Annotation of imach/src/imach.c, revision 1.223
1.223 ! brouard 1: /* $Id: imach.c,v 1.222 2016/02/17 08:14:50 brouard Exp $
1.126 brouard 2: $State: Exp $
1.163 brouard 3: $Log: imach.c,v $
1.223 ! brouard 4: Revision 1.222 2016/02/17 08:14:50 brouard
! 5: Summary: Probably last 0.98 stable version 0.98r6
! 6:
1.222 brouard 7: Revision 1.221 2016/02/15 23:35:36 brouard
8: Summary: minor bug
9:
1.220 brouard 10: Revision 1.219 2016/02/15 00:48:12 brouard
11: *** empty log message ***
12:
1.219 brouard 13: Revision 1.218 2016/02/12 11:29:23 brouard
14: Summary: 0.99 Back projections
15:
1.218 brouard 16: Revision 1.217 2015/12/23 17:18:31 brouard
17: Summary: Experimental backcast
18:
1.217 brouard 19: Revision 1.216 2015/12/18 17:32:11 brouard
20: Summary: 0.98r4 Warning and status=-2
21:
22: Version 0.98r4 is now:
23: - displaying an error when status is -1, date of interview unknown and date of death known;
24: - permitting a status -2 when the vital status is unknown at a known date of right truncation.
25: Older changes concerning s=-2, dating from 2005 have been supersed.
26:
1.216 brouard 27: Revision 1.215 2015/12/16 08:52:24 brouard
28: Summary: 0.98r4 working
29:
1.215 brouard 30: Revision 1.214 2015/12/16 06:57:54 brouard
31: Summary: temporary not working
32:
1.214 brouard 33: Revision 1.213 2015/12/11 18:22:17 brouard
34: Summary: 0.98r4
35:
1.213 brouard 36: Revision 1.212 2015/11/21 12:47:24 brouard
37: Summary: minor typo
38:
1.212 brouard 39: Revision 1.211 2015/11/21 12:41:11 brouard
40: Summary: 0.98r3 with some graph of projected cross-sectional
41:
42: Author: Nicolas Brouard
43:
1.211 brouard 44: Revision 1.210 2015/11/18 17:41:20 brouard
45: Summary: Start working on projected prevalences
46:
1.210 brouard 47: Revision 1.209 2015/11/17 22:12:03 brouard
48: Summary: Adding ftolpl parameter
49: Author: N Brouard
50:
51: We had difficulties to get smoothed confidence intervals. It was due
52: to the period prevalence which wasn't computed accurately. The inner
53: parameter ftolpl is now an outer parameter of the .imach parameter
54: file after estepm. If ftolpl is small 1.e-4 and estepm too,
55: computation are long.
56:
1.209 brouard 57: Revision 1.208 2015/11/17 14:31:57 brouard
58: Summary: temporary
59:
1.208 brouard 60: Revision 1.207 2015/10/27 17:36:57 brouard
61: *** empty log message ***
62:
1.207 brouard 63: Revision 1.206 2015/10/24 07:14:11 brouard
64: *** empty log message ***
65:
1.206 brouard 66: Revision 1.205 2015/10/23 15:50:53 brouard
67: Summary: 0.98r3 some clarification for graphs on likelihood contributions
68:
1.205 brouard 69: Revision 1.204 2015/10/01 16:20:26 brouard
70: Summary: Some new graphs of contribution to likelihood
71:
1.204 brouard 72: Revision 1.203 2015/09/30 17:45:14 brouard
73: Summary: looking at better estimation of the hessian
74:
75: Also a better criteria for convergence to the period prevalence And
76: therefore adding the number of years needed to converge. (The
77: prevalence in any alive state shold sum to one
78:
1.203 brouard 79: Revision 1.202 2015/09/22 19:45:16 brouard
80: Summary: Adding some overall graph on contribution to likelihood. Might change
81:
1.202 brouard 82: Revision 1.201 2015/09/15 17:34:58 brouard
83: Summary: 0.98r0
84:
85: - Some new graphs like suvival functions
86: - Some bugs fixed like model=1+age+V2.
87:
1.201 brouard 88: Revision 1.200 2015/09/09 16:53:55 brouard
89: Summary: Big bug thanks to Flavia
90:
91: Even model=1+age+V2. did not work anymore
92:
1.200 brouard 93: Revision 1.199 2015/09/07 14:09:23 brouard
94: Summary: 0.98q6 changing default small png format for graph to vectorized svg.
95:
1.199 brouard 96: Revision 1.198 2015/09/03 07:14:39 brouard
97: Summary: 0.98q5 Flavia
98:
1.198 brouard 99: Revision 1.197 2015/09/01 18:24:39 brouard
100: *** empty log message ***
101:
1.197 brouard 102: Revision 1.196 2015/08/18 23:17:52 brouard
103: Summary: 0.98q5
104:
1.196 brouard 105: Revision 1.195 2015/08/18 16:28:39 brouard
106: Summary: Adding a hack for testing purpose
107:
108: After reading the title, ftol and model lines, if the comment line has
109: a q, starting with #q, the answer at the end of the run is quit. It
110: permits to run test files in batch with ctest. The former workaround was
111: $ echo q | imach foo.imach
112:
1.195 brouard 113: Revision 1.194 2015/08/18 13:32:00 brouard
114: Summary: Adding error when the covariance matrix doesn't contain the exact number of lines required by the model line.
115:
1.194 brouard 116: Revision 1.193 2015/08/04 07:17:42 brouard
117: Summary: 0.98q4
118:
1.193 brouard 119: Revision 1.192 2015/07/16 16:49:02 brouard
120: Summary: Fixing some outputs
121:
1.192 brouard 122: Revision 1.191 2015/07/14 10:00:33 brouard
123: Summary: Some fixes
124:
1.191 brouard 125: Revision 1.190 2015/05/05 08:51:13 brouard
126: Summary: Adding digits in output parameters (7 digits instead of 6)
127:
128: Fix 1+age+.
129:
1.190 brouard 130: Revision 1.189 2015/04/30 14:45:16 brouard
131: Summary: 0.98q2
132:
1.189 brouard 133: Revision 1.188 2015/04/30 08:27:53 brouard
134: *** empty log message ***
135:
1.188 brouard 136: Revision 1.187 2015/04/29 09:11:15 brouard
137: *** empty log message ***
138:
1.187 brouard 139: Revision 1.186 2015/04/23 12:01:52 brouard
140: Summary: V1*age is working now, version 0.98q1
141:
142: Some codes had been disabled in order to simplify and Vn*age was
143: working in the optimization phase, ie, giving correct MLE parameters,
144: but, as usual, outputs were not correct and program core dumped.
145:
1.186 brouard 146: Revision 1.185 2015/03/11 13:26:42 brouard
147: Summary: Inclusion of compile and links command line for Intel Compiler
148:
1.185 brouard 149: Revision 1.184 2015/03/11 11:52:39 brouard
150: Summary: Back from Windows 8. Intel Compiler
151:
1.184 brouard 152: Revision 1.183 2015/03/10 20:34:32 brouard
153: Summary: 0.98q0, trying with directest, mnbrak fixed
154:
155: We use directest instead of original Powell test; probably no
156: incidence on the results, but better justifications;
157: We fixed Numerical Recipes mnbrak routine which was wrong and gave
158: wrong results.
159:
1.183 brouard 160: Revision 1.182 2015/02/12 08:19:57 brouard
161: Summary: Trying to keep directest which seems simpler and more general
162: Author: Nicolas Brouard
163:
1.182 brouard 164: Revision 1.181 2015/02/11 23:22:24 brouard
165: Summary: Comments on Powell added
166:
167: Author:
168:
1.181 brouard 169: Revision 1.180 2015/02/11 17:33:45 brouard
170: Summary: Finishing move from main to function (hpijx and prevalence_limit)
171:
1.180 brouard 172: Revision 1.179 2015/01/04 09:57:06 brouard
173: Summary: back to OS/X
174:
1.179 brouard 175: Revision 1.178 2015/01/04 09:35:48 brouard
176: *** empty log message ***
177:
1.178 brouard 178: Revision 1.177 2015/01/03 18:40:56 brouard
179: Summary: Still testing ilc32 on OSX
180:
1.177 brouard 181: Revision 1.176 2015/01/03 16:45:04 brouard
182: *** empty log message ***
183:
1.176 brouard 184: Revision 1.175 2015/01/03 16:33:42 brouard
185: *** empty log message ***
186:
1.175 brouard 187: Revision 1.174 2015/01/03 16:15:49 brouard
188: Summary: Still in cross-compilation
189:
1.174 brouard 190: Revision 1.173 2015/01/03 12:06:26 brouard
191: Summary: trying to detect cross-compilation
192:
1.173 brouard 193: Revision 1.172 2014/12/27 12:07:47 brouard
194: Summary: Back from Visual Studio and Intel, options for compiling for Windows XP
195:
1.172 brouard 196: Revision 1.171 2014/12/23 13:26:59 brouard
197: Summary: Back from Visual C
198:
199: Still problem with utsname.h on Windows
200:
1.171 brouard 201: Revision 1.170 2014/12/23 11:17:12 brouard
202: Summary: Cleaning some \%% back to %%
203:
204: The escape was mandatory for a specific compiler (which one?), but too many warnings.
205:
1.170 brouard 206: Revision 1.169 2014/12/22 23:08:31 brouard
207: Summary: 0.98p
208:
209: Outputs some informations on compiler used, OS etc. Testing on different platforms.
210:
1.169 brouard 211: Revision 1.168 2014/12/22 15:17:42 brouard
1.170 brouard 212: Summary: update
1.169 brouard 213:
1.168 brouard 214: Revision 1.167 2014/12/22 13:50:56 brouard
215: Summary: Testing uname and compiler version and if compiled 32 or 64
216:
217: Testing on Linux 64
218:
1.167 brouard 219: Revision 1.166 2014/12/22 11:40:47 brouard
220: *** empty log message ***
221:
1.166 brouard 222: Revision 1.165 2014/12/16 11:20:36 brouard
223: Summary: After compiling on Visual C
224:
225: * imach.c (Module): Merging 1.61 to 1.162
226:
1.165 brouard 227: Revision 1.164 2014/12/16 10:52:11 brouard
228: Summary: Merging with Visual C after suppressing some warnings for unused variables. Also fixing Saito's bug 0.98Xn
229:
230: * imach.c (Module): Merging 1.61 to 1.162
231:
1.164 brouard 232: Revision 1.163 2014/12/16 10:30:11 brouard
233: * imach.c (Module): Merging 1.61 to 1.162
234:
1.163 brouard 235: Revision 1.162 2014/09/25 11:43:39 brouard
236: Summary: temporary backup 0.99!
237:
1.162 brouard 238: Revision 1.1 2014/09/16 11:06:58 brouard
239: Summary: With some code (wrong) for nlopt
240:
241: Author:
242:
243: Revision 1.161 2014/09/15 20:41:41 brouard
244: Summary: Problem with macro SQR on Intel compiler
245:
1.161 brouard 246: Revision 1.160 2014/09/02 09:24:05 brouard
247: *** empty log message ***
248:
1.160 brouard 249: Revision 1.159 2014/09/01 10:34:10 brouard
250: Summary: WIN32
251: Author: Brouard
252:
1.159 brouard 253: Revision 1.158 2014/08/27 17:11:51 brouard
254: *** empty log message ***
255:
1.158 brouard 256: Revision 1.157 2014/08/27 16:26:55 brouard
257: Summary: Preparing windows Visual studio version
258: Author: Brouard
259:
260: In order to compile on Visual studio, time.h is now correct and time_t
261: and tm struct should be used. difftime should be used but sometimes I
262: just make the differences in raw time format (time(&now).
263: Trying to suppress #ifdef LINUX
264: Add xdg-open for __linux in order to open default browser.
265:
1.157 brouard 266: Revision 1.156 2014/08/25 20:10:10 brouard
267: *** empty log message ***
268:
1.156 brouard 269: Revision 1.155 2014/08/25 18:32:34 brouard
270: Summary: New compile, minor changes
271: Author: Brouard
272:
1.155 brouard 273: Revision 1.154 2014/06/20 17:32:08 brouard
274: Summary: Outputs now all graphs of convergence to period prevalence
275:
1.154 brouard 276: Revision 1.153 2014/06/20 16:45:46 brouard
277: Summary: If 3 live state, convergence to period prevalence on same graph
278: Author: Brouard
279:
1.153 brouard 280: Revision 1.152 2014/06/18 17:54:09 brouard
281: Summary: open browser, use gnuplot on same dir than imach if not found in the path
282:
1.152 brouard 283: Revision 1.151 2014/06/18 16:43:30 brouard
284: *** empty log message ***
285:
1.151 brouard 286: Revision 1.150 2014/06/18 16:42:35 brouard
287: Summary: If gnuplot is not in the path try on same directory than imach binary (OSX)
288: Author: brouard
289:
1.150 brouard 290: Revision 1.149 2014/06/18 15:51:14 brouard
291: Summary: Some fixes in parameter files errors
292: Author: Nicolas Brouard
293:
1.149 brouard 294: Revision 1.148 2014/06/17 17:38:48 brouard
295: Summary: Nothing new
296: Author: Brouard
297:
298: Just a new packaging for OS/X version 0.98nS
299:
1.148 brouard 300: Revision 1.147 2014/06/16 10:33:11 brouard
301: *** empty log message ***
302:
1.147 brouard 303: Revision 1.146 2014/06/16 10:20:28 brouard
304: Summary: Merge
305: Author: Brouard
306:
307: Merge, before building revised version.
308:
1.146 brouard 309: Revision 1.145 2014/06/10 21:23:15 brouard
310: Summary: Debugging with valgrind
311: Author: Nicolas Brouard
312:
313: Lot of changes in order to output the results with some covariates
314: After the Edimburgh REVES conference 2014, it seems mandatory to
315: improve the code.
316: No more memory valgrind error but a lot has to be done in order to
317: continue the work of splitting the code into subroutines.
318: Also, decodemodel has been improved. Tricode is still not
319: optimal. nbcode should be improved. Documentation has been added in
320: the source code.
321:
1.144 brouard 322: Revision 1.143 2014/01/26 09:45:38 brouard
323: Summary: Version 0.98nR (to be improved, but gives same optimization results as 0.98k. Nice, promising
324:
325: * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
326: (Module): Version 0.98nR Running ok, but output format still only works for three covariates.
327:
1.143 brouard 328: Revision 1.142 2014/01/26 03:57:36 brouard
329: Summary: gnuplot changed plot w l 1 has to be changed to plot w l lt 2
330:
331: * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
332:
1.142 brouard 333: Revision 1.141 2014/01/26 02:42:01 brouard
334: * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
335:
1.141 brouard 336: Revision 1.140 2011/09/02 10:37:54 brouard
337: Summary: times.h is ok with mingw32 now.
338:
1.140 brouard 339: Revision 1.139 2010/06/14 07:50:17 brouard
340: After the theft of my laptop, I probably lost some lines of codes which were not uploaded to the CVS tree.
341: I remember having already fixed agemin agemax which are pointers now but not cvs saved.
342:
1.139 brouard 343: Revision 1.138 2010/04/30 18:19:40 brouard
344: *** empty log message ***
345:
1.138 brouard 346: Revision 1.137 2010/04/29 18:11:38 brouard
347: (Module): Checking covariates for more complex models
348: than V1+V2. A lot of change to be done. Unstable.
349:
1.137 brouard 350: Revision 1.136 2010/04/26 20:30:53 brouard
351: (Module): merging some libgsl code. Fixing computation
352: of likelione (using inter/intrapolation if mle = 0) in order to
353: get same likelihood as if mle=1.
354: Some cleaning of code and comments added.
355:
1.136 brouard 356: Revision 1.135 2009/10/29 15:33:14 brouard
357: (Module): Now imach stops if date of birth, at least year of birth, is not given. Some cleaning of the code.
358:
1.135 brouard 359: Revision 1.134 2009/10/29 13:18:53 brouard
360: (Module): Now imach stops if date of birth, at least year of birth, is not given. Some cleaning of the code.
361:
1.134 brouard 362: Revision 1.133 2009/07/06 10:21:25 brouard
363: just nforces
364:
1.133 brouard 365: Revision 1.132 2009/07/06 08:22:05 brouard
366: Many tings
367:
1.132 brouard 368: Revision 1.131 2009/06/20 16:22:47 brouard
369: Some dimensions resccaled
370:
1.131 brouard 371: Revision 1.130 2009/05/26 06:44:34 brouard
372: (Module): Max Covariate is now set to 20 instead of 8. A
373: lot of cleaning with variables initialized to 0. Trying to make
374: V2+V3*age+V1+V4 strb=V3*age+V1+V4 working better.
375:
1.130 brouard 376: Revision 1.129 2007/08/31 13:49:27 lievre
377: Modification of the way of exiting when the covariate is not binary in order to see on the window the error message before exiting
378:
1.129 lievre 379: Revision 1.128 2006/06/30 13:02:05 brouard
380: (Module): Clarifications on computing e.j
381:
1.128 brouard 382: Revision 1.127 2006/04/28 18:11:50 brouard
383: (Module): Yes the sum of survivors was wrong since
384: imach-114 because nhstepm was no more computed in the age
385: loop. Now we define nhstepma in the age loop.
386: (Module): In order to speed up (in case of numerous covariates) we
387: compute health expectancies (without variances) in a first step
388: and then all the health expectancies with variances or standard
389: deviation (needs data from the Hessian matrices) which slows the
390: computation.
391: In the future we should be able to stop the program is only health
392: expectancies and graph are needed without standard deviations.
393:
1.127 brouard 394: Revision 1.126 2006/04/28 17:23:28 brouard
395: (Module): Yes the sum of survivors was wrong since
396: imach-114 because nhstepm was no more computed in the age
397: loop. Now we define nhstepma in the age loop.
398: Version 0.98h
399:
1.126 brouard 400: Revision 1.125 2006/04/04 15:20:31 lievre
401: Errors in calculation of health expectancies. Age was not initialized.
402: Forecasting file added.
403:
404: Revision 1.124 2006/03/22 17:13:53 lievre
405: Parameters are printed with %lf instead of %f (more numbers after the comma).
406: The log-likelihood is printed in the log file
407:
408: Revision 1.123 2006/03/20 10:52:43 brouard
409: * imach.c (Module): <title> changed, corresponds to .htm file
410: name. <head> headers where missing.
411:
412: * imach.c (Module): Weights can have a decimal point as for
413: English (a comma might work with a correct LC_NUMERIC environment,
414: otherwise the weight is truncated).
415: Modification of warning when the covariates values are not 0 or
416: 1.
417: Version 0.98g
418:
419: Revision 1.122 2006/03/20 09:45:41 brouard
420: (Module): Weights can have a decimal point as for
421: English (a comma might work with a correct LC_NUMERIC environment,
422: otherwise the weight is truncated).
423: Modification of warning when the covariates values are not 0 or
424: 1.
425: Version 0.98g
426:
427: Revision 1.121 2006/03/16 17:45:01 lievre
428: * imach.c (Module): Comments concerning covariates added
429:
430: * imach.c (Module): refinements in the computation of lli if
431: status=-2 in order to have more reliable computation if stepm is
432: not 1 month. Version 0.98f
433:
434: Revision 1.120 2006/03/16 15:10:38 lievre
435: (Module): refinements in the computation of lli if
436: status=-2 in order to have more reliable computation if stepm is
437: not 1 month. Version 0.98f
438:
439: Revision 1.119 2006/03/15 17:42:26 brouard
440: (Module): Bug if status = -2, the loglikelihood was
441: computed as likelihood omitting the logarithm. Version O.98e
442:
443: Revision 1.118 2006/03/14 18:20:07 brouard
444: (Module): varevsij Comments added explaining the second
445: table of variances if popbased=1 .
446: (Module): Covariances of eij, ekl added, graphs fixed, new html link.
447: (Module): Function pstamp added
448: (Module): Version 0.98d
449:
450: Revision 1.117 2006/03/14 17:16:22 brouard
451: (Module): varevsij Comments added explaining the second
452: table of variances if popbased=1 .
453: (Module): Covariances of eij, ekl added, graphs fixed, new html link.
454: (Module): Function pstamp added
455: (Module): Version 0.98d
456:
457: Revision 1.116 2006/03/06 10:29:27 brouard
458: (Module): Variance-covariance wrong links and
459: varian-covariance of ej. is needed (Saito).
460:
461: Revision 1.115 2006/02/27 12:17:45 brouard
462: (Module): One freematrix added in mlikeli! 0.98c
463:
464: Revision 1.114 2006/02/26 12:57:58 brouard
465: (Module): Some improvements in processing parameter
466: filename with strsep.
467:
468: Revision 1.113 2006/02/24 14:20:24 brouard
469: (Module): Memory leaks checks with valgrind and:
470: datafile was not closed, some imatrix were not freed and on matrix
471: allocation too.
472:
473: Revision 1.112 2006/01/30 09:55:26 brouard
474: (Module): Back to gnuplot.exe instead of wgnuplot.exe
475:
476: Revision 1.111 2006/01/25 20:38:18 brouard
477: (Module): Lots of cleaning and bugs added (Gompertz)
478: (Module): Comments can be added in data file. Missing date values
479: can be a simple dot '.'.
480:
481: Revision 1.110 2006/01/25 00:51:50 brouard
482: (Module): Lots of cleaning and bugs added (Gompertz)
483:
484: Revision 1.109 2006/01/24 19:37:15 brouard
485: (Module): Comments (lines starting with a #) are allowed in data.
486:
487: Revision 1.108 2006/01/19 18:05:42 lievre
488: Gnuplot problem appeared...
489: To be fixed
490:
491: Revision 1.107 2006/01/19 16:20:37 brouard
492: Test existence of gnuplot in imach path
493:
494: Revision 1.106 2006/01/19 13:24:36 brouard
495: Some cleaning and links added in html output
496:
497: Revision 1.105 2006/01/05 20:23:19 lievre
498: *** empty log message ***
499:
500: Revision 1.104 2005/09/30 16:11:43 lievre
501: (Module): sump fixed, loop imx fixed, and simplifications.
502: (Module): If the status is missing at the last wave but we know
503: that the person is alive, then we can code his/her status as -2
504: (instead of missing=-1 in earlier versions) and his/her
505: contributions to the likelihood is 1 - Prob of dying from last
506: health status (= 1-p13= p11+p12 in the easiest case of somebody in
507: the healthy state at last known wave). Version is 0.98
508:
509: Revision 1.103 2005/09/30 15:54:49 lievre
510: (Module): sump fixed, loop imx fixed, and simplifications.
511:
512: Revision 1.102 2004/09/15 17:31:30 brouard
513: Add the possibility to read data file including tab characters.
514:
515: Revision 1.101 2004/09/15 10:38:38 brouard
516: Fix on curr_time
517:
518: Revision 1.100 2004/07/12 18:29:06 brouard
519: Add version for Mac OS X. Just define UNIX in Makefile
520:
521: Revision 1.99 2004/06/05 08:57:40 brouard
522: *** empty log message ***
523:
524: Revision 1.98 2004/05/16 15:05:56 brouard
525: New version 0.97 . First attempt to estimate force of mortality
526: directly from the data i.e. without the need of knowing the health
527: state at each age, but using a Gompertz model: log u =a + b*age .
528: This is the basic analysis of mortality and should be done before any
529: other analysis, in order to test if the mortality estimated from the
530: cross-longitudinal survey is different from the mortality estimated
531: from other sources like vital statistic data.
532:
533: The same imach parameter file can be used but the option for mle should be -3.
534:
1.133 brouard 535: Agnès, who wrote this part of the code, tried to keep most of the
1.126 brouard 536: former routines in order to include the new code within the former code.
537:
538: The output is very simple: only an estimate of the intercept and of
539: the slope with 95% confident intervals.
540:
541: Current limitations:
542: A) Even if you enter covariates, i.e. with the
543: model= V1+V2 equation for example, the programm does only estimate a unique global model without covariates.
544: B) There is no computation of Life Expectancy nor Life Table.
545:
546: Revision 1.97 2004/02/20 13:25:42 lievre
547: Version 0.96d. Population forecasting command line is (temporarily)
548: suppressed.
549:
550: Revision 1.96 2003/07/15 15:38:55 brouard
551: * imach.c (Repository): Errors in subdirf, 2, 3 while printing tmpout is
552: rewritten within the same printf. Workaround: many printfs.
553:
554: Revision 1.95 2003/07/08 07:54:34 brouard
555: * imach.c (Repository):
556: (Repository): Using imachwizard code to output a more meaningful covariance
557: matrix (cov(a12,c31) instead of numbers.
558:
559: Revision 1.94 2003/06/27 13:00:02 brouard
560: Just cleaning
561:
562: Revision 1.93 2003/06/25 16:33:55 brouard
563: (Module): On windows (cygwin) function asctime_r doesn't
564: exist so I changed back to asctime which exists.
565: (Module): Version 0.96b
566:
567: Revision 1.92 2003/06/25 16:30:45 brouard
568: (Module): On windows (cygwin) function asctime_r doesn't
569: exist so I changed back to asctime which exists.
570:
571: Revision 1.91 2003/06/25 15:30:29 brouard
572: * imach.c (Repository): Duplicated warning errors corrected.
573: (Repository): Elapsed time after each iteration is now output. It
574: helps to forecast when convergence will be reached. Elapsed time
575: is stamped in powell. We created a new html file for the graphs
576: concerning matrix of covariance. It has extension -cov.htm.
577:
578: Revision 1.90 2003/06/24 12:34:15 brouard
579: (Module): Some bugs corrected for windows. Also, when
580: mle=-1 a template is output in file "or"mypar.txt with the design
581: of the covariance matrix to be input.
582:
583: Revision 1.89 2003/06/24 12:30:52 brouard
584: (Module): Some bugs corrected for windows. Also, when
585: mle=-1 a template is output in file "or"mypar.txt with the design
586: of the covariance matrix to be input.
587:
588: Revision 1.88 2003/06/23 17:54:56 brouard
589: * 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.
590:
591: Revision 1.87 2003/06/18 12:26:01 brouard
592: Version 0.96
593:
594: Revision 1.86 2003/06/17 20:04:08 brouard
595: (Module): Change position of html and gnuplot routines and added
596: routine fileappend.
597:
598: Revision 1.85 2003/06/17 13:12:43 brouard
599: * imach.c (Repository): Check when date of death was earlier that
600: current date of interview. It may happen when the death was just
601: prior to the death. In this case, dh was negative and likelihood
602: was wrong (infinity). We still send an "Error" but patch by
603: assuming that the date of death was just one stepm after the
604: interview.
605: (Repository): Because some people have very long ID (first column)
606: we changed int to long in num[] and we added a new lvector for
607: memory allocation. But we also truncated to 8 characters (left
608: truncation)
609: (Repository): No more line truncation errors.
610:
611: Revision 1.84 2003/06/13 21:44:43 brouard
612: * imach.c (Repository): Replace "freqsummary" at a correct
613: place. It differs from routine "prevalence" which may be called
614: many times. Probs is memory consuming and must be used with
615: parcimony.
616: Version 0.95a3 (should output exactly the same maximization than 0.8a2)
617:
618: Revision 1.83 2003/06/10 13:39:11 lievre
619: *** empty log message ***
620:
621: Revision 1.82 2003/06/05 15:57:20 brouard
622: Add log in imach.c and fullversion number is now printed.
623:
624: */
625: /*
626: Interpolated Markov Chain
627:
628: Short summary of the programme:
629:
630: This program computes Healthy Life Expectancies from
631: cross-longitudinal data. Cross-longitudinal data consist in: -1- a
632: first survey ("cross") where individuals from different ages are
633: interviewed on their health status or degree of disability (in the
634: case of a health survey which is our main interest) -2- at least a
635: second wave of interviews ("longitudinal") which measure each change
636: (if any) in individual health status. Health expectancies are
637: computed from the time spent in each health state according to a
638: model. More health states you consider, more time is necessary to reach the
639: Maximum Likelihood of the parameters involved in the model. The
640: simplest model is the multinomial logistic model where pij is the
641: probability to be observed in state j at the second wave
642: conditional to be observed in state i at the first wave. Therefore
643: the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where
644: 'age' is age and 'sex' is a covariate. If you want to have a more
645: complex model than "constant and age", you should modify the program
646: where the markup *Covariates have to be included here again* invites
647: you to do it. More covariates you add, slower the
648: convergence.
649:
650: The advantage of this computer programme, compared to a simple
651: multinomial logistic model, is clear when the delay between waves is not
652: identical for each individual. Also, if a individual missed an
653: intermediate interview, the information is lost, but taken into
654: account using an interpolation or extrapolation.
655:
656: hPijx is the probability to be observed in state i at age x+h
657: conditional to the observed state i at age x. The delay 'h' can be
658: split into an exact number (nh*stepm) of unobserved intermediate
659: states. This elementary transition (by month, quarter,
660: semester or year) is modelled as a multinomial logistic. The hPx
661: matrix is simply the matrix product of nh*stepm elementary matrices
662: and the contribution of each individual to the likelihood is simply
663: hPijx.
664:
665: Also this programme outputs the covariance matrix of the parameters but also
1.218 brouard 666: of the life expectancies. It also computes the period (stable) prevalence.
667:
668: Back prevalence and projections:
669: - 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)
670: Computes the back prevalence limit for any combination of covariate values k
671: at any age between ageminpar and agemaxpar and returns it in **bprlim. In the loops,
672: - **bprevalim(**bprlim, ***mobaverage, nlstate, *p, age, **oldm, **savm, **dnewm, **doldm, **dsavm, ftolpl, ncvyearp, k);
673: - hBijx Back Probability to be in state i at age x-h being in j at x
674: Computes for any combination of covariates k and any age between bage and fage
675: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
676: oldm=oldms;savm=savms;
677: - hbxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
678: Computes the transition matrix starting at age 'age' over
679: 'nhstepm*hstepm*stepm' months (i.e. until
680: age (in years) age+nhstepm*hstepm*stepm/12) by multiplying
681: nhstepm*hstepm matrices. Returns p3mat[i][j][h] after calling
682: p3mat[i][j][h]=matprod2(newm, bmij(pmmij,cov,ncovmodel,x,nlstate,prevacurrent, dnewm, doldm, dsavm,ij),\
683: 1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);
684:
1.133 brouard 685: Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).
686: Institut national d'études démographiques, Paris.
1.126 brouard 687: This software have been partly granted by Euro-REVES, a concerted action
688: from the European Union.
689: It is copyrighted identically to a GNU software product, ie programme and
690: software can be distributed freely for non commercial use. Latest version
691: can be accessed at http://euroreves.ined.fr/imach .
692:
693: Help to debug: LD_PRELOAD=/usr/local/lib/libnjamd.so ./imach foo.imach
694: or better on gdb : set env LD_PRELOAD=/usr/local/lib/libnjamd.so
695:
696: **********************************************************************/
697: /*
698: main
699: read parameterfile
700: read datafile
701: concatwav
702: freqsummary
703: if (mle >= 1)
704: mlikeli
705: print results files
706: if mle==1
707: computes hessian
708: read end of parameter file: agemin, agemax, bage, fage, estepm
709: begin-prev-date,...
710: open gnuplot file
711: open html file
1.145 brouard 712: period (stable) prevalence | pl_nom 1-1 2-2 etc by covariate
713: for age prevalim() | #****** V1=0 V2=1 V3=1 V4=0 ******
714: | 65 1 0 2 1 3 1 4 0 0.96326 0.03674
715: freexexit2 possible for memory heap.
716:
717: h Pij x | pij_nom ficrestpij
718: # Cov Agex agex+h hpijx with i,j= 1-1 1-2 1-3 2-1 2-2 2-3
719: 1 85 85 1.00000 0.00000 0.00000 0.00000 1.00000 0.00000
720: 1 85 86 0.68299 0.22291 0.09410 0.71093 0.00000 0.28907
721:
722: 1 65 99 0.00364 0.00322 0.99314 0.00350 0.00310 0.99340
723: 1 65 100 0.00214 0.00204 0.99581 0.00206 0.00196 0.99597
724: variance of p one-step probabilities varprob | prob_nom ficresprob #One-step probabilities and stand. devi in ()
725: Standard deviation of one-step probabilities | probcor_nom ficresprobcor #One-step probabilities and correlation matrix
726: Matrix of variance covariance of one-step probabilities | probcov_nom ficresprobcov #One-step probabilities and covariance matrix
727:
1.126 brouard 728: forecasting if prevfcast==1 prevforecast call prevalence()
729: health expectancies
730: Variance-covariance of DFLE
731: prevalence()
732: movingaverage()
733: varevsij()
734: if popbased==1 varevsij(,popbased)
735: total life expectancies
736: Variance of period (stable) prevalence
737: end
738: */
739:
1.187 brouard 740: /* #define DEBUG */
741: /* #define DEBUGBRENT */
1.203 brouard 742: /* #define DEBUGLINMIN */
743: /* #define DEBUGHESS */
744: #define DEBUGHESSIJ
1.223 ! brouard 745: /* #define LINMINORIGINAL /\* Don't use loop on scale in linmin (accepting nan)*\/ */
1.165 brouard 746: #define POWELL /* Instead of NLOPT */
1.192 brouard 747: #define POWELLF1F3 /* Skip test */
1.186 brouard 748: /* #define POWELLORIGINAL /\* Don't use Directest to decide new direction but original Powell test *\/ */
749: /* #define MNBRAKORIGINAL /\* Don't use mnbrak fix *\/ */
1.126 brouard 750:
751: #include <math.h>
752: #include <stdio.h>
753: #include <stdlib.h>
754: #include <string.h>
1.159 brouard 755:
756: #ifdef _WIN32
757: #include <io.h>
1.172 brouard 758: #include <windows.h>
759: #include <tchar.h>
1.159 brouard 760: #else
1.126 brouard 761: #include <unistd.h>
1.159 brouard 762: #endif
1.126 brouard 763:
764: #include <limits.h>
765: #include <sys/types.h>
1.171 brouard 766:
767: #if defined(__GNUC__)
768: #include <sys/utsname.h> /* Doesn't work on Windows */
769: #endif
770:
1.126 brouard 771: #include <sys/stat.h>
772: #include <errno.h>
1.159 brouard 773: /* extern int errno; */
1.126 brouard 774:
1.157 brouard 775: /* #ifdef LINUX */
776: /* #include <time.h> */
777: /* #include "timeval.h" */
778: /* #else */
779: /* #include <sys/time.h> */
780: /* #endif */
781:
1.126 brouard 782: #include <time.h>
783:
1.136 brouard 784: #ifdef GSL
785: #include <gsl/gsl_errno.h>
786: #include <gsl/gsl_multimin.h>
787: #endif
788:
1.167 brouard 789:
1.162 brouard 790: #ifdef NLOPT
791: #include <nlopt.h>
792: typedef struct {
793: double (* function)(double [] );
794: } myfunc_data ;
795: #endif
796:
1.126 brouard 797: /* #include <libintl.h> */
798: /* #define _(String) gettext (String) */
799:
1.141 brouard 800: #define MAXLINE 1024 /* Was 256. Overflow with 312 with 2 states and 4 covariates. Should be ok */
1.126 brouard 801:
802: #define GNUPLOTPROGRAM "gnuplot"
803: /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
804: #define FILENAMELENGTH 132
805:
806: #define GLOCK_ERROR_NOPATH -1 /* empty path */
807: #define GLOCK_ERROR_GETCWD -2 /* cannot get cwd */
808:
1.144 brouard 809: #define MAXPARM 128 /**< Maximum number of parameters for the optimization */
810: #define NPARMAX 64 /**< (nlstate+ndeath-1)*nlstate*ncovmodel */
1.126 brouard 811:
812: #define NINTERVMAX 8
1.144 brouard 813: #define NLSTATEMAX 8 /**< Maximum number of live states (for func) */
814: #define NDEATHMAX 8 /**< Maximum number of dead states (for func) */
815: #define NCOVMAX 20 /**< Maximum number of covariates, including generated covariates V1*V2 */
1.197 brouard 816: #define codtabm(h,k) (1 & (h-1) >> (k-1))+1
1.211 brouard 817: /*#define decodtabm(h,k,cptcoveff)= (h <= (1<<cptcoveff)?(((h-1) >> (k-1)) & 1) +1 : -1)*/
818: #define decodtabm(h,k,cptcoveff) (((h-1) >> (k-1)) & 1) +1
1.126 brouard 819: #define MAXN 20000
1.144 brouard 820: #define YEARM 12. /**< Number of months per year */
1.218 brouard 821: /* #define AGESUP 130 */
822: #define AGESUP 150
823: #define AGEMARGE 25 /* Marge for agemin and agemax for(iage=agemin-AGEMARGE; iage <= agemax+3+AGEMARGE; iage++) */
1.126 brouard 824: #define AGEBASE 40
1.194 brouard 825: #define AGEOVERFLOW 1.e20
1.164 brouard 826: #define AGEGOMP 10 /**< Minimal age for Gompertz adjustment */
1.157 brouard 827: #ifdef _WIN32
828: #define DIRSEPARATOR '\\'
829: #define CHARSEPARATOR "\\"
830: #define ODIRSEPARATOR '/'
831: #else
1.126 brouard 832: #define DIRSEPARATOR '/'
833: #define CHARSEPARATOR "/"
834: #define ODIRSEPARATOR '\\'
835: #endif
836:
1.223 ! brouard 837: /* $Id: imach.c,v 1.222 2016/02/17 08:14:50 brouard Exp $ */
1.126 brouard 838: /* $State: Exp $ */
1.196 brouard 839: #include "version.h"
840: char version[]=__IMACH_VERSION__;
1.204 brouard 841: 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";
1.223 ! brouard 842: char fullversion[]="$Revision: 1.222 $ $Date: 2016/02/17 08:14:50 $";
1.126 brouard 843: char strstart[80];
844: char optionfilext[10], optionfilefiname[FILENAMELENGTH];
1.130 brouard 845: int erreur=0, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings */
1.187 brouard 846: int nagesqr=0, nforce=0; /* nagesqr=1 if model is including age*age, number of forces */
1.145 brouard 847: /* Number of covariates model=V2+V1+ V3*age+V2*V4 */
848: int cptcovn=0; /**< cptcovn number of covariates added in the model (excepting constant and age and age*product) */
849: int cptcovt=0; /**< cptcovt number of covariates added in the model (excepting constant and age) */
850: int cptcovs=0; /**< cptcovs number of simple covariates V2+V1 =2 */
851: int cptcovage=0; /**< Number of covariates with age: V3*age only =1 */
852: int cptcovprodnoage=0; /**< Number of covariate products without age */
853: int cptcoveff=0; /* Total number of covariates to vary for printing results */
854: int cptcov=0; /* Working variable */
1.218 brouard 855: int ncovcombmax=NCOVMAX; /* Maximum calculated number of covariate combination = pow(2, cptcoveff) */
1.126 brouard 856: int npar=NPARMAX;
857: int nlstate=2; /* Number of live states */
858: int ndeath=1; /* Number of dead states */
1.130 brouard 859: int ncovmodel=0, ncovcol=0; /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
1.223 ! brouard 860: int nqv=0, ntv=0, nqtv=0; /* Total number of quantitative variables, time variable (dummy), quantitative and time variable */
1.126 brouard 861: int popbased=0;
862:
863: int *wav; /* Number of waves for this individuual 0 is possible */
1.130 brouard 864: int maxwav=0; /* Maxim number of waves */
865: int jmin=0, jmax=0; /* min, max spacing between 2 waves */
866: int ijmin=0, ijmax=0; /* Individuals having jmin and jmax */
867: int gipmx=0, gsw=0; /* Global variables on the number of contributions
1.126 brouard 868: to the likelihood and the sum of weights (done by funcone)*/
1.130 brouard 869: int mle=1, weightopt=0;
1.126 brouard 870: int **mw; /* mw[mi][i] is number of the mi wave for this individual */
871: int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
872: int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between
873: * wave mi and wave mi+1 is not an exact multiple of stepm. */
1.162 brouard 874: int countcallfunc=0; /* Count the number of calls to func */
1.130 brouard 875: double jmean=1; /* Mean space between 2 waves */
1.145 brouard 876: double **matprod2(); /* test */
1.126 brouard 877: double **oldm, **newm, **savm; /* Working pointers to matrices */
878: double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
1.218 brouard 879: double **ddnewms, **ddoldms, **ddsavms; /* for freeing later */
880:
1.136 brouard 881: /*FILE *fic ; */ /* Used in readdata only */
1.217 brouard 882: FILE *ficpar, *ficparo,*ficres, *ficresp, *ficresphtm, *ficresphtmfr, *ficrespl, *ficresplb,*ficrespij, *ficrespijb, *ficrest,*ficresf, *ficresfb,*ficrespop;
1.126 brouard 883: FILE *ficlog, *ficrespow;
1.130 brouard 884: int globpr=0; /* Global variable for printing or not */
1.126 brouard 885: double fretone; /* Only one call to likelihood */
1.130 brouard 886: long ipmx=0; /* Number of contributions */
1.126 brouard 887: double sw; /* Sum of weights */
888: char filerespow[FILENAMELENGTH];
889: char fileresilk[FILENAMELENGTH]; /* File of individual contributions to the likelihood */
890: FILE *ficresilk;
891: FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
892: FILE *ficresprobmorprev;
893: FILE *fichtm, *fichtmcov; /* Html File */
894: FILE *ficreseij;
895: char filerese[FILENAMELENGTH];
896: FILE *ficresstdeij;
897: char fileresstde[FILENAMELENGTH];
898: FILE *ficrescveij;
899: char filerescve[FILENAMELENGTH];
900: FILE *ficresvij;
901: char fileresv[FILENAMELENGTH];
902: FILE *ficresvpl;
903: char fileresvpl[FILENAMELENGTH];
904: char title[MAXLINE];
1.217 brouard 905: char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH], filerespl[FILENAMELENGTH], fileresplb[FILENAMELENGTH];
1.126 brouard 906: char plotcmd[FILENAMELENGTH], pplotcmd[FILENAMELENGTH];
907: char tmpout[FILENAMELENGTH], tmpout2[FILENAMELENGTH];
908: char command[FILENAMELENGTH];
909: int outcmd=0;
910:
1.217 brouard 911: char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filerespijb[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
1.202 brouard 912: char fileresu[FILENAMELENGTH]; /* fileres without r in front */
1.126 brouard 913: char filelog[FILENAMELENGTH]; /* Log file */
914: char filerest[FILENAMELENGTH];
915: char fileregp[FILENAMELENGTH];
916: char popfile[FILENAMELENGTH];
917:
918: char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilehtmcov[FILENAMELENGTH] ;
919:
1.157 brouard 920: /* struct timeval start_time, end_time, curr_time, last_time, forecast_time; */
921: /* struct timezone tzp; */
922: /* extern int gettimeofday(); */
923: struct tm tml, *gmtime(), *localtime();
924:
925: extern time_t time();
926:
927: struct tm start_time, end_time, curr_time, last_time, forecast_time;
928: time_t rstart_time, rend_time, rcurr_time, rlast_time, rforecast_time; /* raw time */
929: struct tm tm;
930:
1.126 brouard 931: char strcurr[80], strfor[80];
932:
933: char *endptr;
934: long lval;
935: double dval;
936:
937: #define NR_END 1
938: #define FREE_ARG char*
939: #define FTOL 1.0e-10
940:
941: #define NRANSI
942: #define ITMAX 200
943:
944: #define TOL 2.0e-4
945:
946: #define CGOLD 0.3819660
947: #define ZEPS 1.0e-10
948: #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);
949:
950: #define GOLD 1.618034
951: #define GLIMIT 100.0
952: #define TINY 1.0e-20
953:
954: static double maxarg1,maxarg2;
955: #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
956: #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
957:
958: #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
959: #define rint(a) floor(a+0.5)
1.166 brouard 960: /* http://www.thphys.uni-heidelberg.de/~robbers/cmbeasy/doc/html/myutils_8h-source.html */
1.183 brouard 961: #define mytinydouble 1.0e-16
1.166 brouard 962: /* #define DEQUAL(a,b) (fabs((a)-(b))<mytinydouble) */
963: /* http://www.thphys.uni-heidelberg.de/~robbers/cmbeasy/doc/html/mynrutils_8h-source.html */
964: /* static double dsqrarg; */
965: /* #define DSQR(a) (DEQUAL((dsqrarg=(a)),0.0) ? 0.0 : dsqrarg*dsqrarg) */
1.126 brouard 966: static double sqrarg;
967: #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
968: #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}
969: int agegomp= AGEGOMP;
970:
971: int imx;
972: int stepm=1;
973: /* Stepm, step in month: minimum step interpolation*/
974:
975: int estepm;
976: /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
977:
978: int m,nb;
979: long *num;
1.197 brouard 980: int firstpass=0, lastpass=4,*cod, *cens;
1.192 brouard 981: int *ncodemax; /* ncodemax[j]= Number of modalities of the j th
982: covariate for which somebody answered excluding
983: undefined. Usually 2: 0 and 1. */
984: int *ncodemaxwundef; /* ncodemax[j]= Number of modalities of the j th
985: covariate for which somebody answered including
986: undefined. Usually 3: -1, 0 and 1. */
1.126 brouard 987: double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
1.218 brouard 988: double **pmmij, ***probs; /* Global pointer */
1.219 brouard 989: double ***mobaverage, ***mobaverages; /* New global variable */
1.126 brouard 990: double *ageexmed,*agecens;
991: double dateintmean=0;
992:
993: double *weight;
994: int **s; /* Status */
1.141 brouard 995: double *agedc;
1.145 brouard 996: double **covar; /**< covar[j,i], value of jth covariate for individual i,
1.141 brouard 997: * covar=matrix(0,NCOVMAX,1,n);
1.187 brouard 998: * cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*age; */
1.223 ! brouard 999: double ***cotvar; /* Time varying covariate */
! 1000: double ***cotqvar; /* Time varying quantitative covariate */
! 1001: double **coqvar; /* Fixed quantitative covariate */
1.141 brouard 1002: double idx;
1003: int **nbcode, *Tvar; /**< model=V2 => Tvar[1]= 2 */
1.197 brouard 1004: int *Tage;
1.145 brouard 1005: int *Ndum; /** Freq of modality (tricode */
1.200 brouard 1006: /* int **codtab;*/ /**< codtab=imatrix(1,100,1,10); */
1.220 brouard 1007: int **Tvard, *Tprod, cptcovprod, *Tvaraff, *invalidvarcomb;
1.126 brouard 1008: double *lsurv, *lpop, *tpop;
1009:
1.143 brouard 1010: double ftol=FTOL; /**< Tolerance for computing Max Likelihood */
1011: double ftolhess; /**< Tolerance for computing hessian */
1.126 brouard 1012:
1013: /**************** split *************************/
1014: static int split( char *path, char *dirc, char *name, char *ext, char *finame )
1015: {
1016: /* From a file name with (full) path (either Unix or Windows) we extract the directory (dirc)
1017: the name of the file (name), its extension only (ext) and its first part of the name (finame)
1018: */
1019: char *ss; /* pointer */
1.186 brouard 1020: int l1=0, l2=0; /* length counters */
1.126 brouard 1021:
1022: l1 = strlen(path ); /* length of path */
1023: if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
1024: ss= strrchr( path, DIRSEPARATOR ); /* find last / */
1025: if ( ss == NULL ) { /* no directory, so determine current directory */
1026: strcpy( name, path ); /* we got the fullname name because no directory */
1027: /*if(strrchr(path, ODIRSEPARATOR )==NULL)
1028: printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
1029: /* get current working directory */
1030: /* extern char* getcwd ( char *buf , int len);*/
1.184 brouard 1031: #ifdef WIN32
1032: if (_getcwd( dirc, FILENAME_MAX ) == NULL ) {
1033: #else
1034: if (getcwd(dirc, FILENAME_MAX) == NULL) {
1035: #endif
1.126 brouard 1036: return( GLOCK_ERROR_GETCWD );
1037: }
1038: /* got dirc from getcwd*/
1039: printf(" DIRC = %s \n",dirc);
1.205 brouard 1040: } else { /* strip directory from path */
1.126 brouard 1041: ss++; /* after this, the filename */
1042: l2 = strlen( ss ); /* length of filename */
1043: if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
1044: strcpy( name, ss ); /* save file name */
1045: strncpy( dirc, path, l1 - l2 ); /* now the directory */
1.186 brouard 1046: dirc[l1-l2] = '\0'; /* add zero */
1.126 brouard 1047: printf(" DIRC2 = %s \n",dirc);
1048: }
1049: /* We add a separator at the end of dirc if not exists */
1050: l1 = strlen( dirc ); /* length of directory */
1051: if( dirc[l1-1] != DIRSEPARATOR ){
1052: dirc[l1] = DIRSEPARATOR;
1053: dirc[l1+1] = 0;
1054: printf(" DIRC3 = %s \n",dirc);
1055: }
1056: ss = strrchr( name, '.' ); /* find last / */
1057: if (ss >0){
1058: ss++;
1059: strcpy(ext,ss); /* save extension */
1060: l1= strlen( name);
1061: l2= strlen(ss)+1;
1062: strncpy( finame, name, l1-l2);
1063: finame[l1-l2]= 0;
1064: }
1065:
1066: return( 0 ); /* we're done */
1067: }
1068:
1069:
1070: /******************************************/
1071:
1072: void replace_back_to_slash(char *s, char*t)
1073: {
1074: int i;
1075: int lg=0;
1076: i=0;
1077: lg=strlen(t);
1078: for(i=0; i<= lg; i++) {
1079: (s[i] = t[i]);
1080: if (t[i]== '\\') s[i]='/';
1081: }
1082: }
1083:
1.132 brouard 1084: char *trimbb(char *out, char *in)
1.137 brouard 1085: { /* Trim multiple blanks in line but keeps first blanks if line starts with blanks */
1.132 brouard 1086: char *s;
1087: s=out;
1088: while (*in != '\0'){
1.137 brouard 1089: while( *in == ' ' && *(in+1) == ' '){ /* && *(in+1) != '\0'){*/
1.132 brouard 1090: in++;
1091: }
1092: *out++ = *in++;
1093: }
1094: *out='\0';
1095: return s;
1096: }
1097:
1.187 brouard 1098: /* char *substrchaine(char *out, char *in, char *chain) */
1099: /* { */
1100: /* /\* Substract chain 'chain' from 'in', return and output 'out' *\/ */
1101: /* char *s, *t; */
1102: /* t=in;s=out; */
1103: /* while ((*in != *chain) && (*in != '\0')){ */
1104: /* *out++ = *in++; */
1105: /* } */
1106:
1107: /* /\* *in matches *chain *\/ */
1108: /* while ((*in++ == *chain++) && (*in != '\0')){ */
1109: /* printf("*in = %c, *out= %c *chain= %c \n", *in, *out, *chain); */
1110: /* } */
1111: /* in--; chain--; */
1112: /* while ( (*in != '\0')){ */
1113: /* printf("Bef *in = %c, *out= %c *chain= %c \n", *in, *out, *chain); */
1114: /* *out++ = *in++; */
1115: /* printf("Aft *in = %c, *out= %c *chain= %c \n", *in, *out, *chain); */
1116: /* } */
1117: /* *out='\0'; */
1118: /* out=s; */
1119: /* return out; */
1120: /* } */
1121: char *substrchaine(char *out, char *in, char *chain)
1122: {
1123: /* Substract chain 'chain' from 'in', return and output 'out' */
1124: /* in="V1+V1*age+age*age+V2", chain="age*age" */
1125:
1126: char *strloc;
1127:
1128: strcpy (out, in);
1129: strloc = strstr(out, chain); /* strloc points to out at age*age+V2 */
1130: printf("Bef strloc=%s chain=%s out=%s \n", strloc, chain, out);
1131: if(strloc != NULL){
1132: /* will affect out */ /* strloc+strlenc(chain)=+V2 */ /* Will also work in Unicode */
1133: memmove(strloc,strloc+strlen(chain), strlen(strloc+strlen(chain))+1);
1134: /* strcpy (strloc, strloc +strlen(chain));*/
1135: }
1136: printf("Aft strloc=%s chain=%s in=%s out=%s \n", strloc, chain, in, out);
1137: return out;
1138: }
1139:
1140:
1.145 brouard 1141: char *cutl(char *blocc, char *alocc, char *in, char occ)
1142: {
1.187 brouard 1143: /* cuts string in into blocc and alocc where blocc ends before FIRST occurence of char 'occ'
1.145 brouard 1144: and alocc starts after first occurence of char 'occ' : ex cutv(blocc,alocc,"abcdef2ghi2j",'2')
1.187 brouard 1145: gives blocc="abcdef" and alocc="ghi2j".
1.145 brouard 1146: If occ is not found blocc is null and alocc is equal to in. Returns blocc
1147: */
1.160 brouard 1148: char *s, *t;
1.145 brouard 1149: t=in;s=in;
1150: while ((*in != occ) && (*in != '\0')){
1151: *alocc++ = *in++;
1152: }
1153: if( *in == occ){
1154: *(alocc)='\0';
1155: s=++in;
1156: }
1157:
1158: if (s == t) {/* occ not found */
1159: *(alocc-(in-s))='\0';
1160: in=s;
1161: }
1162: while ( *in != '\0'){
1163: *blocc++ = *in++;
1164: }
1165:
1166: *blocc='\0';
1167: return t;
1168: }
1.137 brouard 1169: char *cutv(char *blocc, char *alocc, char *in, char occ)
1170: {
1.187 brouard 1171: /* cuts string in into blocc and alocc where blocc ends before LAST occurence of char 'occ'
1.137 brouard 1172: and alocc starts after last occurence of char 'occ' : ex cutv(blocc,alocc,"abcdef2ghi2j",'2')
1173: gives blocc="abcdef2ghi" and alocc="j".
1174: If occ is not found blocc is null and alocc is equal to in. Returns alocc
1175: */
1176: char *s, *t;
1177: t=in;s=in;
1178: while (*in != '\0'){
1179: while( *in == occ){
1180: *blocc++ = *in++;
1181: s=in;
1182: }
1183: *blocc++ = *in++;
1184: }
1185: if (s == t) /* occ not found */
1186: *(blocc-(in-s))='\0';
1187: else
1188: *(blocc-(in-s)-1)='\0';
1189: in=s;
1190: while ( *in != '\0'){
1191: *alocc++ = *in++;
1192: }
1193:
1194: *alocc='\0';
1195: return s;
1196: }
1197:
1.126 brouard 1198: int nbocc(char *s, char occ)
1199: {
1200: int i,j=0;
1201: int lg=20;
1202: i=0;
1203: lg=strlen(s);
1204: for(i=0; i<= lg; i++) {
1205: if (s[i] == occ ) j++;
1206: }
1207: return j;
1208: }
1209:
1.137 brouard 1210: /* void cutv(char *u,char *v, char*t, char occ) */
1211: /* { */
1212: /* /\* cuts string t into u and v where u ends before last occurence of char 'occ' */
1213: /* and v starts after last occurence of char 'occ' : ex cutv(u,v,"abcdef2ghi2j",'2') */
1214: /* gives u="abcdef2ghi" and v="j" *\/ */
1215: /* int i,lg,j,p=0; */
1216: /* i=0; */
1217: /* lg=strlen(t); */
1218: /* for(j=0; j<=lg-1; j++) { */
1219: /* if((t[j]!= occ) && (t[j+1]== occ)) p=j+1; */
1220: /* } */
1.126 brouard 1221:
1.137 brouard 1222: /* for(j=0; j<p; j++) { */
1223: /* (u[j] = t[j]); */
1224: /* } */
1225: /* u[p]='\0'; */
1.126 brouard 1226:
1.137 brouard 1227: /* for(j=0; j<= lg; j++) { */
1228: /* if (j>=(p+1))(v[j-p-1] = t[j]); */
1229: /* } */
1230: /* } */
1.126 brouard 1231:
1.160 brouard 1232: #ifdef _WIN32
1233: char * strsep(char **pp, const char *delim)
1234: {
1235: char *p, *q;
1236:
1237: if ((p = *pp) == NULL)
1238: return 0;
1239: if ((q = strpbrk (p, delim)) != NULL)
1240: {
1241: *pp = q + 1;
1242: *q = '\0';
1243: }
1244: else
1245: *pp = 0;
1246: return p;
1247: }
1248: #endif
1249:
1.126 brouard 1250: /********************** nrerror ********************/
1251:
1252: void nrerror(char error_text[])
1253: {
1254: fprintf(stderr,"ERREUR ...\n");
1255: fprintf(stderr,"%s\n",error_text);
1256: exit(EXIT_FAILURE);
1257: }
1258: /*********************** vector *******************/
1259: double *vector(int nl, int nh)
1260: {
1261: double *v;
1262: v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
1263: if (!v) nrerror("allocation failure in vector");
1264: return v-nl+NR_END;
1265: }
1266:
1267: /************************ free vector ******************/
1268: void free_vector(double*v, int nl, int nh)
1269: {
1270: free((FREE_ARG)(v+nl-NR_END));
1271: }
1272:
1273: /************************ivector *******************************/
1274: int *ivector(long nl,long nh)
1275: {
1276: int *v;
1277: v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
1278: if (!v) nrerror("allocation failure in ivector");
1279: return v-nl+NR_END;
1280: }
1281:
1282: /******************free ivector **************************/
1283: void free_ivector(int *v, long nl, long nh)
1284: {
1285: free((FREE_ARG)(v+nl-NR_END));
1286: }
1287:
1288: /************************lvector *******************************/
1289: long *lvector(long nl,long nh)
1290: {
1291: long *v;
1292: v=(long *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(long)));
1293: if (!v) nrerror("allocation failure in ivector");
1294: return v-nl+NR_END;
1295: }
1296:
1297: /******************free lvector **************************/
1298: void free_lvector(long *v, long nl, long nh)
1299: {
1300: free((FREE_ARG)(v+nl-NR_END));
1301: }
1302:
1303: /******************* imatrix *******************************/
1304: int **imatrix(long nrl, long nrh, long ncl, long nch)
1305: /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */
1306: {
1307: long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;
1308: int **m;
1309:
1310: /* allocate pointers to rows */
1311: m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));
1312: if (!m) nrerror("allocation failure 1 in matrix()");
1313: m += NR_END;
1314: m -= nrl;
1315:
1316:
1317: /* allocate rows and set pointers to them */
1318: m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));
1319: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
1320: m[nrl] += NR_END;
1321: m[nrl] -= ncl;
1322:
1323: for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;
1324:
1325: /* return pointer to array of pointers to rows */
1326: return m;
1327: }
1328:
1329: /****************** free_imatrix *************************/
1330: void free_imatrix(m,nrl,nrh,ncl,nch)
1331: int **m;
1332: long nch,ncl,nrh,nrl;
1333: /* free an int matrix allocated by imatrix() */
1334: {
1335: free((FREE_ARG) (m[nrl]+ncl-NR_END));
1336: free((FREE_ARG) (m+nrl-NR_END));
1337: }
1338:
1339: /******************* matrix *******************************/
1340: double **matrix(long nrl, long nrh, long ncl, long nch)
1341: {
1342: long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
1343: double **m;
1344:
1345: m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
1346: if (!m) nrerror("allocation failure 1 in matrix()");
1347: m += NR_END;
1348: m -= nrl;
1349:
1350: m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
1351: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
1352: m[nrl] += NR_END;
1353: m[nrl] -= ncl;
1354:
1355: for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
1356: return m;
1.145 brouard 1357: /* print *(*(m+1)+70) or print m[1][70]; print m+1 or print &(m[1]) or &(m[1][0])
1358: m[i] = address of ith row of the table. &(m[i]) is its value which is another adress
1359: that of m[i][0]. In order to get the value p m[i][0] but it is unitialized.
1.126 brouard 1360: */
1361: }
1362:
1363: /*************************free matrix ************************/
1364: void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
1365: {
1366: free((FREE_ARG)(m[nrl]+ncl-NR_END));
1367: free((FREE_ARG)(m+nrl-NR_END));
1368: }
1369:
1370: /******************* ma3x *******************************/
1371: double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
1372: {
1373: long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
1374: double ***m;
1375:
1376: m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
1377: if (!m) nrerror("allocation failure 1 in matrix()");
1378: m += NR_END;
1379: m -= nrl;
1380:
1381: m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
1382: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
1383: m[nrl] += NR_END;
1384: m[nrl] -= ncl;
1385:
1386: for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
1387:
1388: m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
1389: if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
1390: m[nrl][ncl] += NR_END;
1391: m[nrl][ncl] -= nll;
1392: for (j=ncl+1; j<=nch; j++)
1393: m[nrl][j]=m[nrl][j-1]+nlay;
1394:
1395: for (i=nrl+1; i<=nrh; i++) {
1396: m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
1397: for (j=ncl+1; j<=nch; j++)
1398: m[i][j]=m[i][j-1]+nlay;
1399: }
1400: return m;
1401: /* gdb: p *(m+1) <=> p m[1] and p (m+1) <=> p (m+1) <=> p &(m[1])
1402: &(m[i][j][k]) <=> *((*(m+i) + j)+k)
1403: */
1404: }
1405:
1406: /*************************free ma3x ************************/
1407: void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
1408: {
1409: free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
1410: free((FREE_ARG)(m[nrl]+ncl-NR_END));
1411: free((FREE_ARG)(m+nrl-NR_END));
1412: }
1413:
1414: /*************** function subdirf ***********/
1415: char *subdirf(char fileres[])
1416: {
1417: /* Caution optionfilefiname is hidden */
1418: strcpy(tmpout,optionfilefiname);
1419: strcat(tmpout,"/"); /* Add to the right */
1420: strcat(tmpout,fileres);
1421: return tmpout;
1422: }
1423:
1424: /*************** function subdirf2 ***********/
1425: char *subdirf2(char fileres[], char *preop)
1426: {
1427:
1428: /* Caution optionfilefiname is hidden */
1429: strcpy(tmpout,optionfilefiname);
1430: strcat(tmpout,"/");
1431: strcat(tmpout,preop);
1432: strcat(tmpout,fileres);
1433: return tmpout;
1434: }
1435:
1436: /*************** function subdirf3 ***********/
1437: char *subdirf3(char fileres[], char *preop, char *preop2)
1438: {
1439:
1440: /* Caution optionfilefiname is hidden */
1441: strcpy(tmpout,optionfilefiname);
1442: strcat(tmpout,"/");
1443: strcat(tmpout,preop);
1444: strcat(tmpout,preop2);
1445: strcat(tmpout,fileres);
1446: return tmpout;
1447: }
1.213 brouard 1448:
1449: /*************** function subdirfext ***********/
1450: char *subdirfext(char fileres[], char *preop, char *postop)
1451: {
1452:
1453: strcpy(tmpout,preop);
1454: strcat(tmpout,fileres);
1455: strcat(tmpout,postop);
1456: return tmpout;
1457: }
1.126 brouard 1458:
1.213 brouard 1459: /*************** function subdirfext3 ***********/
1460: char *subdirfext3(char fileres[], char *preop, char *postop)
1461: {
1462:
1463: /* Caution optionfilefiname is hidden */
1464: strcpy(tmpout,optionfilefiname);
1465: strcat(tmpout,"/");
1466: strcat(tmpout,preop);
1467: strcat(tmpout,fileres);
1468: strcat(tmpout,postop);
1469: return tmpout;
1470: }
1471:
1.162 brouard 1472: char *asc_diff_time(long time_sec, char ascdiff[])
1473: {
1474: long sec_left, days, hours, minutes;
1475: days = (time_sec) / (60*60*24);
1476: sec_left = (time_sec) % (60*60*24);
1477: hours = (sec_left) / (60*60) ;
1478: sec_left = (sec_left) %(60*60);
1479: minutes = (sec_left) /60;
1480: sec_left = (sec_left) % (60);
1481: sprintf(ascdiff,"%ld day(s) %ld hour(s) %ld minute(s) %ld second(s)",days, hours, minutes, sec_left);
1482: return ascdiff;
1483: }
1484:
1.126 brouard 1485: /***************** f1dim *************************/
1486: extern int ncom;
1487: extern double *pcom,*xicom;
1488: extern double (*nrfunc)(double []);
1489:
1490: double f1dim(double x)
1491: {
1492: int j;
1493: double f;
1494: double *xt;
1495:
1496: xt=vector(1,ncom);
1497: for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];
1498: f=(*nrfunc)(xt);
1499: free_vector(xt,1,ncom);
1500: return f;
1501: }
1502:
1503: /*****************brent *************************/
1504: double brent(double ax, double bx, double cx, double (*f)(double), double tol, double *xmin)
1.187 brouard 1505: {
1506: /* Given a function f, and given a bracketing triplet of abscissas ax, bx, cx (such that bx is
1507: * between ax and cx, and f(bx) is less than both f(ax) and f(cx) ), this routine isolates
1508: * the minimum to a fractional precision of about tol using Brent’s method. The abscissa of
1509: * the minimum is returned as xmin, and the minimum function value is returned as brent , the
1510: * returned function value.
1511: */
1.126 brouard 1512: int iter;
1513: double a,b,d,etemp;
1.159 brouard 1514: double fu=0,fv,fw,fx;
1.164 brouard 1515: double ftemp=0.;
1.126 brouard 1516: double p,q,r,tol1,tol2,u,v,w,x,xm;
1517: double e=0.0;
1518:
1519: a=(ax < cx ? ax : cx);
1520: b=(ax > cx ? ax : cx);
1521: x=w=v=bx;
1522: fw=fv=fx=(*f)(x);
1523: for (iter=1;iter<=ITMAX;iter++) {
1524: xm=0.5*(a+b);
1525: tol2=2.0*(tol1=tol*fabs(x)+ZEPS);
1526: /* if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
1527: printf(".");fflush(stdout);
1528: fprintf(ficlog,".");fflush(ficlog);
1.162 brouard 1529: #ifdef DEBUGBRENT
1.126 brouard 1530: 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);
1531: 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);
1532: /* if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
1533: #endif
1534: if (fabs(x-xm) <= (tol2-0.5*(b-a))){
1535: *xmin=x;
1536: return fx;
1537: }
1538: ftemp=fu;
1539: if (fabs(e) > tol1) {
1540: r=(x-w)*(fx-fv);
1541: q=(x-v)*(fx-fw);
1542: p=(x-v)*q-(x-w)*r;
1543: q=2.0*(q-r);
1544: if (q > 0.0) p = -p;
1545: q=fabs(q);
1546: etemp=e;
1547: e=d;
1548: if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))
1549: d=CGOLD*(e=(x >= xm ? a-x : b-x));
1550: else {
1551: d=p/q;
1552: u=x+d;
1553: if (u-a < tol2 || b-u < tol2)
1554: d=SIGN(tol1,xm-x);
1555: }
1556: } else {
1557: d=CGOLD*(e=(x >= xm ? a-x : b-x));
1558: }
1559: u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));
1560: fu=(*f)(u);
1561: if (fu <= fx) {
1562: if (u >= x) a=x; else b=x;
1563: SHFT(v,w,x,u)
1.183 brouard 1564: SHFT(fv,fw,fx,fu)
1565: } else {
1566: if (u < x) a=u; else b=u;
1567: if (fu <= fw || w == x) {
1568: v=w;
1569: w=u;
1570: fv=fw;
1571: fw=fu;
1572: } else if (fu <= fv || v == x || v == w) {
1573: v=u;
1574: fv=fu;
1575: }
1576: }
1.126 brouard 1577: }
1578: nrerror("Too many iterations in brent");
1579: *xmin=x;
1580: return fx;
1581: }
1582:
1583: /****************** mnbrak ***********************/
1584:
1585: void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,
1586: double (*func)(double))
1.183 brouard 1587: { /* Given a function func , and given distinct initial points ax and bx , this routine searches in
1588: the downhill direction (defined by the function as evaluated at the initial points) and returns
1589: new points ax , bx , cx that bracket a minimum of the function. Also returned are the function
1590: values at the three points, fa, fb , and fc such that fa > fb and fb < fc.
1591: */
1.126 brouard 1592: double ulim,u,r,q, dum;
1593: double fu;
1.187 brouard 1594:
1595: double scale=10.;
1596: int iterscale=0;
1597:
1598: *fa=(*func)(*ax); /* xta[j]=pcom[j]+(*ax)*xicom[j]; fa=f(xta[j])*/
1599: *fb=(*func)(*bx); /* xtb[j]=pcom[j]+(*bx)*xicom[j]; fb=f(xtb[j]) */
1600:
1601:
1602: /* while(*fb != *fb){ /\* *ax should be ok, reducing distance to *ax *\/ */
1603: /* printf("Warning mnbrak *fb = %lf, *bx=%lf *ax=%lf *fa==%lf iter=%d\n",*fb, *bx, *ax, *fa, iterscale++); */
1604: /* *bx = *ax - (*ax - *bx)/scale; */
1605: /* *fb=(*func)(*bx); /\* xtb[j]=pcom[j]+(*bx)*xicom[j]; fb=f(xtb[j]) *\/ */
1606: /* } */
1607:
1.126 brouard 1608: if (*fb > *fa) {
1609: SHFT(dum,*ax,*bx,dum)
1.183 brouard 1610: SHFT(dum,*fb,*fa,dum)
1611: }
1.126 brouard 1612: *cx=(*bx)+GOLD*(*bx-*ax);
1613: *fc=(*func)(*cx);
1.183 brouard 1614: #ifdef DEBUG
1615: printf("mnbrak0 *fb=%.12e *fc=%.12e\n",*fb,*fc);
1616: fprintf(ficlog,"mnbrak0 *fb=%.12e *fc=%.12e\n",*fb,*fc);
1617: #endif
1618: while (*fb > *fc) { /* Declining a,b,c with fa> fb > fc */
1.126 brouard 1619: r=(*bx-*ax)*(*fb-*fc);
1620: q=(*bx-*cx)*(*fb-*fa);
1621: u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/
1.183 brouard 1622: (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r)); /* Minimum abscissa of a parabolic estimated from (a,fa), (b,fb) and (c,fc). */
1623: ulim=(*bx)+GLIMIT*(*cx-*bx); /* Maximum abscissa where function should be evaluated */
1624: if ((*bx-u)*(u-*cx) > 0.0) { /* if u_p is between b and c */
1.126 brouard 1625: fu=(*func)(u);
1.163 brouard 1626: #ifdef DEBUG
1627: /* f(x)=A(x-u)**2+f(u) */
1628: double A, fparabu;
1629: A= (*fb - *fa)/(*bx-*ax)/(*bx+*ax-2*u);
1630: fparabu= *fa - A*(*ax-u)*(*ax-u);
1631: 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);
1632: 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 1633: /* And thus,it can be that fu > *fc even if fparabu < *fc */
1634: /* mnbrak (*ax=7.666299858533, *fa=299039.693133272231), (*bx=8.595447774979, *fb=298976.598289369489),
1635: (*cx=10.098840694817, *fc=298946.631474258087), (*u=9.852501168332, fu=298948.773013752128, fparabu=298945.434711494134) */
1636: /* In that case, there is no bracket in the output! Routine is wrong with many consequences.*/
1.163 brouard 1637: #endif
1.184 brouard 1638: #ifdef MNBRAKORIGINAL
1.183 brouard 1639: #else
1.191 brouard 1640: /* if (fu > *fc) { */
1641: /* #ifdef DEBUG */
1642: /* printf("mnbrak4 fu > fc \n"); */
1643: /* fprintf(ficlog, "mnbrak4 fu > fc\n"); */
1644: /* #endif */
1645: /* /\* 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 *\\/ *\/ */
1646: /* /\* SHFT(*fa,*fc,fu,*fc) /\\* (b, u, c) is a bracket while test fb > fc will be fu > fc will exit *\\/ *\/ */
1647: /* dum=u; /\* Shifting c and u *\/ */
1648: /* u = *cx; */
1649: /* *cx = dum; */
1650: /* dum = fu; */
1651: /* fu = *fc; */
1652: /* *fc =dum; */
1653: /* } else { /\* end *\/ */
1654: /* #ifdef DEBUG */
1655: /* printf("mnbrak3 fu < fc \n"); */
1656: /* fprintf(ficlog, "mnbrak3 fu < fc\n"); */
1657: /* #endif */
1658: /* dum=u; /\* Shifting c and u *\/ */
1659: /* u = *cx; */
1660: /* *cx = dum; */
1661: /* dum = fu; */
1662: /* fu = *fc; */
1663: /* *fc =dum; */
1664: /* } */
1.183 brouard 1665: #ifdef DEBUG
1.191 brouard 1666: printf("mnbrak34 fu < or >= fc \n");
1667: fprintf(ficlog, "mnbrak34 fu < fc\n");
1.183 brouard 1668: #endif
1.191 brouard 1669: dum=u; /* Shifting c and u */
1670: u = *cx;
1671: *cx = dum;
1672: dum = fu;
1673: fu = *fc;
1674: *fc =dum;
1.183 brouard 1675: #endif
1.162 brouard 1676: } else if ((*cx-u)*(u-ulim) > 0.0) { /* u is after c but before ulim */
1.183 brouard 1677: #ifdef DEBUG
1678: printf("mnbrak2 u after c but before ulim\n");
1679: fprintf(ficlog, "mnbrak2 u after c but before ulim\n");
1680: #endif
1.126 brouard 1681: fu=(*func)(u);
1682: if (fu < *fc) {
1.183 brouard 1683: #ifdef DEBUG
1684: printf("mnbrak2 u after c but before ulim AND fu < fc\n");
1685: fprintf(ficlog, "mnbrak2 u after c but before ulim AND fu <fc \n");
1686: #endif
1.126 brouard 1687: SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))
1.183 brouard 1688: SHFT(*fb,*fc,fu,(*func)(u))
1689: }
1.162 brouard 1690: } else if ((u-ulim)*(ulim-*cx) >= 0.0) { /* u outside ulim (verifying that ulim is beyond c) */
1.183 brouard 1691: #ifdef DEBUG
1692: printf("mnbrak2 u outside ulim (verifying that ulim is beyond c)\n");
1693: fprintf(ficlog, "mnbrak2 u outside ulim (verifying that ulim is beyond c)\n");
1694: #endif
1.126 brouard 1695: u=ulim;
1696: fu=(*func)(u);
1.183 brouard 1697: } else { /* u could be left to b (if r > q parabola has a maximum) */
1698: #ifdef DEBUG
1699: printf("mnbrak2 u could be left to b (if r > q parabola has a maximum)\n");
1700: fprintf(ficlog, "mnbrak2 u could be left to b (if r > q parabola has a maximum)\n");
1701: #endif
1.126 brouard 1702: u=(*cx)+GOLD*(*cx-*bx);
1703: fu=(*func)(u);
1.183 brouard 1704: } /* end tests */
1.126 brouard 1705: SHFT(*ax,*bx,*cx,u)
1.183 brouard 1706: SHFT(*fa,*fb,*fc,fu)
1707: #ifdef DEBUG
1708: 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);
1709: 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);
1710: #endif
1711: } /* 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 1712: }
1713:
1714: /*************** linmin ************************/
1.162 brouard 1715: /* Given an n -dimensional point p[1..n] and an n -dimensional direction xi[1..n] , moves and
1716: resets p to where the function func(p) takes on a minimum along the direction xi from p ,
1717: and replaces xi by the actual vector displacement that p was moved. Also returns as fret
1718: the value of func at the returned location p . This is actually all accomplished by calling the
1719: routines mnbrak and brent .*/
1.126 brouard 1720: int ncom;
1721: double *pcom,*xicom;
1722: double (*nrfunc)(double []);
1723:
1724: void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))
1725: {
1726: double brent(double ax, double bx, double cx,
1727: double (*f)(double), double tol, double *xmin);
1728: double f1dim(double x);
1729: void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,
1730: double *fc, double (*func)(double));
1731: int j;
1732: double xx,xmin,bx,ax;
1733: double fx,fb,fa;
1.187 brouard 1734:
1.203 brouard 1735: #ifdef LINMINORIGINAL
1736: #else
1737: double scale=10., axs, xxs; /* Scale added for infinity */
1738: #endif
1739:
1.126 brouard 1740: ncom=n;
1741: pcom=vector(1,n);
1742: xicom=vector(1,n);
1743: nrfunc=func;
1744: for (j=1;j<=n;j++) {
1745: pcom[j]=p[j];
1.202 brouard 1746: xicom[j]=xi[j]; /* Former scale xi[j] of currrent direction i */
1.126 brouard 1747: }
1.187 brouard 1748:
1.203 brouard 1749: #ifdef LINMINORIGINAL
1750: xx=1.;
1751: #else
1752: axs=0.0;
1753: xxs=1.;
1754: do{
1755: xx= xxs;
1756: #endif
1.187 brouard 1757: ax=0.;
1758: mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim); /* Outputs: xtx[j]=pcom[j]+(*xx)*xicom[j]; fx=f(xtx[j]) */
1759: /* brackets with inputs ax=0 and xx=1, but points, pcom=p, and directions values, xicom=xi, are sent via f1dim(x) */
1760: /* 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)) */
1761: /* Outputs: fa=f(p(j)) and fx=f(p(j) + xxs * xi(j) ) and f(bx)= f(p(j)+ bx* xi(j)) */
1762: /* Given input ax=axs and xx=xxs, xx might be too far from ax to get a finite f(xx) */
1763: /* Searches on line, outputs (ax, xx, bx) such that fx < min(fa and fb) */
1764: /* 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 1765: #ifdef LINMINORIGINAL
1766: #else
1767: if (fx != fx){
1768: xxs=xxs/scale; /* Trying a smaller xx, closer to initial ax=0 */
1769: printf("|");
1770: fprintf(ficlog,"|");
1771: #ifdef DEBUGLINMIN
1772: 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);
1773: #endif
1774: }
1775: }while(fx != fx);
1776: #endif
1777:
1.191 brouard 1778: #ifdef DEBUGLINMIN
1779: 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 1780: 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 1781: #endif
1.187 brouard 1782: *fret=brent(ax,xx,bx,f1dim,TOL,&xmin); /* Giving a bracketting triplet (ax, xx, bx), find a minimum, xmin, according to f1dim, *fret(xmin),*/
1783: /* fa = f(p[j] + ax * xi[j]), fx = f(p[j] + xx * xi[j]), fb = f(p[j] + bx * xi[j]) */
1784: /* fmin = f(p[j] + xmin * xi[j]) */
1785: /* P+lambda n in that direction (lambdamin), with TOL between abscisses */
1786: /* f1dim(xmin): for (j=1;j<=ncom;j++) xt[j]=pcom[j]+xmin*xicom[j]; */
1.126 brouard 1787: #ifdef DEBUG
1788: printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
1789: fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
1790: #endif
1.191 brouard 1791: #ifdef DEBUGLINMIN
1792: printf("linmin end ");
1.202 brouard 1793: fprintf(ficlog,"linmin end ");
1.191 brouard 1794: #endif
1.126 brouard 1795: for (j=1;j<=n;j++) {
1.203 brouard 1796: #ifdef LINMINORIGINAL
1797: xi[j] *= xmin;
1798: #else
1799: #ifdef DEBUGLINMIN
1800: if(xxs <1.0)
1801: printf(" before xi[%d]=%12.8f", j,xi[j]);
1802: #endif
1803: 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) */
1804: #ifdef DEBUGLINMIN
1805: if(xxs <1.0)
1806: 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 );
1807: #endif
1808: #endif
1.187 brouard 1809: p[j] += xi[j]; /* Parameters values are updated accordingly */
1.126 brouard 1810: }
1.191 brouard 1811: #ifdef DEBUGLINMIN
1.203 brouard 1812: printf("\n");
1.191 brouard 1813: printf("Comparing last *frec(xmin=%12.8f)=%12.8f from Brent and frec(0.)=%12.8f \n", xmin, *fret, (*func)(p));
1.202 brouard 1814: 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 1815: for (j=1;j<=n;j++) {
1.202 brouard 1816: printf(" xi[%d]= %14.10f p[%d]= %12.7f",j,xi[j],j,p[j]);
1817: fprintf(ficlog," xi[%d]= %14.10f p[%d]= %12.7f",j,xi[j],j,p[j]);
1818: if(j % ncovmodel == 0){
1.191 brouard 1819: printf("\n");
1.202 brouard 1820: fprintf(ficlog,"\n");
1821: }
1.191 brouard 1822: }
1.203 brouard 1823: #else
1.191 brouard 1824: #endif
1.126 brouard 1825: free_vector(xicom,1,n);
1826: free_vector(pcom,1,n);
1827: }
1828:
1829:
1830: /*************** powell ************************/
1.162 brouard 1831: /*
1832: Minimization of a function func of n variables. Input consists of an initial starting point
1833: p[1..n] ; an initial matrix xi[1..n][1..n] , whose columns contain the initial set of di-
1834: rections (usually the n unit vectors); and ftol , the fractional tolerance in the function value
1835: such that failure to decrease by more than this amount on one iteration signals doneness. On
1836: output, p is set to the best point found, xi is the then-current direction set, fret is the returned
1837: function value at p , and iter is the number of iterations taken. The routine linmin is used.
1838: */
1.126 brouard 1839: void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,
1840: double (*func)(double []))
1841: {
1842: void linmin(double p[], double xi[], int n, double *fret,
1843: double (*func)(double []));
1844: int i,ibig,j;
1845: double del,t,*pt,*ptt,*xit;
1.181 brouard 1846: double directest;
1.126 brouard 1847: double fp,fptt;
1848: double *xits;
1849: int niterf, itmp;
1850:
1851: pt=vector(1,n);
1852: ptt=vector(1,n);
1853: xit=vector(1,n);
1854: xits=vector(1,n);
1855: *fret=(*func)(p);
1856: for (j=1;j<=n;j++) pt[j]=p[j];
1.202 brouard 1857: rcurr_time = time(NULL);
1.126 brouard 1858: for (*iter=1;;++(*iter)) {
1.187 brouard 1859: fp=(*fret); /* From former iteration or initial value */
1.126 brouard 1860: ibig=0;
1861: del=0.0;
1.157 brouard 1862: rlast_time=rcurr_time;
1863: /* (void) gettimeofday(&curr_time,&tzp); */
1864: rcurr_time = time(NULL);
1865: curr_time = *localtime(&rcurr_time);
1866: printf("\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret, rcurr_time-rlast_time, rcurr_time-rstart_time);fflush(stdout);
1867: fprintf(ficlog,"\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret,rcurr_time-rlast_time, rcurr_time-rstart_time); fflush(ficlog);
1868: /* fprintf(ficrespow,"%d %.12f %ld",*iter,*fret,curr_time.tm_sec-start_time.tm_sec); */
1.192 brouard 1869: for (i=1;i<=n;i++) {
1.126 brouard 1870: printf(" %d %.12f",i, p[i]);
1871: fprintf(ficlog," %d %.12lf",i, p[i]);
1872: fprintf(ficrespow," %.12lf", p[i]);
1873: }
1874: printf("\n");
1875: fprintf(ficlog,"\n");
1876: fprintf(ficrespow,"\n");fflush(ficrespow);
1877: if(*iter <=3){
1.157 brouard 1878: tml = *localtime(&rcurr_time);
1879: strcpy(strcurr,asctime(&tml));
1880: rforecast_time=rcurr_time;
1.126 brouard 1881: itmp = strlen(strcurr);
1882: if(strcurr[itmp-1]=='\n') /* Windows outputs with a new line */
1883: strcurr[itmp-1]='\0';
1.162 brouard 1884: printf("\nConsidering the time needed for the last iteration #%d: %ld seconds,\n",*iter,rcurr_time-rlast_time);
1.157 brouard 1885: fprintf(ficlog,"\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,rcurr_time-rlast_time);
1.126 brouard 1886: for(niterf=10;niterf<=30;niterf+=10){
1.157 brouard 1887: rforecast_time=rcurr_time+(niterf-*iter)*(rcurr_time-rlast_time);
1888: forecast_time = *localtime(&rforecast_time);
1889: strcpy(strfor,asctime(&forecast_time));
1.126 brouard 1890: itmp = strlen(strfor);
1891: if(strfor[itmp-1]=='\n')
1892: strfor[itmp-1]='\0';
1.157 brouard 1893: 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);
1894: 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 1895: }
1896: }
1.187 brouard 1897: for (i=1;i<=n;i++) { /* For each direction i */
1898: for (j=1;j<=n;j++) xit[j]=xi[j][i]; /* Directions stored from previous iteration with previous scales */
1.126 brouard 1899: fptt=(*fret);
1900: #ifdef DEBUG
1.203 brouard 1901: printf("fret=%lf, %lf, %lf \n", *fret, *fret, *fret);
1902: fprintf(ficlog, "fret=%lf, %lf, %lf \n", *fret, *fret, *fret);
1.126 brouard 1903: #endif
1.203 brouard 1904: printf("%d",i);fflush(stdout); /* print direction (parameter) i */
1.126 brouard 1905: fprintf(ficlog,"%d",i);fflush(ficlog);
1.188 brouard 1906: linmin(p,xit,n,fret,func); /* Point p[n]. xit[n] has been loaded for direction i as input.*/
1907: /* Outputs are fret(new point p) p is updated and xit rescaled */
1908: if (fabs(fptt-(*fret)) > del) { /* We are keeping the max gain on each of the n directions */
1909: /* because that direction will be replaced unless the gain del is small */
1910: /* in comparison with the 'probable' gain, mu^2, with the last average direction. */
1911: /* Unless the n directions are conjugate some gain in the determinant may be obtained */
1912: /* with the new direction. */
1.126 brouard 1913: del=fabs(fptt-(*fret));
1914: ibig=i;
1915: }
1916: #ifdef DEBUG
1917: printf("%d %.12e",i,(*fret));
1918: fprintf(ficlog,"%d %.12e",i,(*fret));
1919: for (j=1;j<=n;j++) {
1920: xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
1921: printf(" x(%d)=%.12e",j,xit[j]);
1922: fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
1923: }
1924: for(j=1;j<=n;j++) {
1.162 brouard 1925: printf(" p(%d)=%.12e",j,p[j]);
1926: fprintf(ficlog," p(%d)=%.12e",j,p[j]);
1.126 brouard 1927: }
1928: printf("\n");
1929: fprintf(ficlog,"\n");
1930: #endif
1.187 brouard 1931: } /* end loop on each direction i */
1932: /* Convergence test will use last linmin estimation (fret) and compare former iteration (fp) */
1.188 brouard 1933: /* But p and xit have been updated at the end of linmin, *fret corresponds to new p, xit */
1.187 brouard 1934: /* New value of last point Pn is not computed, P(n-1) */
1.182 brouard 1935: if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) { /* Did we reach enough precision? */
1.188 brouard 1936: /* We could compare with a chi^2. chisquare(0.95,ddl=1)=3.84 */
1937: /* By adding age*age in a model, the new -2LL should be lower and the difference follows a */
1938: /* a chisquare statistics with 1 degree. To be significant at the 95% level, it should have */
1939: /* decreased of more than 3.84 */
1940: /* By adding age*age and V1*age the gain (-2LL) should be more than 5.99 (ddl=2) */
1941: /* By using V1+V2+V3, the gain should be 7.82, compared with basic 1+age. */
1942: /* By adding 10 parameters more the gain should be 18.31 */
1943:
1944: /* Starting the program with initial values given by a former maximization will simply change */
1945: /* the scales of the directions and the directions, because the are reset to canonical directions */
1946: /* Thus the first calls to linmin will give new points and better maximizations until fp-(*fret) is */
1947: /* under the tolerance value. If the tolerance is very small 1.e-9, it could last long. */
1.126 brouard 1948: #ifdef DEBUG
1949: int k[2],l;
1950: k[0]=1;
1951: k[1]=-1;
1952: printf("Max: %.12e",(*func)(p));
1953: fprintf(ficlog,"Max: %.12e",(*func)(p));
1954: for (j=1;j<=n;j++) {
1955: printf(" %.12e",p[j]);
1956: fprintf(ficlog," %.12e",p[j]);
1957: }
1958: printf("\n");
1959: fprintf(ficlog,"\n");
1960: for(l=0;l<=1;l++) {
1961: for (j=1;j<=n;j++) {
1962: ptt[j]=p[j]+(p[j]-pt[j])*k[l];
1963: printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
1964: fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
1965: }
1966: printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
1967: fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
1968: }
1969: #endif
1970:
1971:
1972: free_vector(xit,1,n);
1973: free_vector(xits,1,n);
1974: free_vector(ptt,1,n);
1975: free_vector(pt,1,n);
1976: return;
1.192 brouard 1977: } /* enough precision */
1.126 brouard 1978: if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");
1.181 brouard 1979: for (j=1;j<=n;j++) { /* Computes the extrapolated point P_0 + 2 (P_n-P_0) */
1.126 brouard 1980: ptt[j]=2.0*p[j]-pt[j];
1981: xit[j]=p[j]-pt[j];
1982: pt[j]=p[j];
1983: }
1.181 brouard 1984: fptt=(*func)(ptt); /* f_3 */
1.192 brouard 1985: #ifdef POWELLF1F3
1986: #else
1.161 brouard 1987: if (fptt < fp) { /* If extrapolated point is better, decide if we keep that new direction or not */
1.192 brouard 1988: #endif
1.162 brouard 1989: /* (x1 f1=fp), (x2 f2=*fret), (x3 f3=fptt), (xm fm) */
1.161 brouard 1990: /* From x1 (P0) distance of x2 is at h and x3 is 2h */
1.162 brouard 1991: /* Let f"(x2) be the 2nd derivative equal everywhere. */
1992: /* Then the parabolic through (x1,f1), (x2,f2) and (x3,f3) */
1993: /* will reach at f3 = fm + h^2/2 f"m ; f" = (f1 -2f2 +f3 ) / h**2 */
1.181 brouard 1994: /* Conditional for using this new direction is that mu^2 = (f1-2f2+f3)^2 /2 < del */
1.161 brouard 1995: /* t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt); */
1.183 brouard 1996: #ifdef NRCORIGINAL
1997: t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)- del*SQR(fp-fptt); /* Original Numerical Recipes in C*/
1998: #else
1999: 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 2000: t= t- del*SQR(fp-fptt);
1.183 brouard 2001: #endif
1.202 brouard 2002: directest = fp-2.0*(*fret)+fptt - 2.0 * del; /* If delta was big enough we change it for a new direction */
1.161 brouard 2003: #ifdef DEBUG
1.181 brouard 2004: 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);
2005: 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 2006: printf("t3= %.12lf, t4= %.12lf, t3*= %.12lf, t4*= %.12lf\n",SQR(fp-(*fret)-del),SQR(fp-fptt),
2007: (fp-(*fret)-del)*(fp-(*fret)-del),(fp-fptt)*(fp-fptt));
2008: fprintf(ficlog,"t3= %.12lf, t4= %.12lf, t3*= %.12lf, t4*= %.12lf\n",SQR(fp-(*fret)-del),SQR(fp-fptt),
2009: (fp-(*fret)-del)*(fp-(*fret)-del),(fp-fptt)*(fp-fptt));
2010: 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);
2011: 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);
2012: #endif
1.183 brouard 2013: #ifdef POWELLORIGINAL
2014: if (t < 0.0) { /* Then we use it for new direction */
2015: #else
1.182 brouard 2016: if (directest*t < 0.0) { /* Contradiction between both tests */
1.202 brouard 2017: 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 2018: 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 2019: 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 2020: fprintf(ficlog,"f1-2f2+f3= %.12lf, f1-f2-del= %.12lf, f1-f3= %.12lf\n",fp-2.0*(*fret)+fptt, fp -(*fret) -del, fp-fptt);
2021: }
1.181 brouard 2022: if (directest < 0.0) { /* Then we use it for new direction */
2023: #endif
1.191 brouard 2024: #ifdef DEBUGLINMIN
2025: printf("Before linmin in direction P%d-P0\n",n);
2026: for (j=1;j<=n;j++) {
1.202 brouard 2027: printf(" Before xit[%d]= %12.7f p[%d]= %12.7f",j,xit[j],j,p[j]);
2028: fprintf(ficlog," Before xit[%d]= %12.7f p[%d]= %12.7f",j,xit[j],j,p[j]);
2029: if(j % ncovmodel == 0){
1.191 brouard 2030: printf("\n");
1.202 brouard 2031: fprintf(ficlog,"\n");
2032: }
1.191 brouard 2033: }
2034: #endif
1.187 brouard 2035: linmin(p,xit,n,fret,func); /* computes minimum on the extrapolated direction: changes p and rescales xit.*/
1.191 brouard 2036: #ifdef DEBUGLINMIN
2037: for (j=1;j<=n;j++) {
2038: printf("After xit[%d]= %12.7f p[%d]= %12.7f",j,xit[j],j,p[j]);
1.202 brouard 2039: fprintf(ficlog,"After xit[%d]= %12.7f p[%d]= %12.7f",j,xit[j],j,p[j]);
2040: if(j % ncovmodel == 0){
1.191 brouard 2041: printf("\n");
1.202 brouard 2042: fprintf(ficlog,"\n");
2043: }
1.191 brouard 2044: }
2045: #endif
1.126 brouard 2046: for (j=1;j<=n;j++) {
1.181 brouard 2047: xi[j][ibig]=xi[j][n]; /* Replace direction with biggest decrease by last direction n */
2048: xi[j][n]=xit[j]; /* and this nth direction by the by the average p_0 p_n */
1.126 brouard 2049: }
1.181 brouard 2050: printf("Gaining to use new average direction of P0 P%d instead of biggest increase direction %d :\n",n,ibig);
2051: fprintf(ficlog,"Gaining to use new average direction of P0 P%d instead of biggest increase direction %d :\n",n,ibig);
1.161 brouard 2052:
1.126 brouard 2053: #ifdef DEBUG
1.164 brouard 2054: printf("Direction changed last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
2055: fprintf(ficlog,"Direction changed last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
1.126 brouard 2056: for(j=1;j<=n;j++){
2057: printf(" %.12e",xit[j]);
2058: fprintf(ficlog," %.12e",xit[j]);
2059: }
2060: printf("\n");
2061: fprintf(ficlog,"\n");
2062: #endif
1.192 brouard 2063: } /* end of t or directest negative */
2064: #ifdef POWELLF1F3
2065: #else
1.162 brouard 2066: } /* end if (fptt < fp) */
1.192 brouard 2067: #endif
2068: } /* loop iteration */
1.126 brouard 2069: }
2070:
2071: /**** Prevalence limit (stable or period prevalence) ****************/
2072:
1.203 brouard 2073: double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int *ncvyear, int ij)
1.126 brouard 2074: {
1.218 brouard 2075: /* Computes the prevalence limit in each live state at age x and for covariate ij by left multiplying the unit
1.203 brouard 2076: matrix by transitions matrix until convergence is reached with precision ftolpl */
1.206 brouard 2077: /* Wx= Wx-1 Px-1= Wx-2 Px-2 Px-1 = Wx-n Px-n ... Px-2 Px-1 I */
2078: /* Wx is row vector: population in state 1, population in state 2, population dead */
2079: /* or prevalence in state 1, prevalence in state 2, 0 */
2080: /* newm is the matrix after multiplications, its rows are identical at a factor */
2081: /* Initial matrix pimij */
2082: /* {0.85204250825084937, 0.13044499163996345, 0.017512500109187184, */
2083: /* 0.090851990222114765, 0.88271245433047185, 0.026435555447413338, */
2084: /* 0, 0 , 1} */
2085: /*
2086: * and after some iteration: */
2087: /* {0.45504275246439968, 0.42731458730878791, 0.11764266022681241, */
2088: /* 0.45201005341706885, 0.42865420071559901, 0.11933574586733192, */
2089: /* 0, 0 , 1} */
2090: /* And prevalence by suppressing the deaths are close to identical rows in prlim: */
2091: /* {0.51571254859325999, 0.4842874514067399, */
2092: /* 0.51326036147820708, 0.48673963852179264} */
2093: /* If we start from prlim again, prlim tends to a constant matrix */
2094:
1.126 brouard 2095: int i, ii,j,k;
1.209 brouard 2096: double *min, *max, *meandiff, maxmax,sumnew=0.;
1.145 brouard 2097: /* double **matprod2(); */ /* test */
1.218 brouard 2098: double **out, cov[NCOVMAX+1], **pmij(); /* **pmmij is a global variable feeded with oldms etc */
1.126 brouard 2099: double **newm;
1.209 brouard 2100: double agefin, delaymax=200. ; /* 100 Max number of years to converge */
1.203 brouard 2101: int ncvloop=0;
1.169 brouard 2102:
1.209 brouard 2103: min=vector(1,nlstate);
2104: max=vector(1,nlstate);
2105: meandiff=vector(1,nlstate);
2106:
1.218 brouard 2107: /* Starting with matrix unity */
1.126 brouard 2108: for (ii=1;ii<=nlstate+ndeath;ii++)
2109: for (j=1;j<=nlstate+ndeath;j++){
2110: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
2111: }
1.169 brouard 2112:
2113: cov[1]=1.;
2114:
2115: /* Even if hstepm = 1, at least one multiplication by the unit matrix */
1.202 brouard 2116: /* Start at agefin= age, computes the matrix of passage and loops decreasing agefin until convergence is reached */
1.126 brouard 2117: for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
1.202 brouard 2118: ncvloop++;
1.126 brouard 2119: newm=savm;
2120: /* Covariates have to be included here again */
1.138 brouard 2121: cov[2]=agefin;
1.187 brouard 2122: if(nagesqr==1)
2123: cov[3]= agefin*agefin;;
1.138 brouard 2124: for (k=1; k<=cptcovn;k++) {
1.200 brouard 2125: /* cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,Tvar[k])]; */
1.218 brouard 2126: /* Here comes the value of the covariate 'ij' */
1.200 brouard 2127: cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,k)];
1.198 brouard 2128: /* 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 2129: }
1.186 brouard 2130: /*wrong? for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
1.200 brouard 2131: /* for (k=1; k<=cptcovage;k++) cov[2+nagesqr+Tage[k]]=nbcode[Tvar[k]][codtabm(ij,Tvar[k])]*cov[2]; */
2132: for (k=1; k<=cptcovage;k++) cov[2+nagesqr+Tage[k]]=nbcode[Tvar[k]][codtabm(ij,k)]*cov[2];
1.186 brouard 2133: for (k=1; k<=cptcovprod;k++) /* Useless */
1.200 brouard 2134: /* cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,Tvard[k][1])] * nbcode[Tvard[k][2]][codtabm(ij,Tvard[k][2])]; */
2135: cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)] * nbcode[Tvard[k][2]][codtabm(ij,k)];
1.138 brouard 2136:
2137: /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
2138: /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
2139: /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
1.145 brouard 2140: /* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
2141: /* out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /\* Bug Valgrind *\/ */
1.218 brouard 2142: /* age and covariate values of ij are in 'cov' */
1.142 brouard 2143: out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /* Bug Valgrind */
1.138 brouard 2144:
1.126 brouard 2145: savm=oldm;
2146: oldm=newm;
1.209 brouard 2147:
2148: for(j=1; j<=nlstate; j++){
2149: max[j]=0.;
2150: min[j]=1.;
2151: }
2152: for(i=1;i<=nlstate;i++){
2153: sumnew=0;
2154: for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
2155: for(j=1; j<=nlstate; j++){
2156: prlim[i][j]= newm[i][j]/(1-sumnew);
2157: max[j]=FMAX(max[j],prlim[i][j]);
2158: min[j]=FMIN(min[j],prlim[i][j]);
2159: }
2160: }
2161:
1.126 brouard 2162: maxmax=0.;
1.209 brouard 2163: for(j=1; j<=nlstate; j++){
2164: meandiff[j]=(max[j]-min[j])/(max[j]+min[j])*2.; /* mean difference for each column */
2165: maxmax=FMAX(maxmax,meandiff[j]);
2166: /* 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 2167: } /* j loop */
1.203 brouard 2168: *ncvyear= (int)age- (int)agefin;
1.208 brouard 2169: /* 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 2170: if(maxmax < ftolpl){
1.209 brouard 2171: /* printf("maxmax=%lf ncvloop=%ld, age=%d, agefin=%d ncvyear=%d \n", maxmax, ncvloop, (int)age, (int)agefin, *ncvyear); */
2172: free_vector(min,1,nlstate);
2173: free_vector(max,1,nlstate);
2174: free_vector(meandiff,1,nlstate);
1.126 brouard 2175: return prlim;
2176: }
1.169 brouard 2177: } /* age loop */
1.208 brouard 2178: /* After some age loop it doesn't converge */
1.209 brouard 2179: 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 2180: 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 2181: /* 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); */
2182: free_vector(min,1,nlstate);
2183: free_vector(max,1,nlstate);
2184: free_vector(meandiff,1,nlstate);
1.208 brouard 2185:
1.169 brouard 2186: return prlim; /* should not reach here */
1.126 brouard 2187: }
2188:
1.217 brouard 2189:
2190: /**** Back Prevalence limit (stable or period prevalence) ****************/
2191:
1.218 brouard 2192: /* 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) */
2193: /* 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) */
2194: double **bprevalim(double **bprlim, double ***prevacurrent, int nlstate, double x[], double age, double ftolpl, int *ncvyear, int ij)
1.217 brouard 2195: {
1.218 brouard 2196: /* Computes the prevalence limit in each live state at age x and covariate ij by left multiplying the unit
1.217 brouard 2197: matrix by transitions matrix until convergence is reached with precision ftolpl */
2198: /* Wx= Wx-1 Px-1= Wx-2 Px-2 Px-1 = Wx-n Px-n ... Px-2 Px-1 I */
2199: /* Wx is row vector: population in state 1, population in state 2, population dead */
2200: /* or prevalence in state 1, prevalence in state 2, 0 */
2201: /* newm is the matrix after multiplications, its rows are identical at a factor */
2202: /* Initial matrix pimij */
2203: /* {0.85204250825084937, 0.13044499163996345, 0.017512500109187184, */
2204: /* 0.090851990222114765, 0.88271245433047185, 0.026435555447413338, */
2205: /* 0, 0 , 1} */
2206: /*
2207: * and after some iteration: */
2208: /* {0.45504275246439968, 0.42731458730878791, 0.11764266022681241, */
2209: /* 0.45201005341706885, 0.42865420071559901, 0.11933574586733192, */
2210: /* 0, 0 , 1} */
2211: /* And prevalence by suppressing the deaths are close to identical rows in prlim: */
2212: /* {0.51571254859325999, 0.4842874514067399, */
2213: /* 0.51326036147820708, 0.48673963852179264} */
2214: /* If we start from prlim again, prlim tends to a constant matrix */
2215:
2216: int i, ii,j,k;
2217: double *min, *max, *meandiff, maxmax,sumnew=0.;
2218: /* double **matprod2(); */ /* test */
2219: double **out, cov[NCOVMAX+1], **bmij();
2220: double **newm;
1.218 brouard 2221: double **dnewm, **doldm, **dsavm; /* for use */
2222: double **oldm, **savm; /* for use */
2223:
1.217 brouard 2224: double agefin, delaymax=200. ; /* 100 Max number of years to converge */
2225: int ncvloop=0;
2226:
2227: min=vector(1,nlstate);
2228: max=vector(1,nlstate);
2229: meandiff=vector(1,nlstate);
2230:
1.218 brouard 2231: dnewm=ddnewms; doldm=ddoldms; dsavm=ddsavms;
2232: oldm=oldms; savm=savms;
2233:
2234: /* Starting with matrix unity */
2235: for (ii=1;ii<=nlstate+ndeath;ii++)
2236: for (j=1;j<=nlstate+ndeath;j++){
1.217 brouard 2237: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
2238: }
2239:
2240: cov[1]=1.;
2241:
2242: /* Even if hstepm = 1, at least one multiplication by the unit matrix */
2243: /* Start at agefin= age, computes the matrix of passage and loops decreasing agefin until convergence is reached */
1.218 brouard 2244: /* for(agefin=age+stepm/YEARM; agefin<=age+delaymax; agefin=agefin+stepm/YEARM){ /\* A changer en age *\/ */
2245: for(agefin=age; agefin<AGESUP; agefin=agefin+stepm/YEARM){ /* A changer en age */
1.217 brouard 2246: ncvloop++;
1.218 brouard 2247: newm=savm; /* oldm should be kept from previous iteration or unity at start */
2248: /* newm points to the allocated table savm passed by the function it can be written, savm could be reallocated */
1.217 brouard 2249: /* Covariates have to be included here again */
2250: cov[2]=agefin;
2251: if(nagesqr==1)
2252: cov[3]= agefin*agefin;;
2253: for (k=1; k<=cptcovn;k++) {
2254: /* cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,Tvar[k])]; */
2255: cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,k)];
2256: /* 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])]); */
2257: }
2258: /*wrong? for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
2259: /* for (k=1; k<=cptcovage;k++) cov[2+nagesqr+Tage[k]]=nbcode[Tvar[k]][codtabm(ij,Tvar[k])]*cov[2]; */
2260: for (k=1; k<=cptcovage;k++) cov[2+nagesqr+Tage[k]]=nbcode[Tvar[k]][codtabm(ij,k)]*cov[2];
2261: for (k=1; k<=cptcovprod;k++) /* Useless */
2262: /* cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,Tvard[k][1])] * nbcode[Tvard[k][2]][codtabm(ij,Tvard[k][2])]; */
2263: cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)] * nbcode[Tvard[k][2]][codtabm(ij,k)];
2264:
2265: /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
2266: /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
2267: /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
2268: /* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
2269: /* out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /\* Bug Valgrind *\/ */
1.218 brouard 2270: /* ij should be linked to the correct index of cov */
2271: /* age and covariate values ij are in 'cov', but we need to pass
2272: * ij for the observed prevalence at age and status and covariate
2273: * number: prevacurrent[(int)agefin][ii][ij]
2274: */
2275: /* 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 *\/ */
2276: /* 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 *\/ */
2277: 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 2278: savm=oldm;
2279: oldm=newm;
2280: for(j=1; j<=nlstate; j++){
2281: max[j]=0.;
2282: min[j]=1.;
2283: }
2284: for(j=1; j<=nlstate; j++){
2285: for(i=1;i<=nlstate;i++){
1.218 brouard 2286: /* bprlim[i][j]= newm[i][j]/(1-sumnew); */
2287: bprlim[i][j]= newm[i][j];
2288: max[i]=FMAX(max[i],bprlim[i][j]); /* Max in line */
2289: min[i]=FMIN(min[i],bprlim[i][j]);
1.217 brouard 2290: }
2291: }
1.218 brouard 2292:
1.217 brouard 2293: maxmax=0.;
2294: for(i=1; i<=nlstate; i++){
2295: meandiff[i]=(max[i]-min[i])/(max[i]+min[i])*2.; /* mean difference for each column */
2296: maxmax=FMAX(maxmax,meandiff[i]);
2297: /* 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); */
2298: } /* j loop */
2299: *ncvyear= -( (int)age- (int)agefin);
1.218 brouard 2300: /* printf("Back maxmax=%lf ncvloop=%d, age=%d, agefin=%d ncvyear=%d \n", maxmax, ncvloop, (int)age, (int)agefin, *ncvyear);*/
1.217 brouard 2301: if(maxmax < ftolpl){
1.220 brouard 2302: /* printf("OK Back maxmax=%lf ncvloop=%d, age=%d, agefin=%d ncvyear=%d \n", maxmax, ncvloop, (int)age, (int)agefin, *ncvyear); */
1.217 brouard 2303: free_vector(min,1,nlstate);
2304: free_vector(max,1,nlstate);
2305: free_vector(meandiff,1,nlstate);
2306: return bprlim;
2307: }
2308: } /* age loop */
2309: /* After some age loop it doesn't converge */
2310: 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\
2311: 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);
2312: /* 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); */
2313: free_vector(min,1,nlstate);
2314: free_vector(max,1,nlstate);
2315: free_vector(meandiff,1,nlstate);
2316:
2317: return bprlim; /* should not reach here */
2318: }
2319:
1.126 brouard 2320: /*************** transition probabilities ***************/
2321:
2322: double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
2323: {
1.138 brouard 2324: /* According to parameters values stored in x and the covariate's values stored in cov,
2325: computes the probability to be observed in state j being in state i by appying the
2326: model to the ncovmodel covariates (including constant and age).
2327: lnpijopii=ln(pij/pii)= aij+bij*age+cij*v1+dij*v2+... = sum_nc=1^ncovmodel xij(nc)*cov[nc]
2328: and, according on how parameters are entered, the position of the coefficient xij(nc) of the
2329: ncth covariate in the global vector x is given by the formula:
2330: j<i nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel
2331: j>=i nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel
2332: Computes ln(pij/pii) (lnpijopii), deduces pij/pii by exponentiation,
2333: sums on j different of i to get 1-pii/pii, deduces pii, and then all pij.
2334: Outputs ps[i][j] the probability to be observed in j being in j according to
2335: the values of the covariates cov[nc] and corresponding parameter values x[nc+shiftij]
2336: */
2337: double s1, lnpijopii;
1.126 brouard 2338: /*double t34;*/
1.164 brouard 2339: int i,j, nc, ii, jj;
1.126 brouard 2340:
1.223 ! brouard 2341: for(i=1; i<= nlstate; i++){
! 2342: for(j=1; j<i;j++){
! 2343: for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
! 2344: /*lnpijopii += param[i][j][nc]*cov[nc];*/
! 2345: lnpijopii += x[nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel]*cov[nc];
! 2346: /* printf("Int j<i s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
! 2347: }
! 2348: ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
! 2349: /* printf("s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
! 2350: }
! 2351: for(j=i+1; j<=nlstate+ndeath;j++){
! 2352: for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
! 2353: /*lnpijopii += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];*/
! 2354: lnpijopii += x[nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel]*cov[nc];
! 2355: /* printf("Int j>i s1=%.17e, lnpijopii=%.17e %lx %lx\n",s1,lnpijopii,s1,lnpijopii); */
! 2356: }
! 2357: ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
! 2358: }
! 2359: }
1.218 brouard 2360:
1.223 ! brouard 2361: for(i=1; i<= nlstate; i++){
! 2362: s1=0;
! 2363: for(j=1; j<i; j++){
! 2364: s1+=exp(ps[i][j]); /* In fact sums pij/pii */
! 2365: /*printf("debug1 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
! 2366: }
! 2367: for(j=i+1; j<=nlstate+ndeath; j++){
! 2368: s1+=exp(ps[i][j]); /* In fact sums pij/pii */
! 2369: /*printf("debug2 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
! 2370: }
! 2371: /* s1= sum_{j<>i} pij/pii=(1-pii)/pii and thus pii is known from s1 */
! 2372: ps[i][i]=1./(s1+1.);
! 2373: /* Computing other pijs */
! 2374: for(j=1; j<i; j++)
! 2375: ps[i][j]= exp(ps[i][j])*ps[i][i];
! 2376: for(j=i+1; j<=nlstate+ndeath; j++)
! 2377: ps[i][j]= exp(ps[i][j])*ps[i][i];
! 2378: /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
! 2379: } /* end i */
1.218 brouard 2380:
1.223 ! brouard 2381: for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
! 2382: for(jj=1; jj<= nlstate+ndeath; jj++){
! 2383: ps[ii][jj]=0;
! 2384: ps[ii][ii]=1;
! 2385: }
! 2386: }
1.218 brouard 2387:
2388:
1.223 ! brouard 2389: /* for(ii=1; ii<= nlstate+ndeath; ii++){ */
! 2390: /* for(jj=1; jj<= nlstate+ndeath; jj++){ */
! 2391: /* printf(" pmij ps[%d][%d]=%lf ",ii,jj,ps[ii][jj]); */
! 2392: /* } */
! 2393: /* printf("\n "); */
! 2394: /* } */
! 2395: /* printf("\n ");printf("%lf ",cov[2]);*/
! 2396: /*
! 2397: for(i=1; i<= npar; i++) printf("%f ",x[i]);
1.218 brouard 2398: goto end;*/
1.223 ! brouard 2399: return ps;
1.126 brouard 2400: }
2401:
1.218 brouard 2402: /*************** backward transition probabilities ***************/
2403:
2404: /* 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 ) */
2405: /* double **bmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate, double ***prevacurrent, double ***dnewm, double **doldm, double **dsavm, int ij ) */
2406: double **bmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate, double ***prevacurrent, int ij )
2407: {
1.222 brouard 2408: /* Computes the backward probability at age agefin and covariate ij
2409: * and returns in **ps as well as **bmij.
2410: */
1.218 brouard 2411: int i, ii, j,k;
1.222 brouard 2412:
2413: double **out, **pmij();
2414: double sumnew=0.;
1.218 brouard 2415: double agefin;
1.222 brouard 2416:
2417: double **dnewm, **dsavm, **doldm;
2418: double **bbmij;
2419:
1.218 brouard 2420: doldm=ddoldms; /* global pointers */
1.222 brouard 2421: dnewm=ddnewms;
2422: dsavm=ddsavms;
2423:
2424: agefin=cov[2];
2425: /* bmij *//* age is cov[2], ij is included in cov, but we need for
2426: the observed prevalence (with this covariate ij) */
2427: dsavm=pmij(pmmij,cov,ncovmodel,x,nlstate);
2428: /* We do have the matrix Px in savm and we need pij */
2429: for (j=1;j<=nlstate+ndeath;j++){
2430: sumnew=0.; /* w1 p11 + w2 p21 only on live states */
2431: for (ii=1;ii<=nlstate;ii++){
2432: sumnew+=dsavm[ii][j]*prevacurrent[(int)agefin][ii][ij];
2433: } /* sumnew is (N11+N21)/N..= N.1/N.. = sum on i of w_i pij */
2434: for (ii=1;ii<=nlstate+ndeath;ii++){
2435: if(sumnew >= 1.e-10){
2436: /* if(agefin >= agemaxpar && agefin <= agemaxpar+stepm/YEARM){ */
2437: /* doldm[ii][j]=(ii==j ? 1./sumnew : 0.0); */
2438: /* }else if(agefin >= agemaxpar+stepm/YEARM){ */
2439: /* doldm[ii][j]=(ii==j ? 1./sumnew : 0.0); */
2440: /* }else */
2441: doldm[ii][j]=(ii==j ? 1./sumnew : 0.0);
2442: }else{
2443: 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);
2444: }
2445: } /*End ii */
2446: } /* End j, At the end doldm is diag[1/(w_1p1i+w_2 p2i)] */
2447: /* left Product of this diag matrix by dsavm=Px (newm=dsavm*doldm) */
2448: bbmij=matprod2(dnewm, dsavm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, doldm); /* Bug Valgrind */
2449: /* dsavm=doldm; /\* dsavm is now diag [1/(w_1p1i+w_2 p2i)] but can be overwritten*\/ */
2450: /* doldm=dnewm; /\* doldm is now Px * diag [1/(w_1p1i+w_2 p2i)] *\/ */
2451: /* dnewm=dsavm; /\* doldm is now Px * diag [1/(w_1p1i+w_2 p2i)] *\/ */
2452: /* left Product of this matrix by diag matrix of prevalences (savm) */
2453: for (j=1;j<=nlstate+ndeath;j++){
2454: for (ii=1;ii<=nlstate+ndeath;ii++){
2455: dsavm[ii][j]=(ii==j ? prevacurrent[(int)agefin][ii][ij] : 0.0);
2456: }
2457: } /* End j, At the end oldm is diag[1/(w_1p1i+w_2 p2i)] */
2458: ps=matprod2(doldm, dsavm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, dnewm); /* Bug Valgrind */
2459: /* newm or out is now diag[w_i] * Px * diag [1/(w_1p1i+w_2 p2i)] */
2460: /* end bmij */
2461: return ps;
1.218 brouard 2462: }
1.217 brouard 2463: /*************** transition probabilities ***************/
2464:
1.218 brouard 2465: double **bpmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
1.217 brouard 2466: {
2467: /* According to parameters values stored in x and the covariate's values stored in cov,
2468: computes the probability to be observed in state j being in state i by appying the
2469: model to the ncovmodel covariates (including constant and age).
2470: lnpijopii=ln(pij/pii)= aij+bij*age+cij*v1+dij*v2+... = sum_nc=1^ncovmodel xij(nc)*cov[nc]
2471: and, according on how parameters are entered, the position of the coefficient xij(nc) of the
2472: ncth covariate in the global vector x is given by the formula:
2473: j<i nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel
2474: j>=i nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel
2475: Computes ln(pij/pii) (lnpijopii), deduces pij/pii by exponentiation,
2476: sums on j different of i to get 1-pii/pii, deduces pii, and then all pij.
2477: Outputs ps[i][j] the probability to be observed in j being in j according to
2478: the values of the covariates cov[nc] and corresponding parameter values x[nc+shiftij]
2479: */
2480: double s1, lnpijopii;
2481: /*double t34;*/
2482: int i,j, nc, ii, jj;
2483:
1.218 brouard 2484: for(i=1; i<= nlstate; i++){
2485: for(j=1; j<i;j++){
2486: for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
2487: /*lnpijopii += param[i][j][nc]*cov[nc];*/
2488: lnpijopii += x[nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel]*cov[nc];
2489: /* printf("Int j<i s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
2490: }
2491: ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
2492: /* printf("s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
2493: }
2494: for(j=i+1; j<=nlstate+ndeath;j++){
2495: for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
2496: /*lnpijopii += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];*/
2497: lnpijopii += x[nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel]*cov[nc];
2498: /* printf("Int j>i s1=%.17e, lnpijopii=%.17e %lx %lx\n",s1,lnpijopii,s1,lnpijopii); */
2499: }
2500: ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
2501: }
2502: }
2503:
2504: for(i=1; i<= nlstate; i++){
2505: s1=0;
2506: for(j=1; j<i; j++){
2507: s1+=exp(ps[i][j]); /* In fact sums pij/pii */
2508: /*printf("debug1 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
2509: }
2510: for(j=i+1; j<=nlstate+ndeath; j++){
2511: s1+=exp(ps[i][j]); /* In fact sums pij/pii */
2512: /*printf("debug2 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
2513: }
2514: /* s1= sum_{j<>i} pij/pii=(1-pii)/pii and thus pii is known from s1 */
2515: ps[i][i]=1./(s1+1.);
2516: /* Computing other pijs */
2517: for(j=1; j<i; j++)
2518: ps[i][j]= exp(ps[i][j])*ps[i][i];
2519: for(j=i+1; j<=nlstate+ndeath; j++)
2520: ps[i][j]= exp(ps[i][j])*ps[i][i];
2521: /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
2522: } /* end i */
2523:
2524: for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
2525: for(jj=1; jj<= nlstate+ndeath; jj++){
2526: ps[ii][jj]=0;
2527: ps[ii][ii]=1;
2528: }
2529: }
2530: /* Added for backcast */ /* Transposed matrix too */
2531: for(jj=1; jj<= nlstate+ndeath; jj++){
2532: s1=0.;
2533: for(ii=1; ii<= nlstate+ndeath; ii++){
2534: s1+=ps[ii][jj];
2535: }
2536: for(ii=1; ii<= nlstate; ii++){
2537: ps[ii][jj]=ps[ii][jj]/s1;
2538: }
2539: }
2540: /* Transposition */
2541: for(jj=1; jj<= nlstate+ndeath; jj++){
2542: for(ii=jj; ii<= nlstate+ndeath; ii++){
2543: s1=ps[ii][jj];
2544: ps[ii][jj]=ps[jj][ii];
2545: ps[jj][ii]=s1;
2546: }
2547: }
2548: /* for(ii=1; ii<= nlstate+ndeath; ii++){ */
2549: /* for(jj=1; jj<= nlstate+ndeath; jj++){ */
2550: /* printf(" pmij ps[%d][%d]=%lf ",ii,jj,ps[ii][jj]); */
2551: /* } */
2552: /* printf("\n "); */
2553: /* } */
2554: /* printf("\n ");printf("%lf ",cov[2]);*/
2555: /*
2556: for(i=1; i<= npar; i++) printf("%f ",x[i]);
2557: goto end;*/
2558: return ps;
1.217 brouard 2559: }
2560:
2561:
1.126 brouard 2562: /**************** Product of 2 matrices ******************/
2563:
1.145 brouard 2564: double **matprod2(double **out, double **in,int nrl, int nrh, int ncl, int nch, int ncolol, int ncoloh, double **b)
1.126 brouard 2565: {
2566: /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
2567: b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
2568: /* in, b, out are matrice of pointers which should have been initialized
2569: before: only the contents of out is modified. The function returns
2570: a pointer to pointers identical to out */
1.145 brouard 2571: int i, j, k;
1.126 brouard 2572: for(i=nrl; i<= nrh; i++)
1.145 brouard 2573: for(k=ncolol; k<=ncoloh; k++){
2574: out[i][k]=0.;
2575: for(j=ncl; j<=nch; j++)
2576: out[i][k] +=in[i][j]*b[j][k];
2577: }
1.126 brouard 2578: return out;
2579: }
2580:
2581:
2582: /************* Higher Matrix Product ***************/
2583:
2584: double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
2585: {
1.218 brouard 2586: /* Computes the transition matrix starting at age 'age' and combination of covariate values corresponding to ij over
1.126 brouard 2587: 'nhstepm*hstepm*stepm' months (i.e. until
2588: age (in years) age+nhstepm*hstepm*stepm/12) by multiplying
2589: nhstepm*hstepm matrices.
2590: Output is stored in matrix po[i][j][h] for h every 'hstepm' step
2591: (typically every 2 years instead of every month which is too big
2592: for the memory).
2593: Model is determined by parameters x and covariates have to be
2594: included manually here.
2595:
2596: */
2597:
2598: int i, j, d, h, k;
1.131 brouard 2599: double **out, cov[NCOVMAX+1];
1.126 brouard 2600: double **newm;
1.187 brouard 2601: double agexact;
1.214 brouard 2602: double agebegin, ageend;
1.126 brouard 2603:
2604: /* Hstepm could be zero and should return the unit matrix */
2605: for (i=1;i<=nlstate+ndeath;i++)
2606: for (j=1;j<=nlstate+ndeath;j++){
2607: oldm[i][j]=(i==j ? 1.0 : 0.0);
2608: po[i][j][0]=(i==j ? 1.0 : 0.0);
2609: }
2610: /* Even if hstepm = 1, at least one multiplication by the unit matrix */
2611: for(h=1; h <=nhstepm; h++){
2612: for(d=1; d <=hstepm; d++){
2613: newm=savm;
2614: /* Covariates have to be included here again */
2615: cov[1]=1.;
1.214 brouard 2616: agexact=age+((h-1)*hstepm + (d-1))*stepm/YEARM; /* age just before transition */
1.187 brouard 2617: cov[2]=agexact;
2618: if(nagesqr==1)
1.218 brouard 2619: cov[3]= agexact*agexact;
1.131 brouard 2620: for (k=1; k<=cptcovn;k++)
1.218 brouard 2621: cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,k)];
2622: /* cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,Tvar[k])]; */
1.186 brouard 2623: for (k=1; k<=cptcovage;k++) /* Should start at cptcovn+1 */
1.218 brouard 2624: /* cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
2625: cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,k)]*cov[2];
2626: /* cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,Tvar[Tage[k]])]*cov[2]; */
1.145 brouard 2627: for (k=1; k<=cptcovprod;k++) /* Useless because included in cptcovn */
1.218 brouard 2628: cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)]*nbcode[Tvard[k][2]][codtabm(ij,k)];
2629: /* 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 2630:
2631:
2632: /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
2633: /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
1.218 brouard 2634: /* right multiplication of oldm by the current matrix */
1.126 brouard 2635: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,
2636: pmij(pmmij,cov,ncovmodel,x,nlstate));
1.217 brouard 2637: /* if((int)age == 70){ */
2638: /* printf(" Forward hpxij age=%d agexact=%f d=%d nhstepm=%d hstepm=%d\n", (int) age, agexact, d, nhstepm, hstepm); */
2639: /* for(i=1; i<=nlstate+ndeath; i++) { */
2640: /* printf("%d pmmij ",i); */
2641: /* for(j=1;j<=nlstate+ndeath;j++) { */
2642: /* printf("%f ",pmmij[i][j]); */
2643: /* } */
2644: /* printf(" oldm "); */
2645: /* for(j=1;j<=nlstate+ndeath;j++) { */
2646: /* printf("%f ",oldm[i][j]); */
2647: /* } */
2648: /* printf("\n"); */
2649: /* } */
2650: /* } */
1.126 brouard 2651: savm=oldm;
2652: oldm=newm;
2653: }
2654: for(i=1; i<=nlstate+ndeath; i++)
2655: for(j=1;j<=nlstate+ndeath;j++) {
1.218 brouard 2656: po[i][j][h]=newm[i][j];
2657: /*if(h==nhstepm) printf("po[%d][%d][%d]=%f ",i,j,h,po[i][j][h]);*/
1.126 brouard 2658: }
1.128 brouard 2659: /*printf("h=%d ",h);*/
1.126 brouard 2660: } /* end h */
1.218 brouard 2661: /* printf("\n H=%d \n",h); */
1.126 brouard 2662: return po;
2663: }
2664:
1.217 brouard 2665: /************* Higher Back Matrix Product ***************/
1.218 brouard 2666: /* double ***hbxij(double ***po, int nhstepm, double age, int hstepm, double *x, double ***prevacurrent, int nlstate, int stepm, double **oldm, double **savm, double **dnewm, double **doldm, double **dsavm, int ij ) */
1.222 brouard 2667: double ***hbxij(double ***po, int nhstepm, double age, int hstepm, double *x, double ***prevacurrent, int nlstate, int stepm, int ij )
1.217 brouard 2668: {
1.218 brouard 2669: /* Computes the transition matrix starting at age 'age' over
1.217 brouard 2670: 'nhstepm*hstepm*stepm' months (i.e. until
1.218 brouard 2671: age (in years) age+nhstepm*hstepm*stepm/12) by multiplying
2672: nhstepm*hstepm matrices.
2673: Output is stored in matrix po[i][j][h] for h every 'hstepm' step
2674: (typically every 2 years instead of every month which is too big
1.217 brouard 2675: for the memory).
1.218 brouard 2676: Model is determined by parameters x and covariates have to be
2677: included manually here.
1.217 brouard 2678:
1.222 brouard 2679: */
1.217 brouard 2680:
2681: int i, j, d, h, k;
2682: double **out, cov[NCOVMAX+1];
2683: double **newm;
2684: double agexact;
2685: double agebegin, ageend;
1.222 brouard 2686: double **oldm, **savm;
1.217 brouard 2687:
1.222 brouard 2688: oldm=oldms;savm=savms;
1.217 brouard 2689: /* Hstepm could be zero and should return the unit matrix */
2690: for (i=1;i<=nlstate+ndeath;i++)
2691: for (j=1;j<=nlstate+ndeath;j++){
2692: oldm[i][j]=(i==j ? 1.0 : 0.0);
2693: po[i][j][0]=(i==j ? 1.0 : 0.0);
2694: }
2695: /* Even if hstepm = 1, at least one multiplication by the unit matrix */
2696: for(h=1; h <=nhstepm; h++){
2697: for(d=1; d <=hstepm; d++){
2698: newm=savm;
2699: /* Covariates have to be included here again */
2700: cov[1]=1.;
2701: agexact=age-((h-1)*hstepm + (d-1))*stepm/YEARM; /* age just before transition */
2702: /* agexact=age+((h-1)*hstepm + (d-1))*stepm/YEARM; /\* age just before transition *\/ */
2703: cov[2]=agexact;
2704: if(nagesqr==1)
1.222 brouard 2705: cov[3]= agexact*agexact;
1.218 brouard 2706: for (k=1; k<=cptcovn;k++)
1.222 brouard 2707: cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,k)];
2708: /* cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,Tvar[k])]; */
1.217 brouard 2709: for (k=1; k<=cptcovage;k++) /* Should start at cptcovn+1 */
1.222 brouard 2710: /* cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
2711: cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,k)]*cov[2];
2712: /* cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,Tvar[Tage[k]])]*cov[2]; */
1.217 brouard 2713: for (k=1; k<=cptcovprod;k++) /* Useless because included in cptcovn */
1.222 brouard 2714: cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)]*nbcode[Tvard[k][2]][codtabm(ij,k)];
2715: /* cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,Tvard[k][1])]*nbcode[Tvard[k][2]][codtabm(ij,Tvard[k][2])]; */
1.218 brouard 2716:
2717:
1.217 brouard 2718: /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
2719: /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
1.218 brouard 2720: /* Careful transposed matrix */
1.222 brouard 2721: /* age is in cov[2] */
1.218 brouard 2722: /* out=matprod2(newm, bmij(pmmij,cov,ncovmodel,x,nlstate,prevacurrent, dnewm, doldm, dsavm,ij),\ */
1.222 brouard 2723: /* 1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); */
1.218 brouard 2724: out=matprod2(newm, bmij(pmmij,cov,ncovmodel,x,nlstate,prevacurrent,ij),\
1.222 brouard 2725: 1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);
1.217 brouard 2726: /* if((int)age == 70){ */
2727: /* printf(" Backward hbxij age=%d agexact=%f d=%d nhstepm=%d hstepm=%d\n", (int) age, agexact, d, nhstepm, hstepm); */
2728: /* for(i=1; i<=nlstate+ndeath; i++) { */
2729: /* printf("%d pmmij ",i); */
2730: /* for(j=1;j<=nlstate+ndeath;j++) { */
2731: /* printf("%f ",pmmij[i][j]); */
2732: /* } */
2733: /* printf(" oldm "); */
2734: /* for(j=1;j<=nlstate+ndeath;j++) { */
2735: /* printf("%f ",oldm[i][j]); */
2736: /* } */
2737: /* printf("\n"); */
2738: /* } */
2739: /* } */
2740: savm=oldm;
2741: oldm=newm;
2742: }
2743: for(i=1; i<=nlstate+ndeath; i++)
2744: for(j=1;j<=nlstate+ndeath;j++) {
1.222 brouard 2745: po[i][j][h]=newm[i][j];
2746: /*if(h==nhstepm) printf("po[%d][%d][%d]=%f ",i,j,h,po[i][j][h]);*/
1.217 brouard 2747: }
2748: /*printf("h=%d ",h);*/
2749: } /* end h */
1.222 brouard 2750: /* printf("\n H=%d \n",h); */
1.217 brouard 2751: return po;
2752: }
2753:
2754:
1.162 brouard 2755: #ifdef NLOPT
2756: double myfunc(unsigned n, const double *p1, double *grad, void *pd){
2757: double fret;
2758: double *xt;
2759: int j;
2760: myfunc_data *d2 = (myfunc_data *) pd;
2761: /* xt = (p1-1); */
2762: xt=vector(1,n);
2763: for (j=1;j<=n;j++) xt[j]=p1[j-1]; /* xt[1]=p1[0] */
2764:
2765: fret=(d2->function)(xt); /* p xt[1]@8 is fine */
2766: /* fret=(*func)(xt); /\* p xt[1]@8 is fine *\/ */
2767: printf("Function = %.12lf ",fret);
2768: for (j=1;j<=n;j++) printf(" %d %.8lf", j, xt[j]);
2769: printf("\n");
2770: free_vector(xt,1,n);
2771: return fret;
2772: }
2773: #endif
1.126 brouard 2774:
2775: /*************** log-likelihood *************/
2776: double func( double *x)
2777: {
2778: int i, ii, j, k, mi, d, kk;
1.223 ! brouard 2779: int ioffset;
1.131 brouard 2780: double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
1.126 brouard 2781: double **out;
2782: double sw; /* Sum of weights */
2783: double lli; /* Individual log likelihood */
2784: int s1, s2;
1.223 ! brouard 2785: int iv=0, iqv=0, itv=0, iqtv=0 ; /* Index of varying covariate, fixed quantitative cov, time varying covariate */
1.126 brouard 2786: double bbh, survp;
2787: long ipmx;
1.187 brouard 2788: double agexact;
1.126 brouard 2789: /*extern weight */
2790: /* We are differentiating ll according to initial status */
2791: /* for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
2792: /*for(i=1;i<imx;i++)
2793: printf(" %d\n",s[4][i]);
2794: */
1.162 brouard 2795:
2796: ++countcallfunc;
2797:
1.126 brouard 2798: cov[1]=1.;
2799:
2800: for(k=1; k<=nlstate; k++) ll[k]=0.;
2801:
2802: if(mle==1){
2803: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1.138 brouard 2804: /* Computes the values of the ncovmodel covariates of the model
1.223 ! brouard 2805: depending if the covariates are fixed or varying (age dependent) and stores them in cov[]
1.138 brouard 2806: Then computes with function pmij which return a matrix p[i][j] giving the elementary probability
2807: to be observed in j being in i according to the model.
2808: */
1.223 ! brouard 2809: ioffset=2+nagesqr;
1.145 brouard 2810: for (k=1; k<=cptcovn;k++){ /* Simple and product covariates without age* products */
1.223 ! brouard 2811: cov[++ioffset]=covar[Tvar[k]][i];
! 2812: }
! 2813: for(iqv=1; iqv <= nqv; iqv++){ /* Varying quantitatives covariates */
! 2814: /* cov[2+nagesqr+cptcovn+iqv]=varq[mw[mi+1][i]][iqv][i]; */
1.145 brouard 2815: }
1.223 ! brouard 2816:
1.137 brouard 2817: /* In model V2+V1*V4+age*V3+V3*V2 Tvar[1] is V2, Tvar[2=V1*V4]
1.138 brouard 2818: is 6, Tvar[3=age*V3] should not be computed because of age Tvar[4=V3*V2]
1.137 brouard 2819: has been calculated etc */
1.223 ! brouard 2820: /* For an individual i, wav[i] gives the number of effective waves */
! 2821: /* We compute the contribution to Likelihood of each effective transition
! 2822: mw[mi][i] is real wave of the mi th effectve wave */
! 2823: /* Then statuses are computed at each begin and end of an effective wave s1=s[ mw[mi][i] ][i];
! 2824: s2=s[mw[mi+1][i]][i];
! 2825: And the iv th varying covariate is the cotvar[mw[mi+1][i]][iv][i]
! 2826: But if the variable is not in the model TTvar[iv] is the real variable effective in the model:
! 2827: meaning that decodemodel should be used cotvar[mw[mi+1][i]][TTvar[iv]][i]
! 2828: */
1.126 brouard 2829: for(mi=1; mi<= wav[i]-1; mi++){
1.223 ! brouard 2830: for(itv=1; itv <= ntv; itv++){ /* Varying dummy covariates */
! 2831: cov[++ioffset]=cotvar[mw[mi+1][i]][itv][i];
! 2832: }
! 2833: for(iqtv=1; iqtv <= nqtv; iqtv++){ /* Varying quantitatives covariates */
! 2834: /* cov[2+nagesqr+cptcovn+nqv+ntv+iqtv]=varq[mw[mi+1][i]][iqtv][i]; */
! 2835: }
! 2836: ioffset=2+nagesqr+cptcovn+nqv+ntv+nqtv;
1.126 brouard 2837: for (ii=1;ii<=nlstate+ndeath;ii++)
2838: for (j=1;j<=nlstate+ndeath;j++){
2839: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
2840: savm[ii][j]=(ii==j ? 1.0 : 0.0);
2841: }
2842: for(d=0; d<dh[mi][i]; d++){
2843: newm=savm;
1.187 brouard 2844: agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
2845: cov[2]=agexact;
2846: if(nagesqr==1)
1.223 ! brouard 2847: cov[3]= agexact*agexact; /* Should be changed here */
1.126 brouard 2848: for (kk=1; kk<=cptcovage;kk++) {
1.187 brouard 2849: cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact; /* Tage[kk] gives the data-covariate associated with age */
1.126 brouard 2850: }
2851: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
2852: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
2853: savm=oldm;
2854: oldm=newm;
2855: } /* end mult */
2856:
2857: /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
2858: /* But now since version 0.9 we anticipate for bias at large stepm.
2859: * If stepm is larger than one month (smallest stepm) and if the exact delay
2860: * (in months) between two waves is not a multiple of stepm, we rounded to
2861: * the nearest (and in case of equal distance, to the lowest) interval but now
2862: * we keep into memory the bias bh[mi][i] and also the previous matrix product
2863: * (i.e to dh[mi][i]-1) saved in 'savm'. Then we inter(extra)polate the
2864: * probability in order to take into account the bias as a fraction of the way
2865: * from savm to out if bh is negative or even beyond if bh is positive. bh varies
2866: * -stepm/2 to stepm/2 .
2867: * For stepm=1 the results are the same as for previous versions of Imach.
2868: * For stepm > 1 the results are less biased than in previous versions.
2869: */
2870: s1=s[mw[mi][i]][i];
2871: s2=s[mw[mi+1][i]][i];
2872: bbh=(double)bh[mi][i]/(double)stepm;
2873: /* bias bh is positive if real duration
2874: * is higher than the multiple of stepm and negative otherwise.
2875: */
2876: /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
2877: if( s2 > nlstate){
2878: /* i.e. if s2 is a death state and if the date of death is known
2879: then the contribution to the likelihood is the probability to
2880: die between last step unit time and current step unit time,
2881: which is also equal to probability to die before dh
2882: minus probability to die before dh-stepm .
2883: In version up to 0.92 likelihood was computed
2884: as if date of death was unknown. Death was treated as any other
2885: health state: the date of the interview describes the actual state
2886: and not the date of a change in health state. The former idea was
2887: to consider that at each interview the state was recorded
2888: (healthy, disable or death) and IMaCh was corrected; but when we
2889: introduced the exact date of death then we should have modified
2890: the contribution of an exact death to the likelihood. This new
2891: contribution is smaller and very dependent of the step unit
2892: stepm. It is no more the probability to die between last interview
2893: and month of death but the probability to survive from last
2894: interview up to one month before death multiplied by the
2895: probability to die within a month. Thanks to Chris
2896: Jackson for correcting this bug. Former versions increased
2897: mortality artificially. The bad side is that we add another loop
2898: which slows down the processing. The difference can be up to 10%
2899: lower mortality.
2900: */
1.183 brouard 2901: /* If, at the beginning of the maximization mostly, the
2902: cumulative probability or probability to be dead is
2903: constant (ie = 1) over time d, the difference is equal to
2904: 0. out[s1][3] = savm[s1][3]: probability, being at state
2905: s1 at precedent wave, to be dead a month before current
2906: wave is equal to probability, being at state s1 at
2907: precedent wave, to be dead at mont of the current
2908: wave. Then the observed probability (that this person died)
2909: is null according to current estimated parameter. In fact,
2910: it should be very low but not zero otherwise the log go to
2911: infinity.
2912: */
2913: /* #ifdef INFINITYORIGINAL */
2914: /* lli=log(out[s1][s2] - savm[s1][s2]); */
2915: /* #else */
2916: /* if ((out[s1][s2] - savm[s1][s2]) < mytinydouble) */
2917: /* lli=log(mytinydouble); */
2918: /* else */
2919: /* lli=log(out[s1][s2] - savm[s1][s2]); */
2920: /* #endif */
1.216 brouard 2921: lli=log(out[s1][s2] - savm[s1][s2]);
2922:
2923: } else if ( s2==-1 ) { /* alive */
1.126 brouard 2924: for (j=1,survp=0. ; j<=nlstate; j++)
2925: survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
2926: /*survp += out[s1][j]; */
2927: lli= log(survp);
2928: }
2929: else if (s2==-4) {
2930: for (j=3,survp=0. ; j<=nlstate; j++)
2931: survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
2932: lli= log(survp);
2933: }
2934: else if (s2==-5) {
2935: for (j=1,survp=0. ; j<=2; j++)
2936: survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
2937: lli= log(survp);
2938: }
2939: else{
2940: lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
2941: /* 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 */
2942: }
2943: /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
2944: /*if(lli ==000.0)*/
2945: /*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); */
2946: ipmx +=1;
2947: sw += weight[i];
2948: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1.183 brouard 2949: /* if (lli < log(mytinydouble)){ */
2950: /* 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); */
2951: /* 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]); */
2952: /* } */
1.126 brouard 2953: } /* end of wave */
2954: } /* end of individual */
2955: } else if(mle==2){
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]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*(savm[s1][s2])):log((1.+bbh)*out[s1][s2])); /* linear interpolation */
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==3){ /* exponential 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: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
3007: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
3008: savm=oldm;
3009: oldm=newm;
3010: } /* end mult */
3011:
3012: s1=s[mw[mi][i]][i];
3013: s2=s[mw[mi+1][i]][i];
3014: bbh=(double)bh[mi][i]/(double)stepm;
3015: 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 */
3016: ipmx +=1;
3017: sw += weight[i];
3018: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
3019: } /* end of wave */
3020: } /* end of individual */
3021: }else if (mle==4){ /* ml=4 no inter-extrapolation */
3022: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1.187 brouard 3023: for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i];
1.126 brouard 3024: for(mi=1; mi<= wav[i]-1; mi++){
3025: for (ii=1;ii<=nlstate+ndeath;ii++)
3026: for (j=1;j<=nlstate+ndeath;j++){
3027: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
3028: savm[ii][j]=(ii==j ? 1.0 : 0.0);
3029: }
3030: for(d=0; d<dh[mi][i]; d++){
3031: newm=savm;
1.187 brouard 3032: agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
3033: cov[2]=agexact;
3034: if(nagesqr==1)
3035: cov[3]= agexact*agexact;
1.126 brouard 3036: for (kk=1; kk<=cptcovage;kk++) {
1.187 brouard 3037: cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
1.126 brouard 3038: }
3039:
3040: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
3041: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
3042: savm=oldm;
3043: oldm=newm;
3044: } /* end mult */
3045:
3046: s1=s[mw[mi][i]][i];
3047: s2=s[mw[mi+1][i]][i];
3048: if( s2 > nlstate){
3049: lli=log(out[s1][s2] - savm[s1][s2]);
1.216 brouard 3050: } else if ( s2==-1 ) { /* alive */
3051: for (j=1,survp=0. ; j<=nlstate; j++)
3052: survp += out[s1][j];
3053: lli= log(survp);
1.126 brouard 3054: }else{
3055: lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
3056: }
3057: ipmx +=1;
3058: sw += weight[i];
3059: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
3060: /* 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]); */
3061: } /* end of wave */
3062: } /* end of individual */
3063: }else{ /* ml=5 no inter-extrapolation no jackson =0.8a */
3064: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1.187 brouard 3065: for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i];
1.126 brouard 3066: for(mi=1; mi<= wav[i]-1; mi++){
3067: for (ii=1;ii<=nlstate+ndeath;ii++)
3068: for (j=1;j<=nlstate+ndeath;j++){
3069: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
3070: savm[ii][j]=(ii==j ? 1.0 : 0.0);
3071: }
3072: for(d=0; d<dh[mi][i]; d++){
3073: newm=savm;
1.187 brouard 3074: agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
3075: cov[2]=agexact;
3076: if(nagesqr==1)
3077: cov[3]= agexact*agexact;
1.126 brouard 3078: for (kk=1; kk<=cptcovage;kk++) {
1.187 brouard 3079: cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
1.126 brouard 3080: }
3081:
3082: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
3083: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
3084: savm=oldm;
3085: oldm=newm;
3086: } /* end mult */
3087:
3088: s1=s[mw[mi][i]][i];
3089: s2=s[mw[mi+1][i]][i];
3090: lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
3091: ipmx +=1;
3092: sw += weight[i];
3093: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
3094: /*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]);*/
3095: } /* end of wave */
3096: } /* end of individual */
3097: } /* End of if */
3098: for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
3099: /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
3100: l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
3101: return -l;
3102: }
3103:
3104: /*************** log-likelihood *************/
3105: double funcone( double *x)
3106: {
3107: /* Same as likeli but slower because of a lot of printf and if */
3108: int i, ii, j, k, mi, d, kk;
1.131 brouard 3109: double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
1.126 brouard 3110: double **out;
3111: double lli; /* Individual log likelihood */
3112: double llt;
3113: int s1, s2;
3114: double bbh, survp;
1.187 brouard 3115: double agexact;
1.214 brouard 3116: double agebegin, ageend;
1.126 brouard 3117: /*extern weight */
3118: /* We are differentiating ll according to initial status */
3119: /* for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
3120: /*for(i=1;i<imx;i++)
3121: printf(" %d\n",s[4][i]);
3122: */
3123: cov[1]=1.;
3124:
3125: for(k=1; k<=nlstate; k++) ll[k]=0.;
3126:
3127: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1.187 brouard 3128: for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i];
1.126 brouard 3129: for(mi=1; mi<= wav[i]-1; mi++){
3130: for (ii=1;ii<=nlstate+ndeath;ii++)
3131: for (j=1;j<=nlstate+ndeath;j++){
3132: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
3133: savm[ii][j]=(ii==j ? 1.0 : 0.0);
3134: }
1.214 brouard 3135:
3136: agebegin=agev[mw[mi][i]][i]; /* Age at beginning of effective wave */
3137: ageend=agev[mw[mi][i]][i] + (dh[mi][i])*stepm/YEARM; /* Age at end of effective wave and at the end of transition */
3138: for(d=0; d<dh[mi][i]; d++){ /* Delay between two effective waves */
3139: /*dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
3140: and mw[mi+1][i]. dh depends on stepm.*/
1.126 brouard 3141: newm=savm;
1.187 brouard 3142: agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
3143: cov[2]=agexact;
3144: if(nagesqr==1)
3145: cov[3]= agexact*agexact;
1.126 brouard 3146: for (kk=1; kk<=cptcovage;kk++) {
1.187 brouard 3147: cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
1.126 brouard 3148: }
1.187 brouard 3149:
1.145 brouard 3150: /* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
1.126 brouard 3151: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
3152: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1.145 brouard 3153: /* out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath, */
3154: /* 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate)); */
1.126 brouard 3155: savm=oldm;
3156: oldm=newm;
3157: } /* end mult */
3158:
3159: s1=s[mw[mi][i]][i];
3160: s2=s[mw[mi+1][i]][i];
1.217 brouard 3161: /* if(s2==-1){ */
3162: /* printf(" s1=%d, s2=%d i=%d \n", s1, s2, i); */
3163: /* /\* exit(1); *\/ */
3164: /* } */
1.126 brouard 3165: bbh=(double)bh[mi][i]/(double)stepm;
3166: /* bias is positive if real duration
3167: * is higher than the multiple of stepm and negative otherwise.
3168: */
3169: if( s2 > nlstate && (mle <5) ){ /* Jackson */
3170: lli=log(out[s1][s2] - savm[s1][s2]);
1.216 brouard 3171: } else if ( s2==-1 ) { /* alive */
1.126 brouard 3172: for (j=1,survp=0. ; j<=nlstate; j++)
3173: survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
3174: lli= log(survp);
3175: }else if (mle==1){
3176: lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
3177: } else if(mle==2){
3178: 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 */
3179: } else if(mle==3){ /* exponential inter-extrapolation */
3180: 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 */
3181: } else if (mle==4){ /* mle=4 no inter-extrapolation */
3182: lli=log(out[s1][s2]); /* Original formula */
1.136 brouard 3183: } else{ /* mle=0 back to 1 */
3184: lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
3185: /*lli=log(out[s1][s2]); */ /* Original formula */
1.126 brouard 3186: } /* End of if */
3187: ipmx +=1;
3188: sw += weight[i];
3189: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1.132 brouard 3190: /*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 3191: if(globpr){
1.214 brouard 3192: fprintf(ficresilk,"%9ld %6.1f %6.1f %6d %2d %2d %2d %2d %3d %11.6f %8.4f %8.3f\
1.126 brouard 3193: %11.6f %11.6f %11.6f ", \
1.214 brouard 3194: 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 3195: 2*weight[i]*lli,out[s1][s2],savm[s1][s2]);
3196: for(k=1,llt=0.,l=0.; k<=nlstate; k++){
3197: llt +=ll[k]*gipmx/gsw;
3198: fprintf(ficresilk," %10.6f",-ll[k]*gipmx/gsw);
3199: }
3200: fprintf(ficresilk," %10.6f\n", -llt);
3201: }
3202: } /* end of wave */
3203: } /* end of individual */
3204: for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
3205: /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
3206: l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
3207: if(globpr==0){ /* First time we count the contributions and weights */
3208: gipmx=ipmx;
3209: gsw=sw;
3210: }
3211: return -l;
3212: }
3213:
3214:
3215: /*************** function likelione ***********/
3216: void likelione(FILE *ficres,double p[], int npar, int nlstate, int *globpri, long *ipmx, double *sw, double *fretone, double (*funcone)(double []))
3217: {
3218: /* This routine should help understanding what is done with
3219: the selection of individuals/waves and
3220: to check the exact contribution to the likelihood.
3221: Plotting could be done.
3222: */
3223: int k;
3224:
3225: if(*globpri !=0){ /* Just counts and sums, no printings */
1.201 brouard 3226: strcpy(fileresilk,"ILK_");
1.202 brouard 3227: strcat(fileresilk,fileresu);
1.126 brouard 3228: if((ficresilk=fopen(fileresilk,"w"))==NULL) {
3229: printf("Problem with resultfile: %s\n", fileresilk);
3230: fprintf(ficlog,"Problem with resultfile: %s\n", fileresilk);
3231: }
1.214 brouard 3232: 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");
3233: fprintf(ficresilk, "#num_i ageb agend i s1 s2 mi mw dh likeli weight %%weight 2wlli out sav ");
1.126 brouard 3234: /* i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],2*weight[i]*lli,out[s1][s2],savm[s1][s2]); */
3235: for(k=1; k<=nlstate; k++)
3236: fprintf(ficresilk," -2*gipw/gsw*weight*ll[%d]++",k);
3237: fprintf(ficresilk," -2*gipw/gsw*weight*ll(total)\n");
3238: }
3239:
3240: *fretone=(*funcone)(p);
3241: if(*globpri !=0){
3242: fclose(ficresilk);
1.205 brouard 3243: if (mle ==0)
3244: fprintf(fichtm,"\n<br>File of contributions to the likelihood computed with initial parameters and mle = %d.",mle);
3245: else if(mle >=1)
3246: fprintf(fichtm,"\n<br>File of contributions to the likelihood computed with optimized parameters mle = %d.",mle);
3247: 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 3248:
1.208 brouard 3249:
3250: for (k=1; k<= nlstate ; k++) {
1.211 brouard 3251: 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 3252: <img src=\"%s-p%dj.png\">",k,k,subdirf2(optionfilefiname,"ILK_"),k,subdirf2(optionfilefiname,"ILK_"),k,subdirf2(optionfilefiname,"ILK_"),k);
3253: }
1.207 brouard 3254: 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 3255: <img src=\"%s-ori.png\">",subdirf2(optionfilefiname,"ILK_"),subdirf2(optionfilefiname,"ILK_"),subdirf2(optionfilefiname,"ILK_"));
1.207 brouard 3256: fprintf(fichtm,"<br>- and by state of destination <a href=\"%s-dest.png\">%s-dest.png</a><br> \
1.204 brouard 3257: <img src=\"%s-dest.png\">",subdirf2(optionfilefiname,"ILK_"),subdirf2(optionfilefiname,"ILK_"),subdirf2(optionfilefiname,"ILK_"));
1.207 brouard 3258: fflush(fichtm);
1.205 brouard 3259: }
1.126 brouard 3260: return;
3261: }
3262:
3263:
3264: /*********** Maximum Likelihood Estimation ***************/
3265:
3266: void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
3267: {
1.165 brouard 3268: int i,j, iter=0;
1.126 brouard 3269: double **xi;
3270: double fret;
3271: double fretone; /* Only one call to likelihood */
3272: /* char filerespow[FILENAMELENGTH];*/
1.162 brouard 3273:
3274: #ifdef NLOPT
3275: int creturn;
3276: nlopt_opt opt;
3277: /* double lb[9] = { -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL }; /\* lower bounds *\/ */
3278: double *lb;
3279: double minf; /* the minimum objective value, upon return */
3280: double * p1; /* Shifted parameters from 0 instead of 1 */
3281: myfunc_data dinst, *d = &dinst;
3282: #endif
3283:
3284:
1.126 brouard 3285: xi=matrix(1,npar,1,npar);
3286: for (i=1;i<=npar;i++)
3287: for (j=1;j<=npar;j++)
3288: xi[i][j]=(i==j ? 1.0 : 0.0);
3289: printf("Powell\n"); fprintf(ficlog,"Powell\n");
1.201 brouard 3290: strcpy(filerespow,"POW_");
1.126 brouard 3291: strcat(filerespow,fileres);
3292: if((ficrespow=fopen(filerespow,"w"))==NULL) {
3293: printf("Problem with resultfile: %s\n", filerespow);
3294: fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
3295: }
3296: fprintf(ficrespow,"# Powell\n# iter -2*LL");
3297: for (i=1;i<=nlstate;i++)
3298: for(j=1;j<=nlstate+ndeath;j++)
3299: if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
3300: fprintf(ficrespow,"\n");
1.162 brouard 3301: #ifdef POWELL
1.126 brouard 3302: powell(p,xi,npar,ftol,&iter,&fret,func);
1.162 brouard 3303: #endif
1.126 brouard 3304:
1.162 brouard 3305: #ifdef NLOPT
3306: #ifdef NEWUOA
3307: opt = nlopt_create(NLOPT_LN_NEWUOA,npar);
3308: #else
3309: opt = nlopt_create(NLOPT_LN_BOBYQA,npar);
3310: #endif
3311: lb=vector(0,npar-1);
3312: for (i=0;i<npar;i++) lb[i]= -HUGE_VAL;
3313: nlopt_set_lower_bounds(opt, lb);
3314: nlopt_set_initial_step1(opt, 0.1);
3315:
3316: p1= (p+1); /* p *(p+1)@8 and p *(p1)@8 are equal p1[0]=p[1] */
3317: d->function = func;
3318: printf(" Func %.12lf \n",myfunc(npar,p1,NULL,d));
3319: nlopt_set_min_objective(opt, myfunc, d);
3320: nlopt_set_xtol_rel(opt, ftol);
3321: if ((creturn=nlopt_optimize(opt, p1, &minf)) < 0) {
3322: printf("nlopt failed! %d\n",creturn);
3323: }
3324: else {
3325: printf("found minimum after %d evaluations (NLOPT=%d)\n", countcallfunc ,NLOPT);
3326: printf("found minimum at f(%g,%g) = %0.10g\n", p[0], p[1], minf);
3327: iter=1; /* not equal */
3328: }
3329: nlopt_destroy(opt);
3330: #endif
1.126 brouard 3331: free_matrix(xi,1,npar,1,npar);
3332: fclose(ficrespow);
1.203 brouard 3333: printf("\n#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
3334: fprintf(ficlog,"\n#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
1.180 brouard 3335: fprintf(ficres,"#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
1.126 brouard 3336:
3337: }
3338:
3339: /**** Computes Hessian and covariance matrix ***/
1.203 brouard 3340: void hesscov(double **matcov, double **hess, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
1.126 brouard 3341: {
3342: double **a,**y,*x,pd;
1.203 brouard 3343: /* double **hess; */
1.164 brouard 3344: int i, j;
1.126 brouard 3345: int *indx;
3346:
3347: double hessii(double p[], double delta, int theta, double delti[],double (*func)(double []),int npar);
1.203 brouard 3348: double hessij(double p[], double **hess, double delti[], int i, int j,double (*func)(double []),int npar);
1.126 brouard 3349: void lubksb(double **a, int npar, int *indx, double b[]) ;
3350: void ludcmp(double **a, int npar, int *indx, double *d) ;
3351: double gompertz(double p[]);
1.203 brouard 3352: /* hess=matrix(1,npar,1,npar); */
1.126 brouard 3353:
3354: printf("\nCalculation of the hessian matrix. Wait...\n");
3355: fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
3356: for (i=1;i<=npar;i++){
1.203 brouard 3357: printf("%d-",i);fflush(stdout);
3358: fprintf(ficlog,"%d-",i);fflush(ficlog);
1.126 brouard 3359:
3360: hess[i][i]=hessii(p,ftolhess,i,delti,func,npar);
3361:
3362: /* printf(" %f ",p[i]);
3363: printf(" %lf %lf %lf",hess[i][i],ftolhess,delti[i]);*/
3364: }
3365:
3366: for (i=1;i<=npar;i++) {
3367: for (j=1;j<=npar;j++) {
3368: if (j>i) {
1.203 brouard 3369: printf(".%d-%d",i,j);fflush(stdout);
3370: fprintf(ficlog,".%d-%d",i,j);fflush(ficlog);
3371: hess[i][j]=hessij(p,hess, delti,i,j,func,npar);
1.126 brouard 3372:
3373: hess[j][i]=hess[i][j];
3374: /*printf(" %lf ",hess[i][j]);*/
3375: }
3376: }
3377: }
3378: printf("\n");
3379: fprintf(ficlog,"\n");
3380:
3381: printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
3382: fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
3383:
3384: a=matrix(1,npar,1,npar);
3385: y=matrix(1,npar,1,npar);
3386: x=vector(1,npar);
3387: indx=ivector(1,npar);
3388: for (i=1;i<=npar;i++)
3389: for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
3390: ludcmp(a,npar,indx,&pd);
3391:
3392: for (j=1;j<=npar;j++) {
3393: for (i=1;i<=npar;i++) x[i]=0;
3394: x[j]=1;
3395: lubksb(a,npar,indx,x);
3396: for (i=1;i<=npar;i++){
3397: matcov[i][j]=x[i];
3398: }
3399: }
3400:
3401: printf("\n#Hessian matrix#\n");
3402: fprintf(ficlog,"\n#Hessian matrix#\n");
3403: for (i=1;i<=npar;i++) {
3404: for (j=1;j<=npar;j++) {
1.203 brouard 3405: printf("%.6e ",hess[i][j]);
3406: fprintf(ficlog,"%.6e ",hess[i][j]);
1.126 brouard 3407: }
3408: printf("\n");
3409: fprintf(ficlog,"\n");
3410: }
3411:
1.203 brouard 3412: /* printf("\n#Covariance matrix#\n"); */
3413: /* fprintf(ficlog,"\n#Covariance matrix#\n"); */
3414: /* for (i=1;i<=npar;i++) { */
3415: /* for (j=1;j<=npar;j++) { */
3416: /* printf("%.6e ",matcov[i][j]); */
3417: /* fprintf(ficlog,"%.6e ",matcov[i][j]); */
3418: /* } */
3419: /* printf("\n"); */
3420: /* fprintf(ficlog,"\n"); */
3421: /* } */
3422:
1.126 brouard 3423: /* Recompute Inverse */
1.203 brouard 3424: /* for (i=1;i<=npar;i++) */
3425: /* for (j=1;j<=npar;j++) a[i][j]=matcov[i][j]; */
3426: /* ludcmp(a,npar,indx,&pd); */
3427:
3428: /* printf("\n#Hessian matrix recomputed#\n"); */
3429:
3430: /* for (j=1;j<=npar;j++) { */
3431: /* for (i=1;i<=npar;i++) x[i]=0; */
3432: /* x[j]=1; */
3433: /* lubksb(a,npar,indx,x); */
3434: /* for (i=1;i<=npar;i++){ */
3435: /* y[i][j]=x[i]; */
3436: /* printf("%.3e ",y[i][j]); */
3437: /* fprintf(ficlog,"%.3e ",y[i][j]); */
3438: /* } */
3439: /* printf("\n"); */
3440: /* fprintf(ficlog,"\n"); */
3441: /* } */
3442:
3443: /* Verifying the inverse matrix */
3444: #ifdef DEBUGHESS
3445: y=matprod2(y,hess,1,npar,1,npar,1,npar,matcov);
1.126 brouard 3446:
1.203 brouard 3447: printf("\n#Verification: multiplying the matrix of covariance by the Hessian matrix, should be unity:#\n");
3448: fprintf(ficlog,"\n#Verification: multiplying the matrix of covariance by the Hessian matrix. Should be unity:#\n");
1.126 brouard 3449:
3450: for (j=1;j<=npar;j++) {
3451: for (i=1;i<=npar;i++){
1.203 brouard 3452: printf("%.2f ",y[i][j]);
3453: fprintf(ficlog,"%.2f ",y[i][j]);
1.126 brouard 3454: }
3455: printf("\n");
3456: fprintf(ficlog,"\n");
3457: }
1.203 brouard 3458: #endif
1.126 brouard 3459:
3460: free_matrix(a,1,npar,1,npar);
3461: free_matrix(y,1,npar,1,npar);
3462: free_vector(x,1,npar);
3463: free_ivector(indx,1,npar);
1.203 brouard 3464: /* free_matrix(hess,1,npar,1,npar); */
1.126 brouard 3465:
3466:
3467: }
3468:
3469: /*************** hessian matrix ****************/
3470: double hessii(double x[], double delta, int theta, double delti[], double (*func)(double []), int npar)
1.203 brouard 3471: { /* Around values of x, computes the function func and returns the scales delti and hessian */
1.126 brouard 3472: int i;
3473: int l=1, lmax=20;
1.203 brouard 3474: double k1,k2, res, fx;
1.132 brouard 3475: double p2[MAXPARM+1]; /* identical to x */
1.126 brouard 3476: double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4;
3477: int k=0,kmax=10;
3478: double l1;
3479:
3480: fx=func(x);
3481: for (i=1;i<=npar;i++) p2[i]=x[i];
1.145 brouard 3482: for(l=0 ; l <=lmax; l++){ /* Enlarging the zone around the Maximum */
1.126 brouard 3483: l1=pow(10,l);
3484: delts=delt;
3485: for(k=1 ; k <kmax; k=k+1){
3486: delt = delta*(l1*k);
3487: p2[theta]=x[theta] +delt;
1.145 brouard 3488: k1=func(p2)-fx; /* Might be negative if too close to the theoretical maximum */
1.126 brouard 3489: p2[theta]=x[theta]-delt;
3490: k2=func(p2)-fx;
3491: /*res= (k1-2.0*fx+k2)/delt/delt; */
1.203 brouard 3492: res= (k1+k2)/delt/delt/2.; /* Divided by 2 because L and not 2*L */
1.126 brouard 3493:
1.203 brouard 3494: #ifdef DEBUGHESSII
1.126 brouard 3495: 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);
3496: 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);
3497: #endif
3498: /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
3499: if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
3500: k=kmax;
3501: }
3502: else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
1.164 brouard 3503: k=kmax; l=lmax*10;
1.126 brouard 3504: }
3505: else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){
3506: delts=delt;
3507: }
1.203 brouard 3508: } /* End loop k */
1.126 brouard 3509: }
3510: delti[theta]=delts;
3511: return res;
3512:
3513: }
3514:
1.203 brouard 3515: double hessij( double x[], double **hess, double delti[], int thetai,int thetaj,double (*func)(double []),int npar)
1.126 brouard 3516: {
3517: int i;
1.164 brouard 3518: int l=1, lmax=20;
1.126 brouard 3519: double k1,k2,k3,k4,res,fx;
1.132 brouard 3520: double p2[MAXPARM+1];
1.203 brouard 3521: int k, kmax=1;
3522: double v1, v2, cv12, lc1, lc2;
1.208 brouard 3523:
3524: int firstime=0;
1.203 brouard 3525:
1.126 brouard 3526: fx=func(x);
1.203 brouard 3527: for (k=1; k<=kmax; k=k+10) {
1.126 brouard 3528: for (i=1;i<=npar;i++) p2[i]=x[i];
1.203 brouard 3529: p2[thetai]=x[thetai]+delti[thetai]*k;
3530: p2[thetaj]=x[thetaj]+delti[thetaj]*k;
1.126 brouard 3531: k1=func(p2)-fx;
3532:
1.203 brouard 3533: p2[thetai]=x[thetai]+delti[thetai]*k;
3534: p2[thetaj]=x[thetaj]-delti[thetaj]*k;
1.126 brouard 3535: k2=func(p2)-fx;
3536:
1.203 brouard 3537: p2[thetai]=x[thetai]-delti[thetai]*k;
3538: p2[thetaj]=x[thetaj]+delti[thetaj]*k;
1.126 brouard 3539: k3=func(p2)-fx;
3540:
1.203 brouard 3541: p2[thetai]=x[thetai]-delti[thetai]*k;
3542: p2[thetaj]=x[thetaj]-delti[thetaj]*k;
1.126 brouard 3543: k4=func(p2)-fx;
1.203 brouard 3544: res=(k1-k2-k3+k4)/4.0/delti[thetai]/k/delti[thetaj]/k/2.; /* Because of L not 2*L */
3545: if(k1*k2*k3*k4 <0.){
1.208 brouard 3546: firstime=1;
1.203 brouard 3547: kmax=kmax+10;
1.208 brouard 3548: }
3549: if(kmax >=10 || firstime ==1){
1.218 brouard 3550: 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);
3551: 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 3552: 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);
3553: 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);
3554: }
3555: #ifdef DEBUGHESSIJ
3556: v1=hess[thetai][thetai];
3557: v2=hess[thetaj][thetaj];
3558: cv12=res;
3559: /* Computing eigen value of Hessian matrix */
3560: lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
3561: lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
3562: if ((lc2 <0) || (lc1 <0) ){
3563: printf("Warning: sub Hessian matrix '%d%d' does not have positive eigen values \n",thetai,thetaj);
3564: fprintf(ficlog, "Warning: sub Hessian matrix '%d%d' does not have positive eigen values \n",thetai,thetaj);
3565: 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);
3566: 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);
3567: }
1.126 brouard 3568: #endif
3569: }
3570: return res;
3571: }
3572:
1.203 brouard 3573: /* Not done yet: Was supposed to fix if not exactly at the maximum */
3574: /* double hessij( double x[], double delti[], int thetai,int thetaj,double (*func)(double []),int npar) */
3575: /* { */
3576: /* int i; */
3577: /* int l=1, lmax=20; */
3578: /* double k1,k2,k3,k4,res,fx; */
3579: /* double p2[MAXPARM+1]; */
3580: /* double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4; */
3581: /* int k=0,kmax=10; */
3582: /* double l1; */
3583:
3584: /* fx=func(x); */
3585: /* for(l=0 ; l <=lmax; l++){ /\* Enlarging the zone around the Maximum *\/ */
3586: /* l1=pow(10,l); */
3587: /* delts=delt; */
3588: /* for(k=1 ; k <kmax; k=k+1){ */
3589: /* delt = delti*(l1*k); */
3590: /* for (i=1;i<=npar;i++) p2[i]=x[i]; */
3591: /* p2[thetai]=x[thetai]+delti[thetai]/k; */
3592: /* p2[thetaj]=x[thetaj]+delti[thetaj]/k; */
3593: /* k1=func(p2)-fx; */
3594:
3595: /* p2[thetai]=x[thetai]+delti[thetai]/k; */
3596: /* p2[thetaj]=x[thetaj]-delti[thetaj]/k; */
3597: /* k2=func(p2)-fx; */
3598:
3599: /* p2[thetai]=x[thetai]-delti[thetai]/k; */
3600: /* p2[thetaj]=x[thetaj]+delti[thetaj]/k; */
3601: /* k3=func(p2)-fx; */
3602:
3603: /* p2[thetai]=x[thetai]-delti[thetai]/k; */
3604: /* p2[thetaj]=x[thetaj]-delti[thetaj]/k; */
3605: /* k4=func(p2)-fx; */
3606: /* res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /\* Because of L not 2*L *\/ */
3607: /* #ifdef DEBUGHESSIJ */
3608: /* 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); */
3609: /* 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); */
3610: /* #endif */
3611: /* if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)|| (k4 <khi/nkhi/2.)|| (k4 <khi/nkhi/2.)){ */
3612: /* k=kmax; */
3613: /* } */
3614: /* else if((k1 >khi/nkhif) || (k2 >khi/nkhif) || (k4 >khi/nkhif) || (k4 >khi/nkhif)){ /\* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. *\/ */
3615: /* k=kmax; l=lmax*10; */
3616: /* } */
3617: /* else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){ */
3618: /* delts=delt; */
3619: /* } */
3620: /* } /\* End loop k *\/ */
3621: /* } */
3622: /* delti[theta]=delts; */
3623: /* return res; */
3624: /* } */
3625:
3626:
1.126 brouard 3627: /************** Inverse of matrix **************/
3628: void ludcmp(double **a, int n, int *indx, double *d)
3629: {
3630: int i,imax,j,k;
3631: double big,dum,sum,temp;
3632: double *vv;
3633:
3634: vv=vector(1,n);
3635: *d=1.0;
3636: for (i=1;i<=n;i++) {
3637: big=0.0;
3638: for (j=1;j<=n;j++)
3639: if ((temp=fabs(a[i][j])) > big) big=temp;
3640: if (big == 0.0) nrerror("Singular matrix in routine ludcmp");
3641: vv[i]=1.0/big;
3642: }
3643: for (j=1;j<=n;j++) {
3644: for (i=1;i<j;i++) {
3645: sum=a[i][j];
3646: for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];
3647: a[i][j]=sum;
3648: }
3649: big=0.0;
3650: for (i=j;i<=n;i++) {
3651: sum=a[i][j];
3652: for (k=1;k<j;k++)
3653: sum -= a[i][k]*a[k][j];
3654: a[i][j]=sum;
3655: if ( (dum=vv[i]*fabs(sum)) >= big) {
3656: big=dum;
3657: imax=i;
3658: }
3659: }
3660: if (j != imax) {
3661: for (k=1;k<=n;k++) {
3662: dum=a[imax][k];
3663: a[imax][k]=a[j][k];
3664: a[j][k]=dum;
3665: }
3666: *d = -(*d);
3667: vv[imax]=vv[j];
3668: }
3669: indx[j]=imax;
3670: if (a[j][j] == 0.0) a[j][j]=TINY;
3671: if (j != n) {
3672: dum=1.0/(a[j][j]);
3673: for (i=j+1;i<=n;i++) a[i][j] *= dum;
3674: }
3675: }
3676: free_vector(vv,1,n); /* Doesn't work */
3677: ;
3678: }
3679:
3680: void lubksb(double **a, int n, int *indx, double b[])
3681: {
3682: int i,ii=0,ip,j;
3683: double sum;
3684:
3685: for (i=1;i<=n;i++) {
3686: ip=indx[i];
3687: sum=b[ip];
3688: b[ip]=b[i];
3689: if (ii)
3690: for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];
3691: else if (sum) ii=i;
3692: b[i]=sum;
3693: }
3694: for (i=n;i>=1;i--) {
3695: sum=b[i];
3696: for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];
3697: b[i]=sum/a[i][i];
3698: }
3699: }
3700:
3701: void pstamp(FILE *fichier)
3702: {
1.196 brouard 3703: fprintf(fichier,"# %s.%s\n#IMaCh version %s, %s\n#%s\n# %s", optionfilefiname,optionfilext,version,copyright, fullversion, strstart);
1.126 brouard 3704: }
3705:
3706: /************ Frequencies ********************/
1.220 brouard 3707: void freqsummary(char fileres[], int iagemin, int iagemax, int **s, double **agev, int nlstate, int imx, \
3708: int *Tvaraff, int *invalidvarcomb, int **nbcode, int *ncodemax,double **mint,double **anint, char strstart[], \
3709: int firstpass, int lastpass, int stepm, int weightopt, char model[])
3710: { /* Some frequencies */
3711:
3712: int i, m, jk, j1, bool, z1,j;
3713: int iind=0, iage=0;
3714: int mi; /* Effective wave */
3715: int first;
3716: double ***freq; /* Frequencies */
3717: double *pp, **prop, *posprop, *pospropt;
3718: double pos=0., posproptt=0., pospropta=0., k2, dateintsum=0,k2cpt=0;
3719: char fileresp[FILENAMELENGTH], fileresphtm[FILENAMELENGTH], fileresphtmfr[FILENAMELENGTH];
3720: double agebegin, ageend;
3721:
3722: pp=vector(1,nlstate);
3723: prop=matrix(1,nlstate,iagemin-AGEMARGE,iagemax+3+AGEMARGE);
3724: posprop=vector(1,nlstate); /* Counting the number of transition starting from a live state per age */
3725: pospropt=vector(1,nlstate); /* Counting the number of transition starting from a live state */
3726: /* prop=matrix(1,nlstate,iagemin,iagemax+3); */
3727: strcpy(fileresp,"P_");
3728: strcat(fileresp,fileresu);
3729: /*strcat(fileresphtm,fileresu);*/
3730: if((ficresp=fopen(fileresp,"w"))==NULL) {
3731: printf("Problem with prevalence resultfile: %s\n", fileresp);
3732: fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
3733: exit(0);
3734: }
1.214 brouard 3735:
1.220 brouard 3736: strcpy(fileresphtm,subdirfext(optionfilefiname,"PHTM_",".htm"));
3737: if((ficresphtm=fopen(fileresphtm,"w"))==NULL) {
3738: printf("Problem with prevalence HTM resultfile '%s' with errno='%s'\n",fileresphtm,strerror(errno));
3739: fprintf(ficlog,"Problem with prevalence HTM resultfile '%s' with errno='%s'\n",fileresphtm,strerror(errno));
3740: fflush(ficlog);
3741: exit(70);
3742: }
3743: else{
3744: fprintf(ficresphtm,"<html><head>\n<title>IMaCh PHTM_ %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
1.214 brouard 3745: <hr size=\"2\" color=\"#EC5E5E\"> \n\
3746: Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=1+age+%s<br>\n",\
1.220 brouard 3747: fileresphtm,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);
3748: }
3749: 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 3750:
1.220 brouard 3751: strcpy(fileresphtmfr,subdirfext(optionfilefiname,"PHTMFR_",".htm"));
3752: if((ficresphtmfr=fopen(fileresphtmfr,"w"))==NULL) {
3753: printf("Problem with frequency table HTM resultfile '%s' with errno='%s'\n",fileresphtmfr,strerror(errno));
3754: fprintf(ficlog,"Problem with frequency table HTM resultfile '%s' with errno='%s'\n",fileresphtmfr,strerror(errno));
3755: fflush(ficlog);
3756: exit(70);
3757: }
3758: else{
3759: 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 3760: <hr size=\"2\" color=\"#EC5E5E\"> \n\
3761: Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=1+age+%s<br>\n",\
1.220 brouard 3762: fileresphtmfr,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);
3763: }
3764: 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 3765:
1.220 brouard 3766: freq= ma3x(-5,nlstate+ndeath,-5,nlstate+ndeath,iagemin-AGEMARGE,iagemax+3+AGEMARGE);
3767: j1=0;
1.126 brouard 3768:
1.220 brouard 3769: j=cptcoveff;
3770: if (cptcovn<1) {j=1;ncodemax[1]=1;}
3771:
3772: first=1;
3773:
3774: /* Detects if a combination j1 is empty: for a multinomial variable like 3 education levels:
3775: reference=low_education V1=0,V2=0
3776: med_educ V1=1 V2=0,
3777: high_educ V1=0 V2=1
3778: Then V1=1 and V2=1 is a noisy combination that we want to exclude for the list 2**cptcoveff
3779: */
1.126 brouard 3780:
1.220 brouard 3781: for (j1 = 1; j1 <= (int) pow(2,cptcoveff); j1++){ /* Loop on covariates combination */
3782: posproptt=0.;
3783: /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
3784: scanf("%d", i);*/
3785: for (i=-5; i<=nlstate+ndeath; i++)
3786: for (jk=-5; jk<=nlstate+ndeath; jk++)
3787: for(m=iagemin; m <= iagemax+3; m++)
3788: freq[i][jk][m]=0;
3789:
3790: for (i=1; i<=nlstate; i++) {
3791: for(m=iagemin; m <= iagemax+3; m++)
3792: prop[i][m]=0;
3793: posprop[i]=0;
3794: pospropt[i]=0;
3795: }
3796:
3797: dateintsum=0;
3798: k2cpt=0;
1.126 brouard 3799:
1.220 brouard 3800: for (iind=1; iind<=imx; iind++) { /* For each individual iind */
3801: bool=1;
3802: if (cptcovn>0) { /* Filter is here: Must be looked at for model=V1+V2+V3+V4 */
3803: for (z1=1; z1<=cptcoveff; z1++) {
3804: if (covar[Tvaraff[z1]][iind]!= nbcode[Tvaraff[z1]][codtabm(j1,z1)]){
3805: /* Tests if the value of each of the covariates of i is equal to filter j1 */
3806: bool=0;
3807: /* 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 3808: bool,i,z1, z1, Tvaraff[z1],i,covar[Tvaraff[z1]][i],j1,z1,codtabm(j1,z1),
3809: j1,z1,nbcode[Tvaraff[z1]][codtabm(j1,z1)],j1);*/
1.220 brouard 3810: /* For j1=7 in V1+V2+V3+V4 = 0 1 1 0 and codtabm(7,3)=1 and nbcde[3][?]=1*/
3811: }
3812: } /* end z1 */
3813: } /* cptcovn > 0 */
3814:
3815: if (bool==1){
3816: /* for(m=firstpass; m<=lastpass; m++){ */
3817: for(mi=1; mi<wav[iind];mi++){
3818: m=mw[mi][iind];
3819: /* dh[m][iind] or dh[mw[mi][iind]][iind] is the delay between two effective (mi) waves m=mw[mi][iind]
3820: and mw[mi+1][iind]. dh depends on stepm. */
3821: agebegin=agev[m][iind]; /* Age at beginning of wave before transition*/
3822: ageend=agev[m][iind]+(dh[m][iind])*stepm/YEARM; /* Age at end of wave and transition */
3823: if(m >=firstpass && m <=lastpass){
3824: k2=anint[m][iind]+(mint[m][iind]/12.);
3825: /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/
3826: if(agev[m][iind]==0) agev[m][iind]=iagemax+1; /* All ages equal to 0 are in iagemax+1 */
3827: if(agev[m][iind]==1) agev[m][iind]=iagemax+2; /* All ages equal to 1 are in iagemax+2 */
3828: if (s[m][iind]>0 && s[m][iind]<=nlstate) /* If status at wave m is known and a live state */
3829: prop[s[m][iind]][(int)agev[m][iind]] += weight[iind]; /* At age of beginning of transition, where status is known */
3830: if (m<lastpass) {
3831: /* if(s[m][iind]==4 && s[m+1][iind]==4) */
3832: /* 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]); */
3833: if(s[m][iind]==-1)
3834: 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.));
3835: freq[s[m][iind]][s[m+1][iind]][(int)agev[m][iind]] += weight[iind]; /* At age of beginning of transition, where status is known */
3836: /* freq[s[m][iind]][s[m+1][iind]][(int)((agebegin+ageend)/2.)] += weight[iind]; */
3837: 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 */
3838: }
3839: }
3840: if ((agev[m][iind]>1) && (agev[m][iind]< (iagemax+3)) && (anint[m][iind]!=9999) && (mint[m][iind]!=99)) {
3841: dateintsum=dateintsum+k2;
3842: k2cpt++;
3843: /* printf("iind=%ld dateintmean = %lf dateintsum=%lf k2cpt=%lf k2=%lf\n",iind, dateintsum/k2cpt, dateintsum,k2cpt, k2); */
3844: }
3845: /*}*/
3846: } /* end m */
3847: } /* end bool */
3848: } /* end iind = 1 to imx */
3849: /* prop[s][age] is feeded for any initial and valid live state as well as
3850: freq[s1][s2][age] at single age of beginning the transition, for a combination j1 */
3851:
3852:
3853: /* fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
3854: pstamp(ficresp);
3855: if (cptcovn>0) {
3856: fprintf(ficresp, "\n#********** Variable ");
3857: fprintf(ficresphtm, "\n<br/><br/><h3>********** Variable ");
3858: fprintf(ficresphtmfr, "\n<br/><br/><h3>********** Variable ");
3859: for (z1=1; z1<=cptcoveff; z1++){
3860: fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
3861: fprintf(ficresphtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
3862: fprintf(ficresphtmfr, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
3863: }
3864: fprintf(ficresp, "**********\n#");
3865: fprintf(ficresphtm, "**********</h3>\n");
3866: fprintf(ficresphtmfr, "**********</h3>\n");
3867: fprintf(ficlog, "\n#********** Variable ");
3868: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficlog, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
3869: fprintf(ficlog, "**********\n");
3870: }
3871: fprintf(ficresphtm,"<table style=\"text-align:center; border: 1px solid\">");
3872: for(i=1; i<=nlstate;i++) {
3873: fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
3874: fprintf(ficresphtm, "<th>Age</th><th>Prev(%d)</th><th>N(%d)</th><th>N</th>",i,i);
3875: }
3876: fprintf(ficresp, "\n");
3877: fprintf(ficresphtm, "\n");
3878:
3879: /* Header of frequency table by age */
3880: fprintf(ficresphtmfr,"<table style=\"text-align:center; border: 1px solid\">");
3881: fprintf(ficresphtmfr,"<th>Age</th> ");
3882: for(jk=-1; jk <=nlstate+ndeath; jk++){
3883: for(m=-1; m <=nlstate+ndeath; m++){
3884: if(jk!=0 && m!=0)
3885: fprintf(ficresphtmfr,"<th>%d%d</th> ",jk,m);
3886: }
3887: }
3888: fprintf(ficresphtmfr, "\n");
1.214 brouard 3889:
1.220 brouard 3890: /* For each age */
3891: for(iage=iagemin; iage <= iagemax+3; iage++){
3892: fprintf(ficresphtm,"<tr>");
3893: if(iage==iagemax+1){
3894: fprintf(ficlog,"1");
3895: fprintf(ficresphtmfr,"<tr><th>0</th> ");
3896: }else if(iage==iagemax+2){
3897: fprintf(ficlog,"0");
3898: fprintf(ficresphtmfr,"<tr><th>Unknown</th> ");
3899: }else if(iage==iagemax+3){
3900: fprintf(ficlog,"Total");
3901: fprintf(ficresphtmfr,"<tr><th>Total</th> ");
3902: }else{
3903: if(first==1){
3904: first=0;
3905: printf("See log file for details...\n");
3906: }
3907: fprintf(ficresphtmfr,"<tr><th>%d</th> ",iage);
3908: fprintf(ficlog,"Age %d", iage);
3909: }
3910: for(jk=1; jk <=nlstate ; jk++){
3911: for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
3912: pp[jk] += freq[jk][m][iage];
3913: }
3914: for(jk=1; jk <=nlstate ; jk++){
3915: for(m=-1, pos=0; m <=0 ; m++)
3916: pos += freq[jk][m][iage];
3917: if(pp[jk]>=1.e-10){
3918: if(first==1){
3919: printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
3920: }
3921: fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
3922: }else{
3923: if(first==1)
3924: printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
3925: fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
3926: }
3927: }
3928:
3929: for(jk=1; jk <=nlstate ; jk++){
3930: /* posprop[jk]=0; */
3931: for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)/* Summing on all ages */
3932: pp[jk] += freq[jk][m][iage];
3933: } /* pp[jk] is the total number of transitions starting from state jk and any ending status until this age */
3934:
3935: for(jk=1,pos=0, pospropta=0.; jk <=nlstate ; jk++){
3936: pos += pp[jk]; /* pos is the total number of transitions until this age */
3937: posprop[jk] += prop[jk][iage]; /* prop is the number of transitions from a live state
3938: from jk at age iage prop[s[m][iind]][(int)agev[m][iind]] += weight[iind] */
3939: pospropta += prop[jk][iage]; /* prop is the number of transitions from a live state
3940: from jk at age iage prop[s[m][iind]][(int)agev[m][iind]] += weight[iind] */
3941: }
3942: for(jk=1; jk <=nlstate ; jk++){
3943: if(pos>=1.e-5){
3944: if(first==1)
3945: printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
3946: fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
3947: }else{
3948: if(first==1)
3949: printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
3950: fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
3951: }
3952: if( iage <= iagemax){
3953: if(pos>=1.e-5){
3954: fprintf(ficresp," %d %.5f %.0f %.0f",iage,prop[jk][iage]/pospropta, prop[jk][iage],pospropta);
3955: fprintf(ficresphtm,"<th>%d</th><td>%.5f</td><td>%.0f</td><td>%.0f</td>",iage,prop[jk][iage]/pospropta, prop[jk][iage],pospropta);
3956: /*probs[iage][jk][j1]= pp[jk]/pos;*/
3957: /*printf("\niage=%d jk=%d j1=%d %.5f %.0f %.0f %f",iage,jk,j1,pp[jk]/pos, pp[jk],pos,probs[iage][jk][j1]);*/
3958: }
3959: else{
3960: fprintf(ficresp," %d NaNq %.0f %.0f",iage,prop[jk][iage],pospropta);
3961: fprintf(ficresphtm,"<th>%d</th><td>NaNq</td><td>%.0f</td><td>%.0f</td>",iage, prop[jk][iage],pospropta);
3962: }
3963: }
3964: pospropt[jk] +=posprop[jk];
3965: } /* end loop jk */
3966: /* pospropt=0.; */
3967: for(jk=-1; jk <=nlstate+ndeath; jk++){
3968: for(m=-1; m <=nlstate+ndeath; m++){
3969: if(freq[jk][m][iage] !=0 ) { /* minimizing output */
3970: if(first==1){
3971: printf(" %d%d=%.0f",jk,m,freq[jk][m][iage]);
3972: }
3973: fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][iage]);
3974: }
3975: if(jk!=0 && m!=0)
3976: fprintf(ficresphtmfr,"<td>%.0f</td> ",freq[jk][m][iage]);
3977: }
3978: } /* end loop jk */
3979: posproptt=0.;
3980: for(jk=1; jk <=nlstate; jk++){
3981: posproptt += pospropt[jk];
3982: }
3983: fprintf(ficresphtmfr,"</tr>\n ");
3984: if(iage <= iagemax){
3985: fprintf(ficresp,"\n");
3986: fprintf(ficresphtm,"</tr>\n");
3987: }
3988: if(first==1)
3989: printf("Others in log...\n");
3990: fprintf(ficlog,"\n");
3991: } /* end loop age iage */
3992: fprintf(ficresphtm,"<tr><th>Tot</th>");
3993: for(jk=1; jk <=nlstate ; jk++){
3994: if(posproptt < 1.e-5){
1.221 brouard 3995: fprintf(ficresphtm,"<td>Nanq</td><td>%.0f</td><td>%.0f</td>",pospropt[jk],posproptt);
3996: }else{
1.220 brouard 3997: fprintf(ficresphtm,"<td>%.5f</td><td>%.0f</td><td>%.0f</td>",pospropt[jk]/posproptt,pospropt[jk],posproptt);
3998: }
3999: }
4000: fprintf(ficresphtm,"</tr>\n");
4001: fprintf(ficresphtm,"</table>\n");
4002: fprintf(ficresphtmfr,"</table>\n");
4003: if(posproptt < 1.e-5){
4004: fprintf(ficresphtm,"\n <p><b> This combination (%d) is not valid and no result will be produced</b></p>",j1);
4005: fprintf(ficresphtmfr,"\n <p><b> This combination (%d) is not valid and no result will be produced</b></p>",j1);
4006: fprintf(ficres,"\n This combination (%d) is not valid and no result will be produced\n\n",j1);
4007: invalidvarcomb[j1]=1;
4008: }else{
4009: fprintf(ficresphtm,"\n <p> This combination (%d) is valid and result will be produced.</p>",j1);
4010: invalidvarcomb[j1]=0;
4011: }
4012: fprintf(ficresphtmfr,"</table>\n");
4013: } /* end selected combination of covariate j1 */
4014: dateintmean=dateintsum/k2cpt;
4015:
4016: fclose(ficresp);
4017: fclose(ficresphtm);
4018: fclose(ficresphtmfr);
4019: free_ma3x(freq,-5,nlstate+ndeath,-5,nlstate+ndeath, iagemin-AGEMARGE, iagemax+3+AGEMARGE);
4020: free_vector(pospropt,1,nlstate);
4021: free_vector(posprop,1,nlstate);
4022: free_matrix(prop,1,nlstate,iagemin-AGEMARGE, iagemax+3+AGEMARGE);
4023: free_vector(pp,1,nlstate);
4024: /* End of Freq */
4025: }
1.126 brouard 4026:
4027: /************ Prevalence ********************/
1.222 brouard 4028: 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)
4029: {
4030: /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
4031: in each health status at the date of interview (if between dateprev1 and dateprev2).
4032: We still use firstpass and lastpass as another selection.
4033: */
1.126 brouard 4034:
1.222 brouard 4035: int i, m, jk, j1, bool, z1,j;
4036: int mi; /* Effective wave */
4037: int iage;
4038: double agebegin, ageend;
4039:
4040: double **prop;
4041: double posprop;
4042: double y2; /* in fractional years */
4043: int iagemin, iagemax;
4044: int first; /** to stop verbosity which is redirected to log file */
4045:
4046: iagemin= (int) agemin;
4047: iagemax= (int) agemax;
4048: /*pp=vector(1,nlstate);*/
4049: prop=matrix(1,nlstate,iagemin-AGEMARGE,iagemax+3+AGEMARGE);
4050: /* freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
4051: j1=0;
4052:
4053: /*j=cptcoveff;*/
4054: if (cptcovn<1) {j=1;ncodemax[1]=1;}
4055:
4056: first=1;
4057: for(j1=1; j1<= (int) pow(2,cptcoveff);j1++){ /* For each combination of covariate */
4058: for (i=1; i<=nlstate; i++)
4059: for(iage=iagemin-AGEMARGE; iage <= iagemax+3+AGEMARGE; iage++)
4060: prop[i][iage]=0.0;
4061:
4062: for (i=1; i<=imx; i++) { /* Each individual */
4063: bool=1;
4064: if (cptcovn>0) { /* Filter is here: Must be looked at for model=V1+V2+V3+V4 */
4065: 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*/
4066: if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtabm(j1,z1)])
4067: bool=0;
4068: }
4069: if (bool==1) { /* For this combination of covariates values, this individual fits */
4070: /* for(m=firstpass; m<=lastpass; m++){/\* Other selection (we can limit to certain interviews*\/ */
4071: for(mi=1; mi<wav[i];mi++){
4072: m=mw[mi][i];
4073: agebegin=agev[m][i]; /* Age at beginning of wave before transition*/
4074: /* ageend=agev[m][i]+(dh[m][i])*stepm/YEARM; /\* Age at end of wave and transition *\/ */
4075: if(m >=firstpass && m <=lastpass){
4076: y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
4077: if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
4078: if(agev[m][i]==0) agev[m][i]=iagemax+1;
4079: if(agev[m][i]==1) agev[m][i]=iagemax+2;
4080: if((int)agev[m][i] <iagemin-AGEMARGE || (int)agev[m][i] >iagemax+3+AGEMARGE){
4081: 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);
4082: exit(1);
4083: }
4084: if (s[m][i]>0 && s[m][i]<=nlstate) {
4085: /*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]]);*/
4086: prop[s[m][i]][(int)agev[m][i]] += weight[i];/* At age of beginning of transition, where status is known */
4087: prop[s[m][i]][iagemax+3] += weight[i];
4088: } /* end valid statuses */
4089: } /* end selection of dates */
4090: } /* end selection of waves */
4091: } /* end effective waves */
4092: } /* end bool */
4093: }
4094: for(i=iagemin; i <= iagemax+3; i++){
4095: for(jk=1,posprop=0; jk <=nlstate ; jk++) {
4096: posprop += prop[jk][i];
4097: }
4098:
4099: for(jk=1; jk <=nlstate ; jk++){
4100: if( i <= iagemax){
4101: if(posprop>=1.e-5){
4102: probs[i][jk][j1]= prop[jk][i]/posprop;
4103: } else{
4104: if(first==1){
4105: first=0;
4106: 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]);
4107: }
4108: }
4109: }
4110: }/* end jk */
4111: }/* end i */
4112: /*} *//* end i1 */
4113: } /* end j1 */
4114:
4115: /* free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
4116: /*free_vector(pp,1,nlstate);*/
4117: free_matrix(prop,1,nlstate, iagemin-AGEMARGE,iagemax+3+AGEMARGE);
4118: } /* End of prevalence */
1.126 brouard 4119:
4120: /************* Waves Concatenation ***************/
4121:
4122: 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)
4123: {
4124: /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
4125: Death is a valid wave (if date is known).
4126: mw[mi][i] is the mi (mi=1 to wav[i]) effective wave of individual i
4127: dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
4128: and mw[mi+1][i]. dh depends on stepm.
4129: */
4130:
4131: int i, mi, m;
4132: /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
4133: double sum=0., jmean=0.;*/
1.218 brouard 4134: int first, firstwo, firsthree, firstfour;
1.126 brouard 4135: int j, k=0,jk, ju, jl;
4136: double sum=0.;
4137: first=0;
1.214 brouard 4138: firstwo=0;
1.217 brouard 4139: firsthree=0;
1.218 brouard 4140: firstfour=0;
1.164 brouard 4141: jmin=100000;
1.126 brouard 4142: jmax=-1;
4143: jmean=0.;
1.214 brouard 4144: for(i=1; i<=imx; i++){ /* For simple cases and if state is death */
1.126 brouard 4145: mi=0;
4146: m=firstpass;
1.214 brouard 4147: while(s[m][i] <= nlstate){ /* a live state */
1.216 brouard 4148: 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 */
1.223 ! brouard 4149: mw[++mi][i]=m;
1.216 brouard 4150: }
4151: if(m >=lastpass){
1.223 ! brouard 4152: if(s[m][i]==-1 && (int) andc[i] == 9999 && (int)anint[m][i] != 9999){
! 4153: if(firsthree == 0){
! 4154: 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);
! 4155: firsthree=1;
! 4156: }
! 4157: 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);
! 4158: mw[++mi][i]=m;
! 4159: }
! 4160: if(s[m][i]==-2){ /* Vital status is really unknown */
! 4161: nbwarn++;
! 4162: if((int)anint[m][i] == 9999){ /* Has the vital status really been verified? */
! 4163: 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);
! 4164: 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);
! 4165: }
! 4166: break;
! 4167: }
! 4168: break;
1.216 brouard 4169: }
1.126 brouard 4170: else
1.223 ! brouard 4171: m++;
1.126 brouard 4172: }/* end while */
1.216 brouard 4173:
4174: /* After last pass */
1.214 brouard 4175: if (s[m][i] > nlstate){ /* In a death state */
1.126 brouard 4176: mi++; /* Death is another wave */
4177: /* if(mi==0) never been interviewed correctly before death */
1.223 ! brouard 4178: /* Only death is a correct wave */
1.126 brouard 4179: mw[mi][i]=m;
1.216 brouard 4180: }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 */
4181: /* m++; */
4182: /* mi++; */
4183: /* s[m][i]=nlstate+1; /\* We are setting the status to the last of non live state *\/ */
4184: /* mw[mi][i]=m; */
4185: nberr++;
1.218 brouard 4186: if ((int)anint[m][i]!= 9999) { /* date of last interview is known */
1.223 ! brouard 4187: if(firstwo==0){
! 4188: 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 );
! 4189: firstwo=1;
! 4190: }
! 4191: 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 );
1.218 brouard 4192: }else{ /* end date of interview is known */
1.223 ! brouard 4193: /* death is known but not confirmed by death status at any wave */
! 4194: if(firstfour==0){
! 4195: 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 );
! 4196: firstfour=1;
! 4197: }
! 4198: 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 4199: }
1.126 brouard 4200: }
4201: wav[i]=mi;
4202: if(mi==0){
4203: nbwarn++;
4204: if(first==0){
1.223 ! brouard 4205: printf("Warning! No valid information for individual %ld line=%d (skipped) and may be others, see log file\n",num[i],i);
! 4206: first=1;
1.126 brouard 4207: }
4208: if(first==1){
1.223 ! brouard 4209: fprintf(ficlog,"Warning! No valid information for individual %ld line=%d (skipped)\n",num[i],i);
1.126 brouard 4210: }
4211: } /* end mi==0 */
4212: } /* End individuals */
1.214 brouard 4213: /* wav and mw are no more changed */
1.223 ! brouard 4214:
1.214 brouard 4215:
1.126 brouard 4216: for(i=1; i<=imx; i++){
4217: for(mi=1; mi<wav[i];mi++){
4218: if (stepm <=0)
1.223 ! brouard 4219: dh[mi][i]=1;
1.126 brouard 4220: else{
1.223 ! brouard 4221: if (s[mw[mi+1][i]][i] > nlstate) { /* A death */
! 4222: if (agedc[i] < 2*AGESUP) {
! 4223: j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);
! 4224: if(j==0) j=1; /* Survives at least one month after exam */
! 4225: else if(j<0){
! 4226: nberr++;
! 4227: 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]);
! 4228: j=1; /* Temporary Dangerous patch */
! 4229: 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);
! 4230: 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]);
! 4231: 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);
! 4232: }
! 4233: k=k+1;
! 4234: if (j >= jmax){
! 4235: jmax=j;
! 4236: ijmax=i;
! 4237: }
! 4238: if (j <= jmin){
! 4239: jmin=j;
! 4240: ijmin=i;
! 4241: }
! 4242: sum=sum+j;
! 4243: /*if (j<0) printf("j=%d num=%d \n",j,i);*/
! 4244: /* printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
! 4245: }
! 4246: }
! 4247: else{
! 4248: j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
1.126 brouard 4249: /* if (j<0) printf("%d %lf %lf %d %d %d\n", i,agev[mw[mi+1][i]][i], agev[mw[mi][i]][i],j,s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]); */
1.223 ! brouard 4250:
! 4251: k=k+1;
! 4252: if (j >= jmax) {
! 4253: jmax=j;
! 4254: ijmax=i;
! 4255: }
! 4256: else if (j <= jmin){
! 4257: jmin=j;
! 4258: ijmin=i;
! 4259: }
! 4260: /* if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
! 4261: /*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]);*/
! 4262: if(j<0){
! 4263: nberr++;
! 4264: 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]);
! 4265: 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]);
! 4266: }
! 4267: sum=sum+j;
! 4268: }
! 4269: jk= j/stepm;
! 4270: jl= j -jk*stepm;
! 4271: ju= j -(jk+1)*stepm;
! 4272: if(mle <=1){ /* only if we use a the linear-interpoloation pseudo-likelihood */
! 4273: if(jl==0){
! 4274: dh[mi][i]=jk;
! 4275: bh[mi][i]=0;
! 4276: }else{ /* We want a negative bias in order to only have interpolation ie
! 4277: * to avoid the price of an extra matrix product in likelihood */
! 4278: dh[mi][i]=jk+1;
! 4279: bh[mi][i]=ju;
! 4280: }
! 4281: }else{
! 4282: if(jl <= -ju){
! 4283: dh[mi][i]=jk;
! 4284: bh[mi][i]=jl; /* bias is positive if real duration
! 4285: * is higher than the multiple of stepm and negative otherwise.
! 4286: */
! 4287: }
! 4288: else{
! 4289: dh[mi][i]=jk+1;
! 4290: bh[mi][i]=ju;
! 4291: }
! 4292: if(dh[mi][i]==0){
! 4293: dh[mi][i]=1; /* At least one step */
! 4294: bh[mi][i]=ju; /* At least one step */
! 4295: /* 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);*/
! 4296: }
! 4297: } /* end if mle */
1.126 brouard 4298: }
4299: } /* end wave */
4300: }
4301: jmean=sum/k;
4302: 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 4303: 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 4304: }
4305:
4306: /*********** Tricode ****************************/
1.220 brouard 4307: void tricode(int *cptcov, int *Tvar, int **nbcode, int imx, int *Ndum)
1.126 brouard 4308: {
1.144 brouard 4309: /**< Uses cptcovn+2*cptcovprod as the number of covariates */
4310: /* 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 4311: * Boring subroutine which should only output nbcode[Tvar[j]][k]
1.145 brouard 4312: * Tvar[5] in V2+V1+V3*age+V2*V4 is 2 (V2)
1.220 brouard 4313: * nbcode[Tvar[5]][1]= nbcode[2][1]=0, nbcode[2][2]=1 (usually);
1.144 brouard 4314: */
1.130 brouard 4315:
1.145 brouard 4316: int ij=1, k=0, j=0, i=0, maxncov=NCOVMAX;
1.136 brouard 4317: int modmaxcovj=0; /* Modality max of covariates j */
1.145 brouard 4318: int cptcode=0; /* Modality max of covariates j */
4319: int modmincovj=0; /* Modality min of covariates j */
4320:
4321:
1.220 brouard 4322: /* cptcoveff=0; */
4323: *cptcov=0;
1.126 brouard 4324:
1.144 brouard 4325: for (k=1; k <= maxncov; k++) ncodemax[k]=0; /* Horrible constant again replaced by NCOVMAX */
1.126 brouard 4326:
1.145 brouard 4327: /* Loop on covariates without age and products */
1.186 brouard 4328: for (j=1; j<=(cptcovs); j++) { /* From model V1 + V2*age+ V3 + V3*V4 keeps V1 + V3 = 2 only */
1.192 brouard 4329: for (k=-1; k < maxncov; k++) Ndum[k]=0;
1.186 brouard 4330: for (i=1; i<=imx; i++) { /* Loop on individuals: reads the data file to get the maximum value of the
1.219 brouard 4331: modality of this covariate Vj*/
1.145 brouard 4332: ij=(int)(covar[Tvar[j]][i]); /* ij=0 or 1 or -1. Value of the covariate Tvar[j] for individual i
1.219 brouard 4333: * If product of Vn*Vm, still boolean *:
4334: * If it was coded 1, 2, 3, 4 should be splitted into 3 boolean variables
4335: * 1 => 0 0 0, 2 => 0 0 1, 3 => 0 1 1, 4=1 0 0 */
1.145 brouard 4336: /* Finds for covariate j, n=Tvar[j] of Vn . ij is the
1.136 brouard 4337: modality of the nth covariate of individual i. */
1.145 brouard 4338: if (ij > modmaxcovj)
4339: modmaxcovj=ij;
4340: else if (ij < modmincovj)
1.219 brouard 4341: modmincovj=ij;
1.145 brouard 4342: if ((ij < -1) && (ij > NCOVMAX)){
1.219 brouard 4343: printf( "Error: minimal is less than -1 or maximal is bigger than %d. Exiting. \n", NCOVMAX );
4344: exit(1);
1.145 brouard 4345: }else
1.136 brouard 4346: Ndum[ij]++; /*counts and stores the occurence of this modality 0, 1, -1*/
1.145 brouard 4347: /* If coded 1, 2, 3 , counts the number of 1 Ndum[1], number of 2, Ndum[2], etc */
1.126 brouard 4348: /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
1.136 brouard 4349: /* getting the maximum value of the modality of the covariate
4350: (should be 0 or 1 now) Tvar[j]. If V=sex and male is coded 0 and
4351: female is 1, then modmaxcovj=1.*/
1.192 brouard 4352: } /* end for loop on individuals i */
1.145 brouard 4353: printf(" Minimal and maximal values of %d th covariate V%d: min=%d max=%d \n", j, Tvar[j], modmincovj, modmaxcovj);
1.192 brouard 4354: 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 4355: cptcode=modmaxcovj;
1.137 brouard 4356: /* Ndum[0] = frequency of 0 for model-covariate j, Ndum[1] frequency of 1 etc. */
1.145 brouard 4357: /*for (i=0; i<=cptcode; i++) {*/
1.192 brouard 4358: for (k=modmincovj; k<=modmaxcovj; k++) { /* k=-1 ? 0 and 1*//* For each value k of the modality of model-cov j */
4359: printf("Frequencies of covariates %d ie V%d with value %d: %d\n", j, Tvar[j], k, Ndum[k]);
4360: fprintf(ficlog, "Frequencies of covariates %d ie V%d with value %d: %d\n", j, Tvar[j], k, Ndum[k]);
4361: if( Ndum[k] != 0 ){ /* Counts if nobody answered modality k ie empty modality, we skip it and reorder */
1.219 brouard 4362: if( k != -1){
4363: ncodemax[j]++; /* ncodemax[j]= Number of modalities of the j th
4364: covariate for which somebody answered excluding
4365: undefined. Usually 2: 0 and 1. */
4366: }
4367: ncodemaxwundef[j]++; /* ncodemax[j]= Number of modalities of the j th
4368: covariate for which somebody answered including
4369: undefined. Usually 3: -1, 0 and 1. */
1.145 brouard 4370: }
4371: /* In fact ncodemax[j]=2 (dichotom. variables only) but it could be more for
1.219 brouard 4372: historical reasons: 3 if coded 1, 2, 3 and 4 and Ndum[2]=0 */
1.131 brouard 4373: } /* Ndum[-1] number of undefined modalities */
1.219 brouard 4374:
1.136 brouard 4375: /* j is a covariate, n=Tvar[j] of Vn; Fills nbcode */
1.186 brouard 4376: /* For covariate j, modalities could be 1, 2, 3, 4, 5, 6, 7.
4377: 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 4378: modmincovj=3; modmaxcovj = 7;
1.186 brouard 4379: There are only 3 modalities non empty 3, 6, 7 (or 2 if 27 is too few) : ncodemax[j]=3;
4380: which will be coded 0, 1, 2 which in binary on 2=3-1 digits are 0=00 1=01, 2=10;
4381: defining two dummy variables: variables V1_1 and V1_2.
1.145 brouard 4382: nbcode[Tvar[j]][ij]=k;
4383: nbcode[Tvar[j]][1]=0;
4384: nbcode[Tvar[j]][2]=1;
4385: nbcode[Tvar[j]][3]=2;
1.197 brouard 4386: To be continued (not working yet).
1.145 brouard 4387: */
1.197 brouard 4388: ij=0; /* ij is similar to i but can jump over null modalities */
4389: 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*/
4390: if (Ndum[i] == 0) { /* If nobody responded to this modality k */
1.219 brouard 4391: break;
4392: }
1.192 brouard 4393: ij++;
1.197 brouard 4394: 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 4395: cptcode = ij; /* New max modality for covar j */
4396: } /* end of loop on modality i=-1 to 1 or more */
4397:
4398: /* for (k=0; k<= cptcode; k++) { /\* k=-1 ? k=0 to 1 *\//\* Could be 1 to 4 *\//\* cptcode=modmaxcovj *\/ */
4399: /* /\*recode from 0 *\/ */
4400: /* k is a modality. If we have model=V1+V1*sex */
4401: /* then: nbcode[1][1]=0 ; nbcode[1][2]=1; nbcode[2][1]=0 ; nbcode[2][2]=1; */
4402: /* But if some modality were not used, it is recoded from 0 to a newer modmaxcovj=cptcode *\/ */
4403: /* } */
4404: /* /\* cptcode = ij; *\/ /\* New max modality for covar j *\/ */
4405: /* if (ij > ncodemax[j]) { */
4406: /* printf( " Error ij=%d > ncodemax[%d]=%d\n", ij, j, ncodemax[j]); */
4407: /* fprintf(ficlog, " Error ij=%d > ncodemax[%d]=%d\n", ij, j, ncodemax[j]); */
4408: /* break; */
4409: /* } */
4410: /* } /\* end of loop on modality k *\/ */
1.137 brouard 4411: } /* end of loop on model-covariate j. nbcode[Tvarj][1]=0 and nbcode[Tvarj][2]=1 sets the value of covariate j*/
4412:
1.219 brouard 4413: for (k=-1; k< maxncov; k++) Ndum[k]=0;
1.137 brouard 4414:
1.187 brouard 4415: for (i=1; i<=ncovmodel-2-nagesqr; i++) { /* -2, cste and age and eventually age*age */
1.219 brouard 4416: /* Listing of all covariables in statement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/
4417: ij=Tvar[i]; /* Tvar might be -1 if status was unknown */
4418: Ndum[ij]++; /* Might be supersed V1 + V1*age */
4419: }
4420:
4421: ij=0;
4422: for (i=0; i<= maxncov-1; i++) { /* modmaxcovj is unknown here. Only Ndum[2(V2),3(age*V3), 5(V3*V2) 6(V1*V4) */
4423: /*printf("Ndum[%d]=%d\n",i, Ndum[i]);*/
4424: if((Ndum[i]!=0) && (i<=ncovcol)){
4425: ij++;
4426: /*printf("diff Ndum[%d]=%d\n",i, Ndum[i]);*/
4427: Tvaraff[ij]=i; /*For printing (unclear) */
4428: }else{
4429: /* Tvaraff[ij]=0; */
4430: }
4431: }
4432: /* ij--; */
1.220 brouard 4433: /* cptcoveff=ij; /\*Number of total covariates*\/ */
4434: *cptcov=ij; /*Number of total covariates*/
1.219 brouard 4435:
1.126 brouard 4436: }
4437:
1.145 brouard 4438:
1.126 brouard 4439: /*********** Health Expectancies ****************/
4440:
1.127 brouard 4441: 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 4442:
4443: {
4444: /* Health expectancies, no variances */
1.164 brouard 4445: int i, j, nhstepm, hstepm, h, nstepm;
1.126 brouard 4446: int nhstepma, nstepma; /* Decreasing with age */
4447: double age, agelim, hf;
4448: double ***p3mat;
4449: double eip;
4450:
4451: pstamp(ficreseij);
4452: fprintf(ficreseij,"# (a) Life expectancies by health status at initial age and (b) health expectancies by health status at initial age\n");
4453: fprintf(ficreseij,"# Age");
4454: for(i=1; i<=nlstate;i++){
4455: for(j=1; j<=nlstate;j++){
4456: fprintf(ficreseij," e%1d%1d ",i,j);
4457: }
4458: fprintf(ficreseij," e%1d. ",i);
4459: }
4460: fprintf(ficreseij,"\n");
4461:
4462:
4463: if(estepm < stepm){
4464: printf ("Problem %d lower than %d\n",estepm, stepm);
4465: }
4466: else hstepm=estepm;
4467: /* We compute the life expectancy from trapezoids spaced every estepm months
4468: * This is mainly to measure the difference between two models: for example
4469: * if stepm=24 months pijx are given only every 2 years and by summing them
4470: * we are calculating an estimate of the Life Expectancy assuming a linear
4471: * progression in between and thus overestimating or underestimating according
4472: * to the curvature of the survival function. If, for the same date, we
4473: * estimate the model with stepm=1 month, we can keep estepm to 24 months
4474: * to compare the new estimate of Life expectancy with the same linear
4475: * hypothesis. A more precise result, taking into account a more precise
4476: * curvature will be obtained if estepm is as small as stepm. */
4477:
4478: /* For example we decided to compute the life expectancy with the smallest unit */
4479: /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
4480: nhstepm is the number of hstepm from age to agelim
4481: nstepm is the number of stepm from age to agelin.
4482: Look at hpijx to understand the reason of that which relies in memory size
4483: and note for a fixed period like estepm months */
4484: /* We decided (b) to get a life expectancy respecting the most precise curvature of the
4485: survival function given by stepm (the optimization length). Unfortunately it
4486: means that if the survival funtion is printed only each two years of age and if
4487: you sum them up and add 1 year (area under the trapezoids) you won't get the same
4488: results. So we changed our mind and took the option of the best precision.
4489: */
4490: hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
4491:
4492: agelim=AGESUP;
4493: /* If stepm=6 months */
4494: /* Computed by stepm unit matrices, product of hstepm matrices, stored
4495: in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
4496:
4497: /* nhstepm age range expressed in number of stepm */
4498: nstepm=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
4499: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
4500: /* if (stepm >= YEARM) hstepm=1;*/
4501: nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
4502: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4503:
4504: for (age=bage; age<=fage; age ++){
4505: nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
4506: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
4507: /* if (stepm >= YEARM) hstepm=1;*/
4508: nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
4509:
4510: /* If stepm=6 months */
4511: /* Computed by stepm unit matrices, product of hstepma matrices, stored
4512: in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
4513:
4514: hpxij(p3mat,nhstepma,age,hstepm,x,nlstate,stepm,oldm, savm, cij);
4515:
4516: hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
4517:
4518: printf("%d|",(int)age);fflush(stdout);
4519: fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
4520:
4521: /* Computing expectancies */
4522: for(i=1; i<=nlstate;i++)
4523: for(j=1; j<=nlstate;j++)
4524: for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
4525: eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
4526:
4527: /* 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]);*/
4528:
4529: }
4530:
4531: fprintf(ficreseij,"%3.0f",age );
4532: for(i=1; i<=nlstate;i++){
4533: eip=0;
4534: for(j=1; j<=nlstate;j++){
4535: eip +=eij[i][j][(int)age];
4536: fprintf(ficreseij,"%9.4f", eij[i][j][(int)age] );
4537: }
4538: fprintf(ficreseij,"%9.4f", eip );
4539: }
4540: fprintf(ficreseij,"\n");
4541:
4542: }
4543: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4544: printf("\n");
4545: fprintf(ficlog,"\n");
4546:
4547: }
4548:
1.127 brouard 4549: 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 4550:
4551: {
4552: /* Covariances of health expectancies eij and of total life expectancies according
1.222 brouard 4553: to initial status i, ei. .
1.126 brouard 4554: */
4555: int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2, ij, ji;
4556: int nhstepma, nstepma; /* Decreasing with age */
4557: double age, agelim, hf;
4558: double ***p3matp, ***p3matm, ***varhe;
4559: double **dnewm,**doldm;
4560: double *xp, *xm;
4561: double **gp, **gm;
4562: double ***gradg, ***trgradg;
4563: int theta;
4564:
4565: double eip, vip;
4566:
4567: varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage);
4568: xp=vector(1,npar);
4569: xm=vector(1,npar);
4570: dnewm=matrix(1,nlstate*nlstate,1,npar);
4571: doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate);
4572:
4573: pstamp(ficresstdeij);
4574: fprintf(ficresstdeij,"# Health expectancies with standard errors\n");
4575: fprintf(ficresstdeij,"# Age");
4576: for(i=1; i<=nlstate;i++){
4577: for(j=1; j<=nlstate;j++)
4578: fprintf(ficresstdeij," e%1d%1d (SE)",i,j);
4579: fprintf(ficresstdeij," e%1d. ",i);
4580: }
4581: fprintf(ficresstdeij,"\n");
4582:
4583: pstamp(ficrescveij);
4584: fprintf(ficrescveij,"# Subdiagonal matrix of covariances of health expectancies by age: cov(eij,ekl)\n");
4585: fprintf(ficrescveij,"# Age");
4586: for(i=1; i<=nlstate;i++)
4587: for(j=1; j<=nlstate;j++){
4588: cptj= (j-1)*nlstate+i;
4589: for(i2=1; i2<=nlstate;i2++)
4590: for(j2=1; j2<=nlstate;j2++){
4591: cptj2= (j2-1)*nlstate+i2;
4592: if(cptj2 <= cptj)
4593: fprintf(ficrescveij," %1d%1d,%1d%1d",i,j,i2,j2);
4594: }
4595: }
4596: fprintf(ficrescveij,"\n");
4597:
4598: if(estepm < stepm){
4599: printf ("Problem %d lower than %d\n",estepm, stepm);
4600: }
4601: else hstepm=estepm;
4602: /* We compute the life expectancy from trapezoids spaced every estepm months
4603: * This is mainly to measure the difference between two models: for example
4604: * if stepm=24 months pijx are given only every 2 years and by summing them
4605: * we are calculating an estimate of the Life Expectancy assuming a linear
4606: * progression in between and thus overestimating or underestimating according
4607: * to the curvature of the survival function. If, for the same date, we
4608: * estimate the model with stepm=1 month, we can keep estepm to 24 months
4609: * to compare the new estimate of Life expectancy with the same linear
4610: * hypothesis. A more precise result, taking into account a more precise
4611: * curvature will be obtained if estepm is as small as stepm. */
4612:
4613: /* For example we decided to compute the life expectancy with the smallest unit */
4614: /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
4615: nhstepm is the number of hstepm from age to agelim
4616: nstepm is the number of stepm from age to agelin.
4617: Look at hpijx to understand the reason of that which relies in memory size
4618: and note for a fixed period like estepm months */
4619: /* We decided (b) to get a life expectancy respecting the most precise curvature of the
4620: survival function given by stepm (the optimization length). Unfortunately it
4621: means that if the survival funtion is printed only each two years of age and if
4622: you sum them up and add 1 year (area under the trapezoids) you won't get the same
4623: results. So we changed our mind and took the option of the best precision.
4624: */
4625: hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
4626:
4627: /* If stepm=6 months */
4628: /* nhstepm age range expressed in number of stepm */
4629: agelim=AGESUP;
4630: nstepm=(int) rint((agelim-bage)*YEARM/stepm);
4631: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
4632: /* if (stepm >= YEARM) hstepm=1;*/
4633: nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
4634:
4635: p3matp=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4636: p3matm=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4637: gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);
4638: trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar);
4639: gp=matrix(0,nhstepm,1,nlstate*nlstate);
4640: gm=matrix(0,nhstepm,1,nlstate*nlstate);
4641:
4642: for (age=bage; age<=fage; age ++){
4643: nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
4644: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
4645: /* if (stepm >= YEARM) hstepm=1;*/
4646: nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
1.218 brouard 4647:
1.126 brouard 4648: /* If stepm=6 months */
4649: /* Computed by stepm unit matrices, product of hstepma matrices, stored
4650: in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
4651:
4652: hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
1.218 brouard 4653:
1.126 brouard 4654: /* Computing Variances of health expectancies */
4655: /* Gradient is computed with plus gp and minus gm. Code is duplicated in order to
4656: decrease memory allocation */
4657: for(theta=1; theta <=npar; theta++){
4658: for(i=1; i<=npar; i++){
1.222 brouard 4659: xp[i] = x[i] + (i==theta ?delti[theta]:0);
4660: xm[i] = x[i] - (i==theta ?delti[theta]:0);
1.126 brouard 4661: }
4662: hpxij(p3matp,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, cij);
4663: hpxij(p3matm,nhstepm,age,hstepm,xm,nlstate,stepm,oldm,savm, cij);
1.218 brouard 4664:
1.126 brouard 4665: for(j=1; j<= nlstate; j++){
1.222 brouard 4666: for(i=1; i<=nlstate; i++){
4667: for(h=0; h<=nhstepm-1; h++){
4668: gp[h][(j-1)*nlstate + i] = (p3matp[i][j][h]+p3matp[i][j][h+1])/2.;
4669: gm[h][(j-1)*nlstate + i] = (p3matm[i][j][h]+p3matm[i][j][h+1])/2.;
4670: }
4671: }
1.126 brouard 4672: }
1.218 brouard 4673:
1.126 brouard 4674: for(ij=1; ij<= nlstate*nlstate; ij++)
1.222 brouard 4675: for(h=0; h<=nhstepm-1; h++){
4676: gradg[h][theta][ij]= (gp[h][ij]-gm[h][ij])/2./delti[theta];
4677: }
1.126 brouard 4678: }/* End theta */
4679:
4680:
4681: for(h=0; h<=nhstepm-1; h++)
4682: for(j=1; j<=nlstate*nlstate;j++)
1.222 brouard 4683: for(theta=1; theta <=npar; theta++)
4684: trgradg[h][j][theta]=gradg[h][theta][j];
1.126 brouard 4685:
1.218 brouard 4686:
1.222 brouard 4687: for(ij=1;ij<=nlstate*nlstate;ij++)
1.126 brouard 4688: for(ji=1;ji<=nlstate*nlstate;ji++)
1.222 brouard 4689: varhe[ij][ji][(int)age] =0.;
1.218 brouard 4690:
1.222 brouard 4691: printf("%d|",(int)age);fflush(stdout);
4692: fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
4693: for(h=0;h<=nhstepm-1;h++){
1.126 brouard 4694: for(k=0;k<=nhstepm-1;k++){
1.222 brouard 4695: matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov);
4696: matprod2(doldm,dnewm,1,nlstate*nlstate,1,npar,1,nlstate*nlstate,gradg[k]);
4697: for(ij=1;ij<=nlstate*nlstate;ij++)
4698: for(ji=1;ji<=nlstate*nlstate;ji++)
4699: varhe[ij][ji][(int)age] += doldm[ij][ji]*hf*hf;
1.126 brouard 4700: }
4701: }
1.218 brouard 4702:
1.126 brouard 4703: /* Computing expectancies */
4704: hpxij(p3matm,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, cij);
4705: for(i=1; i<=nlstate;i++)
4706: for(j=1; j<=nlstate;j++)
1.222 brouard 4707: for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
4708: eij[i][j][(int)age] += (p3matm[i][j][h]+p3matm[i][j][h+1])/2.0*hf;
1.218 brouard 4709:
1.222 brouard 4710: /* if((int)age==70)printf("i=%2d,j=%2d,h=%2d,age=%3d,%9.4f,%9.4f,%9.4f\n",i,j,h,(int)age,p3mat[i][j][h],hf,eij[i][j][(int)age]);*/
1.218 brouard 4711:
1.222 brouard 4712: }
1.218 brouard 4713:
1.126 brouard 4714: fprintf(ficresstdeij,"%3.0f",age );
4715: for(i=1; i<=nlstate;i++){
4716: eip=0.;
4717: vip=0.;
4718: for(j=1; j<=nlstate;j++){
1.222 brouard 4719: eip += eij[i][j][(int)age];
4720: for(k=1; k<=nlstate;k++) /* Sum on j and k of cov(eij,eik) */
4721: vip += varhe[(j-1)*nlstate+i][(k-1)*nlstate+i][(int)age];
4722: 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 4723: }
4724: fprintf(ficresstdeij," %9.4f (%.4f)", eip, sqrt(vip));
4725: }
4726: fprintf(ficresstdeij,"\n");
1.218 brouard 4727:
1.126 brouard 4728: fprintf(ficrescveij,"%3.0f",age );
4729: for(i=1; i<=nlstate;i++)
4730: for(j=1; j<=nlstate;j++){
1.222 brouard 4731: cptj= (j-1)*nlstate+i;
4732: for(i2=1; i2<=nlstate;i2++)
4733: for(j2=1; j2<=nlstate;j2++){
4734: cptj2= (j2-1)*nlstate+i2;
4735: if(cptj2 <= cptj)
4736: fprintf(ficrescveij," %.4f", varhe[cptj][cptj2][(int)age]);
4737: }
1.126 brouard 4738: }
4739: fprintf(ficrescveij,"\n");
1.218 brouard 4740:
1.126 brouard 4741: }
4742: free_matrix(gm,0,nhstepm,1,nlstate*nlstate);
4743: free_matrix(gp,0,nhstepm,1,nlstate*nlstate);
4744: free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*nlstate);
4745: free_ma3x(trgradg,0,nhstepm,1,nlstate*nlstate,1,npar);
4746: free_ma3x(p3matm,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4747: free_ma3x(p3matp,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4748: printf("\n");
4749: fprintf(ficlog,"\n");
1.218 brouard 4750:
1.126 brouard 4751: free_vector(xm,1,npar);
4752: free_vector(xp,1,npar);
4753: free_matrix(dnewm,1,nlstate*nlstate,1,npar);
4754: free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate);
4755: free_ma3x(varhe,1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int)fage);
4756: }
1.218 brouard 4757:
1.126 brouard 4758: /************ Variance ******************/
1.209 brouard 4759: 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 4760: {
4761: /* Variance of health expectancies */
4762: /* double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
4763: /* double **newm;*/
4764: /* int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav)*/
4765:
4766: /* int movingaverage(); */
4767: double **dnewm,**doldm;
4768: double **dnewmp,**doldmp;
4769: int i, j, nhstepm, hstepm, h, nstepm ;
4770: int k;
4771: double *xp;
4772: double **gp, **gm; /* for var eij */
4773: double ***gradg, ***trgradg; /*for var eij */
4774: double **gradgp, **trgradgp; /* for var p point j */
4775: double *gpp, *gmp; /* for var p point j */
4776: double **varppt; /* for var p point j nlstate to nlstate+ndeath */
4777: double ***p3mat;
4778: double age,agelim, hf;
4779: /* double ***mobaverage; */
4780: int theta;
4781: char digit[4];
4782: char digitp[25];
4783:
4784: char fileresprobmorprev[FILENAMELENGTH];
4785:
4786: if(popbased==1){
4787: if(mobilav!=0)
4788: strcpy(digitp,"-POPULBASED-MOBILAV_");
4789: else strcpy(digitp,"-POPULBASED-NOMOBIL_");
4790: }
4791: else
4792: strcpy(digitp,"-STABLBASED_");
1.126 brouard 4793:
1.218 brouard 4794: /* if (mobilav!=0) { */
4795: /* mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX); */
4796: /* if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){ */
4797: /* fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav); */
4798: /* printf(" Error in movingaverage mobilav=%d\n",mobilav); */
4799: /* } */
4800: /* } */
4801:
4802: strcpy(fileresprobmorprev,"PRMORPREV-");
4803: sprintf(digit,"%-d",ij);
4804: /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
4805: strcat(fileresprobmorprev,digit); /* Tvar to be done */
4806: strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
4807: strcat(fileresprobmorprev,fileresu);
4808: if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
4809: printf("Problem with resultfile: %s\n", fileresprobmorprev);
4810: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
4811: }
4812: printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
4813: fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
4814: pstamp(ficresprobmorprev);
4815: 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);
4816: fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
4817: for(j=nlstate+1; j<=(nlstate+ndeath);j++){
4818: fprintf(ficresprobmorprev," p.%-d SE",j);
4819: for(i=1; i<=nlstate;i++)
4820: fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
4821: }
4822: fprintf(ficresprobmorprev,"\n");
4823:
4824: fprintf(ficgp,"\n# Routine varevsij");
4825: fprintf(ficgp,"\nunset title \n");
4826: /* fprintf(fichtm, "#Local time at start: %s", strstart);*/
4827: 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");
4828: fprintf(fichtm,"\n<br>%s <br>\n",digitp);
4829: /* } */
4830: varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
4831: pstamp(ficresvij);
4832: fprintf(ficresvij,"# Variance and covariance of health expectancies e.j \n# (weighted average of eij where weights are ");
4833: if(popbased==1)
4834: 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);
4835: else
4836: fprintf(ficresvij,"the age specific period (stable) prevalences in each health state \n");
4837: fprintf(ficresvij,"# Age");
4838: for(i=1; i<=nlstate;i++)
4839: for(j=1; j<=nlstate;j++)
4840: fprintf(ficresvij," Cov(e.%1d, e.%1d)",i,j);
4841: fprintf(ficresvij,"\n");
4842:
4843: xp=vector(1,npar);
4844: dnewm=matrix(1,nlstate,1,npar);
4845: doldm=matrix(1,nlstate,1,nlstate);
4846: dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
4847: doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
4848:
4849: gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
4850: gpp=vector(nlstate+1,nlstate+ndeath);
4851: gmp=vector(nlstate+1,nlstate+ndeath);
4852: trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
1.126 brouard 4853:
1.218 brouard 4854: if(estepm < stepm){
4855: printf ("Problem %d lower than %d\n",estepm, stepm);
4856: }
4857: else hstepm=estepm;
4858: /* For example we decided to compute the life expectancy with the smallest unit */
4859: /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
4860: nhstepm is the number of hstepm from age to agelim
4861: nstepm is the number of stepm from age to agelim.
4862: Look at function hpijx to understand why because of memory size limitations,
4863: we decided (b) to get a life expectancy respecting the most precise curvature of the
4864: survival function given by stepm (the optimization length). Unfortunately it
4865: means that if the survival funtion is printed every two years of age and if
4866: you sum them up and add 1 year (area under the trapezoids) you won't get the same
4867: results. So we changed our mind and took the option of the best precision.
4868: */
4869: hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
4870: agelim = AGESUP;
4871: for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
4872: nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
4873: nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
4874: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4875: gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
4876: gp=matrix(0,nhstepm,1,nlstate);
4877: gm=matrix(0,nhstepm,1,nlstate);
4878:
4879:
4880: for(theta=1; theta <=npar; theta++){
4881: for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
4882: xp[i] = x[i] + (i==theta ?delti[theta]:0);
4883: }
4884:
4885: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij);
4886:
4887: if (popbased==1) {
4888: if(mobilav ==0){
4889: for(i=1; i<=nlstate;i++)
4890: prlim[i][i]=probs[(int)age][i][ij];
4891: }else{ /* mobilav */
4892: for(i=1; i<=nlstate;i++)
4893: prlim[i][i]=mobaverage[(int)age][i][ij];
4894: }
4895: }
4896:
4897: hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij); /* Returns p3mat[i][j][h] for h=1 to nhstepm */
4898: for(j=1; j<= nlstate; j++){
4899: for(h=0; h<=nhstepm; h++){
4900: for(i=1, gp[h][j]=0.;i<=nlstate;i++)
4901: gp[h][j] += prlim[i][i]*p3mat[i][j][h];
4902: }
4903: }
4904: /* Next 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,gpp[j]=0.; i<= nlstate; i++)
4910: gpp[j] += prlim[i][i]*p3mat[i][j][1];
4911: }
4912: /* end probability of death */
4913:
4914: for(i=1; i<=npar; i++) /* Computes gradient x - delta */
4915: xp[i] = x[i] - (i==theta ?delti[theta]:0);
4916:
4917: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp, ij);
4918:
4919: if (popbased==1) {
4920: if(mobilav ==0){
4921: for(i=1; i<=nlstate;i++)
4922: prlim[i][i]=probs[(int)age][i][ij];
4923: }else{ /* mobilav */
4924: for(i=1; i<=nlstate;i++)
4925: prlim[i][i]=mobaverage[(int)age][i][ij];
4926: }
4927: }
4928:
4929: hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
4930:
4931: for(j=1; j<= nlstate; j++){ /* Sum of wi * eij = e.j */
4932: for(h=0; h<=nhstepm; h++){
4933: for(i=1, gm[h][j]=0.;i<=nlstate;i++)
4934: gm[h][j] += prlim[i][i]*p3mat[i][j][h];
4935: }
4936: }
4937: /* This for computing probability of death (h=1 means
4938: computed over hstepm matrices product = hstepm*stepm months)
4939: as a weighted average of prlim.
4940: */
4941: for(j=nlstate+1;j<=nlstate+ndeath;j++){
4942: for(i=1,gmp[j]=0.; i<= nlstate; i++)
4943: gmp[j] += prlim[i][i]*p3mat[i][j][1];
4944: }
4945: /* end probability of death */
4946:
4947: for(j=1; j<= nlstate; j++) /* vareij */
4948: for(h=0; h<=nhstepm; h++){
4949: gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
4950: }
4951:
4952: for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
4953: gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
4954: }
4955:
4956: } /* End theta */
4957:
4958: trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
4959:
4960: for(h=0; h<=nhstepm; h++) /* veij */
4961: for(j=1; j<=nlstate;j++)
4962: for(theta=1; theta <=npar; theta++)
4963: trgradg[h][j][theta]=gradg[h][theta][j];
4964:
4965: for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
4966: for(theta=1; theta <=npar; theta++)
4967: trgradgp[j][theta]=gradgp[theta][j];
4968:
4969:
4970: hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
4971: for(i=1;i<=nlstate;i++)
4972: for(j=1;j<=nlstate;j++)
4973: vareij[i][j][(int)age] =0.;
4974:
4975: for(h=0;h<=nhstepm;h++){
4976: for(k=0;k<=nhstepm;k++){
4977: matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
4978: matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
4979: for(i=1;i<=nlstate;i++)
4980: for(j=1;j<=nlstate;j++)
4981: vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
4982: }
4983: }
4984:
4985: /* pptj */
4986: matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
4987: matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
4988: for(j=nlstate+1;j<=nlstate+ndeath;j++)
4989: for(i=nlstate+1;i<=nlstate+ndeath;i++)
4990: varppt[j][i]=doldmp[j][i];
4991: /* end ppptj */
4992: /* x centered again */
4993:
4994: prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ncvyearp,ij);
4995:
4996: if (popbased==1) {
4997: if(mobilav ==0){
4998: for(i=1; i<=nlstate;i++)
4999: prlim[i][i]=probs[(int)age][i][ij];
5000: }else{ /* mobilav */
5001: for(i=1; i<=nlstate;i++)
5002: prlim[i][i]=mobaverage[(int)age][i][ij];
5003: }
5004: }
5005:
5006: /* This for computing probability of death (h=1 means
5007: computed over hstepm (estepm) matrices product = hstepm*stepm months)
5008: as a weighted average of prlim.
5009: */
5010: hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);
5011: for(j=nlstate+1;j<=nlstate+ndeath;j++){
5012: for(i=1,gmp[j]=0.;i<= nlstate; i++)
5013: gmp[j] += prlim[i][i]*p3mat[i][j][1];
5014: }
5015: /* end probability of death */
5016:
5017: fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
5018: for(j=nlstate+1; j<=(nlstate+ndeath);j++){
5019: fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
5020: for(i=1; i<=nlstate;i++){
5021: fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
5022: }
5023: }
5024: fprintf(ficresprobmorprev,"\n");
5025:
5026: fprintf(ficresvij,"%.0f ",age );
5027: for(i=1; i<=nlstate;i++)
5028: for(j=1; j<=nlstate;j++){
5029: fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
5030: }
5031: fprintf(ficresvij,"\n");
5032: free_matrix(gp,0,nhstepm,1,nlstate);
5033: free_matrix(gm,0,nhstepm,1,nlstate);
5034: free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
5035: free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
5036: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
5037: } /* End age */
5038: free_vector(gpp,nlstate+1,nlstate+ndeath);
5039: free_vector(gmp,nlstate+1,nlstate+ndeath);
5040: free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
5041: free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
5042: /* fprintf(ficgp,"\nunset parametric;unset label; set ter png small size 320, 240"); */
5043: fprintf(ficgp,"\nunset parametric;unset label; set ter svg size 640, 480");
5044: /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */
5045: fprintf(ficgp,"\n set log y; unset log x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
5046: fprintf(ficgp,"\nset out \"%s%s.svg\";",subdirf3(optionfilefiname,"VARMUPTJGR-",digitp),digit);
5047: /* fprintf(ficgp,"\n plot \"%s\" u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm); */
5048: /* fprintf(ficgp,"\n replot \"%s\" u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm); */
5049: /* fprintf(ficgp,"\n replot \"%s\" u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm); */
5050: fprintf(ficgp,"\n plot \"%s\" u 1:($3) not w l lt 1 ",subdirf(fileresprobmorprev));
5051: fprintf(ficgp,"\n replot \"%s\" u 1:(($3+1.96*$4)) t \"95%% interval\" w l lt 2 ",subdirf(fileresprobmorprev));
5052: fprintf(ficgp,"\n replot \"%s\" u 1:(($3-1.96*$4)) not w l lt 2 ",subdirf(fileresprobmorprev));
5053: fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",subdirf(fileresprobmorprev),subdirf(fileresprobmorprev));
5054: 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);
5055: /* 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 5056: */
1.218 brouard 5057: /* fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.svg\";replot;",digitp,optionfilefiname,digit); */
5058: fprintf(ficgp,"\nset out;\nset out \"%s%s.svg\";replot;set out;\n",subdirf3(optionfilefiname,"VARMUPTJGR-",digitp),digit);
1.126 brouard 5059:
1.218 brouard 5060: free_vector(xp,1,npar);
5061: free_matrix(doldm,1,nlstate,1,nlstate);
5062: free_matrix(dnewm,1,nlstate,1,npar);
5063: free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
5064: free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
5065: free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
5066: /* if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX); */
5067: fclose(ficresprobmorprev);
5068: fflush(ficgp);
5069: fflush(fichtm);
5070: } /* end varevsij */
1.126 brouard 5071:
5072: /************ Variance of prevlim ******************/
1.209 brouard 5073: 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 5074: {
1.205 brouard 5075: /* Variance of prevalence limit for each state ij using current parameters x[] and estimates of neighbourhood give by delti*/
1.126 brouard 5076: /* double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
1.164 brouard 5077:
1.126 brouard 5078: double **dnewm,**doldm;
5079: int i, j, nhstepm, hstepm;
5080: double *xp;
5081: double *gp, *gm;
5082: double **gradg, **trgradg;
1.208 brouard 5083: double **mgm, **mgp;
1.126 brouard 5084: double age,agelim;
5085: int theta;
5086:
5087: pstamp(ficresvpl);
5088: fprintf(ficresvpl,"# Standard deviation of period (stable) prevalences \n");
5089: fprintf(ficresvpl,"# Age");
5090: for(i=1; i<=nlstate;i++)
5091: fprintf(ficresvpl," %1d-%1d",i,i);
5092: fprintf(ficresvpl,"\n");
5093:
5094: xp=vector(1,npar);
5095: dnewm=matrix(1,nlstate,1,npar);
5096: doldm=matrix(1,nlstate,1,nlstate);
5097:
5098: hstepm=1*YEARM; /* Every year of age */
5099: hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */
5100: agelim = AGESUP;
5101: for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
5102: nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
5103: if (stepm >= YEARM) hstepm=1;
5104: nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
5105: gradg=matrix(1,npar,1,nlstate);
1.208 brouard 5106: mgp=matrix(1,npar,1,nlstate);
5107: mgm=matrix(1,npar,1,nlstate);
1.126 brouard 5108: gp=vector(1,nlstate);
5109: gm=vector(1,nlstate);
5110:
5111: for(theta=1; theta <=npar; theta++){
5112: for(i=1; i<=npar; i++){ /* Computes gradient */
5113: xp[i] = x[i] + (i==theta ?delti[theta]:0);
5114: }
1.209 brouard 5115: if((int)age==79 ||(int)age== 80 ||(int)age== 81 )
5116: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij);
5117: else
5118: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij);
1.208 brouard 5119: for(i=1;i<=nlstate;i++){
1.126 brouard 5120: gp[i] = prlim[i][i];
1.208 brouard 5121: mgp[theta][i] = prlim[i][i];
5122: }
1.126 brouard 5123: for(i=1; i<=npar; i++) /* Computes gradient */
5124: xp[i] = x[i] - (i==theta ?delti[theta]:0);
1.209 brouard 5125: if((int)age==79 ||(int)age== 80 ||(int)age== 81 )
5126: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij);
5127: else
5128: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij);
1.208 brouard 5129: for(i=1;i<=nlstate;i++){
1.126 brouard 5130: gm[i] = prlim[i][i];
1.208 brouard 5131: mgm[theta][i] = prlim[i][i];
5132: }
1.126 brouard 5133: for(i=1;i<=nlstate;i++)
5134: gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
1.209 brouard 5135: /* gradg[theta][2]= -gradg[theta][1]; */ /* For testing if nlstate=2 */
1.126 brouard 5136: } /* End theta */
5137:
5138: trgradg =matrix(1,nlstate,1,npar);
5139:
5140: for(j=1; j<=nlstate;j++)
5141: for(theta=1; theta <=npar; theta++)
5142: trgradg[j][theta]=gradg[theta][j];
1.209 brouard 5143: /* if((int)age==79 ||(int)age== 80 ||(int)age== 81 ){ */
5144: /* printf("\nmgm mgp %d ",(int)age); */
5145: /* for(j=1; j<=nlstate;j++){ */
5146: /* printf(" %d ",j); */
5147: /* for(theta=1; theta <=npar; theta++) */
5148: /* printf(" %d %lf %lf",theta,mgm[theta][j],mgp[theta][j]); */
5149: /* printf("\n "); */
5150: /* } */
5151: /* } */
5152: /* if((int)age==79 ||(int)age== 80 ||(int)age== 81 ){ */
5153: /* printf("\n gradg %d ",(int)age); */
5154: /* for(j=1; j<=nlstate;j++){ */
5155: /* printf("%d ",j); */
5156: /* for(theta=1; theta <=npar; theta++) */
5157: /* printf("%d %lf ",theta,gradg[theta][j]); */
5158: /* printf("\n "); */
5159: /* } */
5160: /* } */
1.126 brouard 5161:
5162: for(i=1;i<=nlstate;i++)
5163: varpl[i][(int)age] =0.;
1.209 brouard 5164: if((int)age==79 ||(int)age== 80 ||(int)age== 81){
1.205 brouard 5165: matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
5166: matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
5167: }else{
1.126 brouard 5168: matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
5169: matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
1.205 brouard 5170: }
1.126 brouard 5171: for(i=1;i<=nlstate;i++)
5172: varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
5173:
5174: fprintf(ficresvpl,"%.0f ",age );
5175: for(i=1; i<=nlstate;i++)
5176: fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
5177: fprintf(ficresvpl,"\n");
5178: free_vector(gp,1,nlstate);
5179: free_vector(gm,1,nlstate);
1.208 brouard 5180: free_matrix(mgm,1,npar,1,nlstate);
5181: free_matrix(mgp,1,npar,1,nlstate);
1.126 brouard 5182: free_matrix(gradg,1,npar,1,nlstate);
5183: free_matrix(trgradg,1,nlstate,1,npar);
5184: } /* End age */
5185:
5186: free_vector(xp,1,npar);
5187: free_matrix(doldm,1,nlstate,1,npar);
5188: free_matrix(dnewm,1,nlstate,1,nlstate);
5189:
5190: }
5191:
5192: /************ Variance of one-step probabilities ******************/
5193: void varprob(char optionfilefiname[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij, int *Tvar, int **nbcode, int *ncodemax, char strstart[])
1.222 brouard 5194: {
5195: int i, j=0, k1, l1, tj;
5196: int k2, l2, j1, z1;
5197: int k=0, l;
5198: int first=1, first1, first2;
5199: double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
5200: double **dnewm,**doldm;
5201: double *xp;
5202: double *gp, *gm;
5203: double **gradg, **trgradg;
5204: double **mu;
5205: double age, cov[NCOVMAX+1];
5206: double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
5207: int theta;
5208: char fileresprob[FILENAMELENGTH];
5209: char fileresprobcov[FILENAMELENGTH];
5210: char fileresprobcor[FILENAMELENGTH];
5211: double ***varpij;
5212:
5213: strcpy(fileresprob,"PROB_");
5214: strcat(fileresprob,fileres);
5215: if((ficresprob=fopen(fileresprob,"w"))==NULL) {
5216: printf("Problem with resultfile: %s\n", fileresprob);
5217: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
5218: }
5219: strcpy(fileresprobcov,"PROBCOV_");
5220: strcat(fileresprobcov,fileresu);
5221: if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
5222: printf("Problem with resultfile: %s\n", fileresprobcov);
5223: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
5224: }
5225: strcpy(fileresprobcor,"PROBCOR_");
5226: strcat(fileresprobcor,fileresu);
5227: if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
5228: printf("Problem with resultfile: %s\n", fileresprobcor);
5229: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
5230: }
5231: printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
5232: fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
5233: printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
5234: fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
5235: printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
5236: fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
5237: pstamp(ficresprob);
5238: fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
5239: fprintf(ficresprob,"# Age");
5240: pstamp(ficresprobcov);
5241: fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
5242: fprintf(ficresprobcov,"# Age");
5243: pstamp(ficresprobcor);
5244: fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
5245: fprintf(ficresprobcor,"# Age");
1.126 brouard 5246:
5247:
1.222 brouard 5248: for(i=1; i<=nlstate;i++)
5249: for(j=1; j<=(nlstate+ndeath);j++){
5250: fprintf(ficresprob," p%1d-%1d (SE)",i,j);
5251: fprintf(ficresprobcov," p%1d-%1d ",i,j);
5252: fprintf(ficresprobcor," p%1d-%1d ",i,j);
5253: }
5254: /* fprintf(ficresprob,"\n");
5255: fprintf(ficresprobcov,"\n");
5256: fprintf(ficresprobcor,"\n");
5257: */
5258: xp=vector(1,npar);
5259: dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
5260: doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
5261: mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
5262: varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
5263: first=1;
5264: fprintf(ficgp,"\n# Routine varprob");
5265: fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
5266: fprintf(fichtm,"\n");
5267:
5268: 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);
5269: 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);
5270: fprintf(fichtmcov,"\nEllipsoids of confidence centered on point (p<inf>ij</inf>, p<inf>kl</inf>) are estimated \
1.126 brouard 5271: and drawn. It helps understanding how is the covariance between two incidences.\
5272: They are expressed in year<sup>-1</sup> in order to be less dependent of stepm.<br>\n");
1.222 brouard 5273: fprintf(fichtmcov,"\n<br> Contour plot corresponding to x'cov<sup>-1</sup>x = 4 (where x is the column vector (pij,pkl)) are drawn. \
1.126 brouard 5274: It can be understood this way: if pij and pkl where uncorrelated the (2x2) matrix of covariance \
5275: would have been (1/(var pij), 0 , 0, 1/(var pkl)), and the confidence interval would be 2 \
5276: standard deviations wide on each axis. <br>\
5277: Now, if both incidences are correlated (usual case) we diagonalised the inverse of the covariance matrix\
5278: and made the appropriate rotation to look at the uncorrelated principal directions.<br>\
5279: To be simple, these graphs help to understand the significativity of each parameter in relation to a second other one.<br> \n");
5280:
1.222 brouard 5281: cov[1]=1;
5282: /* tj=cptcoveff; */
5283: tj = (int) pow(2,cptcoveff);
5284: if (cptcovn<1) {tj=1;ncodemax[1]=1;}
5285: j1=0;
5286: for(j1=1; j1<=tj;j1++){ /* For each valid combination of covariates */
5287: if (cptcovn>0) {
5288: fprintf(ficresprob, "\n#********** Variable ");
5289: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
5290: fprintf(ficresprob, "**********\n#\n");
5291: fprintf(ficresprobcov, "\n#********** Variable ");
5292: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
5293: fprintf(ficresprobcov, "**********\n#\n");
1.220 brouard 5294:
1.222 brouard 5295: fprintf(ficgp, "\n#********** Variable ");
5296: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
5297: fprintf(ficgp, "**********\n#\n");
1.220 brouard 5298:
5299:
1.222 brouard 5300: fprintf(fichtmcov, "\n<hr size=\"2\" color=\"#EC5E5E\">********** Variable ");
5301: for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
5302: fprintf(fichtmcov, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
1.220 brouard 5303:
1.222 brouard 5304: fprintf(ficresprobcor, "\n#********** Variable ");
5305: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
5306: fprintf(ficresprobcor, "**********\n#");
5307: if(invalidvarcomb[j1]){
5308: fprintf(ficgp,"\n#Combination (%d) ignored because no cases \n",j1);
5309: fprintf(fichtmcov,"\n<h3>Combination (%d) ignored because no cases </h3>\n",j1);
5310: continue;
5311: }
5312: }
5313: gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
5314: trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
5315: gp=vector(1,(nlstate)*(nlstate+ndeath));
5316: gm=vector(1,(nlstate)*(nlstate+ndeath));
5317: for (age=bage; age<=fage; age ++){
5318: cov[2]=age;
5319: if(nagesqr==1)
5320: cov[3]= age*age;
5321: for (k=1; k<=cptcovn;k++) {
5322: cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(j1,k)];
5323: /*cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(j1,Tvar[k])];*//* j1 1 2 3 4
5324: * 1 1 1 1 1
5325: * 2 2 1 1 1
5326: * 3 1 2 1 1
5327: */
5328: /* nbcode[1][1]=0 nbcode[1][2]=1;*/
5329: }
5330: /* for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
5331: for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,k)]*cov[2];
5332: for (k=1; k<=cptcovprod;k++)
5333: cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)]*nbcode[Tvard[k][2]][codtabm(ij,k)];
1.220 brouard 5334:
5335:
1.222 brouard 5336: for(theta=1; theta <=npar; theta++){
5337: for(i=1; i<=npar; i++)
5338: xp[i] = x[i] + (i==theta ?delti[theta]:(double)0);
1.220 brouard 5339:
1.222 brouard 5340: pmij(pmmij,cov,ncovmodel,xp,nlstate);
1.220 brouard 5341:
1.222 brouard 5342: k=0;
5343: for(i=1; i<= (nlstate); i++){
5344: for(j=1; j<=(nlstate+ndeath);j++){
5345: k=k+1;
5346: gp[k]=pmmij[i][j];
5347: }
5348: }
1.220 brouard 5349:
1.222 brouard 5350: for(i=1; i<=npar; i++)
5351: xp[i] = x[i] - (i==theta ?delti[theta]:(double)0);
1.220 brouard 5352:
1.222 brouard 5353: pmij(pmmij,cov,ncovmodel,xp,nlstate);
5354: k=0;
5355: for(i=1; i<=(nlstate); i++){
5356: for(j=1; j<=(nlstate+ndeath);j++){
5357: k=k+1;
5358: gm[k]=pmmij[i][j];
5359: }
5360: }
1.220 brouard 5361:
1.222 brouard 5362: for(i=1; i<= (nlstate)*(nlstate+ndeath); i++)
5363: gradg[theta][i]=(gp[i]-gm[i])/(double)2./delti[theta];
5364: }
1.126 brouard 5365:
1.222 brouard 5366: for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
5367: for(theta=1; theta <=npar; theta++)
5368: trgradg[j][theta]=gradg[theta][j];
1.220 brouard 5369:
1.222 brouard 5370: matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov);
5371: matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);
1.220 brouard 5372:
1.222 brouard 5373: pmij(pmmij,cov,ncovmodel,x,nlstate);
1.220 brouard 5374:
1.222 brouard 5375: k=0;
5376: for(i=1; i<=(nlstate); i++){
5377: for(j=1; j<=(nlstate+ndeath);j++){
5378: k=k+1;
5379: mu[k][(int) age]=pmmij[i][j];
5380: }
5381: }
5382: for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
5383: for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
5384: varpij[i][j][(int)age] = doldm[i][j];
1.220 brouard 5385:
1.222 brouard 5386: /*printf("\n%d ",(int)age);
5387: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
5388: printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
5389: fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
5390: }*/
1.220 brouard 5391:
1.222 brouard 5392: fprintf(ficresprob,"\n%d ",(int)age);
5393: fprintf(ficresprobcov,"\n%d ",(int)age);
5394: fprintf(ficresprobcor,"\n%d ",(int)age);
1.220 brouard 5395:
1.222 brouard 5396: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)
5397: fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));
5398: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
5399: fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);
5400: fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
5401: }
5402: i=0;
5403: for (k=1; k<=(nlstate);k++){
5404: for (l=1; l<=(nlstate+ndeath);l++){
5405: i++;
5406: fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
5407: fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
5408: for (j=1; j<=i;j++){
5409: /* printf(" k=%d l=%d i=%d j=%d\n",k,l,i,j);fflush(stdout); */
5410: fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);
5411: fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));
5412: }
5413: }
5414: }/* end of loop for state */
5415: } /* end of loop for age */
5416: free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
5417: free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
5418: free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
5419: free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
5420:
5421: /* Confidence intervalle of pij */
5422: /*
5423: fprintf(ficgp,"\nunset parametric;unset label");
5424: fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");
5425: fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
5426: 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);
5427: fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);
5428: fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);
5429: fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);
5430: */
5431:
5432: /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
5433: first1=1;first2=2;
5434: for (k2=1; k2<=(nlstate);k2++){
5435: for (l2=1; l2<=(nlstate+ndeath);l2++){
5436: if(l2==k2) continue;
5437: j=(k2-1)*(nlstate+ndeath)+l2;
5438: for (k1=1; k1<=(nlstate);k1++){
5439: for (l1=1; l1<=(nlstate+ndeath);l1++){
5440: if(l1==k1) continue;
5441: i=(k1-1)*(nlstate+ndeath)+l1;
5442: if(i<=j) continue;
5443: for (age=bage; age<=fage; age ++){
5444: if ((int)age %5==0){
5445: v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;
5446: v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;
5447: cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;
5448: mu1=mu[i][(int) age]/stepm*YEARM ;
5449: mu2=mu[j][(int) age]/stepm*YEARM;
5450: c12=cv12/sqrt(v1*v2);
5451: /* Computing eigen value of matrix of covariance */
5452: lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
5453: lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
5454: if ((lc2 <0) || (lc1 <0) ){
5455: if(first2==1){
5456: first1=0;
5457: 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);
5458: }
5459: 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);
5460: /* lc1=fabs(lc1); */ /* If we want to have them positive */
5461: /* lc2=fabs(lc2); */
5462: }
1.220 brouard 5463:
1.222 brouard 5464: /* Eigen vectors */
5465: v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
5466: /*v21=sqrt(1.-v11*v11); *//* error */
5467: v21=(lc1-v1)/cv12*v11;
5468: v12=-v21;
5469: v22=v11;
5470: tnalp=v21/v11;
5471: if(first1==1){
5472: first1=0;
5473: 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);
5474: }
5475: 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);
5476: /*printf(fignu*/
5477: /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */
5478: /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */
5479: if(first==1){
5480: first=0;
5481: fprintf(ficgp,"\n# Ellipsoids of confidence\n#\n");
5482: fprintf(ficgp,"\nset parametric;unset label");
5483: 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);
5484: fprintf(ficgp,"\nset ter svg size 640, 480");
5485: fprintf(fichtmcov,"\n<br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup>\
1.220 brouard 5486: :<a href=\"%s_%d%1d%1d-%1d%1d.svg\"> \
1.201 brouard 5487: %s_%d%1d%1d-%1d%1d.svg</A>, ",k1,l1,k2,l2,\
1.222 brouard 5488: subdirf2(optionfilefiname,"VARPIJGR_"), j1,k1,l1,k2,l2, \
5489: subdirf2(optionfilefiname,"VARPIJGR_"), j1,k1,l1,k2,l2);
5490: fprintf(fichtmcov,"\n<br><img src=\"%s_%d%1d%1d-%1d%1d.svg\"> ",subdirf2(optionfilefiname,"VARPIJGR_"), j1,k1,l1,k2,l2);
5491: fprintf(fichtmcov,"\n<br> Correlation at age %d (%.3f),",(int) age, c12);
5492: fprintf(ficgp,"\nset out \"%s_%d%1d%1d-%1d%1d.svg\"",subdirf2(optionfilefiname,"VARPIJGR_"), j1,k1,l1,k2,l2);
5493: fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
5494: fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
5495: 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", \
5496: mu1,std,v11,sqrt(lc1),v12,sqrt(lc2), \
5497: mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
5498: }else{
5499: first=0;
5500: fprintf(fichtmcov," %d (%.3f),",(int) age, c12);
5501: fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
5502: fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
5503: 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", \
5504: mu1,std,v11,sqrt(lc1),v12,sqrt(lc2), \
5505: mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
5506: }/* if first */
5507: } /* age mod 5 */
5508: } /* end loop age */
5509: fprintf(ficgp,"\nset out;\nset out \"%s_%d%1d%1d-%1d%1d.svg\";replot;set out;",subdirf2(optionfilefiname,"VARPIJGR_"), j1,k1,l1,k2,l2);
5510: first=1;
5511: } /*l12 */
5512: } /* k12 */
5513: } /*l1 */
5514: }/* k1 */
5515: } /* loop on combination of covariates j1 */
5516: free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
5517: free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
5518: free_matrix(doldm,1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
5519: free_matrix(dnewm,1,(nlstate)*(nlstate+ndeath),1,npar);
5520: free_vector(xp,1,npar);
5521: fclose(ficresprob);
5522: fclose(ficresprobcov);
5523: fclose(ficresprobcor);
5524: fflush(ficgp);
5525: fflush(fichtmcov);
5526: }
1.126 brouard 5527:
5528:
5529: /******************* Printing html file ***********/
1.201 brouard 5530: void printinghtml(char fileresu[], char title[], char datafile[], int firstpass, \
1.126 brouard 5531: int lastpass, int stepm, int weightopt, char model[],\
5532: int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
1.217 brouard 5533: int popforecast, int prevfcast, int backcast, int estepm , \
1.213 brouard 5534: double jprev1, double mprev1,double anprev1, double dateprev1, \
5535: double jprev2, double mprev2,double anprev2, double dateprev2){
1.126 brouard 5536: int jj1, k1, i1, cpt;
5537:
5538: fprintf(fichtm,"<ul><li><a href='#firstorder'>Result files (first order: no variance)</a>\n \
5539: <li><a href='#secondorder'>Result files (second order (variance)</a>\n \
5540: </ul>");
1.214 brouard 5541: fprintf(fichtm,"<ul><li><h4><a name='firstorder'>Result files (first order: no variance)</a></h4>\n");
5542: 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",
5543: jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirfext3(optionfilefiname,"PHTMFR_",".htm"),subdirfext3(optionfilefiname,"PHTMFR_",".htm"));
5544: 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 5545: jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirfext3(optionfilefiname,"PHTM_",".htm"),subdirfext3(optionfilefiname,"PHTM_",".htm"));
5546: fprintf(fichtm,", <a href=\"%s\">%s</a> (text file) <br>\n",subdirf2(fileresu,"P_"),subdirf2(fileresu,"P_"));
1.126 brouard 5547: fprintf(fichtm,"\
5548: - Estimated transition probabilities over %d (stepm) months: <a href=\"%s\">%s</a><br>\n ",
1.201 brouard 5549: stepm,subdirf2(fileresu,"PIJ_"),subdirf2(fileresu,"PIJ_"));
1.126 brouard 5550: fprintf(fichtm,"\
1.217 brouard 5551: - Estimated back transition probabilities over %d (stepm) months: <a href=\"%s\">%s</a><br>\n ",
5552: stepm,subdirf2(fileresu,"PIJB_"),subdirf2(fileresu,"PIJB_"));
5553: fprintf(fichtm,"\
1.126 brouard 5554: - Period (stable) prevalence in each health state: <a href=\"%s\">%s</a> <br>\n",
1.201 brouard 5555: subdirf2(fileresu,"PL_"),subdirf2(fileresu,"PL_"));
1.126 brouard 5556: fprintf(fichtm,"\
1.217 brouard 5557: - Period (stable) back prevalence in each health state: <a href=\"%s\">%s</a> <br>\n",
5558: subdirf2(fileresu,"PLB_"),subdirf2(fileresu,"PLB_"));
5559: fprintf(fichtm,"\
1.211 brouard 5560: - (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 5561: <a href=\"%s\">%s</a> <br>\n",
1.201 brouard 5562: estepm,subdirf2(fileresu,"E_"),subdirf2(fileresu,"E_"));
1.211 brouard 5563: if(prevfcast==1){
5564: fprintf(fichtm,"\
5565: - Prevalence projections by age and states: \
1.201 brouard 5566: <a href=\"%s\">%s</a> <br>\n</li>", subdirf2(fileresu,"F_"),subdirf2(fileresu,"F_"));
1.211 brouard 5567: }
1.126 brouard 5568:
1.222 brouard 5569: fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
1.126 brouard 5570:
1.222 brouard 5571: m=pow(2,cptcoveff);
5572: if (cptcovn < 1) {m=1;ncodemax[1]=1;}
1.126 brouard 5573:
1.222 brouard 5574: jj1=0;
5575: for(k1=1; k1<=m;k1++){
1.220 brouard 5576:
1.222 brouard 5577: /* for(i1=1; i1<=ncodemax[k1];i1++){ */
5578: jj1++;
5579: if (cptcovn > 0) {
5580: fprintf(fichtm,"<hr size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
5581: for (cpt=1; cpt<=cptcoveff;cpt++){
5582: fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtabm(jj1,cpt)]);
5583: printf(" V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtabm(jj1,cpt)]);fflush(stdout);
5584: }
5585: fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
5586: if(invalidvarcomb[k1]){
5587: fprintf(fichtm,"\n<h3>Combination (%d) ignored because no cases </h3>\n",k1);
5588: printf("\nCombination (%d) ignored because no cases \n",k1);
5589: continue;
5590: }
5591: }
5592: /* aij, bij */
5593: 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 5594: <img src=\"%s_%d-1.svg\">",model,subdirf2(optionfilefiname,"PE_"),jj1,subdirf2(optionfilefiname,"PE_"),jj1,subdirf2(optionfilefiname,"PE_"),jj1);
1.222 brouard 5595: /* Pij */
5596: 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 5597: <img src=\"%s_%d-2.svg\">",stepm,subdirf2(optionfilefiname,"PE_"),jj1,subdirf2(optionfilefiname,"PE_"),jj1,subdirf2(optionfilefiname,"PE_"),jj1);
1.222 brouard 5598: /* Quasi-incidences */
5599: fprintf(fichtm,"<br>\n- I<sub>ij</sub> or Conditional probabilities to be observed in state j being in state i %d (stepm) months\
1.220 brouard 5600: before but expressed in per year i.e. quasi incidences if stepm is small and probabilities too, \
1.211 brouard 5601: incidence (rates) are the limit when h tends to zero of the ratio of the probability <sub>h</sub>P<sub>ij</sub> \
5602: 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 5603: <img src=\"%s_%d-3.svg\">",stepm,subdirf2(optionfilefiname,"PE_"),jj1,subdirf2(optionfilefiname,"PE_"),jj1,subdirf2(optionfilefiname,"PE_"),jj1);
1.222 brouard 5604: /* Survival functions (period) in state j */
5605: for(cpt=1; cpt<=nlstate;cpt++){
5606: 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 5607: <img src=\"%s_%d-%d.svg\">", cpt, cpt, nlstate, subdirf2(optionfilefiname,"LIJ_"),cpt,jj1,subdirf2(optionfilefiname,"LIJ_"),cpt,jj1,subdirf2(optionfilefiname,"LIJ_"),cpt,jj1);
1.222 brouard 5608: }
5609: /* State specific survival functions (period) */
5610: for(cpt=1; cpt<=nlstate;cpt++){
5611: fprintf(fichtm,"<br>\n- Survival functions from state %d in each live state and total.\
1.220 brouard 5612: Or probability to survive in various states (1 to %d) being in state %d at different ages. \
1.201 brouard 5613: <a href=\"%s%d_%d.svg\">%s%d_%d.svg</a><br> <img src=\"%s_%d-%d.svg\">", cpt, nlstate, cpt, subdirf2(optionfilefiname,"LIJT_"),cpt,jj1,subdirf2(optionfilefiname,"LIJT_"),cpt,jj1,subdirf2(optionfilefiname,"LIJT_"),cpt,jj1);
1.222 brouard 5614: }
5615: /* Period (stable) prevalence in each health state */
5616: for(cpt=1; cpt<=nlstate;cpt++){
5617: 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 5618: <img src=\"%s_%d-%d.svg\">", cpt, cpt, nlstate, subdirf2(optionfilefiname,"P_"),cpt,jj1,subdirf2(optionfilefiname,"P_"),cpt,jj1,subdirf2(optionfilefiname,"P_"),cpt,jj1);
1.222 brouard 5619: }
5620: if(backcast==1){
5621: /* Period (stable) back prevalence in each health state */
5622: for(cpt=1; cpt<=nlstate;cpt++){
5623: fprintf(fichtm,"<br>\n- Convergence to period (stable) back prevalence in state %d. Or probability to be in state %d being in state (1 to %d) at different ages. <a href=\"%s_%d-%d.svg\">%s_%d-%d.svg</a><br> \
1.217 brouard 5624: <img src=\"%s_%d-%d.svg\">", cpt, cpt, nlstate, subdirf2(optionfilefiname,"PB_"),cpt,jj1,subdirf2(optionfilefiname,"PB_"),cpt,jj1,subdirf2(optionfilefiname,"PB_"),cpt,jj1);
1.222 brouard 5625: }
1.217 brouard 5626: }
1.222 brouard 5627: if(prevfcast==1){
5628: /* Projection of prevalence up to period (stable) prevalence in each health state */
5629: for(cpt=1; cpt<=nlstate;cpt++){
5630: 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 5631: <img src=\"%s_%d-%d.svg\">", dateprev1, dateprev2, cpt, cpt, nlstate, subdirf2(optionfilefiname,"PROJ_"),cpt,jj1,subdirf2(optionfilefiname,"PROJ_"),cpt,jj1,subdirf2(optionfilefiname,"PROJ_"),cpt,jj1);
1.222 brouard 5632: }
5633: }
1.220 brouard 5634:
1.222 brouard 5635: for(cpt=1; cpt<=nlstate;cpt++) {
5636: 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 5637: <img src=\"%s_%d%d.svg\">",cpt,nlstate,subdirf2(optionfilefiname,"EXP_"),cpt,jj1,subdirf2(optionfilefiname,"EXP_"),cpt,jj1,subdirf2(optionfilefiname,"EXP_"),cpt,jj1);
1.222 brouard 5638: }
5639: /* } /\* end i1 *\/ */
5640: }/* End k1 */
5641: fprintf(fichtm,"</ul>");
1.126 brouard 5642:
1.222 brouard 5643: fprintf(fichtm,"\
1.126 brouard 5644: \n<br><li><h4> <a name='secondorder'>Result files (second order: variances)</a></h4>\n\
1.193 brouard 5645: - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br> \
1.203 brouard 5646: - 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 5647: But because parameters are usually highly correlated (a higher incidence of disability \
5648: and a higher incidence of recovery can give very close observed transition) it might \
5649: be very useful to look not only at linear confidence intervals estimated from the \
5650: variances but at the covariance matrix. And instead of looking at the estimated coefficients \
5651: (parameters) of the logistic regression, it might be more meaningful to visualize the \
5652: covariance matrix of the one-step probabilities. \
5653: See page 'Matrix of variance-covariance of one-step probabilities' below. \n", rfileres,rfileres);
1.126 brouard 5654:
1.222 brouard 5655: fprintf(fichtm," - Standard deviation of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
5656: subdirf2(fileresu,"PROB_"),subdirf2(fileresu,"PROB_"));
5657: fprintf(fichtm,"\
1.126 brouard 5658: - Variance-covariance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
1.222 brouard 5659: subdirf2(fileresu,"PROBCOV_"),subdirf2(fileresu,"PROBCOV_"));
1.126 brouard 5660:
1.222 brouard 5661: fprintf(fichtm,"\
1.126 brouard 5662: - Correlation matrix of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
1.222 brouard 5663: subdirf2(fileresu,"PROBCOR_"),subdirf2(fileresu,"PROBCOR_"));
5664: fprintf(fichtm,"\
1.126 brouard 5665: - 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): \
5666: <a href=\"%s\">%s</a> <br>\n</li>",
1.201 brouard 5667: estepm,subdirf2(fileresu,"CVE_"),subdirf2(fileresu,"CVE_"));
1.222 brouard 5668: fprintf(fichtm,"\
1.126 brouard 5669: - (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): \
5670: <a href=\"%s\">%s</a> <br>\n</li>",
1.201 brouard 5671: estepm,subdirf2(fileresu,"STDE_"),subdirf2(fileresu,"STDE_"));
1.222 brouard 5672: fprintf(fichtm,"\
1.128 brouard 5673: - Variances and covariances of health expectancies by age. Status (i) based health expectancies (in state j), e<sup>ij</sup> are weighted by the period prevalences in each state i (if popbased=1, an additional computation is done using the cross-sectional prevalences, i.e population based) (estepm=%d months): <a href=\"%s\">%s</a><br>\n",
1.222 brouard 5674: estepm, subdirf2(fileresu,"V_"),subdirf2(fileresu,"V_"));
5675: fprintf(fichtm,"\
1.128 brouard 5676: - Total life expectancy and total health expectancies to be spent in each health state e<sup>.j</sup> with their standard errors (if popbased=1, an additional computation is done using the cross-sectional prevalences, i.e population based) (estepm=%d months): <a href=\"%s\">%s</a> <br>\n",
1.222 brouard 5677: estepm, subdirf2(fileresu,"T_"),subdirf2(fileresu,"T_"));
5678: fprintf(fichtm,"\
1.126 brouard 5679: - Standard deviation of period (stable) prevalences: <a href=\"%s\">%s</a> <br>\n",\
1.222 brouard 5680: subdirf2(fileresu,"VPL_"),subdirf2(fileresu,"VPL_"));
1.126 brouard 5681:
5682: /* if(popforecast==1) fprintf(fichtm,"\n */
5683: /* - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n */
5684: /* - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n */
5685: /* <br>",fileres,fileres,fileres,fileres); */
5686: /* else */
5687: /* fprintf(fichtm,"\n No population forecast: popforecast = %d (instead of 1) or stepm = %d (instead of 1) or model=%s (instead of .)<br><br></li>\n",popforecast, stepm, model); */
1.222 brouard 5688: fflush(fichtm);
5689: fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
1.126 brouard 5690:
1.222 brouard 5691: m=pow(2,cptcoveff);
5692: if (cptcovn < 1) {m=1;ncodemax[1]=1;}
1.126 brouard 5693:
1.222 brouard 5694: jj1=0;
5695: for(k1=1; k1<=m;k1++){
5696: /* for(i1=1; i1<=ncodemax[k1];i1++){ */
5697: jj1++;
1.126 brouard 5698: if (cptcovn > 0) {
5699: fprintf(fichtm,"<hr size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
5700: for (cpt=1; cpt<=cptcoveff;cpt++)
1.222 brouard 5701: fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtabm(jj1,cpt)]);
1.126 brouard 5702: fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
1.220 brouard 5703:
1.222 brouard 5704: if(invalidvarcomb[k1]){
5705: fprintf(fichtm,"\n<h4>Combination (%d) ignored because no cases </h4>\n",k1);
5706: continue;
5707: }
1.126 brouard 5708: }
5709: for(cpt=1; cpt<=nlstate;cpt++) {
1.218 brouard 5710: fprintf(fichtm,"\n<br>- Observed (cross-sectional) and period (incidence based) \
5711: prevalence (with 95%% confidence interval) in state (%d): <a href=\"%s_%d-%d.svg\"> %s_%d-%d.svg</a>\n <br>\
1.205 brouard 5712: <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 5713: }
5714: fprintf(fichtm,"\n<br>- Total life expectancy by age and \
1.128 brouard 5715: health expectancies in states (1) and (2). If popbased=1 the smooth (due to the model) \
5716: true period expectancies (those weighted with period prevalences are also\
5717: drawn in addition to the population based expectancies computed using\
1.218 brouard 5718: observed and cahotic prevalences: <a href=\"%s_%d.svg\">%s_%d.svg</a>\n<br>\
1.205 brouard 5719: <img src=\"%s_%d.svg\">",subdirf2(optionfilefiname,"E_"),jj1,subdirf2(optionfilefiname,"E_"),jj1,subdirf2(optionfilefiname,"E_"),jj1);
1.222 brouard 5720: /* } /\* end i1 *\/ */
5721: }/* End k1 */
5722: fprintf(fichtm,"</ul>");
5723: fflush(fichtm);
1.126 brouard 5724: }
5725:
5726: /******************* Gnuplot file **************/
1.223 ! brouard 5727: void printinggnuplot(char fileresu[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , int prevfcast, int backcast, char pathc[], double p[]){
1.126 brouard 5728:
5729: char dirfileres[132],optfileres[132];
1.223 ! brouard 5730: char gplotcondition[132];
1.164 brouard 5731: int cpt=0,k1=0,i=0,k=0,j=0,jk=0,k2=0,k3=0,ij=0,l=0;
1.211 brouard 5732: int lv=0, vlv=0, kl=0;
1.130 brouard 5733: int ng=0;
1.201 brouard 5734: int vpopbased;
1.223 ! brouard 5735: int ioffset; /* variable offset for columns */
1.219 brouard 5736:
1.126 brouard 5737: /* if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) { */
5738: /* printf("Problem with file %s",optionfilegnuplot); */
5739: /* fprintf(ficlog,"Problem with file %s",optionfilegnuplot); */
5740: /* } */
5741:
5742: /*#ifdef windows */
5743: fprintf(ficgp,"cd \"%s\" \n",pathc);
1.223 ! brouard 5744: /*#endif */
1.126 brouard 5745: m=pow(2,cptcoveff);
5746:
1.202 brouard 5747: /* Contribution to likelihood */
5748: /* Plot the probability implied in the likelihood */
1.223 ! brouard 5749: fprintf(ficgp,"\n# Contributions to the Likelihood, mle >=1. For mle=4 no interpolation, pure matrix products.\n#\n");
! 5750: fprintf(ficgp,"\n set log y; unset log x;set xlabel \"Age\"; set ylabel \"Likelihood (-2Log(L))\";");
! 5751: /* fprintf(ficgp,"\nset ter svg size 640, 480"); */ /* Too big for svg */
! 5752: fprintf(ficgp,"\nset ter pngcairo size 640, 480");
1.204 brouard 5753: /* nice for mle=4 plot by number of matrix products.
1.202 brouard 5754: replot "rrtest1/toto.txt" u 2:($4 == 1 && $5==2 ? $9 : 1/0):5 t "p12" with point lc 1 */
5755: /* replot exp(p1+p2*x)/(1+exp(p1+p2*x)+exp(p3+p4*x)+exp(p5+p6*x)) t "p12(x)" */
1.223 ! brouard 5756: /* fprintf(ficgp,"\nset out \"%s.svg\";",subdirf2(optionfilefiname,"ILK_")); */
! 5757: fprintf(ficgp,"\nset out \"%s-dest.png\";",subdirf2(optionfilefiname,"ILK_"));
! 5758: 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));
! 5759: fprintf(ficgp,"\nset out \"%s-ori.png\";",subdirf2(optionfilefiname,"ILK_"));
! 5760: 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));
! 5761: for (i=1; i<= nlstate ; i ++) {
! 5762: fprintf(ficgp,"\nset out \"%s-p%dj.png\";set ylabel \"Probability for each individual/wave\";",subdirf2(optionfilefiname,"ILK_"),i);
! 5763: fprintf(ficgp,"unset log;\n# plot weighted, mean weight should have point size of 0.5\n plot \"%s\"",subdirf(fileresilk));
! 5764: 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);
! 5765: for (j=2; j<= nlstate+ndeath ; j ++) {
! 5766: 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);
! 5767: }
! 5768: fprintf(ficgp,";\nset out; unset ylabel;\n");
! 5769: }
! 5770: /* 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 */
! 5771: /* fprintf(ficgp,"\nset log y;plot \"%s\" u 2:(-$11):3 t \"All sample, all transitions\" with dots lc variable",subdirf(fileresilk)); */
! 5772: /* fprintf(ficgp,"\nreplot \"%s\" u 2:($3 <= 3 ? -$11 : 1/0):3 t \"First 3 individuals\" with line lc variable", subdirf(fileresilk)); */
! 5773: fprintf(ficgp,"\nset out;unset log\n");
! 5774: /* fprintf(ficgp,"\nset out \"%s.svg\"; replot; set out; # bug gnuplot",subdirf2(optionfilefiname,"ILK_")); */
1.202 brouard 5775:
1.126 brouard 5776: strcpy(dirfileres,optionfilefiname);
5777: strcpy(optfileres,"vpl");
1.223 ! brouard 5778: /* 1eme*/
1.211 brouard 5779: for (cpt=1; cpt<= nlstate ; cpt ++) { /* For each live state */
1.220 brouard 5780: for (k1=1; k1<= m ; k1 ++) { /* For each valid combination of covariate */
1.211 brouard 5781: /* plot [100000000000000000000:-100000000000000000000] "mysbiaspar/vplrmysbiaspar.txt to check */
5782: fprintf(ficgp,"\n# 1st: Period (stable) prevalence with CI: 'VPL_' files ");
1.219 brouard 5783: for (k=1; k<=cptcoveff; k++){ /* For each covariate k get corresponding value lv for combination k1 */
1.223 ! brouard 5784: lv= decodtabm(k1,k,cptcoveff); /* Should be the value of the covariate corresponding to k1 combination */
! 5785: /* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
! 5786: /* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
! 5787: /* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
! 5788: vlv= nbcode[Tvaraff[k]][lv]; /* vlv is the value of the covariate lv, 0 or 1 */
! 5789: /* For each combination of covariate k1 (V1=1, V3=0), we printed the current covariate k and its value vlv */
! 5790: fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
1.211 brouard 5791: }
5792: fprintf(ficgp,"\n#\n");
1.223 ! brouard 5793: if(invalidvarcomb[k1]){
! 5794: fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);
! 5795: continue;
! 5796: }
1.211 brouard 5797:
1.223 ! brouard 5798: fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" \n",subdirf2(optionfilefiname,"V_"),cpt,k1);
! 5799: fprintf(ficgp,"\n#set out \"V_%s_%d-%d.svg\" \n",optionfilefiname,cpt,k1);
! 5800: fprintf(ficgp,"set xlabel \"Age\" \n\
1.219 brouard 5801: set ylabel \"Probability\" \n \
5802: set ter svg size 640, 480\n \
1.201 brouard 5803: plot [%.f:%.f] \"%s\" every :::%d::%d u 1:2 \"%%lf",ageminpar,fage,subdirf2(fileresu,"VPL_"),k1-1,k1-1);
1.219 brouard 5804:
1.223 ! brouard 5805: for (i=1; i<= nlstate ; i ++) {
! 5806: if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
! 5807: else fprintf(ficgp," %%*lf (%%*lf)");
! 5808: }
! 5809: 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);
! 5810: for (i=1; i<= nlstate ; i ++) {
! 5811: if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
! 5812: else fprintf(ficgp," %%*lf (%%*lf)");
! 5813: }
! 5814: fprintf(ficgp,"\" t\"95%% CI\" w l lt 1,\"%s\" every :::%d::%d u 1:($2-1.96*$3) \"%%lf",subdirf2(fileresu,"VPL_"),k1-1,k1-1);
! 5815: for (i=1; i<= nlstate ; i ++) {
! 5816: if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
! 5817: else fprintf(ficgp," %%*lf (%%*lf)");
! 5818: }
! 5819: fprintf(ficgp,"\" t\"\" w l lt 1,\"%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence\" w l lt 2",subdirf2(fileresu,"P_"),k1-1,k1-1,2+4*(cpt-1));
! 5820: if(backcast==1){ /* We need to get the corresponding values of the covariates involved in this combination k1 */
! 5821: /* fprintf(ficgp,",\"%s\" every :::%d::%d u 1:($%d) t\"Backward stable prevalence\" w l lt 3",subdirf2(fileresu,"PLB_"),k1-1,k1-1,1+cpt); */
! 5822: fprintf(ficgp,",\"%s\" u 1:((",subdirf2(fileresu,"PLB_")); /* Age is in 1 */
! 5823: if(cptcoveff ==0){
! 5824: fprintf(ficgp,"$%d)) t 'Backward prevalence in state %d' with line ", 2+(cpt-1), cpt );
! 5825: }else{
! 5826: kl=0;
! 5827: for (k=1; k<=cptcoveff; k++){ /* For each combination of covariate */
! 5828: lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate value corresponding to k1 combination and kth covariate */
! 5829: /* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
! 5830: /* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
! 5831: /* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
! 5832: vlv= nbcode[Tvaraff[k]][lv];
! 5833: kl++;
! 5834: /* 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 *\/ */
! 5835: /*6+(cpt-1)*(nlstate+1)+1+(i-1)+(nlstate+1)*nlstate; 6+(1-1)*(2+1)+1+(1-1) +(2+1)*2=13 */
! 5836: /*6+1+(i-1)+(nlstate+1)*nlstate; 6+1+(1-1) +(2+1)*2=13 */
! 5837: /* '' u 6:(($1==1 && $2==0 && $3==2 && $4==0)? $9/(1.-$15) : 1/0):($5==2000? 3:2) t 'p.1' with line lc variable*/
! 5838: if(k==cptcoveff){
! 5839: fprintf(ficgp,"$%d==%d && $%d==%d)? $%d : 1/0) t 'Backward prevalence in state %d' with line ",kl+1, Tvaraff[k],kl+1+1,nbcode[Tvaraff[k]][lv], \
! 5840: 6+(cpt-1), cpt );
! 5841: }else{
! 5842: fprintf(ficgp,"$%d==%d && $%d==%d && ",kl+1, Tvaraff[k],kl+1+1,nbcode[Tvaraff[k]][lv]);
! 5843: kl++;
! 5844: }
! 5845: } /* end covariate */
! 5846: } /* end if no covariate */
! 5847: } /* end if backcast */
! 5848: fprintf(ficgp,"\nset out \n");
1.201 brouard 5849: } /* k1 */
5850: } /* cpt */
1.126 brouard 5851: /*2 eme*/
5852: for (k1=1; k1<= m ; k1 ++) {
1.220 brouard 5853:
1.223 ! brouard 5854: fprintf(ficgp,"\n# 2nd: Total life expectancy with CI: 't' files ");
! 5855: for (k=1; k<=cptcoveff; k++){ /* For each covariate and each value */
! 5856: lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */
! 5857: /* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
! 5858: /* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
! 5859: /* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
! 5860: vlv= nbcode[Tvaraff[k]][lv];
! 5861: fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
! 5862: }
! 5863: fprintf(ficgp,"\n#\n");
! 5864: if(invalidvarcomb[k1]){
! 5865: fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);
! 5866: continue;
! 5867: }
1.219 brouard 5868:
1.223 ! brouard 5869: fprintf(ficgp,"\nset out \"%s_%d.svg\" \n",subdirf2(optionfilefiname,"E_"),k1);
! 5870: for(vpopbased=0; vpopbased <= popbased; vpopbased++){ /* Done for vpopbased=0 and vpopbased=1 if popbased==1*/
! 5871: if(vpopbased==0)
! 5872: fprintf(ficgp,"set ylabel \"Years\" \nset ter svg size 640, 480\nplot [%.f:%.f] ",ageminpar,fage);
! 5873: else
! 5874: fprintf(ficgp,"\nreplot ");
! 5875: for (i=1; i<= nlstate+1 ; i ++) {
! 5876: k=2*i;
! 5877: 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);
! 5878: for (j=1; j<= nlstate+1 ; j ++) {
! 5879: if (j==i) fprintf(ficgp," %%lf (%%lf)");
! 5880: else fprintf(ficgp," %%*lf (%%*lf)");
! 5881: }
! 5882: if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l lt %d, \\\n",i);
! 5883: else fprintf(ficgp,"\" t\"LE in state (%d)\" w l lt %d, \\\n",i-1,i+1);
! 5884: 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);
! 5885: for (j=1; j<= nlstate+1 ; j ++) {
! 5886: if (j==i) fprintf(ficgp," %%lf (%%lf)");
! 5887: else fprintf(ficgp," %%*lf (%%*lf)");
! 5888: }
! 5889: fprintf(ficgp,"\" t\"\" w l lt 0,");
! 5890: fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2==%d && $4!=0 ? $4+$5*2 : 1/0) \"%%lf %%lf %%lf",subdirf2(fileresu,"T_"),k1-1,k1-1,vpopbased);
! 5891: for (j=1; j<= nlstate+1 ; j ++) {
! 5892: if (j==i) fprintf(ficgp," %%lf (%%lf)");
! 5893: else fprintf(ficgp," %%*lf (%%*lf)");
! 5894: }
! 5895: if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l lt 0");
! 5896: else fprintf(ficgp,"\" t\"\" w l lt 0,\\\n");
! 5897: } /* state */
! 5898: } /* vpopbased */
! 5899: fprintf(ficgp,"\nset out;set out \"%s_%d.svg\"; replot; set out; \n",subdirf2(optionfilefiname,"E_"),k1); /* Buggy gnuplot */
1.201 brouard 5900: } /* k1 */
1.219 brouard 5901:
5902:
1.126 brouard 5903: /*3eme*/
5904: for (k1=1; k1<= m ; k1 ++) {
1.220 brouard 5905:
1.126 brouard 5906: for (cpt=1; cpt<= nlstate ; cpt ++) {
1.211 brouard 5907: fprintf(ficgp,"\n# 3d: Life expectancy with EXP_ files: cov=%d state=%d",k1, cpt);
5908: for (k=1; k<=cptcoveff; k++){ /* For each covariate and each value */
1.223 ! brouard 5909: lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */
! 5910: /* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
! 5911: /* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
! 5912: /* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
! 5913: vlv= nbcode[Tvaraff[k]][lv];
! 5914: fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
1.211 brouard 5915: }
5916: fprintf(ficgp,"\n#\n");
1.223 ! brouard 5917: if(invalidvarcomb[k1]){
! 5918: fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);
! 5919: continue;
! 5920: }
1.219 brouard 5921:
1.126 brouard 5922: /* k=2+nlstate*(2*cpt-2); */
5923: k=2+(nlstate+1)*(cpt-1);
1.201 brouard 5924: fprintf(ficgp,"\nset out \"%s_%d%d.svg\" \n",subdirf2(optionfilefiname,"EXP_"),cpt,k1);
1.199 brouard 5925: fprintf(ficgp,"set ter svg size 640, 480\n\
1.201 brouard 5926: plot [%.f:%.f] \"%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,subdirf2(fileresu,"E_"),k1-1,k1-1,k,cpt);
1.126 brouard 5927: /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
1.223 ! brouard 5928: for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
! 5929: fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
! 5930: fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
! 5931: for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
! 5932: fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
1.219 brouard 5933:
1.126 brouard 5934: */
5935: for (i=1; i< nlstate ; i ++) {
1.223 ! brouard 5936: 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);
! 5937: /* fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+2*i,cpt,i+1);*/
1.219 brouard 5938:
1.126 brouard 5939: }
1.201 brouard 5940: 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 5941: }
5942: }
5943:
1.223 ! brouard 5944: /* 4eme */
1.201 brouard 5945: /* Survival functions (period) from state i in state j by initial state i */
5946: for (k1=1; k1<= m ; k1 ++) { /* For each multivariate if any */
1.220 brouard 5947:
1.201 brouard 5948: for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */
1.211 brouard 5949: fprintf(ficgp,"\n#\n#\n# Survival functions in state j : 'LIJ_' files, cov=%d state=%d",k1, cpt);
5950: for (k=1; k<=cptcoveff; k++){ /* For each covariate and each value */
1.223 ! brouard 5951: lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */
! 5952: /* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
! 5953: /* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
! 5954: /* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
! 5955: vlv= nbcode[Tvaraff[k]][lv];
! 5956: fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
1.211 brouard 5957: }
5958: fprintf(ficgp,"\n#\n");
1.223 ! brouard 5959: if(invalidvarcomb[k1]){
! 5960: fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);
! 5961: continue;
! 5962: }
1.220 brouard 5963:
1.201 brouard 5964: fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" \n",subdirf2(optionfilefiname,"LIJ_"),cpt,k1);
5965: fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability to be alive\" \n\
1.220 brouard 5966: set ter svg size 640, 480\n \
5967: unset log y\n \
1.201 brouard 5968: plot [%.f:%.f] ", ageminpar, agemaxpar);
1.211 brouard 5969: k=3;
1.201 brouard 5970: for (i=1; i<= nlstate ; i ++){
1.223 ! brouard 5971: if(i==1){
! 5972: fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"PIJ_"));
! 5973: }else{
! 5974: fprintf(ficgp,", '' ");
! 5975: }
! 5976: l=(nlstate+ndeath)*(i-1)+1;
! 5977: fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d/($%d",k1,k+l+(cpt-1),k+l);
! 5978: for (j=2; j<= nlstate+ndeath ; j ++)
! 5979: fprintf(ficgp,"+$%d",k+l+j-1);
! 5980: fprintf(ficgp,")) t \"l(%d,%d)\" w l",i,cpt);
1.201 brouard 5981: } /* nlstate */
5982: fprintf(ficgp,"\nset out\n");
5983: } /* end cpt state*/
5984: } /* end covariate */
1.220 brouard 5985:
5986: /* 5eme */
1.201 brouard 5987: /* Survival functions (period) from state i in state j by final state j */
1.202 brouard 5988: for (k1=1; k1<= m ; k1 ++) { /* For each covariate if any */
1.201 brouard 5989: for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each inital state */
1.223 ! brouard 5990:
1.201 brouard 5991: 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 5992: for (k=1; k<=cptcoveff; k++){ /* For each covariate and each value */
1.220 brouard 5993: lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */
5994: /* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
5995: /* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
5996: /* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
5997: vlv= nbcode[Tvaraff[k]][lv];
5998: fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
1.211 brouard 5999: }
6000: fprintf(ficgp,"\n#\n");
1.223 ! brouard 6001: if(invalidvarcomb[k1]){
! 6002: fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);
! 6003: continue;
! 6004: }
1.220 brouard 6005:
1.201 brouard 6006: fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" \n",subdirf2(optionfilefiname,"LIJT_"),cpt,k1);
6007: fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability to be alive\" \n\
1.220 brouard 6008: set ter svg size 640, 480\n \
6009: unset log y\n \
1.201 brouard 6010: plot [%.f:%.f] ", ageminpar, agemaxpar);
1.211 brouard 6011: k=3;
1.201 brouard 6012: for (j=1; j<= nlstate ; j ++){ /* Lived in state j */
1.220 brouard 6013: if(j==1)
6014: fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"PIJ_"));
6015: else
6016: fprintf(ficgp,", '' ");
6017: l=(nlstate+ndeath)*(cpt-1) +j;
6018: fprintf(ficgp," u (($1==%d && (floor($2)%%5 == 0)) ? ($3):1/0):($%d",k1,k+l);
6019: /* for (i=2; i<= nlstate+ndeath ; i ++) */
6020: /* fprintf(ficgp,"+$%d",k+l+i-1); */
6021: fprintf(ficgp,") t \"l(%d,%d)\" w l",cpt,j);
1.201 brouard 6022: } /* nlstate */
6023: fprintf(ficgp,", '' ");
6024: fprintf(ficgp," u (($1==%d && (floor($2)%%5 == 0)) ? ($3):1/0):(",k1);
6025: for (j=1; j<= nlstate ; j ++){ /* Lived in state j */
1.220 brouard 6026: l=(nlstate+ndeath)*(cpt-1) +j;
6027: if(j < nlstate)
6028: fprintf(ficgp,"$%d +",k+l);
6029: else
6030: fprintf(ficgp,"$%d) t\"l(%d,.)\" w l",k+l,cpt);
1.201 brouard 6031: }
6032: fprintf(ficgp,"\nset out\n");
6033: } /* end cpt state*/
6034: } /* end covariate */
1.220 brouard 6035:
6036: /* 6eme */
1.202 brouard 6037: /* CV preval stable (period) for each covariate */
1.211 brouard 6038: for (k1=1; k1<= m ; k1 ++) { /* For each covariate combination (1 to m=2**k), if any covariate is present */
1.153 brouard 6039: for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */
1.223 ! brouard 6040:
1.211 brouard 6041: fprintf(ficgp,"\n#\n#\n#CV preval stable (period): 'pij' files, covariatecombination#=%d state=%d",k1, cpt);
6042: for (k=1; k<=cptcoveff; k++){ /* For each covariate and each value */
1.220 brouard 6043: lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */
6044: /* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
6045: /* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
6046: /* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
6047: vlv= nbcode[Tvaraff[k]][lv];
6048: fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
1.211 brouard 6049: }
6050: fprintf(ficgp,"\n#\n");
1.223 ! brouard 6051: if(invalidvarcomb[k1]){
! 6052: fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);
! 6053: continue;
! 6054: }
! 6055:
1.201 brouard 6056: fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" \n",subdirf2(optionfilefiname,"P_"),cpt,k1);
1.126 brouard 6057: fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\
1.223 ! brouard 6058: set ter svg size 640, 480\n \
! 6059: unset log y\n \
1.153 brouard 6060: plot [%.f:%.f] ", ageminpar, agemaxpar);
1.211 brouard 6061: k=3; /* Offset */
1.153 brouard 6062: for (i=1; i<= nlstate ; i ++){
1.220 brouard 6063: if(i==1)
6064: fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"PIJ_"));
6065: else
6066: fprintf(ficgp,", '' ");
6067: l=(nlstate+ndeath)*(i-1)+1;
6068: fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d/($%d",k1,k+l+(cpt-1),k+l);
6069: for (j=2; j<= nlstate ; j ++)
6070: fprintf(ficgp,"+$%d",k+l+j-1);
6071: fprintf(ficgp,")) t \"prev(%d,%d)\" w l",i,cpt);
1.153 brouard 6072: } /* nlstate */
1.201 brouard 6073: fprintf(ficgp,"\nset out\n");
1.153 brouard 6074: } /* end cpt state*/
6075: } /* end covariate */
1.223 ! brouard 6076:
! 6077:
1.220 brouard 6078: /* 7eme */
1.218 brouard 6079: if(backcast == 1){
1.217 brouard 6080: /* CV back preval stable (period) for each covariate */
1.218 brouard 6081: for (k1=1; k1<= m ; k1 ++) { /* For each covariate combination (1 to m=2**k), if any covariate is present */
6082: for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */
1.220 brouard 6083: fprintf(ficgp,"\n#\n#\n#CV Back preval stable (period): 'pij' files, covariatecombination#=%d state=%d",k1, cpt);
6084: for (k=1; k<=cptcoveff; k++){ /* For each covariate and each value */
6085: lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */
6086: /* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
6087: /* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
1.223 ! brouard 6088: /* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
1.220 brouard 6089: vlv= nbcode[Tvaraff[k]][lv];
6090: fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
6091: }
6092: fprintf(ficgp,"\n#\n");
6093: if(invalidvarcomb[k1]){
1.223 ! brouard 6094: fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);
! 6095: continue;
1.220 brouard 6096: }
6097:
6098: fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" \n",subdirf2(optionfilefiname,"PB_"),cpt,k1);
6099: fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\
6100: set ter svg size 640, 480\n \
6101: unset log y\n \
1.218 brouard 6102: plot [%.f:%.f] ", ageminpar, agemaxpar);
1.220 brouard 6103: k=3; /* Offset */
6104: for (i=1; i<= nlstate ; i ++){
6105: if(i==1)
6106: fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"PIJB_"));
6107: else
6108: fprintf(ficgp,", '' ");
6109: /* l=(nlstate+ndeath)*(i-1)+1; */
6110: l=(nlstate+ndeath)*(cpt-1)+1;
6111: /* fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d/($%d",k1,k+l+(cpt-1),k+l); /\* a vérifier *\/ */
6112: /* fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d/($%d",k1,k+l+(cpt-1),k+l+(cpt-1)+i-1); /\* a vérifier *\/ */
6113: fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d",k1,k+l+(cpt-1)+i-1); /* a vérifier */
6114: /* for (j=2; j<= nlstate ; j ++) */
6115: /* fprintf(ficgp,"+$%d",k+l+j-1); */
6116: /* /\* fprintf(ficgp,"+$%d",k+l+j-1); *\/ */
6117: fprintf(ficgp,") t \"bprev(%d,%d)\" w l",i,cpt);
6118: } /* nlstate */
6119: fprintf(ficgp,"\nset out\n");
1.218 brouard 6120: } /* end cpt state*/
6121: } /* end covariate */
6122: } /* End if backcast */
6123:
1.223 ! brouard 6124: /* 8eme */
1.218 brouard 6125: if(prevfcast==1){
6126: /* Projection from cross-sectional to stable (period) for each covariate */
6127:
6128: for (k1=1; k1<= m ; k1 ++) { /* For each covariate combination (1 to m=2**k), if any covariate is present */
1.211 brouard 6129: for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */
1.219 brouard 6130: fprintf(ficgp,"\n#\n#\n#Projection of prevalence to stable (period): 'PROJ_' files, covariatecombination#=%d state=%d",k1, cpt);
6131: for (k=1; k<=cptcoveff; k++){ /* For each correspondig covariate value */
6132: lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate value corresponding to k1 combination and kth covariate */
6133: /* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
6134: /* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
6135: /* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
6136: vlv= nbcode[Tvaraff[k]][lv];
1.220 brouard 6137: fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
1.219 brouard 6138: }
6139: fprintf(ficgp,"\n#\n");
1.220 brouard 6140: if(invalidvarcomb[k1]){
1.223 ! brouard 6141: fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);
! 6142: continue;
1.220 brouard 6143: }
1.219 brouard 6144:
6145: fprintf(ficgp,"# hpijx=probability over h years, hp.jx is weighted by observed prev\n ");
6146: fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" \n",subdirf2(optionfilefiname,"PROJ_"),cpt,k1);
6147: fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Prevalence\" \n\
1.223 ! brouard 6148: set ter svg size 640, 480\n \
! 6149: unset log y\n \
1.219 brouard 6150: plot [%.f:%.f] ", ageminpar, agemaxpar);
6151: for (i=1; i<= nlstate+1 ; i ++){ /* nlstate +1 p11 p21 p.1 */
6152: /*# V1 = 1 V2 = 0 yearproj age p11 p21 p.1 p12 p22 p.2 p13 p23 p.3*/
6153: /*# 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 */
6154: /*# yearproj age p11 p21 p.1 p12 p22 p.2 p13 p23 p.3*/
6155: /*# 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 */
6156: if(i==1){
6157: fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"F_"));
6158: }else{
6159: fprintf(ficgp,",\\\n '' ");
6160: }
6161: if(cptcoveff ==0){ /* No covariate */
6162: ioffset=2; /* Age is in 2 */
6163: /*# yearproj age p11 p21 p31 p.1 p12 p22 p32 p.2 p13 p23 p33 p.3 p14 p24 p34 p.4*/
6164: /*# 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 */
6165: /*# V1 = 1 yearproj age p11 p21 p31 p.1 p12 p22 p32 p.2 p13 p23 p33 p.3 p14 p24 p34 p.4*/
6166: /*# 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 */
6167: fprintf(ficgp," u %d:(", ioffset);
6168: if(i==nlstate+1)
6169: fprintf(ficgp," $%d/(1.-$%d)) t 'pw.%d' with line ", \
6170: ioffset+(cpt-1)*(nlstate+1)+1+(i-1), ioffset+1+(i-1)+(nlstate+1)*nlstate,cpt );
6171: else
6172: fprintf(ficgp," $%d/(1.-$%d)) t 'p%d%d' with line ", \
6173: ioffset+(cpt-1)*(nlstate+1)+1+(i-1), ioffset+1+(i-1)+(nlstate+1)*nlstate,i,cpt );
6174: }else{ /* more than 2 covariates */
6175: if(cptcoveff ==1){
6176: ioffset=4; /* Age is in 4 */
6177: }else{
6178: ioffset=6; /* Age is in 6 */
1.223 ! brouard 6179: /*# V1 = 1 V2 = 0 yearproj age p11 p21 p.1 p12 p22 p.2 p13 p23 p.3*/
! 6180: /*# 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 */
1.219 brouard 6181: }
1.220 brouard 6182: fprintf(ficgp," u %d:(",ioffset);
1.219 brouard 6183: kl=0;
1.220 brouard 6184: strcpy(gplotcondition,"(");
6185: for (k=1; k<=cptcoveff; k++){ /* For each covariate writing the chain of conditions */
1.219 brouard 6186: lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate value corresponding to combination k1 and covariate k */
6187: /* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
6188: /* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
6189: /* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
1.220 brouard 6190: vlv= nbcode[Tvaraff[k]][lv]; /* Value of the modality of Tvaraff[k] */
6191: kl++;
6192: sprintf(gplotcondition+strlen(gplotcondition),"$%d==%d && $%d==%d " ,kl,Tvaraff[k], kl+1, nbcode[Tvaraff[k]][lv]);
1.219 brouard 6193: kl++;
1.220 brouard 6194: if(k <cptcoveff && cptcoveff>1)
6195: sprintf(gplotcondition+strlen(gplotcondition)," && ");
6196: }
6197: strcpy(gplotcondition+strlen(gplotcondition),")");
6198: /* 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 *\/ */
6199: /*6+(cpt-1)*(nlstate+1)+1+(i-1)+(nlstate+1)*nlstate; 6+(1-1)*(2+1)+1+(1-1) +(2+1)*2=13 */
6200: /*6+1+(i-1)+(nlstate+1)*nlstate; 6+1+(1-1) +(2+1)*2=13 */
6201: /* '' 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*/
6202: if(i==nlstate+1){
6203: fprintf(ficgp,"%s ? $%d/(1.-$%d) : 1/0) t 'p.%d' with line ", gplotcondition, \
6204: ioffset+(cpt-1)*(nlstate+1)+1+(i-1), ioffset+1+(i-1)+(nlstate+1)*nlstate,cpt );
6205: }else{
1.223 ! brouard 6206: fprintf(ficgp,"%s ? $%d/(1.-$%d) : 1/0) t 'p%d%d' with line ", gplotcondition, \
! 6207: ioffset+(cpt-1)*(nlstate+1)+1+(i-1), ioffset +1+(i-1)+(nlstate+1)*nlstate,i,cpt );
1.220 brouard 6208: }
1.219 brouard 6209: } /* end if covariate */
6210: } /* nlstate */
6211: fprintf(ficgp,"\nset out\n");
1.223 ! brouard 6212: } /* end cpt state*/
! 6213: } /* end covariate */
! 6214: } /* End if prevfcast */
1.219 brouard 6215:
1.211 brouard 6216:
1.223 ! brouard 6217: /* proba elementaires */
! 6218: fprintf(ficgp,"\n##############\n#MLE estimated parameters\n#############\n");
1.126 brouard 6219: for(i=1,jk=1; i <=nlstate; i++){
1.187 brouard 6220: fprintf(ficgp,"# initial state %d\n",i);
1.126 brouard 6221: for(k=1; k <=(nlstate+ndeath); k++){
6222: if (k != i) {
1.223 ! brouard 6223: fprintf(ficgp,"# current state %d\n",k);
! 6224: for(j=1; j <=ncovmodel; j++){
! 6225: fprintf(ficgp,"p%d=%f; ",jk,p[jk]);
! 6226: jk++;
! 6227: }
! 6228: fprintf(ficgp,"\n");
1.126 brouard 6229: }
6230: }
1.223 ! brouard 6231: }
1.187 brouard 6232: fprintf(ficgp,"##############\n#\n");
1.223 ! brouard 6233:
1.145 brouard 6234: /*goto avoid;*/
1.200 brouard 6235: fprintf(ficgp,"\n##############\n#Graphics of probabilities or incidences\n#############\n");
1.187 brouard 6236: fprintf(ficgp,"# logi(p12/p11)=a12+b12*age+c12age*age+d12*V1+e12*V1*age\n");
6237: fprintf(ficgp,"# logi(p12/p11)=p1 +p2*age +p3*age*age+ p4*V1+ p5*V1*age\n");
6238: fprintf(ficgp,"# logi(p13/p11)=a13+b13*age+c13age*age+d13*V1+e13*V1*age\n");
6239: fprintf(ficgp,"# logi(p13/p11)=p6 +p7*age +p8*age*age+ p9*V1+ p10*V1*age\n");
6240: fprintf(ficgp,"# p12+p13+p14+p11=1=p11(1+exp(a12+b12*age+c12age*age+d12*V1+e12*V1*age)\n");
6241: fprintf(ficgp,"# +exp(a13+b13*age+c13age*age+d13*V1+e13*V1*age)+...)\n");
6242: fprintf(ficgp,"# p11=1/(1+exp(a12+b12*age+c12age*age+d12*V1+e12*V1*age)\n");
6243: fprintf(ficgp,"# +exp(a13+b13*age+c13age*age+d13*V1+e13*V1*age)+...)\n");
6244: fprintf(ficgp,"# p12=exp(a12+b12*age+c12age*age+d12*V1+e12*V1*age)/\n");
6245: fprintf(ficgp,"# (1+exp(a12+b12*age+c12age*age+d12*V1+e12*V1*age)\n");
6246: fprintf(ficgp,"# +exp(a13+b13*age+c13age*age+d13*V1+e13*V1*age))\n");
6247: fprintf(ficgp,"# +exp(a14+b14*age+c14age*age+d14*V1+e14*V1*age)+...)\n");
6248: fprintf(ficgp,"#\n");
1.223 ! brouard 6249: for(ng=1; ng<=3;ng++){ /* Number of graphics: first is logit, 2nd is probabilities, third is incidences per year*/
! 6250: fprintf(ficgp,"# ng=%d\n",ng);
! 6251: fprintf(ficgp,"# jk=1 to 2^%d=%d\n",cptcoveff,m);
! 6252: for(jk=1; jk <=m; jk++) {
! 6253: fprintf(ficgp,"# jk=%d\n",jk);
! 6254: fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" ",subdirf2(optionfilefiname,"PE_"),jk,ng);
! 6255: fprintf(ficgp,"\nset ter svg size 640, 480 ");
! 6256: if (ng==1){
! 6257: fprintf(ficgp,"\nset ylabel \"Value of the logit of the model\"\n"); /* exp(a12+b12*x) could be nice */
! 6258: fprintf(ficgp,"\nunset log y");
! 6259: }else if (ng==2){
! 6260: fprintf(ficgp,"\nset ylabel \"Probability\"\n");
! 6261: fprintf(ficgp,"\nset log y");
! 6262: }else if (ng==3){
! 6263: fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
! 6264: fprintf(ficgp,"\nset log y");
! 6265: }else
! 6266: fprintf(ficgp,"\nunset title ");
! 6267: fprintf(ficgp,"\nplot [%.f:%.f] ",ageminpar,agemaxpar);
! 6268: i=1;
! 6269: for(k2=1; k2<=nlstate; k2++) {
! 6270: k3=i;
! 6271: for(k=1; k<=(nlstate+ndeath); k++) {
! 6272: if (k != k2){
! 6273: switch( ng) {
! 6274: case 1:
! 6275: if(nagesqr==0)
! 6276: fprintf(ficgp," p%d+p%d*x",i,i+1);
! 6277: else /* nagesqr =1 */
! 6278: fprintf(ficgp," p%d+p%d*x+p%d*x*x",i,i+1,i+1+nagesqr);
! 6279: break;
! 6280: case 2: /* ng=2 */
! 6281: if(nagesqr==0)
! 6282: fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
! 6283: else /* nagesqr =1 */
! 6284: fprintf(ficgp," exp(p%d+p%d*x+p%d*x*x",i,i+1,i+1+nagesqr);
! 6285: break;
! 6286: case 3:
! 6287: if(nagesqr==0)
! 6288: fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);
! 6289: else /* nagesqr =1 */
! 6290: fprintf(ficgp," %f*exp(p%d+p%d*x+p%d*x*x",YEARM/stepm,i,i+1,i+1+nagesqr);
! 6291: break;
! 6292: }
! 6293: ij=1;/* To be checked else nbcode[0][0] wrong */
! 6294: for(j=3; j <=ncovmodel-nagesqr; j++) {
! 6295: /* printf("Tage[%d]=%d, j=%d\n", ij, Tage[ij], j); */
! 6296: if(ij <=cptcovage) { /* Bug valgrind */
! 6297: if((j-2)==Tage[ij]) { /* Bug valgrind */
! 6298: fprintf(ficgp,"+p%d*%d*x",i+j+nagesqr-1,nbcode[Tvar[j-2]][codtabm(jk,j-2)]);
! 6299: /* fprintf(ficgp,"+p%d*%d*x",i+j+nagesqr-1,nbcode[Tvar[j-2]][codtabm(jk,Tvar[j-2])]); */
! 6300: ij++;
! 6301: }
! 6302: }
! 6303: else
! 6304: fprintf(ficgp,"+p%d*%d",i+j+nagesqr-1,nbcode[Tvar[j-2]][codtabm(jk,j-2)]);
! 6305: }
! 6306: }else{
! 6307: i=i-ncovmodel;
! 6308: if(ng !=1 ) /* For logit formula of log p11 is more difficult to get */
! 6309: fprintf(ficgp," (1.");
! 6310: }
1.217 brouard 6311:
1.223 ! brouard 6312: if(ng != 1){
! 6313: fprintf(ficgp,")/(1");
1.126 brouard 6314:
1.223 ! brouard 6315: for(k1=1; k1 <=nlstate; k1++){
! 6316: if(nagesqr==0)
! 6317: fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);
! 6318: else /* nagesqr =1 */
! 6319: fprintf(ficgp,"+exp(p%d+p%d*x+p%d*x*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1,k3+(k1-1)*ncovmodel+1+nagesqr);
1.217 brouard 6320:
1.223 ! brouard 6321: ij=1;
! 6322: for(j=3; j <=ncovmodel-nagesqr; j++){
! 6323: if(ij <=cptcovage) { /* Bug valgrind */
! 6324: if((j-2)==Tage[ij]) { /* Bug valgrind */
! 6325: fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2+nagesqr,nbcode[Tvar[j-2]][codtabm(jk,j-2)]);
! 6326: /* fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2+nagesqr,nbcode[Tvar[j-2]][codtabm(jk,Tvar[j-2])]); */
! 6327: ij++;
! 6328: }
! 6329: }
! 6330: else
! 6331: fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2+nagesqr,nbcode[Tvar[j-2]][codtabm(jk,j-2)]);
! 6332: }
! 6333: fprintf(ficgp,")");
! 6334: }
! 6335: fprintf(ficgp,")");
! 6336: if(ng ==2)
! 6337: fprintf(ficgp," t \"p%d%d\" ", k2,k);
! 6338: else /* ng= 3 */
! 6339: fprintf(ficgp," t \"i%d%d\" ", k2,k);
! 6340: }else{ /* end ng <> 1 */
! 6341: if( k !=k2) /* logit p11 is hard to draw */
! 6342: fprintf(ficgp," t \"logit(p%d%d)\" ", k2,k);
! 6343: }
! 6344: if ((k+k2)!= (nlstate*2+ndeath) && ng != 1)
! 6345: fprintf(ficgp,",");
! 6346: if (ng == 1 && k!=k2 && (k+k2)!= (nlstate*2+ndeath))
! 6347: fprintf(ficgp,",");
! 6348: i=i+ncovmodel;
! 6349: } /* end k */
! 6350: } /* end k2 */
! 6351: fprintf(ficgp,"\n set out\n");
! 6352: } /* end jk */
! 6353: } /* end ng */
! 6354: /* avoid: */
! 6355: fflush(ficgp);
1.126 brouard 6356: } /* end gnuplot */
6357:
6358:
6359: /*************** Moving average **************/
1.219 brouard 6360: /* int movingaverage(double ***probs, double bage, double fage, double ***mobaverage, int mobilav, double bageout, double fageout){ */
1.222 brouard 6361: int movingaverage(double ***probs, double bage, double fage, double ***mobaverage, int mobilav){
1.218 brouard 6362:
1.222 brouard 6363: int i, cpt, cptcod;
6364: int modcovmax =1;
6365: int mobilavrange, mob;
6366: int iage=0;
6367:
6368: double sum=0.;
6369: double age;
6370: double *sumnewp, *sumnewm;
6371: double *agemingood, *agemaxgood; /* Currently identical for all covariates */
6372:
6373:
6374: /* modcovmax=2*cptcoveff;/\* Max number of modalities. We suppose */
6375: /* a covariate has 2 modalities, should be equal to ncovcombmax *\/ */
6376:
6377: sumnewp = vector(1,ncovcombmax);
6378: sumnewm = vector(1,ncovcombmax);
6379: agemingood = vector(1,ncovcombmax);
6380: agemaxgood = vector(1,ncovcombmax);
6381:
6382: for (cptcod=1;cptcod<=ncovcombmax;cptcod++){
6383: sumnewm[cptcod]=0.;
6384: sumnewp[cptcod]=0.;
6385: agemingood[cptcod]=0;
6386: agemaxgood[cptcod]=0;
6387: }
6388: if (cptcovn<1) ncovcombmax=1; /* At least 1 pass */
6389:
6390: if(mobilav==1||mobilav ==3 ||mobilav==5 ||mobilav== 7){
6391: if(mobilav==1) mobilavrange=5; /* default */
6392: else mobilavrange=mobilav;
6393: for (age=bage; age<=fage; age++)
6394: for (i=1; i<=nlstate;i++)
6395: for (cptcod=1;cptcod<=ncovcombmax;cptcod++)
6396: mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
6397: /* We keep the original values on the extreme ages bage, fage and for
6398: fage+1 and bage-1 we use a 3 terms moving average; for fage+2 bage+2
6399: we use a 5 terms etc. until the borders are no more concerned.
6400: */
6401: for (mob=3;mob <=mobilavrange;mob=mob+2){
6402: for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){
6403: for (i=1; i<=nlstate;i++){
6404: for (cptcod=1;cptcod<=ncovcombmax;cptcod++){
6405: mobaverage[(int)age][i][cptcod] =probs[(int)age][i][cptcod];
6406: for (cpt=1;cpt<=(mob-1)/2;cpt++){
6407: mobaverage[(int)age][i][cptcod] +=probs[(int)age-cpt][i][cptcod];
6408: mobaverage[(int)age][i][cptcod] +=probs[(int)age+cpt][i][cptcod];
6409: }
6410: mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/mob;
6411: }
6412: }
6413: }/* end age */
6414: }/* end mob */
6415: }else
6416: return -1;
6417: for (cptcod=1;cptcod<=ncovcombmax;cptcod++){
6418: /* for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){ */
6419: if(invalidvarcomb[cptcod]){
6420: printf("\nCombination (%d) ignored because no cases \n",cptcod);
6421: continue;
6422: }
1.219 brouard 6423:
1.222 brouard 6424: agemingood[cptcod]=fage-(mob-1)/2;
6425: for (age=fage-(mob-1)/2; age>=bage; age--){/* From oldest to youngest, finding the youngest wrong */
6426: sumnewm[cptcod]=0.;
6427: for (i=1; i<=nlstate;i++){
6428: sumnewm[cptcod]+=mobaverage[(int)age][i][cptcod];
6429: }
6430: if(fabs(sumnewm[cptcod] - 1.) <= 1.e-3) { /* good */
6431: agemingood[cptcod]=age;
6432: }else{ /* bad */
6433: for (i=1; i<=nlstate;i++){
6434: mobaverage[(int)age][i][cptcod]=mobaverage[(int)agemingood[cptcod]][i][cptcod];
6435: } /* i */
6436: } /* end bad */
6437: }/* age */
6438: sum=0.;
6439: for (i=1; i<=nlstate;i++){
6440: sum+=mobaverage[(int)agemingood[cptcod]][i][cptcod];
6441: }
6442: if(fabs(sum - 1.) > 1.e-3) { /* bad */
6443: 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);
6444: /* for (i=1; i<=nlstate;i++){ */
6445: /* mobaverage[(int)age][i][cptcod]=mobaverage[(int)agemingood[cptcod]][i][cptcod]; */
6446: /* } /\* i *\/ */
6447: } /* end bad */
6448: /* else{ /\* We found some ages summing to one, we will smooth the oldest *\/ */
6449: /* From youngest, finding the oldest wrong */
6450: agemaxgood[cptcod]=bage+(mob-1)/2;
6451: for (age=bage+(mob-1)/2; age<=fage; age++){
6452: sumnewm[cptcod]=0.;
6453: for (i=1; i<=nlstate;i++){
6454: sumnewm[cptcod]+=mobaverage[(int)age][i][cptcod];
6455: }
6456: if(fabs(sumnewm[cptcod] - 1.) <= 1.e-3) { /* good */
6457: agemaxgood[cptcod]=age;
6458: }else{ /* bad */
6459: for (i=1; i<=nlstate;i++){
6460: mobaverage[(int)age][i][cptcod]=mobaverage[(int)agemaxgood[cptcod]][i][cptcod];
6461: } /* i */
6462: } /* end bad */
6463: }/* age */
6464: sum=0.;
6465: for (i=1; i<=nlstate;i++){
6466: sum+=mobaverage[(int)agemaxgood[cptcod]][i][cptcod];
6467: }
6468: if(fabs(sum - 1.) > 1.e-3) { /* bad */
6469: 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);
6470: /* for (i=1; i<=nlstate;i++){ */
6471: /* mobaverage[(int)age][i][cptcod]=mobaverage[(int)agemingood[cptcod]][i][cptcod]; */
6472: /* } /\* i *\/ */
6473: } /* end bad */
6474:
6475: for (age=bage; age<=fage; age++){
6476: printf("%d %d ", cptcod, (int)age);
6477: sumnewp[cptcod]=0.;
6478: sumnewm[cptcod]=0.;
6479: for (i=1; i<=nlstate;i++){
6480: sumnewp[cptcod]+=probs[(int)age][i][cptcod];
6481: sumnewm[cptcod]+=mobaverage[(int)age][i][cptcod];
6482: /* printf("%.4f %.4f ",probs[(int)age][i][cptcod], mobaverage[(int)age][i][cptcod]); */
6483: }
6484: /* printf("%.4f %.4f \n",sumnewp[cptcod], sumnewm[cptcod]); */
6485: }
6486: /* printf("\n"); */
6487: /* } */
6488: /* brutal averaging */
6489: for (i=1; i<=nlstate;i++){
6490: for (age=1; age<=bage; age++){
6491: mobaverage[(int)age][i][cptcod]=mobaverage[(int)agemingood[cptcod]][i][cptcod];
6492: /* printf("age=%d i=%d cptcod=%d mobaverage=%.4f \n",(int)age,i, cptcod, mobaverage[(int)age][i][cptcod]); */
6493: }
6494: for (age=fage; age<=AGESUP; age++){
6495: mobaverage[(int)age][i][cptcod]=mobaverage[(int)agemaxgood[cptcod]][i][cptcod];
6496: /* printf("age=%d i=%d cptcod=%d mobaverage=%.4f \n",(int)age,i, cptcod, mobaverage[(int)age][i][cptcod]); */
6497: }
6498: } /* end i status */
6499: for (i=nlstate+1; i<=nlstate+ndeath;i++){
6500: for (age=1; age<=AGESUP; age++){
6501: /*printf("i=%d, age=%d, cptcod=%d\n",i, (int)age, cptcod);*/
6502: mobaverage[(int)age][i][cptcod]=0.;
6503: }
6504: }
6505: }/* end cptcod */
6506: free_vector(sumnewm,1, ncovcombmax);
6507: free_vector(sumnewp,1, ncovcombmax);
6508: free_vector(agemaxgood,1, ncovcombmax);
6509: free_vector(agemingood,1, ncovcombmax);
6510: return 0;
6511: }/* End movingaverage */
1.218 brouard 6512:
1.126 brouard 6513:
6514: /************** Forecasting ******************/
1.169 brouard 6515: 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 6516: /* proj1, year, month, day of starting projection
6517: agemin, agemax range of age
6518: dateprev1 dateprev2 range of dates during which prevalence is computed
6519: anproj2 year of en of projection (same day and month as proj1).
6520: */
1.164 brouard 6521: int yearp, stepsize, hstepm, nhstepm, j, k, cptcod, i, h, i1;
1.126 brouard 6522: double agec; /* generic age */
6523: double agelim, ppij, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
6524: double *popeffectif,*popcount;
6525: double ***p3mat;
1.218 brouard 6526: /* double ***mobaverage; */
1.126 brouard 6527: char fileresf[FILENAMELENGTH];
6528:
6529: agelim=AGESUP;
1.211 brouard 6530: /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
6531: in each health status at the date of interview (if between dateprev1 and dateprev2).
6532: We still use firstpass and lastpass as another selection.
6533: */
1.214 brouard 6534: /* freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint,strstart,\ */
6535: /* firstpass, lastpass, stepm, weightopt, model); */
1.126 brouard 6536:
1.201 brouard 6537: strcpy(fileresf,"F_");
6538: strcat(fileresf,fileresu);
1.126 brouard 6539: if((ficresf=fopen(fileresf,"w"))==NULL) {
6540: printf("Problem with forecast resultfile: %s\n", fileresf);
6541: fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);
6542: }
1.215 brouard 6543: printf("Computing forecasting: result on file '%s', please wait... \n", fileresf);
6544: fprintf(ficlog,"Computing forecasting: result on file '%s', please wait... \n", fileresf);
1.126 brouard 6545:
6546: if (cptcoveff==0) ncodemax[cptcoveff]=1;
6547:
6548:
6549: stepsize=(int) (stepm+YEARM-1)/YEARM;
6550: if (stepm<=12) stepsize=1;
6551: if(estepm < stepm){
6552: printf ("Problem %d lower than %d\n",estepm, stepm);
6553: }
6554: else hstepm=estepm;
6555:
6556: hstepm=hstepm/stepm;
6557: yp1=modf(dateintmean,&yp);/* extracts integral of datemean in yp and
6558: fractional in yp1 */
6559: anprojmean=yp;
6560: yp2=modf((yp1*12),&yp);
6561: mprojmean=yp;
6562: yp1=modf((yp2*30.5),&yp);
6563: jprojmean=yp;
6564: if(jprojmean==0) jprojmean=1;
6565: if(mprojmean==0) jprojmean=1;
6566:
6567: i1=cptcoveff;
6568: if (cptcovn < 1){i1=1;}
6569:
6570: fprintf(ficresf,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2);
6571:
6572: fprintf(ficresf,"#****** Routine prevforecast **\n");
6573:
6574: /* if (h==(int)(YEARM*yearp)){ */
6575: for(cptcov=1, k=0;cptcov<=i1;cptcov++){
6576: for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
6577: k=k+1;
1.211 brouard 6578: fprintf(ficresf,"\n#****** hpijx=probability over h years, hp.jx is weighted by observed prev \n#");
1.126 brouard 6579: for(j=1;j<=cptcoveff;j++) {
1.219 brouard 6580: fprintf(ficresf," V%d (=) %d",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
1.126 brouard 6581: }
1.211 brouard 6582: fprintf(ficresf," yearproj age");
1.126 brouard 6583: for(j=1; j<=nlstate+ndeath;j++){
1.219 brouard 6584: for(i=1; i<=nlstate;i++)
1.126 brouard 6585: fprintf(ficresf," p%d%d",i,j);
1.219 brouard 6586: fprintf(ficresf," wp.%d",j);
1.126 brouard 6587: }
1.217 brouard 6588: for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) {
1.219 brouard 6589: fprintf(ficresf,"\n");
6590: fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+yearp);
6591: for (agec=fage; agec>=(ageminpar-1); agec--){
6592: nhstepm=(int) rint((agelim-agec)*YEARM/stepm);
6593: nhstepm = nhstepm/hstepm;
6594: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
6595: oldm=oldms;savm=savms;
6596: hpxij(p3mat,nhstepm,agec,hstepm,p,nlstate,stepm,oldm,savm, k);
6597:
6598: for (h=0; h<=nhstepm; h++){
6599: if (h*hstepm/YEARM*stepm ==yearp) {
1.126 brouard 6600: fprintf(ficresf,"\n");
6601: for(j=1;j<=cptcoveff;j++)
1.198 brouard 6602: fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
1.219 brouard 6603: fprintf(ficresf,"%.f %.f ",anproj1+yearp,agec+h*hstepm/YEARM*stepm);
6604: }
6605: for(j=1; j<=nlstate+ndeath;j++) {
6606: ppij=0.;
6607: for(i=1; i<=nlstate;i++) {
6608: if (mobilav==1)
6609: ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][i][cptcod];
6610: else {
6611: ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][cptcod];
6612: }
6613: if (h*hstepm/YEARM*stepm== yearp) {
6614: fprintf(ficresf," %.3f", p3mat[i][j][h]);
6615: }
6616: } /* end i */
6617: if (h*hstepm/YEARM*stepm==yearp) {
6618: fprintf(ficresf," %.3f", ppij);
6619: }
6620: }/* end j */
6621: } /* end h */
6622: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
6623: } /* end agec */
1.126 brouard 6624: } /* end yearp */
6625: } /* end cptcod */
6626: } /* end cptcov */
1.219 brouard 6627:
1.126 brouard 6628: fclose(ficresf);
1.215 brouard 6629: printf("End of Computing forecasting \n");
6630: fprintf(ficlog,"End of Computing forecasting\n");
6631:
1.126 brouard 6632: }
6633:
1.218 brouard 6634: /* /\************** Back Forecasting ******************\/ */
6635: /* 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){ */
6636: /* /\* back1, year, month, day of starting backection */
6637: /* agemin, agemax range of age */
6638: /* dateprev1 dateprev2 range of dates during which prevalence is computed */
6639: /* anback2 year of en of backection (same day and month as back1). */
6640: /* *\/ */
6641: /* int yearp, stepsize, hstepm, nhstepm, j, k, cptcod, i, h, i1; */
6642: /* double agec; /\* generic age *\/ */
6643: /* double agelim, ppij, yp,yp1,yp2,jprojmean,mprojmean,anprojmean; */
6644: /* double *popeffectif,*popcount; */
6645: /* double ***p3mat; */
6646: /* /\* double ***mobaverage; *\/ */
6647: /* char fileresfb[FILENAMELENGTH]; */
6648:
6649: /* agelim=AGESUP; */
6650: /* /\* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people */
6651: /* in each health status at the date of interview (if between dateprev1 and dateprev2). */
6652: /* We still use firstpass and lastpass as another selection. */
6653: /* *\/ */
6654: /* /\* freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint,strstart,\ *\/ */
6655: /* /\* firstpass, lastpass, stepm, weightopt, model); *\/ */
6656: /* prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass); */
6657:
6658: /* strcpy(fileresfb,"FB_"); */
6659: /* strcat(fileresfb,fileresu); */
6660: /* if((ficresfb=fopen(fileresfb,"w"))==NULL) { */
6661: /* printf("Problem with back forecast resultfile: %s\n", fileresfb); */
6662: /* fprintf(ficlog,"Problem with back forecast resultfile: %s\n", fileresfb); */
6663: /* } */
6664: /* printf("Computing back forecasting: result on file '%s', please wait... \n", fileresfb); */
6665: /* fprintf(ficlog,"Computing back forecasting: result on file '%s', please wait... \n", fileresfb); */
6666:
6667: /* if (cptcoveff==0) ncodemax[cptcoveff]=1; */
6668:
6669: /* /\* if (mobilav!=0) { *\/ */
6670: /* /\* mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX); *\/ */
6671: /* /\* if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){ *\/ */
6672: /* /\* fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav); *\/ */
6673: /* /\* printf(" Error in movingaverage mobilav=%d\n",mobilav); *\/ */
6674: /* /\* } *\/ */
6675: /* /\* } *\/ */
6676:
6677: /* stepsize=(int) (stepm+YEARM-1)/YEARM; */
6678: /* if (stepm<=12) stepsize=1; */
6679: /* if(estepm < stepm){ */
6680: /* printf ("Problem %d lower than %d\n",estepm, stepm); */
6681: /* } */
6682: /* else hstepm=estepm; */
6683:
6684: /* hstepm=hstepm/stepm; */
6685: /* yp1=modf(dateintmean,&yp);/\* extracts integral of datemean in yp and */
6686: /* fractional in yp1 *\/ */
6687: /* anprojmean=yp; */
6688: /* yp2=modf((yp1*12),&yp); */
6689: /* mprojmean=yp; */
6690: /* yp1=modf((yp2*30.5),&yp); */
6691: /* jprojmean=yp; */
6692: /* if(jprojmean==0) jprojmean=1; */
6693: /* if(mprojmean==0) jprojmean=1; */
6694:
6695: /* i1=cptcoveff; */
6696: /* if (cptcovn < 1){i1=1;} */
1.217 brouard 6697:
1.218 brouard 6698: /* fprintf(ficresfb,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2); */
1.217 brouard 6699:
1.218 brouard 6700: /* fprintf(ficresfb,"#****** Routine prevbackforecast **\n"); */
6701:
6702: /* /\* if (h==(int)(YEARM*yearp)){ *\/ */
6703: /* for(cptcov=1, k=0;cptcov<=i1;cptcov++){ */
6704: /* for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){ */
6705: /* k=k+1; */
6706: /* fprintf(ficresfb,"\n#****** hbijx=probability over h years, hp.jx is weighted by observed prev \n#"); */
6707: /* for(j=1;j<=cptcoveff;j++) { */
6708: /* fprintf(ficresfb," V%d (=) %d",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]); */
6709: /* } */
6710: /* fprintf(ficresfb," yearbproj age"); */
6711: /* for(j=1; j<=nlstate+ndeath;j++){ */
6712: /* for(i=1; i<=nlstate;i++) */
6713: /* fprintf(ficresfb," p%d%d",i,j); */
6714: /* fprintf(ficresfb," p.%d",j); */
6715: /* } */
6716: /* for (yearp=0; yearp>=(anback2-anback1);yearp -=stepsize) { */
6717: /* /\* for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) { *\/ */
6718: /* fprintf(ficresfb,"\n"); */
6719: /* fprintf(ficresfb,"\n# Back Forecasting at date %.lf/%.lf/%.lf ",jback1,mback1,anback1+yearp); */
6720: /* for (agec=fage; agec>=(ageminpar-1); agec--){ */
6721: /* nhstepm=(int) rint((agelim-agec)*YEARM/stepm); */
6722: /* nhstepm = nhstepm/hstepm; */
6723: /* p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); */
6724: /* oldm=oldms;savm=savms; */
6725: /* hbxij(p3mat,nhstepm,agec,hstepm,p,prevacurrent,nlstate,stepm,oldm,savm,oldm,savm, dnewm, doldm, dsavm, k); */
6726: /* for (h=0; h<=nhstepm; h++){ */
6727: /* if (h*hstepm/YEARM*stepm ==yearp) { */
6728: /* fprintf(ficresfb,"\n"); */
6729: /* for(j=1;j<=cptcoveff;j++) */
6730: /* fprintf(ficresfb,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]); */
6731: /* fprintf(ficresfb,"%.f %.f ",anback1+yearp,agec+h*hstepm/YEARM*stepm); */
6732: /* } */
6733: /* for(j=1; j<=nlstate+ndeath;j++) { */
6734: /* ppij=0.; */
6735: /* for(i=1; i<=nlstate;i++) { */
6736: /* if (mobilav==1) */
6737: /* ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][i][cptcod]; */
6738: /* else { */
6739: /* ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][cptcod]; */
6740: /* } */
6741: /* if (h*hstepm/YEARM*stepm== yearp) { */
6742: /* fprintf(ficresfb," %.3f", p3mat[i][j][h]); */
6743: /* } */
6744: /* } /\* end i *\/ */
6745: /* if (h*hstepm/YEARM*stepm==yearp) { */
6746: /* fprintf(ficresfb," %.3f", ppij); */
6747: /* } */
6748: /* }/\* end j *\/ */
6749: /* } /\* end h *\/ */
6750: /* free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); */
6751: /* } /\* end agec *\/ */
6752: /* } /\* end yearp *\/ */
6753: /* } /\* end cptcod *\/ */
6754: /* } /\* end cptcov *\/ */
6755:
6756: /* /\* if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX); *\/ */
6757:
6758: /* fclose(ficresfb); */
6759: /* printf("End of Computing Back forecasting \n"); */
6760: /* fprintf(ficlog,"End of Computing Back forecasting\n"); */
1.217 brouard 6761:
1.218 brouard 6762: /* } */
1.217 brouard 6763:
1.126 brouard 6764: /************** Forecasting *****not tested NB*************/
1.169 brouard 6765: 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 6766:
6767: int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;
6768: int *popage;
6769: double calagedatem, agelim, kk1, kk2;
6770: double *popeffectif,*popcount;
6771: double ***p3mat,***tabpop,***tabpopprev;
1.218 brouard 6772: /* double ***mobaverage; */
1.126 brouard 6773: char filerespop[FILENAMELENGTH];
6774:
6775: tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
6776: tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
6777: agelim=AGESUP;
6778: calagedatem=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;
6779:
6780: prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
6781:
6782:
1.201 brouard 6783: strcpy(filerespop,"POP_");
6784: strcat(filerespop,fileresu);
1.126 brouard 6785: if((ficrespop=fopen(filerespop,"w"))==NULL) {
6786: printf("Problem with forecast resultfile: %s\n", filerespop);
6787: fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop);
6788: }
6789: printf("Computing forecasting: result on file '%s' \n", filerespop);
6790: fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop);
6791:
6792: if (cptcoveff==0) ncodemax[cptcoveff]=1;
6793:
1.218 brouard 6794: /* if (mobilav!=0) { */
6795: /* mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX); */
6796: /* if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){ */
6797: /* fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav); */
6798: /* printf(" Error in movingaverage mobilav=%d\n",mobilav); */
6799: /* } */
6800: /* } */
1.126 brouard 6801:
6802: stepsize=(int) (stepm+YEARM-1)/YEARM;
6803: if (stepm<=12) stepsize=1;
6804:
6805: agelim=AGESUP;
6806:
6807: hstepm=1;
6808: hstepm=hstepm/stepm;
1.218 brouard 6809:
1.126 brouard 6810: if (popforecast==1) {
6811: if((ficpop=fopen(popfile,"r"))==NULL) {
6812: printf("Problem with population file : %s\n",popfile);exit(0);
6813: fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0);
6814: }
6815: popage=ivector(0,AGESUP);
6816: popeffectif=vector(0,AGESUP);
6817: popcount=vector(0,AGESUP);
6818:
6819: i=1;
6820: while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;
1.218 brouard 6821:
1.126 brouard 6822: imx=i;
6823: for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];
6824: }
1.218 brouard 6825:
1.126 brouard 6826: for(cptcov=1,k=0;cptcov<=i2;cptcov++){
1.218 brouard 6827: for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
1.126 brouard 6828: k=k+1;
6829: fprintf(ficrespop,"\n#******");
6830: for(j=1;j<=cptcoveff;j++) {
1.198 brouard 6831: fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
1.126 brouard 6832: }
6833: fprintf(ficrespop,"******\n");
6834: fprintf(ficrespop,"# Age");
6835: for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);
6836: if (popforecast==1) fprintf(ficrespop," [Population]");
6837:
6838: for (cpt=0; cpt<=0;cpt++) {
6839: fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);
6840:
1.218 brouard 6841: for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){
1.126 brouard 6842: nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);
6843: nhstepm = nhstepm/hstepm;
6844:
6845: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
6846: oldm=oldms;savm=savms;
6847: hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
1.218 brouard 6848:
1.126 brouard 6849: for (h=0; h<=nhstepm; h++){
6850: if (h==(int) (calagedatem+YEARM*cpt)) {
6851: fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
6852: }
6853: for(j=1; j<=nlstate+ndeath;j++) {
6854: kk1=0.;kk2=0;
6855: for(i=1; i<=nlstate;i++) {
6856: if (mobilav==1)
6857: kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];
6858: else {
6859: kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];
6860: }
6861: }
6862: if (h==(int)(calagedatem+12*cpt)){
6863: tabpop[(int)(agedeb)][j][cptcod]=kk1;
1.218 brouard 6864: /*fprintf(ficrespop," %.3f", kk1);
6865: if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/
1.126 brouard 6866: }
6867: }
6868: for(i=1; i<=nlstate;i++){
6869: kk1=0.;
1.218 brouard 6870: for(j=1; j<=nlstate;j++){
6871: kk1= kk1+tabpop[(int)(agedeb)][j][cptcod];
6872: }
6873: tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedatem+12*cpt)*hstepm/YEARM*stepm-1)];
1.126 brouard 6874: }
1.218 brouard 6875:
6876: if (h==(int)(calagedatem+12*cpt))
6877: for(j=1; j<=nlstate;j++)
6878: fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);
1.126 brouard 6879: }
6880: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
6881: }
6882: }
1.218 brouard 6883:
6884: /******/
6885:
1.126 brouard 6886: for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) {
6887: fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);
6888: for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){
6889: nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);
6890: nhstepm = nhstepm/hstepm;
6891:
6892: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
6893: oldm=oldms;savm=savms;
6894: hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
6895: for (h=0; h<=nhstepm; h++){
6896: if (h==(int) (calagedatem+YEARM*cpt)) {
6897: fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
6898: }
6899: for(j=1; j<=nlstate+ndeath;j++) {
6900: kk1=0.;kk2=0;
6901: for(i=1; i<=nlstate;i++) {
6902: kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];
6903: }
6904: if (h==(int)(calagedatem+12*cpt)) fprintf(ficresf," %15.2f", kk1);
6905: }
6906: }
6907: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
6908: }
6909: }
1.218 brouard 6910: }
1.126 brouard 6911: }
1.218 brouard 6912:
6913: /* if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX); */
6914:
1.126 brouard 6915: if (popforecast==1) {
6916: free_ivector(popage,0,AGESUP);
6917: free_vector(popeffectif,0,AGESUP);
6918: free_vector(popcount,0,AGESUP);
6919: }
6920: free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
6921: free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
6922: fclose(ficrespop);
6923: } /* End of popforecast */
1.218 brouard 6924:
1.126 brouard 6925: int fileappend(FILE *fichier, char *optionfich)
6926: {
6927: if((fichier=fopen(optionfich,"a"))==NULL) {
6928: printf("Problem with file: %s\n", optionfich);
6929: fprintf(ficlog,"Problem with file: %s\n", optionfich);
6930: return (0);
6931: }
6932: fflush(fichier);
6933: return (1);
6934: }
6935:
6936:
6937: /**************** function prwizard **********************/
6938: void prwizard(int ncovmodel, int nlstate, int ndeath, char model[], FILE *ficparo)
6939: {
6940:
6941: /* Wizard to print covariance matrix template */
6942:
1.164 brouard 6943: char ca[32], cb[32];
6944: int i,j, k, li, lj, lk, ll, jj, npar, itimes;
1.126 brouard 6945: int numlinepar;
6946:
6947: printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
6948: fprintf(ficparo,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
6949: for(i=1; i <=nlstate; i++){
6950: jj=0;
6951: for(j=1; j <=nlstate+ndeath; j++){
6952: if(j==i) continue;
6953: jj++;
6954: /*ca[0]= k+'a'-1;ca[1]='\0';*/
6955: printf("%1d%1d",i,j);
6956: fprintf(ficparo,"%1d%1d",i,j);
6957: for(k=1; k<=ncovmodel;k++){
6958: /* printf(" %lf",param[i][j][k]); */
6959: /* fprintf(ficparo," %lf",param[i][j][k]); */
6960: printf(" 0.");
6961: fprintf(ficparo," 0.");
6962: }
6963: printf("\n");
6964: fprintf(ficparo,"\n");
6965: }
6966: }
6967: printf("# Scales (for hessian or gradient estimation)\n");
6968: fprintf(ficparo,"# Scales (for hessian or gradient estimation)\n");
6969: npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/
6970: for(i=1; i <=nlstate; i++){
6971: jj=0;
6972: for(j=1; j <=nlstate+ndeath; j++){
6973: if(j==i) continue;
6974: jj++;
6975: fprintf(ficparo,"%1d%1d",i,j);
6976: printf("%1d%1d",i,j);
6977: fflush(stdout);
6978: for(k=1; k<=ncovmodel;k++){
6979: /* printf(" %le",delti3[i][j][k]); */
6980: /* fprintf(ficparo," %le",delti3[i][j][k]); */
6981: printf(" 0.");
6982: fprintf(ficparo," 0.");
6983: }
6984: numlinepar++;
6985: printf("\n");
6986: fprintf(ficparo,"\n");
6987: }
6988: }
6989: printf("# Covariance matrix\n");
6990: /* # 121 Var(a12)\n\ */
6991: /* # 122 Cov(b12,a12) Var(b12)\n\ */
6992: /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
6993: /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
6994: /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
6995: /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
6996: /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
6997: /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
6998: fflush(stdout);
6999: fprintf(ficparo,"# Covariance matrix\n");
7000: /* # 121 Var(a12)\n\ */
7001: /* # 122 Cov(b12,a12) Var(b12)\n\ */
7002: /* # ...\n\ */
7003: /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
7004:
7005: for(itimes=1;itimes<=2;itimes++){
7006: jj=0;
7007: for(i=1; i <=nlstate; i++){
7008: for(j=1; j <=nlstate+ndeath; j++){
7009: if(j==i) continue;
7010: for(k=1; k<=ncovmodel;k++){
7011: jj++;
7012: ca[0]= k+'a'-1;ca[1]='\0';
7013: if(itimes==1){
7014: printf("#%1d%1d%d",i,j,k);
7015: fprintf(ficparo,"#%1d%1d%d",i,j,k);
7016: }else{
7017: printf("%1d%1d%d",i,j,k);
7018: fprintf(ficparo,"%1d%1d%d",i,j,k);
7019: /* printf(" %.5le",matcov[i][j]); */
7020: }
7021: ll=0;
7022: for(li=1;li <=nlstate; li++){
7023: for(lj=1;lj <=nlstate+ndeath; lj++){
7024: if(lj==li) continue;
7025: for(lk=1;lk<=ncovmodel;lk++){
7026: ll++;
7027: if(ll<=jj){
7028: cb[0]= lk +'a'-1;cb[1]='\0';
7029: if(ll<jj){
7030: if(itimes==1){
7031: printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
7032: fprintf(ficparo," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
7033: }else{
7034: printf(" 0.");
7035: fprintf(ficparo," 0.");
7036: }
7037: }else{
7038: if(itimes==1){
7039: printf(" Var(%s%1d%1d)",ca,i,j);
7040: fprintf(ficparo," Var(%s%1d%1d)",ca,i,j);
7041: }else{
7042: printf(" 0.");
7043: fprintf(ficparo," 0.");
7044: }
7045: }
7046: }
7047: } /* end lk */
7048: } /* end lj */
7049: } /* end li */
7050: printf("\n");
7051: fprintf(ficparo,"\n");
7052: numlinepar++;
7053: } /* end k*/
7054: } /*end j */
7055: } /* end i */
7056: } /* end itimes */
7057:
7058: } /* end of prwizard */
7059: /******************* Gompertz Likelihood ******************************/
7060: double gompertz(double x[])
7061: {
7062: double A,B,L=0.0,sump=0.,num=0.;
7063: int i,n=0; /* n is the size of the sample */
7064:
1.220 brouard 7065: for (i=1;i<=imx ; i++) {
1.126 brouard 7066: sump=sump+weight[i];
7067: /* sump=sump+1;*/
7068: num=num+1;
7069: }
7070:
7071:
7072: /* for (i=0; i<=imx; i++)
7073: 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]);*/
7074:
7075: for (i=1;i<=imx ; i++)
7076: {
7077: if (cens[i] == 1 && wav[i]>1)
7078: A=-x[1]/(x[2])*(exp(x[2]*(agecens[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)));
7079:
7080: if (cens[i] == 0 && wav[i]>1)
7081: A=-x[1]/(x[2])*(exp(x[2]*(agedc[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)))
7082: +log(x[1]/YEARM)+x[2]*(agedc[i]-agegomp)+log(YEARM);
7083:
7084: /*if (wav[i] > 1 && agecens[i] > 15) {*/ /* ??? */
7085: if (wav[i] > 1 ) { /* ??? */
7086: L=L+A*weight[i];
7087: /* 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]);*/
7088: }
7089: }
7090:
7091: /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/
7092:
7093: return -2*L*num/sump;
7094: }
7095:
1.136 brouard 7096: #ifdef GSL
7097: /******************* Gompertz_f Likelihood ******************************/
7098: double gompertz_f(const gsl_vector *v, void *params)
7099: {
7100: double A,B,LL=0.0,sump=0.,num=0.;
7101: double *x= (double *) v->data;
7102: int i,n=0; /* n is the size of the sample */
7103:
7104: for (i=0;i<=imx-1 ; i++) {
7105: sump=sump+weight[i];
7106: /* sump=sump+1;*/
7107: num=num+1;
7108: }
7109:
7110:
7111: /* for (i=0; i<=imx; i++)
7112: 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]);*/
7113: printf("x[0]=%lf x[1]=%lf\n",x[0],x[1]);
7114: for (i=1;i<=imx ; i++)
7115: {
7116: if (cens[i] == 1 && wav[i]>1)
7117: A=-x[0]/(x[1])*(exp(x[1]*(agecens[i]-agegomp))-exp(x[1]*(ageexmed[i]-agegomp)));
7118:
7119: if (cens[i] == 0 && wav[i]>1)
7120: A=-x[0]/(x[1])*(exp(x[1]*(agedc[i]-agegomp))-exp(x[1]*(ageexmed[i]-agegomp)))
7121: +log(x[0]/YEARM)+x[1]*(agedc[i]-agegomp)+log(YEARM);
7122:
7123: /*if (wav[i] > 1 && agecens[i] > 15) {*/ /* ??? */
7124: if (wav[i] > 1 ) { /* ??? */
7125: LL=LL+A*weight[i];
7126: /* 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]);*/
7127: }
7128: }
7129:
7130: /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/
7131: printf("x[0]=%lf x[1]=%lf -2*LL*num/sump=%lf\n",x[0],x[1],-2*LL*num/sump);
7132:
7133: return -2*LL*num/sump;
7134: }
7135: #endif
7136:
1.126 brouard 7137: /******************* Printing html file ***********/
1.201 brouard 7138: void printinghtmlmort(char fileresu[], char title[], char datafile[], int firstpass, \
1.126 brouard 7139: int lastpass, int stepm, int weightopt, char model[],\
7140: int imx, double p[],double **matcov,double agemortsup){
7141: int i,k;
7142:
7143: fprintf(fichtm,"<ul><li><h4>Result files </h4>\n Force of mortality. Parameters of the Gompertz fit (with confidence interval in brackets):<br>");
7144: fprintf(fichtm," mu(age) =%lf*exp(%lf*(age-%d)) per year<br><br>",p[1],p[2],agegomp);
7145: for (i=1;i<=2;i++)
7146: 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 7147: fprintf(fichtm,"<br><br><img src=\"graphmort.svg\">");
1.126 brouard 7148: fprintf(fichtm,"</ul>");
7149:
7150: fprintf(fichtm,"<ul><li><h4>Life table</h4>\n <br>");
7151:
7152: 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>");
7153:
7154: for (k=agegomp;k<(agemortsup-2);k++)
7155: 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]);
7156:
7157:
7158: fflush(fichtm);
7159: }
7160:
7161: /******************* Gnuplot file **************/
1.201 brouard 7162: void printinggnuplotmort(char fileresu[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
1.126 brouard 7163:
7164: char dirfileres[132],optfileres[132];
1.164 brouard 7165:
1.126 brouard 7166: int ng;
7167:
7168:
7169: /*#ifdef windows */
7170: fprintf(ficgp,"cd \"%s\" \n",pathc);
7171: /*#endif */
7172:
7173:
7174: strcpy(dirfileres,optionfilefiname);
7175: strcpy(optfileres,"vpl");
1.199 brouard 7176: fprintf(ficgp,"set out \"graphmort.svg\"\n ");
1.126 brouard 7177: fprintf(ficgp,"set xlabel \"Age\"\n set ylabel \"Force of mortality (per year)\" \n ");
1.199 brouard 7178: fprintf(ficgp, "set ter svg size 640, 480\n set log y\n");
1.145 brouard 7179: /* fprintf(ficgp, "set size 0.65,0.65\n"); */
1.126 brouard 7180: fprintf(ficgp,"plot [%d:100] %lf*exp(%lf*(x-%d))",agegomp,p[1],p[2],agegomp);
7181:
7182: }
7183:
1.136 brouard 7184: int readdata(char datafile[], int firstobs, int lastobs, int *imax)
7185: {
1.126 brouard 7186:
1.136 brouard 7187: /*-------- data file ----------*/
7188: FILE *fic;
7189: char dummy[]=" ";
1.223 ! brouard 7190: int i=0, j=0, n=0, iv=0;
! 7191: int lstra;
1.136 brouard 7192: int linei, month, year,iout;
7193: char line[MAXLINE], linetmp[MAXLINE];
1.164 brouard 7194: char stra[MAXLINE], strb[MAXLINE];
1.136 brouard 7195: char *stratrunc;
1.223 ! brouard 7196:
1.126 brouard 7197:
7198:
1.136 brouard 7199: if((fic=fopen(datafile,"r"))==NULL) {
1.218 brouard 7200: printf("Problem while opening datafile: %s with errno='%s'\n", datafile,strerror(errno));fflush(stdout);
7201: fprintf(ficlog,"Problem while opening datafile: %s with errno='%s'\n", datafile,strerror(errno));fflush(ficlog);return 1;
1.136 brouard 7202: }
1.126 brouard 7203:
1.136 brouard 7204: i=1;
7205: linei=0;
7206: while ((fgets(line, MAXLINE, fic) != NULL) &&((i >= firstobs) && (i <=lastobs))) {
7207: linei=linei+1;
7208: for(j=strlen(line); j>=0;j--){ /* Untabifies line */
7209: if(line[j] == '\t')
7210: line[j] = ' ';
7211: }
7212: for(j=strlen(line)-1; (line[j]==' ')||(line[j]==10)||(line[j]==13);j--){
7213: ;
7214: };
7215: line[j+1]=0; /* Trims blanks at end of line */
7216: if(line[0]=='#'){
7217: fprintf(ficlog,"Comment line\n%s\n",line);
7218: printf("Comment line\n%s\n",line);
7219: continue;
7220: }
7221: trimbb(linetmp,line); /* Trims multiple blanks in line */
1.164 brouard 7222: strcpy(line, linetmp);
1.223 ! brouard 7223:
! 7224: /* Loops on waves */
! 7225: for (j=maxwav;j>=1;j--){
! 7226: for (iv=nqtv;iv>=1;iv--){ /* Loop on time varying quantitative variables */
! 7227: cutv(stra, strb, line, ' ');
! 7228: if(strb[0]=='.') { /* Missing value */
! 7229: lval=-1;
! 7230: }else{
! 7231: errno=0;
! 7232: /* what_kind_of_number(strb); */
! 7233: dval=strtod(strb,&endptr);
! 7234: /* if( strb[0]=='\0' || (*endptr != '\0')){ */
! 7235: /* if(strb != endptr && *endptr == '\0') */
! 7236: /* dval=dlval; */
! 7237: /* if (errno == ERANGE && (lval == LONG_MAX || lval == LONG_MIN)) */
! 7238: if( strb[0]=='\0' || (*endptr != '\0')){
! 7239: printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be the %d th quantitative value out of %d measured at wave %d. Setting maxwav=%d might be wrong. Exiting.\n", strb, linei,i,line,iv, nqtv, j,maxwav);
! 7240: fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be the %d th quantitative value out of %d measured at wave %d. Setting maxwav=%d might be wrong. Exiting.\n", strb, linei,i,line, iv, nqtv, j,maxwav);fflush(ficlog);
! 7241: return 1;
! 7242: }
! 7243: cotqvar[j][iv][i]=dval;
! 7244: }
! 7245: strcpy(line,stra);
! 7246: }/* end loop ntqv */
! 7247:
! 7248: for (iv=ntv;iv>=1;iv--){ /* Loop on time varying dummies */
! 7249: cutv(stra, strb, line, ' ');
! 7250: if(strb[0]=='.') { /* Missing value */
! 7251: lval=-1;
! 7252: }else{
! 7253: errno=0;
! 7254: lval=strtol(strb,&endptr,10);
! 7255: /* if (errno == ERANGE && (lval == LONG_MAX || lval == LONG_MIN))*/
! 7256: if( strb[0]=='\0' || (*endptr != '\0')){
! 7257: printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be the %d th dummy covariate out of %d measured at wave %d. Setting maxwav=%d might be wrong. Exiting.\n", strb, linei,i,line,iv, ntv, j,maxwav);
! 7258: fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be the %d dummy covariate out of %d measured wave %d. Setting maxwav=%d might be wrong. Exiting.\n", strb, linei,i,line,iv, ntv,j,maxwav);fflush(ficlog);
! 7259: return 1;
! 7260: }
! 7261: }
! 7262: if(lval <-1 || lval >1){
! 7263: printf("Error reading data around '%ld' at line number %d for individual %d, '%s'\n \
! 7264: Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
! 7265: for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
! 7266: For example, for multinomial values like 1, 2 and 3,\n \
! 7267: build V1=0 V2=0 for the reference value (1),\n \
! 7268: V1=1 V2=0 for (2) \n \
! 7269: and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
! 7270: output of IMaCh is often meaningless.\n \
! 7271: Exiting.\n",lval,linei, i,line,j);
! 7272: fprintf(ficlog,"Error reading data around '%ld' at line number %d for individual %d, '%s'\n \
! 7273: Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
! 7274: for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
! 7275: For example, for multinomial values like 1, 2 and 3,\n \
! 7276: build V1=0 V2=0 for the reference value (1),\n \
! 7277: V1=1 V2=0 for (2) \n \
! 7278: and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
! 7279: output of IMaCh is often meaningless.\n \
! 7280: Exiting.\n",lval,linei, i,line,j);fflush(ficlog);
! 7281: return 1;
! 7282: }
! 7283: cotvar[j][iv][i]=(double)(lval);
! 7284: strcpy(line,stra);
! 7285: }/* end loop ntv */
1.126 brouard 7286:
1.223 ! brouard 7287: /* Statuses at wave */
1.137 brouard 7288: cutv(stra, strb, line, ' ');
1.223 ! brouard 7289: if(strb[0]=='.') { /* Missing value */
! 7290: lval=-1;
1.136 brouard 7291: }else{
1.223 ! brouard 7292: errno=0;
! 7293: lval=strtol(strb,&endptr,10);
! 7294: /* if (errno == ERANGE && (lval == LONG_MAX || lval == LONG_MIN))*/
! 7295: if( strb[0]=='\0' || (*endptr != '\0')){
! 7296: 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);
! 7297: 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);
! 7298: return 1;
! 7299: }
1.136 brouard 7300: }
1.223 ! brouard 7301:
1.136 brouard 7302: s[j][i]=lval;
1.223 ! brouard 7303:
! 7304: /* Date of Interview */
1.136 brouard 7305: strcpy(line,stra);
7306: cutv(stra, strb,line,' ');
1.169 brouard 7307: if( (iout=sscanf(strb,"%d/%d",&month, &year)) != 0){
1.136 brouard 7308: }
1.169 brouard 7309: else if( (iout=sscanf(strb,"%s.",dummy)) != 0){
1.223 ! brouard 7310: month=99;
! 7311: year=9999;
1.136 brouard 7312: }else{
1.223 ! brouard 7313: 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);
! 7314: 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);
! 7315: return 1;
1.136 brouard 7316: }
7317: anint[j][i]= (double) year;
7318: mint[j][i]= (double)month;
7319: strcpy(line,stra);
1.223 ! brouard 7320: } /* End loop on waves */
! 7321:
! 7322: /* Date of death */
1.136 brouard 7323: cutv(stra, strb,line,' ');
1.169 brouard 7324: if( (iout=sscanf(strb,"%d/%d",&month, &year)) != 0){
1.136 brouard 7325: }
1.169 brouard 7326: else if( (iout=sscanf(strb,"%s.",dummy)) != 0){
1.136 brouard 7327: month=99;
7328: year=9999;
7329: }else{
1.141 brouard 7330: printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of death (mm/yyyy or .). Exiting.\n",strb, linei,i,line);
1.223 ! brouard 7331: 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);
! 7332: return 1;
1.136 brouard 7333: }
7334: andc[i]=(double) year;
7335: moisdc[i]=(double) month;
7336: strcpy(line,stra);
7337:
1.223 ! brouard 7338: /* Date of birth */
1.136 brouard 7339: cutv(stra, strb,line,' ');
1.169 brouard 7340: if( (iout=sscanf(strb,"%d/%d",&month, &year)) != 0){
1.136 brouard 7341: }
1.169 brouard 7342: else if( (iout=sscanf(strb,"%s.", dummy)) != 0){
1.136 brouard 7343: month=99;
7344: year=9999;
7345: }else{
1.141 brouard 7346: 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);
7347: 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);
1.223 ! brouard 7348: return 1;
1.136 brouard 7349: }
7350: if (year==9999) {
1.141 brouard 7351: 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);
7352: 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);
1.223 ! brouard 7353: return 1;
1.126 brouard 7354:
1.136 brouard 7355: }
7356: annais[i]=(double)(year);
7357: moisnais[i]=(double)(month);
7358: strcpy(line,stra);
1.223 ! brouard 7359:
! 7360: /* Sample weight */
1.136 brouard 7361: cutv(stra, strb,line,' ');
7362: errno=0;
7363: dval=strtod(strb,&endptr);
7364: if( strb[0]=='\0' || (*endptr != '\0')){
1.141 brouard 7365: printf("Error reading data around '%f' at line number %d, \"%s\" for individual %d\nShould be a weight. Exiting.\n",dval, i,line,linei);
7366: 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 7367: fflush(ficlog);
7368: return 1;
7369: }
7370: weight[i]=dval;
7371: strcpy(line,stra);
1.223 ! brouard 7372:
! 7373: for (iv=nqv;iv>=1;iv--){ /* Loop on fixed quantitative variables */
! 7374: cutv(stra, strb, line, ' ');
! 7375: if(strb[0]=='.') { /* Missing value */
! 7376: lval=-1;
! 7377: }else{
! 7378: errno=0;
! 7379: /* what_kind_of_number(strb); */
! 7380: dval=strtod(strb,&endptr);
! 7381: /* if(strb != endptr && *endptr == '\0') */
! 7382: /* dval=dlval; */
! 7383: /* if (errno == ERANGE && (lval == LONG_MAX || lval == LONG_MIN)) */
! 7384: if( strb[0]=='\0' || (*endptr != '\0')){
! 7385: printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be the %d th quantitative value (out of %d) constant for all waves. Setting maxwav=%d might be wrong. Exiting.\n", strb, linei,i,line, iv, nqv, maxwav);
! 7386: fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be the %d th quantitative value (out of %d) constant for all waves. Setting maxwav=%d might be wrong. Exiting.\n", strb, linei,i,line, iv, nqv, maxwav);fflush(ficlog);
! 7387: return 1;
! 7388: }
! 7389: coqvar[iv][i]=dval;
! 7390: }
! 7391: strcpy(line,stra);
! 7392: }/* end loop nqv */
1.136 brouard 7393:
1.223 ! brouard 7394: /* Covariate values */
1.136 brouard 7395: for (j=ncovcol;j>=1;j--){
7396: cutv(stra, strb,line,' ');
1.223 ! brouard 7397: if(strb[0]=='.') { /* Missing covariate value */
! 7398: lval=-1;
1.136 brouard 7399: }else{
1.223 ! brouard 7400: errno=0;
! 7401: lval=strtol(strb,&endptr,10);
! 7402: if( strb[0]=='\0' || (*endptr != '\0')){
! 7403: 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);
! 7404: 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);
! 7405: return 1;
! 7406: }
1.136 brouard 7407: }
7408: if(lval <-1 || lval >1){
1.223 ! brouard 7409: printf("Error reading data around '%ld' at line number %d for individual %d, '%s'\n \
1.136 brouard 7410: Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
7411: for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
7412: For example, for multinomial values like 1, 2 and 3,\n \
7413: build V1=0 V2=0 for the reference value (1),\n \
7414: V1=1 V2=0 for (2) \n \
7415: and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
7416: output of IMaCh is often meaningless.\n \
7417: Exiting.\n",lval,linei, i,line,j);
1.223 ! brouard 7418: fprintf(ficlog,"Error reading data around '%ld' at line number %d for individual %d, '%s'\n \
1.136 brouard 7419: Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
7420: for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
7421: For example, for multinomial values like 1, 2 and 3,\n \
7422: build V1=0 V2=0 for the reference value (1),\n \
7423: V1=1 V2=0 for (2) \n \
7424: and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
7425: output of IMaCh is often meaningless.\n \
7426: Exiting.\n",lval,linei, i,line,j);fflush(ficlog);
1.223 ! brouard 7427: return 1;
1.136 brouard 7428: }
7429: covar[j][i]=(double)(lval);
7430: strcpy(line,stra);
7431: }
7432: lstra=strlen(stra);
7433:
7434: if(lstra > 9){ /* More than 2**32 or max of what printf can write with %ld */
7435: stratrunc = &(stra[lstra-9]);
7436: num[i]=atol(stratrunc);
7437: }
7438: else
7439: num[i]=atol(stra);
7440: /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){
7441: 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;}*/
7442:
7443: i=i+1;
7444: } /* End loop reading data */
1.126 brouard 7445:
1.136 brouard 7446: *imax=i-1; /* Number of individuals */
7447: fclose(fic);
7448:
7449: return (0);
1.164 brouard 7450: /* endread: */
1.223 ! brouard 7451: printf("Exiting readdata: ");
! 7452: fclose(fic);
! 7453: return (1);
! 7454: }
1.126 brouard 7455:
1.145 brouard 7456: void removespace(char *str) {
7457: char *p1 = str, *p2 = str;
7458: do
7459: while (*p2 == ' ')
7460: p2++;
1.169 brouard 7461: while (*p1++ == *p2++);
1.145 brouard 7462: }
7463:
7464: int decodemodel ( char model[], int lastobs) /**< This routine decode the model and returns:
1.187 brouard 7465: * Model V1+V2+V3+V8+V7*V8+V5*V6+V8*age+V3*age+age*age
7466: * - nagesqr = 1 if age*age in the model, otherwise 0.
7467: * - cptcovt total number of covariates of the model nbocc(+)+1 = 8 excepting constant and age and age*age
7468: * - cptcovn or number of covariates k of the models excluding age*products =6 and age*age
1.145 brouard 7469: * - cptcovage number of covariates with age*products =2
7470: * - cptcovs number of simple covariates
7471: * - 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
7472: * which is a new column after the 9 (ncovcol) variables.
7473: * - if k is a product Vn*Vm covar[k][i] is filled with correct values for each individual
7474: * - Tprod[l] gives the kth covariates of the product Vn*Vm l=1 to cptcovprod-cptcovage
7475: * Tprod[1]@2 {5, 6}: position of first product V7*V8 is 5, and second V5*V6 is 6.
7476: * - Tvard[k] p Tvard[1][1]@4 {7, 8, 5, 6} for V7*V8 and V5*V6 .
7477: */
1.136 brouard 7478: {
1.145 brouard 7479: int i, j, k, ks;
1.164 brouard 7480: int j1, k1, k2;
1.136 brouard 7481: char modelsav[80];
1.145 brouard 7482: char stra[80], strb[80], strc[80], strd[80],stre[80];
1.187 brouard 7483: char *strpt;
1.136 brouard 7484:
1.145 brouard 7485: /*removespace(model);*/
1.136 brouard 7486: if (strlen(model) >1){ /* If there is at least 1 covariate */
1.145 brouard 7487: j=0, j1=0, k1=0, k2=-1, ks=0, cptcovn=0;
1.137 brouard 7488: if (strstr(model,"AGE") !=0){
1.192 brouard 7489: printf("Error. AGE must be in lower case 'age' model=1+age+%s. ",model);
7490: fprintf(ficlog,"Error. AGE must be in lower case model=1+age+%s. ",model);fflush(ficlog);
1.136 brouard 7491: return 1;
7492: }
1.141 brouard 7493: if (strstr(model,"v") !=0){
7494: printf("Error. 'v' must be in upper case 'V' model=%s ",model);
7495: fprintf(ficlog,"Error. 'v' must be in upper case model=%s ",model);fflush(ficlog);
7496: return 1;
7497: }
1.187 brouard 7498: strcpy(modelsav,model);
7499: if ((strpt=strstr(model,"age*age")) !=0){
7500: printf(" strpt=%s, model=%s\n",strpt, model);
7501: if(strpt != model){
7502: printf("Error in model: 'model=%s'; 'age*age' should in first place before other covariates\n \
1.192 brouard 7503: 'model=1+age+age*age+V1.' or 'model=1+age+age*age+V1+V1*age.', please swap as well as \n \
1.187 brouard 7504: corresponding column of parameters.\n",model);
7505: fprintf(ficlog,"Error in model: 'model=%s'; 'age*age' should in first place before other covariates\n \
1.192 brouard 7506: 'model=1+age+age*age+V1.' or 'model=1+age+age*age+V1+V1*age.', please swap as well as \n \
1.187 brouard 7507: corresponding column of parameters.\n",model); fflush(ficlog);
7508: return 1;
7509: }
7510:
7511: nagesqr=1;
7512: if (strstr(model,"+age*age") !=0)
7513: substrchaine(modelsav, model, "+age*age");
7514: else if (strstr(model,"age*age+") !=0)
7515: substrchaine(modelsav, model, "age*age+");
7516: else
7517: substrchaine(modelsav, model, "age*age");
7518: }else
7519: nagesqr=0;
7520: if (strlen(modelsav) >1){
7521: j=nbocc(modelsav,'+'); /**< j=Number of '+' */
7522: j1=nbocc(modelsav,'*'); /**< j1=Number of '*' */
7523: cptcovs=j+1-j1; /**< Number of simple covariates V1+V1*age+V3 +V3*V4+age*age=> V1 + V3 =2 */
7524: cptcovt= j+1; /* Number of total covariates in the model, not including
7525: * cst, age and age*age
7526: * V1+V1*age+ V3 + V3*V4+age*age=> 4*/
7527: /* including age products which are counted in cptcovage.
7528: * but the covariates which are products must be treated
7529: * separately: ncovn=4- 2=2 (V1+V3). */
7530: cptcovprod=j1; /**< Number of products V1*V2 +v3*age = 2 */
7531: cptcovprodnoage=0; /**< Number of covariate products without age: V3*V4 =1 */
7532:
7533:
7534: /* Design
7535: * V1 V2 V3 V4 V5 V6 V7 V8 V9 Weight
7536: * < ncovcol=8 >
7537: * Model V2 + V1 + V3*age + V3 + V5*V6 + V7*V8 + V8*age + V8
7538: * k= 1 2 3 4 5 6 7 8
7539: * cptcovn number of covariates (not including constant and age ) = # of + plus 1 = 7+1=8
7540: * covar[k,i], value of kth covariate if not including age for individual i:
7541: * covar[1][i]= (V2), covar[4][i]=(V3), covar[8][i]=(V8)
7542: * Tvar[k] # of the kth covariate: Tvar[1]=2 Tvar[4]=3 Tvar[8]=8
7543: * if multiplied by age: V3*age Tvar[3=V3*age]=3 (V3) Tvar[7]=8 and
7544: * Tage[++cptcovage]=k
7545: * if products, new covar are created after ncovcol with k1
7546: * Tvar[k]=ncovcol+k1; # of the kth covariate product: Tvar[5]=ncovcol+1=10 Tvar[6]=ncovcol+1=11
7547: * Tprod[k1]=k; Tprod[1]=5 Tprod[2]= 6; gives the position of the k1th product
7548: * 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
7549: * Tvar[cptcovn+k2]=Tvard[k1][1];Tvar[cptcovn+k2+1]=Tvard[k1][2];
7550: * Tvar[8+1]=5;Tvar[8+2]=6;Tvar[8+3]=7;Tvar[8+4]=8 inverted
7551: * V1 V2 V3 V4 V5 V6 V7 V8 V9 V10 V11
7552: * < ncovcol=8 >
7553: * Model V2 + V1 + V3*age + V3 + V5*V6 + V7*V8 + V8*age + V8 d1 d1 d2 d2
7554: * k= 1 2 3 4 5 6 7 8 9 10 11 12
7555: * Tvar[k]= 2 1 3 3 10 11 8 8 5 6 7 8
7556: * p Tvar[1]@12={2, 1, 3, 3, 11, 10, 8, 8, 7, 8, 5, 6}
7557: * p Tprod[1]@2={ 6, 5}
7558: *p Tvard[1][1]@4= {7, 8, 5, 6}
7559: * covar[k][i]= V2 V1 ? V3 V5*V6? V7*V8? ? V8
7560: * cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
7561: *How to reorganize?
7562: * Model V1 + V2 + V3 + V8 + V5*V6 + V7*V8 + V3*age + V8*age
7563: * Tvars {2, 1, 3, 3, 11, 10, 8, 8, 7, 8, 5, 6}
7564: * {2, 1, 4, 8, 5, 6, 3, 7}
7565: * Struct []
7566: */
1.145 brouard 7567:
1.187 brouard 7568: /* This loop fills the array Tvar from the string 'model'.*/
7569: /* j is the number of + signs in the model V1+V2+V3 j=2 i=3 to 1 */
7570: /* modelsav=V2+V1+V4+age*V3 strb=age*V3 stra=V2+V1+V4 */
7571: /* k=4 (age*V3) Tvar[k=4]= 3 (from V3) Tage[cptcovage=1]=4 */
7572: /* k=3 V4 Tvar[k=3]= 4 (from V4) */
7573: /* k=2 V1 Tvar[k=2]= 1 (from V1) */
7574: /* k=1 Tvar[1]=2 (from V2) */
7575: /* k=5 Tvar[5] */
7576: /* for (k=1; k<=cptcovn;k++) { */
1.198 brouard 7577: /* cov[2+k]=nbcode[Tvar[k]][codtabm(ij,Tvar[k])]; */
1.187 brouard 7578: /* } */
1.198 brouard 7579: /* for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,Tvar[Tage[k])]]*cov[2]; */
1.187 brouard 7580: /*
7581: * Treating invertedly V2+V1+V3*age+V2*V4 is as if written V2*V4 +V3*age + V1 + V2 */
7582: for(k=cptcovt; k>=1;k--) /**< Number of covariates */
1.145 brouard 7583: Tvar[k]=0;
1.187 brouard 7584: cptcovage=0;
7585: for(k=1; k<=cptcovt;k++){ /* Loop on total covariates of the model */
1.223 ! brouard 7586: cutl(stra,strb,modelsav,'+'); /* keeps in strb after the first '+'
! 7587: modelsav==V2+V1+V4+V3*age strb=V3*age stra=V2+V1+V4 */
! 7588: if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyzes it */
! 7589: /* printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/
! 7590: /*scanf("%d",i);*/
! 7591: if (strchr(strb,'*')) { /**< Model includes a product V2+V1+V4+V3*age strb=V3*age */
! 7592: cutl(strc,strd,strb,'*'); /**< strd*strc Vm*Vn: strb=V3*age(input) strc=age strd=V3 ; V3*V2 strc=V2, strd=V3 */
! 7593: if (strcmp(strc,"age")==0) { /**< Model includes age: Vn*age */
! 7594: /* covar is not filled and then is empty */
! 7595: cptcovprod--;
! 7596: cutl(stre,strb,strd,'V'); /* strd=V3(input): stre="3" */
! 7597: Tvar[k]=atoi(stre); /* V2+V1+V4+V3*age Tvar[4]=3 ; V1+V2*age Tvar[2]=2; V1+V1*age Tvar[2]=1 */
! 7598: cptcovage++; /* Sums the number of covariates which include age as a product */
! 7599: Tage[cptcovage]=k; /* Tvar[4]=3, Tage[1] = 4 or V1+V1*age Tvar[2]=1, Tage[1]=2 */
! 7600: /*printf("stre=%s ", stre);*/
! 7601: } else if (strcmp(strd,"age")==0) { /* or age*Vn */
! 7602: cptcovprod--;
! 7603: cutl(stre,strb,strc,'V');
! 7604: Tvar[k]=atoi(stre);
! 7605: cptcovage++;
! 7606: Tage[cptcovage]=k;
! 7607: } else { /* Age is not in the model product V2+V1+V1*V4+V3*age+V3*V2 strb=V3*V2*/
! 7608: /* loops on k1=1 (V3*V2) and k1=2 V4*V3 */
! 7609: cptcovn++;
! 7610: cptcovprodnoage++;k1++;
! 7611: cutl(stre,strb,strc,'V'); /* strc= Vn, stre is n; strb=V3*V2 stre=3 strc=*/
! 7612: Tvar[k]=ncovcol+k1; /* For model-covariate k tells which data-covariate to use but
! 7613: because this model-covariate is a construction we invent a new column
! 7614: ncovcol + k1
! 7615: If already ncovcol=4 and model=V2+V1+V1*V4+age*V3+V3*V2
! 7616: Tvar[3=V1*V4]=4+1 Tvar[5=V3*V2]=4 + 2= 6, etc */
! 7617: cutl(strc,strb,strd,'V'); /* strd was Vm, strc is m */
! 7618: Tprod[k1]=k; /* Tprod[1]=3(=V1*V4) for V2+V1+V1*V4+age*V3+V3*V2 */
! 7619: Tvard[k1][1] =atoi(strc); /* m 1 for V1*/
! 7620: Tvard[k1][2] =atoi(stre); /* n 4 for V4*/
! 7621: k2=k2+2;
! 7622: Tvar[cptcovt+k2]=Tvard[k1][1]; /* Tvar[(cptcovt=4+k2=1)=5]= 1 (V1) */
! 7623: Tvar[cptcovt+k2+1]=Tvard[k1][2]; /* Tvar[(cptcovt=4+(k2=1)+1)=6]= 4 (V4) */
! 7624: for (i=1; i<=lastobs;i++){
! 7625: /* Computes the new covariate which is a product of
! 7626: covar[n][i]* covar[m][i] and stores it at ncovol+k1 May not be defined */
! 7627: covar[ncovcol+k1][i]=covar[atoi(stre)][i]*covar[atoi(strc)][i];
! 7628: }
! 7629: } /* End age is not in the model */
! 7630: } /* End if model includes a product */
! 7631: else { /* no more sum */
! 7632: /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/
! 7633: /* scanf("%d",i);*/
! 7634: cutl(strd,strc,strb,'V');
! 7635: ks++; /**< Number of simple covariates */
! 7636: cptcovn++;
! 7637: Tvar[k]=atoi(strd);
! 7638: }
! 7639: strcpy(modelsav,stra); /* modelsav=V2+V1+V4 stra=V2+V1+V4 */
! 7640: /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);
! 7641: scanf("%d",i);*/
1.187 brouard 7642: } /* end of loop + on total covariates */
7643: } /* end if strlen(modelsave == 0) age*age might exist */
7644: } /* end if strlen(model == 0) */
1.136 brouard 7645:
7646: /*The number n of Vn is stored in Tvar. cptcovage =number of age covariate. Tage gives the position of age. cptcovprod= number of products.
7647: If model=V1+V1*age then Tvar[1]=1 Tvar[2]=1 cptcovage=1 Tage[1]=2 cptcovprod=0*/
7648:
7649: /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);
7650: printf("cptcovprod=%d ", cptcovprod);
7651: fprintf(ficlog,"cptcovprod=%d ", cptcovprod);
7652:
7653: scanf("%d ",i);*/
7654:
7655:
1.137 brouard 7656: return (0); /* with covar[new additional covariate if product] and Tage if age */
1.164 brouard 7657: /*endread:*/
1.136 brouard 7658: printf("Exiting decodemodel: ");
7659: return (1);
7660: }
7661:
1.169 brouard 7662: int calandcheckages(int imx, int maxwav, double *agemin, double *agemax, int *nberr, int *nbwarn )
1.136 brouard 7663: {
7664: int i, m;
1.218 brouard 7665: int firstone=0;
7666:
1.136 brouard 7667: for (i=1; i<=imx; i++) {
7668: for(m=2; (m<= maxwav); m++) {
7669: if (((int)mint[m][i]== 99) && (s[m][i] <= nlstate)){
7670: anint[m][i]=9999;
1.216 brouard 7671: if (s[m][i] != -2) /* Keeping initial status of unknown vital status */
7672: s[m][i]=-1;
1.136 brouard 7673: }
7674: if((int)moisdc[i]==99 && (int)andc[i]==9999 && s[m][i]>nlstate){
1.169 brouard 7675: *nberr = *nberr + 1;
1.218 brouard 7676: if(firstone == 0){
7677: firstone=1;
7678: 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);
7679: }
7680: 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 7681: s[m][i]=-1;
7682: }
7683: if((int)moisdc[i]==99 && (int)andc[i]!=9999 && s[m][i]>nlstate){
1.169 brouard 7684: (*nberr)++;
1.136 brouard 7685: 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]);
7686: 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]);
7687: s[m][i]=-1; /* We prefer to skip it (and to skip it in version 0.8a1 too */
7688: }
7689: }
7690: }
7691:
7692: for (i=1; i<=imx; i++) {
7693: agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);
7694: for(m=firstpass; (m<= lastpass); m++){
1.214 brouard 7695: 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 7696: if (s[m][i] >= nlstate+1) {
1.169 brouard 7697: if(agedc[i]>0){
7698: if((int)moisdc[i]!=99 && (int)andc[i]!=9999){
1.136 brouard 7699: agev[m][i]=agedc[i];
1.214 brouard 7700: /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/
1.169 brouard 7701: }else {
1.136 brouard 7702: if ((int)andc[i]!=9999){
7703: nbwarn++;
7704: printf("Warning negative age at death: %ld line:%d\n",num[i],i);
7705: fprintf(ficlog,"Warning negative age at death: %ld line:%d\n",num[i],i);
7706: agev[m][i]=-1;
7707: }
7708: }
1.169 brouard 7709: } /* agedc > 0 */
1.214 brouard 7710: } /* end if */
1.136 brouard 7711: else if(s[m][i] !=9){ /* Standard case, age in fractional
7712: years but with the precision of a month */
7713: agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);
7714: if((int)mint[m][i]==99 || (int)anint[m][i]==9999)
7715: agev[m][i]=1;
7716: else if(agev[m][i] < *agemin){
7717: *agemin=agev[m][i];
7718: printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], *agemin);
7719: }
7720: else if(agev[m][i] >*agemax){
7721: *agemax=agev[m][i];
1.156 brouard 7722: /* printf(" Max anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.2f\n",m,i,anint[m][i], i,annais[i], *agemax);*/
1.136 brouard 7723: }
7724: /*agev[m][i]=anint[m][i]-annais[i];*/
7725: /* agev[m][i] = age[i]+2*m;*/
1.214 brouard 7726: } /* en if 9*/
1.136 brouard 7727: else { /* =9 */
1.214 brouard 7728: /* printf("Debug num[%d]=%ld s[%d][%d]=%d\n",i,num[i], m,i, s[m][i]); */
1.136 brouard 7729: agev[m][i]=1;
7730: s[m][i]=-1;
7731: }
7732: }
1.214 brouard 7733: else if(s[m][i]==0) /*= 0 Unknown */
1.136 brouard 7734: agev[m][i]=1;
1.214 brouard 7735: else{
7736: printf("Warning, num[%d]=%ld, s[%d][%d]=%d\n", i, num[i], m, i,s[m][i]);
7737: fprintf(ficlog, "Warning, num[%d]=%ld, s[%d][%d]=%d\n", i, num[i], m, i,s[m][i]);
7738: agev[m][i]=0;
7739: }
7740: } /* End for lastpass */
7741: }
1.136 brouard 7742:
7743: for (i=1; i<=imx; i++) {
7744: for(m=firstpass; (m<=lastpass); m++){
7745: if (s[m][i] > (nlstate+ndeath)) {
1.169 brouard 7746: (*nberr)++;
1.136 brouard 7747: 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);
7748: 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);
7749: return 1;
7750: }
7751: }
7752: }
7753:
7754: /*for (i=1; i<=imx; i++){
7755: for (m=firstpass; (m<lastpass); m++){
7756: printf("%ld %d %.lf %d %d\n", num[i],(covar[1][i]),agev[m][i],s[m][i],s[m+1][i]);
7757: }
7758:
7759: }*/
7760:
7761:
1.139 brouard 7762: printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, *agemin, *agemax);
7763: fprintf(ficlog,"Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, *agemin, *agemax);
1.136 brouard 7764:
7765: return (0);
1.164 brouard 7766: /* endread:*/
1.136 brouard 7767: printf("Exiting calandcheckages: ");
7768: return (1);
7769: }
7770:
1.172 brouard 7771: #if defined(_MSC_VER)
7772: /*printf("Visual C++ compiler: %s \n;", _MSC_FULL_VER);*/
7773: /*fprintf(ficlog, "Visual C++ compiler: %s \n;", _MSC_FULL_VER);*/
7774: //#include "stdafx.h"
7775: //#include <stdio.h>
7776: //#include <tchar.h>
7777: //#include <windows.h>
7778: //#include <iostream>
7779: typedef BOOL(WINAPI *LPFN_ISWOW64PROCESS) (HANDLE, PBOOL);
7780:
7781: LPFN_ISWOW64PROCESS fnIsWow64Process;
7782:
7783: BOOL IsWow64()
7784: {
7785: BOOL bIsWow64 = FALSE;
7786:
7787: //typedef BOOL (APIENTRY *LPFN_ISWOW64PROCESS)
7788: // (HANDLE, PBOOL);
7789:
7790: //LPFN_ISWOW64PROCESS fnIsWow64Process;
7791:
7792: HMODULE module = GetModuleHandle(_T("kernel32"));
7793: const char funcName[] = "IsWow64Process";
7794: fnIsWow64Process = (LPFN_ISWOW64PROCESS)
7795: GetProcAddress(module, funcName);
7796:
7797: if (NULL != fnIsWow64Process)
7798: {
7799: if (!fnIsWow64Process(GetCurrentProcess(),
7800: &bIsWow64))
7801: //throw std::exception("Unknown error");
7802: printf("Unknown error\n");
7803: }
7804: return bIsWow64 != FALSE;
7805: }
7806: #endif
1.177 brouard 7807:
1.191 brouard 7808: void syscompilerinfo(int logged)
1.167 brouard 7809: {
7810: /* #include "syscompilerinfo.h"*/
1.185 brouard 7811: /* command line Intel compiler 32bit windows, XP compatible:*/
7812: /* /GS /W3 /Gy
7813: /Zc:wchar_t /Zi /O2 /Fd"Release\vc120.pdb" /D "WIN32" /D "NDEBUG" /D
7814: "_CONSOLE" /D "_LIB" /D "_USING_V110_SDK71_" /D "_UNICODE" /D
7815: "UNICODE" /Qipo /Zc:forScope /Gd /Oi /MT /Fa"Release\" /EHsc /nologo
1.186 brouard 7816: /Fo"Release\" /Qprof-dir "Release\" /Fp"Release\IMaCh.pch"
7817: */
7818: /* 64 bits */
1.185 brouard 7819: /*
7820: /GS /W3 /Gy
7821: /Zc:wchar_t /Zi /O2 /Fd"x64\Release\vc120.pdb" /D "WIN32" /D "NDEBUG"
7822: /D "_CONSOLE" /D "_LIB" /D "_UNICODE" /D "UNICODE" /Qipo /Zc:forScope
7823: /Oi /MD /Fa"x64\Release\" /EHsc /nologo /Fo"x64\Release\" /Qprof-dir
7824: "x64\Release\" /Fp"x64\Release\IMaCh.pch" */
7825: /* Optimization are useless and O3 is slower than O2 */
7826: /*
7827: /GS /W3 /Gy /Zc:wchar_t /Zi /O3 /Fd"x64\Release\vc120.pdb" /D "WIN32"
7828: /D "NDEBUG" /D "_CONSOLE" /D "_LIB" /D "_UNICODE" /D "UNICODE" /Qipo
7829: /Zc:forScope /Oi /MD /Fa"x64\Release\" /EHsc /nologo /Qparallel
7830: /Fo"x64\Release\" /Qprof-dir "x64\Release\" /Fp"x64\Release\IMaCh.pch"
7831: */
1.186 brouard 7832: /* Link is */ /* /OUT:"visual studio
1.185 brouard 7833: 2013\Projects\IMaCh\Release\IMaCh.exe" /MANIFEST /NXCOMPAT
7834: /PDB:"visual studio
7835: 2013\Projects\IMaCh\Release\IMaCh.pdb" /DYNAMICBASE
7836: "kernel32.lib" "user32.lib" "gdi32.lib" "winspool.lib"
7837: "comdlg32.lib" "advapi32.lib" "shell32.lib" "ole32.lib"
7838: "oleaut32.lib" "uuid.lib" "odbc32.lib" "odbccp32.lib"
7839: /MACHINE:X86 /OPT:REF /SAFESEH /INCREMENTAL:NO
7840: /SUBSYSTEM:CONSOLE",5.01" /MANIFESTUAC:"level='asInvoker'
7841: uiAccess='false'"
7842: /ManifestFile:"Release\IMaCh.exe.intermediate.manifest" /OPT:ICF
7843: /NOLOGO /TLBID:1
7844: */
1.177 brouard 7845: #if defined __INTEL_COMPILER
1.178 brouard 7846: #if defined(__GNUC__)
7847: struct utsname sysInfo; /* For Intel on Linux and OS/X */
7848: #endif
1.177 brouard 7849: #elif defined(__GNUC__)
1.179 brouard 7850: #ifndef __APPLE__
1.174 brouard 7851: #include <gnu/libc-version.h> /* Only on gnu */
1.179 brouard 7852: #endif
1.177 brouard 7853: struct utsname sysInfo;
1.178 brouard 7854: int cross = CROSS;
7855: if (cross){
7856: printf("Cross-");
1.191 brouard 7857: if(logged) fprintf(ficlog, "Cross-");
1.178 brouard 7858: }
1.174 brouard 7859: #endif
7860:
1.171 brouard 7861: #include <stdint.h>
1.178 brouard 7862:
1.191 brouard 7863: printf("Compiled with:");if(logged)fprintf(ficlog,"Compiled with:");
1.169 brouard 7864: #if defined(__clang__)
1.191 brouard 7865: printf(" Clang/LLVM");if(logged)fprintf(ficlog," Clang/LLVM"); /* Clang/LLVM. ---------------------------------------------- */
1.169 brouard 7866: #endif
7867: #if defined(__ICC) || defined(__INTEL_COMPILER)
1.191 brouard 7868: printf(" Intel ICC/ICPC");if(logged)fprintf(ficlog," Intel ICC/ICPC");/* Intel ICC/ICPC. ------------------------------------------ */
1.169 brouard 7869: #endif
7870: #if defined(__GNUC__) || defined(__GNUG__)
1.191 brouard 7871: printf(" GNU GCC/G++");if(logged)fprintf(ficlog," GNU GCC/G++");/* GNU GCC/G++. --------------------------------------------- */
1.169 brouard 7872: #endif
7873: #if defined(__HP_cc) || defined(__HP_aCC)
1.191 brouard 7874: printf(" Hewlett-Packard C/aC++");if(logged)fprintf(fcilog," Hewlett-Packard C/aC++"); /* Hewlett-Packard C/aC++. ---------------------------------- */
1.169 brouard 7875: #endif
7876: #if defined(__IBMC__) || defined(__IBMCPP__)
1.191 brouard 7877: printf(" IBM XL C/C++"); if(logged) fprintf(ficlog," IBM XL C/C++");/* IBM XL C/C++. -------------------------------------------- */
1.169 brouard 7878: #endif
7879: #if defined(_MSC_VER)
1.191 brouard 7880: printf(" Microsoft Visual Studio");if(logged)fprintf(ficlog," Microsoft Visual Studio");/* Microsoft Visual Studio. --------------------------------- */
1.169 brouard 7881: #endif
7882: #if defined(__PGI)
1.191 brouard 7883: printf(" Portland Group PGCC/PGCPP");if(logged) fprintf(ficlog," Portland Group PGCC/PGCPP");/* Portland Group PGCC/PGCPP. ------------------------------- */
1.169 brouard 7884: #endif
7885: #if defined(__SUNPRO_C) || defined(__SUNPRO_CC)
1.191 brouard 7886: printf(" Oracle Solaris Studio");if(logged)fprintf(ficlog," Oracle Solaris Studio\n");/* Oracle Solaris Studio. ----------------------------------- */
1.167 brouard 7887: #endif
1.191 brouard 7888: printf(" for "); if (logged) fprintf(ficlog, " for ");
1.169 brouard 7889:
1.167 brouard 7890: // http://stackoverflow.com/questions/4605842/how-to-identify-platform-compiler-from-preprocessor-macros
7891: #ifdef _WIN32 // note the underscore: without it, it's not msdn official!
7892: // Windows (x64 and x86)
1.191 brouard 7893: printf("Windows (x64 and x86) ");if(logged) fprintf(ficlog,"Windows (x64 and x86) ");
1.167 brouard 7894: #elif __unix__ // all unices, not all compilers
7895: // Unix
1.191 brouard 7896: printf("Unix ");if(logged) fprintf(ficlog,"Unix ");
1.167 brouard 7897: #elif __linux__
7898: // linux
1.191 brouard 7899: printf("linux ");if(logged) fprintf(ficlog,"linux ");
1.167 brouard 7900: #elif __APPLE__
1.174 brouard 7901: // Mac OS, not sure if this is covered by __posix__ and/or __unix__ though..
1.191 brouard 7902: printf("Mac OS ");if(logged) fprintf(ficlog,"Mac OS ");
1.167 brouard 7903: #endif
7904:
7905: /* __MINGW32__ */
7906: /* __CYGWIN__ */
7907: /* __MINGW64__ */
7908: // http://msdn.microsoft.com/en-us/library/b0084kay.aspx
7909: /* _MSC_VER //the Visual C++ compiler is 17.00.51106.1, the _MSC_VER macro evaluates to 1700. Type cl /? */
7910: /* _MSC_FULL_VER //the Visual C++ compiler is 15.00.20706.01, the _MSC_FULL_VER macro evaluates to 150020706 */
7911: /* _WIN64 // Defined for applications for Win64. */
7912: /* _M_X64 // Defined for compilations that target x64 processors. */
7913: /* _DEBUG // Defined when you compile with /LDd, /MDd, and /MTd. */
1.171 brouard 7914:
1.167 brouard 7915: #if UINTPTR_MAX == 0xffffffff
1.191 brouard 7916: printf(" 32-bit"); if(logged) fprintf(ficlog," 32-bit");/* 32-bit */
1.167 brouard 7917: #elif UINTPTR_MAX == 0xffffffffffffffff
1.191 brouard 7918: printf(" 64-bit"); if(logged) fprintf(ficlog," 64-bit");/* 64-bit */
1.167 brouard 7919: #else
1.191 brouard 7920: printf(" wtf-bit"); if(logged) fprintf(ficlog," wtf-bit");/* wtf */
1.167 brouard 7921: #endif
7922:
1.169 brouard 7923: #if defined(__GNUC__)
7924: # if defined(__GNUC_PATCHLEVEL__)
7925: # define __GNUC_VERSION__ (__GNUC__ * 10000 \
7926: + __GNUC_MINOR__ * 100 \
7927: + __GNUC_PATCHLEVEL__)
7928: # else
7929: # define __GNUC_VERSION__ (__GNUC__ * 10000 \
7930: + __GNUC_MINOR__ * 100)
7931: # endif
1.174 brouard 7932: printf(" using GNU C version %d.\n", __GNUC_VERSION__);
1.191 brouard 7933: if(logged) fprintf(ficlog, " using GNU C version %d.\n", __GNUC_VERSION__);
1.176 brouard 7934:
7935: if (uname(&sysInfo) != -1) {
7936: printf("Running on: %s %s %s %s %s\n",sysInfo.sysname, sysInfo.nodename, sysInfo.release, sysInfo.version, sysInfo.machine);
1.191 brouard 7937: 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 7938: }
7939: else
7940: perror("uname() error");
1.179 brouard 7941: //#ifndef __INTEL_COMPILER
7942: #if !defined (__INTEL_COMPILER) && !defined(__APPLE__)
1.174 brouard 7943: printf("GNU libc version: %s\n", gnu_get_libc_version());
1.191 brouard 7944: if(logged) fprintf(ficlog,"GNU libc version: %s\n", gnu_get_libc_version());
1.177 brouard 7945: #endif
1.169 brouard 7946: #endif
1.172 brouard 7947:
7948: // void main()
7949: // {
1.169 brouard 7950: #if defined(_MSC_VER)
1.174 brouard 7951: if (IsWow64()){
1.191 brouard 7952: printf("\nThe program (probably compiled for 32bit) is running under WOW64 (64bit) emulation.\n");
7953: if (logged) fprintf(ficlog, "\nThe program (probably compiled for 32bit) is running under WOW64 (64bit) emulation.\n");
1.174 brouard 7954: }
7955: else{
1.191 brouard 7956: printf("\nThe program is not running under WOW64 (i.e probably on a 64bit Windows).\n");
7957: if (logged) fprintf(ficlog, "\nThe programm is not running under WOW64 (i.e probably on a 64bit Windows).\n");
1.174 brouard 7958: }
1.172 brouard 7959: // printf("\nPress Enter to continue...");
7960: // getchar();
7961: // }
7962:
1.169 brouard 7963: #endif
7964:
1.167 brouard 7965:
1.219 brouard 7966: }
1.136 brouard 7967:
1.219 brouard 7968: int prevalence_limit(double *p, double **prlim, double ageminpar, double agemaxpar, double ftolpl, int *ncvyearp){
1.180 brouard 7969: /*--------------- Prevalence limit (period or stable prevalence) --------------*/
7970: int i, j, k, i1 ;
1.202 brouard 7971: /* double ftolpl = 1.e-10; */
1.180 brouard 7972: double age, agebase, agelim;
1.203 brouard 7973: double tot;
1.180 brouard 7974:
1.202 brouard 7975: strcpy(filerespl,"PL_");
7976: strcat(filerespl,fileresu);
7977: if((ficrespl=fopen(filerespl,"w"))==NULL) {
7978: printf("Problem with period (stable) prevalence resultfile: %s\n", filerespl);return 1;
7979: fprintf(ficlog,"Problem with period (stable) prevalence resultfile: %s\n", filerespl);return 1;
7980: }
7981: printf("Computing period (stable) prevalence: result on file '%s' \n", filerespl);
7982: fprintf(ficlog,"Computing period (stable) prevalence: result on file '%s' \n", filerespl);
7983: pstamp(ficrespl);
1.203 brouard 7984: fprintf(ficrespl,"# Period (stable) prevalence. Precision given by ftolpl=%g \n", ftolpl);
1.202 brouard 7985: fprintf(ficrespl,"#Age ");
7986: for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);
7987: fprintf(ficrespl,"\n");
1.180 brouard 7988:
1.219 brouard 7989: /* prlim=matrix(1,nlstate,1,nlstate);*/ /* back in main */
1.180 brouard 7990:
1.219 brouard 7991: agebase=ageminpar;
7992: agelim=agemaxpar;
1.180 brouard 7993:
1.219 brouard 7994: i1=pow(2,cptcoveff);
7995: if (cptcovn < 1){i1=1;}
1.180 brouard 7996:
1.220 brouard 7997: for(k=1; k<=i1;k++){
7998: /* for(cptcov=1,k=0;cptcov<=i1;cptcov++){ */
1.180 brouard 7999: /* for(cptcov=1,k=0;cptcov<=1;cptcov++){ */
1.219 brouard 8000: //for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
1.220 brouard 8001: /* k=k+1; */
1.219 brouard 8002: /* to clean */
8003: //printf("cptcov=%d cptcod=%d codtab=%d\n",cptcov, cptcod,codtabm(cptcod,cptcov));
8004: fprintf(ficrespl,"#******");
8005: printf("#******");
8006: fprintf(ficlog,"#******");
8007: for(j=1;j<=cptcoveff;j++) {
8008: fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
8009: printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
8010: fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
8011: }
8012: fprintf(ficrespl,"******\n");
8013: printf("******\n");
8014: fprintf(ficlog,"******\n");
1.220 brouard 8015: if(invalidvarcomb[k]){
8016: printf("\nCombination (%d) ignored because no cases \n",k);
8017: fprintf(ficrespl,"#Combination (%d) ignored because no cases \n",k);
8018: fprintf(ficlog,"\nCombination (%d) ignored because no cases \n",k);
8019: continue;
8020: }
1.219 brouard 8021:
8022: fprintf(ficrespl,"#Age ");
8023: for(j=1;j<=cptcoveff;j++) {
8024: fprintf(ficrespl,"V%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
8025: }
8026: for(i=1; i<=nlstate;i++) fprintf(ficrespl," %d-%d ",i,i);
8027: fprintf(ficrespl,"Total Years_to_converge\n");
8028:
8029: for (age=agebase; age<=agelim; age++){
8030: /* for (age=agebase; age<=agebase; age++){ */
8031: prevalim(prlim, nlstate, p, age, oldm, savm, ftolpl, ncvyearp, k);
8032: fprintf(ficrespl,"%.0f ",age );
8033: for(j=1;j<=cptcoveff;j++)
1.220 brouard 8034: fprintf(ficrespl,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
1.219 brouard 8035: tot=0.;
8036: for(i=1; i<=nlstate;i++){
1.220 brouard 8037: tot += prlim[i][i];
8038: fprintf(ficrespl," %.5f", prlim[i][i]);
1.219 brouard 8039: }
8040: fprintf(ficrespl," %.3f %d\n", tot, *ncvyearp);
8041: } /* Age */
8042: /* was end of cptcod */
8043: } /* cptcov */
8044: return 0;
1.180 brouard 8045: }
8046:
1.218 brouard 8047: 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){
8048: /*--------------- Back Prevalence limit (period or stable prevalence) --------------*/
8049:
8050: /* Computes the back prevalence limit for any combination of covariate values
8051: * at any age between ageminpar and agemaxpar
8052: */
1.217 brouard 8053: int i, j, k, i1 ;
8054: /* double ftolpl = 1.e-10; */
8055: double age, agebase, agelim;
8056: double tot;
1.218 brouard 8057: /* double ***mobaverage; */
8058: /* double **dnewm, **doldm, **dsavm; /\* for use *\/ */
1.217 brouard 8059:
8060: strcpy(fileresplb,"PLB_");
8061: strcat(fileresplb,fileresu);
8062: if((ficresplb=fopen(fileresplb,"w"))==NULL) {
8063: printf("Problem with period (stable) back prevalence resultfile: %s\n", fileresplb);return 1;
8064: fprintf(ficlog,"Problem with period (stable) back prevalence resultfile: %s\n", fileresplb);return 1;
8065: }
8066: printf("Computing period (stable) back prevalence: result on file '%s' \n", fileresplb);
8067: fprintf(ficlog,"Computing period (stable) back prevalence: result on file '%s' \n", fileresplb);
8068: pstamp(ficresplb);
8069: fprintf(ficresplb,"# Period (stable) back prevalence. Precision given by ftolpl=%g \n", ftolpl);
8070: fprintf(ficresplb,"#Age ");
8071: for(i=1; i<=nlstate;i++) fprintf(ficresplb,"%d-%d ",i,i);
8072: fprintf(ficresplb,"\n");
8073:
1.218 brouard 8074:
8075: /* prlim=matrix(1,nlstate,1,nlstate);*/ /* back in main */
8076:
8077: agebase=ageminpar;
8078: agelim=agemaxpar;
8079:
8080:
8081: i1=pow(2,cptcoveff);
8082: if (cptcovn < 1){i1=1;}
1.220 brouard 8083:
8084: for(k=1; k<=i1;k++){
8085: /* for(cptcov=1,k=0;cptcov<=i1;cptcov++){ */
1.217 brouard 8086: /* for(cptcov=1,k=0;cptcov<=1;cptcov++){ */
1.218 brouard 8087: //for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
1.220 brouard 8088: /* k=k+1; */
1.218 brouard 8089: /* to clean */
8090: //printf("cptcov=%d cptcod=%d codtab=%d\n",cptcov, cptcod,codtabm(cptcod,cptcov));
8091: fprintf(ficresplb,"#******");
8092: printf("#******");
8093: fprintf(ficlog,"#******");
8094: for(j=1;j<=cptcoveff;j++) {
8095: fprintf(ficresplb," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
8096: printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
8097: fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
8098: }
8099: fprintf(ficresplb,"******\n");
8100: printf("******\n");
8101: fprintf(ficlog,"******\n");
1.220 brouard 8102: if(invalidvarcomb[k]){
8103: printf("\nCombination (%d) ignored because no cases \n",k);
8104: fprintf(ficresplb,"#Combination (%d) ignored because no cases \n",k);
8105: fprintf(ficlog,"\nCombination (%d) ignored because no cases \n",k);
8106: continue;
8107: }
1.218 brouard 8108:
8109: fprintf(ficresplb,"#Age ");
8110: for(j=1;j<=cptcoveff;j++) {
8111: fprintf(ficresplb,"V%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
8112: }
8113: for(i=1; i<=nlstate;i++) fprintf(ficresplb," %d-%d ",i,i);
8114: fprintf(ficresplb,"Total Years_to_converge\n");
8115:
8116:
8117: for (age=agebase; age<=agelim; age++){
8118: /* for (age=agebase; age<=agebase; age++){ */
8119: if(mobilavproj > 0){
8120: /* bprevalim(bprlim, mobaverage, nlstate, p, age, ageminpar, agemaxpar, oldm, savm, doldm, dsavm, ftolpl, ncvyearp, k); */
8121: /* bprevalim(bprlim, mobaverage, nlstate, p, age, oldm, savm, dnewm, doldm, dsavm, ftolpl, ncvyearp, k); */
1.219 brouard 8122: bprevalim(bprlim, mobaverage, nlstate, p, age, ftolpl, ncvyearp, k);
1.218 brouard 8123: }else if (mobilavproj == 0){
1.219 brouard 8124: 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);
8125: 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);
8126: exit(1);
1.218 brouard 8127: }else{
1.219 brouard 8128: /* bprevalim(bprlim, probs, nlstate, p, age, oldm, savm, dnewm, doldm, dsavm, ftolpl, ncvyearp, k); */
8129: bprevalim(bprlim, probs, nlstate, p, age, ftolpl, ncvyearp, k);
1.218 brouard 8130: }
8131: fprintf(ficresplb,"%.0f ",age );
8132: for(j=1;j<=cptcoveff;j++)
1.219 brouard 8133: fprintf(ficresplb,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
1.218 brouard 8134: tot=0.;
8135: for(i=1; i<=nlstate;i++){
1.219 brouard 8136: tot += bprlim[i][i];
8137: fprintf(ficresplb," %.5f", bprlim[i][i]);
1.218 brouard 8138: }
8139: fprintf(ficresplb," %.3f %d\n", tot, *ncvyearp);
8140: } /* Age */
8141: /* was end of cptcod */
8142: } /* cptcov */
8143:
8144: /* hBijx(p, bage, fage); */
8145: /* fclose(ficrespijb); */
8146:
8147: return 0;
1.217 brouard 8148: }
1.218 brouard 8149:
1.180 brouard 8150: int hPijx(double *p, int bage, int fage){
8151: /*------------- h Pij x at various ages ------------*/
8152:
8153: int stepsize;
8154: int agelim;
8155: int hstepm;
8156: int nhstepm;
8157: int h, i, i1, j, k;
8158:
8159: double agedeb;
8160: double ***p3mat;
8161:
1.201 brouard 8162: strcpy(filerespij,"PIJ_"); strcat(filerespij,fileresu);
1.180 brouard 8163: if((ficrespij=fopen(filerespij,"w"))==NULL) {
8164: printf("Problem with Pij resultfile: %s\n", filerespij); return 1;
8165: fprintf(ficlog,"Problem with Pij resultfile: %s\n", filerespij); return 1;
8166: }
8167: printf("Computing pij: result on file '%s' \n", filerespij);
8168: fprintf(ficlog,"Computing pij: result on file '%s' \n", filerespij);
8169:
8170: stepsize=(int) (stepm+YEARM-1)/YEARM;
8171: /*if (stepm<=24) stepsize=2;*/
8172:
8173: agelim=AGESUP;
8174: hstepm=stepsize*YEARM; /* Every year of age */
8175: hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */
1.218 brouard 8176:
1.180 brouard 8177: /* hstepm=1; aff par mois*/
8178: pstamp(ficrespij);
8179: fprintf(ficrespij,"#****** h Pij x Probability to be in state j at age x+h being in i at x ");
8180: i1= pow(2,cptcoveff);
1.218 brouard 8181: /* for(cptcov=1,k=0;cptcov<=i1;cptcov++){ */
8182: /* /\*for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*\/ */
8183: /* k=k+1; */
1.183 brouard 8184: for (k=1; k <= (int) pow(2,cptcoveff); k++){
8185: fprintf(ficrespij,"\n#****** ");
8186: for(j=1;j<=cptcoveff;j++)
1.198 brouard 8187: fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
1.183 brouard 8188: fprintf(ficrespij,"******\n");
8189:
8190: for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */
8191: nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
8192: nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
8193:
8194: /* nhstepm=nhstepm*YEARM; aff par mois*/
1.180 brouard 8195:
1.183 brouard 8196: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
8197: oldm=oldms;savm=savms;
8198: hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
8199: fprintf(ficrespij,"# Cov Agex agex+h hpijx with i,j=");
8200: for(i=1; i<=nlstate;i++)
8201: for(j=1; j<=nlstate+ndeath;j++)
8202: fprintf(ficrespij," %1d-%1d",i,j);
8203: fprintf(ficrespij,"\n");
8204: for (h=0; h<=nhstepm; h++){
8205: /*agedebphstep = agedeb + h*hstepm/YEARM*stepm;*/
8206: fprintf(ficrespij,"%d %3.f %3.f",k, agedeb, agedeb + h*hstepm/YEARM*stepm );
1.180 brouard 8207: for(i=1; i<=nlstate;i++)
8208: for(j=1; j<=nlstate+ndeath;j++)
1.183 brouard 8209: fprintf(ficrespij," %.5f", p3mat[i][j][h]);
1.180 brouard 8210: fprintf(ficrespij,"\n");
8211: }
1.183 brouard 8212: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
8213: fprintf(ficrespij,"\n");
8214: }
1.180 brouard 8215: /*}*/
8216: }
1.218 brouard 8217: return 0;
1.180 brouard 8218: }
1.218 brouard 8219:
8220: int hBijx(double *p, int bage, int fage, double ***prevacurrent){
1.217 brouard 8221: /*------------- h Bij x at various ages ------------*/
8222:
8223: int stepsize;
1.218 brouard 8224: /* int agelim; */
8225: int ageminl;
1.217 brouard 8226: int hstepm;
8227: int nhstepm;
8228: int h, i, i1, j, k;
1.218 brouard 8229:
1.217 brouard 8230: double agedeb;
8231: double ***p3mat;
1.218 brouard 8232:
8233: strcpy(filerespijb,"PIJB_"); strcat(filerespijb,fileresu);
8234: if((ficrespijb=fopen(filerespijb,"w"))==NULL) {
8235: printf("Problem with Pij back resultfile: %s\n", filerespijb); return 1;
8236: fprintf(ficlog,"Problem with Pij back resultfile: %s\n", filerespijb); return 1;
8237: }
8238: printf("Computing pij back: result on file '%s' \n", filerespijb);
8239: fprintf(ficlog,"Computing pij back: result on file '%s' \n", filerespijb);
8240:
8241: stepsize=(int) (stepm+YEARM-1)/YEARM;
8242: /*if (stepm<=24) stepsize=2;*/
1.217 brouard 8243:
1.218 brouard 8244: /* agelim=AGESUP; */
8245: ageminl=30;
8246: hstepm=stepsize*YEARM; /* Every year of age */
8247: hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */
8248:
8249: /* hstepm=1; aff par mois*/
8250: pstamp(ficrespijb);
8251: fprintf(ficrespijb,"#****** h Pij x Back Probability to be in state i at age x-h being in j at x ");
8252: i1= pow(2,cptcoveff);
8253: /* for(cptcov=1,k=0;cptcov<=i1;cptcov++){ */
8254: /* /\*for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*\/ */
8255: /* k=k+1; */
8256: for (k=1; k <= (int) pow(2,cptcoveff); k++){
8257: fprintf(ficrespijb,"\n#****** ");
8258: for(j=1;j<=cptcoveff;j++)
8259: fprintf(ficrespijb,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
8260: fprintf(ficrespijb,"******\n");
1.222 brouard 8261: if(invalidvarcomb[k]){
8262: fprintf(ficrespijb,"\n#Combination (%d) ignored because no cases \n",k);
8263: continue;
8264: }
1.218 brouard 8265:
8266: /* for (agedeb=fage; agedeb>=bage; agedeb--){ /\* If stepm=6 months *\/ */
8267: for (agedeb=bage; agedeb<=fage; agedeb++){ /* If stepm=6 months and estepm=24 (2 years) */
8268: /* nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /\* Typically 20 years = 20*12/6=40 *\/ */
8269: nhstepm=(int) rint((agedeb-ageminl)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
8270: nhstepm = nhstepm/hstepm; /* Typically 40/4=10, because estepm=24 stepm=6 => hstepm=24/6=4 */
8271:
8272: /* nhstepm=nhstepm*YEARM; aff par mois*/
8273:
8274: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
8275: /* oldm=oldms;savm=savms; */
8276: /* hbxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k); */
8277: hbxij(p3mat,nhstepm,agedeb,hstepm,p,prevacurrent,nlstate,stepm, k);
8278: /* hbxij(p3mat,nhstepm,agedeb,hstepm,p,prevacurrent,nlstate,stepm,oldm,savm, dnewm, doldm, dsavm, k); */
8279: fprintf(ficrespijb,"# Cov Agex agex-h hpijx with i,j=");
8280: for(i=1; i<=nlstate;i++)
8281: for(j=1; j<=nlstate+ndeath;j++)
8282: fprintf(ficrespijb," %1d-%1d",i,j);
8283: fprintf(ficrespijb,"\n");
8284: for (h=0; h<=nhstepm; h++){
8285: /*agedebphstep = agedeb + h*hstepm/YEARM*stepm;*/
8286: fprintf(ficrespijb,"%d %3.f %3.f",k, agedeb, agedeb - h*hstepm/YEARM*stepm );
8287: /* fprintf(ficrespijb,"%d %3.f %3.f",k, agedeb, agedeb + h*hstepm/YEARM*stepm ); */
1.217 brouard 8288: for(i=1; i<=nlstate;i++)
8289: for(j=1; j<=nlstate+ndeath;j++)
1.218 brouard 8290: fprintf(ficrespijb," %.5f", p3mat[i][j][h]);
1.217 brouard 8291: fprintf(ficrespijb,"\n");
8292: }
1.218 brouard 8293: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
8294: fprintf(ficrespijb,"\n");
1.217 brouard 8295: }
1.218 brouard 8296: /*}*/
8297: }
8298: return 0;
8299: } /* hBijx */
1.217 brouard 8300:
1.180 brouard 8301:
1.136 brouard 8302: /***********************************************/
8303: /**************** Main Program *****************/
8304: /***********************************************/
8305:
8306: int main(int argc, char *argv[])
8307: {
8308: #ifdef GSL
8309: const gsl_multimin_fminimizer_type *T;
8310: size_t iteri = 0, it;
8311: int rval = GSL_CONTINUE;
8312: int status = GSL_SUCCESS;
8313: double ssval;
8314: #endif
8315: int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav);
1.164 brouard 8316: int i,j, k, n=MAXN,iter=0,m,size=100, cptcod;
1.209 brouard 8317: int ncvyear=0; /* Number of years needed for the period prevalence to converge */
1.164 brouard 8318: int jj, ll, li, lj, lk;
1.136 brouard 8319: int numlinepar=0; /* Current linenumber of parameter file */
1.197 brouard 8320: int num_filled;
1.136 brouard 8321: int itimes;
8322: int NDIM=2;
8323: int vpopbased=0;
8324:
1.164 brouard 8325: char ca[32], cb[32];
1.136 brouard 8326: /* FILE *fichtm; *//* Html File */
8327: /* FILE *ficgp;*/ /*Gnuplot File */
8328: struct stat info;
1.191 brouard 8329: double agedeb=0.;
1.194 brouard 8330:
8331: double ageminpar=AGEOVERFLOW,agemin=AGEOVERFLOW, agemaxpar=-AGEOVERFLOW, agemax=-AGEOVERFLOW;
1.219 brouard 8332: double ageminout=-AGEOVERFLOW,agemaxout=AGEOVERFLOW; /* Smaller Age range redefined after movingaverage */
1.136 brouard 8333:
1.165 brouard 8334: double fret;
1.191 brouard 8335: double dum=0.; /* Dummy variable */
1.136 brouard 8336: double ***p3mat;
1.218 brouard 8337: /* double ***mobaverage; */
1.164 brouard 8338:
8339: char line[MAXLINE];
1.197 brouard 8340: char path[MAXLINE],pathc[MAXLINE],pathcd[MAXLINE],pathtot[MAXLINE];
8341:
8342: char model[MAXLINE], modeltemp[MAXLINE];
1.136 brouard 8343: char pathr[MAXLINE], pathimach[MAXLINE];
1.164 brouard 8344: char *tok, *val; /* pathtot */
1.136 brouard 8345: int firstobs=1, lastobs=10;
1.195 brouard 8346: int c, h , cpt, c2;
1.191 brouard 8347: int jl=0;
8348: int i1, j1, jk, stepsize=0;
1.194 brouard 8349: int count=0;
8350:
1.164 brouard 8351: int *tab;
1.136 brouard 8352: int mobilavproj=0 , prevfcast=0 ; /* moving average of prev, If prevfcast=1 prevalence projection */
1.217 brouard 8353: int backcast=0;
1.136 brouard 8354: int mobilav=0,popforecast=0;
1.191 brouard 8355: int hstepm=0, nhstepm=0;
1.136 brouard 8356: int agemortsup;
8357: float sumlpop=0.;
8358: double jprev1=1, mprev1=1,anprev1=2000,jprev2=1, mprev2=1,anprev2=2000;
8359: double jpyram=1, mpyram=1,anpyram=2000,jpyram1=1, mpyram1=1,anpyram1=2000;
8360:
1.191 brouard 8361: double bage=0, fage=110., age, agelim=0., agebase=0.;
1.136 brouard 8362: double ftolpl=FTOL;
8363: double **prlim;
1.217 brouard 8364: double **bprlim;
1.136 brouard 8365: double ***param; /* Matrix of parameters */
8366: double *p;
8367: double **matcov; /* Matrix of covariance */
1.203 brouard 8368: double **hess; /* Hessian matrix */
1.136 brouard 8369: double ***delti3; /* Scale */
8370: double *delti; /* Scale */
8371: double ***eij, ***vareij;
8372: double **varpl; /* Variances of prevalence limits by age */
8373: double *epj, vepp;
1.164 brouard 8374:
1.136 brouard 8375: double dateprev1, dateprev2,jproj1=1,mproj1=1,anproj1=2000,jproj2=1,mproj2=1,anproj2=2000;
1.217 brouard 8376: double jback1=1,mback1=1,anback1=2000,jback2=1,mback2=1,anback2=2000;
8377:
1.136 brouard 8378: double **ximort;
1.145 brouard 8379: char *alph[]={"a","a","b","c","d","e"}, str[4]="1234";
1.136 brouard 8380: int *dcwave;
8381:
1.164 brouard 8382: char z[1]="c";
1.136 brouard 8383:
8384: /*char *strt;*/
8385: char strtend[80];
1.126 brouard 8386:
1.164 brouard 8387:
1.126 brouard 8388: /* setlocale (LC_ALL, ""); */
8389: /* bindtextdomain (PACKAGE, LOCALEDIR); */
8390: /* textdomain (PACKAGE); */
8391: /* setlocale (LC_CTYPE, ""); */
8392: /* setlocale (LC_MESSAGES, ""); */
8393:
8394: /* gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */
1.157 brouard 8395: rstart_time = time(NULL);
8396: /* (void) gettimeofday(&start_time,&tzp);*/
8397: start_time = *localtime(&rstart_time);
1.126 brouard 8398: curr_time=start_time;
1.157 brouard 8399: /*tml = *localtime(&start_time.tm_sec);*/
8400: /* strcpy(strstart,asctime(&tml)); */
8401: strcpy(strstart,asctime(&start_time));
1.126 brouard 8402:
8403: /* printf("Localtime (at start)=%s",strstart); */
1.157 brouard 8404: /* tp.tm_sec = tp.tm_sec +86400; */
8405: /* tm = *localtime(&start_time.tm_sec); */
1.126 brouard 8406: /* tmg.tm_year=tmg.tm_year +dsign*dyear; */
8407: /* tmg.tm_mon=tmg.tm_mon +dsign*dmonth; */
8408: /* tmg.tm_hour=tmg.tm_hour + 1; */
1.157 brouard 8409: /* tp.tm_sec = mktime(&tmg); */
1.126 brouard 8410: /* strt=asctime(&tmg); */
8411: /* printf("Time(after) =%s",strstart); */
8412: /* (void) time (&time_value);
8413: * printf("time=%d,t-=%d\n",time_value,time_value-86400);
8414: * tm = *localtime(&time_value);
8415: * strstart=asctime(&tm);
8416: * printf("tim_value=%d,asctime=%s\n",time_value,strstart);
8417: */
8418:
8419: nberr=0; /* Number of errors and warnings */
8420: nbwarn=0;
1.184 brouard 8421: #ifdef WIN32
8422: _getcwd(pathcd, size);
8423: #else
1.126 brouard 8424: getcwd(pathcd, size);
1.184 brouard 8425: #endif
1.191 brouard 8426: syscompilerinfo(0);
1.196 brouard 8427: printf("\nIMaCh version %s, %s\n%s",version, copyright, fullversion);
1.126 brouard 8428: if(argc <=1){
8429: printf("\nEnter the parameter file name: ");
1.205 brouard 8430: if(!fgets(pathr,FILENAMELENGTH,stdin)){
8431: printf("ERROR Empty parameter file name\n");
8432: goto end;
8433: }
1.126 brouard 8434: i=strlen(pathr);
8435: if(pathr[i-1]=='\n')
8436: pathr[i-1]='\0';
1.156 brouard 8437: i=strlen(pathr);
1.205 brouard 8438: if(i >= 1 && pathr[i-1]==' ') {/* This may happen when dragging on oS/X! */
1.156 brouard 8439: pathr[i-1]='\0';
1.205 brouard 8440: }
8441: i=strlen(pathr);
8442: if( i==0 ){
8443: printf("ERROR Empty parameter file name\n");
8444: goto end;
8445: }
8446: for (tok = pathr; tok != NULL; ){
1.126 brouard 8447: printf("Pathr |%s|\n",pathr);
8448: while ((val = strsep(&tok, "\"" )) != NULL && *val == '\0');
8449: printf("val= |%s| pathr=%s\n",val,pathr);
8450: strcpy (pathtot, val);
8451: if(pathr[0] == '\0') break; /* Dirty */
8452: }
8453: }
8454: else{
8455: strcpy(pathtot,argv[1]);
8456: }
8457: /*if(getcwd(pathcd, MAXLINE)!= NULL)printf ("Error pathcd\n");*/
8458: /*cygwin_split_path(pathtot,path,optionfile);
8459: printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/
8460: /* cutv(path,optionfile,pathtot,'\\');*/
8461:
8462: /* Split argv[0], imach program to get pathimach */
8463: printf("\nargv[0]=%s argv[1]=%s, \n",argv[0],argv[1]);
8464: split(argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
8465: printf("\nargv[0]=%s pathimach=%s, \noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
8466: /* strcpy(pathimach,argv[0]); */
8467: /* Split argv[1]=pathtot, parameter file name to get path, optionfile, extension and name */
8468: split(pathtot,path,optionfile,optionfilext,optionfilefiname);
8469: printf("\npathtot=%s,\npath=%s,\noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
1.184 brouard 8470: #ifdef WIN32
8471: _chdir(path); /* Can be a relative path */
8472: if(_getcwd(pathcd,MAXLINE) > 0) /* So pathcd is the full path */
8473: #else
1.126 brouard 8474: chdir(path); /* Can be a relative path */
1.184 brouard 8475: if (getcwd(pathcd, MAXLINE) > 0) /* So pathcd is the full path */
8476: #endif
8477: printf("Current directory %s!\n",pathcd);
1.126 brouard 8478: strcpy(command,"mkdir ");
8479: strcat(command,optionfilefiname);
8480: if((outcmd=system(command)) != 0){
1.169 brouard 8481: printf("Directory already exists (or can't create it) %s%s, err=%d\n",path,optionfilefiname,outcmd);
1.126 brouard 8482: /* fprintf(ficlog,"Problem creating directory %s%s\n",path,optionfilefiname); */
8483: /* fclose(ficlog); */
8484: /* exit(1); */
8485: }
8486: /* if((imk=mkdir(optionfilefiname))<0){ */
8487: /* perror("mkdir"); */
8488: /* } */
8489:
8490: /*-------- arguments in the command line --------*/
8491:
1.186 brouard 8492: /* Main Log file */
1.126 brouard 8493: strcat(filelog, optionfilefiname);
8494: strcat(filelog,".log"); /* */
8495: if((ficlog=fopen(filelog,"w"))==NULL) {
8496: printf("Problem with logfile %s\n",filelog);
8497: goto end;
8498: }
8499: fprintf(ficlog,"Log filename:%s\n",filelog);
1.197 brouard 8500: fprintf(ficlog,"Version %s %s",version,fullversion);
1.126 brouard 8501: fprintf(ficlog,"\nEnter the parameter file name: \n");
8502: fprintf(ficlog,"pathimach=%s\npathtot=%s\n\
8503: path=%s \n\
8504: optionfile=%s\n\
8505: optionfilext=%s\n\
1.156 brouard 8506: optionfilefiname='%s'\n",pathimach,pathtot,path,optionfile,optionfilext,optionfilefiname);
1.126 brouard 8507:
1.197 brouard 8508: syscompilerinfo(1);
1.167 brouard 8509:
1.126 brouard 8510: printf("Local time (at start):%s",strstart);
8511: fprintf(ficlog,"Local time (at start): %s",strstart);
8512: fflush(ficlog);
8513: /* (void) gettimeofday(&curr_time,&tzp); */
1.157 brouard 8514: /* printf("Elapsed time %d\n", asc_diff_time(curr_time.tm_sec-start_time.tm_sec,tmpout)); */
1.126 brouard 8515:
8516: /* */
8517: strcpy(fileres,"r");
8518: strcat(fileres, optionfilefiname);
1.201 brouard 8519: strcat(fileresu, optionfilefiname); /* Without r in front */
1.126 brouard 8520: strcat(fileres,".txt"); /* Other files have txt extension */
1.201 brouard 8521: strcat(fileresu,".txt"); /* Other files have txt extension */
1.126 brouard 8522:
1.186 brouard 8523: /* Main ---------arguments file --------*/
1.126 brouard 8524:
8525: if((ficpar=fopen(optionfile,"r"))==NULL) {
1.155 brouard 8526: printf("Problem with optionfile '%s' with errno='%s'\n",optionfile,strerror(errno));
8527: fprintf(ficlog,"Problem with optionfile '%s' with errno='%s'\n",optionfile,strerror(errno));
1.126 brouard 8528: fflush(ficlog);
1.149 brouard 8529: /* goto end; */
8530: exit(70);
1.126 brouard 8531: }
8532:
8533:
8534:
8535: strcpy(filereso,"o");
1.201 brouard 8536: strcat(filereso,fileresu);
1.126 brouard 8537: if((ficparo=fopen(filereso,"w"))==NULL) { /* opened on subdirectory */
8538: printf("Problem with Output resultfile: %s\n", filereso);
8539: fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso);
8540: fflush(ficlog);
8541: goto end;
8542: }
8543:
8544: /* Reads comments: lines beginning with '#' */
8545: numlinepar=0;
1.197 brouard 8546:
8547: /* First parameter line */
8548: while(fgets(line, MAXLINE, ficpar)) {
8549: /* If line starts with a # it is a comment */
8550: if (line[0] == '#') {
8551: numlinepar++;
8552: fputs(line,stdout);
8553: fputs(line,ficparo);
8554: fputs(line,ficlog);
8555: continue;
8556: }else
8557: break;
8558: }
8559: if((num_filled=sscanf(line,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\n", \
8560: title, datafile, &lastobs, &firstpass,&lastpass)) !=EOF){
8561: if (num_filled != 5) {
8562: printf("Should be 5 parameters\n");
8563: }
1.126 brouard 8564: numlinepar++;
1.197 brouard 8565: printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\n", title, datafile, lastobs, firstpass,lastpass);
8566: }
8567: /* Second parameter line */
8568: while(fgets(line, MAXLINE, ficpar)) {
8569: /* If line starts with a # it is a comment */
8570: if (line[0] == '#') {
8571: numlinepar++;
8572: fputs(line,stdout);
8573: fputs(line,ficparo);
8574: fputs(line,ficlog);
8575: continue;
8576: }else
8577: break;
8578: }
1.223 ! brouard 8579: if((num_filled=sscanf(line,"ftol=%lf stepm=%d ncovcol=%d nqv=%d ntv=%d nqtv=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\n", \
! 8580: &ftol, &stepm, &ncovcol, &nqv, &ntv, &nqtv, &nlstate, &ndeath, &maxwav, &mle, &weightopt)) !=EOF){
! 8581: if (num_filled != 11) {
! 8582: printf("Not 11 parameters, for example:ftol=1.e-8 stepm=12 ncovcol=2 nqv=1 ntv=2 nqtv=1 nlstate=2 ndeath=1 maxwav=3 mle=1 weight=1\n");
1.209 brouard 8583: printf("but line=%s\n",line);
1.197 brouard 8584: }
1.223 ! brouard 8585: printf("ftol=%e stepm=%d ncovcol=%d nqv=%d ntv=%d nqtv=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\n",ftol, stepm, ncovcol, nqv, ntv, nqtv, nlstate, ndeath, maxwav, mle, weightopt);
1.126 brouard 8586: }
1.203 brouard 8587: /* ftolpl=6*ftol*1.e5; /\* 6.e-3 make convergences in less than 80 loops for the prevalence limit *\/ */
1.209 brouard 8588: /*ftolpl=6.e-4; *//* 6.e-3 make convergences in less than 80 loops for the prevalence limit */
1.197 brouard 8589: /* Third parameter line */
8590: while(fgets(line, MAXLINE, ficpar)) {
8591: /* If line starts with a # it is a comment */
8592: if (line[0] == '#') {
8593: numlinepar++;
8594: fputs(line,stdout);
8595: fputs(line,ficparo);
8596: fputs(line,ficlog);
8597: continue;
8598: }else
8599: break;
8600: }
1.201 brouard 8601: if((num_filled=sscanf(line,"model=1+age%[^.\n]", model)) !=EOF){
8602: if (num_filled == 0)
8603: model[0]='\0';
8604: else if (num_filled != 1){
1.197 brouard 8605: printf("ERROR %d: Model should be at minimum 'model=1+age.' %s\n",num_filled, line);
8606: fprintf(ficlog,"ERROR %d: Model should be at minimum 'model=1+age.' %s\n",num_filled, line);
8607: model[0]='\0';
8608: goto end;
8609: }
8610: else{
8611: if (model[0]=='+'){
8612: for(i=1; i<=strlen(model);i++)
8613: modeltemp[i-1]=model[i];
1.201 brouard 8614: strcpy(model,modeltemp);
1.197 brouard 8615: }
8616: }
1.199 brouard 8617: /* printf(" model=1+age%s modeltemp= %s, model=%s\n",model, modeltemp, model);fflush(stdout); */
1.203 brouard 8618: printf("model=1+age+%s\n",model);fflush(stdout);
1.197 brouard 8619: }
8620: /* 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); */
8621: /* numlinepar=numlinepar+3; /\* In general *\/ */
8622: /* printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=1+age+%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate,ndeath, maxwav, mle, weightopt,model); */
1.223 ! brouard 8623: fprintf(ficparo,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nqv=%d ntv=%d nqtv=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=1+age+%s.\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol, nqv, ntv, nqtv, nlstate,ndeath,maxwav, mle, weightopt,model);
! 8624: fprintf(ficlog,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nqv=%d ntv=%d nqtv=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=1+age+%s.\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol, nqv, ntv, nqtv, nlstate,ndeath,maxwav, mle, weightopt,model);
1.126 brouard 8625: fflush(ficlog);
1.190 brouard 8626: /* if(model[0]=='#'|| model[0]== '\0'){ */
8627: if(model[0]=='#'){
1.187 brouard 8628: printf("Error in 'model' line: model should start with 'model=1+age+' and end with '.' \n \
8629: 'model=1+age+.' or 'model=1+age+V1.' or 'model=1+age+age*age+V1+V1*age.' or \n \
8630: 'model=1+age+V1+V2.' or 'model=1+age+V1+V2+V1*V2.' etc. \n"); \
8631: if(mle != -1){
8632: printf("Fix the model line and run imach with mle=-1 to get a correct template of the parameter file.\n");
8633: exit(1);
8634: }
8635: }
1.126 brouard 8636: while((c=getc(ficpar))=='#' && c!= EOF){
8637: ungetc(c,ficpar);
8638: fgets(line, MAXLINE, ficpar);
8639: numlinepar++;
1.195 brouard 8640: if(line[1]=='q'){ /* This #q will quit imach (the answer is q) */
8641: z[0]=line[1];
8642: }
8643: /* printf("****line [1] = %c \n",line[1]); */
1.141 brouard 8644: fputs(line, stdout);
8645: //puts(line);
1.126 brouard 8646: fputs(line,ficparo);
8647: fputs(line,ficlog);
8648: }
8649: ungetc(c,ficpar);
8650:
8651:
1.145 brouard 8652: covar=matrix(0,NCOVMAX,1,n); /**< used in readdata */
1.223 ! brouard 8653: coqvar=matrix(1,nqv,1,n); /**< used in readdata */
! 8654: cotvar=ma3x(1,maxwav,1,ntv,1,n); /**< used in readdata */
! 8655: cotqvar=ma3x(1,maxwav,1,ntqv,1,n); /**< used in readdata */
1.136 brouard 8656: cptcovn=0; /*Number of covariates, i.e. number of '+' in model statement plus one, indepently of n in Vn*/
8657: /* v1+v2+v3+v2*v4+v5*age makes cptcovn = 5
8658: v1+v2*age+v2*v3 makes cptcovn = 3
8659: */
8660: if (strlen(model)>1)
1.187 brouard 8661: 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 8662: else
1.187 brouard 8663: ncovmodel=2; /* Constant and age */
1.133 brouard 8664: nforce= (nlstate+ndeath-1)*nlstate; /* Number of forces ij from state i to j */
8665: npar= nforce*ncovmodel; /* Number of parameters like aij*/
1.131 brouard 8666: if(npar >MAXPARM || nlstate >NLSTATEMAX || ndeath >NDEATHMAX || ncovmodel>NCOVMAX){
8667: 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);
8668: 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);
8669: fflush(stdout);
8670: fclose (ficlog);
8671: goto end;
8672: }
1.126 brouard 8673: delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
8674: delti=delti3[1][1];
8675: /*delti=vector(1,npar); *//* Scale of each paramater (output from hesscov)*/
8676: if(mle==-1){ /* Print a wizard for help writing covariance matrix */
8677: prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
1.191 brouard 8678: printf(" You chose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
8679: fprintf(ficlog," You chose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
1.126 brouard 8680: free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
8681: fclose (ficparo);
8682: fclose (ficlog);
8683: goto end;
8684: exit(0);
1.220 brouard 8685: } else if(mle==-5) { /* Main Wizard */
1.126 brouard 8686: prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
1.192 brouard 8687: printf(" You chose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
8688: fprintf(ficlog," You chose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
1.126 brouard 8689: param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
8690: matcov=matrix(1,npar,1,npar);
1.203 brouard 8691: hess=matrix(1,npar,1,npar);
1.220 brouard 8692: } else{ /* Begin of mle != -1 or -5 */
1.145 brouard 8693: /* Read guessed parameters */
1.126 brouard 8694: /* Reads comments: lines beginning with '#' */
8695: while((c=getc(ficpar))=='#' && c!= EOF){
8696: ungetc(c,ficpar);
8697: fgets(line, MAXLINE, ficpar);
8698: numlinepar++;
1.141 brouard 8699: fputs(line,stdout);
1.126 brouard 8700: fputs(line,ficparo);
8701: fputs(line,ficlog);
8702: }
8703: ungetc(c,ficpar);
8704:
8705: param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
8706: for(i=1; i <=nlstate; i++){
1.220 brouard 8707: j=0;
1.126 brouard 8708: for(jj=1; jj <=nlstate+ndeath; jj++){
1.220 brouard 8709: if(jj==i) continue;
8710: j++;
8711: fscanf(ficpar,"%1d%1d",&i1,&j1);
8712: if ((i1 != i) || (j1 != jj)){
8713: printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n \
1.126 brouard 8714: It might be a problem of design; if ncovcol and the model are correct\n \
8715: run imach with mle=-1 to get a correct template of the parameter file.\n",numlinepar, i,j, i1, j1);
1.220 brouard 8716: exit(1);
8717: }
8718: fprintf(ficparo,"%1d%1d",i1,j1);
8719: if(mle==1)
8720: printf("%1d%1d",i,jj);
8721: fprintf(ficlog,"%1d%1d",i,jj);
8722: for(k=1; k<=ncovmodel;k++){
8723: fscanf(ficpar," %lf",¶m[i][j][k]);
8724: if(mle==1){
8725: printf(" %lf",param[i][j][k]);
8726: fprintf(ficlog," %lf",param[i][j][k]);
8727: }
8728: else
8729: fprintf(ficlog," %lf",param[i][j][k]);
8730: fprintf(ficparo," %lf",param[i][j][k]);
8731: }
8732: fscanf(ficpar,"\n");
8733: numlinepar++;
8734: if(mle==1)
8735: printf("\n");
8736: fprintf(ficlog,"\n");
8737: fprintf(ficparo,"\n");
1.126 brouard 8738: }
8739: }
8740: fflush(ficlog);
8741:
1.145 brouard 8742: /* Reads scales values */
1.126 brouard 8743: p=param[1][1];
8744:
8745: /* Reads comments: lines beginning with '#' */
8746: while((c=getc(ficpar))=='#' && c!= EOF){
8747: ungetc(c,ficpar);
8748: fgets(line, MAXLINE, ficpar);
8749: numlinepar++;
1.141 brouard 8750: fputs(line,stdout);
1.126 brouard 8751: fputs(line,ficparo);
8752: fputs(line,ficlog);
8753: }
8754: ungetc(c,ficpar);
8755:
8756: for(i=1; i <=nlstate; i++){
8757: for(j=1; j <=nlstate+ndeath-1; j++){
1.220 brouard 8758: fscanf(ficpar,"%1d%1d",&i1,&j1);
8759: if ( (i1-i) * (j1-j) != 0){
8760: printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n",numlinepar, i,j, i1, j1);
8761: exit(1);
8762: }
8763: printf("%1d%1d",i,j);
8764: fprintf(ficparo,"%1d%1d",i1,j1);
8765: fprintf(ficlog,"%1d%1d",i1,j1);
8766: for(k=1; k<=ncovmodel;k++){
8767: fscanf(ficpar,"%le",&delti3[i][j][k]);
8768: printf(" %le",delti3[i][j][k]);
8769: fprintf(ficparo," %le",delti3[i][j][k]);
8770: fprintf(ficlog," %le",delti3[i][j][k]);
8771: }
8772: fscanf(ficpar,"\n");
8773: numlinepar++;
8774: printf("\n");
8775: fprintf(ficparo,"\n");
8776: fprintf(ficlog,"\n");
1.126 brouard 8777: }
8778: }
8779: fflush(ficlog);
1.220 brouard 8780:
1.145 brouard 8781: /* Reads covariance matrix */
1.126 brouard 8782: delti=delti3[1][1];
1.220 brouard 8783:
8784:
1.126 brouard 8785: /* 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 8786:
1.126 brouard 8787: /* Reads comments: lines beginning with '#' */
8788: while((c=getc(ficpar))=='#' && c!= EOF){
8789: ungetc(c,ficpar);
8790: fgets(line, MAXLINE, ficpar);
8791: numlinepar++;
1.141 brouard 8792: fputs(line,stdout);
1.126 brouard 8793: fputs(line,ficparo);
8794: fputs(line,ficlog);
8795: }
8796: ungetc(c,ficpar);
1.220 brouard 8797:
1.126 brouard 8798: matcov=matrix(1,npar,1,npar);
1.203 brouard 8799: hess=matrix(1,npar,1,npar);
1.131 brouard 8800: for(i=1; i <=npar; i++)
8801: for(j=1; j <=npar; j++) matcov[i][j]=0.;
1.220 brouard 8802:
1.194 brouard 8803: /* Scans npar lines */
1.126 brouard 8804: for(i=1; i <=npar; i++){
1.194 brouard 8805: count=fscanf(ficpar,"%1d%1d%1d",&i1,&j1,&jk);
8806: if(count != 3){
1.220 brouard 8807: printf("Error! Error in parameter file %s at line %d after line starting with %1d%1d%1d\n\
1.194 brouard 8808: This is probably because your covariance matrix doesn't \n contain exactly %d lines corresponding to your model line '1+age+%s'.\n\
8809: Please run with mle=-1 to get a correct covariance matrix.\n",optionfile,numlinepar, i1,j1,jk, npar, model);
1.220 brouard 8810: fprintf(ficlog,"Error! Error in parameter file %s at line %d after line starting with %1d%1d%1d\n\
1.194 brouard 8811: This is probably because your covariance matrix doesn't \n contain exactly %d lines corresponding to your model line '1+age+%s'.\n\
8812: Please run with mle=-1 to get a correct covariance matrix.\n",optionfile,numlinepar, i1,j1,jk, npar, model);
1.220 brouard 8813: exit(1);
8814: }else{
8815: if(mle==1)
8816: printf("%1d%1d%1d",i1,j1,jk);
8817: }
1.194 brouard 8818: fprintf(ficlog,"%1d%1d%1d",i1,j1,jk);
8819: fprintf(ficparo,"%1d%1d%1d",i1,j1,jk);
1.126 brouard 8820: for(j=1; j <=i; j++){
1.220 brouard 8821: fscanf(ficpar," %le",&matcov[i][j]);
8822: if(mle==1){
8823: printf(" %.5le",matcov[i][j]);
8824: }
8825: fprintf(ficlog," %.5le",matcov[i][j]);
8826: fprintf(ficparo," %.5le",matcov[i][j]);
1.126 brouard 8827: }
8828: fscanf(ficpar,"\n");
8829: numlinepar++;
8830: if(mle==1)
1.220 brouard 8831: printf("\n");
1.126 brouard 8832: fprintf(ficlog,"\n");
8833: fprintf(ficparo,"\n");
8834: }
1.194 brouard 8835: /* End of read covariance matrix npar lines */
1.126 brouard 8836: for(i=1; i <=npar; i++)
8837: for(j=i+1;j<=npar;j++)
1.220 brouard 8838: matcov[i][j]=matcov[j][i];
1.126 brouard 8839:
8840: if(mle==1)
8841: printf("\n");
8842: fprintf(ficlog,"\n");
8843:
8844: fflush(ficlog);
8845:
8846: /*-------- Rewriting parameter file ----------*/
8847: strcpy(rfileres,"r"); /* "Rparameterfile */
8848: strcat(rfileres,optionfilefiname); /* Parameter file first name*/
8849: strcat(rfileres,"."); /* */
8850: strcat(rfileres,optionfilext); /* Other files have txt extension */
8851: if((ficres =fopen(rfileres,"w"))==NULL) {
1.201 brouard 8852: printf("Problem writing new parameter file: %s\n", rfileres);goto end;
8853: fprintf(ficlog,"Problem writing new parameter file: %s\n", rfileres);goto end;
1.126 brouard 8854: }
8855: fprintf(ficres,"#%s\n",version);
8856: } /* End of mle != -3 */
1.218 brouard 8857:
1.186 brouard 8858: /* Main data
8859: */
1.126 brouard 8860: n= lastobs;
8861: num=lvector(1,n);
8862: moisnais=vector(1,n);
8863: annais=vector(1,n);
8864: moisdc=vector(1,n);
8865: andc=vector(1,n);
1.220 brouard 8866: weight=vector(1,n);
1.126 brouard 8867: agedc=vector(1,n);
8868: cod=ivector(1,n);
1.220 brouard 8869: for(i=1;i<=n;i++){
8870: num[i]=0;
8871: moisnais[i]=0;
8872: annais[i]=0;
8873: moisdc[i]=0;
8874: andc[i]=0;
8875: agedc[i]=0;
8876: cod[i]=0;
8877: weight[i]=1.0; /* Equal weights, 1 by default */
8878: }
1.126 brouard 8879: mint=matrix(1,maxwav,1,n);
8880: anint=matrix(1,maxwav,1,n);
1.131 brouard 8881: s=imatrix(1,maxwav+1,1,n); /* s[i][j] health state for wave i and individual j */
1.126 brouard 8882: tab=ivector(1,NCOVMAX);
1.144 brouard 8883: ncodemax=ivector(1,NCOVMAX); /* Number of code per covariate; if O and 1 only, 2**ncov; V1+V2+V3+V4=>16 */
1.192 brouard 8884: 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 8885:
1.136 brouard 8886: /* Reads data from file datafile */
8887: if (readdata(datafile, firstobs, lastobs, &imx)==1)
8888: goto end;
8889:
8890: /* Calculation of the number of parameters from char model */
1.137 brouard 8891: /* modelsav=V2+V1+V4+age*V3 strb=age*V3 stra=V2+V1+V4
8892: k=4 (age*V3) Tvar[k=4]= 3 (from V3) Tag[cptcovage=1]=4
8893: k=3 V4 Tvar[k=3]= 4 (from V4)
8894: k=2 V1 Tvar[k=2]= 1 (from V1)
8895: k=1 Tvar[1]=2 (from V2)
8896: */
8897: Tvar=ivector(1,NCOVMAX); /* Was 15 changed to NCOVMAX. */
8898: /* V2+V1+V4+age*V3 is a model with 4 covariates (3 plus signs).
8899: For each model-covariate stores the data-covariate id. Tvar[1]=2, Tvar[2]=1, Tvar[3]=4,
8900: Tvar[4=age*V3] is 3 and 'age' is recorded in Tage.
8901: */
8902: /* For model-covariate k tells which data-covariate to use but
8903: because this model-covariate is a construction we invent a new column
8904: ncovcol + k1
8905: If already ncovcol=4 and model=V2+V1+V1*V4+age*V3
8906: Tvar[3=V1*V4]=4+1 etc */
1.145 brouard 8907: Tprod=ivector(1,NCOVMAX); /* Gives the position of a product */
1.137 brouard 8908: /* Tprod[k1=1]=3(=V1*V4) for V2+V1+V1*V4+age*V3
8909: if V2+V1+V1*V4+age*V3+V3*V2 TProd[k1=2]=5 (V3*V2)
8910: */
1.145 brouard 8911: Tvaraff=ivector(1,NCOVMAX); /* Unclear */
8912: 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 8913: * For V3*V2 (in V2+V1+V1*V4+age*V3+V3*V2), V3*V2 position is 2nd.
8914: * Tvard[k1=2][1]=3 (V3) Tvard[k1=2][2]=2(V2) */
1.145 brouard 8915: Tage=ivector(1,NCOVMAX); /* Gives the covariate id of covariates associated with age: V2 + V1 + age*V4 + V3*age
1.137 brouard 8916: 4 covariates (3 plus signs)
8917: Tage[1=V3*age]= 4; Tage[2=age*V4] = 3
8918: */
1.136 brouard 8919:
1.186 brouard 8920: /* Main decodemodel */
8921:
1.187 brouard 8922:
1.223 ! brouard 8923: if(decodemodel(model, lastobs) == 1) /* In order to get Tvar[k] V4+V3+V5 p Tvar[1]@3 = {4, 3, 5}*/
1.136 brouard 8924: goto end;
8925:
1.137 brouard 8926: if((double)(lastobs-imx)/(double)imx > 1.10){
8927: nbwarn++;
8928: 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);
8929: 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);
8930: }
1.136 brouard 8931: /* if(mle==1){*/
1.137 brouard 8932: if (weightopt != 1) { /* Maximisation without weights. We can have weights different from 1 but want no weight*/
8933: for(i=1;i<=imx;i++) weight[i]=1.0; /* changed to imx */
1.136 brouard 8934: }
8935:
8936: /*-calculation of age at interview from date of interview and age at death -*/
8937: agev=matrix(1,maxwav,1,imx);
8938:
8939: if(calandcheckages(imx, maxwav, &agemin, &agemax, &nberr, &nbwarn) == 1)
8940: goto end;
8941:
1.126 brouard 8942:
1.136 brouard 8943: agegomp=(int)agemin;
8944: free_vector(moisnais,1,n);
8945: free_vector(annais,1,n);
1.126 brouard 8946: /* free_matrix(mint,1,maxwav,1,n);
8947: free_matrix(anint,1,maxwav,1,n);*/
1.215 brouard 8948: /* free_vector(moisdc,1,n); */
8949: /* free_vector(andc,1,n); */
1.145 brouard 8950: /* */
8951:
1.126 brouard 8952: wav=ivector(1,imx);
1.214 brouard 8953: /* dh=imatrix(1,lastpass-firstpass+1,1,imx); */
8954: /* bh=imatrix(1,lastpass-firstpass+1,1,imx); */
8955: /* mw=imatrix(1,lastpass-firstpass+1,1,imx); */
8956: 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.*/
8957: bh=imatrix(1,lastpass-firstpass+2,1,imx);
8958: mw=imatrix(1,lastpass-firstpass+2,1,imx);
1.126 brouard 8959:
8960: /* Concatenates waves */
1.214 brouard 8961: /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
8962: Death is a valid wave (if date is known).
8963: mw[mi][i] is the number of (mi=1 to wav[i]) effective wave out of mi of individual i
8964: dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
8965: and mw[mi+1][i]. dh depends on stepm.
8966: */
8967:
1.126 brouard 8968: concatwav(wav, dh, bh, mw, s, agedc, agev, firstpass, lastpass, imx, nlstate, stepm);
1.145 brouard 8969: /* */
8970:
1.215 brouard 8971: free_vector(moisdc,1,n);
8972: free_vector(andc,1,n);
8973:
1.126 brouard 8974: /* Routine tricode is to calculate cptcoveff (real number of unique covariates) and to associate covariable number and modality */
8975: nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);
8976: ncodemax[1]=1;
1.145 brouard 8977: Ndum =ivector(-1,NCOVMAX);
1.220 brouard 8978: cptcoveff=0;
8979: if (ncovmodel-nagesqr > 2 ){ /* That is if covariate other than cst, age and age*age */
8980: tricode(&cptcoveff,Tvar,nbcode,imx, Ndum); /**< Fills nbcode[Tvar[j]][l]; */
8981: }
8982:
8983: ncovcombmax=pow(2,cptcoveff);
8984: invalidvarcomb=ivector(1, ncovcombmax);
8985: for(i=1;i<ncovcombmax;i++)
8986: invalidvarcomb[i]=0;
8987:
1.211 brouard 8988: /* Nbcode gives the value of the lth modality (currently 1 to 2) of jth covariate, in
1.186 brouard 8989: V2+V1*age, there are 3 covariates Tvar[2]=1 (V1).*/
1.211 brouard 8990: /* 1 to ncodemax[j] which is the maximum value of this jth covariate */
1.145 brouard 8991:
1.200 brouard 8992: /* codtab=imatrix(1,100,1,10);*/ /* codtab[h,k]=( (h-1) - mod(k-1,2**(k-1) )/2**(k-1) */
1.198 brouard 8993: /*printf(" codtab[1,1],codtab[100,10]=%d,%d\n", codtab[1][1],codtabm(100,10));*/
1.186 brouard 8994: /* codtab gives the value 1 or 2 of the hth combination of k covariates (1 or 2).*/
1.211 brouard 8995: /* nbcode[Tvaraff[j]][codtabm(h,j)]) : if there are only 2 modalities for a covariate j,
8996: * codtabm(h,j) gives its value classified at position h and nbcode gives how it is coded
8997: * (currently 0 or 1) in the data.
8998: * In a loop on h=1 to 2**k, and a loop on j (=1 to k), we get the value of
8999: * corresponding modality (h,j).
9000: */
9001:
1.145 brouard 9002: h=0;
9003: /*if (cptcovn > 0) */
1.126 brouard 9004: m=pow(2,cptcoveff);
9005:
1.144 brouard 9006: /**< codtab(h,k) k = codtab[h,k]=( (h-1) - mod(k-1,2**(k-1) )/2**(k-1) + 1
1.211 brouard 9007: * For k=4 covariates, h goes from 1 to m=2**k
9008: * codtabm(h,k)= (1 & (h-1) >> (k-1)) + 1;
9009: * #define codtabm(h,k) (1 & (h-1) >> (k-1))+1
1.186 brouard 9010: * h\k 1 2 3 4
1.143 brouard 9011: *______________________________
9012: * 1 i=1 1 i=1 1 i=1 1 i=1 1
9013: * 2 2 1 1 1
9014: * 3 i=2 1 2 1 1
9015: * 4 2 2 1 1
9016: * 5 i=3 1 i=2 1 2 1
9017: * 6 2 1 2 1
9018: * 7 i=4 1 2 2 1
9019: * 8 2 2 2 1
1.197 brouard 9020: * 9 i=5 1 i=3 1 i=2 1 2
9021: * 10 2 1 1 2
9022: * 11 i=6 1 2 1 2
9023: * 12 2 2 1 2
9024: * 13 i=7 1 i=4 1 2 2
9025: * 14 2 1 2 2
9026: * 15 i=8 1 2 2 2
9027: * 16 2 2 2 2
1.143 brouard 9028: */
1.212 brouard 9029: /* How to do the opposite? From combination h (=1 to 2**k) how to get the value on the covariates? */
1.211 brouard 9030: /* from h=5 and m, we get then number of covariates k=log(m)/log(2)=4
9031: * and the value of each covariate?
9032: * V1=1, V2=1, V3=2, V4=1 ?
9033: * h-1=4 and 4 is 0100 or reverse 0010, and +1 is 1121 ok.
9034: * h=6, 6-1=5, 5 is 0101, 1010, 2121, V1=2nd, V2=1st, V3=2nd, V4=1st.
9035: * In order to get the real value in the data, we use nbcode
9036: * nbcode[Tvar[3][2nd]]=1 and nbcode[Tvar[4][1]]=0
9037: * We are keeping this crazy system in order to be able (in the future?)
9038: * to have more than 2 values (0 or 1) for a covariate.
9039: * #define codtabm(h,k) (1 & (h-1) >> (k-1))+1
9040: * h=6, k=2? h-1=5=0101, reverse 1010, +1=2121, k=2nd position: value is 1: codtabm(6,2)=1
9041: * bbbbbbbb
9042: * 76543210
9043: * h-1 00000101 (6-1=5)
1.219 brouard 9044: *(h-1)>>(k-1)= 00000010 >> (2-1) = 1 right shift
1.211 brouard 9045: * &
9046: * 1 00000001 (1)
1.219 brouard 9047: * 00000000 = 1 & ((h-1) >> (k-1))
9048: * +1= 00000001 =1
1.211 brouard 9049: *
9050: * h=14, k=3 => h'=h-1=13, k'=k-1=2
9051: * h' 1101 =2^3+2^2+0x2^1+2^0
9052: * >>k' 11
9053: * & 00000001
9054: * = 00000001
9055: * +1 = 00000010=2 = codtabm(14,3)
9056: * Reverse h=6 and m=16?
9057: * cptcoveff=log(16)/log(2)=4 covariate: 6-1=5=0101 reversed=1010 +1=2121 =>V1=2, V2=1, V3=2, V4=1.
9058: * for (j=1 to cptcoveff) Vj=decodtabm(j,h,cptcoveff)
9059: * decodtabm(h,j,cptcoveff)= (((h-1) >> (j-1)) & 1) +1
9060: * decodtabm(h,j,cptcoveff)= (h <= (1<<cptcoveff)?(((h-1) >> (j-1)) & 1) +1 : -1)
9061: * V3=decodtabm(14,3,2**4)=2
9062: * h'=13 1101 =2^3+2^2+0x2^1+2^0
9063: *(h-1) >> (j-1) 0011 =13 >> 2
9064: * &1 000000001
9065: * = 000000001
9066: * +1= 000000010 =2
9067: * 2211
9068: * V1=1+1, V2=0+1, V3=1+1, V4=1+1
9069: * V3=2
1.220 brouard 9070: * codtabm and decodtabm are identical
1.211 brouard 9071: */
9072:
1.145 brouard 9073:
9074: free_ivector(Ndum,-1,NCOVMAX);
9075:
9076:
1.126 brouard 9077:
1.186 brouard 9078: /* Initialisation of ----------- gnuplot -------------*/
1.126 brouard 9079: strcpy(optionfilegnuplot,optionfilefiname);
9080: if(mle==-3)
1.201 brouard 9081: strcat(optionfilegnuplot,"-MORT_");
1.126 brouard 9082: strcat(optionfilegnuplot,".gp");
9083:
9084: if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {
9085: printf("Problem with file %s",optionfilegnuplot);
9086: }
9087: else{
1.204 brouard 9088: fprintf(ficgp,"\n# IMaCh-%s\n", version);
1.126 brouard 9089: fprintf(ficgp,"# %s\n", optionfilegnuplot);
1.141 brouard 9090: //fprintf(ficgp,"set missing 'NaNq'\n");
9091: fprintf(ficgp,"set datafile missing 'NaNq'\n");
1.126 brouard 9092: }
9093: /* fclose(ficgp);*/
1.186 brouard 9094:
9095:
9096: /* Initialisation of --------- index.htm --------*/
1.126 brouard 9097:
9098: strcpy(optionfilehtm,optionfilefiname); /* Main html file */
9099: if(mle==-3)
1.201 brouard 9100: strcat(optionfilehtm,"-MORT_");
1.126 brouard 9101: strcat(optionfilehtm,".htm");
9102: if((fichtm=fopen(optionfilehtm,"w"))==NULL) {
1.131 brouard 9103: printf("Problem with %s \n",optionfilehtm);
9104: exit(0);
1.126 brouard 9105: }
9106:
9107: strcpy(optionfilehtmcov,optionfilefiname); /* Only for matrix of covariance */
9108: strcat(optionfilehtmcov,"-cov.htm");
9109: if((fichtmcov=fopen(optionfilehtmcov,"w"))==NULL) {
9110: printf("Problem with %s \n",optionfilehtmcov), exit(0);
9111: }
9112: else{
9113: fprintf(fichtmcov,"<html><head>\n<title>IMaCh Cov %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
9114: <hr size=\"2\" color=\"#EC5E5E\"> \n\
1.204 brouard 9115: Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=1+age+%s<br>\n",\
1.126 brouard 9116: optionfilehtmcov,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);
9117: }
9118:
1.213 brouard 9119: 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 9120: <hr size=\"2\" color=\"#EC5E5E\"> \n\
9121: <font size=\"2\">IMaCh-%s <br> %s</font> \
1.126 brouard 9122: <hr size=\"2\" color=\"#EC5E5E\"> \n\
1.204 brouard 9123: Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=1+age+%s<br>\n\
1.126 brouard 9124: \n\
9125: <hr size=\"2\" color=\"#EC5E5E\">\
9126: <ul><li><h4>Parameter files</h4>\n\
9127: - Parameter file: <a href=\"%s.%s\">%s.%s</a><br>\n\
9128: - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n\
9129: - Log file of the run: <a href=\"%s\">%s</a><br>\n\
9130: - Gnuplot file name: <a href=\"%s\">%s</a><br>\n\
9131: - Date and time at start: %s</ul>\n",\
9132: optionfilehtm,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model,\
9133: optionfilefiname,optionfilext,optionfilefiname,optionfilext,\
9134: fileres,fileres,\
9135: filelog,filelog,optionfilegnuplot,optionfilegnuplot,strstart);
9136: fflush(fichtm);
9137:
9138: strcpy(pathr,path);
9139: strcat(pathr,optionfilefiname);
1.184 brouard 9140: #ifdef WIN32
9141: _chdir(optionfilefiname); /* Move to directory named optionfile */
9142: #else
1.126 brouard 9143: chdir(optionfilefiname); /* Move to directory named optionfile */
1.184 brouard 9144: #endif
9145:
1.126 brouard 9146:
1.220 brouard 9147: /* Calculates basic frequencies. Computes observed prevalence at single age
9148: and for any valid combination of covariates
1.126 brouard 9149: and prints on file fileres'p'. */
1.220 brouard 9150: freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx, Tvaraff, invalidvarcomb, nbcode, ncodemax,mint,anint,strstart, \
1.223 ! brouard 9151: firstpass, lastpass, stepm, weightopt, model);
1.126 brouard 9152:
9153: fprintf(fichtm,"\n");
9154: fprintf(fichtm,"<br>Total number of observations=%d <br>\n\
9155: Youngest age at first (selected) pass %.2f, oldest age %.2f<br>\n\
9156: Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n",\
9157: imx,agemin,agemax,jmin,jmax,jmean);
9158: pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
1.220 brouard 9159: oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
9160: newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
9161: savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
9162: oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */
1.218 brouard 9163:
1.126 brouard 9164: /* For Powell, parameters are in a vector p[] starting at p[1]
9165: so we point p on param[1][1] so that p[1] maps on param[1][1][1] */
9166: p=param[1][1]; /* *(*(*(param +1)+1)+0) */
9167:
9168: globpr=0; /* To get the number ipmx of contributions and the sum of weights*/
1.186 brouard 9169: /* For mortality only */
1.126 brouard 9170: if (mle==-3){
1.136 brouard 9171: ximort=matrix(1,NDIM,1,NDIM);
1.220 brouard 9172: for(i=1;i<=NDIM;i++)
9173: for(j=1;j<=NDIM;j++)
9174: ximort[i][j]=0.;
1.186 brouard 9175: /* ximort=gsl_matrix_alloc(1,NDIM,1,NDIM); */
1.126 brouard 9176: cens=ivector(1,n);
9177: ageexmed=vector(1,n);
9178: agecens=vector(1,n);
9179: dcwave=ivector(1,n);
1.223 ! brouard 9180:
1.126 brouard 9181: for (i=1; i<=imx; i++){
9182: dcwave[i]=-1;
9183: for (m=firstpass; m<=lastpass; m++)
1.218 brouard 9184: if (s[m][i]>nlstate) {
9185: dcwave[i]=m;
9186: /* printf("i=%d j=%d s=%d dcwave=%d\n",i,j, s[j][i],dcwave[i]);*/
9187: break;
9188: }
1.126 brouard 9189: }
1.218 brouard 9190:
1.126 brouard 9191: for (i=1; i<=imx; i++) {
9192: if (wav[i]>0){
1.218 brouard 9193: ageexmed[i]=agev[mw[1][i]][i];
9194: j=wav[i];
9195: agecens[i]=1.;
9196:
9197: if (ageexmed[i]> 1 && wav[i] > 0){
9198: agecens[i]=agev[mw[j][i]][i];
9199: cens[i]= 1;
9200: }else if (ageexmed[i]< 1)
9201: cens[i]= -1;
9202: if (agedc[i]< AGESUP && agedc[i]>1 && dcwave[i]>firstpass && dcwave[i]<=lastpass)
9203: cens[i]=0 ;
1.126 brouard 9204: }
9205: else cens[i]=-1;
9206: }
9207:
9208: for (i=1;i<=NDIM;i++) {
9209: for (j=1;j<=NDIM;j++)
1.218 brouard 9210: ximort[i][j]=(i == j ? 1.0 : 0.0);
1.126 brouard 9211: }
9212:
1.145 brouard 9213: /*p[1]=0.0268; p[NDIM]=0.083;*/
1.126 brouard 9214: /*printf("%lf %lf", p[1], p[2]);*/
9215:
9216:
1.136 brouard 9217: #ifdef GSL
9218: printf("GSL optimization\n"); fprintf(ficlog,"Powell\n");
1.162 brouard 9219: #else
1.126 brouard 9220: printf("Powell\n"); fprintf(ficlog,"Powell\n");
1.136 brouard 9221: #endif
1.201 brouard 9222: strcpy(filerespow,"POW-MORT_");
9223: strcat(filerespow,fileresu);
1.126 brouard 9224: if((ficrespow=fopen(filerespow,"w"))==NULL) {
9225: printf("Problem with resultfile: %s\n", filerespow);
9226: fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
9227: }
1.136 brouard 9228: #ifdef GSL
9229: fprintf(ficrespow,"# GSL optimization\n# iter -2*LL");
1.162 brouard 9230: #else
1.126 brouard 9231: fprintf(ficrespow,"# Powell\n# iter -2*LL");
1.136 brouard 9232: #endif
1.126 brouard 9233: /* for (i=1;i<=nlstate;i++)
9234: for(j=1;j<=nlstate+ndeath;j++)
9235: if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
9236: */
9237: fprintf(ficrespow,"\n");
1.136 brouard 9238: #ifdef GSL
9239: /* gsl starts here */
9240: T = gsl_multimin_fminimizer_nmsimplex;
9241: gsl_multimin_fminimizer *sfm = NULL;
9242: gsl_vector *ss, *x;
9243: gsl_multimin_function minex_func;
9244:
9245: /* Initial vertex size vector */
9246: ss = gsl_vector_alloc (NDIM);
9247:
9248: if (ss == NULL){
9249: GSL_ERROR_VAL ("failed to allocate space for ss", GSL_ENOMEM, 0);
9250: }
9251: /* Set all step sizes to 1 */
9252: gsl_vector_set_all (ss, 0.001);
9253:
9254: /* Starting point */
1.126 brouard 9255:
1.136 brouard 9256: x = gsl_vector_alloc (NDIM);
9257:
9258: if (x == NULL){
9259: gsl_vector_free(ss);
9260: GSL_ERROR_VAL ("failed to allocate space for x", GSL_ENOMEM, 0);
9261: }
9262:
9263: /* Initialize method and iterate */
9264: /* p[1]=0.0268; p[NDIM]=0.083; */
1.186 brouard 9265: /* gsl_vector_set(x, 0, 0.0268); */
9266: /* gsl_vector_set(x, 1, 0.083); */
1.136 brouard 9267: gsl_vector_set(x, 0, p[1]);
9268: gsl_vector_set(x, 1, p[2]);
9269:
9270: minex_func.f = &gompertz_f;
9271: minex_func.n = NDIM;
9272: minex_func.params = (void *)&p; /* ??? */
9273:
9274: sfm = gsl_multimin_fminimizer_alloc (T, NDIM);
9275: gsl_multimin_fminimizer_set (sfm, &minex_func, x, ss);
9276:
9277: printf("Iterations beginning .....\n\n");
9278: printf("Iter. # Intercept Slope -Log Likelihood Simplex size\n");
9279:
9280: iteri=0;
9281: while (rval == GSL_CONTINUE){
9282: iteri++;
9283: status = gsl_multimin_fminimizer_iterate(sfm);
9284:
9285: if (status) printf("error: %s\n", gsl_strerror (status));
9286: fflush(0);
9287:
9288: if (status)
9289: break;
9290:
9291: rval = gsl_multimin_test_size (gsl_multimin_fminimizer_size (sfm), 1e-6);
9292: ssval = gsl_multimin_fminimizer_size (sfm);
9293:
9294: if (rval == GSL_SUCCESS)
9295: printf ("converged to a local maximum at\n");
9296:
9297: printf("%5d ", iteri);
9298: for (it = 0; it < NDIM; it++){
9299: printf ("%10.5f ", gsl_vector_get (sfm->x, it));
9300: }
9301: printf("f() = %-10.5f ssize = %.7f\n", sfm->fval, ssval);
9302: }
9303:
9304: printf("\n\n Please note: Program should be run many times with varying starting points to detemine global maximum\n\n");
9305:
9306: gsl_vector_free(x); /* initial values */
9307: gsl_vector_free(ss); /* inital step size */
9308: for (it=0; it<NDIM; it++){
9309: p[it+1]=gsl_vector_get(sfm->x,it);
9310: fprintf(ficrespow," %.12lf", p[it]);
9311: }
9312: gsl_multimin_fminimizer_free (sfm); /* p *(sfm.x.data) et p *(sfm.x.data+1) */
9313: #endif
9314: #ifdef POWELL
9315: powell(p,ximort,NDIM,ftol,&iter,&fret,gompertz);
9316: #endif
1.126 brouard 9317: fclose(ficrespow);
9318:
1.203 brouard 9319: hesscov(matcov, hess, p, NDIM, delti, 1e-4, gompertz);
1.126 brouard 9320:
9321: for(i=1; i <=NDIM; i++)
9322: for(j=i+1;j<=NDIM;j++)
1.220 brouard 9323: matcov[i][j]=matcov[j][i];
1.126 brouard 9324:
9325: printf("\nCovariance matrix\n ");
1.203 brouard 9326: fprintf(ficlog,"\nCovariance matrix\n ");
1.126 brouard 9327: for(i=1; i <=NDIM; i++) {
9328: for(j=1;j<=NDIM;j++){
1.220 brouard 9329: printf("%f ",matcov[i][j]);
9330: fprintf(ficlog,"%f ",matcov[i][j]);
1.126 brouard 9331: }
1.203 brouard 9332: printf("\n "); fprintf(ficlog,"\n ");
1.126 brouard 9333: }
9334:
9335: printf("iter=%d MLE=%f Eq=%lf*exp(%lf*(age-%d))\n",iter,-gompertz(p),p[1],p[2],agegomp);
1.193 brouard 9336: for (i=1;i<=NDIM;i++) {
1.126 brouard 9337: printf("%f [%f ; %f]\n",p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
1.193 brouard 9338: fprintf(ficlog,"%f [%f ; %f]\n",p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
9339: }
1.126 brouard 9340: lsurv=vector(1,AGESUP);
9341: lpop=vector(1,AGESUP);
9342: tpop=vector(1,AGESUP);
9343: lsurv[agegomp]=100000;
9344:
9345: for (k=agegomp;k<=AGESUP;k++) {
9346: agemortsup=k;
9347: if (p[1]*exp(p[2]*(k-agegomp))>1) break;
9348: }
9349:
9350: for (k=agegomp;k<agemortsup;k++)
9351: lsurv[k+1]=lsurv[k]-lsurv[k]*(p[1]*exp(p[2]*(k-agegomp)));
9352:
9353: for (k=agegomp;k<agemortsup;k++){
9354: lpop[k]=(lsurv[k]+lsurv[k+1])/2.;
9355: sumlpop=sumlpop+lpop[k];
9356: }
9357:
9358: tpop[agegomp]=sumlpop;
9359: for (k=agegomp;k<(agemortsup-3);k++){
9360: /* tpop[k+1]=2;*/
9361: tpop[k+1]=tpop[k]-lpop[k];
9362: }
9363:
9364:
9365: printf("\nAge lx qx dx Lx Tx e(x)\n");
9366: for (k=agegomp;k<(agemortsup-2);k++)
9367: 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]);
9368:
9369:
9370: replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
1.220 brouard 9371: ageminpar=50;
9372: agemaxpar=100;
1.194 brouard 9373: if(ageminpar == AGEOVERFLOW ||agemaxpar == AGEOVERFLOW){
9374: printf("Warning! Error in gnuplot file with ageminpar %f or agemaxpar %f overflow\n\
9375: This is probably because your parameter file doesn't \n contain the exact number of lines (or columns) corresponding to your model line.\n\
9376: Please run with mle=-1 to get a correct covariance matrix.\n",ageminpar,agemaxpar);
9377: fprintf(ficlog,"Warning! Error in gnuplot file with ageminpar %f or agemaxpar %f overflow\n\
9378: This is probably because your parameter file doesn't \n contain the exact number of lines (or columns) corresponding to your model line.\n\
9379: Please run with mle=-1 to get a correct covariance matrix.\n",ageminpar,agemaxpar);
1.220 brouard 9380: }else{
9381: printf("Warning! ageminpar %f and agemaxpar %f have been fixed because for simplification until it is fixed...\n\n",ageminpar,agemaxpar);
9382: 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 9383: printinggnuplotmort(fileresu, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
1.220 brouard 9384: }
1.201 brouard 9385: printinghtmlmort(fileresu,title,datafile, firstpass, lastpass, \
1.126 brouard 9386: stepm, weightopt,\
9387: model,imx,p,matcov,agemortsup);
9388:
9389: free_vector(lsurv,1,AGESUP);
9390: free_vector(lpop,1,AGESUP);
9391: free_vector(tpop,1,AGESUP);
1.220 brouard 9392: free_matrix(ximort,1,NDIM,1,NDIM);
1.136 brouard 9393: free_ivector(cens,1,n);
9394: free_vector(agecens,1,n);
9395: free_ivector(dcwave,1,n);
1.220 brouard 9396: #ifdef GSL
1.136 brouard 9397: #endif
1.186 brouard 9398: } /* Endof if mle==-3 mortality only */
1.205 brouard 9399: /* Standard */
9400: else{ /* For mle !=- 3, could be 0 or 1 or 4 etc. */
9401: globpr=0;/* Computes sum of likelihood for globpr=1 and funcone */
9402: /* Computes likelihood for initial parameters, uses funcone to compute gpimx and gsw */
1.132 brouard 9403: likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
1.126 brouard 9404: printf("First Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
9405: for (k=1; k<=npar;k++)
9406: printf(" %d %8.5f",k,p[k]);
9407: printf("\n");
1.205 brouard 9408: if(mle>=1){ /* Could be 1 or 2, Real Maximization */
9409: /* mlikeli uses func not funcone */
9410: mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);
9411: }
9412: if(mle==0) {/* No optimization, will print the likelihoods for the datafile */
9413: globpr=0;/* Computes sum of likelihood for globpr=1 and funcone */
9414: /* Computes likelihood for initial parameters, uses funcone to compute gpimx and gsw */
9415: likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
9416: }
9417: globpr=1; /* again, to print the individual contributions using computed gpimx and gsw */
1.126 brouard 9418: likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
9419: printf("Second Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
9420: for (k=1; k<=npar;k++)
9421: printf(" %d %8.5f",k,p[k]);
9422: printf("\n");
9423:
9424: /*--------- results files --------------*/
1.192 brouard 9425: 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 9426:
9427:
9428: fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
9429: printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
9430: fprintf(ficlog,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
9431: for(i=1,jk=1; i <=nlstate; i++){
9432: for(k=1; k <=(nlstate+ndeath); k++){
1.220 brouard 9433: if (k != i) {
9434: printf("%d%d ",i,k);
9435: fprintf(ficlog,"%d%d ",i,k);
9436: fprintf(ficres,"%1d%1d ",i,k);
9437: for(j=1; j <=ncovmodel; j++){
9438: printf("%12.7f ",p[jk]);
9439: fprintf(ficlog,"%12.7f ",p[jk]);
9440: fprintf(ficres,"%12.7f ",p[jk]);
9441: jk++;
9442: }
9443: printf("\n");
9444: fprintf(ficlog,"\n");
9445: fprintf(ficres,"\n");
9446: }
1.126 brouard 9447: }
9448: }
1.203 brouard 9449: if(mle != 0){
9450: /* Computing hessian and covariance matrix only at a peak of the Likelihood, that is after optimization */
1.126 brouard 9451: ftolhess=ftol; /* Usually correct */
1.203 brouard 9452: hesscov(matcov, hess, p, npar, delti, ftolhess, func);
9453: 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");
9454: 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");
9455: for(i=1,jk=1; i <=nlstate; i++){
1.220 brouard 9456: for(k=1; k <=(nlstate+ndeath); k++){
9457: if (k != i) {
9458: printf("%d%d ",i,k);
9459: fprintf(ficlog,"%d%d ",i,k);
9460: for(j=1; j <=ncovmodel; j++){
9461: 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]));
9462: 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]));
9463: jk++;
9464: }
9465: printf("\n");
9466: fprintf(ficlog,"\n");
9467: }
9468: }
1.193 brouard 9469: }
1.203 brouard 9470: } /* end of hesscov and Wald tests */
1.220 brouard 9471:
1.203 brouard 9472: /* */
1.126 brouard 9473: fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");
9474: printf("# Scales (for hessian or gradient estimation)\n");
9475: fprintf(ficlog,"# Scales (for hessian or gradient estimation)\n");
9476: for(i=1,jk=1; i <=nlstate; i++){
9477: for(j=1; j <=nlstate+ndeath; j++){
1.220 brouard 9478: if (j!=i) {
9479: fprintf(ficres,"%1d%1d",i,j);
9480: printf("%1d%1d",i,j);
9481: fprintf(ficlog,"%1d%1d",i,j);
9482: for(k=1; k<=ncovmodel;k++){
9483: printf(" %.5e",delti[jk]);
9484: fprintf(ficlog," %.5e",delti[jk]);
9485: fprintf(ficres," %.5e",delti[jk]);
9486: jk++;
9487: }
9488: printf("\n");
9489: fprintf(ficlog,"\n");
9490: fprintf(ficres,"\n");
9491: }
1.126 brouard 9492: }
9493: }
9494:
9495: 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 9496: if(mle >= 1) /* To big for the screen */
1.126 brouard 9497: 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");
9498: 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");
9499: /* # 121 Var(a12)\n\ */
9500: /* # 122 Cov(b12,a12) Var(b12)\n\ */
9501: /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
9502: /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
9503: /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
9504: /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
9505: /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
9506: /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
9507:
9508:
9509: /* Just to have a covariance matrix which will be more understandable
9510: even is we still don't want to manage dictionary of variables
9511: */
9512: for(itimes=1;itimes<=2;itimes++){
9513: jj=0;
9514: for(i=1; i <=nlstate; i++){
1.220 brouard 9515: for(j=1; j <=nlstate+ndeath; j++){
9516: if(j==i) continue;
9517: for(k=1; k<=ncovmodel;k++){
9518: jj++;
9519: ca[0]= k+'a'-1;ca[1]='\0';
9520: if(itimes==1){
9521: if(mle>=1)
9522: printf("#%1d%1d%d",i,j,k);
9523: fprintf(ficlog,"#%1d%1d%d",i,j,k);
9524: fprintf(ficres,"#%1d%1d%d",i,j,k);
9525: }else{
9526: if(mle>=1)
9527: printf("%1d%1d%d",i,j,k);
9528: fprintf(ficlog,"%1d%1d%d",i,j,k);
9529: fprintf(ficres,"%1d%1d%d",i,j,k);
9530: }
9531: ll=0;
9532: for(li=1;li <=nlstate; li++){
9533: for(lj=1;lj <=nlstate+ndeath; lj++){
9534: if(lj==li) continue;
9535: for(lk=1;lk<=ncovmodel;lk++){
9536: ll++;
9537: if(ll<=jj){
9538: cb[0]= lk +'a'-1;cb[1]='\0';
9539: if(ll<jj){
9540: if(itimes==1){
9541: if(mle>=1)
9542: printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
9543: fprintf(ficlog," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
9544: fprintf(ficres," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
9545: }else{
9546: if(mle>=1)
9547: printf(" %.5e",matcov[jj][ll]);
9548: fprintf(ficlog," %.5e",matcov[jj][ll]);
9549: fprintf(ficres," %.5e",matcov[jj][ll]);
9550: }
9551: }else{
9552: if(itimes==1){
9553: if(mle>=1)
9554: printf(" Var(%s%1d%1d)",ca,i,j);
9555: fprintf(ficlog," Var(%s%1d%1d)",ca,i,j);
9556: fprintf(ficres," Var(%s%1d%1d)",ca,i,j);
9557: }else{
9558: if(mle>=1)
9559: printf(" %.7e",matcov[jj][ll]);
9560: fprintf(ficlog," %.7e",matcov[jj][ll]);
9561: fprintf(ficres," %.7e",matcov[jj][ll]);
9562: }
9563: }
9564: }
9565: } /* end lk */
9566: } /* end lj */
9567: } /* end li */
9568: if(mle>=1)
9569: printf("\n");
9570: fprintf(ficlog,"\n");
9571: fprintf(ficres,"\n");
9572: numlinepar++;
9573: } /* end k*/
9574: } /*end j */
1.126 brouard 9575: } /* end i */
9576: } /* end itimes */
9577:
9578: fflush(ficlog);
9579: fflush(ficres);
1.220 brouard 9580: while(fgets(line, MAXLINE, ficpar)) {
9581: /* If line starts with a # it is a comment */
9582: if (line[0] == '#') {
9583: numlinepar++;
9584: fputs(line,stdout);
9585: fputs(line,ficparo);
9586: fputs(line,ficlog);
9587: continue;
9588: }else
9589: break;
9590: }
9591:
1.209 brouard 9592: /* while((c=getc(ficpar))=='#' && c!= EOF){ */
9593: /* ungetc(c,ficpar); */
9594: /* fgets(line, MAXLINE, ficpar); */
9595: /* fputs(line,stdout); */
9596: /* fputs(line,ficparo); */
9597: /* } */
9598: /* ungetc(c,ficpar); */
1.126 brouard 9599:
9600: estepm=0;
1.209 brouard 9601: 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 9602:
9603: if (num_filled != 6) {
9604: 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);
9605: 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);
9606: goto end;
9607: }
9608: printf("agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d ftolpl=%lf\n",ageminpar,agemaxpar, bage, fage, estepm, ftolpl);
9609: }
9610: /* ftolpl=6*ftol*1.e5; /\* 6.e-3 make convergences in less than 80 loops for the prevalence limit *\/ */
9611: /*ftolpl=6.e-4;*/ /* 6.e-3 make convergences in less than 80 loops for the prevalence limit */
9612:
1.209 brouard 9613: /* fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d ftolpl=%\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm); */
1.126 brouard 9614: if (estepm==0 || estepm < stepm) estepm=stepm;
9615: if (fage <= 2) {
9616: bage = ageminpar;
9617: fage = agemaxpar;
9618: }
9619:
9620: fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");
1.211 brouard 9621: fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d ftolpl=%e\n",ageminpar,agemaxpar,bage,fage, estepm, ftolpl);
9622: fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d, ftolpl=%e\n",ageminpar,agemaxpar,bage,fage, estepm, ftolpl);
1.220 brouard 9623:
1.186 brouard 9624: /* Other stuffs, more or less useful */
1.126 brouard 9625: while((c=getc(ficpar))=='#' && c!= EOF){
9626: ungetc(c,ficpar);
9627: fgets(line, MAXLINE, ficpar);
1.141 brouard 9628: fputs(line,stdout);
1.126 brouard 9629: fputs(line,ficparo);
9630: }
9631: ungetc(c,ficpar);
9632:
9633: 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);
9634: 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);
9635: 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);
9636: printf("begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
9637: 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);
9638:
9639: while((c=getc(ficpar))=='#' && c!= EOF){
9640: ungetc(c,ficpar);
9641: fgets(line, MAXLINE, ficpar);
1.141 brouard 9642: fputs(line,stdout);
1.126 brouard 9643: fputs(line,ficparo);
9644: }
9645: ungetc(c,ficpar);
9646:
9647:
9648: dateprev1=anprev1+(mprev1-1)/12.+(jprev1-1)/365.;
9649: dateprev2=anprev2+(mprev2-1)/12.+(jprev2-1)/365.;
9650:
9651: fscanf(ficpar,"pop_based=%d\n",&popbased);
1.193 brouard 9652: fprintf(ficlog,"pop_based=%d\n",popbased);
1.126 brouard 9653: fprintf(ficparo,"pop_based=%d\n",popbased);
9654: fprintf(ficres,"pop_based=%d\n",popbased);
9655:
9656: while((c=getc(ficpar))=='#' && c!= EOF){
9657: ungetc(c,ficpar);
9658: fgets(line, MAXLINE, ficpar);
1.141 brouard 9659: fputs(line,stdout);
1.126 brouard 9660: fputs(line,ficparo);
9661: }
9662: ungetc(c,ficpar);
9663:
9664: 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);
9665: 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);
9666: 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);
9667: 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);
9668: 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);
9669: /* day and month of proj2 are not used but only year anproj2.*/
9670:
1.217 brouard 9671: while((c=getc(ficpar))=='#' && c!= EOF){
9672: ungetc(c,ficpar);
9673: fgets(line, MAXLINE, ficpar);
9674: fputs(line,stdout);
9675: fputs(line,ficparo);
9676: }
9677: ungetc(c,ficpar);
9678:
9679: fscanf(ficpar,"backcast=%d starting-back-date=%lf/%lf/%lf final-back-date=%lf/%lf/%lf mobil_average=%d\n",&backcast,&jback1,&mback1,&anback1,&jback2,&mback2,&anback2,&mobilavproj);
1.223 ! brouard 9680: 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);
! 9681: 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);
! 9682: 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 9683: /* day and month of proj2 are not used but only year anproj2.*/
1.126 brouard 9684:
9685:
1.220 brouard 9686: /* freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint); */
1.145 brouard 9687: /* ,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2); */
1.126 brouard 9688:
9689: replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
1.194 brouard 9690: if(ageminpar == AGEOVERFLOW ||agemaxpar == -AGEOVERFLOW){
1.220 brouard 9691: printf("Warning! Error in gnuplot file with ageminpar %f or agemaxpar %f overflow\n\
1.194 brouard 9692: This is probably because your parameter file doesn't \n contain the exact number of lines (or columns) corresponding to your model line.\n\
9693: Please run with mle=-1 to get a correct covariance matrix.\n",ageminpar,agemaxpar);
1.220 brouard 9694: fprintf(ficlog,"Warning! Error in gnuplot file with ageminpar %f or agemaxpar %f overflow\n\
1.194 brouard 9695: This is probably because your parameter file doesn't \n contain the exact number of lines (or columns) corresponding to your model line.\n\
9696: Please run with mle=-1 to get a correct covariance matrix.\n",ageminpar,agemaxpar);
1.220 brouard 9697: }else{
1.218 brouard 9698: printinggnuplot(fileresu, optionfilefiname,ageminpar,agemaxpar,fage, prevfcast, backcast, pathc,p);
1.220 brouard 9699: }
9700: printinghtml(fileresu,title,datafile, firstpass, lastpass, stepm, weightopt, \
9701: model,imx,jmin,jmax,jmean,rfileres,popforecast,prevfcast,backcast, estepm, \
9702: jprev1,mprev1,anprev1,dateprev1,jprev2,mprev2,anprev2,dateprev2);
9703:
9704: /*------------ free_vector -------------*/
9705: /* chdir(path); */
9706:
1.215 brouard 9707: /* free_ivector(wav,1,imx); */ /* Moved after last prevalence call */
9708: /* free_imatrix(dh,1,lastpass-firstpass+2,1,imx); */
9709: /* free_imatrix(bh,1,lastpass-firstpass+2,1,imx); */
9710: /* free_imatrix(mw,1,lastpass-firstpass+2,1,imx); */
1.126 brouard 9711: free_lvector(num,1,n);
9712: free_vector(agedc,1,n);
9713: /*free_matrix(covar,0,NCOVMAX,1,n);*/
9714: /*free_matrix(covar,1,NCOVMAX,1,n);*/
9715: fclose(ficparo);
9716: fclose(ficres);
1.220 brouard 9717:
9718:
1.186 brouard 9719: /* Other results (useful)*/
1.220 brouard 9720:
9721:
1.126 brouard 9722: /*--------------- Prevalence limit (period or stable prevalence) --------------*/
1.180 brouard 9723: /*#include "prevlim.h"*/ /* Use ficrespl, ficlog */
9724: prlim=matrix(1,nlstate,1,nlstate);
1.209 brouard 9725: prevalence_limit(p, prlim, ageminpar, agemaxpar, ftolpl, &ncvyear);
1.126 brouard 9726: fclose(ficrespl);
9727:
9728: /*------------- h Pij x at various ages ------------*/
1.180 brouard 9729: /*#include "hpijx.h"*/
9730: hPijx(p, bage, fage);
1.145 brouard 9731: fclose(ficrespij);
1.126 brouard 9732:
1.220 brouard 9733: /* ncovcombmax= pow(2,cptcoveff); */
1.219 brouard 9734: /*-------------- Variance of one-step probabilities---*/
1.145 brouard 9735: k=1;
1.126 brouard 9736: varprob(optionfilefiname, matcov, p, delti, nlstate, bage, fage,k,Tvar,nbcode, ncodemax,strstart);
9737:
1.219 brouard 9738: /* Prevalence for each covariates in probs[age][status][cov] */
1.218 brouard 9739: probs= ma3x(1,AGESUP,1,nlstate+ndeath, 1,ncovcombmax);
1.126 brouard 9740: for(i=1;i<=AGESUP;i++)
1.219 brouard 9741: for(j=1;j<=nlstate+ndeath;j++) /* ndeath is useless but a necessity to be compared with mobaverages */
1.218 brouard 9742: for(k=1;k<=ncovcombmax;k++)
9743: probs[i][j][k]=0.;
1.219 brouard 9744: prevalence(probs, ageminpar, agemaxpar, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
9745: if (mobilav!=0 ||mobilavproj !=0 ) {
9746: mobaverages= ma3x(1, AGESUP,1,nlstate+ndeath, 1,ncovcombmax);
9747: for(i=1;i<=AGESUP;i++)
9748: for(j=1;j<=nlstate;j++)
9749: for(k=1;k<=ncovcombmax;k++)
9750: mobaverages[i][j][k]=0.;
9751: mobaverage=mobaverages;
9752: if (mobilav!=0) {
1.218 brouard 9753: if (movingaverage(probs, ageminpar, agemaxpar, mobaverage, mobilav)!=0){
9754: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
9755: printf(" Error in movingaverage mobilav=%d\n",mobilav);
9756: }
1.219 brouard 9757: }
9758: /* /\* Prevalence for each covariates in probs[age][status][cov] *\/ */
9759: /* prevalence(probs, ageminpar, agemaxpar, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass); */
9760: else if (mobilavproj !=0) {
1.218 brouard 9761: if (movingaverage(probs, ageminpar, agemaxpar, mobaverage, mobilavproj)!=0){
9762: fprintf(ficlog," Error in movingaverage mobilavproj=%d\n",mobilavproj);
9763: printf(" Error in movingaverage mobilavproj=%d\n",mobilavproj);
9764: }
1.219 brouard 9765: }
9766: }/* end if moving average */
9767:
1.126 brouard 9768: /*---------- Forecasting ------------------*/
9769: /*if((stepm == 1) && (strcmp(model,".")==0)){*/
9770: if(prevfcast==1){
9771: /* if(stepm ==1){*/
1.201 brouard 9772: prevforecast(fileresu, anproj1, mproj1, jproj1, agemin, agemax, dateprev1, dateprev2, mobilavproj, bage, fage, firstpass, lastpass, anproj2, p, cptcoveff);
1.126 brouard 9773: }
1.217 brouard 9774: if(backcast==1){
1.219 brouard 9775: ddnewms=matrix(1,nlstate+ndeath,1,nlstate+ndeath);
9776: ddoldms=matrix(1,nlstate+ndeath,1,nlstate+ndeath);
9777: ddsavms=matrix(1,nlstate+ndeath,1,nlstate+ndeath);
9778:
9779: /*--------------- Back Prevalence limit (period or stable prevalence) --------------*/
9780:
9781: bprlim=matrix(1,nlstate,1,nlstate);
9782: back_prevalence_limit(p, bprlim, ageminpar, agemaxpar, ftolpl, &ncvyear, dateprev1, dateprev2, firstpass, lastpass, mobilavproj);
9783: fclose(ficresplb);
9784:
1.222 brouard 9785: hBijx(p, bage, fage, mobaverage);
9786: fclose(ficrespijb);
1.219 brouard 9787: free_matrix(bprlim,1,nlstate,1,nlstate); /*here or after loop ? */
9788:
9789: /* prevbackforecast(fileresu, anback1, mback1, jback1, agemin, agemax, dateprev1, dateprev2, mobilavproj,
9790: bage, fage, firstpass, lastpass, anback2, p, cptcoveff); */
9791: free_matrix(ddnewms, 1, nlstate+ndeath, 1, nlstate+ndeath);
9792: free_matrix(ddsavms, 1, nlstate+ndeath, 1, nlstate+ndeath);
9793: free_matrix(ddoldms, 1, nlstate+ndeath, 1, nlstate+ndeath);
9794: }
1.217 brouard 9795:
1.186 brouard 9796:
9797: /* ------ Other prevalence ratios------------ */
1.126 brouard 9798:
1.215 brouard 9799: free_ivector(wav,1,imx);
9800: free_imatrix(dh,1,lastpass-firstpass+2,1,imx);
9801: free_imatrix(bh,1,lastpass-firstpass+2,1,imx);
9802: free_imatrix(mw,1,lastpass-firstpass+2,1,imx);
1.218 brouard 9803:
9804:
1.127 brouard 9805: /*---------- Health expectancies, no variances ------------*/
1.218 brouard 9806:
1.201 brouard 9807: strcpy(filerese,"E_");
9808: strcat(filerese,fileresu);
1.126 brouard 9809: if((ficreseij=fopen(filerese,"w"))==NULL) {
9810: printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
9811: fprintf(ficlog,"Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
9812: }
1.208 brouard 9813: printf("Computing Health Expectancies: result on file '%s' ...", filerese);fflush(stdout);
9814: fprintf(ficlog,"Computing Health Expectancies: result on file '%s' ...", filerese);fflush(ficlog);
1.219 brouard 9815:
1.145 brouard 9816: for (k=1; k <= (int) pow(2,cptcoveff); k++){
1.219 brouard 9817: fprintf(ficreseij,"\n#****** ");
9818: for(j=1;j<=cptcoveff;j++) {
1.220 brouard 9819: fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
1.219 brouard 9820: }
9821: fprintf(ficreseij,"******\n");
9822:
9823: eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
9824: oldm=oldms;savm=savms;
9825: evsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, strstart);
1.127 brouard 9826:
1.219 brouard 9827: free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
1.127 brouard 9828: }
9829: fclose(ficreseij);
1.208 brouard 9830: printf("done evsij\n");fflush(stdout);
9831: fprintf(ficlog,"done evsij\n");fflush(ficlog);
1.218 brouard 9832:
1.127 brouard 9833: /*---------- Health expectancies and variances ------------*/
1.218 brouard 9834:
9835:
1.201 brouard 9836: strcpy(filerest,"T_");
9837: strcat(filerest,fileresu);
1.127 brouard 9838: if((ficrest=fopen(filerest,"w"))==NULL) {
9839: printf("Problem with total LE resultfile: %s\n", filerest);goto end;
9840: fprintf(ficlog,"Problem with total LE resultfile: %s\n", filerest);goto end;
9841: }
1.208 brouard 9842: printf("Computing Total Life expectancies with their standard errors: file '%s' ...\n", filerest); fflush(stdout);
9843: fprintf(ficlog,"Computing Total Life expectancies with their standard errors: file '%s' ...\n", filerest); fflush(ficlog);
1.218 brouard 9844:
1.126 brouard 9845:
1.201 brouard 9846: strcpy(fileresstde,"STDE_");
9847: strcat(fileresstde,fileresu);
1.126 brouard 9848: if((ficresstdeij=fopen(fileresstde,"w"))==NULL) {
9849: printf("Problem with Health Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
9850: fprintf(ficlog,"Problem with Health Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
9851: }
1.208 brouard 9852: printf(" Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde);
9853: fprintf(ficlog," Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde);
1.126 brouard 9854:
1.201 brouard 9855: strcpy(filerescve,"CVE_");
9856: strcat(filerescve,fileresu);
1.126 brouard 9857: if((ficrescveij=fopen(filerescve,"w"))==NULL) {
9858: printf("Problem with Covar. Health Exp. resultfile: %s\n", filerescve); exit(0);
9859: fprintf(ficlog,"Problem with Covar. Health Exp. resultfile: %s\n", filerescve); exit(0);
9860: }
1.208 brouard 9861: printf(" Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve);
9862: fprintf(ficlog," Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve);
1.126 brouard 9863:
1.201 brouard 9864: strcpy(fileresv,"V_");
9865: strcat(fileresv,fileresu);
1.126 brouard 9866: if((ficresvij=fopen(fileresv,"w"))==NULL) {
9867: printf("Problem with variance resultfile: %s\n", fileresv);exit(0);
9868: fprintf(ficlog,"Problem with variance resultfile: %s\n", fileresv);exit(0);
9869: }
1.208 brouard 9870: printf(" Computing Variance-covariance of DFLEs: file '%s' ... ", fileresv);fflush(stdout);
9871: fprintf(ficlog," Computing Variance-covariance of DFLEs: file '%s' ... ", fileresv);fflush(ficlog);
1.126 brouard 9872:
1.145 brouard 9873: /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){
9874: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/
9875:
9876: for (k=1; k <= (int) pow(2,cptcoveff); k++){
1.208 brouard 9877: fprintf(ficrest,"\n#****** ");
9878: for(j=1;j<=cptcoveff;j++)
1.218 brouard 9879: fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
1.208 brouard 9880: fprintf(ficrest,"******\n");
9881:
9882: fprintf(ficresstdeij,"\n#****** ");
9883: fprintf(ficrescveij,"\n#****** ");
9884: for(j=1;j<=cptcoveff;j++) {
1.218 brouard 9885: fprintf(ficresstdeij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
9886: fprintf(ficrescveij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
1.208 brouard 9887: }
9888: fprintf(ficresstdeij,"******\n");
9889: fprintf(ficrescveij,"******\n");
9890:
9891: fprintf(ficresvij,"\n#****** ");
9892: for(j=1;j<=cptcoveff;j++)
1.218 brouard 9893: fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
1.208 brouard 9894: fprintf(ficresvij,"******\n");
9895:
9896: eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
9897: oldm=oldms;savm=savms;
9898: printf(" cvevsij %d, ",k);
9899: fprintf(ficlog, " cvevsij %d, ",k);
9900: cvevsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov, strstart);
9901: printf(" end cvevsij \n ");
9902: fprintf(ficlog, " end cvevsij \n ");
9903:
9904: /*
9905: */
9906: /* goto endfree; */
9907:
9908: vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
9909: pstamp(ficrest);
9910:
9911:
9912: for(vpopbased=0; vpopbased <= popbased; vpopbased++){ /* Done for vpopbased=0 and vpopbased=1 if popbased==1*/
1.220 brouard 9913: oldm=oldms;savm=savms; /* ZZ Segmentation fault */
9914: cptcod= 0; /* To be deleted */
9915: printf("varevsij %d \n",vpopbased);
9916: fprintf(ficlog, "varevsij %d \n",vpopbased);
9917: 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 */
9918: 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 ");
9919: if(vpopbased==1)
9920: 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);
9921: else
9922: fprintf(ficrest,"the age specific period (stable) prevalences in each health state \n");
9923: fprintf(ficrest,"# Age popbased mobilav e.. (std) ");
9924: for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);
9925: fprintf(ficrest,"\n");
9926: /* printf("Which p?\n"); for(i=1;i<=npar;i++)printf("p[i=%d]=%lf,",i,p[i]);printf("\n"); */
9927: epj=vector(1,nlstate+1);
9928: printf("Computing age specific period (stable) prevalences in each health state \n");
9929: fprintf(ficlog,"Computing age specific period (stable) prevalences in each health state \n");
9930: for(age=bage; age <=fage ;age++){
9931: prevalim(prlim, nlstate, p, age, oldm, savm, ftolpl, &ncvyear, k); /*ZZ Is it the correct prevalim */
9932: if (vpopbased==1) {
9933: if(mobilav ==0){
9934: for(i=1; i<=nlstate;i++)
9935: prlim[i][i]=probs[(int)age][i][k];
9936: }else{ /* mobilav */
9937: for(i=1; i<=nlstate;i++)
9938: prlim[i][i]=mobaverage[(int)age][i][k];
9939: }
9940: }
1.219 brouard 9941:
1.220 brouard 9942: fprintf(ficrest," %4.0f %d %d",age, vpopbased, mobilav);
9943: /* fprintf(ficrest," %4.0f %d %d %d %d",age, vpopbased, mobilav,Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]); */ /* to be done */
9944: /* printf(" age %4.0f ",age); */
9945: for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){
9946: for(i=1, epj[j]=0.;i <=nlstate;i++) {
9947: epj[j] += prlim[i][i]*eij[i][j][(int)age];
9948: /*ZZZ printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/
9949: /* printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]); */
9950: }
9951: epj[nlstate+1] +=epj[j];
9952: }
9953: /* printf(" age %4.0f \n",age); */
1.219 brouard 9954:
1.220 brouard 9955: for(i=1, vepp=0.;i <=nlstate;i++)
9956: for(j=1;j <=nlstate;j++)
9957: vepp += vareij[i][j][(int)age];
9958: fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));
9959: for(j=1;j <=nlstate;j++){
9960: fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));
9961: }
9962: fprintf(ficrest,"\n");
9963: }
1.208 brouard 9964: } /* End vpopbased */
9965: free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
9966: free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);
9967: free_vector(epj,1,nlstate+1);
9968: printf("done \n");fflush(stdout);
9969: fprintf(ficlog,"done\n");fflush(ficlog);
9970:
1.145 brouard 9971: /*}*/
1.208 brouard 9972: } /* End k */
1.126 brouard 9973: free_vector(weight,1,n);
1.145 brouard 9974: free_imatrix(Tvard,1,NCOVMAX,1,2);
1.126 brouard 9975: free_imatrix(s,1,maxwav+1,1,n);
9976: free_matrix(anint,1,maxwav,1,n);
9977: free_matrix(mint,1,maxwav,1,n);
9978: free_ivector(cod,1,n);
9979: free_ivector(tab,1,NCOVMAX);
9980: fclose(ficresstdeij);
9981: fclose(ficrescveij);
9982: fclose(ficresvij);
9983: fclose(ficrest);
1.208 brouard 9984: printf("done Health expectancies\n");fflush(stdout);
9985: fprintf(ficlog,"done Health expectancies\n");fflush(ficlog);
1.126 brouard 9986: fclose(ficpar);
9987:
9988: /*------- Variance of period (stable) prevalence------*/
9989:
1.201 brouard 9990: strcpy(fileresvpl,"VPL_");
9991: strcat(fileresvpl,fileresu);
1.126 brouard 9992: if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {
9993: printf("Problem with variance of period (stable) prevalence resultfile: %s\n", fileresvpl);
9994: exit(0);
9995: }
1.208 brouard 9996: printf("Computing Variance-covariance of period (stable) prevalence: file '%s' ...", fileresvpl);fflush(stdout);
9997: fprintf(ficlog, "Computing Variance-covariance of period (stable) prevalence: file '%s' ...", fileresvpl);fflush(ficlog);
1.126 brouard 9998:
1.145 brouard 9999: /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){
10000: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/
10001:
10002: for (k=1; k <= (int) pow(2,cptcoveff); k++){
10003: fprintf(ficresvpl,"\n#****** ");
1.218 brouard 10004: for(j=1;j<=cptcoveff;j++)
10005: fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
10006: fprintf(ficresvpl,"******\n");
10007:
10008: varpl=matrix(1,nlstate,(int) bage, (int) fage);
10009: oldm=oldms;savm=savms;
10010: varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl, &ncvyear, k, strstart);
10011: free_matrix(varpl,1,nlstate,(int) bage, (int)fage);
1.145 brouard 10012: /*}*/
1.126 brouard 10013: }
1.218 brouard 10014:
1.126 brouard 10015: fclose(ficresvpl);
1.208 brouard 10016: printf("done variance-covariance of period prevalence\n");fflush(stdout);
10017: fprintf(ficlog,"done variance-covariance of period prevalence\n");fflush(ficlog);
1.126 brouard 10018:
10019: /*---------- End : free ----------------*/
1.219 brouard 10020: if (mobilav!=0 ||mobilavproj !=0)
10021: 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 10022: free_ma3x(probs,1,AGESUP,1,nlstate+ndeath, 1,ncovcombmax);
1.220 brouard 10023: free_matrix(prlim,1,nlstate,1,nlstate); /*here or after loop ? */
10024: free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);
1.126 brouard 10025: } /* mle==-3 arrives here for freeing */
1.164 brouard 10026: /* endfree:*/
1.126 brouard 10027: free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);
10028: free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);
10029: free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);
1.223 ! brouard 10030: free_ma3x(cotqvar,1,maxwav,1,ntqv,1,n);
! 10031: free_ma3x(cotvar,1,maxwav,1,ntv,1,n);
! 10032: free_matrix(coqvar,1,maxwav,1,n);
1.126 brouard 10033: free_matrix(covar,0,NCOVMAX,1,n);
10034: free_matrix(matcov,1,npar,1,npar);
1.203 brouard 10035: free_matrix(hess,1,npar,1,npar);
1.126 brouard 10036: /*free_vector(delti,1,npar);*/
10037: free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
10038: free_matrix(agev,1,maxwav,1,imx);
10039: free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
10040:
1.145 brouard 10041: free_ivector(ncodemax,1,NCOVMAX);
1.192 brouard 10042: free_ivector(ncodemaxwundef,1,NCOVMAX);
1.145 brouard 10043: free_ivector(Tvar,1,NCOVMAX);
10044: free_ivector(Tprod,1,NCOVMAX);
10045: free_ivector(Tvaraff,1,NCOVMAX);
1.220 brouard 10046: free_ivector(invalidvarcomb,1,ncovcombmax);
1.145 brouard 10047: free_ivector(Tage,1,NCOVMAX);
1.126 brouard 10048:
10049: free_imatrix(nbcode,0,NCOVMAX,0,NCOVMAX);
1.200 brouard 10050: /* free_imatrix(codtab,1,100,1,10); */
1.126 brouard 10051: fflush(fichtm);
10052: fflush(ficgp);
10053:
10054:
10055: if((nberr >0) || (nbwarn>0)){
1.216 brouard 10056: printf("End of Imach with %d errors and/or %d warnings. Please look at the log file for details.\n",nberr,nbwarn);
10057: 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 10058: }else{
10059: printf("End of Imach\n");
10060: fprintf(ficlog,"End of Imach\n");
10061: }
10062: printf("See log file on %s\n",filelog);
10063: /* gettimeofday(&end_time, (struct timezone*)0);*/ /* after time */
1.157 brouard 10064: /*(void) gettimeofday(&end_time,&tzp);*/
10065: rend_time = time(NULL);
10066: end_time = *localtime(&rend_time);
10067: /* tml = *localtime(&end_time.tm_sec); */
10068: strcpy(strtend,asctime(&end_time));
1.126 brouard 10069: printf("Local time at start %s\nLocal time at end %s",strstart, strtend);
10070: fprintf(ficlog,"Local time at start %s\nLocal time at end %s\n",strstart, strtend);
1.157 brouard 10071: printf("Total time used %s\n", asc_diff_time(rend_time -rstart_time,tmpout));
1.126 brouard 10072:
1.157 brouard 10073: printf("Total time was %.0lf Sec.\n", difftime(rend_time,rstart_time));
10074: fprintf(ficlog,"Total time used %s\n", asc_diff_time(rend_time -rstart_time,tmpout));
10075: fprintf(ficlog,"Total time was %.0lf Sec.\n", difftime(rend_time,rstart_time));
1.126 brouard 10076: /* printf("Total time was %d uSec.\n", total_usecs);*/
10077: /* if(fileappend(fichtm,optionfilehtm)){ */
10078: fprintf(fichtm,"<br>Local time at start %s<br>Local time at end %s<br>\n</body></html>",strstart, strtend);
10079: fclose(fichtm);
10080: fprintf(fichtmcov,"<br>Local time at start %s<br>Local time at end %s<br>\n</body></html>",strstart, strtend);
10081: fclose(fichtmcov);
10082: fclose(ficgp);
10083: fclose(ficlog);
10084: /*------ End -----------*/
10085:
10086:
10087: printf("Before Current directory %s!\n",pathcd);
1.184 brouard 10088: #ifdef WIN32
10089: if (_chdir(pathcd) != 0)
10090: printf("Can't move to directory %s!\n",path);
10091: if(_getcwd(pathcd,MAXLINE) > 0)
10092: #else
1.126 brouard 10093: if(chdir(pathcd) != 0)
1.184 brouard 10094: printf("Can't move to directory %s!\n", path);
10095: if (getcwd(pathcd, MAXLINE) > 0)
10096: #endif
1.126 brouard 10097: printf("Current directory %s!\n",pathcd);
10098: /*strcat(plotcmd,CHARSEPARATOR);*/
10099: sprintf(plotcmd,"gnuplot");
1.157 brouard 10100: #ifdef _WIN32
1.126 brouard 10101: sprintf(plotcmd,"\"%sgnuplot.exe\"",pathimach);
10102: #endif
10103: if(!stat(plotcmd,&info)){
1.158 brouard 10104: printf("Error or gnuplot program not found: '%s'\n",plotcmd);fflush(stdout);
1.126 brouard 10105: if(!stat(getenv("GNUPLOTBIN"),&info)){
1.158 brouard 10106: printf("Error or gnuplot program not found: '%s' Environment GNUPLOTBIN not set.\n",plotcmd);fflush(stdout);
1.126 brouard 10107: }else
10108: strcpy(pplotcmd,plotcmd);
1.157 brouard 10109: #ifdef __unix
1.126 brouard 10110: strcpy(plotcmd,GNUPLOTPROGRAM);
10111: if(!stat(plotcmd,&info)){
1.158 brouard 10112: printf("Error gnuplot program not found: '%s'\n",plotcmd);fflush(stdout);
1.126 brouard 10113: }else
10114: strcpy(pplotcmd,plotcmd);
10115: #endif
10116: }else
10117: strcpy(pplotcmd,plotcmd);
10118:
10119: sprintf(plotcmd,"%s %s",pplotcmd, optionfilegnuplot);
1.158 brouard 10120: printf("Starting graphs with: '%s'\n",plotcmd);fflush(stdout);
1.126 brouard 10121:
10122: if((outcmd=system(plotcmd)) != 0){
1.158 brouard 10123: printf("gnuplot command might not be in your path: '%s', err=%d\n", plotcmd, outcmd);
1.154 brouard 10124: printf("\n Trying if gnuplot resides on the same directory that IMaCh\n");
1.152 brouard 10125: sprintf(plotcmd,"%sgnuplot %s", pathimach, optionfilegnuplot);
1.150 brouard 10126: if((outcmd=system(plotcmd)) != 0)
1.153 brouard 10127: printf("\n Still a problem with gnuplot command %s, err=%d\n", plotcmd, outcmd);
1.126 brouard 10128: }
1.158 brouard 10129: printf(" Successful, please wait...");
1.126 brouard 10130: while (z[0] != 'q') {
10131: /* chdir(path); */
1.154 brouard 10132: printf("\nType e to edit results with your browser, g to graph again and q for exit: ");
1.126 brouard 10133: scanf("%s",z);
10134: /* if (z[0] == 'c') system("./imach"); */
10135: if (z[0] == 'e') {
1.158 brouard 10136: #ifdef __APPLE__
1.152 brouard 10137: sprintf(pplotcmd, "open %s", optionfilehtm);
1.157 brouard 10138: #elif __linux
10139: sprintf(pplotcmd, "xdg-open %s", optionfilehtm);
1.153 brouard 10140: #else
1.152 brouard 10141: sprintf(pplotcmd, "%s", optionfilehtm);
1.153 brouard 10142: #endif
10143: printf("Starting browser with: %s",pplotcmd);fflush(stdout);
10144: system(pplotcmd);
1.126 brouard 10145: }
10146: else if (z[0] == 'g') system(plotcmd);
10147: else if (z[0] == 'q') exit(0);
10148: }
10149: end:
10150: while (z[0] != 'q') {
1.195 brouard 10151: printf("\nType q for exiting: "); fflush(stdout);
1.126 brouard 10152: scanf("%s",z);
10153: }
10154: }
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