1: /* $Id: imach.c,v 1.165 2014/12/16 11:20:36 brouard Exp $
2: $State: Exp $
3: $Log: imach.c,v $
4: Revision 1.165 2014/12/16 11:20:36 brouard
5: Summary: After compiling on Visual C
6:
7: * imach.c (Module): Merging 1.61 to 1.162
8:
9: Revision 1.164 2014/12/16 10:52:11 brouard
10: Summary: Merging with Visual C after suppressing some warnings for unused variables. Also fixing Saito's bug 0.98Xn
11:
12: * imach.c (Module): Merging 1.61 to 1.162
13:
14: Revision 1.163 2014/12/16 10:30:11 brouard
15: * imach.c (Module): Merging 1.61 to 1.162
16:
17: Revision 1.162 2014/09/25 11:43:39 brouard
18: Summary: temporary backup 0.99!
19:
20: Revision 1.1 2014/09/16 11:06:58 brouard
21: Summary: With some code (wrong) for nlopt
22:
23: Author:
24:
25: Revision 1.161 2014/09/15 20:41:41 brouard
26: Summary: Problem with macro SQR on Intel compiler
27:
28: Revision 1.160 2014/09/02 09:24:05 brouard
29: *** empty log message ***
30:
31: Revision 1.159 2014/09/01 10:34:10 brouard
32: Summary: WIN32
33: Author: Brouard
34:
35: Revision 1.158 2014/08/27 17:11:51 brouard
36: *** empty log message ***
37:
38: Revision 1.157 2014/08/27 16:26:55 brouard
39: Summary: Preparing windows Visual studio version
40: Author: Brouard
41:
42: In order to compile on Visual studio, time.h is now correct and time_t
43: and tm struct should be used. difftime should be used but sometimes I
44: just make the differences in raw time format (time(&now).
45: Trying to suppress #ifdef LINUX
46: Add xdg-open for __linux in order to open default browser.
47:
48: Revision 1.156 2014/08/25 20:10:10 brouard
49: *** empty log message ***
50:
51: Revision 1.155 2014/08/25 18:32:34 brouard
52: Summary: New compile, minor changes
53: Author: Brouard
54:
55: Revision 1.154 2014/06/20 17:32:08 brouard
56: Summary: Outputs now all graphs of convergence to period prevalence
57:
58: Revision 1.153 2014/06/20 16:45:46 brouard
59: Summary: If 3 live state, convergence to period prevalence on same graph
60: Author: Brouard
61:
62: Revision 1.152 2014/06/18 17:54:09 brouard
63: Summary: open browser, use gnuplot on same dir than imach if not found in the path
64:
65: Revision 1.151 2014/06/18 16:43:30 brouard
66: *** empty log message ***
67:
68: Revision 1.150 2014/06/18 16:42:35 brouard
69: Summary: If gnuplot is not in the path try on same directory than imach binary (OSX)
70: Author: brouard
71:
72: Revision 1.149 2014/06/18 15:51:14 brouard
73: Summary: Some fixes in parameter files errors
74: Author: Nicolas Brouard
75:
76: Revision 1.148 2014/06/17 17:38:48 brouard
77: Summary: Nothing new
78: Author: Brouard
79:
80: Just a new packaging for OS/X version 0.98nS
81:
82: Revision 1.147 2014/06/16 10:33:11 brouard
83: *** empty log message ***
84:
85: Revision 1.146 2014/06/16 10:20:28 brouard
86: Summary: Merge
87: Author: Brouard
88:
89: Merge, before building revised version.
90:
91: Revision 1.145 2014/06/10 21:23:15 brouard
92: Summary: Debugging with valgrind
93: Author: Nicolas Brouard
94:
95: Lot of changes in order to output the results with some covariates
96: After the Edimburgh REVES conference 2014, it seems mandatory to
97: improve the code.
98: No more memory valgrind error but a lot has to be done in order to
99: continue the work of splitting the code into subroutines.
100: Also, decodemodel has been improved. Tricode is still not
101: optimal. nbcode should be improved. Documentation has been added in
102: the source code.
103:
104: Revision 1.143 2014/01/26 09:45:38 brouard
105: Summary: Version 0.98nR (to be improved, but gives same optimization results as 0.98k. Nice, promising
106:
107: * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
108: (Module): Version 0.98nR Running ok, but output format still only works for three covariates.
109:
110: Revision 1.142 2014/01/26 03:57:36 brouard
111: Summary: gnuplot changed plot w l 1 has to be changed to plot w l lt 2
112:
113: * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
114:
115: Revision 1.141 2014/01/26 02:42:01 brouard
116: * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
117:
118: Revision 1.140 2011/09/02 10:37:54 brouard
119: Summary: times.h is ok with mingw32 now.
120:
121: Revision 1.139 2010/06/14 07:50:17 brouard
122: After the theft of my laptop, I probably lost some lines of codes which were not uploaded to the CVS tree.
123: I remember having already fixed agemin agemax which are pointers now but not cvs saved.
124:
125: Revision 1.138 2010/04/30 18:19:40 brouard
126: *** empty log message ***
127:
128: Revision 1.137 2010/04/29 18:11:38 brouard
129: (Module): Checking covariates for more complex models
130: than V1+V2. A lot of change to be done. Unstable.
131:
132: Revision 1.136 2010/04/26 20:30:53 brouard
133: (Module): merging some libgsl code. Fixing computation
134: of likelione (using inter/intrapolation if mle = 0) in order to
135: get same likelihood as if mle=1.
136: Some cleaning of code and comments added.
137:
138: Revision 1.135 2009/10/29 15:33:14 brouard
139: (Module): Now imach stops if date of birth, at least year of birth, is not given. Some cleaning of the code.
140:
141: Revision 1.134 2009/10/29 13:18:53 brouard
142: (Module): Now imach stops if date of birth, at least year of birth, is not given. Some cleaning of the code.
143:
144: Revision 1.133 2009/07/06 10:21:25 brouard
145: just nforces
146:
147: Revision 1.132 2009/07/06 08:22:05 brouard
148: Many tings
149:
150: Revision 1.131 2009/06/20 16:22:47 brouard
151: Some dimensions resccaled
152:
153: Revision 1.130 2009/05/26 06:44:34 brouard
154: (Module): Max Covariate is now set to 20 instead of 8. A
155: lot of cleaning with variables initialized to 0. Trying to make
156: V2+V3*age+V1+V4 strb=V3*age+V1+V4 working better.
157:
158: Revision 1.129 2007/08/31 13:49:27 lievre
159: Modification of the way of exiting when the covariate is not binary in order to see on the window the error message before exiting
160:
161: Revision 1.128 2006/06/30 13:02:05 brouard
162: (Module): Clarifications on computing e.j
163:
164: Revision 1.127 2006/04/28 18:11:50 brouard
165: (Module): Yes the sum of survivors was wrong since
166: imach-114 because nhstepm was no more computed in the age
167: loop. Now we define nhstepma in the age loop.
168: (Module): In order to speed up (in case of numerous covariates) we
169: compute health expectancies (without variances) in a first step
170: and then all the health expectancies with variances or standard
171: deviation (needs data from the Hessian matrices) which slows the
172: computation.
173: In the future we should be able to stop the program is only health
174: expectancies and graph are needed without standard deviations.
175:
176: Revision 1.126 2006/04/28 17:23:28 brouard
177: (Module): Yes the sum of survivors was wrong since
178: imach-114 because nhstepm was no more computed in the age
179: loop. Now we define nhstepma in the age loop.
180: Version 0.98h
181:
182: Revision 1.125 2006/04/04 15:20:31 lievre
183: Errors in calculation of health expectancies. Age was not initialized.
184: Forecasting file added.
185:
186: Revision 1.124 2006/03/22 17:13:53 lievre
187: Parameters are printed with %lf instead of %f (more numbers after the comma).
188: The log-likelihood is printed in the log file
189:
190: Revision 1.123 2006/03/20 10:52:43 brouard
191: * imach.c (Module): <title> changed, corresponds to .htm file
192: name. <head> headers where missing.
193:
194: * imach.c (Module): Weights can have a decimal point as for
195: English (a comma might work with a correct LC_NUMERIC environment,
196: otherwise the weight is truncated).
197: Modification of warning when the covariates values are not 0 or
198: 1.
199: Version 0.98g
200:
201: Revision 1.122 2006/03/20 09:45:41 brouard
202: (Module): Weights can have a decimal point as for
203: English (a comma might work with a correct LC_NUMERIC environment,
204: otherwise the weight is truncated).
205: Modification of warning when the covariates values are not 0 or
206: 1.
207: Version 0.98g
208:
209: Revision 1.121 2006/03/16 17:45:01 lievre
210: * imach.c (Module): Comments concerning covariates added
211:
212: * imach.c (Module): refinements in the computation of lli if
213: status=-2 in order to have more reliable computation if stepm is
214: not 1 month. Version 0.98f
215:
216: Revision 1.120 2006/03/16 15:10:38 lievre
217: (Module): refinements in the computation of lli if
218: status=-2 in order to have more reliable computation if stepm is
219: not 1 month. Version 0.98f
220:
221: Revision 1.119 2006/03/15 17:42:26 brouard
222: (Module): Bug if status = -2, the loglikelihood was
223: computed as likelihood omitting the logarithm. Version O.98e
224:
225: Revision 1.118 2006/03/14 18:20:07 brouard
226: (Module): varevsij Comments added explaining the second
227: table of variances if popbased=1 .
228: (Module): Covariances of eij, ekl added, graphs fixed, new html link.
229: (Module): Function pstamp added
230: (Module): Version 0.98d
231:
232: Revision 1.117 2006/03/14 17:16:22 brouard
233: (Module): varevsij Comments added explaining the second
234: table of variances if popbased=1 .
235: (Module): Covariances of eij, ekl added, graphs fixed, new html link.
236: (Module): Function pstamp added
237: (Module): Version 0.98d
238:
239: Revision 1.116 2006/03/06 10:29:27 brouard
240: (Module): Variance-covariance wrong links and
241: varian-covariance of ej. is needed (Saito).
242:
243: Revision 1.115 2006/02/27 12:17:45 brouard
244: (Module): One freematrix added in mlikeli! 0.98c
245:
246: Revision 1.114 2006/02/26 12:57:58 brouard
247: (Module): Some improvements in processing parameter
248: filename with strsep.
249:
250: Revision 1.113 2006/02/24 14:20:24 brouard
251: (Module): Memory leaks checks with valgrind and:
252: datafile was not closed, some imatrix were not freed and on matrix
253: allocation too.
254:
255: Revision 1.112 2006/01/30 09:55:26 brouard
256: (Module): Back to gnuplot.exe instead of wgnuplot.exe
257:
258: Revision 1.111 2006/01/25 20:38:18 brouard
259: (Module): Lots of cleaning and bugs added (Gompertz)
260: (Module): Comments can be added in data file. Missing date values
261: can be a simple dot '.'.
262:
263: Revision 1.110 2006/01/25 00:51:50 brouard
264: (Module): Lots of cleaning and bugs added (Gompertz)
265:
266: Revision 1.109 2006/01/24 19:37:15 brouard
267: (Module): Comments (lines starting with a #) are allowed in data.
268:
269: Revision 1.108 2006/01/19 18:05:42 lievre
270: Gnuplot problem appeared...
271: To be fixed
272:
273: Revision 1.107 2006/01/19 16:20:37 brouard
274: Test existence of gnuplot in imach path
275:
276: Revision 1.106 2006/01/19 13:24:36 brouard
277: Some cleaning and links added in html output
278:
279: Revision 1.105 2006/01/05 20:23:19 lievre
280: *** empty log message ***
281:
282: Revision 1.104 2005/09/30 16:11:43 lievre
283: (Module): sump fixed, loop imx fixed, and simplifications.
284: (Module): If the status is missing at the last wave but we know
285: that the person is alive, then we can code his/her status as -2
286: (instead of missing=-1 in earlier versions) and his/her
287: contributions to the likelihood is 1 - Prob of dying from last
288: health status (= 1-p13= p11+p12 in the easiest case of somebody in
289: the healthy state at last known wave). Version is 0.98
290:
291: Revision 1.103 2005/09/30 15:54:49 lievre
292: (Module): sump fixed, loop imx fixed, and simplifications.
293:
294: Revision 1.102 2004/09/15 17:31:30 brouard
295: Add the possibility to read data file including tab characters.
296:
297: Revision 1.101 2004/09/15 10:38:38 brouard
298: Fix on curr_time
299:
300: Revision 1.100 2004/07/12 18:29:06 brouard
301: Add version for Mac OS X. Just define UNIX in Makefile
302:
303: Revision 1.99 2004/06/05 08:57:40 brouard
304: *** empty log message ***
305:
306: Revision 1.98 2004/05/16 15:05:56 brouard
307: New version 0.97 . First attempt to estimate force of mortality
308: directly from the data i.e. without the need of knowing the health
309: state at each age, but using a Gompertz model: log u =a + b*age .
310: This is the basic analysis of mortality and should be done before any
311: other analysis, in order to test if the mortality estimated from the
312: cross-longitudinal survey is different from the mortality estimated
313: from other sources like vital statistic data.
314:
315: The same imach parameter file can be used but the option for mle should be -3.
316:
317: Agnès, who wrote this part of the code, tried to keep most of the
318: former routines in order to include the new code within the former code.
319:
320: The output is very simple: only an estimate of the intercept and of
321: the slope with 95% confident intervals.
322:
323: Current limitations:
324: A) Even if you enter covariates, i.e. with the
325: model= V1+V2 equation for example, the programm does only estimate a unique global model without covariates.
326: B) There is no computation of Life Expectancy nor Life Table.
327:
328: Revision 1.97 2004/02/20 13:25:42 lievre
329: Version 0.96d. Population forecasting command line is (temporarily)
330: suppressed.
331:
332: Revision 1.96 2003/07/15 15:38:55 brouard
333: * imach.c (Repository): Errors in subdirf, 2, 3 while printing tmpout is
334: rewritten within the same printf. Workaround: many printfs.
335:
336: Revision 1.95 2003/07/08 07:54:34 brouard
337: * imach.c (Repository):
338: (Repository): Using imachwizard code to output a more meaningful covariance
339: matrix (cov(a12,c31) instead of numbers.
340:
341: Revision 1.94 2003/06/27 13:00:02 brouard
342: Just cleaning
343:
344: Revision 1.93 2003/06/25 16:33:55 brouard
345: (Module): On windows (cygwin) function asctime_r doesn't
346: exist so I changed back to asctime which exists.
347: (Module): Version 0.96b
348:
349: Revision 1.92 2003/06/25 16:30:45 brouard
350: (Module): On windows (cygwin) function asctime_r doesn't
351: exist so I changed back to asctime which exists.
352:
353: Revision 1.91 2003/06/25 15:30:29 brouard
354: * imach.c (Repository): Duplicated warning errors corrected.
355: (Repository): Elapsed time after each iteration is now output. It
356: helps to forecast when convergence will be reached. Elapsed time
357: is stamped in powell. We created a new html file for the graphs
358: concerning matrix of covariance. It has extension -cov.htm.
359:
360: Revision 1.90 2003/06/24 12:34:15 brouard
361: (Module): Some bugs corrected for windows. Also, when
362: mle=-1 a template is output in file "or"mypar.txt with the design
363: of the covariance matrix to be input.
364:
365: Revision 1.89 2003/06/24 12:30:52 brouard
366: (Module): Some bugs corrected for windows. Also, when
367: mle=-1 a template is output in file "or"mypar.txt with the design
368: of the covariance matrix to be input.
369:
370: Revision 1.88 2003/06/23 17:54:56 brouard
371: * 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.
372:
373: Revision 1.87 2003/06/18 12:26:01 brouard
374: Version 0.96
375:
376: Revision 1.86 2003/06/17 20:04:08 brouard
377: (Module): Change position of html and gnuplot routines and added
378: routine fileappend.
379:
380: Revision 1.85 2003/06/17 13:12:43 brouard
381: * imach.c (Repository): Check when date of death was earlier that
382: current date of interview. It may happen when the death was just
383: prior to the death. In this case, dh was negative and likelihood
384: was wrong (infinity). We still send an "Error" but patch by
385: assuming that the date of death was just one stepm after the
386: interview.
387: (Repository): Because some people have very long ID (first column)
388: we changed int to long in num[] and we added a new lvector for
389: memory allocation. But we also truncated to 8 characters (left
390: truncation)
391: (Repository): No more line truncation errors.
392:
393: Revision 1.84 2003/06/13 21:44:43 brouard
394: * imach.c (Repository): Replace "freqsummary" at a correct
395: place. It differs from routine "prevalence" which may be called
396: many times. Probs is memory consuming and must be used with
397: parcimony.
398: Version 0.95a3 (should output exactly the same maximization than 0.8a2)
399:
400: Revision 1.83 2003/06/10 13:39:11 lievre
401: *** empty log message ***
402:
403: Revision 1.82 2003/06/05 15:57:20 brouard
404: Add log in imach.c and fullversion number is now printed.
405:
406: */
407: /*
408: Interpolated Markov Chain
409:
410: Short summary of the programme:
411:
412: This program computes Healthy Life Expectancies from
413: cross-longitudinal data. Cross-longitudinal data consist in: -1- a
414: first survey ("cross") where individuals from different ages are
415: interviewed on their health status or degree of disability (in the
416: case of a health survey which is our main interest) -2- at least a
417: second wave of interviews ("longitudinal") which measure each change
418: (if any) in individual health status. Health expectancies are
419: computed from the time spent in each health state according to a
420: model. More health states you consider, more time is necessary to reach the
421: Maximum Likelihood of the parameters involved in the model. The
422: simplest model is the multinomial logistic model where pij is the
423: probability to be observed in state j at the second wave
424: conditional to be observed in state i at the first wave. Therefore
425: the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where
426: 'age' is age and 'sex' is a covariate. If you want to have a more
427: complex model than "constant and age", you should modify the program
428: where the markup *Covariates have to be included here again* invites
429: you to do it. More covariates you add, slower the
430: convergence.
431:
432: The advantage of this computer programme, compared to a simple
433: multinomial logistic model, is clear when the delay between waves is not
434: identical for each individual. Also, if a individual missed an
435: intermediate interview, the information is lost, but taken into
436: account using an interpolation or extrapolation.
437:
438: hPijx is the probability to be observed in state i at age x+h
439: conditional to the observed state i at age x. The delay 'h' can be
440: split into an exact number (nh*stepm) of unobserved intermediate
441: states. This elementary transition (by month, quarter,
442: semester or year) is modelled as a multinomial logistic. The hPx
443: matrix is simply the matrix product of nh*stepm elementary matrices
444: and the contribution of each individual to the likelihood is simply
445: hPijx.
446:
447: Also this programme outputs the covariance matrix of the parameters but also
448: of the life expectancies. It also computes the period (stable) prevalence.
449:
450: Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).
451: Institut national d'études démographiques, Paris.
452: This software have been partly granted by Euro-REVES, a concerted action
453: from the European Union.
454: It is copyrighted identically to a GNU software product, ie programme and
455: software can be distributed freely for non commercial use. Latest version
456: can be accessed at http://euroreves.ined.fr/imach .
457:
458: Help to debug: LD_PRELOAD=/usr/local/lib/libnjamd.so ./imach foo.imach
459: or better on gdb : set env LD_PRELOAD=/usr/local/lib/libnjamd.so
460:
461: **********************************************************************/
462: /*
463: main
464: read parameterfile
465: read datafile
466: concatwav
467: freqsummary
468: if (mle >= 1)
469: mlikeli
470: print results files
471: if mle==1
472: computes hessian
473: read end of parameter file: agemin, agemax, bage, fage, estepm
474: begin-prev-date,...
475: open gnuplot file
476: open html file
477: period (stable) prevalence | pl_nom 1-1 2-2 etc by covariate
478: for age prevalim() | #****** V1=0 V2=1 V3=1 V4=0 ******
479: | 65 1 0 2 1 3 1 4 0 0.96326 0.03674
480: freexexit2 possible for memory heap.
481:
482: h Pij x | pij_nom ficrestpij
483: # Cov Agex agex+h hpijx with i,j= 1-1 1-2 1-3 2-1 2-2 2-3
484: 1 85 85 1.00000 0.00000 0.00000 0.00000 1.00000 0.00000
485: 1 85 86 0.68299 0.22291 0.09410 0.71093 0.00000 0.28907
486:
487: 1 65 99 0.00364 0.00322 0.99314 0.00350 0.00310 0.99340
488: 1 65 100 0.00214 0.00204 0.99581 0.00206 0.00196 0.99597
489: variance of p one-step probabilities varprob | prob_nom ficresprob #One-step probabilities and stand. devi in ()
490: Standard deviation of one-step probabilities | probcor_nom ficresprobcor #One-step probabilities and correlation matrix
491: Matrix of variance covariance of one-step probabilities | probcov_nom ficresprobcov #One-step probabilities and covariance matrix
492:
493: forecasting if prevfcast==1 prevforecast call prevalence()
494: health expectancies
495: Variance-covariance of DFLE
496: prevalence()
497: movingaverage()
498: varevsij()
499: if popbased==1 varevsij(,popbased)
500: total life expectancies
501: Variance of period (stable) prevalence
502: end
503: */
504:
505: #define POWELL /* Instead of NLOPT */
506:
507: #include <math.h>
508: #include <stdio.h>
509: #include <stdlib.h>
510: #include <string.h>
511:
512: #ifdef _WIN32
513: #include <io.h>
514: #else
515: #include <unistd.h>
516: #endif
517:
518: #include <limits.h>
519: #include <sys/types.h>
520: #include <sys/stat.h>
521: #include <errno.h>
522: /* extern int errno; */
523:
524: /* #ifdef LINUX */
525: /* #include <time.h> */
526: /* #include "timeval.h" */
527: /* #else */
528: /* #include <sys/time.h> */
529: /* #endif */
530:
531: #include <time.h>
532:
533: #ifdef GSL
534: #include <gsl/gsl_errno.h>
535: #include <gsl/gsl_multimin.h>
536: #endif
537:
538: #ifdef NLOPT
539: #include <nlopt.h>
540: typedef struct {
541: double (* function)(double [] );
542: } myfunc_data ;
543: #endif
544:
545: /* #include <libintl.h> */
546: /* #define _(String) gettext (String) */
547:
548: #define MAXLINE 1024 /* Was 256. Overflow with 312 with 2 states and 4 covariates. Should be ok */
549:
550: #define GNUPLOTPROGRAM "gnuplot"
551: /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
552: #define FILENAMELENGTH 132
553:
554: #define GLOCK_ERROR_NOPATH -1 /* empty path */
555: #define GLOCK_ERROR_GETCWD -2 /* cannot get cwd */
556:
557: #define MAXPARM 128 /**< Maximum number of parameters for the optimization */
558: #define NPARMAX 64 /**< (nlstate+ndeath-1)*nlstate*ncovmodel */
559:
560: #define NINTERVMAX 8
561: #define NLSTATEMAX 8 /**< Maximum number of live states (for func) */
562: #define NDEATHMAX 8 /**< Maximum number of dead states (for func) */
563: #define NCOVMAX 20 /**< Maximum number of covariates, including generated covariates V1*V2 */
564: #define codtabm(h,k) 1 & (h-1) >> (k-1) ;
565: #define MAXN 20000
566: #define YEARM 12. /**< Number of months per year */
567: #define AGESUP 130
568: #define AGEBASE 40
569: #define AGEGOMP 10 /**< Minimal age for Gompertz adjustment */
570: #ifdef _WIN32
571: #define DIRSEPARATOR '\\'
572: #define CHARSEPARATOR "\\"
573: #define ODIRSEPARATOR '/'
574: #else
575: #define DIRSEPARATOR '/'
576: #define CHARSEPARATOR "/"
577: #define ODIRSEPARATOR '\\'
578: #endif
579:
580: /* $Id: imach.c,v 1.165 2014/12/16 11:20:36 brouard Exp $ */
581: /* $State: Exp $ */
582:
583: char version[]="Imach version 0.99, September 2014,INED-EUROREVES-Institut de longevite-Japan Society for the Promotion of Science (Grant-in-Aid for Scientific Research 25293121)";
584: char fullversion[]="$Revision: 1.165 $ $Date: 2014/12/16 11:20:36 $";
585: char strstart[80];
586: char optionfilext[10], optionfilefiname[FILENAMELENGTH];
587: int erreur=0, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings */
588: int nvar=0, nforce=0; /* Number of variables, number of forces */
589: /* Number of covariates model=V2+V1+ V3*age+V2*V4 */
590: int cptcovn=0; /**< cptcovn number of covariates added in the model (excepting constant and age and age*product) */
591: int cptcovt=0; /**< cptcovt number of covariates added in the model (excepting constant and age) */
592: int cptcovs=0; /**< cptcovs number of simple covariates V2+V1 =2 */
593: int cptcovage=0; /**< Number of covariates with age: V3*age only =1 */
594: int cptcovprodnoage=0; /**< Number of covariate products without age */
595: int cptcoveff=0; /* Total number of covariates to vary for printing results */
596: int cptcov=0; /* Working variable */
597: int npar=NPARMAX;
598: int nlstate=2; /* Number of live states */
599: int ndeath=1; /* Number of dead states */
600: int ncovmodel=0, ncovcol=0; /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
601: int popbased=0;
602:
603: int *wav; /* Number of waves for this individuual 0 is possible */
604: int maxwav=0; /* Maxim number of waves */
605: int jmin=0, jmax=0; /* min, max spacing between 2 waves */
606: int ijmin=0, ijmax=0; /* Individuals having jmin and jmax */
607: int gipmx=0, gsw=0; /* Global variables on the number of contributions
608: to the likelihood and the sum of weights (done by funcone)*/
609: int mle=1, weightopt=0;
610: int **mw; /* mw[mi][i] is number of the mi wave for this individual */
611: int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
612: int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between
613: * wave mi and wave mi+1 is not an exact multiple of stepm. */
614: int countcallfunc=0; /* Count the number of calls to func */
615: double jmean=1; /* Mean space between 2 waves */
616: double **matprod2(); /* test */
617: double **oldm, **newm, **savm; /* Working pointers to matrices */
618: double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
619: /*FILE *fic ; */ /* Used in readdata only */
620: FILE *ficpar, *ficparo,*ficres, *ficresp, *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
621: FILE *ficlog, *ficrespow;
622: int globpr=0; /* Global variable for printing or not */
623: double fretone; /* Only one call to likelihood */
624: long ipmx=0; /* Number of contributions */
625: double sw; /* Sum of weights */
626: char filerespow[FILENAMELENGTH];
627: char fileresilk[FILENAMELENGTH]; /* File of individual contributions to the likelihood */
628: FILE *ficresilk;
629: FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
630: FILE *ficresprobmorprev;
631: FILE *fichtm, *fichtmcov; /* Html File */
632: FILE *ficreseij;
633: char filerese[FILENAMELENGTH];
634: FILE *ficresstdeij;
635: char fileresstde[FILENAMELENGTH];
636: FILE *ficrescveij;
637: char filerescve[FILENAMELENGTH];
638: FILE *ficresvij;
639: char fileresv[FILENAMELENGTH];
640: FILE *ficresvpl;
641: char fileresvpl[FILENAMELENGTH];
642: char title[MAXLINE];
643: char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH], filerespl[FILENAMELENGTH];
644: char plotcmd[FILENAMELENGTH], pplotcmd[FILENAMELENGTH];
645: char tmpout[FILENAMELENGTH], tmpout2[FILENAMELENGTH];
646: char command[FILENAMELENGTH];
647: int outcmd=0;
648:
649: char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
650:
651: char filelog[FILENAMELENGTH]; /* Log file */
652: char filerest[FILENAMELENGTH];
653: char fileregp[FILENAMELENGTH];
654: char popfile[FILENAMELENGTH];
655:
656: char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilehtmcov[FILENAMELENGTH] ;
657:
658: /* struct timeval start_time, end_time, curr_time, last_time, forecast_time; */
659: /* struct timezone tzp; */
660: /* extern int gettimeofday(); */
661: struct tm tml, *gmtime(), *localtime();
662:
663: extern time_t time();
664:
665: struct tm start_time, end_time, curr_time, last_time, forecast_time;
666: time_t rstart_time, rend_time, rcurr_time, rlast_time, rforecast_time; /* raw time */
667: struct tm tm;
668:
669: char strcurr[80], strfor[80];
670:
671: char *endptr;
672: long lval;
673: double dval;
674:
675: #define NR_END 1
676: #define FREE_ARG char*
677: #define FTOL 1.0e-10
678:
679: #define NRANSI
680: #define ITMAX 200
681:
682: #define TOL 2.0e-4
683:
684: #define CGOLD 0.3819660
685: #define ZEPS 1.0e-10
686: #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);
687:
688: #define GOLD 1.618034
689: #define GLIMIT 100.0
690: #define TINY 1.0e-20
691:
692: static double maxarg1,maxarg2;
693: #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
694: #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
695:
696: #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
697: #define rint(a) floor(a+0.5)
698:
699: static double sqrarg;
700: #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
701: #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}
702: int agegomp= AGEGOMP;
703:
704: int imx;
705: int stepm=1;
706: /* Stepm, step in month: minimum step interpolation*/
707:
708: int estepm;
709: /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
710:
711: int m,nb;
712: long *num;
713: int firstpass=0, lastpass=4,*cod, *ncodemax, *Tage,*cens;
714: double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
715: double **pmmij, ***probs;
716: double *ageexmed,*agecens;
717: double dateintmean=0;
718:
719: double *weight;
720: int **s; /* Status */
721: double *agedc;
722: double **covar; /**< covar[j,i], value of jth covariate for individual i,
723: * covar=matrix(0,NCOVMAX,1,n);
724: * cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2]; */
725: double idx;
726: int **nbcode, *Tvar; /**< model=V2 => Tvar[1]= 2 */
727: int *Ndum; /** Freq of modality (tricode */
728: int **codtab; /**< codtab=imatrix(1,100,1,10); */
729: int **Tvard, *Tprod, cptcovprod, *Tvaraff;
730: double *lsurv, *lpop, *tpop;
731:
732: double ftol=FTOL; /**< Tolerance for computing Max Likelihood */
733: double ftolhess; /**< Tolerance for computing hessian */
734:
735: /**************** split *************************/
736: static int split( char *path, char *dirc, char *name, char *ext, char *finame )
737: {
738: /* From a file name with (full) path (either Unix or Windows) we extract the directory (dirc)
739: the name of the file (name), its extension only (ext) and its first part of the name (finame)
740: */
741: char *ss; /* pointer */
742: int l1, l2; /* length counters */
743:
744: l1 = strlen(path ); /* length of path */
745: if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
746: ss= strrchr( path, DIRSEPARATOR ); /* find last / */
747: if ( ss == NULL ) { /* no directory, so determine current directory */
748: strcpy( name, path ); /* we got the fullname name because no directory */
749: /*if(strrchr(path, ODIRSEPARATOR )==NULL)
750: printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
751: /* get current working directory */
752: /* extern char* getcwd ( char *buf , int len);*/
753: if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {
754: return( GLOCK_ERROR_GETCWD );
755: }
756: /* got dirc from getcwd*/
757: printf(" DIRC = %s \n",dirc);
758: } else { /* strip direcotry from path */
759: ss++; /* after this, the filename */
760: l2 = strlen( ss ); /* length of filename */
761: if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
762: strcpy( name, ss ); /* save file name */
763: strncpy( dirc, path, l1 - l2 ); /* now the directory */
764: dirc[l1-l2] = 0; /* add zero */
765: printf(" DIRC2 = %s \n",dirc);
766: }
767: /* We add a separator at the end of dirc if not exists */
768: l1 = strlen( dirc ); /* length of directory */
769: if( dirc[l1-1] != DIRSEPARATOR ){
770: dirc[l1] = DIRSEPARATOR;
771: dirc[l1+1] = 0;
772: printf(" DIRC3 = %s \n",dirc);
773: }
774: ss = strrchr( name, '.' ); /* find last / */
775: if (ss >0){
776: ss++;
777: strcpy(ext,ss); /* save extension */
778: l1= strlen( name);
779: l2= strlen(ss)+1;
780: strncpy( finame, name, l1-l2);
781: finame[l1-l2]= 0;
782: }
783:
784: return( 0 ); /* we're done */
785: }
786:
787:
788: /******************************************/
789:
790: void replace_back_to_slash(char *s, char*t)
791: {
792: int i;
793: int lg=0;
794: i=0;
795: lg=strlen(t);
796: for(i=0; i<= lg; i++) {
797: (s[i] = t[i]);
798: if (t[i]== '\\') s[i]='/';
799: }
800: }
801:
802: char *trimbb(char *out, char *in)
803: { /* Trim multiple blanks in line but keeps first blanks if line starts with blanks */
804: char *s;
805: s=out;
806: while (*in != '\0'){
807: while( *in == ' ' && *(in+1) == ' '){ /* && *(in+1) != '\0'){*/
808: in++;
809: }
810: *out++ = *in++;
811: }
812: *out='\0';
813: return s;
814: }
815:
816: char *cutl(char *blocc, char *alocc, char *in, char occ)
817: {
818: /* cuts string in into blocc and alocc where blocc ends before first occurence of char 'occ'
819: and alocc starts after first occurence of char 'occ' : ex cutv(blocc,alocc,"abcdef2ghi2j",'2')
820: gives blocc="abcdef2ghi" and alocc="j".
821: If occ is not found blocc is null and alocc is equal to in. Returns blocc
822: */
823: char *s, *t;
824: t=in;s=in;
825: while ((*in != occ) && (*in != '\0')){
826: *alocc++ = *in++;
827: }
828: if( *in == occ){
829: *(alocc)='\0';
830: s=++in;
831: }
832:
833: if (s == t) {/* occ not found */
834: *(alocc-(in-s))='\0';
835: in=s;
836: }
837: while ( *in != '\0'){
838: *blocc++ = *in++;
839: }
840:
841: *blocc='\0';
842: return t;
843: }
844: char *cutv(char *blocc, char *alocc, char *in, char occ)
845: {
846: /* cuts string in into blocc and alocc where blocc ends before last occurence of char 'occ'
847: and alocc starts after last occurence of char 'occ' : ex cutv(blocc,alocc,"abcdef2ghi2j",'2')
848: gives blocc="abcdef2ghi" and alocc="j".
849: If occ is not found blocc is null and alocc is equal to in. Returns alocc
850: */
851: char *s, *t;
852: t=in;s=in;
853: while (*in != '\0'){
854: while( *in == occ){
855: *blocc++ = *in++;
856: s=in;
857: }
858: *blocc++ = *in++;
859: }
860: if (s == t) /* occ not found */
861: *(blocc-(in-s))='\0';
862: else
863: *(blocc-(in-s)-1)='\0';
864: in=s;
865: while ( *in != '\0'){
866: *alocc++ = *in++;
867: }
868:
869: *alocc='\0';
870: return s;
871: }
872:
873: int nbocc(char *s, char occ)
874: {
875: int i,j=0;
876: int lg=20;
877: i=0;
878: lg=strlen(s);
879: for(i=0; i<= lg; i++) {
880: if (s[i] == occ ) j++;
881: }
882: return j;
883: }
884:
885: /* void cutv(char *u,char *v, char*t, char occ) */
886: /* { */
887: /* /\* cuts string t into u and v where u ends before last occurence of char 'occ' */
888: /* and v starts after last occurence of char 'occ' : ex cutv(u,v,"abcdef2ghi2j",'2') */
889: /* gives u="abcdef2ghi" and v="j" *\/ */
890: /* int i,lg,j,p=0; */
891: /* i=0; */
892: /* lg=strlen(t); */
893: /* for(j=0; j<=lg-1; j++) { */
894: /* if((t[j]!= occ) && (t[j+1]== occ)) p=j+1; */
895: /* } */
896:
897: /* for(j=0; j<p; j++) { */
898: /* (u[j] = t[j]); */
899: /* } */
900: /* u[p]='\0'; */
901:
902: /* for(j=0; j<= lg; j++) { */
903: /* if (j>=(p+1))(v[j-p-1] = t[j]); */
904: /* } */
905: /* } */
906:
907: #ifdef _WIN32
908: char * strsep(char **pp, const char *delim)
909: {
910: char *p, *q;
911:
912: if ((p = *pp) == NULL)
913: return 0;
914: if ((q = strpbrk (p, delim)) != NULL)
915: {
916: *pp = q + 1;
917: *q = '\0';
918: }
919: else
920: *pp = 0;
921: return p;
922: }
923: #endif
924:
925: /********************** nrerror ********************/
926:
927: void nrerror(char error_text[])
928: {
929: fprintf(stderr,"ERREUR ...\n");
930: fprintf(stderr,"%s\n",error_text);
931: exit(EXIT_FAILURE);
932: }
933: /*********************** vector *******************/
934: double *vector(int nl, int nh)
935: {
936: double *v;
937: v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
938: if (!v) nrerror("allocation failure in vector");
939: return v-nl+NR_END;
940: }
941:
942: /************************ free vector ******************/
943: void free_vector(double*v, int nl, int nh)
944: {
945: free((FREE_ARG)(v+nl-NR_END));
946: }
947:
948: /************************ivector *******************************/
949: int *ivector(long nl,long nh)
950: {
951: int *v;
952: v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
953: if (!v) nrerror("allocation failure in ivector");
954: return v-nl+NR_END;
955: }
956:
957: /******************free ivector **************************/
958: void free_ivector(int *v, long nl, long nh)
959: {
960: free((FREE_ARG)(v+nl-NR_END));
961: }
962:
963: /************************lvector *******************************/
964: long *lvector(long nl,long nh)
965: {
966: long *v;
967: v=(long *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(long)));
968: if (!v) nrerror("allocation failure in ivector");
969: return v-nl+NR_END;
970: }
971:
972: /******************free lvector **************************/
973: void free_lvector(long *v, long nl, long nh)
974: {
975: free((FREE_ARG)(v+nl-NR_END));
976: }
977:
978: /******************* imatrix *******************************/
979: int **imatrix(long nrl, long nrh, long ncl, long nch)
980: /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */
981: {
982: long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;
983: int **m;
984:
985: /* allocate pointers to rows */
986: m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));
987: if (!m) nrerror("allocation failure 1 in matrix()");
988: m += NR_END;
989: m -= nrl;
990:
991:
992: /* allocate rows and set pointers to them */
993: m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));
994: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
995: m[nrl] += NR_END;
996: m[nrl] -= ncl;
997:
998: for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;
999:
1000: /* return pointer to array of pointers to rows */
1001: return m;
1002: }
1003:
1004: /****************** free_imatrix *************************/
1005: void free_imatrix(m,nrl,nrh,ncl,nch)
1006: int **m;
1007: long nch,ncl,nrh,nrl;
1008: /* free an int matrix allocated by imatrix() */
1009: {
1010: free((FREE_ARG) (m[nrl]+ncl-NR_END));
1011: free((FREE_ARG) (m+nrl-NR_END));
1012: }
1013:
1014: /******************* matrix *******************************/
1015: double **matrix(long nrl, long nrh, long ncl, long nch)
1016: {
1017: long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
1018: double **m;
1019:
1020: m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
1021: if (!m) nrerror("allocation failure 1 in matrix()");
1022: m += NR_END;
1023: m -= nrl;
1024:
1025: m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
1026: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
1027: m[nrl] += NR_END;
1028: m[nrl] -= ncl;
1029:
1030: for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
1031: return m;
1032: /* print *(*(m+1)+70) or print m[1][70]; print m+1 or print &(m[1]) or &(m[1][0])
1033: m[i] = address of ith row of the table. &(m[i]) is its value which is another adress
1034: that of m[i][0]. In order to get the value p m[i][0] but it is unitialized.
1035: */
1036: }
1037:
1038: /*************************free matrix ************************/
1039: void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
1040: {
1041: free((FREE_ARG)(m[nrl]+ncl-NR_END));
1042: free((FREE_ARG)(m+nrl-NR_END));
1043: }
1044:
1045: /******************* ma3x *******************************/
1046: double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
1047: {
1048: long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
1049: double ***m;
1050:
1051: m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
1052: if (!m) nrerror("allocation failure 1 in matrix()");
1053: m += NR_END;
1054: m -= nrl;
1055:
1056: m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
1057: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
1058: m[nrl] += NR_END;
1059: m[nrl] -= ncl;
1060:
1061: for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
1062:
1063: m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
1064: if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
1065: m[nrl][ncl] += NR_END;
1066: m[nrl][ncl] -= nll;
1067: for (j=ncl+1; j<=nch; j++)
1068: m[nrl][j]=m[nrl][j-1]+nlay;
1069:
1070: for (i=nrl+1; i<=nrh; i++) {
1071: m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
1072: for (j=ncl+1; j<=nch; j++)
1073: m[i][j]=m[i][j-1]+nlay;
1074: }
1075: return m;
1076: /* gdb: p *(m+1) <=> p m[1] and p (m+1) <=> p (m+1) <=> p &(m[1])
1077: &(m[i][j][k]) <=> *((*(m+i) + j)+k)
1078: */
1079: }
1080:
1081: /*************************free ma3x ************************/
1082: void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
1083: {
1084: free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
1085: free((FREE_ARG)(m[nrl]+ncl-NR_END));
1086: free((FREE_ARG)(m+nrl-NR_END));
1087: }
1088:
1089: /*************** function subdirf ***********/
1090: char *subdirf(char fileres[])
1091: {
1092: /* Caution optionfilefiname is hidden */
1093: strcpy(tmpout,optionfilefiname);
1094: strcat(tmpout,"/"); /* Add to the right */
1095: strcat(tmpout,fileres);
1096: return tmpout;
1097: }
1098:
1099: /*************** function subdirf2 ***********/
1100: char *subdirf2(char fileres[], char *preop)
1101: {
1102:
1103: /* Caution optionfilefiname is hidden */
1104: strcpy(tmpout,optionfilefiname);
1105: strcat(tmpout,"/");
1106: strcat(tmpout,preop);
1107: strcat(tmpout,fileres);
1108: return tmpout;
1109: }
1110:
1111: /*************** function subdirf3 ***********/
1112: char *subdirf3(char fileres[], char *preop, char *preop2)
1113: {
1114:
1115: /* Caution optionfilefiname is hidden */
1116: strcpy(tmpout,optionfilefiname);
1117: strcat(tmpout,"/");
1118: strcat(tmpout,preop);
1119: strcat(tmpout,preop2);
1120: strcat(tmpout,fileres);
1121: return tmpout;
1122: }
1123:
1124: char *asc_diff_time(long time_sec, char ascdiff[])
1125: {
1126: long sec_left, days, hours, minutes;
1127: days = (time_sec) / (60*60*24);
1128: sec_left = (time_sec) % (60*60*24);
1129: hours = (sec_left) / (60*60) ;
1130: sec_left = (sec_left) %(60*60);
1131: minutes = (sec_left) /60;
1132: sec_left = (sec_left) % (60);
1133: sprintf(ascdiff,"%ld day(s) %ld hour(s) %ld minute(s) %ld second(s)",days, hours, minutes, sec_left);
1134: return ascdiff;
1135: }
1136:
1137: /***************** f1dim *************************/
1138: extern int ncom;
1139: extern double *pcom,*xicom;
1140: extern double (*nrfunc)(double []);
1141:
1142: double f1dim(double x)
1143: {
1144: int j;
1145: double f;
1146: double *xt;
1147:
1148: xt=vector(1,ncom);
1149: for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];
1150: f=(*nrfunc)(xt);
1151: free_vector(xt,1,ncom);
1152: return f;
1153: }
1154:
1155: /*****************brent *************************/
1156: double brent(double ax, double bx, double cx, double (*f)(double), double tol, double *xmin)
1157: {
1158: int iter;
1159: double a,b,d,etemp;
1160: double fu=0,fv,fw,fx;
1161: double ftemp=0.;
1162: double p,q,r,tol1,tol2,u,v,w,x,xm;
1163: double e=0.0;
1164:
1165: a=(ax < cx ? ax : cx);
1166: b=(ax > cx ? ax : cx);
1167: x=w=v=bx;
1168: fw=fv=fx=(*f)(x);
1169: for (iter=1;iter<=ITMAX;iter++) {
1170: xm=0.5*(a+b);
1171: tol2=2.0*(tol1=tol*fabs(x)+ZEPS);
1172: /* if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
1173: printf(".");fflush(stdout);
1174: fprintf(ficlog,".");fflush(ficlog);
1175: #ifdef DEBUGBRENT
1176: 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);
1177: 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);
1178: /* if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
1179: #endif
1180: if (fabs(x-xm) <= (tol2-0.5*(b-a))){
1181: *xmin=x;
1182: return fx;
1183: }
1184: ftemp=fu;
1185: if (fabs(e) > tol1) {
1186: r=(x-w)*(fx-fv);
1187: q=(x-v)*(fx-fw);
1188: p=(x-v)*q-(x-w)*r;
1189: q=2.0*(q-r);
1190: if (q > 0.0) p = -p;
1191: q=fabs(q);
1192: etemp=e;
1193: e=d;
1194: if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))
1195: d=CGOLD*(e=(x >= xm ? a-x : b-x));
1196: else {
1197: d=p/q;
1198: u=x+d;
1199: if (u-a < tol2 || b-u < tol2)
1200: d=SIGN(tol1,xm-x);
1201: }
1202: } else {
1203: d=CGOLD*(e=(x >= xm ? a-x : b-x));
1204: }
1205: u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));
1206: fu=(*f)(u);
1207: if (fu <= fx) {
1208: if (u >= x) a=x; else b=x;
1209: SHFT(v,w,x,u)
1210: SHFT(fv,fw,fx,fu)
1211: } else {
1212: if (u < x) a=u; else b=u;
1213: if (fu <= fw || w == x) {
1214: v=w;
1215: w=u;
1216: fv=fw;
1217: fw=fu;
1218: } else if (fu <= fv || v == x || v == w) {
1219: v=u;
1220: fv=fu;
1221: }
1222: }
1223: }
1224: nrerror("Too many iterations in brent");
1225: *xmin=x;
1226: return fx;
1227: }
1228:
1229: /****************** mnbrak ***********************/
1230:
1231: void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,
1232: double (*func)(double))
1233: {
1234: double ulim,u,r,q, dum;
1235: double fu;
1236:
1237: *fa=(*func)(*ax);
1238: *fb=(*func)(*bx);
1239: if (*fb > *fa) {
1240: SHFT(dum,*ax,*bx,dum)
1241: SHFT(dum,*fb,*fa,dum)
1242: }
1243: *cx=(*bx)+GOLD*(*bx-*ax);
1244: *fc=(*func)(*cx);
1245: while (*fb > *fc) { /* Declining fa, fb, fc */
1246: r=(*bx-*ax)*(*fb-*fc);
1247: q=(*bx-*cx)*(*fb-*fa);
1248: u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/
1249: (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r)); /* Minimum abscisse of a parabolic estimated from (a,fa), (b,fb) and (c,fc). */
1250: ulim=(*bx)+GLIMIT*(*cx-*bx); /* Maximum abscisse where function can be evaluated */
1251: if ((*bx-u)*(u-*cx) > 0.0) { /* if u between b and c */
1252: fu=(*func)(u);
1253: #ifdef DEBUG
1254: /* f(x)=A(x-u)**2+f(u) */
1255: double A, fparabu;
1256: A= (*fb - *fa)/(*bx-*ax)/(*bx+*ax-2*u);
1257: fparabu= *fa - A*(*ax-u)*(*ax-u);
1258: 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);
1259: 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);
1260: #endif
1261: } else if ((*cx-u)*(u-ulim) > 0.0) { /* u is after c but before ulim */
1262: fu=(*func)(u);
1263: if (fu < *fc) {
1264: SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))
1265: SHFT(*fb,*fc,fu,(*func)(u))
1266: }
1267: } else if ((u-ulim)*(ulim-*cx) >= 0.0) { /* u outside ulim (verifying that ulim is beyond c) */
1268: u=ulim;
1269: fu=(*func)(u);
1270: } else {
1271: u=(*cx)+GOLD*(*cx-*bx);
1272: fu=(*func)(u);
1273: }
1274: SHFT(*ax,*bx,*cx,u)
1275: SHFT(*fa,*fb,*fc,fu)
1276: }
1277: }
1278:
1279: /*************** linmin ************************/
1280: /* Given an n -dimensional point p[1..n] and an n -dimensional direction xi[1..n] , moves and
1281: resets p to where the function func(p) takes on a minimum along the direction xi from p ,
1282: and replaces xi by the actual vector displacement that p was moved. Also returns as fret
1283: the value of func at the returned location p . This is actually all accomplished by calling the
1284: routines mnbrak and brent .*/
1285: int ncom;
1286: double *pcom,*xicom;
1287: double (*nrfunc)(double []);
1288:
1289: void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))
1290: {
1291: double brent(double ax, double bx, double cx,
1292: double (*f)(double), double tol, double *xmin);
1293: double f1dim(double x);
1294: void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,
1295: double *fc, double (*func)(double));
1296: int j;
1297: double xx,xmin,bx,ax;
1298: double fx,fb,fa;
1299:
1300: ncom=n;
1301: pcom=vector(1,n);
1302: xicom=vector(1,n);
1303: nrfunc=func;
1304: for (j=1;j<=n;j++) {
1305: pcom[j]=p[j];
1306: xicom[j]=xi[j];
1307: }
1308: ax=0.0;
1309: xx=1.0;
1310: mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim); /* Find a bracket a,x,b in direction n=xi ie xicom */
1311: *fret=brent(ax,xx,bx,f1dim,TOL,&xmin); /* Find a minimum P+lambda n in that direction (lambdamin), with TOL between abscisses */
1312: #ifdef DEBUG
1313: printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
1314: fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
1315: #endif
1316: for (j=1;j<=n;j++) {
1317: xi[j] *= xmin;
1318: p[j] += xi[j];
1319: }
1320: free_vector(xicom,1,n);
1321: free_vector(pcom,1,n);
1322: }
1323:
1324:
1325: /*************** powell ************************/
1326: /*
1327: Minimization of a function func of n variables. Input consists of an initial starting point
1328: p[1..n] ; an initial matrix xi[1..n][1..n] , whose columns contain the initial set of di-
1329: rections (usually the n unit vectors); and ftol , the fractional tolerance in the function value
1330: such that failure to decrease by more than this amount on one iteration signals doneness. On
1331: output, p is set to the best point found, xi is the then-current direction set, fret is the returned
1332: function value at p , and iter is the number of iterations taken. The routine linmin is used.
1333: */
1334: void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,
1335: double (*func)(double []))
1336: {
1337: void linmin(double p[], double xi[], int n, double *fret,
1338: double (*func)(double []));
1339: int i,ibig,j;
1340: double del,t,*pt,*ptt,*xit;
1341: double fp,fptt;
1342: double *xits;
1343: int niterf, itmp;
1344:
1345: pt=vector(1,n);
1346: ptt=vector(1,n);
1347: xit=vector(1,n);
1348: xits=vector(1,n);
1349: *fret=(*func)(p);
1350: for (j=1;j<=n;j++) pt[j]=p[j];
1351: rcurr_time = time(NULL);
1352: for (*iter=1;;++(*iter)) {
1353: fp=(*fret);
1354: ibig=0;
1355: del=0.0;
1356: rlast_time=rcurr_time;
1357: /* (void) gettimeofday(&curr_time,&tzp); */
1358: rcurr_time = time(NULL);
1359: curr_time = *localtime(&rcurr_time);
1360: printf("\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret, rcurr_time-rlast_time, rcurr_time-rstart_time);fflush(stdout);
1361: fprintf(ficlog,"\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret,rcurr_time-rlast_time, rcurr_time-rstart_time); fflush(ficlog);
1362: /* fprintf(ficrespow,"%d %.12f %ld",*iter,*fret,curr_time.tm_sec-start_time.tm_sec); */
1363: for (i=1;i<=n;i++) {
1364: printf(" %d %.12f",i, p[i]);
1365: fprintf(ficlog," %d %.12lf",i, p[i]);
1366: fprintf(ficrespow," %.12lf", p[i]);
1367: }
1368: printf("\n");
1369: fprintf(ficlog,"\n");
1370: fprintf(ficrespow,"\n");fflush(ficrespow);
1371: if(*iter <=3){
1372: tml = *localtime(&rcurr_time);
1373: strcpy(strcurr,asctime(&tml));
1374: rforecast_time=rcurr_time;
1375: itmp = strlen(strcurr);
1376: if(strcurr[itmp-1]=='\n') /* Windows outputs with a new line */
1377: strcurr[itmp-1]='\0';
1378: printf("\nConsidering the time needed for the last iteration #%d: %ld seconds,\n",*iter,rcurr_time-rlast_time);
1379: fprintf(ficlog,"\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,rcurr_time-rlast_time);
1380: for(niterf=10;niterf<=30;niterf+=10){
1381: rforecast_time=rcurr_time+(niterf-*iter)*(rcurr_time-rlast_time);
1382: forecast_time = *localtime(&rforecast_time);
1383: strcpy(strfor,asctime(&forecast_time));
1384: itmp = strlen(strfor);
1385: if(strfor[itmp-1]=='\n')
1386: strfor[itmp-1]='\0';
1387: 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);
1388: 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);
1389: }
1390: }
1391: for (i=1;i<=n;i++) {
1392: for (j=1;j<=n;j++) xit[j]=xi[j][i];
1393: fptt=(*fret);
1394: #ifdef DEBUG
1395: printf("fret=%lf, %lf, %lf \n", *fret, *fret, *fret);
1396: fprintf(ficlog, "fret=%lf, %lf, %lf \n", *fret, *fret, *fret);
1397: #endif
1398: printf("%d",i);fflush(stdout);
1399: fprintf(ficlog,"%d",i);fflush(ficlog);
1400: linmin(p,xit,n,fret,func);
1401: if (fabs(fptt-(*fret)) > del) {
1402: del=fabs(fptt-(*fret));
1403: ibig=i;
1404: }
1405: #ifdef DEBUG
1406: printf("%d %.12e",i,(*fret));
1407: fprintf(ficlog,"%d %.12e",i,(*fret));
1408: for (j=1;j<=n;j++) {
1409: xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
1410: printf(" x(%d)=%.12e",j,xit[j]);
1411: fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
1412: }
1413: for(j=1;j<=n;j++) {
1414: printf(" p(%d)=%.12e",j,p[j]);
1415: fprintf(ficlog," p(%d)=%.12e",j,p[j]);
1416: }
1417: printf("\n");
1418: fprintf(ficlog,"\n");
1419: #endif
1420: } /* end i */
1421: if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {
1422: #ifdef DEBUG
1423: int k[2],l;
1424: k[0]=1;
1425: k[1]=-1;
1426: printf("Max: %.12e",(*func)(p));
1427: fprintf(ficlog,"Max: %.12e",(*func)(p));
1428: for (j=1;j<=n;j++) {
1429: printf(" %.12e",p[j]);
1430: fprintf(ficlog," %.12e",p[j]);
1431: }
1432: printf("\n");
1433: fprintf(ficlog,"\n");
1434: for(l=0;l<=1;l++) {
1435: for (j=1;j<=n;j++) {
1436: ptt[j]=p[j]+(p[j]-pt[j])*k[l];
1437: printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
1438: fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
1439: }
1440: printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
1441: fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
1442: }
1443: #endif
1444:
1445:
1446: free_vector(xit,1,n);
1447: free_vector(xits,1,n);
1448: free_vector(ptt,1,n);
1449: free_vector(pt,1,n);
1450: return;
1451: }
1452: if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");
1453: for (j=1;j<=n;j++) { /* Computes an extrapolated point */
1454: ptt[j]=2.0*p[j]-pt[j];
1455: xit[j]=p[j]-pt[j];
1456: pt[j]=p[j];
1457: }
1458: fptt=(*func)(ptt);
1459: if (fptt < fp) { /* If extrapolated point is better, decide if we keep that new direction or not */
1460: /* (x1 f1=fp), (x2 f2=*fret), (x3 f3=fptt), (xm fm) */
1461: /* From x1 (P0) distance of x2 is at h and x3 is 2h */
1462: /* Let f"(x2) be the 2nd derivative equal everywhere. */
1463: /* Then the parabolic through (x1,f1), (x2,f2) and (x3,f3) */
1464: /* will reach at f3 = fm + h^2/2 f"m ; f" = (f1 -2f2 +f3 ) / h**2 */
1465: /* f1-f3 = delta(2h) = 2 h**2 f'' = 2(f1- 2f2 +f3) */
1466: /* Thus we compare delta(2h) with observed f1-f3 */
1467: /* or best gain on one ancient line 'del' with total */
1468: /* gain f1-f2 = f1 - f2 - 'del' with del */
1469: /* t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt); */
1470:
1471: t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del);
1472: t= t- del*SQR(fp-fptt);
1473: printf("t1= %.12lf, t2= %.12lf, t=%.12lf\n", 2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del),del*SQR(fp-fptt),t);
1474: fprintf(ficlog,"t1= %.12lf, t2= %.12lf, t=%.12lf\n", 2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del),del*SQR(fp-fptt),t);
1475: #ifdef DEBUG
1476: printf("t3= %.12lf, t4= %.12lf, t3*= %.12lf, t4*= %.12lf\n",SQR(fp-(*fret)-del),SQR(fp-fptt),
1477: (fp-(*fret)-del)*(fp-(*fret)-del),(fp-fptt)*(fp-fptt));
1478: fprintf(ficlog,"t3= %.12lf, t4= %.12lf, t3*= %.12lf, t4*= %.12lf\n",SQR(fp-(*fret)-del),SQR(fp-fptt),
1479: (fp-(*fret)-del)*(fp-(*fret)-del),(fp-fptt)*(fp-fptt));
1480: 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);
1481: 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);
1482: #endif
1483: if (t < 0.0) { /* Then we use it for last direction */
1484: linmin(p,xit,n,fret,func); /* computes mean on the extrapolated direction.*/
1485: for (j=1;j<=n;j++) {
1486: xi[j][ibig]=xi[j][n]; /* Replace the direction with biggest decrease by n */
1487: xi[j][n]=xit[j]; /* and nth direction by the extrapolated */
1488: }
1489: printf("Gaining to use average direction of P0 P%d instead of biggest increase direction %d :\n",n,ibig);
1490: fprintf(ficlog,"Gaining to use average direction of P0 P%d instead of biggest increase direction :\n",n,ibig);
1491:
1492: #ifdef DEBUG
1493: printf("Direction changed last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
1494: fprintf(ficlog,"Direction changed last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
1495: for(j=1;j<=n;j++){
1496: printf(" %.12e",xit[j]);
1497: fprintf(ficlog," %.12e",xit[j]);
1498: }
1499: printf("\n");
1500: fprintf(ficlog,"\n");
1501: #endif
1502: } /* end of t negative */
1503: } /* end if (fptt < fp) */
1504: }
1505: }
1506:
1507: /**** Prevalence limit (stable or period prevalence) ****************/
1508:
1509: double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)
1510: {
1511: /* Computes the prevalence limit in each live state at age x by left multiplying the unit
1512: matrix by transitions matrix until convergence is reached */
1513:
1514: int i, ii,j,k;
1515: double min, max, maxmin, maxmax,sumnew=0.;
1516: /* double **matprod2(); */ /* test */
1517: double **out, cov[NCOVMAX+1], **pmij();
1518: double **newm;
1519: double agefin, delaymax=50 ; /* Max number of years to converge */
1520:
1521: for (ii=1;ii<=nlstate+ndeath;ii++)
1522: for (j=1;j<=nlstate+ndeath;j++){
1523: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1524: }
1525:
1526: cov[1]=1.;
1527:
1528: /* Even if hstepm = 1, at least one multiplication by the unit matrix */
1529: for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
1530: newm=savm;
1531: /* Covariates have to be included here again */
1532: cov[2]=agefin;
1533:
1534: for (k=1; k<=cptcovn;k++) {
1535: cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
1536: /*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]]);*/
1537: }
1538: /* for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
1539: /* for (k=1; k<=cptcovprod;k++) /\* Useless *\/ */
1540: /* cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]] * nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]]; */
1541:
1542: /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
1543: /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
1544: /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
1545: /* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
1546: /* out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /\* Bug Valgrind *\/ */
1547: out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /* Bug Valgrind */
1548:
1549: savm=oldm;
1550: oldm=newm;
1551: maxmax=0.;
1552: for(j=1;j<=nlstate;j++){
1553: min=1.;
1554: max=0.;
1555: for(i=1; i<=nlstate; i++) {
1556: sumnew=0;
1557: for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
1558: prlim[i][j]= newm[i][j]/(1-sumnew);
1559: /*printf(" prevalim i=%d, j=%d, prmlim[%d][%d]=%f, agefin=%d \n", i, j, i, j, prlim[i][j],(int)agefin);*/
1560: max=FMAX(max,prlim[i][j]);
1561: min=FMIN(min,prlim[i][j]);
1562: }
1563: maxmin=max-min;
1564: maxmax=FMAX(maxmax,maxmin);
1565: }
1566: if(maxmax < ftolpl){
1567: return prlim;
1568: }
1569: }
1570: }
1571:
1572: /*************** transition probabilities ***************/
1573:
1574: double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
1575: {
1576: /* According to parameters values stored in x and the covariate's values stored in cov,
1577: computes the probability to be observed in state j being in state i by appying the
1578: model to the ncovmodel covariates (including constant and age).
1579: lnpijopii=ln(pij/pii)= aij+bij*age+cij*v1+dij*v2+... = sum_nc=1^ncovmodel xij(nc)*cov[nc]
1580: and, according on how parameters are entered, the position of the coefficient xij(nc) of the
1581: ncth covariate in the global vector x is given by the formula:
1582: j<i nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel
1583: j>=i nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel
1584: Computes ln(pij/pii) (lnpijopii), deduces pij/pii by exponentiation,
1585: sums on j different of i to get 1-pii/pii, deduces pii, and then all pij.
1586: Outputs ps[i][j] the probability to be observed in j being in j according to
1587: the values of the covariates cov[nc] and corresponding parameter values x[nc+shiftij]
1588: */
1589: double s1, lnpijopii;
1590: /*double t34;*/
1591: int i,j, nc, ii, jj;
1592:
1593: for(i=1; i<= nlstate; i++){
1594: for(j=1; j<i;j++){
1595: for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
1596: /*lnpijopii += param[i][j][nc]*cov[nc];*/
1597: lnpijopii += x[nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel]*cov[nc];
1598: /* printf("Int j<i s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
1599: }
1600: ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
1601: /* printf("s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
1602: }
1603: for(j=i+1; j<=nlstate+ndeath;j++){
1604: for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
1605: /*lnpijopii += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];*/
1606: lnpijopii += x[nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel]*cov[nc];
1607: /* printf("Int j>i s1=%.17e, lnpijopii=%.17e %lx %lx\n",s1,lnpijopii,s1,lnpijopii); */
1608: }
1609: ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
1610: }
1611: }
1612:
1613: for(i=1; i<= nlstate; i++){
1614: s1=0;
1615: for(j=1; j<i; j++){
1616: s1+=exp(ps[i][j]); /* In fact sums pij/pii */
1617: /*printf("debug1 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
1618: }
1619: for(j=i+1; j<=nlstate+ndeath; j++){
1620: s1+=exp(ps[i][j]); /* In fact sums pij/pii */
1621: /*printf("debug2 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
1622: }
1623: /* s1= sum_{j<>i} pij/pii=(1-pii)/pii and thus pii is known from s1 */
1624: ps[i][i]=1./(s1+1.);
1625: /* Computing other pijs */
1626: for(j=1; j<i; j++)
1627: ps[i][j]= exp(ps[i][j])*ps[i][i];
1628: for(j=i+1; j<=nlstate+ndeath; j++)
1629: ps[i][j]= exp(ps[i][j])*ps[i][i];
1630: /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
1631: } /* end i */
1632:
1633: for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
1634: for(jj=1; jj<= nlstate+ndeath; jj++){
1635: ps[ii][jj]=0;
1636: ps[ii][ii]=1;
1637: }
1638: }
1639:
1640:
1641: /* for(ii=1; ii<= nlstate+ndeath; ii++){ */
1642: /* for(jj=1; jj<= nlstate+ndeath; jj++){ */
1643: /* printf(" pmij ps[%d][%d]=%lf ",ii,jj,ps[ii][jj]); */
1644: /* } */
1645: /* printf("\n "); */
1646: /* } */
1647: /* printf("\n ");printf("%lf ",cov[2]);*/
1648: /*
1649: for(i=1; i<= npar; i++) printf("%f ",x[i]);
1650: goto end;*/
1651: return ps;
1652: }
1653:
1654: /**************** Product of 2 matrices ******************/
1655:
1656: double **matprod2(double **out, double **in,int nrl, int nrh, int ncl, int nch, int ncolol, int ncoloh, double **b)
1657: {
1658: /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
1659: b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
1660: /* in, b, out are matrice of pointers which should have been initialized
1661: before: only the contents of out is modified. The function returns
1662: a pointer to pointers identical to out */
1663: int i, j, k;
1664: for(i=nrl; i<= nrh; i++)
1665: for(k=ncolol; k<=ncoloh; k++){
1666: out[i][k]=0.;
1667: for(j=ncl; j<=nch; j++)
1668: out[i][k] +=in[i][j]*b[j][k];
1669: }
1670: return out;
1671: }
1672:
1673:
1674: /************* Higher Matrix Product ***************/
1675:
1676: double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
1677: {
1678: /* Computes the transition matrix starting at age 'age' over
1679: 'nhstepm*hstepm*stepm' months (i.e. until
1680: age (in years) age+nhstepm*hstepm*stepm/12) by multiplying
1681: nhstepm*hstepm matrices.
1682: Output is stored in matrix po[i][j][h] for h every 'hstepm' step
1683: (typically every 2 years instead of every month which is too big
1684: for the memory).
1685: Model is determined by parameters x and covariates have to be
1686: included manually here.
1687:
1688: */
1689:
1690: int i, j, d, h, k;
1691: double **out, cov[NCOVMAX+1];
1692: double **newm;
1693:
1694: /* Hstepm could be zero and should return the unit matrix */
1695: for (i=1;i<=nlstate+ndeath;i++)
1696: for (j=1;j<=nlstate+ndeath;j++){
1697: oldm[i][j]=(i==j ? 1.0 : 0.0);
1698: po[i][j][0]=(i==j ? 1.0 : 0.0);
1699: }
1700: /* Even if hstepm = 1, at least one multiplication by the unit matrix */
1701: for(h=1; h <=nhstepm; h++){
1702: for(d=1; d <=hstepm; d++){
1703: newm=savm;
1704: /* Covariates have to be included here again */
1705: cov[1]=1.;
1706: cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
1707: for (k=1; k<=cptcovn;k++)
1708: cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
1709: for (k=1; k<=cptcovage;k++)
1710: cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
1711: for (k=1; k<=cptcovprod;k++) /* Useless because included in cptcovn */
1712: cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
1713:
1714:
1715: /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
1716: /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
1717: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,
1718: pmij(pmmij,cov,ncovmodel,x,nlstate));
1719: savm=oldm;
1720: oldm=newm;
1721: }
1722: for(i=1; i<=nlstate+ndeath; i++)
1723: for(j=1;j<=nlstate+ndeath;j++) {
1724: po[i][j][h]=newm[i][j];
1725: /*if(h==nhstepm) printf("po[%d][%d][%d]=%f ",i,j,h,po[i][j][h]);*/
1726: }
1727: /*printf("h=%d ",h);*/
1728: } /* end h */
1729: /* printf("\n H=%d \n",h); */
1730: return po;
1731: }
1732:
1733: #ifdef NLOPT
1734: double myfunc(unsigned n, const double *p1, double *grad, void *pd){
1735: double fret;
1736: double *xt;
1737: int j;
1738: myfunc_data *d2 = (myfunc_data *) pd;
1739: /* xt = (p1-1); */
1740: xt=vector(1,n);
1741: for (j=1;j<=n;j++) xt[j]=p1[j-1]; /* xt[1]=p1[0] */
1742:
1743: fret=(d2->function)(xt); /* p xt[1]@8 is fine */
1744: /* fret=(*func)(xt); /\* p xt[1]@8 is fine *\/ */
1745: printf("Function = %.12lf ",fret);
1746: for (j=1;j<=n;j++) printf(" %d %.8lf", j, xt[j]);
1747: printf("\n");
1748: free_vector(xt,1,n);
1749: return fret;
1750: }
1751: #endif
1752:
1753: /*************** log-likelihood *************/
1754: double func( double *x)
1755: {
1756: int i, ii, j, k, mi, d, kk;
1757: double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
1758: double **out;
1759: double sw; /* Sum of weights */
1760: double lli; /* Individual log likelihood */
1761: int s1, s2;
1762: double bbh, survp;
1763: long ipmx;
1764: /*extern weight */
1765: /* We are differentiating ll according to initial status */
1766: /* for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
1767: /*for(i=1;i<imx;i++)
1768: printf(" %d\n",s[4][i]);
1769: */
1770:
1771: ++countcallfunc;
1772:
1773: cov[1]=1.;
1774:
1775: for(k=1; k<=nlstate; k++) ll[k]=0.;
1776:
1777: if(mle==1){
1778: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1779: /* Computes the values of the ncovmodel covariates of the model
1780: depending if the covariates are fixed or variying (age dependent) and stores them in cov[]
1781: Then computes with function pmij which return a matrix p[i][j] giving the elementary probability
1782: to be observed in j being in i according to the model.
1783: */
1784: for (k=1; k<=cptcovn;k++){ /* Simple and product covariates without age* products */
1785: cov[2+k]=covar[Tvar[k]][i];
1786: }
1787: /* In model V2+V1*V4+age*V3+V3*V2 Tvar[1] is V2, Tvar[2=V1*V4]
1788: is 6, Tvar[3=age*V3] should not be computed because of age Tvar[4=V3*V2]
1789: has been calculated etc */
1790: for(mi=1; mi<= wav[i]-1; mi++){
1791: for (ii=1;ii<=nlstate+ndeath;ii++)
1792: for (j=1;j<=nlstate+ndeath;j++){
1793: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1794: savm[ii][j]=(ii==j ? 1.0 : 0.0);
1795: }
1796: for(d=0; d<dh[mi][i]; d++){
1797: newm=savm;
1798: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
1799: for (kk=1; kk<=cptcovage;kk++) {
1800: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2]; /* Tage[kk] gives the data-covariate associated with age */
1801: }
1802: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1803: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1804: savm=oldm;
1805: oldm=newm;
1806: } /* end mult */
1807:
1808: /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
1809: /* But now since version 0.9 we anticipate for bias at large stepm.
1810: * If stepm is larger than one month (smallest stepm) and if the exact delay
1811: * (in months) between two waves is not a multiple of stepm, we rounded to
1812: * the nearest (and in case of equal distance, to the lowest) interval but now
1813: * we keep into memory the bias bh[mi][i] and also the previous matrix product
1814: * (i.e to dh[mi][i]-1) saved in 'savm'. Then we inter(extra)polate the
1815: * probability in order to take into account the bias as a fraction of the way
1816: * from savm to out if bh is negative or even beyond if bh is positive. bh varies
1817: * -stepm/2 to stepm/2 .
1818: * For stepm=1 the results are the same as for previous versions of Imach.
1819: * For stepm > 1 the results are less biased than in previous versions.
1820: */
1821: s1=s[mw[mi][i]][i];
1822: s2=s[mw[mi+1][i]][i];
1823: bbh=(double)bh[mi][i]/(double)stepm;
1824: /* bias bh is positive if real duration
1825: * is higher than the multiple of stepm and negative otherwise.
1826: */
1827: /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
1828: if( s2 > nlstate){
1829: /* i.e. if s2 is a death state and if the date of death is known
1830: then the contribution to the likelihood is the probability to
1831: die between last step unit time and current step unit time,
1832: which is also equal to probability to die before dh
1833: minus probability to die before dh-stepm .
1834: In version up to 0.92 likelihood was computed
1835: as if date of death was unknown. Death was treated as any other
1836: health state: the date of the interview describes the actual state
1837: and not the date of a change in health state. The former idea was
1838: to consider that at each interview the state was recorded
1839: (healthy, disable or death) and IMaCh was corrected; but when we
1840: introduced the exact date of death then we should have modified
1841: the contribution of an exact death to the likelihood. This new
1842: contribution is smaller and very dependent of the step unit
1843: stepm. It is no more the probability to die between last interview
1844: and month of death but the probability to survive from last
1845: interview up to one month before death multiplied by the
1846: probability to die within a month. Thanks to Chris
1847: Jackson for correcting this bug. Former versions increased
1848: mortality artificially. The bad side is that we add another loop
1849: which slows down the processing. The difference can be up to 10%
1850: lower mortality.
1851: */
1852: lli=log(out[s1][s2] - savm[s1][s2]);
1853:
1854:
1855: } else if (s2==-2) {
1856: for (j=1,survp=0. ; j<=nlstate; j++)
1857: survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
1858: /*survp += out[s1][j]; */
1859: lli= log(survp);
1860: }
1861:
1862: else if (s2==-4) {
1863: for (j=3,survp=0. ; j<=nlstate; j++)
1864: survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
1865: lli= log(survp);
1866: }
1867:
1868: else if (s2==-5) {
1869: for (j=1,survp=0. ; j<=2; j++)
1870: survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
1871: lli= log(survp);
1872: }
1873:
1874: else{
1875: lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
1876: /* 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 */
1877: }
1878: /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
1879: /*if(lli ==000.0)*/
1880: /*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); */
1881: ipmx +=1;
1882: sw += weight[i];
1883: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1884: } /* end of wave */
1885: } /* end of individual */
1886: } else if(mle==2){
1887: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1888: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
1889: for(mi=1; mi<= wav[i]-1; mi++){
1890: for (ii=1;ii<=nlstate+ndeath;ii++)
1891: for (j=1;j<=nlstate+ndeath;j++){
1892: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1893: savm[ii][j]=(ii==j ? 1.0 : 0.0);
1894: }
1895: for(d=0; d<=dh[mi][i]; d++){
1896: newm=savm;
1897: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
1898: for (kk=1; kk<=cptcovage;kk++) {
1899: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
1900: }
1901: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1902: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1903: savm=oldm;
1904: oldm=newm;
1905: } /* end mult */
1906:
1907: s1=s[mw[mi][i]][i];
1908: s2=s[mw[mi+1][i]][i];
1909: bbh=(double)bh[mi][i]/(double)stepm;
1910: 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 */
1911: ipmx +=1;
1912: sw += weight[i];
1913: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1914: } /* end of wave */
1915: } /* end of individual */
1916: } else if(mle==3){ /* exponential inter-extrapolation */
1917: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1918: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
1919: for(mi=1; mi<= wav[i]-1; mi++){
1920: for (ii=1;ii<=nlstate+ndeath;ii++)
1921: for (j=1;j<=nlstate+ndeath;j++){
1922: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1923: savm[ii][j]=(ii==j ? 1.0 : 0.0);
1924: }
1925: for(d=0; d<dh[mi][i]; d++){
1926: newm=savm;
1927: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
1928: for (kk=1; kk<=cptcovage;kk++) {
1929: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
1930: }
1931: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1932: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1933: savm=oldm;
1934: oldm=newm;
1935: } /* end mult */
1936:
1937: s1=s[mw[mi][i]][i];
1938: s2=s[mw[mi+1][i]][i];
1939: bbh=(double)bh[mi][i]/(double)stepm;
1940: 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 */
1941: ipmx +=1;
1942: sw += weight[i];
1943: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1944: } /* end of wave */
1945: } /* end of individual */
1946: }else if (mle==4){ /* ml=4 no inter-extrapolation */
1947: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1948: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
1949: for(mi=1; mi<= wav[i]-1; mi++){
1950: for (ii=1;ii<=nlstate+ndeath;ii++)
1951: for (j=1;j<=nlstate+ndeath;j++){
1952: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1953: savm[ii][j]=(ii==j ? 1.0 : 0.0);
1954: }
1955: for(d=0; d<dh[mi][i]; d++){
1956: newm=savm;
1957: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
1958: for (kk=1; kk<=cptcovage;kk++) {
1959: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
1960: }
1961:
1962: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1963: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1964: savm=oldm;
1965: oldm=newm;
1966: } /* end mult */
1967:
1968: s1=s[mw[mi][i]][i];
1969: s2=s[mw[mi+1][i]][i];
1970: if( s2 > nlstate){
1971: lli=log(out[s1][s2] - savm[s1][s2]);
1972: }else{
1973: lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
1974: }
1975: ipmx +=1;
1976: sw += weight[i];
1977: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1978: /* 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]); */
1979: } /* end of wave */
1980: } /* end of individual */
1981: }else{ /* ml=5 no inter-extrapolation no jackson =0.8a */
1982: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1983: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
1984: for(mi=1; mi<= wav[i]-1; mi++){
1985: for (ii=1;ii<=nlstate+ndeath;ii++)
1986: for (j=1;j<=nlstate+ndeath;j++){
1987: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1988: savm[ii][j]=(ii==j ? 1.0 : 0.0);
1989: }
1990: for(d=0; d<dh[mi][i]; d++){
1991: newm=savm;
1992: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
1993: for (kk=1; kk<=cptcovage;kk++) {
1994: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
1995: }
1996:
1997: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1998: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1999: savm=oldm;
2000: oldm=newm;
2001: } /* end mult */
2002:
2003: s1=s[mw[mi][i]][i];
2004: s2=s[mw[mi+1][i]][i];
2005: lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
2006: ipmx +=1;
2007: sw += weight[i];
2008: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
2009: /*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]);*/
2010: } /* end of wave */
2011: } /* end of individual */
2012: } /* End of if */
2013: for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
2014: /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
2015: l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
2016: return -l;
2017: }
2018:
2019: /*************** log-likelihood *************/
2020: double funcone( double *x)
2021: {
2022: /* Same as likeli but slower because of a lot of printf and if */
2023: int i, ii, j, k, mi, d, kk;
2024: double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
2025: double **out;
2026: double lli; /* Individual log likelihood */
2027: double llt;
2028: int s1, s2;
2029: double bbh, survp;
2030: /*extern weight */
2031: /* We are differentiating ll according to initial status */
2032: /* for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
2033: /*for(i=1;i<imx;i++)
2034: printf(" %d\n",s[4][i]);
2035: */
2036: cov[1]=1.;
2037:
2038: for(k=1; k<=nlstate; k++) ll[k]=0.;
2039:
2040: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
2041: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
2042: for(mi=1; mi<= wav[i]-1; mi++){
2043: for (ii=1;ii<=nlstate+ndeath;ii++)
2044: for (j=1;j<=nlstate+ndeath;j++){
2045: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
2046: savm[ii][j]=(ii==j ? 1.0 : 0.0);
2047: }
2048: for(d=0; d<dh[mi][i]; d++){
2049: newm=savm;
2050: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
2051: for (kk=1; kk<=cptcovage;kk++) {
2052: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
2053: }
2054: /* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
2055: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
2056: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
2057: /* out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath, */
2058: /* 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate)); */
2059: savm=oldm;
2060: oldm=newm;
2061: } /* end mult */
2062:
2063: s1=s[mw[mi][i]][i];
2064: s2=s[mw[mi+1][i]][i];
2065: bbh=(double)bh[mi][i]/(double)stepm;
2066: /* bias is positive if real duration
2067: * is higher than the multiple of stepm and negative otherwise.
2068: */
2069: if( s2 > nlstate && (mle <5) ){ /* Jackson */
2070: lli=log(out[s1][s2] - savm[s1][s2]);
2071: } else if (s2==-2) {
2072: for (j=1,survp=0. ; j<=nlstate; j++)
2073: survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
2074: lli= log(survp);
2075: }else if (mle==1){
2076: lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
2077: } else if(mle==2){
2078: 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 */
2079: } else if(mle==3){ /* exponential inter-extrapolation */
2080: 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 */
2081: } else if (mle==4){ /* mle=4 no inter-extrapolation */
2082: lli=log(out[s1][s2]); /* Original formula */
2083: } else{ /* mle=0 back to 1 */
2084: lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
2085: /*lli=log(out[s1][s2]); */ /* Original formula */
2086: } /* End of if */
2087: ipmx +=1;
2088: sw += weight[i];
2089: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
2090: /*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]); */
2091: if(globpr){
2092: fprintf(ficresilk,"%9ld %6d %2d %2d %1d %1d %3d %11.6f %8.4f\
2093: %11.6f %11.6f %11.6f ", \
2094: num[i],i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],
2095: 2*weight[i]*lli,out[s1][s2],savm[s1][s2]);
2096: for(k=1,llt=0.,l=0.; k<=nlstate; k++){
2097: llt +=ll[k]*gipmx/gsw;
2098: fprintf(ficresilk," %10.6f",-ll[k]*gipmx/gsw);
2099: }
2100: fprintf(ficresilk," %10.6f\n", -llt);
2101: }
2102: } /* end of wave */
2103: } /* end of individual */
2104: for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
2105: /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
2106: l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
2107: if(globpr==0){ /* First time we count the contributions and weights */
2108: gipmx=ipmx;
2109: gsw=sw;
2110: }
2111: return -l;
2112: }
2113:
2114:
2115: /*************** function likelione ***********/
2116: void likelione(FILE *ficres,double p[], int npar, int nlstate, int *globpri, long *ipmx, double *sw, double *fretone, double (*funcone)(double []))
2117: {
2118: /* This routine should help understanding what is done with
2119: the selection of individuals/waves and
2120: to check the exact contribution to the likelihood.
2121: Plotting could be done.
2122: */
2123: int k;
2124:
2125: if(*globpri !=0){ /* Just counts and sums, no printings */
2126: strcpy(fileresilk,"ilk");
2127: strcat(fileresilk,fileres);
2128: if((ficresilk=fopen(fileresilk,"w"))==NULL) {
2129: printf("Problem with resultfile: %s\n", fileresilk);
2130: fprintf(ficlog,"Problem with resultfile: %s\n", fileresilk);
2131: }
2132: 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");
2133: fprintf(ficresilk, "#num_i i s1 s2 mi mw dh likeli weight 2wlli out sav ");
2134: /* i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],2*weight[i]*lli,out[s1][s2],savm[s1][s2]); */
2135: for(k=1; k<=nlstate; k++)
2136: fprintf(ficresilk," -2*gipw/gsw*weight*ll[%d]++",k);
2137: fprintf(ficresilk," -2*gipw/gsw*weight*ll(total)\n");
2138: }
2139:
2140: *fretone=(*funcone)(p);
2141: if(*globpri !=0){
2142: fclose(ficresilk);
2143: fprintf(fichtm,"\n<br>File of contributions to the likelihood: <a href=\"%s\">%s</a><br>\n",subdirf(fileresilk),subdirf(fileresilk));
2144: fflush(fichtm);
2145: }
2146: return;
2147: }
2148:
2149:
2150: /*********** Maximum Likelihood Estimation ***************/
2151:
2152: void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
2153: {
2154: int i,j, iter=0;
2155: double **xi;
2156: double fret;
2157: double fretone; /* Only one call to likelihood */
2158: /* char filerespow[FILENAMELENGTH];*/
2159:
2160: #ifdef NLOPT
2161: int creturn;
2162: nlopt_opt opt;
2163: /* double lb[9] = { -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL }; /\* lower bounds *\/ */
2164: double *lb;
2165: double minf; /* the minimum objective value, upon return */
2166: double * p1; /* Shifted parameters from 0 instead of 1 */
2167: myfunc_data dinst, *d = &dinst;
2168: #endif
2169:
2170:
2171: xi=matrix(1,npar,1,npar);
2172: for (i=1;i<=npar;i++)
2173: for (j=1;j<=npar;j++)
2174: xi[i][j]=(i==j ? 1.0 : 0.0);
2175: printf("Powell\n"); fprintf(ficlog,"Powell\n");
2176: strcpy(filerespow,"pow");
2177: strcat(filerespow,fileres);
2178: if((ficrespow=fopen(filerespow,"w"))==NULL) {
2179: printf("Problem with resultfile: %s\n", filerespow);
2180: fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
2181: }
2182: fprintf(ficrespow,"# Powell\n# iter -2*LL");
2183: for (i=1;i<=nlstate;i++)
2184: for(j=1;j<=nlstate+ndeath;j++)
2185: if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
2186: fprintf(ficrespow,"\n");
2187: #ifdef POWELL
2188: powell(p,xi,npar,ftol,&iter,&fret,func);
2189: #endif
2190:
2191: #ifdef NLOPT
2192: #ifdef NEWUOA
2193: opt = nlopt_create(NLOPT_LN_NEWUOA,npar);
2194: #else
2195: opt = nlopt_create(NLOPT_LN_BOBYQA,npar);
2196: #endif
2197: lb=vector(0,npar-1);
2198: for (i=0;i<npar;i++) lb[i]= -HUGE_VAL;
2199: nlopt_set_lower_bounds(opt, lb);
2200: nlopt_set_initial_step1(opt, 0.1);
2201:
2202: p1= (p+1); /* p *(p+1)@8 and p *(p1)@8 are equal p1[0]=p[1] */
2203: d->function = func;
2204: printf(" Func %.12lf \n",myfunc(npar,p1,NULL,d));
2205: nlopt_set_min_objective(opt, myfunc, d);
2206: nlopt_set_xtol_rel(opt, ftol);
2207: if ((creturn=nlopt_optimize(opt, p1, &minf)) < 0) {
2208: printf("nlopt failed! %d\n",creturn);
2209: }
2210: else {
2211: printf("found minimum after %d evaluations (NLOPT=%d)\n", countcallfunc ,NLOPT);
2212: printf("found minimum at f(%g,%g) = %0.10g\n", p[0], p[1], minf);
2213: iter=1; /* not equal */
2214: }
2215: nlopt_destroy(opt);
2216: #endif
2217: free_matrix(xi,1,npar,1,npar);
2218: fclose(ficrespow);
2219: printf("\n#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
2220: fprintf(ficlog,"\n#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
2221: fprintf(ficres,"\n#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
2222:
2223: }
2224:
2225: /**** Computes Hessian and covariance matrix ***/
2226: void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
2227: {
2228: double **a,**y,*x,pd;
2229: double **hess;
2230: int i, j;
2231: int *indx;
2232:
2233: double hessii(double p[], double delta, int theta, double delti[],double (*func)(double []),int npar);
2234: double hessij(double p[], double delti[], int i, int j,double (*func)(double []),int npar);
2235: void lubksb(double **a, int npar, int *indx, double b[]) ;
2236: void ludcmp(double **a, int npar, int *indx, double *d) ;
2237: double gompertz(double p[]);
2238: hess=matrix(1,npar,1,npar);
2239:
2240: printf("\nCalculation of the hessian matrix. Wait...\n");
2241: fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
2242: for (i=1;i<=npar;i++){
2243: printf("%d",i);fflush(stdout);
2244: fprintf(ficlog,"%d",i);fflush(ficlog);
2245:
2246: hess[i][i]=hessii(p,ftolhess,i,delti,func,npar);
2247:
2248: /* printf(" %f ",p[i]);
2249: printf(" %lf %lf %lf",hess[i][i],ftolhess,delti[i]);*/
2250: }
2251:
2252: for (i=1;i<=npar;i++) {
2253: for (j=1;j<=npar;j++) {
2254: if (j>i) {
2255: printf(".%d%d",i,j);fflush(stdout);
2256: fprintf(ficlog,".%d%d",i,j);fflush(ficlog);
2257: hess[i][j]=hessij(p,delti,i,j,func,npar);
2258:
2259: hess[j][i]=hess[i][j];
2260: /*printf(" %lf ",hess[i][j]);*/
2261: }
2262: }
2263: }
2264: printf("\n");
2265: fprintf(ficlog,"\n");
2266:
2267: printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
2268: fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
2269:
2270: a=matrix(1,npar,1,npar);
2271: y=matrix(1,npar,1,npar);
2272: x=vector(1,npar);
2273: indx=ivector(1,npar);
2274: for (i=1;i<=npar;i++)
2275: for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
2276: ludcmp(a,npar,indx,&pd);
2277:
2278: for (j=1;j<=npar;j++) {
2279: for (i=1;i<=npar;i++) x[i]=0;
2280: x[j]=1;
2281: lubksb(a,npar,indx,x);
2282: for (i=1;i<=npar;i++){
2283: matcov[i][j]=x[i];
2284: }
2285: }
2286:
2287: printf("\n#Hessian matrix#\n");
2288: fprintf(ficlog,"\n#Hessian matrix#\n");
2289: for (i=1;i<=npar;i++) {
2290: for (j=1;j<=npar;j++) {
2291: printf("%.3e ",hess[i][j]);
2292: fprintf(ficlog,"%.3e ",hess[i][j]);
2293: }
2294: printf("\n");
2295: fprintf(ficlog,"\n");
2296: }
2297:
2298: /* Recompute Inverse */
2299: for (i=1;i<=npar;i++)
2300: for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];
2301: ludcmp(a,npar,indx,&pd);
2302:
2303: /* printf("\n#Hessian matrix recomputed#\n");
2304:
2305: for (j=1;j<=npar;j++) {
2306: for (i=1;i<=npar;i++) x[i]=0;
2307: x[j]=1;
2308: lubksb(a,npar,indx,x);
2309: for (i=1;i<=npar;i++){
2310: y[i][j]=x[i];
2311: printf("%.3e ",y[i][j]);
2312: fprintf(ficlog,"%.3e ",y[i][j]);
2313: }
2314: printf("\n");
2315: fprintf(ficlog,"\n");
2316: }
2317: */
2318:
2319: free_matrix(a,1,npar,1,npar);
2320: free_matrix(y,1,npar,1,npar);
2321: free_vector(x,1,npar);
2322: free_ivector(indx,1,npar);
2323: free_matrix(hess,1,npar,1,npar);
2324:
2325:
2326: }
2327:
2328: /*************** hessian matrix ****************/
2329: double hessii(double x[], double delta, int theta, double delti[], double (*func)(double []), int npar)
2330: {
2331: int i;
2332: int l=1, lmax=20;
2333: double k1,k2;
2334: double p2[MAXPARM+1]; /* identical to x */
2335: double res;
2336: double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4;
2337: double fx;
2338: int k=0,kmax=10;
2339: double l1;
2340:
2341: fx=func(x);
2342: for (i=1;i<=npar;i++) p2[i]=x[i];
2343: for(l=0 ; l <=lmax; l++){ /* Enlarging the zone around the Maximum */
2344: l1=pow(10,l);
2345: delts=delt;
2346: for(k=1 ; k <kmax; k=k+1){
2347: delt = delta*(l1*k);
2348: p2[theta]=x[theta] +delt;
2349: k1=func(p2)-fx; /* Might be negative if too close to the theoretical maximum */
2350: p2[theta]=x[theta]-delt;
2351: k2=func(p2)-fx;
2352: /*res= (k1-2.0*fx+k2)/delt/delt; */
2353: res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */
2354:
2355: #ifdef DEBUGHESS
2356: 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);
2357: 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);
2358: #endif
2359: /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
2360: if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
2361: k=kmax;
2362: }
2363: else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
2364: k=kmax; l=lmax*10;
2365: }
2366: else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){
2367: delts=delt;
2368: }
2369: }
2370: }
2371: delti[theta]=delts;
2372: return res;
2373:
2374: }
2375:
2376: double hessij( double x[], double delti[], int thetai,int thetaj,double (*func)(double []),int npar)
2377: {
2378: int i;
2379: int l=1, lmax=20;
2380: double k1,k2,k3,k4,res,fx;
2381: double p2[MAXPARM+1];
2382: int k;
2383:
2384: fx=func(x);
2385: for (k=1; k<=2; k++) {
2386: for (i=1;i<=npar;i++) p2[i]=x[i];
2387: p2[thetai]=x[thetai]+delti[thetai]/k;
2388: p2[thetaj]=x[thetaj]+delti[thetaj]/k;
2389: k1=func(p2)-fx;
2390:
2391: p2[thetai]=x[thetai]+delti[thetai]/k;
2392: p2[thetaj]=x[thetaj]-delti[thetaj]/k;
2393: k2=func(p2)-fx;
2394:
2395: p2[thetai]=x[thetai]-delti[thetai]/k;
2396: p2[thetaj]=x[thetaj]+delti[thetaj]/k;
2397: k3=func(p2)-fx;
2398:
2399: p2[thetai]=x[thetai]-delti[thetai]/k;
2400: p2[thetaj]=x[thetaj]-delti[thetaj]/k;
2401: k4=func(p2)-fx;
2402: res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */
2403: #ifdef DEBUG
2404: 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);
2405: 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);
2406: #endif
2407: }
2408: return res;
2409: }
2410:
2411: /************** Inverse of matrix **************/
2412: void ludcmp(double **a, int n, int *indx, double *d)
2413: {
2414: int i,imax,j,k;
2415: double big,dum,sum,temp;
2416: double *vv;
2417:
2418: vv=vector(1,n);
2419: *d=1.0;
2420: for (i=1;i<=n;i++) {
2421: big=0.0;
2422: for (j=1;j<=n;j++)
2423: if ((temp=fabs(a[i][j])) > big) big=temp;
2424: if (big == 0.0) nrerror("Singular matrix in routine ludcmp");
2425: vv[i]=1.0/big;
2426: }
2427: for (j=1;j<=n;j++) {
2428: for (i=1;i<j;i++) {
2429: sum=a[i][j];
2430: for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];
2431: a[i][j]=sum;
2432: }
2433: big=0.0;
2434: for (i=j;i<=n;i++) {
2435: sum=a[i][j];
2436: for (k=1;k<j;k++)
2437: sum -= a[i][k]*a[k][j];
2438: a[i][j]=sum;
2439: if ( (dum=vv[i]*fabs(sum)) >= big) {
2440: big=dum;
2441: imax=i;
2442: }
2443: }
2444: if (j != imax) {
2445: for (k=1;k<=n;k++) {
2446: dum=a[imax][k];
2447: a[imax][k]=a[j][k];
2448: a[j][k]=dum;
2449: }
2450: *d = -(*d);
2451: vv[imax]=vv[j];
2452: }
2453: indx[j]=imax;
2454: if (a[j][j] == 0.0) a[j][j]=TINY;
2455: if (j != n) {
2456: dum=1.0/(a[j][j]);
2457: for (i=j+1;i<=n;i++) a[i][j] *= dum;
2458: }
2459: }
2460: free_vector(vv,1,n); /* Doesn't work */
2461: ;
2462: }
2463:
2464: void lubksb(double **a, int n, int *indx, double b[])
2465: {
2466: int i,ii=0,ip,j;
2467: double sum;
2468:
2469: for (i=1;i<=n;i++) {
2470: ip=indx[i];
2471: sum=b[ip];
2472: b[ip]=b[i];
2473: if (ii)
2474: for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];
2475: else if (sum) ii=i;
2476: b[i]=sum;
2477: }
2478: for (i=n;i>=1;i--) {
2479: sum=b[i];
2480: for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];
2481: b[i]=sum/a[i][i];
2482: }
2483: }
2484:
2485: void pstamp(FILE *fichier)
2486: {
2487: fprintf(fichier,"# %s.%s\n#%s\n#%s\n# %s", optionfilefiname,optionfilext,version,fullversion,strstart);
2488: }
2489:
2490: /************ Frequencies ********************/
2491: 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[])
2492: { /* Some frequencies */
2493:
2494: int i, m, jk, j1, bool, z1,j;
2495: int first;
2496: double ***freq; /* Frequencies */
2497: double *pp, **prop;
2498: double pos,posprop, k2, dateintsum=0,k2cpt=0;
2499: char fileresp[FILENAMELENGTH];
2500:
2501: pp=vector(1,nlstate);
2502: prop=matrix(1,nlstate,iagemin,iagemax+3);
2503: strcpy(fileresp,"p");
2504: strcat(fileresp,fileres);
2505: if((ficresp=fopen(fileresp,"w"))==NULL) {
2506: printf("Problem with prevalence resultfile: %s\n", fileresp);
2507: fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
2508: exit(0);
2509: }
2510: freq= ma3x(-5,nlstate+ndeath,-5,nlstate+ndeath,iagemin,iagemax+3);
2511: j1=0;
2512:
2513: j=cptcoveff;
2514: if (cptcovn<1) {j=1;ncodemax[1]=1;}
2515:
2516: first=1;
2517:
2518: /* for(k1=1; k1<=j ; k1++){ /* Loop on covariates */
2519: /* for(i1=1; i1<=ncodemax[k1];i1++){ /* Now it is 2 */
2520: /* j1++;
2521: */
2522: for (j1 = 1; j1 <= (int) pow(2,cptcoveff); j1++){
2523: /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
2524: scanf("%d", i);*/
2525: for (i=-5; i<=nlstate+ndeath; i++)
2526: for (jk=-5; jk<=nlstate+ndeath; jk++)
2527: for(m=iagemin; m <= iagemax+3; m++)
2528: freq[i][jk][m]=0;
2529:
2530: for (i=1; i<=nlstate; i++)
2531: for(m=iagemin; m <= iagemax+3; m++)
2532: prop[i][m]=0;
2533:
2534: dateintsum=0;
2535: k2cpt=0;
2536: for (i=1; i<=imx; i++) {
2537: bool=1;
2538: if (cptcovn>0) { /* Filter is here: Must be looked at for model=V1+V2+V3+V4 */
2539: for (z1=1; z1<=cptcoveff; z1++)
2540: if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]){
2541: /* Tests if the value of each of the covariates of i is equal to filter j1 */
2542: bool=0;
2543: /* 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",
2544: bool,i,z1, z1, Tvaraff[z1],i,covar[Tvaraff[z1]][i],j1,z1,codtab[j1][z1],
2545: j1,z1,nbcode[Tvaraff[z1]][codtab[j1][z1]],j1);*/
2546: /* For j1=7 in V1+V2+V3+V4 = 0 1 1 0 and codtab[7][3]=1 and nbcde[3][?]=1*/
2547: }
2548: }
2549:
2550: if (bool==1){
2551: for(m=firstpass; m<=lastpass; m++){
2552: k2=anint[m][i]+(mint[m][i]/12.);
2553: /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/
2554: if(agev[m][i]==0) agev[m][i]=iagemax+1;
2555: if(agev[m][i]==1) agev[m][i]=iagemax+2;
2556: if (s[m][i]>0 && s[m][i]<=nlstate) prop[s[m][i]][(int)agev[m][i]] += weight[i];
2557: if (m<lastpass) {
2558: freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
2559: freq[s[m][i]][s[m+1][i]][iagemax+3] += weight[i];
2560: }
2561:
2562: if ((agev[m][i]>1) && (agev[m][i]< (iagemax+3))) {
2563: dateintsum=dateintsum+k2;
2564: k2cpt++;
2565: }
2566: /*}*/
2567: }
2568: }
2569: } /* end i */
2570:
2571: /* fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
2572: pstamp(ficresp);
2573: if (cptcovn>0) {
2574: fprintf(ficresp, "\n#********** Variable ");
2575: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
2576: fprintf(ficresp, "**********\n#");
2577: fprintf(ficlog, "\n#********** Variable ");
2578: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficlog, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
2579: fprintf(ficlog, "**********\n#");
2580: }
2581: for(i=1; i<=nlstate;i++)
2582: fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
2583: fprintf(ficresp, "\n");
2584:
2585: for(i=iagemin; i <= iagemax+3; i++){
2586: if(i==iagemax+3){
2587: fprintf(ficlog,"Total");
2588: }else{
2589: if(first==1){
2590: first=0;
2591: printf("See log file for details...\n");
2592: }
2593: fprintf(ficlog,"Age %d", i);
2594: }
2595: for(jk=1; jk <=nlstate ; jk++){
2596: for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
2597: pp[jk] += freq[jk][m][i];
2598: }
2599: for(jk=1; jk <=nlstate ; jk++){
2600: for(m=-1, pos=0; m <=0 ; m++)
2601: pos += freq[jk][m][i];
2602: if(pp[jk]>=1.e-10){
2603: if(first==1){
2604: printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
2605: }
2606: fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
2607: }else{
2608: if(first==1)
2609: printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
2610: fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
2611: }
2612: }
2613:
2614: for(jk=1; jk <=nlstate ; jk++){
2615: for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
2616: pp[jk] += freq[jk][m][i];
2617: }
2618: for(jk=1,pos=0,posprop=0; jk <=nlstate ; jk++){
2619: pos += pp[jk];
2620: posprop += prop[jk][i];
2621: }
2622: for(jk=1; jk <=nlstate ; jk++){
2623: if(pos>=1.e-5){
2624: if(first==1)
2625: printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
2626: fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
2627: }else{
2628: if(first==1)
2629: printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
2630: fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
2631: }
2632: if( i <= iagemax){
2633: if(pos>=1.e-5){
2634: fprintf(ficresp," %d %.5f %.0f %.0f",i,prop[jk][i]/posprop, prop[jk][i],posprop);
2635: /*probs[i][jk][j1]= pp[jk]/pos;*/
2636: /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/
2637: }
2638: else
2639: fprintf(ficresp," %d NaNq %.0f %.0f",i,prop[jk][i],posprop);
2640: }
2641: }
2642:
2643: for(jk=-1; jk <=nlstate+ndeath; jk++)
2644: for(m=-1; m <=nlstate+ndeath; m++)
2645: if(freq[jk][m][i] !=0 ) {
2646: if(first==1)
2647: printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
2648: fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
2649: }
2650: if(i <= iagemax)
2651: fprintf(ficresp,"\n");
2652: if(first==1)
2653: printf("Others in log...\n");
2654: fprintf(ficlog,"\n");
2655: }
2656: /*}*/
2657: }
2658: dateintmean=dateintsum/k2cpt;
2659:
2660: fclose(ficresp);
2661: free_ma3x(freq,-5,nlstate+ndeath,-5,nlstate+ndeath, iagemin, iagemax+3);
2662: free_vector(pp,1,nlstate);
2663: free_matrix(prop,1,nlstate,iagemin, iagemax+3);
2664: /* End of Freq */
2665: }
2666:
2667: /************ Prevalence ********************/
2668: 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)
2669: {
2670: /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
2671: in each health status at the date of interview (if between dateprev1 and dateprev2).
2672: We still use firstpass and lastpass as another selection.
2673: */
2674:
2675: int i, m, jk, j1, bool, z1,j;
2676:
2677: double **prop;
2678: double posprop;
2679: double y2; /* in fractional years */
2680: int iagemin, iagemax;
2681: int first; /** to stop verbosity which is redirected to log file */
2682:
2683: iagemin= (int) agemin;
2684: iagemax= (int) agemax;
2685: /*pp=vector(1,nlstate);*/
2686: prop=matrix(1,nlstate,iagemin,iagemax+3);
2687: /* freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
2688: j1=0;
2689:
2690: /*j=cptcoveff;*/
2691: if (cptcovn<1) {j=1;ncodemax[1]=1;}
2692:
2693: first=1;
2694: for(j1=1; j1<= (int) pow(2,cptcoveff);j1++){
2695: /*for(i1=1; i1<=ncodemax[k1];i1++){
2696: j1++;*/
2697:
2698: for (i=1; i<=nlstate; i++)
2699: for(m=iagemin; m <= iagemax+3; m++)
2700: prop[i][m]=0.0;
2701:
2702: for (i=1; i<=imx; i++) { /* Each individual */
2703: bool=1;
2704: if (cptcovn>0) {
2705: for (z1=1; z1<=cptcoveff; z1++)
2706: if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])
2707: bool=0;
2708: }
2709: if (bool==1) {
2710: for(m=firstpass; m<=lastpass; m++){/* Other selection (we can limit to certain interviews*/
2711: y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
2712: if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
2713: if(agev[m][i]==0) agev[m][i]=iagemax+1;
2714: if(agev[m][i]==1) agev[m][i]=iagemax+2;
2715: 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);
2716: if (s[m][i]>0 && s[m][i]<=nlstate) {
2717: /*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]]);*/
2718: prop[s[m][i]][(int)agev[m][i]] += weight[i];
2719: prop[s[m][i]][iagemax+3] += weight[i];
2720: }
2721: }
2722: } /* end selection of waves */
2723: }
2724: }
2725: for(i=iagemin; i <= iagemax+3; i++){
2726: for(jk=1,posprop=0; jk <=nlstate ; jk++) {
2727: posprop += prop[jk][i];
2728: }
2729:
2730: for(jk=1; jk <=nlstate ; jk++){
2731: if( i <= iagemax){
2732: if(posprop>=1.e-5){
2733: probs[i][jk][j1]= prop[jk][i]/posprop;
2734: } else{
2735: if(first==1){
2736: first=0;
2737: 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]);
2738: }
2739: }
2740: }
2741: }/* end jk */
2742: }/* end i */
2743: /*} *//* end i1 */
2744: } /* end j1 */
2745:
2746: /* free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
2747: /*free_vector(pp,1,nlstate);*/
2748: free_matrix(prop,1,nlstate, iagemin,iagemax+3);
2749: } /* End of prevalence */
2750:
2751: /************* Waves Concatenation ***************/
2752:
2753: 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)
2754: {
2755: /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
2756: Death is a valid wave (if date is known).
2757: mw[mi][i] is the mi (mi=1 to wav[i]) effective wave of individual i
2758: dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
2759: and mw[mi+1][i]. dh depends on stepm.
2760: */
2761:
2762: int i, mi, m;
2763: /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
2764: double sum=0., jmean=0.;*/
2765: int first;
2766: int j, k=0,jk, ju, jl;
2767: double sum=0.;
2768: first=0;
2769: jmin=100000;
2770: jmax=-1;
2771: jmean=0.;
2772: for(i=1; i<=imx; i++){
2773: mi=0;
2774: m=firstpass;
2775: while(s[m][i] <= nlstate){
2776: if(s[m][i]>=1 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5)
2777: mw[++mi][i]=m;
2778: if(m >=lastpass)
2779: break;
2780: else
2781: m++;
2782: }/* end while */
2783: if (s[m][i] > nlstate){
2784: mi++; /* Death is another wave */
2785: /* if(mi==0) never been interviewed correctly before death */
2786: /* Only death is a correct wave */
2787: mw[mi][i]=m;
2788: }
2789:
2790: wav[i]=mi;
2791: if(mi==0){
2792: nbwarn++;
2793: if(first==0){
2794: printf("Warning! No valid information for individual %ld line=%d (skipped) and may be others, see log file\n",num[i],i);
2795: first=1;
2796: }
2797: if(first==1){
2798: fprintf(ficlog,"Warning! No valid information for individual %ld line=%d (skipped)\n",num[i],i);
2799: }
2800: } /* end mi==0 */
2801: } /* End individuals */
2802:
2803: for(i=1; i<=imx; i++){
2804: for(mi=1; mi<wav[i];mi++){
2805: if (stepm <=0)
2806: dh[mi][i]=1;
2807: else{
2808: if (s[mw[mi+1][i]][i] > nlstate) { /* A death */
2809: if (agedc[i] < 2*AGESUP) {
2810: j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);
2811: if(j==0) j=1; /* Survives at least one month after exam */
2812: else if(j<0){
2813: nberr++;
2814: 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]);
2815: j=1; /* Temporary Dangerous patch */
2816: 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);
2817: 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]);
2818: 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);
2819: }
2820: k=k+1;
2821: if (j >= jmax){
2822: jmax=j;
2823: ijmax=i;
2824: }
2825: if (j <= jmin){
2826: jmin=j;
2827: ijmin=i;
2828: }
2829: sum=sum+j;
2830: /*if (j<0) printf("j=%d num=%d \n",j,i);*/
2831: /* printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
2832: }
2833: }
2834: else{
2835: j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
2836: /* 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]); */
2837:
2838: k=k+1;
2839: if (j >= jmax) {
2840: jmax=j;
2841: ijmax=i;
2842: }
2843: else if (j <= jmin){
2844: jmin=j;
2845: ijmin=i;
2846: }
2847: /* if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
2848: /*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]);*/
2849: if(j<0){
2850: nberr++;
2851: 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]);
2852: 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]);
2853: }
2854: sum=sum+j;
2855: }
2856: jk= j/stepm;
2857: jl= j -jk*stepm;
2858: ju= j -(jk+1)*stepm;
2859: if(mle <=1){ /* only if we use a the linear-interpoloation pseudo-likelihood */
2860: if(jl==0){
2861: dh[mi][i]=jk;
2862: bh[mi][i]=0;
2863: }else{ /* We want a negative bias in order to only have interpolation ie
2864: * to avoid the price of an extra matrix product in likelihood */
2865: dh[mi][i]=jk+1;
2866: bh[mi][i]=ju;
2867: }
2868: }else{
2869: if(jl <= -ju){
2870: dh[mi][i]=jk;
2871: bh[mi][i]=jl; /* bias is positive if real duration
2872: * is higher than the multiple of stepm and negative otherwise.
2873: */
2874: }
2875: else{
2876: dh[mi][i]=jk+1;
2877: bh[mi][i]=ju;
2878: }
2879: if(dh[mi][i]==0){
2880: dh[mi][i]=1; /* At least one step */
2881: bh[mi][i]=ju; /* At least one step */
2882: /* 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);*/
2883: }
2884: } /* end if mle */
2885: }
2886: } /* end wave */
2887: }
2888: jmean=sum/k;
2889: 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);
2890: 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);
2891: }
2892:
2893: /*********** Tricode ****************************/
2894: void tricode(int *Tvar, int **nbcode, int imx, int *Ndum)
2895: {
2896: /**< Uses cptcovn+2*cptcovprod as the number of covariates */
2897: /* Tvar[i]=atoi(stre); find 'n' in Vn and stores in Tvar. If model=V2+V1 Tvar[1]=2 and Tvar[2]=1
2898: /* Boring subroutine which should only output nbcode[Tvar[j]][k]
2899: * Tvar[5] in V2+V1+V3*age+V2*V4 is 2 (V2)
2900: /* nbcode[Tvar[j]][1]=
2901: */
2902:
2903: int ij=1, k=0, j=0, i=0, maxncov=NCOVMAX;
2904: int modmaxcovj=0; /* Modality max of covariates j */
2905: int cptcode=0; /* Modality max of covariates j */
2906: int modmincovj=0; /* Modality min of covariates j */
2907:
2908:
2909: cptcoveff=0;
2910:
2911: for (k=-1; k < maxncov; k++) Ndum[k]=0;
2912: for (k=1; k <= maxncov; k++) ncodemax[k]=0; /* Horrible constant again replaced by NCOVMAX */
2913:
2914: /* Loop on covariates without age and products */
2915: for (j=1; j<=(cptcovs); j++) { /* model V1 + V2*age+ V3 + V3*V4 : V1 + V3 = 2 only */
2916: for (i=1; i<=imx; i++) { /* Lopp on individuals: reads the data file to get the maximum value of the
2917: modality of this covariate Vj*/
2918: ij=(int)(covar[Tvar[j]][i]); /* ij=0 or 1 or -1. Value of the covariate Tvar[j] for individual i
2919: * If product of Vn*Vm, still boolean *:
2920: * If it was coded 1, 2, 3, 4 should be splitted into 3 boolean variables
2921: * 1 => 0 0 0, 2 => 0 0 1, 3 => 0 1 1, 4=1 0 0 */
2922: /* Finds for covariate j, n=Tvar[j] of Vn . ij is the
2923: modality of the nth covariate of individual i. */
2924: if (ij > modmaxcovj)
2925: modmaxcovj=ij;
2926: else if (ij < modmincovj)
2927: modmincovj=ij;
2928: if ((ij < -1) && (ij > NCOVMAX)){
2929: printf( "Error: minimal is less than -1 or maximal is bigger than %d. Exiting. \n", NCOVMAX );
2930: exit(1);
2931: }else
2932: Ndum[ij]++; /*counts and stores the occurence of this modality 0, 1, -1*/
2933: /* If coded 1, 2, 3 , counts the number of 1 Ndum[1], number of 2, Ndum[2], etc */
2934: /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
2935: /* getting the maximum value of the modality of the covariate
2936: (should be 0 or 1 now) Tvar[j]. If V=sex and male is coded 0 and
2937: female is 1, then modmaxcovj=1.*/
2938: }
2939: printf(" Minimal and maximal values of %d th covariate V%d: min=%d max=%d \n", j, Tvar[j], modmincovj, modmaxcovj);
2940: cptcode=modmaxcovj;
2941: /* Ndum[0] = frequency of 0 for model-covariate j, Ndum[1] frequency of 1 etc. */
2942: /*for (i=0; i<=cptcode; i++) {*/
2943: for (i=modmincovj; i<=modmaxcovj; i++) { /* i=-1 ? 0 and 1*//* For each value of the modality of model-cov j */
2944: printf("Frequencies of covariates %d V%d %d\n", j, Tvar[j], Ndum[i]);
2945: if( Ndum[i] != 0 ){ /* Counts if nobody answered, empty modality */
2946: ncodemax[j]++; /* ncodemax[j]= Number of non-null modalities of the j th covariate. */
2947: }
2948: /* In fact ncodemax[j]=2 (dichotom. variables only) but it could be more for
2949: historical reasons: 3 if coded 1, 2, 3 and 4 and Ndum[2]=0 */
2950: } /* Ndum[-1] number of undefined modalities */
2951:
2952: /* j is a covariate, n=Tvar[j] of Vn; Fills nbcode */
2953: /* For covariate j, modalities could be 1, 2, 3, 4. If Ndum[2]=0 ncodemax[j] is not 4 but 3 */
2954: /* If Ndum[3}= 635; Ndum[4]=0; Ndum[5]=0; Ndum[6]=27; Ndum[7]=125;
2955: modmincovj=3; modmaxcovj = 7;
2956: There are only 3 modalities non empty (or 2 if 27 is too few) : ncodemax[j]=3;
2957: which will be coded 0, 1, 2 which in binary on 3-1 digits are 0=00 1=01, 2=10; defining two dummy
2958: variables V1_1 and V1_2.
2959: nbcode[Tvar[j]][ij]=k;
2960: nbcode[Tvar[j]][1]=0;
2961: nbcode[Tvar[j]][2]=1;
2962: nbcode[Tvar[j]][3]=2;
2963: */
2964: ij=1; /* ij is similar to i but can jumps over null modalities */
2965: for (i=modmincovj; i<=modmaxcovj; i++) { /* i= 1 to 2 for dichotomous, or from 1 to 3 */
2966: for (k=0; k<= cptcode; k++) { /* k=-1 ? k=0 to 1 *//* Could be 1 to 4 */
2967: /*recode from 0 */
2968: if (Ndum[k] != 0) { /* If at least one individual responded to this modality k */
2969: nbcode[Tvar[j]][ij]=k; /* stores the modality in an array nbcode.
2970: k is a modality. If we have model=V1+V1*sex
2971: then: nbcode[1][1]=0 ; nbcode[1][2]=1; nbcode[2][1]=0 ; nbcode[2][2]=1; */
2972: ij++;
2973: }
2974: if (ij > ncodemax[j]) break;
2975: } /* end of loop on */
2976: } /* end of loop on modality */
2977: } /* end of loop on model-covariate j. nbcode[Tvarj][1]=0 and nbcode[Tvarj][2]=1 sets the value of covariate j*/
2978:
2979: for (k=-1; k< maxncov; k++) Ndum[k]=0;
2980:
2981: for (i=1; i<=ncovmodel-2; i++) { /* -2, cste and age */
2982: /* Listing of all covariables in statement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/
2983: ij=Tvar[i]; /* Tvar might be -1 if status was unknown */
2984: Ndum[ij]++;
2985: }
2986:
2987: ij=1;
2988: for (i=0; i<= maxncov-1; i++) { /* modmaxcovj is unknown here. Only Ndum[2(V2),3(age*V3), 5(V3*V2) 6(V1*V4) */
2989: /*printf("Ndum[%d]=%d\n",i, Ndum[i]);*/
2990: if((Ndum[i]!=0) && (i<=ncovcol)){
2991: /*printf("diff Ndum[%d]=%d\n",i, Ndum[i]);*/
2992: Tvaraff[ij]=i; /*For printing (unclear) */
2993: ij++;
2994: }else
2995: Tvaraff[ij]=0;
2996: }
2997: ij--;
2998: cptcoveff=ij; /*Number of total covariates*/
2999:
3000: }
3001:
3002:
3003: /*********** Health Expectancies ****************/
3004:
3005: void evsij(double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int cij, int estepm,char strstart[] )
3006:
3007: {
3008: /* Health expectancies, no variances */
3009: int i, j, nhstepm, hstepm, h, nstepm;
3010: int nhstepma, nstepma; /* Decreasing with age */
3011: double age, agelim, hf;
3012: double ***p3mat;
3013: double eip;
3014:
3015: pstamp(ficreseij);
3016: fprintf(ficreseij,"# (a) Life expectancies by health status at initial age and (b) health expectancies by health status at initial age\n");
3017: fprintf(ficreseij,"# Age");
3018: for(i=1; i<=nlstate;i++){
3019: for(j=1; j<=nlstate;j++){
3020: fprintf(ficreseij," e%1d%1d ",i,j);
3021: }
3022: fprintf(ficreseij," e%1d. ",i);
3023: }
3024: fprintf(ficreseij,"\n");
3025:
3026:
3027: if(estepm < stepm){
3028: printf ("Problem %d lower than %d\n",estepm, stepm);
3029: }
3030: else hstepm=estepm;
3031: /* We compute the life expectancy from trapezoids spaced every estepm months
3032: * This is mainly to measure the difference between two models: for example
3033: * if stepm=24 months pijx are given only every 2 years and by summing them
3034: * we are calculating an estimate of the Life Expectancy assuming a linear
3035: * progression in between and thus overestimating or underestimating according
3036: * to the curvature of the survival function. If, for the same date, we
3037: * estimate the model with stepm=1 month, we can keep estepm to 24 months
3038: * to compare the new estimate of Life expectancy with the same linear
3039: * hypothesis. A more precise result, taking into account a more precise
3040: * curvature will be obtained if estepm is as small as stepm. */
3041:
3042: /* For example we decided to compute the life expectancy with the smallest unit */
3043: /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
3044: nhstepm is the number of hstepm from age to agelim
3045: nstepm is the number of stepm from age to agelin.
3046: Look at hpijx to understand the reason of that which relies in memory size
3047: and note for a fixed period like estepm months */
3048: /* We decided (b) to get a life expectancy respecting the most precise curvature of the
3049: survival function given by stepm (the optimization length). Unfortunately it
3050: means that if the survival funtion is printed only each two years of age and if
3051: you sum them up and add 1 year (area under the trapezoids) you won't get the same
3052: results. So we changed our mind and took the option of the best precision.
3053: */
3054: hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
3055:
3056: agelim=AGESUP;
3057: /* If stepm=6 months */
3058: /* Computed by stepm unit matrices, product of hstepm matrices, stored
3059: in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
3060:
3061: /* nhstepm age range expressed in number of stepm */
3062: nstepm=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
3063: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
3064: /* if (stepm >= YEARM) hstepm=1;*/
3065: nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
3066: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3067:
3068: for (age=bage; age<=fage; age ++){
3069: nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
3070: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
3071: /* if (stepm >= YEARM) hstepm=1;*/
3072: nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
3073:
3074: /* If stepm=6 months */
3075: /* Computed by stepm unit matrices, product of hstepma matrices, stored
3076: in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
3077:
3078: hpxij(p3mat,nhstepma,age,hstepm,x,nlstate,stepm,oldm, savm, cij);
3079:
3080: hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
3081:
3082: printf("%d|",(int)age);fflush(stdout);
3083: fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
3084:
3085: /* Computing expectancies */
3086: for(i=1; i<=nlstate;i++)
3087: for(j=1; j<=nlstate;j++)
3088: for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
3089: eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
3090:
3091: /* 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]);*/
3092:
3093: }
3094:
3095: fprintf(ficreseij,"%3.0f",age );
3096: for(i=1; i<=nlstate;i++){
3097: eip=0;
3098: for(j=1; j<=nlstate;j++){
3099: eip +=eij[i][j][(int)age];
3100: fprintf(ficreseij,"%9.4f", eij[i][j][(int)age] );
3101: }
3102: fprintf(ficreseij,"%9.4f", eip );
3103: }
3104: fprintf(ficreseij,"\n");
3105:
3106: }
3107: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3108: printf("\n");
3109: fprintf(ficlog,"\n");
3110:
3111: }
3112:
3113: 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[] )
3114:
3115: {
3116: /* Covariances of health expectancies eij and of total life expectancies according
3117: to initial status i, ei. .
3118: */
3119: int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2, ij, ji;
3120: int nhstepma, nstepma; /* Decreasing with age */
3121: double age, agelim, hf;
3122: double ***p3matp, ***p3matm, ***varhe;
3123: double **dnewm,**doldm;
3124: double *xp, *xm;
3125: double **gp, **gm;
3126: double ***gradg, ***trgradg;
3127: int theta;
3128:
3129: double eip, vip;
3130:
3131: varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage);
3132: xp=vector(1,npar);
3133: xm=vector(1,npar);
3134: dnewm=matrix(1,nlstate*nlstate,1,npar);
3135: doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate);
3136:
3137: pstamp(ficresstdeij);
3138: fprintf(ficresstdeij,"# Health expectancies with standard errors\n");
3139: fprintf(ficresstdeij,"# Age");
3140: for(i=1; i<=nlstate;i++){
3141: for(j=1; j<=nlstate;j++)
3142: fprintf(ficresstdeij," e%1d%1d (SE)",i,j);
3143: fprintf(ficresstdeij," e%1d. ",i);
3144: }
3145: fprintf(ficresstdeij,"\n");
3146:
3147: pstamp(ficrescveij);
3148: fprintf(ficrescveij,"# Subdiagonal matrix of covariances of health expectancies by age: cov(eij,ekl)\n");
3149: fprintf(ficrescveij,"# Age");
3150: for(i=1; i<=nlstate;i++)
3151: for(j=1; j<=nlstate;j++){
3152: cptj= (j-1)*nlstate+i;
3153: for(i2=1; i2<=nlstate;i2++)
3154: for(j2=1; j2<=nlstate;j2++){
3155: cptj2= (j2-1)*nlstate+i2;
3156: if(cptj2 <= cptj)
3157: fprintf(ficrescveij," %1d%1d,%1d%1d",i,j,i2,j2);
3158: }
3159: }
3160: fprintf(ficrescveij,"\n");
3161:
3162: if(estepm < stepm){
3163: printf ("Problem %d lower than %d\n",estepm, stepm);
3164: }
3165: else hstepm=estepm;
3166: /* We compute the life expectancy from trapezoids spaced every estepm months
3167: * This is mainly to measure the difference between two models: for example
3168: * if stepm=24 months pijx are given only every 2 years and by summing them
3169: * we are calculating an estimate of the Life Expectancy assuming a linear
3170: * progression in between and thus overestimating or underestimating according
3171: * to the curvature of the survival function. If, for the same date, we
3172: * estimate the model with stepm=1 month, we can keep estepm to 24 months
3173: * to compare the new estimate of Life expectancy with the same linear
3174: * hypothesis. A more precise result, taking into account a more precise
3175: * curvature will be obtained if estepm is as small as stepm. */
3176:
3177: /* For example we decided to compute the life expectancy with the smallest unit */
3178: /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
3179: nhstepm is the number of hstepm from age to agelim
3180: nstepm is the number of stepm from age to agelin.
3181: Look at hpijx to understand the reason of that which relies in memory size
3182: and note for a fixed period like estepm months */
3183: /* We decided (b) to get a life expectancy respecting the most precise curvature of the
3184: survival function given by stepm (the optimization length). Unfortunately it
3185: means that if the survival funtion is printed only each two years of age and if
3186: you sum them up and add 1 year (area under the trapezoids) you won't get the same
3187: results. So we changed our mind and took the option of the best precision.
3188: */
3189: hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
3190:
3191: /* If stepm=6 months */
3192: /* nhstepm age range expressed in number of stepm */
3193: agelim=AGESUP;
3194: nstepm=(int) rint((agelim-bage)*YEARM/stepm);
3195: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
3196: /* if (stepm >= YEARM) hstepm=1;*/
3197: nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
3198:
3199: p3matp=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3200: p3matm=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3201: gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);
3202: trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar);
3203: gp=matrix(0,nhstepm,1,nlstate*nlstate);
3204: gm=matrix(0,nhstepm,1,nlstate*nlstate);
3205:
3206: for (age=bage; age<=fage; age ++){
3207: nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
3208: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
3209: /* if (stepm >= YEARM) hstepm=1;*/
3210: nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
3211:
3212: /* If stepm=6 months */
3213: /* Computed by stepm unit matrices, product of hstepma matrices, stored
3214: in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
3215:
3216: hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
3217:
3218: /* Computing Variances of health expectancies */
3219: /* Gradient is computed with plus gp and minus gm. Code is duplicated in order to
3220: decrease memory allocation */
3221: for(theta=1; theta <=npar; theta++){
3222: for(i=1; i<=npar; i++){
3223: xp[i] = x[i] + (i==theta ?delti[theta]:0);
3224: xm[i] = x[i] - (i==theta ?delti[theta]:0);
3225: }
3226: hpxij(p3matp,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, cij);
3227: hpxij(p3matm,nhstepm,age,hstepm,xm,nlstate,stepm,oldm,savm, cij);
3228:
3229: for(j=1; j<= nlstate; j++){
3230: for(i=1; i<=nlstate; i++){
3231: for(h=0; h<=nhstepm-1; h++){
3232: gp[h][(j-1)*nlstate + i] = (p3matp[i][j][h]+p3matp[i][j][h+1])/2.;
3233: gm[h][(j-1)*nlstate + i] = (p3matm[i][j][h]+p3matm[i][j][h+1])/2.;
3234: }
3235: }
3236: }
3237:
3238: for(ij=1; ij<= nlstate*nlstate; ij++)
3239: for(h=0; h<=nhstepm-1; h++){
3240: gradg[h][theta][ij]= (gp[h][ij]-gm[h][ij])/2./delti[theta];
3241: }
3242: }/* End theta */
3243:
3244:
3245: for(h=0; h<=nhstepm-1; h++)
3246: for(j=1; j<=nlstate*nlstate;j++)
3247: for(theta=1; theta <=npar; theta++)
3248: trgradg[h][j][theta]=gradg[h][theta][j];
3249:
3250:
3251: for(ij=1;ij<=nlstate*nlstate;ij++)
3252: for(ji=1;ji<=nlstate*nlstate;ji++)
3253: varhe[ij][ji][(int)age] =0.;
3254:
3255: printf("%d|",(int)age);fflush(stdout);
3256: fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
3257: for(h=0;h<=nhstepm-1;h++){
3258: for(k=0;k<=nhstepm-1;k++){
3259: matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov);
3260: matprod2(doldm,dnewm,1,nlstate*nlstate,1,npar,1,nlstate*nlstate,gradg[k]);
3261: for(ij=1;ij<=nlstate*nlstate;ij++)
3262: for(ji=1;ji<=nlstate*nlstate;ji++)
3263: varhe[ij][ji][(int)age] += doldm[ij][ji]*hf*hf;
3264: }
3265: }
3266:
3267: /* Computing expectancies */
3268: hpxij(p3matm,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, cij);
3269: for(i=1; i<=nlstate;i++)
3270: for(j=1; j<=nlstate;j++)
3271: for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
3272: eij[i][j][(int)age] += (p3matm[i][j][h]+p3matm[i][j][h+1])/2.0*hf;
3273:
3274: /* 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]);*/
3275:
3276: }
3277:
3278: fprintf(ficresstdeij,"%3.0f",age );
3279: for(i=1; i<=nlstate;i++){
3280: eip=0.;
3281: vip=0.;
3282: for(j=1; j<=nlstate;j++){
3283: eip += eij[i][j][(int)age];
3284: for(k=1; k<=nlstate;k++) /* Sum on j and k of cov(eij,eik) */
3285: vip += varhe[(j-1)*nlstate+i][(k-1)*nlstate+i][(int)age];
3286: fprintf(ficresstdeij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[(j-1)*nlstate+i][(j-1)*nlstate+i][(int)age]) );
3287: }
3288: fprintf(ficresstdeij," %9.4f (%.4f)", eip, sqrt(vip));
3289: }
3290: fprintf(ficresstdeij,"\n");
3291:
3292: fprintf(ficrescveij,"%3.0f",age );
3293: for(i=1; i<=nlstate;i++)
3294: for(j=1; j<=nlstate;j++){
3295: cptj= (j-1)*nlstate+i;
3296: for(i2=1; i2<=nlstate;i2++)
3297: for(j2=1; j2<=nlstate;j2++){
3298: cptj2= (j2-1)*nlstate+i2;
3299: if(cptj2 <= cptj)
3300: fprintf(ficrescveij," %.4f", varhe[cptj][cptj2][(int)age]);
3301: }
3302: }
3303: fprintf(ficrescveij,"\n");
3304:
3305: }
3306: free_matrix(gm,0,nhstepm,1,nlstate*nlstate);
3307: free_matrix(gp,0,nhstepm,1,nlstate*nlstate);
3308: free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*nlstate);
3309: free_ma3x(trgradg,0,nhstepm,1,nlstate*nlstate,1,npar);
3310: free_ma3x(p3matm,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3311: free_ma3x(p3matp,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3312: printf("\n");
3313: fprintf(ficlog,"\n");
3314:
3315: free_vector(xm,1,npar);
3316: free_vector(xp,1,npar);
3317: free_matrix(dnewm,1,nlstate*nlstate,1,npar);
3318: free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate);
3319: free_ma3x(varhe,1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int)fage);
3320: }
3321:
3322: /************ Variance ******************/
3323: 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[])
3324: {
3325: /* Variance of health expectancies */
3326: /* double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
3327: /* double **newm;*/
3328: double **dnewm,**doldm;
3329: double **dnewmp,**doldmp;
3330: int i, j, nhstepm, hstepm, h, nstepm ;
3331: int k;
3332: double *xp;
3333: double **gp, **gm; /* for var eij */
3334: double ***gradg, ***trgradg; /*for var eij */
3335: double **gradgp, **trgradgp; /* for var p point j */
3336: double *gpp, *gmp; /* for var p point j */
3337: double **varppt; /* for var p point j nlstate to nlstate+ndeath */
3338: double ***p3mat;
3339: double age,agelim, hf;
3340: double ***mobaverage;
3341: int theta;
3342: char digit[4];
3343: char digitp[25];
3344:
3345: char fileresprobmorprev[FILENAMELENGTH];
3346:
3347: if(popbased==1){
3348: if(mobilav!=0)
3349: strcpy(digitp,"-populbased-mobilav-");
3350: else strcpy(digitp,"-populbased-nomobil-");
3351: }
3352: else
3353: strcpy(digitp,"-stablbased-");
3354:
3355: if (mobilav!=0) {
3356: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
3357: if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
3358: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
3359: printf(" Error in movingaverage mobilav=%d\n",mobilav);
3360: }
3361: }
3362:
3363: strcpy(fileresprobmorprev,"prmorprev");
3364: sprintf(digit,"%-d",ij);
3365: /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
3366: strcat(fileresprobmorprev,digit); /* Tvar to be done */
3367: strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
3368: strcat(fileresprobmorprev,fileres);
3369: if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
3370: printf("Problem with resultfile: %s\n", fileresprobmorprev);
3371: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
3372: }
3373: printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
3374:
3375: fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
3376: pstamp(ficresprobmorprev);
3377: 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);
3378: fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
3379: for(j=nlstate+1; j<=(nlstate+ndeath);j++){
3380: fprintf(ficresprobmorprev," p.%-d SE",j);
3381: for(i=1; i<=nlstate;i++)
3382: fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
3383: }
3384: fprintf(ficresprobmorprev,"\n");
3385: fprintf(ficgp,"\n# Routine varevsij");
3386: /* fprintf(fichtm, "#Local time at start: %s", strstart);*/
3387: 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");
3388: fprintf(fichtm,"\n<br>%s <br>\n",digitp);
3389: /* } */
3390: varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
3391: pstamp(ficresvij);
3392: fprintf(ficresvij,"# Variance and covariance of health expectancies e.j \n# (weighted average of eij where weights are ");
3393: if(popbased==1)
3394: 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);
3395: else
3396: fprintf(ficresvij,"the age specific period (stable) prevalences in each health state \n");
3397: fprintf(ficresvij,"# Age");
3398: for(i=1; i<=nlstate;i++)
3399: for(j=1; j<=nlstate;j++)
3400: fprintf(ficresvij," Cov(e.%1d, e.%1d)",i,j);
3401: fprintf(ficresvij,"\n");
3402:
3403: xp=vector(1,npar);
3404: dnewm=matrix(1,nlstate,1,npar);
3405: doldm=matrix(1,nlstate,1,nlstate);
3406: dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
3407: doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
3408:
3409: gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
3410: gpp=vector(nlstate+1,nlstate+ndeath);
3411: gmp=vector(nlstate+1,nlstate+ndeath);
3412: trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
3413:
3414: if(estepm < stepm){
3415: printf ("Problem %d lower than %d\n",estepm, stepm);
3416: }
3417: else hstepm=estepm;
3418: /* For example we decided to compute the life expectancy with the smallest unit */
3419: /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
3420: nhstepm is the number of hstepm from age to agelim
3421: nstepm is the number of stepm from age to agelin.
3422: Look at function hpijx to understand why (it is linked to memory size questions) */
3423: /* We decided (b) to get a life expectancy respecting the most precise curvature of the
3424: survival function given by stepm (the optimization length). Unfortunately it
3425: means that if the survival funtion is printed every two years of age and if
3426: you sum them up and add 1 year (area under the trapezoids) you won't get the same
3427: results. So we changed our mind and took the option of the best precision.
3428: */
3429: hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
3430: agelim = AGESUP;
3431: for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
3432: nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
3433: nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
3434: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3435: gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
3436: gp=matrix(0,nhstepm,1,nlstate);
3437: gm=matrix(0,nhstepm,1,nlstate);
3438:
3439:
3440: for(theta=1; theta <=npar; theta++){
3441: for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
3442: xp[i] = x[i] + (i==theta ?delti[theta]:0);
3443: }
3444: hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
3445: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
3446:
3447: if (popbased==1) {
3448: if(mobilav ==0){
3449: for(i=1; i<=nlstate;i++)
3450: prlim[i][i]=probs[(int)age][i][ij];
3451: }else{ /* mobilav */
3452: for(i=1; i<=nlstate;i++)
3453: prlim[i][i]=mobaverage[(int)age][i][ij];
3454: }
3455: }
3456:
3457: for(j=1; j<= nlstate; j++){
3458: for(h=0; h<=nhstepm; h++){
3459: for(i=1, gp[h][j]=0.;i<=nlstate;i++)
3460: gp[h][j] += prlim[i][i]*p3mat[i][j][h];
3461: }
3462: }
3463: /* This for computing probability of death (h=1 means
3464: computed over hstepm matrices product = hstepm*stepm months)
3465: as a weighted average of prlim.
3466: */
3467: for(j=nlstate+1;j<=nlstate+ndeath;j++){
3468: for(i=1,gpp[j]=0.; i<= nlstate; i++)
3469: gpp[j] += prlim[i][i]*p3mat[i][j][1];
3470: }
3471: /* end probability of death */
3472:
3473: for(i=1; i<=npar; i++) /* Computes gradient x - delta */
3474: xp[i] = x[i] - (i==theta ?delti[theta]:0);
3475: hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
3476: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
3477:
3478: if (popbased==1) {
3479: if(mobilav ==0){
3480: for(i=1; i<=nlstate;i++)
3481: prlim[i][i]=probs[(int)age][i][ij];
3482: }else{ /* mobilav */
3483: for(i=1; i<=nlstate;i++)
3484: prlim[i][i]=mobaverage[(int)age][i][ij];
3485: }
3486: }
3487:
3488: for(j=1; j<= nlstate; j++){ /* Sum of wi * eij = e.j */
3489: for(h=0; h<=nhstepm; h++){
3490: for(i=1, gm[h][j]=0.;i<=nlstate;i++)
3491: gm[h][j] += prlim[i][i]*p3mat[i][j][h];
3492: }
3493: }
3494: /* This for computing probability of death (h=1 means
3495: computed over hstepm matrices product = hstepm*stepm months)
3496: as a weighted average of prlim.
3497: */
3498: for(j=nlstate+1;j<=nlstate+ndeath;j++){
3499: for(i=1,gmp[j]=0.; i<= nlstate; i++)
3500: gmp[j] += prlim[i][i]*p3mat[i][j][1];
3501: }
3502: /* end probability of death */
3503:
3504: for(j=1; j<= nlstate; j++) /* vareij */
3505: for(h=0; h<=nhstepm; h++){
3506: gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
3507: }
3508:
3509: for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
3510: gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
3511: }
3512:
3513: } /* End theta */
3514:
3515: trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
3516:
3517: for(h=0; h<=nhstepm; h++) /* veij */
3518: for(j=1; j<=nlstate;j++)
3519: for(theta=1; theta <=npar; theta++)
3520: trgradg[h][j][theta]=gradg[h][theta][j];
3521:
3522: for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
3523: for(theta=1; theta <=npar; theta++)
3524: trgradgp[j][theta]=gradgp[theta][j];
3525:
3526:
3527: hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
3528: for(i=1;i<=nlstate;i++)
3529: for(j=1;j<=nlstate;j++)
3530: vareij[i][j][(int)age] =0.;
3531:
3532: for(h=0;h<=nhstepm;h++){
3533: for(k=0;k<=nhstepm;k++){
3534: matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
3535: matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
3536: for(i=1;i<=nlstate;i++)
3537: for(j=1;j<=nlstate;j++)
3538: vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
3539: }
3540: }
3541:
3542: /* pptj */
3543: matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
3544: matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
3545: for(j=nlstate+1;j<=nlstate+ndeath;j++)
3546: for(i=nlstate+1;i<=nlstate+ndeath;i++)
3547: varppt[j][i]=doldmp[j][i];
3548: /* end ppptj */
3549: /* x centered again */
3550: hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);
3551: prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);
3552:
3553: if (popbased==1) {
3554: if(mobilav ==0){
3555: for(i=1; i<=nlstate;i++)
3556: prlim[i][i]=probs[(int)age][i][ij];
3557: }else{ /* mobilav */
3558: for(i=1; i<=nlstate;i++)
3559: prlim[i][i]=mobaverage[(int)age][i][ij];
3560: }
3561: }
3562:
3563: /* This for computing probability of death (h=1 means
3564: computed over hstepm (estepm) matrices product = hstepm*stepm months)
3565: as a weighted average of prlim.
3566: */
3567: for(j=nlstate+1;j<=nlstate+ndeath;j++){
3568: for(i=1,gmp[j]=0.;i<= nlstate; i++)
3569: gmp[j] += prlim[i][i]*p3mat[i][j][1];
3570: }
3571: /* end probability of death */
3572:
3573: fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
3574: for(j=nlstate+1; j<=(nlstate+ndeath);j++){
3575: fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
3576: for(i=1; i<=nlstate;i++){
3577: fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
3578: }
3579: }
3580: fprintf(ficresprobmorprev,"\n");
3581:
3582: fprintf(ficresvij,"%.0f ",age );
3583: for(i=1; i<=nlstate;i++)
3584: for(j=1; j<=nlstate;j++){
3585: fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
3586: }
3587: fprintf(ficresvij,"\n");
3588: free_matrix(gp,0,nhstepm,1,nlstate);
3589: free_matrix(gm,0,nhstepm,1,nlstate);
3590: free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
3591: free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
3592: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3593: } /* End age */
3594: free_vector(gpp,nlstate+1,nlstate+ndeath);
3595: free_vector(gmp,nlstate+1,nlstate+ndeath);
3596: free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
3597: free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
3598: fprintf(ficgp,"\nunset parametric;unset label; set ter png small size 320, 240");
3599: /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */
3600: fprintf(ficgp,"\n set log y; unset log x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
3601: /* fprintf(ficgp,"\n plot \"%s\" u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm); */
3602: /* fprintf(ficgp,"\n replot \"%s\" u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm); */
3603: /* fprintf(ficgp,"\n replot \"%s\" u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm); */
3604: fprintf(ficgp,"\n plot \"%s\" u 1:($3) not w l lt 1 ",subdirf(fileresprobmorprev));
3605: fprintf(ficgp,"\n replot \"%s\" u 1:(($3+1.96*$4)) t \"95\%% interval\" w l lt 2 ",subdirf(fileresprobmorprev));
3606: fprintf(ficgp,"\n replot \"%s\" u 1:(($3-1.96*$4)) not w l lt 2 ",subdirf(fileresprobmorprev));
3607: fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",subdirf(fileresprobmorprev),subdirf(fileresprobmorprev));
3608: 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);
3609: /* 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);
3610: */
3611: /* fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.png\";replot;",digitp,optionfilefiname,digit); */
3612: fprintf(ficgp,"\nset out \"%s%s.png\";replot;\n",subdirf3(optionfilefiname,"varmuptjgr",digitp),digit);
3613:
3614: free_vector(xp,1,npar);
3615: free_matrix(doldm,1,nlstate,1,nlstate);
3616: free_matrix(dnewm,1,nlstate,1,npar);
3617: free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
3618: free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
3619: free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
3620: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
3621: fclose(ficresprobmorprev);
3622: fflush(ficgp);
3623: fflush(fichtm);
3624: } /* end varevsij */
3625:
3626: /************ Variance of prevlim ******************/
3627: 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[])
3628: {
3629: /* Variance of prevalence limit */
3630: /* double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
3631:
3632: double **dnewm,**doldm;
3633: int i, j, nhstepm, hstepm;
3634: double *xp;
3635: double *gp, *gm;
3636: double **gradg, **trgradg;
3637: double age,agelim;
3638: int theta;
3639:
3640: pstamp(ficresvpl);
3641: fprintf(ficresvpl,"# Standard deviation of period (stable) prevalences \n");
3642: fprintf(ficresvpl,"# Age");
3643: for(i=1; i<=nlstate;i++)
3644: fprintf(ficresvpl," %1d-%1d",i,i);
3645: fprintf(ficresvpl,"\n");
3646:
3647: xp=vector(1,npar);
3648: dnewm=matrix(1,nlstate,1,npar);
3649: doldm=matrix(1,nlstate,1,nlstate);
3650:
3651: hstepm=1*YEARM; /* Every year of age */
3652: hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */
3653: agelim = AGESUP;
3654: for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
3655: nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
3656: if (stepm >= YEARM) hstepm=1;
3657: nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
3658: gradg=matrix(1,npar,1,nlstate);
3659: gp=vector(1,nlstate);
3660: gm=vector(1,nlstate);
3661:
3662: for(theta=1; theta <=npar; theta++){
3663: for(i=1; i<=npar; i++){ /* Computes gradient */
3664: xp[i] = x[i] + (i==theta ?delti[theta]:0);
3665: }
3666: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
3667: for(i=1;i<=nlstate;i++)
3668: gp[i] = prlim[i][i];
3669:
3670: for(i=1; i<=npar; i++) /* Computes gradient */
3671: xp[i] = x[i] - (i==theta ?delti[theta]:0);
3672: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
3673: for(i=1;i<=nlstate;i++)
3674: gm[i] = prlim[i][i];
3675:
3676: for(i=1;i<=nlstate;i++)
3677: gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
3678: } /* End theta */
3679:
3680: trgradg =matrix(1,nlstate,1,npar);
3681:
3682: for(j=1; j<=nlstate;j++)
3683: for(theta=1; theta <=npar; theta++)
3684: trgradg[j][theta]=gradg[theta][j];
3685:
3686: for(i=1;i<=nlstate;i++)
3687: varpl[i][(int)age] =0.;
3688: matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
3689: matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
3690: for(i=1;i<=nlstate;i++)
3691: varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
3692:
3693: fprintf(ficresvpl,"%.0f ",age );
3694: for(i=1; i<=nlstate;i++)
3695: fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
3696: fprintf(ficresvpl,"\n");
3697: free_vector(gp,1,nlstate);
3698: free_vector(gm,1,nlstate);
3699: free_matrix(gradg,1,npar,1,nlstate);
3700: free_matrix(trgradg,1,nlstate,1,npar);
3701: } /* End age */
3702:
3703: free_vector(xp,1,npar);
3704: free_matrix(doldm,1,nlstate,1,npar);
3705: free_matrix(dnewm,1,nlstate,1,nlstate);
3706:
3707: }
3708:
3709: /************ Variance of one-step probabilities ******************/
3710: 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[])
3711: {
3712: int i, j=0, k1, l1, tj;
3713: int k2, l2, j1, z1;
3714: int k=0, l;
3715: int first=1, first1, first2;
3716: double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
3717: double **dnewm,**doldm;
3718: double *xp;
3719: double *gp, *gm;
3720: double **gradg, **trgradg;
3721: double **mu;
3722: double age, cov[NCOVMAX+1];
3723: double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
3724: int theta;
3725: char fileresprob[FILENAMELENGTH];
3726: char fileresprobcov[FILENAMELENGTH];
3727: char fileresprobcor[FILENAMELENGTH];
3728: double ***varpij;
3729:
3730: strcpy(fileresprob,"prob");
3731: strcat(fileresprob,fileres);
3732: if((ficresprob=fopen(fileresprob,"w"))==NULL) {
3733: printf("Problem with resultfile: %s\n", fileresprob);
3734: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
3735: }
3736: strcpy(fileresprobcov,"probcov");
3737: strcat(fileresprobcov,fileres);
3738: if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
3739: printf("Problem with resultfile: %s\n", fileresprobcov);
3740: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
3741: }
3742: strcpy(fileresprobcor,"probcor");
3743: strcat(fileresprobcor,fileres);
3744: if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
3745: printf("Problem with resultfile: %s\n", fileresprobcor);
3746: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
3747: }
3748: printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
3749: fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
3750: printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
3751: fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
3752: printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
3753: fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
3754: pstamp(ficresprob);
3755: fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
3756: fprintf(ficresprob,"# Age");
3757: pstamp(ficresprobcov);
3758: fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
3759: fprintf(ficresprobcov,"# Age");
3760: pstamp(ficresprobcor);
3761: fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
3762: fprintf(ficresprobcor,"# Age");
3763:
3764:
3765: for(i=1; i<=nlstate;i++)
3766: for(j=1; j<=(nlstate+ndeath);j++){
3767: fprintf(ficresprob," p%1d-%1d (SE)",i,j);
3768: fprintf(ficresprobcov," p%1d-%1d ",i,j);
3769: fprintf(ficresprobcor," p%1d-%1d ",i,j);
3770: }
3771: /* fprintf(ficresprob,"\n");
3772: fprintf(ficresprobcov,"\n");
3773: fprintf(ficresprobcor,"\n");
3774: */
3775: xp=vector(1,npar);
3776: dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
3777: doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
3778: mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
3779: varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
3780: first=1;
3781: fprintf(ficgp,"\n# Routine varprob");
3782: fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
3783: fprintf(fichtm,"\n");
3784:
3785: fprintf(fichtm,"\n<li><h4> <a href=\"%s\">Matrix of variance-covariance of pairs of step probabilities (drawings)</a></h4></li>\n",optionfilehtmcov);
3786: fprintf(fichtmcov,"\n<h4>Matrix of variance-covariance of pairs of step probabilities</h4>\n\
3787: file %s<br>\n",optionfilehtmcov);
3788: fprintf(fichtmcov,"\nEllipsoids of confidence centered on point (p<inf>ij</inf>, p<inf>kl</inf>) are estimated\
3789: and drawn. It helps understanding how is the covariance between two incidences.\
3790: They are expressed in year<sup>-1</sup> in order to be less dependent of stepm.<br>\n");
3791: 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. \
3792: It can be understood this way: if pij and pkl where uncorrelated the (2x2) matrix of covariance \
3793: would have been (1/(var pij), 0 , 0, 1/(var pkl)), and the confidence interval would be 2 \
3794: standard deviations wide on each axis. <br>\
3795: Now, if both incidences are correlated (usual case) we diagonalised the inverse of the covariance matrix\
3796: and made the appropriate rotation to look at the uncorrelated principal directions.<br>\
3797: To be simple, these graphs help to understand the significativity of each parameter in relation to a second other one.<br> \n");
3798:
3799: cov[1]=1;
3800: /* tj=cptcoveff; */
3801: tj = (int) pow(2,cptcoveff);
3802: if (cptcovn<1) {tj=1;ncodemax[1]=1;}
3803: j1=0;
3804: for(j1=1; j1<=tj;j1++){
3805: /*for(i1=1; i1<=ncodemax[t];i1++){ */
3806: /*j1++;*/
3807: if (cptcovn>0) {
3808: fprintf(ficresprob, "\n#********** Variable ");
3809: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
3810: fprintf(ficresprob, "**********\n#\n");
3811: fprintf(ficresprobcov, "\n#********** Variable ");
3812: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
3813: fprintf(ficresprobcov, "**********\n#\n");
3814:
3815: fprintf(ficgp, "\n#********** Variable ");
3816: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
3817: fprintf(ficgp, "**********\n#\n");
3818:
3819:
3820: fprintf(fichtmcov, "\n<hr size=\"2\" color=\"#EC5E5E\">********** Variable ");
3821: for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
3822: fprintf(fichtmcov, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
3823:
3824: fprintf(ficresprobcor, "\n#********** Variable ");
3825: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
3826: fprintf(ficresprobcor, "**********\n#");
3827: }
3828:
3829: gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
3830: trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
3831: gp=vector(1,(nlstate)*(nlstate+ndeath));
3832: gm=vector(1,(nlstate)*(nlstate+ndeath));
3833: for (age=bage; age<=fage; age ++){
3834: cov[2]=age;
3835: for (k=1; k<=cptcovn;k++) {
3836: cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];/* j1 1 2 3 4
3837: * 1 1 1 1 1
3838: * 2 2 1 1 1
3839: * 3 1 2 1 1
3840: */
3841: /* nbcode[1][1]=0 nbcode[1][2]=1;*/
3842: }
3843: for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
3844: for (k=1; k<=cptcovprod;k++)
3845: cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
3846:
3847:
3848: for(theta=1; theta <=npar; theta++){
3849: for(i=1; i<=npar; i++)
3850: xp[i] = x[i] + (i==theta ?delti[theta]:(double)0);
3851:
3852: pmij(pmmij,cov,ncovmodel,xp,nlstate);
3853:
3854: k=0;
3855: for(i=1; i<= (nlstate); i++){
3856: for(j=1; j<=(nlstate+ndeath);j++){
3857: k=k+1;
3858: gp[k]=pmmij[i][j];
3859: }
3860: }
3861:
3862: for(i=1; i<=npar; i++)
3863: xp[i] = x[i] - (i==theta ?delti[theta]:(double)0);
3864:
3865: pmij(pmmij,cov,ncovmodel,xp,nlstate);
3866: k=0;
3867: for(i=1; i<=(nlstate); i++){
3868: for(j=1; j<=(nlstate+ndeath);j++){
3869: k=k+1;
3870: gm[k]=pmmij[i][j];
3871: }
3872: }
3873:
3874: for(i=1; i<= (nlstate)*(nlstate+ndeath); i++)
3875: gradg[theta][i]=(gp[i]-gm[i])/(double)2./delti[theta];
3876: }
3877:
3878: for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
3879: for(theta=1; theta <=npar; theta++)
3880: trgradg[j][theta]=gradg[theta][j];
3881:
3882: matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov);
3883: matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);
3884:
3885: pmij(pmmij,cov,ncovmodel,x,nlstate);
3886:
3887: k=0;
3888: for(i=1; i<=(nlstate); i++){
3889: for(j=1; j<=(nlstate+ndeath);j++){
3890: k=k+1;
3891: mu[k][(int) age]=pmmij[i][j];
3892: }
3893: }
3894: for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
3895: for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
3896: varpij[i][j][(int)age] = doldm[i][j];
3897:
3898: /*printf("\n%d ",(int)age);
3899: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
3900: printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
3901: fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
3902: }*/
3903:
3904: fprintf(ficresprob,"\n%d ",(int)age);
3905: fprintf(ficresprobcov,"\n%d ",(int)age);
3906: fprintf(ficresprobcor,"\n%d ",(int)age);
3907:
3908: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)
3909: fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));
3910: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
3911: fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);
3912: fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
3913: }
3914: i=0;
3915: for (k=1; k<=(nlstate);k++){
3916: for (l=1; l<=(nlstate+ndeath);l++){
3917: i++;
3918: fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
3919: fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
3920: for (j=1; j<=i;j++){
3921: /* printf(" k=%d l=%d i=%d j=%d\n",k,l,i,j);fflush(stdout); */
3922: fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);
3923: fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));
3924: }
3925: }
3926: }/* end of loop for state */
3927: } /* end of loop for age */
3928: free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
3929: free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
3930: free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
3931: free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
3932:
3933: /* Confidence intervalle of pij */
3934: /*
3935: fprintf(ficgp,"\nunset parametric;unset label");
3936: fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");
3937: fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
3938: 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);
3939: fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);
3940: fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);
3941: fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);
3942: */
3943:
3944: /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
3945: first1=1;first2=2;
3946: for (k2=1; k2<=(nlstate);k2++){
3947: for (l2=1; l2<=(nlstate+ndeath);l2++){
3948: if(l2==k2) continue;
3949: j=(k2-1)*(nlstate+ndeath)+l2;
3950: for (k1=1; k1<=(nlstate);k1++){
3951: for (l1=1; l1<=(nlstate+ndeath);l1++){
3952: if(l1==k1) continue;
3953: i=(k1-1)*(nlstate+ndeath)+l1;
3954: if(i<=j) continue;
3955: for (age=bage; age<=fage; age ++){
3956: if ((int)age %5==0){
3957: v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;
3958: v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;
3959: cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;
3960: mu1=mu[i][(int) age]/stepm*YEARM ;
3961: mu2=mu[j][(int) age]/stepm*YEARM;
3962: c12=cv12/sqrt(v1*v2);
3963: /* Computing eigen value of matrix of covariance */
3964: lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
3965: lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
3966: if ((lc2 <0) || (lc1 <0) ){
3967: if(first2==1){
3968: first1=0;
3969: 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);
3970: }
3971: 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);
3972: /* lc1=fabs(lc1); */ /* If we want to have them positive */
3973: /* lc2=fabs(lc2); */
3974: }
3975:
3976: /* Eigen vectors */
3977: v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
3978: /*v21=sqrt(1.-v11*v11); *//* error */
3979: v21=(lc1-v1)/cv12*v11;
3980: v12=-v21;
3981: v22=v11;
3982: tnalp=v21/v11;
3983: if(first1==1){
3984: first1=0;
3985: 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);
3986: }
3987: 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);
3988: /*printf(fignu*/
3989: /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */
3990: /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */
3991: if(first==1){
3992: first=0;
3993: fprintf(ficgp,"\nset parametric;unset label");
3994: 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);
3995: fprintf(ficgp,"\nset ter png small size 320, 240");
3996: fprintf(fichtmcov,"\n<br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup>\
3997: :<a href=\"%s%d%1d%1d-%1d%1d.png\">\
3998: %s%d%1d%1d-%1d%1d.png</A>, ",k1,l1,k2,l2,\
3999: subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2,\
4000: subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
4001: fprintf(fichtmcov,"\n<br><img src=\"%s%d%1d%1d-%1d%1d.png\"> ",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
4002: fprintf(fichtmcov,"\n<br> Correlation at age %d (%.3f),",(int) age, c12);
4003: fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\"",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
4004: fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
4005: fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
4006: 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",\
4007: mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
4008: mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
4009: }else{
4010: first=0;
4011: fprintf(fichtmcov," %d (%.3f),",(int) age, c12);
4012: fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
4013: fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
4014: 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",\
4015: mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
4016: mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
4017: }/* if first */
4018: } /* age mod 5 */
4019: } /* end loop age */
4020: fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\";replot;",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
4021: first=1;
4022: } /*l12 */
4023: } /* k12 */
4024: } /*l1 */
4025: }/* k1 */
4026: /* } /* loop covariates */
4027: }
4028: free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
4029: free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
4030: free_matrix(doldm,1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
4031: free_matrix(dnewm,1,(nlstate)*(nlstate+ndeath),1,npar);
4032: free_vector(xp,1,npar);
4033: fclose(ficresprob);
4034: fclose(ficresprobcov);
4035: fclose(ficresprobcor);
4036: fflush(ficgp);
4037: fflush(fichtmcov);
4038: }
4039:
4040:
4041: /******************* Printing html file ***********/
4042: void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \
4043: int lastpass, int stepm, int weightopt, char model[],\
4044: int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
4045: int popforecast, int estepm ,\
4046: double jprev1, double mprev1,double anprev1, \
4047: double jprev2, double mprev2,double anprev2){
4048: int jj1, k1, i1, cpt;
4049:
4050: fprintf(fichtm,"<ul><li><a href='#firstorder'>Result files (first order: no variance)</a>\n \
4051: <li><a href='#secondorder'>Result files (second order (variance)</a>\n \
4052: </ul>");
4053: fprintf(fichtm,"<ul><li><h4><a name='firstorder'>Result files (first order: no variance)</a></h4>\n \
4054: - Observed prevalence in each state (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"%s\">%s</a> <br>\n ",
4055: jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirf2(fileres,"p"),subdirf2(fileres,"p"));
4056: fprintf(fichtm,"\
4057: - Estimated transition probabilities over %d (stepm) months: <a href=\"%s\">%s</a><br>\n ",
4058: stepm,subdirf2(fileres,"pij"),subdirf2(fileres,"pij"));
4059: fprintf(fichtm,"\
4060: - Period (stable) prevalence in each health state: <a href=\"%s\">%s</a> <br>\n",
4061: subdirf2(fileres,"pl"),subdirf2(fileres,"pl"));
4062: fprintf(fichtm,"\
4063: - (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): \
4064: <a href=\"%s\">%s</a> <br>\n",
4065: estepm,subdirf2(fileres,"e"),subdirf2(fileres,"e"));
4066: fprintf(fichtm,"\
4067: - Population projections by age and states: \
4068: <a href=\"%s\">%s</a> <br>\n</li>", subdirf2(fileres,"f"),subdirf2(fileres,"f"));
4069:
4070: fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
4071:
4072: m=pow(2,cptcoveff);
4073: if (cptcovn < 1) {m=1;ncodemax[1]=1;}
4074:
4075: jj1=0;
4076: for(k1=1; k1<=m;k1++){
4077: for(i1=1; i1<=ncodemax[k1];i1++){
4078: jj1++;
4079: if (cptcovn > 0) {
4080: fprintf(fichtm,"<hr size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
4081: for (cpt=1; cpt<=cptcoveff;cpt++)
4082: fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
4083: fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
4084: }
4085: /* Pij */
4086: 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> \
4087: <img src=\"%s%d_1.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);
4088: /* Quasi-incidences */
4089: fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months\
4090: 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> \
4091: <img src=\"%s%d_2.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);
4092: /* Period (stable) prevalence in each health state */
4093: for(cpt=1; cpt<=nlstate;cpt++){
4094: fprintf(fichtm,"<br>- Convergence from cross-sectional prevalence in each state (1 to %d) to period (stable) prevalence in specific state %d <a href=\"%s%d_%d.png\">%s%d_%d.png</a><br> \
4095: <img src=\"%s%d_%d.png\">",nlstate, cpt, subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1);
4096: }
4097: for(cpt=1; cpt<=nlstate;cpt++) {
4098: 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> \
4099: <img src=\"%s%d%d.png\">",cpt,nlstate,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1);
4100: }
4101: } /* end i1 */
4102: }/* End k1 */
4103: fprintf(fichtm,"</ul>");
4104:
4105:
4106: fprintf(fichtm,"\
4107: \n<br><li><h4> <a name='secondorder'>Result files (second order: variances)</a></h4>\n\
4108: - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n", rfileres,rfileres);
4109:
4110: fprintf(fichtm," - Variance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
4111: subdirf2(fileres,"prob"),subdirf2(fileres,"prob"));
4112: fprintf(fichtm,"\
4113: - Variance-covariance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
4114: subdirf2(fileres,"probcov"),subdirf2(fileres,"probcov"));
4115:
4116: fprintf(fichtm,"\
4117: - Correlation matrix of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
4118: subdirf2(fileres,"probcor"),subdirf2(fileres,"probcor"));
4119: fprintf(fichtm,"\
4120: - 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): \
4121: <a href=\"%s\">%s</a> <br>\n</li>",
4122: estepm,subdirf2(fileres,"cve"),subdirf2(fileres,"cve"));
4123: fprintf(fichtm,"\
4124: - (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): \
4125: <a href=\"%s\">%s</a> <br>\n</li>",
4126: estepm,subdirf2(fileres,"stde"),subdirf2(fileres,"stde"));
4127: fprintf(fichtm,"\
4128: - 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",
4129: estepm, subdirf2(fileres,"v"),subdirf2(fileres,"v"));
4130: fprintf(fichtm,"\
4131: - 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",
4132: estepm, subdirf2(fileres,"t"),subdirf2(fileres,"t"));
4133: fprintf(fichtm,"\
4134: - Standard deviation of period (stable) prevalences: <a href=\"%s\">%s</a> <br>\n",\
4135: subdirf2(fileres,"vpl"),subdirf2(fileres,"vpl"));
4136:
4137: /* if(popforecast==1) fprintf(fichtm,"\n */
4138: /* - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n */
4139: /* - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n */
4140: /* <br>",fileres,fileres,fileres,fileres); */
4141: /* else */
4142: /* 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); */
4143: fflush(fichtm);
4144: fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
4145:
4146: m=pow(2,cptcoveff);
4147: if (cptcovn < 1) {m=1;ncodemax[1]=1;}
4148:
4149: jj1=0;
4150: for(k1=1; k1<=m;k1++){
4151: for(i1=1; i1<=ncodemax[k1];i1++){
4152: jj1++;
4153: if (cptcovn > 0) {
4154: fprintf(fichtm,"<hr size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
4155: for (cpt=1; cpt<=cptcoveff;cpt++)
4156: fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
4157: fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
4158: }
4159: for(cpt=1; cpt<=nlstate;cpt++) {
4160: fprintf(fichtm,"<br>- Observed (cross-sectional) and period (incidence based) \
4161: prevalence (with 95%% confidence interval) in state (%d): %s%d_%d.png <br>\
4162: <img src=\"%s%d_%d.png\">",cpt,subdirf2(optionfilefiname,"v"),cpt,jj1,subdirf2(optionfilefiname,"v"),cpt,jj1);
4163: }
4164: fprintf(fichtm,"\n<br>- Total life expectancy by age and \
4165: health expectancies in states (1) and (2). If popbased=1 the smooth (due to the model) \
4166: true period expectancies (those weighted with period prevalences are also\
4167: drawn in addition to the population based expectancies computed using\
4168: observed and cahotic prevalences: %s%d.png<br>\
4169: <img src=\"%s%d.png\">",subdirf2(optionfilefiname,"e"),jj1,subdirf2(optionfilefiname,"e"),jj1);
4170: } /* end i1 */
4171: }/* End k1 */
4172: fprintf(fichtm,"</ul>");
4173: fflush(fichtm);
4174: }
4175:
4176: /******************* Gnuplot file **************/
4177: void printinggnuplot(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
4178:
4179: char dirfileres[132],optfileres[132];
4180: int cpt=0,k1=0,i=0,k=0,j=0,jk=0,k2=0,k3=0,ij=0,l=0;
4181: int ng=0;
4182: /* if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) { */
4183: /* printf("Problem with file %s",optionfilegnuplot); */
4184: /* fprintf(ficlog,"Problem with file %s",optionfilegnuplot); */
4185: /* } */
4186:
4187: /*#ifdef windows */
4188: fprintf(ficgp,"cd \"%s\" \n",pathc);
4189: /*#endif */
4190: m=pow(2,cptcoveff);
4191:
4192: strcpy(dirfileres,optionfilefiname);
4193: strcpy(optfileres,"vpl");
4194: /* 1eme*/
4195: fprintf(ficgp,"\n# 1st: Period (stable) prevalence with CI: 'vpl' files\n");
4196: for (cpt=1; cpt<= nlstate ; cpt ++) {
4197: for (k1=1; k1<= m ; k1 ++) { /* plot [100000000000000000000:-100000000000000000000] "mysbiaspar/vplrmysbiaspar.txt to check */
4198: fprintf(ficgp,"\nset out \"%s%d_%d.png\" \n",subdirf2(optionfilefiname,"v"),cpt,k1);
4199: fprintf(ficgp,"\n#set out \"v%s%d_%d.png\" \n",optionfilefiname,cpt,k1);
4200: fprintf(ficgp,"set xlabel \"Age\" \n\
4201: set ylabel \"Probability\" \n\
4202: set ter png small size 320, 240\n\
4203: plot [%.f:%.f] \"%s\" every :::%d::%d u 1:2 \"\%%lf",ageminpar,fage,subdirf2(fileres,"vpl"),k1-1,k1-1);
4204:
4205: for (i=1; i<= nlstate ; i ++) {
4206: if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
4207: else fprintf(ficgp," \%%*lf (\%%*lf)");
4208: }
4209: 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);
4210: for (i=1; i<= nlstate ; i ++) {
4211: if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
4212: else fprintf(ficgp," \%%*lf (\%%*lf)");
4213: }
4214: fprintf(ficgp,"\" t\"95\%% CI\" w l lt 1,\"%s\" every :::%d::%d u 1:($2-1.96*$3) \"\%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1);
4215: for (i=1; i<= nlstate ; i ++) {
4216: if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
4217: else fprintf(ficgp," \%%*lf (\%%*lf)");
4218: }
4219: fprintf(ficgp,"\" t\"\" w l lt 1,\"%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l lt 2",subdirf2(fileres,"p"),k1-1,k1-1,2+4*(cpt-1));
4220: }
4221: }
4222: /*2 eme*/
4223: fprintf(ficgp,"\n# 2nd: Total life expectancy with CI: 't' files\n");
4224: for (k1=1; k1<= m ; k1 ++) {
4225: fprintf(ficgp,"\nset out \"%s%d.png\" \n",subdirf2(optionfilefiname,"e"),k1);
4226: fprintf(ficgp,"set ylabel \"Years\" \nset ter png small size 320, 240\nplot [%.f:%.f] ",ageminpar,fage);
4227:
4228: for (i=1; i<= nlstate+1 ; i ++) {
4229: k=2*i;
4230: fprintf(ficgp,"\"%s\" every :::%d::%d u 1:2 \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
4231: for (j=1; j<= nlstate+1 ; j ++) {
4232: if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
4233: else fprintf(ficgp," \%%*lf (\%%*lf)");
4234: }
4235: if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");
4236: else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);
4237: fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
4238: for (j=1; j<= nlstate+1 ; j ++) {
4239: if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
4240: else fprintf(ficgp," \%%*lf (\%%*lf)");
4241: }
4242: fprintf(ficgp,"\" t\"\" w l lt 0,");
4243: fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
4244: for (j=1; j<= nlstate+1 ; j ++) {
4245: if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
4246: else fprintf(ficgp," \%%*lf (\%%*lf)");
4247: }
4248: if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l lt 0");
4249: else fprintf(ficgp,"\" t\"\" w l lt 0,");
4250: }
4251: }
4252:
4253: /*3eme*/
4254:
4255: for (k1=1; k1<= m ; k1 ++) {
4256: for (cpt=1; cpt<= nlstate ; cpt ++) {
4257: /* k=2+nlstate*(2*cpt-2); */
4258: k=2+(nlstate+1)*(cpt-1);
4259: fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"exp"),cpt,k1);
4260: fprintf(ficgp,"set ter png small size 320, 240\n\
4261: plot [%.f:%.f] \"%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,subdirf2(fileres,"e"),k1-1,k1-1,k,cpt);
4262: /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
4263: for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
4264: fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
4265: fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
4266: for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
4267: fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
4268:
4269: */
4270: for (i=1; i< nlstate ; i ++) {
4271: 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);
4272: /* 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);*/
4273:
4274: }
4275: fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d.\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+nlstate,cpt);
4276: }
4277: }
4278:
4279: /* CV preval stable (period) */
4280: for (k1=1; k1<= m ; k1 ++) { /* For each multivariate if any */
4281: for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */
4282: k=3;
4283: fprintf(ficgp,"\n#\n#\n#CV preval stable (period): 'pij' files, cov=%d state=%d",k1, cpt);
4284: fprintf(ficgp,"\nset out \"%s%d_%d.png\" \n",subdirf2(optionfilefiname,"p"),cpt,k1);
4285: fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\
4286: set ter png small size 320, 240\n\
4287: unset log y\n\
4288: plot [%.f:%.f] ", ageminpar, agemaxpar);
4289: for (i=1; i<= nlstate ; i ++){
4290: if(i==1)
4291: fprintf(ficgp,"\"%s\"",subdirf2(fileres,"pij"));
4292: else
4293: fprintf(ficgp,", '' ");
4294: l=(nlstate+ndeath)*(i-1)+1;
4295: fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d/($%d",k1,k+l+(cpt-1),k+l);
4296: for (j=1; j<= (nlstate-1) ; j ++)
4297: fprintf(ficgp,"+$%d",k+l+j);
4298: fprintf(ficgp,")) t \"prev(%d,%d)\" w l",i,cpt);
4299: } /* nlstate */
4300: fprintf(ficgp,"\n");
4301: } /* end cpt state*/
4302: } /* end covariate */
4303:
4304: /* proba elementaires */
4305: for(i=1,jk=1; i <=nlstate; i++){
4306: for(k=1; k <=(nlstate+ndeath); k++){
4307: if (k != i) {
4308: for(j=1; j <=ncovmodel; j++){
4309: fprintf(ficgp,"p%d=%f ",jk,p[jk]);
4310: jk++;
4311: fprintf(ficgp,"\n");
4312: }
4313: }
4314: }
4315: }
4316: /*goto avoid;*/
4317: for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/
4318: for(jk=1; jk <=m; jk++) {
4319: fprintf(ficgp,"\nset out \"%s%d_%d.png\" \n",subdirf2(optionfilefiname,"pe"),jk,ng);
4320: if (ng==2)
4321: fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
4322: else
4323: fprintf(ficgp,"\nset title \"Probability\"\n");
4324: fprintf(ficgp,"\nset ter png small size 320, 240\nset log y\nplot [%.f:%.f] ",ageminpar,agemaxpar);
4325: i=1;
4326: for(k2=1; k2<=nlstate; k2++) {
4327: k3=i;
4328: for(k=1; k<=(nlstate+ndeath); k++) {
4329: if (k != k2){
4330: if(ng==2)
4331: fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);
4332: else
4333: fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
4334: ij=1;/* To be checked else nbcode[0][0] wrong */
4335: for(j=3; j <=ncovmodel; j++) {
4336: /* if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) { /\* Bug valgrind *\/ */
4337: /* /\*fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);*\/ */
4338: /* ij++; */
4339: /* } */
4340: /* else */
4341: fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
4342: }
4343: fprintf(ficgp,")/(1");
4344:
4345: for(k1=1; k1 <=nlstate; k1++){
4346: fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);
4347: ij=1;
4348: for(j=3; j <=ncovmodel; j++){
4349: /* if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) { */
4350: /* fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]); */
4351: /* ij++; */
4352: /* } */
4353: /* else */
4354: fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
4355: }
4356: fprintf(ficgp,")");
4357: }
4358: fprintf(ficgp,") t \"p%d%d\" ", k2,k);
4359: if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");
4360: i=i+ncovmodel;
4361: }
4362: } /* end k */
4363: } /* end k2 */
4364: } /* end jk */
4365: } /* end ng */
4366: /* avoid: */
4367: fflush(ficgp);
4368: } /* end gnuplot */
4369:
4370:
4371: /*************** Moving average **************/
4372: int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav){
4373:
4374: int i, cpt, cptcod;
4375: int modcovmax =1;
4376: int mobilavrange, mob;
4377: double age;
4378:
4379: modcovmax=2*cptcoveff;/* Max number of modalities. We suppose
4380: a covariate has 2 modalities */
4381: if (cptcovn<1) modcovmax=1; /* At least 1 pass */
4382:
4383: if(mobilav==1||mobilav ==3 ||mobilav==5 ||mobilav== 7){
4384: if(mobilav==1) mobilavrange=5; /* default */
4385: else mobilavrange=mobilav;
4386: for (age=bage; age<=fage; age++)
4387: for (i=1; i<=nlstate;i++)
4388: for (cptcod=1;cptcod<=modcovmax;cptcod++)
4389: mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
4390: /* We keep the original values on the extreme ages bage, fage and for
4391: fage+1 and bage-1 we use a 3 terms moving average; for fage+2 bage+2
4392: we use a 5 terms etc. until the borders are no more concerned.
4393: */
4394: for (mob=3;mob <=mobilavrange;mob=mob+2){
4395: for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){
4396: for (i=1; i<=nlstate;i++){
4397: for (cptcod=1;cptcod<=modcovmax;cptcod++){
4398: mobaverage[(int)age][i][cptcod] =probs[(int)age][i][cptcod];
4399: for (cpt=1;cpt<=(mob-1)/2;cpt++){
4400: mobaverage[(int)age][i][cptcod] +=probs[(int)age-cpt][i][cptcod];
4401: mobaverage[(int)age][i][cptcod] +=probs[(int)age+cpt][i][cptcod];
4402: }
4403: mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/mob;
4404: }
4405: }
4406: }/* end age */
4407: }/* end mob */
4408: }else return -1;
4409: return 0;
4410: }/* End movingaverage */
4411:
4412:
4413: /************** Forecasting ******************/
4414: 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){
4415: /* proj1, year, month, day of starting projection
4416: agemin, agemax range of age
4417: dateprev1 dateprev2 range of dates during which prevalence is computed
4418: anproj2 year of en of projection (same day and month as proj1).
4419: */
4420: int yearp, stepsize, hstepm, nhstepm, j, k, cptcod, i, h, i1;
4421: double agec; /* generic age */
4422: double agelim, ppij, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
4423: double *popeffectif,*popcount;
4424: double ***p3mat;
4425: double ***mobaverage;
4426: char fileresf[FILENAMELENGTH];
4427:
4428: agelim=AGESUP;
4429: prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
4430:
4431: strcpy(fileresf,"f");
4432: strcat(fileresf,fileres);
4433: if((ficresf=fopen(fileresf,"w"))==NULL) {
4434: printf("Problem with forecast resultfile: %s\n", fileresf);
4435: fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);
4436: }
4437: printf("Computing forecasting: result on file '%s' \n", fileresf);
4438: fprintf(ficlog,"Computing forecasting: result on file '%s' \n", fileresf);
4439:
4440: if (cptcoveff==0) ncodemax[cptcoveff]=1;
4441:
4442: if (mobilav!=0) {
4443: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
4444: if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
4445: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
4446: printf(" Error in movingaverage mobilav=%d\n",mobilav);
4447: }
4448: }
4449:
4450: stepsize=(int) (stepm+YEARM-1)/YEARM;
4451: if (stepm<=12) stepsize=1;
4452: if(estepm < stepm){
4453: printf ("Problem %d lower than %d\n",estepm, stepm);
4454: }
4455: else hstepm=estepm;
4456:
4457: hstepm=hstepm/stepm;
4458: yp1=modf(dateintmean,&yp);/* extracts integral of datemean in yp and
4459: fractional in yp1 */
4460: anprojmean=yp;
4461: yp2=modf((yp1*12),&yp);
4462: mprojmean=yp;
4463: yp1=modf((yp2*30.5),&yp);
4464: jprojmean=yp;
4465: if(jprojmean==0) jprojmean=1;
4466: if(mprojmean==0) jprojmean=1;
4467:
4468: i1=cptcoveff;
4469: if (cptcovn < 1){i1=1;}
4470:
4471: fprintf(ficresf,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2);
4472:
4473: fprintf(ficresf,"#****** Routine prevforecast **\n");
4474:
4475: /* if (h==(int)(YEARM*yearp)){ */
4476: for(cptcov=1, k=0;cptcov<=i1;cptcov++){
4477: for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
4478: k=k+1;
4479: fprintf(ficresf,"\n#******");
4480: for(j=1;j<=cptcoveff;j++) {
4481: 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]]);
4482: }
4483: fprintf(ficresf,"******\n");
4484: fprintf(ficresf,"# Covariate valuofcovar yearproj age");
4485: for(j=1; j<=nlstate+ndeath;j++){
4486: for(i=1; i<=nlstate;i++)
4487: fprintf(ficresf," p%d%d",i,j);
4488: fprintf(ficresf," p.%d",j);
4489: }
4490: for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) {
4491: fprintf(ficresf,"\n");
4492: fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+yearp);
4493:
4494: for (agec=fage; agec>=(ageminpar-1); agec--){
4495: nhstepm=(int) rint((agelim-agec)*YEARM/stepm);
4496: nhstepm = nhstepm/hstepm;
4497: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4498: oldm=oldms;savm=savms;
4499: hpxij(p3mat,nhstepm,agec,hstepm,p,nlstate,stepm,oldm,savm, k);
4500:
4501: for (h=0; h<=nhstepm; h++){
4502: if (h*hstepm/YEARM*stepm ==yearp) {
4503: fprintf(ficresf,"\n");
4504: for(j=1;j<=cptcoveff;j++)
4505: fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
4506: fprintf(ficresf,"%.f %.f ",anproj1+yearp,agec+h*hstepm/YEARM*stepm);
4507: }
4508: for(j=1; j<=nlstate+ndeath;j++) {
4509: ppij=0.;
4510: for(i=1; i<=nlstate;i++) {
4511: if (mobilav==1)
4512: ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][i][cptcod];
4513: else {
4514: ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][cptcod];
4515: }
4516: if (h*hstepm/YEARM*stepm== yearp) {
4517: fprintf(ficresf," %.3f", p3mat[i][j][h]);
4518: }
4519: } /* end i */
4520: if (h*hstepm/YEARM*stepm==yearp) {
4521: fprintf(ficresf," %.3f", ppij);
4522: }
4523: }/* end j */
4524: } /* end h */
4525: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4526: } /* end agec */
4527: } /* end yearp */
4528: } /* end cptcod */
4529: } /* end cptcov */
4530:
4531: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
4532:
4533: fclose(ficresf);
4534: }
4535:
4536: /************** Forecasting *****not tested NB*************/
4537: 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){
4538:
4539: int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;
4540: int *popage;
4541: double calagedatem, agelim, kk1, kk2;
4542: double *popeffectif,*popcount;
4543: double ***p3mat,***tabpop,***tabpopprev;
4544: double ***mobaverage;
4545: char filerespop[FILENAMELENGTH];
4546:
4547: tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
4548: tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
4549: agelim=AGESUP;
4550: calagedatem=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;
4551:
4552: prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
4553:
4554:
4555: strcpy(filerespop,"pop");
4556: strcat(filerespop,fileres);
4557: if((ficrespop=fopen(filerespop,"w"))==NULL) {
4558: printf("Problem with forecast resultfile: %s\n", filerespop);
4559: fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop);
4560: }
4561: printf("Computing forecasting: result on file '%s' \n", filerespop);
4562: fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop);
4563:
4564: if (cptcoveff==0) ncodemax[cptcoveff]=1;
4565:
4566: if (mobilav!=0) {
4567: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
4568: if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
4569: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
4570: printf(" Error in movingaverage mobilav=%d\n",mobilav);
4571: }
4572: }
4573:
4574: stepsize=(int) (stepm+YEARM-1)/YEARM;
4575: if (stepm<=12) stepsize=1;
4576:
4577: agelim=AGESUP;
4578:
4579: hstepm=1;
4580: hstepm=hstepm/stepm;
4581:
4582: if (popforecast==1) {
4583: if((ficpop=fopen(popfile,"r"))==NULL) {
4584: printf("Problem with population file : %s\n",popfile);exit(0);
4585: fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0);
4586: }
4587: popage=ivector(0,AGESUP);
4588: popeffectif=vector(0,AGESUP);
4589: popcount=vector(0,AGESUP);
4590:
4591: i=1;
4592: while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;
4593:
4594: imx=i;
4595: for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];
4596: }
4597:
4598: for(cptcov=1,k=0;cptcov<=i2;cptcov++){
4599: for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
4600: k=k+1;
4601: fprintf(ficrespop,"\n#******");
4602: for(j=1;j<=cptcoveff;j++) {
4603: fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
4604: }
4605: fprintf(ficrespop,"******\n");
4606: fprintf(ficrespop,"# Age");
4607: for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);
4608: if (popforecast==1) fprintf(ficrespop," [Population]");
4609:
4610: for (cpt=0; cpt<=0;cpt++) {
4611: fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);
4612:
4613: for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){
4614: nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);
4615: nhstepm = nhstepm/hstepm;
4616:
4617: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4618: oldm=oldms;savm=savms;
4619: hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
4620:
4621: for (h=0; h<=nhstepm; h++){
4622: if (h==(int) (calagedatem+YEARM*cpt)) {
4623: fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
4624: }
4625: for(j=1; j<=nlstate+ndeath;j++) {
4626: kk1=0.;kk2=0;
4627: for(i=1; i<=nlstate;i++) {
4628: if (mobilav==1)
4629: kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];
4630: else {
4631: kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];
4632: }
4633: }
4634: if (h==(int)(calagedatem+12*cpt)){
4635: tabpop[(int)(agedeb)][j][cptcod]=kk1;
4636: /*fprintf(ficrespop," %.3f", kk1);
4637: if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/
4638: }
4639: }
4640: for(i=1; i<=nlstate;i++){
4641: kk1=0.;
4642: for(j=1; j<=nlstate;j++){
4643: kk1= kk1+tabpop[(int)(agedeb)][j][cptcod];
4644: }
4645: tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedatem+12*cpt)*hstepm/YEARM*stepm-1)];
4646: }
4647:
4648: if (h==(int)(calagedatem+12*cpt)) for(j=1; j<=nlstate;j++)
4649: fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);
4650: }
4651: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4652: }
4653: }
4654:
4655: /******/
4656:
4657: for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) {
4658: fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);
4659: for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){
4660: nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);
4661: nhstepm = nhstepm/hstepm;
4662:
4663: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4664: oldm=oldms;savm=savms;
4665: hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
4666: for (h=0; h<=nhstepm; h++){
4667: if (h==(int) (calagedatem+YEARM*cpt)) {
4668: fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
4669: }
4670: for(j=1; j<=nlstate+ndeath;j++) {
4671: kk1=0.;kk2=0;
4672: for(i=1; i<=nlstate;i++) {
4673: kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];
4674: }
4675: if (h==(int)(calagedatem+12*cpt)) fprintf(ficresf," %15.2f", kk1);
4676: }
4677: }
4678: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4679: }
4680: }
4681: }
4682: }
4683:
4684: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
4685:
4686: if (popforecast==1) {
4687: free_ivector(popage,0,AGESUP);
4688: free_vector(popeffectif,0,AGESUP);
4689: free_vector(popcount,0,AGESUP);
4690: }
4691: free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
4692: free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
4693: fclose(ficrespop);
4694: } /* End of popforecast */
4695:
4696: int fileappend(FILE *fichier, char *optionfich)
4697: {
4698: if((fichier=fopen(optionfich,"a"))==NULL) {
4699: printf("Problem with file: %s\n", optionfich);
4700: fprintf(ficlog,"Problem with file: %s\n", optionfich);
4701: return (0);
4702: }
4703: fflush(fichier);
4704: return (1);
4705: }
4706:
4707:
4708: /**************** function prwizard **********************/
4709: void prwizard(int ncovmodel, int nlstate, int ndeath, char model[], FILE *ficparo)
4710: {
4711:
4712: /* Wizard to print covariance matrix template */
4713:
4714: char ca[32], cb[32];
4715: int i,j, k, li, lj, lk, ll, jj, npar, itimes;
4716: int numlinepar;
4717:
4718: printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
4719: fprintf(ficparo,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
4720: for(i=1; i <=nlstate; i++){
4721: jj=0;
4722: for(j=1; j <=nlstate+ndeath; j++){
4723: if(j==i) continue;
4724: jj++;
4725: /*ca[0]= k+'a'-1;ca[1]='\0';*/
4726: printf("%1d%1d",i,j);
4727: fprintf(ficparo,"%1d%1d",i,j);
4728: for(k=1; k<=ncovmodel;k++){
4729: /* printf(" %lf",param[i][j][k]); */
4730: /* fprintf(ficparo," %lf",param[i][j][k]); */
4731: printf(" 0.");
4732: fprintf(ficparo," 0.");
4733: }
4734: printf("\n");
4735: fprintf(ficparo,"\n");
4736: }
4737: }
4738: printf("# Scales (for hessian or gradient estimation)\n");
4739: fprintf(ficparo,"# Scales (for hessian or gradient estimation)\n");
4740: npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/
4741: for(i=1; i <=nlstate; i++){
4742: jj=0;
4743: for(j=1; j <=nlstate+ndeath; j++){
4744: if(j==i) continue;
4745: jj++;
4746: fprintf(ficparo,"%1d%1d",i,j);
4747: printf("%1d%1d",i,j);
4748: fflush(stdout);
4749: for(k=1; k<=ncovmodel;k++){
4750: /* printf(" %le",delti3[i][j][k]); */
4751: /* fprintf(ficparo," %le",delti3[i][j][k]); */
4752: printf(" 0.");
4753: fprintf(ficparo," 0.");
4754: }
4755: numlinepar++;
4756: printf("\n");
4757: fprintf(ficparo,"\n");
4758: }
4759: }
4760: printf("# Covariance matrix\n");
4761: /* # 121 Var(a12)\n\ */
4762: /* # 122 Cov(b12,a12) Var(b12)\n\ */
4763: /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
4764: /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
4765: /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
4766: /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
4767: /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
4768: /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
4769: fflush(stdout);
4770: fprintf(ficparo,"# Covariance matrix\n");
4771: /* # 121 Var(a12)\n\ */
4772: /* # 122 Cov(b12,a12) Var(b12)\n\ */
4773: /* # ...\n\ */
4774: /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
4775:
4776: for(itimes=1;itimes<=2;itimes++){
4777: jj=0;
4778: for(i=1; i <=nlstate; i++){
4779: for(j=1; j <=nlstate+ndeath; j++){
4780: if(j==i) continue;
4781: for(k=1; k<=ncovmodel;k++){
4782: jj++;
4783: ca[0]= k+'a'-1;ca[1]='\0';
4784: if(itimes==1){
4785: printf("#%1d%1d%d",i,j,k);
4786: fprintf(ficparo,"#%1d%1d%d",i,j,k);
4787: }else{
4788: printf("%1d%1d%d",i,j,k);
4789: fprintf(ficparo,"%1d%1d%d",i,j,k);
4790: /* printf(" %.5le",matcov[i][j]); */
4791: }
4792: ll=0;
4793: for(li=1;li <=nlstate; li++){
4794: for(lj=1;lj <=nlstate+ndeath; lj++){
4795: if(lj==li) continue;
4796: for(lk=1;lk<=ncovmodel;lk++){
4797: ll++;
4798: if(ll<=jj){
4799: cb[0]= lk +'a'-1;cb[1]='\0';
4800: if(ll<jj){
4801: if(itimes==1){
4802: printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
4803: fprintf(ficparo," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
4804: }else{
4805: printf(" 0.");
4806: fprintf(ficparo," 0.");
4807: }
4808: }else{
4809: if(itimes==1){
4810: printf(" Var(%s%1d%1d)",ca,i,j);
4811: fprintf(ficparo," Var(%s%1d%1d)",ca,i,j);
4812: }else{
4813: printf(" 0.");
4814: fprintf(ficparo," 0.");
4815: }
4816: }
4817: }
4818: } /* end lk */
4819: } /* end lj */
4820: } /* end li */
4821: printf("\n");
4822: fprintf(ficparo,"\n");
4823: numlinepar++;
4824: } /* end k*/
4825: } /*end j */
4826: } /* end i */
4827: } /* end itimes */
4828:
4829: } /* end of prwizard */
4830: /******************* Gompertz Likelihood ******************************/
4831: double gompertz(double x[])
4832: {
4833: double A,B,L=0.0,sump=0.,num=0.;
4834: int i,n=0; /* n is the size of the sample */
4835:
4836: for (i=0;i<=imx-1 ; i++) {
4837: sump=sump+weight[i];
4838: /* sump=sump+1;*/
4839: num=num+1;
4840: }
4841:
4842:
4843: /* for (i=0; i<=imx; i++)
4844: 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]);*/
4845:
4846: for (i=1;i<=imx ; i++)
4847: {
4848: if (cens[i] == 1 && wav[i]>1)
4849: A=-x[1]/(x[2])*(exp(x[2]*(agecens[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)));
4850:
4851: if (cens[i] == 0 && wav[i]>1)
4852: A=-x[1]/(x[2])*(exp(x[2]*(agedc[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)))
4853: +log(x[1]/YEARM)+x[2]*(agedc[i]-agegomp)+log(YEARM);
4854:
4855: /*if (wav[i] > 1 && agecens[i] > 15) {*/ /* ??? */
4856: if (wav[i] > 1 ) { /* ??? */
4857: L=L+A*weight[i];
4858: /* 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]);*/
4859: }
4860: }
4861:
4862: /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/
4863:
4864: return -2*L*num/sump;
4865: }
4866:
4867: #ifdef GSL
4868: /******************* Gompertz_f Likelihood ******************************/
4869: double gompertz_f(const gsl_vector *v, void *params)
4870: {
4871: double A,B,LL=0.0,sump=0.,num=0.;
4872: double *x= (double *) v->data;
4873: int i,n=0; /* n is the size of the sample */
4874:
4875: for (i=0;i<=imx-1 ; i++) {
4876: sump=sump+weight[i];
4877: /* sump=sump+1;*/
4878: num=num+1;
4879: }
4880:
4881:
4882: /* for (i=0; i<=imx; i++)
4883: 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]);*/
4884: printf("x[0]=%lf x[1]=%lf\n",x[0],x[1]);
4885: for (i=1;i<=imx ; i++)
4886: {
4887: if (cens[i] == 1 && wav[i]>1)
4888: A=-x[0]/(x[1])*(exp(x[1]*(agecens[i]-agegomp))-exp(x[1]*(ageexmed[i]-agegomp)));
4889:
4890: if (cens[i] == 0 && wav[i]>1)
4891: A=-x[0]/(x[1])*(exp(x[1]*(agedc[i]-agegomp))-exp(x[1]*(ageexmed[i]-agegomp)))
4892: +log(x[0]/YEARM)+x[1]*(agedc[i]-agegomp)+log(YEARM);
4893:
4894: /*if (wav[i] > 1 && agecens[i] > 15) {*/ /* ??? */
4895: if (wav[i] > 1 ) { /* ??? */
4896: LL=LL+A*weight[i];
4897: /* 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]);*/
4898: }
4899: }
4900:
4901: /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/
4902: printf("x[0]=%lf x[1]=%lf -2*LL*num/sump=%lf\n",x[0],x[1],-2*LL*num/sump);
4903:
4904: return -2*LL*num/sump;
4905: }
4906: #endif
4907:
4908: /******************* Printing html file ***********/
4909: void printinghtmlmort(char fileres[], char title[], char datafile[], int firstpass, \
4910: int lastpass, int stepm, int weightopt, char model[],\
4911: int imx, double p[],double **matcov,double agemortsup){
4912: int i,k;
4913:
4914: fprintf(fichtm,"<ul><li><h4>Result files </h4>\n Force of mortality. Parameters of the Gompertz fit (with confidence interval in brackets):<br>");
4915: fprintf(fichtm," mu(age) =%lf*exp(%lf*(age-%d)) per year<br><br>",p[1],p[2],agegomp);
4916: for (i=1;i<=2;i++)
4917: 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]));
4918: fprintf(fichtm,"<br><br><img src=\"graphmort.png\">");
4919: fprintf(fichtm,"</ul>");
4920:
4921: fprintf(fichtm,"<ul><li><h4>Life table</h4>\n <br>");
4922:
4923: 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>");
4924:
4925: for (k=agegomp;k<(agemortsup-2);k++)
4926: 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]);
4927:
4928:
4929: fflush(fichtm);
4930: }
4931:
4932: /******************* Gnuplot file **************/
4933: void printinggnuplotmort(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
4934:
4935: char dirfileres[132],optfileres[132];
4936:
4937: int ng;
4938:
4939:
4940: /*#ifdef windows */
4941: fprintf(ficgp,"cd \"%s\" \n",pathc);
4942: /*#endif */
4943:
4944:
4945: strcpy(dirfileres,optionfilefiname);
4946: strcpy(optfileres,"vpl");
4947: fprintf(ficgp,"set out \"graphmort.png\"\n ");
4948: fprintf(ficgp,"set xlabel \"Age\"\n set ylabel \"Force of mortality (per year)\" \n ");
4949: fprintf(ficgp, "set ter png small size 320, 240\n set log y\n");
4950: /* fprintf(ficgp, "set size 0.65,0.65\n"); */
4951: fprintf(ficgp,"plot [%d:100] %lf*exp(%lf*(x-%d))",agegomp,p[1],p[2],agegomp);
4952:
4953: }
4954:
4955: int readdata(char datafile[], int firstobs, int lastobs, int *imax)
4956: {
4957:
4958: /*-------- data file ----------*/
4959: FILE *fic;
4960: char dummy[]=" ";
4961: int i=0, j=0, n=0;
4962: int linei, month, year,iout;
4963: char line[MAXLINE], linetmp[MAXLINE];
4964: char stra[MAXLINE], strb[MAXLINE];
4965: char *stratrunc;
4966: int lstra;
4967:
4968:
4969: if((fic=fopen(datafile,"r"))==NULL) {
4970: printf("Problem while opening datafile: %s\n", datafile);return 1;
4971: fprintf(ficlog,"Problem while opening datafile: %s\n", datafile);return 1;
4972: }
4973:
4974: i=1;
4975: linei=0;
4976: while ((fgets(line, MAXLINE, fic) != NULL) &&((i >= firstobs) && (i <=lastobs))) {
4977: linei=linei+1;
4978: for(j=strlen(line); j>=0;j--){ /* Untabifies line */
4979: if(line[j] == '\t')
4980: line[j] = ' ';
4981: }
4982: for(j=strlen(line)-1; (line[j]==' ')||(line[j]==10)||(line[j]==13);j--){
4983: ;
4984: };
4985: line[j+1]=0; /* Trims blanks at end of line */
4986: if(line[0]=='#'){
4987: fprintf(ficlog,"Comment line\n%s\n",line);
4988: printf("Comment line\n%s\n",line);
4989: continue;
4990: }
4991: trimbb(linetmp,line); /* Trims multiple blanks in line */
4992: strcpy(line, linetmp);
4993:
4994:
4995: for (j=maxwav;j>=1;j--){
4996: cutv(stra, strb, line, ' ');
4997: if(strb[0]=='.') { /* Missing status */
4998: lval=-1;
4999: }else{
5000: errno=0;
5001: lval=strtol(strb,&endptr,10);
5002: /* if (errno == ERANGE && (lval == LONG_MAX || lval == LONG_MIN))*/
5003: if( strb[0]=='\0' || (*endptr != '\0')){
5004: 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);
5005: 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);
5006: return 1;
5007: }
5008: }
5009: s[j][i]=lval;
5010:
5011: strcpy(line,stra);
5012: cutv(stra, strb,line,' ');
5013: if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){
5014: }
5015: else if(iout=sscanf(strb,"%s.",dummy) != 0){
5016: month=99;
5017: year=9999;
5018: }else{
5019: 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);
5020: 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);
5021: return 1;
5022: }
5023: anint[j][i]= (double) year;
5024: mint[j][i]= (double)month;
5025: strcpy(line,stra);
5026: } /* ENd Waves */
5027:
5028: cutv(stra, strb,line,' ');
5029: if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){
5030: }
5031: else if(iout=sscanf(strb,"%s.",dummy) != 0){
5032: month=99;
5033: year=9999;
5034: }else{
5035: 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);
5036: 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);
5037: return 1;
5038: }
5039: andc[i]=(double) year;
5040: moisdc[i]=(double) month;
5041: strcpy(line,stra);
5042:
5043: cutv(stra, strb,line,' ');
5044: if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){
5045: }
5046: else if(iout=sscanf(strb,"%s.", dummy) != 0){
5047: month=99;
5048: year=9999;
5049: }else{
5050: 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);
5051: 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);
5052: return 1;
5053: }
5054: if (year==9999) {
5055: 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);
5056: 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);
5057: return 1;
5058:
5059: }
5060: annais[i]=(double)(year);
5061: moisnais[i]=(double)(month);
5062: strcpy(line,stra);
5063:
5064: cutv(stra, strb,line,' ');
5065: errno=0;
5066: dval=strtod(strb,&endptr);
5067: if( strb[0]=='\0' || (*endptr != '\0')){
5068: printf("Error reading data around '%f' at line number %d, \"%s\" for individual %d\nShould be a weight. Exiting.\n",dval, i,line,linei);
5069: 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);
5070: fflush(ficlog);
5071: return 1;
5072: }
5073: weight[i]=dval;
5074: strcpy(line,stra);
5075:
5076: for (j=ncovcol;j>=1;j--){
5077: cutv(stra, strb,line,' ');
5078: if(strb[0]=='.') { /* Missing status */
5079: lval=-1;
5080: }else{
5081: errno=0;
5082: lval=strtol(strb,&endptr,10);
5083: if( strb[0]=='\0' || (*endptr != '\0')){
5084: 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);
5085: 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);
5086: return 1;
5087: }
5088: }
5089: if(lval <-1 || lval >1){
5090: printf("Error reading data around '%ld' at line number %d for individual %d, '%s'\n \
5091: Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
5092: for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
5093: For example, for multinomial values like 1, 2 and 3,\n \
5094: build V1=0 V2=0 for the reference value (1),\n \
5095: V1=1 V2=0 for (2) \n \
5096: and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
5097: output of IMaCh is often meaningless.\n \
5098: Exiting.\n",lval,linei, i,line,j);
5099: fprintf(ficlog,"Error reading data around '%ld' at line number %d for individual %d, '%s'\n \
5100: Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
5101: for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
5102: For example, for multinomial values like 1, 2 and 3,\n \
5103: build V1=0 V2=0 for the reference value (1),\n \
5104: V1=1 V2=0 for (2) \n \
5105: and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
5106: output of IMaCh is often meaningless.\n \
5107: Exiting.\n",lval,linei, i,line,j);fflush(ficlog);
5108: return 1;
5109: }
5110: covar[j][i]=(double)(lval);
5111: strcpy(line,stra);
5112: }
5113: lstra=strlen(stra);
5114:
5115: if(lstra > 9){ /* More than 2**32 or max of what printf can write with %ld */
5116: stratrunc = &(stra[lstra-9]);
5117: num[i]=atol(stratrunc);
5118: }
5119: else
5120: num[i]=atol(stra);
5121: /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){
5122: 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;}*/
5123:
5124: i=i+1;
5125: } /* End loop reading data */
5126:
5127: *imax=i-1; /* Number of individuals */
5128: fclose(fic);
5129:
5130: return (0);
5131: /* endread: */
5132: printf("Exiting readdata: ");
5133: fclose(fic);
5134: return (1);
5135:
5136:
5137:
5138: }
5139: void removespace(char *str) {
5140: char *p1 = str, *p2 = str;
5141: do
5142: while (*p2 == ' ')
5143: p2++;
5144: while (*p1++ = *p2++);
5145: }
5146:
5147: int decodemodel ( char model[], int lastobs) /**< This routine decode the model and returns:
5148: * Model V1+V2+V3+V8+V7*V8+V5*V6+V8*age+V3*age
5149: * - cptcovt total number of covariates of the model nbocc(+)+1 = 8
5150: * - cptcovn or number of covariates k of the models excluding age*products =6
5151: * - cptcovage number of covariates with age*products =2
5152: * - cptcovs number of simple covariates
5153: * - 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
5154: * which is a new column after the 9 (ncovcol) variables.
5155: * - if k is a product Vn*Vm covar[k][i] is filled with correct values for each individual
5156: * - Tprod[l] gives the kth covariates of the product Vn*Vm l=1 to cptcovprod-cptcovage
5157: * Tprod[1]@2 {5, 6}: position of first product V7*V8 is 5, and second V5*V6 is 6.
5158: * - Tvard[k] p Tvard[1][1]@4 {7, 8, 5, 6} for V7*V8 and V5*V6 .
5159: */
5160: {
5161: int i, j, k, ks;
5162: int j1, k1, k2;
5163: char modelsav[80];
5164: char stra[80], strb[80], strc[80], strd[80],stre[80];
5165:
5166: /*removespace(model);*/
5167: if (strlen(model) >1){ /* If there is at least 1 covariate */
5168: j=0, j1=0, k1=0, k2=-1, ks=0, cptcovn=0;
5169: j=nbocc(model,'+'); /**< j=Number of '+' */
5170: j1=nbocc(model,'*'); /**< j1=Number of '*' */
5171: cptcovs=j+1-j1; /**< Number of simple covariates V1+V2*age+V3 +V3*V4=> V1 + V3 =2 */
5172: cptcovt= j+1; /* Number of total covariates in the model V1 + V2*age+ V3 + V3*V4=> 4*/
5173: /* including age products which are counted in cptcovage.
5174: /* but the covariates which are products must be treated separately: ncovn=4- 2=2 (V1+V3). */
5175: cptcovprod=j1; /**< Number of products V1*V2 +v3*age = 2 */
5176: cptcovprodnoage=0; /**< Number of covariate products without age: V3*V4 =1 */
5177: strcpy(modelsav,model);
5178: if (strstr(model,"AGE") !=0){
5179: printf("Error. AGE must be in lower case 'age' model=%s ",model);
5180: fprintf(ficlog,"Error. AGE must be in lower case model=%s ",model);fflush(ficlog);
5181: return 1;
5182: }
5183: if (strstr(model,"v") !=0){
5184: printf("Error. 'v' must be in upper case 'V' model=%s ",model);
5185: fprintf(ficlog,"Error. 'v' must be in upper case model=%s ",model);fflush(ficlog);
5186: return 1;
5187: }
5188:
5189: /* Design
5190: * V1 V2 V3 V4 V5 V6 V7 V8 V9 Weight
5191: * < ncovcol=8 >
5192: * Model V2 + V1 + V3*age + V3 + V5*V6 + V7*V8 + V8*age + V8
5193: * k= 1 2 3 4 5 6 7 8
5194: * cptcovn number of covariates (not including constant and age ) = # of + plus 1 = 7+1=8
5195: * covar[k,i], value of kth covariate if not including age for individual i:
5196: * covar[1][i]= (V2), covar[4][i]=(V3), covar[8][i]=(V8)
5197: * Tvar[k] # of the kth covariate: Tvar[1]=2 Tvar[4]=3 Tvar[8]=8
5198: * if multiplied by age: V3*age Tvar[3=V3*age]=3 (V3) Tvar[7]=8 and
5199: * Tage[++cptcovage]=k
5200: * if products, new covar are created after ncovcol with k1
5201: * Tvar[k]=ncovcol+k1; # of the kth covariate product: Tvar[5]=ncovcol+1=10 Tvar[6]=ncovcol+1=11
5202: * Tprod[k1]=k; Tprod[1]=5 Tprod[2]= 6; gives the position of the k1th product
5203: * 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
5204: * Tvar[cptcovn+k2]=Tvard[k1][1];Tvar[cptcovn+k2+1]=Tvard[k1][2];
5205: * Tvar[8+1]=5;Tvar[8+2]=6;Tvar[8+3]=7;Tvar[8+4]=8 inverted
5206: * V1 V2 V3 V4 V5 V6 V7 V8 V9 V10 V11
5207: * < ncovcol=8 >
5208: * Model V2 + V1 + V3*age + V3 + V5*V6 + V7*V8 + V8*age + V8 d1 d1 d2 d2
5209: * k= 1 2 3 4 5 6 7 8 9 10 11 12
5210: * Tvar[k]= 2 1 3 3 10 11 8 8 5 6 7 8
5211: * p Tvar[1]@12={2, 1, 3, 3, 11, 10, 8, 8, 7, 8, 5, 6}
5212: * p Tprod[1]@2={ 6, 5}
5213: *p Tvard[1][1]@4= {7, 8, 5, 6}
5214: * covar[k][i]= V2 V1 ? V3 V5*V6? V7*V8? ? V8
5215: * cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
5216: *How to reorganize?
5217: * Model V1 + V2 + V3 + V8 + V5*V6 + V7*V8 + V3*age + V8*age
5218: * Tvars {2, 1, 3, 3, 11, 10, 8, 8, 7, 8, 5, 6}
5219: * {2, 1, 4, 8, 5, 6, 3, 7}
5220: * Struct []
5221: */
5222:
5223: /* This loop fills the array Tvar from the string 'model'.*/
5224: /* j is the number of + signs in the model V1+V2+V3 j=2 i=3 to 1 */
5225: /* modelsav=V2+V1+V4+age*V3 strb=age*V3 stra=V2+V1+V4 */
5226: /* k=4 (age*V3) Tvar[k=4]= 3 (from V3) Tage[cptcovage=1]=4 */
5227: /* k=3 V4 Tvar[k=3]= 4 (from V4) */
5228: /* k=2 V1 Tvar[k=2]= 1 (from V1) */
5229: /* k=1 Tvar[1]=2 (from V2) */
5230: /* k=5 Tvar[5] */
5231: /* for (k=1; k<=cptcovn;k++) { */
5232: /* cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]]; */
5233: /* } */
5234: /* for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
5235: /*
5236: * Treating invertedly V2+V1+V3*age+V2*V4 is as if written V2*V4 +V3*age + V1 + V2 */
5237: for(k=cptcovt; k>=1;k--) /**< Number of covariates */
5238: Tvar[k]=0;
5239: cptcovage=0;
5240: for(k=1; k<=cptcovt;k++){ /* Loop on total covariates of the model */
5241: cutl(stra,strb,modelsav,'+'); /* keeps in strb after the first '+'
5242: modelsav==V2+V1+V4+V3*age strb=V3*age stra=V2+V1+V4 */
5243: if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyzes it */
5244: /* printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/
5245: /*scanf("%d",i);*/
5246: if (strchr(strb,'*')) { /**< Model includes a product V2+V1+V4+V3*age strb=V3*age */
5247: cutl(strc,strd,strb,'*'); /**< strd*strc Vm*Vn: strb=V3*age(input) strc=age strd=V3 ; V3*V2 strc=V2, strd=V3 */
5248: if (strcmp(strc,"age")==0) { /**< Model includes age: Vn*age */
5249: /* covar is not filled and then is empty */
5250: cptcovprod--;
5251: cutl(stre,strb,strd,'V'); /* strd=V3(input): stre="3" */
5252: Tvar[k]=atoi(stre); /* V2+V1+V4+V3*age Tvar[4]=3 ; V1+V2*age Tvar[2]=2 */
5253: cptcovage++; /* Sums the number of covariates which include age as a product */
5254: Tage[cptcovage]=k; /* Tage[1] = 4 */
5255: /*printf("stre=%s ", stre);*/
5256: } else if (strcmp(strd,"age")==0) { /* or age*Vn */
5257: cptcovprod--;
5258: cutl(stre,strb,strc,'V');
5259: Tvar[k]=atoi(stre);
5260: cptcovage++;
5261: Tage[cptcovage]=k;
5262: } else { /* Age is not in the model product V2+V1+V1*V4+V3*age+V3*V2 strb=V3*V2*/
5263: /* loops on k1=1 (V3*V2) and k1=2 V4*V3 */
5264: cptcovn++;
5265: cptcovprodnoage++;k1++;
5266: cutl(stre,strb,strc,'V'); /* strc= Vn, stre is n; strb=V3*V2 stre=3 strc=*/
5267: Tvar[k]=ncovcol+k1; /* For model-covariate k tells which data-covariate to use but
5268: because this model-covariate is a construction we invent a new column
5269: ncovcol + k1
5270: If already ncovcol=4 and model=V2+V1+V1*V4+age*V3+V3*V2
5271: Tvar[3=V1*V4]=4+1 Tvar[5=V3*V2]=4 + 2= 6, etc */
5272: cutl(strc,strb,strd,'V'); /* strd was Vm, strc is m */
5273: Tprod[k1]=k; /* Tprod[1]=3(=V1*V4) for V2+V1+V1*V4+age*V3+V3*V2 */
5274: Tvard[k1][1] =atoi(strc); /* m 1 for V1*/
5275: Tvard[k1][2] =atoi(stre); /* n 4 for V4*/
5276: k2=k2+2;
5277: Tvar[cptcovt+k2]=Tvard[k1][1]; /* Tvar[(cptcovt=4+k2=1)=5]= 1 (V1) */
5278: Tvar[cptcovt+k2+1]=Tvard[k1][2]; /* Tvar[(cptcovt=4+(k2=1)+1)=6]= 4 (V4) */
5279: for (i=1; i<=lastobs;i++){
5280: /* Computes the new covariate which is a product of
5281: covar[n][i]* covar[m][i] and stores it at ncovol+k1 May not be defined */
5282: covar[ncovcol+k1][i]=covar[atoi(stre)][i]*covar[atoi(strc)][i];
5283: }
5284: } /* End age is not in the model */
5285: } /* End if model includes a product */
5286: else { /* no more sum */
5287: /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/
5288: /* scanf("%d",i);*/
5289: cutl(strd,strc,strb,'V');
5290: ks++; /**< Number of simple covariates */
5291: cptcovn++;
5292: Tvar[k]=atoi(strd);
5293: }
5294: strcpy(modelsav,stra); /* modelsav=V2+V1+V4 stra=V2+V1+V4 */
5295: /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);
5296: scanf("%d",i);*/
5297: } /* end of loop + */
5298: } /* end model */
5299:
5300: /*The number n of Vn is stored in Tvar. cptcovage =number of age covariate. Tage gives the position of age. cptcovprod= number of products.
5301: If model=V1+V1*age then Tvar[1]=1 Tvar[2]=1 cptcovage=1 Tage[1]=2 cptcovprod=0*/
5302:
5303: /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);
5304: printf("cptcovprod=%d ", cptcovprod);
5305: fprintf(ficlog,"cptcovprod=%d ", cptcovprod);
5306:
5307: scanf("%d ",i);*/
5308:
5309:
5310: return (0); /* with covar[new additional covariate if product] and Tage if age */
5311: /*endread:*/
5312: printf("Exiting decodemodel: ");
5313: return (1);
5314: }
5315:
5316: calandcheckages(int imx, int maxwav, double *agemin, double *agemax, int *nberr, int *nbwarn )
5317: {
5318: int i, m;
5319:
5320: for (i=1; i<=imx; i++) {
5321: for(m=2; (m<= maxwav); m++) {
5322: if (((int)mint[m][i]== 99) && (s[m][i] <= nlstate)){
5323: anint[m][i]=9999;
5324: s[m][i]=-1;
5325: }
5326: if((int)moisdc[i]==99 && (int)andc[i]==9999 && s[m][i]>nlstate){
5327: *nberr++;
5328: 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\n",(int)moisdc[i],(int)andc[i],num[i],i);
5329: 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\n",(int)moisdc[i],(int)andc[i],num[i],i);
5330: s[m][i]=-1;
5331: }
5332: if((int)moisdc[i]==99 && (int)andc[i]!=9999 && s[m][i]>nlstate){
5333: *nberr++;
5334: 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]);
5335: 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]);
5336: s[m][i]=-1; /* We prefer to skip it (and to skip it in version 0.8a1 too */
5337: }
5338: }
5339: }
5340:
5341: for (i=1; i<=imx; i++) {
5342: agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);
5343: for(m=firstpass; (m<= lastpass); m++){
5344: if(s[m][i] >0 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5){
5345: if (s[m][i] >= nlstate+1) {
5346: if(agedc[i]>0)
5347: if((int)moisdc[i]!=99 && (int)andc[i]!=9999)
5348: agev[m][i]=agedc[i];
5349: /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/
5350: else {
5351: if ((int)andc[i]!=9999){
5352: nbwarn++;
5353: printf("Warning negative age at death: %ld line:%d\n",num[i],i);
5354: fprintf(ficlog,"Warning negative age at death: %ld line:%d\n",num[i],i);
5355: agev[m][i]=-1;
5356: }
5357: }
5358: }
5359: else if(s[m][i] !=9){ /* Standard case, age in fractional
5360: years but with the precision of a month */
5361: agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);
5362: if((int)mint[m][i]==99 || (int)anint[m][i]==9999)
5363: agev[m][i]=1;
5364: else if(agev[m][i] < *agemin){
5365: *agemin=agev[m][i];
5366: printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], *agemin);
5367: }
5368: else if(agev[m][i] >*agemax){
5369: *agemax=agev[m][i];
5370: /* printf(" Max anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.2f\n",m,i,anint[m][i], i,annais[i], *agemax);*/
5371: }
5372: /*agev[m][i]=anint[m][i]-annais[i];*/
5373: /* agev[m][i] = age[i]+2*m;*/
5374: }
5375: else { /* =9 */
5376: agev[m][i]=1;
5377: s[m][i]=-1;
5378: }
5379: }
5380: else /*= 0 Unknown */
5381: agev[m][i]=1;
5382: }
5383:
5384: }
5385: for (i=1; i<=imx; i++) {
5386: for(m=firstpass; (m<=lastpass); m++){
5387: if (s[m][i] > (nlstate+ndeath)) {
5388: *nberr++;
5389: 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);
5390: 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);
5391: return 1;
5392: }
5393: }
5394: }
5395:
5396: /*for (i=1; i<=imx; i++){
5397: for (m=firstpass; (m<lastpass); m++){
5398: printf("%ld %d %.lf %d %d\n", num[i],(covar[1][i]),agev[m][i],s[m][i],s[m+1][i]);
5399: }
5400:
5401: }*/
5402:
5403:
5404: printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, *agemin, *agemax);
5405: fprintf(ficlog,"Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, *agemin, *agemax);
5406:
5407: return (0);
5408: /* endread:*/
5409: printf("Exiting calandcheckages: ");
5410: return (1);
5411: }
5412:
5413:
5414: /***********************************************/
5415: /**************** Main Program *****************/
5416: /***********************************************/
5417:
5418: int main(int argc, char *argv[])
5419: {
5420: #ifdef GSL
5421: const gsl_multimin_fminimizer_type *T;
5422: size_t iteri = 0, it;
5423: int rval = GSL_CONTINUE;
5424: int status = GSL_SUCCESS;
5425: double ssval;
5426: #endif
5427: int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav);
5428: int i,j, k, n=MAXN,iter=0,m,size=100, cptcod;
5429:
5430: int jj, ll, li, lj, lk;
5431: int numlinepar=0; /* Current linenumber of parameter file */
5432: int itimes;
5433: int NDIM=2;
5434: int vpopbased=0;
5435:
5436: char ca[32], cb[32];
5437: /* FILE *fichtm; *//* Html File */
5438: /* FILE *ficgp;*/ /*Gnuplot File */
5439: struct stat info;
5440: double agedeb;
5441: double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;
5442:
5443: double fret;
5444: double dum; /* Dummy variable */
5445: double ***p3mat;
5446: double ***mobaverage;
5447:
5448: char line[MAXLINE];
5449: char path[MAXLINE],pathc[MAXLINE],pathcd[MAXLINE],pathtot[MAXLINE],model[MAXLINE];
5450: char pathr[MAXLINE], pathimach[MAXLINE];
5451: char *tok, *val; /* pathtot */
5452: int firstobs=1, lastobs=10;
5453: int c, h , cpt;
5454: int jl;
5455: int i1, j1, jk, stepsize;
5456: int *tab;
5457: int mobilavproj=0 , prevfcast=0 ; /* moving average of prev, If prevfcast=1 prevalence projection */
5458: int mobilav=0,popforecast=0;
5459: int hstepm, nhstepm;
5460: int agemortsup;
5461: float sumlpop=0.;
5462: double jprev1=1, mprev1=1,anprev1=2000,jprev2=1, mprev2=1,anprev2=2000;
5463: double jpyram=1, mpyram=1,anpyram=2000,jpyram1=1, mpyram1=1,anpyram1=2000;
5464:
5465: double bage=0, fage=110, age, agelim, agebase;
5466: double ftolpl=FTOL;
5467: double **prlim;
5468: double ***param; /* Matrix of parameters */
5469: double *p;
5470: double **matcov; /* Matrix of covariance */
5471: double ***delti3; /* Scale */
5472: double *delti; /* Scale */
5473: double ***eij, ***vareij;
5474: double **varpl; /* Variances of prevalence limits by age */
5475: double *epj, vepp;
5476:
5477: double dateprev1, dateprev2,jproj1=1,mproj1=1,anproj1=2000,jproj2=1,mproj2=1,anproj2=2000;
5478: double **ximort;
5479: char *alph[]={"a","a","b","c","d","e"}, str[4]="1234";
5480: int *dcwave;
5481:
5482: char z[1]="c";
5483:
5484: /*char *strt;*/
5485: char strtend[80];
5486:
5487:
5488: /* setlocale (LC_ALL, ""); */
5489: /* bindtextdomain (PACKAGE, LOCALEDIR); */
5490: /* textdomain (PACKAGE); */
5491: /* setlocale (LC_CTYPE, ""); */
5492: /* setlocale (LC_MESSAGES, ""); */
5493:
5494: /* gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */
5495: rstart_time = time(NULL);
5496: /* (void) gettimeofday(&start_time,&tzp);*/
5497: start_time = *localtime(&rstart_time);
5498: curr_time=start_time;
5499: /*tml = *localtime(&start_time.tm_sec);*/
5500: /* strcpy(strstart,asctime(&tml)); */
5501: strcpy(strstart,asctime(&start_time));
5502:
5503: /* printf("Localtime (at start)=%s",strstart); */
5504: /* tp.tm_sec = tp.tm_sec +86400; */
5505: /* tm = *localtime(&start_time.tm_sec); */
5506: /* tmg.tm_year=tmg.tm_year +dsign*dyear; */
5507: /* tmg.tm_mon=tmg.tm_mon +dsign*dmonth; */
5508: /* tmg.tm_hour=tmg.tm_hour + 1; */
5509: /* tp.tm_sec = mktime(&tmg); */
5510: /* strt=asctime(&tmg); */
5511: /* printf("Time(after) =%s",strstart); */
5512: /* (void) time (&time_value);
5513: * printf("time=%d,t-=%d\n",time_value,time_value-86400);
5514: * tm = *localtime(&time_value);
5515: * strstart=asctime(&tm);
5516: * printf("tim_value=%d,asctime=%s\n",time_value,strstart);
5517: */
5518:
5519: nberr=0; /* Number of errors and warnings */
5520: nbwarn=0;
5521: getcwd(pathcd, size);
5522:
5523: printf("\n%s\n%s",version,fullversion);
5524: if(argc <=1){
5525: printf("\nEnter the parameter file name: ");
5526: fgets(pathr,FILENAMELENGTH,stdin);
5527: i=strlen(pathr);
5528: if(pathr[i-1]=='\n')
5529: pathr[i-1]='\0';
5530: i=strlen(pathr);
5531: if(pathr[i-1]==' ') /* This may happen when dragging on oS/X! */
5532: pathr[i-1]='\0';
5533: for (tok = pathr; tok != NULL; ){
5534: printf("Pathr |%s|\n",pathr);
5535: while ((val = strsep(&tok, "\"" )) != NULL && *val == '\0');
5536: printf("val= |%s| pathr=%s\n",val,pathr);
5537: strcpy (pathtot, val);
5538: if(pathr[0] == '\0') break; /* Dirty */
5539: }
5540: }
5541: else{
5542: strcpy(pathtot,argv[1]);
5543: }
5544: /*if(getcwd(pathcd, MAXLINE)!= NULL)printf ("Error pathcd\n");*/
5545: /*cygwin_split_path(pathtot,path,optionfile);
5546: printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/
5547: /* cutv(path,optionfile,pathtot,'\\');*/
5548:
5549: /* Split argv[0], imach program to get pathimach */
5550: printf("\nargv[0]=%s argv[1]=%s, \n",argv[0],argv[1]);
5551: split(argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
5552: printf("\nargv[0]=%s pathimach=%s, \noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
5553: /* strcpy(pathimach,argv[0]); */
5554: /* Split argv[1]=pathtot, parameter file name to get path, optionfile, extension and name */
5555: split(pathtot,path,optionfile,optionfilext,optionfilefiname);
5556: printf("\npathtot=%s,\npath=%s,\noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
5557: chdir(path); /* Can be a relative path */
5558: if(getcwd(pathcd,MAXLINE) > 0) /* So pathcd is the full path */
5559: printf("Current directory %s!\n",pathcd);
5560: strcpy(command,"mkdir ");
5561: strcat(command,optionfilefiname);
5562: if((outcmd=system(command)) != 0){
5563: printf("Problem creating directory or it already exists %s%s, err=%d\n",path,optionfilefiname,outcmd);
5564: /* fprintf(ficlog,"Problem creating directory %s%s\n",path,optionfilefiname); */
5565: /* fclose(ficlog); */
5566: /* exit(1); */
5567: }
5568: /* if((imk=mkdir(optionfilefiname))<0){ */
5569: /* perror("mkdir"); */
5570: /* } */
5571:
5572: /*-------- arguments in the command line --------*/
5573:
5574: /* Log file */
5575: strcat(filelog, optionfilefiname);
5576: strcat(filelog,".log"); /* */
5577: if((ficlog=fopen(filelog,"w"))==NULL) {
5578: printf("Problem with logfile %s\n",filelog);
5579: goto end;
5580: }
5581: fprintf(ficlog,"Log filename:%s\n",filelog);
5582: fprintf(ficlog,"\n%s\n%s",version,fullversion);
5583: fprintf(ficlog,"\nEnter the parameter file name: \n");
5584: fprintf(ficlog,"pathimach=%s\npathtot=%s\n\
5585: path=%s \n\
5586: optionfile=%s\n\
5587: optionfilext=%s\n\
5588: optionfilefiname='%s'\n",pathimach,pathtot,path,optionfile,optionfilext,optionfilefiname);
5589:
5590: printf("Local time (at start):%s",strstart);
5591: fprintf(ficlog,"Local time (at start): %s",strstart);
5592: fflush(ficlog);
5593: /* (void) gettimeofday(&curr_time,&tzp); */
5594: /* printf("Elapsed time %d\n", asc_diff_time(curr_time.tm_sec-start_time.tm_sec,tmpout)); */
5595:
5596: /* */
5597: strcpy(fileres,"r");
5598: strcat(fileres, optionfilefiname);
5599: strcat(fileres,".txt"); /* Other files have txt extension */
5600:
5601: /*---------arguments file --------*/
5602:
5603: if((ficpar=fopen(optionfile,"r"))==NULL) {
5604: printf("Problem with optionfile '%s' with errno='%s'\n",optionfile,strerror(errno));
5605: fprintf(ficlog,"Problem with optionfile '%s' with errno='%s'\n",optionfile,strerror(errno));
5606: fflush(ficlog);
5607: /* goto end; */
5608: exit(70);
5609: }
5610:
5611:
5612:
5613: strcpy(filereso,"o");
5614: strcat(filereso,fileres);
5615: if((ficparo=fopen(filereso,"w"))==NULL) { /* opened on subdirectory */
5616: printf("Problem with Output resultfile: %s\n", filereso);
5617: fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso);
5618: fflush(ficlog);
5619: goto end;
5620: }
5621:
5622: /* Reads comments: lines beginning with '#' */
5623: numlinepar=0;
5624: while((c=getc(ficpar))=='#' && c!= EOF){
5625: ungetc(c,ficpar);
5626: fgets(line, MAXLINE, ficpar);
5627: numlinepar++;
5628: fputs(line,stdout);
5629: fputs(line,ficparo);
5630: fputs(line,ficlog);
5631: }
5632: ungetc(c,ficpar);
5633:
5634: 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=%s\n",title, datafile, &lastobs, &firstpass,&lastpass,&ftol, &stepm, &ncovcol, &nlstate,&ndeath, &maxwav, &mle, &weightopt,model);
5635: numlinepar++;
5636: 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=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate,ndeath, maxwav, mle, weightopt,model);
5637: 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=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol,nlstate,ndeath,maxwav, mle, weightopt,model);
5638: 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=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol,nlstate,ndeath,maxwav, mle, weightopt,model);
5639: fflush(ficlog);
5640: while((c=getc(ficpar))=='#' && c!= EOF){
5641: ungetc(c,ficpar);
5642: fgets(line, MAXLINE, ficpar);
5643: numlinepar++;
5644: fputs(line, stdout);
5645: //puts(line);
5646: fputs(line,ficparo);
5647: fputs(line,ficlog);
5648: }
5649: ungetc(c,ficpar);
5650:
5651:
5652: covar=matrix(0,NCOVMAX,1,n); /**< used in readdata */
5653: cptcovn=0; /*Number of covariates, i.e. number of '+' in model statement plus one, indepently of n in Vn*/
5654: /* v1+v2+v3+v2*v4+v5*age makes cptcovn = 5
5655: v1+v2*age+v2*v3 makes cptcovn = 3
5656: */
5657: if (strlen(model)>1)
5658: 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*/
5659: else
5660: ncovmodel=2;
5661: nvar=ncovmodel-1; /* Suppressing age as a basic covariate */
5662: nforce= (nlstate+ndeath-1)*nlstate; /* Number of forces ij from state i to j */
5663: npar= nforce*ncovmodel; /* Number of parameters like aij*/
5664: if(npar >MAXPARM || nlstate >NLSTATEMAX || ndeath >NDEATHMAX || ncovmodel>NCOVMAX){
5665: 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);
5666: 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);
5667: fflush(stdout);
5668: fclose (ficlog);
5669: goto end;
5670: }
5671: delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
5672: delti=delti3[1][1];
5673: /*delti=vector(1,npar); *//* Scale of each paramater (output from hesscov)*/
5674: if(mle==-1){ /* Print a wizard for help writing covariance matrix */
5675: prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
5676: printf(" You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
5677: fprintf(ficlog," You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
5678: free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
5679: fclose (ficparo);
5680: fclose (ficlog);
5681: goto end;
5682: exit(0);
5683: }
5684: else if(mle==-3) {
5685: prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
5686: printf(" You choose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
5687: fprintf(ficlog," You choose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
5688: param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
5689: matcov=matrix(1,npar,1,npar);
5690: }
5691: else{
5692: /* Read guessed parameters */
5693: /* Reads comments: lines beginning with '#' */
5694: while((c=getc(ficpar))=='#' && c!= EOF){
5695: ungetc(c,ficpar);
5696: fgets(line, MAXLINE, ficpar);
5697: numlinepar++;
5698: fputs(line,stdout);
5699: fputs(line,ficparo);
5700: fputs(line,ficlog);
5701: }
5702: ungetc(c,ficpar);
5703:
5704: param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
5705: for(i=1; i <=nlstate; i++){
5706: j=0;
5707: for(jj=1; jj <=nlstate+ndeath; jj++){
5708: if(jj==i) continue;
5709: j++;
5710: fscanf(ficpar,"%1d%1d",&i1,&j1);
5711: if ((i1 != i) && (j1 != j)){
5712: printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n \
5713: It might be a problem of design; if ncovcol and the model are correct\n \
5714: run imach with mle=-1 to get a correct template of the parameter file.\n",numlinepar, i,j, i1, j1);
5715: exit(1);
5716: }
5717: fprintf(ficparo,"%1d%1d",i1,j1);
5718: if(mle==1)
5719: printf("%1d%1d",i,j);
5720: fprintf(ficlog,"%1d%1d",i,j);
5721: for(k=1; k<=ncovmodel;k++){
5722: fscanf(ficpar," %lf",¶m[i][j][k]);
5723: if(mle==1){
5724: printf(" %lf",param[i][j][k]);
5725: fprintf(ficlog," %lf",param[i][j][k]);
5726: }
5727: else
5728: fprintf(ficlog," %lf",param[i][j][k]);
5729: fprintf(ficparo," %lf",param[i][j][k]);
5730: }
5731: fscanf(ficpar,"\n");
5732: numlinepar++;
5733: if(mle==1)
5734: printf("\n");
5735: fprintf(ficlog,"\n");
5736: fprintf(ficparo,"\n");
5737: }
5738: }
5739: fflush(ficlog);
5740:
5741: /* Reads scales values */
5742: p=param[1][1];
5743:
5744: /* Reads comments: lines beginning with '#' */
5745: while((c=getc(ficpar))=='#' && c!= EOF){
5746: ungetc(c,ficpar);
5747: fgets(line, MAXLINE, ficpar);
5748: numlinepar++;
5749: fputs(line,stdout);
5750: fputs(line,ficparo);
5751: fputs(line,ficlog);
5752: }
5753: ungetc(c,ficpar);
5754:
5755: for(i=1; i <=nlstate; i++){
5756: for(j=1; j <=nlstate+ndeath-1; j++){
5757: fscanf(ficpar,"%1d%1d",&i1,&j1);
5758: if ( (i1-i) * (j1-j) != 0){
5759: printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n",numlinepar, i,j, i1, j1);
5760: exit(1);
5761: }
5762: printf("%1d%1d",i,j);
5763: fprintf(ficparo,"%1d%1d",i1,j1);
5764: fprintf(ficlog,"%1d%1d",i1,j1);
5765: for(k=1; k<=ncovmodel;k++){
5766: fscanf(ficpar,"%le",&delti3[i][j][k]);
5767: printf(" %le",delti3[i][j][k]);
5768: fprintf(ficparo," %le",delti3[i][j][k]);
5769: fprintf(ficlog," %le",delti3[i][j][k]);
5770: }
5771: fscanf(ficpar,"\n");
5772: numlinepar++;
5773: printf("\n");
5774: fprintf(ficparo,"\n");
5775: fprintf(ficlog,"\n");
5776: }
5777: }
5778: fflush(ficlog);
5779:
5780: /* Reads covariance matrix */
5781: delti=delti3[1][1];
5782:
5783:
5784: /* free_ma3x(delti3,1,nlstate,1,nlstate+ndeath-1,1,ncovmodel); */ /* Hasn't to to freed here otherwise delti is no more allocated */
5785:
5786: /* Reads comments: lines beginning with '#' */
5787: while((c=getc(ficpar))=='#' && c!= EOF){
5788: ungetc(c,ficpar);
5789: fgets(line, MAXLINE, ficpar);
5790: numlinepar++;
5791: fputs(line,stdout);
5792: fputs(line,ficparo);
5793: fputs(line,ficlog);
5794: }
5795: ungetc(c,ficpar);
5796:
5797: matcov=matrix(1,npar,1,npar);
5798: for(i=1; i <=npar; i++)
5799: for(j=1; j <=npar; j++) matcov[i][j]=0.;
5800:
5801: for(i=1; i <=npar; i++){
5802: fscanf(ficpar,"%s",str);
5803: if(mle==1)
5804: printf("%s",str);
5805: fprintf(ficlog,"%s",str);
5806: fprintf(ficparo,"%s",str);
5807: for(j=1; j <=i; j++){
5808: fscanf(ficpar," %le",&matcov[i][j]);
5809: if(mle==1){
5810: printf(" %.5le",matcov[i][j]);
5811: }
5812: fprintf(ficlog," %.5le",matcov[i][j]);
5813: fprintf(ficparo," %.5le",matcov[i][j]);
5814: }
5815: fscanf(ficpar,"\n");
5816: numlinepar++;
5817: if(mle==1)
5818: printf("\n");
5819: fprintf(ficlog,"\n");
5820: fprintf(ficparo,"\n");
5821: }
5822: for(i=1; i <=npar; i++)
5823: for(j=i+1;j<=npar;j++)
5824: matcov[i][j]=matcov[j][i];
5825:
5826: if(mle==1)
5827: printf("\n");
5828: fprintf(ficlog,"\n");
5829:
5830: fflush(ficlog);
5831:
5832: /*-------- Rewriting parameter file ----------*/
5833: strcpy(rfileres,"r"); /* "Rparameterfile */
5834: strcat(rfileres,optionfilefiname); /* Parameter file first name*/
5835: strcat(rfileres,"."); /* */
5836: strcat(rfileres,optionfilext); /* Other files have txt extension */
5837: if((ficres =fopen(rfileres,"w"))==NULL) {
5838: printf("Problem writing new parameter file: %s\n", fileres);goto end;
5839: fprintf(ficlog,"Problem writing new parameter file: %s\n", fileres);goto end;
5840: }
5841: fprintf(ficres,"#%s\n",version);
5842: } /* End of mle != -3 */
5843:
5844:
5845: n= lastobs;
5846: num=lvector(1,n);
5847: moisnais=vector(1,n);
5848: annais=vector(1,n);
5849: moisdc=vector(1,n);
5850: andc=vector(1,n);
5851: agedc=vector(1,n);
5852: cod=ivector(1,n);
5853: weight=vector(1,n);
5854: for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */
5855: mint=matrix(1,maxwav,1,n);
5856: anint=matrix(1,maxwav,1,n);
5857: s=imatrix(1,maxwav+1,1,n); /* s[i][j] health state for wave i and individual j */
5858: tab=ivector(1,NCOVMAX);
5859: ncodemax=ivector(1,NCOVMAX); /* Number of code per covariate; if O and 1 only, 2**ncov; V1+V2+V3+V4=>16 */
5860:
5861: /* Reads data from file datafile */
5862: if (readdata(datafile, firstobs, lastobs, &imx)==1)
5863: goto end;
5864:
5865: /* Calculation of the number of parameters from char model */
5866: /* modelsav=V2+V1+V4+age*V3 strb=age*V3 stra=V2+V1+V4
5867: k=4 (age*V3) Tvar[k=4]= 3 (from V3) Tag[cptcovage=1]=4
5868: k=3 V4 Tvar[k=3]= 4 (from V4)
5869: k=2 V1 Tvar[k=2]= 1 (from V1)
5870: k=1 Tvar[1]=2 (from V2)
5871: */
5872: Tvar=ivector(1,NCOVMAX); /* Was 15 changed to NCOVMAX. */
5873: /* V2+V1+V4+age*V3 is a model with 4 covariates (3 plus signs).
5874: For each model-covariate stores the data-covariate id. Tvar[1]=2, Tvar[2]=1, Tvar[3]=4,
5875: Tvar[4=age*V3] is 3 and 'age' is recorded in Tage.
5876: */
5877: /* For model-covariate k tells which data-covariate to use but
5878: because this model-covariate is a construction we invent a new column
5879: ncovcol + k1
5880: If already ncovcol=4 and model=V2+V1+V1*V4+age*V3
5881: Tvar[3=V1*V4]=4+1 etc */
5882: Tprod=ivector(1,NCOVMAX); /* Gives the position of a product */
5883: /* Tprod[k1=1]=3(=V1*V4) for V2+V1+V1*V4+age*V3
5884: if V2+V1+V1*V4+age*V3+V3*V2 TProd[k1=2]=5 (V3*V2)
5885: */
5886: Tvaraff=ivector(1,NCOVMAX); /* Unclear */
5887: 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
5888: * For V3*V2 (in V2+V1+V1*V4+age*V3+V3*V2), V3*V2 position is 2nd.
5889: * Tvard[k1=2][1]=3 (V3) Tvard[k1=2][2]=2(V2) */
5890: Tage=ivector(1,NCOVMAX); /* Gives the covariate id of covariates associated with age: V2 + V1 + age*V4 + V3*age
5891: 4 covariates (3 plus signs)
5892: Tage[1=V3*age]= 4; Tage[2=age*V4] = 3
5893: */
5894:
5895: if(decodemodel(model, lastobs) == 1)
5896: goto end;
5897:
5898: if((double)(lastobs-imx)/(double)imx > 1.10){
5899: nbwarn++;
5900: 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);
5901: 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);
5902: }
5903: /* if(mle==1){*/
5904: if (weightopt != 1) { /* Maximisation without weights. We can have weights different from 1 but want no weight*/
5905: for(i=1;i<=imx;i++) weight[i]=1.0; /* changed to imx */
5906: }
5907:
5908: /*-calculation of age at interview from date of interview and age at death -*/
5909: agev=matrix(1,maxwav,1,imx);
5910:
5911: if(calandcheckages(imx, maxwav, &agemin, &agemax, &nberr, &nbwarn) == 1)
5912: goto end;
5913:
5914:
5915: agegomp=(int)agemin;
5916: free_vector(moisnais,1,n);
5917: free_vector(annais,1,n);
5918: /* free_matrix(mint,1,maxwav,1,n);
5919: free_matrix(anint,1,maxwav,1,n);*/
5920: free_vector(moisdc,1,n);
5921: free_vector(andc,1,n);
5922: /* */
5923:
5924: wav=ivector(1,imx);
5925: dh=imatrix(1,lastpass-firstpass+1,1,imx);
5926: bh=imatrix(1,lastpass-firstpass+1,1,imx);
5927: mw=imatrix(1,lastpass-firstpass+1,1,imx);
5928:
5929: /* Concatenates waves */
5930: concatwav(wav, dh, bh, mw, s, agedc, agev, firstpass, lastpass, imx, nlstate, stepm);
5931: /* */
5932:
5933: /* Routine tricode is to calculate cptcoveff (real number of unique covariates) and to associate covariable number and modality */
5934:
5935: nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);
5936: ncodemax[1]=1;
5937: Ndum =ivector(-1,NCOVMAX);
5938: if (ncovmodel > 2)
5939: tricode(Tvar,nbcode,imx, Ndum); /**< Fills nbcode[Tvar[j]][l]; */
5940:
5941: codtab=imatrix(1,100,1,10); /* codtab[h,k]=( (h-1) - mod(k-1,2**(k-1) )/2**(k-1) */
5942: /*printf(" codtab[1,1],codtab[100,10]=%d,%d\n", codtab[1][1],codtab[100][10]);*/
5943: h=0;
5944:
5945:
5946: /*if (cptcovn > 0) */
5947:
5948:
5949: m=pow(2,cptcoveff);
5950:
5951: for(k=1;k<=cptcoveff; k++){ /* scans any effective covariate */
5952: 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 */
5953: for(j=1; j <= ncodemax[k]; j++){ /* For each modality of this covariate ncodemax=2*/
5954: for(cpt=1; cpt <=pow(2,k-1); cpt++){ /* cpt=1 to 8/2**(3+1-1 or 3+1-3) =1 or 4 */
5955: h++;
5956: if (h>m)
5957: h=1;
5958: /**< codtab(h,k) k = codtab[h,k]=( (h-1) - mod(k-1,2**(k-1) )/2**(k-1) + 1
5959: * h 1 2 3 4
5960: *______________________________
5961: * 1 i=1 1 i=1 1 i=1 1 i=1 1
5962: * 2 2 1 1 1
5963: * 3 i=2 1 2 1 1
5964: * 4 2 2 1 1
5965: * 5 i=3 1 i=2 1 2 1
5966: * 6 2 1 2 1
5967: * 7 i=4 1 2 2 1
5968: * 8 2 2 2 1
5969: * 9 i=5 1 i=3 1 i=2 1 1
5970: * 10 2 1 1 1
5971: * 11 i=6 1 2 1 1
5972: * 12 2 2 1 1
5973: * 13 i=7 1 i=4 1 2 1
5974: * 14 2 1 2 1
5975: * 15 i=8 1 2 2 1
5976: * 16 2 2 2 1
5977: */
5978: codtab[h][k]=j;
5979: /*codtab[h][Tvar[k]]=j;*/
5980: 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]]);
5981: }
5982: }
5983: }
5984: }
5985: /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]);
5986: codtab[1][2]=1;codtab[2][2]=2; */
5987: /* for(i=1; i <=m ;i++){
5988: for(k=1; k <=cptcovn; k++){
5989: printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);
5990: }
5991: printf("\n");
5992: }
5993: scanf("%d",i);*/
5994:
5995: free_ivector(Ndum,-1,NCOVMAX);
5996:
5997:
5998:
5999: /*------------ gnuplot -------------*/
6000: strcpy(optionfilegnuplot,optionfilefiname);
6001: if(mle==-3)
6002: strcat(optionfilegnuplot,"-mort");
6003: strcat(optionfilegnuplot,".gp");
6004:
6005: if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {
6006: printf("Problem with file %s",optionfilegnuplot);
6007: }
6008: else{
6009: fprintf(ficgp,"\n# %s\n", version);
6010: fprintf(ficgp,"# %s\n", optionfilegnuplot);
6011: //fprintf(ficgp,"set missing 'NaNq'\n");
6012: fprintf(ficgp,"set datafile missing 'NaNq'\n");
6013: }
6014: /* fclose(ficgp);*/
6015: /*--------- index.htm --------*/
6016:
6017: strcpy(optionfilehtm,optionfilefiname); /* Main html file */
6018: if(mle==-3)
6019: strcat(optionfilehtm,"-mort");
6020: strcat(optionfilehtm,".htm");
6021: if((fichtm=fopen(optionfilehtm,"w"))==NULL) {
6022: printf("Problem with %s \n",optionfilehtm);
6023: exit(0);
6024: }
6025:
6026: strcpy(optionfilehtmcov,optionfilefiname); /* Only for matrix of covariance */
6027: strcat(optionfilehtmcov,"-cov.htm");
6028: if((fichtmcov=fopen(optionfilehtmcov,"w"))==NULL) {
6029: printf("Problem with %s \n",optionfilehtmcov), exit(0);
6030: }
6031: else{
6032: fprintf(fichtmcov,"<html><head>\n<title>IMaCh Cov %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
6033: <hr size=\"2\" color=\"#EC5E5E\"> \n\
6034: Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n",\
6035: optionfilehtmcov,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);
6036: }
6037:
6038: fprintf(fichtm,"<html><head>\n<title>IMaCh %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
6039: <hr size=\"2\" color=\"#EC5E5E\"> \n\
6040: Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n\
6041: \n\
6042: <hr size=\"2\" color=\"#EC5E5E\">\
6043: <ul><li><h4>Parameter files</h4>\n\
6044: - Parameter file: <a href=\"%s.%s\">%s.%s</a><br>\n\
6045: - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n\
6046: - Log file of the run: <a href=\"%s\">%s</a><br>\n\
6047: - Gnuplot file name: <a href=\"%s\">%s</a><br>\n\
6048: - Date and time at start: %s</ul>\n",\
6049: optionfilehtm,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model,\
6050: optionfilefiname,optionfilext,optionfilefiname,optionfilext,\
6051: fileres,fileres,\
6052: filelog,filelog,optionfilegnuplot,optionfilegnuplot,strstart);
6053: fflush(fichtm);
6054:
6055: strcpy(pathr,path);
6056: strcat(pathr,optionfilefiname);
6057: chdir(optionfilefiname); /* Move to directory named optionfile */
6058:
6059: /* Calculates basic frequencies. Computes observed prevalence at single age
6060: and prints on file fileres'p'. */
6061: freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint,strstart);
6062:
6063: fprintf(fichtm,"\n");
6064: fprintf(fichtm,"<br>Total number of observations=%d <br>\n\
6065: Youngest age at first (selected) pass %.2f, oldest age %.2f<br>\n\
6066: Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n",\
6067: imx,agemin,agemax,jmin,jmax,jmean);
6068: pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
6069: oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
6070: newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
6071: savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
6072: oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */
6073:
6074:
6075: /* For Powell, parameters are in a vector p[] starting at p[1]
6076: so we point p on param[1][1] so that p[1] maps on param[1][1][1] */
6077: p=param[1][1]; /* *(*(*(param +1)+1)+0) */
6078:
6079: globpr=0; /* To get the number ipmx of contributions and the sum of weights*/
6080:
6081: if (mle==-3){
6082: ximort=matrix(1,NDIM,1,NDIM);
6083: /* ximort=gsl_matrix_alloc(1,NDIM,1,NDIM); */
6084: cens=ivector(1,n);
6085: ageexmed=vector(1,n);
6086: agecens=vector(1,n);
6087: dcwave=ivector(1,n);
6088:
6089: for (i=1; i<=imx; i++){
6090: dcwave[i]=-1;
6091: for (m=firstpass; m<=lastpass; m++)
6092: if (s[m][i]>nlstate) {
6093: dcwave[i]=m;
6094: /* printf("i=%d j=%d s=%d dcwave=%d\n",i,j, s[j][i],dcwave[i]);*/
6095: break;
6096: }
6097: }
6098:
6099: for (i=1; i<=imx; i++) {
6100: if (wav[i]>0){
6101: ageexmed[i]=agev[mw[1][i]][i];
6102: j=wav[i];
6103: agecens[i]=1.;
6104:
6105: if (ageexmed[i]> 1 && wav[i] > 0){
6106: agecens[i]=agev[mw[j][i]][i];
6107: cens[i]= 1;
6108: }else if (ageexmed[i]< 1)
6109: cens[i]= -1;
6110: if (agedc[i]< AGESUP && agedc[i]>1 && dcwave[i]>firstpass && dcwave[i]<=lastpass)
6111: cens[i]=0 ;
6112: }
6113: else cens[i]=-1;
6114: }
6115:
6116: for (i=1;i<=NDIM;i++) {
6117: for (j=1;j<=NDIM;j++)
6118: ximort[i][j]=(i == j ? 1.0 : 0.0);
6119: }
6120:
6121: /*p[1]=0.0268; p[NDIM]=0.083;*/
6122: /*printf("%lf %lf", p[1], p[2]);*/
6123:
6124:
6125: #ifdef GSL
6126: printf("GSL optimization\n"); fprintf(ficlog,"Powell\n");
6127: #else
6128: printf("Powell\n"); fprintf(ficlog,"Powell\n");
6129: #endif
6130: strcpy(filerespow,"pow-mort");
6131: strcat(filerespow,fileres);
6132: if((ficrespow=fopen(filerespow,"w"))==NULL) {
6133: printf("Problem with resultfile: %s\n", filerespow);
6134: fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
6135: }
6136: #ifdef GSL
6137: fprintf(ficrespow,"# GSL optimization\n# iter -2*LL");
6138: #else
6139: fprintf(ficrespow,"# Powell\n# iter -2*LL");
6140: #endif
6141: /* for (i=1;i<=nlstate;i++)
6142: for(j=1;j<=nlstate+ndeath;j++)
6143: if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
6144: */
6145: fprintf(ficrespow,"\n");
6146: #ifdef GSL
6147: /* gsl starts here */
6148: T = gsl_multimin_fminimizer_nmsimplex;
6149: gsl_multimin_fminimizer *sfm = NULL;
6150: gsl_vector *ss, *x;
6151: gsl_multimin_function minex_func;
6152:
6153: /* Initial vertex size vector */
6154: ss = gsl_vector_alloc (NDIM);
6155:
6156: if (ss == NULL){
6157: GSL_ERROR_VAL ("failed to allocate space for ss", GSL_ENOMEM, 0);
6158: }
6159: /* Set all step sizes to 1 */
6160: gsl_vector_set_all (ss, 0.001);
6161:
6162: /* Starting point */
6163:
6164: x = gsl_vector_alloc (NDIM);
6165:
6166: if (x == NULL){
6167: gsl_vector_free(ss);
6168: GSL_ERROR_VAL ("failed to allocate space for x", GSL_ENOMEM, 0);
6169: }
6170:
6171: /* Initialize method and iterate */
6172: /* p[1]=0.0268; p[NDIM]=0.083; */
6173: /* gsl_vector_set(x, 0, 0.0268); */
6174: /* gsl_vector_set(x, 1, 0.083); */
6175: gsl_vector_set(x, 0, p[1]);
6176: gsl_vector_set(x, 1, p[2]);
6177:
6178: minex_func.f = &gompertz_f;
6179: minex_func.n = NDIM;
6180: minex_func.params = (void *)&p; /* ??? */
6181:
6182: sfm = gsl_multimin_fminimizer_alloc (T, NDIM);
6183: gsl_multimin_fminimizer_set (sfm, &minex_func, x, ss);
6184:
6185: printf("Iterations beginning .....\n\n");
6186: printf("Iter. # Intercept Slope -Log Likelihood Simplex size\n");
6187:
6188: iteri=0;
6189: while (rval == GSL_CONTINUE){
6190: iteri++;
6191: status = gsl_multimin_fminimizer_iterate(sfm);
6192:
6193: if (status) printf("error: %s\n", gsl_strerror (status));
6194: fflush(0);
6195:
6196: if (status)
6197: break;
6198:
6199: rval = gsl_multimin_test_size (gsl_multimin_fminimizer_size (sfm), 1e-6);
6200: ssval = gsl_multimin_fminimizer_size (sfm);
6201:
6202: if (rval == GSL_SUCCESS)
6203: printf ("converged to a local maximum at\n");
6204:
6205: printf("%5d ", iteri);
6206: for (it = 0; it < NDIM; it++){
6207: printf ("%10.5f ", gsl_vector_get (sfm->x, it));
6208: }
6209: printf("f() = %-10.5f ssize = %.7f\n", sfm->fval, ssval);
6210: }
6211:
6212: printf("\n\n Please note: Program should be run many times with varying starting points to detemine global maximum\n\n");
6213:
6214: gsl_vector_free(x); /* initial values */
6215: gsl_vector_free(ss); /* inital step size */
6216: for (it=0; it<NDIM; it++){
6217: p[it+1]=gsl_vector_get(sfm->x,it);
6218: fprintf(ficrespow," %.12lf", p[it]);
6219: }
6220: gsl_multimin_fminimizer_free (sfm); /* p *(sfm.x.data) et p *(sfm.x.data+1) */
6221: #endif
6222: #ifdef POWELL
6223: powell(p,ximort,NDIM,ftol,&iter,&fret,gompertz);
6224: #endif
6225: fclose(ficrespow);
6226:
6227: hesscov(matcov, p, NDIM, delti, 1e-4, gompertz);
6228:
6229: for(i=1; i <=NDIM; i++)
6230: for(j=i+1;j<=NDIM;j++)
6231: matcov[i][j]=matcov[j][i];
6232:
6233: printf("\nCovariance matrix\n ");
6234: for(i=1; i <=NDIM; i++) {
6235: for(j=1;j<=NDIM;j++){
6236: printf("%f ",matcov[i][j]);
6237: }
6238: printf("\n ");
6239: }
6240:
6241: printf("iter=%d MLE=%f Eq=%lf*exp(%lf*(age-%d))\n",iter,-gompertz(p),p[1],p[2],agegomp);
6242: for (i=1;i<=NDIM;i++)
6243: printf("%f [%f ; %f]\n",p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
6244:
6245: lsurv=vector(1,AGESUP);
6246: lpop=vector(1,AGESUP);
6247: tpop=vector(1,AGESUP);
6248: lsurv[agegomp]=100000;
6249:
6250: for (k=agegomp;k<=AGESUP;k++) {
6251: agemortsup=k;
6252: if (p[1]*exp(p[2]*(k-agegomp))>1) break;
6253: }
6254:
6255: for (k=agegomp;k<agemortsup;k++)
6256: lsurv[k+1]=lsurv[k]-lsurv[k]*(p[1]*exp(p[2]*(k-agegomp)));
6257:
6258: for (k=agegomp;k<agemortsup;k++){
6259: lpop[k]=(lsurv[k]+lsurv[k+1])/2.;
6260: sumlpop=sumlpop+lpop[k];
6261: }
6262:
6263: tpop[agegomp]=sumlpop;
6264: for (k=agegomp;k<(agemortsup-3);k++){
6265: /* tpop[k+1]=2;*/
6266: tpop[k+1]=tpop[k]-lpop[k];
6267: }
6268:
6269:
6270: printf("\nAge lx qx dx Lx Tx e(x)\n");
6271: for (k=agegomp;k<(agemortsup-2);k++)
6272: 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]);
6273:
6274:
6275: replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
6276: printinggnuplotmort(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
6277:
6278: printinghtmlmort(fileres,title,datafile, firstpass, lastpass, \
6279: stepm, weightopt,\
6280: model,imx,p,matcov,agemortsup);
6281:
6282: free_vector(lsurv,1,AGESUP);
6283: free_vector(lpop,1,AGESUP);
6284: free_vector(tpop,1,AGESUP);
6285: #ifdef GSL
6286: free_ivector(cens,1,n);
6287: free_vector(agecens,1,n);
6288: free_ivector(dcwave,1,n);
6289: free_matrix(ximort,1,NDIM,1,NDIM);
6290: #endif
6291: } /* Endof if mle==-3 */
6292:
6293: else{ /* For mle >=1 */
6294: globpr=0;/* debug */
6295: likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
6296: printf("First Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
6297: for (k=1; k<=npar;k++)
6298: printf(" %d %8.5f",k,p[k]);
6299: printf("\n");
6300: globpr=1; /* to print the contributions */
6301: likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
6302: printf("Second Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
6303: for (k=1; k<=npar;k++)
6304: printf(" %d %8.5f",k,p[k]);
6305: printf("\n");
6306: if(mle>=1){ /* Could be 1 or 2 */
6307: mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);
6308: }
6309:
6310: /*--------- results files --------------*/
6311: 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=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate, ndeath, maxwav, weightopt,model);
6312:
6313:
6314: fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
6315: printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
6316: fprintf(ficlog,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
6317: for(i=1,jk=1; i <=nlstate; i++){
6318: for(k=1; k <=(nlstate+ndeath); k++){
6319: if (k != i) {
6320: printf("%d%d ",i,k);
6321: fprintf(ficlog,"%d%d ",i,k);
6322: fprintf(ficres,"%1d%1d ",i,k);
6323: for(j=1; j <=ncovmodel; j++){
6324: printf("%lf ",p[jk]);
6325: fprintf(ficlog,"%lf ",p[jk]);
6326: fprintf(ficres,"%lf ",p[jk]);
6327: jk++;
6328: }
6329: printf("\n");
6330: fprintf(ficlog,"\n");
6331: fprintf(ficres,"\n");
6332: }
6333: }
6334: }
6335: if(mle!=0){
6336: /* Computing hessian and covariance matrix */
6337: ftolhess=ftol; /* Usually correct */
6338: hesscov(matcov, p, npar, delti, ftolhess, func);
6339: }
6340: fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");
6341: printf("# Scales (for hessian or gradient estimation)\n");
6342: fprintf(ficlog,"# Scales (for hessian or gradient estimation)\n");
6343: for(i=1,jk=1; i <=nlstate; i++){
6344: for(j=1; j <=nlstate+ndeath; j++){
6345: if (j!=i) {
6346: fprintf(ficres,"%1d%1d",i,j);
6347: printf("%1d%1d",i,j);
6348: fprintf(ficlog,"%1d%1d",i,j);
6349: for(k=1; k<=ncovmodel;k++){
6350: printf(" %.5e",delti[jk]);
6351: fprintf(ficlog," %.5e",delti[jk]);
6352: fprintf(ficres," %.5e",delti[jk]);
6353: jk++;
6354: }
6355: printf("\n");
6356: fprintf(ficlog,"\n");
6357: fprintf(ficres,"\n");
6358: }
6359: }
6360: }
6361:
6362: 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");
6363: if(mle>=1)
6364: 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");
6365: 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");
6366: /* # 121 Var(a12)\n\ */
6367: /* # 122 Cov(b12,a12) Var(b12)\n\ */
6368: /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
6369: /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
6370: /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
6371: /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
6372: /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
6373: /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
6374:
6375:
6376: /* Just to have a covariance matrix which will be more understandable
6377: even is we still don't want to manage dictionary of variables
6378: */
6379: for(itimes=1;itimes<=2;itimes++){
6380: jj=0;
6381: for(i=1; i <=nlstate; i++){
6382: for(j=1; j <=nlstate+ndeath; j++){
6383: if(j==i) continue;
6384: for(k=1; k<=ncovmodel;k++){
6385: jj++;
6386: ca[0]= k+'a'-1;ca[1]='\0';
6387: if(itimes==1){
6388: if(mle>=1)
6389: printf("#%1d%1d%d",i,j,k);
6390: fprintf(ficlog,"#%1d%1d%d",i,j,k);
6391: fprintf(ficres,"#%1d%1d%d",i,j,k);
6392: }else{
6393: if(mle>=1)
6394: printf("%1d%1d%d",i,j,k);
6395: fprintf(ficlog,"%1d%1d%d",i,j,k);
6396: fprintf(ficres,"%1d%1d%d",i,j,k);
6397: }
6398: ll=0;
6399: for(li=1;li <=nlstate; li++){
6400: for(lj=1;lj <=nlstate+ndeath; lj++){
6401: if(lj==li) continue;
6402: for(lk=1;lk<=ncovmodel;lk++){
6403: ll++;
6404: if(ll<=jj){
6405: cb[0]= lk +'a'-1;cb[1]='\0';
6406: if(ll<jj){
6407: if(itimes==1){
6408: if(mle>=1)
6409: printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
6410: fprintf(ficlog," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
6411: fprintf(ficres," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
6412: }else{
6413: if(mle>=1)
6414: printf(" %.5e",matcov[jj][ll]);
6415: fprintf(ficlog," %.5e",matcov[jj][ll]);
6416: fprintf(ficres," %.5e",matcov[jj][ll]);
6417: }
6418: }else{
6419: if(itimes==1){
6420: if(mle>=1)
6421: printf(" Var(%s%1d%1d)",ca,i,j);
6422: fprintf(ficlog," Var(%s%1d%1d)",ca,i,j);
6423: fprintf(ficres," Var(%s%1d%1d)",ca,i,j);
6424: }else{
6425: if(mle>=1)
6426: printf(" %.5e",matcov[jj][ll]);
6427: fprintf(ficlog," %.5e",matcov[jj][ll]);
6428: fprintf(ficres," %.5e",matcov[jj][ll]);
6429: }
6430: }
6431: }
6432: } /* end lk */
6433: } /* end lj */
6434: } /* end li */
6435: if(mle>=1)
6436: printf("\n");
6437: fprintf(ficlog,"\n");
6438: fprintf(ficres,"\n");
6439: numlinepar++;
6440: } /* end k*/
6441: } /*end j */
6442: } /* end i */
6443: } /* end itimes */
6444:
6445: fflush(ficlog);
6446: fflush(ficres);
6447:
6448: while((c=getc(ficpar))=='#' && c!= EOF){
6449: ungetc(c,ficpar);
6450: fgets(line, MAXLINE, ficpar);
6451: fputs(line,stdout);
6452: fputs(line,ficparo);
6453: }
6454: ungetc(c,ficpar);
6455:
6456: estepm=0;
6457: fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm);
6458: if (estepm==0 || estepm < stepm) estepm=stepm;
6459: if (fage <= 2) {
6460: bage = ageminpar;
6461: fage = agemaxpar;
6462: }
6463:
6464: fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");
6465: fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
6466: fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
6467:
6468: while((c=getc(ficpar))=='#' && c!= EOF){
6469: ungetc(c,ficpar);
6470: fgets(line, MAXLINE, ficpar);
6471: fputs(line,stdout);
6472: fputs(line,ficparo);
6473: }
6474: ungetc(c,ficpar);
6475:
6476: 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);
6477: 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);
6478: 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);
6479: printf("begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
6480: 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);
6481:
6482: while((c=getc(ficpar))=='#' && c!= EOF){
6483: ungetc(c,ficpar);
6484: fgets(line, MAXLINE, ficpar);
6485: fputs(line,stdout);
6486: fputs(line,ficparo);
6487: }
6488: ungetc(c,ficpar);
6489:
6490:
6491: dateprev1=anprev1+(mprev1-1)/12.+(jprev1-1)/365.;
6492: dateprev2=anprev2+(mprev2-1)/12.+(jprev2-1)/365.;
6493:
6494: fscanf(ficpar,"pop_based=%d\n",&popbased);
6495: fprintf(ficparo,"pop_based=%d\n",popbased);
6496: fprintf(ficres,"pop_based=%d\n",popbased);
6497:
6498: while((c=getc(ficpar))=='#' && c!= EOF){
6499: ungetc(c,ficpar);
6500: fgets(line, MAXLINE, ficpar);
6501: fputs(line,stdout);
6502: fputs(line,ficparo);
6503: }
6504: ungetc(c,ficpar);
6505:
6506: 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);
6507: 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);
6508: 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);
6509: 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);
6510: 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);
6511: /* day and month of proj2 are not used but only year anproj2.*/
6512:
6513:
6514:
6515: /* freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint); */
6516: /* ,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2); */
6517:
6518: replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
6519: printinggnuplot(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
6520:
6521: printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,\
6522: model,imx,jmin,jmax,jmean,rfileres,popforecast,estepm,\
6523: jprev1,mprev1,anprev1,jprev2,mprev2,anprev2);
6524:
6525: /*------------ free_vector -------------*/
6526: /* chdir(path); */
6527:
6528: free_ivector(wav,1,imx);
6529: free_imatrix(dh,1,lastpass-firstpass+1,1,imx);
6530: free_imatrix(bh,1,lastpass-firstpass+1,1,imx);
6531: free_imatrix(mw,1,lastpass-firstpass+1,1,imx);
6532: free_lvector(num,1,n);
6533: free_vector(agedc,1,n);
6534: /*free_matrix(covar,0,NCOVMAX,1,n);*/
6535: /*free_matrix(covar,1,NCOVMAX,1,n);*/
6536: fclose(ficparo);
6537: fclose(ficres);
6538:
6539:
6540: /*--------------- Prevalence limit (period or stable prevalence) --------------*/
6541: #include "prevlim.h" /* Use ficrespl, ficlog */
6542: fclose(ficrespl);
6543:
6544: #ifdef FREEEXIT2
6545: #include "freeexit2.h"
6546: #endif
6547:
6548: /*------------- h Pij x at various ages ------------*/
6549: #include "hpijx.h"
6550: fclose(ficrespij);
6551:
6552: /*-------------- Variance of one-step probabilities---*/
6553: k=1;
6554: varprob(optionfilefiname, matcov, p, delti, nlstate, bage, fage,k,Tvar,nbcode, ncodemax,strstart);
6555:
6556:
6557: probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
6558: for(i=1;i<=AGESUP;i++)
6559: for(j=1;j<=NCOVMAX;j++)
6560: for(k=1;k<=NCOVMAX;k++)
6561: probs[i][j][k]=0.;
6562:
6563: /*---------- Forecasting ------------------*/
6564: /*if((stepm == 1) && (strcmp(model,".")==0)){*/
6565: if(prevfcast==1){
6566: /* if(stepm ==1){*/
6567: prevforecast(fileres, anproj1, mproj1, jproj1, agemin, agemax, dateprev1, dateprev2, mobilavproj, bage, fage, firstpass, lastpass, anproj2, p, cptcoveff);
6568: /* (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);*/
6569: /* } */
6570: /* else{ */
6571: /* erreur=108; */
6572: /* 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); */
6573: /* 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); */
6574: /* } */
6575: }
6576:
6577:
6578: /* Computes prevalence between agemin (i.e minimal age computed) and no more ageminpar */
6579:
6580: prevalence(probs, agemin, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
6581: /* 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",\
6582: ageminpar, agemax, s[lastpass][imx], agev[lastpass][imx], nlstate, imx, mint[lastpass][imx],anint[lastpass][imx], dateprev1, dateprev2, firstpass, lastpass);
6583: */
6584:
6585: if (mobilav!=0) {
6586: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
6587: if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
6588: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
6589: printf(" Error in movingaverage mobilav=%d\n",mobilav);
6590: }
6591: }
6592:
6593:
6594: /*---------- Health expectancies, no variances ------------*/
6595:
6596: strcpy(filerese,"e");
6597: strcat(filerese,fileres);
6598: if((ficreseij=fopen(filerese,"w"))==NULL) {
6599: printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
6600: fprintf(ficlog,"Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
6601: }
6602: printf("Computing Health Expectancies: result on file '%s' \n", filerese);
6603: fprintf(ficlog,"Computing Health Expectancies: result on file '%s' \n", filerese);
6604: /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){
6605: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/
6606:
6607: for (k=1; k <= (int) pow(2,cptcoveff); k++){
6608: fprintf(ficreseij,"\n#****** ");
6609: for(j=1;j<=cptcoveff;j++) {
6610: fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
6611: }
6612: fprintf(ficreseij,"******\n");
6613:
6614: eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
6615: oldm=oldms;savm=savms;
6616: evsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, strstart);
6617:
6618: free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
6619: /*}*/
6620: }
6621: fclose(ficreseij);
6622:
6623:
6624: /*---------- Health expectancies and variances ------------*/
6625:
6626:
6627: strcpy(filerest,"t");
6628: strcat(filerest,fileres);
6629: if((ficrest=fopen(filerest,"w"))==NULL) {
6630: printf("Problem with total LE resultfile: %s\n", filerest);goto end;
6631: fprintf(ficlog,"Problem with total LE resultfile: %s\n", filerest);goto end;
6632: }
6633: printf("Computing Total Life expectancies with their standard errors: file '%s' \n", filerest);
6634: fprintf(ficlog,"Computing Total Life expectancies with their standard errors: file '%s' \n", filerest);
6635:
6636:
6637: strcpy(fileresstde,"stde");
6638: strcat(fileresstde,fileres);
6639: if((ficresstdeij=fopen(fileresstde,"w"))==NULL) {
6640: printf("Problem with Health Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
6641: fprintf(ficlog,"Problem with Health Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
6642: }
6643: printf("Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde);
6644: fprintf(ficlog,"Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde);
6645:
6646: strcpy(filerescve,"cve");
6647: strcat(filerescve,fileres);
6648: if((ficrescveij=fopen(filerescve,"w"))==NULL) {
6649: printf("Problem with Covar. Health Exp. resultfile: %s\n", filerescve); exit(0);
6650: fprintf(ficlog,"Problem with Covar. Health Exp. resultfile: %s\n", filerescve); exit(0);
6651: }
6652: printf("Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve);
6653: fprintf(ficlog,"Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve);
6654:
6655: strcpy(fileresv,"v");
6656: strcat(fileresv,fileres);
6657: if((ficresvij=fopen(fileresv,"w"))==NULL) {
6658: printf("Problem with variance resultfile: %s\n", fileresv);exit(0);
6659: fprintf(ficlog,"Problem with variance resultfile: %s\n", fileresv);exit(0);
6660: }
6661: printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
6662: fprintf(ficlog,"Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
6663:
6664: /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){
6665: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/
6666:
6667: for (k=1; k <= (int) pow(2,cptcoveff); k++){
6668: fprintf(ficrest,"\n#****** ");
6669: for(j=1;j<=cptcoveff;j++)
6670: fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
6671: fprintf(ficrest,"******\n");
6672:
6673: fprintf(ficresstdeij,"\n#****** ");
6674: fprintf(ficrescveij,"\n#****** ");
6675: for(j=1;j<=cptcoveff;j++) {
6676: fprintf(ficresstdeij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
6677: fprintf(ficrescveij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
6678: }
6679: fprintf(ficresstdeij,"******\n");
6680: fprintf(ficrescveij,"******\n");
6681:
6682: fprintf(ficresvij,"\n#****** ");
6683: for(j=1;j<=cptcoveff;j++)
6684: fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
6685: fprintf(ficresvij,"******\n");
6686:
6687: eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
6688: oldm=oldms;savm=savms;
6689: cvevsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov, strstart);
6690: /*
6691: */
6692: /* goto endfree; */
6693:
6694: vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
6695: pstamp(ficrest);
6696:
6697:
6698: for(vpopbased=0; vpopbased <= popbased; vpopbased++){ /* Done for vpopbased=0 and vpopbased=1 if popbased==1*/
6699: oldm=oldms;savm=savms; /* Segmentation fault */
6700: cptcod= 0; /* To be deleted */
6701: 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 */
6702: 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 ");
6703: if(vpopbased==1)
6704: 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);
6705: else
6706: fprintf(ficrest,"the age specific period (stable) prevalences in each health state \n");
6707: fprintf(ficrest,"# Age e.. (std) ");
6708: for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);
6709: fprintf(ficrest,"\n");
6710:
6711: epj=vector(1,nlstate+1);
6712: for(age=bage; age <=fage ;age++){
6713: prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
6714: if (vpopbased==1) {
6715: if(mobilav ==0){
6716: for(i=1; i<=nlstate;i++)
6717: prlim[i][i]=probs[(int)age][i][k];
6718: }else{ /* mobilav */
6719: for(i=1; i<=nlstate;i++)
6720: prlim[i][i]=mobaverage[(int)age][i][k];
6721: }
6722: }
6723:
6724: fprintf(ficrest," %4.0f",age);
6725: for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){
6726: for(i=1, epj[j]=0.;i <=nlstate;i++) {
6727: epj[j] += prlim[i][i]*eij[i][j][(int)age];
6728: /* printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/
6729: }
6730: epj[nlstate+1] +=epj[j];
6731: }
6732:
6733: for(i=1, vepp=0.;i <=nlstate;i++)
6734: for(j=1;j <=nlstate;j++)
6735: vepp += vareij[i][j][(int)age];
6736: fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));
6737: for(j=1;j <=nlstate;j++){
6738: fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));
6739: }
6740: fprintf(ficrest,"\n");
6741: }
6742: }
6743: free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
6744: free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);
6745: free_vector(epj,1,nlstate+1);
6746: /*}*/
6747: }
6748: free_vector(weight,1,n);
6749: free_imatrix(Tvard,1,NCOVMAX,1,2);
6750: free_imatrix(s,1,maxwav+1,1,n);
6751: free_matrix(anint,1,maxwav,1,n);
6752: free_matrix(mint,1,maxwav,1,n);
6753: free_ivector(cod,1,n);
6754: free_ivector(tab,1,NCOVMAX);
6755: fclose(ficresstdeij);
6756: fclose(ficrescveij);
6757: fclose(ficresvij);
6758: fclose(ficrest);
6759: fclose(ficpar);
6760:
6761: /*------- Variance of period (stable) prevalence------*/
6762:
6763: strcpy(fileresvpl,"vpl");
6764: strcat(fileresvpl,fileres);
6765: if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {
6766: printf("Problem with variance of period (stable) prevalence resultfile: %s\n", fileresvpl);
6767: exit(0);
6768: }
6769: printf("Computing Variance-covariance of period (stable) prevalence: file '%s' \n", fileresvpl);
6770:
6771: /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){
6772: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/
6773:
6774: for (k=1; k <= (int) pow(2,cptcoveff); k++){
6775: fprintf(ficresvpl,"\n#****** ");
6776: for(j=1;j<=cptcoveff;j++)
6777: fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
6778: fprintf(ficresvpl,"******\n");
6779:
6780: varpl=matrix(1,nlstate,(int) bage, (int) fage);
6781: oldm=oldms;savm=savms;
6782: varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k,strstart);
6783: free_matrix(varpl,1,nlstate,(int) bage, (int)fage);
6784: /*}*/
6785: }
6786:
6787: fclose(ficresvpl);
6788:
6789: /*---------- End : free ----------------*/
6790: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
6791: free_ma3x(probs,1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
6792: } /* mle==-3 arrives here for freeing */
6793: /* endfree:*/
6794: free_matrix(prlim,1,nlstate,1,nlstate); /*here or after loop ? */
6795: free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);
6796: free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);
6797: free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);
6798: free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);
6799: free_matrix(covar,0,NCOVMAX,1,n);
6800: free_matrix(matcov,1,npar,1,npar);
6801: /*free_vector(delti,1,npar);*/
6802: free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
6803: free_matrix(agev,1,maxwav,1,imx);
6804: free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
6805:
6806: free_ivector(ncodemax,1,NCOVMAX);
6807: free_ivector(Tvar,1,NCOVMAX);
6808: free_ivector(Tprod,1,NCOVMAX);
6809: free_ivector(Tvaraff,1,NCOVMAX);
6810: free_ivector(Tage,1,NCOVMAX);
6811:
6812: free_imatrix(nbcode,0,NCOVMAX,0,NCOVMAX);
6813: free_imatrix(codtab,1,100,1,10);
6814: fflush(fichtm);
6815: fflush(ficgp);
6816:
6817:
6818: if((nberr >0) || (nbwarn>0)){
6819: printf("End of Imach with %d errors and/or %d warnings\n",nberr,nbwarn);
6820: fprintf(ficlog,"End of Imach with %d errors and/or warnings %d\n",nberr,nbwarn);
6821: }else{
6822: printf("End of Imach\n");
6823: fprintf(ficlog,"End of Imach\n");
6824: }
6825: printf("See log file on %s\n",filelog);
6826: /* gettimeofday(&end_time, (struct timezone*)0);*/ /* after time */
6827: /*(void) gettimeofday(&end_time,&tzp);*/
6828: rend_time = time(NULL);
6829: end_time = *localtime(&rend_time);
6830: /* tml = *localtime(&end_time.tm_sec); */
6831: strcpy(strtend,asctime(&end_time));
6832: printf("Local time at start %s\nLocal time at end %s",strstart, strtend);
6833: fprintf(ficlog,"Local time at start %s\nLocal time at end %s\n",strstart, strtend);
6834: printf("Total time used %s\n", asc_diff_time(rend_time -rstart_time,tmpout));
6835:
6836: printf("Total time was %.0lf Sec.\n", difftime(rend_time,rstart_time));
6837: fprintf(ficlog,"Total time used %s\n", asc_diff_time(rend_time -rstart_time,tmpout));
6838: fprintf(ficlog,"Total time was %.0lf Sec.\n", difftime(rend_time,rstart_time));
6839: /* printf("Total time was %d uSec.\n", total_usecs);*/
6840: /* if(fileappend(fichtm,optionfilehtm)){ */
6841: fprintf(fichtm,"<br>Local time at start %s<br>Local time at end %s<br>\n</body></html>",strstart, strtend);
6842: fclose(fichtm);
6843: fprintf(fichtmcov,"<br>Local time at start %s<br>Local time at end %s<br>\n</body></html>",strstart, strtend);
6844: fclose(fichtmcov);
6845: fclose(ficgp);
6846: fclose(ficlog);
6847: /*------ End -----------*/
6848:
6849:
6850: printf("Before Current directory %s!\n",pathcd);
6851: if(chdir(pathcd) != 0)
6852: printf("Can't move to directory %s!\n",path);
6853: if(getcwd(pathcd,MAXLINE) > 0)
6854: printf("Current directory %s!\n",pathcd);
6855: /*strcat(plotcmd,CHARSEPARATOR);*/
6856: sprintf(plotcmd,"gnuplot");
6857: #ifdef _WIN32
6858: sprintf(plotcmd,"\"%sgnuplot.exe\"",pathimach);
6859: #endif
6860: if(!stat(plotcmd,&info)){
6861: printf("Error or gnuplot program not found: '%s'\n",plotcmd);fflush(stdout);
6862: if(!stat(getenv("GNUPLOTBIN"),&info)){
6863: printf("Error or gnuplot program not found: '%s' Environment GNUPLOTBIN not set.\n",plotcmd);fflush(stdout);
6864: }else
6865: strcpy(pplotcmd,plotcmd);
6866: #ifdef __unix
6867: strcpy(plotcmd,GNUPLOTPROGRAM);
6868: if(!stat(plotcmd,&info)){
6869: printf("Error gnuplot program not found: '%s'\n",plotcmd);fflush(stdout);
6870: }else
6871: strcpy(pplotcmd,plotcmd);
6872: #endif
6873: }else
6874: strcpy(pplotcmd,plotcmd);
6875:
6876: sprintf(plotcmd,"%s %s",pplotcmd, optionfilegnuplot);
6877: printf("Starting graphs with: '%s'\n",plotcmd);fflush(stdout);
6878:
6879: if((outcmd=system(plotcmd)) != 0){
6880: printf("gnuplot command might not be in your path: '%s', err=%d\n", plotcmd, outcmd);
6881: printf("\n Trying if gnuplot resides on the same directory that IMaCh\n");
6882: sprintf(plotcmd,"%sgnuplot %s", pathimach, optionfilegnuplot);
6883: if((outcmd=system(plotcmd)) != 0)
6884: printf("\n Still a problem with gnuplot command %s, err=%d\n", plotcmd, outcmd);
6885: }
6886: printf(" Successful, please wait...");
6887: while (z[0] != 'q') {
6888: /* chdir(path); */
6889: printf("\nType e to edit results with your browser, g to graph again and q for exit: ");
6890: scanf("%s",z);
6891: /* if (z[0] == 'c') system("./imach"); */
6892: if (z[0] == 'e') {
6893: #ifdef __APPLE__
6894: sprintf(pplotcmd, "open %s", optionfilehtm);
6895: #elif __linux
6896: sprintf(pplotcmd, "xdg-open %s", optionfilehtm);
6897: #else
6898: sprintf(pplotcmd, "%s", optionfilehtm);
6899: #endif
6900: printf("Starting browser with: %s",pplotcmd);fflush(stdout);
6901: system(pplotcmd);
6902: }
6903: else if (z[0] == 'g') system(plotcmd);
6904: else if (z[0] == 'q') exit(0);
6905: }
6906: end:
6907: while (z[0] != 'q') {
6908: printf("\nType q for exiting: ");
6909: scanf("%s",z);
6910: }
6911: }
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