Annotation of imach/src/imach.c, revision 1.216
1.216 ! brouard 1: /* $Id: imach.c,v 1.215 2015/12/16 08:52:24 brouard Exp $
1.126 brouard 2: $State: Exp $
1.163 brouard 3: $Log: imach.c,v $
1.216 ! brouard 4: Revision 1.215 2015/12/16 08:52:24 brouard
! 5: Summary: 0.98r4 working
! 6:
1.215 brouard 7: Revision 1.214 2015/12/16 06:57:54 brouard
8: Summary: temporary not working
9:
1.214 brouard 10: Revision 1.213 2015/12/11 18:22:17 brouard
11: Summary: 0.98r4
12:
1.213 brouard 13: Revision 1.212 2015/11/21 12:47:24 brouard
14: Summary: minor typo
15:
1.212 brouard 16: Revision 1.211 2015/11/21 12:41:11 brouard
17: Summary: 0.98r3 with some graph of projected cross-sectional
18:
19: Author: Nicolas Brouard
20:
1.211 brouard 21: Revision 1.210 2015/11/18 17:41:20 brouard
22: Summary: Start working on projected prevalences
23:
1.210 brouard 24: Revision 1.209 2015/11/17 22:12:03 brouard
25: Summary: Adding ftolpl parameter
26: Author: N Brouard
27:
28: We had difficulties to get smoothed confidence intervals. It was due
29: to the period prevalence which wasn't computed accurately. The inner
30: parameter ftolpl is now an outer parameter of the .imach parameter
31: file after estepm. If ftolpl is small 1.e-4 and estepm too,
32: computation are long.
33:
1.209 brouard 34: Revision 1.208 2015/11/17 14:31:57 brouard
35: Summary: temporary
36:
1.208 brouard 37: Revision 1.207 2015/10/27 17:36:57 brouard
38: *** empty log message ***
39:
1.207 brouard 40: Revision 1.206 2015/10/24 07:14:11 brouard
41: *** empty log message ***
42:
1.206 brouard 43: Revision 1.205 2015/10/23 15:50:53 brouard
44: Summary: 0.98r3 some clarification for graphs on likelihood contributions
45:
1.205 brouard 46: Revision 1.204 2015/10/01 16:20:26 brouard
47: Summary: Some new graphs of contribution to likelihood
48:
1.204 brouard 49: Revision 1.203 2015/09/30 17:45:14 brouard
50: Summary: looking at better estimation of the hessian
51:
52: Also a better criteria for convergence to the period prevalence And
53: therefore adding the number of years needed to converge. (The
54: prevalence in any alive state shold sum to one
55:
1.203 brouard 56: Revision 1.202 2015/09/22 19:45:16 brouard
57: Summary: Adding some overall graph on contribution to likelihood. Might change
58:
1.202 brouard 59: Revision 1.201 2015/09/15 17:34:58 brouard
60: Summary: 0.98r0
61:
62: - Some new graphs like suvival functions
63: - Some bugs fixed like model=1+age+V2.
64:
1.201 brouard 65: Revision 1.200 2015/09/09 16:53:55 brouard
66: Summary: Big bug thanks to Flavia
67:
68: Even model=1+age+V2. did not work anymore
69:
1.200 brouard 70: Revision 1.199 2015/09/07 14:09:23 brouard
71: Summary: 0.98q6 changing default small png format for graph to vectorized svg.
72:
1.199 brouard 73: Revision 1.198 2015/09/03 07:14:39 brouard
74: Summary: 0.98q5 Flavia
75:
1.198 brouard 76: Revision 1.197 2015/09/01 18:24:39 brouard
77: *** empty log message ***
78:
1.197 brouard 79: Revision 1.196 2015/08/18 23:17:52 brouard
80: Summary: 0.98q5
81:
1.196 brouard 82: Revision 1.195 2015/08/18 16:28:39 brouard
83: Summary: Adding a hack for testing purpose
84:
85: After reading the title, ftol and model lines, if the comment line has
86: a q, starting with #q, the answer at the end of the run is quit. It
87: permits to run test files in batch with ctest. The former workaround was
88: $ echo q | imach foo.imach
89:
1.195 brouard 90: Revision 1.194 2015/08/18 13:32:00 brouard
91: Summary: Adding error when the covariance matrix doesn't contain the exact number of lines required by the model line.
92:
1.194 brouard 93: Revision 1.193 2015/08/04 07:17:42 brouard
94: Summary: 0.98q4
95:
1.193 brouard 96: Revision 1.192 2015/07/16 16:49:02 brouard
97: Summary: Fixing some outputs
98:
1.192 brouard 99: Revision 1.191 2015/07/14 10:00:33 brouard
100: Summary: Some fixes
101:
1.191 brouard 102: Revision 1.190 2015/05/05 08:51:13 brouard
103: Summary: Adding digits in output parameters (7 digits instead of 6)
104:
105: Fix 1+age+.
106:
1.190 brouard 107: Revision 1.189 2015/04/30 14:45:16 brouard
108: Summary: 0.98q2
109:
1.189 brouard 110: Revision 1.188 2015/04/30 08:27:53 brouard
111: *** empty log message ***
112:
1.188 brouard 113: Revision 1.187 2015/04/29 09:11:15 brouard
114: *** empty log message ***
115:
1.187 brouard 116: Revision 1.186 2015/04/23 12:01:52 brouard
117: Summary: V1*age is working now, version 0.98q1
118:
119: Some codes had been disabled in order to simplify and Vn*age was
120: working in the optimization phase, ie, giving correct MLE parameters,
121: but, as usual, outputs were not correct and program core dumped.
122:
1.186 brouard 123: Revision 1.185 2015/03/11 13:26:42 brouard
124: Summary: Inclusion of compile and links command line for Intel Compiler
125:
1.185 brouard 126: Revision 1.184 2015/03/11 11:52:39 brouard
127: Summary: Back from Windows 8. Intel Compiler
128:
1.184 brouard 129: Revision 1.183 2015/03/10 20:34:32 brouard
130: Summary: 0.98q0, trying with directest, mnbrak fixed
131:
132: We use directest instead of original Powell test; probably no
133: incidence on the results, but better justifications;
134: We fixed Numerical Recipes mnbrak routine which was wrong and gave
135: wrong results.
136:
1.183 brouard 137: Revision 1.182 2015/02/12 08:19:57 brouard
138: Summary: Trying to keep directest which seems simpler and more general
139: Author: Nicolas Brouard
140:
1.182 brouard 141: Revision 1.181 2015/02/11 23:22:24 brouard
142: Summary: Comments on Powell added
143:
144: Author:
145:
1.181 brouard 146: Revision 1.180 2015/02/11 17:33:45 brouard
147: Summary: Finishing move from main to function (hpijx and prevalence_limit)
148:
1.180 brouard 149: Revision 1.179 2015/01/04 09:57:06 brouard
150: Summary: back to OS/X
151:
1.179 brouard 152: Revision 1.178 2015/01/04 09:35:48 brouard
153: *** empty log message ***
154:
1.178 brouard 155: Revision 1.177 2015/01/03 18:40:56 brouard
156: Summary: Still testing ilc32 on OSX
157:
1.177 brouard 158: Revision 1.176 2015/01/03 16:45:04 brouard
159: *** empty log message ***
160:
1.176 brouard 161: Revision 1.175 2015/01/03 16:33:42 brouard
162: *** empty log message ***
163:
1.175 brouard 164: Revision 1.174 2015/01/03 16:15:49 brouard
165: Summary: Still in cross-compilation
166:
1.174 brouard 167: Revision 1.173 2015/01/03 12:06:26 brouard
168: Summary: trying to detect cross-compilation
169:
1.173 brouard 170: Revision 1.172 2014/12/27 12:07:47 brouard
171: Summary: Back from Visual Studio and Intel, options for compiling for Windows XP
172:
1.172 brouard 173: Revision 1.171 2014/12/23 13:26:59 brouard
174: Summary: Back from Visual C
175:
176: Still problem with utsname.h on Windows
177:
1.171 brouard 178: Revision 1.170 2014/12/23 11:17:12 brouard
179: Summary: Cleaning some \%% back to %%
180:
181: The escape was mandatory for a specific compiler (which one?), but too many warnings.
182:
1.170 brouard 183: Revision 1.169 2014/12/22 23:08:31 brouard
184: Summary: 0.98p
185:
186: Outputs some informations on compiler used, OS etc. Testing on different platforms.
187:
1.169 brouard 188: Revision 1.168 2014/12/22 15:17:42 brouard
1.170 brouard 189: Summary: update
1.169 brouard 190:
1.168 brouard 191: Revision 1.167 2014/12/22 13:50:56 brouard
192: Summary: Testing uname and compiler version and if compiled 32 or 64
193:
194: Testing on Linux 64
195:
1.167 brouard 196: Revision 1.166 2014/12/22 11:40:47 brouard
197: *** empty log message ***
198:
1.166 brouard 199: Revision 1.165 2014/12/16 11:20:36 brouard
200: Summary: After compiling on Visual C
201:
202: * imach.c (Module): Merging 1.61 to 1.162
203:
1.165 brouard 204: Revision 1.164 2014/12/16 10:52:11 brouard
205: Summary: Merging with Visual C after suppressing some warnings for unused variables. Also fixing Saito's bug 0.98Xn
206:
207: * imach.c (Module): Merging 1.61 to 1.162
208:
1.164 brouard 209: Revision 1.163 2014/12/16 10:30:11 brouard
210: * imach.c (Module): Merging 1.61 to 1.162
211:
1.163 brouard 212: Revision 1.162 2014/09/25 11:43:39 brouard
213: Summary: temporary backup 0.99!
214:
1.162 brouard 215: Revision 1.1 2014/09/16 11:06:58 brouard
216: Summary: With some code (wrong) for nlopt
217:
218: Author:
219:
220: Revision 1.161 2014/09/15 20:41:41 brouard
221: Summary: Problem with macro SQR on Intel compiler
222:
1.161 brouard 223: Revision 1.160 2014/09/02 09:24:05 brouard
224: *** empty log message ***
225:
1.160 brouard 226: Revision 1.159 2014/09/01 10:34:10 brouard
227: Summary: WIN32
228: Author: Brouard
229:
1.159 brouard 230: Revision 1.158 2014/08/27 17:11:51 brouard
231: *** empty log message ***
232:
1.158 brouard 233: Revision 1.157 2014/08/27 16:26:55 brouard
234: Summary: Preparing windows Visual studio version
235: Author: Brouard
236:
237: In order to compile on Visual studio, time.h is now correct and time_t
238: and tm struct should be used. difftime should be used but sometimes I
239: just make the differences in raw time format (time(&now).
240: Trying to suppress #ifdef LINUX
241: Add xdg-open for __linux in order to open default browser.
242:
1.157 brouard 243: Revision 1.156 2014/08/25 20:10:10 brouard
244: *** empty log message ***
245:
1.156 brouard 246: Revision 1.155 2014/08/25 18:32:34 brouard
247: Summary: New compile, minor changes
248: Author: Brouard
249:
1.155 brouard 250: Revision 1.154 2014/06/20 17:32:08 brouard
251: Summary: Outputs now all graphs of convergence to period prevalence
252:
1.154 brouard 253: Revision 1.153 2014/06/20 16:45:46 brouard
254: Summary: If 3 live state, convergence to period prevalence on same graph
255: Author: Brouard
256:
1.153 brouard 257: Revision 1.152 2014/06/18 17:54:09 brouard
258: Summary: open browser, use gnuplot on same dir than imach if not found in the path
259:
1.152 brouard 260: Revision 1.151 2014/06/18 16:43:30 brouard
261: *** empty log message ***
262:
1.151 brouard 263: Revision 1.150 2014/06/18 16:42:35 brouard
264: Summary: If gnuplot is not in the path try on same directory than imach binary (OSX)
265: Author: brouard
266:
1.150 brouard 267: Revision 1.149 2014/06/18 15:51:14 brouard
268: Summary: Some fixes in parameter files errors
269: Author: Nicolas Brouard
270:
1.149 brouard 271: Revision 1.148 2014/06/17 17:38:48 brouard
272: Summary: Nothing new
273: Author: Brouard
274:
275: Just a new packaging for OS/X version 0.98nS
276:
1.148 brouard 277: Revision 1.147 2014/06/16 10:33:11 brouard
278: *** empty log message ***
279:
1.147 brouard 280: Revision 1.146 2014/06/16 10:20:28 brouard
281: Summary: Merge
282: Author: Brouard
283:
284: Merge, before building revised version.
285:
1.146 brouard 286: Revision 1.145 2014/06/10 21:23:15 brouard
287: Summary: Debugging with valgrind
288: Author: Nicolas Brouard
289:
290: Lot of changes in order to output the results with some covariates
291: After the Edimburgh REVES conference 2014, it seems mandatory to
292: improve the code.
293: No more memory valgrind error but a lot has to be done in order to
294: continue the work of splitting the code into subroutines.
295: Also, decodemodel has been improved. Tricode is still not
296: optimal. nbcode should be improved. Documentation has been added in
297: the source code.
298:
1.144 brouard 299: Revision 1.143 2014/01/26 09:45:38 brouard
300: Summary: Version 0.98nR (to be improved, but gives same optimization results as 0.98k. Nice, promising
301:
302: * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
303: (Module): Version 0.98nR Running ok, but output format still only works for three covariates.
304:
1.143 brouard 305: Revision 1.142 2014/01/26 03:57:36 brouard
306: Summary: gnuplot changed plot w l 1 has to be changed to plot w l lt 2
307:
308: * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
309:
1.142 brouard 310: Revision 1.141 2014/01/26 02:42:01 brouard
311: * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
312:
1.141 brouard 313: Revision 1.140 2011/09/02 10:37:54 brouard
314: Summary: times.h is ok with mingw32 now.
315:
1.140 brouard 316: Revision 1.139 2010/06/14 07:50:17 brouard
317: After the theft of my laptop, I probably lost some lines of codes which were not uploaded to the CVS tree.
318: I remember having already fixed agemin agemax which are pointers now but not cvs saved.
319:
1.139 brouard 320: Revision 1.138 2010/04/30 18:19:40 brouard
321: *** empty log message ***
322:
1.138 brouard 323: Revision 1.137 2010/04/29 18:11:38 brouard
324: (Module): Checking covariates for more complex models
325: than V1+V2. A lot of change to be done. Unstable.
326:
1.137 brouard 327: Revision 1.136 2010/04/26 20:30:53 brouard
328: (Module): merging some libgsl code. Fixing computation
329: of likelione (using inter/intrapolation if mle = 0) in order to
330: get same likelihood as if mle=1.
331: Some cleaning of code and comments added.
332:
1.136 brouard 333: Revision 1.135 2009/10/29 15:33:14 brouard
334: (Module): Now imach stops if date of birth, at least year of birth, is not given. Some cleaning of the code.
335:
1.135 brouard 336: Revision 1.134 2009/10/29 13:18:53 brouard
337: (Module): Now imach stops if date of birth, at least year of birth, is not given. Some cleaning of the code.
338:
1.134 brouard 339: Revision 1.133 2009/07/06 10:21:25 brouard
340: just nforces
341:
1.133 brouard 342: Revision 1.132 2009/07/06 08:22:05 brouard
343: Many tings
344:
1.132 brouard 345: Revision 1.131 2009/06/20 16:22:47 brouard
346: Some dimensions resccaled
347:
1.131 brouard 348: Revision 1.130 2009/05/26 06:44:34 brouard
349: (Module): Max Covariate is now set to 20 instead of 8. A
350: lot of cleaning with variables initialized to 0. Trying to make
351: V2+V3*age+V1+V4 strb=V3*age+V1+V4 working better.
352:
1.130 brouard 353: Revision 1.129 2007/08/31 13:49:27 lievre
354: Modification of the way of exiting when the covariate is not binary in order to see on the window the error message before exiting
355:
1.129 lievre 356: Revision 1.128 2006/06/30 13:02:05 brouard
357: (Module): Clarifications on computing e.j
358:
1.128 brouard 359: Revision 1.127 2006/04/28 18:11:50 brouard
360: (Module): Yes the sum of survivors was wrong since
361: imach-114 because nhstepm was no more computed in the age
362: loop. Now we define nhstepma in the age loop.
363: (Module): In order to speed up (in case of numerous covariates) we
364: compute health expectancies (without variances) in a first step
365: and then all the health expectancies with variances or standard
366: deviation (needs data from the Hessian matrices) which slows the
367: computation.
368: In the future we should be able to stop the program is only health
369: expectancies and graph are needed without standard deviations.
370:
1.127 brouard 371: Revision 1.126 2006/04/28 17:23:28 brouard
372: (Module): Yes the sum of survivors was wrong since
373: imach-114 because nhstepm was no more computed in the age
374: loop. Now we define nhstepma in the age loop.
375: Version 0.98h
376:
1.126 brouard 377: Revision 1.125 2006/04/04 15:20:31 lievre
378: Errors in calculation of health expectancies. Age was not initialized.
379: Forecasting file added.
380:
381: Revision 1.124 2006/03/22 17:13:53 lievre
382: Parameters are printed with %lf instead of %f (more numbers after the comma).
383: The log-likelihood is printed in the log file
384:
385: Revision 1.123 2006/03/20 10:52:43 brouard
386: * imach.c (Module): <title> changed, corresponds to .htm file
387: name. <head> headers where missing.
388:
389: * imach.c (Module): Weights can have a decimal point as for
390: English (a comma might work with a correct LC_NUMERIC environment,
391: otherwise the weight is truncated).
392: Modification of warning when the covariates values are not 0 or
393: 1.
394: Version 0.98g
395:
396: Revision 1.122 2006/03/20 09:45:41 brouard
397: (Module): Weights can have a decimal point as for
398: English (a comma might work with a correct LC_NUMERIC environment,
399: otherwise the weight is truncated).
400: Modification of warning when the covariates values are not 0 or
401: 1.
402: Version 0.98g
403:
404: Revision 1.121 2006/03/16 17:45:01 lievre
405: * imach.c (Module): Comments concerning covariates added
406:
407: * imach.c (Module): refinements in the computation of lli if
408: status=-2 in order to have more reliable computation if stepm is
409: not 1 month. Version 0.98f
410:
411: Revision 1.120 2006/03/16 15:10:38 lievre
412: (Module): refinements in the computation of lli if
413: status=-2 in order to have more reliable computation if stepm is
414: not 1 month. Version 0.98f
415:
416: Revision 1.119 2006/03/15 17:42:26 brouard
417: (Module): Bug if status = -2, the loglikelihood was
418: computed as likelihood omitting the logarithm. Version O.98e
419:
420: Revision 1.118 2006/03/14 18:20:07 brouard
421: (Module): varevsij Comments added explaining the second
422: table of variances if popbased=1 .
423: (Module): Covariances of eij, ekl added, graphs fixed, new html link.
424: (Module): Function pstamp added
425: (Module): Version 0.98d
426:
427: Revision 1.117 2006/03/14 17:16:22 brouard
428: (Module): varevsij Comments added explaining the second
429: table of variances if popbased=1 .
430: (Module): Covariances of eij, ekl added, graphs fixed, new html link.
431: (Module): Function pstamp added
432: (Module): Version 0.98d
433:
434: Revision 1.116 2006/03/06 10:29:27 brouard
435: (Module): Variance-covariance wrong links and
436: varian-covariance of ej. is needed (Saito).
437:
438: Revision 1.115 2006/02/27 12:17:45 brouard
439: (Module): One freematrix added in mlikeli! 0.98c
440:
441: Revision 1.114 2006/02/26 12:57:58 brouard
442: (Module): Some improvements in processing parameter
443: filename with strsep.
444:
445: Revision 1.113 2006/02/24 14:20:24 brouard
446: (Module): Memory leaks checks with valgrind and:
447: datafile was not closed, some imatrix were not freed and on matrix
448: allocation too.
449:
450: Revision 1.112 2006/01/30 09:55:26 brouard
451: (Module): Back to gnuplot.exe instead of wgnuplot.exe
452:
453: Revision 1.111 2006/01/25 20:38:18 brouard
454: (Module): Lots of cleaning and bugs added (Gompertz)
455: (Module): Comments can be added in data file. Missing date values
456: can be a simple dot '.'.
457:
458: Revision 1.110 2006/01/25 00:51:50 brouard
459: (Module): Lots of cleaning and bugs added (Gompertz)
460:
461: Revision 1.109 2006/01/24 19:37:15 brouard
462: (Module): Comments (lines starting with a #) are allowed in data.
463:
464: Revision 1.108 2006/01/19 18:05:42 lievre
465: Gnuplot problem appeared...
466: To be fixed
467:
468: Revision 1.107 2006/01/19 16:20:37 brouard
469: Test existence of gnuplot in imach path
470:
471: Revision 1.106 2006/01/19 13:24:36 brouard
472: Some cleaning and links added in html output
473:
474: Revision 1.105 2006/01/05 20:23:19 lievre
475: *** empty log message ***
476:
477: Revision 1.104 2005/09/30 16:11:43 lievre
478: (Module): sump fixed, loop imx fixed, and simplifications.
479: (Module): If the status is missing at the last wave but we know
480: that the person is alive, then we can code his/her status as -2
481: (instead of missing=-1 in earlier versions) and his/her
482: contributions to the likelihood is 1 - Prob of dying from last
483: health status (= 1-p13= p11+p12 in the easiest case of somebody in
484: the healthy state at last known wave). Version is 0.98
485:
486: Revision 1.103 2005/09/30 15:54:49 lievre
487: (Module): sump fixed, loop imx fixed, and simplifications.
488:
489: Revision 1.102 2004/09/15 17:31:30 brouard
490: Add the possibility to read data file including tab characters.
491:
492: Revision 1.101 2004/09/15 10:38:38 brouard
493: Fix on curr_time
494:
495: Revision 1.100 2004/07/12 18:29:06 brouard
496: Add version for Mac OS X. Just define UNIX in Makefile
497:
498: Revision 1.99 2004/06/05 08:57:40 brouard
499: *** empty log message ***
500:
501: Revision 1.98 2004/05/16 15:05:56 brouard
502: New version 0.97 . First attempt to estimate force of mortality
503: directly from the data i.e. without the need of knowing the health
504: state at each age, but using a Gompertz model: log u =a + b*age .
505: This is the basic analysis of mortality and should be done before any
506: other analysis, in order to test if the mortality estimated from the
507: cross-longitudinal survey is different from the mortality estimated
508: from other sources like vital statistic data.
509:
510: The same imach parameter file can be used but the option for mle should be -3.
511:
1.133 brouard 512: Agnès, who wrote this part of the code, tried to keep most of the
1.126 brouard 513: former routines in order to include the new code within the former code.
514:
515: The output is very simple: only an estimate of the intercept and of
516: the slope with 95% confident intervals.
517:
518: Current limitations:
519: A) Even if you enter covariates, i.e. with the
520: model= V1+V2 equation for example, the programm does only estimate a unique global model without covariates.
521: B) There is no computation of Life Expectancy nor Life Table.
522:
523: Revision 1.97 2004/02/20 13:25:42 lievre
524: Version 0.96d. Population forecasting command line is (temporarily)
525: suppressed.
526:
527: Revision 1.96 2003/07/15 15:38:55 brouard
528: * imach.c (Repository): Errors in subdirf, 2, 3 while printing tmpout is
529: rewritten within the same printf. Workaround: many printfs.
530:
531: Revision 1.95 2003/07/08 07:54:34 brouard
532: * imach.c (Repository):
533: (Repository): Using imachwizard code to output a more meaningful covariance
534: matrix (cov(a12,c31) instead of numbers.
535:
536: Revision 1.94 2003/06/27 13:00:02 brouard
537: Just cleaning
538:
539: Revision 1.93 2003/06/25 16:33:55 brouard
540: (Module): On windows (cygwin) function asctime_r doesn't
541: exist so I changed back to asctime which exists.
542: (Module): Version 0.96b
543:
544: Revision 1.92 2003/06/25 16:30:45 brouard
545: (Module): On windows (cygwin) function asctime_r doesn't
546: exist so I changed back to asctime which exists.
547:
548: Revision 1.91 2003/06/25 15:30:29 brouard
549: * imach.c (Repository): Duplicated warning errors corrected.
550: (Repository): Elapsed time after each iteration is now output. It
551: helps to forecast when convergence will be reached. Elapsed time
552: is stamped in powell. We created a new html file for the graphs
553: concerning matrix of covariance. It has extension -cov.htm.
554:
555: Revision 1.90 2003/06/24 12:34:15 brouard
556: (Module): Some bugs corrected for windows. Also, when
557: mle=-1 a template is output in file "or"mypar.txt with the design
558: of the covariance matrix to be input.
559:
560: Revision 1.89 2003/06/24 12:30:52 brouard
561: (Module): Some bugs corrected for windows. Also, when
562: mle=-1 a template is output in file "or"mypar.txt with the design
563: of the covariance matrix to be input.
564:
565: Revision 1.88 2003/06/23 17:54:56 brouard
566: * 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.
567:
568: Revision 1.87 2003/06/18 12:26:01 brouard
569: Version 0.96
570:
571: Revision 1.86 2003/06/17 20:04:08 brouard
572: (Module): Change position of html and gnuplot routines and added
573: routine fileappend.
574:
575: Revision 1.85 2003/06/17 13:12:43 brouard
576: * imach.c (Repository): Check when date of death was earlier that
577: current date of interview. It may happen when the death was just
578: prior to the death. In this case, dh was negative and likelihood
579: was wrong (infinity). We still send an "Error" but patch by
580: assuming that the date of death was just one stepm after the
581: interview.
582: (Repository): Because some people have very long ID (first column)
583: we changed int to long in num[] and we added a new lvector for
584: memory allocation. But we also truncated to 8 characters (left
585: truncation)
586: (Repository): No more line truncation errors.
587:
588: Revision 1.84 2003/06/13 21:44:43 brouard
589: * imach.c (Repository): Replace "freqsummary" at a correct
590: place. It differs from routine "prevalence" which may be called
591: many times. Probs is memory consuming and must be used with
592: parcimony.
593: Version 0.95a3 (should output exactly the same maximization than 0.8a2)
594:
595: Revision 1.83 2003/06/10 13:39:11 lievre
596: *** empty log message ***
597:
598: Revision 1.82 2003/06/05 15:57:20 brouard
599: Add log in imach.c and fullversion number is now printed.
600:
601: */
602: /*
603: Interpolated Markov Chain
604:
605: Short summary of the programme:
606:
607: This program computes Healthy Life Expectancies from
608: cross-longitudinal data. Cross-longitudinal data consist in: -1- a
609: first survey ("cross") where individuals from different ages are
610: interviewed on their health status or degree of disability (in the
611: case of a health survey which is our main interest) -2- at least a
612: second wave of interviews ("longitudinal") which measure each change
613: (if any) in individual health status. Health expectancies are
614: computed from the time spent in each health state according to a
615: model. More health states you consider, more time is necessary to reach the
616: Maximum Likelihood of the parameters involved in the model. The
617: simplest model is the multinomial logistic model where pij is the
618: probability to be observed in state j at the second wave
619: conditional to be observed in state i at the first wave. Therefore
620: the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where
621: 'age' is age and 'sex' is a covariate. If you want to have a more
622: complex model than "constant and age", you should modify the program
623: where the markup *Covariates have to be included here again* invites
624: you to do it. More covariates you add, slower the
625: convergence.
626:
627: The advantage of this computer programme, compared to a simple
628: multinomial logistic model, is clear when the delay between waves is not
629: identical for each individual. Also, if a individual missed an
630: intermediate interview, the information is lost, but taken into
631: account using an interpolation or extrapolation.
632:
633: hPijx is the probability to be observed in state i at age x+h
634: conditional to the observed state i at age x. The delay 'h' can be
635: split into an exact number (nh*stepm) of unobserved intermediate
636: states. This elementary transition (by month, quarter,
637: semester or year) is modelled as a multinomial logistic. The hPx
638: matrix is simply the matrix product of nh*stepm elementary matrices
639: and the contribution of each individual to the likelihood is simply
640: hPijx.
641:
642: Also this programme outputs the covariance matrix of the parameters but also
643: of the life expectancies. It also computes the period (stable) prevalence.
644:
1.133 brouard 645: Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).
646: Institut national d'études démographiques, Paris.
1.126 brouard 647: This software have been partly granted by Euro-REVES, a concerted action
648: from the European Union.
649: It is copyrighted identically to a GNU software product, ie programme and
650: software can be distributed freely for non commercial use. Latest version
651: can be accessed at http://euroreves.ined.fr/imach .
652:
653: Help to debug: LD_PRELOAD=/usr/local/lib/libnjamd.so ./imach foo.imach
654: or better on gdb : set env LD_PRELOAD=/usr/local/lib/libnjamd.so
655:
656: **********************************************************************/
657: /*
658: main
659: read parameterfile
660: read datafile
661: concatwav
662: freqsummary
663: if (mle >= 1)
664: mlikeli
665: print results files
666: if mle==1
667: computes hessian
668: read end of parameter file: agemin, agemax, bage, fage, estepm
669: begin-prev-date,...
670: open gnuplot file
671: open html file
1.145 brouard 672: period (stable) prevalence | pl_nom 1-1 2-2 etc by covariate
673: for age prevalim() | #****** V1=0 V2=1 V3=1 V4=0 ******
674: | 65 1 0 2 1 3 1 4 0 0.96326 0.03674
675: freexexit2 possible for memory heap.
676:
677: h Pij x | pij_nom ficrestpij
678: # Cov Agex agex+h hpijx with i,j= 1-1 1-2 1-3 2-1 2-2 2-3
679: 1 85 85 1.00000 0.00000 0.00000 0.00000 1.00000 0.00000
680: 1 85 86 0.68299 0.22291 0.09410 0.71093 0.00000 0.28907
681:
682: 1 65 99 0.00364 0.00322 0.99314 0.00350 0.00310 0.99340
683: 1 65 100 0.00214 0.00204 0.99581 0.00206 0.00196 0.99597
684: variance of p one-step probabilities varprob | prob_nom ficresprob #One-step probabilities and stand. devi in ()
685: Standard deviation of one-step probabilities | probcor_nom ficresprobcor #One-step probabilities and correlation matrix
686: Matrix of variance covariance of one-step probabilities | probcov_nom ficresprobcov #One-step probabilities and covariance matrix
687:
1.126 brouard 688: forecasting if prevfcast==1 prevforecast call prevalence()
689: health expectancies
690: Variance-covariance of DFLE
691: prevalence()
692: movingaverage()
693: varevsij()
694: if popbased==1 varevsij(,popbased)
695: total life expectancies
696: Variance of period (stable) prevalence
697: end
698: */
699:
1.187 brouard 700: /* #define DEBUG */
701: /* #define DEBUGBRENT */
1.203 brouard 702: /* #define DEBUGLINMIN */
703: /* #define DEBUGHESS */
704: #define DEBUGHESSIJ
705: /* #define LINMINORIGINAL /\* Don't use loop on scale in linmin (accepting nan)*\/ */
1.165 brouard 706: #define POWELL /* Instead of NLOPT */
1.192 brouard 707: #define POWELLF1F3 /* Skip test */
1.186 brouard 708: /* #define POWELLORIGINAL /\* Don't use Directest to decide new direction but original Powell test *\/ */
709: /* #define MNBRAKORIGINAL /\* Don't use mnbrak fix *\/ */
1.126 brouard 710:
711: #include <math.h>
712: #include <stdio.h>
713: #include <stdlib.h>
714: #include <string.h>
1.159 brouard 715:
716: #ifdef _WIN32
717: #include <io.h>
1.172 brouard 718: #include <windows.h>
719: #include <tchar.h>
1.159 brouard 720: #else
1.126 brouard 721: #include <unistd.h>
1.159 brouard 722: #endif
1.126 brouard 723:
724: #include <limits.h>
725: #include <sys/types.h>
1.171 brouard 726:
727: #if defined(__GNUC__)
728: #include <sys/utsname.h> /* Doesn't work on Windows */
729: #endif
730:
1.126 brouard 731: #include <sys/stat.h>
732: #include <errno.h>
1.159 brouard 733: /* extern int errno; */
1.126 brouard 734:
1.157 brouard 735: /* #ifdef LINUX */
736: /* #include <time.h> */
737: /* #include "timeval.h" */
738: /* #else */
739: /* #include <sys/time.h> */
740: /* #endif */
741:
1.126 brouard 742: #include <time.h>
743:
1.136 brouard 744: #ifdef GSL
745: #include <gsl/gsl_errno.h>
746: #include <gsl/gsl_multimin.h>
747: #endif
748:
1.167 brouard 749:
1.162 brouard 750: #ifdef NLOPT
751: #include <nlopt.h>
752: typedef struct {
753: double (* function)(double [] );
754: } myfunc_data ;
755: #endif
756:
1.126 brouard 757: /* #include <libintl.h> */
758: /* #define _(String) gettext (String) */
759:
1.141 brouard 760: #define MAXLINE 1024 /* Was 256. Overflow with 312 with 2 states and 4 covariates. Should be ok */
1.126 brouard 761:
762: #define GNUPLOTPROGRAM "gnuplot"
763: /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
764: #define FILENAMELENGTH 132
765:
766: #define GLOCK_ERROR_NOPATH -1 /* empty path */
767: #define GLOCK_ERROR_GETCWD -2 /* cannot get cwd */
768:
1.144 brouard 769: #define MAXPARM 128 /**< Maximum number of parameters for the optimization */
770: #define NPARMAX 64 /**< (nlstate+ndeath-1)*nlstate*ncovmodel */
1.126 brouard 771:
772: #define NINTERVMAX 8
1.144 brouard 773: #define NLSTATEMAX 8 /**< Maximum number of live states (for func) */
774: #define NDEATHMAX 8 /**< Maximum number of dead states (for func) */
775: #define NCOVMAX 20 /**< Maximum number of covariates, including generated covariates V1*V2 */
1.197 brouard 776: #define codtabm(h,k) (1 & (h-1) >> (k-1))+1
1.211 brouard 777: /*#define decodtabm(h,k,cptcoveff)= (h <= (1<<cptcoveff)?(((h-1) >> (k-1)) & 1) +1 : -1)*/
778: #define decodtabm(h,k,cptcoveff) (((h-1) >> (k-1)) & 1) +1
1.126 brouard 779: #define MAXN 20000
1.144 brouard 780: #define YEARM 12. /**< Number of months per year */
1.126 brouard 781: #define AGESUP 130
782: #define AGEBASE 40
1.194 brouard 783: #define AGEOVERFLOW 1.e20
1.164 brouard 784: #define AGEGOMP 10 /**< Minimal age for Gompertz adjustment */
1.157 brouard 785: #ifdef _WIN32
786: #define DIRSEPARATOR '\\'
787: #define CHARSEPARATOR "\\"
788: #define ODIRSEPARATOR '/'
789: #else
1.126 brouard 790: #define DIRSEPARATOR '/'
791: #define CHARSEPARATOR "/"
792: #define ODIRSEPARATOR '\\'
793: #endif
794:
1.216 ! brouard 795: /* $Id: imach.c,v 1.215 2015/12/16 08:52:24 brouard Exp $ */
1.126 brouard 796: /* $State: Exp $ */
1.196 brouard 797: #include "version.h"
798: char version[]=__IMACH_VERSION__;
1.204 brouard 799: 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";
1.216 ! brouard 800: char fullversion[]="$Revision: 1.215 $ $Date: 2015/12/16 08:52:24 $";
1.126 brouard 801: char strstart[80];
802: char optionfilext[10], optionfilefiname[FILENAMELENGTH];
1.130 brouard 803: int erreur=0, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings */
1.187 brouard 804: int nagesqr=0, nforce=0; /* nagesqr=1 if model is including age*age, number of forces */
1.145 brouard 805: /* Number of covariates model=V2+V1+ V3*age+V2*V4 */
806: int cptcovn=0; /**< cptcovn number of covariates added in the model (excepting constant and age and age*product) */
807: int cptcovt=0; /**< cptcovt number of covariates added in the model (excepting constant and age) */
808: int cptcovs=0; /**< cptcovs number of simple covariates V2+V1 =2 */
809: int cptcovage=0; /**< Number of covariates with age: V3*age only =1 */
810: int cptcovprodnoage=0; /**< Number of covariate products without age */
811: int cptcoveff=0; /* Total number of covariates to vary for printing results */
812: int cptcov=0; /* Working variable */
1.126 brouard 813: int npar=NPARMAX;
814: int nlstate=2; /* Number of live states */
815: int ndeath=1; /* Number of dead states */
1.130 brouard 816: int ncovmodel=0, ncovcol=0; /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
1.126 brouard 817: int popbased=0;
818:
819: int *wav; /* Number of waves for this individuual 0 is possible */
1.130 brouard 820: int maxwav=0; /* Maxim number of waves */
821: int jmin=0, jmax=0; /* min, max spacing between 2 waves */
822: int ijmin=0, ijmax=0; /* Individuals having jmin and jmax */
823: int gipmx=0, gsw=0; /* Global variables on the number of contributions
1.126 brouard 824: to the likelihood and the sum of weights (done by funcone)*/
1.130 brouard 825: int mle=1, weightopt=0;
1.126 brouard 826: int **mw; /* mw[mi][i] is number of the mi wave for this individual */
827: int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
828: int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between
829: * wave mi and wave mi+1 is not an exact multiple of stepm. */
1.162 brouard 830: int countcallfunc=0; /* Count the number of calls to func */
1.130 brouard 831: double jmean=1; /* Mean space between 2 waves */
1.145 brouard 832: double **matprod2(); /* test */
1.126 brouard 833: double **oldm, **newm, **savm; /* Working pointers to matrices */
834: double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
1.136 brouard 835: /*FILE *fic ; */ /* Used in readdata only */
1.214 brouard 836: FILE *ficpar, *ficparo,*ficres, *ficresp, *ficresphtm, *ficresphtmfr, *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
1.126 brouard 837: FILE *ficlog, *ficrespow;
1.130 brouard 838: int globpr=0; /* Global variable for printing or not */
1.126 brouard 839: double fretone; /* Only one call to likelihood */
1.130 brouard 840: long ipmx=0; /* Number of contributions */
1.126 brouard 841: double sw; /* Sum of weights */
842: char filerespow[FILENAMELENGTH];
843: char fileresilk[FILENAMELENGTH]; /* File of individual contributions to the likelihood */
844: FILE *ficresilk;
845: FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
846: FILE *ficresprobmorprev;
847: FILE *fichtm, *fichtmcov; /* Html File */
848: FILE *ficreseij;
849: char filerese[FILENAMELENGTH];
850: FILE *ficresstdeij;
851: char fileresstde[FILENAMELENGTH];
852: FILE *ficrescveij;
853: char filerescve[FILENAMELENGTH];
854: FILE *ficresvij;
855: char fileresv[FILENAMELENGTH];
856: FILE *ficresvpl;
857: char fileresvpl[FILENAMELENGTH];
858: char title[MAXLINE];
859: char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH], filerespl[FILENAMELENGTH];
860: char plotcmd[FILENAMELENGTH], pplotcmd[FILENAMELENGTH];
861: char tmpout[FILENAMELENGTH], tmpout2[FILENAMELENGTH];
862: char command[FILENAMELENGTH];
863: int outcmd=0;
864:
865: char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
1.202 brouard 866: char fileresu[FILENAMELENGTH]; /* fileres without r in front */
1.126 brouard 867: char filelog[FILENAMELENGTH]; /* Log file */
868: char filerest[FILENAMELENGTH];
869: char fileregp[FILENAMELENGTH];
870: char popfile[FILENAMELENGTH];
871:
872: char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilehtmcov[FILENAMELENGTH] ;
873:
1.157 brouard 874: /* struct timeval start_time, end_time, curr_time, last_time, forecast_time; */
875: /* struct timezone tzp; */
876: /* extern int gettimeofday(); */
877: struct tm tml, *gmtime(), *localtime();
878:
879: extern time_t time();
880:
881: struct tm start_time, end_time, curr_time, last_time, forecast_time;
882: time_t rstart_time, rend_time, rcurr_time, rlast_time, rforecast_time; /* raw time */
883: struct tm tm;
884:
1.126 brouard 885: char strcurr[80], strfor[80];
886:
887: char *endptr;
888: long lval;
889: double dval;
890:
891: #define NR_END 1
892: #define FREE_ARG char*
893: #define FTOL 1.0e-10
894:
895: #define NRANSI
896: #define ITMAX 200
897:
898: #define TOL 2.0e-4
899:
900: #define CGOLD 0.3819660
901: #define ZEPS 1.0e-10
902: #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);
903:
904: #define GOLD 1.618034
905: #define GLIMIT 100.0
906: #define TINY 1.0e-20
907:
908: static double maxarg1,maxarg2;
909: #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
910: #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
911:
912: #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
913: #define rint(a) floor(a+0.5)
1.166 brouard 914: /* http://www.thphys.uni-heidelberg.de/~robbers/cmbeasy/doc/html/myutils_8h-source.html */
1.183 brouard 915: #define mytinydouble 1.0e-16
1.166 brouard 916: /* #define DEQUAL(a,b) (fabs((a)-(b))<mytinydouble) */
917: /* http://www.thphys.uni-heidelberg.de/~robbers/cmbeasy/doc/html/mynrutils_8h-source.html */
918: /* static double dsqrarg; */
919: /* #define DSQR(a) (DEQUAL((dsqrarg=(a)),0.0) ? 0.0 : dsqrarg*dsqrarg) */
1.126 brouard 920: static double sqrarg;
921: #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
922: #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}
923: int agegomp= AGEGOMP;
924:
925: int imx;
926: int stepm=1;
927: /* Stepm, step in month: minimum step interpolation*/
928:
929: int estepm;
930: /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
931:
932: int m,nb;
933: long *num;
1.197 brouard 934: int firstpass=0, lastpass=4,*cod, *cens;
1.192 brouard 935: int *ncodemax; /* ncodemax[j]= Number of modalities of the j th
936: covariate for which somebody answered excluding
937: undefined. Usually 2: 0 and 1. */
938: int *ncodemaxwundef; /* ncodemax[j]= Number of modalities of the j th
939: covariate for which somebody answered including
940: undefined. Usually 3: -1, 0 and 1. */
1.126 brouard 941: double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
942: double **pmmij, ***probs;
943: double *ageexmed,*agecens;
944: double dateintmean=0;
945:
946: double *weight;
947: int **s; /* Status */
1.141 brouard 948: double *agedc;
1.145 brouard 949: double **covar; /**< covar[j,i], value of jth covariate for individual i,
1.141 brouard 950: * covar=matrix(0,NCOVMAX,1,n);
1.187 brouard 951: * cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*age; */
1.141 brouard 952: double idx;
953: int **nbcode, *Tvar; /**< model=V2 => Tvar[1]= 2 */
1.197 brouard 954: int *Tage;
1.145 brouard 955: int *Ndum; /** Freq of modality (tricode */
1.200 brouard 956: /* int **codtab;*/ /**< codtab=imatrix(1,100,1,10); */
1.141 brouard 957: int **Tvard, *Tprod, cptcovprod, *Tvaraff;
1.126 brouard 958: double *lsurv, *lpop, *tpop;
959:
1.143 brouard 960: double ftol=FTOL; /**< Tolerance for computing Max Likelihood */
961: double ftolhess; /**< Tolerance for computing hessian */
1.126 brouard 962:
963: /**************** split *************************/
964: static int split( char *path, char *dirc, char *name, char *ext, char *finame )
965: {
966: /* From a file name with (full) path (either Unix or Windows) we extract the directory (dirc)
967: the name of the file (name), its extension only (ext) and its first part of the name (finame)
968: */
969: char *ss; /* pointer */
1.186 brouard 970: int l1=0, l2=0; /* length counters */
1.126 brouard 971:
972: l1 = strlen(path ); /* length of path */
973: if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
974: ss= strrchr( path, DIRSEPARATOR ); /* find last / */
975: if ( ss == NULL ) { /* no directory, so determine current directory */
976: strcpy( name, path ); /* we got the fullname name because no directory */
977: /*if(strrchr(path, ODIRSEPARATOR )==NULL)
978: printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
979: /* get current working directory */
980: /* extern char* getcwd ( char *buf , int len);*/
1.184 brouard 981: #ifdef WIN32
982: if (_getcwd( dirc, FILENAME_MAX ) == NULL ) {
983: #else
984: if (getcwd(dirc, FILENAME_MAX) == NULL) {
985: #endif
1.126 brouard 986: return( GLOCK_ERROR_GETCWD );
987: }
988: /* got dirc from getcwd*/
989: printf(" DIRC = %s \n",dirc);
1.205 brouard 990: } else { /* strip directory from path */
1.126 brouard 991: ss++; /* after this, the filename */
992: l2 = strlen( ss ); /* length of filename */
993: if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
994: strcpy( name, ss ); /* save file name */
995: strncpy( dirc, path, l1 - l2 ); /* now the directory */
1.186 brouard 996: dirc[l1-l2] = '\0'; /* add zero */
1.126 brouard 997: printf(" DIRC2 = %s \n",dirc);
998: }
999: /* We add a separator at the end of dirc if not exists */
1000: l1 = strlen( dirc ); /* length of directory */
1001: if( dirc[l1-1] != DIRSEPARATOR ){
1002: dirc[l1] = DIRSEPARATOR;
1003: dirc[l1+1] = 0;
1004: printf(" DIRC3 = %s \n",dirc);
1005: }
1006: ss = strrchr( name, '.' ); /* find last / */
1007: if (ss >0){
1008: ss++;
1009: strcpy(ext,ss); /* save extension */
1010: l1= strlen( name);
1011: l2= strlen(ss)+1;
1012: strncpy( finame, name, l1-l2);
1013: finame[l1-l2]= 0;
1014: }
1015:
1016: return( 0 ); /* we're done */
1017: }
1018:
1019:
1020: /******************************************/
1021:
1022: void replace_back_to_slash(char *s, char*t)
1023: {
1024: int i;
1025: int lg=0;
1026: i=0;
1027: lg=strlen(t);
1028: for(i=0; i<= lg; i++) {
1029: (s[i] = t[i]);
1030: if (t[i]== '\\') s[i]='/';
1031: }
1032: }
1033:
1.132 brouard 1034: char *trimbb(char *out, char *in)
1.137 brouard 1035: { /* Trim multiple blanks in line but keeps first blanks if line starts with blanks */
1.132 brouard 1036: char *s;
1037: s=out;
1038: while (*in != '\0'){
1.137 brouard 1039: while( *in == ' ' && *(in+1) == ' '){ /* && *(in+1) != '\0'){*/
1.132 brouard 1040: in++;
1041: }
1042: *out++ = *in++;
1043: }
1044: *out='\0';
1045: return s;
1046: }
1047:
1.187 brouard 1048: /* char *substrchaine(char *out, char *in, char *chain) */
1049: /* { */
1050: /* /\* Substract chain 'chain' from 'in', return and output 'out' *\/ */
1051: /* char *s, *t; */
1052: /* t=in;s=out; */
1053: /* while ((*in != *chain) && (*in != '\0')){ */
1054: /* *out++ = *in++; */
1055: /* } */
1056:
1057: /* /\* *in matches *chain *\/ */
1058: /* while ((*in++ == *chain++) && (*in != '\0')){ */
1059: /* printf("*in = %c, *out= %c *chain= %c \n", *in, *out, *chain); */
1060: /* } */
1061: /* in--; chain--; */
1062: /* while ( (*in != '\0')){ */
1063: /* printf("Bef *in = %c, *out= %c *chain= %c \n", *in, *out, *chain); */
1064: /* *out++ = *in++; */
1065: /* printf("Aft *in = %c, *out= %c *chain= %c \n", *in, *out, *chain); */
1066: /* } */
1067: /* *out='\0'; */
1068: /* out=s; */
1069: /* return out; */
1070: /* } */
1071: char *substrchaine(char *out, char *in, char *chain)
1072: {
1073: /* Substract chain 'chain' from 'in', return and output 'out' */
1074: /* in="V1+V1*age+age*age+V2", chain="age*age" */
1075:
1076: char *strloc;
1077:
1078: strcpy (out, in);
1079: strloc = strstr(out, chain); /* strloc points to out at age*age+V2 */
1080: printf("Bef strloc=%s chain=%s out=%s \n", strloc, chain, out);
1081: if(strloc != NULL){
1082: /* will affect out */ /* strloc+strlenc(chain)=+V2 */ /* Will also work in Unicode */
1083: memmove(strloc,strloc+strlen(chain), strlen(strloc+strlen(chain))+1);
1084: /* strcpy (strloc, strloc +strlen(chain));*/
1085: }
1086: printf("Aft strloc=%s chain=%s in=%s out=%s \n", strloc, chain, in, out);
1087: return out;
1088: }
1089:
1090:
1.145 brouard 1091: char *cutl(char *blocc, char *alocc, char *in, char occ)
1092: {
1.187 brouard 1093: /* cuts string in into blocc and alocc where blocc ends before FIRST occurence of char 'occ'
1.145 brouard 1094: and alocc starts after first occurence of char 'occ' : ex cutv(blocc,alocc,"abcdef2ghi2j",'2')
1.187 brouard 1095: gives blocc="abcdef" and alocc="ghi2j".
1.145 brouard 1096: If occ is not found blocc is null and alocc is equal to in. Returns blocc
1097: */
1.160 brouard 1098: char *s, *t;
1.145 brouard 1099: t=in;s=in;
1100: while ((*in != occ) && (*in != '\0')){
1101: *alocc++ = *in++;
1102: }
1103: if( *in == occ){
1104: *(alocc)='\0';
1105: s=++in;
1106: }
1107:
1108: if (s == t) {/* occ not found */
1109: *(alocc-(in-s))='\0';
1110: in=s;
1111: }
1112: while ( *in != '\0'){
1113: *blocc++ = *in++;
1114: }
1115:
1116: *blocc='\0';
1117: return t;
1118: }
1.137 brouard 1119: char *cutv(char *blocc, char *alocc, char *in, char occ)
1120: {
1.187 brouard 1121: /* cuts string in into blocc and alocc where blocc ends before LAST occurence of char 'occ'
1.137 brouard 1122: and alocc starts after last occurence of char 'occ' : ex cutv(blocc,alocc,"abcdef2ghi2j",'2')
1123: gives blocc="abcdef2ghi" and alocc="j".
1124: If occ is not found blocc is null and alocc is equal to in. Returns alocc
1125: */
1126: char *s, *t;
1127: t=in;s=in;
1128: while (*in != '\0'){
1129: while( *in == occ){
1130: *blocc++ = *in++;
1131: s=in;
1132: }
1133: *blocc++ = *in++;
1134: }
1135: if (s == t) /* occ not found */
1136: *(blocc-(in-s))='\0';
1137: else
1138: *(blocc-(in-s)-1)='\0';
1139: in=s;
1140: while ( *in != '\0'){
1141: *alocc++ = *in++;
1142: }
1143:
1144: *alocc='\0';
1145: return s;
1146: }
1147:
1.126 brouard 1148: int nbocc(char *s, char occ)
1149: {
1150: int i,j=0;
1151: int lg=20;
1152: i=0;
1153: lg=strlen(s);
1154: for(i=0; i<= lg; i++) {
1155: if (s[i] == occ ) j++;
1156: }
1157: return j;
1158: }
1159:
1.137 brouard 1160: /* void cutv(char *u,char *v, char*t, char occ) */
1161: /* { */
1162: /* /\* cuts string t into u and v where u ends before last occurence of char 'occ' */
1163: /* and v starts after last occurence of char 'occ' : ex cutv(u,v,"abcdef2ghi2j",'2') */
1164: /* gives u="abcdef2ghi" and v="j" *\/ */
1165: /* int i,lg,j,p=0; */
1166: /* i=0; */
1167: /* lg=strlen(t); */
1168: /* for(j=0; j<=lg-1; j++) { */
1169: /* if((t[j]!= occ) && (t[j+1]== occ)) p=j+1; */
1170: /* } */
1.126 brouard 1171:
1.137 brouard 1172: /* for(j=0; j<p; j++) { */
1173: /* (u[j] = t[j]); */
1174: /* } */
1175: /* u[p]='\0'; */
1.126 brouard 1176:
1.137 brouard 1177: /* for(j=0; j<= lg; j++) { */
1178: /* if (j>=(p+1))(v[j-p-1] = t[j]); */
1179: /* } */
1180: /* } */
1.126 brouard 1181:
1.160 brouard 1182: #ifdef _WIN32
1183: char * strsep(char **pp, const char *delim)
1184: {
1185: char *p, *q;
1186:
1187: if ((p = *pp) == NULL)
1188: return 0;
1189: if ((q = strpbrk (p, delim)) != NULL)
1190: {
1191: *pp = q + 1;
1192: *q = '\0';
1193: }
1194: else
1195: *pp = 0;
1196: return p;
1197: }
1198: #endif
1199:
1.126 brouard 1200: /********************** nrerror ********************/
1201:
1202: void nrerror(char error_text[])
1203: {
1204: fprintf(stderr,"ERREUR ...\n");
1205: fprintf(stderr,"%s\n",error_text);
1206: exit(EXIT_FAILURE);
1207: }
1208: /*********************** vector *******************/
1209: double *vector(int nl, int nh)
1210: {
1211: double *v;
1212: v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
1213: if (!v) nrerror("allocation failure in vector");
1214: return v-nl+NR_END;
1215: }
1216:
1217: /************************ free vector ******************/
1218: void free_vector(double*v, int nl, int nh)
1219: {
1220: free((FREE_ARG)(v+nl-NR_END));
1221: }
1222:
1223: /************************ivector *******************************/
1224: int *ivector(long nl,long nh)
1225: {
1226: int *v;
1227: v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
1228: if (!v) nrerror("allocation failure in ivector");
1229: return v-nl+NR_END;
1230: }
1231:
1232: /******************free ivector **************************/
1233: void free_ivector(int *v, long nl, long nh)
1234: {
1235: free((FREE_ARG)(v+nl-NR_END));
1236: }
1237:
1238: /************************lvector *******************************/
1239: long *lvector(long nl,long nh)
1240: {
1241: long *v;
1242: v=(long *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(long)));
1243: if (!v) nrerror("allocation failure in ivector");
1244: return v-nl+NR_END;
1245: }
1246:
1247: /******************free lvector **************************/
1248: void free_lvector(long *v, long nl, long nh)
1249: {
1250: free((FREE_ARG)(v+nl-NR_END));
1251: }
1252:
1253: /******************* imatrix *******************************/
1254: int **imatrix(long nrl, long nrh, long ncl, long nch)
1255: /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */
1256: {
1257: long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;
1258: int **m;
1259:
1260: /* allocate pointers to rows */
1261: m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));
1262: if (!m) nrerror("allocation failure 1 in matrix()");
1263: m += NR_END;
1264: m -= nrl;
1265:
1266:
1267: /* allocate rows and set pointers to them */
1268: m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));
1269: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
1270: m[nrl] += NR_END;
1271: m[nrl] -= ncl;
1272:
1273: for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;
1274:
1275: /* return pointer to array of pointers to rows */
1276: return m;
1277: }
1278:
1279: /****************** free_imatrix *************************/
1280: void free_imatrix(m,nrl,nrh,ncl,nch)
1281: int **m;
1282: long nch,ncl,nrh,nrl;
1283: /* free an int matrix allocated by imatrix() */
1284: {
1285: free((FREE_ARG) (m[nrl]+ncl-NR_END));
1286: free((FREE_ARG) (m+nrl-NR_END));
1287: }
1288:
1289: /******************* matrix *******************************/
1290: double **matrix(long nrl, long nrh, long ncl, long nch)
1291: {
1292: long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
1293: double **m;
1294:
1295: m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
1296: if (!m) nrerror("allocation failure 1 in matrix()");
1297: m += NR_END;
1298: m -= nrl;
1299:
1300: m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
1301: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
1302: m[nrl] += NR_END;
1303: m[nrl] -= ncl;
1304:
1305: for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
1306: return m;
1.145 brouard 1307: /* print *(*(m+1)+70) or print m[1][70]; print m+1 or print &(m[1]) or &(m[1][0])
1308: m[i] = address of ith row of the table. &(m[i]) is its value which is another adress
1309: that of m[i][0]. In order to get the value p m[i][0] but it is unitialized.
1.126 brouard 1310: */
1311: }
1312:
1313: /*************************free matrix ************************/
1314: void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
1315: {
1316: free((FREE_ARG)(m[nrl]+ncl-NR_END));
1317: free((FREE_ARG)(m+nrl-NR_END));
1318: }
1319:
1320: /******************* ma3x *******************************/
1321: double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
1322: {
1323: long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
1324: double ***m;
1325:
1326: m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
1327: if (!m) nrerror("allocation failure 1 in matrix()");
1328: m += NR_END;
1329: m -= nrl;
1330:
1331: m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
1332: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
1333: m[nrl] += NR_END;
1334: m[nrl] -= ncl;
1335:
1336: for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
1337:
1338: m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
1339: if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
1340: m[nrl][ncl] += NR_END;
1341: m[nrl][ncl] -= nll;
1342: for (j=ncl+1; j<=nch; j++)
1343: m[nrl][j]=m[nrl][j-1]+nlay;
1344:
1345: for (i=nrl+1; i<=nrh; i++) {
1346: m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
1347: for (j=ncl+1; j<=nch; j++)
1348: m[i][j]=m[i][j-1]+nlay;
1349: }
1350: return m;
1351: /* gdb: p *(m+1) <=> p m[1] and p (m+1) <=> p (m+1) <=> p &(m[1])
1352: &(m[i][j][k]) <=> *((*(m+i) + j)+k)
1353: */
1354: }
1355:
1356: /*************************free ma3x ************************/
1357: void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
1358: {
1359: free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
1360: free((FREE_ARG)(m[nrl]+ncl-NR_END));
1361: free((FREE_ARG)(m+nrl-NR_END));
1362: }
1363:
1364: /*************** function subdirf ***********/
1365: char *subdirf(char fileres[])
1366: {
1367: /* Caution optionfilefiname is hidden */
1368: strcpy(tmpout,optionfilefiname);
1369: strcat(tmpout,"/"); /* Add to the right */
1370: strcat(tmpout,fileres);
1371: return tmpout;
1372: }
1373:
1374: /*************** function subdirf2 ***********/
1375: char *subdirf2(char fileres[], char *preop)
1376: {
1377:
1378: /* Caution optionfilefiname is hidden */
1379: strcpy(tmpout,optionfilefiname);
1380: strcat(tmpout,"/");
1381: strcat(tmpout,preop);
1382: strcat(tmpout,fileres);
1383: return tmpout;
1384: }
1385:
1386: /*************** function subdirf3 ***********/
1387: char *subdirf3(char fileres[], char *preop, char *preop2)
1388: {
1389:
1390: /* Caution optionfilefiname is hidden */
1391: strcpy(tmpout,optionfilefiname);
1392: strcat(tmpout,"/");
1393: strcat(tmpout,preop);
1394: strcat(tmpout,preop2);
1395: strcat(tmpout,fileres);
1396: return tmpout;
1397: }
1.213 brouard 1398:
1399: /*************** function subdirfext ***********/
1400: char *subdirfext(char fileres[], char *preop, char *postop)
1401: {
1402:
1403: strcpy(tmpout,preop);
1404: strcat(tmpout,fileres);
1405: strcat(tmpout,postop);
1406: return tmpout;
1407: }
1.126 brouard 1408:
1.213 brouard 1409: /*************** function subdirfext3 ***********/
1410: char *subdirfext3(char fileres[], char *preop, char *postop)
1411: {
1412:
1413: /* Caution optionfilefiname is hidden */
1414: strcpy(tmpout,optionfilefiname);
1415: strcat(tmpout,"/");
1416: strcat(tmpout,preop);
1417: strcat(tmpout,fileres);
1418: strcat(tmpout,postop);
1419: return tmpout;
1420: }
1421:
1.162 brouard 1422: char *asc_diff_time(long time_sec, char ascdiff[])
1423: {
1424: long sec_left, days, hours, minutes;
1425: days = (time_sec) / (60*60*24);
1426: sec_left = (time_sec) % (60*60*24);
1427: hours = (sec_left) / (60*60) ;
1428: sec_left = (sec_left) %(60*60);
1429: minutes = (sec_left) /60;
1430: sec_left = (sec_left) % (60);
1431: sprintf(ascdiff,"%ld day(s) %ld hour(s) %ld minute(s) %ld second(s)",days, hours, minutes, sec_left);
1432: return ascdiff;
1433: }
1434:
1.126 brouard 1435: /***************** f1dim *************************/
1436: extern int ncom;
1437: extern double *pcom,*xicom;
1438: extern double (*nrfunc)(double []);
1439:
1440: double f1dim(double x)
1441: {
1442: int j;
1443: double f;
1444: double *xt;
1445:
1446: xt=vector(1,ncom);
1447: for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];
1448: f=(*nrfunc)(xt);
1449: free_vector(xt,1,ncom);
1450: return f;
1451: }
1452:
1453: /*****************brent *************************/
1454: double brent(double ax, double bx, double cx, double (*f)(double), double tol, double *xmin)
1.187 brouard 1455: {
1456: /* Given a function f, and given a bracketing triplet of abscissas ax, bx, cx (such that bx is
1457: * between ax and cx, and f(bx) is less than both f(ax) and f(cx) ), this routine isolates
1458: * the minimum to a fractional precision of about tol using Brent’s method. The abscissa of
1459: * the minimum is returned as xmin, and the minimum function value is returned as brent , the
1460: * returned function value.
1461: */
1.126 brouard 1462: int iter;
1463: double a,b,d,etemp;
1.159 brouard 1464: double fu=0,fv,fw,fx;
1.164 brouard 1465: double ftemp=0.;
1.126 brouard 1466: double p,q,r,tol1,tol2,u,v,w,x,xm;
1467: double e=0.0;
1468:
1469: a=(ax < cx ? ax : cx);
1470: b=(ax > cx ? ax : cx);
1471: x=w=v=bx;
1472: fw=fv=fx=(*f)(x);
1473: for (iter=1;iter<=ITMAX;iter++) {
1474: xm=0.5*(a+b);
1475: tol2=2.0*(tol1=tol*fabs(x)+ZEPS);
1476: /* if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
1477: printf(".");fflush(stdout);
1478: fprintf(ficlog,".");fflush(ficlog);
1.162 brouard 1479: #ifdef DEBUGBRENT
1.126 brouard 1480: 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);
1481: 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);
1482: /* if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
1483: #endif
1484: if (fabs(x-xm) <= (tol2-0.5*(b-a))){
1485: *xmin=x;
1486: return fx;
1487: }
1488: ftemp=fu;
1489: if (fabs(e) > tol1) {
1490: r=(x-w)*(fx-fv);
1491: q=(x-v)*(fx-fw);
1492: p=(x-v)*q-(x-w)*r;
1493: q=2.0*(q-r);
1494: if (q > 0.0) p = -p;
1495: q=fabs(q);
1496: etemp=e;
1497: e=d;
1498: if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))
1499: d=CGOLD*(e=(x >= xm ? a-x : b-x));
1500: else {
1501: d=p/q;
1502: u=x+d;
1503: if (u-a < tol2 || b-u < tol2)
1504: d=SIGN(tol1,xm-x);
1505: }
1506: } else {
1507: d=CGOLD*(e=(x >= xm ? a-x : b-x));
1508: }
1509: u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));
1510: fu=(*f)(u);
1511: if (fu <= fx) {
1512: if (u >= x) a=x; else b=x;
1513: SHFT(v,w,x,u)
1.183 brouard 1514: SHFT(fv,fw,fx,fu)
1515: } else {
1516: if (u < x) a=u; else b=u;
1517: if (fu <= fw || w == x) {
1518: v=w;
1519: w=u;
1520: fv=fw;
1521: fw=fu;
1522: } else if (fu <= fv || v == x || v == w) {
1523: v=u;
1524: fv=fu;
1525: }
1526: }
1.126 brouard 1527: }
1528: nrerror("Too many iterations in brent");
1529: *xmin=x;
1530: return fx;
1531: }
1532:
1533: /****************** mnbrak ***********************/
1534:
1535: void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,
1536: double (*func)(double))
1.183 brouard 1537: { /* Given a function func , and given distinct initial points ax and bx , this routine searches in
1538: the downhill direction (defined by the function as evaluated at the initial points) and returns
1539: new points ax , bx , cx that bracket a minimum of the function. Also returned are the function
1540: values at the three points, fa, fb , and fc such that fa > fb and fb < fc.
1541: */
1.126 brouard 1542: double ulim,u,r,q, dum;
1543: double fu;
1.187 brouard 1544:
1545: double scale=10.;
1546: int iterscale=0;
1547:
1548: *fa=(*func)(*ax); /* xta[j]=pcom[j]+(*ax)*xicom[j]; fa=f(xta[j])*/
1549: *fb=(*func)(*bx); /* xtb[j]=pcom[j]+(*bx)*xicom[j]; fb=f(xtb[j]) */
1550:
1551:
1552: /* while(*fb != *fb){ /\* *ax should be ok, reducing distance to *ax *\/ */
1553: /* printf("Warning mnbrak *fb = %lf, *bx=%lf *ax=%lf *fa==%lf iter=%d\n",*fb, *bx, *ax, *fa, iterscale++); */
1554: /* *bx = *ax - (*ax - *bx)/scale; */
1555: /* *fb=(*func)(*bx); /\* xtb[j]=pcom[j]+(*bx)*xicom[j]; fb=f(xtb[j]) *\/ */
1556: /* } */
1557:
1.126 brouard 1558: if (*fb > *fa) {
1559: SHFT(dum,*ax,*bx,dum)
1.183 brouard 1560: SHFT(dum,*fb,*fa,dum)
1561: }
1.126 brouard 1562: *cx=(*bx)+GOLD*(*bx-*ax);
1563: *fc=(*func)(*cx);
1.183 brouard 1564: #ifdef DEBUG
1565: printf("mnbrak0 *fb=%.12e *fc=%.12e\n",*fb,*fc);
1566: fprintf(ficlog,"mnbrak0 *fb=%.12e *fc=%.12e\n",*fb,*fc);
1567: #endif
1568: while (*fb > *fc) { /* Declining a,b,c with fa> fb > fc */
1.126 brouard 1569: r=(*bx-*ax)*(*fb-*fc);
1570: q=(*bx-*cx)*(*fb-*fa);
1571: u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/
1.183 brouard 1572: (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r)); /* Minimum abscissa of a parabolic estimated from (a,fa), (b,fb) and (c,fc). */
1573: ulim=(*bx)+GLIMIT*(*cx-*bx); /* Maximum abscissa where function should be evaluated */
1574: if ((*bx-u)*(u-*cx) > 0.0) { /* if u_p is between b and c */
1.126 brouard 1575: fu=(*func)(u);
1.163 brouard 1576: #ifdef DEBUG
1577: /* f(x)=A(x-u)**2+f(u) */
1578: double A, fparabu;
1579: A= (*fb - *fa)/(*bx-*ax)/(*bx+*ax-2*u);
1580: fparabu= *fa - A*(*ax-u)*(*ax-u);
1581: 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);
1582: 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 1583: /* And thus,it can be that fu > *fc even if fparabu < *fc */
1584: /* mnbrak (*ax=7.666299858533, *fa=299039.693133272231), (*bx=8.595447774979, *fb=298976.598289369489),
1585: (*cx=10.098840694817, *fc=298946.631474258087), (*u=9.852501168332, fu=298948.773013752128, fparabu=298945.434711494134) */
1586: /* In that case, there is no bracket in the output! Routine is wrong with many consequences.*/
1.163 brouard 1587: #endif
1.184 brouard 1588: #ifdef MNBRAKORIGINAL
1.183 brouard 1589: #else
1.191 brouard 1590: /* if (fu > *fc) { */
1591: /* #ifdef DEBUG */
1592: /* printf("mnbrak4 fu > fc \n"); */
1593: /* fprintf(ficlog, "mnbrak4 fu > fc\n"); */
1594: /* #endif */
1595: /* /\* 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 *\\/ *\/ */
1596: /* /\* SHFT(*fa,*fc,fu,*fc) /\\* (b, u, c) is a bracket while test fb > fc will be fu > fc will exit *\\/ *\/ */
1597: /* dum=u; /\* Shifting c and u *\/ */
1598: /* u = *cx; */
1599: /* *cx = dum; */
1600: /* dum = fu; */
1601: /* fu = *fc; */
1602: /* *fc =dum; */
1603: /* } else { /\* end *\/ */
1604: /* #ifdef DEBUG */
1605: /* printf("mnbrak3 fu < fc \n"); */
1606: /* fprintf(ficlog, "mnbrak3 fu < fc\n"); */
1607: /* #endif */
1608: /* dum=u; /\* Shifting c and u *\/ */
1609: /* u = *cx; */
1610: /* *cx = dum; */
1611: /* dum = fu; */
1612: /* fu = *fc; */
1613: /* *fc =dum; */
1614: /* } */
1.183 brouard 1615: #ifdef DEBUG
1.191 brouard 1616: printf("mnbrak34 fu < or >= fc \n");
1617: fprintf(ficlog, "mnbrak34 fu < fc\n");
1.183 brouard 1618: #endif
1.191 brouard 1619: dum=u; /* Shifting c and u */
1620: u = *cx;
1621: *cx = dum;
1622: dum = fu;
1623: fu = *fc;
1624: *fc =dum;
1.183 brouard 1625: #endif
1.162 brouard 1626: } else if ((*cx-u)*(u-ulim) > 0.0) { /* u is after c but before ulim */
1.183 brouard 1627: #ifdef DEBUG
1628: printf("mnbrak2 u after c but before ulim\n");
1629: fprintf(ficlog, "mnbrak2 u after c but before ulim\n");
1630: #endif
1.126 brouard 1631: fu=(*func)(u);
1632: if (fu < *fc) {
1.183 brouard 1633: #ifdef DEBUG
1634: printf("mnbrak2 u after c but before ulim AND fu < fc\n");
1635: fprintf(ficlog, "mnbrak2 u after c but before ulim AND fu <fc \n");
1636: #endif
1.126 brouard 1637: SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))
1.183 brouard 1638: SHFT(*fb,*fc,fu,(*func)(u))
1639: }
1.162 brouard 1640: } else if ((u-ulim)*(ulim-*cx) >= 0.0) { /* u outside ulim (verifying that ulim is beyond c) */
1.183 brouard 1641: #ifdef DEBUG
1642: printf("mnbrak2 u outside ulim (verifying that ulim is beyond c)\n");
1643: fprintf(ficlog, "mnbrak2 u outside ulim (verifying that ulim is beyond c)\n");
1644: #endif
1.126 brouard 1645: u=ulim;
1646: fu=(*func)(u);
1.183 brouard 1647: } else { /* u could be left to b (if r > q parabola has a maximum) */
1648: #ifdef DEBUG
1649: printf("mnbrak2 u could be left to b (if r > q parabola has a maximum)\n");
1650: fprintf(ficlog, "mnbrak2 u could be left to b (if r > q parabola has a maximum)\n");
1651: #endif
1.126 brouard 1652: u=(*cx)+GOLD*(*cx-*bx);
1653: fu=(*func)(u);
1.183 brouard 1654: } /* end tests */
1.126 brouard 1655: SHFT(*ax,*bx,*cx,u)
1.183 brouard 1656: SHFT(*fa,*fb,*fc,fu)
1657: #ifdef DEBUG
1658: 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);
1659: 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);
1660: #endif
1661: } /* 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 1662: }
1663:
1664: /*************** linmin ************************/
1.162 brouard 1665: /* Given an n -dimensional point p[1..n] and an n -dimensional direction xi[1..n] , moves and
1666: resets p to where the function func(p) takes on a minimum along the direction xi from p ,
1667: and replaces xi by the actual vector displacement that p was moved. Also returns as fret
1668: the value of func at the returned location p . This is actually all accomplished by calling the
1669: routines mnbrak and brent .*/
1.126 brouard 1670: int ncom;
1671: double *pcom,*xicom;
1672: double (*nrfunc)(double []);
1673:
1674: void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))
1675: {
1676: double brent(double ax, double bx, double cx,
1677: double (*f)(double), double tol, double *xmin);
1678: double f1dim(double x);
1679: void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,
1680: double *fc, double (*func)(double));
1681: int j;
1682: double xx,xmin,bx,ax;
1683: double fx,fb,fa;
1.187 brouard 1684:
1.203 brouard 1685: #ifdef LINMINORIGINAL
1686: #else
1687: double scale=10., axs, xxs; /* Scale added for infinity */
1688: #endif
1689:
1.126 brouard 1690: ncom=n;
1691: pcom=vector(1,n);
1692: xicom=vector(1,n);
1693: nrfunc=func;
1694: for (j=1;j<=n;j++) {
1695: pcom[j]=p[j];
1.202 brouard 1696: xicom[j]=xi[j]; /* Former scale xi[j] of currrent direction i */
1.126 brouard 1697: }
1.187 brouard 1698:
1.203 brouard 1699: #ifdef LINMINORIGINAL
1700: xx=1.;
1701: #else
1702: axs=0.0;
1703: xxs=1.;
1704: do{
1705: xx= xxs;
1706: #endif
1.187 brouard 1707: ax=0.;
1708: mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim); /* Outputs: xtx[j]=pcom[j]+(*xx)*xicom[j]; fx=f(xtx[j]) */
1709: /* brackets with inputs ax=0 and xx=1, but points, pcom=p, and directions values, xicom=xi, are sent via f1dim(x) */
1710: /* 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)) */
1711: /* Outputs: fa=f(p(j)) and fx=f(p(j) + xxs * xi(j) ) and f(bx)= f(p(j)+ bx* xi(j)) */
1712: /* Given input ax=axs and xx=xxs, xx might be too far from ax to get a finite f(xx) */
1713: /* Searches on line, outputs (ax, xx, bx) such that fx < min(fa and fb) */
1714: /* 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 1715: #ifdef LINMINORIGINAL
1716: #else
1717: if (fx != fx){
1718: xxs=xxs/scale; /* Trying a smaller xx, closer to initial ax=0 */
1719: printf("|");
1720: fprintf(ficlog,"|");
1721: #ifdef DEBUGLINMIN
1722: 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);
1723: #endif
1724: }
1725: }while(fx != fx);
1726: #endif
1727:
1.191 brouard 1728: #ifdef DEBUGLINMIN
1729: 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 1730: 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 1731: #endif
1.187 brouard 1732: *fret=brent(ax,xx,bx,f1dim,TOL,&xmin); /* Giving a bracketting triplet (ax, xx, bx), find a minimum, xmin, according to f1dim, *fret(xmin),*/
1733: /* fa = f(p[j] + ax * xi[j]), fx = f(p[j] + xx * xi[j]), fb = f(p[j] + bx * xi[j]) */
1734: /* fmin = f(p[j] + xmin * xi[j]) */
1735: /* P+lambda n in that direction (lambdamin), with TOL between abscisses */
1736: /* f1dim(xmin): for (j=1;j<=ncom;j++) xt[j]=pcom[j]+xmin*xicom[j]; */
1.126 brouard 1737: #ifdef DEBUG
1738: printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
1739: fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
1740: #endif
1.191 brouard 1741: #ifdef DEBUGLINMIN
1742: printf("linmin end ");
1.202 brouard 1743: fprintf(ficlog,"linmin end ");
1.191 brouard 1744: #endif
1.126 brouard 1745: for (j=1;j<=n;j++) {
1.203 brouard 1746: #ifdef LINMINORIGINAL
1747: xi[j] *= xmin;
1748: #else
1749: #ifdef DEBUGLINMIN
1750: if(xxs <1.0)
1751: printf(" before xi[%d]=%12.8f", j,xi[j]);
1752: #endif
1753: 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) */
1754: #ifdef DEBUGLINMIN
1755: if(xxs <1.0)
1756: 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 );
1757: #endif
1758: #endif
1.187 brouard 1759: p[j] += xi[j]; /* Parameters values are updated accordingly */
1.126 brouard 1760: }
1.191 brouard 1761: #ifdef DEBUGLINMIN
1.203 brouard 1762: printf("\n");
1.191 brouard 1763: printf("Comparing last *frec(xmin=%12.8f)=%12.8f from Brent and frec(0.)=%12.8f \n", xmin, *fret, (*func)(p));
1.202 brouard 1764: 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 1765: for (j=1;j<=n;j++) {
1.202 brouard 1766: printf(" xi[%d]= %14.10f p[%d]= %12.7f",j,xi[j],j,p[j]);
1767: fprintf(ficlog," xi[%d]= %14.10f p[%d]= %12.7f",j,xi[j],j,p[j]);
1768: if(j % ncovmodel == 0){
1.191 brouard 1769: printf("\n");
1.202 brouard 1770: fprintf(ficlog,"\n");
1771: }
1.191 brouard 1772: }
1.203 brouard 1773: #else
1.191 brouard 1774: #endif
1.126 brouard 1775: free_vector(xicom,1,n);
1776: free_vector(pcom,1,n);
1777: }
1778:
1779:
1780: /*************** powell ************************/
1.162 brouard 1781: /*
1782: Minimization of a function func of n variables. Input consists of an initial starting point
1783: p[1..n] ; an initial matrix xi[1..n][1..n] , whose columns contain the initial set of di-
1784: rections (usually the n unit vectors); and ftol , the fractional tolerance in the function value
1785: such that failure to decrease by more than this amount on one iteration signals doneness. On
1786: output, p is set to the best point found, xi is the then-current direction set, fret is the returned
1787: function value at p , and iter is the number of iterations taken. The routine linmin is used.
1788: */
1.126 brouard 1789: void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,
1790: double (*func)(double []))
1791: {
1792: void linmin(double p[], double xi[], int n, double *fret,
1793: double (*func)(double []));
1794: int i,ibig,j;
1795: double del,t,*pt,*ptt,*xit;
1.181 brouard 1796: double directest;
1.126 brouard 1797: double fp,fptt;
1798: double *xits;
1799: int niterf, itmp;
1800:
1801: pt=vector(1,n);
1802: ptt=vector(1,n);
1803: xit=vector(1,n);
1804: xits=vector(1,n);
1805: *fret=(*func)(p);
1806: for (j=1;j<=n;j++) pt[j]=p[j];
1.202 brouard 1807: rcurr_time = time(NULL);
1.126 brouard 1808: for (*iter=1;;++(*iter)) {
1.187 brouard 1809: fp=(*fret); /* From former iteration or initial value */
1.126 brouard 1810: ibig=0;
1811: del=0.0;
1.157 brouard 1812: rlast_time=rcurr_time;
1813: /* (void) gettimeofday(&curr_time,&tzp); */
1814: rcurr_time = time(NULL);
1815: curr_time = *localtime(&rcurr_time);
1816: printf("\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret, rcurr_time-rlast_time, rcurr_time-rstart_time);fflush(stdout);
1817: fprintf(ficlog,"\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret,rcurr_time-rlast_time, rcurr_time-rstart_time); fflush(ficlog);
1818: /* fprintf(ficrespow,"%d %.12f %ld",*iter,*fret,curr_time.tm_sec-start_time.tm_sec); */
1.192 brouard 1819: for (i=1;i<=n;i++) {
1.126 brouard 1820: printf(" %d %.12f",i, p[i]);
1821: fprintf(ficlog," %d %.12lf",i, p[i]);
1822: fprintf(ficrespow," %.12lf", p[i]);
1823: }
1824: printf("\n");
1825: fprintf(ficlog,"\n");
1826: fprintf(ficrespow,"\n");fflush(ficrespow);
1827: if(*iter <=3){
1.157 brouard 1828: tml = *localtime(&rcurr_time);
1829: strcpy(strcurr,asctime(&tml));
1830: rforecast_time=rcurr_time;
1.126 brouard 1831: itmp = strlen(strcurr);
1832: if(strcurr[itmp-1]=='\n') /* Windows outputs with a new line */
1833: strcurr[itmp-1]='\0';
1.162 brouard 1834: printf("\nConsidering the time needed for the last iteration #%d: %ld seconds,\n",*iter,rcurr_time-rlast_time);
1.157 brouard 1835: fprintf(ficlog,"\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,rcurr_time-rlast_time);
1.126 brouard 1836: for(niterf=10;niterf<=30;niterf+=10){
1.157 brouard 1837: rforecast_time=rcurr_time+(niterf-*iter)*(rcurr_time-rlast_time);
1838: forecast_time = *localtime(&rforecast_time);
1839: strcpy(strfor,asctime(&forecast_time));
1.126 brouard 1840: itmp = strlen(strfor);
1841: if(strfor[itmp-1]=='\n')
1842: strfor[itmp-1]='\0';
1.157 brouard 1843: 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);
1844: 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 1845: }
1846: }
1.187 brouard 1847: for (i=1;i<=n;i++) { /* For each direction i */
1848: for (j=1;j<=n;j++) xit[j]=xi[j][i]; /* Directions stored from previous iteration with previous scales */
1.126 brouard 1849: fptt=(*fret);
1850: #ifdef DEBUG
1.203 brouard 1851: printf("fret=%lf, %lf, %lf \n", *fret, *fret, *fret);
1852: fprintf(ficlog, "fret=%lf, %lf, %lf \n", *fret, *fret, *fret);
1.126 brouard 1853: #endif
1.203 brouard 1854: printf("%d",i);fflush(stdout); /* print direction (parameter) i */
1.126 brouard 1855: fprintf(ficlog,"%d",i);fflush(ficlog);
1.188 brouard 1856: linmin(p,xit,n,fret,func); /* Point p[n]. xit[n] has been loaded for direction i as input.*/
1857: /* Outputs are fret(new point p) p is updated and xit rescaled */
1858: if (fabs(fptt-(*fret)) > del) { /* We are keeping the max gain on each of the n directions */
1859: /* because that direction will be replaced unless the gain del is small */
1860: /* in comparison with the 'probable' gain, mu^2, with the last average direction. */
1861: /* Unless the n directions are conjugate some gain in the determinant may be obtained */
1862: /* with the new direction. */
1.126 brouard 1863: del=fabs(fptt-(*fret));
1864: ibig=i;
1865: }
1866: #ifdef DEBUG
1867: printf("%d %.12e",i,(*fret));
1868: fprintf(ficlog,"%d %.12e",i,(*fret));
1869: for (j=1;j<=n;j++) {
1870: xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
1871: printf(" x(%d)=%.12e",j,xit[j]);
1872: fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
1873: }
1874: for(j=1;j<=n;j++) {
1.162 brouard 1875: printf(" p(%d)=%.12e",j,p[j]);
1876: fprintf(ficlog," p(%d)=%.12e",j,p[j]);
1.126 brouard 1877: }
1878: printf("\n");
1879: fprintf(ficlog,"\n");
1880: #endif
1.187 brouard 1881: } /* end loop on each direction i */
1882: /* Convergence test will use last linmin estimation (fret) and compare former iteration (fp) */
1.188 brouard 1883: /* But p and xit have been updated at the end of linmin, *fret corresponds to new p, xit */
1.187 brouard 1884: /* New value of last point Pn is not computed, P(n-1) */
1.182 brouard 1885: if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) { /* Did we reach enough precision? */
1.188 brouard 1886: /* We could compare with a chi^2. chisquare(0.95,ddl=1)=3.84 */
1887: /* By adding age*age in a model, the new -2LL should be lower and the difference follows a */
1888: /* a chisquare statistics with 1 degree. To be significant at the 95% level, it should have */
1889: /* decreased of more than 3.84 */
1890: /* By adding age*age and V1*age the gain (-2LL) should be more than 5.99 (ddl=2) */
1891: /* By using V1+V2+V3, the gain should be 7.82, compared with basic 1+age. */
1892: /* By adding 10 parameters more the gain should be 18.31 */
1893:
1894: /* Starting the program with initial values given by a former maximization will simply change */
1895: /* the scales of the directions and the directions, because the are reset to canonical directions */
1896: /* Thus the first calls to linmin will give new points and better maximizations until fp-(*fret) is */
1897: /* under the tolerance value. If the tolerance is very small 1.e-9, it could last long. */
1.126 brouard 1898: #ifdef DEBUG
1899: int k[2],l;
1900: k[0]=1;
1901: k[1]=-1;
1902: printf("Max: %.12e",(*func)(p));
1903: fprintf(ficlog,"Max: %.12e",(*func)(p));
1904: for (j=1;j<=n;j++) {
1905: printf(" %.12e",p[j]);
1906: fprintf(ficlog," %.12e",p[j]);
1907: }
1908: printf("\n");
1909: fprintf(ficlog,"\n");
1910: for(l=0;l<=1;l++) {
1911: for (j=1;j<=n;j++) {
1912: ptt[j]=p[j]+(p[j]-pt[j])*k[l];
1913: printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
1914: fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
1915: }
1916: printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
1917: fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
1918: }
1919: #endif
1920:
1921:
1922: free_vector(xit,1,n);
1923: free_vector(xits,1,n);
1924: free_vector(ptt,1,n);
1925: free_vector(pt,1,n);
1926: return;
1.192 brouard 1927: } /* enough precision */
1.126 brouard 1928: if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");
1.181 brouard 1929: for (j=1;j<=n;j++) { /* Computes the extrapolated point P_0 + 2 (P_n-P_0) */
1.126 brouard 1930: ptt[j]=2.0*p[j]-pt[j];
1931: xit[j]=p[j]-pt[j];
1932: pt[j]=p[j];
1933: }
1.181 brouard 1934: fptt=(*func)(ptt); /* f_3 */
1.192 brouard 1935: #ifdef POWELLF1F3
1936: #else
1.161 brouard 1937: if (fptt < fp) { /* If extrapolated point is better, decide if we keep that new direction or not */
1.192 brouard 1938: #endif
1.162 brouard 1939: /* (x1 f1=fp), (x2 f2=*fret), (x3 f3=fptt), (xm fm) */
1.161 brouard 1940: /* From x1 (P0) distance of x2 is at h and x3 is 2h */
1.162 brouard 1941: /* Let f"(x2) be the 2nd derivative equal everywhere. */
1942: /* Then the parabolic through (x1,f1), (x2,f2) and (x3,f3) */
1943: /* will reach at f3 = fm + h^2/2 f"m ; f" = (f1 -2f2 +f3 ) / h**2 */
1.181 brouard 1944: /* Conditional for using this new direction is that mu^2 = (f1-2f2+f3)^2 /2 < del */
1.161 brouard 1945: /* t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt); */
1.183 brouard 1946: #ifdef NRCORIGINAL
1947: t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)- del*SQR(fp-fptt); /* Original Numerical Recipes in C*/
1948: #else
1949: 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 1950: t= t- del*SQR(fp-fptt);
1.183 brouard 1951: #endif
1.202 brouard 1952: directest = fp-2.0*(*fret)+fptt - 2.0 * del; /* If delta was big enough we change it for a new direction */
1.161 brouard 1953: #ifdef DEBUG
1.181 brouard 1954: 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);
1955: 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 1956: printf("t3= %.12lf, t4= %.12lf, t3*= %.12lf, t4*= %.12lf\n",SQR(fp-(*fret)-del),SQR(fp-fptt),
1957: (fp-(*fret)-del)*(fp-(*fret)-del),(fp-fptt)*(fp-fptt));
1958: fprintf(ficlog,"t3= %.12lf, t4= %.12lf, t3*= %.12lf, t4*= %.12lf\n",SQR(fp-(*fret)-del),SQR(fp-fptt),
1959: (fp-(*fret)-del)*(fp-(*fret)-del),(fp-fptt)*(fp-fptt));
1960: 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);
1961: 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);
1962: #endif
1.183 brouard 1963: #ifdef POWELLORIGINAL
1964: if (t < 0.0) { /* Then we use it for new direction */
1965: #else
1.182 brouard 1966: if (directest*t < 0.0) { /* Contradiction between both tests */
1.202 brouard 1967: 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 1968: 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 1969: 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 1970: fprintf(ficlog,"f1-2f2+f3= %.12lf, f1-f2-del= %.12lf, f1-f3= %.12lf\n",fp-2.0*(*fret)+fptt, fp -(*fret) -del, fp-fptt);
1971: }
1.181 brouard 1972: if (directest < 0.0) { /* Then we use it for new direction */
1973: #endif
1.191 brouard 1974: #ifdef DEBUGLINMIN
1975: printf("Before linmin in direction P%d-P0\n",n);
1976: for (j=1;j<=n;j++) {
1.202 brouard 1977: printf(" Before xit[%d]= %12.7f p[%d]= %12.7f",j,xit[j],j,p[j]);
1978: fprintf(ficlog," Before xit[%d]= %12.7f p[%d]= %12.7f",j,xit[j],j,p[j]);
1979: if(j % ncovmodel == 0){
1.191 brouard 1980: printf("\n");
1.202 brouard 1981: fprintf(ficlog,"\n");
1982: }
1.191 brouard 1983: }
1984: #endif
1.187 brouard 1985: linmin(p,xit,n,fret,func); /* computes minimum on the extrapolated direction: changes p and rescales xit.*/
1.191 brouard 1986: #ifdef DEBUGLINMIN
1987: for (j=1;j<=n;j++) {
1988: printf("After xit[%d]= %12.7f p[%d]= %12.7f",j,xit[j],j,p[j]);
1.202 brouard 1989: fprintf(ficlog,"After xit[%d]= %12.7f p[%d]= %12.7f",j,xit[j],j,p[j]);
1990: if(j % ncovmodel == 0){
1.191 brouard 1991: printf("\n");
1.202 brouard 1992: fprintf(ficlog,"\n");
1993: }
1.191 brouard 1994: }
1995: #endif
1.126 brouard 1996: for (j=1;j<=n;j++) {
1.181 brouard 1997: xi[j][ibig]=xi[j][n]; /* Replace direction with biggest decrease by last direction n */
1998: xi[j][n]=xit[j]; /* and this nth direction by the by the average p_0 p_n */
1.126 brouard 1999: }
1.181 brouard 2000: printf("Gaining to use new average direction of P0 P%d instead of biggest increase direction %d :\n",n,ibig);
2001: fprintf(ficlog,"Gaining to use new average direction of P0 P%d instead of biggest increase direction %d :\n",n,ibig);
1.161 brouard 2002:
1.126 brouard 2003: #ifdef DEBUG
1.164 brouard 2004: printf("Direction changed last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
2005: fprintf(ficlog,"Direction changed last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
1.126 brouard 2006: for(j=1;j<=n;j++){
2007: printf(" %.12e",xit[j]);
2008: fprintf(ficlog," %.12e",xit[j]);
2009: }
2010: printf("\n");
2011: fprintf(ficlog,"\n");
2012: #endif
1.192 brouard 2013: } /* end of t or directest negative */
2014: #ifdef POWELLF1F3
2015: #else
1.162 brouard 2016: } /* end if (fptt < fp) */
1.192 brouard 2017: #endif
2018: } /* loop iteration */
1.126 brouard 2019: }
2020:
2021: /**** Prevalence limit (stable or period prevalence) ****************/
2022:
1.203 brouard 2023: double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int *ncvyear, int ij)
1.126 brouard 2024: {
2025: /* Computes the prevalence limit in each live state at age x by left multiplying the unit
1.203 brouard 2026: matrix by transitions matrix until convergence is reached with precision ftolpl */
1.206 brouard 2027: /* Wx= Wx-1 Px-1= Wx-2 Px-2 Px-1 = Wx-n Px-n ... Px-2 Px-1 I */
2028: /* Wx is row vector: population in state 1, population in state 2, population dead */
2029: /* or prevalence in state 1, prevalence in state 2, 0 */
2030: /* newm is the matrix after multiplications, its rows are identical at a factor */
2031: /* Initial matrix pimij */
2032: /* {0.85204250825084937, 0.13044499163996345, 0.017512500109187184, */
2033: /* 0.090851990222114765, 0.88271245433047185, 0.026435555447413338, */
2034: /* 0, 0 , 1} */
2035: /*
2036: * and after some iteration: */
2037: /* {0.45504275246439968, 0.42731458730878791, 0.11764266022681241, */
2038: /* 0.45201005341706885, 0.42865420071559901, 0.11933574586733192, */
2039: /* 0, 0 , 1} */
2040: /* And prevalence by suppressing the deaths are close to identical rows in prlim: */
2041: /* {0.51571254859325999, 0.4842874514067399, */
2042: /* 0.51326036147820708, 0.48673963852179264} */
2043: /* If we start from prlim again, prlim tends to a constant matrix */
2044:
1.126 brouard 2045: int i, ii,j,k;
1.209 brouard 2046: double *min, *max, *meandiff, maxmax,sumnew=0.;
1.145 brouard 2047: /* double **matprod2(); */ /* test */
1.131 brouard 2048: double **out, cov[NCOVMAX+1], **pmij();
1.126 brouard 2049: double **newm;
1.209 brouard 2050: double agefin, delaymax=200. ; /* 100 Max number of years to converge */
1.203 brouard 2051: int ncvloop=0;
1.169 brouard 2052:
1.209 brouard 2053: min=vector(1,nlstate);
2054: max=vector(1,nlstate);
2055: meandiff=vector(1,nlstate);
2056:
1.126 brouard 2057: for (ii=1;ii<=nlstate+ndeath;ii++)
2058: for (j=1;j<=nlstate+ndeath;j++){
2059: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
2060: }
1.169 brouard 2061:
2062: cov[1]=1.;
2063:
2064: /* Even if hstepm = 1, at least one multiplication by the unit matrix */
1.202 brouard 2065: /* Start at agefin= age, computes the matrix of passage and loops decreasing agefin until convergence is reached */
1.126 brouard 2066: for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
1.202 brouard 2067: ncvloop++;
1.126 brouard 2068: newm=savm;
2069: /* Covariates have to be included here again */
1.138 brouard 2070: cov[2]=agefin;
1.187 brouard 2071: if(nagesqr==1)
2072: cov[3]= agefin*agefin;;
1.138 brouard 2073: for (k=1; k<=cptcovn;k++) {
1.200 brouard 2074: /* cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,Tvar[k])]; */
2075: cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,k)];
1.198 brouard 2076: /* 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 2077: }
1.186 brouard 2078: /*wrong? for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
1.200 brouard 2079: /* for (k=1; k<=cptcovage;k++) cov[2+nagesqr+Tage[k]]=nbcode[Tvar[k]][codtabm(ij,Tvar[k])]*cov[2]; */
2080: for (k=1; k<=cptcovage;k++) cov[2+nagesqr+Tage[k]]=nbcode[Tvar[k]][codtabm(ij,k)]*cov[2];
1.186 brouard 2081: for (k=1; k<=cptcovprod;k++) /* Useless */
1.200 brouard 2082: /* cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,Tvard[k][1])] * nbcode[Tvard[k][2]][codtabm(ij,Tvard[k][2])]; */
2083: cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)] * nbcode[Tvard[k][2]][codtabm(ij,k)];
1.138 brouard 2084:
2085: /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
2086: /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
2087: /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
1.145 brouard 2088: /* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
2089: /* out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /\* Bug Valgrind *\/ */
1.142 brouard 2090: out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /* Bug Valgrind */
1.138 brouard 2091:
1.126 brouard 2092: savm=oldm;
2093: oldm=newm;
1.209 brouard 2094:
2095: for(j=1; j<=nlstate; j++){
2096: max[j]=0.;
2097: min[j]=1.;
2098: }
2099: for(i=1;i<=nlstate;i++){
2100: sumnew=0;
2101: for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
2102: for(j=1; j<=nlstate; j++){
2103: prlim[i][j]= newm[i][j]/(1-sumnew);
2104: max[j]=FMAX(max[j],prlim[i][j]);
2105: min[j]=FMIN(min[j],prlim[i][j]);
2106: }
2107: }
2108:
1.126 brouard 2109: maxmax=0.;
1.209 brouard 2110: for(j=1; j<=nlstate; j++){
2111: meandiff[j]=(max[j]-min[j])/(max[j]+min[j])*2.; /* mean difference for each column */
2112: maxmax=FMAX(maxmax,meandiff[j]);
2113: /* 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 2114: } /* j loop */
1.203 brouard 2115: *ncvyear= (int)age- (int)agefin;
1.208 brouard 2116: /* 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 2117: if(maxmax < ftolpl){
1.209 brouard 2118: /* printf("maxmax=%lf ncvloop=%ld, age=%d, agefin=%d ncvyear=%d \n", maxmax, ncvloop, (int)age, (int)agefin, *ncvyear); */
2119: free_vector(min,1,nlstate);
2120: free_vector(max,1,nlstate);
2121: free_vector(meandiff,1,nlstate);
1.126 brouard 2122: return prlim;
2123: }
1.169 brouard 2124: } /* age loop */
1.208 brouard 2125: /* After some age loop it doesn't converge */
1.209 brouard 2126: 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 2127: 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 2128: /* 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); */
2129: free_vector(min,1,nlstate);
2130: free_vector(max,1,nlstate);
2131: free_vector(meandiff,1,nlstate);
1.208 brouard 2132:
1.169 brouard 2133: return prlim; /* should not reach here */
1.126 brouard 2134: }
2135:
2136: /*************** transition probabilities ***************/
2137:
2138: double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
2139: {
1.138 brouard 2140: /* According to parameters values stored in x and the covariate's values stored in cov,
2141: computes the probability to be observed in state j being in state i by appying the
2142: model to the ncovmodel covariates (including constant and age).
2143: lnpijopii=ln(pij/pii)= aij+bij*age+cij*v1+dij*v2+... = sum_nc=1^ncovmodel xij(nc)*cov[nc]
2144: and, according on how parameters are entered, the position of the coefficient xij(nc) of the
2145: ncth covariate in the global vector x is given by the formula:
2146: j<i nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel
2147: j>=i nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel
2148: Computes ln(pij/pii) (lnpijopii), deduces pij/pii by exponentiation,
2149: sums on j different of i to get 1-pii/pii, deduces pii, and then all pij.
2150: Outputs ps[i][j] the probability to be observed in j being in j according to
2151: the values of the covariates cov[nc] and corresponding parameter values x[nc+shiftij]
2152: */
2153: double s1, lnpijopii;
1.126 brouard 2154: /*double t34;*/
1.164 brouard 2155: int i,j, nc, ii, jj;
1.126 brouard 2156:
2157: for(i=1; i<= nlstate; i++){
2158: for(j=1; j<i;j++){
1.138 brouard 2159: for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
2160: /*lnpijopii += param[i][j][nc]*cov[nc];*/
2161: lnpijopii += x[nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel]*cov[nc];
2162: /* printf("Int j<i s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
1.126 brouard 2163: }
1.138 brouard 2164: ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
2165: /* printf("s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
1.126 brouard 2166: }
2167: for(j=i+1; j<=nlstate+ndeath;j++){
1.138 brouard 2168: for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
2169: /*lnpijopii += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];*/
2170: lnpijopii += x[nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel]*cov[nc];
2171: /* printf("Int j>i s1=%.17e, lnpijopii=%.17e %lx %lx\n",s1,lnpijopii,s1,lnpijopii); */
1.126 brouard 2172: }
1.138 brouard 2173: ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
1.126 brouard 2174: }
2175: }
2176:
2177: for(i=1; i<= nlstate; i++){
2178: s1=0;
1.131 brouard 2179: for(j=1; j<i; j++){
1.138 brouard 2180: s1+=exp(ps[i][j]); /* In fact sums pij/pii */
1.131 brouard 2181: /*printf("debug1 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
2182: }
2183: for(j=i+1; j<=nlstate+ndeath; j++){
1.138 brouard 2184: s1+=exp(ps[i][j]); /* In fact sums pij/pii */
1.131 brouard 2185: /*printf("debug2 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
2186: }
1.138 brouard 2187: /* s1= sum_{j<>i} pij/pii=(1-pii)/pii and thus pii is known from s1 */
1.126 brouard 2188: ps[i][i]=1./(s1+1.);
1.138 brouard 2189: /* Computing other pijs */
1.126 brouard 2190: for(j=1; j<i; j++)
2191: ps[i][j]= exp(ps[i][j])*ps[i][i];
2192: for(j=i+1; j<=nlstate+ndeath; j++)
2193: ps[i][j]= exp(ps[i][j])*ps[i][i];
2194: /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
2195: } /* end i */
2196:
2197: for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
2198: for(jj=1; jj<= nlstate+ndeath; jj++){
2199: ps[ii][jj]=0;
2200: ps[ii][ii]=1;
2201: }
2202: }
2203:
1.145 brouard 2204:
2205: /* for(ii=1; ii<= nlstate+ndeath; ii++){ */
2206: /* for(jj=1; jj<= nlstate+ndeath; jj++){ */
2207: /* printf(" pmij ps[%d][%d]=%lf ",ii,jj,ps[ii][jj]); */
2208: /* } */
2209: /* printf("\n "); */
2210: /* } */
2211: /* printf("\n ");printf("%lf ",cov[2]);*/
2212: /*
1.126 brouard 2213: for(i=1; i<= npar; i++) printf("%f ",x[i]);
2214: goto end;*/
2215: return ps;
2216: }
2217:
2218: /**************** Product of 2 matrices ******************/
2219:
1.145 brouard 2220: double **matprod2(double **out, double **in,int nrl, int nrh, int ncl, int nch, int ncolol, int ncoloh, double **b)
1.126 brouard 2221: {
2222: /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
2223: b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
2224: /* in, b, out are matrice of pointers which should have been initialized
2225: before: only the contents of out is modified. The function returns
2226: a pointer to pointers identical to out */
1.145 brouard 2227: int i, j, k;
1.126 brouard 2228: for(i=nrl; i<= nrh; i++)
1.145 brouard 2229: for(k=ncolol; k<=ncoloh; k++){
2230: out[i][k]=0.;
2231: for(j=ncl; j<=nch; j++)
2232: out[i][k] +=in[i][j]*b[j][k];
2233: }
1.126 brouard 2234: return out;
2235: }
2236:
2237:
2238: /************* Higher Matrix Product ***************/
2239:
2240: double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
2241: {
2242: /* Computes the transition matrix starting at age 'age' over
2243: 'nhstepm*hstepm*stepm' months (i.e. until
2244: age (in years) age+nhstepm*hstepm*stepm/12) by multiplying
2245: nhstepm*hstepm matrices.
2246: Output is stored in matrix po[i][j][h] for h every 'hstepm' step
2247: (typically every 2 years instead of every month which is too big
2248: for the memory).
2249: Model is determined by parameters x and covariates have to be
2250: included manually here.
2251:
2252: */
2253:
2254: int i, j, d, h, k;
1.131 brouard 2255: double **out, cov[NCOVMAX+1];
1.126 brouard 2256: double **newm;
1.187 brouard 2257: double agexact;
1.214 brouard 2258: double agebegin, ageend;
1.126 brouard 2259:
2260: /* Hstepm could be zero and should return the unit matrix */
2261: for (i=1;i<=nlstate+ndeath;i++)
2262: for (j=1;j<=nlstate+ndeath;j++){
2263: oldm[i][j]=(i==j ? 1.0 : 0.0);
2264: po[i][j][0]=(i==j ? 1.0 : 0.0);
2265: }
2266: /* Even if hstepm = 1, at least one multiplication by the unit matrix */
2267: for(h=1; h <=nhstepm; h++){
2268: for(d=1; d <=hstepm; d++){
2269: newm=savm;
2270: /* Covariates have to be included here again */
2271: cov[1]=1.;
1.214 brouard 2272: agexact=age+((h-1)*hstepm + (d-1))*stepm/YEARM; /* age just before transition */
1.187 brouard 2273: cov[2]=agexact;
2274: if(nagesqr==1)
2275: cov[3]= agexact*agexact;
1.131 brouard 2276: for (k=1; k<=cptcovn;k++)
1.200 brouard 2277: cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,k)];
2278: /* cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,Tvar[k])]; */
1.186 brouard 2279: for (k=1; k<=cptcovage;k++) /* Should start at cptcovn+1 */
2280: /* cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
1.200 brouard 2281: cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,k)]*cov[2];
2282: /* cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,Tvar[Tage[k]])]*cov[2]; */
1.145 brouard 2283: for (k=1; k<=cptcovprod;k++) /* Useless because included in cptcovn */
1.200 brouard 2284: cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)]*nbcode[Tvard[k][2]][codtabm(ij,k)];
2285: /* 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 2286:
2287:
2288: /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
2289: /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
2290: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,
2291: pmij(pmmij,cov,ncovmodel,x,nlstate));
2292: savm=oldm;
2293: oldm=newm;
2294: }
2295: for(i=1; i<=nlstate+ndeath; i++)
2296: for(j=1;j<=nlstate+ndeath;j++) {
2297: po[i][j][h]=newm[i][j];
1.128 brouard 2298: /*if(h==nhstepm) printf("po[%d][%d][%d]=%f ",i,j,h,po[i][j][h]);*/
1.126 brouard 2299: }
1.128 brouard 2300: /*printf("h=%d ",h);*/
1.126 brouard 2301: } /* end h */
1.128 brouard 2302: /* printf("\n H=%d \n",h); */
1.126 brouard 2303: return po;
2304: }
2305:
1.162 brouard 2306: #ifdef NLOPT
2307: double myfunc(unsigned n, const double *p1, double *grad, void *pd){
2308: double fret;
2309: double *xt;
2310: int j;
2311: myfunc_data *d2 = (myfunc_data *) pd;
2312: /* xt = (p1-1); */
2313: xt=vector(1,n);
2314: for (j=1;j<=n;j++) xt[j]=p1[j-1]; /* xt[1]=p1[0] */
2315:
2316: fret=(d2->function)(xt); /* p xt[1]@8 is fine */
2317: /* fret=(*func)(xt); /\* p xt[1]@8 is fine *\/ */
2318: printf("Function = %.12lf ",fret);
2319: for (j=1;j<=n;j++) printf(" %d %.8lf", j, xt[j]);
2320: printf("\n");
2321: free_vector(xt,1,n);
2322: return fret;
2323: }
2324: #endif
1.126 brouard 2325:
2326: /*************** log-likelihood *************/
2327: double func( double *x)
2328: {
2329: int i, ii, j, k, mi, d, kk;
1.131 brouard 2330: double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
1.126 brouard 2331: double **out;
2332: double sw; /* Sum of weights */
2333: double lli; /* Individual log likelihood */
2334: int s1, s2;
2335: double bbh, survp;
2336: long ipmx;
1.187 brouard 2337: double agexact;
1.126 brouard 2338: /*extern weight */
2339: /* We are differentiating ll according to initial status */
2340: /* for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
2341: /*for(i=1;i<imx;i++)
2342: printf(" %d\n",s[4][i]);
2343: */
1.162 brouard 2344:
2345: ++countcallfunc;
2346:
1.126 brouard 2347: cov[1]=1.;
2348:
2349: for(k=1; k<=nlstate; k++) ll[k]=0.;
2350:
2351: if(mle==1){
2352: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1.138 brouard 2353: /* Computes the values of the ncovmodel covariates of the model
2354: depending if the covariates are fixed or variying (age dependent) and stores them in cov[]
2355: Then computes with function pmij which return a matrix p[i][j] giving the elementary probability
2356: to be observed in j being in i according to the model.
2357: */
1.145 brouard 2358: for (k=1; k<=cptcovn;k++){ /* Simple and product covariates without age* products */
1.187 brouard 2359: cov[2+nagesqr+k]=covar[Tvar[k]][i];
1.145 brouard 2360: }
1.137 brouard 2361: /* In model V2+V1*V4+age*V3+V3*V2 Tvar[1] is V2, Tvar[2=V1*V4]
1.138 brouard 2362: is 6, Tvar[3=age*V3] should not be computed because of age Tvar[4=V3*V2]
1.137 brouard 2363: has been calculated etc */
1.126 brouard 2364: for(mi=1; mi<= wav[i]-1; mi++){
2365: for (ii=1;ii<=nlstate+ndeath;ii++)
2366: for (j=1;j<=nlstate+ndeath;j++){
2367: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
2368: savm[ii][j]=(ii==j ? 1.0 : 0.0);
2369: }
2370: for(d=0; d<dh[mi][i]; d++){
2371: newm=savm;
1.187 brouard 2372: agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
2373: cov[2]=agexact;
2374: if(nagesqr==1)
2375: cov[3]= agexact*agexact;
1.126 brouard 2376: for (kk=1; kk<=cptcovage;kk++) {
1.187 brouard 2377: cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact; /* Tage[kk] gives the data-covariate associated with age */
1.126 brouard 2378: }
2379: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
2380: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
2381: savm=oldm;
2382: oldm=newm;
2383: } /* end mult */
2384:
2385: /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
2386: /* But now since version 0.9 we anticipate for bias at large stepm.
2387: * If stepm is larger than one month (smallest stepm) and if the exact delay
2388: * (in months) between two waves is not a multiple of stepm, we rounded to
2389: * the nearest (and in case of equal distance, to the lowest) interval but now
2390: * we keep into memory the bias bh[mi][i] and also the previous matrix product
2391: * (i.e to dh[mi][i]-1) saved in 'savm'. Then we inter(extra)polate the
2392: * probability in order to take into account the bias as a fraction of the way
2393: * from savm to out if bh is negative or even beyond if bh is positive. bh varies
2394: * -stepm/2 to stepm/2 .
2395: * For stepm=1 the results are the same as for previous versions of Imach.
2396: * For stepm > 1 the results are less biased than in previous versions.
2397: */
2398: s1=s[mw[mi][i]][i];
2399: s2=s[mw[mi+1][i]][i];
2400: bbh=(double)bh[mi][i]/(double)stepm;
2401: /* bias bh is positive if real duration
2402: * is higher than the multiple of stepm and negative otherwise.
2403: */
2404: /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
2405: if( s2 > nlstate){
2406: /* i.e. if s2 is a death state and if the date of death is known
2407: then the contribution to the likelihood is the probability to
2408: die between last step unit time and current step unit time,
2409: which is also equal to probability to die before dh
2410: minus probability to die before dh-stepm .
2411: In version up to 0.92 likelihood was computed
2412: as if date of death was unknown. Death was treated as any other
2413: health state: the date of the interview describes the actual state
2414: and not the date of a change in health state. The former idea was
2415: to consider that at each interview the state was recorded
2416: (healthy, disable or death) and IMaCh was corrected; but when we
2417: introduced the exact date of death then we should have modified
2418: the contribution of an exact death to the likelihood. This new
2419: contribution is smaller and very dependent of the step unit
2420: stepm. It is no more the probability to die between last interview
2421: and month of death but the probability to survive from last
2422: interview up to one month before death multiplied by the
2423: probability to die within a month. Thanks to Chris
2424: Jackson for correcting this bug. Former versions increased
2425: mortality artificially. The bad side is that we add another loop
2426: which slows down the processing. The difference can be up to 10%
2427: lower mortality.
2428: */
1.183 brouard 2429: /* If, at the beginning of the maximization mostly, the
2430: cumulative probability or probability to be dead is
2431: constant (ie = 1) over time d, the difference is equal to
2432: 0. out[s1][3] = savm[s1][3]: probability, being at state
2433: s1 at precedent wave, to be dead a month before current
2434: wave is equal to probability, being at state s1 at
2435: precedent wave, to be dead at mont of the current
2436: wave. Then the observed probability (that this person died)
2437: is null according to current estimated parameter. In fact,
2438: it should be very low but not zero otherwise the log go to
2439: infinity.
2440: */
2441: /* #ifdef INFINITYORIGINAL */
2442: /* lli=log(out[s1][s2] - savm[s1][s2]); */
2443: /* #else */
2444: /* if ((out[s1][s2] - savm[s1][s2]) < mytinydouble) */
2445: /* lli=log(mytinydouble); */
2446: /* else */
2447: /* lli=log(out[s1][s2] - savm[s1][s2]); */
2448: /* #endif */
1.216 ! brouard 2449: lli=log(out[s1][s2] - savm[s1][s2]);
! 2450:
! 2451: } else if ( s2==-1 ) { /* alive */
1.126 brouard 2452: for (j=1,survp=0. ; j<=nlstate; j++)
2453: survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
2454: /*survp += out[s1][j]; */
2455: lli= log(survp);
2456: }
2457: else if (s2==-4) {
2458: for (j=3,survp=0. ; j<=nlstate; j++)
2459: survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
2460: lli= log(survp);
2461: }
2462: else if (s2==-5) {
2463: for (j=1,survp=0. ; j<=2; j++)
2464: survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
2465: lli= log(survp);
2466: }
2467: else{
2468: lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
2469: /* 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 */
2470: }
2471: /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
2472: /*if(lli ==000.0)*/
2473: /*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); */
2474: ipmx +=1;
2475: sw += weight[i];
2476: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1.183 brouard 2477: /* if (lli < log(mytinydouble)){ */
2478: /* 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); */
2479: /* 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]); */
2480: /* } */
1.126 brouard 2481: } /* end of wave */
2482: } /* end of individual */
2483: } else if(mle==2){
2484: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1.187 brouard 2485: for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i];
1.126 brouard 2486: for(mi=1; mi<= wav[i]-1; mi++){
2487: for (ii=1;ii<=nlstate+ndeath;ii++)
2488: for (j=1;j<=nlstate+ndeath;j++){
2489: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
2490: savm[ii][j]=(ii==j ? 1.0 : 0.0);
2491: }
2492: for(d=0; d<=dh[mi][i]; d++){
2493: newm=savm;
1.187 brouard 2494: agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
2495: cov[2]=agexact;
2496: if(nagesqr==1)
2497: cov[3]= agexact*agexact;
1.126 brouard 2498: for (kk=1; kk<=cptcovage;kk++) {
1.187 brouard 2499: cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
1.126 brouard 2500: }
2501: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
2502: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
2503: savm=oldm;
2504: oldm=newm;
2505: } /* end mult */
2506:
2507: s1=s[mw[mi][i]][i];
2508: s2=s[mw[mi+1][i]][i];
2509: bbh=(double)bh[mi][i]/(double)stepm;
2510: 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 */
2511: ipmx +=1;
2512: sw += weight[i];
2513: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
2514: } /* end of wave */
2515: } /* end of individual */
2516: } else if(mle==3){ /* exponential inter-extrapolation */
2517: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1.187 brouard 2518: for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i];
1.126 brouard 2519: for(mi=1; mi<= wav[i]-1; mi++){
2520: for (ii=1;ii<=nlstate+ndeath;ii++)
2521: for (j=1;j<=nlstate+ndeath;j++){
2522: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
2523: savm[ii][j]=(ii==j ? 1.0 : 0.0);
2524: }
2525: for(d=0; d<dh[mi][i]; d++){
2526: newm=savm;
1.187 brouard 2527: agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
2528: cov[2]=agexact;
2529: if(nagesqr==1)
2530: cov[3]= agexact*agexact;
1.126 brouard 2531: for (kk=1; kk<=cptcovage;kk++) {
1.187 brouard 2532: cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
1.126 brouard 2533: }
2534: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
2535: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
2536: savm=oldm;
2537: oldm=newm;
2538: } /* end mult */
2539:
2540: s1=s[mw[mi][i]][i];
2541: s2=s[mw[mi+1][i]][i];
2542: bbh=(double)bh[mi][i]/(double)stepm;
2543: 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 */
2544: ipmx +=1;
2545: sw += weight[i];
2546: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
2547: } /* end of wave */
2548: } /* end of individual */
2549: }else if (mle==4){ /* ml=4 no inter-extrapolation */
2550: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1.187 brouard 2551: for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i];
1.126 brouard 2552: for(mi=1; mi<= wav[i]-1; mi++){
2553: for (ii=1;ii<=nlstate+ndeath;ii++)
2554: for (j=1;j<=nlstate+ndeath;j++){
2555: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
2556: savm[ii][j]=(ii==j ? 1.0 : 0.0);
2557: }
2558: for(d=0; d<dh[mi][i]; d++){
2559: newm=savm;
1.187 brouard 2560: agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
2561: cov[2]=agexact;
2562: if(nagesqr==1)
2563: cov[3]= agexact*agexact;
1.126 brouard 2564: for (kk=1; kk<=cptcovage;kk++) {
1.187 brouard 2565: cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
1.126 brouard 2566: }
2567:
2568: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
2569: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
2570: savm=oldm;
2571: oldm=newm;
2572: } /* end mult */
2573:
2574: s1=s[mw[mi][i]][i];
2575: s2=s[mw[mi+1][i]][i];
2576: if( s2 > nlstate){
2577: lli=log(out[s1][s2] - savm[s1][s2]);
1.216 ! brouard 2578: } else if ( s2==-1 ) { /* alive */
! 2579: for (j=1,survp=0. ; j<=nlstate; j++)
! 2580: survp += out[s1][j];
! 2581: lli= log(survp);
1.126 brouard 2582: }else{
2583: lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
2584: }
2585: ipmx +=1;
2586: sw += weight[i];
2587: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
2588: /* 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]); */
2589: } /* end of wave */
2590: } /* end of individual */
2591: }else{ /* ml=5 no inter-extrapolation no jackson =0.8a */
2592: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1.187 brouard 2593: for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i];
1.126 brouard 2594: for(mi=1; mi<= wav[i]-1; mi++){
2595: for (ii=1;ii<=nlstate+ndeath;ii++)
2596: for (j=1;j<=nlstate+ndeath;j++){
2597: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
2598: savm[ii][j]=(ii==j ? 1.0 : 0.0);
2599: }
2600: for(d=0; d<dh[mi][i]; d++){
2601: newm=savm;
1.187 brouard 2602: agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
2603: cov[2]=agexact;
2604: if(nagesqr==1)
2605: cov[3]= agexact*agexact;
1.126 brouard 2606: for (kk=1; kk<=cptcovage;kk++) {
1.187 brouard 2607: cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
1.126 brouard 2608: }
2609:
2610: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
2611: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
2612: savm=oldm;
2613: oldm=newm;
2614: } /* end mult */
2615:
2616: s1=s[mw[mi][i]][i];
2617: s2=s[mw[mi+1][i]][i];
2618: lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
2619: ipmx +=1;
2620: sw += weight[i];
2621: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
2622: /*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]);*/
2623: } /* end of wave */
2624: } /* end of individual */
2625: } /* End of if */
2626: for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
2627: /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
2628: l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
2629: return -l;
2630: }
2631:
2632: /*************** log-likelihood *************/
2633: double funcone( double *x)
2634: {
2635: /* Same as likeli but slower because of a lot of printf and if */
2636: int i, ii, j, k, mi, d, kk;
1.131 brouard 2637: double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
1.126 brouard 2638: double **out;
2639: double lli; /* Individual log likelihood */
2640: double llt;
2641: int s1, s2;
2642: double bbh, survp;
1.187 brouard 2643: double agexact;
1.214 brouard 2644: double agebegin, ageend;
1.126 brouard 2645: /*extern weight */
2646: /* We are differentiating ll according to initial status */
2647: /* for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
2648: /*for(i=1;i<imx;i++)
2649: printf(" %d\n",s[4][i]);
2650: */
2651: cov[1]=1.;
2652:
2653: for(k=1; k<=nlstate; k++) ll[k]=0.;
2654:
2655: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1.187 brouard 2656: for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i];
1.126 brouard 2657: for(mi=1; mi<= wav[i]-1; mi++){
2658: for (ii=1;ii<=nlstate+ndeath;ii++)
2659: for (j=1;j<=nlstate+ndeath;j++){
2660: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
2661: savm[ii][j]=(ii==j ? 1.0 : 0.0);
2662: }
1.214 brouard 2663:
2664: agebegin=agev[mw[mi][i]][i]; /* Age at beginning of effective wave */
2665: ageend=agev[mw[mi][i]][i] + (dh[mi][i])*stepm/YEARM; /* Age at end of effective wave and at the end of transition */
2666: for(d=0; d<dh[mi][i]; d++){ /* Delay between two effective waves */
2667: /*dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
2668: and mw[mi+1][i]. dh depends on stepm.*/
1.126 brouard 2669: newm=savm;
1.187 brouard 2670: agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
2671: cov[2]=agexact;
2672: if(nagesqr==1)
2673: cov[3]= agexact*agexact;
1.126 brouard 2674: for (kk=1; kk<=cptcovage;kk++) {
1.187 brouard 2675: cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
1.126 brouard 2676: }
1.187 brouard 2677:
1.145 brouard 2678: /* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
1.126 brouard 2679: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
2680: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1.145 brouard 2681: /* out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath, */
2682: /* 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate)); */
1.126 brouard 2683: savm=oldm;
2684: oldm=newm;
2685: } /* end mult */
2686:
2687: s1=s[mw[mi][i]][i];
2688: s2=s[mw[mi+1][i]][i];
1.216 ! brouard 2689: if(s2==-1){
! 2690: printf(" s1=%d, s2=%d i=%d \n", s1, s2, i);
! 2691: /* exit(1); */
! 2692: }
1.126 brouard 2693: bbh=(double)bh[mi][i]/(double)stepm;
2694: /* bias is positive if real duration
2695: * is higher than the multiple of stepm and negative otherwise.
2696: */
2697: if( s2 > nlstate && (mle <5) ){ /* Jackson */
2698: lli=log(out[s1][s2] - savm[s1][s2]);
1.216 ! brouard 2699: } else if ( s2==-1 ) { /* alive */
1.126 brouard 2700: for (j=1,survp=0. ; j<=nlstate; j++)
2701: survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
2702: lli= log(survp);
2703: }else if (mle==1){
2704: lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
2705: } else if(mle==2){
2706: 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 */
2707: } else if(mle==3){ /* exponential inter-extrapolation */
2708: 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 */
2709: } else if (mle==4){ /* mle=4 no inter-extrapolation */
2710: lli=log(out[s1][s2]); /* Original formula */
1.136 brouard 2711: } else{ /* mle=0 back to 1 */
2712: lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
2713: /*lli=log(out[s1][s2]); */ /* Original formula */
1.126 brouard 2714: } /* End of if */
2715: ipmx +=1;
2716: sw += weight[i];
2717: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1.132 brouard 2718: /*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 2719: if(globpr){
1.214 brouard 2720: fprintf(ficresilk,"%9ld %6.1f %6.1f %6d %2d %2d %2d %2d %3d %11.6f %8.4f %8.3f\
1.126 brouard 2721: %11.6f %11.6f %11.6f ", \
1.214 brouard 2722: 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 2723: 2*weight[i]*lli,out[s1][s2],savm[s1][s2]);
2724: for(k=1,llt=0.,l=0.; k<=nlstate; k++){
2725: llt +=ll[k]*gipmx/gsw;
2726: fprintf(ficresilk," %10.6f",-ll[k]*gipmx/gsw);
2727: }
2728: fprintf(ficresilk," %10.6f\n", -llt);
2729: }
2730: } /* end of wave */
2731: } /* end of individual */
2732: for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
2733: /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
2734: l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
2735: if(globpr==0){ /* First time we count the contributions and weights */
2736: gipmx=ipmx;
2737: gsw=sw;
2738: }
2739: return -l;
2740: }
2741:
2742:
2743: /*************** function likelione ***********/
2744: void likelione(FILE *ficres,double p[], int npar, int nlstate, int *globpri, long *ipmx, double *sw, double *fretone, double (*funcone)(double []))
2745: {
2746: /* This routine should help understanding what is done with
2747: the selection of individuals/waves and
2748: to check the exact contribution to the likelihood.
2749: Plotting could be done.
2750: */
2751: int k;
2752:
2753: if(*globpri !=0){ /* Just counts and sums, no printings */
1.201 brouard 2754: strcpy(fileresilk,"ILK_");
1.202 brouard 2755: strcat(fileresilk,fileresu);
1.126 brouard 2756: if((ficresilk=fopen(fileresilk,"w"))==NULL) {
2757: printf("Problem with resultfile: %s\n", fileresilk);
2758: fprintf(ficlog,"Problem with resultfile: %s\n", fileresilk);
2759: }
1.214 brouard 2760: 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");
2761: fprintf(ficresilk, "#num_i ageb agend i s1 s2 mi mw dh likeli weight %%weight 2wlli out sav ");
1.126 brouard 2762: /* i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],2*weight[i]*lli,out[s1][s2],savm[s1][s2]); */
2763: for(k=1; k<=nlstate; k++)
2764: fprintf(ficresilk," -2*gipw/gsw*weight*ll[%d]++",k);
2765: fprintf(ficresilk," -2*gipw/gsw*weight*ll(total)\n");
2766: }
2767:
2768: *fretone=(*funcone)(p);
2769: if(*globpri !=0){
2770: fclose(ficresilk);
1.205 brouard 2771: if (mle ==0)
2772: fprintf(fichtm,"\n<br>File of contributions to the likelihood computed with initial parameters and mle = %d.",mle);
2773: else if(mle >=1)
2774: fprintf(fichtm,"\n<br>File of contributions to the likelihood computed with optimized parameters mle = %d.",mle);
2775: 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 2776:
1.208 brouard 2777:
2778: for (k=1; k<= nlstate ; k++) {
1.211 brouard 2779: 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 2780: <img src=\"%s-p%dj.png\">",k,k,subdirf2(optionfilefiname,"ILK_"),k,subdirf2(optionfilefiname,"ILK_"),k,subdirf2(optionfilefiname,"ILK_"),k);
2781: }
1.207 brouard 2782: 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 2783: <img src=\"%s-ori.png\">",subdirf2(optionfilefiname,"ILK_"),subdirf2(optionfilefiname,"ILK_"),subdirf2(optionfilefiname,"ILK_"));
1.207 brouard 2784: fprintf(fichtm,"<br>- and by state of destination <a href=\"%s-dest.png\">%s-dest.png</a><br> \
1.204 brouard 2785: <img src=\"%s-dest.png\">",subdirf2(optionfilefiname,"ILK_"),subdirf2(optionfilefiname,"ILK_"),subdirf2(optionfilefiname,"ILK_"));
1.207 brouard 2786: fflush(fichtm);
1.205 brouard 2787: }
1.126 brouard 2788: return;
2789: }
2790:
2791:
2792: /*********** Maximum Likelihood Estimation ***************/
2793:
2794: void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
2795: {
1.165 brouard 2796: int i,j, iter=0;
1.126 brouard 2797: double **xi;
2798: double fret;
2799: double fretone; /* Only one call to likelihood */
2800: /* char filerespow[FILENAMELENGTH];*/
1.162 brouard 2801:
2802: #ifdef NLOPT
2803: int creturn;
2804: nlopt_opt opt;
2805: /* double lb[9] = { -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL }; /\* lower bounds *\/ */
2806: double *lb;
2807: double minf; /* the minimum objective value, upon return */
2808: double * p1; /* Shifted parameters from 0 instead of 1 */
2809: myfunc_data dinst, *d = &dinst;
2810: #endif
2811:
2812:
1.126 brouard 2813: xi=matrix(1,npar,1,npar);
2814: for (i=1;i<=npar;i++)
2815: for (j=1;j<=npar;j++)
2816: xi[i][j]=(i==j ? 1.0 : 0.0);
2817: printf("Powell\n"); fprintf(ficlog,"Powell\n");
1.201 brouard 2818: strcpy(filerespow,"POW_");
1.126 brouard 2819: strcat(filerespow,fileres);
2820: if((ficrespow=fopen(filerespow,"w"))==NULL) {
2821: printf("Problem with resultfile: %s\n", filerespow);
2822: fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
2823: }
2824: fprintf(ficrespow,"# Powell\n# iter -2*LL");
2825: for (i=1;i<=nlstate;i++)
2826: for(j=1;j<=nlstate+ndeath;j++)
2827: if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
2828: fprintf(ficrespow,"\n");
1.162 brouard 2829: #ifdef POWELL
1.126 brouard 2830: powell(p,xi,npar,ftol,&iter,&fret,func);
1.162 brouard 2831: #endif
1.126 brouard 2832:
1.162 brouard 2833: #ifdef NLOPT
2834: #ifdef NEWUOA
2835: opt = nlopt_create(NLOPT_LN_NEWUOA,npar);
2836: #else
2837: opt = nlopt_create(NLOPT_LN_BOBYQA,npar);
2838: #endif
2839: lb=vector(0,npar-1);
2840: for (i=0;i<npar;i++) lb[i]= -HUGE_VAL;
2841: nlopt_set_lower_bounds(opt, lb);
2842: nlopt_set_initial_step1(opt, 0.1);
2843:
2844: p1= (p+1); /* p *(p+1)@8 and p *(p1)@8 are equal p1[0]=p[1] */
2845: d->function = func;
2846: printf(" Func %.12lf \n",myfunc(npar,p1,NULL,d));
2847: nlopt_set_min_objective(opt, myfunc, d);
2848: nlopt_set_xtol_rel(opt, ftol);
2849: if ((creturn=nlopt_optimize(opt, p1, &minf)) < 0) {
2850: printf("nlopt failed! %d\n",creturn);
2851: }
2852: else {
2853: printf("found minimum after %d evaluations (NLOPT=%d)\n", countcallfunc ,NLOPT);
2854: printf("found minimum at f(%g,%g) = %0.10g\n", p[0], p[1], minf);
2855: iter=1; /* not equal */
2856: }
2857: nlopt_destroy(opt);
2858: #endif
1.126 brouard 2859: free_matrix(xi,1,npar,1,npar);
2860: fclose(ficrespow);
1.203 brouard 2861: printf("\n#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
2862: fprintf(ficlog,"\n#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
1.180 brouard 2863: fprintf(ficres,"#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
1.126 brouard 2864:
2865: }
2866:
2867: /**** Computes Hessian and covariance matrix ***/
1.203 brouard 2868: void hesscov(double **matcov, double **hess, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
1.126 brouard 2869: {
2870: double **a,**y,*x,pd;
1.203 brouard 2871: /* double **hess; */
1.164 brouard 2872: int i, j;
1.126 brouard 2873: int *indx;
2874:
2875: double hessii(double p[], double delta, int theta, double delti[],double (*func)(double []),int npar);
1.203 brouard 2876: double hessij(double p[], double **hess, double delti[], int i, int j,double (*func)(double []),int npar);
1.126 brouard 2877: void lubksb(double **a, int npar, int *indx, double b[]) ;
2878: void ludcmp(double **a, int npar, int *indx, double *d) ;
2879: double gompertz(double p[]);
1.203 brouard 2880: /* hess=matrix(1,npar,1,npar); */
1.126 brouard 2881:
2882: printf("\nCalculation of the hessian matrix. Wait...\n");
2883: fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
2884: for (i=1;i<=npar;i++){
1.203 brouard 2885: printf("%d-",i);fflush(stdout);
2886: fprintf(ficlog,"%d-",i);fflush(ficlog);
1.126 brouard 2887:
2888: hess[i][i]=hessii(p,ftolhess,i,delti,func,npar);
2889:
2890: /* printf(" %f ",p[i]);
2891: printf(" %lf %lf %lf",hess[i][i],ftolhess,delti[i]);*/
2892: }
2893:
2894: for (i=1;i<=npar;i++) {
2895: for (j=1;j<=npar;j++) {
2896: if (j>i) {
1.203 brouard 2897: printf(".%d-%d",i,j);fflush(stdout);
2898: fprintf(ficlog,".%d-%d",i,j);fflush(ficlog);
2899: hess[i][j]=hessij(p,hess, delti,i,j,func,npar);
1.126 brouard 2900:
2901: hess[j][i]=hess[i][j];
2902: /*printf(" %lf ",hess[i][j]);*/
2903: }
2904: }
2905: }
2906: printf("\n");
2907: fprintf(ficlog,"\n");
2908:
2909: printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
2910: fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
2911:
2912: a=matrix(1,npar,1,npar);
2913: y=matrix(1,npar,1,npar);
2914: x=vector(1,npar);
2915: indx=ivector(1,npar);
2916: for (i=1;i<=npar;i++)
2917: for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
2918: ludcmp(a,npar,indx,&pd);
2919:
2920: for (j=1;j<=npar;j++) {
2921: for (i=1;i<=npar;i++) x[i]=0;
2922: x[j]=1;
2923: lubksb(a,npar,indx,x);
2924: for (i=1;i<=npar;i++){
2925: matcov[i][j]=x[i];
2926: }
2927: }
2928:
2929: printf("\n#Hessian matrix#\n");
2930: fprintf(ficlog,"\n#Hessian matrix#\n");
2931: for (i=1;i<=npar;i++) {
2932: for (j=1;j<=npar;j++) {
1.203 brouard 2933: printf("%.6e ",hess[i][j]);
2934: fprintf(ficlog,"%.6e ",hess[i][j]);
1.126 brouard 2935: }
2936: printf("\n");
2937: fprintf(ficlog,"\n");
2938: }
2939:
1.203 brouard 2940: /* printf("\n#Covariance matrix#\n"); */
2941: /* fprintf(ficlog,"\n#Covariance matrix#\n"); */
2942: /* for (i=1;i<=npar;i++) { */
2943: /* for (j=1;j<=npar;j++) { */
2944: /* printf("%.6e ",matcov[i][j]); */
2945: /* fprintf(ficlog,"%.6e ",matcov[i][j]); */
2946: /* } */
2947: /* printf("\n"); */
2948: /* fprintf(ficlog,"\n"); */
2949: /* } */
2950:
1.126 brouard 2951: /* Recompute Inverse */
1.203 brouard 2952: /* for (i=1;i<=npar;i++) */
2953: /* for (j=1;j<=npar;j++) a[i][j]=matcov[i][j]; */
2954: /* ludcmp(a,npar,indx,&pd); */
2955:
2956: /* printf("\n#Hessian matrix recomputed#\n"); */
2957:
2958: /* for (j=1;j<=npar;j++) { */
2959: /* for (i=1;i<=npar;i++) x[i]=0; */
2960: /* x[j]=1; */
2961: /* lubksb(a,npar,indx,x); */
2962: /* for (i=1;i<=npar;i++){ */
2963: /* y[i][j]=x[i]; */
2964: /* printf("%.3e ",y[i][j]); */
2965: /* fprintf(ficlog,"%.3e ",y[i][j]); */
2966: /* } */
2967: /* printf("\n"); */
2968: /* fprintf(ficlog,"\n"); */
2969: /* } */
2970:
2971: /* Verifying the inverse matrix */
2972: #ifdef DEBUGHESS
2973: y=matprod2(y,hess,1,npar,1,npar,1,npar,matcov);
1.126 brouard 2974:
1.203 brouard 2975: printf("\n#Verification: multiplying the matrix of covariance by the Hessian matrix, should be unity:#\n");
2976: fprintf(ficlog,"\n#Verification: multiplying the matrix of covariance by the Hessian matrix. Should be unity:#\n");
1.126 brouard 2977:
2978: for (j=1;j<=npar;j++) {
2979: for (i=1;i<=npar;i++){
1.203 brouard 2980: printf("%.2f ",y[i][j]);
2981: fprintf(ficlog,"%.2f ",y[i][j]);
1.126 brouard 2982: }
2983: printf("\n");
2984: fprintf(ficlog,"\n");
2985: }
1.203 brouard 2986: #endif
1.126 brouard 2987:
2988: free_matrix(a,1,npar,1,npar);
2989: free_matrix(y,1,npar,1,npar);
2990: free_vector(x,1,npar);
2991: free_ivector(indx,1,npar);
1.203 brouard 2992: /* free_matrix(hess,1,npar,1,npar); */
1.126 brouard 2993:
2994:
2995: }
2996:
2997: /*************** hessian matrix ****************/
2998: double hessii(double x[], double delta, int theta, double delti[], double (*func)(double []), int npar)
1.203 brouard 2999: { /* Around values of x, computes the function func and returns the scales delti and hessian */
1.126 brouard 3000: int i;
3001: int l=1, lmax=20;
1.203 brouard 3002: double k1,k2, res, fx;
1.132 brouard 3003: double p2[MAXPARM+1]; /* identical to x */
1.126 brouard 3004: double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4;
3005: int k=0,kmax=10;
3006: double l1;
3007:
3008: fx=func(x);
3009: for (i=1;i<=npar;i++) p2[i]=x[i];
1.145 brouard 3010: for(l=0 ; l <=lmax; l++){ /* Enlarging the zone around the Maximum */
1.126 brouard 3011: l1=pow(10,l);
3012: delts=delt;
3013: for(k=1 ; k <kmax; k=k+1){
3014: delt = delta*(l1*k);
3015: p2[theta]=x[theta] +delt;
1.145 brouard 3016: k1=func(p2)-fx; /* Might be negative if too close to the theoretical maximum */
1.126 brouard 3017: p2[theta]=x[theta]-delt;
3018: k2=func(p2)-fx;
3019: /*res= (k1-2.0*fx+k2)/delt/delt; */
1.203 brouard 3020: res= (k1+k2)/delt/delt/2.; /* Divided by 2 because L and not 2*L */
1.126 brouard 3021:
1.203 brouard 3022: #ifdef DEBUGHESSII
1.126 brouard 3023: 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);
3024: 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);
3025: #endif
3026: /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
3027: if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
3028: k=kmax;
3029: }
3030: else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
1.164 brouard 3031: k=kmax; l=lmax*10;
1.126 brouard 3032: }
3033: else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){
3034: delts=delt;
3035: }
1.203 brouard 3036: } /* End loop k */
1.126 brouard 3037: }
3038: delti[theta]=delts;
3039: return res;
3040:
3041: }
3042:
1.203 brouard 3043: double hessij( double x[], double **hess, double delti[], int thetai,int thetaj,double (*func)(double []),int npar)
1.126 brouard 3044: {
3045: int i;
1.164 brouard 3046: int l=1, lmax=20;
1.126 brouard 3047: double k1,k2,k3,k4,res,fx;
1.132 brouard 3048: double p2[MAXPARM+1];
1.203 brouard 3049: int k, kmax=1;
3050: double v1, v2, cv12, lc1, lc2;
1.208 brouard 3051:
3052: int firstime=0;
1.203 brouard 3053:
1.126 brouard 3054: fx=func(x);
1.203 brouard 3055: for (k=1; k<=kmax; k=k+10) {
1.126 brouard 3056: for (i=1;i<=npar;i++) p2[i]=x[i];
1.203 brouard 3057: p2[thetai]=x[thetai]+delti[thetai]*k;
3058: p2[thetaj]=x[thetaj]+delti[thetaj]*k;
1.126 brouard 3059: k1=func(p2)-fx;
3060:
1.203 brouard 3061: p2[thetai]=x[thetai]+delti[thetai]*k;
3062: p2[thetaj]=x[thetaj]-delti[thetaj]*k;
1.126 brouard 3063: k2=func(p2)-fx;
3064:
1.203 brouard 3065: p2[thetai]=x[thetai]-delti[thetai]*k;
3066: p2[thetaj]=x[thetaj]+delti[thetaj]*k;
1.126 brouard 3067: k3=func(p2)-fx;
3068:
1.203 brouard 3069: p2[thetai]=x[thetai]-delti[thetai]*k;
3070: p2[thetaj]=x[thetaj]-delti[thetaj]*k;
1.126 brouard 3071: k4=func(p2)-fx;
1.203 brouard 3072: res=(k1-k2-k3+k4)/4.0/delti[thetai]/k/delti[thetaj]/k/2.; /* Because of L not 2*L */
3073: if(k1*k2*k3*k4 <0.){
1.208 brouard 3074: firstime=1;
1.203 brouard 3075: kmax=kmax+10;
1.208 brouard 3076: }
3077: if(kmax >=10 || firstime ==1){
1.203 brouard 3078: printf("Warning: directions %d-%d, you are not estimating the Hessian at the exact maximum likelihood; increase ftol=%.2e\n",thetai,thetaj, ftol);
3079: fprintf(ficlog,"Warning: directions %d-%d, you are not estimating the Hessian at the exact maximum likelihood; increase ftol=%.2e\n",thetai,thetaj, ftol);
3080: 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);
3081: 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);
3082: }
3083: #ifdef DEBUGHESSIJ
3084: v1=hess[thetai][thetai];
3085: v2=hess[thetaj][thetaj];
3086: cv12=res;
3087: /* Computing eigen value of Hessian matrix */
3088: lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
3089: lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
3090: if ((lc2 <0) || (lc1 <0) ){
3091: printf("Warning: sub Hessian matrix '%d%d' does not have positive eigen values \n",thetai,thetaj);
3092: fprintf(ficlog, "Warning: sub Hessian matrix '%d%d' does not have positive eigen values \n",thetai,thetaj);
3093: 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);
3094: 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);
3095: }
1.126 brouard 3096: #endif
3097: }
3098: return res;
3099: }
3100:
1.203 brouard 3101: /* Not done yet: Was supposed to fix if not exactly at the maximum */
3102: /* double hessij( double x[], double delti[], int thetai,int thetaj,double (*func)(double []),int npar) */
3103: /* { */
3104: /* int i; */
3105: /* int l=1, lmax=20; */
3106: /* double k1,k2,k3,k4,res,fx; */
3107: /* double p2[MAXPARM+1]; */
3108: /* double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4; */
3109: /* int k=0,kmax=10; */
3110: /* double l1; */
3111:
3112: /* fx=func(x); */
3113: /* for(l=0 ; l <=lmax; l++){ /\* Enlarging the zone around the Maximum *\/ */
3114: /* l1=pow(10,l); */
3115: /* delts=delt; */
3116: /* for(k=1 ; k <kmax; k=k+1){ */
3117: /* delt = delti*(l1*k); */
3118: /* for (i=1;i<=npar;i++) p2[i]=x[i]; */
3119: /* p2[thetai]=x[thetai]+delti[thetai]/k; */
3120: /* p2[thetaj]=x[thetaj]+delti[thetaj]/k; */
3121: /* k1=func(p2)-fx; */
3122:
3123: /* p2[thetai]=x[thetai]+delti[thetai]/k; */
3124: /* p2[thetaj]=x[thetaj]-delti[thetaj]/k; */
3125: /* k2=func(p2)-fx; */
3126:
3127: /* p2[thetai]=x[thetai]-delti[thetai]/k; */
3128: /* p2[thetaj]=x[thetaj]+delti[thetaj]/k; */
3129: /* k3=func(p2)-fx; */
3130:
3131: /* p2[thetai]=x[thetai]-delti[thetai]/k; */
3132: /* p2[thetaj]=x[thetaj]-delti[thetaj]/k; */
3133: /* k4=func(p2)-fx; */
3134: /* res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /\* Because of L not 2*L *\/ */
3135: /* #ifdef DEBUGHESSIJ */
3136: /* 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); */
3137: /* 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); */
3138: /* #endif */
3139: /* if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)|| (k4 <khi/nkhi/2.)|| (k4 <khi/nkhi/2.)){ */
3140: /* k=kmax; */
3141: /* } */
3142: /* else if((k1 >khi/nkhif) || (k2 >khi/nkhif) || (k4 >khi/nkhif) || (k4 >khi/nkhif)){ /\* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. *\/ */
3143: /* k=kmax; l=lmax*10; */
3144: /* } */
3145: /* else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){ */
3146: /* delts=delt; */
3147: /* } */
3148: /* } /\* End loop k *\/ */
3149: /* } */
3150: /* delti[theta]=delts; */
3151: /* return res; */
3152: /* } */
3153:
3154:
1.126 brouard 3155: /************** Inverse of matrix **************/
3156: void ludcmp(double **a, int n, int *indx, double *d)
3157: {
3158: int i,imax,j,k;
3159: double big,dum,sum,temp;
3160: double *vv;
3161:
3162: vv=vector(1,n);
3163: *d=1.0;
3164: for (i=1;i<=n;i++) {
3165: big=0.0;
3166: for (j=1;j<=n;j++)
3167: if ((temp=fabs(a[i][j])) > big) big=temp;
3168: if (big == 0.0) nrerror("Singular matrix in routine ludcmp");
3169: vv[i]=1.0/big;
3170: }
3171: for (j=1;j<=n;j++) {
3172: for (i=1;i<j;i++) {
3173: sum=a[i][j];
3174: for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];
3175: a[i][j]=sum;
3176: }
3177: big=0.0;
3178: for (i=j;i<=n;i++) {
3179: sum=a[i][j];
3180: for (k=1;k<j;k++)
3181: sum -= a[i][k]*a[k][j];
3182: a[i][j]=sum;
3183: if ( (dum=vv[i]*fabs(sum)) >= big) {
3184: big=dum;
3185: imax=i;
3186: }
3187: }
3188: if (j != imax) {
3189: for (k=1;k<=n;k++) {
3190: dum=a[imax][k];
3191: a[imax][k]=a[j][k];
3192: a[j][k]=dum;
3193: }
3194: *d = -(*d);
3195: vv[imax]=vv[j];
3196: }
3197: indx[j]=imax;
3198: if (a[j][j] == 0.0) a[j][j]=TINY;
3199: if (j != n) {
3200: dum=1.0/(a[j][j]);
3201: for (i=j+1;i<=n;i++) a[i][j] *= dum;
3202: }
3203: }
3204: free_vector(vv,1,n); /* Doesn't work */
3205: ;
3206: }
3207:
3208: void lubksb(double **a, int n, int *indx, double b[])
3209: {
3210: int i,ii=0,ip,j;
3211: double sum;
3212:
3213: for (i=1;i<=n;i++) {
3214: ip=indx[i];
3215: sum=b[ip];
3216: b[ip]=b[i];
3217: if (ii)
3218: for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];
3219: else if (sum) ii=i;
3220: b[i]=sum;
3221: }
3222: for (i=n;i>=1;i--) {
3223: sum=b[i];
3224: for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];
3225: b[i]=sum/a[i][i];
3226: }
3227: }
3228:
3229: void pstamp(FILE *fichier)
3230: {
1.196 brouard 3231: fprintf(fichier,"# %s.%s\n#IMaCh version %s, %s\n#%s\n# %s", optionfilefiname,optionfilext,version,copyright, fullversion, strstart);
1.126 brouard 3232: }
3233:
3234: /************ Frequencies ********************/
1.214 brouard 3235: void freqsummary(char fileres[], int iagemin, int iagemax, int **s, double **agev, int nlstate, int imx, \
3236: int *Tvaraff, int **nbcode, int *ncodemax,double **mint,double **anint, char strstart[],\
3237: int firstpass, int lastpass, int stepm, int weightopt, char model[])
1.126 brouard 3238: { /* Some frequencies */
3239:
1.164 brouard 3240: int i, m, jk, j1, bool, z1,j;
1.214 brouard 3241: int mi; /* Effective wave */
1.126 brouard 3242: int first;
3243: double ***freq; /* Frequencies */
3244: double *pp, **prop;
3245: double pos,posprop, k2, dateintsum=0,k2cpt=0;
1.214 brouard 3246: char fileresp[FILENAMELENGTH], fileresphtm[FILENAMELENGTH], fileresphtmfr[FILENAMELENGTH];
3247: double agebegin, ageend;
3248:
1.126 brouard 3249: pp=vector(1,nlstate);
3250: prop=matrix(1,nlstate,iagemin,iagemax+3);
1.201 brouard 3251: strcpy(fileresp,"P_");
3252: strcat(fileresp,fileresu);
1.213 brouard 3253: /*strcat(fileresphtm,fileresu);*/
1.126 brouard 3254: if((ficresp=fopen(fileresp,"w"))==NULL) {
3255: printf("Problem with prevalence resultfile: %s\n", fileresp);
3256: fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
3257: exit(0);
3258: }
1.214 brouard 3259:
1.213 brouard 3260: strcpy(fileresphtm,subdirfext(optionfilefiname,"PHTM_",".htm"));
3261: if((ficresphtm=fopen(fileresphtm,"w"))==NULL) {
3262: printf("Problem with prevalence HTM resultfile '%s' with errno='%s'\n",fileresphtm,strerror(errno));
3263: fprintf(ficlog,"Problem with prevalence HTM resultfile '%s' with errno='%s'\n",fileresphtm,strerror(errno));
3264: fflush(ficlog);
3265: exit(70);
3266: }
1.214 brouard 3267: else{
3268: fprintf(ficresphtm,"<html><head>\n<title>IMaCh PHTM_ %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
3269: <hr size=\"2\" color=\"#EC5E5E\"> \n\
3270: Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=1+age+%s<br>\n",\
3271: fileresphtm,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);
3272: }
3273: 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);
3274:
3275: strcpy(fileresphtmfr,subdirfext(optionfilefiname,"PHTMFR_",".htm"));
3276: if((ficresphtmfr=fopen(fileresphtmfr,"w"))==NULL) {
3277: printf("Problem with frequency table HTM resultfile '%s' with errno='%s'\n",fileresphtmfr,strerror(errno));
3278: fprintf(ficlog,"Problem with frequency table HTM resultfile '%s' with errno='%s'\n",fileresphtmfr,strerror(errno));
3279: fflush(ficlog);
3280: exit(70);
3281: }
3282: else{
3283: fprintf(ficresphtmfr,"<html><head>\n<title>IMaCh PHTM_Frequency table %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
3284: <hr size=\"2\" color=\"#EC5E5E\"> \n\
3285: Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=1+age+%s<br>\n",\
3286: fileresphtmfr,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);
3287: }
3288: 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);
3289:
1.126 brouard 3290: freq= ma3x(-5,nlstate+ndeath,-5,nlstate+ndeath,iagemin,iagemax+3);
3291: j1=0;
3292:
3293: j=cptcoveff;
3294: if (cptcovn<1) {j=1;ncodemax[1]=1;}
3295:
3296: first=1;
3297:
1.214 brouard 3298: for (j1 = 1; j1 <= (int) pow(2,cptcoveff); j1++){ /* Loop on covariates combination */
1.126 brouard 3299: /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
3300: scanf("%d", i);*/
3301: for (i=-5; i<=nlstate+ndeath; i++)
3302: for (jk=-5; jk<=nlstate+ndeath; jk++)
3303: for(m=iagemin; m <= iagemax+3; m++)
3304: freq[i][jk][m]=0;
1.143 brouard 3305:
3306: for (i=1; i<=nlstate; i++)
3307: for(m=iagemin; m <= iagemax+3; m++)
3308: prop[i][m]=0;
1.126 brouard 3309:
3310: dateintsum=0;
3311: k2cpt=0;
1.214 brouard 3312: for (i=1; i<=imx; i++) { /* For each individual i */
1.126 brouard 3313: bool=1;
1.210 brouard 3314: if (cptcovn>0) { /* Filter is here: Must be looked at for model=V1+V2+V3+V4 */
1.144 brouard 3315: for (z1=1; z1<=cptcoveff; z1++)
1.198 brouard 3316: if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtabm(j1,z1)]){
1.145 brouard 3317: /* Tests if the value of each of the covariates of i is equal to filter j1 */
1.144 brouard 3318: bool=0;
1.198 brouard 3319: /* 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",
3320: bool,i,z1, z1, Tvaraff[z1],i,covar[Tvaraff[z1]][i],j1,z1,codtabm(j1,z1),
3321: j1,z1,nbcode[Tvaraff[z1]][codtabm(j1,z1)],j1);*/
3322: /* For j1=7 in V1+V2+V3+V4 = 0 1 1 0 and codtabm(7,3)=1 and nbcde[3][?]=1*/
1.144 brouard 3323: }
1.210 brouard 3324: } /* cptcovn > 0 */
1.214 brouard 3325:
1.126 brouard 3326: if (bool==1){
1.214 brouard 3327: /* for(m=firstpass; m<=lastpass; m++){ */
3328: for(mi=1; mi<wav[i];mi++){
3329: m=mw[mi][i];
3330: /* dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective (mi) waves m=mw[mi][i]
3331: and mw[mi+1][i]. dh depends on stepm. */
3332: agebegin=agev[m][i]; /* Age at beginning of wave before transition*/
3333: ageend=agev[m][i]+(dh[m][i])*stepm/YEARM; /* Age at end of wave and transition */
3334: if(m >=firstpass && m <=lastpass){
3335: k2=anint[m][i]+(mint[m][i]/12.);
3336: /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/
3337: if(agev[m][i]==0) agev[m][i]=iagemax+1; /* All ages equal to 0 are in iagemax+1 */
3338: if(agev[m][i]==1) agev[m][i]=iagemax+2; /* All ages equal to 1 are in iagemax+2 */
3339: if (s[m][i]>0 && s[m][i]<=nlstate) /* If status at wave m is known and a live state */
3340: prop[s[m][i]][(int)agev[m][i]] += weight[i]; /* At age of beginning of transition, where status is known */
1.126 brouard 3341: if (m<lastpass) {
1.214 brouard 3342: /* if(s[m][i]==4 && s[m+1][i]==4) */
3343: /* printf(" num=%ld m=%d, i=%d s1=%d s2=%d agev at m=%d\n", num[i], m, i,s[m][i],s[m+1][i], (int)agev[m][i]); */
3344: if(s[m][i]==-1)
3345: printf(" num=%ld m=%d, i=%d s1=%d s2=%d agev at m=%d agebegin=%.2f ageend=%.2f, agemed=%d\n", num[i], m, i,s[m][i],s[m+1][i], (int)agev[m][i],agebegin, ageend, (int)((agebegin+ageend)/2.));
3346: freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i]; /* At age of beginning of transition, where status is known */
3347: /* freq[s[m][i]][s[m+1][i]][(int)((agebegin+ageend)/2.)] += weight[i]; */
3348: freq[s[m][i]][s[m+1][i]][iagemax+3] += weight[i]; /* Total is in iagemax+3 *//* At age of beginning of transition, where status is known */
1.126 brouard 3349: }
1.214 brouard 3350: }
3351: if ((agev[m][i]>1) && (agev[m][i]< (iagemax+3)) && (anint[m][i]!=9999) && (mint[m][i]!=99)) {
3352: dateintsum=dateintsum+k2;
3353: k2cpt++;
3354: /* printf("i=%ld dateintmean = %lf dateintsum=%lf k2cpt=%lf k2=%lf\n",i, dateintsum/k2cpt, dateintsum,k2cpt, k2); */
3355: }
3356: /*}*/
1.210 brouard 3357: } /* end m */
3358: } /* end bool */
3359: } /* end i = 1 to imx */
1.126 brouard 3360:
3361: /* fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
3362: pstamp(ficresp);
3363: if (cptcovn>0) {
3364: fprintf(ficresp, "\n#********** Variable ");
1.214 brouard 3365: fprintf(ficresphtm, "\n<br/><br/><h3>********** Variable ");
3366: fprintf(ficresphtmfr, "\n<br/><br/><h3>********** Variable ");
1.213 brouard 3367: for (z1=1; z1<=cptcoveff; z1++){
3368: fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
3369: fprintf(ficresphtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
1.214 brouard 3370: fprintf(ficresphtmfr, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
1.213 brouard 3371: }
3372: fprintf(ficresp, "**********\n#");
1.214 brouard 3373: fprintf(ficresphtm, "**********</h3>\n");
3374: fprintf(ficresphtmfr, "**********</h3>\n");
1.143 brouard 3375: fprintf(ficlog, "\n#********** Variable ");
1.198 brouard 3376: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficlog, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
1.214 brouard 3377: fprintf(ficlog, "**********\n");
1.126 brouard 3378: }
1.214 brouard 3379: fprintf(ficresphtm,"<table style=\"text-align:center; border: 1px solid\">");
1.213 brouard 3380: for(i=1; i<=nlstate;i++) {
1.126 brouard 3381: fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
1.213 brouard 3382: fprintf(ficresphtm, "<th>Age</th><th>Prev(%d)</th><th>N(%d)</th><th>N</th>",i,i);
3383: }
1.126 brouard 3384: fprintf(ficresp, "\n");
1.213 brouard 3385: fprintf(ficresphtm, "\n");
1.126 brouard 3386:
1.214 brouard 3387: /* Header of frequency table by age */
3388: fprintf(ficresphtmfr,"<table style=\"text-align:center; border: 1px solid\">");
3389: fprintf(ficresphtmfr,"<th>Age</th> ");
3390: for(jk=-1; jk <=nlstate+ndeath; jk++){
3391: for(m=-1; m <=nlstate+ndeath; m++){
3392: if(jk!=0 && m!=0)
3393: fprintf(ficresphtmfr,"<th>%d%d</th> ",jk,m);
3394: }
3395: }
3396: fprintf(ficresphtmfr, "\n");
3397:
3398: /* For each age */
1.126 brouard 3399: for(i=iagemin; i <= iagemax+3; i++){
1.213 brouard 3400: fprintf(ficresphtm,"<tr>");
1.214 brouard 3401: if(i==iagemax+1){
3402: fprintf(ficlog,"1");
3403: fprintf(ficresphtmfr,"<tr><th>0</th> ");
3404: }else if(i==iagemax+2){
3405: fprintf(ficlog,"0");
3406: fprintf(ficresphtmfr,"<tr><th>Unknown</th> ");
3407: }else if(i==iagemax+3){
1.126 brouard 3408: fprintf(ficlog,"Total");
1.214 brouard 3409: fprintf(ficresphtmfr,"<tr><th>Total</th> ");
1.126 brouard 3410: }else{
3411: if(first==1){
3412: first=0;
3413: printf("See log file for details...\n");
3414: }
1.214 brouard 3415: fprintf(ficresphtmfr,"<tr><th>%d</th> ",i);
1.126 brouard 3416: fprintf(ficlog,"Age %d", i);
3417: }
3418: for(jk=1; jk <=nlstate ; jk++){
3419: for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
3420: pp[jk] += freq[jk][m][i];
3421: }
3422: for(jk=1; jk <=nlstate ; jk++){
3423: for(m=-1, pos=0; m <=0 ; m++)
3424: pos += freq[jk][m][i];
3425: if(pp[jk]>=1.e-10){
3426: if(first==1){
1.132 brouard 3427: printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
1.126 brouard 3428: }
3429: fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
3430: }else{
3431: if(first==1)
3432: printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
3433: fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
3434: }
3435: }
3436:
3437: for(jk=1; jk <=nlstate ; jk++){
3438: for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
3439: pp[jk] += freq[jk][m][i];
3440: }
3441: for(jk=1,pos=0,posprop=0; jk <=nlstate ; jk++){
3442: pos += pp[jk];
3443: posprop += prop[jk][i];
3444: }
3445: for(jk=1; jk <=nlstate ; jk++){
3446: if(pos>=1.e-5){
3447: if(first==1)
3448: printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
3449: fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
3450: }else{
3451: if(first==1)
3452: printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
3453: fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
3454: }
3455: if( i <= iagemax){
3456: if(pos>=1.e-5){
3457: fprintf(ficresp," %d %.5f %.0f %.0f",i,prop[jk][i]/posprop, prop[jk][i],posprop);
1.213 brouard 3458: fprintf(ficresphtm,"<th>%d</th><td>%.5f</td><td>%.0f</td><td>%.0f</td>",i,prop[jk][i]/posprop, prop[jk][i],posprop);
1.126 brouard 3459: /*probs[i][jk][j1]= pp[jk]/pos;*/
3460: /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/
3461: }
1.213 brouard 3462: else{
1.126 brouard 3463: fprintf(ficresp," %d NaNq %.0f %.0f",i,prop[jk][i],posprop);
1.213 brouard 3464: fprintf(ficresphtm,"<th>%d</th><td>NaNq</td><td>%.0f</td><td>%.0f</td>",i, prop[jk][i],posprop);
3465: }
1.126 brouard 3466: }
3467: }
3468:
1.214 brouard 3469: for(jk=-1; jk <=nlstate+ndeath; jk++){
3470: for(m=-1; m <=nlstate+ndeath; m++){
3471: if(freq[jk][m][i] !=0 ) { /* minimizing output */
3472: if(first==1){
3473: printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
3474: }
1.126 brouard 3475: fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
3476: }
1.214 brouard 3477: if(jk!=0 && m!=0)
3478: fprintf(ficresphtmfr,"<td>%.0f</td> ",freq[jk][m][i]);
3479: }
3480: }
3481: fprintf(ficresphtmfr,"</tr>\n ");
1.213 brouard 3482: if(i <= iagemax){
1.126 brouard 3483: fprintf(ficresp,"\n");
1.213 brouard 3484: fprintf(ficresphtm,"</tr>\n");
3485: }
1.126 brouard 3486: if(first==1)
3487: printf("Others in log...\n");
3488: fprintf(ficlog,"\n");
1.210 brouard 3489: } /* end loop i */
1.213 brouard 3490: fprintf(ficresphtm,"</table>\n");
1.214 brouard 3491: fprintf(ficresphtmfr,"</table>\n");
1.145 brouard 3492: /*}*/
1.210 brouard 3493: } /* end j1 */
1.126 brouard 3494: dateintmean=dateintsum/k2cpt;
3495:
3496: fclose(ficresp);
1.213 brouard 3497: fclose(ficresphtm);
1.214 brouard 3498: fclose(ficresphtmfr);
1.126 brouard 3499: free_ma3x(freq,-5,nlstate+ndeath,-5,nlstate+ndeath, iagemin, iagemax+3);
3500: free_vector(pp,1,nlstate);
3501: free_matrix(prop,1,nlstate,iagemin, iagemax+3);
3502: /* End of Freq */
3503: }
3504:
3505: /************ Prevalence ********************/
3506: 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)
3507: {
3508: /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
3509: in each health status at the date of interview (if between dateprev1 and dateprev2).
3510: We still use firstpass and lastpass as another selection.
3511: */
3512:
1.164 brouard 3513: int i, m, jk, j1, bool, z1,j;
1.214 brouard 3514: int mi; /* Effective wave */
3515: int iage;
3516: double agebegin, ageend;
1.164 brouard 3517:
3518: double **prop;
3519: double posprop;
1.126 brouard 3520: double y2; /* in fractional years */
3521: int iagemin, iagemax;
1.145 brouard 3522: int first; /** to stop verbosity which is redirected to log file */
1.126 brouard 3523:
3524: iagemin= (int) agemin;
3525: iagemax= (int) agemax;
3526: /*pp=vector(1,nlstate);*/
3527: prop=matrix(1,nlstate,iagemin,iagemax+3);
3528: /* freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
3529: j1=0;
3530:
1.145 brouard 3531: /*j=cptcoveff;*/
1.126 brouard 3532: if (cptcovn<1) {j=1;ncodemax[1]=1;}
3533:
1.145 brouard 3534: first=1;
3535: for(j1=1; j1<= (int) pow(2,cptcoveff);j1++){
1.214 brouard 3536: for (i=1; i<=nlstate; i++)
3537: for(iage=iagemin; iage <= iagemax+3; iage++)
3538: prop[i][iage]=0.0;
3539:
3540: for (i=1; i<=imx; i++) { /* Each individual */
3541: bool=1;
3542: if (cptcovn>0) { /* Filter is here: Must be looked at for model=V1+V2+V3+V4 */
3543: for (z1=1; z1<=cptcoveff; z1++)
3544: if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtabm(j1,z1)])
3545: bool=0;
3546: }
3547: if (bool==1) {
3548: /* for(m=firstpass; m<=lastpass; m++){/\* Other selection (we can limit to certain interviews*\/ */
3549: for(mi=1; mi<wav[i];mi++){
3550: m=mw[mi][i];
3551: agebegin=agev[m][i]; /* Age at beginning of wave before transition*/
3552: /* ageend=agev[m][i]+(dh[m][i])*stepm/YEARM; /\* Age at end of wave and transition *\/ */
3553: if(m >=firstpass && m <=lastpass){
1.126 brouard 3554: y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
3555: if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
3556: if(agev[m][i]==0) agev[m][i]=iagemax+1;
3557: if(agev[m][i]==1) agev[m][i]=iagemax+2;
3558: if((int)agev[m][i] <iagemin || (int)agev[m][i] >iagemax+3) printf("Error on individual =%d agev[m][i]=%f m=%d\n",i, agev[m][i],m);
1.214 brouard 3559: if (s[m][i]>0 && s[m][i]<=nlstate) {
1.126 brouard 3560: /*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]]);*/
1.214 brouard 3561: prop[s[m][i]][(int)agev[m][i]] += weight[i];/* At age of beginning of transition, where status is known */
3562: prop[s[m][i]][iagemax+3] += weight[i];
3563: } /* end valid statuses */
3564: } /* end selection of dates */
1.126 brouard 3565: } /* end selection of waves */
1.214 brouard 3566: } /* end effective waves */
3567: } /* end bool */
3568: }
3569: for(i=iagemin; i <= iagemax+3; i++){
3570: for(jk=1,posprop=0; jk <=nlstate ; jk++) {
3571: posprop += prop[jk][i];
3572: }
3573:
3574: for(jk=1; jk <=nlstate ; jk++){
3575: if( i <= iagemax){
3576: if(posprop>=1.e-5){
3577: probs[i][jk][j1]= prop[jk][i]/posprop;
3578: } else{
3579: if(first==1){
3580: first=0;
3581: 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]);
1.145 brouard 3582: }
1.214 brouard 3583: }
3584: }
3585: }/* end jk */
3586: }/* end i */
1.145 brouard 3587: /*} *//* end i1 */
3588: } /* end j1 */
1.126 brouard 3589:
3590: /* free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
3591: /*free_vector(pp,1,nlstate);*/
3592: free_matrix(prop,1,nlstate, iagemin,iagemax+3);
3593: } /* End of prevalence */
3594:
3595: /************* Waves Concatenation ***************/
3596:
3597: 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)
3598: {
3599: /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
3600: Death is a valid wave (if date is known).
3601: mw[mi][i] is the mi (mi=1 to wav[i]) effective wave of individual i
3602: dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
3603: and mw[mi+1][i]. dh depends on stepm.
3604: */
3605:
3606: int i, mi, m;
3607: /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
3608: double sum=0., jmean=0.;*/
1.214 brouard 3609: int first, firstwo;
1.126 brouard 3610: int j, k=0,jk, ju, jl;
3611: double sum=0.;
3612: first=0;
1.214 brouard 3613: firstwo=0;
1.164 brouard 3614: jmin=100000;
1.126 brouard 3615: jmax=-1;
3616: jmean=0.;
1.214 brouard 3617: for(i=1; i<=imx; i++){ /* For simple cases and if state is death */
1.126 brouard 3618: mi=0;
3619: m=firstpass;
1.214 brouard 3620: while(s[m][i] <= nlstate){ /* a live state */
1.216 ! brouard 3621: if(s[m][i]>=1 || s[m][i]==-4 || s[m][i]==-5){ /* Since 0.98r4 if status=-2 vital status is really unknown, wave should be skipped */
1.126 brouard 3622: mw[++mi][i]=m;
1.216 ! brouard 3623: }
! 3624: if(m >=lastpass){
! 3625: if(s[m][i]==-1 && (int) andc[i] == 9999 && (int)anint[m][i] != 9999){
! 3626: 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);
! 3627: 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.\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);
! 3628: mw[++mi][i]=m;
! 3629: }
! 3630: if(s[m][i]==-2){ /* Vital status is really unknown */
! 3631: nbwarn++;
! 3632: if((int)anint[m][i] == 9999){ /* Has the vital status really been verified? */
! 3633: 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);
! 3634: 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);
! 3635: }
! 3636: break;
! 3637: }
1.126 brouard 3638: break;
1.216 ! brouard 3639: }
1.126 brouard 3640: else
3641: m++;
3642: }/* end while */
1.216 ! brouard 3643:
! 3644: /* After last pass */
1.214 brouard 3645: if (s[m][i] > nlstate){ /* In a death state */
1.126 brouard 3646: mi++; /* Death is another wave */
3647: /* if(mi==0) never been interviewed correctly before death */
3648: /* Only death is a correct wave */
3649: mw[mi][i]=m;
1.216 ! brouard 3650: }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 */
! 3651: /* m++; */
! 3652: /* mi++; */
! 3653: /* s[m][i]=nlstate+1; /\* We are setting the status to the last of non live state *\/ */
! 3654: /* mw[mi][i]=m; */
! 3655: nberr++;
1.214 brouard 3656: if(firstwo==0){
1.216 ! brouard 3657: 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 );
! 3658: 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.\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 );
1.214 brouard 3659: firstwo=1;
1.216 ! brouard 3660: }else if(firstwo==1){
! 3661: 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.\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 );
1.214 brouard 3662: }
1.126 brouard 3663: }
3664: wav[i]=mi;
3665: if(mi==0){
3666: nbwarn++;
3667: if(first==0){
3668: printf("Warning! No valid information for individual %ld line=%d (skipped) and may be others, see log file\n",num[i],i);
3669: first=1;
3670: }
3671: if(first==1){
3672: fprintf(ficlog,"Warning! No valid information for individual %ld line=%d (skipped)\n",num[i],i);
3673: }
3674: } /* end mi==0 */
3675: } /* End individuals */
1.214 brouard 3676: /* wav and mw are no more changed */
1.126 brouard 3677:
1.214 brouard 3678:
1.126 brouard 3679: for(i=1; i<=imx; i++){
3680: for(mi=1; mi<wav[i];mi++){
3681: if (stepm <=0)
3682: dh[mi][i]=1;
3683: else{
3684: if (s[mw[mi+1][i]][i] > nlstate) { /* A death */
3685: if (agedc[i] < 2*AGESUP) {
3686: j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);
3687: if(j==0) j=1; /* Survives at least one month after exam */
3688: else if(j<0){
3689: nberr++;
3690: 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]);
3691: j=1; /* Temporary Dangerous patch */
3692: 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);
3693: 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]);
3694: 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);
3695: }
3696: k=k+1;
3697: if (j >= jmax){
3698: jmax=j;
3699: ijmax=i;
3700: }
3701: if (j <= jmin){
3702: jmin=j;
3703: ijmin=i;
3704: }
3705: sum=sum+j;
3706: /*if (j<0) printf("j=%d num=%d \n",j,i);*/
3707: /* printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
3708: }
3709: }
3710: else{
3711: j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
3712: /* 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]); */
3713:
3714: k=k+1;
3715: if (j >= jmax) {
3716: jmax=j;
3717: ijmax=i;
3718: }
3719: else if (j <= jmin){
3720: jmin=j;
3721: ijmin=i;
3722: }
3723: /* if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
3724: /*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]);*/
3725: if(j<0){
3726: nberr++;
3727: 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]);
3728: 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]);
3729: }
3730: sum=sum+j;
3731: }
3732: jk= j/stepm;
3733: jl= j -jk*stepm;
3734: ju= j -(jk+1)*stepm;
3735: if(mle <=1){ /* only if we use a the linear-interpoloation pseudo-likelihood */
3736: if(jl==0){
3737: dh[mi][i]=jk;
3738: bh[mi][i]=0;
3739: }else{ /* We want a negative bias in order to only have interpolation ie
1.136 brouard 3740: * to avoid the price of an extra matrix product in likelihood */
1.126 brouard 3741: dh[mi][i]=jk+1;
3742: bh[mi][i]=ju;
3743: }
3744: }else{
3745: if(jl <= -ju){
3746: dh[mi][i]=jk;
3747: bh[mi][i]=jl; /* bias is positive if real duration
3748: * is higher than the multiple of stepm and negative otherwise.
3749: */
3750: }
3751: else{
3752: dh[mi][i]=jk+1;
3753: bh[mi][i]=ju;
3754: }
3755: if(dh[mi][i]==0){
3756: dh[mi][i]=1; /* At least one step */
3757: bh[mi][i]=ju; /* At least one step */
3758: /* 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);*/
3759: }
3760: } /* end if mle */
3761: }
3762: } /* end wave */
3763: }
3764: jmean=sum/k;
3765: 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 3766: 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 3767: }
3768:
3769: /*********** Tricode ****************************/
1.145 brouard 3770: void tricode(int *Tvar, int **nbcode, int imx, int *Ndum)
1.126 brouard 3771: {
1.144 brouard 3772: /**< Uses cptcovn+2*cptcovprod as the number of covariates */
3773: /* 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 3774: * Boring subroutine which should only output nbcode[Tvar[j]][k]
1.145 brouard 3775: * Tvar[5] in V2+V1+V3*age+V2*V4 is 2 (V2)
1.169 brouard 3776: * nbcode[Tvar[j]][1]=
1.144 brouard 3777: */
1.130 brouard 3778:
1.145 brouard 3779: int ij=1, k=0, j=0, i=0, maxncov=NCOVMAX;
1.136 brouard 3780: int modmaxcovj=0; /* Modality max of covariates j */
1.145 brouard 3781: int cptcode=0; /* Modality max of covariates j */
3782: int modmincovj=0; /* Modality min of covariates j */
3783:
3784:
1.126 brouard 3785: cptcoveff=0;
3786:
1.144 brouard 3787: for (k=1; k <= maxncov; k++) ncodemax[k]=0; /* Horrible constant again replaced by NCOVMAX */
1.126 brouard 3788:
1.145 brouard 3789: /* Loop on covariates without age and products */
1.186 brouard 3790: for (j=1; j<=(cptcovs); j++) { /* From model V1 + V2*age+ V3 + V3*V4 keeps V1 + V3 = 2 only */
1.192 brouard 3791: for (k=-1; k < maxncov; k++) Ndum[k]=0;
1.186 brouard 3792: for (i=1; i<=imx; i++) { /* Loop on individuals: reads the data file to get the maximum value of the
1.136 brouard 3793: modality of this covariate Vj*/
1.145 brouard 3794: ij=(int)(covar[Tvar[j]][i]); /* ij=0 or 1 or -1. Value of the covariate Tvar[j] for individual i
3795: * If product of Vn*Vm, still boolean *:
3796: * If it was coded 1, 2, 3, 4 should be splitted into 3 boolean variables
3797: * 1 => 0 0 0, 2 => 0 0 1, 3 => 0 1 1, 4=1 0 0 */
3798: /* Finds for covariate j, n=Tvar[j] of Vn . ij is the
1.136 brouard 3799: modality of the nth covariate of individual i. */
1.145 brouard 3800: if (ij > modmaxcovj)
3801: modmaxcovj=ij;
3802: else if (ij < modmincovj)
3803: modmincovj=ij;
3804: if ((ij < -1) && (ij > NCOVMAX)){
3805: printf( "Error: minimal is less than -1 or maximal is bigger than %d. Exiting. \n", NCOVMAX );
3806: exit(1);
3807: }else
1.136 brouard 3808: Ndum[ij]++; /*counts and stores the occurence of this modality 0, 1, -1*/
1.145 brouard 3809: /* If coded 1, 2, 3 , counts the number of 1 Ndum[1], number of 2, Ndum[2], etc */
1.126 brouard 3810: /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
1.136 brouard 3811: /* getting the maximum value of the modality of the covariate
3812: (should be 0 or 1 now) Tvar[j]. If V=sex and male is coded 0 and
3813: female is 1, then modmaxcovj=1.*/
1.192 brouard 3814: } /* end for loop on individuals i */
1.145 brouard 3815: printf(" Minimal and maximal values of %d th covariate V%d: min=%d max=%d \n", j, Tvar[j], modmincovj, modmaxcovj);
1.192 brouard 3816: 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 3817: cptcode=modmaxcovj;
1.137 brouard 3818: /* Ndum[0] = frequency of 0 for model-covariate j, Ndum[1] frequency of 1 etc. */
1.145 brouard 3819: /*for (i=0; i<=cptcode; i++) {*/
1.192 brouard 3820: for (k=modmincovj; k<=modmaxcovj; k++) { /* k=-1 ? 0 and 1*//* For each value k of the modality of model-cov j */
3821: printf("Frequencies of covariates %d ie V%d with value %d: %d\n", j, Tvar[j], k, Ndum[k]);
3822: fprintf(ficlog, "Frequencies of covariates %d ie V%d with value %d: %d\n", j, Tvar[j], k, Ndum[k]);
3823: if( Ndum[k] != 0 ){ /* Counts if nobody answered modality k ie empty modality, we skip it and reorder */
3824: if( k != -1){
3825: ncodemax[j]++; /* ncodemax[j]= Number of modalities of the j th
3826: covariate for which somebody answered excluding
3827: undefined. Usually 2: 0 and 1. */
3828: }
3829: ncodemaxwundef[j]++; /* ncodemax[j]= Number of modalities of the j th
3830: covariate for which somebody answered including
3831: undefined. Usually 3: -1, 0 and 1. */
1.145 brouard 3832: }
3833: /* In fact ncodemax[j]=2 (dichotom. variables only) but it could be more for
3834: historical reasons: 3 if coded 1, 2, 3 and 4 and Ndum[2]=0 */
1.131 brouard 3835: } /* Ndum[-1] number of undefined modalities */
1.126 brouard 3836:
1.136 brouard 3837: /* j is a covariate, n=Tvar[j] of Vn; Fills nbcode */
1.186 brouard 3838: /* For covariate j, modalities could be 1, 2, 3, 4, 5, 6, 7.
3839: 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 3840: modmincovj=3; modmaxcovj = 7;
1.186 brouard 3841: There are only 3 modalities non empty 3, 6, 7 (or 2 if 27 is too few) : ncodemax[j]=3;
3842: which will be coded 0, 1, 2 which in binary on 2=3-1 digits are 0=00 1=01, 2=10;
3843: defining two dummy variables: variables V1_1 and V1_2.
1.145 brouard 3844: nbcode[Tvar[j]][ij]=k;
3845: nbcode[Tvar[j]][1]=0;
3846: nbcode[Tvar[j]][2]=1;
3847: nbcode[Tvar[j]][3]=2;
1.197 brouard 3848: To be continued (not working yet).
1.145 brouard 3849: */
1.197 brouard 3850: ij=0; /* ij is similar to i but can jump over null modalities */
3851: 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*/
3852: if (Ndum[i] == 0) { /* If nobody responded to this modality k */
1.192 brouard 3853: break;
3854: }
3855: ij++;
1.197 brouard 3856: 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 3857: cptcode = ij; /* New max modality for covar j */
3858: } /* end of loop on modality i=-1 to 1 or more */
3859:
3860: /* for (k=0; k<= cptcode; k++) { /\* k=-1 ? k=0 to 1 *\//\* Could be 1 to 4 *\//\* cptcode=modmaxcovj *\/ */
3861: /* /\*recode from 0 *\/ */
3862: /* k is a modality. If we have model=V1+V1*sex */
3863: /* then: nbcode[1][1]=0 ; nbcode[1][2]=1; nbcode[2][1]=0 ; nbcode[2][2]=1; */
3864: /* But if some modality were not used, it is recoded from 0 to a newer modmaxcovj=cptcode *\/ */
3865: /* } */
3866: /* /\* cptcode = ij; *\/ /\* New max modality for covar j *\/ */
3867: /* if (ij > ncodemax[j]) { */
3868: /* printf( " Error ij=%d > ncodemax[%d]=%d\n", ij, j, ncodemax[j]); */
3869: /* fprintf(ficlog, " Error ij=%d > ncodemax[%d]=%d\n", ij, j, ncodemax[j]); */
3870: /* break; */
3871: /* } */
3872: /* } /\* end of loop on modality k *\/ */
1.137 brouard 3873: } /* end of loop on model-covariate j. nbcode[Tvarj][1]=0 and nbcode[Tvarj][2]=1 sets the value of covariate j*/
3874:
1.145 brouard 3875: for (k=-1; k< maxncov; k++) Ndum[k]=0;
1.137 brouard 3876:
1.187 brouard 3877: for (i=1; i<=ncovmodel-2-nagesqr; i++) { /* -2, cste and age and eventually age*age */
1.145 brouard 3878: /* Listing of all covariables in statement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/
3879: ij=Tvar[i]; /* Tvar might be -1 if status was unknown */
1.187 brouard 3880: Ndum[ij]++; /* Might be supersed V1 + V1*age */
1.145 brouard 3881: }
1.126 brouard 3882:
1.192 brouard 3883: ij=0;
1.145 brouard 3884: for (i=0; i<= maxncov-1; i++) { /* modmaxcovj is unknown here. Only Ndum[2(V2),3(age*V3), 5(V3*V2) 6(V1*V4) */
3885: /*printf("Ndum[%d]=%d\n",i, Ndum[i]);*/
1.126 brouard 3886: if((Ndum[i]!=0) && (i<=ncovcol)){
1.192 brouard 3887: ij++;
1.145 brouard 3888: /*printf("diff Ndum[%d]=%d\n",i, Ndum[i]);*/
3889: Tvaraff[ij]=i; /*For printing (unclear) */
1.192 brouard 3890: }else{
3891: /* Tvaraff[ij]=0; */
3892: }
1.126 brouard 3893: }
1.192 brouard 3894: /* ij--; */
1.144 brouard 3895: cptcoveff=ij; /*Number of total covariates*/
1.145 brouard 3896:
1.126 brouard 3897: }
3898:
1.145 brouard 3899:
1.126 brouard 3900: /*********** Health Expectancies ****************/
3901:
1.127 brouard 3902: 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 3903:
3904: {
3905: /* Health expectancies, no variances */
1.164 brouard 3906: int i, j, nhstepm, hstepm, h, nstepm;
1.126 brouard 3907: int nhstepma, nstepma; /* Decreasing with age */
3908: double age, agelim, hf;
3909: double ***p3mat;
3910: double eip;
3911:
3912: pstamp(ficreseij);
3913: fprintf(ficreseij,"# (a) Life expectancies by health status at initial age and (b) health expectancies by health status at initial age\n");
3914: fprintf(ficreseij,"# Age");
3915: for(i=1; i<=nlstate;i++){
3916: for(j=1; j<=nlstate;j++){
3917: fprintf(ficreseij," e%1d%1d ",i,j);
3918: }
3919: fprintf(ficreseij," e%1d. ",i);
3920: }
3921: fprintf(ficreseij,"\n");
3922:
3923:
3924: if(estepm < stepm){
3925: printf ("Problem %d lower than %d\n",estepm, stepm);
3926: }
3927: else hstepm=estepm;
3928: /* We compute the life expectancy from trapezoids spaced every estepm months
3929: * This is mainly to measure the difference between two models: for example
3930: * if stepm=24 months pijx are given only every 2 years and by summing them
3931: * we are calculating an estimate of the Life Expectancy assuming a linear
3932: * progression in between and thus overestimating or underestimating according
3933: * to the curvature of the survival function. If, for the same date, we
3934: * estimate the model with stepm=1 month, we can keep estepm to 24 months
3935: * to compare the new estimate of Life expectancy with the same linear
3936: * hypothesis. A more precise result, taking into account a more precise
3937: * curvature will be obtained if estepm is as small as stepm. */
3938:
3939: /* For example we decided to compute the life expectancy with the smallest unit */
3940: /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
3941: nhstepm is the number of hstepm from age to agelim
3942: nstepm is the number of stepm from age to agelin.
3943: Look at hpijx to understand the reason of that which relies in memory size
3944: and note for a fixed period like estepm months */
3945: /* We decided (b) to get a life expectancy respecting the most precise curvature of the
3946: survival function given by stepm (the optimization length). Unfortunately it
3947: means that if the survival funtion is printed only each two years of age and if
3948: you sum them up and add 1 year (area under the trapezoids) you won't get the same
3949: results. So we changed our mind and took the option of the best precision.
3950: */
3951: hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
3952:
3953: agelim=AGESUP;
3954: /* If stepm=6 months */
3955: /* Computed by stepm unit matrices, product of hstepm matrices, stored
3956: in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
3957:
3958: /* nhstepm age range expressed in number of stepm */
3959: nstepm=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
3960: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
3961: /* if (stepm >= YEARM) hstepm=1;*/
3962: nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
3963: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3964:
3965: for (age=bage; age<=fage; age ++){
3966: nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
3967: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
3968: /* if (stepm >= YEARM) hstepm=1;*/
3969: nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
3970:
3971: /* If stepm=6 months */
3972: /* Computed by stepm unit matrices, product of hstepma matrices, stored
3973: in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
3974:
3975: hpxij(p3mat,nhstepma,age,hstepm,x,nlstate,stepm,oldm, savm, cij);
3976:
3977: hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
3978:
3979: printf("%d|",(int)age);fflush(stdout);
3980: fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
3981:
3982: /* Computing expectancies */
3983: for(i=1; i<=nlstate;i++)
3984: for(j=1; j<=nlstate;j++)
3985: for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
3986: eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
3987:
3988: /* 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]);*/
3989:
3990: }
3991:
3992: fprintf(ficreseij,"%3.0f",age );
3993: for(i=1; i<=nlstate;i++){
3994: eip=0;
3995: for(j=1; j<=nlstate;j++){
3996: eip +=eij[i][j][(int)age];
3997: fprintf(ficreseij,"%9.4f", eij[i][j][(int)age] );
3998: }
3999: fprintf(ficreseij,"%9.4f", eip );
4000: }
4001: fprintf(ficreseij,"\n");
4002:
4003: }
4004: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4005: printf("\n");
4006: fprintf(ficlog,"\n");
4007:
4008: }
4009:
1.127 brouard 4010: 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 4011:
4012: {
4013: /* Covariances of health expectancies eij and of total life expectancies according
4014: to initial status i, ei. .
4015: */
4016: int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2, ij, ji;
4017: int nhstepma, nstepma; /* Decreasing with age */
4018: double age, agelim, hf;
4019: double ***p3matp, ***p3matm, ***varhe;
4020: double **dnewm,**doldm;
4021: double *xp, *xm;
4022: double **gp, **gm;
4023: double ***gradg, ***trgradg;
4024: int theta;
4025:
4026: double eip, vip;
4027:
4028: varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage);
4029: xp=vector(1,npar);
4030: xm=vector(1,npar);
4031: dnewm=matrix(1,nlstate*nlstate,1,npar);
4032: doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate);
4033:
4034: pstamp(ficresstdeij);
4035: fprintf(ficresstdeij,"# Health expectancies with standard errors\n");
4036: fprintf(ficresstdeij,"# Age");
4037: for(i=1; i<=nlstate;i++){
4038: for(j=1; j<=nlstate;j++)
4039: fprintf(ficresstdeij," e%1d%1d (SE)",i,j);
4040: fprintf(ficresstdeij," e%1d. ",i);
4041: }
4042: fprintf(ficresstdeij,"\n");
4043:
4044: pstamp(ficrescveij);
4045: fprintf(ficrescveij,"# Subdiagonal matrix of covariances of health expectancies by age: cov(eij,ekl)\n");
4046: fprintf(ficrescveij,"# Age");
4047: for(i=1; i<=nlstate;i++)
4048: for(j=1; j<=nlstate;j++){
4049: cptj= (j-1)*nlstate+i;
4050: for(i2=1; i2<=nlstate;i2++)
4051: for(j2=1; j2<=nlstate;j2++){
4052: cptj2= (j2-1)*nlstate+i2;
4053: if(cptj2 <= cptj)
4054: fprintf(ficrescveij," %1d%1d,%1d%1d",i,j,i2,j2);
4055: }
4056: }
4057: fprintf(ficrescveij,"\n");
4058:
4059: if(estepm < stepm){
4060: printf ("Problem %d lower than %d\n",estepm, stepm);
4061: }
4062: else hstepm=estepm;
4063: /* We compute the life expectancy from trapezoids spaced every estepm months
4064: * This is mainly to measure the difference between two models: for example
4065: * if stepm=24 months pijx are given only every 2 years and by summing them
4066: * we are calculating an estimate of the Life Expectancy assuming a linear
4067: * progression in between and thus overestimating or underestimating according
4068: * to the curvature of the survival function. If, for the same date, we
4069: * estimate the model with stepm=1 month, we can keep estepm to 24 months
4070: * to compare the new estimate of Life expectancy with the same linear
4071: * hypothesis. A more precise result, taking into account a more precise
4072: * curvature will be obtained if estepm is as small as stepm. */
4073:
4074: /* For example we decided to compute the life expectancy with the smallest unit */
4075: /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
4076: nhstepm is the number of hstepm from age to agelim
4077: nstepm is the number of stepm from age to agelin.
4078: Look at hpijx to understand the reason of that which relies in memory size
4079: and note for a fixed period like estepm months */
4080: /* We decided (b) to get a life expectancy respecting the most precise curvature of the
4081: survival function given by stepm (the optimization length). Unfortunately it
4082: means that if the survival funtion is printed only each two years of age and if
4083: you sum them up and add 1 year (area under the trapezoids) you won't get the same
4084: results. So we changed our mind and took the option of the best precision.
4085: */
4086: hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
4087:
4088: /* If stepm=6 months */
4089: /* nhstepm age range expressed in number of stepm */
4090: agelim=AGESUP;
4091: nstepm=(int) rint((agelim-bage)*YEARM/stepm);
4092: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
4093: /* if (stepm >= YEARM) hstepm=1;*/
4094: nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
4095:
4096: p3matp=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4097: p3matm=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4098: gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);
4099: trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar);
4100: gp=matrix(0,nhstepm,1,nlstate*nlstate);
4101: gm=matrix(0,nhstepm,1,nlstate*nlstate);
4102:
4103: for (age=bage; age<=fage; age ++){
4104: nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
4105: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
4106: /* if (stepm >= YEARM) hstepm=1;*/
4107: nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
4108:
4109: /* If stepm=6 months */
4110: /* Computed by stepm unit matrices, product of hstepma matrices, stored
4111: in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
4112:
4113: hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
4114:
4115: /* Computing Variances of health expectancies */
4116: /* Gradient is computed with plus gp and minus gm. Code is duplicated in order to
4117: decrease memory allocation */
4118: for(theta=1; theta <=npar; theta++){
4119: for(i=1; i<=npar; i++){
4120: xp[i] = x[i] + (i==theta ?delti[theta]:0);
4121: xm[i] = x[i] - (i==theta ?delti[theta]:0);
4122: }
4123: hpxij(p3matp,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, cij);
4124: hpxij(p3matm,nhstepm,age,hstepm,xm,nlstate,stepm,oldm,savm, cij);
4125:
4126: for(j=1; j<= nlstate; j++){
4127: for(i=1; i<=nlstate; i++){
4128: for(h=0; h<=nhstepm-1; h++){
4129: gp[h][(j-1)*nlstate + i] = (p3matp[i][j][h]+p3matp[i][j][h+1])/2.;
4130: gm[h][(j-1)*nlstate + i] = (p3matm[i][j][h]+p3matm[i][j][h+1])/2.;
4131: }
4132: }
4133: }
4134:
4135: for(ij=1; ij<= nlstate*nlstate; ij++)
4136: for(h=0; h<=nhstepm-1; h++){
4137: gradg[h][theta][ij]= (gp[h][ij]-gm[h][ij])/2./delti[theta];
4138: }
4139: }/* End theta */
4140:
4141:
4142: for(h=0; h<=nhstepm-1; h++)
4143: for(j=1; j<=nlstate*nlstate;j++)
4144: for(theta=1; theta <=npar; theta++)
4145: trgradg[h][j][theta]=gradg[h][theta][j];
4146:
4147:
4148: for(ij=1;ij<=nlstate*nlstate;ij++)
4149: for(ji=1;ji<=nlstate*nlstate;ji++)
4150: varhe[ij][ji][(int)age] =0.;
4151:
4152: printf("%d|",(int)age);fflush(stdout);
4153: fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
4154: for(h=0;h<=nhstepm-1;h++){
4155: for(k=0;k<=nhstepm-1;k++){
4156: matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov);
4157: matprod2(doldm,dnewm,1,nlstate*nlstate,1,npar,1,nlstate*nlstate,gradg[k]);
4158: for(ij=1;ij<=nlstate*nlstate;ij++)
4159: for(ji=1;ji<=nlstate*nlstate;ji++)
4160: varhe[ij][ji][(int)age] += doldm[ij][ji]*hf*hf;
4161: }
4162: }
4163:
4164: /* Computing expectancies */
4165: hpxij(p3matm,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, cij);
4166: for(i=1; i<=nlstate;i++)
4167: for(j=1; j<=nlstate;j++)
4168: for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
4169: eij[i][j][(int)age] += (p3matm[i][j][h]+p3matm[i][j][h+1])/2.0*hf;
4170:
4171: /* 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]);*/
4172:
4173: }
4174:
4175: fprintf(ficresstdeij,"%3.0f",age );
4176: for(i=1; i<=nlstate;i++){
4177: eip=0.;
4178: vip=0.;
4179: for(j=1; j<=nlstate;j++){
4180: eip += eij[i][j][(int)age];
4181: for(k=1; k<=nlstate;k++) /* Sum on j and k of cov(eij,eik) */
4182: vip += varhe[(j-1)*nlstate+i][(k-1)*nlstate+i][(int)age];
4183: fprintf(ficresstdeij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[(j-1)*nlstate+i][(j-1)*nlstate+i][(int)age]) );
4184: }
4185: fprintf(ficresstdeij," %9.4f (%.4f)", eip, sqrt(vip));
4186: }
4187: fprintf(ficresstdeij,"\n");
4188:
4189: fprintf(ficrescveij,"%3.0f",age );
4190: for(i=1; i<=nlstate;i++)
4191: for(j=1; j<=nlstate;j++){
4192: cptj= (j-1)*nlstate+i;
4193: for(i2=1; i2<=nlstate;i2++)
4194: for(j2=1; j2<=nlstate;j2++){
4195: cptj2= (j2-1)*nlstate+i2;
4196: if(cptj2 <= cptj)
4197: fprintf(ficrescveij," %.4f", varhe[cptj][cptj2][(int)age]);
4198: }
4199: }
4200: fprintf(ficrescveij,"\n");
4201:
4202: }
4203: free_matrix(gm,0,nhstepm,1,nlstate*nlstate);
4204: free_matrix(gp,0,nhstepm,1,nlstate*nlstate);
4205: free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*nlstate);
4206: free_ma3x(trgradg,0,nhstepm,1,nlstate*nlstate,1,npar);
4207: free_ma3x(p3matm,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4208: free_ma3x(p3matp,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4209: printf("\n");
4210: fprintf(ficlog,"\n");
4211:
4212: free_vector(xm,1,npar);
4213: free_vector(xp,1,npar);
4214: free_matrix(dnewm,1,nlstate*nlstate,1,npar);
4215: free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate);
4216: free_ma3x(varhe,1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int)fage);
4217: }
4218:
4219: /************ Variance ******************/
1.209 brouard 4220: 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[])
1.126 brouard 4221: {
4222: /* Variance of health expectancies */
4223: /* double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
4224: /* double **newm;*/
1.169 brouard 4225: /* int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav)*/
4226:
4227: int movingaverage();
1.126 brouard 4228: double **dnewm,**doldm;
4229: double **dnewmp,**doldmp;
4230: int i, j, nhstepm, hstepm, h, nstepm ;
1.164 brouard 4231: int k;
1.126 brouard 4232: double *xp;
4233: double **gp, **gm; /* for var eij */
4234: double ***gradg, ***trgradg; /*for var eij */
4235: double **gradgp, **trgradgp; /* for var p point j */
4236: double *gpp, *gmp; /* for var p point j */
4237: double **varppt; /* for var p point j nlstate to nlstate+ndeath */
4238: double ***p3mat;
4239: double age,agelim, hf;
4240: double ***mobaverage;
4241: int theta;
4242: char digit[4];
4243: char digitp[25];
4244:
4245: char fileresprobmorprev[FILENAMELENGTH];
4246:
4247: if(popbased==1){
4248: if(mobilav!=0)
1.201 brouard 4249: strcpy(digitp,"-POPULBASED-MOBILAV_");
4250: else strcpy(digitp,"-POPULBASED-NOMOBIL_");
1.126 brouard 4251: }
4252: else
1.201 brouard 4253: strcpy(digitp,"-STABLBASED_");
1.126 brouard 4254:
4255: if (mobilav!=0) {
4256: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
4257: if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
4258: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
4259: printf(" Error in movingaverage mobilav=%d\n",mobilav);
4260: }
4261: }
4262:
1.201 brouard 4263: strcpy(fileresprobmorprev,"PRMORPREV-");
1.126 brouard 4264: sprintf(digit,"%-d",ij);
4265: /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
4266: strcat(fileresprobmorprev,digit); /* Tvar to be done */
4267: strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
1.202 brouard 4268: strcat(fileresprobmorprev,fileresu);
1.126 brouard 4269: if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
4270: printf("Problem with resultfile: %s\n", fileresprobmorprev);
4271: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
4272: }
4273: printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
4274: fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
4275: pstamp(ficresprobmorprev);
4276: 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);
4277: fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
4278: for(j=nlstate+1; j<=(nlstate+ndeath);j++){
4279: fprintf(ficresprobmorprev," p.%-d SE",j);
4280: for(i=1; i<=nlstate;i++)
4281: fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
4282: }
4283: fprintf(ficresprobmorprev,"\n");
1.208 brouard 4284:
1.126 brouard 4285: fprintf(ficgp,"\n# Routine varevsij");
1.200 brouard 4286: fprintf(ficgp,"\nunset title \n");
4287: /* fprintf(fichtm, "#Local time at start: %s", strstart);*/
1.126 brouard 4288: 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");
4289: fprintf(fichtm,"\n<br>%s <br>\n",digitp);
4290: /* } */
4291: varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
4292: pstamp(ficresvij);
4293: fprintf(ficresvij,"# Variance and covariance of health expectancies e.j \n# (weighted average of eij where weights are ");
4294: if(popbased==1)
1.128 brouard 4295: 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);
1.126 brouard 4296: else
4297: fprintf(ficresvij,"the age specific period (stable) prevalences in each health state \n");
4298: fprintf(ficresvij,"# Age");
4299: for(i=1; i<=nlstate;i++)
4300: for(j=1; j<=nlstate;j++)
4301: fprintf(ficresvij," Cov(e.%1d, e.%1d)",i,j);
4302: fprintf(ficresvij,"\n");
4303:
4304: xp=vector(1,npar);
4305: dnewm=matrix(1,nlstate,1,npar);
4306: doldm=matrix(1,nlstate,1,nlstate);
4307: dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
4308: doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
4309:
4310: gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
4311: gpp=vector(nlstate+1,nlstate+ndeath);
4312: gmp=vector(nlstate+1,nlstate+ndeath);
4313: trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
4314:
4315: if(estepm < stepm){
4316: printf ("Problem %d lower than %d\n",estepm, stepm);
4317: }
4318: else hstepm=estepm;
4319: /* For example we decided to compute the life expectancy with the smallest unit */
4320: /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
4321: nhstepm is the number of hstepm from age to agelim
1.208 brouard 4322: nstepm is the number of stepm from age to agelim.
1.209 brouard 4323: Look at function hpijx to understand why because of memory size limitations,
1.208 brouard 4324: we decided (b) to get a life expectancy respecting the most precise curvature of the
1.126 brouard 4325: survival function given by stepm (the optimization length). Unfortunately it
4326: means that if the survival funtion is printed every two years of age and if
4327: you sum them up and add 1 year (area under the trapezoids) you won't get the same
4328: results. So we changed our mind and took the option of the best precision.
4329: */
4330: hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
4331: agelim = AGESUP;
4332: for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
4333: nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
4334: nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
4335: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4336: gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
4337: gp=matrix(0,nhstepm,1,nlstate);
4338: gm=matrix(0,nhstepm,1,nlstate);
4339:
4340:
4341: for(theta=1; theta <=npar; theta++){
4342: for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
4343: xp[i] = x[i] + (i==theta ?delti[theta]:0);
4344: }
1.209 brouard 4345:
4346: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij);
1.126 brouard 4347:
4348: if (popbased==1) {
4349: if(mobilav ==0){
4350: for(i=1; i<=nlstate;i++)
4351: prlim[i][i]=probs[(int)age][i][ij];
4352: }else{ /* mobilav */
4353: for(i=1; i<=nlstate;i++)
4354: prlim[i][i]=mobaverage[(int)age][i][ij];
4355: }
4356: }
4357:
1.209 brouard 4358: hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij); /* Returns p3mat[i][j][h] for h=1 to nhstepm */
1.126 brouard 4359: for(j=1; j<= nlstate; j++){
4360: for(h=0; h<=nhstepm; h++){
4361: for(i=1, gp[h][j]=0.;i<=nlstate;i++)
4362: gp[h][j] += prlim[i][i]*p3mat[i][j][h];
4363: }
4364: }
1.209 brouard 4365: /* Next for computing probability of death (h=1 means
1.126 brouard 4366: computed over hstepm matrices product = hstepm*stepm months)
4367: as a weighted average of prlim.
4368: */
4369: for(j=nlstate+1;j<=nlstate+ndeath;j++){
4370: for(i=1,gpp[j]=0.; i<= nlstate; i++)
4371: gpp[j] += prlim[i][i]*p3mat[i][j][1];
4372: }
4373: /* end probability of death */
4374:
4375: for(i=1; i<=npar; i++) /* Computes gradient x - delta */
4376: xp[i] = x[i] - (i==theta ?delti[theta]:0);
1.209 brouard 4377:
4378: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp, ij);
1.126 brouard 4379:
4380: if (popbased==1) {
4381: if(mobilav ==0){
4382: for(i=1; i<=nlstate;i++)
4383: prlim[i][i]=probs[(int)age][i][ij];
4384: }else{ /* mobilav */
4385: for(i=1; i<=nlstate;i++)
4386: prlim[i][i]=mobaverage[(int)age][i][ij];
4387: }
4388: }
4389:
1.209 brouard 4390: hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
4391:
1.128 brouard 4392: for(j=1; j<= nlstate; j++){ /* Sum of wi * eij = e.j */
1.126 brouard 4393: for(h=0; h<=nhstepm; h++){
4394: for(i=1, gm[h][j]=0.;i<=nlstate;i++)
4395: gm[h][j] += prlim[i][i]*p3mat[i][j][h];
4396: }
4397: }
4398: /* This for computing probability of death (h=1 means
4399: computed over hstepm matrices product = hstepm*stepm months)
4400: as a weighted average of prlim.
4401: */
4402: for(j=nlstate+1;j<=nlstate+ndeath;j++){
4403: for(i=1,gmp[j]=0.; i<= nlstate; i++)
4404: gmp[j] += prlim[i][i]*p3mat[i][j][1];
4405: }
4406: /* end probability of death */
4407:
4408: for(j=1; j<= nlstate; j++) /* vareij */
4409: for(h=0; h<=nhstepm; h++){
4410: gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
4411: }
4412:
4413: for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
4414: gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
4415: }
4416:
4417: } /* End theta */
4418:
4419: trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
4420:
4421: for(h=0; h<=nhstepm; h++) /* veij */
4422: for(j=1; j<=nlstate;j++)
4423: for(theta=1; theta <=npar; theta++)
4424: trgradg[h][j][theta]=gradg[h][theta][j];
4425:
4426: for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
4427: for(theta=1; theta <=npar; theta++)
4428: trgradgp[j][theta]=gradgp[theta][j];
4429:
4430:
4431: hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
4432: for(i=1;i<=nlstate;i++)
4433: for(j=1;j<=nlstate;j++)
4434: vareij[i][j][(int)age] =0.;
4435:
4436: for(h=0;h<=nhstepm;h++){
4437: for(k=0;k<=nhstepm;k++){
4438: matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
4439: matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
4440: for(i=1;i<=nlstate;i++)
4441: for(j=1;j<=nlstate;j++)
4442: vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
4443: }
4444: }
4445:
4446: /* pptj */
4447: matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
4448: matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
4449: for(j=nlstate+1;j<=nlstate+ndeath;j++)
4450: for(i=nlstate+1;i<=nlstate+ndeath;i++)
4451: varppt[j][i]=doldmp[j][i];
4452: /* end ppptj */
4453: /* x centered again */
1.209 brouard 4454:
4455: prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ncvyearp,ij);
1.126 brouard 4456:
4457: if (popbased==1) {
4458: if(mobilav ==0){
4459: for(i=1; i<=nlstate;i++)
4460: prlim[i][i]=probs[(int)age][i][ij];
4461: }else{ /* mobilav */
4462: for(i=1; i<=nlstate;i++)
4463: prlim[i][i]=mobaverage[(int)age][i][ij];
4464: }
4465: }
4466:
4467: /* This for computing probability of death (h=1 means
4468: computed over hstepm (estepm) matrices product = hstepm*stepm months)
4469: as a weighted average of prlim.
4470: */
1.209 brouard 4471: hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);
1.126 brouard 4472: for(j=nlstate+1;j<=nlstate+ndeath;j++){
4473: for(i=1,gmp[j]=0.;i<= nlstate; i++)
4474: gmp[j] += prlim[i][i]*p3mat[i][j][1];
4475: }
4476: /* end probability of death */
4477:
4478: fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
4479: for(j=nlstate+1; j<=(nlstate+ndeath);j++){
4480: fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
4481: for(i=1; i<=nlstate;i++){
4482: fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
4483: }
4484: }
4485: fprintf(ficresprobmorprev,"\n");
4486:
4487: fprintf(ficresvij,"%.0f ",age );
4488: for(i=1; i<=nlstate;i++)
4489: for(j=1; j<=nlstate;j++){
4490: fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
4491: }
4492: fprintf(ficresvij,"\n");
4493: free_matrix(gp,0,nhstepm,1,nlstate);
4494: free_matrix(gm,0,nhstepm,1,nlstate);
4495: free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
4496: free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
4497: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4498: } /* End age */
4499: free_vector(gpp,nlstate+1,nlstate+ndeath);
4500: free_vector(gmp,nlstate+1,nlstate+ndeath);
4501: free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
4502: free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
1.199 brouard 4503: /* fprintf(ficgp,"\nunset parametric;unset label; set ter png small size 320, 240"); */
4504: fprintf(ficgp,"\nunset parametric;unset label; set ter svg size 640, 480");
1.126 brouard 4505: /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */
1.131 brouard 4506: fprintf(ficgp,"\n set log y; unset log x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
1.201 brouard 4507: fprintf(ficgp,"\nset out \"%s%s.svg\";",subdirf3(optionfilefiname,"VARMUPTJGR-",digitp),digit);
1.126 brouard 4508: /* fprintf(ficgp,"\n plot \"%s\" u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm); */
4509: /* fprintf(ficgp,"\n replot \"%s\" u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm); */
4510: /* fprintf(ficgp,"\n replot \"%s\" u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm); */
1.145 brouard 4511: fprintf(ficgp,"\n plot \"%s\" u 1:($3) not w l lt 1 ",subdirf(fileresprobmorprev));
1.170 brouard 4512: fprintf(ficgp,"\n replot \"%s\" u 1:(($3+1.96*$4)) t \"95%% interval\" w l lt 2 ",subdirf(fileresprobmorprev));
1.145 brouard 4513: fprintf(ficgp,"\n replot \"%s\" u 1:(($3-1.96*$4)) not w l lt 2 ",subdirf(fileresprobmorprev));
1.126 brouard 4514: fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",subdirf(fileresprobmorprev),subdirf(fileresprobmorprev));
1.201 brouard 4515: 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);
1.199 brouard 4516: /* 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 4517: */
1.199 brouard 4518: /* fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.svg\";replot;",digitp,optionfilefiname,digit); */
1.201 brouard 4519: fprintf(ficgp,"\nset out;\nset out \"%s%s.svg\";replot;set out;\n",subdirf3(optionfilefiname,"VARMUPTJGR-",digitp),digit);
1.126 brouard 4520:
4521: free_vector(xp,1,npar);
4522: free_matrix(doldm,1,nlstate,1,nlstate);
4523: free_matrix(dnewm,1,nlstate,1,npar);
4524: free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
4525: free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
4526: free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
4527: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
4528: fclose(ficresprobmorprev);
4529: fflush(ficgp);
4530: fflush(fichtm);
4531: } /* end varevsij */
4532:
4533: /************ Variance of prevlim ******************/
1.209 brouard 4534: 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 4535: {
1.205 brouard 4536: /* Variance of prevalence limit for each state ij using current parameters x[] and estimates of neighbourhood give by delti*/
1.126 brouard 4537: /* double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
1.164 brouard 4538:
1.126 brouard 4539: double **dnewm,**doldm;
4540: int i, j, nhstepm, hstepm;
4541: double *xp;
4542: double *gp, *gm;
4543: double **gradg, **trgradg;
1.208 brouard 4544: double **mgm, **mgp;
1.126 brouard 4545: double age,agelim;
4546: int theta;
4547:
4548: pstamp(ficresvpl);
4549: fprintf(ficresvpl,"# Standard deviation of period (stable) prevalences \n");
4550: fprintf(ficresvpl,"# Age");
4551: for(i=1; i<=nlstate;i++)
4552: fprintf(ficresvpl," %1d-%1d",i,i);
4553: fprintf(ficresvpl,"\n");
4554:
4555: xp=vector(1,npar);
4556: dnewm=matrix(1,nlstate,1,npar);
4557: doldm=matrix(1,nlstate,1,nlstate);
4558:
4559: hstepm=1*YEARM; /* Every year of age */
4560: hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */
4561: agelim = AGESUP;
4562: for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
4563: nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
4564: if (stepm >= YEARM) hstepm=1;
4565: nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
4566: gradg=matrix(1,npar,1,nlstate);
1.208 brouard 4567: mgp=matrix(1,npar,1,nlstate);
4568: mgm=matrix(1,npar,1,nlstate);
1.126 brouard 4569: gp=vector(1,nlstate);
4570: gm=vector(1,nlstate);
4571:
4572: for(theta=1; theta <=npar; theta++){
4573: for(i=1; i<=npar; i++){ /* Computes gradient */
4574: xp[i] = x[i] + (i==theta ?delti[theta]:0);
4575: }
1.209 brouard 4576: if((int)age==79 ||(int)age== 80 ||(int)age== 81 )
4577: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij);
4578: else
4579: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij);
1.208 brouard 4580: for(i=1;i<=nlstate;i++){
1.126 brouard 4581: gp[i] = prlim[i][i];
1.208 brouard 4582: mgp[theta][i] = prlim[i][i];
4583: }
1.126 brouard 4584: for(i=1; i<=npar; i++) /* Computes gradient */
4585: xp[i] = x[i] - (i==theta ?delti[theta]:0);
1.209 brouard 4586: if((int)age==79 ||(int)age== 80 ||(int)age== 81 )
4587: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij);
4588: else
4589: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij);
1.208 brouard 4590: for(i=1;i<=nlstate;i++){
1.126 brouard 4591: gm[i] = prlim[i][i];
1.208 brouard 4592: mgm[theta][i] = prlim[i][i];
4593: }
1.126 brouard 4594: for(i=1;i<=nlstate;i++)
4595: gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
1.209 brouard 4596: /* gradg[theta][2]= -gradg[theta][1]; */ /* For testing if nlstate=2 */
1.126 brouard 4597: } /* End theta */
4598:
4599: trgradg =matrix(1,nlstate,1,npar);
4600:
4601: for(j=1; j<=nlstate;j++)
4602: for(theta=1; theta <=npar; theta++)
4603: trgradg[j][theta]=gradg[theta][j];
1.209 brouard 4604: /* if((int)age==79 ||(int)age== 80 ||(int)age== 81 ){ */
4605: /* printf("\nmgm mgp %d ",(int)age); */
4606: /* for(j=1; j<=nlstate;j++){ */
4607: /* printf(" %d ",j); */
4608: /* for(theta=1; theta <=npar; theta++) */
4609: /* printf(" %d %lf %lf",theta,mgm[theta][j],mgp[theta][j]); */
4610: /* printf("\n "); */
4611: /* } */
4612: /* } */
4613: /* if((int)age==79 ||(int)age== 80 ||(int)age== 81 ){ */
4614: /* printf("\n gradg %d ",(int)age); */
4615: /* for(j=1; j<=nlstate;j++){ */
4616: /* printf("%d ",j); */
4617: /* for(theta=1; theta <=npar; theta++) */
4618: /* printf("%d %lf ",theta,gradg[theta][j]); */
4619: /* printf("\n "); */
4620: /* } */
4621: /* } */
1.126 brouard 4622:
4623: for(i=1;i<=nlstate;i++)
4624: varpl[i][(int)age] =0.;
1.209 brouard 4625: if((int)age==79 ||(int)age== 80 ||(int)age== 81){
1.205 brouard 4626: matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
4627: matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
4628: }else{
1.126 brouard 4629: matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
4630: matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
1.205 brouard 4631: }
1.126 brouard 4632: for(i=1;i<=nlstate;i++)
4633: varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
4634:
4635: fprintf(ficresvpl,"%.0f ",age );
4636: for(i=1; i<=nlstate;i++)
4637: fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
4638: fprintf(ficresvpl,"\n");
4639: free_vector(gp,1,nlstate);
4640: free_vector(gm,1,nlstate);
1.208 brouard 4641: free_matrix(mgm,1,npar,1,nlstate);
4642: free_matrix(mgp,1,npar,1,nlstate);
1.126 brouard 4643: free_matrix(gradg,1,npar,1,nlstate);
4644: free_matrix(trgradg,1,nlstate,1,npar);
4645: } /* End age */
4646:
4647: free_vector(xp,1,npar);
4648: free_matrix(doldm,1,nlstate,1,npar);
4649: free_matrix(dnewm,1,nlstate,1,nlstate);
4650:
4651: }
4652:
4653: /************ Variance of one-step probabilities ******************/
4654: 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[])
4655: {
1.164 brouard 4656: int i, j=0, k1, l1, tj;
1.126 brouard 4657: int k2, l2, j1, z1;
1.164 brouard 4658: int k=0, l;
1.145 brouard 4659: int first=1, first1, first2;
1.126 brouard 4660: double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
4661: double **dnewm,**doldm;
4662: double *xp;
4663: double *gp, *gm;
4664: double **gradg, **trgradg;
4665: double **mu;
1.164 brouard 4666: double age, cov[NCOVMAX+1];
1.126 brouard 4667: double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
4668: int theta;
4669: char fileresprob[FILENAMELENGTH];
4670: char fileresprobcov[FILENAMELENGTH];
4671: char fileresprobcor[FILENAMELENGTH];
4672: double ***varpij;
4673:
1.201 brouard 4674: strcpy(fileresprob,"PROB_");
1.126 brouard 4675: strcat(fileresprob,fileres);
4676: if((ficresprob=fopen(fileresprob,"w"))==NULL) {
4677: printf("Problem with resultfile: %s\n", fileresprob);
4678: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
4679: }
1.201 brouard 4680: strcpy(fileresprobcov,"PROBCOV_");
1.202 brouard 4681: strcat(fileresprobcov,fileresu);
1.126 brouard 4682: if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
4683: printf("Problem with resultfile: %s\n", fileresprobcov);
4684: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
4685: }
1.201 brouard 4686: strcpy(fileresprobcor,"PROBCOR_");
1.202 brouard 4687: strcat(fileresprobcor,fileresu);
1.126 brouard 4688: if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
4689: printf("Problem with resultfile: %s\n", fileresprobcor);
4690: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
4691: }
4692: printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
4693: fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
4694: printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
4695: fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
4696: printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
4697: fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
4698: pstamp(ficresprob);
4699: fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
4700: fprintf(ficresprob,"# Age");
4701: pstamp(ficresprobcov);
4702: fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
4703: fprintf(ficresprobcov,"# Age");
4704: pstamp(ficresprobcor);
4705: fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
4706: fprintf(ficresprobcor,"# Age");
4707:
4708:
4709: for(i=1; i<=nlstate;i++)
4710: for(j=1; j<=(nlstate+ndeath);j++){
4711: fprintf(ficresprob," p%1d-%1d (SE)",i,j);
4712: fprintf(ficresprobcov," p%1d-%1d ",i,j);
4713: fprintf(ficresprobcor," p%1d-%1d ",i,j);
4714: }
4715: /* fprintf(ficresprob,"\n");
4716: fprintf(ficresprobcov,"\n");
4717: fprintf(ficresprobcor,"\n");
4718: */
1.131 brouard 4719: xp=vector(1,npar);
1.126 brouard 4720: dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
4721: doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
4722: mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
4723: varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
4724: first=1;
4725: fprintf(ficgp,"\n# Routine varprob");
4726: fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
4727: fprintf(fichtm,"\n");
4728:
1.200 brouard 4729: fprintf(fichtm,"\n<li><h4> <a href=\"%s\">Matrix of variance-covariance of one-step probabilities (drawings)</a></h4> this page is important in order to visualize confidence intervals and especially correlation between disability and recovery, or more generally, way in and way back.</li>\n",optionfilehtmcov);
1.197 brouard 4730: 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);
4731: fprintf(fichtmcov,"\nEllipsoids of confidence centered on point (p<inf>ij</inf>, p<inf>kl</inf>) are estimated \
1.126 brouard 4732: and drawn. It helps understanding how is the covariance between two incidences.\
4733: They are expressed in year<sup>-1</sup> in order to be less dependent of stepm.<br>\n");
4734: 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. \
4735: It can be understood this way: if pij and pkl where uncorrelated the (2x2) matrix of covariance \
4736: would have been (1/(var pij), 0 , 0, 1/(var pkl)), and the confidence interval would be 2 \
4737: standard deviations wide on each axis. <br>\
4738: Now, if both incidences are correlated (usual case) we diagonalised the inverse of the covariance matrix\
4739: and made the appropriate rotation to look at the uncorrelated principal directions.<br>\
4740: To be simple, these graphs help to understand the significativity of each parameter in relation to a second other one.<br> \n");
4741:
4742: cov[1]=1;
1.145 brouard 4743: /* tj=cptcoveff; */
4744: tj = (int) pow(2,cptcoveff);
1.126 brouard 4745: if (cptcovn<1) {tj=1;ncodemax[1]=1;}
4746: j1=0;
1.145 brouard 4747: for(j1=1; j1<=tj;j1++){
4748: /*for(i1=1; i1<=ncodemax[t];i1++){ */
4749: /*j1++;*/
1.126 brouard 4750: if (cptcovn>0) {
4751: fprintf(ficresprob, "\n#********** Variable ");
1.198 brouard 4752: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
1.126 brouard 4753: fprintf(ficresprob, "**********\n#\n");
4754: fprintf(ficresprobcov, "\n#********** Variable ");
1.198 brouard 4755: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
1.126 brouard 4756: fprintf(ficresprobcov, "**********\n#\n");
4757:
4758: fprintf(ficgp, "\n#********** Variable ");
1.198 brouard 4759: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
1.126 brouard 4760: fprintf(ficgp, "**********\n#\n");
4761:
4762:
4763: fprintf(fichtmcov, "\n<hr size=\"2\" color=\"#EC5E5E\">********** Variable ");
1.198 brouard 4764: for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
1.126 brouard 4765: fprintf(fichtmcov, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
4766:
4767: fprintf(ficresprobcor, "\n#********** Variable ");
1.198 brouard 4768: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
1.126 brouard 4769: fprintf(ficresprobcor, "**********\n#");
4770: }
4771:
1.145 brouard 4772: gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
4773: trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
4774: gp=vector(1,(nlstate)*(nlstate+ndeath));
4775: gm=vector(1,(nlstate)*(nlstate+ndeath));
1.126 brouard 4776: for (age=bage; age<=fage; age ++){
4777: cov[2]=age;
1.187 brouard 4778: if(nagesqr==1)
4779: cov[3]= age*age;
1.126 brouard 4780: for (k=1; k<=cptcovn;k++) {
1.200 brouard 4781: cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(j1,k)];
4782: /*cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(j1,Tvar[k])];*//* j1 1 2 3 4
1.145 brouard 4783: * 1 1 1 1 1
4784: * 2 2 1 1 1
4785: * 3 1 2 1 1
4786: */
4787: /* nbcode[1][1]=0 nbcode[1][2]=1;*/
1.126 brouard 4788: }
1.186 brouard 4789: /* for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
1.200 brouard 4790: for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,k)]*cov[2];
1.126 brouard 4791: for (k=1; k<=cptcovprod;k++)
1.200 brouard 4792: cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)]*nbcode[Tvard[k][2]][codtabm(ij,k)];
1.126 brouard 4793:
4794:
4795: for(theta=1; theta <=npar; theta++){
4796: for(i=1; i<=npar; i++)
4797: xp[i] = x[i] + (i==theta ?delti[theta]:(double)0);
4798:
4799: pmij(pmmij,cov,ncovmodel,xp,nlstate);
4800:
4801: k=0;
4802: for(i=1; i<= (nlstate); i++){
4803: for(j=1; j<=(nlstate+ndeath);j++){
4804: k=k+1;
4805: gp[k]=pmmij[i][j];
4806: }
4807: }
4808:
4809: for(i=1; i<=npar; i++)
4810: xp[i] = x[i] - (i==theta ?delti[theta]:(double)0);
4811:
4812: pmij(pmmij,cov,ncovmodel,xp,nlstate);
4813: k=0;
4814: for(i=1; i<=(nlstate); i++){
4815: for(j=1; j<=(nlstate+ndeath);j++){
4816: k=k+1;
4817: gm[k]=pmmij[i][j];
4818: }
4819: }
4820:
4821: for(i=1; i<= (nlstate)*(nlstate+ndeath); i++)
4822: gradg[theta][i]=(gp[i]-gm[i])/(double)2./delti[theta];
4823: }
4824:
4825: for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
4826: for(theta=1; theta <=npar; theta++)
4827: trgradg[j][theta]=gradg[theta][j];
4828:
4829: matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov);
4830: matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);
4831:
4832: pmij(pmmij,cov,ncovmodel,x,nlstate);
4833:
4834: k=0;
4835: for(i=1; i<=(nlstate); i++){
4836: for(j=1; j<=(nlstate+ndeath);j++){
4837: k=k+1;
4838: mu[k][(int) age]=pmmij[i][j];
4839: }
4840: }
4841: for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
4842: for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
4843: varpij[i][j][(int)age] = doldm[i][j];
4844:
4845: /*printf("\n%d ",(int)age);
4846: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
4847: printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
4848: fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
4849: }*/
4850:
4851: fprintf(ficresprob,"\n%d ",(int)age);
4852: fprintf(ficresprobcov,"\n%d ",(int)age);
4853: fprintf(ficresprobcor,"\n%d ",(int)age);
4854:
4855: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)
4856: fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));
4857: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
4858: fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);
4859: fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
4860: }
4861: i=0;
4862: for (k=1; k<=(nlstate);k++){
4863: for (l=1; l<=(nlstate+ndeath);l++){
1.145 brouard 4864: i++;
1.126 brouard 4865: fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
4866: fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
4867: for (j=1; j<=i;j++){
1.145 brouard 4868: /* printf(" k=%d l=%d i=%d j=%d\n",k,l,i,j);fflush(stdout); */
1.126 brouard 4869: fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);
4870: fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));
4871: }
4872: }
4873: }/* end of loop for state */
4874: } /* end of loop for age */
1.145 brouard 4875: free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
4876: free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
4877: free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
4878: free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
4879:
1.126 brouard 4880: /* Confidence intervalle of pij */
4881: /*
1.131 brouard 4882: fprintf(ficgp,"\nunset parametric;unset label");
1.126 brouard 4883: fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");
4884: fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
4885: 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);
4886: fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);
4887: fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);
4888: fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);
4889: */
4890:
4891: /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
1.145 brouard 4892: first1=1;first2=2;
1.126 brouard 4893: for (k2=1; k2<=(nlstate);k2++){
4894: for (l2=1; l2<=(nlstate+ndeath);l2++){
4895: if(l2==k2) continue;
4896: j=(k2-1)*(nlstate+ndeath)+l2;
4897: for (k1=1; k1<=(nlstate);k1++){
4898: for (l1=1; l1<=(nlstate+ndeath);l1++){
4899: if(l1==k1) continue;
4900: i=(k1-1)*(nlstate+ndeath)+l1;
4901: if(i<=j) continue;
4902: for (age=bage; age<=fage; age ++){
4903: if ((int)age %5==0){
4904: v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;
4905: v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;
4906: cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;
4907: mu1=mu[i][(int) age]/stepm*YEARM ;
4908: mu2=mu[j][(int) age]/stepm*YEARM;
4909: c12=cv12/sqrt(v1*v2);
4910: /* Computing eigen value of matrix of covariance */
4911: lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
4912: lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
1.135 brouard 4913: if ((lc2 <0) || (lc1 <0) ){
1.145 brouard 4914: if(first2==1){
4915: first1=0;
4916: 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);
4917: }
4918: 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);
4919: /* lc1=fabs(lc1); */ /* If we want to have them positive */
4920: /* lc2=fabs(lc2); */
1.135 brouard 4921: }
4922:
1.126 brouard 4923: /* Eigen vectors */
4924: v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
4925: /*v21=sqrt(1.-v11*v11); *//* error */
4926: v21=(lc1-v1)/cv12*v11;
4927: v12=-v21;
4928: v22=v11;
4929: tnalp=v21/v11;
4930: if(first1==1){
4931: first1=0;
4932: 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);
4933: }
4934: 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);
4935: /*printf(fignu*/
4936: /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */
4937: /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */
4938: if(first==1){
4939: first=0;
1.200 brouard 4940: fprintf(ficgp,"\n# Ellipsoids of confidence\n#\n");
1.126 brouard 4941: fprintf(ficgp,"\nset parametric;unset label");
4942: 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);
1.199 brouard 4943: fprintf(ficgp,"\nset ter svg size 640, 480");
1.126 brouard 4944: fprintf(fichtmcov,"\n<br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup>\
1.201 brouard 4945: :<a href=\"%s_%d%1d%1d-%1d%1d.svg\">\
4946: %s_%d%1d%1d-%1d%1d.svg</A>, ",k1,l1,k2,l2,\
4947: subdirf2(optionfilefiname,"VARPIJGR_"), j1,k1,l1,k2,l2,\
4948: subdirf2(optionfilefiname,"VARPIJGR_"), j1,k1,l1,k2,l2);
4949: fprintf(fichtmcov,"\n<br><img src=\"%s_%d%1d%1d-%1d%1d.svg\"> ",subdirf2(optionfilefiname,"VARPIJGR_"), j1,k1,l1,k2,l2);
1.126 brouard 4950: fprintf(fichtmcov,"\n<br> Correlation at age %d (%.3f),",(int) age, c12);
1.201 brouard 4951: fprintf(ficgp,"\nset out \"%s_%d%1d%1d-%1d%1d.svg\"",subdirf2(optionfilefiname,"VARPIJGR_"), j1,k1,l1,k2,l2);
1.126 brouard 4952: fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
4953: fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
4954: 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",\
4955: mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
4956: mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
4957: }else{
4958: first=0;
4959: fprintf(fichtmcov," %d (%.3f),",(int) age, c12);
4960: fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
4961: fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
4962: 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",\
4963: mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
4964: mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
4965: }/* if first */
4966: } /* age mod 5 */
4967: } /* end loop age */
1.201 brouard 4968: fprintf(ficgp,"\nset out;\nset out \"%s_%d%1d%1d-%1d%1d.svg\";replot;set out;",subdirf2(optionfilefiname,"VARPIJGR_"), j1,k1,l1,k2,l2);
1.126 brouard 4969: first=1;
4970: } /*l12 */
4971: } /* k12 */
4972: } /*l1 */
4973: }/* k1 */
1.169 brouard 4974: /* } */ /* loop covariates */
1.126 brouard 4975: }
4976: free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
4977: free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
4978: free_matrix(doldm,1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
4979: free_matrix(dnewm,1,(nlstate)*(nlstate+ndeath),1,npar);
4980: free_vector(xp,1,npar);
4981: fclose(ficresprob);
4982: fclose(ficresprobcov);
4983: fclose(ficresprobcor);
4984: fflush(ficgp);
4985: fflush(fichtmcov);
4986: }
4987:
4988:
4989: /******************* Printing html file ***********/
1.201 brouard 4990: void printinghtml(char fileresu[], char title[], char datafile[], int firstpass, \
1.126 brouard 4991: int lastpass, int stepm, int weightopt, char model[],\
4992: int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
1.211 brouard 4993: int popforecast, int prevfcast, int estepm , \
1.213 brouard 4994: double jprev1, double mprev1,double anprev1, double dateprev1, \
4995: double jprev2, double mprev2,double anprev2, double dateprev2){
1.126 brouard 4996: int jj1, k1, i1, cpt;
4997:
4998: fprintf(fichtm,"<ul><li><a href='#firstorder'>Result files (first order: no variance)</a>\n \
4999: <li><a href='#secondorder'>Result files (second order (variance)</a>\n \
5000: </ul>");
1.214 brouard 5001: fprintf(fichtm,"<ul><li><h4><a name='firstorder'>Result files (first order: no variance)</a></h4>\n");
5002: 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",
5003: jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirfext3(optionfilefiname,"PHTMFR_",".htm"),subdirfext3(optionfilefiname,"PHTMFR_",".htm"));
5004: 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 5005: jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirfext3(optionfilefiname,"PHTM_",".htm"),subdirfext3(optionfilefiname,"PHTM_",".htm"));
5006: fprintf(fichtm,", <a href=\"%s\">%s</a> (text file) <br>\n",subdirf2(fileresu,"P_"),subdirf2(fileresu,"P_"));
1.126 brouard 5007: fprintf(fichtm,"\
5008: - Estimated transition probabilities over %d (stepm) months: <a href=\"%s\">%s</a><br>\n ",
1.201 brouard 5009: stepm,subdirf2(fileresu,"PIJ_"),subdirf2(fileresu,"PIJ_"));
1.126 brouard 5010: fprintf(fichtm,"\
5011: - Period (stable) prevalence in each health state: <a href=\"%s\">%s</a> <br>\n",
1.201 brouard 5012: subdirf2(fileresu,"PL_"),subdirf2(fileresu,"PL_"));
1.126 brouard 5013: fprintf(fichtm,"\
1.211 brouard 5014: - (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 5015: <a href=\"%s\">%s</a> <br>\n",
1.201 brouard 5016: estepm,subdirf2(fileresu,"E_"),subdirf2(fileresu,"E_"));
1.211 brouard 5017: if(prevfcast==1){
5018: fprintf(fichtm,"\
5019: - Prevalence projections by age and states: \
1.201 brouard 5020: <a href=\"%s\">%s</a> <br>\n</li>", subdirf2(fileresu,"F_"),subdirf2(fileresu,"F_"));
1.211 brouard 5021: }
1.126 brouard 5022:
5023: fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
5024:
1.145 brouard 5025: m=pow(2,cptcoveff);
1.126 brouard 5026: if (cptcovn < 1) {m=1;ncodemax[1]=1;}
5027:
5028: jj1=0;
5029: for(k1=1; k1<=m;k1++){
1.192 brouard 5030: /* for(i1=1; i1<=ncodemax[k1];i1++){ */
1.126 brouard 5031: jj1++;
5032: if (cptcovn > 0) {
5033: fprintf(fichtm,"<hr size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
1.192 brouard 5034: for (cpt=1; cpt<=cptcoveff;cpt++){
1.198 brouard 5035: fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtabm(jj1,cpt)]);
5036: printf(" V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtabm(jj1,cpt)]);fflush(stdout);
1.192 brouard 5037: }
1.126 brouard 5038: fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
5039: }
1.201 brouard 5040: /* aij, bij */
1.211 brouard 5041: 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> \
5042: <img src=\"%s_%d-1.svg\">",model,subdirf2(optionfilefiname,"PE_"),jj1,subdirf2(optionfilefiname,"PE_"),jj1,subdirf2(optionfilefiname,"PE_"),jj1);
1.126 brouard 5043: /* Pij */
1.211 brouard 5044: 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 5045: <img src=\"%s_%d-2.svg\">",stepm,subdirf2(optionfilefiname,"PE_"),jj1,subdirf2(optionfilefiname,"PE_"),jj1,subdirf2(optionfilefiname,"PE_"),jj1);
1.126 brouard 5046: /* Quasi-incidences */
1.211 brouard 5047: fprintf(fichtm,"<br>\n- I<sub>ij</sub> or Conditional probabilities to be observed in state j being in state i %d (stepm) months\
1.201 brouard 5048: before but expressed in per year i.e. quasi incidences if stepm is small and probabilities too,\
1.211 brouard 5049: incidence (rates) are the limit when h tends to zero of the ratio of the probability <sub>h</sub>P<sub>ij</sub> \
5050: 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 5051: <img src=\"%s_%d-3.svg\">",stepm,subdirf2(optionfilefiname,"PE_"),jj1,subdirf2(optionfilefiname,"PE_"),jj1,subdirf2(optionfilefiname,"PE_"),jj1);
5052: /* Survival functions (period) in state j */
5053: for(cpt=1; cpt<=nlstate;cpt++){
5054: 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> \
5055: <img src=\"%s_%d-%d.svg\">", cpt, cpt, nlstate, subdirf2(optionfilefiname,"LIJ_"),cpt,jj1,subdirf2(optionfilefiname,"LIJ_"),cpt,jj1,subdirf2(optionfilefiname,"LIJ_"),cpt,jj1);
5056: }
5057: /* State specific survival functions (period) */
5058: for(cpt=1; cpt<=nlstate;cpt++){
1.208 brouard 5059: fprintf(fichtm,"<br>\n- Survival functions from state %d in each live state and total.\
1.201 brouard 5060: Or probability to survive in various states (1 to %d) being in state %d at different ages.\
5061: <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);
5062: }
5063: /* Period (stable) prevalence in each health state */
5064: for(cpt=1; cpt<=nlstate;cpt++){
5065: 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> \
5066: <img src=\"%s_%d-%d.svg\">", cpt, cpt, nlstate, subdirf2(optionfilefiname,"P_"),cpt,jj1,subdirf2(optionfilefiname,"P_"),cpt,jj1,subdirf2(optionfilefiname,"P_"),cpt,jj1);
5067: }
1.211 brouard 5068: if(prevfcast==1){
5069: /* Projection of prevalence up to period (stable) prevalence in each health state */
5070: for(cpt=1; cpt<=nlstate;cpt++){
1.214 brouard 5071: 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 5072: <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);
1.211 brouard 5073: }
5074: }
5075:
1.126 brouard 5076: for(cpt=1; cpt<=nlstate;cpt++) {
1.205 brouard 5077: 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 5078: <img src=\"%s_%d%d.svg\">",cpt,nlstate,subdirf2(optionfilefiname,"EXP_"),cpt,jj1,subdirf2(optionfilefiname,"EXP_"),cpt,jj1,subdirf2(optionfilefiname,"EXP_"),cpt,jj1);
1.126 brouard 5079: }
1.192 brouard 5080: /* } /\* end i1 *\/ */
1.126 brouard 5081: }/* End k1 */
5082: fprintf(fichtm,"</ul>");
5083:
5084: fprintf(fichtm,"\
5085: \n<br><li><h4> <a name='secondorder'>Result files (second order: variances)</a></h4>\n\
1.193 brouard 5086: - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br> \
1.203 brouard 5087: - 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 5088: But because parameters are usually highly correlated (a higher incidence of disability \
5089: and a higher incidence of recovery can give very close observed transition) it might \
5090: be very useful to look not only at linear confidence intervals estimated from the \
5091: variances but at the covariance matrix. And instead of looking at the estimated coefficients \
5092: (parameters) of the logistic regression, it might be more meaningful to visualize the \
5093: covariance matrix of the one-step probabilities. \
5094: See page 'Matrix of variance-covariance of one-step probabilities' below. \n", rfileres,rfileres);
1.126 brouard 5095:
1.193 brouard 5096: fprintf(fichtm," - Standard deviation of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
1.201 brouard 5097: subdirf2(fileresu,"PROB_"),subdirf2(fileresu,"PROB_"));
1.126 brouard 5098: fprintf(fichtm,"\
5099: - Variance-covariance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
1.201 brouard 5100: subdirf2(fileresu,"PROBCOV_"),subdirf2(fileresu,"PROBCOV_"));
1.126 brouard 5101:
5102: fprintf(fichtm,"\
5103: - Correlation matrix of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
1.201 brouard 5104: subdirf2(fileresu,"PROBCOR_"),subdirf2(fileresu,"PROBCOR_"));
1.126 brouard 5105: fprintf(fichtm,"\
5106: - 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): \
5107: <a href=\"%s\">%s</a> <br>\n</li>",
1.201 brouard 5108: estepm,subdirf2(fileresu,"CVE_"),subdirf2(fileresu,"CVE_"));
1.126 brouard 5109: fprintf(fichtm,"\
5110: - (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): \
5111: <a href=\"%s\">%s</a> <br>\n</li>",
1.201 brouard 5112: estepm,subdirf2(fileresu,"STDE_"),subdirf2(fileresu,"STDE_"));
1.126 brouard 5113: fprintf(fichtm,"\
1.128 brouard 5114: - Variances and covariances of health expectancies by age. Status (i) based health expectancies (in state j), e<sup>ij</sup> are weighted by the period prevalences in each state i (if popbased=1, an additional computation is done using the cross-sectional prevalences, i.e population based) (estepm=%d months): <a href=\"%s\">%s</a><br>\n",
1.201 brouard 5115: estepm, subdirf2(fileresu,"V_"),subdirf2(fileresu,"V_"));
1.126 brouard 5116: fprintf(fichtm,"\
1.128 brouard 5117: - Total life expectancy and total health expectancies to be spent in each health state e<sup>.j</sup> with their standard errors (if popbased=1, an additional computation is done using the cross-sectional prevalences, i.e population based) (estepm=%d months): <a href=\"%s\">%s</a> <br>\n",
1.201 brouard 5118: estepm, subdirf2(fileresu,"T_"),subdirf2(fileresu,"T_"));
1.126 brouard 5119: fprintf(fichtm,"\
5120: - Standard deviation of period (stable) prevalences: <a href=\"%s\">%s</a> <br>\n",\
1.201 brouard 5121: subdirf2(fileresu,"VPL_"),subdirf2(fileresu,"VPL_"));
1.126 brouard 5122:
5123: /* if(popforecast==1) fprintf(fichtm,"\n */
5124: /* - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n */
5125: /* - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n */
5126: /* <br>",fileres,fileres,fileres,fileres); */
5127: /* else */
5128: /* 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); */
5129: fflush(fichtm);
5130: fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
5131:
1.145 brouard 5132: m=pow(2,cptcoveff);
1.126 brouard 5133: if (cptcovn < 1) {m=1;ncodemax[1]=1;}
5134:
5135: jj1=0;
5136: for(k1=1; k1<=m;k1++){
1.192 brouard 5137: /* for(i1=1; i1<=ncodemax[k1];i1++){ */
1.126 brouard 5138: jj1++;
5139: if (cptcovn > 0) {
5140: fprintf(fichtm,"<hr size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
5141: for (cpt=1; cpt<=cptcoveff;cpt++)
1.198 brouard 5142: fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtabm(jj1,cpt)]);
1.126 brouard 5143: fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
5144: }
5145: for(cpt=1; cpt<=nlstate;cpt++) {
5146: fprintf(fichtm,"<br>- Observed (cross-sectional) and period (incidence based) \
1.205 brouard 5147: prevalence (with 95%% confidence interval) in state (%d): <a href=\"%s_%d%d.svg\"> %s_%d-%d.svg <br>\
5148: <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 5149: }
5150: fprintf(fichtm,"\n<br>- Total life expectancy by age and \
1.128 brouard 5151: health expectancies in states (1) and (2). If popbased=1 the smooth (due to the model) \
5152: true period expectancies (those weighted with period prevalences are also\
5153: drawn in addition to the population based expectancies computed using\
1.205 brouard 5154: observed and cahotic prevalences: <a href=\"%s_%d.svg\">%s_%d.svg<br>\
5155: <img src=\"%s_%d.svg\">",subdirf2(optionfilefiname,"E_"),jj1,subdirf2(optionfilefiname,"E_"),jj1,subdirf2(optionfilefiname,"E_"),jj1);
1.192 brouard 5156: /* } /\* end i1 *\/ */
1.126 brouard 5157: }/* End k1 */
5158: fprintf(fichtm,"</ul>");
5159: fflush(fichtm);
5160: }
5161:
5162: /******************* Gnuplot file **************/
1.211 brouard 5163: void printinggnuplot(char fileresu[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , int prevfcast, char pathc[], double p[]){
1.126 brouard 5164:
5165: char dirfileres[132],optfileres[132];
1.164 brouard 5166: int cpt=0,k1=0,i=0,k=0,j=0,jk=0,k2=0,k3=0,ij=0,l=0;
1.211 brouard 5167: int lv=0, vlv=0, kl=0;
1.130 brouard 5168: int ng=0;
1.201 brouard 5169: int vpopbased;
1.126 brouard 5170: /* if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) { */
5171: /* printf("Problem with file %s",optionfilegnuplot); */
5172: /* fprintf(ficlog,"Problem with file %s",optionfilegnuplot); */
5173: /* } */
5174:
5175: /*#ifdef windows */
5176: fprintf(ficgp,"cd \"%s\" \n",pathc);
5177: /*#endif */
5178: m=pow(2,cptcoveff);
5179:
1.202 brouard 5180: /* Contribution to likelihood */
5181: /* Plot the probability implied in the likelihood */
5182: fprintf(ficgp,"\n# Contributions to the Likelihood, mle >=1. For mle=4 no interpolation, pure matrix products.\n#\n");
5183: fprintf(ficgp,"\n set log y; unset log x;set xlabel \"Age\"; set ylabel \"Likelihood (-2Log(L))\";");
5184: /* fprintf(ficgp,"\nset ter svg size 640, 480"); */ /* Too big for svg */
1.205 brouard 5185: fprintf(ficgp,"\nset ter pngcairo size 640, 480");
1.204 brouard 5186: /* nice for mle=4 plot by number of matrix products.
1.202 brouard 5187: replot "rrtest1/toto.txt" u 2:($4 == 1 && $5==2 ? $9 : 1/0):5 t "p12" with point lc 1 */
5188: /* replot exp(p1+p2*x)/(1+exp(p1+p2*x)+exp(p3+p4*x)+exp(p5+p6*x)) t "p12(x)" */
5189: /* fprintf(ficgp,"\nset out \"%s.svg\";",subdirf2(optionfilefiname,"ILK_")); */
1.204 brouard 5190: fprintf(ficgp,"\nset out \"%s-dest.png\";",subdirf2(optionfilefiname,"ILK_"));
1.214 brouard 5191: fprintf(ficgp,"\nset log y;plot \"%s\" u 2:(-$13):6 t \"All sample, transitions colored by destination\" with dots lc variable; set out;\n",subdirf(fileresilk));
1.204 brouard 5192: fprintf(ficgp,"\nset out \"%s-ori.png\";",subdirf2(optionfilefiname,"ILK_"));
1.214 brouard 5193: fprintf(ficgp,"\nset log y;plot \"%s\" u 2:(-$13):5 t \"All sample, transitions colored by origin\" with dots lc variable; set out;\n\n",subdirf(fileresilk));
1.204 brouard 5194: for (i=1; i<= nlstate ; i ++) {
5195: fprintf(ficgp,"\nset out \"%s-p%dj.png\";set ylabel \"Probability for each individual/wave\";",subdirf2(optionfilefiname,"ILK_"),i);
1.205 brouard 5196: fprintf(ficgp,"unset log;\n# plot weighted, mean weight should have point size of 0.5\n plot \"%s\"",subdirf(fileresilk));
1.214 brouard 5197: fprintf(ficgp," u 2:($5 == %d && $6==%d ? $10 : 1/0):($12/4.):6 t \"p%d%d\" with points pointtype 7 ps variable lc variable \\\n",i,1,i,1);
1.204 brouard 5198: for (j=2; j<= nlstate+ndeath ; j ++) {
1.214 brouard 5199: fprintf(ficgp,",\\\n \"\" u 2:($5 == %d && $6==%d ? $10 : 1/0):($12/4.):6 t \"p%d%d\" with points pointtype 7 ps variable lc variable ",i,j,i,j);
1.204 brouard 5200: }
5201: fprintf(ficgp,";\nset out; unset ylabel;\n");
5202: }
5203: /* 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 */
5204: /* fprintf(ficgp,"\nset log y;plot \"%s\" u 2:(-$11):3 t \"All sample, all transitions\" with dots lc variable",subdirf(fileresilk)); */
5205: /* fprintf(ficgp,"\nreplot \"%s\" u 2:($3 <= 3 ? -$11 : 1/0):3 t \"First 3 individuals\" with line lc variable", subdirf(fileresilk)); */
1.203 brouard 5206: fprintf(ficgp,"\nset out;unset log\n");
1.202 brouard 5207: /* fprintf(ficgp,"\nset out \"%s.svg\"; replot; set out; # bug gnuplot",subdirf2(optionfilefiname,"ILK_")); */
5208:
1.126 brouard 5209: strcpy(dirfileres,optionfilefiname);
5210: strcpy(optfileres,"vpl");
5211: /* 1eme*/
1.211 brouard 5212: for (cpt=1; cpt<= nlstate ; cpt ++) { /* For each live state */
5213: for (k1=1; k1<= m ; k1 ++) { /* For each combination of covariate */
5214: /* plot [100000000000000000000:-100000000000000000000] "mysbiaspar/vplrmysbiaspar.txt to check */
5215: fprintf(ficgp,"\n# 1st: Period (stable) prevalence with CI: 'VPL_' files ");
5216: for (k=1; k<=cptcoveff; k++){ /* For each covariate and each value */
5217: lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */
5218: /* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
5219: /* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
5220: /* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
5221: vlv= nbcode[Tvaraff[lv]][lv];
5222: fprintf(ficgp," V%d=%d ",k,vlv);
5223: }
5224: fprintf(ficgp,"\n#\n");
5225:
1.201 brouard 5226: fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" \n",subdirf2(optionfilefiname,"V_"),cpt,k1);
5227: fprintf(ficgp,"\n#set out \"V_%s_%d-%d.svg\" \n",optionfilefiname,cpt,k1);
1.126 brouard 5228: fprintf(ficgp,"set xlabel \"Age\" \n\
5229: set ylabel \"Probability\" \n\
1.199 brouard 5230: set ter svg size 640, 480\n\
1.201 brouard 5231: plot [%.f:%.f] \"%s\" every :::%d::%d u 1:2 \"%%lf",ageminpar,fage,subdirf2(fileresu,"VPL_"),k1-1,k1-1);
1.126 brouard 5232:
5233: for (i=1; i<= nlstate ; i ++) {
1.170 brouard 5234: if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
5235: else fprintf(ficgp," %%*lf (%%*lf)");
1.126 brouard 5236: }
1.201 brouard 5237: 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);
1.126 brouard 5238: for (i=1; i<= nlstate ; i ++) {
1.170 brouard 5239: if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
5240: else fprintf(ficgp," %%*lf (%%*lf)");
1.126 brouard 5241: }
1.201 brouard 5242: fprintf(ficgp,"\" t\"95%% CI\" w l lt 1,\"%s\" every :::%d::%d u 1:($2-1.96*$3) \"%%lf",subdirf2(fileresu,"VPL_"),k1-1,k1-1);
1.126 brouard 5243: for (i=1; i<= nlstate ; i ++) {
1.170 brouard 5244: if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
5245: else fprintf(ficgp," %%*lf (%%*lf)");
1.126 brouard 5246: }
1.201 brouard 5247: fprintf(ficgp,"\" t\"\" w l lt 1,\"%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l lt 2",subdirf2(fileresu,"P_"),k1-1,k1-1,2+4*(cpt-1));
5248: fprintf(ficgp,"\nset out \n");
5249: } /* k1 */
5250: } /* cpt */
1.126 brouard 5251: /*2 eme*/
5252: for (k1=1; k1<= m ; k1 ++) {
1.211 brouard 5253: fprintf(ficgp,"\n# 2nd: Total life expectancy with CI: 't' files ");
5254: for (k=1; k<=cptcoveff; k++){ /* For each covariate and each value */
5255: lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */
5256: /* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
5257: /* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
5258: /* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
5259: vlv= nbcode[Tvaraff[lv]][lv];
5260: fprintf(ficgp," V%d=%d ",k,vlv);
5261: }
5262: fprintf(ficgp,"\n#\n");
5263:
1.201 brouard 5264: fprintf(ficgp,"\nset out \"%s_%d.svg\" \n",subdirf2(optionfilefiname,"E_"),k1);
5265: for(vpopbased=0; vpopbased <= popbased; vpopbased++){ /* Done for vpopbased=0 and vpopbased=1 if popbased==1*/
5266: if(vpopbased==0)
5267: fprintf(ficgp,"set ylabel \"Years\" \nset ter svg size 640, 480\nplot [%.f:%.f] ",ageminpar,fage);
5268: else
5269: fprintf(ficgp,"\nreplot ");
5270: for (i=1; i<= nlstate+1 ; i ++) {
5271: k=2*i;
5272: 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);
5273: for (j=1; j<= nlstate+1 ; j ++) {
5274: if (j==i) fprintf(ficgp," %%lf (%%lf)");
5275: else fprintf(ficgp," %%*lf (%%*lf)");
5276: }
5277: if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l lt %d, \\\n",i);
5278: else fprintf(ficgp,"\" t\"LE in state (%d)\" w l lt %d, \\\n",i-1,i+1);
5279: 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);
5280: for (j=1; j<= nlstate+1 ; j ++) {
5281: if (j==i) fprintf(ficgp," %%lf (%%lf)");
5282: else fprintf(ficgp," %%*lf (%%*lf)");
5283: }
5284: fprintf(ficgp,"\" t\"\" w l lt 0,");
5285: fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2==%d && $4!=0 ? $4+$5*2 : 1/0) \"%%lf %%lf %%lf",subdirf2(fileresu,"T_"),k1-1,k1-1,vpopbased);
5286: for (j=1; j<= nlstate+1 ; j ++) {
5287: if (j==i) fprintf(ficgp," %%lf (%%lf)");
5288: else fprintf(ficgp," %%*lf (%%*lf)");
5289: }
5290: if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l lt 0");
5291: else fprintf(ficgp,"\" t\"\" w l lt 0,\\\n");
5292: } /* state */
5293: } /* vpopbased */
5294: fprintf(ficgp,"\nset out;set out \"%s_%d.svg\"; replot; set out; \n",subdirf2(optionfilefiname,"E_"),k1); /* Buggy gnuplot */
5295: } /* k1 */
1.211 brouard 5296:
5297:
1.126 brouard 5298: /*3eme*/
5299: for (k1=1; k1<= m ; k1 ++) {
5300: for (cpt=1; cpt<= nlstate ; cpt ++) {
1.211 brouard 5301: fprintf(ficgp,"\n# 3d: Life expectancy with EXP_ files: cov=%d state=%d",k1, cpt);
5302: for (k=1; k<=cptcoveff; k++){ /* For each covariate and each value */
5303: lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */
5304: /* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
5305: /* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
5306: /* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
5307: vlv= nbcode[Tvaraff[lv]][lv];
5308: fprintf(ficgp," V%d=%d ",k,vlv);
5309: }
5310: fprintf(ficgp,"\n#\n");
5311:
1.126 brouard 5312: /* k=2+nlstate*(2*cpt-2); */
5313: k=2+(nlstate+1)*(cpt-1);
1.201 brouard 5314: fprintf(ficgp,"\nset out \"%s_%d%d.svg\" \n",subdirf2(optionfilefiname,"EXP_"),cpt,k1);
1.199 brouard 5315: fprintf(ficgp,"set ter svg size 640, 480\n\
1.201 brouard 5316: plot [%.f:%.f] \"%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,subdirf2(fileresu,"E_"),k1-1,k1-1,k,cpt);
1.126 brouard 5317: /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
5318: for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
5319: fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
5320: fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
5321: for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
5322: fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
5323:
5324: */
5325: for (i=1; i< nlstate ; i ++) {
1.201 brouard 5326: 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);
1.126 brouard 5327: /* 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);*/
5328:
5329: }
1.201 brouard 5330: 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 5331: }
5332: }
5333:
1.201 brouard 5334: /* Survival functions (period) from state i in state j by initial state i */
5335: for (k1=1; k1<= m ; k1 ++) { /* For each multivariate if any */
5336: for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */
1.211 brouard 5337: fprintf(ficgp,"\n#\n#\n# Survival functions in state j : 'LIJ_' files, cov=%d state=%d",k1, cpt);
5338: for (k=1; k<=cptcoveff; k++){ /* For each covariate and each value */
5339: lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */
5340: /* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
5341: /* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
5342: /* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
5343: vlv= nbcode[Tvaraff[lv]][lv];
5344: fprintf(ficgp," V%d=%d ",k,vlv);
5345: }
5346: fprintf(ficgp,"\n#\n");
5347:
1.201 brouard 5348: fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" \n",subdirf2(optionfilefiname,"LIJ_"),cpt,k1);
5349: fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability to be alive\" \n\
5350: set ter svg size 640, 480\n\
5351: unset log y\n\
5352: plot [%.f:%.f] ", ageminpar, agemaxpar);
1.211 brouard 5353: k=3;
1.201 brouard 5354: for (i=1; i<= nlstate ; i ++){
5355: if(i==1)
5356: fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"PIJ_"));
5357: else
5358: fprintf(ficgp,", '' ");
5359: l=(nlstate+ndeath)*(i-1)+1;
5360: fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d/($%d",k1,k+l+(cpt-1),k+l);
5361: for (j=2; j<= nlstate+ndeath ; j ++)
5362: fprintf(ficgp,"+$%d",k+l+j-1);
5363: fprintf(ficgp,")) t \"l(%d,%d)\" w l",i,cpt);
5364: } /* nlstate */
5365: fprintf(ficgp,"\nset out\n");
5366: } /* end cpt state*/
5367: } /* end covariate */
5368:
5369: /* Survival functions (period) from state i in state j by final state j */
1.202 brouard 5370: for (k1=1; k1<= m ; k1 ++) { /* For each covariate if any */
1.201 brouard 5371: for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each inital state */
5372: 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 5373: for (k=1; k<=cptcoveff; k++){ /* For each covariate and each value */
5374: lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */
5375: /* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
5376: /* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
5377: /* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
5378: vlv= nbcode[Tvaraff[lv]][lv];
5379: fprintf(ficgp," V%d=%d ",k,vlv);
5380: }
5381: fprintf(ficgp,"\n#\n");
5382:
1.201 brouard 5383: fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" \n",subdirf2(optionfilefiname,"LIJT_"),cpt,k1);
5384: fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability to be alive\" \n\
5385: set ter svg size 640, 480\n\
5386: unset log y\n\
5387: plot [%.f:%.f] ", ageminpar, agemaxpar);
1.211 brouard 5388: k=3;
1.201 brouard 5389: for (j=1; j<= nlstate ; j ++){ /* Lived in state j */
5390: if(j==1)
5391: fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"PIJ_"));
5392: else
5393: fprintf(ficgp,", '' ");
5394: l=(nlstate+ndeath)*(cpt-1) +j;
5395: fprintf(ficgp," u (($1==%d && (floor($2)%%5 == 0)) ? ($3):1/0):($%d",k1,k+l);
5396: /* for (i=2; i<= nlstate+ndeath ; i ++) */
5397: /* fprintf(ficgp,"+$%d",k+l+i-1); */
5398: fprintf(ficgp,") t \"l(%d,%d)\" w l",cpt,j);
5399: } /* nlstate */
5400: fprintf(ficgp,", '' ");
5401: fprintf(ficgp," u (($1==%d && (floor($2)%%5 == 0)) ? ($3):1/0):(",k1);
5402: for (j=1; j<= nlstate ; j ++){ /* Lived in state j */
5403: l=(nlstate+ndeath)*(cpt-1) +j;
5404: if(j < nlstate)
5405: fprintf(ficgp,"$%d +",k+l);
5406: else
5407: fprintf(ficgp,"$%d) t\"l(%d,.)\" w l",k+l,cpt);
5408: }
5409: fprintf(ficgp,"\nset out\n");
5410: } /* end cpt state*/
5411: } /* end covariate */
5412:
1.202 brouard 5413: /* CV preval stable (period) for each covariate */
1.211 brouard 5414: for (k1=1; k1<= m ; k1 ++) { /* For each covariate combination (1 to m=2**k), if any covariate is present */
1.153 brouard 5415: for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */
1.211 brouard 5416: fprintf(ficgp,"\n#\n#\n#CV preval stable (period): 'pij' files, covariatecombination#=%d state=%d",k1, cpt);
5417: for (k=1; k<=cptcoveff; k++){ /* For each covariate and each value */
5418: lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */
5419: /* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
5420: /* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
5421: /* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
5422: vlv= nbcode[Tvaraff[lv]][lv];
5423: fprintf(ficgp," V%d=%d ",k,vlv);
5424: }
5425: fprintf(ficgp,"\n#\n");
5426:
1.201 brouard 5427: fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" \n",subdirf2(optionfilefiname,"P_"),cpt,k1);
1.126 brouard 5428: fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\
1.199 brouard 5429: set ter svg size 640, 480\n\
1.126 brouard 5430: unset log y\n\
1.153 brouard 5431: plot [%.f:%.f] ", ageminpar, agemaxpar);
1.211 brouard 5432: k=3; /* Offset */
1.153 brouard 5433: for (i=1; i<= nlstate ; i ++){
5434: if(i==1)
1.201 brouard 5435: fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"PIJ_"));
1.153 brouard 5436: else
5437: fprintf(ficgp,", '' ");
1.154 brouard 5438: l=(nlstate+ndeath)*(i-1)+1;
5439: fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d/($%d",k1,k+l+(cpt-1),k+l);
1.201 brouard 5440: for (j=2; j<= nlstate ; j ++)
5441: fprintf(ficgp,"+$%d",k+l+j-1);
1.153 brouard 5442: fprintf(ficgp,")) t \"prev(%d,%d)\" w l",i,cpt);
5443: } /* nlstate */
1.201 brouard 5444: fprintf(ficgp,"\nset out\n");
1.153 brouard 5445: } /* end cpt state*/
5446: } /* end covariate */
1.201 brouard 5447:
1.211 brouard 5448: if(prevfcast==1){
5449: /* Projection from cross-sectional to stable (period) for each covariate */
5450:
5451: for (k1=1; k1<= m ; k1 ++) { /* For each covariate combination (1 to m=2**k), if any covariate is present */
5452: for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */
5453: fprintf(ficgp,"\n#\n#\n#Projection of prevalence to stable (period): 'PROJ_' files, covariatecombination#=%d state=%d",k1, cpt);
5454: for (k=1; k<=cptcoveff; k++){ /* For each correspondig covariate value */
5455: lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate value corresponding to k1 combination and kth covariate */
5456: /* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
5457: /* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
5458: /* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
5459: vlv= nbcode[Tvaraff[lv]][lv];
5460: fprintf(ficgp," V%d=%d ",k,vlv);
5461: }
5462: fprintf(ficgp,"\n#\n");
5463:
5464: fprintf(ficgp,"# hpijx=probability over h years, hp.jx is weighted by observed prev\n ");
5465: fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" \n",subdirf2(optionfilefiname,"PROJ_"),cpt,k1);
5466: fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Prevalence\" \n\
5467: set ter svg size 640, 480\n\
5468: unset log y\n\
5469: plot [%.f:%.f] ", ageminpar, agemaxpar);
5470: for (i=1; i<= nlstate+1 ; i ++){ /* nlstate +1 p11 p21 p.1 */
5471: /*# V1 = 1 V2 = 0 yearproj age p11 p21 p.1 p12 p22 p.2 p13 p23 p.3*/
5472: /*# 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 */
5473: /*# yearproj age p11 p21 p.1 p12 p22 p.2 p13 p23 p.3*/
5474: /*# 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 */
5475: if(i==1){
5476: fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"F_"));
5477: }else{
5478: fprintf(ficgp,",\\\n '' ");
5479: }
5480: if(cptcoveff ==0){ /* No covariate */
5481: fprintf(ficgp," u 2:("); /* Age is in 2 */
5482: /*# yearproj age p11 p21 p31 p.1 p12 p22 p32 p.2 p13 p23 p33 p.3 p14 p24 p34 p.4*/
5483: /*# 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 */
5484: if(i==nlstate+1)
5485: fprintf(ficgp," $%d/(1.-$%d)) t 'p.%d' with line ", \
5486: 2+(cpt-1)*(nlstate+1)+1+(i-1), 2+1+(i-1)+(nlstate+1)*nlstate,cpt );
5487: else
5488: fprintf(ficgp," $%d/(1.-$%d)) t 'p%d%d' with line ", \
5489: 2+(cpt-1)*(nlstate+1)+1+(i-1), 2+1+(i-1)+(nlstate+1)*nlstate,i,cpt );
5490: }else{
5491: fprintf(ficgp,"u 6:(("); /* Age is in 6 */
5492: /*# V1 = 1 V2 = 0 yearproj age p11 p21 p.1 p12 p22 p.2 p13 p23 p.3*/
5493: /*# 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 */
5494: kl=0;
5495: for (k=1; k<=cptcoveff; k++){ /* For each covariate */
5496: lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate value corresponding to k1 combination and kth covariate */
5497: /* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
5498: /* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
5499: /* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
5500: vlv= nbcode[Tvaraff[lv]][lv];
5501: kl++;
5502: /* 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 *\/ */
5503: /*6+(cpt-1)*(nlstate+1)+1+(i-1)+(nlstate+1)*nlstate; 6+(1-1)*(2+1)+1+(1-1) +(2+1)*2=13 */
5504: /*6+1+(i-1)+(nlstate+1)*nlstate; 6+1+(1-1) +(2+1)*2=13 */
5505: /* '' u 6:(($1==1 && $2==0 && $3==2 && $4==0)? $9/(1.-$15) : 1/0):($5==2000? 3:2) t 'p.1' with line lc variable*/
5506: if(k==cptcoveff)
5507: if(i==nlstate+1)
5508: fprintf(ficgp,"$%d==%d && $%d==%d)? $%d/(1.-$%d) : 1/0) t 'p.%d' with line ",kl, k,kl+1,nbcode[Tvaraff[lv]][lv], \
5509: 6+(cpt-1)*(nlstate+1)+1+(i-1), 6+1+(i-1)+(nlstate+1)*nlstate,cpt );
5510: else
5511: fprintf(ficgp,"$%d==%d && $%d==%d)? $%d/(1.-$%d) : 1/0) t 'p%d%d' with line ",kl, k,kl+1,nbcode[Tvaraff[lv]][lv], \
5512: 6+(cpt-1)*(nlstate+1)+1+(i-1), 6+1+(i-1)+(nlstate+1)*nlstate,i,cpt );
5513: else{
5514: fprintf(ficgp,"$%d==%d && $%d==%d && ",kl, k,kl+1,nbcode[Tvaraff[lv]][lv]);
5515: kl++;
5516: }
5517: } /* end covariate */
5518: } /* end if covariate */
5519: } /* nlstate */
5520: fprintf(ficgp,"\nset out\n");
5521: } /* end cpt state*/
5522: } /* end covariate */
5523: } /* End if prevfcast */
5524:
5525:
1.126 brouard 5526: /* proba elementaires */
1.187 brouard 5527: fprintf(ficgp,"\n##############\n#MLE estimated parameters\n#############\n");
1.126 brouard 5528: for(i=1,jk=1; i <=nlstate; i++){
1.187 brouard 5529: fprintf(ficgp,"# initial state %d\n",i);
1.126 brouard 5530: for(k=1; k <=(nlstate+ndeath); k++){
5531: if (k != i) {
1.187 brouard 5532: fprintf(ficgp,"# current state %d\n",k);
1.126 brouard 5533: for(j=1; j <=ncovmodel; j++){
1.187 brouard 5534: fprintf(ficgp,"p%d=%f; ",jk,p[jk]);
1.126 brouard 5535: jk++;
5536: }
1.187 brouard 5537: fprintf(ficgp,"\n");
1.126 brouard 5538: }
5539: }
5540: }
1.187 brouard 5541: fprintf(ficgp,"##############\n#\n");
5542:
1.145 brouard 5543: /*goto avoid;*/
1.200 brouard 5544: fprintf(ficgp,"\n##############\n#Graphics of probabilities or incidences\n#############\n");
1.187 brouard 5545: fprintf(ficgp,"# logi(p12/p11)=a12+b12*age+c12age*age+d12*V1+e12*V1*age\n");
5546: fprintf(ficgp,"# logi(p12/p11)=p1 +p2*age +p3*age*age+ p4*V1+ p5*V1*age\n");
5547: fprintf(ficgp,"# logi(p13/p11)=a13+b13*age+c13age*age+d13*V1+e13*V1*age\n");
5548: fprintf(ficgp,"# logi(p13/p11)=p6 +p7*age +p8*age*age+ p9*V1+ p10*V1*age\n");
5549: fprintf(ficgp,"# p12+p13+p14+p11=1=p11(1+exp(a12+b12*age+c12age*age+d12*V1+e12*V1*age)\n");
5550: fprintf(ficgp,"# +exp(a13+b13*age+c13age*age+d13*V1+e13*V1*age)+...)\n");
5551: fprintf(ficgp,"# p11=1/(1+exp(a12+b12*age+c12age*age+d12*V1+e12*V1*age)\n");
5552: fprintf(ficgp,"# +exp(a13+b13*age+c13age*age+d13*V1+e13*V1*age)+...)\n");
5553: fprintf(ficgp,"# p12=exp(a12+b12*age+c12age*age+d12*V1+e12*V1*age)/\n");
5554: fprintf(ficgp,"# (1+exp(a12+b12*age+c12age*age+d12*V1+e12*V1*age)\n");
5555: fprintf(ficgp,"# +exp(a13+b13*age+c13age*age+d13*V1+e13*V1*age))\n");
5556: fprintf(ficgp,"# +exp(a14+b14*age+c14age*age+d14*V1+e14*V1*age)+...)\n");
5557: fprintf(ficgp,"#\n");
1.201 brouard 5558: for(ng=1; ng<=3;ng++){ /* Number of graphics: first is logit, 2nd is probabilities, third is incidences per year*/
1.187 brouard 5559: fprintf(ficgp,"# ng=%d\n",ng);
5560: fprintf(ficgp,"# jk=1 to 2^%d=%d\n",cptcoveff,m);
1.126 brouard 5561: for(jk=1; jk <=m; jk++) {
1.187 brouard 5562: fprintf(ficgp,"# jk=%d\n",jk);
1.201 brouard 5563: fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" ",subdirf2(optionfilefiname,"PE_"),jk,ng);
5564: fprintf(ficgp,"\nset ter svg size 640, 480 ");
5565: if (ng==1){
5566: fprintf(ficgp,"\nset ylabel \"Value of the logit of the model\"\n"); /* exp(a12+b12*x) could be nice */
5567: fprintf(ficgp,"\nunset log y");
5568: }else if (ng==2){
5569: fprintf(ficgp,"\nset ylabel \"Probability\"\n");
5570: fprintf(ficgp,"\nset log y");
5571: }else if (ng==3){
1.126 brouard 5572: fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
1.201 brouard 5573: fprintf(ficgp,"\nset log y");
5574: }else
5575: fprintf(ficgp,"\nunset title ");
5576: fprintf(ficgp,"\nplot [%.f:%.f] ",ageminpar,agemaxpar);
1.126 brouard 5577: i=1;
5578: for(k2=1; k2<=nlstate; k2++) {
5579: k3=i;
5580: for(k=1; k<=(nlstate+ndeath); k++) {
5581: if (k != k2){
1.201 brouard 5582: switch( ng) {
5583: case 1:
1.187 brouard 5584: if(nagesqr==0)
1.201 brouard 5585: fprintf(ficgp," p%d+p%d*x",i,i+1);
1.187 brouard 5586: else /* nagesqr =1 */
1.201 brouard 5587: fprintf(ficgp," p%d+p%d*x+p%d*x*x",i,i+1,i+1+nagesqr);
5588: break;
5589: case 2: /* ng=2 */
1.187 brouard 5590: if(nagesqr==0)
5591: fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
5592: else /* nagesqr =1 */
1.201 brouard 5593: fprintf(ficgp," exp(p%d+p%d*x+p%d*x*x",i,i+1,i+1+nagesqr);
5594: break;
5595: case 3:
5596: if(nagesqr==0)
5597: fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);
5598: else /* nagesqr =1 */
5599: fprintf(ficgp," %f*exp(p%d+p%d*x+p%d*x*x",YEARM/stepm,i,i+1,i+1+nagesqr);
5600: break;
5601: }
1.141 brouard 5602: ij=1;/* To be checked else nbcode[0][0] wrong */
1.187 brouard 5603: for(j=3; j <=ncovmodel-nagesqr; j++) {
1.197 brouard 5604: /* printf("Tage[%d]=%d, j=%d\n", ij, Tage[ij], j); */
5605: if(ij <=cptcovage) { /* Bug valgrind */
5606: if((j-2)==Tage[ij]) { /* Bug valgrind */
1.200 brouard 5607: fprintf(ficgp,"+p%d*%d*x",i+j+nagesqr-1,nbcode[Tvar[j-2]][codtabm(jk,j-2)]);
5608: /* fprintf(ficgp,"+p%d*%d*x",i+j+nagesqr-1,nbcode[Tvar[j-2]][codtabm(jk,Tvar[j-2])]); */
1.197 brouard 5609: ij++;
5610: }
1.186 brouard 5611: }
5612: else
1.198 brouard 5613: fprintf(ficgp,"+p%d*%d",i+j+nagesqr-1,nbcode[Tvar[j-2]][codtabm(jk,j-2)]);
1.126 brouard 5614: }
1.201 brouard 5615: if(ng != 1){
5616: fprintf(ficgp,")/(1");
1.126 brouard 5617:
1.201 brouard 5618: for(k1=1; k1 <=nlstate; k1++){
5619: if(nagesqr==0)
5620: fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);
5621: else /* nagesqr =1 */
5622: 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);
5623:
5624: ij=1;
5625: for(j=3; j <=ncovmodel-nagesqr; j++){
5626: if(ij <=cptcovage) { /* Bug valgrind */
5627: if((j-2)==Tage[ij]) { /* Bug valgrind */
5628: fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2+nagesqr,nbcode[Tvar[j-2]][codtabm(jk,j-2)]);
5629: /* fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2+nagesqr,nbcode[Tvar[j-2]][codtabm(jk,Tvar[j-2])]); */
5630: ij++;
5631: }
1.197 brouard 5632: }
1.201 brouard 5633: else
5634: fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2+nagesqr,nbcode[Tvar[j-2]][codtabm(jk,j-2)]);
1.186 brouard 5635: }
1.201 brouard 5636: fprintf(ficgp,")");
1.126 brouard 5637: }
5638: fprintf(ficgp,")");
1.201 brouard 5639: if(ng ==2)
5640: fprintf(ficgp," t \"p%d%d\" ", k2,k);
5641: else /* ng= 3 */
5642: fprintf(ficgp," t \"i%d%d\" ", k2,k);
5643: }else{ /* end ng <> 1 */
5644: fprintf(ficgp," t \"logit(p%d%d)\" ", k2,k);
1.126 brouard 5645: }
5646: if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");
5647: i=i+ncovmodel;
5648: }
5649: } /* end k */
5650: } /* end k2 */
1.201 brouard 5651: fprintf(ficgp,"\n set out\n");
1.126 brouard 5652: } /* end jk */
5653: } /* end ng */
1.164 brouard 5654: /* avoid: */
1.126 brouard 5655: fflush(ficgp);
5656: } /* end gnuplot */
5657:
5658:
5659: /*************** Moving average **************/
5660: int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav){
5661:
5662: int i, cpt, cptcod;
5663: int modcovmax =1;
5664: int mobilavrange, mob;
5665: double age;
5666:
5667: modcovmax=2*cptcoveff;/* Max number of modalities. We suppose
5668: a covariate has 2 modalities */
5669: if (cptcovn<1) modcovmax=1; /* At least 1 pass */
5670:
5671: if(mobilav==1||mobilav ==3 ||mobilav==5 ||mobilav== 7){
5672: if(mobilav==1) mobilavrange=5; /* default */
5673: else mobilavrange=mobilav;
5674: for (age=bage; age<=fage; age++)
5675: for (i=1; i<=nlstate;i++)
5676: for (cptcod=1;cptcod<=modcovmax;cptcod++)
5677: mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
5678: /* We keep the original values on the extreme ages bage, fage and for
5679: fage+1 and bage-1 we use a 3 terms moving average; for fage+2 bage+2
5680: we use a 5 terms etc. until the borders are no more concerned.
5681: */
5682: for (mob=3;mob <=mobilavrange;mob=mob+2){
5683: for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){
5684: for (i=1; i<=nlstate;i++){
5685: for (cptcod=1;cptcod<=modcovmax;cptcod++){
5686: mobaverage[(int)age][i][cptcod] =probs[(int)age][i][cptcod];
5687: for (cpt=1;cpt<=(mob-1)/2;cpt++){
5688: mobaverage[(int)age][i][cptcod] +=probs[(int)age-cpt][i][cptcod];
5689: mobaverage[(int)age][i][cptcod] +=probs[(int)age+cpt][i][cptcod];
5690: }
5691: mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/mob;
5692: }
5693: }
5694: }/* end age */
5695: }/* end mob */
5696: }else return -1;
5697: return 0;
5698: }/* End movingaverage */
5699:
5700:
5701: /************** Forecasting ******************/
1.169 brouard 5702: 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 5703: /* proj1, year, month, day of starting projection
5704: agemin, agemax range of age
5705: dateprev1 dateprev2 range of dates during which prevalence is computed
5706: anproj2 year of en of projection (same day and month as proj1).
5707: */
1.164 brouard 5708: int yearp, stepsize, hstepm, nhstepm, j, k, cptcod, i, h, i1;
1.126 brouard 5709: double agec; /* generic age */
5710: double agelim, ppij, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
5711: double *popeffectif,*popcount;
5712: double ***p3mat;
5713: double ***mobaverage;
5714: char fileresf[FILENAMELENGTH];
5715:
5716: agelim=AGESUP;
1.211 brouard 5717: /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
5718: in each health status at the date of interview (if between dateprev1 and dateprev2).
5719: We still use firstpass and lastpass as another selection.
5720: */
1.214 brouard 5721: /* freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint,strstart,\ */
5722: /* firstpass, lastpass, stepm, weightopt, model); */
1.126 brouard 5723: prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
5724:
1.201 brouard 5725: strcpy(fileresf,"F_");
5726: strcat(fileresf,fileresu);
1.126 brouard 5727: if((ficresf=fopen(fileresf,"w"))==NULL) {
5728: printf("Problem with forecast resultfile: %s\n", fileresf);
5729: fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);
5730: }
1.215 brouard 5731: printf("Computing forecasting: result on file '%s', please wait... \n", fileresf);
5732: fprintf(ficlog,"Computing forecasting: result on file '%s', please wait... \n", fileresf);
1.126 brouard 5733:
5734: if (cptcoveff==0) ncodemax[cptcoveff]=1;
5735:
5736: if (mobilav!=0) {
5737: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
5738: if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
5739: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
5740: printf(" Error in movingaverage mobilav=%d\n",mobilav);
5741: }
5742: }
5743:
5744: stepsize=(int) (stepm+YEARM-1)/YEARM;
5745: if (stepm<=12) stepsize=1;
5746: if(estepm < stepm){
5747: printf ("Problem %d lower than %d\n",estepm, stepm);
5748: }
5749: else hstepm=estepm;
5750:
5751: hstepm=hstepm/stepm;
5752: yp1=modf(dateintmean,&yp);/* extracts integral of datemean in yp and
5753: fractional in yp1 */
5754: anprojmean=yp;
5755: yp2=modf((yp1*12),&yp);
5756: mprojmean=yp;
5757: yp1=modf((yp2*30.5),&yp);
5758: jprojmean=yp;
5759: if(jprojmean==0) jprojmean=1;
5760: if(mprojmean==0) jprojmean=1;
5761:
5762: i1=cptcoveff;
5763: if (cptcovn < 1){i1=1;}
5764:
5765: fprintf(ficresf,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2);
5766:
5767: fprintf(ficresf,"#****** Routine prevforecast **\n");
5768:
5769: /* if (h==(int)(YEARM*yearp)){ */
5770: for(cptcov=1, k=0;cptcov<=i1;cptcov++){
5771: for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
5772: k=k+1;
1.211 brouard 5773: fprintf(ficresf,"\n#****** hpijx=probability over h years, hp.jx is weighted by observed prev \n#");
1.126 brouard 5774: for(j=1;j<=cptcoveff;j++) {
1.211 brouard 5775: fprintf(ficresf," V%d (=) %d",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
1.126 brouard 5776: }
1.211 brouard 5777: fprintf(ficresf," yearproj age");
1.126 brouard 5778: for(j=1; j<=nlstate+ndeath;j++){
5779: for(i=1; i<=nlstate;i++)
5780: fprintf(ficresf," p%d%d",i,j);
5781: fprintf(ficresf," p.%d",j);
5782: }
5783: for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) {
5784: fprintf(ficresf,"\n");
5785: fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+yearp);
5786:
5787: for (agec=fage; agec>=(ageminpar-1); agec--){
5788: nhstepm=(int) rint((agelim-agec)*YEARM/stepm);
5789: nhstepm = nhstepm/hstepm;
5790: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
5791: oldm=oldms;savm=savms;
5792: hpxij(p3mat,nhstepm,agec,hstepm,p,nlstate,stepm,oldm,savm, k);
5793:
5794: for (h=0; h<=nhstepm; h++){
5795: if (h*hstepm/YEARM*stepm ==yearp) {
5796: fprintf(ficresf,"\n");
5797: for(j=1;j<=cptcoveff;j++)
1.198 brouard 5798: fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
1.126 brouard 5799: fprintf(ficresf,"%.f %.f ",anproj1+yearp,agec+h*hstepm/YEARM*stepm);
5800: }
5801: for(j=1; j<=nlstate+ndeath;j++) {
5802: ppij=0.;
5803: for(i=1; i<=nlstate;i++) {
5804: if (mobilav==1)
5805: ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][i][cptcod];
5806: else {
5807: ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][cptcod];
5808: }
5809: if (h*hstepm/YEARM*stepm== yearp) {
5810: fprintf(ficresf," %.3f", p3mat[i][j][h]);
5811: }
5812: } /* end i */
5813: if (h*hstepm/YEARM*stepm==yearp) {
5814: fprintf(ficresf," %.3f", ppij);
5815: }
5816: }/* end j */
5817: } /* end h */
5818: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
5819: } /* end agec */
5820: } /* end yearp */
5821: } /* end cptcod */
5822: } /* end cptcov */
5823:
5824: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
5825:
5826: fclose(ficresf);
1.215 brouard 5827: printf("End of Computing forecasting \n");
5828: fprintf(ficlog,"End of Computing forecasting\n");
5829:
1.126 brouard 5830: }
5831:
5832: /************** Forecasting *****not tested NB*************/
1.169 brouard 5833: 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 5834:
5835: int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;
5836: int *popage;
5837: double calagedatem, agelim, kk1, kk2;
5838: double *popeffectif,*popcount;
5839: double ***p3mat,***tabpop,***tabpopprev;
5840: double ***mobaverage;
5841: char filerespop[FILENAMELENGTH];
5842:
5843: tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
5844: tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
5845: agelim=AGESUP;
5846: calagedatem=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;
5847:
5848: prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
5849:
5850:
1.201 brouard 5851: strcpy(filerespop,"POP_");
5852: strcat(filerespop,fileresu);
1.126 brouard 5853: if((ficrespop=fopen(filerespop,"w"))==NULL) {
5854: printf("Problem with forecast resultfile: %s\n", filerespop);
5855: fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop);
5856: }
5857: printf("Computing forecasting: result on file '%s' \n", filerespop);
5858: fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop);
5859:
5860: if (cptcoveff==0) ncodemax[cptcoveff]=1;
5861:
5862: if (mobilav!=0) {
5863: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
5864: if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
5865: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
5866: printf(" Error in movingaverage mobilav=%d\n",mobilav);
5867: }
5868: }
5869:
5870: stepsize=(int) (stepm+YEARM-1)/YEARM;
5871: if (stepm<=12) stepsize=1;
5872:
5873: agelim=AGESUP;
5874:
5875: hstepm=1;
5876: hstepm=hstepm/stepm;
5877:
5878: if (popforecast==1) {
5879: if((ficpop=fopen(popfile,"r"))==NULL) {
5880: printf("Problem with population file : %s\n",popfile);exit(0);
5881: fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0);
5882: }
5883: popage=ivector(0,AGESUP);
5884: popeffectif=vector(0,AGESUP);
5885: popcount=vector(0,AGESUP);
5886:
5887: i=1;
5888: while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;
5889:
5890: imx=i;
5891: for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];
5892: }
5893:
5894: for(cptcov=1,k=0;cptcov<=i2;cptcov++){
5895: for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
5896: k=k+1;
5897: fprintf(ficrespop,"\n#******");
5898: for(j=1;j<=cptcoveff;j++) {
1.198 brouard 5899: fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
1.126 brouard 5900: }
5901: fprintf(ficrespop,"******\n");
5902: fprintf(ficrespop,"# Age");
5903: for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);
5904: if (popforecast==1) fprintf(ficrespop," [Population]");
5905:
5906: for (cpt=0; cpt<=0;cpt++) {
5907: fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);
5908:
5909: for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){
5910: nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);
5911: nhstepm = nhstepm/hstepm;
5912:
5913: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
5914: oldm=oldms;savm=savms;
5915: hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
5916:
5917: for (h=0; h<=nhstepm; h++){
5918: if (h==(int) (calagedatem+YEARM*cpt)) {
5919: fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
5920: }
5921: for(j=1; j<=nlstate+ndeath;j++) {
5922: kk1=0.;kk2=0;
5923: for(i=1; i<=nlstate;i++) {
5924: if (mobilav==1)
5925: kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];
5926: else {
5927: kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];
5928: }
5929: }
5930: if (h==(int)(calagedatem+12*cpt)){
5931: tabpop[(int)(agedeb)][j][cptcod]=kk1;
5932: /*fprintf(ficrespop," %.3f", kk1);
5933: if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/
5934: }
5935: }
5936: for(i=1; i<=nlstate;i++){
5937: kk1=0.;
5938: for(j=1; j<=nlstate;j++){
5939: kk1= kk1+tabpop[(int)(agedeb)][j][cptcod];
5940: }
5941: tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedatem+12*cpt)*hstepm/YEARM*stepm-1)];
5942: }
5943:
5944: if (h==(int)(calagedatem+12*cpt)) for(j=1; j<=nlstate;j++)
5945: fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);
5946: }
5947: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
5948: }
5949: }
5950:
5951: /******/
5952:
5953: for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) {
5954: fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);
5955: for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){
5956: nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);
5957: nhstepm = nhstepm/hstepm;
5958:
5959: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
5960: oldm=oldms;savm=savms;
5961: hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
5962: for (h=0; h<=nhstepm; h++){
5963: if (h==(int) (calagedatem+YEARM*cpt)) {
5964: fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
5965: }
5966: for(j=1; j<=nlstate+ndeath;j++) {
5967: kk1=0.;kk2=0;
5968: for(i=1; i<=nlstate;i++) {
5969: kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];
5970: }
5971: if (h==(int)(calagedatem+12*cpt)) fprintf(ficresf," %15.2f", kk1);
5972: }
5973: }
5974: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
5975: }
5976: }
5977: }
5978: }
5979:
5980: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
5981:
5982: if (popforecast==1) {
5983: free_ivector(popage,0,AGESUP);
5984: free_vector(popeffectif,0,AGESUP);
5985: free_vector(popcount,0,AGESUP);
5986: }
5987: free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
5988: free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
5989: fclose(ficrespop);
5990: } /* End of popforecast */
5991:
5992: int fileappend(FILE *fichier, char *optionfich)
5993: {
5994: if((fichier=fopen(optionfich,"a"))==NULL) {
5995: printf("Problem with file: %s\n", optionfich);
5996: fprintf(ficlog,"Problem with file: %s\n", optionfich);
5997: return (0);
5998: }
5999: fflush(fichier);
6000: return (1);
6001: }
6002:
6003:
6004: /**************** function prwizard **********************/
6005: void prwizard(int ncovmodel, int nlstate, int ndeath, char model[], FILE *ficparo)
6006: {
6007:
6008: /* Wizard to print covariance matrix template */
6009:
1.164 brouard 6010: char ca[32], cb[32];
6011: int i,j, k, li, lj, lk, ll, jj, npar, itimes;
1.126 brouard 6012: int numlinepar;
6013:
6014: printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
6015: fprintf(ficparo,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
6016: for(i=1; i <=nlstate; i++){
6017: jj=0;
6018: for(j=1; j <=nlstate+ndeath; j++){
6019: if(j==i) continue;
6020: jj++;
6021: /*ca[0]= k+'a'-1;ca[1]='\0';*/
6022: printf("%1d%1d",i,j);
6023: fprintf(ficparo,"%1d%1d",i,j);
6024: for(k=1; k<=ncovmodel;k++){
6025: /* printf(" %lf",param[i][j][k]); */
6026: /* fprintf(ficparo," %lf",param[i][j][k]); */
6027: printf(" 0.");
6028: fprintf(ficparo," 0.");
6029: }
6030: printf("\n");
6031: fprintf(ficparo,"\n");
6032: }
6033: }
6034: printf("# Scales (for hessian or gradient estimation)\n");
6035: fprintf(ficparo,"# Scales (for hessian or gradient estimation)\n");
6036: npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/
6037: for(i=1; i <=nlstate; i++){
6038: jj=0;
6039: for(j=1; j <=nlstate+ndeath; j++){
6040: if(j==i) continue;
6041: jj++;
6042: fprintf(ficparo,"%1d%1d",i,j);
6043: printf("%1d%1d",i,j);
6044: fflush(stdout);
6045: for(k=1; k<=ncovmodel;k++){
6046: /* printf(" %le",delti3[i][j][k]); */
6047: /* fprintf(ficparo," %le",delti3[i][j][k]); */
6048: printf(" 0.");
6049: fprintf(ficparo," 0.");
6050: }
6051: numlinepar++;
6052: printf("\n");
6053: fprintf(ficparo,"\n");
6054: }
6055: }
6056: printf("# Covariance matrix\n");
6057: /* # 121 Var(a12)\n\ */
6058: /* # 122 Cov(b12,a12) Var(b12)\n\ */
6059: /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
6060: /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
6061: /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
6062: /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
6063: /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
6064: /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
6065: fflush(stdout);
6066: fprintf(ficparo,"# Covariance matrix\n");
6067: /* # 121 Var(a12)\n\ */
6068: /* # 122 Cov(b12,a12) Var(b12)\n\ */
6069: /* # ...\n\ */
6070: /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
6071:
6072: for(itimes=1;itimes<=2;itimes++){
6073: jj=0;
6074: for(i=1; i <=nlstate; i++){
6075: for(j=1; j <=nlstate+ndeath; j++){
6076: if(j==i) continue;
6077: for(k=1; k<=ncovmodel;k++){
6078: jj++;
6079: ca[0]= k+'a'-1;ca[1]='\0';
6080: if(itimes==1){
6081: printf("#%1d%1d%d",i,j,k);
6082: fprintf(ficparo,"#%1d%1d%d",i,j,k);
6083: }else{
6084: printf("%1d%1d%d",i,j,k);
6085: fprintf(ficparo,"%1d%1d%d",i,j,k);
6086: /* printf(" %.5le",matcov[i][j]); */
6087: }
6088: ll=0;
6089: for(li=1;li <=nlstate; li++){
6090: for(lj=1;lj <=nlstate+ndeath; lj++){
6091: if(lj==li) continue;
6092: for(lk=1;lk<=ncovmodel;lk++){
6093: ll++;
6094: if(ll<=jj){
6095: cb[0]= lk +'a'-1;cb[1]='\0';
6096: if(ll<jj){
6097: if(itimes==1){
6098: printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
6099: fprintf(ficparo," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
6100: }else{
6101: printf(" 0.");
6102: fprintf(ficparo," 0.");
6103: }
6104: }else{
6105: if(itimes==1){
6106: printf(" Var(%s%1d%1d)",ca,i,j);
6107: fprintf(ficparo," Var(%s%1d%1d)",ca,i,j);
6108: }else{
6109: printf(" 0.");
6110: fprintf(ficparo," 0.");
6111: }
6112: }
6113: }
6114: } /* end lk */
6115: } /* end lj */
6116: } /* end li */
6117: printf("\n");
6118: fprintf(ficparo,"\n");
6119: numlinepar++;
6120: } /* end k*/
6121: } /*end j */
6122: } /* end i */
6123: } /* end itimes */
6124:
6125: } /* end of prwizard */
6126: /******************* Gompertz Likelihood ******************************/
6127: double gompertz(double x[])
6128: {
6129: double A,B,L=0.0,sump=0.,num=0.;
6130: int i,n=0; /* n is the size of the sample */
6131:
6132: for (i=0;i<=imx-1 ; i++) {
6133: sump=sump+weight[i];
6134: /* sump=sump+1;*/
6135: num=num+1;
6136: }
6137:
6138:
6139: /* for (i=0; i<=imx; i++)
6140: 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]);*/
6141:
6142: for (i=1;i<=imx ; i++)
6143: {
6144: if (cens[i] == 1 && wav[i]>1)
6145: A=-x[1]/(x[2])*(exp(x[2]*(agecens[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)));
6146:
6147: if (cens[i] == 0 && wav[i]>1)
6148: A=-x[1]/(x[2])*(exp(x[2]*(agedc[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)))
6149: +log(x[1]/YEARM)+x[2]*(agedc[i]-agegomp)+log(YEARM);
6150:
6151: /*if (wav[i] > 1 && agecens[i] > 15) {*/ /* ??? */
6152: if (wav[i] > 1 ) { /* ??? */
6153: L=L+A*weight[i];
6154: /* 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]);*/
6155: }
6156: }
6157:
6158: /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/
6159:
6160: return -2*L*num/sump;
6161: }
6162:
1.136 brouard 6163: #ifdef GSL
6164: /******************* Gompertz_f Likelihood ******************************/
6165: double gompertz_f(const gsl_vector *v, void *params)
6166: {
6167: double A,B,LL=0.0,sump=0.,num=0.;
6168: double *x= (double *) v->data;
6169: int i,n=0; /* n is the size of the sample */
6170:
6171: for (i=0;i<=imx-1 ; i++) {
6172: sump=sump+weight[i];
6173: /* sump=sump+1;*/
6174: num=num+1;
6175: }
6176:
6177:
6178: /* for (i=0; i<=imx; i++)
6179: 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]);*/
6180: printf("x[0]=%lf x[1]=%lf\n",x[0],x[1]);
6181: for (i=1;i<=imx ; i++)
6182: {
6183: if (cens[i] == 1 && wav[i]>1)
6184: A=-x[0]/(x[1])*(exp(x[1]*(agecens[i]-agegomp))-exp(x[1]*(ageexmed[i]-agegomp)));
6185:
6186: if (cens[i] == 0 && wav[i]>1)
6187: A=-x[0]/(x[1])*(exp(x[1]*(agedc[i]-agegomp))-exp(x[1]*(ageexmed[i]-agegomp)))
6188: +log(x[0]/YEARM)+x[1]*(agedc[i]-agegomp)+log(YEARM);
6189:
6190: /*if (wav[i] > 1 && agecens[i] > 15) {*/ /* ??? */
6191: if (wav[i] > 1 ) { /* ??? */
6192: LL=LL+A*weight[i];
6193: /* 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]);*/
6194: }
6195: }
6196:
6197: /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/
6198: printf("x[0]=%lf x[1]=%lf -2*LL*num/sump=%lf\n",x[0],x[1],-2*LL*num/sump);
6199:
6200: return -2*LL*num/sump;
6201: }
6202: #endif
6203:
1.126 brouard 6204: /******************* Printing html file ***********/
1.201 brouard 6205: void printinghtmlmort(char fileresu[], char title[], char datafile[], int firstpass, \
1.126 brouard 6206: int lastpass, int stepm, int weightopt, char model[],\
6207: int imx, double p[],double **matcov,double agemortsup){
6208: int i,k;
6209:
6210: fprintf(fichtm,"<ul><li><h4>Result files </h4>\n Force of mortality. Parameters of the Gompertz fit (with confidence interval in brackets):<br>");
6211: fprintf(fichtm," mu(age) =%lf*exp(%lf*(age-%d)) per year<br><br>",p[1],p[2],agegomp);
6212: for (i=1;i<=2;i++)
6213: 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 6214: fprintf(fichtm,"<br><br><img src=\"graphmort.svg\">");
1.126 brouard 6215: fprintf(fichtm,"</ul>");
6216:
6217: fprintf(fichtm,"<ul><li><h4>Life table</h4>\n <br>");
6218:
6219: 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>");
6220:
6221: for (k=agegomp;k<(agemortsup-2);k++)
6222: 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]);
6223:
6224:
6225: fflush(fichtm);
6226: }
6227:
6228: /******************* Gnuplot file **************/
1.201 brouard 6229: void printinggnuplotmort(char fileresu[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
1.126 brouard 6230:
6231: char dirfileres[132],optfileres[132];
1.164 brouard 6232:
1.126 brouard 6233: int ng;
6234:
6235:
6236: /*#ifdef windows */
6237: fprintf(ficgp,"cd \"%s\" \n",pathc);
6238: /*#endif */
6239:
6240:
6241: strcpy(dirfileres,optionfilefiname);
6242: strcpy(optfileres,"vpl");
1.199 brouard 6243: fprintf(ficgp,"set out \"graphmort.svg\"\n ");
1.126 brouard 6244: fprintf(ficgp,"set xlabel \"Age\"\n set ylabel \"Force of mortality (per year)\" \n ");
1.199 brouard 6245: fprintf(ficgp, "set ter svg size 640, 480\n set log y\n");
1.145 brouard 6246: /* fprintf(ficgp, "set size 0.65,0.65\n"); */
1.126 brouard 6247: fprintf(ficgp,"plot [%d:100] %lf*exp(%lf*(x-%d))",agegomp,p[1],p[2],agegomp);
6248:
6249: }
6250:
1.136 brouard 6251: int readdata(char datafile[], int firstobs, int lastobs, int *imax)
6252: {
1.126 brouard 6253:
1.136 brouard 6254: /*-------- data file ----------*/
6255: FILE *fic;
6256: char dummy[]=" ";
1.164 brouard 6257: int i=0, j=0, n=0;
1.136 brouard 6258: int linei, month, year,iout;
6259: char line[MAXLINE], linetmp[MAXLINE];
1.164 brouard 6260: char stra[MAXLINE], strb[MAXLINE];
1.136 brouard 6261: char *stratrunc;
6262: int lstra;
1.126 brouard 6263:
6264:
1.136 brouard 6265: if((fic=fopen(datafile,"r"))==NULL) {
1.195 brouard 6266: printf("Problem while opening datafile: %s\n", datafile);fflush(stdout);
6267: fprintf(ficlog,"Problem while opening datafile: %s\n", datafile);fflush(ficlog);return 1;
1.136 brouard 6268: }
1.126 brouard 6269:
1.136 brouard 6270: i=1;
6271: linei=0;
6272: while ((fgets(line, MAXLINE, fic) != NULL) &&((i >= firstobs) && (i <=lastobs))) {
6273: linei=linei+1;
6274: for(j=strlen(line); j>=0;j--){ /* Untabifies line */
6275: if(line[j] == '\t')
6276: line[j] = ' ';
6277: }
6278: for(j=strlen(line)-1; (line[j]==' ')||(line[j]==10)||(line[j]==13);j--){
6279: ;
6280: };
6281: line[j+1]=0; /* Trims blanks at end of line */
6282: if(line[0]=='#'){
6283: fprintf(ficlog,"Comment line\n%s\n",line);
6284: printf("Comment line\n%s\n",line);
6285: continue;
6286: }
6287: trimbb(linetmp,line); /* Trims multiple blanks in line */
1.164 brouard 6288: strcpy(line, linetmp);
1.136 brouard 6289:
1.126 brouard 6290:
1.136 brouard 6291: for (j=maxwav;j>=1;j--){
1.137 brouard 6292: cutv(stra, strb, line, ' ');
1.136 brouard 6293: if(strb[0]=='.') { /* Missing status */
6294: lval=-1;
6295: }else{
6296: errno=0;
6297: lval=strtol(strb,&endptr,10);
6298: /* if (errno == ERANGE && (lval == LONG_MAX || lval == LONG_MIN))*/
6299: if( strb[0]=='\0' || (*endptr != '\0')){
1.141 brouard 6300: 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);
6301: fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a status of wave %d. Setting maxwav=%d might be wrong. Exiting.\n", strb, linei,i,line,j,maxwav);fflush(ficlog);
1.136 brouard 6302: return 1;
6303: }
6304: }
6305: s[j][i]=lval;
6306:
6307: strcpy(line,stra);
6308: cutv(stra, strb,line,' ');
1.169 brouard 6309: if( (iout=sscanf(strb,"%d/%d",&month, &year)) != 0){
1.136 brouard 6310: }
1.169 brouard 6311: else if( (iout=sscanf(strb,"%s.",dummy)) != 0){
1.136 brouard 6312: month=99;
6313: year=9999;
6314: }else{
1.141 brouard 6315: 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);
6316: fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of interview (mm/yyyy or .) at wave %d. Exiting.\n",strb, linei,i, line,j);fflush(ficlog);
1.136 brouard 6317: return 1;
6318: }
6319: anint[j][i]= (double) year;
6320: mint[j][i]= (double)month;
6321: strcpy(line,stra);
6322: } /* ENd Waves */
6323:
6324: cutv(stra, strb,line,' ');
1.169 brouard 6325: if( (iout=sscanf(strb,"%d/%d",&month, &year)) != 0){
1.136 brouard 6326: }
1.169 brouard 6327: else if( (iout=sscanf(strb,"%s.",dummy)) != 0){
1.136 brouard 6328: month=99;
6329: year=9999;
6330: }else{
1.141 brouard 6331: 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);
6332: fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of death (mm/yyyy or .). Exiting.\n",strb, linei,i,line);fflush(ficlog);
1.136 brouard 6333: return 1;
6334: }
6335: andc[i]=(double) year;
6336: moisdc[i]=(double) month;
6337: strcpy(line,stra);
6338:
6339: cutv(stra, strb,line,' ');
1.169 brouard 6340: if( (iout=sscanf(strb,"%d/%d",&month, &year)) != 0){
1.136 brouard 6341: }
1.169 brouard 6342: else if( (iout=sscanf(strb,"%s.", dummy)) != 0){
1.136 brouard 6343: month=99;
6344: year=9999;
6345: }else{
1.141 brouard 6346: 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);
6347: fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of birth (mm/yyyy or .). Exiting.\n",strb, linei,i,line);fflush(ficlog);
1.136 brouard 6348: return 1;
6349: }
6350: if (year==9999) {
1.141 brouard 6351: 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);
6352: fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of birth (mm/yyyy) but at least the year of birth should be given. Exiting.\n",strb, linei,i,line);fflush(ficlog);
1.136 brouard 6353: return 1;
1.126 brouard 6354:
1.136 brouard 6355: }
6356: annais[i]=(double)(year);
6357: moisnais[i]=(double)(month);
6358: strcpy(line,stra);
6359:
6360: cutv(stra, strb,line,' ');
6361: errno=0;
6362: dval=strtod(strb,&endptr);
6363: if( strb[0]=='\0' || (*endptr != '\0')){
1.141 brouard 6364: printf("Error reading data around '%f' at line number %d, \"%s\" for individual %d\nShould be a weight. Exiting.\n",dval, i,line,linei);
6365: 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 6366: fflush(ficlog);
6367: return 1;
6368: }
6369: weight[i]=dval;
6370: strcpy(line,stra);
6371:
6372: for (j=ncovcol;j>=1;j--){
6373: cutv(stra, strb,line,' ');
6374: if(strb[0]=='.') { /* Missing status */
6375: lval=-1;
6376: }else{
6377: errno=0;
6378: lval=strtol(strb,&endptr,10);
6379: if( strb[0]=='\0' || (*endptr != '\0')){
1.141 brouard 6380: 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);
6381: fprintf(ficlog,"Error reading data around '%ld' at line number %d for individual %d, '%s'\nShould be a covariate value (=0 for the reference or 1 for alternative). Exiting.\n",lval, linei,i, line);fflush(ficlog);
1.136 brouard 6382: return 1;
6383: }
6384: }
6385: if(lval <-1 || lval >1){
1.141 brouard 6386: printf("Error reading data around '%ld' at line number %d for individual %d, '%s'\n \
1.136 brouard 6387: Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
6388: for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
6389: For example, for multinomial values like 1, 2 and 3,\n \
6390: build V1=0 V2=0 for the reference value (1),\n \
6391: V1=1 V2=0 for (2) \n \
6392: and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
6393: output of IMaCh is often meaningless.\n \
6394: Exiting.\n",lval,linei, i,line,j);
1.141 brouard 6395: fprintf(ficlog,"Error reading data around '%ld' at line number %d for individual %d, '%s'\n \
1.136 brouard 6396: Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
6397: for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
6398: For example, for multinomial values like 1, 2 and 3,\n \
6399: build V1=0 V2=0 for the reference value (1),\n \
6400: V1=1 V2=0 for (2) \n \
6401: and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
6402: output of IMaCh is often meaningless.\n \
6403: Exiting.\n",lval,linei, i,line,j);fflush(ficlog);
6404: return 1;
6405: }
6406: covar[j][i]=(double)(lval);
6407: strcpy(line,stra);
6408: }
6409: lstra=strlen(stra);
6410:
6411: if(lstra > 9){ /* More than 2**32 or max of what printf can write with %ld */
6412: stratrunc = &(stra[lstra-9]);
6413: num[i]=atol(stratrunc);
6414: }
6415: else
6416: num[i]=atol(stra);
6417: /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){
6418: 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;}*/
6419:
6420: i=i+1;
6421: } /* End loop reading data */
1.126 brouard 6422:
1.136 brouard 6423: *imax=i-1; /* Number of individuals */
6424: fclose(fic);
6425:
6426: return (0);
1.164 brouard 6427: /* endread: */
1.136 brouard 6428: printf("Exiting readdata: ");
6429: fclose(fic);
6430: return (1);
1.126 brouard 6431:
6432:
6433:
1.136 brouard 6434: }
1.145 brouard 6435: void removespace(char *str) {
6436: char *p1 = str, *p2 = str;
6437: do
6438: while (*p2 == ' ')
6439: p2++;
1.169 brouard 6440: while (*p1++ == *p2++);
1.145 brouard 6441: }
6442:
6443: int decodemodel ( char model[], int lastobs) /**< This routine decode the model and returns:
1.187 brouard 6444: * Model V1+V2+V3+V8+V7*V8+V5*V6+V8*age+V3*age+age*age
6445: * - nagesqr = 1 if age*age in the model, otherwise 0.
6446: * - cptcovt total number of covariates of the model nbocc(+)+1 = 8 excepting constant and age and age*age
6447: * - cptcovn or number of covariates k of the models excluding age*products =6 and age*age
1.145 brouard 6448: * - cptcovage number of covariates with age*products =2
6449: * - cptcovs number of simple covariates
6450: * - 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
6451: * which is a new column after the 9 (ncovcol) variables.
6452: * - if k is a product Vn*Vm covar[k][i] is filled with correct values for each individual
6453: * - Tprod[l] gives the kth covariates of the product Vn*Vm l=1 to cptcovprod-cptcovage
6454: * Tprod[1]@2 {5, 6}: position of first product V7*V8 is 5, and second V5*V6 is 6.
6455: * - Tvard[k] p Tvard[1][1]@4 {7, 8, 5, 6} for V7*V8 and V5*V6 .
6456: */
1.136 brouard 6457: {
1.145 brouard 6458: int i, j, k, ks;
1.164 brouard 6459: int j1, k1, k2;
1.136 brouard 6460: char modelsav[80];
1.145 brouard 6461: char stra[80], strb[80], strc[80], strd[80],stre[80];
1.187 brouard 6462: char *strpt;
1.136 brouard 6463:
1.145 brouard 6464: /*removespace(model);*/
1.136 brouard 6465: if (strlen(model) >1){ /* If there is at least 1 covariate */
1.145 brouard 6466: j=0, j1=0, k1=0, k2=-1, ks=0, cptcovn=0;
1.137 brouard 6467: if (strstr(model,"AGE") !=0){
1.192 brouard 6468: printf("Error. AGE must be in lower case 'age' model=1+age+%s. ",model);
6469: fprintf(ficlog,"Error. AGE must be in lower case model=1+age+%s. ",model);fflush(ficlog);
1.136 brouard 6470: return 1;
6471: }
1.141 brouard 6472: if (strstr(model,"v") !=0){
6473: printf("Error. 'v' must be in upper case 'V' model=%s ",model);
6474: fprintf(ficlog,"Error. 'v' must be in upper case model=%s ",model);fflush(ficlog);
6475: return 1;
6476: }
1.187 brouard 6477: strcpy(modelsav,model);
6478: if ((strpt=strstr(model,"age*age")) !=0){
6479: printf(" strpt=%s, model=%s\n",strpt, model);
6480: if(strpt != model){
6481: printf("Error in model: 'model=%s'; 'age*age' should in first place before other covariates\n \
1.192 brouard 6482: 'model=1+age+age*age+V1.' or 'model=1+age+age*age+V1+V1*age.', please swap as well as \n \
1.187 brouard 6483: corresponding column of parameters.\n",model);
6484: fprintf(ficlog,"Error in model: 'model=%s'; 'age*age' should in first place before other covariates\n \
1.192 brouard 6485: 'model=1+age+age*age+V1.' or 'model=1+age+age*age+V1+V1*age.', please swap as well as \n \
1.187 brouard 6486: corresponding column of parameters.\n",model); fflush(ficlog);
6487: return 1;
6488: }
6489:
6490: nagesqr=1;
6491: if (strstr(model,"+age*age") !=0)
6492: substrchaine(modelsav, model, "+age*age");
6493: else if (strstr(model,"age*age+") !=0)
6494: substrchaine(modelsav, model, "age*age+");
6495: else
6496: substrchaine(modelsav, model, "age*age");
6497: }else
6498: nagesqr=0;
6499: if (strlen(modelsav) >1){
6500: j=nbocc(modelsav,'+'); /**< j=Number of '+' */
6501: j1=nbocc(modelsav,'*'); /**< j1=Number of '*' */
6502: cptcovs=j+1-j1; /**< Number of simple covariates V1+V1*age+V3 +V3*V4+age*age=> V1 + V3 =2 */
6503: cptcovt= j+1; /* Number of total covariates in the model, not including
6504: * cst, age and age*age
6505: * V1+V1*age+ V3 + V3*V4+age*age=> 4*/
6506: /* including age products which are counted in cptcovage.
6507: * but the covariates which are products must be treated
6508: * separately: ncovn=4- 2=2 (V1+V3). */
6509: cptcovprod=j1; /**< Number of products V1*V2 +v3*age = 2 */
6510: cptcovprodnoage=0; /**< Number of covariate products without age: V3*V4 =1 */
6511:
6512:
6513: /* Design
6514: * V1 V2 V3 V4 V5 V6 V7 V8 V9 Weight
6515: * < ncovcol=8 >
6516: * Model V2 + V1 + V3*age + V3 + V5*V6 + V7*V8 + V8*age + V8
6517: * k= 1 2 3 4 5 6 7 8
6518: * cptcovn number of covariates (not including constant and age ) = # of + plus 1 = 7+1=8
6519: * covar[k,i], value of kth covariate if not including age for individual i:
6520: * covar[1][i]= (V2), covar[4][i]=(V3), covar[8][i]=(V8)
6521: * Tvar[k] # of the kth covariate: Tvar[1]=2 Tvar[4]=3 Tvar[8]=8
6522: * if multiplied by age: V3*age Tvar[3=V3*age]=3 (V3) Tvar[7]=8 and
6523: * Tage[++cptcovage]=k
6524: * if products, new covar are created after ncovcol with k1
6525: * Tvar[k]=ncovcol+k1; # of the kth covariate product: Tvar[5]=ncovcol+1=10 Tvar[6]=ncovcol+1=11
6526: * Tprod[k1]=k; Tprod[1]=5 Tprod[2]= 6; gives the position of the k1th product
6527: * 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
6528: * Tvar[cptcovn+k2]=Tvard[k1][1];Tvar[cptcovn+k2+1]=Tvard[k1][2];
6529: * Tvar[8+1]=5;Tvar[8+2]=6;Tvar[8+3]=7;Tvar[8+4]=8 inverted
6530: * V1 V2 V3 V4 V5 V6 V7 V8 V9 V10 V11
6531: * < ncovcol=8 >
6532: * Model V2 + V1 + V3*age + V3 + V5*V6 + V7*V8 + V8*age + V8 d1 d1 d2 d2
6533: * k= 1 2 3 4 5 6 7 8 9 10 11 12
6534: * Tvar[k]= 2 1 3 3 10 11 8 8 5 6 7 8
6535: * p Tvar[1]@12={2, 1, 3, 3, 11, 10, 8, 8, 7, 8, 5, 6}
6536: * p Tprod[1]@2={ 6, 5}
6537: *p Tvard[1][1]@4= {7, 8, 5, 6}
6538: * covar[k][i]= V2 V1 ? V3 V5*V6? V7*V8? ? V8
6539: * cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
6540: *How to reorganize?
6541: * Model V1 + V2 + V3 + V8 + V5*V6 + V7*V8 + V3*age + V8*age
6542: * Tvars {2, 1, 3, 3, 11, 10, 8, 8, 7, 8, 5, 6}
6543: * {2, 1, 4, 8, 5, 6, 3, 7}
6544: * Struct []
6545: */
1.145 brouard 6546:
1.187 brouard 6547: /* This loop fills the array Tvar from the string 'model'.*/
6548: /* j is the number of + signs in the model V1+V2+V3 j=2 i=3 to 1 */
6549: /* modelsav=V2+V1+V4+age*V3 strb=age*V3 stra=V2+V1+V4 */
6550: /* k=4 (age*V3) Tvar[k=4]= 3 (from V3) Tage[cptcovage=1]=4 */
6551: /* k=3 V4 Tvar[k=3]= 4 (from V4) */
6552: /* k=2 V1 Tvar[k=2]= 1 (from V1) */
6553: /* k=1 Tvar[1]=2 (from V2) */
6554: /* k=5 Tvar[5] */
6555: /* for (k=1; k<=cptcovn;k++) { */
1.198 brouard 6556: /* cov[2+k]=nbcode[Tvar[k]][codtabm(ij,Tvar[k])]; */
1.187 brouard 6557: /* } */
1.198 brouard 6558: /* for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,Tvar[Tage[k])]]*cov[2]; */
1.187 brouard 6559: /*
6560: * Treating invertedly V2+V1+V3*age+V2*V4 is as if written V2*V4 +V3*age + V1 + V2 */
6561: for(k=cptcovt; k>=1;k--) /**< Number of covariates */
1.145 brouard 6562: Tvar[k]=0;
1.187 brouard 6563: cptcovage=0;
6564: for(k=1; k<=cptcovt;k++){ /* Loop on total covariates of the model */
6565: cutl(stra,strb,modelsav,'+'); /* keeps in strb after the first '+'
6566: modelsav==V2+V1+V4+V3*age strb=V3*age stra=V2+V1+V4 */
6567: if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyzes it */
6568: /* printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/
6569: /*scanf("%d",i);*/
6570: if (strchr(strb,'*')) { /**< Model includes a product V2+V1+V4+V3*age strb=V3*age */
6571: cutl(strc,strd,strb,'*'); /**< strd*strc Vm*Vn: strb=V3*age(input) strc=age strd=V3 ; V3*V2 strc=V2, strd=V3 */
6572: if (strcmp(strc,"age")==0) { /**< Model includes age: Vn*age */
6573: /* covar is not filled and then is empty */
6574: cptcovprod--;
6575: cutl(stre,strb,strd,'V'); /* strd=V3(input): stre="3" */
6576: Tvar[k]=atoi(stre); /* V2+V1+V4+V3*age Tvar[4]=3 ; V1+V2*age Tvar[2]=2; V1+V1*age Tvar[2]=1 */
6577: cptcovage++; /* Sums the number of covariates which include age as a product */
6578: Tage[cptcovage]=k; /* Tvar[4]=3, Tage[1] = 4 or V1+V1*age Tvar[2]=1, Tage[1]=2 */
6579: /*printf("stre=%s ", stre);*/
6580: } else if (strcmp(strd,"age")==0) { /* or age*Vn */
6581: cptcovprod--;
6582: cutl(stre,strb,strc,'V');
6583: Tvar[k]=atoi(stre);
6584: cptcovage++;
6585: Tage[cptcovage]=k;
6586: } else { /* Age is not in the model product V2+V1+V1*V4+V3*age+V3*V2 strb=V3*V2*/
6587: /* loops on k1=1 (V3*V2) and k1=2 V4*V3 */
6588: cptcovn++;
6589: cptcovprodnoage++;k1++;
6590: cutl(stre,strb,strc,'V'); /* strc= Vn, stre is n; strb=V3*V2 stre=3 strc=*/
6591: Tvar[k]=ncovcol+k1; /* For model-covariate k tells which data-covariate to use but
6592: because this model-covariate is a construction we invent a new column
6593: ncovcol + k1
6594: If already ncovcol=4 and model=V2+V1+V1*V4+age*V3+V3*V2
6595: Tvar[3=V1*V4]=4+1 Tvar[5=V3*V2]=4 + 2= 6, etc */
6596: cutl(strc,strb,strd,'V'); /* strd was Vm, strc is m */
6597: Tprod[k1]=k; /* Tprod[1]=3(=V1*V4) for V2+V1+V1*V4+age*V3+V3*V2 */
6598: Tvard[k1][1] =atoi(strc); /* m 1 for V1*/
6599: Tvard[k1][2] =atoi(stre); /* n 4 for V4*/
6600: k2=k2+2;
6601: Tvar[cptcovt+k2]=Tvard[k1][1]; /* Tvar[(cptcovt=4+k2=1)=5]= 1 (V1) */
6602: Tvar[cptcovt+k2+1]=Tvard[k1][2]; /* Tvar[(cptcovt=4+(k2=1)+1)=6]= 4 (V4) */
6603: for (i=1; i<=lastobs;i++){
6604: /* Computes the new covariate which is a product of
6605: covar[n][i]* covar[m][i] and stores it at ncovol+k1 May not be defined */
6606: covar[ncovcol+k1][i]=covar[atoi(stre)][i]*covar[atoi(strc)][i];
6607: }
6608: } /* End age is not in the model */
6609: } /* End if model includes a product */
6610: else { /* no more sum */
6611: /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/
6612: /* scanf("%d",i);*/
6613: cutl(strd,strc,strb,'V');
6614: ks++; /**< Number of simple covariates */
1.145 brouard 6615: cptcovn++;
1.187 brouard 6616: Tvar[k]=atoi(strd);
6617: }
6618: strcpy(modelsav,stra); /* modelsav=V2+V1+V4 stra=V2+V1+V4 */
6619: /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);
6620: scanf("%d",i);*/
6621: } /* end of loop + on total covariates */
6622: } /* end if strlen(modelsave == 0) age*age might exist */
6623: } /* end if strlen(model == 0) */
1.136 brouard 6624:
6625: /*The number n of Vn is stored in Tvar. cptcovage =number of age covariate. Tage gives the position of age. cptcovprod= number of products.
6626: If model=V1+V1*age then Tvar[1]=1 Tvar[2]=1 cptcovage=1 Tage[1]=2 cptcovprod=0*/
6627:
6628: /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);
6629: printf("cptcovprod=%d ", cptcovprod);
6630: fprintf(ficlog,"cptcovprod=%d ", cptcovprod);
6631:
6632: scanf("%d ",i);*/
6633:
6634:
1.137 brouard 6635: return (0); /* with covar[new additional covariate if product] and Tage if age */
1.164 brouard 6636: /*endread:*/
1.136 brouard 6637: printf("Exiting decodemodel: ");
6638: return (1);
6639: }
6640:
1.169 brouard 6641: int calandcheckages(int imx, int maxwav, double *agemin, double *agemax, int *nberr, int *nbwarn )
1.136 brouard 6642: {
6643: int i, m;
6644:
6645: for (i=1; i<=imx; i++) {
6646: for(m=2; (m<= maxwav); m++) {
6647: if (((int)mint[m][i]== 99) && (s[m][i] <= nlstate)){
6648: anint[m][i]=9999;
1.216 ! brouard 6649: if (s[m][i] != -2) /* Keeping initial status of unknown vital status */
! 6650: s[m][i]=-1;
1.136 brouard 6651: }
6652: if((int)moisdc[i]==99 && (int)andc[i]==9999 && s[m][i]>nlstate){
1.169 brouard 6653: *nberr = *nberr + 1;
6654: 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 are biased (%d)\n",(int)moisdc[i],(int)andc[i],num[i],i, *nberr);
6655: 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 are biased (%d)\n",(int)moisdc[i],(int)andc[i],num[i],i, *nberr);
1.136 brouard 6656: s[m][i]=-1;
6657: }
6658: if((int)moisdc[i]==99 && (int)andc[i]!=9999 && s[m][i]>nlstate){
1.169 brouard 6659: (*nberr)++;
1.136 brouard 6660: 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]);
6661: 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]);
6662: s[m][i]=-1; /* We prefer to skip it (and to skip it in version 0.8a1 too */
6663: }
6664: }
6665: }
6666:
6667: for (i=1; i<=imx; i++) {
6668: agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);
6669: for(m=firstpass; (m<= lastpass); m++){
1.214 brouard 6670: 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 6671: if (s[m][i] >= nlstate+1) {
1.169 brouard 6672: if(agedc[i]>0){
6673: if((int)moisdc[i]!=99 && (int)andc[i]!=9999){
1.136 brouard 6674: agev[m][i]=agedc[i];
1.214 brouard 6675: /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/
1.169 brouard 6676: }else {
1.136 brouard 6677: if ((int)andc[i]!=9999){
6678: nbwarn++;
6679: printf("Warning negative age at death: %ld line:%d\n",num[i],i);
6680: fprintf(ficlog,"Warning negative age at death: %ld line:%d\n",num[i],i);
6681: agev[m][i]=-1;
6682: }
6683: }
1.169 brouard 6684: } /* agedc > 0 */
1.214 brouard 6685: } /* end if */
1.136 brouard 6686: else if(s[m][i] !=9){ /* Standard case, age in fractional
6687: years but with the precision of a month */
6688: agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);
6689: if((int)mint[m][i]==99 || (int)anint[m][i]==9999)
6690: agev[m][i]=1;
6691: else if(agev[m][i] < *agemin){
6692: *agemin=agev[m][i];
6693: printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], *agemin);
6694: }
6695: else if(agev[m][i] >*agemax){
6696: *agemax=agev[m][i];
1.156 brouard 6697: /* printf(" Max anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.2f\n",m,i,anint[m][i], i,annais[i], *agemax);*/
1.136 brouard 6698: }
6699: /*agev[m][i]=anint[m][i]-annais[i];*/
6700: /* agev[m][i] = age[i]+2*m;*/
1.214 brouard 6701: } /* en if 9*/
1.136 brouard 6702: else { /* =9 */
1.214 brouard 6703: /* printf("Debug num[%d]=%ld s[%d][%d]=%d\n",i,num[i], m,i, s[m][i]); */
1.136 brouard 6704: agev[m][i]=1;
6705: s[m][i]=-1;
6706: }
6707: }
1.214 brouard 6708: else if(s[m][i]==0) /*= 0 Unknown */
1.136 brouard 6709: agev[m][i]=1;
1.214 brouard 6710: else{
6711: printf("Warning, num[%d]=%ld, s[%d][%d]=%d\n", i, num[i], m, i,s[m][i]);
6712: fprintf(ficlog, "Warning, num[%d]=%ld, s[%d][%d]=%d\n", i, num[i], m, i,s[m][i]);
6713: agev[m][i]=0;
6714: }
6715: } /* End for lastpass */
6716: }
1.136 brouard 6717:
6718: for (i=1; i<=imx; i++) {
6719: for(m=firstpass; (m<=lastpass); m++){
6720: if (s[m][i] > (nlstate+ndeath)) {
1.169 brouard 6721: (*nberr)++;
1.136 brouard 6722: 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);
6723: 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);
6724: return 1;
6725: }
6726: }
6727: }
6728:
6729: /*for (i=1; i<=imx; i++){
6730: for (m=firstpass; (m<lastpass); m++){
6731: printf("%ld %d %.lf %d %d\n", num[i],(covar[1][i]),agev[m][i],s[m][i],s[m+1][i]);
6732: }
6733:
6734: }*/
6735:
6736:
1.139 brouard 6737: printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, *agemin, *agemax);
6738: fprintf(ficlog,"Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, *agemin, *agemax);
1.136 brouard 6739:
6740: return (0);
1.164 brouard 6741: /* endread:*/
1.136 brouard 6742: printf("Exiting calandcheckages: ");
6743: return (1);
6744: }
6745:
1.172 brouard 6746: #if defined(_MSC_VER)
6747: /*printf("Visual C++ compiler: %s \n;", _MSC_FULL_VER);*/
6748: /*fprintf(ficlog, "Visual C++ compiler: %s \n;", _MSC_FULL_VER);*/
6749: //#include "stdafx.h"
6750: //#include <stdio.h>
6751: //#include <tchar.h>
6752: //#include <windows.h>
6753: //#include <iostream>
6754: typedef BOOL(WINAPI *LPFN_ISWOW64PROCESS) (HANDLE, PBOOL);
6755:
6756: LPFN_ISWOW64PROCESS fnIsWow64Process;
6757:
6758: BOOL IsWow64()
6759: {
6760: BOOL bIsWow64 = FALSE;
6761:
6762: //typedef BOOL (APIENTRY *LPFN_ISWOW64PROCESS)
6763: // (HANDLE, PBOOL);
6764:
6765: //LPFN_ISWOW64PROCESS fnIsWow64Process;
6766:
6767: HMODULE module = GetModuleHandle(_T("kernel32"));
6768: const char funcName[] = "IsWow64Process";
6769: fnIsWow64Process = (LPFN_ISWOW64PROCESS)
6770: GetProcAddress(module, funcName);
6771:
6772: if (NULL != fnIsWow64Process)
6773: {
6774: if (!fnIsWow64Process(GetCurrentProcess(),
6775: &bIsWow64))
6776: //throw std::exception("Unknown error");
6777: printf("Unknown error\n");
6778: }
6779: return bIsWow64 != FALSE;
6780: }
6781: #endif
1.177 brouard 6782:
1.191 brouard 6783: void syscompilerinfo(int logged)
1.167 brouard 6784: {
6785: /* #include "syscompilerinfo.h"*/
1.185 brouard 6786: /* command line Intel compiler 32bit windows, XP compatible:*/
6787: /* /GS /W3 /Gy
6788: /Zc:wchar_t /Zi /O2 /Fd"Release\vc120.pdb" /D "WIN32" /D "NDEBUG" /D
6789: "_CONSOLE" /D "_LIB" /D "_USING_V110_SDK71_" /D "_UNICODE" /D
6790: "UNICODE" /Qipo /Zc:forScope /Gd /Oi /MT /Fa"Release\" /EHsc /nologo
1.186 brouard 6791: /Fo"Release\" /Qprof-dir "Release\" /Fp"Release\IMaCh.pch"
6792: */
6793: /* 64 bits */
1.185 brouard 6794: /*
6795: /GS /W3 /Gy
6796: /Zc:wchar_t /Zi /O2 /Fd"x64\Release\vc120.pdb" /D "WIN32" /D "NDEBUG"
6797: /D "_CONSOLE" /D "_LIB" /D "_UNICODE" /D "UNICODE" /Qipo /Zc:forScope
6798: /Oi /MD /Fa"x64\Release\" /EHsc /nologo /Fo"x64\Release\" /Qprof-dir
6799: "x64\Release\" /Fp"x64\Release\IMaCh.pch" */
6800: /* Optimization are useless and O3 is slower than O2 */
6801: /*
6802: /GS /W3 /Gy /Zc:wchar_t /Zi /O3 /Fd"x64\Release\vc120.pdb" /D "WIN32"
6803: /D "NDEBUG" /D "_CONSOLE" /D "_LIB" /D "_UNICODE" /D "UNICODE" /Qipo
6804: /Zc:forScope /Oi /MD /Fa"x64\Release\" /EHsc /nologo /Qparallel
6805: /Fo"x64\Release\" /Qprof-dir "x64\Release\" /Fp"x64\Release\IMaCh.pch"
6806: */
1.186 brouard 6807: /* Link is */ /* /OUT:"visual studio
1.185 brouard 6808: 2013\Projects\IMaCh\Release\IMaCh.exe" /MANIFEST /NXCOMPAT
6809: /PDB:"visual studio
6810: 2013\Projects\IMaCh\Release\IMaCh.pdb" /DYNAMICBASE
6811: "kernel32.lib" "user32.lib" "gdi32.lib" "winspool.lib"
6812: "comdlg32.lib" "advapi32.lib" "shell32.lib" "ole32.lib"
6813: "oleaut32.lib" "uuid.lib" "odbc32.lib" "odbccp32.lib"
6814: /MACHINE:X86 /OPT:REF /SAFESEH /INCREMENTAL:NO
6815: /SUBSYSTEM:CONSOLE",5.01" /MANIFESTUAC:"level='asInvoker'
6816: uiAccess='false'"
6817: /ManifestFile:"Release\IMaCh.exe.intermediate.manifest" /OPT:ICF
6818: /NOLOGO /TLBID:1
6819: */
1.177 brouard 6820: #if defined __INTEL_COMPILER
1.178 brouard 6821: #if defined(__GNUC__)
6822: struct utsname sysInfo; /* For Intel on Linux and OS/X */
6823: #endif
1.177 brouard 6824: #elif defined(__GNUC__)
1.179 brouard 6825: #ifndef __APPLE__
1.174 brouard 6826: #include <gnu/libc-version.h> /* Only on gnu */
1.179 brouard 6827: #endif
1.177 brouard 6828: struct utsname sysInfo;
1.178 brouard 6829: int cross = CROSS;
6830: if (cross){
6831: printf("Cross-");
1.191 brouard 6832: if(logged) fprintf(ficlog, "Cross-");
1.178 brouard 6833: }
1.174 brouard 6834: #endif
6835:
1.171 brouard 6836: #include <stdint.h>
1.178 brouard 6837:
1.191 brouard 6838: printf("Compiled with:");if(logged)fprintf(ficlog,"Compiled with:");
1.169 brouard 6839: #if defined(__clang__)
1.191 brouard 6840: printf(" Clang/LLVM");if(logged)fprintf(ficlog," Clang/LLVM"); /* Clang/LLVM. ---------------------------------------------- */
1.169 brouard 6841: #endif
6842: #if defined(__ICC) || defined(__INTEL_COMPILER)
1.191 brouard 6843: printf(" Intel ICC/ICPC");if(logged)fprintf(ficlog," Intel ICC/ICPC");/* Intel ICC/ICPC. ------------------------------------------ */
1.169 brouard 6844: #endif
6845: #if defined(__GNUC__) || defined(__GNUG__)
1.191 brouard 6846: printf(" GNU GCC/G++");if(logged)fprintf(ficlog," GNU GCC/G++");/* GNU GCC/G++. --------------------------------------------- */
1.169 brouard 6847: #endif
6848: #if defined(__HP_cc) || defined(__HP_aCC)
1.191 brouard 6849: printf(" Hewlett-Packard C/aC++");if(logged)fprintf(fcilog," Hewlett-Packard C/aC++"); /* Hewlett-Packard C/aC++. ---------------------------------- */
1.169 brouard 6850: #endif
6851: #if defined(__IBMC__) || defined(__IBMCPP__)
1.191 brouard 6852: printf(" IBM XL C/C++"); if(logged) fprintf(ficlog," IBM XL C/C++");/* IBM XL C/C++. -------------------------------------------- */
1.169 brouard 6853: #endif
6854: #if defined(_MSC_VER)
1.191 brouard 6855: printf(" Microsoft Visual Studio");if(logged)fprintf(ficlog," Microsoft Visual Studio");/* Microsoft Visual Studio. --------------------------------- */
1.169 brouard 6856: #endif
6857: #if defined(__PGI)
1.191 brouard 6858: printf(" Portland Group PGCC/PGCPP");if(logged) fprintf(ficlog," Portland Group PGCC/PGCPP");/* Portland Group PGCC/PGCPP. ------------------------------- */
1.169 brouard 6859: #endif
6860: #if defined(__SUNPRO_C) || defined(__SUNPRO_CC)
1.191 brouard 6861: printf(" Oracle Solaris Studio");if(logged)fprintf(ficlog," Oracle Solaris Studio\n");/* Oracle Solaris Studio. ----------------------------------- */
1.167 brouard 6862: #endif
1.191 brouard 6863: printf(" for "); if (logged) fprintf(ficlog, " for ");
1.169 brouard 6864:
1.167 brouard 6865: // http://stackoverflow.com/questions/4605842/how-to-identify-platform-compiler-from-preprocessor-macros
6866: #ifdef _WIN32 // note the underscore: without it, it's not msdn official!
6867: // Windows (x64 and x86)
1.191 brouard 6868: printf("Windows (x64 and x86) ");if(logged) fprintf(ficlog,"Windows (x64 and x86) ");
1.167 brouard 6869: #elif __unix__ // all unices, not all compilers
6870: // Unix
1.191 brouard 6871: printf("Unix ");if(logged) fprintf(ficlog,"Unix ");
1.167 brouard 6872: #elif __linux__
6873: // linux
1.191 brouard 6874: printf("linux ");if(logged) fprintf(ficlog,"linux ");
1.167 brouard 6875: #elif __APPLE__
1.174 brouard 6876: // Mac OS, not sure if this is covered by __posix__ and/or __unix__ though..
1.191 brouard 6877: printf("Mac OS ");if(logged) fprintf(ficlog,"Mac OS ");
1.167 brouard 6878: #endif
6879:
6880: /* __MINGW32__ */
6881: /* __CYGWIN__ */
6882: /* __MINGW64__ */
6883: // http://msdn.microsoft.com/en-us/library/b0084kay.aspx
6884: /* _MSC_VER //the Visual C++ compiler is 17.00.51106.1, the _MSC_VER macro evaluates to 1700. Type cl /? */
6885: /* _MSC_FULL_VER //the Visual C++ compiler is 15.00.20706.01, the _MSC_FULL_VER macro evaluates to 150020706 */
6886: /* _WIN64 // Defined for applications for Win64. */
6887: /* _M_X64 // Defined for compilations that target x64 processors. */
6888: /* _DEBUG // Defined when you compile with /LDd, /MDd, and /MTd. */
1.171 brouard 6889:
1.167 brouard 6890: #if UINTPTR_MAX == 0xffffffff
1.191 brouard 6891: printf(" 32-bit"); if(logged) fprintf(ficlog," 32-bit");/* 32-bit */
1.167 brouard 6892: #elif UINTPTR_MAX == 0xffffffffffffffff
1.191 brouard 6893: printf(" 64-bit"); if(logged) fprintf(ficlog," 64-bit");/* 64-bit */
1.167 brouard 6894: #else
1.191 brouard 6895: printf(" wtf-bit"); if(logged) fprintf(ficlog," wtf-bit");/* wtf */
1.167 brouard 6896: #endif
6897:
1.169 brouard 6898: #if defined(__GNUC__)
6899: # if defined(__GNUC_PATCHLEVEL__)
6900: # define __GNUC_VERSION__ (__GNUC__ * 10000 \
6901: + __GNUC_MINOR__ * 100 \
6902: + __GNUC_PATCHLEVEL__)
6903: # else
6904: # define __GNUC_VERSION__ (__GNUC__ * 10000 \
6905: + __GNUC_MINOR__ * 100)
6906: # endif
1.174 brouard 6907: printf(" using GNU C version %d.\n", __GNUC_VERSION__);
1.191 brouard 6908: if(logged) fprintf(ficlog, " using GNU C version %d.\n", __GNUC_VERSION__);
1.176 brouard 6909:
6910: if (uname(&sysInfo) != -1) {
6911: printf("Running on: %s %s %s %s %s\n",sysInfo.sysname, sysInfo.nodename, sysInfo.release, sysInfo.version, sysInfo.machine);
1.191 brouard 6912: 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 6913: }
6914: else
6915: perror("uname() error");
1.179 brouard 6916: //#ifndef __INTEL_COMPILER
6917: #if !defined (__INTEL_COMPILER) && !defined(__APPLE__)
1.174 brouard 6918: printf("GNU libc version: %s\n", gnu_get_libc_version());
1.191 brouard 6919: if(logged) fprintf(ficlog,"GNU libc version: %s\n", gnu_get_libc_version());
1.177 brouard 6920: #endif
1.169 brouard 6921: #endif
1.172 brouard 6922:
6923: // void main()
6924: // {
1.169 brouard 6925: #if defined(_MSC_VER)
1.174 brouard 6926: if (IsWow64()){
1.191 brouard 6927: printf("\nThe program (probably compiled for 32bit) is running under WOW64 (64bit) emulation.\n");
6928: if (logged) fprintf(ficlog, "\nThe program (probably compiled for 32bit) is running under WOW64 (64bit) emulation.\n");
1.174 brouard 6929: }
6930: else{
1.191 brouard 6931: printf("\nThe program is not running under WOW64 (i.e probably on a 64bit Windows).\n");
6932: if (logged) fprintf(ficlog, "\nThe programm is not running under WOW64 (i.e probably on a 64bit Windows).\n");
1.174 brouard 6933: }
1.172 brouard 6934: // printf("\nPress Enter to continue...");
6935: // getchar();
6936: // }
6937:
1.169 brouard 6938: #endif
6939:
1.167 brouard 6940:
6941: }
1.136 brouard 6942:
1.209 brouard 6943: int prevalence_limit(double *p, double **prlim, double ageminpar, double agemaxpar, double ftolpl, int *ncvyearp){
1.180 brouard 6944: /*--------------- Prevalence limit (period or stable prevalence) --------------*/
6945: int i, j, k, i1 ;
1.202 brouard 6946: /* double ftolpl = 1.e-10; */
1.180 brouard 6947: double age, agebase, agelim;
1.203 brouard 6948: double tot;
1.180 brouard 6949:
1.202 brouard 6950: strcpy(filerespl,"PL_");
6951: strcat(filerespl,fileresu);
6952: if((ficrespl=fopen(filerespl,"w"))==NULL) {
6953: printf("Problem with period (stable) prevalence resultfile: %s\n", filerespl);return 1;
6954: fprintf(ficlog,"Problem with period (stable) prevalence resultfile: %s\n", filerespl);return 1;
6955: }
6956: printf("Computing period (stable) prevalence: result on file '%s' \n", filerespl);
6957: fprintf(ficlog,"Computing period (stable) prevalence: result on file '%s' \n", filerespl);
6958: pstamp(ficrespl);
1.203 brouard 6959: fprintf(ficrespl,"# Period (stable) prevalence. Precision given by ftolpl=%g \n", ftolpl);
1.202 brouard 6960: fprintf(ficrespl,"#Age ");
6961: for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);
6962: fprintf(ficrespl,"\n");
1.180 brouard 6963:
6964: /* prlim=matrix(1,nlstate,1,nlstate);*/ /* back in main */
6965:
6966: agebase=ageminpar;
6967: agelim=agemaxpar;
6968:
6969: i1=pow(2,cptcoveff);
6970: if (cptcovn < 1){i1=1;}
6971:
6972: for(cptcov=1,k=0;cptcov<=i1;cptcov++){
6973: /* for(cptcov=1,k=0;cptcov<=1;cptcov++){ */
6974: //for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
6975: k=k+1;
6976: /* to clean */
1.198 brouard 6977: //printf("cptcov=%d cptcod=%d codtab=%d\n",cptcov, cptcod,codtabm(cptcod,cptcov));
1.200 brouard 6978: fprintf(ficrespl,"#******");
6979: printf("#******");
6980: fprintf(ficlog,"#******");
1.180 brouard 6981: for(j=1;j<=cptcoveff;j++) {
1.198 brouard 6982: fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
6983: printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
6984: fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
1.180 brouard 6985: }
6986: fprintf(ficrespl,"******\n");
6987: printf("******\n");
6988: fprintf(ficlog,"******\n");
6989:
6990: fprintf(ficrespl,"#Age ");
6991: for(j=1;j<=cptcoveff;j++) {
1.200 brouard 6992: fprintf(ficrespl,"V%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
1.180 brouard 6993: }
1.203 brouard 6994: for(i=1; i<=nlstate;i++) fprintf(ficrespl," %d-%d ",i,i);
6995: fprintf(ficrespl,"Total Years_to_converge\n");
1.180 brouard 6996:
6997: for (age=agebase; age<=agelim; age++){
6998: /* for (age=agebase; age<=agebase; age++){ */
1.209 brouard 6999: prevalim(prlim, nlstate, p, age, oldm, savm, ftolpl, ncvyearp, k);
1.180 brouard 7000: fprintf(ficrespl,"%.0f ",age );
7001: for(j=1;j<=cptcoveff;j++)
1.198 brouard 7002: fprintf(ficrespl,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
1.203 brouard 7003: tot=0.;
7004: for(i=1; i<=nlstate;i++){
7005: tot += prlim[i][i];
1.180 brouard 7006: fprintf(ficrespl," %.5f", prlim[i][i]);
1.203 brouard 7007: }
1.209 brouard 7008: fprintf(ficrespl," %.3f %d\n", tot, *ncvyearp);
1.180 brouard 7009: } /* Age */
7010: /* was end of cptcod */
7011: } /* cptcov */
1.184 brouard 7012: return 0;
1.180 brouard 7013: }
7014:
7015: int hPijx(double *p, int bage, int fage){
7016: /*------------- h Pij x at various ages ------------*/
7017:
7018: int stepsize;
7019: int agelim;
7020: int hstepm;
7021: int nhstepm;
7022: int h, i, i1, j, k;
7023:
7024: double agedeb;
7025: double ***p3mat;
7026:
1.201 brouard 7027: strcpy(filerespij,"PIJ_"); strcat(filerespij,fileresu);
1.180 brouard 7028: if((ficrespij=fopen(filerespij,"w"))==NULL) {
7029: printf("Problem with Pij resultfile: %s\n", filerespij); return 1;
7030: fprintf(ficlog,"Problem with Pij resultfile: %s\n", filerespij); return 1;
7031: }
7032: printf("Computing pij: result on file '%s' \n", filerespij);
7033: fprintf(ficlog,"Computing pij: result on file '%s' \n", filerespij);
7034:
7035: stepsize=(int) (stepm+YEARM-1)/YEARM;
7036: /*if (stepm<=24) stepsize=2;*/
7037:
7038: agelim=AGESUP;
7039: hstepm=stepsize*YEARM; /* Every year of age */
7040: hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */
7041:
7042: /* hstepm=1; aff par mois*/
7043: pstamp(ficrespij);
7044: fprintf(ficrespij,"#****** h Pij x Probability to be in state j at age x+h being in i at x ");
7045: i1= pow(2,cptcoveff);
1.183 brouard 7046: /* for(cptcov=1,k=0;cptcov<=i1;cptcov++){ */
7047: /* /\*for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*\/ */
7048: /* k=k+1; */
7049: for (k=1; k <= (int) pow(2,cptcoveff); k++){
7050: fprintf(ficrespij,"\n#****** ");
7051: for(j=1;j<=cptcoveff;j++)
1.198 brouard 7052: fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
1.183 brouard 7053: fprintf(ficrespij,"******\n");
7054:
7055: for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */
7056: nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
7057: nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
7058:
7059: /* nhstepm=nhstepm*YEARM; aff par mois*/
1.180 brouard 7060:
1.183 brouard 7061: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
7062: oldm=oldms;savm=savms;
7063: hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
7064: fprintf(ficrespij,"# Cov Agex agex+h hpijx with i,j=");
7065: for(i=1; i<=nlstate;i++)
7066: for(j=1; j<=nlstate+ndeath;j++)
7067: fprintf(ficrespij," %1d-%1d",i,j);
7068: fprintf(ficrespij,"\n");
7069: for (h=0; h<=nhstepm; h++){
7070: /*agedebphstep = agedeb + h*hstepm/YEARM*stepm;*/
7071: fprintf(ficrespij,"%d %3.f %3.f",k, agedeb, agedeb + h*hstepm/YEARM*stepm );
1.180 brouard 7072: for(i=1; i<=nlstate;i++)
7073: for(j=1; j<=nlstate+ndeath;j++)
1.183 brouard 7074: fprintf(ficrespij," %.5f", p3mat[i][j][h]);
1.180 brouard 7075: fprintf(ficrespij,"\n");
7076: }
1.183 brouard 7077: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
7078: fprintf(ficrespij,"\n");
7079: }
1.180 brouard 7080: /*}*/
7081: }
1.184 brouard 7082: return 0;
1.180 brouard 7083: }
7084:
7085:
1.136 brouard 7086: /***********************************************/
7087: /**************** Main Program *****************/
7088: /***********************************************/
7089:
7090: int main(int argc, char *argv[])
7091: {
7092: #ifdef GSL
7093: const gsl_multimin_fminimizer_type *T;
7094: size_t iteri = 0, it;
7095: int rval = GSL_CONTINUE;
7096: int status = GSL_SUCCESS;
7097: double ssval;
7098: #endif
7099: int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav);
1.164 brouard 7100: int i,j, k, n=MAXN,iter=0,m,size=100, cptcod;
1.209 brouard 7101: int ncvyear=0; /* Number of years needed for the period prevalence to converge */
1.164 brouard 7102: int jj, ll, li, lj, lk;
1.136 brouard 7103: int numlinepar=0; /* Current linenumber of parameter file */
1.197 brouard 7104: int num_filled;
1.136 brouard 7105: int itimes;
7106: int NDIM=2;
7107: int vpopbased=0;
7108:
1.164 brouard 7109: char ca[32], cb[32];
1.136 brouard 7110: /* FILE *fichtm; *//* Html File */
7111: /* FILE *ficgp;*/ /*Gnuplot File */
7112: struct stat info;
1.191 brouard 7113: double agedeb=0.;
1.194 brouard 7114:
7115: double ageminpar=AGEOVERFLOW,agemin=AGEOVERFLOW, agemaxpar=-AGEOVERFLOW, agemax=-AGEOVERFLOW;
1.136 brouard 7116:
1.165 brouard 7117: double fret;
1.191 brouard 7118: double dum=0.; /* Dummy variable */
1.136 brouard 7119: double ***p3mat;
7120: double ***mobaverage;
1.164 brouard 7121:
7122: char line[MAXLINE];
1.197 brouard 7123: char path[MAXLINE],pathc[MAXLINE],pathcd[MAXLINE],pathtot[MAXLINE];
7124:
7125: char model[MAXLINE], modeltemp[MAXLINE];
1.136 brouard 7126: char pathr[MAXLINE], pathimach[MAXLINE];
1.164 brouard 7127: char *tok, *val; /* pathtot */
1.136 brouard 7128: int firstobs=1, lastobs=10;
1.195 brouard 7129: int c, h , cpt, c2;
1.191 brouard 7130: int jl=0;
7131: int i1, j1, jk, stepsize=0;
1.194 brouard 7132: int count=0;
7133:
1.164 brouard 7134: int *tab;
1.136 brouard 7135: int mobilavproj=0 , prevfcast=0 ; /* moving average of prev, If prevfcast=1 prevalence projection */
7136: int mobilav=0,popforecast=0;
1.191 brouard 7137: int hstepm=0, nhstepm=0;
1.136 brouard 7138: int agemortsup;
7139: float sumlpop=0.;
7140: double jprev1=1, mprev1=1,anprev1=2000,jprev2=1, mprev2=1,anprev2=2000;
7141: double jpyram=1, mpyram=1,anpyram=2000,jpyram1=1, mpyram1=1,anpyram1=2000;
7142:
1.191 brouard 7143: double bage=0, fage=110., age, agelim=0., agebase=0.;
1.136 brouard 7144: double ftolpl=FTOL;
7145: double **prlim;
7146: double ***param; /* Matrix of parameters */
7147: double *p;
7148: double **matcov; /* Matrix of covariance */
1.203 brouard 7149: double **hess; /* Hessian matrix */
1.136 brouard 7150: double ***delti3; /* Scale */
7151: double *delti; /* Scale */
7152: double ***eij, ***vareij;
7153: double **varpl; /* Variances of prevalence limits by age */
7154: double *epj, vepp;
1.164 brouard 7155:
1.136 brouard 7156: double dateprev1, dateprev2,jproj1=1,mproj1=1,anproj1=2000,jproj2=1,mproj2=1,anproj2=2000;
7157: double **ximort;
1.145 brouard 7158: char *alph[]={"a","a","b","c","d","e"}, str[4]="1234";
1.136 brouard 7159: int *dcwave;
7160:
1.164 brouard 7161: char z[1]="c";
1.136 brouard 7162:
7163: /*char *strt;*/
7164: char strtend[80];
1.126 brouard 7165:
1.164 brouard 7166:
1.126 brouard 7167: /* setlocale (LC_ALL, ""); */
7168: /* bindtextdomain (PACKAGE, LOCALEDIR); */
7169: /* textdomain (PACKAGE); */
7170: /* setlocale (LC_CTYPE, ""); */
7171: /* setlocale (LC_MESSAGES, ""); */
7172:
7173: /* gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */
1.157 brouard 7174: rstart_time = time(NULL);
7175: /* (void) gettimeofday(&start_time,&tzp);*/
7176: start_time = *localtime(&rstart_time);
1.126 brouard 7177: curr_time=start_time;
1.157 brouard 7178: /*tml = *localtime(&start_time.tm_sec);*/
7179: /* strcpy(strstart,asctime(&tml)); */
7180: strcpy(strstart,asctime(&start_time));
1.126 brouard 7181:
7182: /* printf("Localtime (at start)=%s",strstart); */
1.157 brouard 7183: /* tp.tm_sec = tp.tm_sec +86400; */
7184: /* tm = *localtime(&start_time.tm_sec); */
1.126 brouard 7185: /* tmg.tm_year=tmg.tm_year +dsign*dyear; */
7186: /* tmg.tm_mon=tmg.tm_mon +dsign*dmonth; */
7187: /* tmg.tm_hour=tmg.tm_hour + 1; */
1.157 brouard 7188: /* tp.tm_sec = mktime(&tmg); */
1.126 brouard 7189: /* strt=asctime(&tmg); */
7190: /* printf("Time(after) =%s",strstart); */
7191: /* (void) time (&time_value);
7192: * printf("time=%d,t-=%d\n",time_value,time_value-86400);
7193: * tm = *localtime(&time_value);
7194: * strstart=asctime(&tm);
7195: * printf("tim_value=%d,asctime=%s\n",time_value,strstart);
7196: */
7197:
7198: nberr=0; /* Number of errors and warnings */
7199: nbwarn=0;
1.184 brouard 7200: #ifdef WIN32
7201: _getcwd(pathcd, size);
7202: #else
1.126 brouard 7203: getcwd(pathcd, size);
1.184 brouard 7204: #endif
1.191 brouard 7205: syscompilerinfo(0);
1.196 brouard 7206: printf("\nIMaCh version %s, %s\n%s",version, copyright, fullversion);
1.126 brouard 7207: if(argc <=1){
7208: printf("\nEnter the parameter file name: ");
1.205 brouard 7209: if(!fgets(pathr,FILENAMELENGTH,stdin)){
7210: printf("ERROR Empty parameter file name\n");
7211: goto end;
7212: }
1.126 brouard 7213: i=strlen(pathr);
7214: if(pathr[i-1]=='\n')
7215: pathr[i-1]='\0';
1.156 brouard 7216: i=strlen(pathr);
1.205 brouard 7217: if(i >= 1 && pathr[i-1]==' ') {/* This may happen when dragging on oS/X! */
1.156 brouard 7218: pathr[i-1]='\0';
1.205 brouard 7219: }
7220: i=strlen(pathr);
7221: if( i==0 ){
7222: printf("ERROR Empty parameter file name\n");
7223: goto end;
7224: }
7225: for (tok = pathr; tok != NULL; ){
1.126 brouard 7226: printf("Pathr |%s|\n",pathr);
7227: while ((val = strsep(&tok, "\"" )) != NULL && *val == '\0');
7228: printf("val= |%s| pathr=%s\n",val,pathr);
7229: strcpy (pathtot, val);
7230: if(pathr[0] == '\0') break; /* Dirty */
7231: }
7232: }
7233: else{
7234: strcpy(pathtot,argv[1]);
7235: }
7236: /*if(getcwd(pathcd, MAXLINE)!= NULL)printf ("Error pathcd\n");*/
7237: /*cygwin_split_path(pathtot,path,optionfile);
7238: printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/
7239: /* cutv(path,optionfile,pathtot,'\\');*/
7240:
7241: /* Split argv[0], imach program to get pathimach */
7242: printf("\nargv[0]=%s argv[1]=%s, \n",argv[0],argv[1]);
7243: split(argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
7244: printf("\nargv[0]=%s pathimach=%s, \noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
7245: /* strcpy(pathimach,argv[0]); */
7246: /* Split argv[1]=pathtot, parameter file name to get path, optionfile, extension and name */
7247: split(pathtot,path,optionfile,optionfilext,optionfilefiname);
7248: printf("\npathtot=%s,\npath=%s,\noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
1.184 brouard 7249: #ifdef WIN32
7250: _chdir(path); /* Can be a relative path */
7251: if(_getcwd(pathcd,MAXLINE) > 0) /* So pathcd is the full path */
7252: #else
1.126 brouard 7253: chdir(path); /* Can be a relative path */
1.184 brouard 7254: if (getcwd(pathcd, MAXLINE) > 0) /* So pathcd is the full path */
7255: #endif
7256: printf("Current directory %s!\n",pathcd);
1.126 brouard 7257: strcpy(command,"mkdir ");
7258: strcat(command,optionfilefiname);
7259: if((outcmd=system(command)) != 0){
1.169 brouard 7260: printf("Directory already exists (or can't create it) %s%s, err=%d\n",path,optionfilefiname,outcmd);
1.126 brouard 7261: /* fprintf(ficlog,"Problem creating directory %s%s\n",path,optionfilefiname); */
7262: /* fclose(ficlog); */
7263: /* exit(1); */
7264: }
7265: /* if((imk=mkdir(optionfilefiname))<0){ */
7266: /* perror("mkdir"); */
7267: /* } */
7268:
7269: /*-------- arguments in the command line --------*/
7270:
1.186 brouard 7271: /* Main Log file */
1.126 brouard 7272: strcat(filelog, optionfilefiname);
7273: strcat(filelog,".log"); /* */
7274: if((ficlog=fopen(filelog,"w"))==NULL) {
7275: printf("Problem with logfile %s\n",filelog);
7276: goto end;
7277: }
7278: fprintf(ficlog,"Log filename:%s\n",filelog);
1.197 brouard 7279: fprintf(ficlog,"Version %s %s",version,fullversion);
1.126 brouard 7280: fprintf(ficlog,"\nEnter the parameter file name: \n");
7281: fprintf(ficlog,"pathimach=%s\npathtot=%s\n\
7282: path=%s \n\
7283: optionfile=%s\n\
7284: optionfilext=%s\n\
1.156 brouard 7285: optionfilefiname='%s'\n",pathimach,pathtot,path,optionfile,optionfilext,optionfilefiname);
1.126 brouard 7286:
1.197 brouard 7287: syscompilerinfo(1);
1.167 brouard 7288:
1.126 brouard 7289: printf("Local time (at start):%s",strstart);
7290: fprintf(ficlog,"Local time (at start): %s",strstart);
7291: fflush(ficlog);
7292: /* (void) gettimeofday(&curr_time,&tzp); */
1.157 brouard 7293: /* printf("Elapsed time %d\n", asc_diff_time(curr_time.tm_sec-start_time.tm_sec,tmpout)); */
1.126 brouard 7294:
7295: /* */
7296: strcpy(fileres,"r");
7297: strcat(fileres, optionfilefiname);
1.201 brouard 7298: strcat(fileresu, optionfilefiname); /* Without r in front */
1.126 brouard 7299: strcat(fileres,".txt"); /* Other files have txt extension */
1.201 brouard 7300: strcat(fileresu,".txt"); /* Other files have txt extension */
1.126 brouard 7301:
1.186 brouard 7302: /* Main ---------arguments file --------*/
1.126 brouard 7303:
7304: if((ficpar=fopen(optionfile,"r"))==NULL) {
1.155 brouard 7305: printf("Problem with optionfile '%s' with errno='%s'\n",optionfile,strerror(errno));
7306: fprintf(ficlog,"Problem with optionfile '%s' with errno='%s'\n",optionfile,strerror(errno));
1.126 brouard 7307: fflush(ficlog);
1.149 brouard 7308: /* goto end; */
7309: exit(70);
1.126 brouard 7310: }
7311:
7312:
7313:
7314: strcpy(filereso,"o");
1.201 brouard 7315: strcat(filereso,fileresu);
1.126 brouard 7316: if((ficparo=fopen(filereso,"w"))==NULL) { /* opened on subdirectory */
7317: printf("Problem with Output resultfile: %s\n", filereso);
7318: fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso);
7319: fflush(ficlog);
7320: goto end;
7321: }
7322:
7323: /* Reads comments: lines beginning with '#' */
7324: numlinepar=0;
1.197 brouard 7325:
7326: /* First parameter line */
7327: while(fgets(line, MAXLINE, ficpar)) {
7328: /* If line starts with a # it is a comment */
7329: if (line[0] == '#') {
7330: numlinepar++;
7331: fputs(line,stdout);
7332: fputs(line,ficparo);
7333: fputs(line,ficlog);
7334: continue;
7335: }else
7336: break;
7337: }
7338: if((num_filled=sscanf(line,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\n", \
7339: title, datafile, &lastobs, &firstpass,&lastpass)) !=EOF){
7340: if (num_filled != 5) {
7341: printf("Should be 5 parameters\n");
7342: }
1.126 brouard 7343: numlinepar++;
1.197 brouard 7344: printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\n", title, datafile, lastobs, firstpass,lastpass);
7345: }
7346: /* Second parameter line */
7347: while(fgets(line, MAXLINE, ficpar)) {
7348: /* If line starts with a # it is a comment */
7349: if (line[0] == '#') {
7350: numlinepar++;
7351: fputs(line,stdout);
7352: fputs(line,ficparo);
7353: fputs(line,ficlog);
7354: continue;
7355: }else
7356: break;
7357: }
7358: if((num_filled=sscanf(line,"ftol=%lf stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\n", \
7359: &ftol, &stepm, &ncovcol, &nlstate, &ndeath, &maxwav, &mle, &weightopt)) !=EOF){
7360: if (num_filled != 8) {
1.209 brouard 7361: printf("Not 8 parameters, for example:ftol=1.e-8 stepm=12 ncovcol=2 nlstate=2 ndeath=1 maxwav=3 mle=1 weight=1\n");
7362: printf("but line=%s\n",line);
1.197 brouard 7363: }
7364: printf("ftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\n",ftol, stepm, ncovcol, nlstate,ndeath, maxwav, mle, weightopt);
1.126 brouard 7365: }
1.203 brouard 7366: /* ftolpl=6*ftol*1.e5; /\* 6.e-3 make convergences in less than 80 loops for the prevalence limit *\/ */
1.209 brouard 7367: /*ftolpl=6.e-4; *//* 6.e-3 make convergences in less than 80 loops for the prevalence limit */
1.197 brouard 7368: /* Third parameter line */
7369: while(fgets(line, MAXLINE, ficpar)) {
7370: /* If line starts with a # it is a comment */
7371: if (line[0] == '#') {
7372: numlinepar++;
7373: fputs(line,stdout);
7374: fputs(line,ficparo);
7375: fputs(line,ficlog);
7376: continue;
7377: }else
7378: break;
7379: }
1.201 brouard 7380: if((num_filled=sscanf(line,"model=1+age%[^.\n]", model)) !=EOF){
7381: if (num_filled == 0)
7382: model[0]='\0';
7383: else if (num_filled != 1){
1.197 brouard 7384: printf("ERROR %d: Model should be at minimum 'model=1+age.' %s\n",num_filled, line);
7385: fprintf(ficlog,"ERROR %d: Model should be at minimum 'model=1+age.' %s\n",num_filled, line);
7386: model[0]='\0';
7387: goto end;
7388: }
7389: else{
7390: if (model[0]=='+'){
7391: for(i=1; i<=strlen(model);i++)
7392: modeltemp[i-1]=model[i];
1.201 brouard 7393: strcpy(model,modeltemp);
1.197 brouard 7394: }
7395: }
1.199 brouard 7396: /* printf(" model=1+age%s modeltemp= %s, model=%s\n",model, modeltemp, model);fflush(stdout); */
1.203 brouard 7397: printf("model=1+age+%s\n",model);fflush(stdout);
1.197 brouard 7398: }
7399: /* 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); */
7400: /* numlinepar=numlinepar+3; /\* In general *\/ */
7401: /* printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=1+age+%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate,ndeath, maxwav, mle, weightopt,model); */
1.203 brouard 7402: fprintf(ficparo,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=1+age+%s.\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol,nlstate,ndeath,maxwav, mle, weightopt,model);
7403: fprintf(ficlog,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=1+age+%s.\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol,nlstate,ndeath,maxwav, mle, weightopt,model);
1.126 brouard 7404: fflush(ficlog);
1.190 brouard 7405: /* if(model[0]=='#'|| model[0]== '\0'){ */
7406: if(model[0]=='#'){
1.187 brouard 7407: printf("Error in 'model' line: model should start with 'model=1+age+' and end with '.' \n \
7408: 'model=1+age+.' or 'model=1+age+V1.' or 'model=1+age+age*age+V1+V1*age.' or \n \
7409: 'model=1+age+V1+V2.' or 'model=1+age+V1+V2+V1*V2.' etc. \n"); \
7410: if(mle != -1){
7411: printf("Fix the model line and run imach with mle=-1 to get a correct template of the parameter file.\n");
7412: exit(1);
7413: }
7414: }
1.126 brouard 7415: while((c=getc(ficpar))=='#' && c!= EOF){
7416: ungetc(c,ficpar);
7417: fgets(line, MAXLINE, ficpar);
7418: numlinepar++;
1.195 brouard 7419: if(line[1]=='q'){ /* This #q will quit imach (the answer is q) */
7420: z[0]=line[1];
7421: }
7422: /* printf("****line [1] = %c \n",line[1]); */
1.141 brouard 7423: fputs(line, stdout);
7424: //puts(line);
1.126 brouard 7425: fputs(line,ficparo);
7426: fputs(line,ficlog);
7427: }
7428: ungetc(c,ficpar);
7429:
7430:
1.145 brouard 7431: covar=matrix(0,NCOVMAX,1,n); /**< used in readdata */
1.136 brouard 7432: cptcovn=0; /*Number of covariates, i.e. number of '+' in model statement plus one, indepently of n in Vn*/
7433: /* v1+v2+v3+v2*v4+v5*age makes cptcovn = 5
7434: v1+v2*age+v2*v3 makes cptcovn = 3
7435: */
7436: if (strlen(model)>1)
1.187 brouard 7437: 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 7438: else
1.187 brouard 7439: ncovmodel=2; /* Constant and age */
1.133 brouard 7440: nforce= (nlstate+ndeath-1)*nlstate; /* Number of forces ij from state i to j */
7441: npar= nforce*ncovmodel; /* Number of parameters like aij*/
1.131 brouard 7442: if(npar >MAXPARM || nlstate >NLSTATEMAX || ndeath >NDEATHMAX || ncovmodel>NCOVMAX){
7443: 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);
7444: 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);
7445: fflush(stdout);
7446: fclose (ficlog);
7447: goto end;
7448: }
1.126 brouard 7449: delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
7450: delti=delti3[1][1];
7451: /*delti=vector(1,npar); *//* Scale of each paramater (output from hesscov)*/
7452: if(mle==-1){ /* Print a wizard for help writing covariance matrix */
7453: prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
1.191 brouard 7454: printf(" You chose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
7455: fprintf(ficlog," You chose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
1.126 brouard 7456: free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
7457: fclose (ficparo);
7458: fclose (ficlog);
7459: goto end;
7460: exit(0);
7461: }
1.186 brouard 7462: else if(mle==-3) { /* Main Wizard */
1.126 brouard 7463: prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
1.192 brouard 7464: printf(" You chose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
7465: fprintf(ficlog," You chose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
1.126 brouard 7466: param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
7467: matcov=matrix(1,npar,1,npar);
1.203 brouard 7468: hess=matrix(1,npar,1,npar);
1.126 brouard 7469: }
7470: else{
1.145 brouard 7471: /* Read guessed parameters */
1.126 brouard 7472: /* Reads comments: lines beginning with '#' */
7473: while((c=getc(ficpar))=='#' && c!= EOF){
7474: ungetc(c,ficpar);
7475: fgets(line, MAXLINE, ficpar);
7476: numlinepar++;
1.141 brouard 7477: fputs(line,stdout);
1.126 brouard 7478: fputs(line,ficparo);
7479: fputs(line,ficlog);
7480: }
7481: ungetc(c,ficpar);
7482:
7483: param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
7484: for(i=1; i <=nlstate; i++){
7485: j=0;
7486: for(jj=1; jj <=nlstate+ndeath; jj++){
7487: if(jj==i) continue;
7488: j++;
7489: fscanf(ficpar,"%1d%1d",&i1,&j1);
1.193 brouard 7490: if ((i1 != i) || (j1 != jj)){
1.126 brouard 7491: printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n \
7492: It might be a problem of design; if ncovcol and the model are correct\n \
7493: run imach with mle=-1 to get a correct template of the parameter file.\n",numlinepar, i,j, i1, j1);
7494: exit(1);
7495: }
7496: fprintf(ficparo,"%1d%1d",i1,j1);
7497: if(mle==1)
1.193 brouard 7498: printf("%1d%1d",i,jj);
7499: fprintf(ficlog,"%1d%1d",i,jj);
1.126 brouard 7500: for(k=1; k<=ncovmodel;k++){
7501: fscanf(ficpar," %lf",¶m[i][j][k]);
7502: if(mle==1){
7503: printf(" %lf",param[i][j][k]);
7504: fprintf(ficlog," %lf",param[i][j][k]);
7505: }
7506: else
7507: fprintf(ficlog," %lf",param[i][j][k]);
7508: fprintf(ficparo," %lf",param[i][j][k]);
7509: }
7510: fscanf(ficpar,"\n");
7511: numlinepar++;
7512: if(mle==1)
7513: printf("\n");
7514: fprintf(ficlog,"\n");
7515: fprintf(ficparo,"\n");
7516: }
7517: }
7518: fflush(ficlog);
7519:
1.145 brouard 7520: /* Reads scales values */
1.126 brouard 7521: p=param[1][1];
7522:
7523: /* Reads comments: lines beginning with '#' */
7524: while((c=getc(ficpar))=='#' && c!= EOF){
7525: ungetc(c,ficpar);
7526: fgets(line, MAXLINE, ficpar);
7527: numlinepar++;
1.141 brouard 7528: fputs(line,stdout);
1.126 brouard 7529: fputs(line,ficparo);
7530: fputs(line,ficlog);
7531: }
7532: ungetc(c,ficpar);
7533:
7534: for(i=1; i <=nlstate; i++){
7535: for(j=1; j <=nlstate+ndeath-1; j++){
7536: fscanf(ficpar,"%1d%1d",&i1,&j1);
1.164 brouard 7537: if ( (i1-i) * (j1-j) != 0){
1.126 brouard 7538: printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n",numlinepar, i,j, i1, j1);
7539: exit(1);
7540: }
7541: printf("%1d%1d",i,j);
7542: fprintf(ficparo,"%1d%1d",i1,j1);
7543: fprintf(ficlog,"%1d%1d",i1,j1);
7544: for(k=1; k<=ncovmodel;k++){
7545: fscanf(ficpar,"%le",&delti3[i][j][k]);
7546: printf(" %le",delti3[i][j][k]);
7547: fprintf(ficparo," %le",delti3[i][j][k]);
7548: fprintf(ficlog," %le",delti3[i][j][k]);
7549: }
7550: fscanf(ficpar,"\n");
7551: numlinepar++;
7552: printf("\n");
7553: fprintf(ficparo,"\n");
7554: fprintf(ficlog,"\n");
7555: }
7556: }
7557: fflush(ficlog);
7558:
1.145 brouard 7559: /* Reads covariance matrix */
1.126 brouard 7560: delti=delti3[1][1];
7561:
7562:
7563: /* free_ma3x(delti3,1,nlstate,1,nlstate+ndeath-1,1,ncovmodel); */ /* Hasn't to to freed here otherwise delti is no more allocated */
7564:
7565: /* Reads comments: lines beginning with '#' */
7566: while((c=getc(ficpar))=='#' && c!= EOF){
7567: ungetc(c,ficpar);
7568: fgets(line, MAXLINE, ficpar);
7569: numlinepar++;
1.141 brouard 7570: fputs(line,stdout);
1.126 brouard 7571: fputs(line,ficparo);
7572: fputs(line,ficlog);
7573: }
7574: ungetc(c,ficpar);
7575:
7576: matcov=matrix(1,npar,1,npar);
1.203 brouard 7577: hess=matrix(1,npar,1,npar);
1.131 brouard 7578: for(i=1; i <=npar; i++)
7579: for(j=1; j <=npar; j++) matcov[i][j]=0.;
7580:
1.194 brouard 7581: /* Scans npar lines */
1.126 brouard 7582: for(i=1; i <=npar; i++){
1.194 brouard 7583: count=fscanf(ficpar,"%1d%1d%1d",&i1,&j1,&jk);
7584: if(count != 3){
7585: printf("Error! Error in parameter file %s at line %d after line starting with %1d%1d%1d\n\
7586: This is probably because your covariance matrix doesn't \n contain exactly %d lines corresponding to your model line '1+age+%s'.\n\
7587: Please run with mle=-1 to get a correct covariance matrix.\n",optionfile,numlinepar, i1,j1,jk, npar, model);
7588: fprintf(ficlog,"Error! Error in parameter file %s at line %d after line starting with %1d%1d%1d\n\
7589: This is probably because your covariance matrix doesn't \n contain exactly %d lines corresponding to your model line '1+age+%s'.\n\
7590: Please run with mle=-1 to get a correct covariance matrix.\n",optionfile,numlinepar, i1,j1,jk, npar, model);
7591: exit(1);
7592: }else
1.126 brouard 7593: if(mle==1)
1.194 brouard 7594: printf("%1d%1d%1d",i1,j1,jk);
7595: fprintf(ficlog,"%1d%1d%1d",i1,j1,jk);
7596: fprintf(ficparo,"%1d%1d%1d",i1,j1,jk);
1.126 brouard 7597: for(j=1; j <=i; j++){
7598: fscanf(ficpar," %le",&matcov[i][j]);
7599: if(mle==1){
7600: printf(" %.5le",matcov[i][j]);
7601: }
7602: fprintf(ficlog," %.5le",matcov[i][j]);
7603: fprintf(ficparo," %.5le",matcov[i][j]);
7604: }
7605: fscanf(ficpar,"\n");
7606: numlinepar++;
7607: if(mle==1)
7608: printf("\n");
7609: fprintf(ficlog,"\n");
7610: fprintf(ficparo,"\n");
7611: }
1.194 brouard 7612: /* End of read covariance matrix npar lines */
1.126 brouard 7613: for(i=1; i <=npar; i++)
7614: for(j=i+1;j<=npar;j++)
7615: matcov[i][j]=matcov[j][i];
7616:
7617: if(mle==1)
7618: printf("\n");
7619: fprintf(ficlog,"\n");
7620:
7621: fflush(ficlog);
7622:
7623: /*-------- Rewriting parameter file ----------*/
7624: strcpy(rfileres,"r"); /* "Rparameterfile */
7625: strcat(rfileres,optionfilefiname); /* Parameter file first name*/
7626: strcat(rfileres,"."); /* */
7627: strcat(rfileres,optionfilext); /* Other files have txt extension */
7628: if((ficres =fopen(rfileres,"w"))==NULL) {
1.201 brouard 7629: printf("Problem writing new parameter file: %s\n", rfileres);goto end;
7630: fprintf(ficlog,"Problem writing new parameter file: %s\n", rfileres);goto end;
1.126 brouard 7631: }
7632: fprintf(ficres,"#%s\n",version);
7633: } /* End of mle != -3 */
7634:
1.186 brouard 7635: /* Main data
7636: */
1.126 brouard 7637: n= lastobs;
7638: num=lvector(1,n);
7639: moisnais=vector(1,n);
7640: annais=vector(1,n);
7641: moisdc=vector(1,n);
7642: andc=vector(1,n);
7643: agedc=vector(1,n);
7644: cod=ivector(1,n);
7645: weight=vector(1,n);
7646: for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */
7647: mint=matrix(1,maxwav,1,n);
7648: anint=matrix(1,maxwav,1,n);
1.131 brouard 7649: s=imatrix(1,maxwav+1,1,n); /* s[i][j] health state for wave i and individual j */
1.126 brouard 7650: tab=ivector(1,NCOVMAX);
1.144 brouard 7651: ncodemax=ivector(1,NCOVMAX); /* Number of code per covariate; if O and 1 only, 2**ncov; V1+V2+V3+V4=>16 */
1.192 brouard 7652: 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 7653:
1.136 brouard 7654: /* Reads data from file datafile */
7655: if (readdata(datafile, firstobs, lastobs, &imx)==1)
7656: goto end;
7657:
7658: /* Calculation of the number of parameters from char model */
1.137 brouard 7659: /* modelsav=V2+V1+V4+age*V3 strb=age*V3 stra=V2+V1+V4
7660: k=4 (age*V3) Tvar[k=4]= 3 (from V3) Tag[cptcovage=1]=4
7661: k=3 V4 Tvar[k=3]= 4 (from V4)
7662: k=2 V1 Tvar[k=2]= 1 (from V1)
7663: k=1 Tvar[1]=2 (from V2)
7664: */
7665: Tvar=ivector(1,NCOVMAX); /* Was 15 changed to NCOVMAX. */
7666: /* V2+V1+V4+age*V3 is a model with 4 covariates (3 plus signs).
7667: For each model-covariate stores the data-covariate id. Tvar[1]=2, Tvar[2]=1, Tvar[3]=4,
7668: Tvar[4=age*V3] is 3 and 'age' is recorded in Tage.
7669: */
7670: /* For model-covariate k tells which data-covariate to use but
7671: because this model-covariate is a construction we invent a new column
7672: ncovcol + k1
7673: If already ncovcol=4 and model=V2+V1+V1*V4+age*V3
7674: Tvar[3=V1*V4]=4+1 etc */
1.145 brouard 7675: Tprod=ivector(1,NCOVMAX); /* Gives the position of a product */
1.137 brouard 7676: /* Tprod[k1=1]=3(=V1*V4) for V2+V1+V1*V4+age*V3
7677: if V2+V1+V1*V4+age*V3+V3*V2 TProd[k1=2]=5 (V3*V2)
7678: */
1.145 brouard 7679: Tvaraff=ivector(1,NCOVMAX); /* Unclear */
7680: 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 7681: * For V3*V2 (in V2+V1+V1*V4+age*V3+V3*V2), V3*V2 position is 2nd.
7682: * Tvard[k1=2][1]=3 (V3) Tvard[k1=2][2]=2(V2) */
1.145 brouard 7683: Tage=ivector(1,NCOVMAX); /* Gives the covariate id of covariates associated with age: V2 + V1 + age*V4 + V3*age
1.137 brouard 7684: 4 covariates (3 plus signs)
7685: Tage[1=V3*age]= 4; Tage[2=age*V4] = 3
7686: */
1.136 brouard 7687:
1.186 brouard 7688: /* Main decodemodel */
7689:
1.187 brouard 7690:
1.136 brouard 7691: if(decodemodel(model, lastobs) == 1)
7692: goto end;
7693:
1.137 brouard 7694: if((double)(lastobs-imx)/(double)imx > 1.10){
7695: nbwarn++;
7696: 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);
7697: 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);
7698: }
1.136 brouard 7699: /* if(mle==1){*/
1.137 brouard 7700: if (weightopt != 1) { /* Maximisation without weights. We can have weights different from 1 but want no weight*/
7701: for(i=1;i<=imx;i++) weight[i]=1.0; /* changed to imx */
1.136 brouard 7702: }
7703:
7704: /*-calculation of age at interview from date of interview and age at death -*/
7705: agev=matrix(1,maxwav,1,imx);
7706:
7707: if(calandcheckages(imx, maxwav, &agemin, &agemax, &nberr, &nbwarn) == 1)
7708: goto end;
7709:
1.126 brouard 7710:
1.136 brouard 7711: agegomp=(int)agemin;
7712: free_vector(moisnais,1,n);
7713: free_vector(annais,1,n);
1.126 brouard 7714: /* free_matrix(mint,1,maxwav,1,n);
7715: free_matrix(anint,1,maxwav,1,n);*/
1.215 brouard 7716: /* free_vector(moisdc,1,n); */
7717: /* free_vector(andc,1,n); */
1.145 brouard 7718: /* */
7719:
1.126 brouard 7720: wav=ivector(1,imx);
1.214 brouard 7721: /* dh=imatrix(1,lastpass-firstpass+1,1,imx); */
7722: /* bh=imatrix(1,lastpass-firstpass+1,1,imx); */
7723: /* mw=imatrix(1,lastpass-firstpass+1,1,imx); */
7724: 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.*/
7725: bh=imatrix(1,lastpass-firstpass+2,1,imx);
7726: mw=imatrix(1,lastpass-firstpass+2,1,imx);
1.126 brouard 7727:
7728: /* Concatenates waves */
1.214 brouard 7729: /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
7730: Death is a valid wave (if date is known).
7731: mw[mi][i] is the number of (mi=1 to wav[i]) effective wave out of mi of individual i
7732: dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
7733: and mw[mi+1][i]. dh depends on stepm.
7734: */
7735:
1.126 brouard 7736: concatwav(wav, dh, bh, mw, s, agedc, agev, firstpass, lastpass, imx, nlstate, stepm);
1.145 brouard 7737: /* */
7738:
1.215 brouard 7739: free_vector(moisdc,1,n);
7740: free_vector(andc,1,n);
7741:
1.126 brouard 7742: /* Routine tricode is to calculate cptcoveff (real number of unique covariates) and to associate covariable number and modality */
7743:
7744: nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);
7745: ncodemax[1]=1;
1.145 brouard 7746: Ndum =ivector(-1,NCOVMAX);
1.187 brouard 7747: if (ncovmodel-nagesqr > 2 ) /* That is if covariate other than cst, age and age*age */
1.145 brouard 7748: tricode(Tvar,nbcode,imx, Ndum); /**< Fills nbcode[Tvar[j]][l]; */
1.211 brouard 7749: /* Nbcode gives the value of the lth modality (currently 1 to 2) of jth covariate, in
1.186 brouard 7750: V2+V1*age, there are 3 covariates Tvar[2]=1 (V1).*/
1.211 brouard 7751: /* 1 to ncodemax[j] which is the maximum value of this jth covariate */
1.145 brouard 7752:
1.200 brouard 7753: /* codtab=imatrix(1,100,1,10);*/ /* codtab[h,k]=( (h-1) - mod(k-1,2**(k-1) )/2**(k-1) */
1.198 brouard 7754: /*printf(" codtab[1,1],codtab[100,10]=%d,%d\n", codtab[1][1],codtabm(100,10));*/
1.186 brouard 7755: /* codtab gives the value 1 or 2 of the hth combination of k covariates (1 or 2).*/
1.211 brouard 7756: /* nbcode[Tvaraff[j]][codtabm(h,j)]) : if there are only 2 modalities for a covariate j,
7757: * codtabm(h,j) gives its value classified at position h and nbcode gives how it is coded
7758: * (currently 0 or 1) in the data.
7759: * In a loop on h=1 to 2**k, and a loop on j (=1 to k), we get the value of
7760: * corresponding modality (h,j).
7761: */
7762:
1.145 brouard 7763: h=0;
7764:
7765:
7766: /*if (cptcovn > 0) */
1.126 brouard 7767:
1.145 brouard 7768:
1.126 brouard 7769: m=pow(2,cptcoveff);
7770:
1.144 brouard 7771: /**< codtab(h,k) k = codtab[h,k]=( (h-1) - mod(k-1,2**(k-1) )/2**(k-1) + 1
1.211 brouard 7772: * For k=4 covariates, h goes from 1 to m=2**k
7773: * codtabm(h,k)= (1 & (h-1) >> (k-1)) + 1;
7774: * #define codtabm(h,k) (1 & (h-1) >> (k-1))+1
1.186 brouard 7775: * h\k 1 2 3 4
1.143 brouard 7776: *______________________________
7777: * 1 i=1 1 i=1 1 i=1 1 i=1 1
7778: * 2 2 1 1 1
7779: * 3 i=2 1 2 1 1
7780: * 4 2 2 1 1
7781: * 5 i=3 1 i=2 1 2 1
7782: * 6 2 1 2 1
7783: * 7 i=4 1 2 2 1
7784: * 8 2 2 2 1
1.197 brouard 7785: * 9 i=5 1 i=3 1 i=2 1 2
7786: * 10 2 1 1 2
7787: * 11 i=6 1 2 1 2
7788: * 12 2 2 1 2
7789: * 13 i=7 1 i=4 1 2 2
7790: * 14 2 1 2 2
7791: * 15 i=8 1 2 2 2
7792: * 16 2 2 2 2
1.143 brouard 7793: */
1.212 brouard 7794: /* How to do the opposite? From combination h (=1 to 2**k) how to get the value on the covariates? */
1.211 brouard 7795: /* from h=5 and m, we get then number of covariates k=log(m)/log(2)=4
7796: * and the value of each covariate?
7797: * V1=1, V2=1, V3=2, V4=1 ?
7798: * h-1=4 and 4 is 0100 or reverse 0010, and +1 is 1121 ok.
7799: * h=6, 6-1=5, 5 is 0101, 1010, 2121, V1=2nd, V2=1st, V3=2nd, V4=1st.
7800: * In order to get the real value in the data, we use nbcode
7801: * nbcode[Tvar[3][2nd]]=1 and nbcode[Tvar[4][1]]=0
7802: * We are keeping this crazy system in order to be able (in the future?)
7803: * to have more than 2 values (0 or 1) for a covariate.
7804: * #define codtabm(h,k) (1 & (h-1) >> (k-1))+1
7805: * h=6, k=2? h-1=5=0101, reverse 1010, +1=2121, k=2nd position: value is 1: codtabm(6,2)=1
7806: * bbbbbbbb
7807: * 76543210
7808: * h-1 00000101 (6-1=5)
7809: *(h-1)>>(k-1)= 00000001 >> (2-1) = 1 right shift
7810: * &
7811: * 1 00000001 (1)
7812: * 00000001 = 1 & ((h-1) >> (k-1))
7813: * +1= 00000010 =2
7814: *
7815: * h=14, k=3 => h'=h-1=13, k'=k-1=2
7816: * h' 1101 =2^3+2^2+0x2^1+2^0
7817: * >>k' 11
7818: * & 00000001
7819: * = 00000001
7820: * +1 = 00000010=2 = codtabm(14,3)
7821: * Reverse h=6 and m=16?
7822: * cptcoveff=log(16)/log(2)=4 covariate: 6-1=5=0101 reversed=1010 +1=2121 =>V1=2, V2=1, V3=2, V4=1.
7823: * for (j=1 to cptcoveff) Vj=decodtabm(j,h,cptcoveff)
7824: * decodtabm(h,j,cptcoveff)= (((h-1) >> (j-1)) & 1) +1
7825: * decodtabm(h,j,cptcoveff)= (h <= (1<<cptcoveff)?(((h-1) >> (j-1)) & 1) +1 : -1)
7826: * V3=decodtabm(14,3,2**4)=2
7827: * h'=13 1101 =2^3+2^2+0x2^1+2^0
7828: *(h-1) >> (j-1) 0011 =13 >> 2
7829: * &1 000000001
7830: * = 000000001
7831: * +1= 000000010 =2
7832: * 2211
7833: * V1=1+1, V2=0+1, V3=1+1, V4=1+1
7834: * V3=2
7835: */
7836:
1.202 brouard 7837: /* /\* for(h=1; h <=100 ;h++){ *\/ */
7838: /* /\* printf("h=%2d ", h); *\/ */
7839: /* /\* for(k=1; k <=10; k++){ *\/ */
7840: /* /\* printf("k=%d %d ",k,codtabm(h,k)); *\/ */
7841: /* /\* codtab[h][k]=codtabm(h,k); *\/ */
7842: /* /\* } *\/ */
7843: /* /\* printf("\n"); *\/ */
7844: /* } */
1.197 brouard 7845: /* for(k=1;k<=cptcoveff; k++){ /\* scans any effective covariate *\/ */
7846: /* for(i=1; i <=pow(2,cptcoveff-k);i++){ /\* i=1 to 8/1=8; i=1 to 8/2=4; i=1 to 8/8=1 *\/ */
7847: /* for(j=1; j <= ncodemax[k]; j++){ /\* For each modality of this covariate ncodemax=2*\/ */
7848: /* for(cpt=1; cpt <=pow(2,k-1); cpt++){ /\* cpt=1 to 8/2**(3+1-1 or 3+1-3) =1 or 4 *\/ */
7849: /* h++; */
7850: /* if (h>m) */
7851: /* h=1; */
7852: /* codtab[h][k]=j; */
7853: /* /\* codtab[12][3]=1; *\/ */
7854: /* /\*codtab[h][Tvar[k]]=j;*\/ */
7855: /* /\* printf("h=%d k=%d j=%d codtab[h][k]=%d Tvar[k]=%d codtab[h][Tvar[k]]=%d \n",h, k,j,codtab[h][k],Tvar[k],codtab[h][Tvar[k]]); *\/ */
7856: /* } */
7857: /* } */
7858: /* } */
7859: /* } */
1.126 brouard 7860: /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]);
7861: codtab[1][2]=1;codtab[2][2]=2; */
1.197 brouard 7862: /* for(i=1; i <=m ;i++){ */
7863: /* for(k=1; k <=cptcovn; k++){ */
7864: /* printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff); */
7865: /* } */
7866: /* printf("\n"); */
7867: /* } */
7868: /* scanf("%d",i);*/
1.145 brouard 7869:
7870: free_ivector(Ndum,-1,NCOVMAX);
7871:
7872:
1.126 brouard 7873:
1.186 brouard 7874: /* Initialisation of ----------- gnuplot -------------*/
1.126 brouard 7875: strcpy(optionfilegnuplot,optionfilefiname);
7876: if(mle==-3)
1.201 brouard 7877: strcat(optionfilegnuplot,"-MORT_");
1.126 brouard 7878: strcat(optionfilegnuplot,".gp");
7879:
7880: if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {
7881: printf("Problem with file %s",optionfilegnuplot);
7882: }
7883: else{
1.204 brouard 7884: fprintf(ficgp,"\n# IMaCh-%s\n", version);
1.126 brouard 7885: fprintf(ficgp,"# %s\n", optionfilegnuplot);
1.141 brouard 7886: //fprintf(ficgp,"set missing 'NaNq'\n");
7887: fprintf(ficgp,"set datafile missing 'NaNq'\n");
1.126 brouard 7888: }
7889: /* fclose(ficgp);*/
1.186 brouard 7890:
7891:
7892: /* Initialisation of --------- index.htm --------*/
1.126 brouard 7893:
7894: strcpy(optionfilehtm,optionfilefiname); /* Main html file */
7895: if(mle==-3)
1.201 brouard 7896: strcat(optionfilehtm,"-MORT_");
1.126 brouard 7897: strcat(optionfilehtm,".htm");
7898: if((fichtm=fopen(optionfilehtm,"w"))==NULL) {
1.131 brouard 7899: printf("Problem with %s \n",optionfilehtm);
7900: exit(0);
1.126 brouard 7901: }
7902:
7903: strcpy(optionfilehtmcov,optionfilefiname); /* Only for matrix of covariance */
7904: strcat(optionfilehtmcov,"-cov.htm");
7905: if((fichtmcov=fopen(optionfilehtmcov,"w"))==NULL) {
7906: printf("Problem with %s \n",optionfilehtmcov), exit(0);
7907: }
7908: else{
7909: fprintf(fichtmcov,"<html><head>\n<title>IMaCh Cov %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
7910: <hr size=\"2\" color=\"#EC5E5E\"> \n\
1.204 brouard 7911: Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=1+age+%s<br>\n",\
1.126 brouard 7912: optionfilehtmcov,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);
7913: }
7914:
1.213 brouard 7915: 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 7916: <hr size=\"2\" color=\"#EC5E5E\"> \n\
7917: <font size=\"2\">IMaCh-%s <br> %s</font> \
1.126 brouard 7918: <hr size=\"2\" color=\"#EC5E5E\"> \n\
1.204 brouard 7919: Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=1+age+%s<br>\n\
1.126 brouard 7920: \n\
7921: <hr size=\"2\" color=\"#EC5E5E\">\
7922: <ul><li><h4>Parameter files</h4>\n\
7923: - Parameter file: <a href=\"%s.%s\">%s.%s</a><br>\n\
7924: - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n\
7925: - Log file of the run: <a href=\"%s\">%s</a><br>\n\
7926: - Gnuplot file name: <a href=\"%s\">%s</a><br>\n\
7927: - Date and time at start: %s</ul>\n",\
7928: optionfilehtm,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model,\
7929: optionfilefiname,optionfilext,optionfilefiname,optionfilext,\
7930: fileres,fileres,\
7931: filelog,filelog,optionfilegnuplot,optionfilegnuplot,strstart);
7932: fflush(fichtm);
7933:
7934: strcpy(pathr,path);
7935: strcat(pathr,optionfilefiname);
1.184 brouard 7936: #ifdef WIN32
7937: _chdir(optionfilefiname); /* Move to directory named optionfile */
7938: #else
1.126 brouard 7939: chdir(optionfilefiname); /* Move to directory named optionfile */
1.184 brouard 7940: #endif
7941:
1.126 brouard 7942:
7943: /* Calculates basic frequencies. Computes observed prevalence at single age
7944: and prints on file fileres'p'. */
1.214 brouard 7945: freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint,strstart,\
7946: firstpass, lastpass, stepm, weightopt, model);
1.126 brouard 7947:
7948: fprintf(fichtm,"\n");
7949: fprintf(fichtm,"<br>Total number of observations=%d <br>\n\
7950: Youngest age at first (selected) pass %.2f, oldest age %.2f<br>\n\
7951: Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n",\
7952: imx,agemin,agemax,jmin,jmax,jmean);
7953: pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
7954: oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
7955: newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
7956: savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
7957: oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */
7958:
7959:
7960: /* For Powell, parameters are in a vector p[] starting at p[1]
7961: so we point p on param[1][1] so that p[1] maps on param[1][1][1] */
7962: p=param[1][1]; /* *(*(*(param +1)+1)+0) */
7963:
7964: globpr=0; /* To get the number ipmx of contributions and the sum of weights*/
1.186 brouard 7965: /* For mortality only */
1.126 brouard 7966: if (mle==-3){
1.136 brouard 7967: ximort=matrix(1,NDIM,1,NDIM);
1.186 brouard 7968: /* ximort=gsl_matrix_alloc(1,NDIM,1,NDIM); */
1.126 brouard 7969: cens=ivector(1,n);
7970: ageexmed=vector(1,n);
7971: agecens=vector(1,n);
7972: dcwave=ivector(1,n);
7973:
7974: for (i=1; i<=imx; i++){
7975: dcwave[i]=-1;
7976: for (m=firstpass; m<=lastpass; m++)
7977: if (s[m][i]>nlstate) {
7978: dcwave[i]=m;
7979: /* printf("i=%d j=%d s=%d dcwave=%d\n",i,j, s[j][i],dcwave[i]);*/
7980: break;
7981: }
7982: }
7983:
7984: for (i=1; i<=imx; i++) {
7985: if (wav[i]>0){
7986: ageexmed[i]=agev[mw[1][i]][i];
7987: j=wav[i];
7988: agecens[i]=1.;
7989:
7990: if (ageexmed[i]> 1 && wav[i] > 0){
7991: agecens[i]=agev[mw[j][i]][i];
7992: cens[i]= 1;
7993: }else if (ageexmed[i]< 1)
7994: cens[i]= -1;
7995: if (agedc[i]< AGESUP && agedc[i]>1 && dcwave[i]>firstpass && dcwave[i]<=lastpass)
7996: cens[i]=0 ;
7997: }
7998: else cens[i]=-1;
7999: }
8000:
8001: for (i=1;i<=NDIM;i++) {
8002: for (j=1;j<=NDIM;j++)
8003: ximort[i][j]=(i == j ? 1.0 : 0.0);
8004: }
8005:
1.145 brouard 8006: /*p[1]=0.0268; p[NDIM]=0.083;*/
1.126 brouard 8007: /*printf("%lf %lf", p[1], p[2]);*/
8008:
8009:
1.136 brouard 8010: #ifdef GSL
8011: printf("GSL optimization\n"); fprintf(ficlog,"Powell\n");
1.162 brouard 8012: #else
1.126 brouard 8013: printf("Powell\n"); fprintf(ficlog,"Powell\n");
1.136 brouard 8014: #endif
1.201 brouard 8015: strcpy(filerespow,"POW-MORT_");
8016: strcat(filerespow,fileresu);
1.126 brouard 8017: if((ficrespow=fopen(filerespow,"w"))==NULL) {
8018: printf("Problem with resultfile: %s\n", filerespow);
8019: fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
8020: }
1.136 brouard 8021: #ifdef GSL
8022: fprintf(ficrespow,"# GSL optimization\n# iter -2*LL");
1.162 brouard 8023: #else
1.126 brouard 8024: fprintf(ficrespow,"# Powell\n# iter -2*LL");
1.136 brouard 8025: #endif
1.126 brouard 8026: /* for (i=1;i<=nlstate;i++)
8027: for(j=1;j<=nlstate+ndeath;j++)
8028: if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
8029: */
8030: fprintf(ficrespow,"\n");
1.136 brouard 8031: #ifdef GSL
8032: /* gsl starts here */
8033: T = gsl_multimin_fminimizer_nmsimplex;
8034: gsl_multimin_fminimizer *sfm = NULL;
8035: gsl_vector *ss, *x;
8036: gsl_multimin_function minex_func;
8037:
8038: /* Initial vertex size vector */
8039: ss = gsl_vector_alloc (NDIM);
8040:
8041: if (ss == NULL){
8042: GSL_ERROR_VAL ("failed to allocate space for ss", GSL_ENOMEM, 0);
8043: }
8044: /* Set all step sizes to 1 */
8045: gsl_vector_set_all (ss, 0.001);
8046:
8047: /* Starting point */
1.126 brouard 8048:
1.136 brouard 8049: x = gsl_vector_alloc (NDIM);
8050:
8051: if (x == NULL){
8052: gsl_vector_free(ss);
8053: GSL_ERROR_VAL ("failed to allocate space for x", GSL_ENOMEM, 0);
8054: }
8055:
8056: /* Initialize method and iterate */
8057: /* p[1]=0.0268; p[NDIM]=0.083; */
1.186 brouard 8058: /* gsl_vector_set(x, 0, 0.0268); */
8059: /* gsl_vector_set(x, 1, 0.083); */
1.136 brouard 8060: gsl_vector_set(x, 0, p[1]);
8061: gsl_vector_set(x, 1, p[2]);
8062:
8063: minex_func.f = &gompertz_f;
8064: minex_func.n = NDIM;
8065: minex_func.params = (void *)&p; /* ??? */
8066:
8067: sfm = gsl_multimin_fminimizer_alloc (T, NDIM);
8068: gsl_multimin_fminimizer_set (sfm, &minex_func, x, ss);
8069:
8070: printf("Iterations beginning .....\n\n");
8071: printf("Iter. # Intercept Slope -Log Likelihood Simplex size\n");
8072:
8073: iteri=0;
8074: while (rval == GSL_CONTINUE){
8075: iteri++;
8076: status = gsl_multimin_fminimizer_iterate(sfm);
8077:
8078: if (status) printf("error: %s\n", gsl_strerror (status));
8079: fflush(0);
8080:
8081: if (status)
8082: break;
8083:
8084: rval = gsl_multimin_test_size (gsl_multimin_fminimizer_size (sfm), 1e-6);
8085: ssval = gsl_multimin_fminimizer_size (sfm);
8086:
8087: if (rval == GSL_SUCCESS)
8088: printf ("converged to a local maximum at\n");
8089:
8090: printf("%5d ", iteri);
8091: for (it = 0; it < NDIM; it++){
8092: printf ("%10.5f ", gsl_vector_get (sfm->x, it));
8093: }
8094: printf("f() = %-10.5f ssize = %.7f\n", sfm->fval, ssval);
8095: }
8096:
8097: printf("\n\n Please note: Program should be run many times with varying starting points to detemine global maximum\n\n");
8098:
8099: gsl_vector_free(x); /* initial values */
8100: gsl_vector_free(ss); /* inital step size */
8101: for (it=0; it<NDIM; it++){
8102: p[it+1]=gsl_vector_get(sfm->x,it);
8103: fprintf(ficrespow," %.12lf", p[it]);
8104: }
8105: gsl_multimin_fminimizer_free (sfm); /* p *(sfm.x.data) et p *(sfm.x.data+1) */
8106: #endif
8107: #ifdef POWELL
8108: powell(p,ximort,NDIM,ftol,&iter,&fret,gompertz);
8109: #endif
1.126 brouard 8110: fclose(ficrespow);
8111:
1.203 brouard 8112: hesscov(matcov, hess, p, NDIM, delti, 1e-4, gompertz);
1.126 brouard 8113:
8114: for(i=1; i <=NDIM; i++)
8115: for(j=i+1;j<=NDIM;j++)
8116: matcov[i][j]=matcov[j][i];
8117:
8118: printf("\nCovariance matrix\n ");
1.203 brouard 8119: fprintf(ficlog,"\nCovariance matrix\n ");
1.126 brouard 8120: for(i=1; i <=NDIM; i++) {
8121: for(j=1;j<=NDIM;j++){
8122: printf("%f ",matcov[i][j]);
1.203 brouard 8123: fprintf(ficlog,"%f ",matcov[i][j]);
1.126 brouard 8124: }
1.203 brouard 8125: printf("\n "); fprintf(ficlog,"\n ");
1.126 brouard 8126: }
8127:
8128: printf("iter=%d MLE=%f Eq=%lf*exp(%lf*(age-%d))\n",iter,-gompertz(p),p[1],p[2],agegomp);
1.193 brouard 8129: for (i=1;i<=NDIM;i++) {
1.126 brouard 8130: printf("%f [%f ; %f]\n",p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
1.193 brouard 8131: fprintf(ficlog,"%f [%f ; %f]\n",p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
8132: }
1.126 brouard 8133: lsurv=vector(1,AGESUP);
8134: lpop=vector(1,AGESUP);
8135: tpop=vector(1,AGESUP);
8136: lsurv[agegomp]=100000;
8137:
8138: for (k=agegomp;k<=AGESUP;k++) {
8139: agemortsup=k;
8140: if (p[1]*exp(p[2]*(k-agegomp))>1) break;
8141: }
8142:
8143: for (k=agegomp;k<agemortsup;k++)
8144: lsurv[k+1]=lsurv[k]-lsurv[k]*(p[1]*exp(p[2]*(k-agegomp)));
8145:
8146: for (k=agegomp;k<agemortsup;k++){
8147: lpop[k]=(lsurv[k]+lsurv[k+1])/2.;
8148: sumlpop=sumlpop+lpop[k];
8149: }
8150:
8151: tpop[agegomp]=sumlpop;
8152: for (k=agegomp;k<(agemortsup-3);k++){
8153: /* tpop[k+1]=2;*/
8154: tpop[k+1]=tpop[k]-lpop[k];
8155: }
8156:
8157:
8158: printf("\nAge lx qx dx Lx Tx e(x)\n");
8159: for (k=agegomp;k<(agemortsup-2);k++)
8160: 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]);
8161:
8162:
8163: replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
1.194 brouard 8164: if(ageminpar == AGEOVERFLOW ||agemaxpar == AGEOVERFLOW){
8165: printf("Warning! Error in gnuplot file with ageminpar %f or agemaxpar %f overflow\n\
8166: This is probably because your parameter file doesn't \n contain the exact number of lines (or columns) corresponding to your model line.\n\
8167: Please run with mle=-1 to get a correct covariance matrix.\n",ageminpar,agemaxpar);
8168: fprintf(ficlog,"Warning! Error in gnuplot file with ageminpar %f or agemaxpar %f overflow\n\
8169: This is probably because your parameter file doesn't \n contain the exact number of lines (or columns) corresponding to your model line.\n\
8170: Please run with mle=-1 to get a correct covariance matrix.\n",ageminpar,agemaxpar);
8171: }else
1.201 brouard 8172: printinggnuplotmort(fileresu, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
8173: printinghtmlmort(fileresu,title,datafile, firstpass, lastpass, \
1.126 brouard 8174: stepm, weightopt,\
8175: model,imx,p,matcov,agemortsup);
8176:
8177: free_vector(lsurv,1,AGESUP);
8178: free_vector(lpop,1,AGESUP);
8179: free_vector(tpop,1,AGESUP);
1.136 brouard 8180: #ifdef GSL
8181: free_ivector(cens,1,n);
8182: free_vector(agecens,1,n);
8183: free_ivector(dcwave,1,n);
8184: free_matrix(ximort,1,NDIM,1,NDIM);
8185: #endif
1.186 brouard 8186: } /* Endof if mle==-3 mortality only */
1.205 brouard 8187: /* Standard */
8188: else{ /* For mle !=- 3, could be 0 or 1 or 4 etc. */
8189: globpr=0;/* Computes sum of likelihood for globpr=1 and funcone */
8190: /* Computes likelihood for initial parameters, uses funcone to compute gpimx and gsw */
1.132 brouard 8191: likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
1.126 brouard 8192: printf("First Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
8193: for (k=1; k<=npar;k++)
8194: printf(" %d %8.5f",k,p[k]);
8195: printf("\n");
1.205 brouard 8196: if(mle>=1){ /* Could be 1 or 2, Real Maximization */
8197: /* mlikeli uses func not funcone */
8198: mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);
8199: }
8200: if(mle==0) {/* No optimization, will print the likelihoods for the datafile */
8201: globpr=0;/* Computes sum of likelihood for globpr=1 and funcone */
8202: /* Computes likelihood for initial parameters, uses funcone to compute gpimx and gsw */
8203: likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
8204: }
8205: globpr=1; /* again, to print the individual contributions using computed gpimx and gsw */
1.126 brouard 8206: likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
8207: printf("Second Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
8208: for (k=1; k<=npar;k++)
8209: printf(" %d %8.5f",k,p[k]);
8210: printf("\n");
8211:
8212: /*--------- results files --------------*/
1.192 brouard 8213: 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 8214:
8215:
8216: fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
8217: printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
8218: fprintf(ficlog,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
8219: for(i=1,jk=1; i <=nlstate; i++){
8220: for(k=1; k <=(nlstate+ndeath); k++){
8221: if (k != i) {
8222: printf("%d%d ",i,k);
8223: fprintf(ficlog,"%d%d ",i,k);
8224: fprintf(ficres,"%1d%1d ",i,k);
8225: for(j=1; j <=ncovmodel; j++){
1.190 brouard 8226: printf("%12.7f ",p[jk]);
8227: fprintf(ficlog,"%12.7f ",p[jk]);
8228: fprintf(ficres,"%12.7f ",p[jk]);
1.126 brouard 8229: jk++;
8230: }
8231: printf("\n");
8232: fprintf(ficlog,"\n");
8233: fprintf(ficres,"\n");
8234: }
8235: }
8236: }
1.203 brouard 8237: if(mle != 0){
8238: /* Computing hessian and covariance matrix only at a peak of the Likelihood, that is after optimization */
1.126 brouard 8239: ftolhess=ftol; /* Usually correct */
1.203 brouard 8240: hesscov(matcov, hess, p, npar, delti, ftolhess, func);
8241: 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");
8242: 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");
8243: for(i=1,jk=1; i <=nlstate; i++){
8244: for(k=1; k <=(nlstate+ndeath); k++){
8245: if (k != i) {
8246: printf("%d%d ",i,k);
8247: fprintf(ficlog,"%d%d ",i,k);
8248: for(j=1; j <=ncovmodel; j++){
8249: 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]));
8250: 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]));
8251: jk++;
8252: }
8253: printf("\n");
8254: fprintf(ficlog,"\n");
1.193 brouard 8255: }
8256: }
8257: }
1.203 brouard 8258: } /* end of hesscov and Wald tests */
1.193 brouard 8259:
1.203 brouard 8260: /* */
1.126 brouard 8261: fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");
8262: printf("# Scales (for hessian or gradient estimation)\n");
8263: fprintf(ficlog,"# Scales (for hessian or gradient estimation)\n");
8264: for(i=1,jk=1; i <=nlstate; i++){
8265: for(j=1; j <=nlstate+ndeath; j++){
8266: if (j!=i) {
8267: fprintf(ficres,"%1d%1d",i,j);
8268: printf("%1d%1d",i,j);
8269: fprintf(ficlog,"%1d%1d",i,j);
8270: for(k=1; k<=ncovmodel;k++){
8271: printf(" %.5e",delti[jk]);
8272: fprintf(ficlog," %.5e",delti[jk]);
8273: fprintf(ficres," %.5e",delti[jk]);
8274: jk++;
8275: }
8276: printf("\n");
8277: fprintf(ficlog,"\n");
8278: fprintf(ficres,"\n");
8279: }
8280: }
8281: }
8282:
8283: 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 8284: if(mle >= 1) /* To big for the screen */
1.126 brouard 8285: 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");
8286: 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");
8287: /* # 121 Var(a12)\n\ */
8288: /* # 122 Cov(b12,a12) Var(b12)\n\ */
8289: /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
8290: /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
8291: /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
8292: /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
8293: /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
8294: /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
8295:
8296:
8297: /* Just to have a covariance matrix which will be more understandable
8298: even is we still don't want to manage dictionary of variables
8299: */
8300: for(itimes=1;itimes<=2;itimes++){
8301: jj=0;
8302: for(i=1; i <=nlstate; i++){
8303: for(j=1; j <=nlstate+ndeath; j++){
8304: if(j==i) continue;
8305: for(k=1; k<=ncovmodel;k++){
8306: jj++;
8307: ca[0]= k+'a'-1;ca[1]='\0';
8308: if(itimes==1){
8309: if(mle>=1)
8310: printf("#%1d%1d%d",i,j,k);
8311: fprintf(ficlog,"#%1d%1d%d",i,j,k);
8312: fprintf(ficres,"#%1d%1d%d",i,j,k);
8313: }else{
8314: if(mle>=1)
8315: printf("%1d%1d%d",i,j,k);
8316: fprintf(ficlog,"%1d%1d%d",i,j,k);
8317: fprintf(ficres,"%1d%1d%d",i,j,k);
8318: }
8319: ll=0;
8320: for(li=1;li <=nlstate; li++){
8321: for(lj=1;lj <=nlstate+ndeath; lj++){
8322: if(lj==li) continue;
8323: for(lk=1;lk<=ncovmodel;lk++){
8324: ll++;
8325: if(ll<=jj){
8326: cb[0]= lk +'a'-1;cb[1]='\0';
8327: if(ll<jj){
8328: if(itimes==1){
8329: if(mle>=1)
8330: printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
8331: fprintf(ficlog," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
8332: fprintf(ficres," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
8333: }else{
8334: if(mle>=1)
8335: printf(" %.5e",matcov[jj][ll]);
8336: fprintf(ficlog," %.5e",matcov[jj][ll]);
8337: fprintf(ficres," %.5e",matcov[jj][ll]);
8338: }
8339: }else{
8340: if(itimes==1){
8341: if(mle>=1)
8342: printf(" Var(%s%1d%1d)",ca,i,j);
8343: fprintf(ficlog," Var(%s%1d%1d)",ca,i,j);
8344: fprintf(ficres," Var(%s%1d%1d)",ca,i,j);
8345: }else{
8346: if(mle>=1)
1.203 brouard 8347: printf(" %.7e",matcov[jj][ll]);
8348: fprintf(ficlog," %.7e",matcov[jj][ll]);
8349: fprintf(ficres," %.7e",matcov[jj][ll]);
1.126 brouard 8350: }
8351: }
8352: }
8353: } /* end lk */
8354: } /* end lj */
8355: } /* end li */
8356: if(mle>=1)
8357: printf("\n");
8358: fprintf(ficlog,"\n");
8359: fprintf(ficres,"\n");
8360: numlinepar++;
8361: } /* end k*/
8362: } /*end j */
8363: } /* end i */
8364: } /* end itimes */
8365:
8366: fflush(ficlog);
8367: fflush(ficres);
1.209 brouard 8368: while(fgets(line, MAXLINE, ficpar)) {
8369: /* If line starts with a # it is a comment */
8370: if (line[0] == '#') {
8371: numlinepar++;
1.141 brouard 8372: fputs(line,stdout);
1.126 brouard 8373: fputs(line,ficparo);
1.209 brouard 8374: fputs(line,ficlog);
8375: continue;
8376: }else
8377: break;
8378: }
8379:
8380: /* while((c=getc(ficpar))=='#' && c!= EOF){ */
8381: /* ungetc(c,ficpar); */
8382: /* fgets(line, MAXLINE, ficpar); */
8383: /* fputs(line,stdout); */
8384: /* fputs(line,ficparo); */
8385: /* } */
8386: /* ungetc(c,ficpar); */
1.126 brouard 8387:
8388: estepm=0;
1.209 brouard 8389: 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){
8390:
8391: if (num_filled != 6) {
8392: printf("Not 6 parameters in line, for example:agemin=60 agemax=95 bage=55 fage=95 estepm=24 ftolpl=6e-4\n");
8393: printf("but line=%s\n",line);
8394: goto end;
8395: }
8396: printf("agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d ftolpl=%lf\n",ageminpar,agemaxpar, bage, fage, estepm, ftolpl);
8397: }
8398: /* ftolpl=6*ftol*1.e5; /\* 6.e-3 make convergences in less than 80 loops for the prevalence limit *\/ */
8399: /*ftolpl=6.e-4;*/ /* 6.e-3 make convergences in less than 80 loops for the prevalence limit */
8400:
8401: /* fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d ftolpl=%\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm); */
1.126 brouard 8402: if (estepm==0 || estepm < stepm) estepm=stepm;
8403: if (fage <= 2) {
8404: bage = ageminpar;
8405: fage = agemaxpar;
8406: }
8407:
8408: fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");
1.211 brouard 8409: fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d ftolpl=%e\n",ageminpar,agemaxpar,bage,fage, estepm, ftolpl);
8410: fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d, ftolpl=%e\n",ageminpar,agemaxpar,bage,fage, estepm, ftolpl);
1.186 brouard 8411:
8412: /* Other stuffs, more or less useful */
1.126 brouard 8413: while((c=getc(ficpar))=='#' && c!= EOF){
8414: ungetc(c,ficpar);
8415: fgets(line, MAXLINE, ficpar);
1.141 brouard 8416: fputs(line,stdout);
1.126 brouard 8417: fputs(line,ficparo);
8418: }
8419: ungetc(c,ficpar);
8420:
8421: 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);
8422: 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);
8423: 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);
8424: printf("begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
8425: 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);
8426:
8427: while((c=getc(ficpar))=='#' && c!= EOF){
8428: ungetc(c,ficpar);
8429: fgets(line, MAXLINE, ficpar);
1.141 brouard 8430: fputs(line,stdout);
1.126 brouard 8431: fputs(line,ficparo);
8432: }
8433: ungetc(c,ficpar);
8434:
8435:
8436: dateprev1=anprev1+(mprev1-1)/12.+(jprev1-1)/365.;
8437: dateprev2=anprev2+(mprev2-1)/12.+(jprev2-1)/365.;
8438:
8439: fscanf(ficpar,"pop_based=%d\n",&popbased);
1.193 brouard 8440: fprintf(ficlog,"pop_based=%d\n",popbased);
1.126 brouard 8441: fprintf(ficparo,"pop_based=%d\n",popbased);
8442: fprintf(ficres,"pop_based=%d\n",popbased);
8443:
8444: while((c=getc(ficpar))=='#' && c!= EOF){
8445: ungetc(c,ficpar);
8446: fgets(line, MAXLINE, ficpar);
1.141 brouard 8447: fputs(line,stdout);
1.126 brouard 8448: fputs(line,ficparo);
8449: }
8450: ungetc(c,ficpar);
8451:
8452: 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);
8453: 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);
8454: 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);
8455: 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);
8456: 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);
8457: /* day and month of proj2 are not used but only year anproj2.*/
8458:
8459:
8460:
1.145 brouard 8461: /* freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint); */
8462: /* ,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2); */
1.126 brouard 8463:
8464: replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
1.194 brouard 8465: if(ageminpar == AGEOVERFLOW ||agemaxpar == -AGEOVERFLOW){
8466: printf("Warning! Error in gnuplot file with ageminpar %f or agemaxpar %f overflow\n\
8467: This is probably because your parameter file doesn't \n contain the exact number of lines (or columns) corresponding to your model line.\n\
8468: Please run with mle=-1 to get a correct covariance matrix.\n",ageminpar,agemaxpar);
8469: fprintf(ficlog,"Warning! Error in gnuplot file with ageminpar %f or agemaxpar %f overflow\n\
8470: This is probably because your parameter file doesn't \n contain the exact number of lines (or columns) corresponding to your model line.\n\
8471: Please run with mle=-1 to get a correct covariance matrix.\n",ageminpar,agemaxpar);
8472: }else
1.211 brouard 8473: printinggnuplot(fileresu, optionfilefiname,ageminpar,agemaxpar,fage, prevfcast, pathc,p);
1.126 brouard 8474:
1.201 brouard 8475: printinghtml(fileresu,title,datafile, firstpass, lastpass, stepm, weightopt,\
1.211 brouard 8476: model,imx,jmin,jmax,jmean,rfileres,popforecast,prevfcast,estepm, \
1.213 brouard 8477: jprev1,mprev1,anprev1,dateprev1,jprev2,mprev2,anprev2,dateprev2);
1.126 brouard 8478:
8479: /*------------ free_vector -------------*/
8480: /* chdir(path); */
8481:
1.215 brouard 8482: /* free_ivector(wav,1,imx); */ /* Moved after last prevalence call */
8483: /* free_imatrix(dh,1,lastpass-firstpass+2,1,imx); */
8484: /* free_imatrix(bh,1,lastpass-firstpass+2,1,imx); */
8485: /* free_imatrix(mw,1,lastpass-firstpass+2,1,imx); */
1.126 brouard 8486: free_lvector(num,1,n);
8487: free_vector(agedc,1,n);
8488: /*free_matrix(covar,0,NCOVMAX,1,n);*/
8489: /*free_matrix(covar,1,NCOVMAX,1,n);*/
8490: fclose(ficparo);
8491: fclose(ficres);
8492:
8493:
1.186 brouard 8494: /* Other results (useful)*/
8495:
8496:
1.126 brouard 8497: /*--------------- Prevalence limit (period or stable prevalence) --------------*/
1.180 brouard 8498: /*#include "prevlim.h"*/ /* Use ficrespl, ficlog */
8499: prlim=matrix(1,nlstate,1,nlstate);
1.209 brouard 8500: prevalence_limit(p, prlim, ageminpar, agemaxpar, ftolpl, &ncvyear);
1.126 brouard 8501: fclose(ficrespl);
8502:
1.145 brouard 8503: #ifdef FREEEXIT2
8504: #include "freeexit2.h"
8505: #endif
8506:
1.126 brouard 8507: /*------------- h Pij x at various ages ------------*/
1.180 brouard 8508: /*#include "hpijx.h"*/
8509: hPijx(p, bage, fage);
1.145 brouard 8510: fclose(ficrespij);
1.126 brouard 8511:
1.145 brouard 8512: /*-------------- Variance of one-step probabilities---*/
8513: k=1;
1.126 brouard 8514: varprob(optionfilefiname, matcov, p, delti, nlstate, bage, fage,k,Tvar,nbcode, ncodemax,strstart);
8515:
8516:
8517: probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
8518: for(i=1;i<=AGESUP;i++)
8519: for(j=1;j<=NCOVMAX;j++)
8520: for(k=1;k<=NCOVMAX;k++)
8521: probs[i][j][k]=0.;
8522:
8523: /*---------- Forecasting ------------------*/
8524: /*if((stepm == 1) && (strcmp(model,".")==0)){*/
8525: if(prevfcast==1){
8526: /* if(stepm ==1){*/
1.201 brouard 8527: prevforecast(fileresu, anproj1, mproj1, jproj1, agemin, agemax, dateprev1, dateprev2, mobilavproj, bage, fage, firstpass, lastpass, anproj2, p, cptcoveff);
1.126 brouard 8528: /* (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);*/
8529: /* } */
8530: /* else{ */
8531: /* erreur=108; */
8532: /* printf("Warning %d!! You can only forecast the prevalences if the optimization\n has been performed with stepm = 1 (month) instead of %d or model=. instead of '%s'\n", erreur, stepm, model); */
8533: /* fprintf(ficlog,"Warning %d!! You can only forecast the prevalences if the optimization\n has been performed with stepm = 1 (month) instead of %d or model=. instead of '%s'\n", erreur, stepm, model); */
8534: /* } */
8535: }
1.186 brouard 8536:
8537: /* ------ Other prevalence ratios------------ */
1.126 brouard 8538:
1.127 brouard 8539: /* Computes prevalence between agemin (i.e minimal age computed) and no more ageminpar */
8540:
8541: prevalence(probs, agemin, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
8542: /* printf("ageminpar=%f, agemax=%f, s[lastpass][imx]=%d, agev[lastpass][imx]=%f, nlstate=%d, imx=%d, mint[lastpass][imx]=%f, anint[lastpass][imx]=%f,dateprev1=%f, dateprev2=%f, firstpass=%d, lastpass=%d\n",\
8543: ageminpar, agemax, s[lastpass][imx], agev[lastpass][imx], nlstate, imx, mint[lastpass][imx],anint[lastpass][imx], dateprev1, dateprev2, firstpass, lastpass);
8544: */
1.215 brouard 8545: free_ivector(wav,1,imx);
8546: free_imatrix(dh,1,lastpass-firstpass+2,1,imx);
8547: free_imatrix(bh,1,lastpass-firstpass+2,1,imx);
8548: free_imatrix(mw,1,lastpass-firstpass+2,1,imx);
8549:
1.126 brouard 8550:
1.127 brouard 8551: if (mobilav!=0) {
8552: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
8553: if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
8554: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
8555: printf(" Error in movingaverage mobilav=%d\n",mobilav);
8556: }
1.126 brouard 8557: }
8558:
8559:
1.127 brouard 8560: /*---------- Health expectancies, no variances ------------*/
8561:
1.201 brouard 8562: strcpy(filerese,"E_");
8563: strcat(filerese,fileresu);
1.126 brouard 8564: if((ficreseij=fopen(filerese,"w"))==NULL) {
8565: printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
8566: fprintf(ficlog,"Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
8567: }
1.208 brouard 8568: printf("Computing Health Expectancies: result on file '%s' ...", filerese);fflush(stdout);
8569: fprintf(ficlog,"Computing Health Expectancies: result on file '%s' ...", filerese);fflush(ficlog);
1.145 brouard 8570: /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){
8571: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/
8572:
8573: for (k=1; k <= (int) pow(2,cptcoveff); k++){
1.127 brouard 8574: fprintf(ficreseij,"\n#****** ");
8575: for(j=1;j<=cptcoveff;j++) {
1.200 brouard 8576: fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
1.127 brouard 8577: }
8578: fprintf(ficreseij,"******\n");
8579:
8580: eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
8581: oldm=oldms;savm=savms;
8582: evsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, strstart);
8583:
8584: free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
1.145 brouard 8585: /*}*/
1.127 brouard 8586: }
8587: fclose(ficreseij);
1.208 brouard 8588: printf("done evsij\n");fflush(stdout);
8589: fprintf(ficlog,"done evsij\n");fflush(ficlog);
1.127 brouard 8590:
8591: /*---------- Health expectancies and variances ------------*/
8592:
8593:
1.201 brouard 8594: strcpy(filerest,"T_");
8595: strcat(filerest,fileresu);
1.127 brouard 8596: if((ficrest=fopen(filerest,"w"))==NULL) {
8597: printf("Problem with total LE resultfile: %s\n", filerest);goto end;
8598: fprintf(ficlog,"Problem with total LE resultfile: %s\n", filerest);goto end;
8599: }
1.208 brouard 8600: printf("Computing Total Life expectancies with their standard errors: file '%s' ...\n", filerest); fflush(stdout);
8601: fprintf(ficlog,"Computing Total Life expectancies with their standard errors: file '%s' ...\n", filerest); fflush(ficlog);
1.127 brouard 8602:
1.126 brouard 8603:
1.201 brouard 8604: strcpy(fileresstde,"STDE_");
8605: strcat(fileresstde,fileresu);
1.126 brouard 8606: if((ficresstdeij=fopen(fileresstde,"w"))==NULL) {
8607: printf("Problem with Health Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
8608: fprintf(ficlog,"Problem with Health Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
8609: }
1.208 brouard 8610: printf(" Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde);
8611: fprintf(ficlog," Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde);
1.126 brouard 8612:
1.201 brouard 8613: strcpy(filerescve,"CVE_");
8614: strcat(filerescve,fileresu);
1.126 brouard 8615: if((ficrescveij=fopen(filerescve,"w"))==NULL) {
8616: printf("Problem with Covar. Health Exp. resultfile: %s\n", filerescve); exit(0);
8617: fprintf(ficlog,"Problem with Covar. Health Exp. resultfile: %s\n", filerescve); exit(0);
8618: }
1.208 brouard 8619: printf(" Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve);
8620: fprintf(ficlog," Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve);
1.126 brouard 8621:
1.201 brouard 8622: strcpy(fileresv,"V_");
8623: strcat(fileresv,fileresu);
1.126 brouard 8624: if((ficresvij=fopen(fileresv,"w"))==NULL) {
8625: printf("Problem with variance resultfile: %s\n", fileresv);exit(0);
8626: fprintf(ficlog,"Problem with variance resultfile: %s\n", fileresv);exit(0);
8627: }
1.208 brouard 8628: printf(" Computing Variance-covariance of DFLEs: file '%s' ... ", fileresv);fflush(stdout);
8629: fprintf(ficlog," Computing Variance-covariance of DFLEs: file '%s' ... ", fileresv);fflush(ficlog);
1.126 brouard 8630:
1.145 brouard 8631: /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){
8632: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/
8633:
8634: for (k=1; k <= (int) pow(2,cptcoveff); k++){
1.208 brouard 8635: fprintf(ficrest,"\n#****** ");
8636: for(j=1;j<=cptcoveff;j++)
8637: fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
8638: fprintf(ficrest,"******\n");
8639:
8640: fprintf(ficresstdeij,"\n#****** ");
8641: fprintf(ficrescveij,"\n#****** ");
8642: for(j=1;j<=cptcoveff;j++) {
8643: fprintf(ficresstdeij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
8644: fprintf(ficrescveij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
8645: }
8646: fprintf(ficresstdeij,"******\n");
8647: fprintf(ficrescveij,"******\n");
8648:
8649: fprintf(ficresvij,"\n#****** ");
8650: for(j=1;j<=cptcoveff;j++)
8651: fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
8652: fprintf(ficresvij,"******\n");
8653:
8654: eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
8655: oldm=oldms;savm=savms;
8656: printf(" cvevsij %d, ",k);
8657: fprintf(ficlog, " cvevsij %d, ",k);
8658: cvevsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov, strstart);
8659: printf(" end cvevsij \n ");
8660: fprintf(ficlog, " end cvevsij \n ");
8661:
8662: /*
8663: */
8664: /* goto endfree; */
8665:
8666: vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
8667: pstamp(ficrest);
8668:
8669:
8670: for(vpopbased=0; vpopbased <= popbased; vpopbased++){ /* Done for vpopbased=0 and vpopbased=1 if popbased==1*/
8671: oldm=oldms;savm=savms; /* ZZ Segmentation fault */
8672: cptcod= 0; /* To be deleted */
8673: printf("varevsij %d \n",vpopbased);
8674: fprintf(ficlog, "varevsij %d \n",vpopbased);
1.209 brouard 8675: 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 */
1.208 brouard 8676: 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 ");
8677: if(vpopbased==1)
8678: 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);
8679: else
8680: fprintf(ficrest,"the age specific period (stable) prevalences in each health state \n");
8681: fprintf(ficrest,"# Age popbased mobilav e.. (std) ");
8682: for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);
8683: fprintf(ficrest,"\n");
8684: /* printf("Which p?\n"); for(i=1;i<=npar;i++)printf("p[i=%d]=%lf,",i,p[i]);printf("\n"); */
8685: epj=vector(1,nlstate+1);
8686: printf("Computing age specific period (stable) prevalences in each health state \n");
8687: fprintf(ficlog,"Computing age specific period (stable) prevalences in each health state \n");
8688: for(age=bage; age <=fage ;age++){
1.209 brouard 8689: prevalim(prlim, nlstate, p, age, oldm, savm, ftolpl, &ncvyear, k); /*ZZ Is it the correct prevalim */
1.208 brouard 8690: if (vpopbased==1) {
8691: if(mobilav ==0){
8692: for(i=1; i<=nlstate;i++)
8693: prlim[i][i]=probs[(int)age][i][k];
8694: }else{ /* mobilav */
8695: for(i=1; i<=nlstate;i++)
8696: prlim[i][i]=mobaverage[(int)age][i][k];
1.126 brouard 8697: }
1.208 brouard 8698: }
8699:
8700: fprintf(ficrest," %4.0f %d %d",age, vpopbased, mobilav);
8701: /* fprintf(ficrest," %4.0f %d %d %d %d",age, vpopbased, mobilav,Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]); */ /* to be done */
8702: /* printf(" age %4.0f ",age); */
8703: for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){
8704: for(i=1, epj[j]=0.;i <=nlstate;i++) {
8705: epj[j] += prlim[i][i]*eij[i][j][(int)age];
8706: /*ZZZ printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/
8707: /* printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]); */
1.126 brouard 8708: }
1.208 brouard 8709: epj[nlstate+1] +=epj[j];
8710: }
8711: /* printf(" age %4.0f \n",age); */
8712:
8713: for(i=1, vepp=0.;i <=nlstate;i++)
8714: for(j=1;j <=nlstate;j++)
8715: vepp += vareij[i][j][(int)age];
8716: fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));
8717: for(j=1;j <=nlstate;j++){
8718: fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));
1.126 brouard 8719: }
1.208 brouard 8720: fprintf(ficrest,"\n");
1.126 brouard 8721: }
1.208 brouard 8722: } /* End vpopbased */
8723: free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
8724: free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);
8725: free_vector(epj,1,nlstate+1);
8726: printf("done \n");fflush(stdout);
8727: fprintf(ficlog,"done\n");fflush(ficlog);
8728:
1.145 brouard 8729: /*}*/
1.208 brouard 8730: } /* End k */
1.126 brouard 8731: free_vector(weight,1,n);
1.145 brouard 8732: free_imatrix(Tvard,1,NCOVMAX,1,2);
1.126 brouard 8733: free_imatrix(s,1,maxwav+1,1,n);
8734: free_matrix(anint,1,maxwav,1,n);
8735: free_matrix(mint,1,maxwav,1,n);
8736: free_ivector(cod,1,n);
8737: free_ivector(tab,1,NCOVMAX);
8738: fclose(ficresstdeij);
8739: fclose(ficrescveij);
8740: fclose(ficresvij);
8741: fclose(ficrest);
1.208 brouard 8742: printf("done Health expectancies\n");fflush(stdout);
8743: fprintf(ficlog,"done Health expectancies\n");fflush(ficlog);
1.126 brouard 8744: fclose(ficpar);
8745:
8746: /*------- Variance of period (stable) prevalence------*/
8747:
1.201 brouard 8748: strcpy(fileresvpl,"VPL_");
8749: strcat(fileresvpl,fileresu);
1.126 brouard 8750: if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {
8751: printf("Problem with variance of period (stable) prevalence resultfile: %s\n", fileresvpl);
8752: exit(0);
8753: }
1.208 brouard 8754: printf("Computing Variance-covariance of period (stable) prevalence: file '%s' ...", fileresvpl);fflush(stdout);
8755: fprintf(ficlog, "Computing Variance-covariance of period (stable) prevalence: file '%s' ...", fileresvpl);fflush(ficlog);
1.126 brouard 8756:
1.145 brouard 8757: /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){
8758: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/
8759:
8760: for (k=1; k <= (int) pow(2,cptcoveff); k++){
8761: fprintf(ficresvpl,"\n#****** ");
1.126 brouard 8762: for(j=1;j<=cptcoveff;j++)
1.200 brouard 8763: fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
1.126 brouard 8764: fprintf(ficresvpl,"******\n");
8765:
8766: varpl=matrix(1,nlstate,(int) bage, (int) fage);
8767: oldm=oldms;savm=savms;
1.209 brouard 8768: varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl, &ncvyear, k, strstart);
1.126 brouard 8769: free_matrix(varpl,1,nlstate,(int) bage, (int)fage);
1.145 brouard 8770: /*}*/
1.126 brouard 8771: }
8772:
8773: fclose(ficresvpl);
1.208 brouard 8774: printf("done variance-covariance of period prevalence\n");fflush(stdout);
8775: fprintf(ficlog,"done variance-covariance of period prevalence\n");fflush(ficlog);
1.126 brouard 8776:
8777: /*---------- End : free ----------------*/
8778: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
8779: free_ma3x(probs,1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
8780: } /* mle==-3 arrives here for freeing */
1.164 brouard 8781: /* endfree:*/
1.141 brouard 8782: free_matrix(prlim,1,nlstate,1,nlstate); /*here or after loop ? */
1.126 brouard 8783: free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);
8784: free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);
8785: free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);
8786: free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);
8787: free_matrix(covar,0,NCOVMAX,1,n);
8788: free_matrix(matcov,1,npar,1,npar);
1.203 brouard 8789: free_matrix(hess,1,npar,1,npar);
1.126 brouard 8790: /*free_vector(delti,1,npar);*/
8791: free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
8792: free_matrix(agev,1,maxwav,1,imx);
8793: free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
8794:
1.145 brouard 8795: free_ivector(ncodemax,1,NCOVMAX);
1.192 brouard 8796: free_ivector(ncodemaxwundef,1,NCOVMAX);
1.145 brouard 8797: free_ivector(Tvar,1,NCOVMAX);
8798: free_ivector(Tprod,1,NCOVMAX);
8799: free_ivector(Tvaraff,1,NCOVMAX);
8800: free_ivector(Tage,1,NCOVMAX);
1.126 brouard 8801:
8802: free_imatrix(nbcode,0,NCOVMAX,0,NCOVMAX);
1.200 brouard 8803: /* free_imatrix(codtab,1,100,1,10); */
1.126 brouard 8804: fflush(fichtm);
8805: fflush(ficgp);
8806:
8807:
8808: if((nberr >0) || (nbwarn>0)){
1.216 ! brouard 8809: printf("End of Imach with %d errors and/or %d warnings. Please look at the log file for details.\n",nberr,nbwarn);
! 8810: 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 8811: }else{
8812: printf("End of Imach\n");
8813: fprintf(ficlog,"End of Imach\n");
8814: }
8815: printf("See log file on %s\n",filelog);
8816: /* gettimeofday(&end_time, (struct timezone*)0);*/ /* after time */
1.157 brouard 8817: /*(void) gettimeofday(&end_time,&tzp);*/
8818: rend_time = time(NULL);
8819: end_time = *localtime(&rend_time);
8820: /* tml = *localtime(&end_time.tm_sec); */
8821: strcpy(strtend,asctime(&end_time));
1.126 brouard 8822: printf("Local time at start %s\nLocal time at end %s",strstart, strtend);
8823: fprintf(ficlog,"Local time at start %s\nLocal time at end %s\n",strstart, strtend);
1.157 brouard 8824: printf("Total time used %s\n", asc_diff_time(rend_time -rstart_time,tmpout));
1.126 brouard 8825:
1.157 brouard 8826: printf("Total time was %.0lf Sec.\n", difftime(rend_time,rstart_time));
8827: fprintf(ficlog,"Total time used %s\n", asc_diff_time(rend_time -rstart_time,tmpout));
8828: fprintf(ficlog,"Total time was %.0lf Sec.\n", difftime(rend_time,rstart_time));
1.126 brouard 8829: /* printf("Total time was %d uSec.\n", total_usecs);*/
8830: /* if(fileappend(fichtm,optionfilehtm)){ */
8831: fprintf(fichtm,"<br>Local time at start %s<br>Local time at end %s<br>\n</body></html>",strstart, strtend);
8832: fclose(fichtm);
8833: fprintf(fichtmcov,"<br>Local time at start %s<br>Local time at end %s<br>\n</body></html>",strstart, strtend);
8834: fclose(fichtmcov);
8835: fclose(ficgp);
8836: fclose(ficlog);
8837: /*------ End -----------*/
8838:
8839:
8840: printf("Before Current directory %s!\n",pathcd);
1.184 brouard 8841: #ifdef WIN32
8842: if (_chdir(pathcd) != 0)
8843: printf("Can't move to directory %s!\n",path);
8844: if(_getcwd(pathcd,MAXLINE) > 0)
8845: #else
1.126 brouard 8846: if(chdir(pathcd) != 0)
1.184 brouard 8847: printf("Can't move to directory %s!\n", path);
8848: if (getcwd(pathcd, MAXLINE) > 0)
8849: #endif
1.126 brouard 8850: printf("Current directory %s!\n",pathcd);
8851: /*strcat(plotcmd,CHARSEPARATOR);*/
8852: sprintf(plotcmd,"gnuplot");
1.157 brouard 8853: #ifdef _WIN32
1.126 brouard 8854: sprintf(plotcmd,"\"%sgnuplot.exe\"",pathimach);
8855: #endif
8856: if(!stat(plotcmd,&info)){
1.158 brouard 8857: printf("Error or gnuplot program not found: '%s'\n",plotcmd);fflush(stdout);
1.126 brouard 8858: if(!stat(getenv("GNUPLOTBIN"),&info)){
1.158 brouard 8859: printf("Error or gnuplot program not found: '%s' Environment GNUPLOTBIN not set.\n",plotcmd);fflush(stdout);
1.126 brouard 8860: }else
8861: strcpy(pplotcmd,plotcmd);
1.157 brouard 8862: #ifdef __unix
1.126 brouard 8863: strcpy(plotcmd,GNUPLOTPROGRAM);
8864: if(!stat(plotcmd,&info)){
1.158 brouard 8865: printf("Error gnuplot program not found: '%s'\n",plotcmd);fflush(stdout);
1.126 brouard 8866: }else
8867: strcpy(pplotcmd,plotcmd);
8868: #endif
8869: }else
8870: strcpy(pplotcmd,plotcmd);
8871:
8872: sprintf(plotcmd,"%s %s",pplotcmd, optionfilegnuplot);
1.158 brouard 8873: printf("Starting graphs with: '%s'\n",plotcmd);fflush(stdout);
1.126 brouard 8874:
8875: if((outcmd=system(plotcmd)) != 0){
1.158 brouard 8876: printf("gnuplot command might not be in your path: '%s', err=%d\n", plotcmd, outcmd);
1.154 brouard 8877: printf("\n Trying if gnuplot resides on the same directory that IMaCh\n");
1.152 brouard 8878: sprintf(plotcmd,"%sgnuplot %s", pathimach, optionfilegnuplot);
1.150 brouard 8879: if((outcmd=system(plotcmd)) != 0)
1.153 brouard 8880: printf("\n Still a problem with gnuplot command %s, err=%d\n", plotcmd, outcmd);
1.126 brouard 8881: }
1.158 brouard 8882: printf(" Successful, please wait...");
1.126 brouard 8883: while (z[0] != 'q') {
8884: /* chdir(path); */
1.154 brouard 8885: printf("\nType e to edit results with your browser, g to graph again and q for exit: ");
1.126 brouard 8886: scanf("%s",z);
8887: /* if (z[0] == 'c') system("./imach"); */
8888: if (z[0] == 'e') {
1.158 brouard 8889: #ifdef __APPLE__
1.152 brouard 8890: sprintf(pplotcmd, "open %s", optionfilehtm);
1.157 brouard 8891: #elif __linux
8892: sprintf(pplotcmd, "xdg-open %s", optionfilehtm);
1.153 brouard 8893: #else
1.152 brouard 8894: sprintf(pplotcmd, "%s", optionfilehtm);
1.153 brouard 8895: #endif
8896: printf("Starting browser with: %s",pplotcmd);fflush(stdout);
8897: system(pplotcmd);
1.126 brouard 8898: }
8899: else if (z[0] == 'g') system(plotcmd);
8900: else if (z[0] == 'q') exit(0);
8901: }
8902: end:
8903: while (z[0] != 'q') {
1.195 brouard 8904: printf("\nType q for exiting: "); fflush(stdout);
1.126 brouard 8905: scanf("%s",z);
8906: }
8907: }
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