Annotation of imach/src/imach.c, revision 1.195
1.195 ! brouard 1: /* $Id: imach.c,v 1.194 2015/08/18 13:32:00 brouard Exp $
1.126 brouard 2: $State: Exp $
1.163 brouard 3: $Log: imach.c,v $
1.195 ! brouard 4: Revision 1.194 2015/08/18 13:32:00 brouard
! 5: Summary: Adding error when the covariance matrix doesn't contain the exact number of lines required by the model line.
! 6:
1.194 brouard 7: Revision 1.193 2015/08/04 07:17:42 brouard
8: Summary: 0.98q4
9:
1.193 brouard 10: Revision 1.192 2015/07/16 16:49:02 brouard
11: Summary: Fixing some outputs
12:
1.192 brouard 13: Revision 1.191 2015/07/14 10:00:33 brouard
14: Summary: Some fixes
15:
1.191 brouard 16: Revision 1.190 2015/05/05 08:51:13 brouard
17: Summary: Adding digits in output parameters (7 digits instead of 6)
18:
19: Fix 1+age+.
20:
1.190 brouard 21: Revision 1.189 2015/04/30 14:45:16 brouard
22: Summary: 0.98q2
23:
1.189 brouard 24: Revision 1.188 2015/04/30 08:27:53 brouard
25: *** empty log message ***
26:
1.188 brouard 27: Revision 1.187 2015/04/29 09:11:15 brouard
28: *** empty log message ***
29:
1.187 brouard 30: Revision 1.186 2015/04/23 12:01:52 brouard
31: Summary: V1*age is working now, version 0.98q1
32:
33: Some codes had been disabled in order to simplify and Vn*age was
34: working in the optimization phase, ie, giving correct MLE parameters,
35: but, as usual, outputs were not correct and program core dumped.
36:
1.186 brouard 37: Revision 1.185 2015/03/11 13:26:42 brouard
38: Summary: Inclusion of compile and links command line for Intel Compiler
39:
1.185 brouard 40: Revision 1.184 2015/03/11 11:52:39 brouard
41: Summary: Back from Windows 8. Intel Compiler
42:
1.184 brouard 43: Revision 1.183 2015/03/10 20:34:32 brouard
44: Summary: 0.98q0, trying with directest, mnbrak fixed
45:
46: We use directest instead of original Powell test; probably no
47: incidence on the results, but better justifications;
48: We fixed Numerical Recipes mnbrak routine which was wrong and gave
49: wrong results.
50:
1.183 brouard 51: Revision 1.182 2015/02/12 08:19:57 brouard
52: Summary: Trying to keep directest which seems simpler and more general
53: Author: Nicolas Brouard
54:
1.182 brouard 55: Revision 1.181 2015/02/11 23:22:24 brouard
56: Summary: Comments on Powell added
57:
58: Author:
59:
1.181 brouard 60: Revision 1.180 2015/02/11 17:33:45 brouard
61: Summary: Finishing move from main to function (hpijx and prevalence_limit)
62:
1.180 brouard 63: Revision 1.179 2015/01/04 09:57:06 brouard
64: Summary: back to OS/X
65:
1.179 brouard 66: Revision 1.178 2015/01/04 09:35:48 brouard
67: *** empty log message ***
68:
1.178 brouard 69: Revision 1.177 2015/01/03 18:40:56 brouard
70: Summary: Still testing ilc32 on OSX
71:
1.177 brouard 72: Revision 1.176 2015/01/03 16:45:04 brouard
73: *** empty log message ***
74:
1.176 brouard 75: Revision 1.175 2015/01/03 16:33:42 brouard
76: *** empty log message ***
77:
1.175 brouard 78: Revision 1.174 2015/01/03 16:15:49 brouard
79: Summary: Still in cross-compilation
80:
1.174 brouard 81: Revision 1.173 2015/01/03 12:06:26 brouard
82: Summary: trying to detect cross-compilation
83:
1.173 brouard 84: Revision 1.172 2014/12/27 12:07:47 brouard
85: Summary: Back from Visual Studio and Intel, options for compiling for Windows XP
86:
1.172 brouard 87: Revision 1.171 2014/12/23 13:26:59 brouard
88: Summary: Back from Visual C
89:
90: Still problem with utsname.h on Windows
91:
1.171 brouard 92: Revision 1.170 2014/12/23 11:17:12 brouard
93: Summary: Cleaning some \%% back to %%
94:
95: The escape was mandatory for a specific compiler (which one?), but too many warnings.
96:
1.170 brouard 97: Revision 1.169 2014/12/22 23:08:31 brouard
98: Summary: 0.98p
99:
100: Outputs some informations on compiler used, OS etc. Testing on different platforms.
101:
1.169 brouard 102: Revision 1.168 2014/12/22 15:17:42 brouard
1.170 brouard 103: Summary: update
1.169 brouard 104:
1.168 brouard 105: Revision 1.167 2014/12/22 13:50:56 brouard
106: Summary: Testing uname and compiler version and if compiled 32 or 64
107:
108: Testing on Linux 64
109:
1.167 brouard 110: Revision 1.166 2014/12/22 11:40:47 brouard
111: *** empty log message ***
112:
1.166 brouard 113: Revision 1.165 2014/12/16 11:20:36 brouard
114: Summary: After compiling on Visual C
115:
116: * imach.c (Module): Merging 1.61 to 1.162
117:
1.165 brouard 118: Revision 1.164 2014/12/16 10:52:11 brouard
119: Summary: Merging with Visual C after suppressing some warnings for unused variables. Also fixing Saito's bug 0.98Xn
120:
121: * imach.c (Module): Merging 1.61 to 1.162
122:
1.164 brouard 123: Revision 1.163 2014/12/16 10:30:11 brouard
124: * imach.c (Module): Merging 1.61 to 1.162
125:
1.163 brouard 126: Revision 1.162 2014/09/25 11:43:39 brouard
127: Summary: temporary backup 0.99!
128:
1.162 brouard 129: Revision 1.1 2014/09/16 11:06:58 brouard
130: Summary: With some code (wrong) for nlopt
131:
132: Author:
133:
134: Revision 1.161 2014/09/15 20:41:41 brouard
135: Summary: Problem with macro SQR on Intel compiler
136:
1.161 brouard 137: Revision 1.160 2014/09/02 09:24:05 brouard
138: *** empty log message ***
139:
1.160 brouard 140: Revision 1.159 2014/09/01 10:34:10 brouard
141: Summary: WIN32
142: Author: Brouard
143:
1.159 brouard 144: Revision 1.158 2014/08/27 17:11:51 brouard
145: *** empty log message ***
146:
1.158 brouard 147: Revision 1.157 2014/08/27 16:26:55 brouard
148: Summary: Preparing windows Visual studio version
149: Author: Brouard
150:
151: In order to compile on Visual studio, time.h is now correct and time_t
152: and tm struct should be used. difftime should be used but sometimes I
153: just make the differences in raw time format (time(&now).
154: Trying to suppress #ifdef LINUX
155: Add xdg-open for __linux in order to open default browser.
156:
1.157 brouard 157: Revision 1.156 2014/08/25 20:10:10 brouard
158: *** empty log message ***
159:
1.156 brouard 160: Revision 1.155 2014/08/25 18:32:34 brouard
161: Summary: New compile, minor changes
162: Author: Brouard
163:
1.155 brouard 164: Revision 1.154 2014/06/20 17:32:08 brouard
165: Summary: Outputs now all graphs of convergence to period prevalence
166:
1.154 brouard 167: Revision 1.153 2014/06/20 16:45:46 brouard
168: Summary: If 3 live state, convergence to period prevalence on same graph
169: Author: Brouard
170:
1.153 brouard 171: Revision 1.152 2014/06/18 17:54:09 brouard
172: Summary: open browser, use gnuplot on same dir than imach if not found in the path
173:
1.152 brouard 174: Revision 1.151 2014/06/18 16:43:30 brouard
175: *** empty log message ***
176:
1.151 brouard 177: Revision 1.150 2014/06/18 16:42:35 brouard
178: Summary: If gnuplot is not in the path try on same directory than imach binary (OSX)
179: Author: brouard
180:
1.150 brouard 181: Revision 1.149 2014/06/18 15:51:14 brouard
182: Summary: Some fixes in parameter files errors
183: Author: Nicolas Brouard
184:
1.149 brouard 185: Revision 1.148 2014/06/17 17:38:48 brouard
186: Summary: Nothing new
187: Author: Brouard
188:
189: Just a new packaging for OS/X version 0.98nS
190:
1.148 brouard 191: Revision 1.147 2014/06/16 10:33:11 brouard
192: *** empty log message ***
193:
1.147 brouard 194: Revision 1.146 2014/06/16 10:20:28 brouard
195: Summary: Merge
196: Author: Brouard
197:
198: Merge, before building revised version.
199:
1.146 brouard 200: Revision 1.145 2014/06/10 21:23:15 brouard
201: Summary: Debugging with valgrind
202: Author: Nicolas Brouard
203:
204: Lot of changes in order to output the results with some covariates
205: After the Edimburgh REVES conference 2014, it seems mandatory to
206: improve the code.
207: No more memory valgrind error but a lot has to be done in order to
208: continue the work of splitting the code into subroutines.
209: Also, decodemodel has been improved. Tricode is still not
210: optimal. nbcode should be improved. Documentation has been added in
211: the source code.
212:
1.144 brouard 213: Revision 1.143 2014/01/26 09:45:38 brouard
214: Summary: Version 0.98nR (to be improved, but gives same optimization results as 0.98k. Nice, promising
215:
216: * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
217: (Module): Version 0.98nR Running ok, but output format still only works for three covariates.
218:
1.143 brouard 219: Revision 1.142 2014/01/26 03:57:36 brouard
220: Summary: gnuplot changed plot w l 1 has to be changed to plot w l lt 2
221:
222: * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
223:
1.142 brouard 224: Revision 1.141 2014/01/26 02:42:01 brouard
225: * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
226:
1.141 brouard 227: Revision 1.140 2011/09/02 10:37:54 brouard
228: Summary: times.h is ok with mingw32 now.
229:
1.140 brouard 230: Revision 1.139 2010/06/14 07:50:17 brouard
231: After the theft of my laptop, I probably lost some lines of codes which were not uploaded to the CVS tree.
232: I remember having already fixed agemin agemax which are pointers now but not cvs saved.
233:
1.139 brouard 234: Revision 1.138 2010/04/30 18:19:40 brouard
235: *** empty log message ***
236:
1.138 brouard 237: Revision 1.137 2010/04/29 18:11:38 brouard
238: (Module): Checking covariates for more complex models
239: than V1+V2. A lot of change to be done. Unstable.
240:
1.137 brouard 241: Revision 1.136 2010/04/26 20:30:53 brouard
242: (Module): merging some libgsl code. Fixing computation
243: of likelione (using inter/intrapolation if mle = 0) in order to
244: get same likelihood as if mle=1.
245: Some cleaning of code and comments added.
246:
1.136 brouard 247: Revision 1.135 2009/10/29 15:33:14 brouard
248: (Module): Now imach stops if date of birth, at least year of birth, is not given. Some cleaning of the code.
249:
1.135 brouard 250: Revision 1.134 2009/10/29 13:18:53 brouard
251: (Module): Now imach stops if date of birth, at least year of birth, is not given. Some cleaning of the code.
252:
1.134 brouard 253: Revision 1.133 2009/07/06 10:21:25 brouard
254: just nforces
255:
1.133 brouard 256: Revision 1.132 2009/07/06 08:22:05 brouard
257: Many tings
258:
1.132 brouard 259: Revision 1.131 2009/06/20 16:22:47 brouard
260: Some dimensions resccaled
261:
1.131 brouard 262: Revision 1.130 2009/05/26 06:44:34 brouard
263: (Module): Max Covariate is now set to 20 instead of 8. A
264: lot of cleaning with variables initialized to 0. Trying to make
265: V2+V3*age+V1+V4 strb=V3*age+V1+V4 working better.
266:
1.130 brouard 267: Revision 1.129 2007/08/31 13:49:27 lievre
268: Modification of the way of exiting when the covariate is not binary in order to see on the window the error message before exiting
269:
1.129 lievre 270: Revision 1.128 2006/06/30 13:02:05 brouard
271: (Module): Clarifications on computing e.j
272:
1.128 brouard 273: Revision 1.127 2006/04/28 18:11:50 brouard
274: (Module): Yes the sum of survivors was wrong since
275: imach-114 because nhstepm was no more computed in the age
276: loop. Now we define nhstepma in the age loop.
277: (Module): In order to speed up (in case of numerous covariates) we
278: compute health expectancies (without variances) in a first step
279: and then all the health expectancies with variances or standard
280: deviation (needs data from the Hessian matrices) which slows the
281: computation.
282: In the future we should be able to stop the program is only health
283: expectancies and graph are needed without standard deviations.
284:
1.127 brouard 285: Revision 1.126 2006/04/28 17:23:28 brouard
286: (Module): Yes the sum of survivors was wrong since
287: imach-114 because nhstepm was no more computed in the age
288: loop. Now we define nhstepma in the age loop.
289: Version 0.98h
290:
1.126 brouard 291: Revision 1.125 2006/04/04 15:20:31 lievre
292: Errors in calculation of health expectancies. Age was not initialized.
293: Forecasting file added.
294:
295: Revision 1.124 2006/03/22 17:13:53 lievre
296: Parameters are printed with %lf instead of %f (more numbers after the comma).
297: The log-likelihood is printed in the log file
298:
299: Revision 1.123 2006/03/20 10:52:43 brouard
300: * imach.c (Module): <title> changed, corresponds to .htm file
301: name. <head> headers where missing.
302:
303: * imach.c (Module): Weights can have a decimal point as for
304: English (a comma might work with a correct LC_NUMERIC environment,
305: otherwise the weight is truncated).
306: Modification of warning when the covariates values are not 0 or
307: 1.
308: Version 0.98g
309:
310: Revision 1.122 2006/03/20 09:45:41 brouard
311: (Module): Weights can have a decimal point as for
312: English (a comma might work with a correct LC_NUMERIC environment,
313: otherwise the weight is truncated).
314: Modification of warning when the covariates values are not 0 or
315: 1.
316: Version 0.98g
317:
318: Revision 1.121 2006/03/16 17:45:01 lievre
319: * imach.c (Module): Comments concerning covariates added
320:
321: * imach.c (Module): refinements in the computation of lli if
322: status=-2 in order to have more reliable computation if stepm is
323: not 1 month. Version 0.98f
324:
325: Revision 1.120 2006/03/16 15:10:38 lievre
326: (Module): refinements in the computation of lli if
327: status=-2 in order to have more reliable computation if stepm is
328: not 1 month. Version 0.98f
329:
330: Revision 1.119 2006/03/15 17:42:26 brouard
331: (Module): Bug if status = -2, the loglikelihood was
332: computed as likelihood omitting the logarithm. Version O.98e
333:
334: Revision 1.118 2006/03/14 18:20:07 brouard
335: (Module): varevsij Comments added explaining the second
336: table of variances if popbased=1 .
337: (Module): Covariances of eij, ekl added, graphs fixed, new html link.
338: (Module): Function pstamp added
339: (Module): Version 0.98d
340:
341: Revision 1.117 2006/03/14 17:16:22 brouard
342: (Module): varevsij Comments added explaining the second
343: table of variances if popbased=1 .
344: (Module): Covariances of eij, ekl added, graphs fixed, new html link.
345: (Module): Function pstamp added
346: (Module): Version 0.98d
347:
348: Revision 1.116 2006/03/06 10:29:27 brouard
349: (Module): Variance-covariance wrong links and
350: varian-covariance of ej. is needed (Saito).
351:
352: Revision 1.115 2006/02/27 12:17:45 brouard
353: (Module): One freematrix added in mlikeli! 0.98c
354:
355: Revision 1.114 2006/02/26 12:57:58 brouard
356: (Module): Some improvements in processing parameter
357: filename with strsep.
358:
359: Revision 1.113 2006/02/24 14:20:24 brouard
360: (Module): Memory leaks checks with valgrind and:
361: datafile was not closed, some imatrix were not freed and on matrix
362: allocation too.
363:
364: Revision 1.112 2006/01/30 09:55:26 brouard
365: (Module): Back to gnuplot.exe instead of wgnuplot.exe
366:
367: Revision 1.111 2006/01/25 20:38:18 brouard
368: (Module): Lots of cleaning and bugs added (Gompertz)
369: (Module): Comments can be added in data file. Missing date values
370: can be a simple dot '.'.
371:
372: Revision 1.110 2006/01/25 00:51:50 brouard
373: (Module): Lots of cleaning and bugs added (Gompertz)
374:
375: Revision 1.109 2006/01/24 19:37:15 brouard
376: (Module): Comments (lines starting with a #) are allowed in data.
377:
378: Revision 1.108 2006/01/19 18:05:42 lievre
379: Gnuplot problem appeared...
380: To be fixed
381:
382: Revision 1.107 2006/01/19 16:20:37 brouard
383: Test existence of gnuplot in imach path
384:
385: Revision 1.106 2006/01/19 13:24:36 brouard
386: Some cleaning and links added in html output
387:
388: Revision 1.105 2006/01/05 20:23:19 lievre
389: *** empty log message ***
390:
391: Revision 1.104 2005/09/30 16:11:43 lievre
392: (Module): sump fixed, loop imx fixed, and simplifications.
393: (Module): If the status is missing at the last wave but we know
394: that the person is alive, then we can code his/her status as -2
395: (instead of missing=-1 in earlier versions) and his/her
396: contributions to the likelihood is 1 - Prob of dying from last
397: health status (= 1-p13= p11+p12 in the easiest case of somebody in
398: the healthy state at last known wave). Version is 0.98
399:
400: Revision 1.103 2005/09/30 15:54:49 lievre
401: (Module): sump fixed, loop imx fixed, and simplifications.
402:
403: Revision 1.102 2004/09/15 17:31:30 brouard
404: Add the possibility to read data file including tab characters.
405:
406: Revision 1.101 2004/09/15 10:38:38 brouard
407: Fix on curr_time
408:
409: Revision 1.100 2004/07/12 18:29:06 brouard
410: Add version for Mac OS X. Just define UNIX in Makefile
411:
412: Revision 1.99 2004/06/05 08:57:40 brouard
413: *** empty log message ***
414:
415: Revision 1.98 2004/05/16 15:05:56 brouard
416: New version 0.97 . First attempt to estimate force of mortality
417: directly from the data i.e. without the need of knowing the health
418: state at each age, but using a Gompertz model: log u =a + b*age .
419: This is the basic analysis of mortality and should be done before any
420: other analysis, in order to test if the mortality estimated from the
421: cross-longitudinal survey is different from the mortality estimated
422: from other sources like vital statistic data.
423:
424: The same imach parameter file can be used but the option for mle should be -3.
425:
1.133 brouard 426: Agnès, who wrote this part of the code, tried to keep most of the
1.126 brouard 427: former routines in order to include the new code within the former code.
428:
429: The output is very simple: only an estimate of the intercept and of
430: the slope with 95% confident intervals.
431:
432: Current limitations:
433: A) Even if you enter covariates, i.e. with the
434: model= V1+V2 equation for example, the programm does only estimate a unique global model without covariates.
435: B) There is no computation of Life Expectancy nor Life Table.
436:
437: Revision 1.97 2004/02/20 13:25:42 lievre
438: Version 0.96d. Population forecasting command line is (temporarily)
439: suppressed.
440:
441: Revision 1.96 2003/07/15 15:38:55 brouard
442: * imach.c (Repository): Errors in subdirf, 2, 3 while printing tmpout is
443: rewritten within the same printf. Workaround: many printfs.
444:
445: Revision 1.95 2003/07/08 07:54:34 brouard
446: * imach.c (Repository):
447: (Repository): Using imachwizard code to output a more meaningful covariance
448: matrix (cov(a12,c31) instead of numbers.
449:
450: Revision 1.94 2003/06/27 13:00:02 brouard
451: Just cleaning
452:
453: Revision 1.93 2003/06/25 16:33:55 brouard
454: (Module): On windows (cygwin) function asctime_r doesn't
455: exist so I changed back to asctime which exists.
456: (Module): Version 0.96b
457:
458: Revision 1.92 2003/06/25 16:30:45 brouard
459: (Module): On windows (cygwin) function asctime_r doesn't
460: exist so I changed back to asctime which exists.
461:
462: Revision 1.91 2003/06/25 15:30:29 brouard
463: * imach.c (Repository): Duplicated warning errors corrected.
464: (Repository): Elapsed time after each iteration is now output. It
465: helps to forecast when convergence will be reached. Elapsed time
466: is stamped in powell. We created a new html file for the graphs
467: concerning matrix of covariance. It has extension -cov.htm.
468:
469: Revision 1.90 2003/06/24 12:34:15 brouard
470: (Module): Some bugs corrected for windows. Also, when
471: mle=-1 a template is output in file "or"mypar.txt with the design
472: of the covariance matrix to be input.
473:
474: Revision 1.89 2003/06/24 12:30:52 brouard
475: (Module): Some bugs corrected for windows. Also, when
476: mle=-1 a template is output in file "or"mypar.txt with the design
477: of the covariance matrix to be input.
478:
479: Revision 1.88 2003/06/23 17:54:56 brouard
480: * 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.
481:
482: Revision 1.87 2003/06/18 12:26:01 brouard
483: Version 0.96
484:
485: Revision 1.86 2003/06/17 20:04:08 brouard
486: (Module): Change position of html and gnuplot routines and added
487: routine fileappend.
488:
489: Revision 1.85 2003/06/17 13:12:43 brouard
490: * imach.c (Repository): Check when date of death was earlier that
491: current date of interview. It may happen when the death was just
492: prior to the death. In this case, dh was negative and likelihood
493: was wrong (infinity). We still send an "Error" but patch by
494: assuming that the date of death was just one stepm after the
495: interview.
496: (Repository): Because some people have very long ID (first column)
497: we changed int to long in num[] and we added a new lvector for
498: memory allocation. But we also truncated to 8 characters (left
499: truncation)
500: (Repository): No more line truncation errors.
501:
502: Revision 1.84 2003/06/13 21:44:43 brouard
503: * imach.c (Repository): Replace "freqsummary" at a correct
504: place. It differs from routine "prevalence" which may be called
505: many times. Probs is memory consuming and must be used with
506: parcimony.
507: Version 0.95a3 (should output exactly the same maximization than 0.8a2)
508:
509: Revision 1.83 2003/06/10 13:39:11 lievre
510: *** empty log message ***
511:
512: Revision 1.82 2003/06/05 15:57:20 brouard
513: Add log in imach.c and fullversion number is now printed.
514:
515: */
516: /*
517: Interpolated Markov Chain
518:
519: Short summary of the programme:
520:
521: This program computes Healthy Life Expectancies from
522: cross-longitudinal data. Cross-longitudinal data consist in: -1- a
523: first survey ("cross") where individuals from different ages are
524: interviewed on their health status or degree of disability (in the
525: case of a health survey which is our main interest) -2- at least a
526: second wave of interviews ("longitudinal") which measure each change
527: (if any) in individual health status. Health expectancies are
528: computed from the time spent in each health state according to a
529: model. More health states you consider, more time is necessary to reach the
530: Maximum Likelihood of the parameters involved in the model. The
531: simplest model is the multinomial logistic model where pij is the
532: probability to be observed in state j at the second wave
533: conditional to be observed in state i at the first wave. Therefore
534: the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where
535: 'age' is age and 'sex' is a covariate. If you want to have a more
536: complex model than "constant and age", you should modify the program
537: where the markup *Covariates have to be included here again* invites
538: you to do it. More covariates you add, slower the
539: convergence.
540:
541: The advantage of this computer programme, compared to a simple
542: multinomial logistic model, is clear when the delay between waves is not
543: identical for each individual. Also, if a individual missed an
544: intermediate interview, the information is lost, but taken into
545: account using an interpolation or extrapolation.
546:
547: hPijx is the probability to be observed in state i at age x+h
548: conditional to the observed state i at age x. The delay 'h' can be
549: split into an exact number (nh*stepm) of unobserved intermediate
550: states. This elementary transition (by month, quarter,
551: semester or year) is modelled as a multinomial logistic. The hPx
552: matrix is simply the matrix product of nh*stepm elementary matrices
553: and the contribution of each individual to the likelihood is simply
554: hPijx.
555:
556: Also this programme outputs the covariance matrix of the parameters but also
557: of the life expectancies. It also computes the period (stable) prevalence.
558:
1.133 brouard 559: Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).
560: Institut national d'études démographiques, Paris.
1.126 brouard 561: This software have been partly granted by Euro-REVES, a concerted action
562: from the European Union.
563: It is copyrighted identically to a GNU software product, ie programme and
564: software can be distributed freely for non commercial use. Latest version
565: can be accessed at http://euroreves.ined.fr/imach .
566:
567: Help to debug: LD_PRELOAD=/usr/local/lib/libnjamd.so ./imach foo.imach
568: or better on gdb : set env LD_PRELOAD=/usr/local/lib/libnjamd.so
569:
570: **********************************************************************/
571: /*
572: main
573: read parameterfile
574: read datafile
575: concatwav
576: freqsummary
577: if (mle >= 1)
578: mlikeli
579: print results files
580: if mle==1
581: computes hessian
582: read end of parameter file: agemin, agemax, bage, fage, estepm
583: begin-prev-date,...
584: open gnuplot file
585: open html file
1.145 brouard 586: period (stable) prevalence | pl_nom 1-1 2-2 etc by covariate
587: for age prevalim() | #****** V1=0 V2=1 V3=1 V4=0 ******
588: | 65 1 0 2 1 3 1 4 0 0.96326 0.03674
589: freexexit2 possible for memory heap.
590:
591: h Pij x | pij_nom ficrestpij
592: # Cov Agex agex+h hpijx with i,j= 1-1 1-2 1-3 2-1 2-2 2-3
593: 1 85 85 1.00000 0.00000 0.00000 0.00000 1.00000 0.00000
594: 1 85 86 0.68299 0.22291 0.09410 0.71093 0.00000 0.28907
595:
596: 1 65 99 0.00364 0.00322 0.99314 0.00350 0.00310 0.99340
597: 1 65 100 0.00214 0.00204 0.99581 0.00206 0.00196 0.99597
598: variance of p one-step probabilities varprob | prob_nom ficresprob #One-step probabilities and stand. devi in ()
599: Standard deviation of one-step probabilities | probcor_nom ficresprobcor #One-step probabilities and correlation matrix
600: Matrix of variance covariance of one-step probabilities | probcov_nom ficresprobcov #One-step probabilities and covariance matrix
601:
1.126 brouard 602: forecasting if prevfcast==1 prevforecast call prevalence()
603: health expectancies
604: Variance-covariance of DFLE
605: prevalence()
606: movingaverage()
607: varevsij()
608: if popbased==1 varevsij(,popbased)
609: total life expectancies
610: Variance of period (stable) prevalence
611: end
612: */
613:
1.187 brouard 614: /* #define DEBUG */
615: /* #define DEBUGBRENT */
1.165 brouard 616: #define POWELL /* Instead of NLOPT */
1.192 brouard 617: #define POWELLF1F3 /* Skip test */
1.186 brouard 618: /* #define POWELLORIGINAL /\* Don't use Directest to decide new direction but original Powell test *\/ */
619: /* #define MNBRAKORIGINAL /\* Don't use mnbrak fix *\/ */
1.126 brouard 620:
621: #include <math.h>
622: #include <stdio.h>
623: #include <stdlib.h>
624: #include <string.h>
1.159 brouard 625:
626: #ifdef _WIN32
627: #include <io.h>
1.172 brouard 628: #include <windows.h>
629: #include <tchar.h>
1.159 brouard 630: #else
1.126 brouard 631: #include <unistd.h>
1.159 brouard 632: #endif
1.126 brouard 633:
634: #include <limits.h>
635: #include <sys/types.h>
1.171 brouard 636:
637: #if defined(__GNUC__)
638: #include <sys/utsname.h> /* Doesn't work on Windows */
639: #endif
640:
1.126 brouard 641: #include <sys/stat.h>
642: #include <errno.h>
1.159 brouard 643: /* extern int errno; */
1.126 brouard 644:
1.157 brouard 645: /* #ifdef LINUX */
646: /* #include <time.h> */
647: /* #include "timeval.h" */
648: /* #else */
649: /* #include <sys/time.h> */
650: /* #endif */
651:
1.126 brouard 652: #include <time.h>
653:
1.136 brouard 654: #ifdef GSL
655: #include <gsl/gsl_errno.h>
656: #include <gsl/gsl_multimin.h>
657: #endif
658:
1.167 brouard 659:
1.162 brouard 660: #ifdef NLOPT
661: #include <nlopt.h>
662: typedef struct {
663: double (* function)(double [] );
664: } myfunc_data ;
665: #endif
666:
1.126 brouard 667: /* #include <libintl.h> */
668: /* #define _(String) gettext (String) */
669:
1.141 brouard 670: #define MAXLINE 1024 /* Was 256. Overflow with 312 with 2 states and 4 covariates. Should be ok */
1.126 brouard 671:
672: #define GNUPLOTPROGRAM "gnuplot"
673: /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
674: #define FILENAMELENGTH 132
675:
676: #define GLOCK_ERROR_NOPATH -1 /* empty path */
677: #define GLOCK_ERROR_GETCWD -2 /* cannot get cwd */
678:
1.144 brouard 679: #define MAXPARM 128 /**< Maximum number of parameters for the optimization */
680: #define NPARMAX 64 /**< (nlstate+ndeath-1)*nlstate*ncovmodel */
1.126 brouard 681:
682: #define NINTERVMAX 8
1.144 brouard 683: #define NLSTATEMAX 8 /**< Maximum number of live states (for func) */
684: #define NDEATHMAX 8 /**< Maximum number of dead states (for func) */
685: #define NCOVMAX 20 /**< Maximum number of covariates, including generated covariates V1*V2 */
1.145 brouard 686: #define codtabm(h,k) 1 & (h-1) >> (k-1) ;
1.126 brouard 687: #define MAXN 20000
1.144 brouard 688: #define YEARM 12. /**< Number of months per year */
1.126 brouard 689: #define AGESUP 130
690: #define AGEBASE 40
1.194 brouard 691: #define AGEOVERFLOW 1.e20
1.164 brouard 692: #define AGEGOMP 10 /**< Minimal age for Gompertz adjustment */
1.157 brouard 693: #ifdef _WIN32
694: #define DIRSEPARATOR '\\'
695: #define CHARSEPARATOR "\\"
696: #define ODIRSEPARATOR '/'
697: #else
1.126 brouard 698: #define DIRSEPARATOR '/'
699: #define CHARSEPARATOR "/"
700: #define ODIRSEPARATOR '\\'
701: #endif
702:
1.195 ! brouard 703: /* $Id: imach.c,v 1.194 2015/08/18 13:32:00 brouard Exp $ */
1.126 brouard 704: /* $State: Exp $ */
705:
1.194 brouard 706: char version[]="Imach version 0.98q5, August 2015,INED-EUROREVES-Institut de longevite-Japan Society for the Promotion of Science (Grant-in-Aid for Scientific Research 25293121), Intel Software 2015";
1.195 ! brouard 707: char fullversion[]="$Revision: 1.194 $ $Date: 2015/08/18 13:32:00 $";
1.126 brouard 708: char strstart[80];
709: char optionfilext[10], optionfilefiname[FILENAMELENGTH];
1.130 brouard 710: int erreur=0, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings */
1.187 brouard 711: int nagesqr=0, nforce=0; /* nagesqr=1 if model is including age*age, number of forces */
1.145 brouard 712: /* Number of covariates model=V2+V1+ V3*age+V2*V4 */
713: int cptcovn=0; /**< cptcovn number of covariates added in the model (excepting constant and age and age*product) */
714: int cptcovt=0; /**< cptcovt number of covariates added in the model (excepting constant and age) */
715: int cptcovs=0; /**< cptcovs number of simple covariates V2+V1 =2 */
716: int cptcovage=0; /**< Number of covariates with age: V3*age only =1 */
717: int cptcovprodnoage=0; /**< Number of covariate products without age */
718: int cptcoveff=0; /* Total number of covariates to vary for printing results */
719: int cptcov=0; /* Working variable */
1.126 brouard 720: int npar=NPARMAX;
721: int nlstate=2; /* Number of live states */
722: int ndeath=1; /* Number of dead states */
1.130 brouard 723: int ncovmodel=0, ncovcol=0; /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
1.126 brouard 724: int popbased=0;
725:
726: int *wav; /* Number of waves for this individuual 0 is possible */
1.130 brouard 727: int maxwav=0; /* Maxim number of waves */
728: int jmin=0, jmax=0; /* min, max spacing between 2 waves */
729: int ijmin=0, ijmax=0; /* Individuals having jmin and jmax */
730: int gipmx=0, gsw=0; /* Global variables on the number of contributions
1.126 brouard 731: to the likelihood and the sum of weights (done by funcone)*/
1.130 brouard 732: int mle=1, weightopt=0;
1.126 brouard 733: int **mw; /* mw[mi][i] is number of the mi wave for this individual */
734: int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
735: int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between
736: * wave mi and wave mi+1 is not an exact multiple of stepm. */
1.162 brouard 737: int countcallfunc=0; /* Count the number of calls to func */
1.130 brouard 738: double jmean=1; /* Mean space between 2 waves */
1.145 brouard 739: double **matprod2(); /* test */
1.126 brouard 740: double **oldm, **newm, **savm; /* Working pointers to matrices */
741: double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
1.136 brouard 742: /*FILE *fic ; */ /* Used in readdata only */
743: FILE *ficpar, *ficparo,*ficres, *ficresp, *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
1.126 brouard 744: FILE *ficlog, *ficrespow;
1.130 brouard 745: int globpr=0; /* Global variable for printing or not */
1.126 brouard 746: double fretone; /* Only one call to likelihood */
1.130 brouard 747: long ipmx=0; /* Number of contributions */
1.126 brouard 748: double sw; /* Sum of weights */
749: char filerespow[FILENAMELENGTH];
750: char fileresilk[FILENAMELENGTH]; /* File of individual contributions to the likelihood */
751: FILE *ficresilk;
752: FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
753: FILE *ficresprobmorprev;
754: FILE *fichtm, *fichtmcov; /* Html File */
755: FILE *ficreseij;
756: char filerese[FILENAMELENGTH];
757: FILE *ficresstdeij;
758: char fileresstde[FILENAMELENGTH];
759: FILE *ficrescveij;
760: char filerescve[FILENAMELENGTH];
761: FILE *ficresvij;
762: char fileresv[FILENAMELENGTH];
763: FILE *ficresvpl;
764: char fileresvpl[FILENAMELENGTH];
765: char title[MAXLINE];
766: char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH], filerespl[FILENAMELENGTH];
767: char plotcmd[FILENAMELENGTH], pplotcmd[FILENAMELENGTH];
768: char tmpout[FILENAMELENGTH], tmpout2[FILENAMELENGTH];
769: char command[FILENAMELENGTH];
770: int outcmd=0;
771:
772: char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
773:
774: char filelog[FILENAMELENGTH]; /* Log file */
775: char filerest[FILENAMELENGTH];
776: char fileregp[FILENAMELENGTH];
777: char popfile[FILENAMELENGTH];
778:
779: char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilehtmcov[FILENAMELENGTH] ;
780:
1.157 brouard 781: /* struct timeval start_time, end_time, curr_time, last_time, forecast_time; */
782: /* struct timezone tzp; */
783: /* extern int gettimeofday(); */
784: struct tm tml, *gmtime(), *localtime();
785:
786: extern time_t time();
787:
788: struct tm start_time, end_time, curr_time, last_time, forecast_time;
789: time_t rstart_time, rend_time, rcurr_time, rlast_time, rforecast_time; /* raw time */
790: struct tm tm;
791:
1.126 brouard 792: char strcurr[80], strfor[80];
793:
794: char *endptr;
795: long lval;
796: double dval;
797:
798: #define NR_END 1
799: #define FREE_ARG char*
800: #define FTOL 1.0e-10
801:
802: #define NRANSI
803: #define ITMAX 200
804:
805: #define TOL 2.0e-4
806:
807: #define CGOLD 0.3819660
808: #define ZEPS 1.0e-10
809: #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);
810:
811: #define GOLD 1.618034
812: #define GLIMIT 100.0
813: #define TINY 1.0e-20
814:
815: static double maxarg1,maxarg2;
816: #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
817: #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
818:
819: #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
820: #define rint(a) floor(a+0.5)
1.166 brouard 821: /* http://www.thphys.uni-heidelberg.de/~robbers/cmbeasy/doc/html/myutils_8h-source.html */
1.183 brouard 822: #define mytinydouble 1.0e-16
1.166 brouard 823: /* #define DEQUAL(a,b) (fabs((a)-(b))<mytinydouble) */
824: /* http://www.thphys.uni-heidelberg.de/~robbers/cmbeasy/doc/html/mynrutils_8h-source.html */
825: /* static double dsqrarg; */
826: /* #define DSQR(a) (DEQUAL((dsqrarg=(a)),0.0) ? 0.0 : dsqrarg*dsqrarg) */
1.126 brouard 827: static double sqrarg;
828: #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
829: #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}
830: int agegomp= AGEGOMP;
831:
832: int imx;
833: int stepm=1;
834: /* Stepm, step in month: minimum step interpolation*/
835:
836: int estepm;
837: /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
838:
839: int m,nb;
840: long *num;
1.192 brouard 841: int firstpass=0, lastpass=4,*cod, *Tage,*cens;
842: int *ncodemax; /* ncodemax[j]= Number of modalities of the j th
843: covariate for which somebody answered excluding
844: undefined. Usually 2: 0 and 1. */
845: int *ncodemaxwundef; /* ncodemax[j]= Number of modalities of the j th
846: covariate for which somebody answered including
847: undefined. Usually 3: -1, 0 and 1. */
1.126 brouard 848: double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
849: double **pmmij, ***probs;
850: double *ageexmed,*agecens;
851: double dateintmean=0;
852:
853: double *weight;
854: int **s; /* Status */
1.141 brouard 855: double *agedc;
1.145 brouard 856: double **covar; /**< covar[j,i], value of jth covariate for individual i,
1.141 brouard 857: * covar=matrix(0,NCOVMAX,1,n);
1.187 brouard 858: * cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*age; */
1.141 brouard 859: double idx;
860: int **nbcode, *Tvar; /**< model=V2 => Tvar[1]= 2 */
1.145 brouard 861: int *Ndum; /** Freq of modality (tricode */
1.141 brouard 862: int **codtab; /**< codtab=imatrix(1,100,1,10); */
863: int **Tvard, *Tprod, cptcovprod, *Tvaraff;
1.126 brouard 864: double *lsurv, *lpop, *tpop;
865:
1.143 brouard 866: double ftol=FTOL; /**< Tolerance for computing Max Likelihood */
867: double ftolhess; /**< Tolerance for computing hessian */
1.126 brouard 868:
869: /**************** split *************************/
870: static int split( char *path, char *dirc, char *name, char *ext, char *finame )
871: {
872: /* From a file name with (full) path (either Unix or Windows) we extract the directory (dirc)
873: the name of the file (name), its extension only (ext) and its first part of the name (finame)
874: */
875: char *ss; /* pointer */
1.186 brouard 876: int l1=0, l2=0; /* length counters */
1.126 brouard 877:
878: l1 = strlen(path ); /* length of path */
879: if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
880: ss= strrchr( path, DIRSEPARATOR ); /* find last / */
881: if ( ss == NULL ) { /* no directory, so determine current directory */
882: strcpy( name, path ); /* we got the fullname name because no directory */
883: /*if(strrchr(path, ODIRSEPARATOR )==NULL)
884: printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
885: /* get current working directory */
886: /* extern char* getcwd ( char *buf , int len);*/
1.184 brouard 887: #ifdef WIN32
888: if (_getcwd( dirc, FILENAME_MAX ) == NULL ) {
889: #else
890: if (getcwd(dirc, FILENAME_MAX) == NULL) {
891: #endif
1.126 brouard 892: return( GLOCK_ERROR_GETCWD );
893: }
894: /* got dirc from getcwd*/
895: printf(" DIRC = %s \n",dirc);
896: } else { /* strip direcotry from path */
897: ss++; /* after this, the filename */
898: l2 = strlen( ss ); /* length of filename */
899: if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
900: strcpy( name, ss ); /* save file name */
901: strncpy( dirc, path, l1 - l2 ); /* now the directory */
1.186 brouard 902: dirc[l1-l2] = '\0'; /* add zero */
1.126 brouard 903: printf(" DIRC2 = %s \n",dirc);
904: }
905: /* We add a separator at the end of dirc if not exists */
906: l1 = strlen( dirc ); /* length of directory */
907: if( dirc[l1-1] != DIRSEPARATOR ){
908: dirc[l1] = DIRSEPARATOR;
909: dirc[l1+1] = 0;
910: printf(" DIRC3 = %s \n",dirc);
911: }
912: ss = strrchr( name, '.' ); /* find last / */
913: if (ss >0){
914: ss++;
915: strcpy(ext,ss); /* save extension */
916: l1= strlen( name);
917: l2= strlen(ss)+1;
918: strncpy( finame, name, l1-l2);
919: finame[l1-l2]= 0;
920: }
921:
922: return( 0 ); /* we're done */
923: }
924:
925:
926: /******************************************/
927:
928: void replace_back_to_slash(char *s, char*t)
929: {
930: int i;
931: int lg=0;
932: i=0;
933: lg=strlen(t);
934: for(i=0; i<= lg; i++) {
935: (s[i] = t[i]);
936: if (t[i]== '\\') s[i]='/';
937: }
938: }
939:
1.132 brouard 940: char *trimbb(char *out, char *in)
1.137 brouard 941: { /* Trim multiple blanks in line but keeps first blanks if line starts with blanks */
1.132 brouard 942: char *s;
943: s=out;
944: while (*in != '\0'){
1.137 brouard 945: while( *in == ' ' && *(in+1) == ' '){ /* && *(in+1) != '\0'){*/
1.132 brouard 946: in++;
947: }
948: *out++ = *in++;
949: }
950: *out='\0';
951: return s;
952: }
953:
1.187 brouard 954: /* char *substrchaine(char *out, char *in, char *chain) */
955: /* { */
956: /* /\* Substract chain 'chain' from 'in', return and output 'out' *\/ */
957: /* char *s, *t; */
958: /* t=in;s=out; */
959: /* while ((*in != *chain) && (*in != '\0')){ */
960: /* *out++ = *in++; */
961: /* } */
962:
963: /* /\* *in matches *chain *\/ */
964: /* while ((*in++ == *chain++) && (*in != '\0')){ */
965: /* printf("*in = %c, *out= %c *chain= %c \n", *in, *out, *chain); */
966: /* } */
967: /* in--; chain--; */
968: /* while ( (*in != '\0')){ */
969: /* printf("Bef *in = %c, *out= %c *chain= %c \n", *in, *out, *chain); */
970: /* *out++ = *in++; */
971: /* printf("Aft *in = %c, *out= %c *chain= %c \n", *in, *out, *chain); */
972: /* } */
973: /* *out='\0'; */
974: /* out=s; */
975: /* return out; */
976: /* } */
977: char *substrchaine(char *out, char *in, char *chain)
978: {
979: /* Substract chain 'chain' from 'in', return and output 'out' */
980: /* in="V1+V1*age+age*age+V2", chain="age*age" */
981:
982: char *strloc;
983:
984: strcpy (out, in);
985: strloc = strstr(out, chain); /* strloc points to out at age*age+V2 */
986: printf("Bef strloc=%s chain=%s out=%s \n", strloc, chain, out);
987: if(strloc != NULL){
988: /* will affect out */ /* strloc+strlenc(chain)=+V2 */ /* Will also work in Unicode */
989: memmove(strloc,strloc+strlen(chain), strlen(strloc+strlen(chain))+1);
990: /* strcpy (strloc, strloc +strlen(chain));*/
991: }
992: printf("Aft strloc=%s chain=%s in=%s out=%s \n", strloc, chain, in, out);
993: return out;
994: }
995:
996:
1.145 brouard 997: char *cutl(char *blocc, char *alocc, char *in, char occ)
998: {
1.187 brouard 999: /* cuts string in into blocc and alocc where blocc ends before FIRST occurence of char 'occ'
1.145 brouard 1000: and alocc starts after first occurence of char 'occ' : ex cutv(blocc,alocc,"abcdef2ghi2j",'2')
1.187 brouard 1001: gives blocc="abcdef" and alocc="ghi2j".
1.145 brouard 1002: If occ is not found blocc is null and alocc is equal to in. Returns blocc
1003: */
1.160 brouard 1004: char *s, *t;
1.145 brouard 1005: t=in;s=in;
1006: while ((*in != occ) && (*in != '\0')){
1007: *alocc++ = *in++;
1008: }
1009: if( *in == occ){
1010: *(alocc)='\0';
1011: s=++in;
1012: }
1013:
1014: if (s == t) {/* occ not found */
1015: *(alocc-(in-s))='\0';
1016: in=s;
1017: }
1018: while ( *in != '\0'){
1019: *blocc++ = *in++;
1020: }
1021:
1022: *blocc='\0';
1023: return t;
1024: }
1.137 brouard 1025: char *cutv(char *blocc, char *alocc, char *in, char occ)
1026: {
1.187 brouard 1027: /* cuts string in into blocc and alocc where blocc ends before LAST occurence of char 'occ'
1.137 brouard 1028: and alocc starts after last occurence of char 'occ' : ex cutv(blocc,alocc,"abcdef2ghi2j",'2')
1029: gives blocc="abcdef2ghi" and alocc="j".
1030: If occ is not found blocc is null and alocc is equal to in. Returns alocc
1031: */
1032: char *s, *t;
1033: t=in;s=in;
1034: while (*in != '\0'){
1035: while( *in == occ){
1036: *blocc++ = *in++;
1037: s=in;
1038: }
1039: *blocc++ = *in++;
1040: }
1041: if (s == t) /* occ not found */
1042: *(blocc-(in-s))='\0';
1043: else
1044: *(blocc-(in-s)-1)='\0';
1045: in=s;
1046: while ( *in != '\0'){
1047: *alocc++ = *in++;
1048: }
1049:
1050: *alocc='\0';
1051: return s;
1052: }
1053:
1.126 brouard 1054: int nbocc(char *s, char occ)
1055: {
1056: int i,j=0;
1057: int lg=20;
1058: i=0;
1059: lg=strlen(s);
1060: for(i=0; i<= lg; i++) {
1061: if (s[i] == occ ) j++;
1062: }
1063: return j;
1064: }
1065:
1.137 brouard 1066: /* void cutv(char *u,char *v, char*t, char occ) */
1067: /* { */
1068: /* /\* cuts string t into u and v where u ends before last occurence of char 'occ' */
1069: /* and v starts after last occurence of char 'occ' : ex cutv(u,v,"abcdef2ghi2j",'2') */
1070: /* gives u="abcdef2ghi" and v="j" *\/ */
1071: /* int i,lg,j,p=0; */
1072: /* i=0; */
1073: /* lg=strlen(t); */
1074: /* for(j=0; j<=lg-1; j++) { */
1075: /* if((t[j]!= occ) && (t[j+1]== occ)) p=j+1; */
1076: /* } */
1.126 brouard 1077:
1.137 brouard 1078: /* for(j=0; j<p; j++) { */
1079: /* (u[j] = t[j]); */
1080: /* } */
1081: /* u[p]='\0'; */
1.126 brouard 1082:
1.137 brouard 1083: /* for(j=0; j<= lg; j++) { */
1084: /* if (j>=(p+1))(v[j-p-1] = t[j]); */
1085: /* } */
1086: /* } */
1.126 brouard 1087:
1.160 brouard 1088: #ifdef _WIN32
1089: char * strsep(char **pp, const char *delim)
1090: {
1091: char *p, *q;
1092:
1093: if ((p = *pp) == NULL)
1094: return 0;
1095: if ((q = strpbrk (p, delim)) != NULL)
1096: {
1097: *pp = q + 1;
1098: *q = '\0';
1099: }
1100: else
1101: *pp = 0;
1102: return p;
1103: }
1104: #endif
1105:
1.126 brouard 1106: /********************** nrerror ********************/
1107:
1108: void nrerror(char error_text[])
1109: {
1110: fprintf(stderr,"ERREUR ...\n");
1111: fprintf(stderr,"%s\n",error_text);
1112: exit(EXIT_FAILURE);
1113: }
1114: /*********************** vector *******************/
1115: double *vector(int nl, int nh)
1116: {
1117: double *v;
1118: v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
1119: if (!v) nrerror("allocation failure in vector");
1120: return v-nl+NR_END;
1121: }
1122:
1123: /************************ free vector ******************/
1124: void free_vector(double*v, int nl, int nh)
1125: {
1126: free((FREE_ARG)(v+nl-NR_END));
1127: }
1128:
1129: /************************ivector *******************************/
1130: int *ivector(long nl,long nh)
1131: {
1132: int *v;
1133: v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
1134: if (!v) nrerror("allocation failure in ivector");
1135: return v-nl+NR_END;
1136: }
1137:
1138: /******************free ivector **************************/
1139: void free_ivector(int *v, long nl, long nh)
1140: {
1141: free((FREE_ARG)(v+nl-NR_END));
1142: }
1143:
1144: /************************lvector *******************************/
1145: long *lvector(long nl,long nh)
1146: {
1147: long *v;
1148: v=(long *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(long)));
1149: if (!v) nrerror("allocation failure in ivector");
1150: return v-nl+NR_END;
1151: }
1152:
1153: /******************free lvector **************************/
1154: void free_lvector(long *v, long nl, long nh)
1155: {
1156: free((FREE_ARG)(v+nl-NR_END));
1157: }
1158:
1159: /******************* imatrix *******************************/
1160: int **imatrix(long nrl, long nrh, long ncl, long nch)
1161: /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */
1162: {
1163: long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;
1164: int **m;
1165:
1166: /* allocate pointers to rows */
1167: m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));
1168: if (!m) nrerror("allocation failure 1 in matrix()");
1169: m += NR_END;
1170: m -= nrl;
1171:
1172:
1173: /* allocate rows and set pointers to them */
1174: m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));
1175: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
1176: m[nrl] += NR_END;
1177: m[nrl] -= ncl;
1178:
1179: for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;
1180:
1181: /* return pointer to array of pointers to rows */
1182: return m;
1183: }
1184:
1185: /****************** free_imatrix *************************/
1186: void free_imatrix(m,nrl,nrh,ncl,nch)
1187: int **m;
1188: long nch,ncl,nrh,nrl;
1189: /* free an int matrix allocated by imatrix() */
1190: {
1191: free((FREE_ARG) (m[nrl]+ncl-NR_END));
1192: free((FREE_ARG) (m+nrl-NR_END));
1193: }
1194:
1195: /******************* matrix *******************************/
1196: double **matrix(long nrl, long nrh, long ncl, long nch)
1197: {
1198: long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
1199: double **m;
1200:
1201: m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
1202: if (!m) nrerror("allocation failure 1 in matrix()");
1203: m += NR_END;
1204: m -= nrl;
1205:
1206: m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
1207: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
1208: m[nrl] += NR_END;
1209: m[nrl] -= ncl;
1210:
1211: for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
1212: return m;
1.145 brouard 1213: /* print *(*(m+1)+70) or print m[1][70]; print m+1 or print &(m[1]) or &(m[1][0])
1214: m[i] = address of ith row of the table. &(m[i]) is its value which is another adress
1215: that of m[i][0]. In order to get the value p m[i][0] but it is unitialized.
1.126 brouard 1216: */
1217: }
1218:
1219: /*************************free matrix ************************/
1220: void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
1221: {
1222: free((FREE_ARG)(m[nrl]+ncl-NR_END));
1223: free((FREE_ARG)(m+nrl-NR_END));
1224: }
1225:
1226: /******************* ma3x *******************************/
1227: double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
1228: {
1229: long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
1230: double ***m;
1231:
1232: m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
1233: if (!m) nrerror("allocation failure 1 in matrix()");
1234: m += NR_END;
1235: m -= nrl;
1236:
1237: m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
1238: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
1239: m[nrl] += NR_END;
1240: m[nrl] -= ncl;
1241:
1242: for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
1243:
1244: m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
1245: if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
1246: m[nrl][ncl] += NR_END;
1247: m[nrl][ncl] -= nll;
1248: for (j=ncl+1; j<=nch; j++)
1249: m[nrl][j]=m[nrl][j-1]+nlay;
1250:
1251: for (i=nrl+1; i<=nrh; i++) {
1252: m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
1253: for (j=ncl+1; j<=nch; j++)
1254: m[i][j]=m[i][j-1]+nlay;
1255: }
1256: return m;
1257: /* gdb: p *(m+1) <=> p m[1] and p (m+1) <=> p (m+1) <=> p &(m[1])
1258: &(m[i][j][k]) <=> *((*(m+i) + j)+k)
1259: */
1260: }
1261:
1262: /*************************free ma3x ************************/
1263: void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
1264: {
1265: free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
1266: free((FREE_ARG)(m[nrl]+ncl-NR_END));
1267: free((FREE_ARG)(m+nrl-NR_END));
1268: }
1269:
1270: /*************** function subdirf ***********/
1271: char *subdirf(char fileres[])
1272: {
1273: /* Caution optionfilefiname is hidden */
1274: strcpy(tmpout,optionfilefiname);
1275: strcat(tmpout,"/"); /* Add to the right */
1276: strcat(tmpout,fileres);
1277: return tmpout;
1278: }
1279:
1280: /*************** function subdirf2 ***********/
1281: char *subdirf2(char fileres[], char *preop)
1282: {
1283:
1284: /* Caution optionfilefiname is hidden */
1285: strcpy(tmpout,optionfilefiname);
1286: strcat(tmpout,"/");
1287: strcat(tmpout,preop);
1288: strcat(tmpout,fileres);
1289: return tmpout;
1290: }
1291:
1292: /*************** function subdirf3 ***********/
1293: char *subdirf3(char fileres[], char *preop, char *preop2)
1294: {
1295:
1296: /* Caution optionfilefiname is hidden */
1297: strcpy(tmpout,optionfilefiname);
1298: strcat(tmpout,"/");
1299: strcat(tmpout,preop);
1300: strcat(tmpout,preop2);
1301: strcat(tmpout,fileres);
1302: return tmpout;
1303: }
1304:
1.162 brouard 1305: char *asc_diff_time(long time_sec, char ascdiff[])
1306: {
1307: long sec_left, days, hours, minutes;
1308: days = (time_sec) / (60*60*24);
1309: sec_left = (time_sec) % (60*60*24);
1310: hours = (sec_left) / (60*60) ;
1311: sec_left = (sec_left) %(60*60);
1312: minutes = (sec_left) /60;
1313: sec_left = (sec_left) % (60);
1314: sprintf(ascdiff,"%ld day(s) %ld hour(s) %ld minute(s) %ld second(s)",days, hours, minutes, sec_left);
1315: return ascdiff;
1316: }
1317:
1.126 brouard 1318: /***************** f1dim *************************/
1319: extern int ncom;
1320: extern double *pcom,*xicom;
1321: extern double (*nrfunc)(double []);
1322:
1323: double f1dim(double x)
1324: {
1325: int j;
1326: double f;
1327: double *xt;
1328:
1329: xt=vector(1,ncom);
1330: for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];
1331: f=(*nrfunc)(xt);
1332: free_vector(xt,1,ncom);
1333: return f;
1334: }
1335:
1336: /*****************brent *************************/
1337: double brent(double ax, double bx, double cx, double (*f)(double), double tol, double *xmin)
1.187 brouard 1338: {
1339: /* Given a function f, and given a bracketing triplet of abscissas ax, bx, cx (such that bx is
1340: * between ax and cx, and f(bx) is less than both f(ax) and f(cx) ), this routine isolates
1341: * the minimum to a fractional precision of about tol using Brent’s method. The abscissa of
1342: * the minimum is returned as xmin, and the minimum function value is returned as brent , the
1343: * returned function value.
1344: */
1.126 brouard 1345: int iter;
1346: double a,b,d,etemp;
1.159 brouard 1347: double fu=0,fv,fw,fx;
1.164 brouard 1348: double ftemp=0.;
1.126 brouard 1349: double p,q,r,tol1,tol2,u,v,w,x,xm;
1350: double e=0.0;
1351:
1352: a=(ax < cx ? ax : cx);
1353: b=(ax > cx ? ax : cx);
1354: x=w=v=bx;
1355: fw=fv=fx=(*f)(x);
1356: for (iter=1;iter<=ITMAX;iter++) {
1357: xm=0.5*(a+b);
1358: tol2=2.0*(tol1=tol*fabs(x)+ZEPS);
1359: /* if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
1360: printf(".");fflush(stdout);
1361: fprintf(ficlog,".");fflush(ficlog);
1.162 brouard 1362: #ifdef DEBUGBRENT
1.126 brouard 1363: 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);
1364: 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);
1365: /* if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
1366: #endif
1367: if (fabs(x-xm) <= (tol2-0.5*(b-a))){
1368: *xmin=x;
1369: return fx;
1370: }
1371: ftemp=fu;
1372: if (fabs(e) > tol1) {
1373: r=(x-w)*(fx-fv);
1374: q=(x-v)*(fx-fw);
1375: p=(x-v)*q-(x-w)*r;
1376: q=2.0*(q-r);
1377: if (q > 0.0) p = -p;
1378: q=fabs(q);
1379: etemp=e;
1380: e=d;
1381: if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))
1382: d=CGOLD*(e=(x >= xm ? a-x : b-x));
1383: else {
1384: d=p/q;
1385: u=x+d;
1386: if (u-a < tol2 || b-u < tol2)
1387: d=SIGN(tol1,xm-x);
1388: }
1389: } else {
1390: d=CGOLD*(e=(x >= xm ? a-x : b-x));
1391: }
1392: u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));
1393: fu=(*f)(u);
1394: if (fu <= fx) {
1395: if (u >= x) a=x; else b=x;
1396: SHFT(v,w,x,u)
1.183 brouard 1397: SHFT(fv,fw,fx,fu)
1398: } else {
1399: if (u < x) a=u; else b=u;
1400: if (fu <= fw || w == x) {
1401: v=w;
1402: w=u;
1403: fv=fw;
1404: fw=fu;
1405: } else if (fu <= fv || v == x || v == w) {
1406: v=u;
1407: fv=fu;
1408: }
1409: }
1.126 brouard 1410: }
1411: nrerror("Too many iterations in brent");
1412: *xmin=x;
1413: return fx;
1414: }
1415:
1416: /****************** mnbrak ***********************/
1417:
1418: void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,
1419: double (*func)(double))
1.183 brouard 1420: { /* Given a function func , and given distinct initial points ax and bx , this routine searches in
1421: the downhill direction (defined by the function as evaluated at the initial points) and returns
1422: new points ax , bx , cx that bracket a minimum of the function. Also returned are the function
1423: values at the three points, fa, fb , and fc such that fa > fb and fb < fc.
1424: */
1.126 brouard 1425: double ulim,u,r,q, dum;
1426: double fu;
1.187 brouard 1427:
1428: double scale=10.;
1429: int iterscale=0;
1430:
1431: *fa=(*func)(*ax); /* xta[j]=pcom[j]+(*ax)*xicom[j]; fa=f(xta[j])*/
1432: *fb=(*func)(*bx); /* xtb[j]=pcom[j]+(*bx)*xicom[j]; fb=f(xtb[j]) */
1433:
1434:
1435: /* while(*fb != *fb){ /\* *ax should be ok, reducing distance to *ax *\/ */
1436: /* printf("Warning mnbrak *fb = %lf, *bx=%lf *ax=%lf *fa==%lf iter=%d\n",*fb, *bx, *ax, *fa, iterscale++); */
1437: /* *bx = *ax - (*ax - *bx)/scale; */
1438: /* *fb=(*func)(*bx); /\* xtb[j]=pcom[j]+(*bx)*xicom[j]; fb=f(xtb[j]) *\/ */
1439: /* } */
1440:
1.126 brouard 1441: if (*fb > *fa) {
1442: SHFT(dum,*ax,*bx,dum)
1.183 brouard 1443: SHFT(dum,*fb,*fa,dum)
1444: }
1.126 brouard 1445: *cx=(*bx)+GOLD*(*bx-*ax);
1446: *fc=(*func)(*cx);
1.183 brouard 1447: #ifdef DEBUG
1448: printf("mnbrak0 *fb=%.12e *fc=%.12e\n",*fb,*fc);
1449: fprintf(ficlog,"mnbrak0 *fb=%.12e *fc=%.12e\n",*fb,*fc);
1450: #endif
1451: while (*fb > *fc) { /* Declining a,b,c with fa> fb > fc */
1.126 brouard 1452: r=(*bx-*ax)*(*fb-*fc);
1453: q=(*bx-*cx)*(*fb-*fa);
1454: u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/
1.183 brouard 1455: (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r)); /* Minimum abscissa of a parabolic estimated from (a,fa), (b,fb) and (c,fc). */
1456: ulim=(*bx)+GLIMIT*(*cx-*bx); /* Maximum abscissa where function should be evaluated */
1457: if ((*bx-u)*(u-*cx) > 0.0) { /* if u_p is between b and c */
1.126 brouard 1458: fu=(*func)(u);
1.163 brouard 1459: #ifdef DEBUG
1460: /* f(x)=A(x-u)**2+f(u) */
1461: double A, fparabu;
1462: A= (*fb - *fa)/(*bx-*ax)/(*bx+*ax-2*u);
1463: fparabu= *fa - A*(*ax-u)*(*ax-u);
1464: 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);
1465: 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 1466: /* And thus,it can be that fu > *fc even if fparabu < *fc */
1467: /* mnbrak (*ax=7.666299858533, *fa=299039.693133272231), (*bx=8.595447774979, *fb=298976.598289369489),
1468: (*cx=10.098840694817, *fc=298946.631474258087), (*u=9.852501168332, fu=298948.773013752128, fparabu=298945.434711494134) */
1469: /* In that case, there is no bracket in the output! Routine is wrong with many consequences.*/
1.163 brouard 1470: #endif
1.184 brouard 1471: #ifdef MNBRAKORIGINAL
1.183 brouard 1472: #else
1.191 brouard 1473: /* if (fu > *fc) { */
1474: /* #ifdef DEBUG */
1475: /* printf("mnbrak4 fu > fc \n"); */
1476: /* fprintf(ficlog, "mnbrak4 fu > fc\n"); */
1477: /* #endif */
1478: /* /\* 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 *\\/ *\/ */
1479: /* /\* SHFT(*fa,*fc,fu,*fc) /\\* (b, u, c) is a bracket while test fb > fc will be fu > fc will exit *\\/ *\/ */
1480: /* dum=u; /\* Shifting c and u *\/ */
1481: /* u = *cx; */
1482: /* *cx = dum; */
1483: /* dum = fu; */
1484: /* fu = *fc; */
1485: /* *fc =dum; */
1486: /* } else { /\* end *\/ */
1487: /* #ifdef DEBUG */
1488: /* printf("mnbrak3 fu < fc \n"); */
1489: /* fprintf(ficlog, "mnbrak3 fu < fc\n"); */
1490: /* #endif */
1491: /* dum=u; /\* Shifting c and u *\/ */
1492: /* u = *cx; */
1493: /* *cx = dum; */
1494: /* dum = fu; */
1495: /* fu = *fc; */
1496: /* *fc =dum; */
1497: /* } */
1.183 brouard 1498: #ifdef DEBUG
1.191 brouard 1499: printf("mnbrak34 fu < or >= fc \n");
1500: fprintf(ficlog, "mnbrak34 fu < fc\n");
1.183 brouard 1501: #endif
1.191 brouard 1502: dum=u; /* Shifting c and u */
1503: u = *cx;
1504: *cx = dum;
1505: dum = fu;
1506: fu = *fc;
1507: *fc =dum;
1.183 brouard 1508: #endif
1.162 brouard 1509: } else if ((*cx-u)*(u-ulim) > 0.0) { /* u is after c but before ulim */
1.183 brouard 1510: #ifdef DEBUG
1511: printf("mnbrak2 u after c but before ulim\n");
1512: fprintf(ficlog, "mnbrak2 u after c but before ulim\n");
1513: #endif
1.126 brouard 1514: fu=(*func)(u);
1515: if (fu < *fc) {
1.183 brouard 1516: #ifdef DEBUG
1517: printf("mnbrak2 u after c but before ulim AND fu < fc\n");
1518: fprintf(ficlog, "mnbrak2 u after c but before ulim AND fu <fc \n");
1519: #endif
1.126 brouard 1520: SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))
1.183 brouard 1521: SHFT(*fb,*fc,fu,(*func)(u))
1522: }
1.162 brouard 1523: } else if ((u-ulim)*(ulim-*cx) >= 0.0) { /* u outside ulim (verifying that ulim is beyond c) */
1.183 brouard 1524: #ifdef DEBUG
1525: printf("mnbrak2 u outside ulim (verifying that ulim is beyond c)\n");
1526: fprintf(ficlog, "mnbrak2 u outside ulim (verifying that ulim is beyond c)\n");
1527: #endif
1.126 brouard 1528: u=ulim;
1529: fu=(*func)(u);
1.183 brouard 1530: } else { /* u could be left to b (if r > q parabola has a maximum) */
1531: #ifdef DEBUG
1532: printf("mnbrak2 u could be left to b (if r > q parabola has a maximum)\n");
1533: fprintf(ficlog, "mnbrak2 u could be left to b (if r > q parabola has a maximum)\n");
1534: #endif
1.126 brouard 1535: u=(*cx)+GOLD*(*cx-*bx);
1536: fu=(*func)(u);
1.183 brouard 1537: } /* end tests */
1.126 brouard 1538: SHFT(*ax,*bx,*cx,u)
1.183 brouard 1539: SHFT(*fa,*fb,*fc,fu)
1540: #ifdef DEBUG
1541: 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);
1542: 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);
1543: #endif
1544: } /* 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 1545: }
1546:
1547: /*************** linmin ************************/
1.162 brouard 1548: /* Given an n -dimensional point p[1..n] and an n -dimensional direction xi[1..n] , moves and
1549: resets p to where the function func(p) takes on a minimum along the direction xi from p ,
1550: and replaces xi by the actual vector displacement that p was moved. Also returns as fret
1551: the value of func at the returned location p . This is actually all accomplished by calling the
1552: routines mnbrak and brent .*/
1.126 brouard 1553: int ncom;
1554: double *pcom,*xicom;
1555: double (*nrfunc)(double []);
1556:
1557: void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))
1558: {
1559: double brent(double ax, double bx, double cx,
1560: double (*f)(double), double tol, double *xmin);
1561: double f1dim(double x);
1562: void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,
1563: double *fc, double (*func)(double));
1564: int j;
1565: double xx,xmin,bx,ax;
1566: double fx,fb,fa;
1.187 brouard 1567:
1568: double scale=10., axs, xxs, xxss; /* Scale added for infinity */
1.126 brouard 1569:
1570: ncom=n;
1571: pcom=vector(1,n);
1572: xicom=vector(1,n);
1573: nrfunc=func;
1574: for (j=1;j<=n;j++) {
1575: pcom[j]=p[j];
1576: xicom[j]=xi[j];
1577: }
1.187 brouard 1578:
1.192 brouard 1579: /* axs=0.0; */
1580: /* xxss=1; /\* 1 and using scale *\/ */
1.187 brouard 1581: xxs=1;
1.192 brouard 1582: /* do{ */
1.187 brouard 1583: ax=0.;
1584: xx= xxs;
1585: mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim); /* Outputs: xtx[j]=pcom[j]+(*xx)*xicom[j]; fx=f(xtx[j]) */
1586: /* brackets with inputs ax=0 and xx=1, but points, pcom=p, and directions values, xicom=xi, are sent via f1dim(x) */
1587: /* 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)) */
1588: /* Outputs: fa=f(p(j)) and fx=f(p(j) + xxs * xi(j) ) and f(bx)= f(p(j)+ bx* xi(j)) */
1589: /* Given input ax=axs and xx=xxs, xx might be too far from ax to get a finite f(xx) */
1590: /* Searches on line, outputs (ax, xx, bx) such that fx < min(fa and fb) */
1591: /* 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]]*/
1.192 brouard 1592: /* if (fx != fx){ */
1593: /* xxs=xxs/scale; /\* Trying a smaller xx, closer to initial ax=0 *\/ */
1594: /* 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); */
1595: /* } */
1596: /* }while(fx != fx); */
1.187 brouard 1597:
1.191 brouard 1598: #ifdef DEBUGLINMIN
1599: 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);
1600: #endif
1.187 brouard 1601: *fret=brent(ax,xx,bx,f1dim,TOL,&xmin); /* Giving a bracketting triplet (ax, xx, bx), find a minimum, xmin, according to f1dim, *fret(xmin),*/
1602: /* fa = f(p[j] + ax * xi[j]), fx = f(p[j] + xx * xi[j]), fb = f(p[j] + bx * xi[j]) */
1603: /* fmin = f(p[j] + xmin * xi[j]) */
1604: /* P+lambda n in that direction (lambdamin), with TOL between abscisses */
1605: /* f1dim(xmin): for (j=1;j<=ncom;j++) xt[j]=pcom[j]+xmin*xicom[j]; */
1.126 brouard 1606: #ifdef DEBUG
1607: printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
1608: fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
1609: #endif
1.191 brouard 1610: #ifdef DEBUGLINMIN
1611: printf("linmin end ");
1612: #endif
1.126 brouard 1613: for (j=1;j<=n;j++) {
1.188 brouard 1614: /* printf(" before xi[%d]=%12.8f", j,xi[j]); */
1.187 brouard 1615: xi[j] *= xmin; /* xi rescaled by xmin: if xmin=-1.237 and xi=(1,0,...,0) xi=(-1.237,0,...,0) */
1.189 brouard 1616: /* if(xxs <1.0) */
1617: /* 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 ); */
1.187 brouard 1618: p[j] += xi[j]; /* Parameters values are updated accordingly */
1.126 brouard 1619: }
1.189 brouard 1620: /* printf("\n"); */
1.191 brouard 1621: #ifdef DEBUGLINMIN
1622: printf("Comparing last *frec(xmin=%12.8f)=%12.8f from Brent and frec(0.)=%12.8f \n", xmin, *fret, (*func)(p));
1623: for (j=1;j<=n;j++) {
1624: printf(" xi[%d]= %12.7f p[%d]= %12.7f",j,xi[j],j,p[j]);
1625: if(j % ncovmodel == 0)
1626: printf("\n");
1627: }
1628: #endif
1.126 brouard 1629: free_vector(xicom,1,n);
1630: free_vector(pcom,1,n);
1631: }
1632:
1633:
1634: /*************** powell ************************/
1.162 brouard 1635: /*
1636: Minimization of a function func of n variables. Input consists of an initial starting point
1637: p[1..n] ; an initial matrix xi[1..n][1..n] , whose columns contain the initial set of di-
1638: rections (usually the n unit vectors); and ftol , the fractional tolerance in the function value
1639: such that failure to decrease by more than this amount on one iteration signals doneness. On
1640: output, p is set to the best point found, xi is the then-current direction set, fret is the returned
1641: function value at p , and iter is the number of iterations taken. The routine linmin is used.
1642: */
1.126 brouard 1643: void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,
1644: double (*func)(double []))
1645: {
1646: void linmin(double p[], double xi[], int n, double *fret,
1647: double (*func)(double []));
1648: int i,ibig,j;
1649: double del,t,*pt,*ptt,*xit;
1.181 brouard 1650: double directest;
1.126 brouard 1651: double fp,fptt;
1652: double *xits;
1653: int niterf, itmp;
1654:
1655: pt=vector(1,n);
1656: ptt=vector(1,n);
1657: xit=vector(1,n);
1658: xits=vector(1,n);
1659: *fret=(*func)(p);
1660: for (j=1;j<=n;j++) pt[j]=p[j];
1.157 brouard 1661: rcurr_time = time(NULL);
1.126 brouard 1662: for (*iter=1;;++(*iter)) {
1.187 brouard 1663: fp=(*fret); /* From former iteration or initial value */
1.126 brouard 1664: ibig=0;
1665: del=0.0;
1.157 brouard 1666: rlast_time=rcurr_time;
1667: /* (void) gettimeofday(&curr_time,&tzp); */
1668: rcurr_time = time(NULL);
1669: curr_time = *localtime(&rcurr_time);
1670: printf("\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret, rcurr_time-rlast_time, rcurr_time-rstart_time);fflush(stdout);
1671: fprintf(ficlog,"\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret,rcurr_time-rlast_time, rcurr_time-rstart_time); fflush(ficlog);
1672: /* fprintf(ficrespow,"%d %.12f %ld",*iter,*fret,curr_time.tm_sec-start_time.tm_sec); */
1.192 brouard 1673: for (i=1;i<=n;i++) {
1.126 brouard 1674: printf(" %d %.12f",i, p[i]);
1675: fprintf(ficlog," %d %.12lf",i, p[i]);
1676: fprintf(ficrespow," %.12lf", p[i]);
1677: }
1678: printf("\n");
1679: fprintf(ficlog,"\n");
1680: fprintf(ficrespow,"\n");fflush(ficrespow);
1681: if(*iter <=3){
1.157 brouard 1682: tml = *localtime(&rcurr_time);
1683: strcpy(strcurr,asctime(&tml));
1684: rforecast_time=rcurr_time;
1.126 brouard 1685: itmp = strlen(strcurr);
1686: if(strcurr[itmp-1]=='\n') /* Windows outputs with a new line */
1687: strcurr[itmp-1]='\0';
1.162 brouard 1688: printf("\nConsidering the time needed for the last iteration #%d: %ld seconds,\n",*iter,rcurr_time-rlast_time);
1.157 brouard 1689: fprintf(ficlog,"\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,rcurr_time-rlast_time);
1.126 brouard 1690: for(niterf=10;niterf<=30;niterf+=10){
1.157 brouard 1691: rforecast_time=rcurr_time+(niterf-*iter)*(rcurr_time-rlast_time);
1692: forecast_time = *localtime(&rforecast_time);
1693: strcpy(strfor,asctime(&forecast_time));
1.126 brouard 1694: itmp = strlen(strfor);
1695: if(strfor[itmp-1]=='\n')
1696: strfor[itmp-1]='\0';
1.157 brouard 1697: 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);
1698: 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 1699: }
1700: }
1.187 brouard 1701: for (i=1;i<=n;i++) { /* For each direction i */
1702: for (j=1;j<=n;j++) xit[j]=xi[j][i]; /* Directions stored from previous iteration with previous scales */
1.126 brouard 1703: fptt=(*fret);
1704: #ifdef DEBUG
1.164 brouard 1705: printf("fret=%lf, %lf, %lf \n", *fret, *fret, *fret);
1706: fprintf(ficlog, "fret=%lf, %lf, %lf \n", *fret, *fret, *fret);
1.126 brouard 1707: #endif
1.187 brouard 1708: printf("%d",i);fflush(stdout); /* print direction (parameter) i */
1.126 brouard 1709: fprintf(ficlog,"%d",i);fflush(ficlog);
1.188 brouard 1710: linmin(p,xit,n,fret,func); /* Point p[n]. xit[n] has been loaded for direction i as input.*/
1711: /* Outputs are fret(new point p) p is updated and xit rescaled */
1712: if (fabs(fptt-(*fret)) > del) { /* We are keeping the max gain on each of the n directions */
1713: /* because that direction will be replaced unless the gain del is small */
1714: /* in comparison with the 'probable' gain, mu^2, with the last average direction. */
1715: /* Unless the n directions are conjugate some gain in the determinant may be obtained */
1716: /* with the new direction. */
1.126 brouard 1717: del=fabs(fptt-(*fret));
1718: ibig=i;
1719: }
1720: #ifdef DEBUG
1721: printf("%d %.12e",i,(*fret));
1722: fprintf(ficlog,"%d %.12e",i,(*fret));
1723: for (j=1;j<=n;j++) {
1724: xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
1725: printf(" x(%d)=%.12e",j,xit[j]);
1726: fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
1727: }
1728: for(j=1;j<=n;j++) {
1.162 brouard 1729: printf(" p(%d)=%.12e",j,p[j]);
1730: fprintf(ficlog," p(%d)=%.12e",j,p[j]);
1.126 brouard 1731: }
1732: printf("\n");
1733: fprintf(ficlog,"\n");
1734: #endif
1.187 brouard 1735: } /* end loop on each direction i */
1736: /* Convergence test will use last linmin estimation (fret) and compare former iteration (fp) */
1.188 brouard 1737: /* But p and xit have been updated at the end of linmin, *fret corresponds to new p, xit */
1.187 brouard 1738: /* New value of last point Pn is not computed, P(n-1) */
1.182 brouard 1739: if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) { /* Did we reach enough precision? */
1.188 brouard 1740: /* We could compare with a chi^2. chisquare(0.95,ddl=1)=3.84 */
1741: /* By adding age*age in a model, the new -2LL should be lower and the difference follows a */
1742: /* a chisquare statistics with 1 degree. To be significant at the 95% level, it should have */
1743: /* decreased of more than 3.84 */
1744: /* By adding age*age and V1*age the gain (-2LL) should be more than 5.99 (ddl=2) */
1745: /* By using V1+V2+V3, the gain should be 7.82, compared with basic 1+age. */
1746: /* By adding 10 parameters more the gain should be 18.31 */
1747:
1748: /* Starting the program with initial values given by a former maximization will simply change */
1749: /* the scales of the directions and the directions, because the are reset to canonical directions */
1750: /* Thus the first calls to linmin will give new points and better maximizations until fp-(*fret) is */
1751: /* under the tolerance value. If the tolerance is very small 1.e-9, it could last long. */
1.126 brouard 1752: #ifdef DEBUG
1753: int k[2],l;
1754: k[0]=1;
1755: k[1]=-1;
1756: printf("Max: %.12e",(*func)(p));
1757: fprintf(ficlog,"Max: %.12e",(*func)(p));
1758: for (j=1;j<=n;j++) {
1759: printf(" %.12e",p[j]);
1760: fprintf(ficlog," %.12e",p[j]);
1761: }
1762: printf("\n");
1763: fprintf(ficlog,"\n");
1764: for(l=0;l<=1;l++) {
1765: for (j=1;j<=n;j++) {
1766: ptt[j]=p[j]+(p[j]-pt[j])*k[l];
1767: printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
1768: fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
1769: }
1770: printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
1771: fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
1772: }
1773: #endif
1774:
1775:
1776: free_vector(xit,1,n);
1777: free_vector(xits,1,n);
1778: free_vector(ptt,1,n);
1779: free_vector(pt,1,n);
1780: return;
1.192 brouard 1781: } /* enough precision */
1.126 brouard 1782: if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");
1.181 brouard 1783: for (j=1;j<=n;j++) { /* Computes the extrapolated point P_0 + 2 (P_n-P_0) */
1.126 brouard 1784: ptt[j]=2.0*p[j]-pt[j];
1785: xit[j]=p[j]-pt[j];
1786: pt[j]=p[j];
1787: }
1.181 brouard 1788: fptt=(*func)(ptt); /* f_3 */
1.192 brouard 1789: #ifdef POWELLF1F3
1790: #else
1.161 brouard 1791: if (fptt < fp) { /* If extrapolated point is better, decide if we keep that new direction or not */
1.192 brouard 1792: #endif
1.162 brouard 1793: /* (x1 f1=fp), (x2 f2=*fret), (x3 f3=fptt), (xm fm) */
1.161 brouard 1794: /* From x1 (P0) distance of x2 is at h and x3 is 2h */
1.162 brouard 1795: /* Let f"(x2) be the 2nd derivative equal everywhere. */
1796: /* Then the parabolic through (x1,f1), (x2,f2) and (x3,f3) */
1797: /* will reach at f3 = fm + h^2/2 f"m ; f" = (f1 -2f2 +f3 ) / h**2 */
1.181 brouard 1798: /* Conditional for using this new direction is that mu^2 = (f1-2f2+f3)^2 /2 < del */
1.161 brouard 1799: /* t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt); */
1.183 brouard 1800: #ifdef NRCORIGINAL
1801: t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)- del*SQR(fp-fptt); /* Original Numerical Recipes in C*/
1802: #else
1803: 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 1804: t= t- del*SQR(fp-fptt);
1.183 brouard 1805: #endif
1.182 brouard 1806: directest = fp-2.0*(*fret)+fptt - 2.0 * del; /* If del was big enough we change it for a new direction */
1.161 brouard 1807: #ifdef DEBUG
1.181 brouard 1808: 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);
1809: 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 1810: printf("t3= %.12lf, t4= %.12lf, t3*= %.12lf, t4*= %.12lf\n",SQR(fp-(*fret)-del),SQR(fp-fptt),
1811: (fp-(*fret)-del)*(fp-(*fret)-del),(fp-fptt)*(fp-fptt));
1812: fprintf(ficlog,"t3= %.12lf, t4= %.12lf, t3*= %.12lf, t4*= %.12lf\n",SQR(fp-(*fret)-del),SQR(fp-fptt),
1813: (fp-(*fret)-del)*(fp-(*fret)-del),(fp-fptt)*(fp-fptt));
1814: 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);
1815: 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);
1816: #endif
1.183 brouard 1817: #ifdef POWELLORIGINAL
1818: if (t < 0.0) { /* Then we use it for new direction */
1819: #else
1.182 brouard 1820: if (directest*t < 0.0) { /* Contradiction between both tests */
1.192 brouard 1821: printf("directest= %.12lf, t= %.12lf, f1= %.12lf,f2= %.12lf,f3= %.12lf, del= %.12lf\n",directest, t, fp,(*fret),fptt,del);
1822: printf("f1-2f2+f3= %.12lf, f1-f2-del= %.12lf, f1-f3= %.12lf\n",fp-2.0*(*fret)+fptt, fp -(*fret) -del, fp-fptt);
1823: fprintf(ficlog,"directest= %.12lf, t= %.12lf, f1= %.12lf,f2= %.12lf,f3= %.12lf, del= %.12lf\n",directest, t, fp,(*fret),fptt, del);
1824: fprintf(ficlog,"f1-2f2+f3= %.12lf, f1-f2-del= %.12lf, f1-f3= %.12lf\n",fp-2.0*(*fret)+fptt, fp -(*fret) -del, fp-fptt);
1825: }
1.181 brouard 1826: if (directest < 0.0) { /* Then we use it for new direction */
1827: #endif
1.191 brouard 1828: #ifdef DEBUGLINMIN
1829: printf("Before linmin in direction P%d-P0\n",n);
1830: for (j=1;j<=n;j++) {
1831: printf("Before xit[%d]= %12.7f p[%d]= %12.7f",j,xit[j],j,p[j]);
1832: if(j % ncovmodel == 0)
1833: printf("\n");
1834: }
1835: #endif
1.187 brouard 1836: linmin(p,xit,n,fret,func); /* computes minimum on the extrapolated direction: changes p and rescales xit.*/
1.191 brouard 1837: #ifdef DEBUGLINMIN
1838: for (j=1;j<=n;j++) {
1839: printf("After xit[%d]= %12.7f p[%d]= %12.7f",j,xit[j],j,p[j]);
1840: if(j % ncovmodel == 0)
1841: printf("\n");
1842: }
1843: #endif
1.126 brouard 1844: for (j=1;j<=n;j++) {
1.181 brouard 1845: xi[j][ibig]=xi[j][n]; /* Replace direction with biggest decrease by last direction n */
1846: xi[j][n]=xit[j]; /* and this nth direction by the by the average p_0 p_n */
1.126 brouard 1847: }
1.181 brouard 1848: printf("Gaining to use new average direction of P0 P%d instead of biggest increase direction %d :\n",n,ibig);
1849: fprintf(ficlog,"Gaining to use new average direction of P0 P%d instead of biggest increase direction %d :\n",n,ibig);
1.161 brouard 1850:
1.126 brouard 1851: #ifdef DEBUG
1.164 brouard 1852: printf("Direction changed last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
1853: fprintf(ficlog,"Direction changed last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
1.126 brouard 1854: for(j=1;j<=n;j++){
1855: printf(" %.12e",xit[j]);
1856: fprintf(ficlog," %.12e",xit[j]);
1857: }
1858: printf("\n");
1859: fprintf(ficlog,"\n");
1860: #endif
1.192 brouard 1861: } /* end of t or directest negative */
1862: #ifdef POWELLF1F3
1863: #else
1.162 brouard 1864: } /* end if (fptt < fp) */
1.192 brouard 1865: #endif
1866: } /* loop iteration */
1.126 brouard 1867: }
1868:
1869: /**** Prevalence limit (stable or period prevalence) ****************/
1870:
1871: double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)
1872: {
1873: /* Computes the prevalence limit in each live state at age x by left multiplying the unit
1874: matrix by transitions matrix until convergence is reached */
1.169 brouard 1875:
1.126 brouard 1876: int i, ii,j,k;
1877: double min, max, maxmin, maxmax,sumnew=0.;
1.145 brouard 1878: /* double **matprod2(); */ /* test */
1.131 brouard 1879: double **out, cov[NCOVMAX+1], **pmij();
1.126 brouard 1880: double **newm;
1881: double agefin, delaymax=50 ; /* Max number of years to converge */
1.169 brouard 1882:
1.126 brouard 1883: for (ii=1;ii<=nlstate+ndeath;ii++)
1884: for (j=1;j<=nlstate+ndeath;j++){
1885: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1886: }
1.169 brouard 1887:
1888: cov[1]=1.;
1889:
1890: /* Even if hstepm = 1, at least one multiplication by the unit matrix */
1.126 brouard 1891: for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
1892: newm=savm;
1893: /* Covariates have to be included here again */
1.138 brouard 1894: cov[2]=agefin;
1.187 brouard 1895: if(nagesqr==1)
1896: cov[3]= agefin*agefin;;
1.138 brouard 1897: for (k=1; k<=cptcovn;k++) {
1.187 brouard 1898: cov[2+nagesqr+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
1.145 brouard 1899: /*printf("prevalim ij=%d k=%d Tvar[%d]=%d nbcode=%d cov=%lf codtab[%d][Tvar[%d]]=%d \n",ij,k, k, Tvar[k],nbcode[Tvar[k]][codtab[ij][Tvar[k]]],cov[2+k], ij, k, codtab[ij][Tvar[k]]);*/
1.138 brouard 1900: }
1.186 brouard 1901: /*wrong? for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
1.187 brouard 1902: for (k=1; k<=cptcovage;k++) cov[2+nagesqr+Tage[k]]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]]*cov[2];
1.186 brouard 1903: for (k=1; k<=cptcovprod;k++) /* Useless */
1.187 brouard 1904: cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]] * nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
1.138 brouard 1905:
1906: /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
1907: /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
1908: /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
1.145 brouard 1909: /* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
1910: /* out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /\* Bug Valgrind *\/ */
1.142 brouard 1911: out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /* Bug Valgrind */
1.138 brouard 1912:
1.126 brouard 1913: savm=oldm;
1914: oldm=newm;
1915: maxmax=0.;
1916: for(j=1;j<=nlstate;j++){
1917: min=1.;
1918: max=0.;
1919: for(i=1; i<=nlstate; i++) {
1920: sumnew=0;
1921: for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
1922: prlim[i][j]= newm[i][j]/(1-sumnew);
1.145 brouard 1923: /*printf(" prevalim i=%d, j=%d, prmlim[%d][%d]=%f, agefin=%d \n", i, j, i, j, prlim[i][j],(int)agefin);*/
1.126 brouard 1924: max=FMAX(max,prlim[i][j]);
1925: min=FMIN(min,prlim[i][j]);
1926: }
1927: maxmin=max-min;
1928: maxmax=FMAX(maxmax,maxmin);
1.169 brouard 1929: } /* j loop */
1.126 brouard 1930: if(maxmax < ftolpl){
1931: return prlim;
1932: }
1.169 brouard 1933: } /* age loop */
1934: return prlim; /* should not reach here */
1.126 brouard 1935: }
1936:
1937: /*************** transition probabilities ***************/
1938:
1939: double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
1940: {
1.138 brouard 1941: /* According to parameters values stored in x and the covariate's values stored in cov,
1942: computes the probability to be observed in state j being in state i by appying the
1943: model to the ncovmodel covariates (including constant and age).
1944: lnpijopii=ln(pij/pii)= aij+bij*age+cij*v1+dij*v2+... = sum_nc=1^ncovmodel xij(nc)*cov[nc]
1945: and, according on how parameters are entered, the position of the coefficient xij(nc) of the
1946: ncth covariate in the global vector x is given by the formula:
1947: j<i nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel
1948: j>=i nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel
1949: Computes ln(pij/pii) (lnpijopii), deduces pij/pii by exponentiation,
1950: sums on j different of i to get 1-pii/pii, deduces pii, and then all pij.
1951: Outputs ps[i][j] the probability to be observed in j being in j according to
1952: the values of the covariates cov[nc] and corresponding parameter values x[nc+shiftij]
1953: */
1954: double s1, lnpijopii;
1.126 brouard 1955: /*double t34;*/
1.164 brouard 1956: int i,j, nc, ii, jj;
1.126 brouard 1957:
1958: for(i=1; i<= nlstate; i++){
1959: for(j=1; j<i;j++){
1.138 brouard 1960: for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
1961: /*lnpijopii += param[i][j][nc]*cov[nc];*/
1962: lnpijopii += x[nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel]*cov[nc];
1963: /* printf("Int j<i s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
1.126 brouard 1964: }
1.138 brouard 1965: ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
1966: /* printf("s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
1.126 brouard 1967: }
1968: for(j=i+1; j<=nlstate+ndeath;j++){
1.138 brouard 1969: for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
1970: /*lnpijopii += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];*/
1971: lnpijopii += x[nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel]*cov[nc];
1972: /* printf("Int j>i s1=%.17e, lnpijopii=%.17e %lx %lx\n",s1,lnpijopii,s1,lnpijopii); */
1.126 brouard 1973: }
1.138 brouard 1974: ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
1.126 brouard 1975: }
1976: }
1977:
1978: for(i=1; i<= nlstate; i++){
1979: s1=0;
1.131 brouard 1980: for(j=1; j<i; j++){
1.138 brouard 1981: s1+=exp(ps[i][j]); /* In fact sums pij/pii */
1.131 brouard 1982: /*printf("debug1 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
1983: }
1984: for(j=i+1; j<=nlstate+ndeath; j++){
1.138 brouard 1985: s1+=exp(ps[i][j]); /* In fact sums pij/pii */
1.131 brouard 1986: /*printf("debug2 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
1987: }
1.138 brouard 1988: /* s1= sum_{j<>i} pij/pii=(1-pii)/pii and thus pii is known from s1 */
1.126 brouard 1989: ps[i][i]=1./(s1+1.);
1.138 brouard 1990: /* Computing other pijs */
1.126 brouard 1991: for(j=1; j<i; j++)
1992: ps[i][j]= exp(ps[i][j])*ps[i][i];
1993: for(j=i+1; j<=nlstate+ndeath; j++)
1994: ps[i][j]= exp(ps[i][j])*ps[i][i];
1995: /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
1996: } /* end i */
1997:
1998: for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
1999: for(jj=1; jj<= nlstate+ndeath; jj++){
2000: ps[ii][jj]=0;
2001: ps[ii][ii]=1;
2002: }
2003: }
2004:
1.145 brouard 2005:
2006: /* for(ii=1; ii<= nlstate+ndeath; ii++){ */
2007: /* for(jj=1; jj<= nlstate+ndeath; jj++){ */
2008: /* printf(" pmij ps[%d][%d]=%lf ",ii,jj,ps[ii][jj]); */
2009: /* } */
2010: /* printf("\n "); */
2011: /* } */
2012: /* printf("\n ");printf("%lf ",cov[2]);*/
2013: /*
1.126 brouard 2014: for(i=1; i<= npar; i++) printf("%f ",x[i]);
2015: goto end;*/
2016: return ps;
2017: }
2018:
2019: /**************** Product of 2 matrices ******************/
2020:
1.145 brouard 2021: double **matprod2(double **out, double **in,int nrl, int nrh, int ncl, int nch, int ncolol, int ncoloh, double **b)
1.126 brouard 2022: {
2023: /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
2024: b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
2025: /* in, b, out are matrice of pointers which should have been initialized
2026: before: only the contents of out is modified. The function returns
2027: a pointer to pointers identical to out */
1.145 brouard 2028: int i, j, k;
1.126 brouard 2029: for(i=nrl; i<= nrh; i++)
1.145 brouard 2030: for(k=ncolol; k<=ncoloh; k++){
2031: out[i][k]=0.;
2032: for(j=ncl; j<=nch; j++)
2033: out[i][k] +=in[i][j]*b[j][k];
2034: }
1.126 brouard 2035: return out;
2036: }
2037:
2038:
2039: /************* Higher Matrix Product ***************/
2040:
2041: double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
2042: {
2043: /* Computes the transition matrix starting at age 'age' over
2044: 'nhstepm*hstepm*stepm' months (i.e. until
2045: age (in years) age+nhstepm*hstepm*stepm/12) by multiplying
2046: nhstepm*hstepm matrices.
2047: Output is stored in matrix po[i][j][h] for h every 'hstepm' step
2048: (typically every 2 years instead of every month which is too big
2049: for the memory).
2050: Model is determined by parameters x and covariates have to be
2051: included manually here.
2052:
2053: */
2054:
2055: int i, j, d, h, k;
1.131 brouard 2056: double **out, cov[NCOVMAX+1];
1.126 brouard 2057: double **newm;
1.187 brouard 2058: double agexact;
1.126 brouard 2059:
2060: /* Hstepm could be zero and should return the unit matrix */
2061: for (i=1;i<=nlstate+ndeath;i++)
2062: for (j=1;j<=nlstate+ndeath;j++){
2063: oldm[i][j]=(i==j ? 1.0 : 0.0);
2064: po[i][j][0]=(i==j ? 1.0 : 0.0);
2065: }
2066: /* Even if hstepm = 1, at least one multiplication by the unit matrix */
2067: for(h=1; h <=nhstepm; h++){
2068: for(d=1; d <=hstepm; d++){
2069: newm=savm;
2070: /* Covariates have to be included here again */
2071: cov[1]=1.;
1.187 brouard 2072: agexact=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
2073: cov[2]=agexact;
2074: if(nagesqr==1)
2075: cov[3]= agexact*agexact;
1.131 brouard 2076: for (k=1; k<=cptcovn;k++)
1.187 brouard 2077: cov[2+nagesqr+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
1.186 brouard 2078: for (k=1; k<=cptcovage;k++) /* Should start at cptcovn+1 */
2079: /* cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
1.187 brouard 2080: cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtab[ij][Tvar[Tage[k]]]]*cov[2];
1.145 brouard 2081: for (k=1; k<=cptcovprod;k++) /* Useless because included in cptcovn */
1.187 brouard 2082: cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
1.126 brouard 2083:
2084:
2085: /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
2086: /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
2087: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,
2088: pmij(pmmij,cov,ncovmodel,x,nlstate));
2089: savm=oldm;
2090: oldm=newm;
2091: }
2092: for(i=1; i<=nlstate+ndeath; i++)
2093: for(j=1;j<=nlstate+ndeath;j++) {
2094: po[i][j][h]=newm[i][j];
1.128 brouard 2095: /*if(h==nhstepm) printf("po[%d][%d][%d]=%f ",i,j,h,po[i][j][h]);*/
1.126 brouard 2096: }
1.128 brouard 2097: /*printf("h=%d ",h);*/
1.126 brouard 2098: } /* end h */
1.128 brouard 2099: /* printf("\n H=%d \n",h); */
1.126 brouard 2100: return po;
2101: }
2102:
1.162 brouard 2103: #ifdef NLOPT
2104: double myfunc(unsigned n, const double *p1, double *grad, void *pd){
2105: double fret;
2106: double *xt;
2107: int j;
2108: myfunc_data *d2 = (myfunc_data *) pd;
2109: /* xt = (p1-1); */
2110: xt=vector(1,n);
2111: for (j=1;j<=n;j++) xt[j]=p1[j-1]; /* xt[1]=p1[0] */
2112:
2113: fret=(d2->function)(xt); /* p xt[1]@8 is fine */
2114: /* fret=(*func)(xt); /\* p xt[1]@8 is fine *\/ */
2115: printf("Function = %.12lf ",fret);
2116: for (j=1;j<=n;j++) printf(" %d %.8lf", j, xt[j]);
2117: printf("\n");
2118: free_vector(xt,1,n);
2119: return fret;
2120: }
2121: #endif
1.126 brouard 2122:
2123: /*************** log-likelihood *************/
2124: double func( double *x)
2125: {
2126: int i, ii, j, k, mi, d, kk;
1.131 brouard 2127: double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
1.126 brouard 2128: double **out;
2129: double sw; /* Sum of weights */
2130: double lli; /* Individual log likelihood */
2131: int s1, s2;
2132: double bbh, survp;
2133: long ipmx;
1.187 brouard 2134: double agexact;
1.126 brouard 2135: /*extern weight */
2136: /* We are differentiating ll according to initial status */
2137: /* for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
2138: /*for(i=1;i<imx;i++)
2139: printf(" %d\n",s[4][i]);
2140: */
1.162 brouard 2141:
2142: ++countcallfunc;
2143:
1.126 brouard 2144: cov[1]=1.;
2145:
2146: for(k=1; k<=nlstate; k++) ll[k]=0.;
2147:
2148: if(mle==1){
2149: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1.138 brouard 2150: /* Computes the values of the ncovmodel covariates of the model
2151: depending if the covariates are fixed or variying (age dependent) and stores them in cov[]
2152: Then computes with function pmij which return a matrix p[i][j] giving the elementary probability
2153: to be observed in j being in i according to the model.
2154: */
1.145 brouard 2155: for (k=1; k<=cptcovn;k++){ /* Simple and product covariates without age* products */
1.187 brouard 2156: cov[2+nagesqr+k]=covar[Tvar[k]][i];
1.145 brouard 2157: }
1.137 brouard 2158: /* In model V2+V1*V4+age*V3+V3*V2 Tvar[1] is V2, Tvar[2=V1*V4]
1.138 brouard 2159: is 6, Tvar[3=age*V3] should not be computed because of age Tvar[4=V3*V2]
1.137 brouard 2160: has been calculated etc */
1.126 brouard 2161: for(mi=1; mi<= wav[i]-1; mi++){
2162: for (ii=1;ii<=nlstate+ndeath;ii++)
2163: for (j=1;j<=nlstate+ndeath;j++){
2164: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
2165: savm[ii][j]=(ii==j ? 1.0 : 0.0);
2166: }
2167: for(d=0; d<dh[mi][i]; d++){
2168: newm=savm;
1.187 brouard 2169: agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
2170: cov[2]=agexact;
2171: if(nagesqr==1)
2172: cov[3]= agexact*agexact;
1.126 brouard 2173: for (kk=1; kk<=cptcovage;kk++) {
1.187 brouard 2174: cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact; /* Tage[kk] gives the data-covariate associated with age */
1.126 brouard 2175: }
2176: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
2177: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
2178: savm=oldm;
2179: oldm=newm;
2180: } /* end mult */
2181:
2182: /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
2183: /* But now since version 0.9 we anticipate for bias at large stepm.
2184: * If stepm is larger than one month (smallest stepm) and if the exact delay
2185: * (in months) between two waves is not a multiple of stepm, we rounded to
2186: * the nearest (and in case of equal distance, to the lowest) interval but now
2187: * we keep into memory the bias bh[mi][i] and also the previous matrix product
2188: * (i.e to dh[mi][i]-1) saved in 'savm'. Then we inter(extra)polate the
2189: * probability in order to take into account the bias as a fraction of the way
2190: * from savm to out if bh is negative or even beyond if bh is positive. bh varies
2191: * -stepm/2 to stepm/2 .
2192: * For stepm=1 the results are the same as for previous versions of Imach.
2193: * For stepm > 1 the results are less biased than in previous versions.
2194: */
2195: s1=s[mw[mi][i]][i];
2196: s2=s[mw[mi+1][i]][i];
2197: bbh=(double)bh[mi][i]/(double)stepm;
2198: /* bias bh is positive if real duration
2199: * is higher than the multiple of stepm and negative otherwise.
2200: */
2201: /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
2202: if( s2 > nlstate){
2203: /* i.e. if s2 is a death state and if the date of death is known
2204: then the contribution to the likelihood is the probability to
2205: die between last step unit time and current step unit time,
2206: which is also equal to probability to die before dh
2207: minus probability to die before dh-stepm .
2208: In version up to 0.92 likelihood was computed
2209: as if date of death was unknown. Death was treated as any other
2210: health state: the date of the interview describes the actual state
2211: and not the date of a change in health state. The former idea was
2212: to consider that at each interview the state was recorded
2213: (healthy, disable or death) and IMaCh was corrected; but when we
2214: introduced the exact date of death then we should have modified
2215: the contribution of an exact death to the likelihood. This new
2216: contribution is smaller and very dependent of the step unit
2217: stepm. It is no more the probability to die between last interview
2218: and month of death but the probability to survive from last
2219: interview up to one month before death multiplied by the
2220: probability to die within a month. Thanks to Chris
2221: Jackson for correcting this bug. Former versions increased
2222: mortality artificially. The bad side is that we add another loop
2223: which slows down the processing. The difference can be up to 10%
2224: lower mortality.
2225: */
1.183 brouard 2226: /* If, at the beginning of the maximization mostly, the
2227: cumulative probability or probability to be dead is
2228: constant (ie = 1) over time d, the difference is equal to
2229: 0. out[s1][3] = savm[s1][3]: probability, being at state
2230: s1 at precedent wave, to be dead a month before current
2231: wave is equal to probability, being at state s1 at
2232: precedent wave, to be dead at mont of the current
2233: wave. Then the observed probability (that this person died)
2234: is null according to current estimated parameter. In fact,
2235: it should be very low but not zero otherwise the log go to
2236: infinity.
2237: */
2238: /* #ifdef INFINITYORIGINAL */
2239: /* lli=log(out[s1][s2] - savm[s1][s2]); */
2240: /* #else */
2241: /* if ((out[s1][s2] - savm[s1][s2]) < mytinydouble) */
2242: /* lli=log(mytinydouble); */
2243: /* else */
2244: /* lli=log(out[s1][s2] - savm[s1][s2]); */
2245: /* #endif */
2246: lli=log(out[s1][s2] - savm[s1][s2]);
1.126 brouard 2247:
2248: } else if (s2==-2) {
2249: for (j=1,survp=0. ; j<=nlstate; j++)
2250: survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
2251: /*survp += out[s1][j]; */
2252: lli= log(survp);
2253: }
2254:
2255: else if (s2==-4) {
2256: for (j=3,survp=0. ; j<=nlstate; j++)
2257: survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
2258: lli= log(survp);
2259: }
2260:
2261: else if (s2==-5) {
2262: for (j=1,survp=0. ; j<=2; j++)
2263: survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
2264: lli= log(survp);
2265: }
2266:
2267: else{
2268: lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
2269: /* 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 */
2270: }
2271: /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
2272: /*if(lli ==000.0)*/
2273: /*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); */
2274: ipmx +=1;
2275: sw += weight[i];
2276: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1.183 brouard 2277: /* if (lli < log(mytinydouble)){ */
2278: /* 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); */
2279: /* 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]); */
2280: /* } */
1.126 brouard 2281: } /* end of wave */
2282: } /* end of individual */
2283: } else if(mle==2){
2284: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1.187 brouard 2285: for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i];
1.126 brouard 2286: for(mi=1; mi<= wav[i]-1; mi++){
2287: for (ii=1;ii<=nlstate+ndeath;ii++)
2288: for (j=1;j<=nlstate+ndeath;j++){
2289: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
2290: savm[ii][j]=(ii==j ? 1.0 : 0.0);
2291: }
2292: for(d=0; d<=dh[mi][i]; d++){
2293: newm=savm;
1.187 brouard 2294: agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
2295: cov[2]=agexact;
2296: if(nagesqr==1)
2297: cov[3]= agexact*agexact;
1.126 brouard 2298: for (kk=1; kk<=cptcovage;kk++) {
1.187 brouard 2299: cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
1.126 brouard 2300: }
2301: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
2302: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
2303: savm=oldm;
2304: oldm=newm;
2305: } /* end mult */
2306:
2307: s1=s[mw[mi][i]][i];
2308: s2=s[mw[mi+1][i]][i];
2309: bbh=(double)bh[mi][i]/(double)stepm;
2310: 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 */
2311: ipmx +=1;
2312: sw += weight[i];
2313: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
2314: } /* end of wave */
2315: } /* end of individual */
2316: } else if(mle==3){ /* exponential inter-extrapolation */
2317: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1.187 brouard 2318: for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i];
1.126 brouard 2319: for(mi=1; mi<= wav[i]-1; mi++){
2320: for (ii=1;ii<=nlstate+ndeath;ii++)
2321: for (j=1;j<=nlstate+ndeath;j++){
2322: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
2323: savm[ii][j]=(ii==j ? 1.0 : 0.0);
2324: }
2325: for(d=0; d<dh[mi][i]; d++){
2326: newm=savm;
1.187 brouard 2327: agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
2328: cov[2]=agexact;
2329: if(nagesqr==1)
2330: cov[3]= agexact*agexact;
1.126 brouard 2331: for (kk=1; kk<=cptcovage;kk++) {
1.187 brouard 2332: cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
1.126 brouard 2333: }
2334: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
2335: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
2336: savm=oldm;
2337: oldm=newm;
2338: } /* end mult */
2339:
2340: s1=s[mw[mi][i]][i];
2341: s2=s[mw[mi+1][i]][i];
2342: bbh=(double)bh[mi][i]/(double)stepm;
2343: 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 */
2344: ipmx +=1;
2345: sw += weight[i];
2346: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
2347: } /* end of wave */
2348: } /* end of individual */
2349: }else if (mle==4){ /* ml=4 no inter-extrapolation */
2350: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1.187 brouard 2351: for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i];
1.126 brouard 2352: for(mi=1; mi<= wav[i]-1; mi++){
2353: for (ii=1;ii<=nlstate+ndeath;ii++)
2354: for (j=1;j<=nlstate+ndeath;j++){
2355: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
2356: savm[ii][j]=(ii==j ? 1.0 : 0.0);
2357: }
2358: for(d=0; d<dh[mi][i]; d++){
2359: newm=savm;
1.187 brouard 2360: agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
2361: cov[2]=agexact;
2362: if(nagesqr==1)
2363: cov[3]= agexact*agexact;
1.126 brouard 2364: for (kk=1; kk<=cptcovage;kk++) {
1.187 brouard 2365: cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
1.126 brouard 2366: }
2367:
2368: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
2369: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
2370: savm=oldm;
2371: oldm=newm;
2372: } /* end mult */
2373:
2374: s1=s[mw[mi][i]][i];
2375: s2=s[mw[mi+1][i]][i];
2376: if( s2 > nlstate){
2377: lli=log(out[s1][s2] - savm[s1][s2]);
2378: }else{
2379: lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
2380: }
2381: ipmx +=1;
2382: sw += weight[i];
2383: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
2384: /* 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]); */
2385: } /* end of wave */
2386: } /* end of individual */
2387: }else{ /* ml=5 no inter-extrapolation no jackson =0.8a */
2388: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1.187 brouard 2389: for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i];
1.126 brouard 2390: for(mi=1; mi<= wav[i]-1; mi++){
2391: for (ii=1;ii<=nlstate+ndeath;ii++)
2392: for (j=1;j<=nlstate+ndeath;j++){
2393: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
2394: savm[ii][j]=(ii==j ? 1.0 : 0.0);
2395: }
2396: for(d=0; d<dh[mi][i]; d++){
2397: newm=savm;
1.187 brouard 2398: agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
2399: cov[2]=agexact;
2400: if(nagesqr==1)
2401: cov[3]= agexact*agexact;
1.126 brouard 2402: for (kk=1; kk<=cptcovage;kk++) {
1.187 brouard 2403: cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
1.126 brouard 2404: }
2405:
2406: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
2407: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
2408: savm=oldm;
2409: oldm=newm;
2410: } /* end mult */
2411:
2412: s1=s[mw[mi][i]][i];
2413: s2=s[mw[mi+1][i]][i];
2414: lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
2415: ipmx +=1;
2416: sw += weight[i];
2417: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
2418: /*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]);*/
2419: } /* end of wave */
2420: } /* end of individual */
2421: } /* End of if */
2422: for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
2423: /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
2424: l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
2425: return -l;
2426: }
2427:
2428: /*************** log-likelihood *************/
2429: double funcone( double *x)
2430: {
2431: /* Same as likeli but slower because of a lot of printf and if */
2432: int i, ii, j, k, mi, d, kk;
1.131 brouard 2433: double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
1.126 brouard 2434: double **out;
2435: double lli; /* Individual log likelihood */
2436: double llt;
2437: int s1, s2;
2438: double bbh, survp;
1.187 brouard 2439: double agexact;
1.126 brouard 2440: /*extern weight */
2441: /* We are differentiating ll according to initial status */
2442: /* for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
2443: /*for(i=1;i<imx;i++)
2444: printf(" %d\n",s[4][i]);
2445: */
2446: cov[1]=1.;
2447:
2448: for(k=1; k<=nlstate; k++) ll[k]=0.;
2449:
2450: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1.187 brouard 2451: for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i];
1.126 brouard 2452: for(mi=1; mi<= wav[i]-1; mi++){
2453: for (ii=1;ii<=nlstate+ndeath;ii++)
2454: for (j=1;j<=nlstate+ndeath;j++){
2455: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
2456: savm[ii][j]=(ii==j ? 1.0 : 0.0);
2457: }
2458: for(d=0; d<dh[mi][i]; d++){
2459: newm=savm;
1.187 brouard 2460: agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
2461: cov[2]=agexact;
2462: if(nagesqr==1)
2463: cov[3]= agexact*agexact;
1.126 brouard 2464: for (kk=1; kk<=cptcovage;kk++) {
1.187 brouard 2465: cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
1.126 brouard 2466: }
1.187 brouard 2467:
1.145 brouard 2468: /* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
1.126 brouard 2469: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
2470: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1.145 brouard 2471: /* out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath, */
2472: /* 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate)); */
1.126 brouard 2473: savm=oldm;
2474: oldm=newm;
2475: } /* end mult */
2476:
2477: s1=s[mw[mi][i]][i];
2478: s2=s[mw[mi+1][i]][i];
2479: bbh=(double)bh[mi][i]/(double)stepm;
2480: /* bias is positive if real duration
2481: * is higher than the multiple of stepm and negative otherwise.
2482: */
2483: if( s2 > nlstate && (mle <5) ){ /* Jackson */
2484: lli=log(out[s1][s2] - savm[s1][s2]);
2485: } else if (s2==-2) {
2486: for (j=1,survp=0. ; j<=nlstate; j++)
2487: survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
2488: lli= log(survp);
2489: }else if (mle==1){
2490: lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
2491: } else if(mle==2){
2492: 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 */
2493: } else if(mle==3){ /* exponential inter-extrapolation */
2494: 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 */
2495: } else if (mle==4){ /* mle=4 no inter-extrapolation */
2496: lli=log(out[s1][s2]); /* Original formula */
1.136 brouard 2497: } else{ /* mle=0 back to 1 */
2498: lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
2499: /*lli=log(out[s1][s2]); */ /* Original formula */
1.126 brouard 2500: } /* End of if */
2501: ipmx +=1;
2502: sw += weight[i];
2503: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1.132 brouard 2504: /*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 2505: if(globpr){
1.141 brouard 2506: fprintf(ficresilk,"%9ld %6d %2d %2d %1d %1d %3d %11.6f %8.4f\
1.126 brouard 2507: %11.6f %11.6f %11.6f ", \
2508: num[i],i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],
2509: 2*weight[i]*lli,out[s1][s2],savm[s1][s2]);
2510: for(k=1,llt=0.,l=0.; k<=nlstate; k++){
2511: llt +=ll[k]*gipmx/gsw;
2512: fprintf(ficresilk," %10.6f",-ll[k]*gipmx/gsw);
2513: }
2514: fprintf(ficresilk," %10.6f\n", -llt);
2515: }
2516: } /* end of wave */
2517: } /* end of individual */
2518: for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
2519: /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
2520: l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
2521: if(globpr==0){ /* First time we count the contributions and weights */
2522: gipmx=ipmx;
2523: gsw=sw;
2524: }
2525: return -l;
2526: }
2527:
2528:
2529: /*************** function likelione ***********/
2530: void likelione(FILE *ficres,double p[], int npar, int nlstate, int *globpri, long *ipmx, double *sw, double *fretone, double (*funcone)(double []))
2531: {
2532: /* This routine should help understanding what is done with
2533: the selection of individuals/waves and
2534: to check the exact contribution to the likelihood.
2535: Plotting could be done.
2536: */
2537: int k;
2538:
2539: if(*globpri !=0){ /* Just counts and sums, no printings */
2540: strcpy(fileresilk,"ilk");
2541: strcat(fileresilk,fileres);
2542: if((ficresilk=fopen(fileresilk,"w"))==NULL) {
2543: printf("Problem with resultfile: %s\n", fileresilk);
2544: fprintf(ficlog,"Problem with resultfile: %s\n", fileresilk);
2545: }
2546: fprintf(ficresilk, "#individual(line's_record) s1 s2 wave# effective_wave# number_of_matrices_product pij weight -2ln(pij)*weight 0pij_x 0pij_(x-stepm) cumulating_loglikeli_by_health_state(reweighted=-2ll*weightXnumber_of_contribs/sum_of_weights) and_total\n");
2547: fprintf(ficresilk, "#num_i i s1 s2 mi mw dh likeli weight 2wlli out sav ");
2548: /* i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],2*weight[i]*lli,out[s1][s2],savm[s1][s2]); */
2549: for(k=1; k<=nlstate; k++)
2550: fprintf(ficresilk," -2*gipw/gsw*weight*ll[%d]++",k);
2551: fprintf(ficresilk," -2*gipw/gsw*weight*ll(total)\n");
2552: }
2553:
2554: *fretone=(*funcone)(p);
2555: if(*globpri !=0){
2556: fclose(ficresilk);
2557: fprintf(fichtm,"\n<br>File of contributions to the likelihood: <a href=\"%s\">%s</a><br>\n",subdirf(fileresilk),subdirf(fileresilk));
2558: fflush(fichtm);
2559: }
2560: return;
2561: }
2562:
2563:
2564: /*********** Maximum Likelihood Estimation ***************/
2565:
2566: void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
2567: {
1.165 brouard 2568: int i,j, iter=0;
1.126 brouard 2569: double **xi;
2570: double fret;
2571: double fretone; /* Only one call to likelihood */
2572: /* char filerespow[FILENAMELENGTH];*/
1.162 brouard 2573:
2574: #ifdef NLOPT
2575: int creturn;
2576: nlopt_opt opt;
2577: /* double lb[9] = { -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL }; /\* lower bounds *\/ */
2578: double *lb;
2579: double minf; /* the minimum objective value, upon return */
2580: double * p1; /* Shifted parameters from 0 instead of 1 */
2581: myfunc_data dinst, *d = &dinst;
2582: #endif
2583:
2584:
1.126 brouard 2585: xi=matrix(1,npar,1,npar);
2586: for (i=1;i<=npar;i++)
2587: for (j=1;j<=npar;j++)
2588: xi[i][j]=(i==j ? 1.0 : 0.0);
2589: printf("Powell\n"); fprintf(ficlog,"Powell\n");
2590: strcpy(filerespow,"pow");
2591: strcat(filerespow,fileres);
2592: if((ficrespow=fopen(filerespow,"w"))==NULL) {
2593: printf("Problem with resultfile: %s\n", filerespow);
2594: fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
2595: }
2596: fprintf(ficrespow,"# Powell\n# iter -2*LL");
2597: for (i=1;i<=nlstate;i++)
2598: for(j=1;j<=nlstate+ndeath;j++)
2599: if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
2600: fprintf(ficrespow,"\n");
1.162 brouard 2601: #ifdef POWELL
1.126 brouard 2602: powell(p,xi,npar,ftol,&iter,&fret,func);
1.162 brouard 2603: #endif
1.126 brouard 2604:
1.162 brouard 2605: #ifdef NLOPT
2606: #ifdef NEWUOA
2607: opt = nlopt_create(NLOPT_LN_NEWUOA,npar);
2608: #else
2609: opt = nlopt_create(NLOPT_LN_BOBYQA,npar);
2610: #endif
2611: lb=vector(0,npar-1);
2612: for (i=0;i<npar;i++) lb[i]= -HUGE_VAL;
2613: nlopt_set_lower_bounds(opt, lb);
2614: nlopt_set_initial_step1(opt, 0.1);
2615:
2616: p1= (p+1); /* p *(p+1)@8 and p *(p1)@8 are equal p1[0]=p[1] */
2617: d->function = func;
2618: printf(" Func %.12lf \n",myfunc(npar,p1,NULL,d));
2619: nlopt_set_min_objective(opt, myfunc, d);
2620: nlopt_set_xtol_rel(opt, ftol);
2621: if ((creturn=nlopt_optimize(opt, p1, &minf)) < 0) {
2622: printf("nlopt failed! %d\n",creturn);
2623: }
2624: else {
2625: printf("found minimum after %d evaluations (NLOPT=%d)\n", countcallfunc ,NLOPT);
2626: printf("found minimum at f(%g,%g) = %0.10g\n", p[0], p[1], minf);
2627: iter=1; /* not equal */
2628: }
2629: nlopt_destroy(opt);
2630: #endif
1.126 brouard 2631: free_matrix(xi,1,npar,1,npar);
2632: fclose(ficrespow);
1.180 brouard 2633: printf("#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
2634: fprintf(ficlog,"#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
2635: fprintf(ficres,"#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
1.126 brouard 2636:
2637: }
2638:
2639: /**** Computes Hessian and covariance matrix ***/
2640: void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
2641: {
2642: double **a,**y,*x,pd;
2643: double **hess;
1.164 brouard 2644: int i, j;
1.126 brouard 2645: int *indx;
2646:
2647: double hessii(double p[], double delta, int theta, double delti[],double (*func)(double []),int npar);
2648: double hessij(double p[], double delti[], int i, int j,double (*func)(double []),int npar);
2649: void lubksb(double **a, int npar, int *indx, double b[]) ;
2650: void ludcmp(double **a, int npar, int *indx, double *d) ;
2651: double gompertz(double p[]);
2652: hess=matrix(1,npar,1,npar);
2653:
2654: printf("\nCalculation of the hessian matrix. Wait...\n");
2655: fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
2656: for (i=1;i<=npar;i++){
2657: printf("%d",i);fflush(stdout);
2658: fprintf(ficlog,"%d",i);fflush(ficlog);
2659:
2660: hess[i][i]=hessii(p,ftolhess,i,delti,func,npar);
2661:
2662: /* printf(" %f ",p[i]);
2663: printf(" %lf %lf %lf",hess[i][i],ftolhess,delti[i]);*/
2664: }
2665:
2666: for (i=1;i<=npar;i++) {
2667: for (j=1;j<=npar;j++) {
2668: if (j>i) {
2669: printf(".%d%d",i,j);fflush(stdout);
2670: fprintf(ficlog,".%d%d",i,j);fflush(ficlog);
2671: hess[i][j]=hessij(p,delti,i,j,func,npar);
2672:
2673: hess[j][i]=hess[i][j];
2674: /*printf(" %lf ",hess[i][j]);*/
2675: }
2676: }
2677: }
2678: printf("\n");
2679: fprintf(ficlog,"\n");
2680:
2681: printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
2682: fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
2683:
2684: a=matrix(1,npar,1,npar);
2685: y=matrix(1,npar,1,npar);
2686: x=vector(1,npar);
2687: indx=ivector(1,npar);
2688: for (i=1;i<=npar;i++)
2689: for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
2690: ludcmp(a,npar,indx,&pd);
2691:
2692: for (j=1;j<=npar;j++) {
2693: for (i=1;i<=npar;i++) x[i]=0;
2694: x[j]=1;
2695: lubksb(a,npar,indx,x);
2696: for (i=1;i<=npar;i++){
2697: matcov[i][j]=x[i];
2698: }
2699: }
2700:
2701: printf("\n#Hessian matrix#\n");
2702: fprintf(ficlog,"\n#Hessian matrix#\n");
2703: for (i=1;i<=npar;i++) {
2704: for (j=1;j<=npar;j++) {
2705: printf("%.3e ",hess[i][j]);
2706: fprintf(ficlog,"%.3e ",hess[i][j]);
2707: }
2708: printf("\n");
2709: fprintf(ficlog,"\n");
2710: }
2711:
2712: /* Recompute Inverse */
2713: for (i=1;i<=npar;i++)
2714: for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];
2715: ludcmp(a,npar,indx,&pd);
2716:
2717: /* printf("\n#Hessian matrix recomputed#\n");
2718:
2719: for (j=1;j<=npar;j++) {
2720: for (i=1;i<=npar;i++) x[i]=0;
2721: x[j]=1;
2722: lubksb(a,npar,indx,x);
2723: for (i=1;i<=npar;i++){
2724: y[i][j]=x[i];
2725: printf("%.3e ",y[i][j]);
2726: fprintf(ficlog,"%.3e ",y[i][j]);
2727: }
2728: printf("\n");
2729: fprintf(ficlog,"\n");
2730: }
2731: */
2732:
2733: free_matrix(a,1,npar,1,npar);
2734: free_matrix(y,1,npar,1,npar);
2735: free_vector(x,1,npar);
2736: free_ivector(indx,1,npar);
2737: free_matrix(hess,1,npar,1,npar);
2738:
2739:
2740: }
2741:
2742: /*************** hessian matrix ****************/
2743: double hessii(double x[], double delta, int theta, double delti[], double (*func)(double []), int npar)
2744: {
2745: int i;
2746: int l=1, lmax=20;
2747: double k1,k2;
1.132 brouard 2748: double p2[MAXPARM+1]; /* identical to x */
1.126 brouard 2749: double res;
2750: double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4;
2751: double fx;
2752: int k=0,kmax=10;
2753: double l1;
2754:
2755: fx=func(x);
2756: for (i=1;i<=npar;i++) p2[i]=x[i];
1.145 brouard 2757: for(l=0 ; l <=lmax; l++){ /* Enlarging the zone around the Maximum */
1.126 brouard 2758: l1=pow(10,l);
2759: delts=delt;
2760: for(k=1 ; k <kmax; k=k+1){
2761: delt = delta*(l1*k);
2762: p2[theta]=x[theta] +delt;
1.145 brouard 2763: k1=func(p2)-fx; /* Might be negative if too close to the theoretical maximum */
1.126 brouard 2764: p2[theta]=x[theta]-delt;
2765: k2=func(p2)-fx;
2766: /*res= (k1-2.0*fx+k2)/delt/delt; */
2767: res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */
2768:
1.132 brouard 2769: #ifdef DEBUGHESS
1.126 brouard 2770: 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);
2771: 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);
2772: #endif
2773: /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
2774: if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
2775: k=kmax;
2776: }
2777: else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
1.164 brouard 2778: k=kmax; l=lmax*10;
1.126 brouard 2779: }
2780: else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){
2781: delts=delt;
2782: }
2783: }
2784: }
2785: delti[theta]=delts;
2786: return res;
2787:
2788: }
2789:
2790: double hessij( double x[], double delti[], int thetai,int thetaj,double (*func)(double []),int npar)
2791: {
2792: int i;
1.164 brouard 2793: int l=1, lmax=20;
1.126 brouard 2794: double k1,k2,k3,k4,res,fx;
1.132 brouard 2795: double p2[MAXPARM+1];
1.126 brouard 2796: int k;
2797:
2798: fx=func(x);
2799: for (k=1; k<=2; k++) {
2800: for (i=1;i<=npar;i++) p2[i]=x[i];
2801: p2[thetai]=x[thetai]+delti[thetai]/k;
2802: p2[thetaj]=x[thetaj]+delti[thetaj]/k;
2803: k1=func(p2)-fx;
2804:
2805: p2[thetai]=x[thetai]+delti[thetai]/k;
2806: p2[thetaj]=x[thetaj]-delti[thetaj]/k;
2807: k2=func(p2)-fx;
2808:
2809: p2[thetai]=x[thetai]-delti[thetai]/k;
2810: p2[thetaj]=x[thetaj]+delti[thetaj]/k;
2811: k3=func(p2)-fx;
2812:
2813: p2[thetai]=x[thetai]-delti[thetai]/k;
2814: p2[thetaj]=x[thetaj]-delti[thetaj]/k;
2815: k4=func(p2)-fx;
2816: res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */
2817: #ifdef DEBUG
2818: 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);
2819: 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);
2820: #endif
2821: }
2822: return res;
2823: }
2824:
2825: /************** Inverse of matrix **************/
2826: void ludcmp(double **a, int n, int *indx, double *d)
2827: {
2828: int i,imax,j,k;
2829: double big,dum,sum,temp;
2830: double *vv;
2831:
2832: vv=vector(1,n);
2833: *d=1.0;
2834: for (i=1;i<=n;i++) {
2835: big=0.0;
2836: for (j=1;j<=n;j++)
2837: if ((temp=fabs(a[i][j])) > big) big=temp;
2838: if (big == 0.0) nrerror("Singular matrix in routine ludcmp");
2839: vv[i]=1.0/big;
2840: }
2841: for (j=1;j<=n;j++) {
2842: for (i=1;i<j;i++) {
2843: sum=a[i][j];
2844: for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];
2845: a[i][j]=sum;
2846: }
2847: big=0.0;
2848: for (i=j;i<=n;i++) {
2849: sum=a[i][j];
2850: for (k=1;k<j;k++)
2851: sum -= a[i][k]*a[k][j];
2852: a[i][j]=sum;
2853: if ( (dum=vv[i]*fabs(sum)) >= big) {
2854: big=dum;
2855: imax=i;
2856: }
2857: }
2858: if (j != imax) {
2859: for (k=1;k<=n;k++) {
2860: dum=a[imax][k];
2861: a[imax][k]=a[j][k];
2862: a[j][k]=dum;
2863: }
2864: *d = -(*d);
2865: vv[imax]=vv[j];
2866: }
2867: indx[j]=imax;
2868: if (a[j][j] == 0.0) a[j][j]=TINY;
2869: if (j != n) {
2870: dum=1.0/(a[j][j]);
2871: for (i=j+1;i<=n;i++) a[i][j] *= dum;
2872: }
2873: }
2874: free_vector(vv,1,n); /* Doesn't work */
2875: ;
2876: }
2877:
2878: void lubksb(double **a, int n, int *indx, double b[])
2879: {
2880: int i,ii=0,ip,j;
2881: double sum;
2882:
2883: for (i=1;i<=n;i++) {
2884: ip=indx[i];
2885: sum=b[ip];
2886: b[ip]=b[i];
2887: if (ii)
2888: for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];
2889: else if (sum) ii=i;
2890: b[i]=sum;
2891: }
2892: for (i=n;i>=1;i--) {
2893: sum=b[i];
2894: for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];
2895: b[i]=sum/a[i][i];
2896: }
2897: }
2898:
2899: void pstamp(FILE *fichier)
2900: {
2901: fprintf(fichier,"# %s.%s\n#%s\n#%s\n# %s", optionfilefiname,optionfilext,version,fullversion,strstart);
2902: }
2903:
2904: /************ Frequencies ********************/
2905: void freqsummary(char fileres[], int iagemin, int iagemax, int **s, double **agev, int nlstate, int imx, int *Tvaraff, int **nbcode, int *ncodemax,double **mint,double **anint, char strstart[])
2906: { /* Some frequencies */
2907:
1.164 brouard 2908: int i, m, jk, j1, bool, z1,j;
1.126 brouard 2909: int first;
2910: double ***freq; /* Frequencies */
2911: double *pp, **prop;
2912: double pos,posprop, k2, dateintsum=0,k2cpt=0;
2913: char fileresp[FILENAMELENGTH];
2914:
2915: pp=vector(1,nlstate);
2916: prop=matrix(1,nlstate,iagemin,iagemax+3);
2917: strcpy(fileresp,"p");
2918: strcat(fileresp,fileres);
2919: if((ficresp=fopen(fileresp,"w"))==NULL) {
2920: printf("Problem with prevalence resultfile: %s\n", fileresp);
2921: fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
2922: exit(0);
2923: }
2924: freq= ma3x(-5,nlstate+ndeath,-5,nlstate+ndeath,iagemin,iagemax+3);
2925: j1=0;
2926:
2927: j=cptcoveff;
2928: if (cptcovn<1) {j=1;ncodemax[1]=1;}
2929:
2930: first=1;
2931:
1.169 brouard 2932: /* for(k1=1; k1<=j ; k1++){ */ /* Loop on covariates */
2933: /* for(i1=1; i1<=ncodemax[k1];i1++){ */ /* Now it is 2 */
2934: /* j1++; */
1.145 brouard 2935: for (j1 = 1; j1 <= (int) pow(2,cptcoveff); j1++){
1.126 brouard 2936: /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
2937: scanf("%d", i);*/
2938: for (i=-5; i<=nlstate+ndeath; i++)
2939: for (jk=-5; jk<=nlstate+ndeath; jk++)
2940: for(m=iagemin; m <= iagemax+3; m++)
2941: freq[i][jk][m]=0;
1.143 brouard 2942:
2943: for (i=1; i<=nlstate; i++)
2944: for(m=iagemin; m <= iagemax+3; m++)
2945: prop[i][m]=0;
1.126 brouard 2946:
2947: dateintsum=0;
2948: k2cpt=0;
2949: for (i=1; i<=imx; i++) {
2950: bool=1;
1.144 brouard 2951: if (cptcovn>0) { /* Filter is here: Must be looked at for model=V1+V2+V3+V4 */
2952: for (z1=1; z1<=cptcoveff; z1++)
2953: if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]){
1.145 brouard 2954: /* Tests if the value of each of the covariates of i is equal to filter j1 */
1.144 brouard 2955: bool=0;
1.145 brouard 2956: /* printf("bool=%d i=%d, z1=%d, Tvaraff[%d]=%d, covar[Tvarff][%d]=%2f, codtab[%d][%d]=%d, nbcode[Tvaraff][codtab[%d][%d]=%d, j1=%d\n",
2957: bool,i,z1, z1, Tvaraff[z1],i,covar[Tvaraff[z1]][i],j1,z1,codtab[j1][z1],
2958: j1,z1,nbcode[Tvaraff[z1]][codtab[j1][z1]],j1);*/
1.144 brouard 2959: /* For j1=7 in V1+V2+V3+V4 = 0 1 1 0 and codtab[7][3]=1 and nbcde[3][?]=1*/
2960: }
1.126 brouard 2961: }
1.144 brouard 2962:
1.126 brouard 2963: if (bool==1){
2964: for(m=firstpass; m<=lastpass; m++){
2965: k2=anint[m][i]+(mint[m][i]/12.);
2966: /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/
2967: if(agev[m][i]==0) agev[m][i]=iagemax+1;
2968: if(agev[m][i]==1) agev[m][i]=iagemax+2;
2969: if (s[m][i]>0 && s[m][i]<=nlstate) prop[s[m][i]][(int)agev[m][i]] += weight[i];
2970: if (m<lastpass) {
2971: freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
2972: freq[s[m][i]][s[m+1][i]][iagemax+3] += weight[i];
2973: }
2974:
2975: if ((agev[m][i]>1) && (agev[m][i]< (iagemax+3))) {
2976: dateintsum=dateintsum+k2;
2977: k2cpt++;
2978: }
2979: /*}*/
2980: }
2981: }
1.145 brouard 2982: } /* end i */
1.126 brouard 2983:
2984: /* fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
2985: pstamp(ficresp);
2986: if (cptcovn>0) {
2987: fprintf(ficresp, "\n#********** Variable ");
2988: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
2989: fprintf(ficresp, "**********\n#");
1.143 brouard 2990: fprintf(ficlog, "\n#********** Variable ");
2991: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficlog, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
2992: fprintf(ficlog, "**********\n#");
1.126 brouard 2993: }
2994: for(i=1; i<=nlstate;i++)
2995: fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
2996: fprintf(ficresp, "\n");
2997:
2998: for(i=iagemin; i <= iagemax+3; i++){
2999: if(i==iagemax+3){
3000: fprintf(ficlog,"Total");
3001: }else{
3002: if(first==1){
3003: first=0;
3004: printf("See log file for details...\n");
3005: }
3006: fprintf(ficlog,"Age %d", i);
3007: }
3008: for(jk=1; jk <=nlstate ; jk++){
3009: for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
3010: pp[jk] += freq[jk][m][i];
3011: }
3012: for(jk=1; jk <=nlstate ; jk++){
3013: for(m=-1, pos=0; m <=0 ; m++)
3014: pos += freq[jk][m][i];
3015: if(pp[jk]>=1.e-10){
3016: if(first==1){
1.132 brouard 3017: printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
1.126 brouard 3018: }
3019: fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
3020: }else{
3021: if(first==1)
3022: printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
3023: fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
3024: }
3025: }
3026:
3027: for(jk=1; jk <=nlstate ; jk++){
3028: for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
3029: pp[jk] += freq[jk][m][i];
3030: }
3031: for(jk=1,pos=0,posprop=0; jk <=nlstate ; jk++){
3032: pos += pp[jk];
3033: posprop += prop[jk][i];
3034: }
3035: for(jk=1; jk <=nlstate ; jk++){
3036: if(pos>=1.e-5){
3037: if(first==1)
3038: printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
3039: fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
3040: }else{
3041: if(first==1)
3042: printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
3043: fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
3044: }
3045: if( i <= iagemax){
3046: if(pos>=1.e-5){
3047: fprintf(ficresp," %d %.5f %.0f %.0f",i,prop[jk][i]/posprop, prop[jk][i],posprop);
3048: /*probs[i][jk][j1]= pp[jk]/pos;*/
3049: /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/
3050: }
3051: else
3052: fprintf(ficresp," %d NaNq %.0f %.0f",i,prop[jk][i],posprop);
3053: }
3054: }
3055:
3056: for(jk=-1; jk <=nlstate+ndeath; jk++)
3057: for(m=-1; m <=nlstate+ndeath; m++)
3058: if(freq[jk][m][i] !=0 ) {
3059: if(first==1)
3060: printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
3061: fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
3062: }
3063: if(i <= iagemax)
3064: fprintf(ficresp,"\n");
3065: if(first==1)
3066: printf("Others in log...\n");
3067: fprintf(ficlog,"\n");
3068: }
1.145 brouard 3069: /*}*/
1.126 brouard 3070: }
3071: dateintmean=dateintsum/k2cpt;
3072:
3073: fclose(ficresp);
3074: free_ma3x(freq,-5,nlstate+ndeath,-5,nlstate+ndeath, iagemin, iagemax+3);
3075: free_vector(pp,1,nlstate);
3076: free_matrix(prop,1,nlstate,iagemin, iagemax+3);
3077: /* End of Freq */
3078: }
3079:
3080: /************ Prevalence ********************/
3081: 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)
3082: {
3083: /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
3084: in each health status at the date of interview (if between dateprev1 and dateprev2).
3085: We still use firstpass and lastpass as another selection.
3086: */
3087:
1.164 brouard 3088: int i, m, jk, j1, bool, z1,j;
3089:
3090: double **prop;
3091: double posprop;
1.126 brouard 3092: double y2; /* in fractional years */
3093: int iagemin, iagemax;
1.145 brouard 3094: int first; /** to stop verbosity which is redirected to log file */
1.126 brouard 3095:
3096: iagemin= (int) agemin;
3097: iagemax= (int) agemax;
3098: /*pp=vector(1,nlstate);*/
3099: prop=matrix(1,nlstate,iagemin,iagemax+3);
3100: /* freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
3101: j1=0;
3102:
1.145 brouard 3103: /*j=cptcoveff;*/
1.126 brouard 3104: if (cptcovn<1) {j=1;ncodemax[1]=1;}
3105:
1.145 brouard 3106: first=1;
3107: for(j1=1; j1<= (int) pow(2,cptcoveff);j1++){
3108: /*for(i1=1; i1<=ncodemax[k1];i1++){
3109: j1++;*/
1.126 brouard 3110:
3111: for (i=1; i<=nlstate; i++)
3112: for(m=iagemin; m <= iagemax+3; m++)
3113: prop[i][m]=0.0;
3114:
3115: for (i=1; i<=imx; i++) { /* Each individual */
3116: bool=1;
3117: if (cptcovn>0) {
3118: for (z1=1; z1<=cptcoveff; z1++)
3119: if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])
3120: bool=0;
3121: }
3122: if (bool==1) {
3123: for(m=firstpass; m<=lastpass; m++){/* Other selection (we can limit to certain interviews*/
3124: y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
3125: if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
3126: if(agev[m][i]==0) agev[m][i]=iagemax+1;
3127: if(agev[m][i]==1) agev[m][i]=iagemax+2;
3128: 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);
3129: if (s[m][i]>0 && s[m][i]<=nlstate) {
3130: /*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]]);*/
3131: prop[s[m][i]][(int)agev[m][i]] += weight[i];
3132: prop[s[m][i]][iagemax+3] += weight[i];
3133: }
3134: }
3135: } /* end selection of waves */
3136: }
3137: }
3138: for(i=iagemin; i <= iagemax+3; i++){
3139: for(jk=1,posprop=0; jk <=nlstate ; jk++) {
3140: posprop += prop[jk][i];
3141: }
1.145 brouard 3142:
1.126 brouard 3143: for(jk=1; jk <=nlstate ; jk++){
3144: if( i <= iagemax){
3145: if(posprop>=1.e-5){
3146: probs[i][jk][j1]= prop[jk][i]/posprop;
1.145 brouard 3147: } else{
3148: if(first==1){
3149: first=0;
3150: 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]);
3151: }
3152: }
1.126 brouard 3153: }
3154: }/* end jk */
3155: }/* end i */
1.145 brouard 3156: /*} *//* end i1 */
3157: } /* end j1 */
1.126 brouard 3158:
3159: /* free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
3160: /*free_vector(pp,1,nlstate);*/
3161: free_matrix(prop,1,nlstate, iagemin,iagemax+3);
3162: } /* End of prevalence */
3163:
3164: /************* Waves Concatenation ***************/
3165:
3166: 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)
3167: {
3168: /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
3169: Death is a valid wave (if date is known).
3170: mw[mi][i] is the mi (mi=1 to wav[i]) effective wave of individual i
3171: dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
3172: and mw[mi+1][i]. dh depends on stepm.
3173: */
3174:
3175: int i, mi, m;
3176: /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
3177: double sum=0., jmean=0.;*/
3178: int first;
3179: int j, k=0,jk, ju, jl;
3180: double sum=0.;
3181: first=0;
1.164 brouard 3182: jmin=100000;
1.126 brouard 3183: jmax=-1;
3184: jmean=0.;
3185: for(i=1; i<=imx; i++){
3186: mi=0;
3187: m=firstpass;
3188: while(s[m][i] <= nlstate){
3189: if(s[m][i]>=1 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5)
3190: mw[++mi][i]=m;
3191: if(m >=lastpass)
3192: break;
3193: else
3194: m++;
3195: }/* end while */
3196: if (s[m][i] > nlstate){
3197: mi++; /* Death is another wave */
3198: /* if(mi==0) never been interviewed correctly before death */
3199: /* Only death is a correct wave */
3200: mw[mi][i]=m;
3201: }
3202:
3203: wav[i]=mi;
3204: if(mi==0){
3205: nbwarn++;
3206: if(first==0){
3207: printf("Warning! No valid information for individual %ld line=%d (skipped) and may be others, see log file\n",num[i],i);
3208: first=1;
3209: }
3210: if(first==1){
3211: fprintf(ficlog,"Warning! No valid information for individual %ld line=%d (skipped)\n",num[i],i);
3212: }
3213: } /* end mi==0 */
3214: } /* End individuals */
3215:
3216: for(i=1; i<=imx; i++){
3217: for(mi=1; mi<wav[i];mi++){
3218: if (stepm <=0)
3219: dh[mi][i]=1;
3220: else{
3221: if (s[mw[mi+1][i]][i] > nlstate) { /* A death */
3222: if (agedc[i] < 2*AGESUP) {
3223: j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);
3224: if(j==0) j=1; /* Survives at least one month after exam */
3225: else if(j<0){
3226: nberr++;
3227: 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]);
3228: j=1; /* Temporary Dangerous patch */
3229: 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);
3230: 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]);
3231: 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);
3232: }
3233: k=k+1;
3234: if (j >= jmax){
3235: jmax=j;
3236: ijmax=i;
3237: }
3238: if (j <= jmin){
3239: jmin=j;
3240: ijmin=i;
3241: }
3242: sum=sum+j;
3243: /*if (j<0) printf("j=%d num=%d \n",j,i);*/
3244: /* printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
3245: }
3246: }
3247: else{
3248: j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
3249: /* 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]); */
3250:
3251: k=k+1;
3252: if (j >= jmax) {
3253: jmax=j;
3254: ijmax=i;
3255: }
3256: else if (j <= jmin){
3257: jmin=j;
3258: ijmin=i;
3259: }
3260: /* if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
3261: /*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]);*/
3262: if(j<0){
3263: nberr++;
3264: 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]);
3265: 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]);
3266: }
3267: sum=sum+j;
3268: }
3269: jk= j/stepm;
3270: jl= j -jk*stepm;
3271: ju= j -(jk+1)*stepm;
3272: if(mle <=1){ /* only if we use a the linear-interpoloation pseudo-likelihood */
3273: if(jl==0){
3274: dh[mi][i]=jk;
3275: bh[mi][i]=0;
3276: }else{ /* We want a negative bias in order to only have interpolation ie
1.136 brouard 3277: * to avoid the price of an extra matrix product in likelihood */
1.126 brouard 3278: dh[mi][i]=jk+1;
3279: bh[mi][i]=ju;
3280: }
3281: }else{
3282: if(jl <= -ju){
3283: dh[mi][i]=jk;
3284: bh[mi][i]=jl; /* bias is positive if real duration
3285: * is higher than the multiple of stepm and negative otherwise.
3286: */
3287: }
3288: else{
3289: dh[mi][i]=jk+1;
3290: bh[mi][i]=ju;
3291: }
3292: if(dh[mi][i]==0){
3293: dh[mi][i]=1; /* At least one step */
3294: bh[mi][i]=ju; /* At least one step */
3295: /* 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);*/
3296: }
3297: } /* end if mle */
3298: }
3299: } /* end wave */
3300: }
3301: jmean=sum/k;
3302: 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 3303: 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 3304: }
3305:
3306: /*********** Tricode ****************************/
1.145 brouard 3307: void tricode(int *Tvar, int **nbcode, int imx, int *Ndum)
1.126 brouard 3308: {
1.144 brouard 3309: /**< Uses cptcovn+2*cptcovprod as the number of covariates */
3310: /* 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 3311: * Boring subroutine which should only output nbcode[Tvar[j]][k]
1.145 brouard 3312: * Tvar[5] in V2+V1+V3*age+V2*V4 is 2 (V2)
1.169 brouard 3313: * nbcode[Tvar[j]][1]=
1.144 brouard 3314: */
1.130 brouard 3315:
1.145 brouard 3316: int ij=1, k=0, j=0, i=0, maxncov=NCOVMAX;
1.136 brouard 3317: int modmaxcovj=0; /* Modality max of covariates j */
1.145 brouard 3318: int cptcode=0; /* Modality max of covariates j */
3319: int modmincovj=0; /* Modality min of covariates j */
3320:
3321:
1.126 brouard 3322: cptcoveff=0;
3323:
1.144 brouard 3324: for (k=1; k <= maxncov; k++) ncodemax[k]=0; /* Horrible constant again replaced by NCOVMAX */
1.126 brouard 3325:
1.145 brouard 3326: /* Loop on covariates without age and products */
1.186 brouard 3327: for (j=1; j<=(cptcovs); j++) { /* From model V1 + V2*age+ V3 + V3*V4 keeps V1 + V3 = 2 only */
1.192 brouard 3328: for (k=-1; k < maxncov; k++) Ndum[k]=0;
1.186 brouard 3329: for (i=1; i<=imx; i++) { /* Loop on individuals: reads the data file to get the maximum value of the
1.136 brouard 3330: modality of this covariate Vj*/
1.145 brouard 3331: ij=(int)(covar[Tvar[j]][i]); /* ij=0 or 1 or -1. Value of the covariate Tvar[j] for individual i
3332: * If product of Vn*Vm, still boolean *:
3333: * If it was coded 1, 2, 3, 4 should be splitted into 3 boolean variables
3334: * 1 => 0 0 0, 2 => 0 0 1, 3 => 0 1 1, 4=1 0 0 */
3335: /* Finds for covariate j, n=Tvar[j] of Vn . ij is the
1.136 brouard 3336: modality of the nth covariate of individual i. */
1.145 brouard 3337: if (ij > modmaxcovj)
3338: modmaxcovj=ij;
3339: else if (ij < modmincovj)
3340: modmincovj=ij;
3341: if ((ij < -1) && (ij > NCOVMAX)){
3342: printf( "Error: minimal is less than -1 or maximal is bigger than %d. Exiting. \n", NCOVMAX );
3343: exit(1);
3344: }else
1.136 brouard 3345: Ndum[ij]++; /*counts and stores the occurence of this modality 0, 1, -1*/
1.145 brouard 3346: /* If coded 1, 2, 3 , counts the number of 1 Ndum[1], number of 2, Ndum[2], etc */
1.126 brouard 3347: /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
1.136 brouard 3348: /* getting the maximum value of the modality of the covariate
3349: (should be 0 or 1 now) Tvar[j]. If V=sex and male is coded 0 and
3350: female is 1, then modmaxcovj=1.*/
1.192 brouard 3351: } /* end for loop on individuals i */
1.145 brouard 3352: printf(" Minimal and maximal values of %d th covariate V%d: min=%d max=%d \n", j, Tvar[j], modmincovj, modmaxcovj);
1.192 brouard 3353: 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 3354: cptcode=modmaxcovj;
1.137 brouard 3355: /* Ndum[0] = frequency of 0 for model-covariate j, Ndum[1] frequency of 1 etc. */
1.145 brouard 3356: /*for (i=0; i<=cptcode; i++) {*/
1.192 brouard 3357: for (k=modmincovj; k<=modmaxcovj; k++) { /* k=-1 ? 0 and 1*//* For each value k of the modality of model-cov j */
3358: printf("Frequencies of covariates %d ie V%d with value %d: %d\n", j, Tvar[j], k, Ndum[k]);
3359: fprintf(ficlog, "Frequencies of covariates %d ie V%d with value %d: %d\n", j, Tvar[j], k, Ndum[k]);
3360: if( Ndum[k] != 0 ){ /* Counts if nobody answered modality k ie empty modality, we skip it and reorder */
3361: if( k != -1){
3362: ncodemax[j]++; /* ncodemax[j]= Number of modalities of the j th
3363: covariate for which somebody answered excluding
3364: undefined. Usually 2: 0 and 1. */
3365: }
3366: ncodemaxwundef[j]++; /* ncodemax[j]= Number of modalities of the j th
3367: covariate for which somebody answered including
3368: undefined. Usually 3: -1, 0 and 1. */
1.145 brouard 3369: }
3370: /* In fact ncodemax[j]=2 (dichotom. variables only) but it could be more for
3371: historical reasons: 3 if coded 1, 2, 3 and 4 and Ndum[2]=0 */
1.131 brouard 3372: } /* Ndum[-1] number of undefined modalities */
1.126 brouard 3373:
1.136 brouard 3374: /* j is a covariate, n=Tvar[j] of Vn; Fills nbcode */
1.186 brouard 3375: /* For covariate j, modalities could be 1, 2, 3, 4, 5, 6, 7.
3376: 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 3377: modmincovj=3; modmaxcovj = 7;
1.186 brouard 3378: There are only 3 modalities non empty 3, 6, 7 (or 2 if 27 is too few) : ncodemax[j]=3;
3379: which will be coded 0, 1, 2 which in binary on 2=3-1 digits are 0=00 1=01, 2=10;
3380: defining two dummy variables: variables V1_1 and V1_2.
1.145 brouard 3381: nbcode[Tvar[j]][ij]=k;
3382: nbcode[Tvar[j]][1]=0;
3383: nbcode[Tvar[j]][2]=1;
3384: nbcode[Tvar[j]][3]=2;
3385: */
1.192 brouard 3386: ij=0; /* ij is similar to i but can jumps over null modalities */
3387: for (i=modmincovj; i<=modmaxcovj; i++) { /* i= 1 to 2 for dichotomous, or from 1 to 3 or from -1 to 1*/
3388: if (Ndum[i] == 0) { /* If at least one individual responded to this modality k */
3389: break;
3390: }
3391: ij++;
3392: nbcode[Tvar[j]][ij]=i; /* stores the original modality i in an array nbcode, ij modality from 1 to last non-nul modality.*/
3393: cptcode = ij; /* New max modality for covar j */
3394: } /* end of loop on modality i=-1 to 1 or more */
3395:
3396: /* for (k=0; k<= cptcode; k++) { /\* k=-1 ? k=0 to 1 *\//\* Could be 1 to 4 *\//\* cptcode=modmaxcovj *\/ */
3397: /* /\*recode from 0 *\/ */
3398: /* k is a modality. If we have model=V1+V1*sex */
3399: /* then: nbcode[1][1]=0 ; nbcode[1][2]=1; nbcode[2][1]=0 ; nbcode[2][2]=1; */
3400: /* But if some modality were not used, it is recoded from 0 to a newer modmaxcovj=cptcode *\/ */
3401: /* } */
3402: /* /\* cptcode = ij; *\/ /\* New max modality for covar j *\/ */
3403: /* if (ij > ncodemax[j]) { */
3404: /* printf( " Error ij=%d > ncodemax[%d]=%d\n", ij, j, ncodemax[j]); */
3405: /* fprintf(ficlog, " Error ij=%d > ncodemax[%d]=%d\n", ij, j, ncodemax[j]); */
3406: /* break; */
3407: /* } */
3408: /* } /\* end of loop on modality k *\/ */
1.137 brouard 3409: } /* end of loop on model-covariate j. nbcode[Tvarj][1]=0 and nbcode[Tvarj][2]=1 sets the value of covariate j*/
3410:
1.145 brouard 3411: for (k=-1; k< maxncov; k++) Ndum[k]=0;
1.137 brouard 3412:
1.187 brouard 3413: for (i=1; i<=ncovmodel-2-nagesqr; i++) { /* -2, cste and age and eventually age*age */
1.145 brouard 3414: /* Listing of all covariables in statement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/
3415: ij=Tvar[i]; /* Tvar might be -1 if status was unknown */
1.187 brouard 3416: Ndum[ij]++; /* Might be supersed V1 + V1*age */
1.145 brouard 3417: }
1.126 brouard 3418:
1.192 brouard 3419: ij=0;
1.145 brouard 3420: for (i=0; i<= maxncov-1; i++) { /* modmaxcovj is unknown here. Only Ndum[2(V2),3(age*V3), 5(V3*V2) 6(V1*V4) */
3421: /*printf("Ndum[%d]=%d\n",i, Ndum[i]);*/
1.126 brouard 3422: if((Ndum[i]!=0) && (i<=ncovcol)){
1.192 brouard 3423: ij++;
1.145 brouard 3424: /*printf("diff Ndum[%d]=%d\n",i, Ndum[i]);*/
3425: Tvaraff[ij]=i; /*For printing (unclear) */
1.192 brouard 3426: }else{
3427: /* Tvaraff[ij]=0; */
3428: }
1.126 brouard 3429: }
1.192 brouard 3430: /* ij--; */
1.144 brouard 3431: cptcoveff=ij; /*Number of total covariates*/
1.145 brouard 3432:
1.126 brouard 3433: }
3434:
1.145 brouard 3435:
1.126 brouard 3436: /*********** Health Expectancies ****************/
3437:
1.127 brouard 3438: 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 3439:
3440: {
3441: /* Health expectancies, no variances */
1.164 brouard 3442: int i, j, nhstepm, hstepm, h, nstepm;
1.126 brouard 3443: int nhstepma, nstepma; /* Decreasing with age */
3444: double age, agelim, hf;
3445: double ***p3mat;
3446: double eip;
3447:
3448: pstamp(ficreseij);
3449: fprintf(ficreseij,"# (a) Life expectancies by health status at initial age and (b) health expectancies by health status at initial age\n");
3450: fprintf(ficreseij,"# Age");
3451: for(i=1; i<=nlstate;i++){
3452: for(j=1; j<=nlstate;j++){
3453: fprintf(ficreseij," e%1d%1d ",i,j);
3454: }
3455: fprintf(ficreseij," e%1d. ",i);
3456: }
3457: fprintf(ficreseij,"\n");
3458:
3459:
3460: if(estepm < stepm){
3461: printf ("Problem %d lower than %d\n",estepm, stepm);
3462: }
3463: else hstepm=estepm;
3464: /* We compute the life expectancy from trapezoids spaced every estepm months
3465: * This is mainly to measure the difference between two models: for example
3466: * if stepm=24 months pijx are given only every 2 years and by summing them
3467: * we are calculating an estimate of the Life Expectancy assuming a linear
3468: * progression in between and thus overestimating or underestimating according
3469: * to the curvature of the survival function. If, for the same date, we
3470: * estimate the model with stepm=1 month, we can keep estepm to 24 months
3471: * to compare the new estimate of Life expectancy with the same linear
3472: * hypothesis. A more precise result, taking into account a more precise
3473: * curvature will be obtained if estepm is as small as stepm. */
3474:
3475: /* For example we decided to compute the life expectancy with the smallest unit */
3476: /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
3477: nhstepm is the number of hstepm from age to agelim
3478: nstepm is the number of stepm from age to agelin.
3479: Look at hpijx to understand the reason of that which relies in memory size
3480: and note for a fixed period like estepm months */
3481: /* We decided (b) to get a life expectancy respecting the most precise curvature of the
3482: survival function given by stepm (the optimization length). Unfortunately it
3483: means that if the survival funtion is printed only each two years of age and if
3484: you sum them up and add 1 year (area under the trapezoids) you won't get the same
3485: results. So we changed our mind and took the option of the best precision.
3486: */
3487: hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
3488:
3489: agelim=AGESUP;
3490: /* If stepm=6 months */
3491: /* Computed by stepm unit matrices, product of hstepm matrices, stored
3492: in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
3493:
3494: /* nhstepm age range expressed in number of stepm */
3495: nstepm=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
3496: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
3497: /* if (stepm >= YEARM) hstepm=1;*/
3498: nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
3499: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3500:
3501: for (age=bage; age<=fage; age ++){
3502: nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
3503: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
3504: /* if (stepm >= YEARM) hstepm=1;*/
3505: nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
3506:
3507: /* If stepm=6 months */
3508: /* Computed by stepm unit matrices, product of hstepma matrices, stored
3509: in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
3510:
3511: hpxij(p3mat,nhstepma,age,hstepm,x,nlstate,stepm,oldm, savm, cij);
3512:
3513: hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
3514:
3515: printf("%d|",(int)age);fflush(stdout);
3516: fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
3517:
3518: /* Computing expectancies */
3519: for(i=1; i<=nlstate;i++)
3520: for(j=1; j<=nlstate;j++)
3521: for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
3522: eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
3523:
3524: /* 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]);*/
3525:
3526: }
3527:
3528: fprintf(ficreseij,"%3.0f",age );
3529: for(i=1; i<=nlstate;i++){
3530: eip=0;
3531: for(j=1; j<=nlstate;j++){
3532: eip +=eij[i][j][(int)age];
3533: fprintf(ficreseij,"%9.4f", eij[i][j][(int)age] );
3534: }
3535: fprintf(ficreseij,"%9.4f", eip );
3536: }
3537: fprintf(ficreseij,"\n");
3538:
3539: }
3540: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3541: printf("\n");
3542: fprintf(ficlog,"\n");
3543:
3544: }
3545:
1.127 brouard 3546: 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 3547:
3548: {
3549: /* Covariances of health expectancies eij and of total life expectancies according
3550: to initial status i, ei. .
3551: */
3552: int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2, ij, ji;
3553: int nhstepma, nstepma; /* Decreasing with age */
3554: double age, agelim, hf;
3555: double ***p3matp, ***p3matm, ***varhe;
3556: double **dnewm,**doldm;
3557: double *xp, *xm;
3558: double **gp, **gm;
3559: double ***gradg, ***trgradg;
3560: int theta;
3561:
3562: double eip, vip;
3563:
3564: varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage);
3565: xp=vector(1,npar);
3566: xm=vector(1,npar);
3567: dnewm=matrix(1,nlstate*nlstate,1,npar);
3568: doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate);
3569:
3570: pstamp(ficresstdeij);
3571: fprintf(ficresstdeij,"# Health expectancies with standard errors\n");
3572: fprintf(ficresstdeij,"# Age");
3573: for(i=1; i<=nlstate;i++){
3574: for(j=1; j<=nlstate;j++)
3575: fprintf(ficresstdeij," e%1d%1d (SE)",i,j);
3576: fprintf(ficresstdeij," e%1d. ",i);
3577: }
3578: fprintf(ficresstdeij,"\n");
3579:
3580: pstamp(ficrescveij);
3581: fprintf(ficrescveij,"# Subdiagonal matrix of covariances of health expectancies by age: cov(eij,ekl)\n");
3582: fprintf(ficrescveij,"# Age");
3583: for(i=1; i<=nlstate;i++)
3584: for(j=1; j<=nlstate;j++){
3585: cptj= (j-1)*nlstate+i;
3586: for(i2=1; i2<=nlstate;i2++)
3587: for(j2=1; j2<=nlstate;j2++){
3588: cptj2= (j2-1)*nlstate+i2;
3589: if(cptj2 <= cptj)
3590: fprintf(ficrescveij," %1d%1d,%1d%1d",i,j,i2,j2);
3591: }
3592: }
3593: fprintf(ficrescveij,"\n");
3594:
3595: if(estepm < stepm){
3596: printf ("Problem %d lower than %d\n",estepm, stepm);
3597: }
3598: else hstepm=estepm;
3599: /* We compute the life expectancy from trapezoids spaced every estepm months
3600: * This is mainly to measure the difference between two models: for example
3601: * if stepm=24 months pijx are given only every 2 years and by summing them
3602: * we are calculating an estimate of the Life Expectancy assuming a linear
3603: * progression in between and thus overestimating or underestimating according
3604: * to the curvature of the survival function. If, for the same date, we
3605: * estimate the model with stepm=1 month, we can keep estepm to 24 months
3606: * to compare the new estimate of Life expectancy with the same linear
3607: * hypothesis. A more precise result, taking into account a more precise
3608: * curvature will be obtained if estepm is as small as stepm. */
3609:
3610: /* For example we decided to compute the life expectancy with the smallest unit */
3611: /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
3612: nhstepm is the number of hstepm from age to agelim
3613: nstepm is the number of stepm from age to agelin.
3614: Look at hpijx to understand the reason of that which relies in memory size
3615: and note for a fixed period like estepm months */
3616: /* We decided (b) to get a life expectancy respecting the most precise curvature of the
3617: survival function given by stepm (the optimization length). Unfortunately it
3618: means that if the survival funtion is printed only each two years of age and if
3619: you sum them up and add 1 year (area under the trapezoids) you won't get the same
3620: results. So we changed our mind and took the option of the best precision.
3621: */
3622: hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
3623:
3624: /* If stepm=6 months */
3625: /* nhstepm age range expressed in number of stepm */
3626: agelim=AGESUP;
3627: nstepm=(int) rint((agelim-bage)*YEARM/stepm);
3628: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
3629: /* if (stepm >= YEARM) hstepm=1;*/
3630: nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
3631:
3632: p3matp=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3633: p3matm=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3634: gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);
3635: trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar);
3636: gp=matrix(0,nhstepm,1,nlstate*nlstate);
3637: gm=matrix(0,nhstepm,1,nlstate*nlstate);
3638:
3639: for (age=bage; age<=fage; age ++){
3640: nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
3641: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
3642: /* if (stepm >= YEARM) hstepm=1;*/
3643: nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
3644:
3645: /* If stepm=6 months */
3646: /* Computed by stepm unit matrices, product of hstepma matrices, stored
3647: in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
3648:
3649: hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
3650:
3651: /* Computing Variances of health expectancies */
3652: /* Gradient is computed with plus gp and minus gm. Code is duplicated in order to
3653: decrease memory allocation */
3654: for(theta=1; theta <=npar; theta++){
3655: for(i=1; i<=npar; i++){
3656: xp[i] = x[i] + (i==theta ?delti[theta]:0);
3657: xm[i] = x[i] - (i==theta ?delti[theta]:0);
3658: }
3659: hpxij(p3matp,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, cij);
3660: hpxij(p3matm,nhstepm,age,hstepm,xm,nlstate,stepm,oldm,savm, cij);
3661:
3662: for(j=1; j<= nlstate; j++){
3663: for(i=1; i<=nlstate; i++){
3664: for(h=0; h<=nhstepm-1; h++){
3665: gp[h][(j-1)*nlstate + i] = (p3matp[i][j][h]+p3matp[i][j][h+1])/2.;
3666: gm[h][(j-1)*nlstate + i] = (p3matm[i][j][h]+p3matm[i][j][h+1])/2.;
3667: }
3668: }
3669: }
3670:
3671: for(ij=1; ij<= nlstate*nlstate; ij++)
3672: for(h=0; h<=nhstepm-1; h++){
3673: gradg[h][theta][ij]= (gp[h][ij]-gm[h][ij])/2./delti[theta];
3674: }
3675: }/* End theta */
3676:
3677:
3678: for(h=0; h<=nhstepm-1; h++)
3679: for(j=1; j<=nlstate*nlstate;j++)
3680: for(theta=1; theta <=npar; theta++)
3681: trgradg[h][j][theta]=gradg[h][theta][j];
3682:
3683:
3684: for(ij=1;ij<=nlstate*nlstate;ij++)
3685: for(ji=1;ji<=nlstate*nlstate;ji++)
3686: varhe[ij][ji][(int)age] =0.;
3687:
3688: printf("%d|",(int)age);fflush(stdout);
3689: fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
3690: for(h=0;h<=nhstepm-1;h++){
3691: for(k=0;k<=nhstepm-1;k++){
3692: matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov);
3693: matprod2(doldm,dnewm,1,nlstate*nlstate,1,npar,1,nlstate*nlstate,gradg[k]);
3694: for(ij=1;ij<=nlstate*nlstate;ij++)
3695: for(ji=1;ji<=nlstate*nlstate;ji++)
3696: varhe[ij][ji][(int)age] += doldm[ij][ji]*hf*hf;
3697: }
3698: }
3699:
3700: /* Computing expectancies */
3701: hpxij(p3matm,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, cij);
3702: for(i=1; i<=nlstate;i++)
3703: for(j=1; j<=nlstate;j++)
3704: for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
3705: eij[i][j][(int)age] += (p3matm[i][j][h]+p3matm[i][j][h+1])/2.0*hf;
3706:
3707: /* 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]);*/
3708:
3709: }
3710:
3711: fprintf(ficresstdeij,"%3.0f",age );
3712: for(i=1; i<=nlstate;i++){
3713: eip=0.;
3714: vip=0.;
3715: for(j=1; j<=nlstate;j++){
3716: eip += eij[i][j][(int)age];
3717: for(k=1; k<=nlstate;k++) /* Sum on j and k of cov(eij,eik) */
3718: vip += varhe[(j-1)*nlstate+i][(k-1)*nlstate+i][(int)age];
3719: fprintf(ficresstdeij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[(j-1)*nlstate+i][(j-1)*nlstate+i][(int)age]) );
3720: }
3721: fprintf(ficresstdeij," %9.4f (%.4f)", eip, sqrt(vip));
3722: }
3723: fprintf(ficresstdeij,"\n");
3724:
3725: fprintf(ficrescveij,"%3.0f",age );
3726: for(i=1; i<=nlstate;i++)
3727: for(j=1; j<=nlstate;j++){
3728: cptj= (j-1)*nlstate+i;
3729: for(i2=1; i2<=nlstate;i2++)
3730: for(j2=1; j2<=nlstate;j2++){
3731: cptj2= (j2-1)*nlstate+i2;
3732: if(cptj2 <= cptj)
3733: fprintf(ficrescveij," %.4f", varhe[cptj][cptj2][(int)age]);
3734: }
3735: }
3736: fprintf(ficrescveij,"\n");
3737:
3738: }
3739: free_matrix(gm,0,nhstepm,1,nlstate*nlstate);
3740: free_matrix(gp,0,nhstepm,1,nlstate*nlstate);
3741: free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*nlstate);
3742: free_ma3x(trgradg,0,nhstepm,1,nlstate*nlstate,1,npar);
3743: free_ma3x(p3matm,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3744: free_ma3x(p3matp,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3745: printf("\n");
3746: fprintf(ficlog,"\n");
3747:
3748: free_vector(xm,1,npar);
3749: free_vector(xp,1,npar);
3750: free_matrix(dnewm,1,nlstate*nlstate,1,npar);
3751: free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate);
3752: free_ma3x(varhe,1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int)fage);
3753: }
3754:
3755: /************ Variance ******************/
3756: 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 ij, int estepm, int cptcov, int cptcod, int popbased, int mobilav, char strstart[])
3757: {
3758: /* Variance of health expectancies */
3759: /* double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
3760: /* double **newm;*/
1.169 brouard 3761: /* int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav)*/
3762:
3763: int movingaverage();
1.126 brouard 3764: double **dnewm,**doldm;
3765: double **dnewmp,**doldmp;
3766: int i, j, nhstepm, hstepm, h, nstepm ;
1.164 brouard 3767: int k;
1.126 brouard 3768: double *xp;
3769: double **gp, **gm; /* for var eij */
3770: double ***gradg, ***trgradg; /*for var eij */
3771: double **gradgp, **trgradgp; /* for var p point j */
3772: double *gpp, *gmp; /* for var p point j */
3773: double **varppt; /* for var p point j nlstate to nlstate+ndeath */
3774: double ***p3mat;
3775: double age,agelim, hf;
3776: double ***mobaverage;
3777: int theta;
3778: char digit[4];
3779: char digitp[25];
3780:
3781: char fileresprobmorprev[FILENAMELENGTH];
3782:
3783: if(popbased==1){
3784: if(mobilav!=0)
3785: strcpy(digitp,"-populbased-mobilav-");
3786: else strcpy(digitp,"-populbased-nomobil-");
3787: }
3788: else
3789: strcpy(digitp,"-stablbased-");
3790:
3791: if (mobilav!=0) {
3792: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
3793: if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
3794: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
3795: printf(" Error in movingaverage mobilav=%d\n",mobilav);
3796: }
3797: }
3798:
3799: strcpy(fileresprobmorprev,"prmorprev");
3800: sprintf(digit,"%-d",ij);
3801: /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
3802: strcat(fileresprobmorprev,digit); /* Tvar to be done */
3803: strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
3804: strcat(fileresprobmorprev,fileres);
3805: if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
3806: printf("Problem with resultfile: %s\n", fileresprobmorprev);
3807: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
3808: }
3809: printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
3810:
3811: fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
3812: pstamp(ficresprobmorprev);
3813: 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);
3814: fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
3815: for(j=nlstate+1; j<=(nlstate+ndeath);j++){
3816: fprintf(ficresprobmorprev," p.%-d SE",j);
3817: for(i=1; i<=nlstate;i++)
3818: fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
3819: }
3820: fprintf(ficresprobmorprev,"\n");
3821: fprintf(ficgp,"\n# Routine varevsij");
3822: /* fprintf(fichtm, "#Local time at start: %s", strstart);*/
3823: 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");
3824: fprintf(fichtm,"\n<br>%s <br>\n",digitp);
3825: /* } */
3826: varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
3827: pstamp(ficresvij);
3828: fprintf(ficresvij,"# Variance and covariance of health expectancies e.j \n# (weighted average of eij where weights are ");
3829: if(popbased==1)
1.128 brouard 3830: 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 3831: else
3832: fprintf(ficresvij,"the age specific period (stable) prevalences in each health state \n");
3833: fprintf(ficresvij,"# Age");
3834: for(i=1; i<=nlstate;i++)
3835: for(j=1; j<=nlstate;j++)
3836: fprintf(ficresvij," Cov(e.%1d, e.%1d)",i,j);
3837: fprintf(ficresvij,"\n");
3838:
3839: xp=vector(1,npar);
3840: dnewm=matrix(1,nlstate,1,npar);
3841: doldm=matrix(1,nlstate,1,nlstate);
3842: dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
3843: doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
3844:
3845: gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
3846: gpp=vector(nlstate+1,nlstate+ndeath);
3847: gmp=vector(nlstate+1,nlstate+ndeath);
3848: trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
3849:
3850: if(estepm < stepm){
3851: printf ("Problem %d lower than %d\n",estepm, stepm);
3852: }
3853: else hstepm=estepm;
3854: /* For example we decided to compute the life expectancy with the smallest unit */
3855: /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
3856: nhstepm is the number of hstepm from age to agelim
3857: nstepm is the number of stepm from age to agelin.
1.128 brouard 3858: Look at function hpijx to understand why (it is linked to memory size questions) */
1.126 brouard 3859: /* We decided (b) to get a life expectancy respecting the most precise curvature of the
3860: survival function given by stepm (the optimization length). Unfortunately it
3861: means that if the survival funtion is printed every two years of age and if
3862: you sum them up and add 1 year (area under the trapezoids) you won't get the same
3863: results. So we changed our mind and took the option of the best precision.
3864: */
3865: hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
3866: agelim = AGESUP;
3867: for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
3868: nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
3869: nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
3870: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3871: gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
3872: gp=matrix(0,nhstepm,1,nlstate);
3873: gm=matrix(0,nhstepm,1,nlstate);
3874:
3875:
3876: for(theta=1; theta <=npar; theta++){
3877: for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
3878: xp[i] = x[i] + (i==theta ?delti[theta]:0);
3879: }
3880: hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
3881: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
3882:
3883: if (popbased==1) {
3884: if(mobilav ==0){
3885: for(i=1; i<=nlstate;i++)
3886: prlim[i][i]=probs[(int)age][i][ij];
3887: }else{ /* mobilav */
3888: for(i=1; i<=nlstate;i++)
3889: prlim[i][i]=mobaverage[(int)age][i][ij];
3890: }
3891: }
3892:
3893: for(j=1; j<= nlstate; j++){
3894: for(h=0; h<=nhstepm; h++){
3895: for(i=1, gp[h][j]=0.;i<=nlstate;i++)
3896: gp[h][j] += prlim[i][i]*p3mat[i][j][h];
3897: }
3898: }
3899: /* This for computing probability of death (h=1 means
3900: computed over hstepm matrices product = hstepm*stepm months)
3901: as a weighted average of prlim.
3902: */
3903: for(j=nlstate+1;j<=nlstate+ndeath;j++){
3904: for(i=1,gpp[j]=0.; i<= nlstate; i++)
3905: gpp[j] += prlim[i][i]*p3mat[i][j][1];
3906: }
3907: /* end probability of death */
3908:
3909: for(i=1; i<=npar; i++) /* Computes gradient x - delta */
3910: xp[i] = x[i] - (i==theta ?delti[theta]:0);
3911: hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
3912: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
3913:
3914: if (popbased==1) {
3915: if(mobilav ==0){
3916: for(i=1; i<=nlstate;i++)
3917: prlim[i][i]=probs[(int)age][i][ij];
3918: }else{ /* mobilav */
3919: for(i=1; i<=nlstate;i++)
3920: prlim[i][i]=mobaverage[(int)age][i][ij];
3921: }
3922: }
3923:
1.128 brouard 3924: for(j=1; j<= nlstate; j++){ /* Sum of wi * eij = e.j */
1.126 brouard 3925: for(h=0; h<=nhstepm; h++){
3926: for(i=1, gm[h][j]=0.;i<=nlstate;i++)
3927: gm[h][j] += prlim[i][i]*p3mat[i][j][h];
3928: }
3929: }
3930: /* This for computing probability of death (h=1 means
3931: computed over hstepm matrices product = hstepm*stepm months)
3932: as a weighted average of prlim.
3933: */
3934: for(j=nlstate+1;j<=nlstate+ndeath;j++){
3935: for(i=1,gmp[j]=0.; i<= nlstate; i++)
3936: gmp[j] += prlim[i][i]*p3mat[i][j][1];
3937: }
3938: /* end probability of death */
3939:
3940: for(j=1; j<= nlstate; j++) /* vareij */
3941: for(h=0; h<=nhstepm; h++){
3942: gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
3943: }
3944:
3945: for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
3946: gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
3947: }
3948:
3949: } /* End theta */
3950:
3951: trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
3952:
3953: for(h=0; h<=nhstepm; h++) /* veij */
3954: for(j=1; j<=nlstate;j++)
3955: for(theta=1; theta <=npar; theta++)
3956: trgradg[h][j][theta]=gradg[h][theta][j];
3957:
3958: for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
3959: for(theta=1; theta <=npar; theta++)
3960: trgradgp[j][theta]=gradgp[theta][j];
3961:
3962:
3963: hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
3964: for(i=1;i<=nlstate;i++)
3965: for(j=1;j<=nlstate;j++)
3966: vareij[i][j][(int)age] =0.;
3967:
3968: for(h=0;h<=nhstepm;h++){
3969: for(k=0;k<=nhstepm;k++){
3970: matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
3971: matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
3972: for(i=1;i<=nlstate;i++)
3973: for(j=1;j<=nlstate;j++)
3974: vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
3975: }
3976: }
3977:
3978: /* pptj */
3979: matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
3980: matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
3981: for(j=nlstate+1;j<=nlstate+ndeath;j++)
3982: for(i=nlstate+1;i<=nlstate+ndeath;i++)
3983: varppt[j][i]=doldmp[j][i];
3984: /* end ppptj */
3985: /* x centered again */
3986: hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);
3987: prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);
3988:
3989: if (popbased==1) {
3990: if(mobilav ==0){
3991: for(i=1; i<=nlstate;i++)
3992: prlim[i][i]=probs[(int)age][i][ij];
3993: }else{ /* mobilav */
3994: for(i=1; i<=nlstate;i++)
3995: prlim[i][i]=mobaverage[(int)age][i][ij];
3996: }
3997: }
3998:
3999: /* This for computing probability of death (h=1 means
4000: computed over hstepm (estepm) matrices product = hstepm*stepm months)
4001: as a weighted average of prlim.
4002: */
4003: for(j=nlstate+1;j<=nlstate+ndeath;j++){
4004: for(i=1,gmp[j]=0.;i<= nlstate; i++)
4005: gmp[j] += prlim[i][i]*p3mat[i][j][1];
4006: }
4007: /* end probability of death */
4008:
4009: fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
4010: for(j=nlstate+1; j<=(nlstate+ndeath);j++){
4011: fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
4012: for(i=1; i<=nlstate;i++){
4013: fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
4014: }
4015: }
4016: fprintf(ficresprobmorprev,"\n");
4017:
4018: fprintf(ficresvij,"%.0f ",age );
4019: for(i=1; i<=nlstate;i++)
4020: for(j=1; j<=nlstate;j++){
4021: fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
4022: }
4023: fprintf(ficresvij,"\n");
4024: free_matrix(gp,0,nhstepm,1,nlstate);
4025: free_matrix(gm,0,nhstepm,1,nlstate);
4026: free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
4027: free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
4028: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4029: } /* End age */
4030: free_vector(gpp,nlstate+1,nlstate+ndeath);
4031: free_vector(gmp,nlstate+1,nlstate+ndeath);
4032: free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
4033: free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
1.145 brouard 4034: fprintf(ficgp,"\nunset parametric;unset label; set ter png small size 320, 240");
1.126 brouard 4035: /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */
1.131 brouard 4036: fprintf(ficgp,"\n set log y; unset log x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
1.126 brouard 4037: /* fprintf(ficgp,"\n plot \"%s\" u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm); */
4038: /* fprintf(ficgp,"\n replot \"%s\" u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm); */
4039: /* fprintf(ficgp,"\n replot \"%s\" u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm); */
1.145 brouard 4040: fprintf(ficgp,"\n plot \"%s\" u 1:($3) not w l lt 1 ",subdirf(fileresprobmorprev));
1.170 brouard 4041: fprintf(ficgp,"\n replot \"%s\" u 1:(($3+1.96*$4)) t \"95%% interval\" w l lt 2 ",subdirf(fileresprobmorprev));
1.145 brouard 4042: fprintf(ficgp,"\n replot \"%s\" u 1:(($3-1.96*$4)) not w l lt 2 ",subdirf(fileresprobmorprev));
1.126 brouard 4043: fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",subdirf(fileresprobmorprev),subdirf(fileresprobmorprev));
4044: fprintf(fichtm,"\n<br> Probability is computed over estepm=%d months. <br> <img src=\"%s%s.png\"> <br>\n", estepm,subdirf3(optionfilefiname,"varmuptjgr",digitp),digit);
4045: /* 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.png\"> <br>\n", stepm,YEARM,digitp,digit);
4046: */
4047: /* fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.png\";replot;",digitp,optionfilefiname,digit); */
4048: fprintf(ficgp,"\nset out \"%s%s.png\";replot;\n",subdirf3(optionfilefiname,"varmuptjgr",digitp),digit);
4049:
4050: free_vector(xp,1,npar);
4051: free_matrix(doldm,1,nlstate,1,nlstate);
4052: free_matrix(dnewm,1,nlstate,1,npar);
4053: free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
4054: free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
4055: free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
4056: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
4057: fclose(ficresprobmorprev);
4058: fflush(ficgp);
4059: fflush(fichtm);
4060: } /* end varevsij */
4061:
4062: /************ Variance of prevlim ******************/
4063: 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 ij, char strstart[])
4064: {
4065: /* Variance of prevalence limit */
4066: /* double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
1.164 brouard 4067:
1.126 brouard 4068: double **dnewm,**doldm;
4069: int i, j, nhstepm, hstepm;
4070: double *xp;
4071: double *gp, *gm;
4072: double **gradg, **trgradg;
4073: double age,agelim;
4074: int theta;
4075:
4076: pstamp(ficresvpl);
4077: fprintf(ficresvpl,"# Standard deviation of period (stable) prevalences \n");
4078: fprintf(ficresvpl,"# Age");
4079: for(i=1; i<=nlstate;i++)
4080: fprintf(ficresvpl," %1d-%1d",i,i);
4081: fprintf(ficresvpl,"\n");
4082:
4083: xp=vector(1,npar);
4084: dnewm=matrix(1,nlstate,1,npar);
4085: doldm=matrix(1,nlstate,1,nlstate);
4086:
4087: hstepm=1*YEARM; /* Every year of age */
4088: hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */
4089: agelim = AGESUP;
4090: for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
4091: nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
4092: if (stepm >= YEARM) hstepm=1;
4093: nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
4094: gradg=matrix(1,npar,1,nlstate);
4095: gp=vector(1,nlstate);
4096: gm=vector(1,nlstate);
4097:
4098: for(theta=1; theta <=npar; theta++){
4099: for(i=1; i<=npar; i++){ /* Computes gradient */
4100: xp[i] = x[i] + (i==theta ?delti[theta]:0);
4101: }
4102: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
4103: for(i=1;i<=nlstate;i++)
4104: gp[i] = prlim[i][i];
4105:
4106: for(i=1; i<=npar; i++) /* Computes gradient */
4107: xp[i] = x[i] - (i==theta ?delti[theta]:0);
4108: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
4109: for(i=1;i<=nlstate;i++)
4110: gm[i] = prlim[i][i];
4111:
4112: for(i=1;i<=nlstate;i++)
4113: gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
4114: } /* End theta */
4115:
4116: trgradg =matrix(1,nlstate,1,npar);
4117:
4118: for(j=1; j<=nlstate;j++)
4119: for(theta=1; theta <=npar; theta++)
4120: trgradg[j][theta]=gradg[theta][j];
4121:
4122: for(i=1;i<=nlstate;i++)
4123: varpl[i][(int)age] =0.;
4124: matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
4125: matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
4126: for(i=1;i<=nlstate;i++)
4127: varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
4128:
4129: fprintf(ficresvpl,"%.0f ",age );
4130: for(i=1; i<=nlstate;i++)
4131: fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
4132: fprintf(ficresvpl,"\n");
4133: free_vector(gp,1,nlstate);
4134: free_vector(gm,1,nlstate);
4135: free_matrix(gradg,1,npar,1,nlstate);
4136: free_matrix(trgradg,1,nlstate,1,npar);
4137: } /* End age */
4138:
4139: free_vector(xp,1,npar);
4140: free_matrix(doldm,1,nlstate,1,npar);
4141: free_matrix(dnewm,1,nlstate,1,nlstate);
4142:
4143: }
4144:
4145: /************ Variance of one-step probabilities ******************/
4146: 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[])
4147: {
1.164 brouard 4148: int i, j=0, k1, l1, tj;
1.126 brouard 4149: int k2, l2, j1, z1;
1.164 brouard 4150: int k=0, l;
1.145 brouard 4151: int first=1, first1, first2;
1.126 brouard 4152: double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
4153: double **dnewm,**doldm;
4154: double *xp;
4155: double *gp, *gm;
4156: double **gradg, **trgradg;
4157: double **mu;
1.164 brouard 4158: double age, cov[NCOVMAX+1];
1.126 brouard 4159: double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
4160: int theta;
4161: char fileresprob[FILENAMELENGTH];
4162: char fileresprobcov[FILENAMELENGTH];
4163: char fileresprobcor[FILENAMELENGTH];
4164: double ***varpij;
4165:
4166: strcpy(fileresprob,"prob");
4167: strcat(fileresprob,fileres);
4168: if((ficresprob=fopen(fileresprob,"w"))==NULL) {
4169: printf("Problem with resultfile: %s\n", fileresprob);
4170: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
4171: }
4172: strcpy(fileresprobcov,"probcov");
4173: strcat(fileresprobcov,fileres);
4174: if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
4175: printf("Problem with resultfile: %s\n", fileresprobcov);
4176: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
4177: }
4178: strcpy(fileresprobcor,"probcor");
4179: strcat(fileresprobcor,fileres);
4180: if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
4181: printf("Problem with resultfile: %s\n", fileresprobcor);
4182: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
4183: }
4184: printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
4185: fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
4186: printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
4187: fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
4188: printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
4189: fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
4190: pstamp(ficresprob);
4191: fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
4192: fprintf(ficresprob,"# Age");
4193: pstamp(ficresprobcov);
4194: fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
4195: fprintf(ficresprobcov,"# Age");
4196: pstamp(ficresprobcor);
4197: fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
4198: fprintf(ficresprobcor,"# Age");
4199:
4200:
4201: for(i=1; i<=nlstate;i++)
4202: for(j=1; j<=(nlstate+ndeath);j++){
4203: fprintf(ficresprob," p%1d-%1d (SE)",i,j);
4204: fprintf(ficresprobcov," p%1d-%1d ",i,j);
4205: fprintf(ficresprobcor," p%1d-%1d ",i,j);
4206: }
4207: /* fprintf(ficresprob,"\n");
4208: fprintf(ficresprobcov,"\n");
4209: fprintf(ficresprobcor,"\n");
4210: */
1.131 brouard 4211: xp=vector(1,npar);
1.126 brouard 4212: dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
4213: doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
4214: mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
4215: varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
4216: first=1;
4217: fprintf(ficgp,"\n# Routine varprob");
4218: fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
4219: fprintf(fichtm,"\n");
4220:
4221: fprintf(fichtm,"\n<li><h4> <a href=\"%s\">Matrix of variance-covariance of pairs of step probabilities (drawings)</a></h4></li>\n",optionfilehtmcov);
4222: fprintf(fichtmcov,"\n<h4>Matrix of variance-covariance of pairs of step probabilities</h4>\n\
4223: file %s<br>\n",optionfilehtmcov);
4224: fprintf(fichtmcov,"\nEllipsoids of confidence centered on point (p<inf>ij</inf>, p<inf>kl</inf>) are estimated\
4225: and drawn. It helps understanding how is the covariance between two incidences.\
4226: They are expressed in year<sup>-1</sup> in order to be less dependent of stepm.<br>\n");
4227: 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. \
4228: It can be understood this way: if pij and pkl where uncorrelated the (2x2) matrix of covariance \
4229: would have been (1/(var pij), 0 , 0, 1/(var pkl)), and the confidence interval would be 2 \
4230: standard deviations wide on each axis. <br>\
4231: Now, if both incidences are correlated (usual case) we diagonalised the inverse of the covariance matrix\
4232: and made the appropriate rotation to look at the uncorrelated principal directions.<br>\
4233: To be simple, these graphs help to understand the significativity of each parameter in relation to a second other one.<br> \n");
4234:
4235: cov[1]=1;
1.145 brouard 4236: /* tj=cptcoveff; */
4237: tj = (int) pow(2,cptcoveff);
1.126 brouard 4238: if (cptcovn<1) {tj=1;ncodemax[1]=1;}
4239: j1=0;
1.145 brouard 4240: for(j1=1; j1<=tj;j1++){
4241: /*for(i1=1; i1<=ncodemax[t];i1++){ */
4242: /*j1++;*/
1.126 brouard 4243: if (cptcovn>0) {
4244: fprintf(ficresprob, "\n#********** Variable ");
4245: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
4246: fprintf(ficresprob, "**********\n#\n");
4247: fprintf(ficresprobcov, "\n#********** Variable ");
4248: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
4249: fprintf(ficresprobcov, "**********\n#\n");
4250:
4251: fprintf(ficgp, "\n#********** Variable ");
4252: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
4253: fprintf(ficgp, "**********\n#\n");
4254:
4255:
4256: fprintf(fichtmcov, "\n<hr size=\"2\" color=\"#EC5E5E\">********** Variable ");
4257: for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
4258: fprintf(fichtmcov, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
4259:
4260: fprintf(ficresprobcor, "\n#********** Variable ");
4261: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
4262: fprintf(ficresprobcor, "**********\n#");
4263: }
4264:
1.145 brouard 4265: gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
4266: trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
4267: gp=vector(1,(nlstate)*(nlstate+ndeath));
4268: gm=vector(1,(nlstate)*(nlstate+ndeath));
1.126 brouard 4269: for (age=bage; age<=fage; age ++){
4270: cov[2]=age;
1.187 brouard 4271: if(nagesqr==1)
4272: cov[3]= age*age;
1.126 brouard 4273: for (k=1; k<=cptcovn;k++) {
1.187 brouard 4274: cov[2+nagesqr+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];/* j1 1 2 3 4
1.145 brouard 4275: * 1 1 1 1 1
4276: * 2 2 1 1 1
4277: * 3 1 2 1 1
4278: */
4279: /* nbcode[1][1]=0 nbcode[1][2]=1;*/
1.126 brouard 4280: }
1.186 brouard 4281: /* for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
4282: for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=nbcode[Tvar[Tage[k]]][codtab[ij][Tvar[Tage[k]]]]*cov[2];
1.126 brouard 4283: for (k=1; k<=cptcovprod;k++)
1.187 brouard 4284: cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
1.126 brouard 4285:
4286:
4287: for(theta=1; theta <=npar; theta++){
4288: for(i=1; i<=npar; i++)
4289: xp[i] = x[i] + (i==theta ?delti[theta]:(double)0);
4290:
4291: pmij(pmmij,cov,ncovmodel,xp,nlstate);
4292:
4293: k=0;
4294: for(i=1; i<= (nlstate); i++){
4295: for(j=1; j<=(nlstate+ndeath);j++){
4296: k=k+1;
4297: gp[k]=pmmij[i][j];
4298: }
4299: }
4300:
4301: for(i=1; i<=npar; i++)
4302: xp[i] = x[i] - (i==theta ?delti[theta]:(double)0);
4303:
4304: pmij(pmmij,cov,ncovmodel,xp,nlstate);
4305: k=0;
4306: for(i=1; i<=(nlstate); i++){
4307: for(j=1; j<=(nlstate+ndeath);j++){
4308: k=k+1;
4309: gm[k]=pmmij[i][j];
4310: }
4311: }
4312:
4313: for(i=1; i<= (nlstate)*(nlstate+ndeath); i++)
4314: gradg[theta][i]=(gp[i]-gm[i])/(double)2./delti[theta];
4315: }
4316:
4317: for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
4318: for(theta=1; theta <=npar; theta++)
4319: trgradg[j][theta]=gradg[theta][j];
4320:
4321: matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov);
4322: matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);
4323:
4324: pmij(pmmij,cov,ncovmodel,x,nlstate);
4325:
4326: k=0;
4327: for(i=1; i<=(nlstate); i++){
4328: for(j=1; j<=(nlstate+ndeath);j++){
4329: k=k+1;
4330: mu[k][(int) age]=pmmij[i][j];
4331: }
4332: }
4333: for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
4334: for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
4335: varpij[i][j][(int)age] = doldm[i][j];
4336:
4337: /*printf("\n%d ",(int)age);
4338: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
4339: printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
4340: fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
4341: }*/
4342:
4343: fprintf(ficresprob,"\n%d ",(int)age);
4344: fprintf(ficresprobcov,"\n%d ",(int)age);
4345: fprintf(ficresprobcor,"\n%d ",(int)age);
4346:
4347: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)
4348: fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));
4349: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
4350: fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);
4351: fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
4352: }
4353: i=0;
4354: for (k=1; k<=(nlstate);k++){
4355: for (l=1; l<=(nlstate+ndeath);l++){
1.145 brouard 4356: i++;
1.126 brouard 4357: fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
4358: fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
4359: for (j=1; j<=i;j++){
1.145 brouard 4360: /* printf(" k=%d l=%d i=%d j=%d\n",k,l,i,j);fflush(stdout); */
1.126 brouard 4361: fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);
4362: fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));
4363: }
4364: }
4365: }/* end of loop for state */
4366: } /* end of loop for age */
1.145 brouard 4367: free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
4368: free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
4369: free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
4370: free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
4371:
1.126 brouard 4372: /* Confidence intervalle of pij */
4373: /*
1.131 brouard 4374: fprintf(ficgp,"\nunset parametric;unset label");
1.126 brouard 4375: fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");
4376: fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
4377: 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);
4378: fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);
4379: fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);
4380: fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);
4381: */
4382:
4383: /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
1.145 brouard 4384: first1=1;first2=2;
1.126 brouard 4385: for (k2=1; k2<=(nlstate);k2++){
4386: for (l2=1; l2<=(nlstate+ndeath);l2++){
4387: if(l2==k2) continue;
4388: j=(k2-1)*(nlstate+ndeath)+l2;
4389: for (k1=1; k1<=(nlstate);k1++){
4390: for (l1=1; l1<=(nlstate+ndeath);l1++){
4391: if(l1==k1) continue;
4392: i=(k1-1)*(nlstate+ndeath)+l1;
4393: if(i<=j) continue;
4394: for (age=bage; age<=fage; age ++){
4395: if ((int)age %5==0){
4396: v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;
4397: v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;
4398: cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;
4399: mu1=mu[i][(int) age]/stepm*YEARM ;
4400: mu2=mu[j][(int) age]/stepm*YEARM;
4401: c12=cv12/sqrt(v1*v2);
4402: /* Computing eigen value of matrix of covariance */
4403: lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
4404: lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
1.135 brouard 4405: if ((lc2 <0) || (lc1 <0) ){
1.145 brouard 4406: if(first2==1){
4407: first1=0;
4408: 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);
4409: }
4410: 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);
4411: /* lc1=fabs(lc1); */ /* If we want to have them positive */
4412: /* lc2=fabs(lc2); */
1.135 brouard 4413: }
4414:
1.126 brouard 4415: /* Eigen vectors */
4416: v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
4417: /*v21=sqrt(1.-v11*v11); *//* error */
4418: v21=(lc1-v1)/cv12*v11;
4419: v12=-v21;
4420: v22=v11;
4421: tnalp=v21/v11;
4422: if(first1==1){
4423: first1=0;
4424: 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);
4425: }
4426: 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);
4427: /*printf(fignu*/
4428: /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */
4429: /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */
4430: if(first==1){
4431: first=0;
4432: fprintf(ficgp,"\nset parametric;unset label");
4433: 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);
1.145 brouard 4434: fprintf(ficgp,"\nset ter png small size 320, 240");
1.126 brouard 4435: fprintf(fichtmcov,"\n<br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup>\
4436: :<a href=\"%s%d%1d%1d-%1d%1d.png\">\
4437: %s%d%1d%1d-%1d%1d.png</A>, ",k1,l1,k2,l2,\
4438: subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2,\
4439: subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
4440: fprintf(fichtmcov,"\n<br><img src=\"%s%d%1d%1d-%1d%1d.png\"> ",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
4441: fprintf(fichtmcov,"\n<br> Correlation at age %d (%.3f),",(int) age, c12);
4442: fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\"",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
4443: fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
4444: fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
4445: 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",\
4446: mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
4447: mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
4448: }else{
4449: first=0;
4450: fprintf(fichtmcov," %d (%.3f),",(int) age, c12);
4451: fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
4452: fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
4453: 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",\
4454: mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
4455: mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
4456: }/* if first */
4457: } /* age mod 5 */
4458: } /* end loop age */
4459: fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\";replot;",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
4460: first=1;
4461: } /*l12 */
4462: } /* k12 */
4463: } /*l1 */
4464: }/* k1 */
1.169 brouard 4465: /* } */ /* loop covariates */
1.126 brouard 4466: }
4467: free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
4468: free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
4469: free_matrix(doldm,1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
4470: free_matrix(dnewm,1,(nlstate)*(nlstate+ndeath),1,npar);
4471: free_vector(xp,1,npar);
4472: fclose(ficresprob);
4473: fclose(ficresprobcov);
4474: fclose(ficresprobcor);
4475: fflush(ficgp);
4476: fflush(fichtmcov);
4477: }
4478:
4479:
4480: /******************* Printing html file ***********/
4481: void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \
4482: int lastpass, int stepm, int weightopt, char model[],\
4483: int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
4484: int popforecast, int estepm ,\
4485: double jprev1, double mprev1,double anprev1, \
4486: double jprev2, double mprev2,double anprev2){
4487: int jj1, k1, i1, cpt;
4488:
4489: fprintf(fichtm,"<ul><li><a href='#firstorder'>Result files (first order: no variance)</a>\n \
4490: <li><a href='#secondorder'>Result files (second order (variance)</a>\n \
4491: </ul>");
4492: fprintf(fichtm,"<ul><li><h4><a name='firstorder'>Result files (first order: no variance)</a></h4>\n \
4493: - Observed prevalence in each state (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"%s\">%s</a> <br>\n ",
4494: jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirf2(fileres,"p"),subdirf2(fileres,"p"));
4495: fprintf(fichtm,"\
4496: - Estimated transition probabilities over %d (stepm) months: <a href=\"%s\">%s</a><br>\n ",
4497: stepm,subdirf2(fileres,"pij"),subdirf2(fileres,"pij"));
4498: fprintf(fichtm,"\
4499: - Period (stable) prevalence in each health state: <a href=\"%s\">%s</a> <br>\n",
4500: subdirf2(fileres,"pl"),subdirf2(fileres,"pl"));
4501: fprintf(fichtm,"\
1.128 brouard 4502: - (a) Life expectancies by health status at initial age, ei. (b) health expectancies by health status at initial age, eij . 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 4503: <a href=\"%s\">%s</a> <br>\n",
4504: estepm,subdirf2(fileres,"e"),subdirf2(fileres,"e"));
4505: fprintf(fichtm,"\
4506: - Population projections by age and states: \
4507: <a href=\"%s\">%s</a> <br>\n</li>", subdirf2(fileres,"f"),subdirf2(fileres,"f"));
4508:
4509: fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
4510:
1.145 brouard 4511: m=pow(2,cptcoveff);
1.126 brouard 4512: if (cptcovn < 1) {m=1;ncodemax[1]=1;}
4513:
4514: jj1=0;
4515: for(k1=1; k1<=m;k1++){
1.192 brouard 4516: /* for(i1=1; i1<=ncodemax[k1];i1++){ */
1.126 brouard 4517: jj1++;
4518: if (cptcovn > 0) {
4519: fprintf(fichtm,"<hr size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
1.192 brouard 4520: for (cpt=1; cpt<=cptcoveff;cpt++){
1.126 brouard 4521: fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
1.192 brouard 4522: printf(" V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);fflush(stdout);
4523: }
1.126 brouard 4524: fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
4525: }
4526: /* Pij */
1.145 brouard 4527: fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i, %d (stepm) months before: <a href=\"%s%d_1.png\">%s%d_1.png</a><br> \
4528: <img src=\"%s%d_1.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);
1.126 brouard 4529: /* Quasi-incidences */
4530: fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months\
1.145 brouard 4531: before but expressed in per year i.e. quasi incidences if stepm is small and probabilities too: <a href=\"%s%d_2.png\">%s%d_2.png</a><br> \
4532: <img src=\"%s%d_2.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);
1.126 brouard 4533: /* Period (stable) prevalence in each health state */
1.154 brouard 4534: for(cpt=1; cpt<=nlstate;cpt++){
1.166 brouard 4535: fprintf(fichtm,"<br>- 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.png\">%s%d_%d.png</a><br> \
4536: <img src=\"%s%d_%d.png\">", cpt, cpt, nlstate, subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1);
1.126 brouard 4537: }
4538: for(cpt=1; cpt<=nlstate;cpt++) {
1.154 brouard 4539: 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) : <a href=\"%s%d%d.png\">%s%d%d.png</a> <br> \
4540: <img src=\"%s%d%d.png\">",cpt,nlstate,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1);
1.126 brouard 4541: }
1.192 brouard 4542: /* } /\* end i1 *\/ */
1.126 brouard 4543: }/* End k1 */
4544: fprintf(fichtm,"</ul>");
4545:
4546: fprintf(fichtm,"\
4547: \n<br><li><h4> <a name='secondorder'>Result files (second order: variances)</a></h4>\n\
1.193 brouard 4548: - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br> \
4549: - 95%% confidence intervals and T statistics are in the log file.<br>\n", rfileres,rfileres);
1.126 brouard 4550:
1.193 brouard 4551: fprintf(fichtm," - Standard deviation of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
1.126 brouard 4552: subdirf2(fileres,"prob"),subdirf2(fileres,"prob"));
4553: fprintf(fichtm,"\
4554: - Variance-covariance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
4555: subdirf2(fileres,"probcov"),subdirf2(fileres,"probcov"));
4556:
4557: fprintf(fichtm,"\
4558: - Correlation matrix of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
4559: subdirf2(fileres,"probcor"),subdirf2(fileres,"probcor"));
4560: fprintf(fichtm,"\
4561: - 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): \
4562: <a href=\"%s\">%s</a> <br>\n</li>",
4563: estepm,subdirf2(fileres,"cve"),subdirf2(fileres,"cve"));
4564: fprintf(fichtm,"\
4565: - (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): \
4566: <a href=\"%s\">%s</a> <br>\n</li>",
4567: estepm,subdirf2(fileres,"stde"),subdirf2(fileres,"stde"));
4568: fprintf(fichtm,"\
1.128 brouard 4569: - 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",
1.126 brouard 4570: estepm, subdirf2(fileres,"v"),subdirf2(fileres,"v"));
4571: fprintf(fichtm,"\
1.128 brouard 4572: - 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",
4573: estepm, subdirf2(fileres,"t"),subdirf2(fileres,"t"));
1.126 brouard 4574: fprintf(fichtm,"\
4575: - Standard deviation of period (stable) prevalences: <a href=\"%s\">%s</a> <br>\n",\
4576: subdirf2(fileres,"vpl"),subdirf2(fileres,"vpl"));
4577:
4578: /* if(popforecast==1) fprintf(fichtm,"\n */
4579: /* - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n */
4580: /* - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n */
4581: /* <br>",fileres,fileres,fileres,fileres); */
4582: /* else */
4583: /* 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); */
4584: fflush(fichtm);
4585: fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
4586:
1.145 brouard 4587: m=pow(2,cptcoveff);
1.126 brouard 4588: if (cptcovn < 1) {m=1;ncodemax[1]=1;}
4589:
4590: jj1=0;
4591: for(k1=1; k1<=m;k1++){
1.192 brouard 4592: /* for(i1=1; i1<=ncodemax[k1];i1++){ */
1.126 brouard 4593: jj1++;
4594: if (cptcovn > 0) {
4595: fprintf(fichtm,"<hr size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
4596: for (cpt=1; cpt<=cptcoveff;cpt++)
4597: fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
4598: fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
4599: }
4600: for(cpt=1; cpt<=nlstate;cpt++) {
4601: fprintf(fichtm,"<br>- Observed (cross-sectional) and period (incidence based) \
1.145 brouard 4602: prevalence (with 95%% confidence interval) in state (%d): %s%d_%d.png <br>\
4603: <img src=\"%s%d_%d.png\">",cpt,subdirf2(optionfilefiname,"v"),cpt,jj1,subdirf2(optionfilefiname,"v"),cpt,jj1);
1.126 brouard 4604: }
4605: fprintf(fichtm,"\n<br>- Total life expectancy by age and \
1.128 brouard 4606: health expectancies in states (1) and (2). If popbased=1 the smooth (due to the model) \
4607: true period expectancies (those weighted with period prevalences are also\
4608: drawn in addition to the population based expectancies computed using\
4609: observed and cahotic prevalences: %s%d.png<br>\
1.126 brouard 4610: <img src=\"%s%d.png\">",subdirf2(optionfilefiname,"e"),jj1,subdirf2(optionfilefiname,"e"),jj1);
1.192 brouard 4611: /* } /\* end i1 *\/ */
1.126 brouard 4612: }/* End k1 */
4613: fprintf(fichtm,"</ul>");
4614: fflush(fichtm);
4615: }
4616:
4617: /******************* Gnuplot file **************/
4618: void printinggnuplot(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
4619:
4620: char dirfileres[132],optfileres[132];
1.164 brouard 4621: int cpt=0,k1=0,i=0,k=0,j=0,jk=0,k2=0,k3=0,ij=0,l=0;
1.130 brouard 4622: int ng=0;
1.126 brouard 4623: /* if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) { */
4624: /* printf("Problem with file %s",optionfilegnuplot); */
4625: /* fprintf(ficlog,"Problem with file %s",optionfilegnuplot); */
4626: /* } */
4627:
4628: /*#ifdef windows */
4629: fprintf(ficgp,"cd \"%s\" \n",pathc);
4630: /*#endif */
4631: m=pow(2,cptcoveff);
4632:
4633: strcpy(dirfileres,optionfilefiname);
4634: strcpy(optfileres,"vpl");
4635: /* 1eme*/
1.153 brouard 4636: fprintf(ficgp,"\n# 1st: Period (stable) prevalence with CI: 'vpl' files\n");
1.126 brouard 4637: for (cpt=1; cpt<= nlstate ; cpt ++) {
1.145 brouard 4638: for (k1=1; k1<= m ; k1 ++) { /* plot [100000000000000000000:-100000000000000000000] "mysbiaspar/vplrmysbiaspar.txt to check */
4639: fprintf(ficgp,"\nset out \"%s%d_%d.png\" \n",subdirf2(optionfilefiname,"v"),cpt,k1);
4640: fprintf(ficgp,"\n#set out \"v%s%d_%d.png\" \n",optionfilefiname,cpt,k1);
1.126 brouard 4641: fprintf(ficgp,"set xlabel \"Age\" \n\
4642: set ylabel \"Probability\" \n\
1.145 brouard 4643: set ter png small size 320, 240\n\
1.170 brouard 4644: plot [%.f:%.f] \"%s\" every :::%d::%d u 1:2 \"%%lf",ageminpar,fage,subdirf2(fileres,"vpl"),k1-1,k1-1);
1.126 brouard 4645:
4646: for (i=1; i<= nlstate ; i ++) {
1.170 brouard 4647: if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
4648: else fprintf(ficgp," %%*lf (%%*lf)");
1.126 brouard 4649: }
1.170 brouard 4650: fprintf(ficgp,"\" t\"Period (stable) prevalence\" w l lt 0,\"%s\" every :::%d::%d u 1:($2+1.96*$3) \"%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1);
1.126 brouard 4651: for (i=1; i<= nlstate ; i ++) {
1.170 brouard 4652: if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
4653: else fprintf(ficgp," %%*lf (%%*lf)");
1.126 brouard 4654: }
1.170 brouard 4655: fprintf(ficgp,"\" t\"95%% CI\" w l lt 1,\"%s\" every :::%d::%d u 1:($2-1.96*$3) \"%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1);
1.126 brouard 4656: for (i=1; i<= nlstate ; i ++) {
1.170 brouard 4657: if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
4658: else fprintf(ficgp," %%*lf (%%*lf)");
1.126 brouard 4659: }
1.145 brouard 4660: fprintf(ficgp,"\" t\"\" w l lt 1,\"%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l lt 2",subdirf2(fileres,"p"),k1-1,k1-1,2+4*(cpt-1));
1.126 brouard 4661: }
4662: }
4663: /*2 eme*/
1.153 brouard 4664: fprintf(ficgp,"\n# 2nd: Total life expectancy with CI: 't' files\n");
1.126 brouard 4665: for (k1=1; k1<= m ; k1 ++) {
4666: fprintf(ficgp,"\nset out \"%s%d.png\" \n",subdirf2(optionfilefiname,"e"),k1);
1.145 brouard 4667: fprintf(ficgp,"set ylabel \"Years\" \nset ter png small size 320, 240\nplot [%.f:%.f] ",ageminpar,fage);
1.126 brouard 4668:
4669: for (i=1; i<= nlstate+1 ; i ++) {
4670: k=2*i;
1.170 brouard 4671: fprintf(ficgp,"\"%s\" every :::%d::%d u 1:2 \"%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
1.126 brouard 4672: for (j=1; j<= nlstate+1 ; j ++) {
1.170 brouard 4673: if (j==i) fprintf(ficgp," %%lf (%%lf)");
4674: else fprintf(ficgp," %%*lf (%%*lf)");
1.126 brouard 4675: }
4676: if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");
4677: else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);
1.170 brouard 4678: fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2-$3*2) \"%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
1.126 brouard 4679: for (j=1; j<= nlstate+1 ; j ++) {
1.170 brouard 4680: if (j==i) fprintf(ficgp," %%lf (%%lf)");
4681: else fprintf(ficgp," %%*lf (%%*lf)");
1.126 brouard 4682: }
1.145 brouard 4683: fprintf(ficgp,"\" t\"\" w l lt 0,");
1.170 brouard 4684: fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2+$3*2) \"%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
1.126 brouard 4685: for (j=1; j<= nlstate+1 ; j ++) {
1.170 brouard 4686: if (j==i) fprintf(ficgp," %%lf (%%lf)");
4687: else fprintf(ficgp," %%*lf (%%*lf)");
1.126 brouard 4688: }
1.145 brouard 4689: if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l lt 0");
4690: else fprintf(ficgp,"\" t\"\" w l lt 0,");
1.126 brouard 4691: }
4692: }
4693:
4694: /*3eme*/
4695:
4696: for (k1=1; k1<= m ; k1 ++) {
4697: for (cpt=1; cpt<= nlstate ; cpt ++) {
4698: /* k=2+nlstate*(2*cpt-2); */
4699: k=2+(nlstate+1)*(cpt-1);
4700: fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"exp"),cpt,k1);
1.145 brouard 4701: fprintf(ficgp,"set ter png small size 320, 240\n\
1.126 brouard 4702: plot [%.f:%.f] \"%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,subdirf2(fileres,"e"),k1-1,k1-1,k,cpt);
4703: /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
4704: for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
4705: fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
4706: fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
4707: for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
4708: fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
4709:
4710: */
4711: for (i=1; i< nlstate ; i ++) {
4712: fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+i,cpt,i+1);
4713: /* 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);*/
4714:
4715: }
4716: fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d.\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+nlstate,cpt);
4717: }
4718: }
4719:
4720: /* CV preval stable (period) */
1.153 brouard 4721: for (k1=1; k1<= m ; k1 ++) { /* For each multivariate if any */
4722: for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */
1.126 brouard 4723: k=3;
1.153 brouard 4724: fprintf(ficgp,"\n#\n#\n#CV preval stable (period): 'pij' files, cov=%d state=%d",k1, cpt);
1.145 brouard 4725: fprintf(ficgp,"\nset out \"%s%d_%d.png\" \n",subdirf2(optionfilefiname,"p"),cpt,k1);
1.126 brouard 4726: fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\
1.145 brouard 4727: set ter png small size 320, 240\n\
1.126 brouard 4728: unset log y\n\
1.153 brouard 4729: plot [%.f:%.f] ", ageminpar, agemaxpar);
4730: for (i=1; i<= nlstate ; i ++){
4731: if(i==1)
4732: fprintf(ficgp,"\"%s\"",subdirf2(fileres,"pij"));
4733: else
4734: fprintf(ficgp,", '' ");
1.154 brouard 4735: l=(nlstate+ndeath)*(i-1)+1;
4736: fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d/($%d",k1,k+l+(cpt-1),k+l);
1.153 brouard 4737: for (j=1; j<= (nlstate-1) ; j ++)
4738: fprintf(ficgp,"+$%d",k+l+j);
4739: fprintf(ficgp,")) t \"prev(%d,%d)\" w l",i,cpt);
4740: } /* nlstate */
4741: fprintf(ficgp,"\n");
4742: } /* end cpt state*/
4743: } /* end covariate */
1.126 brouard 4744:
4745: /* proba elementaires */
1.187 brouard 4746: fprintf(ficgp,"\n##############\n#MLE estimated parameters\n#############\n");
1.126 brouard 4747: for(i=1,jk=1; i <=nlstate; i++){
1.187 brouard 4748: fprintf(ficgp,"# initial state %d\n",i);
1.126 brouard 4749: for(k=1; k <=(nlstate+ndeath); k++){
4750: if (k != i) {
1.187 brouard 4751: fprintf(ficgp,"# current state %d\n",k);
1.126 brouard 4752: for(j=1; j <=ncovmodel; j++){
1.187 brouard 4753: fprintf(ficgp,"p%d=%f; ",jk,p[jk]);
1.126 brouard 4754: jk++;
4755: }
1.187 brouard 4756: fprintf(ficgp,"\n");
1.126 brouard 4757: }
4758: }
4759: }
1.187 brouard 4760: fprintf(ficgp,"##############\n#\n");
4761:
1.145 brouard 4762: /*goto avoid;*/
1.187 brouard 4763: fprintf(ficgp,"\n##############\n#Graphics of of probabilities or incidences\n#############\n");
4764: fprintf(ficgp,"# logi(p12/p11)=a12+b12*age+c12age*age+d12*V1+e12*V1*age\n");
4765: fprintf(ficgp,"# logi(p12/p11)=p1 +p2*age +p3*age*age+ p4*V1+ p5*V1*age\n");
4766: fprintf(ficgp,"# logi(p13/p11)=a13+b13*age+c13age*age+d13*V1+e13*V1*age\n");
4767: fprintf(ficgp,"# logi(p13/p11)=p6 +p7*age +p8*age*age+ p9*V1+ p10*V1*age\n");
4768: fprintf(ficgp,"# p12+p13+p14+p11=1=p11(1+exp(a12+b12*age+c12age*age+d12*V1+e12*V1*age)\n");
4769: fprintf(ficgp,"# +exp(a13+b13*age+c13age*age+d13*V1+e13*V1*age)+...)\n");
4770: fprintf(ficgp,"# p11=1/(1+exp(a12+b12*age+c12age*age+d12*V1+e12*V1*age)\n");
4771: fprintf(ficgp,"# +exp(a13+b13*age+c13age*age+d13*V1+e13*V1*age)+...)\n");
4772: fprintf(ficgp,"# p12=exp(a12+b12*age+c12age*age+d12*V1+e12*V1*age)/\n");
4773: fprintf(ficgp,"# (1+exp(a12+b12*age+c12age*age+d12*V1+e12*V1*age)\n");
4774: fprintf(ficgp,"# +exp(a13+b13*age+c13age*age+d13*V1+e13*V1*age))\n");
4775: fprintf(ficgp,"# +exp(a14+b14*age+c14age*age+d14*V1+e14*V1*age)+...)\n");
4776: fprintf(ficgp,"#\n");
1.126 brouard 4777: for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/
1.187 brouard 4778: fprintf(ficgp,"# ng=%d\n",ng);
4779: fprintf(ficgp,"# jk=1 to 2^%d=%d\n",cptcoveff,m);
1.126 brouard 4780: for(jk=1; jk <=m; jk++) {
1.187 brouard 4781: fprintf(ficgp,"# jk=%d\n",jk);
1.145 brouard 4782: fprintf(ficgp,"\nset out \"%s%d_%d.png\" \n",subdirf2(optionfilefiname,"pe"),jk,ng);
1.126 brouard 4783: if (ng==2)
4784: fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
4785: else
4786: fprintf(ficgp,"\nset title \"Probability\"\n");
1.145 brouard 4787: fprintf(ficgp,"\nset ter png small size 320, 240\nset log y\nplot [%.f:%.f] ",ageminpar,agemaxpar);
1.126 brouard 4788: i=1;
4789: for(k2=1; k2<=nlstate; k2++) {
4790: k3=i;
4791: for(k=1; k<=(nlstate+ndeath); k++) {
4792: if (k != k2){
4793: if(ng==2)
1.187 brouard 4794: if(nagesqr==0)
4795: fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);
4796: else /* nagesqr =1 */
4797: fprintf(ficgp," %f*exp(p%d+p%d*x+p%d*x*x",YEARM/stepm,i,i+1,i+1+nagesqr);
1.126 brouard 4798: else
1.187 brouard 4799: if(nagesqr==0)
4800: fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
4801: else /* nagesqr =1 */
4802: fprintf(ficgp," exp(p%d+p%d*x+p%d*x*x",i,i+1,i+1+nagesqr);
1.141 brouard 4803: ij=1;/* To be checked else nbcode[0][0] wrong */
1.187 brouard 4804: for(j=3; j <=ncovmodel-nagesqr; j++) {
1.186 brouard 4805: if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) { /* Bug valgrind */
1.187 brouard 4806: fprintf(ficgp,"+p%d*%d*x",i+j+nagesqr-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
1.186 brouard 4807: ij++;
4808: }
4809: else
1.187 brouard 4810: fprintf(ficgp,"+p%d*%d",i+j+nagesqr-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
1.126 brouard 4811: }
4812: fprintf(ficgp,")/(1");
4813:
1.187 brouard 4814: for(k1=1; k1 <=nlstate; k1++){
4815: if(nagesqr==0)
4816: fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);
4817: else /* nagesqr =1 */
4818: 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);
4819:
1.126 brouard 4820: ij=1;
1.187 brouard 4821: for(j=3; j <=ncovmodel-nagesqr; j++){
1.186 brouard 4822: if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
1.187 brouard 4823: fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2+nagesqr,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
1.186 brouard 4824: ij++;
4825: }
4826: else
1.187 brouard 4827: fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2+nagesqr,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
1.126 brouard 4828: }
4829: fprintf(ficgp,")");
4830: }
4831: fprintf(ficgp,") t \"p%d%d\" ", k2,k);
4832: if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");
4833: i=i+ncovmodel;
4834: }
4835: } /* end k */
4836: } /* end k2 */
4837: } /* end jk */
4838: } /* end ng */
1.164 brouard 4839: /* avoid: */
1.126 brouard 4840: fflush(ficgp);
4841: } /* end gnuplot */
4842:
4843:
4844: /*************** Moving average **************/
4845: int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav){
4846:
4847: int i, cpt, cptcod;
4848: int modcovmax =1;
4849: int mobilavrange, mob;
4850: double age;
4851:
4852: modcovmax=2*cptcoveff;/* Max number of modalities. We suppose
4853: a covariate has 2 modalities */
4854: if (cptcovn<1) modcovmax=1; /* At least 1 pass */
4855:
4856: if(mobilav==1||mobilav ==3 ||mobilav==5 ||mobilav== 7){
4857: if(mobilav==1) mobilavrange=5; /* default */
4858: else mobilavrange=mobilav;
4859: for (age=bage; age<=fage; age++)
4860: for (i=1; i<=nlstate;i++)
4861: for (cptcod=1;cptcod<=modcovmax;cptcod++)
4862: mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
4863: /* We keep the original values on the extreme ages bage, fage and for
4864: fage+1 and bage-1 we use a 3 terms moving average; for fage+2 bage+2
4865: we use a 5 terms etc. until the borders are no more concerned.
4866: */
4867: for (mob=3;mob <=mobilavrange;mob=mob+2){
4868: for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){
4869: for (i=1; i<=nlstate;i++){
4870: for (cptcod=1;cptcod<=modcovmax;cptcod++){
4871: mobaverage[(int)age][i][cptcod] =probs[(int)age][i][cptcod];
4872: for (cpt=1;cpt<=(mob-1)/2;cpt++){
4873: mobaverage[(int)age][i][cptcod] +=probs[(int)age-cpt][i][cptcod];
4874: mobaverage[(int)age][i][cptcod] +=probs[(int)age+cpt][i][cptcod];
4875: }
4876: mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/mob;
4877: }
4878: }
4879: }/* end age */
4880: }/* end mob */
4881: }else return -1;
4882: return 0;
4883: }/* End movingaverage */
4884:
4885:
4886: /************** Forecasting ******************/
1.169 brouard 4887: 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 4888: /* proj1, year, month, day of starting projection
4889: agemin, agemax range of age
4890: dateprev1 dateprev2 range of dates during which prevalence is computed
4891: anproj2 year of en of projection (same day and month as proj1).
4892: */
1.164 brouard 4893: int yearp, stepsize, hstepm, nhstepm, j, k, cptcod, i, h, i1;
1.126 brouard 4894: double agec; /* generic age */
4895: double agelim, ppij, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
4896: double *popeffectif,*popcount;
4897: double ***p3mat;
4898: double ***mobaverage;
4899: char fileresf[FILENAMELENGTH];
4900:
4901: agelim=AGESUP;
4902: prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
4903:
4904: strcpy(fileresf,"f");
4905: strcat(fileresf,fileres);
4906: if((ficresf=fopen(fileresf,"w"))==NULL) {
4907: printf("Problem with forecast resultfile: %s\n", fileresf);
4908: fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);
4909: }
4910: printf("Computing forecasting: result on file '%s' \n", fileresf);
4911: fprintf(ficlog,"Computing forecasting: result on file '%s' \n", fileresf);
4912:
4913: if (cptcoveff==0) ncodemax[cptcoveff]=1;
4914:
4915: if (mobilav!=0) {
4916: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
4917: if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
4918: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
4919: printf(" Error in movingaverage mobilav=%d\n",mobilav);
4920: }
4921: }
4922:
4923: stepsize=(int) (stepm+YEARM-1)/YEARM;
4924: if (stepm<=12) stepsize=1;
4925: if(estepm < stepm){
4926: printf ("Problem %d lower than %d\n",estepm, stepm);
4927: }
4928: else hstepm=estepm;
4929:
4930: hstepm=hstepm/stepm;
4931: yp1=modf(dateintmean,&yp);/* extracts integral of datemean in yp and
4932: fractional in yp1 */
4933: anprojmean=yp;
4934: yp2=modf((yp1*12),&yp);
4935: mprojmean=yp;
4936: yp1=modf((yp2*30.5),&yp);
4937: jprojmean=yp;
4938: if(jprojmean==0) jprojmean=1;
4939: if(mprojmean==0) jprojmean=1;
4940:
4941: i1=cptcoveff;
4942: if (cptcovn < 1){i1=1;}
4943:
4944: fprintf(ficresf,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2);
4945:
4946: fprintf(ficresf,"#****** Routine prevforecast **\n");
4947:
4948: /* if (h==(int)(YEARM*yearp)){ */
4949: for(cptcov=1, k=0;cptcov<=i1;cptcov++){
4950: for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
4951: k=k+1;
4952: fprintf(ficresf,"\n#******");
4953: for(j=1;j<=cptcoveff;j++) {
4954: fprintf(ficresf," V%d=%d, hpijx=probability over h years, hp.jx is weighted by observed prev ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
4955: }
4956: fprintf(ficresf,"******\n");
4957: fprintf(ficresf,"# Covariate valuofcovar yearproj age");
4958: for(j=1; j<=nlstate+ndeath;j++){
4959: for(i=1; i<=nlstate;i++)
4960: fprintf(ficresf," p%d%d",i,j);
4961: fprintf(ficresf," p.%d",j);
4962: }
4963: for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) {
4964: fprintf(ficresf,"\n");
4965: fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+yearp);
4966:
4967: for (agec=fage; agec>=(ageminpar-1); agec--){
4968: nhstepm=(int) rint((agelim-agec)*YEARM/stepm);
4969: nhstepm = nhstepm/hstepm;
4970: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4971: oldm=oldms;savm=savms;
4972: hpxij(p3mat,nhstepm,agec,hstepm,p,nlstate,stepm,oldm,savm, k);
4973:
4974: for (h=0; h<=nhstepm; h++){
4975: if (h*hstepm/YEARM*stepm ==yearp) {
4976: fprintf(ficresf,"\n");
4977: for(j=1;j<=cptcoveff;j++)
4978: fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
4979: fprintf(ficresf,"%.f %.f ",anproj1+yearp,agec+h*hstepm/YEARM*stepm);
4980: }
4981: for(j=1; j<=nlstate+ndeath;j++) {
4982: ppij=0.;
4983: for(i=1; i<=nlstate;i++) {
4984: if (mobilav==1)
4985: ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][i][cptcod];
4986: else {
4987: ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][cptcod];
4988: }
4989: if (h*hstepm/YEARM*stepm== yearp) {
4990: fprintf(ficresf," %.3f", p3mat[i][j][h]);
4991: }
4992: } /* end i */
4993: if (h*hstepm/YEARM*stepm==yearp) {
4994: fprintf(ficresf," %.3f", ppij);
4995: }
4996: }/* end j */
4997: } /* end h */
4998: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4999: } /* end agec */
5000: } /* end yearp */
5001: } /* end cptcod */
5002: } /* end cptcov */
5003:
5004: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
5005:
5006: fclose(ficresf);
5007: }
5008:
5009: /************** Forecasting *****not tested NB*************/
1.169 brouard 5010: 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 5011:
5012: int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;
5013: int *popage;
5014: double calagedatem, agelim, kk1, kk2;
5015: double *popeffectif,*popcount;
5016: double ***p3mat,***tabpop,***tabpopprev;
5017: double ***mobaverage;
5018: char filerespop[FILENAMELENGTH];
5019:
5020: tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
5021: tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
5022: agelim=AGESUP;
5023: calagedatem=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;
5024:
5025: prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
5026:
5027:
5028: strcpy(filerespop,"pop");
5029: strcat(filerespop,fileres);
5030: if((ficrespop=fopen(filerespop,"w"))==NULL) {
5031: printf("Problem with forecast resultfile: %s\n", filerespop);
5032: fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop);
5033: }
5034: printf("Computing forecasting: result on file '%s' \n", filerespop);
5035: fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop);
5036:
5037: if (cptcoveff==0) ncodemax[cptcoveff]=1;
5038:
5039: if (mobilav!=0) {
5040: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
5041: if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
5042: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
5043: printf(" Error in movingaverage mobilav=%d\n",mobilav);
5044: }
5045: }
5046:
5047: stepsize=(int) (stepm+YEARM-1)/YEARM;
5048: if (stepm<=12) stepsize=1;
5049:
5050: agelim=AGESUP;
5051:
5052: hstepm=1;
5053: hstepm=hstepm/stepm;
5054:
5055: if (popforecast==1) {
5056: if((ficpop=fopen(popfile,"r"))==NULL) {
5057: printf("Problem with population file : %s\n",popfile);exit(0);
5058: fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0);
5059: }
5060: popage=ivector(0,AGESUP);
5061: popeffectif=vector(0,AGESUP);
5062: popcount=vector(0,AGESUP);
5063:
5064: i=1;
5065: while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;
5066:
5067: imx=i;
5068: for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];
5069: }
5070:
5071: for(cptcov=1,k=0;cptcov<=i2;cptcov++){
5072: for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
5073: k=k+1;
5074: fprintf(ficrespop,"\n#******");
5075: for(j=1;j<=cptcoveff;j++) {
5076: fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
5077: }
5078: fprintf(ficrespop,"******\n");
5079: fprintf(ficrespop,"# Age");
5080: for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);
5081: if (popforecast==1) fprintf(ficrespop," [Population]");
5082:
5083: for (cpt=0; cpt<=0;cpt++) {
5084: fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);
5085:
5086: for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){
5087: nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);
5088: nhstepm = nhstepm/hstepm;
5089:
5090: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
5091: oldm=oldms;savm=savms;
5092: hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
5093:
5094: for (h=0; h<=nhstepm; h++){
5095: if (h==(int) (calagedatem+YEARM*cpt)) {
5096: fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
5097: }
5098: for(j=1; j<=nlstate+ndeath;j++) {
5099: kk1=0.;kk2=0;
5100: for(i=1; i<=nlstate;i++) {
5101: if (mobilav==1)
5102: kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];
5103: else {
5104: kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];
5105: }
5106: }
5107: if (h==(int)(calagedatem+12*cpt)){
5108: tabpop[(int)(agedeb)][j][cptcod]=kk1;
5109: /*fprintf(ficrespop," %.3f", kk1);
5110: if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/
5111: }
5112: }
5113: for(i=1; i<=nlstate;i++){
5114: kk1=0.;
5115: for(j=1; j<=nlstate;j++){
5116: kk1= kk1+tabpop[(int)(agedeb)][j][cptcod];
5117: }
5118: tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedatem+12*cpt)*hstepm/YEARM*stepm-1)];
5119: }
5120:
5121: if (h==(int)(calagedatem+12*cpt)) for(j=1; j<=nlstate;j++)
5122: fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);
5123: }
5124: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
5125: }
5126: }
5127:
5128: /******/
5129:
5130: for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) {
5131: fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);
5132: for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){
5133: nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);
5134: nhstepm = nhstepm/hstepm;
5135:
5136: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
5137: oldm=oldms;savm=savms;
5138: hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
5139: for (h=0; h<=nhstepm; h++){
5140: if (h==(int) (calagedatem+YEARM*cpt)) {
5141: fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
5142: }
5143: for(j=1; j<=nlstate+ndeath;j++) {
5144: kk1=0.;kk2=0;
5145: for(i=1; i<=nlstate;i++) {
5146: kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];
5147: }
5148: if (h==(int)(calagedatem+12*cpt)) fprintf(ficresf," %15.2f", kk1);
5149: }
5150: }
5151: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
5152: }
5153: }
5154: }
5155: }
5156:
5157: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
5158:
5159: if (popforecast==1) {
5160: free_ivector(popage,0,AGESUP);
5161: free_vector(popeffectif,0,AGESUP);
5162: free_vector(popcount,0,AGESUP);
5163: }
5164: free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
5165: free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
5166: fclose(ficrespop);
5167: } /* End of popforecast */
5168:
5169: int fileappend(FILE *fichier, char *optionfich)
5170: {
5171: if((fichier=fopen(optionfich,"a"))==NULL) {
5172: printf("Problem with file: %s\n", optionfich);
5173: fprintf(ficlog,"Problem with file: %s\n", optionfich);
5174: return (0);
5175: }
5176: fflush(fichier);
5177: return (1);
5178: }
5179:
5180:
5181: /**************** function prwizard **********************/
5182: void prwizard(int ncovmodel, int nlstate, int ndeath, char model[], FILE *ficparo)
5183: {
5184:
5185: /* Wizard to print covariance matrix template */
5186:
1.164 brouard 5187: char ca[32], cb[32];
5188: int i,j, k, li, lj, lk, ll, jj, npar, itimes;
1.126 brouard 5189: int numlinepar;
5190:
5191: printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
5192: fprintf(ficparo,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
5193: for(i=1; i <=nlstate; i++){
5194: jj=0;
5195: for(j=1; j <=nlstate+ndeath; j++){
5196: if(j==i) continue;
5197: jj++;
5198: /*ca[0]= k+'a'-1;ca[1]='\0';*/
5199: printf("%1d%1d",i,j);
5200: fprintf(ficparo,"%1d%1d",i,j);
5201: for(k=1; k<=ncovmodel;k++){
5202: /* printf(" %lf",param[i][j][k]); */
5203: /* fprintf(ficparo," %lf",param[i][j][k]); */
5204: printf(" 0.");
5205: fprintf(ficparo," 0.");
5206: }
5207: printf("\n");
5208: fprintf(ficparo,"\n");
5209: }
5210: }
5211: printf("# Scales (for hessian or gradient estimation)\n");
5212: fprintf(ficparo,"# Scales (for hessian or gradient estimation)\n");
5213: npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/
5214: for(i=1; i <=nlstate; i++){
5215: jj=0;
5216: for(j=1; j <=nlstate+ndeath; j++){
5217: if(j==i) continue;
5218: jj++;
5219: fprintf(ficparo,"%1d%1d",i,j);
5220: printf("%1d%1d",i,j);
5221: fflush(stdout);
5222: for(k=1; k<=ncovmodel;k++){
5223: /* printf(" %le",delti3[i][j][k]); */
5224: /* fprintf(ficparo," %le",delti3[i][j][k]); */
5225: printf(" 0.");
5226: fprintf(ficparo," 0.");
5227: }
5228: numlinepar++;
5229: printf("\n");
5230: fprintf(ficparo,"\n");
5231: }
5232: }
5233: printf("# Covariance matrix\n");
5234: /* # 121 Var(a12)\n\ */
5235: /* # 122 Cov(b12,a12) Var(b12)\n\ */
5236: /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
5237: /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
5238: /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
5239: /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
5240: /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
5241: /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
5242: fflush(stdout);
5243: fprintf(ficparo,"# Covariance matrix\n");
5244: /* # 121 Var(a12)\n\ */
5245: /* # 122 Cov(b12,a12) Var(b12)\n\ */
5246: /* # ...\n\ */
5247: /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
5248:
5249: for(itimes=1;itimes<=2;itimes++){
5250: jj=0;
5251: for(i=1; i <=nlstate; i++){
5252: for(j=1; j <=nlstate+ndeath; j++){
5253: if(j==i) continue;
5254: for(k=1; k<=ncovmodel;k++){
5255: jj++;
5256: ca[0]= k+'a'-1;ca[1]='\0';
5257: if(itimes==1){
5258: printf("#%1d%1d%d",i,j,k);
5259: fprintf(ficparo,"#%1d%1d%d",i,j,k);
5260: }else{
5261: printf("%1d%1d%d",i,j,k);
5262: fprintf(ficparo,"%1d%1d%d",i,j,k);
5263: /* printf(" %.5le",matcov[i][j]); */
5264: }
5265: ll=0;
5266: for(li=1;li <=nlstate; li++){
5267: for(lj=1;lj <=nlstate+ndeath; lj++){
5268: if(lj==li) continue;
5269: for(lk=1;lk<=ncovmodel;lk++){
5270: ll++;
5271: if(ll<=jj){
5272: cb[0]= lk +'a'-1;cb[1]='\0';
5273: if(ll<jj){
5274: if(itimes==1){
5275: printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
5276: fprintf(ficparo," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
5277: }else{
5278: printf(" 0.");
5279: fprintf(ficparo," 0.");
5280: }
5281: }else{
5282: if(itimes==1){
5283: printf(" Var(%s%1d%1d)",ca,i,j);
5284: fprintf(ficparo," Var(%s%1d%1d)",ca,i,j);
5285: }else{
5286: printf(" 0.");
5287: fprintf(ficparo," 0.");
5288: }
5289: }
5290: }
5291: } /* end lk */
5292: } /* end lj */
5293: } /* end li */
5294: printf("\n");
5295: fprintf(ficparo,"\n");
5296: numlinepar++;
5297: } /* end k*/
5298: } /*end j */
5299: } /* end i */
5300: } /* end itimes */
5301:
5302: } /* end of prwizard */
5303: /******************* Gompertz Likelihood ******************************/
5304: double gompertz(double x[])
5305: {
5306: double A,B,L=0.0,sump=0.,num=0.;
5307: int i,n=0; /* n is the size of the sample */
5308:
5309: for (i=0;i<=imx-1 ; i++) {
5310: sump=sump+weight[i];
5311: /* sump=sump+1;*/
5312: num=num+1;
5313: }
5314:
5315:
5316: /* for (i=0; i<=imx; i++)
5317: 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]);*/
5318:
5319: for (i=1;i<=imx ; i++)
5320: {
5321: if (cens[i] == 1 && wav[i]>1)
5322: A=-x[1]/(x[2])*(exp(x[2]*(agecens[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)));
5323:
5324: if (cens[i] == 0 && wav[i]>1)
5325: A=-x[1]/(x[2])*(exp(x[2]*(agedc[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)))
5326: +log(x[1]/YEARM)+x[2]*(agedc[i]-agegomp)+log(YEARM);
5327:
5328: /*if (wav[i] > 1 && agecens[i] > 15) {*/ /* ??? */
5329: if (wav[i] > 1 ) { /* ??? */
5330: L=L+A*weight[i];
5331: /* 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]);*/
5332: }
5333: }
5334:
5335: /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/
5336:
5337: return -2*L*num/sump;
5338: }
5339:
1.136 brouard 5340: #ifdef GSL
5341: /******************* Gompertz_f Likelihood ******************************/
5342: double gompertz_f(const gsl_vector *v, void *params)
5343: {
5344: double A,B,LL=0.0,sump=0.,num=0.;
5345: double *x= (double *) v->data;
5346: int i,n=0; /* n is the size of the sample */
5347:
5348: for (i=0;i<=imx-1 ; i++) {
5349: sump=sump+weight[i];
5350: /* sump=sump+1;*/
5351: num=num+1;
5352: }
5353:
5354:
5355: /* for (i=0; i<=imx; i++)
5356: 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]);*/
5357: printf("x[0]=%lf x[1]=%lf\n",x[0],x[1]);
5358: for (i=1;i<=imx ; i++)
5359: {
5360: if (cens[i] == 1 && wav[i]>1)
5361: A=-x[0]/(x[1])*(exp(x[1]*(agecens[i]-agegomp))-exp(x[1]*(ageexmed[i]-agegomp)));
5362:
5363: if (cens[i] == 0 && wav[i]>1)
5364: A=-x[0]/(x[1])*(exp(x[1]*(agedc[i]-agegomp))-exp(x[1]*(ageexmed[i]-agegomp)))
5365: +log(x[0]/YEARM)+x[1]*(agedc[i]-agegomp)+log(YEARM);
5366:
5367: /*if (wav[i] > 1 && agecens[i] > 15) {*/ /* ??? */
5368: if (wav[i] > 1 ) { /* ??? */
5369: LL=LL+A*weight[i];
5370: /* 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]);*/
5371: }
5372: }
5373:
5374: /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/
5375: printf("x[0]=%lf x[1]=%lf -2*LL*num/sump=%lf\n",x[0],x[1],-2*LL*num/sump);
5376:
5377: return -2*LL*num/sump;
5378: }
5379: #endif
5380:
1.126 brouard 5381: /******************* Printing html file ***********/
5382: void printinghtmlmort(char fileres[], char title[], char datafile[], int firstpass, \
5383: int lastpass, int stepm, int weightopt, char model[],\
5384: int imx, double p[],double **matcov,double agemortsup){
5385: int i,k;
5386:
5387: fprintf(fichtm,"<ul><li><h4>Result files </h4>\n Force of mortality. Parameters of the Gompertz fit (with confidence interval in brackets):<br>");
5388: fprintf(fichtm," mu(age) =%lf*exp(%lf*(age-%d)) per year<br><br>",p[1],p[2],agegomp);
5389: for (i=1;i<=2;i++)
5390: 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]));
5391: fprintf(fichtm,"<br><br><img src=\"graphmort.png\">");
5392: fprintf(fichtm,"</ul>");
5393:
5394: fprintf(fichtm,"<ul><li><h4>Life table</h4>\n <br>");
5395:
5396: 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>");
5397:
5398: for (k=agegomp;k<(agemortsup-2);k++)
5399: 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]);
5400:
5401:
5402: fflush(fichtm);
5403: }
5404:
5405: /******************* Gnuplot file **************/
5406: void printinggnuplotmort(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
5407:
5408: char dirfileres[132],optfileres[132];
1.164 brouard 5409:
1.126 brouard 5410: int ng;
5411:
5412:
5413: /*#ifdef windows */
5414: fprintf(ficgp,"cd \"%s\" \n",pathc);
5415: /*#endif */
5416:
5417:
5418: strcpy(dirfileres,optionfilefiname);
5419: strcpy(optfileres,"vpl");
5420: fprintf(ficgp,"set out \"graphmort.png\"\n ");
5421: fprintf(ficgp,"set xlabel \"Age\"\n set ylabel \"Force of mortality (per year)\" \n ");
1.145 brouard 5422: fprintf(ficgp, "set ter png small size 320, 240\n set log y\n");
5423: /* fprintf(ficgp, "set size 0.65,0.65\n"); */
1.126 brouard 5424: fprintf(ficgp,"plot [%d:100] %lf*exp(%lf*(x-%d))",agegomp,p[1],p[2],agegomp);
5425:
5426: }
5427:
1.136 brouard 5428: int readdata(char datafile[], int firstobs, int lastobs, int *imax)
5429: {
1.126 brouard 5430:
1.136 brouard 5431: /*-------- data file ----------*/
5432: FILE *fic;
5433: char dummy[]=" ";
1.164 brouard 5434: int i=0, j=0, n=0;
1.136 brouard 5435: int linei, month, year,iout;
5436: char line[MAXLINE], linetmp[MAXLINE];
1.164 brouard 5437: char stra[MAXLINE], strb[MAXLINE];
1.136 brouard 5438: char *stratrunc;
5439: int lstra;
1.126 brouard 5440:
5441:
1.136 brouard 5442: if((fic=fopen(datafile,"r"))==NULL) {
1.195 ! brouard 5443: printf("Problem while opening datafile: %s\n", datafile);fflush(stdout);
! 5444: fprintf(ficlog,"Problem while opening datafile: %s\n", datafile);fflush(ficlog);return 1;
1.136 brouard 5445: }
1.126 brouard 5446:
1.136 brouard 5447: i=1;
5448: linei=0;
5449: while ((fgets(line, MAXLINE, fic) != NULL) &&((i >= firstobs) && (i <=lastobs))) {
5450: linei=linei+1;
5451: for(j=strlen(line); j>=0;j--){ /* Untabifies line */
5452: if(line[j] == '\t')
5453: line[j] = ' ';
5454: }
5455: for(j=strlen(line)-1; (line[j]==' ')||(line[j]==10)||(line[j]==13);j--){
5456: ;
5457: };
5458: line[j+1]=0; /* Trims blanks at end of line */
5459: if(line[0]=='#'){
5460: fprintf(ficlog,"Comment line\n%s\n",line);
5461: printf("Comment line\n%s\n",line);
5462: continue;
5463: }
5464: trimbb(linetmp,line); /* Trims multiple blanks in line */
1.164 brouard 5465: strcpy(line, linetmp);
1.136 brouard 5466:
1.126 brouard 5467:
1.136 brouard 5468: for (j=maxwav;j>=1;j--){
1.137 brouard 5469: cutv(stra, strb, line, ' ');
1.136 brouard 5470: if(strb[0]=='.') { /* Missing status */
5471: lval=-1;
5472: }else{
5473: errno=0;
5474: lval=strtol(strb,&endptr,10);
5475: /* if (errno == ERANGE && (lval == LONG_MAX || lval == LONG_MIN))*/
5476: if( strb[0]=='\0' || (*endptr != '\0')){
1.141 brouard 5477: 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);
5478: 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 5479: return 1;
5480: }
5481: }
5482: s[j][i]=lval;
5483:
5484: strcpy(line,stra);
5485: cutv(stra, strb,line,' ');
1.169 brouard 5486: if( (iout=sscanf(strb,"%d/%d",&month, &year)) != 0){
1.136 brouard 5487: }
1.169 brouard 5488: else if( (iout=sscanf(strb,"%s.",dummy)) != 0){
1.136 brouard 5489: month=99;
5490: year=9999;
5491: }else{
1.141 brouard 5492: 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);
5493: 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 5494: return 1;
5495: }
5496: anint[j][i]= (double) year;
5497: mint[j][i]= (double)month;
5498: strcpy(line,stra);
5499: } /* ENd Waves */
5500:
5501: cutv(stra, strb,line,' ');
1.169 brouard 5502: if( (iout=sscanf(strb,"%d/%d",&month, &year)) != 0){
1.136 brouard 5503: }
1.169 brouard 5504: else if( (iout=sscanf(strb,"%s.",dummy)) != 0){
1.136 brouard 5505: month=99;
5506: year=9999;
5507: }else{
1.141 brouard 5508: 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);
5509: 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 5510: return 1;
5511: }
5512: andc[i]=(double) year;
5513: moisdc[i]=(double) month;
5514: strcpy(line,stra);
5515:
5516: cutv(stra, strb,line,' ');
1.169 brouard 5517: if( (iout=sscanf(strb,"%d/%d",&month, &year)) != 0){
1.136 brouard 5518: }
1.169 brouard 5519: else if( (iout=sscanf(strb,"%s.", dummy)) != 0){
1.136 brouard 5520: month=99;
5521: year=9999;
5522: }else{
1.141 brouard 5523: 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);
5524: 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 5525: return 1;
5526: }
5527: if (year==9999) {
1.141 brouard 5528: 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);
5529: 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 5530: return 1;
1.126 brouard 5531:
1.136 brouard 5532: }
5533: annais[i]=(double)(year);
5534: moisnais[i]=(double)(month);
5535: strcpy(line,stra);
5536:
5537: cutv(stra, strb,line,' ');
5538: errno=0;
5539: dval=strtod(strb,&endptr);
5540: if( strb[0]=='\0' || (*endptr != '\0')){
1.141 brouard 5541: printf("Error reading data around '%f' at line number %d, \"%s\" for individual %d\nShould be a weight. Exiting.\n",dval, i,line,linei);
5542: 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 5543: fflush(ficlog);
5544: return 1;
5545: }
5546: weight[i]=dval;
5547: strcpy(line,stra);
5548:
5549: for (j=ncovcol;j>=1;j--){
5550: cutv(stra, strb,line,' ');
5551: if(strb[0]=='.') { /* Missing status */
5552: lval=-1;
5553: }else{
5554: errno=0;
5555: lval=strtol(strb,&endptr,10);
5556: if( strb[0]=='\0' || (*endptr != '\0')){
1.141 brouard 5557: 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);
5558: 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 5559: return 1;
5560: }
5561: }
5562: if(lval <-1 || lval >1){
1.141 brouard 5563: printf("Error reading data around '%ld' at line number %d for individual %d, '%s'\n \
1.136 brouard 5564: Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
5565: for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
5566: For example, for multinomial values like 1, 2 and 3,\n \
5567: build V1=0 V2=0 for the reference value (1),\n \
5568: V1=1 V2=0 for (2) \n \
5569: and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
5570: output of IMaCh is often meaningless.\n \
5571: Exiting.\n",lval,linei, i,line,j);
1.141 brouard 5572: fprintf(ficlog,"Error reading data around '%ld' at line number %d for individual %d, '%s'\n \
1.136 brouard 5573: Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
5574: for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
5575: For example, for multinomial values like 1, 2 and 3,\n \
5576: build V1=0 V2=0 for the reference value (1),\n \
5577: V1=1 V2=0 for (2) \n \
5578: and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
5579: output of IMaCh is often meaningless.\n \
5580: Exiting.\n",lval,linei, i,line,j);fflush(ficlog);
5581: return 1;
5582: }
5583: covar[j][i]=(double)(lval);
5584: strcpy(line,stra);
5585: }
5586: lstra=strlen(stra);
5587:
5588: if(lstra > 9){ /* More than 2**32 or max of what printf can write with %ld */
5589: stratrunc = &(stra[lstra-9]);
5590: num[i]=atol(stratrunc);
5591: }
5592: else
5593: num[i]=atol(stra);
5594: /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){
5595: 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;}*/
5596:
5597: i=i+1;
5598: } /* End loop reading data */
1.126 brouard 5599:
1.136 brouard 5600: *imax=i-1; /* Number of individuals */
5601: fclose(fic);
5602:
5603: return (0);
1.164 brouard 5604: /* endread: */
1.136 brouard 5605: printf("Exiting readdata: ");
5606: fclose(fic);
5607: return (1);
1.126 brouard 5608:
5609:
5610:
1.136 brouard 5611: }
1.145 brouard 5612: void removespace(char *str) {
5613: char *p1 = str, *p2 = str;
5614: do
5615: while (*p2 == ' ')
5616: p2++;
1.169 brouard 5617: while (*p1++ == *p2++);
1.145 brouard 5618: }
5619:
5620: int decodemodel ( char model[], int lastobs) /**< This routine decode the model and returns:
1.187 brouard 5621: * Model V1+V2+V3+V8+V7*V8+V5*V6+V8*age+V3*age+age*age
5622: * - nagesqr = 1 if age*age in the model, otherwise 0.
5623: * - cptcovt total number of covariates of the model nbocc(+)+1 = 8 excepting constant and age and age*age
5624: * - cptcovn or number of covariates k of the models excluding age*products =6 and age*age
1.145 brouard 5625: * - cptcovage number of covariates with age*products =2
5626: * - cptcovs number of simple covariates
5627: * - 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
5628: * which is a new column after the 9 (ncovcol) variables.
5629: * - if k is a product Vn*Vm covar[k][i] is filled with correct values for each individual
5630: * - Tprod[l] gives the kth covariates of the product Vn*Vm l=1 to cptcovprod-cptcovage
5631: * Tprod[1]@2 {5, 6}: position of first product V7*V8 is 5, and second V5*V6 is 6.
5632: * - Tvard[k] p Tvard[1][1]@4 {7, 8, 5, 6} for V7*V8 and V5*V6 .
5633: */
1.136 brouard 5634: {
1.145 brouard 5635: int i, j, k, ks;
1.164 brouard 5636: int j1, k1, k2;
1.136 brouard 5637: char modelsav[80];
1.145 brouard 5638: char stra[80], strb[80], strc[80], strd[80],stre[80];
1.187 brouard 5639: char *strpt;
1.136 brouard 5640:
1.145 brouard 5641: /*removespace(model);*/
1.136 brouard 5642: if (strlen(model) >1){ /* If there is at least 1 covariate */
1.145 brouard 5643: j=0, j1=0, k1=0, k2=-1, ks=0, cptcovn=0;
1.137 brouard 5644: if (strstr(model,"AGE") !=0){
1.192 brouard 5645: printf("Error. AGE must be in lower case 'age' model=1+age+%s. ",model);
5646: fprintf(ficlog,"Error. AGE must be in lower case model=1+age+%s. ",model);fflush(ficlog);
1.136 brouard 5647: return 1;
5648: }
1.141 brouard 5649: if (strstr(model,"v") !=0){
5650: printf("Error. 'v' must be in upper case 'V' model=%s ",model);
5651: fprintf(ficlog,"Error. 'v' must be in upper case model=%s ",model);fflush(ficlog);
5652: return 1;
5653: }
1.187 brouard 5654: strcpy(modelsav,model);
5655: if ((strpt=strstr(model,"age*age")) !=0){
5656: printf(" strpt=%s, model=%s\n",strpt, model);
5657: if(strpt != model){
5658: printf("Error in model: 'model=%s'; 'age*age' should in first place before other covariates\n \
1.192 brouard 5659: 'model=1+age+age*age+V1.' or 'model=1+age+age*age+V1+V1*age.', please swap as well as \n \
1.187 brouard 5660: corresponding column of parameters.\n",model);
5661: fprintf(ficlog,"Error in model: 'model=%s'; 'age*age' should in first place before other covariates\n \
1.192 brouard 5662: 'model=1+age+age*age+V1.' or 'model=1+age+age*age+V1+V1*age.', please swap as well as \n \
1.187 brouard 5663: corresponding column of parameters.\n",model); fflush(ficlog);
5664: return 1;
5665: }
5666:
5667: nagesqr=1;
5668: if (strstr(model,"+age*age") !=0)
5669: substrchaine(modelsav, model, "+age*age");
5670: else if (strstr(model,"age*age+") !=0)
5671: substrchaine(modelsav, model, "age*age+");
5672: else
5673: substrchaine(modelsav, model, "age*age");
5674: }else
5675: nagesqr=0;
5676: if (strlen(modelsav) >1){
5677: j=nbocc(modelsav,'+'); /**< j=Number of '+' */
5678: j1=nbocc(modelsav,'*'); /**< j1=Number of '*' */
5679: cptcovs=j+1-j1; /**< Number of simple covariates V1+V1*age+V3 +V3*V4+age*age=> V1 + V3 =2 */
5680: cptcovt= j+1; /* Number of total covariates in the model, not including
5681: * cst, age and age*age
5682: * V1+V1*age+ V3 + V3*V4+age*age=> 4*/
5683: /* including age products which are counted in cptcovage.
5684: * but the covariates which are products must be treated
5685: * separately: ncovn=4- 2=2 (V1+V3). */
5686: cptcovprod=j1; /**< Number of products V1*V2 +v3*age = 2 */
5687: cptcovprodnoage=0; /**< Number of covariate products without age: V3*V4 =1 */
5688:
5689:
5690: /* Design
5691: * V1 V2 V3 V4 V5 V6 V7 V8 V9 Weight
5692: * < ncovcol=8 >
5693: * Model V2 + V1 + V3*age + V3 + V5*V6 + V7*V8 + V8*age + V8
5694: * k= 1 2 3 4 5 6 7 8
5695: * cptcovn number of covariates (not including constant and age ) = # of + plus 1 = 7+1=8
5696: * covar[k,i], value of kth covariate if not including age for individual i:
5697: * covar[1][i]= (V2), covar[4][i]=(V3), covar[8][i]=(V8)
5698: * Tvar[k] # of the kth covariate: Tvar[1]=2 Tvar[4]=3 Tvar[8]=8
5699: * if multiplied by age: V3*age Tvar[3=V3*age]=3 (V3) Tvar[7]=8 and
5700: * Tage[++cptcovage]=k
5701: * if products, new covar are created after ncovcol with k1
5702: * Tvar[k]=ncovcol+k1; # of the kth covariate product: Tvar[5]=ncovcol+1=10 Tvar[6]=ncovcol+1=11
5703: * Tprod[k1]=k; Tprod[1]=5 Tprod[2]= 6; gives the position of the k1th product
5704: * 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
5705: * Tvar[cptcovn+k2]=Tvard[k1][1];Tvar[cptcovn+k2+1]=Tvard[k1][2];
5706: * Tvar[8+1]=5;Tvar[8+2]=6;Tvar[8+3]=7;Tvar[8+4]=8 inverted
5707: * V1 V2 V3 V4 V5 V6 V7 V8 V9 V10 V11
5708: * < ncovcol=8 >
5709: * Model V2 + V1 + V3*age + V3 + V5*V6 + V7*V8 + V8*age + V8 d1 d1 d2 d2
5710: * k= 1 2 3 4 5 6 7 8 9 10 11 12
5711: * Tvar[k]= 2 1 3 3 10 11 8 8 5 6 7 8
5712: * p Tvar[1]@12={2, 1, 3, 3, 11, 10, 8, 8, 7, 8, 5, 6}
5713: * p Tprod[1]@2={ 6, 5}
5714: *p Tvard[1][1]@4= {7, 8, 5, 6}
5715: * covar[k][i]= V2 V1 ? V3 V5*V6? V7*V8? ? V8
5716: * cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
5717: *How to reorganize?
5718: * Model V1 + V2 + V3 + V8 + V5*V6 + V7*V8 + V3*age + V8*age
5719: * Tvars {2, 1, 3, 3, 11, 10, 8, 8, 7, 8, 5, 6}
5720: * {2, 1, 4, 8, 5, 6, 3, 7}
5721: * Struct []
5722: */
1.145 brouard 5723:
1.187 brouard 5724: /* This loop fills the array Tvar from the string 'model'.*/
5725: /* j is the number of + signs in the model V1+V2+V3 j=2 i=3 to 1 */
5726: /* modelsav=V2+V1+V4+age*V3 strb=age*V3 stra=V2+V1+V4 */
5727: /* k=4 (age*V3) Tvar[k=4]= 3 (from V3) Tage[cptcovage=1]=4 */
5728: /* k=3 V4 Tvar[k=3]= 4 (from V4) */
5729: /* k=2 V1 Tvar[k=2]= 1 (from V1) */
5730: /* k=1 Tvar[1]=2 (from V2) */
5731: /* k=5 Tvar[5] */
5732: /* for (k=1; k<=cptcovn;k++) { */
5733: /* cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]]; */
5734: /* } */
5735: /* for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=nbcode[Tvar[Tage[k]]][codtab[ij][Tvar[Tage[k]]]]*cov[2]; */
5736: /*
5737: * Treating invertedly V2+V1+V3*age+V2*V4 is as if written V2*V4 +V3*age + V1 + V2 */
5738: for(k=cptcovt; k>=1;k--) /**< Number of covariates */
1.145 brouard 5739: Tvar[k]=0;
1.187 brouard 5740: cptcovage=0;
5741: for(k=1; k<=cptcovt;k++){ /* Loop on total covariates of the model */
5742: cutl(stra,strb,modelsav,'+'); /* keeps in strb after the first '+'
5743: modelsav==V2+V1+V4+V3*age strb=V3*age stra=V2+V1+V4 */
5744: if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyzes it */
5745: /* printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/
5746: /*scanf("%d",i);*/
5747: if (strchr(strb,'*')) { /**< Model includes a product V2+V1+V4+V3*age strb=V3*age */
5748: cutl(strc,strd,strb,'*'); /**< strd*strc Vm*Vn: strb=V3*age(input) strc=age strd=V3 ; V3*V2 strc=V2, strd=V3 */
5749: if (strcmp(strc,"age")==0) { /**< Model includes age: Vn*age */
5750: /* covar is not filled and then is empty */
5751: cptcovprod--;
5752: cutl(stre,strb,strd,'V'); /* strd=V3(input): stre="3" */
5753: Tvar[k]=atoi(stre); /* V2+V1+V4+V3*age Tvar[4]=3 ; V1+V2*age Tvar[2]=2; V1+V1*age Tvar[2]=1 */
5754: cptcovage++; /* Sums the number of covariates which include age as a product */
5755: Tage[cptcovage]=k; /* Tvar[4]=3, Tage[1] = 4 or V1+V1*age Tvar[2]=1, Tage[1]=2 */
5756: /*printf("stre=%s ", stre);*/
5757: } else if (strcmp(strd,"age")==0) { /* or age*Vn */
5758: cptcovprod--;
5759: cutl(stre,strb,strc,'V');
5760: Tvar[k]=atoi(stre);
5761: cptcovage++;
5762: Tage[cptcovage]=k;
5763: } else { /* Age is not in the model product V2+V1+V1*V4+V3*age+V3*V2 strb=V3*V2*/
5764: /* loops on k1=1 (V3*V2) and k1=2 V4*V3 */
5765: cptcovn++;
5766: cptcovprodnoage++;k1++;
5767: cutl(stre,strb,strc,'V'); /* strc= Vn, stre is n; strb=V3*V2 stre=3 strc=*/
5768: Tvar[k]=ncovcol+k1; /* For model-covariate k tells which data-covariate to use but
5769: because this model-covariate is a construction we invent a new column
5770: ncovcol + k1
5771: If already ncovcol=4 and model=V2+V1+V1*V4+age*V3+V3*V2
5772: Tvar[3=V1*V4]=4+1 Tvar[5=V3*V2]=4 + 2= 6, etc */
5773: cutl(strc,strb,strd,'V'); /* strd was Vm, strc is m */
5774: Tprod[k1]=k; /* Tprod[1]=3(=V1*V4) for V2+V1+V1*V4+age*V3+V3*V2 */
5775: Tvard[k1][1] =atoi(strc); /* m 1 for V1*/
5776: Tvard[k1][2] =atoi(stre); /* n 4 for V4*/
5777: k2=k2+2;
5778: Tvar[cptcovt+k2]=Tvard[k1][1]; /* Tvar[(cptcovt=4+k2=1)=5]= 1 (V1) */
5779: Tvar[cptcovt+k2+1]=Tvard[k1][2]; /* Tvar[(cptcovt=4+(k2=1)+1)=6]= 4 (V4) */
5780: for (i=1; i<=lastobs;i++){
5781: /* Computes the new covariate which is a product of
5782: covar[n][i]* covar[m][i] and stores it at ncovol+k1 May not be defined */
5783: covar[ncovcol+k1][i]=covar[atoi(stre)][i]*covar[atoi(strc)][i];
5784: }
5785: } /* End age is not in the model */
5786: } /* End if model includes a product */
5787: else { /* no more sum */
5788: /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/
5789: /* scanf("%d",i);*/
5790: cutl(strd,strc,strb,'V');
5791: ks++; /**< Number of simple covariates */
1.145 brouard 5792: cptcovn++;
1.187 brouard 5793: Tvar[k]=atoi(strd);
5794: }
5795: strcpy(modelsav,stra); /* modelsav=V2+V1+V4 stra=V2+V1+V4 */
5796: /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);
5797: scanf("%d",i);*/
5798: } /* end of loop + on total covariates */
5799: } /* end if strlen(modelsave == 0) age*age might exist */
5800: } /* end if strlen(model == 0) */
1.136 brouard 5801:
5802: /*The number n of Vn is stored in Tvar. cptcovage =number of age covariate. Tage gives the position of age. cptcovprod= number of products.
5803: If model=V1+V1*age then Tvar[1]=1 Tvar[2]=1 cptcovage=1 Tage[1]=2 cptcovprod=0*/
5804:
5805: /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);
5806: printf("cptcovprod=%d ", cptcovprod);
5807: fprintf(ficlog,"cptcovprod=%d ", cptcovprod);
5808:
5809: scanf("%d ",i);*/
5810:
5811:
1.137 brouard 5812: return (0); /* with covar[new additional covariate if product] and Tage if age */
1.164 brouard 5813: /*endread:*/
1.136 brouard 5814: printf("Exiting decodemodel: ");
5815: return (1);
5816: }
5817:
1.169 brouard 5818: int calandcheckages(int imx, int maxwav, double *agemin, double *agemax, int *nberr, int *nbwarn )
1.136 brouard 5819: {
5820: int i, m;
5821:
5822: for (i=1; i<=imx; i++) {
5823: for(m=2; (m<= maxwav); m++) {
5824: if (((int)mint[m][i]== 99) && (s[m][i] <= nlstate)){
5825: anint[m][i]=9999;
5826: s[m][i]=-1;
5827: }
5828: if((int)moisdc[i]==99 && (int)andc[i]==9999 && s[m][i]>nlstate){
1.169 brouard 5829: *nberr = *nberr + 1;
5830: 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);
5831: 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 5832: s[m][i]=-1;
5833: }
5834: if((int)moisdc[i]==99 && (int)andc[i]!=9999 && s[m][i]>nlstate){
1.169 brouard 5835: (*nberr)++;
1.136 brouard 5836: 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]);
5837: 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]);
5838: s[m][i]=-1; /* We prefer to skip it (and to skip it in version 0.8a1 too */
5839: }
5840: }
5841: }
5842:
5843: for (i=1; i<=imx; i++) {
5844: agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);
5845: for(m=firstpass; (m<= lastpass); m++){
5846: if(s[m][i] >0 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5){
5847: if (s[m][i] >= nlstate+1) {
1.169 brouard 5848: if(agedc[i]>0){
5849: if((int)moisdc[i]!=99 && (int)andc[i]!=9999){
1.136 brouard 5850: agev[m][i]=agedc[i];
5851: /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/
1.169 brouard 5852: }else {
1.136 brouard 5853: if ((int)andc[i]!=9999){
5854: nbwarn++;
5855: printf("Warning negative age at death: %ld line:%d\n",num[i],i);
5856: fprintf(ficlog,"Warning negative age at death: %ld line:%d\n",num[i],i);
5857: agev[m][i]=-1;
5858: }
5859: }
1.169 brouard 5860: } /* agedc > 0 */
1.136 brouard 5861: }
5862: else if(s[m][i] !=9){ /* Standard case, age in fractional
5863: years but with the precision of a month */
5864: agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);
5865: if((int)mint[m][i]==99 || (int)anint[m][i]==9999)
5866: agev[m][i]=1;
5867: else if(agev[m][i] < *agemin){
5868: *agemin=agev[m][i];
5869: printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], *agemin);
5870: }
5871: else if(agev[m][i] >*agemax){
5872: *agemax=agev[m][i];
1.156 brouard 5873: /* printf(" Max anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.2f\n",m,i,anint[m][i], i,annais[i], *agemax);*/
1.136 brouard 5874: }
5875: /*agev[m][i]=anint[m][i]-annais[i];*/
5876: /* agev[m][i] = age[i]+2*m;*/
5877: }
5878: else { /* =9 */
5879: agev[m][i]=1;
5880: s[m][i]=-1;
5881: }
5882: }
5883: else /*= 0 Unknown */
5884: agev[m][i]=1;
5885: }
5886:
5887: }
5888: for (i=1; i<=imx; i++) {
5889: for(m=firstpass; (m<=lastpass); m++){
5890: if (s[m][i] > (nlstate+ndeath)) {
1.169 brouard 5891: (*nberr)++;
1.136 brouard 5892: 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);
5893: 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);
5894: return 1;
5895: }
5896: }
5897: }
5898:
5899: /*for (i=1; i<=imx; i++){
5900: for (m=firstpass; (m<lastpass); m++){
5901: printf("%ld %d %.lf %d %d\n", num[i],(covar[1][i]),agev[m][i],s[m][i],s[m+1][i]);
5902: }
5903:
5904: }*/
5905:
5906:
1.139 brouard 5907: printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, *agemin, *agemax);
5908: fprintf(ficlog,"Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, *agemin, *agemax);
1.136 brouard 5909:
5910: return (0);
1.164 brouard 5911: /* endread:*/
1.136 brouard 5912: printf("Exiting calandcheckages: ");
5913: return (1);
5914: }
5915:
1.172 brouard 5916: #if defined(_MSC_VER)
5917: /*printf("Visual C++ compiler: %s \n;", _MSC_FULL_VER);*/
5918: /*fprintf(ficlog, "Visual C++ compiler: %s \n;", _MSC_FULL_VER);*/
5919: //#include "stdafx.h"
5920: //#include <stdio.h>
5921: //#include <tchar.h>
5922: //#include <windows.h>
5923: //#include <iostream>
5924: typedef BOOL(WINAPI *LPFN_ISWOW64PROCESS) (HANDLE, PBOOL);
5925:
5926: LPFN_ISWOW64PROCESS fnIsWow64Process;
5927:
5928: BOOL IsWow64()
5929: {
5930: BOOL bIsWow64 = FALSE;
5931:
5932: //typedef BOOL (APIENTRY *LPFN_ISWOW64PROCESS)
5933: // (HANDLE, PBOOL);
5934:
5935: //LPFN_ISWOW64PROCESS fnIsWow64Process;
5936:
5937: HMODULE module = GetModuleHandle(_T("kernel32"));
5938: const char funcName[] = "IsWow64Process";
5939: fnIsWow64Process = (LPFN_ISWOW64PROCESS)
5940: GetProcAddress(module, funcName);
5941:
5942: if (NULL != fnIsWow64Process)
5943: {
5944: if (!fnIsWow64Process(GetCurrentProcess(),
5945: &bIsWow64))
5946: //throw std::exception("Unknown error");
5947: printf("Unknown error\n");
5948: }
5949: return bIsWow64 != FALSE;
5950: }
5951: #endif
1.177 brouard 5952:
1.191 brouard 5953: void syscompilerinfo(int logged)
1.167 brouard 5954: {
5955: /* #include "syscompilerinfo.h"*/
1.185 brouard 5956: /* command line Intel compiler 32bit windows, XP compatible:*/
5957: /* /GS /W3 /Gy
5958: /Zc:wchar_t /Zi /O2 /Fd"Release\vc120.pdb" /D "WIN32" /D "NDEBUG" /D
5959: "_CONSOLE" /D "_LIB" /D "_USING_V110_SDK71_" /D "_UNICODE" /D
5960: "UNICODE" /Qipo /Zc:forScope /Gd /Oi /MT /Fa"Release\" /EHsc /nologo
1.186 brouard 5961: /Fo"Release\" /Qprof-dir "Release\" /Fp"Release\IMaCh.pch"
5962: */
5963: /* 64 bits */
1.185 brouard 5964: /*
5965: /GS /W3 /Gy
5966: /Zc:wchar_t /Zi /O2 /Fd"x64\Release\vc120.pdb" /D "WIN32" /D "NDEBUG"
5967: /D "_CONSOLE" /D "_LIB" /D "_UNICODE" /D "UNICODE" /Qipo /Zc:forScope
5968: /Oi /MD /Fa"x64\Release\" /EHsc /nologo /Fo"x64\Release\" /Qprof-dir
5969: "x64\Release\" /Fp"x64\Release\IMaCh.pch" */
5970: /* Optimization are useless and O3 is slower than O2 */
5971: /*
5972: /GS /W3 /Gy /Zc:wchar_t /Zi /O3 /Fd"x64\Release\vc120.pdb" /D "WIN32"
5973: /D "NDEBUG" /D "_CONSOLE" /D "_LIB" /D "_UNICODE" /D "UNICODE" /Qipo
5974: /Zc:forScope /Oi /MD /Fa"x64\Release\" /EHsc /nologo /Qparallel
5975: /Fo"x64\Release\" /Qprof-dir "x64\Release\" /Fp"x64\Release\IMaCh.pch"
5976: */
1.186 brouard 5977: /* Link is */ /* /OUT:"visual studio
1.185 brouard 5978: 2013\Projects\IMaCh\Release\IMaCh.exe" /MANIFEST /NXCOMPAT
5979: /PDB:"visual studio
5980: 2013\Projects\IMaCh\Release\IMaCh.pdb" /DYNAMICBASE
5981: "kernel32.lib" "user32.lib" "gdi32.lib" "winspool.lib"
5982: "comdlg32.lib" "advapi32.lib" "shell32.lib" "ole32.lib"
5983: "oleaut32.lib" "uuid.lib" "odbc32.lib" "odbccp32.lib"
5984: /MACHINE:X86 /OPT:REF /SAFESEH /INCREMENTAL:NO
5985: /SUBSYSTEM:CONSOLE",5.01" /MANIFESTUAC:"level='asInvoker'
5986: uiAccess='false'"
5987: /ManifestFile:"Release\IMaCh.exe.intermediate.manifest" /OPT:ICF
5988: /NOLOGO /TLBID:1
5989: */
1.177 brouard 5990: #if defined __INTEL_COMPILER
1.178 brouard 5991: #if defined(__GNUC__)
5992: struct utsname sysInfo; /* For Intel on Linux and OS/X */
5993: #endif
1.177 brouard 5994: #elif defined(__GNUC__)
1.179 brouard 5995: #ifndef __APPLE__
1.174 brouard 5996: #include <gnu/libc-version.h> /* Only on gnu */
1.179 brouard 5997: #endif
1.177 brouard 5998: struct utsname sysInfo;
1.178 brouard 5999: int cross = CROSS;
6000: if (cross){
6001: printf("Cross-");
1.191 brouard 6002: if(logged) fprintf(ficlog, "Cross-");
1.178 brouard 6003: }
1.174 brouard 6004: #endif
6005:
1.171 brouard 6006: #include <stdint.h>
1.178 brouard 6007:
1.191 brouard 6008: printf("Compiled with:");if(logged)fprintf(ficlog,"Compiled with:");
1.169 brouard 6009: #if defined(__clang__)
1.191 brouard 6010: printf(" Clang/LLVM");if(logged)fprintf(ficlog," Clang/LLVM"); /* Clang/LLVM. ---------------------------------------------- */
1.169 brouard 6011: #endif
6012: #if defined(__ICC) || defined(__INTEL_COMPILER)
1.191 brouard 6013: printf(" Intel ICC/ICPC");if(logged)fprintf(ficlog," Intel ICC/ICPC");/* Intel ICC/ICPC. ------------------------------------------ */
1.169 brouard 6014: #endif
6015: #if defined(__GNUC__) || defined(__GNUG__)
1.191 brouard 6016: printf(" GNU GCC/G++");if(logged)fprintf(ficlog," GNU GCC/G++");/* GNU GCC/G++. --------------------------------------------- */
1.169 brouard 6017: #endif
6018: #if defined(__HP_cc) || defined(__HP_aCC)
1.191 brouard 6019: printf(" Hewlett-Packard C/aC++");if(logged)fprintf(fcilog," Hewlett-Packard C/aC++"); /* Hewlett-Packard C/aC++. ---------------------------------- */
1.169 brouard 6020: #endif
6021: #if defined(__IBMC__) || defined(__IBMCPP__)
1.191 brouard 6022: printf(" IBM XL C/C++"); if(logged) fprintf(ficlog," IBM XL C/C++");/* IBM XL C/C++. -------------------------------------------- */
1.169 brouard 6023: #endif
6024: #if defined(_MSC_VER)
1.191 brouard 6025: printf(" Microsoft Visual Studio");if(logged)fprintf(ficlog," Microsoft Visual Studio");/* Microsoft Visual Studio. --------------------------------- */
1.169 brouard 6026: #endif
6027: #if defined(__PGI)
1.191 brouard 6028: printf(" Portland Group PGCC/PGCPP");if(logged) fprintf(ficlog," Portland Group PGCC/PGCPP");/* Portland Group PGCC/PGCPP. ------------------------------- */
1.169 brouard 6029: #endif
6030: #if defined(__SUNPRO_C) || defined(__SUNPRO_CC)
1.191 brouard 6031: printf(" Oracle Solaris Studio");if(logged)fprintf(ficlog," Oracle Solaris Studio\n");/* Oracle Solaris Studio. ----------------------------------- */
1.167 brouard 6032: #endif
1.191 brouard 6033: printf(" for "); if (logged) fprintf(ficlog, " for ");
1.169 brouard 6034:
1.167 brouard 6035: // http://stackoverflow.com/questions/4605842/how-to-identify-platform-compiler-from-preprocessor-macros
6036: #ifdef _WIN32 // note the underscore: without it, it's not msdn official!
6037: // Windows (x64 and x86)
1.191 brouard 6038: printf("Windows (x64 and x86) ");if(logged) fprintf(ficlog,"Windows (x64 and x86) ");
1.167 brouard 6039: #elif __unix__ // all unices, not all compilers
6040: // Unix
1.191 brouard 6041: printf("Unix ");if(logged) fprintf(ficlog,"Unix ");
1.167 brouard 6042: #elif __linux__
6043: // linux
1.191 brouard 6044: printf("linux ");if(logged) fprintf(ficlog,"linux ");
1.167 brouard 6045: #elif __APPLE__
1.174 brouard 6046: // Mac OS, not sure if this is covered by __posix__ and/or __unix__ though..
1.191 brouard 6047: printf("Mac OS ");if(logged) fprintf(ficlog,"Mac OS ");
1.167 brouard 6048: #endif
6049:
6050: /* __MINGW32__ */
6051: /* __CYGWIN__ */
6052: /* __MINGW64__ */
6053: // http://msdn.microsoft.com/en-us/library/b0084kay.aspx
6054: /* _MSC_VER //the Visual C++ compiler is 17.00.51106.1, the _MSC_VER macro evaluates to 1700. Type cl /? */
6055: /* _MSC_FULL_VER //the Visual C++ compiler is 15.00.20706.01, the _MSC_FULL_VER macro evaluates to 150020706 */
6056: /* _WIN64 // Defined for applications for Win64. */
6057: /* _M_X64 // Defined for compilations that target x64 processors. */
6058: /* _DEBUG // Defined when you compile with /LDd, /MDd, and /MTd. */
1.171 brouard 6059:
1.167 brouard 6060: #if UINTPTR_MAX == 0xffffffff
1.191 brouard 6061: printf(" 32-bit"); if(logged) fprintf(ficlog," 32-bit");/* 32-bit */
1.167 brouard 6062: #elif UINTPTR_MAX == 0xffffffffffffffff
1.191 brouard 6063: printf(" 64-bit"); if(logged) fprintf(ficlog," 64-bit");/* 64-bit */
1.167 brouard 6064: #else
1.191 brouard 6065: printf(" wtf-bit"); if(logged) fprintf(ficlog," wtf-bit");/* wtf */
1.167 brouard 6066: #endif
6067:
1.169 brouard 6068: #if defined(__GNUC__)
6069: # if defined(__GNUC_PATCHLEVEL__)
6070: # define __GNUC_VERSION__ (__GNUC__ * 10000 \
6071: + __GNUC_MINOR__ * 100 \
6072: + __GNUC_PATCHLEVEL__)
6073: # else
6074: # define __GNUC_VERSION__ (__GNUC__ * 10000 \
6075: + __GNUC_MINOR__ * 100)
6076: # endif
1.174 brouard 6077: printf(" using GNU C version %d.\n", __GNUC_VERSION__);
1.191 brouard 6078: if(logged) fprintf(ficlog, " using GNU C version %d.\n", __GNUC_VERSION__);
1.176 brouard 6079:
6080: if (uname(&sysInfo) != -1) {
6081: printf("Running on: %s %s %s %s %s\n",sysInfo.sysname, sysInfo.nodename, sysInfo.release, sysInfo.version, sysInfo.machine);
1.191 brouard 6082: 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 6083: }
6084: else
6085: perror("uname() error");
1.179 brouard 6086: //#ifndef __INTEL_COMPILER
6087: #if !defined (__INTEL_COMPILER) && !defined(__APPLE__)
1.174 brouard 6088: printf("GNU libc version: %s\n", gnu_get_libc_version());
1.191 brouard 6089: if(logged) fprintf(ficlog,"GNU libc version: %s\n", gnu_get_libc_version());
1.177 brouard 6090: #endif
1.169 brouard 6091: #endif
1.172 brouard 6092:
6093: // void main()
6094: // {
1.169 brouard 6095: #if defined(_MSC_VER)
1.174 brouard 6096: if (IsWow64()){
1.191 brouard 6097: printf("\nThe program (probably compiled for 32bit) is running under WOW64 (64bit) emulation.\n");
6098: if (logged) fprintf(ficlog, "\nThe program (probably compiled for 32bit) is running under WOW64 (64bit) emulation.\n");
1.174 brouard 6099: }
6100: else{
1.191 brouard 6101: printf("\nThe program is not running under WOW64 (i.e probably on a 64bit Windows).\n");
6102: if (logged) fprintf(ficlog, "\nThe programm is not running under WOW64 (i.e probably on a 64bit Windows).\n");
1.174 brouard 6103: }
1.172 brouard 6104: // printf("\nPress Enter to continue...");
6105: // getchar();
6106: // }
6107:
1.169 brouard 6108: #endif
6109:
1.167 brouard 6110:
6111: }
1.136 brouard 6112:
1.180 brouard 6113: int prevalence_limit(double *p, double **prlim, double ageminpar, double agemaxpar){
6114: /*--------------- Prevalence limit (period or stable prevalence) --------------*/
6115: int i, j, k, i1 ;
6116: double ftolpl = 1.e-10;
6117: double age, agebase, agelim;
6118:
6119: strcpy(filerespl,"pl");
6120: strcat(filerespl,fileres);
6121: if((ficrespl=fopen(filerespl,"w"))==NULL) {
6122: printf("Problem with period (stable) prevalence resultfile: %s\n", filerespl);return 1;
6123: fprintf(ficlog,"Problem with period (stable) prevalence resultfile: %s\n", filerespl);return 1;
6124: }
6125: printf("Computing period (stable) prevalence: result on file '%s' \n", filerespl);
6126: fprintf(ficlog,"Computing period (stable) prevalence: result on file '%s' \n", filerespl);
6127: pstamp(ficrespl);
6128: fprintf(ficrespl,"# Period (stable) prevalence \n");
6129: fprintf(ficrespl,"#Age ");
6130: for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);
6131: fprintf(ficrespl,"\n");
6132:
6133: /* prlim=matrix(1,nlstate,1,nlstate);*/ /* back in main */
6134:
6135: agebase=ageminpar;
6136: agelim=agemaxpar;
6137:
6138: i1=pow(2,cptcoveff);
6139: if (cptcovn < 1){i1=1;}
6140:
6141: for(cptcov=1,k=0;cptcov<=i1;cptcov++){
6142: /* for(cptcov=1,k=0;cptcov<=1;cptcov++){ */
6143: //for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
6144: k=k+1;
6145: /* to clean */
6146: //printf("cptcov=%d cptcod=%d codtab=%d\n",cptcov, cptcod,codtab[cptcod][cptcov]);
6147: fprintf(ficrespl,"\n#******");
6148: printf("\n#******");
6149: fprintf(ficlog,"\n#******");
6150: for(j=1;j<=cptcoveff;j++) {
6151: fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
6152: printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
6153: fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
6154: }
6155: fprintf(ficrespl,"******\n");
6156: printf("******\n");
6157: fprintf(ficlog,"******\n");
6158:
6159: fprintf(ficrespl,"#Age ");
6160: for(j=1;j<=cptcoveff;j++) {
6161: fprintf(ficrespl,"V%d %d",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
6162: }
6163: for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);
6164: fprintf(ficrespl,"\n");
6165:
6166: for (age=agebase; age<=agelim; age++){
6167: /* for (age=agebase; age<=agebase; age++){ */
6168: prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
6169: fprintf(ficrespl,"%.0f ",age );
6170: for(j=1;j<=cptcoveff;j++)
6171: fprintf(ficrespl,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
6172: for(i=1; i<=nlstate;i++)
6173: fprintf(ficrespl," %.5f", prlim[i][i]);
6174: fprintf(ficrespl,"\n");
6175: } /* Age */
6176: /* was end of cptcod */
6177: } /* cptcov */
1.184 brouard 6178: return 0;
1.180 brouard 6179: }
6180:
6181: int hPijx(double *p, int bage, int fage){
6182: /*------------- h Pij x at various ages ------------*/
6183:
6184: int stepsize;
6185: int agelim;
6186: int hstepm;
6187: int nhstepm;
6188: int h, i, i1, j, k;
6189:
6190: double agedeb;
6191: double ***p3mat;
6192:
6193: strcpy(filerespij,"pij"); strcat(filerespij,fileres);
6194: if((ficrespij=fopen(filerespij,"w"))==NULL) {
6195: printf("Problem with Pij resultfile: %s\n", filerespij); return 1;
6196: fprintf(ficlog,"Problem with Pij resultfile: %s\n", filerespij); return 1;
6197: }
6198: printf("Computing pij: result on file '%s' \n", filerespij);
6199: fprintf(ficlog,"Computing pij: result on file '%s' \n", filerespij);
6200:
6201: stepsize=(int) (stepm+YEARM-1)/YEARM;
6202: /*if (stepm<=24) stepsize=2;*/
6203:
6204: agelim=AGESUP;
6205: hstepm=stepsize*YEARM; /* Every year of age */
6206: hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */
6207:
6208: /* hstepm=1; aff par mois*/
6209: pstamp(ficrespij);
6210: fprintf(ficrespij,"#****** h Pij x Probability to be in state j at age x+h being in i at x ");
6211: i1= pow(2,cptcoveff);
1.183 brouard 6212: /* for(cptcov=1,k=0;cptcov<=i1;cptcov++){ */
6213: /* /\*for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*\/ */
6214: /* k=k+1; */
6215: for (k=1; k <= (int) pow(2,cptcoveff); k++){
6216: fprintf(ficrespij,"\n#****** ");
6217: for(j=1;j<=cptcoveff;j++)
6218: fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
6219: fprintf(ficrespij,"******\n");
6220:
6221: for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */
6222: nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
6223: nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
6224:
6225: /* nhstepm=nhstepm*YEARM; aff par mois*/
1.180 brouard 6226:
1.183 brouard 6227: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
6228: oldm=oldms;savm=savms;
6229: hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
6230: fprintf(ficrespij,"# Cov Agex agex+h hpijx with i,j=");
6231: for(i=1; i<=nlstate;i++)
6232: for(j=1; j<=nlstate+ndeath;j++)
6233: fprintf(ficrespij," %1d-%1d",i,j);
6234: fprintf(ficrespij,"\n");
6235: for (h=0; h<=nhstepm; h++){
6236: /*agedebphstep = agedeb + h*hstepm/YEARM*stepm;*/
6237: fprintf(ficrespij,"%d %3.f %3.f",k, agedeb, agedeb + h*hstepm/YEARM*stepm );
1.180 brouard 6238: for(i=1; i<=nlstate;i++)
6239: for(j=1; j<=nlstate+ndeath;j++)
1.183 brouard 6240: fprintf(ficrespij," %.5f", p3mat[i][j][h]);
1.180 brouard 6241: fprintf(ficrespij,"\n");
6242: }
1.183 brouard 6243: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
6244: fprintf(ficrespij,"\n");
6245: }
1.180 brouard 6246: /*}*/
6247: }
1.184 brouard 6248: return 0;
1.180 brouard 6249: }
6250:
6251:
1.136 brouard 6252: /***********************************************/
6253: /**************** Main Program *****************/
6254: /***********************************************/
6255:
6256: int main(int argc, char *argv[])
6257: {
6258: #ifdef GSL
6259: const gsl_multimin_fminimizer_type *T;
6260: size_t iteri = 0, it;
6261: int rval = GSL_CONTINUE;
6262: int status = GSL_SUCCESS;
6263: double ssval;
6264: #endif
6265: int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav);
1.164 brouard 6266: int i,j, k, n=MAXN,iter=0,m,size=100, cptcod;
6267:
6268: int jj, ll, li, lj, lk;
1.136 brouard 6269: int numlinepar=0; /* Current linenumber of parameter file */
6270: int itimes;
6271: int NDIM=2;
6272: int vpopbased=0;
6273:
1.164 brouard 6274: char ca[32], cb[32];
1.136 brouard 6275: /* FILE *fichtm; *//* Html File */
6276: /* FILE *ficgp;*/ /*Gnuplot File */
6277: struct stat info;
1.191 brouard 6278: double agedeb=0.;
1.194 brouard 6279:
6280: double ageminpar=AGEOVERFLOW,agemin=AGEOVERFLOW, agemaxpar=-AGEOVERFLOW, agemax=-AGEOVERFLOW;
1.136 brouard 6281:
1.165 brouard 6282: double fret;
1.191 brouard 6283: double dum=0.; /* Dummy variable */
1.136 brouard 6284: double ***p3mat;
6285: double ***mobaverage;
1.164 brouard 6286:
6287: char line[MAXLINE];
1.136 brouard 6288: char path[MAXLINE],pathc[MAXLINE],pathcd[MAXLINE],pathtot[MAXLINE],model[MAXLINE];
6289: char pathr[MAXLINE], pathimach[MAXLINE];
1.164 brouard 6290: char *tok, *val; /* pathtot */
1.136 brouard 6291: int firstobs=1, lastobs=10;
1.195 ! brouard 6292: int c, h , cpt, c2;
1.191 brouard 6293: int jl=0;
6294: int i1, j1, jk, stepsize=0;
1.194 brouard 6295: int count=0;
6296:
1.164 brouard 6297: int *tab;
1.136 brouard 6298: int mobilavproj=0 , prevfcast=0 ; /* moving average of prev, If prevfcast=1 prevalence projection */
6299: int mobilav=0,popforecast=0;
1.191 brouard 6300: int hstepm=0, nhstepm=0;
1.136 brouard 6301: int agemortsup;
6302: float sumlpop=0.;
6303: double jprev1=1, mprev1=1,anprev1=2000,jprev2=1, mprev2=1,anprev2=2000;
6304: double jpyram=1, mpyram=1,anpyram=2000,jpyram1=1, mpyram1=1,anpyram1=2000;
6305:
1.191 brouard 6306: double bage=0, fage=110., age, agelim=0., agebase=0.;
1.136 brouard 6307: double ftolpl=FTOL;
6308: double **prlim;
6309: double ***param; /* Matrix of parameters */
6310: double *p;
6311: double **matcov; /* Matrix of covariance */
6312: double ***delti3; /* Scale */
6313: double *delti; /* Scale */
6314: double ***eij, ***vareij;
6315: double **varpl; /* Variances of prevalence limits by age */
6316: double *epj, vepp;
1.164 brouard 6317:
1.136 brouard 6318: double dateprev1, dateprev2,jproj1=1,mproj1=1,anproj1=2000,jproj2=1,mproj2=1,anproj2=2000;
6319: double **ximort;
1.145 brouard 6320: char *alph[]={"a","a","b","c","d","e"}, str[4]="1234";
1.136 brouard 6321: int *dcwave;
6322:
1.164 brouard 6323: char z[1]="c";
1.136 brouard 6324:
6325: /*char *strt;*/
6326: char strtend[80];
1.126 brouard 6327:
1.164 brouard 6328:
1.126 brouard 6329: /* setlocale (LC_ALL, ""); */
6330: /* bindtextdomain (PACKAGE, LOCALEDIR); */
6331: /* textdomain (PACKAGE); */
6332: /* setlocale (LC_CTYPE, ""); */
6333: /* setlocale (LC_MESSAGES, ""); */
6334:
6335: /* gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */
1.157 brouard 6336: rstart_time = time(NULL);
6337: /* (void) gettimeofday(&start_time,&tzp);*/
6338: start_time = *localtime(&rstart_time);
1.126 brouard 6339: curr_time=start_time;
1.157 brouard 6340: /*tml = *localtime(&start_time.tm_sec);*/
6341: /* strcpy(strstart,asctime(&tml)); */
6342: strcpy(strstart,asctime(&start_time));
1.126 brouard 6343:
6344: /* printf("Localtime (at start)=%s",strstart); */
1.157 brouard 6345: /* tp.tm_sec = tp.tm_sec +86400; */
6346: /* tm = *localtime(&start_time.tm_sec); */
1.126 brouard 6347: /* tmg.tm_year=tmg.tm_year +dsign*dyear; */
6348: /* tmg.tm_mon=tmg.tm_mon +dsign*dmonth; */
6349: /* tmg.tm_hour=tmg.tm_hour + 1; */
1.157 brouard 6350: /* tp.tm_sec = mktime(&tmg); */
1.126 brouard 6351: /* strt=asctime(&tmg); */
6352: /* printf("Time(after) =%s",strstart); */
6353: /* (void) time (&time_value);
6354: * printf("time=%d,t-=%d\n",time_value,time_value-86400);
6355: * tm = *localtime(&time_value);
6356: * strstart=asctime(&tm);
6357: * printf("tim_value=%d,asctime=%s\n",time_value,strstart);
6358: */
6359:
6360: nberr=0; /* Number of errors and warnings */
6361: nbwarn=0;
1.184 brouard 6362: #ifdef WIN32
6363: _getcwd(pathcd, size);
6364: #else
1.126 brouard 6365: getcwd(pathcd, size);
1.184 brouard 6366: #endif
1.191 brouard 6367: syscompilerinfo(0);
1.126 brouard 6368: printf("\n%s\n%s",version,fullversion);
6369: if(argc <=1){
6370: printf("\nEnter the parameter file name: ");
6371: fgets(pathr,FILENAMELENGTH,stdin);
6372: i=strlen(pathr);
6373: if(pathr[i-1]=='\n')
6374: pathr[i-1]='\0';
1.156 brouard 6375: i=strlen(pathr);
6376: if(pathr[i-1]==' ') /* This may happen when dragging on oS/X! */
6377: pathr[i-1]='\0';
1.126 brouard 6378: for (tok = pathr; tok != NULL; ){
6379: printf("Pathr |%s|\n",pathr);
6380: while ((val = strsep(&tok, "\"" )) != NULL && *val == '\0');
6381: printf("val= |%s| pathr=%s\n",val,pathr);
6382: strcpy (pathtot, val);
6383: if(pathr[0] == '\0') break; /* Dirty */
6384: }
6385: }
6386: else{
6387: strcpy(pathtot,argv[1]);
6388: }
6389: /*if(getcwd(pathcd, MAXLINE)!= NULL)printf ("Error pathcd\n");*/
6390: /*cygwin_split_path(pathtot,path,optionfile);
6391: printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/
6392: /* cutv(path,optionfile,pathtot,'\\');*/
6393:
6394: /* Split argv[0], imach program to get pathimach */
6395: printf("\nargv[0]=%s argv[1]=%s, \n",argv[0],argv[1]);
6396: split(argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
6397: printf("\nargv[0]=%s pathimach=%s, \noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
6398: /* strcpy(pathimach,argv[0]); */
6399: /* Split argv[1]=pathtot, parameter file name to get path, optionfile, extension and name */
6400: split(pathtot,path,optionfile,optionfilext,optionfilefiname);
6401: printf("\npathtot=%s,\npath=%s,\noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
1.184 brouard 6402: #ifdef WIN32
6403: _chdir(path); /* Can be a relative path */
6404: if(_getcwd(pathcd,MAXLINE) > 0) /* So pathcd is the full path */
6405: #else
1.126 brouard 6406: chdir(path); /* Can be a relative path */
1.184 brouard 6407: if (getcwd(pathcd, MAXLINE) > 0) /* So pathcd is the full path */
6408: #endif
6409: printf("Current directory %s!\n",pathcd);
1.126 brouard 6410: strcpy(command,"mkdir ");
6411: strcat(command,optionfilefiname);
6412: if((outcmd=system(command)) != 0){
1.169 brouard 6413: printf("Directory already exists (or can't create it) %s%s, err=%d\n",path,optionfilefiname,outcmd);
1.126 brouard 6414: /* fprintf(ficlog,"Problem creating directory %s%s\n",path,optionfilefiname); */
6415: /* fclose(ficlog); */
6416: /* exit(1); */
6417: }
6418: /* if((imk=mkdir(optionfilefiname))<0){ */
6419: /* perror("mkdir"); */
6420: /* } */
6421:
6422: /*-------- arguments in the command line --------*/
6423:
1.186 brouard 6424: /* Main Log file */
1.126 brouard 6425: strcat(filelog, optionfilefiname);
6426: strcat(filelog,".log"); /* */
6427: if((ficlog=fopen(filelog,"w"))==NULL) {
6428: printf("Problem with logfile %s\n",filelog);
6429: goto end;
6430: }
6431: fprintf(ficlog,"Log filename:%s\n",filelog);
6432: fprintf(ficlog,"\n%s\n%s",version,fullversion);
6433: fprintf(ficlog,"\nEnter the parameter file name: \n");
6434: fprintf(ficlog,"pathimach=%s\npathtot=%s\n\
6435: path=%s \n\
6436: optionfile=%s\n\
6437: optionfilext=%s\n\
1.156 brouard 6438: optionfilefiname='%s'\n",pathimach,pathtot,path,optionfile,optionfilext,optionfilefiname);
1.126 brouard 6439:
1.191 brouard 6440: syscompilerinfo(0);
1.167 brouard 6441:
1.126 brouard 6442: printf("Local time (at start):%s",strstart);
6443: fprintf(ficlog,"Local time (at start): %s",strstart);
6444: fflush(ficlog);
6445: /* (void) gettimeofday(&curr_time,&tzp); */
1.157 brouard 6446: /* printf("Elapsed time %d\n", asc_diff_time(curr_time.tm_sec-start_time.tm_sec,tmpout)); */
1.126 brouard 6447:
6448: /* */
6449: strcpy(fileres,"r");
6450: strcat(fileres, optionfilefiname);
6451: strcat(fileres,".txt"); /* Other files have txt extension */
6452:
1.186 brouard 6453: /* Main ---------arguments file --------*/
1.126 brouard 6454:
6455: if((ficpar=fopen(optionfile,"r"))==NULL) {
1.155 brouard 6456: printf("Problem with optionfile '%s' with errno='%s'\n",optionfile,strerror(errno));
6457: fprintf(ficlog,"Problem with optionfile '%s' with errno='%s'\n",optionfile,strerror(errno));
1.126 brouard 6458: fflush(ficlog);
1.149 brouard 6459: /* goto end; */
6460: exit(70);
1.126 brouard 6461: }
6462:
6463:
6464:
6465: strcpy(filereso,"o");
6466: strcat(filereso,fileres);
6467: if((ficparo=fopen(filereso,"w"))==NULL) { /* opened on subdirectory */
6468: printf("Problem with Output resultfile: %s\n", filereso);
6469: fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso);
6470: fflush(ficlog);
6471: goto end;
6472: }
6473:
6474: /* Reads comments: lines beginning with '#' */
6475: numlinepar=0;
6476: while((c=getc(ficpar))=='#' && c!= EOF){
6477: ungetc(c,ficpar);
6478: fgets(line, MAXLINE, ficpar);
6479: numlinepar++;
1.141 brouard 6480: fputs(line,stdout);
1.126 brouard 6481: fputs(line,ficparo);
6482: fputs(line,ficlog);
6483: }
6484: ungetc(c,ficpar);
6485:
1.187 brouard 6486: 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);
1.194 brouard 6487: numlinepar=numlinepar+3; /* In general */
1.187 brouard 6488: 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);
6489: if(model[strlen(model)-1]=='.') /* Suppressing leading dot in the model */
6490: model[strlen(model)-1]='\0';
6491: 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);
6492: 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 6493: fflush(ficlog);
1.190 brouard 6494: /* if(model[0]=='#'|| model[0]== '\0'){ */
6495: if(model[0]=='#'){
1.187 brouard 6496: printf("Error in 'model' line: model should start with 'model=1+age+' and end with '.' \n \
6497: 'model=1+age+.' or 'model=1+age+V1.' or 'model=1+age+age*age+V1+V1*age.' or \n \
6498: 'model=1+age+V1+V2.' or 'model=1+age+V1+V2+V1*V2.' etc. \n"); \
6499: if(mle != -1){
6500: printf("Fix the model line and run imach with mle=-1 to get a correct template of the parameter file.\n");
6501: exit(1);
6502: }
6503: }
1.126 brouard 6504: while((c=getc(ficpar))=='#' && c!= EOF){
6505: ungetc(c,ficpar);
6506: fgets(line, MAXLINE, ficpar);
6507: numlinepar++;
1.195 ! brouard 6508: if(line[1]=='q'){ /* This #q will quit imach (the answer is q) */
! 6509: z[0]=line[1];
! 6510: }
! 6511: /* printf("****line [1] = %c \n",line[1]); */
1.141 brouard 6512: fputs(line, stdout);
6513: //puts(line);
1.126 brouard 6514: fputs(line,ficparo);
6515: fputs(line,ficlog);
6516: }
6517: ungetc(c,ficpar);
6518:
6519:
1.145 brouard 6520: covar=matrix(0,NCOVMAX,1,n); /**< used in readdata */
1.136 brouard 6521: cptcovn=0; /*Number of covariates, i.e. number of '+' in model statement plus one, indepently of n in Vn*/
6522: /* v1+v2+v3+v2*v4+v5*age makes cptcovn = 5
6523: v1+v2*age+v2*v3 makes cptcovn = 3
6524: */
6525: if (strlen(model)>1)
1.187 brouard 6526: 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 6527: else
1.187 brouard 6528: ncovmodel=2; /* Constant and age */
1.133 brouard 6529: nforce= (nlstate+ndeath-1)*nlstate; /* Number of forces ij from state i to j */
6530: npar= nforce*ncovmodel; /* Number of parameters like aij*/
1.131 brouard 6531: if(npar >MAXPARM || nlstate >NLSTATEMAX || ndeath >NDEATHMAX || ncovmodel>NCOVMAX){
6532: 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);
6533: 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);
6534: fflush(stdout);
6535: fclose (ficlog);
6536: goto end;
6537: }
1.126 brouard 6538: delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
6539: delti=delti3[1][1];
6540: /*delti=vector(1,npar); *//* Scale of each paramater (output from hesscov)*/
6541: if(mle==-1){ /* Print a wizard for help writing covariance matrix */
6542: prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
1.191 brouard 6543: printf(" You chose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
6544: fprintf(ficlog," You chose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
1.126 brouard 6545: free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
6546: fclose (ficparo);
6547: fclose (ficlog);
6548: goto end;
6549: exit(0);
6550: }
1.186 brouard 6551: else if(mle==-3) { /* Main Wizard */
1.126 brouard 6552: prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
1.192 brouard 6553: printf(" You chose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
6554: fprintf(ficlog," You chose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
1.126 brouard 6555: param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
6556: matcov=matrix(1,npar,1,npar);
6557: }
6558: else{
1.145 brouard 6559: /* Read guessed parameters */
1.126 brouard 6560: /* Reads comments: lines beginning with '#' */
6561: while((c=getc(ficpar))=='#' && c!= EOF){
6562: ungetc(c,ficpar);
6563: fgets(line, MAXLINE, ficpar);
6564: numlinepar++;
1.141 brouard 6565: fputs(line,stdout);
1.126 brouard 6566: fputs(line,ficparo);
6567: fputs(line,ficlog);
6568: }
6569: ungetc(c,ficpar);
6570:
6571: param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
6572: for(i=1; i <=nlstate; i++){
6573: j=0;
6574: for(jj=1; jj <=nlstate+ndeath; jj++){
6575: if(jj==i) continue;
6576: j++;
6577: fscanf(ficpar,"%1d%1d",&i1,&j1);
1.193 brouard 6578: if ((i1 != i) || (j1 != jj)){
1.126 brouard 6579: printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n \
6580: It might be a problem of design; if ncovcol and the model are correct\n \
6581: run imach with mle=-1 to get a correct template of the parameter file.\n",numlinepar, i,j, i1, j1);
6582: exit(1);
6583: }
6584: fprintf(ficparo,"%1d%1d",i1,j1);
6585: if(mle==1)
1.193 brouard 6586: printf("%1d%1d",i,jj);
6587: fprintf(ficlog,"%1d%1d",i,jj);
1.126 brouard 6588: for(k=1; k<=ncovmodel;k++){
6589: fscanf(ficpar," %lf",¶m[i][j][k]);
6590: if(mle==1){
6591: printf(" %lf",param[i][j][k]);
6592: fprintf(ficlog," %lf",param[i][j][k]);
6593: }
6594: else
6595: fprintf(ficlog," %lf",param[i][j][k]);
6596: fprintf(ficparo," %lf",param[i][j][k]);
6597: }
6598: fscanf(ficpar,"\n");
6599: numlinepar++;
6600: if(mle==1)
6601: printf("\n");
6602: fprintf(ficlog,"\n");
6603: fprintf(ficparo,"\n");
6604: }
6605: }
6606: fflush(ficlog);
6607:
1.145 brouard 6608: /* Reads scales values */
1.126 brouard 6609: p=param[1][1];
6610:
6611: /* Reads comments: lines beginning with '#' */
6612: while((c=getc(ficpar))=='#' && c!= EOF){
6613: ungetc(c,ficpar);
6614: fgets(line, MAXLINE, ficpar);
6615: numlinepar++;
1.141 brouard 6616: fputs(line,stdout);
1.126 brouard 6617: fputs(line,ficparo);
6618: fputs(line,ficlog);
6619: }
6620: ungetc(c,ficpar);
6621:
6622: for(i=1; i <=nlstate; i++){
6623: for(j=1; j <=nlstate+ndeath-1; j++){
6624: fscanf(ficpar,"%1d%1d",&i1,&j1);
1.164 brouard 6625: if ( (i1-i) * (j1-j) != 0){
1.126 brouard 6626: printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n",numlinepar, i,j, i1, j1);
6627: exit(1);
6628: }
6629: printf("%1d%1d",i,j);
6630: fprintf(ficparo,"%1d%1d",i1,j1);
6631: fprintf(ficlog,"%1d%1d",i1,j1);
6632: for(k=1; k<=ncovmodel;k++){
6633: fscanf(ficpar,"%le",&delti3[i][j][k]);
6634: printf(" %le",delti3[i][j][k]);
6635: fprintf(ficparo," %le",delti3[i][j][k]);
6636: fprintf(ficlog," %le",delti3[i][j][k]);
6637: }
6638: fscanf(ficpar,"\n");
6639: numlinepar++;
6640: printf("\n");
6641: fprintf(ficparo,"\n");
6642: fprintf(ficlog,"\n");
6643: }
6644: }
6645: fflush(ficlog);
6646:
1.145 brouard 6647: /* Reads covariance matrix */
1.126 brouard 6648: delti=delti3[1][1];
6649:
6650:
6651: /* free_ma3x(delti3,1,nlstate,1,nlstate+ndeath-1,1,ncovmodel); */ /* Hasn't to to freed here otherwise delti is no more allocated */
6652:
6653: /* Reads comments: lines beginning with '#' */
6654: while((c=getc(ficpar))=='#' && c!= EOF){
6655: ungetc(c,ficpar);
6656: fgets(line, MAXLINE, ficpar);
6657: numlinepar++;
1.141 brouard 6658: fputs(line,stdout);
1.126 brouard 6659: fputs(line,ficparo);
6660: fputs(line,ficlog);
6661: }
6662: ungetc(c,ficpar);
6663:
6664: matcov=matrix(1,npar,1,npar);
1.131 brouard 6665: for(i=1; i <=npar; i++)
6666: for(j=1; j <=npar; j++) matcov[i][j]=0.;
6667:
1.194 brouard 6668: /* Scans npar lines */
1.126 brouard 6669: for(i=1; i <=npar; i++){
1.194 brouard 6670: count=fscanf(ficpar,"%1d%1d%1d",&i1,&j1,&jk);
6671: if(count != 3){
6672: printf("Error! Error in parameter file %s at line %d after line starting with %1d%1d%1d\n\
6673: This is probably because your covariance matrix doesn't \n contain exactly %d lines corresponding to your model line '1+age+%s'.\n\
6674: Please run with mle=-1 to get a correct covariance matrix.\n",optionfile,numlinepar, i1,j1,jk, npar, model);
6675: fprintf(ficlog,"Error! Error in parameter file %s at line %d after line starting with %1d%1d%1d\n\
6676: This is probably because your covariance matrix doesn't \n contain exactly %d lines corresponding to your model line '1+age+%s'.\n\
6677: Please run with mle=-1 to get a correct covariance matrix.\n",optionfile,numlinepar, i1,j1,jk, npar, model);
6678: exit(1);
6679: }else
1.126 brouard 6680: if(mle==1)
1.194 brouard 6681: printf("%1d%1d%1d",i1,j1,jk);
6682: fprintf(ficlog,"%1d%1d%1d",i1,j1,jk);
6683: fprintf(ficparo,"%1d%1d%1d",i1,j1,jk);
1.126 brouard 6684: for(j=1; j <=i; j++){
6685: fscanf(ficpar," %le",&matcov[i][j]);
6686: if(mle==1){
6687: printf(" %.5le",matcov[i][j]);
6688: }
6689: fprintf(ficlog," %.5le",matcov[i][j]);
6690: fprintf(ficparo," %.5le",matcov[i][j]);
6691: }
6692: fscanf(ficpar,"\n");
6693: numlinepar++;
6694: if(mle==1)
6695: printf("\n");
6696: fprintf(ficlog,"\n");
6697: fprintf(ficparo,"\n");
6698: }
1.194 brouard 6699: /* End of read covariance matrix npar lines */
1.126 brouard 6700: for(i=1; i <=npar; i++)
6701: for(j=i+1;j<=npar;j++)
6702: matcov[i][j]=matcov[j][i];
6703:
6704: if(mle==1)
6705: printf("\n");
6706: fprintf(ficlog,"\n");
6707:
6708: fflush(ficlog);
6709:
6710: /*-------- Rewriting parameter file ----------*/
6711: strcpy(rfileres,"r"); /* "Rparameterfile */
6712: strcat(rfileres,optionfilefiname); /* Parameter file first name*/
6713: strcat(rfileres,"."); /* */
6714: strcat(rfileres,optionfilext); /* Other files have txt extension */
6715: if((ficres =fopen(rfileres,"w"))==NULL) {
6716: printf("Problem writing new parameter file: %s\n", fileres);goto end;
6717: fprintf(ficlog,"Problem writing new parameter file: %s\n", fileres);goto end;
6718: }
6719: fprintf(ficres,"#%s\n",version);
6720: } /* End of mle != -3 */
6721:
1.186 brouard 6722: /* Main data
6723: */
1.126 brouard 6724: n= lastobs;
6725: num=lvector(1,n);
6726: moisnais=vector(1,n);
6727: annais=vector(1,n);
6728: moisdc=vector(1,n);
6729: andc=vector(1,n);
6730: agedc=vector(1,n);
6731: cod=ivector(1,n);
6732: weight=vector(1,n);
6733: for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */
6734: mint=matrix(1,maxwav,1,n);
6735: anint=matrix(1,maxwav,1,n);
1.131 brouard 6736: s=imatrix(1,maxwav+1,1,n); /* s[i][j] health state for wave i and individual j */
1.126 brouard 6737: tab=ivector(1,NCOVMAX);
1.144 brouard 6738: ncodemax=ivector(1,NCOVMAX); /* Number of code per covariate; if O and 1 only, 2**ncov; V1+V2+V3+V4=>16 */
1.192 brouard 6739: 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 6740:
1.136 brouard 6741: /* Reads data from file datafile */
6742: if (readdata(datafile, firstobs, lastobs, &imx)==1)
6743: goto end;
6744:
6745: /* Calculation of the number of parameters from char model */
1.137 brouard 6746: /* modelsav=V2+V1+V4+age*V3 strb=age*V3 stra=V2+V1+V4
6747: k=4 (age*V3) Tvar[k=4]= 3 (from V3) Tag[cptcovage=1]=4
6748: k=3 V4 Tvar[k=3]= 4 (from V4)
6749: k=2 V1 Tvar[k=2]= 1 (from V1)
6750: k=1 Tvar[1]=2 (from V2)
6751: */
6752: Tvar=ivector(1,NCOVMAX); /* Was 15 changed to NCOVMAX. */
6753: /* V2+V1+V4+age*V3 is a model with 4 covariates (3 plus signs).
6754: For each model-covariate stores the data-covariate id. Tvar[1]=2, Tvar[2]=1, Tvar[3]=4,
6755: Tvar[4=age*V3] is 3 and 'age' is recorded in Tage.
6756: */
6757: /* For model-covariate k tells which data-covariate to use but
6758: because this model-covariate is a construction we invent a new column
6759: ncovcol + k1
6760: If already ncovcol=4 and model=V2+V1+V1*V4+age*V3
6761: Tvar[3=V1*V4]=4+1 etc */
1.145 brouard 6762: Tprod=ivector(1,NCOVMAX); /* Gives the position of a product */
1.137 brouard 6763: /* Tprod[k1=1]=3(=V1*V4) for V2+V1+V1*V4+age*V3
6764: if V2+V1+V1*V4+age*V3+V3*V2 TProd[k1=2]=5 (V3*V2)
6765: */
1.145 brouard 6766: Tvaraff=ivector(1,NCOVMAX); /* Unclear */
6767: 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 6768: * For V3*V2 (in V2+V1+V1*V4+age*V3+V3*V2), V3*V2 position is 2nd.
6769: * Tvard[k1=2][1]=3 (V3) Tvard[k1=2][2]=2(V2) */
1.145 brouard 6770: Tage=ivector(1,NCOVMAX); /* Gives the covariate id of covariates associated with age: V2 + V1 + age*V4 + V3*age
1.137 brouard 6771: 4 covariates (3 plus signs)
6772: Tage[1=V3*age]= 4; Tage[2=age*V4] = 3
6773: */
1.136 brouard 6774:
1.186 brouard 6775: /* Main decodemodel */
6776:
1.187 brouard 6777:
1.136 brouard 6778: if(decodemodel(model, lastobs) == 1)
6779: goto end;
6780:
1.137 brouard 6781: if((double)(lastobs-imx)/(double)imx > 1.10){
6782: nbwarn++;
6783: 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);
6784: 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);
6785: }
1.136 brouard 6786: /* if(mle==1){*/
1.137 brouard 6787: if (weightopt != 1) { /* Maximisation without weights. We can have weights different from 1 but want no weight*/
6788: for(i=1;i<=imx;i++) weight[i]=1.0; /* changed to imx */
1.136 brouard 6789: }
6790:
6791: /*-calculation of age at interview from date of interview and age at death -*/
6792: agev=matrix(1,maxwav,1,imx);
6793:
6794: if(calandcheckages(imx, maxwav, &agemin, &agemax, &nberr, &nbwarn) == 1)
6795: goto end;
6796:
1.126 brouard 6797:
1.136 brouard 6798: agegomp=(int)agemin;
6799: free_vector(moisnais,1,n);
6800: free_vector(annais,1,n);
1.126 brouard 6801: /* free_matrix(mint,1,maxwav,1,n);
6802: free_matrix(anint,1,maxwav,1,n);*/
6803: free_vector(moisdc,1,n);
6804: free_vector(andc,1,n);
1.145 brouard 6805: /* */
6806:
1.126 brouard 6807: wav=ivector(1,imx);
6808: dh=imatrix(1,lastpass-firstpass+1,1,imx);
6809: bh=imatrix(1,lastpass-firstpass+1,1,imx);
6810: mw=imatrix(1,lastpass-firstpass+1,1,imx);
6811:
6812: /* Concatenates waves */
6813: concatwav(wav, dh, bh, mw, s, agedc, agev, firstpass, lastpass, imx, nlstate, stepm);
1.145 brouard 6814: /* */
6815:
1.126 brouard 6816: /* Routine tricode is to calculate cptcoveff (real number of unique covariates) and to associate covariable number and modality */
6817:
6818: nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);
6819: ncodemax[1]=1;
1.145 brouard 6820: Ndum =ivector(-1,NCOVMAX);
1.187 brouard 6821: if (ncovmodel-nagesqr > 2 ) /* That is if covariate other than cst, age and age*age */
1.145 brouard 6822: tricode(Tvar,nbcode,imx, Ndum); /**< Fills nbcode[Tvar[j]][l]; */
1.186 brouard 6823: /* Nbcode gives the value of the lth modality of jth covariate, in
6824: V2+V1*age, there are 3 covariates Tvar[2]=1 (V1).*/
6825: /* 1 to ncodemax[j] is the maximum value of this jth covariate */
1.145 brouard 6826:
6827: codtab=imatrix(1,100,1,10); /* codtab[h,k]=( (h-1) - mod(k-1,2**(k-1) )/2**(k-1) */
6828: /*printf(" codtab[1,1],codtab[100,10]=%d,%d\n", codtab[1][1],codtab[100][10]);*/
1.186 brouard 6829: /* codtab gives the value 1 or 2 of the hth combination of k covariates (1 or 2).*/
1.145 brouard 6830: h=0;
6831:
6832:
6833: /*if (cptcovn > 0) */
1.126 brouard 6834:
1.145 brouard 6835:
1.126 brouard 6836: m=pow(2,cptcoveff);
6837:
1.131 brouard 6838: for(k=1;k<=cptcoveff; k++){ /* scans any effective covariate */
1.143 brouard 6839: 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 */
6840: for(j=1; j <= ncodemax[k]; j++){ /* For each modality of this covariate ncodemax=2*/
6841: for(cpt=1; cpt <=pow(2,k-1); cpt++){ /* cpt=1 to 8/2**(3+1-1 or 3+1-3) =1 or 4 */
1.126 brouard 6842: h++;
1.141 brouard 6843: if (h>m)
1.136 brouard 6844: h=1;
1.144 brouard 6845: /**< codtab(h,k) k = codtab[h,k]=( (h-1) - mod(k-1,2**(k-1) )/2**(k-1) + 1
1.186 brouard 6846: * For k=4 covariates, h goes from 1 to 2**k
6847: * codtabm(h,k)= 1 & (h-1) >> (k-1) ;
6848: * h\k 1 2 3 4
1.143 brouard 6849: *______________________________
6850: * 1 i=1 1 i=1 1 i=1 1 i=1 1
6851: * 2 2 1 1 1
6852: * 3 i=2 1 2 1 1
6853: * 4 2 2 1 1
6854: * 5 i=3 1 i=2 1 2 1
6855: * 6 2 1 2 1
6856: * 7 i=4 1 2 2 1
6857: * 8 2 2 2 1
6858: * 9 i=5 1 i=3 1 i=2 1 1
6859: * 10 2 1 1 1
6860: * 11 i=6 1 2 1 1
6861: * 12 2 2 1 1
6862: * 13 i=7 1 i=4 1 2 1
6863: * 14 2 1 2 1
6864: * 15 i=8 1 2 2 1
6865: * 16 2 2 2 1
6866: */
1.141 brouard 6867: codtab[h][k]=j;
1.186 brouard 6868: /* codtab[12][3]=1; */
1.145 brouard 6869: /*codtab[h][Tvar[k]]=j;*/
1.130 brouard 6870: 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]]);
1.126 brouard 6871: }
6872: }
6873: }
6874: }
6875: /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]);
6876: codtab[1][2]=1;codtab[2][2]=2; */
6877: /* for(i=1; i <=m ;i++){
6878: for(k=1; k <=cptcovn; k++){
1.131 brouard 6879: printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);
1.126 brouard 6880: }
6881: printf("\n");
6882: }
6883: scanf("%d",i);*/
1.145 brouard 6884:
6885: free_ivector(Ndum,-1,NCOVMAX);
6886:
6887:
1.126 brouard 6888:
1.186 brouard 6889: /* Initialisation of ----------- gnuplot -------------*/
1.126 brouard 6890: strcpy(optionfilegnuplot,optionfilefiname);
6891: if(mle==-3)
6892: strcat(optionfilegnuplot,"-mort");
6893: strcat(optionfilegnuplot,".gp");
6894:
6895: if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {
6896: printf("Problem with file %s",optionfilegnuplot);
6897: }
6898: else{
6899: fprintf(ficgp,"\n# %s\n", version);
6900: fprintf(ficgp,"# %s\n", optionfilegnuplot);
1.141 brouard 6901: //fprintf(ficgp,"set missing 'NaNq'\n");
6902: fprintf(ficgp,"set datafile missing 'NaNq'\n");
1.126 brouard 6903: }
6904: /* fclose(ficgp);*/
1.186 brouard 6905:
6906:
6907: /* Initialisation of --------- index.htm --------*/
1.126 brouard 6908:
6909: strcpy(optionfilehtm,optionfilefiname); /* Main html file */
6910: if(mle==-3)
6911: strcat(optionfilehtm,"-mort");
6912: strcat(optionfilehtm,".htm");
6913: if((fichtm=fopen(optionfilehtm,"w"))==NULL) {
1.131 brouard 6914: printf("Problem with %s \n",optionfilehtm);
6915: exit(0);
1.126 brouard 6916: }
6917:
6918: strcpy(optionfilehtmcov,optionfilefiname); /* Only for matrix of covariance */
6919: strcat(optionfilehtmcov,"-cov.htm");
6920: if((fichtmcov=fopen(optionfilehtmcov,"w"))==NULL) {
6921: printf("Problem with %s \n",optionfilehtmcov), exit(0);
6922: }
6923: else{
6924: fprintf(fichtmcov,"<html><head>\n<title>IMaCh Cov %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
6925: <hr size=\"2\" color=\"#EC5E5E\"> \n\
6926: Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n",\
6927: optionfilehtmcov,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);
6928: }
6929:
6930: fprintf(fichtm,"<html><head>\n<title>IMaCh %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
6931: <hr size=\"2\" color=\"#EC5E5E\"> \n\
6932: Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n\
6933: \n\
6934: <hr size=\"2\" color=\"#EC5E5E\">\
6935: <ul><li><h4>Parameter files</h4>\n\
6936: - Parameter file: <a href=\"%s.%s\">%s.%s</a><br>\n\
6937: - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n\
6938: - Log file of the run: <a href=\"%s\">%s</a><br>\n\
6939: - Gnuplot file name: <a href=\"%s\">%s</a><br>\n\
6940: - Date and time at start: %s</ul>\n",\
6941: optionfilehtm,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model,\
6942: optionfilefiname,optionfilext,optionfilefiname,optionfilext,\
6943: fileres,fileres,\
6944: filelog,filelog,optionfilegnuplot,optionfilegnuplot,strstart);
6945: fflush(fichtm);
6946:
6947: strcpy(pathr,path);
6948: strcat(pathr,optionfilefiname);
1.184 brouard 6949: #ifdef WIN32
6950: _chdir(optionfilefiname); /* Move to directory named optionfile */
6951: #else
1.126 brouard 6952: chdir(optionfilefiname); /* Move to directory named optionfile */
1.184 brouard 6953: #endif
6954:
1.126 brouard 6955:
6956: /* Calculates basic frequencies. Computes observed prevalence at single age
6957: and prints on file fileres'p'. */
6958: freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint,strstart);
6959:
6960: fprintf(fichtm,"\n");
6961: fprintf(fichtm,"<br>Total number of observations=%d <br>\n\
6962: Youngest age at first (selected) pass %.2f, oldest age %.2f<br>\n\
6963: Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n",\
6964: imx,agemin,agemax,jmin,jmax,jmean);
6965: pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
6966: oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
6967: newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
6968: savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
6969: oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */
6970:
6971:
6972: /* For Powell, parameters are in a vector p[] starting at p[1]
6973: so we point p on param[1][1] so that p[1] maps on param[1][1][1] */
6974: p=param[1][1]; /* *(*(*(param +1)+1)+0) */
6975:
6976: globpr=0; /* To get the number ipmx of contributions and the sum of weights*/
1.186 brouard 6977: /* For mortality only */
1.126 brouard 6978: if (mle==-3){
1.136 brouard 6979: ximort=matrix(1,NDIM,1,NDIM);
1.186 brouard 6980: /* ximort=gsl_matrix_alloc(1,NDIM,1,NDIM); */
1.126 brouard 6981: cens=ivector(1,n);
6982: ageexmed=vector(1,n);
6983: agecens=vector(1,n);
6984: dcwave=ivector(1,n);
6985:
6986: for (i=1; i<=imx; i++){
6987: dcwave[i]=-1;
6988: for (m=firstpass; m<=lastpass; m++)
6989: if (s[m][i]>nlstate) {
6990: dcwave[i]=m;
6991: /* printf("i=%d j=%d s=%d dcwave=%d\n",i,j, s[j][i],dcwave[i]);*/
6992: break;
6993: }
6994: }
6995:
6996: for (i=1; i<=imx; i++) {
6997: if (wav[i]>0){
6998: ageexmed[i]=agev[mw[1][i]][i];
6999: j=wav[i];
7000: agecens[i]=1.;
7001:
7002: if (ageexmed[i]> 1 && wav[i] > 0){
7003: agecens[i]=agev[mw[j][i]][i];
7004: cens[i]= 1;
7005: }else if (ageexmed[i]< 1)
7006: cens[i]= -1;
7007: if (agedc[i]< AGESUP && agedc[i]>1 && dcwave[i]>firstpass && dcwave[i]<=lastpass)
7008: cens[i]=0 ;
7009: }
7010: else cens[i]=-1;
7011: }
7012:
7013: for (i=1;i<=NDIM;i++) {
7014: for (j=1;j<=NDIM;j++)
7015: ximort[i][j]=(i == j ? 1.0 : 0.0);
7016: }
7017:
1.145 brouard 7018: /*p[1]=0.0268; p[NDIM]=0.083;*/
1.126 brouard 7019: /*printf("%lf %lf", p[1], p[2]);*/
7020:
7021:
1.136 brouard 7022: #ifdef GSL
7023: printf("GSL optimization\n"); fprintf(ficlog,"Powell\n");
1.162 brouard 7024: #else
1.126 brouard 7025: printf("Powell\n"); fprintf(ficlog,"Powell\n");
1.136 brouard 7026: #endif
1.126 brouard 7027: strcpy(filerespow,"pow-mort");
7028: strcat(filerespow,fileres);
7029: if((ficrespow=fopen(filerespow,"w"))==NULL) {
7030: printf("Problem with resultfile: %s\n", filerespow);
7031: fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
7032: }
1.136 brouard 7033: #ifdef GSL
7034: fprintf(ficrespow,"# GSL optimization\n# iter -2*LL");
1.162 brouard 7035: #else
1.126 brouard 7036: fprintf(ficrespow,"# Powell\n# iter -2*LL");
1.136 brouard 7037: #endif
1.126 brouard 7038: /* for (i=1;i<=nlstate;i++)
7039: for(j=1;j<=nlstate+ndeath;j++)
7040: if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
7041: */
7042: fprintf(ficrespow,"\n");
1.136 brouard 7043: #ifdef GSL
7044: /* gsl starts here */
7045: T = gsl_multimin_fminimizer_nmsimplex;
7046: gsl_multimin_fminimizer *sfm = NULL;
7047: gsl_vector *ss, *x;
7048: gsl_multimin_function minex_func;
7049:
7050: /* Initial vertex size vector */
7051: ss = gsl_vector_alloc (NDIM);
7052:
7053: if (ss == NULL){
7054: GSL_ERROR_VAL ("failed to allocate space for ss", GSL_ENOMEM, 0);
7055: }
7056: /* Set all step sizes to 1 */
7057: gsl_vector_set_all (ss, 0.001);
7058:
7059: /* Starting point */
1.126 brouard 7060:
1.136 brouard 7061: x = gsl_vector_alloc (NDIM);
7062:
7063: if (x == NULL){
7064: gsl_vector_free(ss);
7065: GSL_ERROR_VAL ("failed to allocate space for x", GSL_ENOMEM, 0);
7066: }
7067:
7068: /* Initialize method and iterate */
7069: /* p[1]=0.0268; p[NDIM]=0.083; */
1.186 brouard 7070: /* gsl_vector_set(x, 0, 0.0268); */
7071: /* gsl_vector_set(x, 1, 0.083); */
1.136 brouard 7072: gsl_vector_set(x, 0, p[1]);
7073: gsl_vector_set(x, 1, p[2]);
7074:
7075: minex_func.f = &gompertz_f;
7076: minex_func.n = NDIM;
7077: minex_func.params = (void *)&p; /* ??? */
7078:
7079: sfm = gsl_multimin_fminimizer_alloc (T, NDIM);
7080: gsl_multimin_fminimizer_set (sfm, &minex_func, x, ss);
7081:
7082: printf("Iterations beginning .....\n\n");
7083: printf("Iter. # Intercept Slope -Log Likelihood Simplex size\n");
7084:
7085: iteri=0;
7086: while (rval == GSL_CONTINUE){
7087: iteri++;
7088: status = gsl_multimin_fminimizer_iterate(sfm);
7089:
7090: if (status) printf("error: %s\n", gsl_strerror (status));
7091: fflush(0);
7092:
7093: if (status)
7094: break;
7095:
7096: rval = gsl_multimin_test_size (gsl_multimin_fminimizer_size (sfm), 1e-6);
7097: ssval = gsl_multimin_fminimizer_size (sfm);
7098:
7099: if (rval == GSL_SUCCESS)
7100: printf ("converged to a local maximum at\n");
7101:
7102: printf("%5d ", iteri);
7103: for (it = 0; it < NDIM; it++){
7104: printf ("%10.5f ", gsl_vector_get (sfm->x, it));
7105: }
7106: printf("f() = %-10.5f ssize = %.7f\n", sfm->fval, ssval);
7107: }
7108:
7109: printf("\n\n Please note: Program should be run many times with varying starting points to detemine global maximum\n\n");
7110:
7111: gsl_vector_free(x); /* initial values */
7112: gsl_vector_free(ss); /* inital step size */
7113: for (it=0; it<NDIM; it++){
7114: p[it+1]=gsl_vector_get(sfm->x,it);
7115: fprintf(ficrespow," %.12lf", p[it]);
7116: }
7117: gsl_multimin_fminimizer_free (sfm); /* p *(sfm.x.data) et p *(sfm.x.data+1) */
7118: #endif
7119: #ifdef POWELL
7120: powell(p,ximort,NDIM,ftol,&iter,&fret,gompertz);
7121: #endif
1.126 brouard 7122: fclose(ficrespow);
7123:
7124: hesscov(matcov, p, NDIM, delti, 1e-4, gompertz);
7125:
7126: for(i=1; i <=NDIM; i++)
7127: for(j=i+1;j<=NDIM;j++)
7128: matcov[i][j]=matcov[j][i];
7129:
7130: printf("\nCovariance matrix\n ");
7131: for(i=1; i <=NDIM; i++) {
7132: for(j=1;j<=NDIM;j++){
7133: printf("%f ",matcov[i][j]);
7134: }
7135: printf("\n ");
7136: }
7137:
7138: printf("iter=%d MLE=%f Eq=%lf*exp(%lf*(age-%d))\n",iter,-gompertz(p),p[1],p[2],agegomp);
1.193 brouard 7139: for (i=1;i<=NDIM;i++) {
1.126 brouard 7140: printf("%f [%f ; %f]\n",p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
1.193 brouard 7141: fprintf(ficlog,"%f [%f ; %f]\n",p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
7142: }
1.126 brouard 7143: lsurv=vector(1,AGESUP);
7144: lpop=vector(1,AGESUP);
7145: tpop=vector(1,AGESUP);
7146: lsurv[agegomp]=100000;
7147:
7148: for (k=agegomp;k<=AGESUP;k++) {
7149: agemortsup=k;
7150: if (p[1]*exp(p[2]*(k-agegomp))>1) break;
7151: }
7152:
7153: for (k=agegomp;k<agemortsup;k++)
7154: lsurv[k+1]=lsurv[k]-lsurv[k]*(p[1]*exp(p[2]*(k-agegomp)));
7155:
7156: for (k=agegomp;k<agemortsup;k++){
7157: lpop[k]=(lsurv[k]+lsurv[k+1])/2.;
7158: sumlpop=sumlpop+lpop[k];
7159: }
7160:
7161: tpop[agegomp]=sumlpop;
7162: for (k=agegomp;k<(agemortsup-3);k++){
7163: /* tpop[k+1]=2;*/
7164: tpop[k+1]=tpop[k]-lpop[k];
7165: }
7166:
7167:
7168: printf("\nAge lx qx dx Lx Tx e(x)\n");
7169: for (k=agegomp;k<(agemortsup-2);k++)
7170: 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]);
7171:
7172:
7173: replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
1.194 brouard 7174: if(ageminpar == AGEOVERFLOW ||agemaxpar == AGEOVERFLOW){
7175: printf("Warning! Error in gnuplot file with ageminpar %f or agemaxpar %f overflow\n\
7176: This is probably because your parameter file doesn't \n contain the exact number of lines (or columns) corresponding to your model line.\n\
7177: Please run with mle=-1 to get a correct covariance matrix.\n",ageminpar,agemaxpar);
7178: fprintf(ficlog,"Warning! Error in gnuplot file with ageminpar %f or agemaxpar %f overflow\n\
7179: This is probably because your parameter file doesn't \n contain the exact number of lines (or columns) corresponding to your model line.\n\
7180: Please run with mle=-1 to get a correct covariance matrix.\n",ageminpar,agemaxpar);
7181: }else
7182: printinggnuplotmort(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
1.126 brouard 7183: printinghtmlmort(fileres,title,datafile, firstpass, lastpass, \
7184: stepm, weightopt,\
7185: model,imx,p,matcov,agemortsup);
7186:
7187: free_vector(lsurv,1,AGESUP);
7188: free_vector(lpop,1,AGESUP);
7189: free_vector(tpop,1,AGESUP);
1.136 brouard 7190: #ifdef GSL
7191: free_ivector(cens,1,n);
7192: free_vector(agecens,1,n);
7193: free_ivector(dcwave,1,n);
7194: free_matrix(ximort,1,NDIM,1,NDIM);
7195: #endif
1.186 brouard 7196: } /* Endof if mle==-3 mortality only */
7197: /* Standard maximisation */
1.126 brouard 7198: else{ /* For mle >=1 */
1.132 brouard 7199: globpr=0;/* debug */
1.186 brouard 7200: /* Computes likelihood for initial parameters */
1.132 brouard 7201: likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
1.126 brouard 7202: printf("First Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
7203: for (k=1; k<=npar;k++)
7204: printf(" %d %8.5f",k,p[k]);
7205: printf("\n");
1.186 brouard 7206: globpr=1; /* again, to print the contributions */
1.126 brouard 7207: likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
7208: printf("Second Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
7209: for (k=1; k<=npar;k++)
7210: printf(" %d %8.5f",k,p[k]);
7211: printf("\n");
1.186 brouard 7212: if(mle>=1){ /* Could be 1 or 2, Real Maximisation */
1.126 brouard 7213: mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);
7214: }
7215:
7216: /*--------- results files --------------*/
1.192 brouard 7217: 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 7218:
7219:
7220: fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
7221: printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
7222: fprintf(ficlog,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
7223: for(i=1,jk=1; i <=nlstate; i++){
7224: for(k=1; k <=(nlstate+ndeath); k++){
7225: if (k != i) {
7226: printf("%d%d ",i,k);
7227: fprintf(ficlog,"%d%d ",i,k);
7228: fprintf(ficres,"%1d%1d ",i,k);
7229: for(j=1; j <=ncovmodel; j++){
1.190 brouard 7230: printf("%12.7f ",p[jk]);
7231: fprintf(ficlog,"%12.7f ",p[jk]);
7232: fprintf(ficres,"%12.7f ",p[jk]);
1.126 brouard 7233: jk++;
7234: }
7235: printf("\n");
7236: fprintf(ficlog,"\n");
7237: fprintf(ficres,"\n");
7238: }
7239: }
7240: }
7241: if(mle!=0){
7242: /* Computing hessian and covariance matrix */
7243: ftolhess=ftol; /* Usually correct */
7244: hesscov(matcov, p, npar, delti, ftolhess, func);
7245: }
1.193 brouard 7246: printf("Parameters and 95%% confidence intervals\n");
7247: fprintf(ficlog, "Parameters, T and confidence intervals\n");
7248: for(i=1,jk=1; i <=nlstate; i++){
7249: for(k=1; k <=(nlstate+ndeath); k++){
7250: if (k != i) {
7251: printf("%d%d ",i,k);
7252: fprintf(ficlog,"%d%d ",i,k);
7253: for(j=1; j <=ncovmodel; j++){
7254: printf("%12.7f T=%8.3f CI=[%12.7f ; %12.7f] ",p[jk], p[jk]/sqrt(matcov[jk][jk]), p[jk]-2*sqrt(matcov[jk][jk]),p[jk]+2*sqrt(matcov[jk][jk]));
7255: fprintf(ficlog,"%12.7f T=%8.3f CI=[%12.7f ; %12.7f] ",p[jk], p[jk]/sqrt(matcov[jk][jk]), p[jk]-2*sqrt(matcov[jk][jk]),p[jk]+2*sqrt(matcov[jk][jk]));
7256: jk++;
7257: }
7258: printf("\n");
7259: fprintf(ficlog,"\n");
7260: }
7261: }
7262: }
7263:
1.126 brouard 7264: fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");
7265: printf("# Scales (for hessian or gradient estimation)\n");
7266: fprintf(ficlog,"# Scales (for hessian or gradient estimation)\n");
7267: for(i=1,jk=1; i <=nlstate; i++){
7268: for(j=1; j <=nlstate+ndeath; j++){
7269: if (j!=i) {
7270: fprintf(ficres,"%1d%1d",i,j);
7271: printf("%1d%1d",i,j);
7272: fprintf(ficlog,"%1d%1d",i,j);
7273: for(k=1; k<=ncovmodel;k++){
7274: printf(" %.5e",delti[jk]);
7275: fprintf(ficlog," %.5e",delti[jk]);
7276: fprintf(ficres," %.5e",delti[jk]);
7277: jk++;
7278: }
7279: printf("\n");
7280: fprintf(ficlog,"\n");
7281: fprintf(ficres,"\n");
7282: }
7283: }
7284: }
7285:
7286: 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");
7287: if(mle>=1)
7288: 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");
7289: 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");
7290: /* # 121 Var(a12)\n\ */
7291: /* # 122 Cov(b12,a12) Var(b12)\n\ */
7292: /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
7293: /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
7294: /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
7295: /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
7296: /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
7297: /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
7298:
7299:
7300: /* Just to have a covariance matrix which will be more understandable
7301: even is we still don't want to manage dictionary of variables
7302: */
7303: for(itimes=1;itimes<=2;itimes++){
7304: jj=0;
7305: for(i=1; i <=nlstate; i++){
7306: for(j=1; j <=nlstate+ndeath; j++){
7307: if(j==i) continue;
7308: for(k=1; k<=ncovmodel;k++){
7309: jj++;
7310: ca[0]= k+'a'-1;ca[1]='\0';
7311: if(itimes==1){
7312: if(mle>=1)
7313: printf("#%1d%1d%d",i,j,k);
7314: fprintf(ficlog,"#%1d%1d%d",i,j,k);
7315: fprintf(ficres,"#%1d%1d%d",i,j,k);
7316: }else{
7317: if(mle>=1)
7318: printf("%1d%1d%d",i,j,k);
7319: fprintf(ficlog,"%1d%1d%d",i,j,k);
7320: fprintf(ficres,"%1d%1d%d",i,j,k);
7321: }
7322: ll=0;
7323: for(li=1;li <=nlstate; li++){
7324: for(lj=1;lj <=nlstate+ndeath; lj++){
7325: if(lj==li) continue;
7326: for(lk=1;lk<=ncovmodel;lk++){
7327: ll++;
7328: if(ll<=jj){
7329: cb[0]= lk +'a'-1;cb[1]='\0';
7330: if(ll<jj){
7331: if(itimes==1){
7332: if(mle>=1)
7333: printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
7334: fprintf(ficlog," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
7335: fprintf(ficres," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
7336: }else{
7337: if(mle>=1)
7338: printf(" %.5e",matcov[jj][ll]);
7339: fprintf(ficlog," %.5e",matcov[jj][ll]);
7340: fprintf(ficres," %.5e",matcov[jj][ll]);
7341: }
7342: }else{
7343: if(itimes==1){
7344: if(mle>=1)
7345: printf(" Var(%s%1d%1d)",ca,i,j);
7346: fprintf(ficlog," Var(%s%1d%1d)",ca,i,j);
7347: fprintf(ficres," Var(%s%1d%1d)",ca,i,j);
7348: }else{
7349: if(mle>=1)
7350: printf(" %.5e",matcov[jj][ll]);
7351: fprintf(ficlog," %.5e",matcov[jj][ll]);
7352: fprintf(ficres," %.5e",matcov[jj][ll]);
7353: }
7354: }
7355: }
7356: } /* end lk */
7357: } /* end lj */
7358: } /* end li */
7359: if(mle>=1)
7360: printf("\n");
7361: fprintf(ficlog,"\n");
7362: fprintf(ficres,"\n");
7363: numlinepar++;
7364: } /* end k*/
7365: } /*end j */
7366: } /* end i */
7367: } /* end itimes */
7368:
7369: fflush(ficlog);
7370: fflush(ficres);
7371:
7372: while((c=getc(ficpar))=='#' && c!= EOF){
7373: ungetc(c,ficpar);
7374: fgets(line, MAXLINE, ficpar);
1.141 brouard 7375: fputs(line,stdout);
1.126 brouard 7376: fputs(line,ficparo);
7377: }
7378: ungetc(c,ficpar);
7379:
7380: estepm=0;
7381: fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm);
7382: if (estepm==0 || estepm < stepm) estepm=stepm;
7383: if (fage <= 2) {
7384: bage = ageminpar;
7385: fage = agemaxpar;
7386: }
7387:
7388: fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");
7389: fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
7390: fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
1.186 brouard 7391:
7392: /* Other stuffs, more or less useful */
1.126 brouard 7393: while((c=getc(ficpar))=='#' && c!= EOF){
7394: ungetc(c,ficpar);
7395: fgets(line, MAXLINE, ficpar);
1.141 brouard 7396: fputs(line,stdout);
1.126 brouard 7397: fputs(line,ficparo);
7398: }
7399: ungetc(c,ficpar);
7400:
7401: 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);
7402: 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);
7403: 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);
7404: printf("begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
7405: 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);
7406:
7407: while((c=getc(ficpar))=='#' && c!= EOF){
7408: ungetc(c,ficpar);
7409: fgets(line, MAXLINE, ficpar);
1.141 brouard 7410: fputs(line,stdout);
1.126 brouard 7411: fputs(line,ficparo);
7412: }
7413: ungetc(c,ficpar);
7414:
7415:
7416: dateprev1=anprev1+(mprev1-1)/12.+(jprev1-1)/365.;
7417: dateprev2=anprev2+(mprev2-1)/12.+(jprev2-1)/365.;
7418:
7419: fscanf(ficpar,"pop_based=%d\n",&popbased);
1.193 brouard 7420: fprintf(ficlog,"pop_based=%d\n",popbased);
1.126 brouard 7421: fprintf(ficparo,"pop_based=%d\n",popbased);
7422: fprintf(ficres,"pop_based=%d\n",popbased);
7423:
7424: while((c=getc(ficpar))=='#' && c!= EOF){
7425: ungetc(c,ficpar);
7426: fgets(line, MAXLINE, ficpar);
1.141 brouard 7427: fputs(line,stdout);
1.126 brouard 7428: fputs(line,ficparo);
7429: }
7430: ungetc(c,ficpar);
7431:
7432: 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);
7433: 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);
7434: 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);
7435: 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);
7436: 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);
7437: /* day and month of proj2 are not used but only year anproj2.*/
7438:
7439:
7440:
1.145 brouard 7441: /* freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint); */
7442: /* ,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2); */
1.126 brouard 7443:
7444: replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
1.194 brouard 7445: if(ageminpar == AGEOVERFLOW ||agemaxpar == -AGEOVERFLOW){
7446: printf("Warning! Error in gnuplot file with ageminpar %f or agemaxpar %f overflow\n\
7447: This is probably because your parameter file doesn't \n contain the exact number of lines (or columns) corresponding to your model line.\n\
7448: Please run with mle=-1 to get a correct covariance matrix.\n",ageminpar,agemaxpar);
7449: fprintf(ficlog,"Warning! Error in gnuplot file with ageminpar %f or agemaxpar %f overflow\n\
7450: This is probably because your parameter file doesn't \n contain the exact number of lines (or columns) corresponding to your model line.\n\
7451: Please run with mle=-1 to get a correct covariance matrix.\n",ageminpar,agemaxpar);
7452: }else
7453: printinggnuplot(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
1.126 brouard 7454:
7455: printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,\
7456: model,imx,jmin,jmax,jmean,rfileres,popforecast,estepm,\
7457: jprev1,mprev1,anprev1,jprev2,mprev2,anprev2);
7458:
7459: /*------------ free_vector -------------*/
7460: /* chdir(path); */
7461:
7462: free_ivector(wav,1,imx);
7463: free_imatrix(dh,1,lastpass-firstpass+1,1,imx);
7464: free_imatrix(bh,1,lastpass-firstpass+1,1,imx);
7465: free_imatrix(mw,1,lastpass-firstpass+1,1,imx);
7466: free_lvector(num,1,n);
7467: free_vector(agedc,1,n);
7468: /*free_matrix(covar,0,NCOVMAX,1,n);*/
7469: /*free_matrix(covar,1,NCOVMAX,1,n);*/
7470: fclose(ficparo);
7471: fclose(ficres);
7472:
7473:
1.186 brouard 7474: /* Other results (useful)*/
7475:
7476:
1.126 brouard 7477: /*--------------- Prevalence limit (period or stable prevalence) --------------*/
1.180 brouard 7478: /*#include "prevlim.h"*/ /* Use ficrespl, ficlog */
7479: prlim=matrix(1,nlstate,1,nlstate);
7480: prevalence_limit(p, prlim, ageminpar, agemaxpar);
1.126 brouard 7481: fclose(ficrespl);
7482:
1.145 brouard 7483: #ifdef FREEEXIT2
7484: #include "freeexit2.h"
7485: #endif
7486:
1.126 brouard 7487: /*------------- h Pij x at various ages ------------*/
1.180 brouard 7488: /*#include "hpijx.h"*/
7489: hPijx(p, bage, fage);
1.145 brouard 7490: fclose(ficrespij);
1.126 brouard 7491:
1.145 brouard 7492: /*-------------- Variance of one-step probabilities---*/
7493: k=1;
1.126 brouard 7494: varprob(optionfilefiname, matcov, p, delti, nlstate, bage, fage,k,Tvar,nbcode, ncodemax,strstart);
7495:
7496:
7497: probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
7498: for(i=1;i<=AGESUP;i++)
7499: for(j=1;j<=NCOVMAX;j++)
7500: for(k=1;k<=NCOVMAX;k++)
7501: probs[i][j][k]=0.;
7502:
7503: /*---------- Forecasting ------------------*/
7504: /*if((stepm == 1) && (strcmp(model,".")==0)){*/
7505: if(prevfcast==1){
7506: /* if(stepm ==1){*/
7507: prevforecast(fileres, anproj1, mproj1, jproj1, agemin, agemax, dateprev1, dateprev2, mobilavproj, bage, fage, firstpass, lastpass, anproj2, p, cptcoveff);
7508: /* (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);*/
7509: /* } */
7510: /* else{ */
7511: /* erreur=108; */
7512: /* 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); */
7513: /* 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); */
7514: /* } */
7515: }
1.186 brouard 7516:
7517: /* ------ Other prevalence ratios------------ */
1.126 brouard 7518:
1.127 brouard 7519: /* Computes prevalence between agemin (i.e minimal age computed) and no more ageminpar */
7520:
7521: prevalence(probs, agemin, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
7522: /* 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",\
7523: ageminpar, agemax, s[lastpass][imx], agev[lastpass][imx], nlstate, imx, mint[lastpass][imx],anint[lastpass][imx], dateprev1, dateprev2, firstpass, lastpass);
7524: */
1.126 brouard 7525:
1.127 brouard 7526: if (mobilav!=0) {
7527: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
7528: if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
7529: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
7530: printf(" Error in movingaverage mobilav=%d\n",mobilav);
7531: }
1.126 brouard 7532: }
7533:
7534:
1.127 brouard 7535: /*---------- Health expectancies, no variances ------------*/
7536:
1.126 brouard 7537: strcpy(filerese,"e");
7538: strcat(filerese,fileres);
7539: if((ficreseij=fopen(filerese,"w"))==NULL) {
7540: printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
7541: fprintf(ficlog,"Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
7542: }
7543: printf("Computing Health Expectancies: result on file '%s' \n", filerese);
7544: fprintf(ficlog,"Computing Health Expectancies: result on file '%s' \n", filerese);
1.145 brouard 7545: /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){
7546: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/
7547:
7548: for (k=1; k <= (int) pow(2,cptcoveff); k++){
1.127 brouard 7549: fprintf(ficreseij,"\n#****** ");
7550: for(j=1;j<=cptcoveff;j++) {
7551: fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
7552: }
7553: fprintf(ficreseij,"******\n");
7554:
7555: eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
7556: oldm=oldms;savm=savms;
7557: evsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, strstart);
7558:
7559: free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
1.145 brouard 7560: /*}*/
1.127 brouard 7561: }
7562: fclose(ficreseij);
7563:
7564:
7565: /*---------- Health expectancies and variances ------------*/
7566:
7567:
7568: strcpy(filerest,"t");
7569: strcat(filerest,fileres);
7570: if((ficrest=fopen(filerest,"w"))==NULL) {
7571: printf("Problem with total LE resultfile: %s\n", filerest);goto end;
7572: fprintf(ficlog,"Problem with total LE resultfile: %s\n", filerest);goto end;
7573: }
7574: printf("Computing Total Life expectancies with their standard errors: file '%s' \n", filerest);
7575: fprintf(ficlog,"Computing Total Life expectancies with their standard errors: file '%s' \n", filerest);
7576:
1.126 brouard 7577:
7578: strcpy(fileresstde,"stde");
7579: strcat(fileresstde,fileres);
7580: if((ficresstdeij=fopen(fileresstde,"w"))==NULL) {
7581: printf("Problem with Health Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
7582: fprintf(ficlog,"Problem with Health Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
7583: }
7584: printf("Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde);
7585: fprintf(ficlog,"Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde);
7586:
7587: strcpy(filerescve,"cve");
7588: strcat(filerescve,fileres);
7589: if((ficrescveij=fopen(filerescve,"w"))==NULL) {
7590: printf("Problem with Covar. Health Exp. resultfile: %s\n", filerescve); exit(0);
7591: fprintf(ficlog,"Problem with Covar. Health Exp. resultfile: %s\n", filerescve); exit(0);
7592: }
7593: printf("Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve);
7594: fprintf(ficlog,"Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve);
7595:
7596: strcpy(fileresv,"v");
7597: strcat(fileresv,fileres);
7598: if((ficresvij=fopen(fileresv,"w"))==NULL) {
7599: printf("Problem with variance resultfile: %s\n", fileresv);exit(0);
7600: fprintf(ficlog,"Problem with variance resultfile: %s\n", fileresv);exit(0);
7601: }
7602: printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
7603: fprintf(ficlog,"Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
7604:
1.145 brouard 7605: /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){
7606: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/
7607:
7608: for (k=1; k <= (int) pow(2,cptcoveff); k++){
7609: fprintf(ficrest,"\n#****** ");
1.126 brouard 7610: for(j=1;j<=cptcoveff;j++)
7611: fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
7612: fprintf(ficrest,"******\n");
7613:
7614: fprintf(ficresstdeij,"\n#****** ");
7615: fprintf(ficrescveij,"\n#****** ");
7616: for(j=1;j<=cptcoveff;j++) {
7617: fprintf(ficresstdeij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
7618: fprintf(ficrescveij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
7619: }
7620: fprintf(ficresstdeij,"******\n");
7621: fprintf(ficrescveij,"******\n");
7622:
7623: fprintf(ficresvij,"\n#****** ");
7624: for(j=1;j<=cptcoveff;j++)
7625: fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
7626: fprintf(ficresvij,"******\n");
7627:
7628: eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
7629: oldm=oldms;savm=savms;
1.127 brouard 7630: cvevsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov, strstart);
1.145 brouard 7631: /*
7632: */
7633: /* goto endfree; */
1.126 brouard 7634:
7635: vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
7636: pstamp(ficrest);
1.145 brouard 7637:
7638:
1.128 brouard 7639: for(vpopbased=0; vpopbased <= popbased; vpopbased++){ /* Done for vpopbased=0 and vpopbased=1 if popbased==1*/
1.145 brouard 7640: oldm=oldms;savm=savms; /* Segmentation fault */
1.161 brouard 7641: cptcod= 0; /* To be deleted */
7642: varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,vpopbased,mobilav, strstart); /* cptcod not initialized Intel */
1.145 brouard 7643: 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 ");
1.128 brouard 7644: if(vpopbased==1)
7645: 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);
7646: else
7647: fprintf(ficrest,"the age specific period (stable) prevalences in each health state \n");
7648: fprintf(ficrest,"# Age e.. (std) ");
7649: for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);
7650: fprintf(ficrest,"\n");
1.126 brouard 7651:
1.128 brouard 7652: epj=vector(1,nlstate+1);
7653: for(age=bage; age <=fage ;age++){
7654: prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
7655: if (vpopbased==1) {
7656: if(mobilav ==0){
7657: for(i=1; i<=nlstate;i++)
7658: prlim[i][i]=probs[(int)age][i][k];
7659: }else{ /* mobilav */
7660: for(i=1; i<=nlstate;i++)
7661: prlim[i][i]=mobaverage[(int)age][i][k];
7662: }
1.126 brouard 7663: }
7664:
1.128 brouard 7665: fprintf(ficrest," %4.0f",age);
7666: for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){
7667: for(i=1, epj[j]=0.;i <=nlstate;i++) {
7668: epj[j] += prlim[i][i]*eij[i][j][(int)age];
7669: /* printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/
7670: }
7671: epj[nlstate+1] +=epj[j];
1.126 brouard 7672: }
7673:
1.128 brouard 7674: for(i=1, vepp=0.;i <=nlstate;i++)
7675: for(j=1;j <=nlstate;j++)
7676: vepp += vareij[i][j][(int)age];
7677: fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));
7678: for(j=1;j <=nlstate;j++){
7679: fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));
7680: }
7681: fprintf(ficrest,"\n");
1.126 brouard 7682: }
7683: }
7684: free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
7685: free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);
7686: free_vector(epj,1,nlstate+1);
1.145 brouard 7687: /*}*/
1.126 brouard 7688: }
7689: free_vector(weight,1,n);
1.145 brouard 7690: free_imatrix(Tvard,1,NCOVMAX,1,2);
1.126 brouard 7691: free_imatrix(s,1,maxwav+1,1,n);
7692: free_matrix(anint,1,maxwav,1,n);
7693: free_matrix(mint,1,maxwav,1,n);
7694: free_ivector(cod,1,n);
7695: free_ivector(tab,1,NCOVMAX);
7696: fclose(ficresstdeij);
7697: fclose(ficrescveij);
7698: fclose(ficresvij);
7699: fclose(ficrest);
7700: fclose(ficpar);
7701:
7702: /*------- Variance of period (stable) prevalence------*/
7703:
7704: strcpy(fileresvpl,"vpl");
7705: strcat(fileresvpl,fileres);
7706: if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {
7707: printf("Problem with variance of period (stable) prevalence resultfile: %s\n", fileresvpl);
7708: exit(0);
7709: }
7710: printf("Computing Variance-covariance of period (stable) prevalence: file '%s' \n", fileresvpl);
7711:
1.145 brouard 7712: /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){
7713: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/
7714:
7715: for (k=1; k <= (int) pow(2,cptcoveff); k++){
7716: fprintf(ficresvpl,"\n#****** ");
1.126 brouard 7717: for(j=1;j<=cptcoveff;j++)
7718: fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
7719: fprintf(ficresvpl,"******\n");
7720:
7721: varpl=matrix(1,nlstate,(int) bage, (int) fage);
7722: oldm=oldms;savm=savms;
7723: varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k,strstart);
7724: free_matrix(varpl,1,nlstate,(int) bage, (int)fage);
1.145 brouard 7725: /*}*/
1.126 brouard 7726: }
7727:
7728: fclose(ficresvpl);
7729:
7730: /*---------- End : free ----------------*/
7731: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
7732: free_ma3x(probs,1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
7733: } /* mle==-3 arrives here for freeing */
1.164 brouard 7734: /* endfree:*/
1.141 brouard 7735: free_matrix(prlim,1,nlstate,1,nlstate); /*here or after loop ? */
1.126 brouard 7736: free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);
7737: free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);
7738: free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);
7739: free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);
7740: free_matrix(covar,0,NCOVMAX,1,n);
7741: free_matrix(matcov,1,npar,1,npar);
7742: /*free_vector(delti,1,npar);*/
7743: free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
7744: free_matrix(agev,1,maxwav,1,imx);
7745: free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
7746:
1.145 brouard 7747: free_ivector(ncodemax,1,NCOVMAX);
1.192 brouard 7748: free_ivector(ncodemaxwundef,1,NCOVMAX);
1.145 brouard 7749: free_ivector(Tvar,1,NCOVMAX);
7750: free_ivector(Tprod,1,NCOVMAX);
7751: free_ivector(Tvaraff,1,NCOVMAX);
7752: free_ivector(Tage,1,NCOVMAX);
1.126 brouard 7753:
7754: free_imatrix(nbcode,0,NCOVMAX,0,NCOVMAX);
7755: free_imatrix(codtab,1,100,1,10);
7756: fflush(fichtm);
7757: fflush(ficgp);
7758:
7759:
7760: if((nberr >0) || (nbwarn>0)){
7761: printf("End of Imach with %d errors and/or %d warnings\n",nberr,nbwarn);
7762: fprintf(ficlog,"End of Imach with %d errors and/or warnings %d\n",nberr,nbwarn);
7763: }else{
7764: printf("End of Imach\n");
7765: fprintf(ficlog,"End of Imach\n");
7766: }
7767: printf("See log file on %s\n",filelog);
7768: /* gettimeofday(&end_time, (struct timezone*)0);*/ /* after time */
1.157 brouard 7769: /*(void) gettimeofday(&end_time,&tzp);*/
7770: rend_time = time(NULL);
7771: end_time = *localtime(&rend_time);
7772: /* tml = *localtime(&end_time.tm_sec); */
7773: strcpy(strtend,asctime(&end_time));
1.126 brouard 7774: printf("Local time at start %s\nLocal time at end %s",strstart, strtend);
7775: fprintf(ficlog,"Local time at start %s\nLocal time at end %s\n",strstart, strtend);
1.157 brouard 7776: printf("Total time used %s\n", asc_diff_time(rend_time -rstart_time,tmpout));
1.126 brouard 7777:
1.157 brouard 7778: printf("Total time was %.0lf Sec.\n", difftime(rend_time,rstart_time));
7779: fprintf(ficlog,"Total time used %s\n", asc_diff_time(rend_time -rstart_time,tmpout));
7780: fprintf(ficlog,"Total time was %.0lf Sec.\n", difftime(rend_time,rstart_time));
1.126 brouard 7781: /* printf("Total time was %d uSec.\n", total_usecs);*/
7782: /* if(fileappend(fichtm,optionfilehtm)){ */
7783: fprintf(fichtm,"<br>Local time at start %s<br>Local time at end %s<br>\n</body></html>",strstart, strtend);
7784: fclose(fichtm);
7785: fprintf(fichtmcov,"<br>Local time at start %s<br>Local time at end %s<br>\n</body></html>",strstart, strtend);
7786: fclose(fichtmcov);
7787: fclose(ficgp);
7788: fclose(ficlog);
7789: /*------ End -----------*/
7790:
7791:
7792: printf("Before Current directory %s!\n",pathcd);
1.184 brouard 7793: #ifdef WIN32
7794: if (_chdir(pathcd) != 0)
7795: printf("Can't move to directory %s!\n",path);
7796: if(_getcwd(pathcd,MAXLINE) > 0)
7797: #else
1.126 brouard 7798: if(chdir(pathcd) != 0)
1.184 brouard 7799: printf("Can't move to directory %s!\n", path);
7800: if (getcwd(pathcd, MAXLINE) > 0)
7801: #endif
1.126 brouard 7802: printf("Current directory %s!\n",pathcd);
7803: /*strcat(plotcmd,CHARSEPARATOR);*/
7804: sprintf(plotcmd,"gnuplot");
1.157 brouard 7805: #ifdef _WIN32
1.126 brouard 7806: sprintf(plotcmd,"\"%sgnuplot.exe\"",pathimach);
7807: #endif
7808: if(!stat(plotcmd,&info)){
1.158 brouard 7809: printf("Error or gnuplot program not found: '%s'\n",plotcmd);fflush(stdout);
1.126 brouard 7810: if(!stat(getenv("GNUPLOTBIN"),&info)){
1.158 brouard 7811: printf("Error or gnuplot program not found: '%s' Environment GNUPLOTBIN not set.\n",plotcmd);fflush(stdout);
1.126 brouard 7812: }else
7813: strcpy(pplotcmd,plotcmd);
1.157 brouard 7814: #ifdef __unix
1.126 brouard 7815: strcpy(plotcmd,GNUPLOTPROGRAM);
7816: if(!stat(plotcmd,&info)){
1.158 brouard 7817: printf("Error gnuplot program not found: '%s'\n",plotcmd);fflush(stdout);
1.126 brouard 7818: }else
7819: strcpy(pplotcmd,plotcmd);
7820: #endif
7821: }else
7822: strcpy(pplotcmd,plotcmd);
7823:
7824: sprintf(plotcmd,"%s %s",pplotcmd, optionfilegnuplot);
1.158 brouard 7825: printf("Starting graphs with: '%s'\n",plotcmd);fflush(stdout);
1.126 brouard 7826:
7827: if((outcmd=system(plotcmd)) != 0){
1.158 brouard 7828: printf("gnuplot command might not be in your path: '%s', err=%d\n", plotcmd, outcmd);
1.154 brouard 7829: printf("\n Trying if gnuplot resides on the same directory that IMaCh\n");
1.152 brouard 7830: sprintf(plotcmd,"%sgnuplot %s", pathimach, optionfilegnuplot);
1.150 brouard 7831: if((outcmd=system(plotcmd)) != 0)
1.153 brouard 7832: printf("\n Still a problem with gnuplot command %s, err=%d\n", plotcmd, outcmd);
1.126 brouard 7833: }
1.158 brouard 7834: printf(" Successful, please wait...");
1.126 brouard 7835: while (z[0] != 'q') {
7836: /* chdir(path); */
1.154 brouard 7837: printf("\nType e to edit results with your browser, g to graph again and q for exit: ");
1.126 brouard 7838: scanf("%s",z);
7839: /* if (z[0] == 'c') system("./imach"); */
7840: if (z[0] == 'e') {
1.158 brouard 7841: #ifdef __APPLE__
1.152 brouard 7842: sprintf(pplotcmd, "open %s", optionfilehtm);
1.157 brouard 7843: #elif __linux
7844: sprintf(pplotcmd, "xdg-open %s", optionfilehtm);
1.153 brouard 7845: #else
1.152 brouard 7846: sprintf(pplotcmd, "%s", optionfilehtm);
1.153 brouard 7847: #endif
7848: printf("Starting browser with: %s",pplotcmd);fflush(stdout);
7849: system(pplotcmd);
1.126 brouard 7850: }
7851: else if (z[0] == 'g') system(plotcmd);
7852: else if (z[0] == 'q') exit(0);
7853: }
7854: end:
7855: while (z[0] != 'q') {
1.195 ! brouard 7856: printf("\nType q for exiting: "); fflush(stdout);
1.126 brouard 7857: scanf("%s",z);
7858: }
7859: }
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