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Tue Mar 14 18:20:07 2006 UTC (18 years, 3 months ago) by
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(Module): varevsij Comments added explaining the second
table of variances if popbased=1 .
(Module): Covariances of eij, ekl added, graphs fixed, new html link.
(Module): Function pstamp added
(Module): Version 0.98d
1: /* $Id: imach.c,v 1.118 2006/03/14 18:20:07 brouard Exp $
2: $State: Exp $
3: $Log: imach.c,v $
4: Revision 1.118 2006/03/14 18:20:07 brouard
5: (Module): varevsij Comments added explaining the second
6: table of variances if popbased=1 .
7: (Module): Covariances of eij, ekl added, graphs fixed, new html link.
8: (Module): Function pstamp added
9: (Module): Version 0.98d
10:
11: Revision 1.117 2006/03/14 17:16:22 brouard
12: (Module): varevsij Comments added explaining the second
13: table of variances if popbased=1 .
14: (Module): Covariances of eij, ekl added, graphs fixed, new html link.
15: (Module): Function pstamp added
16: (Module): Version 0.98d
17:
18: Revision 1.116 2006/03/06 10:29:27 brouard
19: (Module): Variance-covariance wrong links and
20: varian-covariance of ej. is needed (Saito).
21:
22: Revision 1.115 2006/02/27 12:17:45 brouard
23: (Module): One freematrix added in mlikeli! 0.98c
24:
25: Revision 1.114 2006/02/26 12:57:58 brouard
26: (Module): Some improvements in processing parameter
27: filename with strsep.
28:
29: Revision 1.113 2006/02/24 14:20:24 brouard
30: (Module): Memory leaks checks with valgrind and:
31: datafile was not closed, some imatrix were not freed and on matrix
32: allocation too.
33:
34: Revision 1.112 2006/01/30 09:55:26 brouard
35: (Module): Back to gnuplot.exe instead of wgnuplot.exe
36:
37: Revision 1.111 2006/01/25 20:38:18 brouard
38: (Module): Lots of cleaning and bugs added (Gompertz)
39: (Module): Comments can be added in data file. Missing date values
40: can be a simple dot '.'.
41:
42: Revision 1.110 2006/01/25 00:51:50 brouard
43: (Module): Lots of cleaning and bugs added (Gompertz)
44:
45: Revision 1.109 2006/01/24 19:37:15 brouard
46: (Module): Comments (lines starting with a #) are allowed in data.
47:
48: Revision 1.108 2006/01/19 18:05:42 lievre
49: Gnuplot problem appeared...
50: To be fixed
51:
52: Revision 1.107 2006/01/19 16:20:37 brouard
53: Test existence of gnuplot in imach path
54:
55: Revision 1.106 2006/01/19 13:24:36 brouard
56: Some cleaning and links added in html output
57:
58: Revision 1.105 2006/01/05 20:23:19 lievre
59: *** empty log message ***
60:
61: Revision 1.104 2005/09/30 16:11:43 lievre
62: (Module): sump fixed, loop imx fixed, and simplifications.
63: (Module): If the status is missing at the last wave but we know
64: that the person is alive, then we can code his/her status as -2
65: (instead of missing=-1 in earlier versions) and his/her
66: contributions to the likelihood is 1 - Prob of dying from last
67: health status (= 1-p13= p11+p12 in the easiest case of somebody in
68: the healthy state at last known wave). Version is 0.98
69:
70: Revision 1.103 2005/09/30 15:54:49 lievre
71: (Module): sump fixed, loop imx fixed, and simplifications.
72:
73: Revision 1.102 2004/09/15 17:31:30 brouard
74: Add the possibility to read data file including tab characters.
75:
76: Revision 1.101 2004/09/15 10:38:38 brouard
77: Fix on curr_time
78:
79: Revision 1.100 2004/07/12 18:29:06 brouard
80: Add version for Mac OS X. Just define UNIX in Makefile
81:
82: Revision 1.99 2004/06/05 08:57:40 brouard
83: *** empty log message ***
84:
85: Revision 1.98 2004/05/16 15:05:56 brouard
86: New version 0.97 . First attempt to estimate force of mortality
87: directly from the data i.e. without the need of knowing the health
88: state at each age, but using a Gompertz model: log u =a + b*age .
89: This is the basic analysis of mortality and should be done before any
90: other analysis, in order to test if the mortality estimated from the
91: cross-longitudinal survey is different from the mortality estimated
92: from other sources like vital statistic data.
93:
94: The same imach parameter file can be used but the option for mle should be -3.
95:
96: Agnès, who wrote this part of the code, tried to keep most of the
97: former routines in order to include the new code within the former code.
98:
99: The output is very simple: only an estimate of the intercept and of
100: the slope with 95% confident intervals.
101:
102: Current limitations:
103: A) Even if you enter covariates, i.e. with the
104: model= V1+V2 equation for example, the programm does only estimate a unique global model without covariates.
105: B) There is no computation of Life Expectancy nor Life Table.
106:
107: Revision 1.97 2004/02/20 13:25:42 lievre
108: Version 0.96d. Population forecasting command line is (temporarily)
109: suppressed.
110:
111: Revision 1.96 2003/07/15 15:38:55 brouard
112: * imach.c (Repository): Errors in subdirf, 2, 3 while printing tmpout is
113: rewritten within the same printf. Workaround: many printfs.
114:
115: Revision 1.95 2003/07/08 07:54:34 brouard
116: * imach.c (Repository):
117: (Repository): Using imachwizard code to output a more meaningful covariance
118: matrix (cov(a12,c31) instead of numbers.
119:
120: Revision 1.94 2003/06/27 13:00:02 brouard
121: Just cleaning
122:
123: Revision 1.93 2003/06/25 16:33:55 brouard
124: (Module): On windows (cygwin) function asctime_r doesn't
125: exist so I changed back to asctime which exists.
126: (Module): Version 0.96b
127:
128: Revision 1.92 2003/06/25 16:30:45 brouard
129: (Module): On windows (cygwin) function asctime_r doesn't
130: exist so I changed back to asctime which exists.
131:
132: Revision 1.91 2003/06/25 15:30:29 brouard
133: * imach.c (Repository): Duplicated warning errors corrected.
134: (Repository): Elapsed time after each iteration is now output. It
135: helps to forecast when convergence will be reached. Elapsed time
136: is stamped in powell. We created a new html file for the graphs
137: concerning matrix of covariance. It has extension -cov.htm.
138:
139: Revision 1.90 2003/06/24 12:34:15 brouard
140: (Module): Some bugs corrected for windows. Also, when
141: mle=-1 a template is output in file "or"mypar.txt with the design
142: of the covariance matrix to be input.
143:
144: Revision 1.89 2003/06/24 12:30:52 brouard
145: (Module): Some bugs corrected for windows. Also, when
146: mle=-1 a template is output in file "or"mypar.txt with the design
147: of the covariance matrix to be input.
148:
149: Revision 1.88 2003/06/23 17:54:56 brouard
150: * 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.
151:
152: Revision 1.87 2003/06/18 12:26:01 brouard
153: Version 0.96
154:
155: Revision 1.86 2003/06/17 20:04:08 brouard
156: (Module): Change position of html and gnuplot routines and added
157: routine fileappend.
158:
159: Revision 1.85 2003/06/17 13:12:43 brouard
160: * imach.c (Repository): Check when date of death was earlier that
161: current date of interview. It may happen when the death was just
162: prior to the death. In this case, dh was negative and likelihood
163: was wrong (infinity). We still send an "Error" but patch by
164: assuming that the date of death was just one stepm after the
165: interview.
166: (Repository): Because some people have very long ID (first column)
167: we changed int to long in num[] and we added a new lvector for
168: memory allocation. But we also truncated to 8 characters (left
169: truncation)
170: (Repository): No more line truncation errors.
171:
172: Revision 1.84 2003/06/13 21:44:43 brouard
173: * imach.c (Repository): Replace "freqsummary" at a correct
174: place. It differs from routine "prevalence" which may be called
175: many times. Probs is memory consuming and must be used with
176: parcimony.
177: Version 0.95a3 (should output exactly the same maximization than 0.8a2)
178:
179: Revision 1.83 2003/06/10 13:39:11 lievre
180: *** empty log message ***
181:
182: Revision 1.82 2003/06/05 15:57:20 brouard
183: Add log in imach.c and fullversion number is now printed.
184:
185: */
186: /*
187: Interpolated Markov Chain
188:
189: Short summary of the programme:
190:
191: This program computes Healthy Life Expectancies from
192: cross-longitudinal data. Cross-longitudinal data consist in: -1- a
193: first survey ("cross") where individuals from different ages are
194: interviewed on their health status or degree of disability (in the
195: case of a health survey which is our main interest) -2- at least a
196: second wave of interviews ("longitudinal") which measure each change
197: (if any) in individual health status. Health expectancies are
198: computed from the time spent in each health state according to a
199: model. More health states you consider, more time is necessary to reach the
200: Maximum Likelihood of the parameters involved in the model. The
201: simplest model is the multinomial logistic model where pij is the
202: probability to be observed in state j at the second wave
203: conditional to be observed in state i at the first wave. Therefore
204: the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where
205: 'age' is age and 'sex' is a covariate. If you want to have a more
206: complex model than "constant and age", you should modify the program
207: where the markup *Covariates have to be included here again* invites
208: you to do it. More covariates you add, slower the
209: convergence.
210:
211: The advantage of this computer programme, compared to a simple
212: multinomial logistic model, is clear when the delay between waves is not
213: identical for each individual. Also, if a individual missed an
214: intermediate interview, the information is lost, but taken into
215: account using an interpolation or extrapolation.
216:
217: hPijx is the probability to be observed in state i at age x+h
218: conditional to the observed state i at age x. The delay 'h' can be
219: split into an exact number (nh*stepm) of unobserved intermediate
220: states. This elementary transition (by month, quarter,
221: semester or year) is modelled as a multinomial logistic. The hPx
222: matrix is simply the matrix product of nh*stepm elementary matrices
223: and the contribution of each individual to the likelihood is simply
224: hPijx.
225:
226: Also this programme outputs the covariance matrix of the parameters but also
227: of the life expectancies. It also computes the period (stable) prevalence.
228:
229: Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).
230: Institut national d'études démographiques, Paris.
231: This software have been partly granted by Euro-REVES, a concerted action
232: from the European Union.
233: It is copyrighted identically to a GNU software product, ie programme and
234: software can be distributed freely for non commercial use. Latest version
235: can be accessed at http://euroreves.ined.fr/imach .
236:
237: Help to debug: LD_PRELOAD=/usr/local/lib/libnjamd.so ./imach foo.imach
238: or better on gdb : set env LD_PRELOAD=/usr/local/lib/libnjamd.so
239:
240: **********************************************************************/
241: /*
242: main
243: read parameterfile
244: read datafile
245: concatwav
246: freqsummary
247: if (mle >= 1)
248: mlikeli
249: print results files
250: if mle==1
251: computes hessian
252: read end of parameter file: agemin, agemax, bage, fage, estepm
253: begin-prev-date,...
254: open gnuplot file
255: open html file
256: period (stable) prevalence
257: for age prevalim()
258: h Pij x
259: variance of p varprob
260: forecasting if prevfcast==1 prevforecast call prevalence()
261: health expectancies
262: Variance-covariance of DFLE
263: prevalence()
264: movingaverage()
265: varevsij()
266: if popbased==1 varevsij(,popbased)
267: total life expectancies
268: Variance of period (stable) prevalence
269: end
270: */
271:
272:
273:
274:
275: #include <math.h>
276: #include <stdio.h>
277: #include <stdlib.h>
278: #include <string.h>
279: #include <unistd.h>
280:
281: #include <limits.h>
282: #include <sys/types.h>
283: #include <sys/stat.h>
284: #include <errno.h>
285: extern int errno;
286:
287: /* #include <sys/time.h> */
288: #include <time.h>
289: #include "timeval.h"
290:
291: /* #include <libintl.h> */
292: /* #define _(String) gettext (String) */
293:
294: #define MAXLINE 256
295:
296: #define GNUPLOTPROGRAM "gnuplot"
297: /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
298: #define FILENAMELENGTH 132
299:
300: #define GLOCK_ERROR_NOPATH -1 /* empty path */
301: #define GLOCK_ERROR_GETCWD -2 /* cannot get cwd */
302:
303: #define MAXPARM 30 /* Maximum number of parameters for the optimization */
304: #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */
305:
306: #define NINTERVMAX 8
307: #define NLSTATEMAX 8 /* Maximum number of live states (for func) */
308: #define NDEATHMAX 8 /* Maximum number of dead states (for func) */
309: #define NCOVMAX 8 /* Maximum number of covariates */
310: #define MAXN 20000
311: #define YEARM 12. /* Number of months per year */
312: #define AGESUP 130
313: #define AGEBASE 40
314: #define AGEGOMP 10. /* Minimal age for Gompertz adjustment */
315: #ifdef UNIX
316: #define DIRSEPARATOR '/'
317: #define CHARSEPARATOR "/"
318: #define ODIRSEPARATOR '\\'
319: #else
320: #define DIRSEPARATOR '\\'
321: #define CHARSEPARATOR "\\"
322: #define ODIRSEPARATOR '/'
323: #endif
324:
325: /* $Id: imach.c,v 1.118 2006/03/14 18:20:07 brouard Exp $ */
326: /* $State: Exp $ */
327:
328: char version[]="Imach version 0.98d, March 2006, INED-EUROREVES-Institut de longevite ";
329: char fullversion[]="$Revision: 1.118 $ $Date: 2006/03/14 18:20:07 $";
330: char strstart[80];
331: char optionfilext[10], optionfilefiname[FILENAMELENGTH];
332: int erreur, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings */
333: int nvar;
334: int cptcovn=0, cptcovage=0, cptcoveff=0,cptcov;
335: int npar=NPARMAX;
336: int nlstate=2; /* Number of live states */
337: int ndeath=1; /* Number of dead states */
338: int ncovmodel, ncovcol; /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
339: int popbased=0;
340:
341: int *wav; /* Number of waves for this individuual 0 is possible */
342: int maxwav; /* Maxim number of waves */
343: int jmin, jmax; /* min, max spacing between 2 waves */
344: int ijmin, ijmax; /* Individuals having jmin and jmax */
345: int gipmx, gsw; /* Global variables on the number of contributions
346: to the likelihood and the sum of weights (done by funcone)*/
347: int mle, weightopt;
348: int **mw; /* mw[mi][i] is number of the mi wave for this individual */
349: int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
350: int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between
351: * wave mi and wave mi+1 is not an exact multiple of stepm. */
352: double jmean; /* Mean space between 2 waves */
353: double **oldm, **newm, **savm; /* Working pointers to matrices */
354: double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
355: FILE *fic,*ficpar, *ficparo,*ficres, *ficresp, *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
356: FILE *ficlog, *ficrespow;
357: int globpr; /* Global variable for printing or not */
358: double fretone; /* Only one call to likelihood */
359: long ipmx; /* Number of contributions */
360: double sw; /* Sum of weights */
361: char filerespow[FILENAMELENGTH];
362: char fileresilk[FILENAMELENGTH]; /* File of individual contributions to the likelihood */
363: FILE *ficresilk;
364: FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
365: FILE *ficresprobmorprev;
366: FILE *fichtm, *fichtmcov; /* Html File */
367: FILE *ficreseij;
368: char filerese[FILENAMELENGTH];
369: FILE *ficresstdeij;
370: char fileresstde[FILENAMELENGTH];
371: FILE *ficrescveij;
372: char filerescve[FILENAMELENGTH];
373: FILE *ficresvij;
374: char fileresv[FILENAMELENGTH];
375: FILE *ficresvpl;
376: char fileresvpl[FILENAMELENGTH];
377: char title[MAXLINE];
378: char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH], filerespl[FILENAMELENGTH];
379: char plotcmd[FILENAMELENGTH], pplotcmd[FILENAMELENGTH];
380: char tmpout[FILENAMELENGTH], tmpout2[FILENAMELENGTH];
381: char command[FILENAMELENGTH];
382: int outcmd=0;
383:
384: char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
385:
386: char filelog[FILENAMELENGTH]; /* Log file */
387: char filerest[FILENAMELENGTH];
388: char fileregp[FILENAMELENGTH];
389: char popfile[FILENAMELENGTH];
390:
391: char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilehtmcov[FILENAMELENGTH] ;
392:
393: struct timeval start_time, end_time, curr_time, last_time, forecast_time;
394: struct timezone tzp;
395: extern int gettimeofday();
396: struct tm tmg, tm, tmf, *gmtime(), *localtime();
397: long time_value;
398: extern long time();
399: char strcurr[80], strfor[80];
400:
401: char *endptr;
402: long lval;
403:
404: #define NR_END 1
405: #define FREE_ARG char*
406: #define FTOL 1.0e-10
407:
408: #define NRANSI
409: #define ITMAX 200
410:
411: #define TOL 2.0e-4
412:
413: #define CGOLD 0.3819660
414: #define ZEPS 1.0e-10
415: #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);
416:
417: #define GOLD 1.618034
418: #define GLIMIT 100.0
419: #define TINY 1.0e-20
420:
421: static double maxarg1,maxarg2;
422: #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
423: #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
424:
425: #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
426: #define rint(a) floor(a+0.5)
427:
428: static double sqrarg;
429: #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
430: #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}
431: int agegomp= AGEGOMP;
432:
433: int imx;
434: int stepm=1;
435: /* Stepm, step in month: minimum step interpolation*/
436:
437: int estepm;
438: /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
439:
440: int m,nb;
441: long *num;
442: int firstpass=0, lastpass=4,*cod, *ncodemax, *Tage,*cens;
443: double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
444: double **pmmij, ***probs;
445: double *ageexmed,*agecens;
446: double dateintmean=0;
447:
448: double *weight;
449: int **s; /* Status */
450: double *agedc, **covar, idx;
451: int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;
452: double *lsurv, *lpop, *tpop;
453:
454: double ftol=FTOL; /* Tolerance for computing Max Likelihood */
455: double ftolhess; /* Tolerance for computing hessian */
456:
457: /**************** split *************************/
458: static int split( char *path, char *dirc, char *name, char *ext, char *finame )
459: {
460: /* From a file name with (full) path (either Unix or Windows) we extract the directory (dirc)
461: the name of the file (name), its extension only (ext) and its first part of the name (finame)
462: */
463: char *ss; /* pointer */
464: int l1, l2; /* length counters */
465:
466: l1 = strlen(path ); /* length of path */
467: if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
468: ss= strrchr( path, DIRSEPARATOR ); /* find last / */
469: if ( ss == NULL ) { /* no directory, so determine current directory */
470: strcpy( name, path ); /* we got the fullname name because no directory */
471: /*if(strrchr(path, ODIRSEPARATOR )==NULL)
472: printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
473: /* get current working directory */
474: /* extern char* getcwd ( char *buf , int len);*/
475: if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {
476: return( GLOCK_ERROR_GETCWD );
477: }
478: /* got dirc from getcwd*/
479: printf(" DIRC = %s \n",dirc);
480: } else { /* strip direcotry from path */
481: ss++; /* after this, the filename */
482: l2 = strlen( ss ); /* length of filename */
483: if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
484: strcpy( name, ss ); /* save file name */
485: strncpy( dirc, path, l1 - l2 ); /* now the directory */
486: dirc[l1-l2] = 0; /* add zero */
487: printf(" DIRC2 = %s \n",dirc);
488: }
489: /* We add a separator at the end of dirc if not exists */
490: l1 = strlen( dirc ); /* length of directory */
491: if( dirc[l1-1] != DIRSEPARATOR ){
492: dirc[l1] = DIRSEPARATOR;
493: dirc[l1+1] = 0;
494: printf(" DIRC3 = %s \n",dirc);
495: }
496: ss = strrchr( name, '.' ); /* find last / */
497: if (ss >0){
498: ss++;
499: strcpy(ext,ss); /* save extension */
500: l1= strlen( name);
501: l2= strlen(ss)+1;
502: strncpy( finame, name, l1-l2);
503: finame[l1-l2]= 0;
504: }
505:
506: return( 0 ); /* we're done */
507: }
508:
509:
510: /******************************************/
511:
512: void replace_back_to_slash(char *s, char*t)
513: {
514: int i;
515: int lg=0;
516: i=0;
517: lg=strlen(t);
518: for(i=0; i<= lg; i++) {
519: (s[i] = t[i]);
520: if (t[i]== '\\') s[i]='/';
521: }
522: }
523:
524: int nbocc(char *s, char occ)
525: {
526: int i,j=0;
527: int lg=20;
528: i=0;
529: lg=strlen(s);
530: for(i=0; i<= lg; i++) {
531: if (s[i] == occ ) j++;
532: }
533: return j;
534: }
535:
536: void cutv(char *u,char *v, char*t, char occ)
537: {
538: /* cuts string t into u and v where u ends before first occurence of char 'occ'
539: and v starts after first occurence of char 'occ' : ex cutv(u,v,"abcdef2ghi2j",'2')
540: gives u="abcedf" and v="ghi2j" */
541: int i,lg,j,p=0;
542: i=0;
543: for(j=0; j<=strlen(t)-1; j++) {
544: if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;
545: }
546:
547: lg=strlen(t);
548: for(j=0; j<p; j++) {
549: (u[j] = t[j]);
550: }
551: u[p]='\0';
552:
553: for(j=0; j<= lg; j++) {
554: if (j>=(p+1))(v[j-p-1] = t[j]);
555: }
556: }
557:
558: /********************** nrerror ********************/
559:
560: void nrerror(char error_text[])
561: {
562: fprintf(stderr,"ERREUR ...\n");
563: fprintf(stderr,"%s\n",error_text);
564: exit(EXIT_FAILURE);
565: }
566: /*********************** vector *******************/
567: double *vector(int nl, int nh)
568: {
569: double *v;
570: v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
571: if (!v) nrerror("allocation failure in vector");
572: return v-nl+NR_END;
573: }
574:
575: /************************ free vector ******************/
576: void free_vector(double*v, int nl, int nh)
577: {
578: free((FREE_ARG)(v+nl-NR_END));
579: }
580:
581: /************************ivector *******************************/
582: int *ivector(long nl,long nh)
583: {
584: int *v;
585: v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
586: if (!v) nrerror("allocation failure in ivector");
587: return v-nl+NR_END;
588: }
589:
590: /******************free ivector **************************/
591: void free_ivector(int *v, long nl, long nh)
592: {
593: free((FREE_ARG)(v+nl-NR_END));
594: }
595:
596: /************************lvector *******************************/
597: long *lvector(long nl,long nh)
598: {
599: long *v;
600: v=(long *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(long)));
601: if (!v) nrerror("allocation failure in ivector");
602: return v-nl+NR_END;
603: }
604:
605: /******************free lvector **************************/
606: void free_lvector(long *v, long nl, long nh)
607: {
608: free((FREE_ARG)(v+nl-NR_END));
609: }
610:
611: /******************* imatrix *******************************/
612: int **imatrix(long nrl, long nrh, long ncl, long nch)
613: /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */
614: {
615: long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;
616: int **m;
617:
618: /* allocate pointers to rows */
619: m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));
620: if (!m) nrerror("allocation failure 1 in matrix()");
621: m += NR_END;
622: m -= nrl;
623:
624:
625: /* allocate rows and set pointers to them */
626: m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));
627: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
628: m[nrl] += NR_END;
629: m[nrl] -= ncl;
630:
631: for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;
632:
633: /* return pointer to array of pointers to rows */
634: return m;
635: }
636:
637: /****************** free_imatrix *************************/
638: void free_imatrix(m,nrl,nrh,ncl,nch)
639: int **m;
640: long nch,ncl,nrh,nrl;
641: /* free an int matrix allocated by imatrix() */
642: {
643: free((FREE_ARG) (m[nrl]+ncl-NR_END));
644: free((FREE_ARG) (m+nrl-NR_END));
645: }
646:
647: /******************* matrix *******************************/
648: double **matrix(long nrl, long nrh, long ncl, long nch)
649: {
650: long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
651: double **m;
652:
653: m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
654: if (!m) nrerror("allocation failure 1 in matrix()");
655: m += NR_END;
656: m -= nrl;
657:
658: m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
659: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
660: m[nrl] += NR_END;
661: m[nrl] -= ncl;
662:
663: for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
664: return m;
665: /* print *(*(m+1)+70) or print m[1][70]; print m+1 or print &(m[1])
666: */
667: }
668:
669: /*************************free matrix ************************/
670: void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
671: {
672: free((FREE_ARG)(m[nrl]+ncl-NR_END));
673: free((FREE_ARG)(m+nrl-NR_END));
674: }
675:
676: /******************* ma3x *******************************/
677: double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
678: {
679: long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
680: double ***m;
681:
682: m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
683: if (!m) nrerror("allocation failure 1 in matrix()");
684: m += NR_END;
685: m -= nrl;
686:
687: m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
688: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
689: m[nrl] += NR_END;
690: m[nrl] -= ncl;
691:
692: for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
693:
694: m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
695: if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
696: m[nrl][ncl] += NR_END;
697: m[nrl][ncl] -= nll;
698: for (j=ncl+1; j<=nch; j++)
699: m[nrl][j]=m[nrl][j-1]+nlay;
700:
701: for (i=nrl+1; i<=nrh; i++) {
702: m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
703: for (j=ncl+1; j<=nch; j++)
704: m[i][j]=m[i][j-1]+nlay;
705: }
706: return m;
707: /* gdb: p *(m+1) <=> p m[1] and p (m+1) <=> p (m+1) <=> p &(m[1])
708: &(m[i][j][k]) <=> *((*(m+i) + j)+k)
709: */
710: }
711:
712: /*************************free ma3x ************************/
713: void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
714: {
715: free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
716: free((FREE_ARG)(m[nrl]+ncl-NR_END));
717: free((FREE_ARG)(m+nrl-NR_END));
718: }
719:
720: /*************** function subdirf ***********/
721: char *subdirf(char fileres[])
722: {
723: /* Caution optionfilefiname is hidden */
724: strcpy(tmpout,optionfilefiname);
725: strcat(tmpout,"/"); /* Add to the right */
726: strcat(tmpout,fileres);
727: return tmpout;
728: }
729:
730: /*************** function subdirf2 ***********/
731: char *subdirf2(char fileres[], char *preop)
732: {
733:
734: /* Caution optionfilefiname is hidden */
735: strcpy(tmpout,optionfilefiname);
736: strcat(tmpout,"/");
737: strcat(tmpout,preop);
738: strcat(tmpout,fileres);
739: return tmpout;
740: }
741:
742: /*************** function subdirf3 ***********/
743: char *subdirf3(char fileres[], char *preop, char *preop2)
744: {
745:
746: /* Caution optionfilefiname is hidden */
747: strcpy(tmpout,optionfilefiname);
748: strcat(tmpout,"/");
749: strcat(tmpout,preop);
750: strcat(tmpout,preop2);
751: strcat(tmpout,fileres);
752: return tmpout;
753: }
754:
755: /***************** f1dim *************************/
756: extern int ncom;
757: extern double *pcom,*xicom;
758: extern double (*nrfunc)(double []);
759:
760: double f1dim(double x)
761: {
762: int j;
763: double f;
764: double *xt;
765:
766: xt=vector(1,ncom);
767: for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];
768: f=(*nrfunc)(xt);
769: free_vector(xt,1,ncom);
770: return f;
771: }
772:
773: /*****************brent *************************/
774: double brent(double ax, double bx, double cx, double (*f)(double), double tol, double *xmin)
775: {
776: int iter;
777: double a,b,d,etemp;
778: double fu,fv,fw,fx;
779: double ftemp;
780: double p,q,r,tol1,tol2,u,v,w,x,xm;
781: double e=0.0;
782:
783: a=(ax < cx ? ax : cx);
784: b=(ax > cx ? ax : cx);
785: x=w=v=bx;
786: fw=fv=fx=(*f)(x);
787: for (iter=1;iter<=ITMAX;iter++) {
788: xm=0.5*(a+b);
789: tol2=2.0*(tol1=tol*fabs(x)+ZEPS);
790: /* if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
791: printf(".");fflush(stdout);
792: fprintf(ficlog,".");fflush(ficlog);
793: #ifdef DEBUG
794: 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);
795: 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);
796: /* if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
797: #endif
798: if (fabs(x-xm) <= (tol2-0.5*(b-a))){
799: *xmin=x;
800: return fx;
801: }
802: ftemp=fu;
803: if (fabs(e) > tol1) {
804: r=(x-w)*(fx-fv);
805: q=(x-v)*(fx-fw);
806: p=(x-v)*q-(x-w)*r;
807: q=2.0*(q-r);
808: if (q > 0.0) p = -p;
809: q=fabs(q);
810: etemp=e;
811: e=d;
812: if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))
813: d=CGOLD*(e=(x >= xm ? a-x : b-x));
814: else {
815: d=p/q;
816: u=x+d;
817: if (u-a < tol2 || b-u < tol2)
818: d=SIGN(tol1,xm-x);
819: }
820: } else {
821: d=CGOLD*(e=(x >= xm ? a-x : b-x));
822: }
823: u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));
824: fu=(*f)(u);
825: if (fu <= fx) {
826: if (u >= x) a=x; else b=x;
827: SHFT(v,w,x,u)
828: SHFT(fv,fw,fx,fu)
829: } else {
830: if (u < x) a=u; else b=u;
831: if (fu <= fw || w == x) {
832: v=w;
833: w=u;
834: fv=fw;
835: fw=fu;
836: } else if (fu <= fv || v == x || v == w) {
837: v=u;
838: fv=fu;
839: }
840: }
841: }
842: nrerror("Too many iterations in brent");
843: *xmin=x;
844: return fx;
845: }
846:
847: /****************** mnbrak ***********************/
848:
849: void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,
850: double (*func)(double))
851: {
852: double ulim,u,r,q, dum;
853: double fu;
854:
855: *fa=(*func)(*ax);
856: *fb=(*func)(*bx);
857: if (*fb > *fa) {
858: SHFT(dum,*ax,*bx,dum)
859: SHFT(dum,*fb,*fa,dum)
860: }
861: *cx=(*bx)+GOLD*(*bx-*ax);
862: *fc=(*func)(*cx);
863: while (*fb > *fc) {
864: r=(*bx-*ax)*(*fb-*fc);
865: q=(*bx-*cx)*(*fb-*fa);
866: u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/
867: (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r));
868: ulim=(*bx)+GLIMIT*(*cx-*bx);
869: if ((*bx-u)*(u-*cx) > 0.0) {
870: fu=(*func)(u);
871: } else if ((*cx-u)*(u-ulim) > 0.0) {
872: fu=(*func)(u);
873: if (fu < *fc) {
874: SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))
875: SHFT(*fb,*fc,fu,(*func)(u))
876: }
877: } else if ((u-ulim)*(ulim-*cx) >= 0.0) {
878: u=ulim;
879: fu=(*func)(u);
880: } else {
881: u=(*cx)+GOLD*(*cx-*bx);
882: fu=(*func)(u);
883: }
884: SHFT(*ax,*bx,*cx,u)
885: SHFT(*fa,*fb,*fc,fu)
886: }
887: }
888:
889: /*************** linmin ************************/
890:
891: int ncom;
892: double *pcom,*xicom;
893: double (*nrfunc)(double []);
894:
895: void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))
896: {
897: double brent(double ax, double bx, double cx,
898: double (*f)(double), double tol, double *xmin);
899: double f1dim(double x);
900: void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,
901: double *fc, double (*func)(double));
902: int j;
903: double xx,xmin,bx,ax;
904: double fx,fb,fa;
905:
906: ncom=n;
907: pcom=vector(1,n);
908: xicom=vector(1,n);
909: nrfunc=func;
910: for (j=1;j<=n;j++) {
911: pcom[j]=p[j];
912: xicom[j]=xi[j];
913: }
914: ax=0.0;
915: xx=1.0;
916: mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim);
917: *fret=brent(ax,xx,bx,f1dim,TOL,&xmin);
918: #ifdef DEBUG
919: printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
920: fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
921: #endif
922: for (j=1;j<=n;j++) {
923: xi[j] *= xmin;
924: p[j] += xi[j];
925: }
926: free_vector(xicom,1,n);
927: free_vector(pcom,1,n);
928: }
929:
930: char *asc_diff_time(long time_sec, char ascdiff[])
931: {
932: long sec_left, days, hours, minutes;
933: days = (time_sec) / (60*60*24);
934: sec_left = (time_sec) % (60*60*24);
935: hours = (sec_left) / (60*60) ;
936: sec_left = (sec_left) %(60*60);
937: minutes = (sec_left) /60;
938: sec_left = (sec_left) % (60);
939: sprintf(ascdiff,"%d day(s) %d hour(s) %d minute(s) %d second(s)",days, hours, minutes, sec_left);
940: return ascdiff;
941: }
942:
943: /*************** powell ************************/
944: void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,
945: double (*func)(double []))
946: {
947: void linmin(double p[], double xi[], int n, double *fret,
948: double (*func)(double []));
949: int i,ibig,j;
950: double del,t,*pt,*ptt,*xit;
951: double fp,fptt;
952: double *xits;
953: int niterf, itmp;
954:
955: pt=vector(1,n);
956: ptt=vector(1,n);
957: xit=vector(1,n);
958: xits=vector(1,n);
959: *fret=(*func)(p);
960: for (j=1;j<=n;j++) pt[j]=p[j];
961: for (*iter=1;;++(*iter)) {
962: fp=(*fret);
963: ibig=0;
964: del=0.0;
965: last_time=curr_time;
966: (void) gettimeofday(&curr_time,&tzp);
967: printf("\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret, curr_time.tv_sec-last_time.tv_sec, curr_time.tv_sec-start_time.tv_sec);fflush(stdout);
968: /* fprintf(ficlog,"\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret, curr_time.tv_sec-last_time.tv_sec, curr_time.tv_sec-start_time.tv_sec);
969: fprintf(ficrespow,"%d %.12f %ld",*iter,*fret,curr_time.tv_sec-start_time.tv_sec);
970: */
971: for (i=1;i<=n;i++) {
972: printf(" %d %.12f",i, p[i]);
973: fprintf(ficlog," %d %.12lf",i, p[i]);
974: fprintf(ficrespow," %.12lf", p[i]);
975: }
976: printf("\n");
977: fprintf(ficlog,"\n");
978: fprintf(ficrespow,"\n");fflush(ficrespow);
979: if(*iter <=3){
980: tm = *localtime(&curr_time.tv_sec);
981: strcpy(strcurr,asctime(&tm));
982: /* asctime_r(&tm,strcurr); */
983: forecast_time=curr_time;
984: itmp = strlen(strcurr);
985: if(strcurr[itmp-1]=='\n') /* Windows outputs with a new line */
986: strcurr[itmp-1]='\0';
987: printf("\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,curr_time.tv_sec-last_time.tv_sec);
988: fprintf(ficlog,"\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,curr_time.tv_sec-last_time.tv_sec);
989: for(niterf=10;niterf<=30;niterf+=10){
990: forecast_time.tv_sec=curr_time.tv_sec+(niterf-*iter)*(curr_time.tv_sec-last_time.tv_sec);
991: tmf = *localtime(&forecast_time.tv_sec);
992: /* asctime_r(&tmf,strfor); */
993: strcpy(strfor,asctime(&tmf));
994: itmp = strlen(strfor);
995: if(strfor[itmp-1]=='\n')
996: strfor[itmp-1]='\0';
997: 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(forecast_time.tv_sec-curr_time.tv_sec,tmpout),strfor,strcurr);
998: 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(forecast_time.tv_sec-curr_time.tv_sec,tmpout),strfor,strcurr);
999: }
1000: }
1001: for (i=1;i<=n;i++) {
1002: for (j=1;j<=n;j++) xit[j]=xi[j][i];
1003: fptt=(*fret);
1004: #ifdef DEBUG
1005: printf("fret=%lf \n",*fret);
1006: fprintf(ficlog,"fret=%lf \n",*fret);
1007: #endif
1008: printf("%d",i);fflush(stdout);
1009: fprintf(ficlog,"%d",i);fflush(ficlog);
1010: linmin(p,xit,n,fret,func);
1011: if (fabs(fptt-(*fret)) > del) {
1012: del=fabs(fptt-(*fret));
1013: ibig=i;
1014: }
1015: #ifdef DEBUG
1016: printf("%d %.12e",i,(*fret));
1017: fprintf(ficlog,"%d %.12e",i,(*fret));
1018: for (j=1;j<=n;j++) {
1019: xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
1020: printf(" x(%d)=%.12e",j,xit[j]);
1021: fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
1022: }
1023: for(j=1;j<=n;j++) {
1024: printf(" p=%.12e",p[j]);
1025: fprintf(ficlog," p=%.12e",p[j]);
1026: }
1027: printf("\n");
1028: fprintf(ficlog,"\n");
1029: #endif
1030: }
1031: if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {
1032: #ifdef DEBUG
1033: int k[2],l;
1034: k[0]=1;
1035: k[1]=-1;
1036: printf("Max: %.12e",(*func)(p));
1037: fprintf(ficlog,"Max: %.12e",(*func)(p));
1038: for (j=1;j<=n;j++) {
1039: printf(" %.12e",p[j]);
1040: fprintf(ficlog," %.12e",p[j]);
1041: }
1042: printf("\n");
1043: fprintf(ficlog,"\n");
1044: for(l=0;l<=1;l++) {
1045: for (j=1;j<=n;j++) {
1046: ptt[j]=p[j]+(p[j]-pt[j])*k[l];
1047: printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
1048: fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
1049: }
1050: printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
1051: fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
1052: }
1053: #endif
1054:
1055:
1056: free_vector(xit,1,n);
1057: free_vector(xits,1,n);
1058: free_vector(ptt,1,n);
1059: free_vector(pt,1,n);
1060: return;
1061: }
1062: if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");
1063: for (j=1;j<=n;j++) {
1064: ptt[j]=2.0*p[j]-pt[j];
1065: xit[j]=p[j]-pt[j];
1066: pt[j]=p[j];
1067: }
1068: fptt=(*func)(ptt);
1069: if (fptt < fp) {
1070: t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt);
1071: if (t < 0.0) {
1072: linmin(p,xit,n,fret,func);
1073: for (j=1;j<=n;j++) {
1074: xi[j][ibig]=xi[j][n];
1075: xi[j][n]=xit[j];
1076: }
1077: #ifdef DEBUG
1078: printf("Direction changed last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
1079: fprintf(ficlog,"Direction changed last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
1080: for(j=1;j<=n;j++){
1081: printf(" %.12e",xit[j]);
1082: fprintf(ficlog," %.12e",xit[j]);
1083: }
1084: printf("\n");
1085: fprintf(ficlog,"\n");
1086: #endif
1087: }
1088: }
1089: }
1090: }
1091:
1092: /**** Prevalence limit (stable or period prevalence) ****************/
1093:
1094: double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)
1095: {
1096: /* Computes the prevalence limit in each live state at age x by left multiplying the unit
1097: matrix by transitions matrix until convergence is reached */
1098:
1099: int i, ii,j,k;
1100: double min, max, maxmin, maxmax,sumnew=0.;
1101: double **matprod2();
1102: double **out, cov[NCOVMAX], **pmij();
1103: double **newm;
1104: double agefin, delaymax=50 ; /* Max number of years to converge */
1105:
1106: for (ii=1;ii<=nlstate+ndeath;ii++)
1107: for (j=1;j<=nlstate+ndeath;j++){
1108: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1109: }
1110:
1111: cov[1]=1.;
1112:
1113: /* Even if hstepm = 1, at least one multiplication by the unit matrix */
1114: for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
1115: newm=savm;
1116: /* Covariates have to be included here again */
1117: cov[2]=agefin;
1118:
1119: for (k=1; k<=cptcovn;k++) {
1120: cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
1121: /* printf("ij=%d k=%d Tvar[k]=%d nbcode=%d cov=%lf codtab[ij][Tvar[k]]=%d \n",ij,k, Tvar[k],nbcode[Tvar[k]][codtab[ij][Tvar[k]]],cov[2+k], codtab[ij][Tvar[k]]);*/
1122: }
1123: for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
1124: for (k=1; k<=cptcovprod;k++)
1125: cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
1126:
1127: /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
1128: /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
1129: /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
1130: out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);
1131:
1132: savm=oldm;
1133: oldm=newm;
1134: maxmax=0.;
1135: for(j=1;j<=nlstate;j++){
1136: min=1.;
1137: max=0.;
1138: for(i=1; i<=nlstate; i++) {
1139: sumnew=0;
1140: for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
1141: prlim[i][j]= newm[i][j]/(1-sumnew);
1142: max=FMAX(max,prlim[i][j]);
1143: min=FMIN(min,prlim[i][j]);
1144: }
1145: maxmin=max-min;
1146: maxmax=FMAX(maxmax,maxmin);
1147: }
1148: if(maxmax < ftolpl){
1149: return prlim;
1150: }
1151: }
1152: }
1153:
1154: /*************** transition probabilities ***************/
1155:
1156: double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
1157: {
1158: double s1, s2;
1159: /*double t34;*/
1160: int i,j,j1, nc, ii, jj;
1161:
1162: for(i=1; i<= nlstate; i++){
1163: for(j=1; j<i;j++){
1164: for (nc=1, s2=0.;nc <=ncovmodel; nc++){
1165: /*s2 += param[i][j][nc]*cov[nc];*/
1166: s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
1167: /* printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2); */
1168: }
1169: ps[i][j]=s2;
1170: /* printf("s1=%.17e, s2=%.17e\n",s1,s2); */
1171: }
1172: for(j=i+1; j<=nlstate+ndeath;j++){
1173: for (nc=1, s2=0.;nc <=ncovmodel; nc++){
1174: s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
1175: /* printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2); */
1176: }
1177: ps[i][j]=s2;
1178: }
1179: }
1180: /*ps[3][2]=1;*/
1181:
1182: for(i=1; i<= nlstate; i++){
1183: s1=0;
1184: for(j=1; j<i; j++)
1185: s1+=exp(ps[i][j]);
1186: for(j=i+1; j<=nlstate+ndeath; j++)
1187: s1+=exp(ps[i][j]);
1188: ps[i][i]=1./(s1+1.);
1189: for(j=1; j<i; j++)
1190: ps[i][j]= exp(ps[i][j])*ps[i][i];
1191: for(j=i+1; j<=nlstate+ndeath; j++)
1192: ps[i][j]= exp(ps[i][j])*ps[i][i];
1193: /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
1194: } /* end i */
1195:
1196: for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
1197: for(jj=1; jj<= nlstate+ndeath; jj++){
1198: ps[ii][jj]=0;
1199: ps[ii][ii]=1;
1200: }
1201: }
1202:
1203:
1204: /* for(ii=1; ii<= nlstate+ndeath; ii++){ */
1205: /* for(jj=1; jj<= nlstate+ndeath; jj++){ */
1206: /* printf("ddd %lf ",ps[ii][jj]); */
1207: /* } */
1208: /* printf("\n "); */
1209: /* } */
1210: /* printf("\n ");printf("%lf ",cov[2]); */
1211: /*
1212: for(i=1; i<= npar; i++) printf("%f ",x[i]);
1213: goto end;*/
1214: return ps;
1215: }
1216:
1217: /**************** Product of 2 matrices ******************/
1218:
1219: double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)
1220: {
1221: /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
1222: b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
1223: /* in, b, out are matrice of pointers which should have been initialized
1224: before: only the contents of out is modified. The function returns
1225: a pointer to pointers identical to out */
1226: long i, j, k;
1227: for(i=nrl; i<= nrh; i++)
1228: for(k=ncolol; k<=ncoloh; k++)
1229: for(j=ncl,out[i][k]=0.; j<=nch; j++)
1230: out[i][k] +=in[i][j]*b[j][k];
1231:
1232: return out;
1233: }
1234:
1235:
1236: /************* Higher Matrix Product ***************/
1237:
1238: double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
1239: {
1240: /* Computes the transition matrix starting at age 'age' over
1241: 'nhstepm*hstepm*stepm' months (i.e. until
1242: age (in years) age+nhstepm*hstepm*stepm/12) by multiplying
1243: nhstepm*hstepm matrices.
1244: Output is stored in matrix po[i][j][h] for h every 'hstepm' step
1245: (typically every 2 years instead of every month which is too big
1246: for the memory).
1247: Model is determined by parameters x and covariates have to be
1248: included manually here.
1249:
1250: */
1251:
1252: int i, j, d, h, k;
1253: double **out, cov[NCOVMAX];
1254: double **newm;
1255:
1256: /* Hstepm could be zero and should return the unit matrix */
1257: for (i=1;i<=nlstate+ndeath;i++)
1258: for (j=1;j<=nlstate+ndeath;j++){
1259: oldm[i][j]=(i==j ? 1.0 : 0.0);
1260: po[i][j][0]=(i==j ? 1.0 : 0.0);
1261: }
1262: /* Even if hstepm = 1, at least one multiplication by the unit matrix */
1263: for(h=1; h <=nhstepm; h++){
1264: for(d=1; d <=hstepm; d++){
1265: newm=savm;
1266: /* Covariates have to be included here again */
1267: cov[1]=1.;
1268: cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
1269: for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
1270: for (k=1; k<=cptcovage;k++)
1271: cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
1272: for (k=1; k<=cptcovprod;k++)
1273: cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
1274:
1275:
1276: /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
1277: /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
1278: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,
1279: pmij(pmmij,cov,ncovmodel,x,nlstate));
1280: savm=oldm;
1281: oldm=newm;
1282: }
1283: for(i=1; i<=nlstate+ndeath; i++)
1284: for(j=1;j<=nlstate+ndeath;j++) {
1285: po[i][j][h]=newm[i][j];
1286: /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);
1287: */
1288: }
1289: } /* end h */
1290: return po;
1291: }
1292:
1293:
1294: /*************** log-likelihood *************/
1295: double func( double *x)
1296: {
1297: int i, ii, j, k, mi, d, kk;
1298: double l, ll[NLSTATEMAX], cov[NCOVMAX];
1299: double **out;
1300: double sw; /* Sum of weights */
1301: double lli; /* Individual log likelihood */
1302: int s1, s2;
1303: double bbh, survp;
1304: long ipmx;
1305: /*extern weight */
1306: /* We are differentiating ll according to initial status */
1307: /* for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
1308: /*for(i=1;i<imx;i++)
1309: printf(" %d\n",s[4][i]);
1310: */
1311: cov[1]=1.;
1312:
1313: for(k=1; k<=nlstate; k++) ll[k]=0.;
1314:
1315: if(mle==1){
1316: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1317: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
1318: for(mi=1; mi<= wav[i]-1; mi++){
1319: for (ii=1;ii<=nlstate+ndeath;ii++)
1320: for (j=1;j<=nlstate+ndeath;j++){
1321: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1322: savm[ii][j]=(ii==j ? 1.0 : 0.0);
1323: }
1324: for(d=0; d<dh[mi][i]; d++){
1325: newm=savm;
1326: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
1327: for (kk=1; kk<=cptcovage;kk++) {
1328: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
1329: }
1330: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1331: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1332: savm=oldm;
1333: oldm=newm;
1334: } /* end mult */
1335:
1336: /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
1337: /* But now since version 0.9 we anticipate for bias at large stepm.
1338: * If stepm is larger than one month (smallest stepm) and if the exact delay
1339: * (in months) between two waves is not a multiple of stepm, we rounded to
1340: * the nearest (and in case of equal distance, to the lowest) interval but now
1341: * we keep into memory the bias bh[mi][i] and also the previous matrix product
1342: * (i.e to dh[mi][i]-1) saved in 'savm'. Then we inter(extra)polate the
1343: * probability in order to take into account the bias as a fraction of the way
1344: * from savm to out if bh is negative or even beyond if bh is positive. bh varies
1345: * -stepm/2 to stepm/2 .
1346: * For stepm=1 the results are the same as for previous versions of Imach.
1347: * For stepm > 1 the results are less biased than in previous versions.
1348: */
1349: s1=s[mw[mi][i]][i];
1350: s2=s[mw[mi+1][i]][i];
1351: bbh=(double)bh[mi][i]/(double)stepm;
1352: /* bias bh is positive if real duration
1353: * is higher than the multiple of stepm and negative otherwise.
1354: */
1355: /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
1356: if( s2 > nlstate){
1357: /* i.e. if s2 is a death state and if the date of death is known
1358: then the contribution to the likelihood is the probability to
1359: die between last step unit time and current step unit time,
1360: which is also equal to probability to die before dh
1361: minus probability to die before dh-stepm .
1362: In version up to 0.92 likelihood was computed
1363: as if date of death was unknown. Death was treated as any other
1364: health state: the date of the interview describes the actual state
1365: and not the date of a change in health state. The former idea was
1366: to consider that at each interview the state was recorded
1367: (healthy, disable or death) and IMaCh was corrected; but when we
1368: introduced the exact date of death then we should have modified
1369: the contribution of an exact death to the likelihood. This new
1370: contribution is smaller and very dependent of the step unit
1371: stepm. It is no more the probability to die between last interview
1372: and month of death but the probability to survive from last
1373: interview up to one month before death multiplied by the
1374: probability to die within a month. Thanks to Chris
1375: Jackson for correcting this bug. Former versions increased
1376: mortality artificially. The bad side is that we add another loop
1377: which slows down the processing. The difference can be up to 10%
1378: lower mortality.
1379: */
1380: lli=log(out[s1][s2] - savm[s1][s2]);
1381:
1382:
1383: } else if (s2==-2) {
1384: for (j=1,survp=0. ; j<=nlstate; j++)
1385: survp += out[s1][j];
1386: lli= survp;
1387: }
1388:
1389: else if (s2==-4) {
1390: for (j=3,survp=0. ; j<=nlstate; j++)
1391: survp += out[s1][j];
1392: lli= survp;
1393: }
1394:
1395: else if (s2==-5) {
1396: for (j=1,survp=0. ; j<=2; j++)
1397: survp += out[s1][j];
1398: lli= survp;
1399: }
1400:
1401:
1402: else{
1403: lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
1404: /* 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 */
1405: }
1406: /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
1407: /*if(lli ==000.0)*/
1408: /*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); */
1409: ipmx +=1;
1410: sw += weight[i];
1411: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1412: } /* end of wave */
1413: } /* end of individual */
1414: } else if(mle==2){
1415: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1416: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
1417: for(mi=1; mi<= wav[i]-1; mi++){
1418: for (ii=1;ii<=nlstate+ndeath;ii++)
1419: for (j=1;j<=nlstate+ndeath;j++){
1420: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1421: savm[ii][j]=(ii==j ? 1.0 : 0.0);
1422: }
1423: for(d=0; d<=dh[mi][i]; d++){
1424: newm=savm;
1425: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
1426: for (kk=1; kk<=cptcovage;kk++) {
1427: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
1428: }
1429: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1430: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1431: savm=oldm;
1432: oldm=newm;
1433: } /* end mult */
1434:
1435: s1=s[mw[mi][i]][i];
1436: s2=s[mw[mi+1][i]][i];
1437: bbh=(double)bh[mi][i]/(double)stepm;
1438: 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 */
1439: ipmx +=1;
1440: sw += weight[i];
1441: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1442: } /* end of wave */
1443: } /* end of individual */
1444: } else if(mle==3){ /* exponential inter-extrapolation */
1445: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1446: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
1447: for(mi=1; mi<= wav[i]-1; mi++){
1448: for (ii=1;ii<=nlstate+ndeath;ii++)
1449: for (j=1;j<=nlstate+ndeath;j++){
1450: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1451: savm[ii][j]=(ii==j ? 1.0 : 0.0);
1452: }
1453: for(d=0; d<dh[mi][i]; d++){
1454: newm=savm;
1455: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
1456: for (kk=1; kk<=cptcovage;kk++) {
1457: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
1458: }
1459: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1460: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1461: savm=oldm;
1462: oldm=newm;
1463: } /* end mult */
1464:
1465: s1=s[mw[mi][i]][i];
1466: s2=s[mw[mi+1][i]][i];
1467: bbh=(double)bh[mi][i]/(double)stepm;
1468: 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 */
1469: ipmx +=1;
1470: sw += weight[i];
1471: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1472: } /* end of wave */
1473: } /* end of individual */
1474: }else if (mle==4){ /* ml=4 no inter-extrapolation */
1475: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1476: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
1477: for(mi=1; mi<= wav[i]-1; mi++){
1478: for (ii=1;ii<=nlstate+ndeath;ii++)
1479: for (j=1;j<=nlstate+ndeath;j++){
1480: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1481: savm[ii][j]=(ii==j ? 1.0 : 0.0);
1482: }
1483: for(d=0; d<dh[mi][i]; d++){
1484: newm=savm;
1485: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
1486: for (kk=1; kk<=cptcovage;kk++) {
1487: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
1488: }
1489:
1490: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1491: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1492: savm=oldm;
1493: oldm=newm;
1494: } /* end mult */
1495:
1496: s1=s[mw[mi][i]][i];
1497: s2=s[mw[mi+1][i]][i];
1498: if( s2 > nlstate){
1499: lli=log(out[s1][s2] - savm[s1][s2]);
1500: }else{
1501: lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
1502: }
1503: ipmx +=1;
1504: sw += weight[i];
1505: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1506: /* 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]); */
1507: } /* end of wave */
1508: } /* end of individual */
1509: }else{ /* ml=5 no inter-extrapolation no jackson =0.8a */
1510: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1511: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
1512: for(mi=1; mi<= wav[i]-1; mi++){
1513: for (ii=1;ii<=nlstate+ndeath;ii++)
1514: for (j=1;j<=nlstate+ndeath;j++){
1515: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1516: savm[ii][j]=(ii==j ? 1.0 : 0.0);
1517: }
1518: for(d=0; d<dh[mi][i]; d++){
1519: newm=savm;
1520: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
1521: for (kk=1; kk<=cptcovage;kk++) {
1522: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
1523: }
1524:
1525: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1526: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1527: savm=oldm;
1528: oldm=newm;
1529: } /* end mult */
1530:
1531: s1=s[mw[mi][i]][i];
1532: s2=s[mw[mi+1][i]][i];
1533: lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
1534: ipmx +=1;
1535: sw += weight[i];
1536: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1537: /*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]);*/
1538: } /* end of wave */
1539: } /* end of individual */
1540: } /* End of if */
1541: for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
1542: /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
1543: l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
1544: return -l;
1545: }
1546:
1547: /*************** log-likelihood *************/
1548: double funcone( double *x)
1549: {
1550: /* Same as likeli but slower because of a lot of printf and if */
1551: int i, ii, j, k, mi, d, kk;
1552: double l, ll[NLSTATEMAX], cov[NCOVMAX];
1553: double **out;
1554: double lli; /* Individual log likelihood */
1555: double llt;
1556: int s1, s2;
1557: double bbh, survp;
1558: /*extern weight */
1559: /* We are differentiating ll according to initial status */
1560: /* for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
1561: /*for(i=1;i<imx;i++)
1562: printf(" %d\n",s[4][i]);
1563: */
1564: cov[1]=1.;
1565:
1566: for(k=1; k<=nlstate; k++) ll[k]=0.;
1567:
1568: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1569: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
1570: for(mi=1; mi<= wav[i]-1; mi++){
1571: for (ii=1;ii<=nlstate+ndeath;ii++)
1572: for (j=1;j<=nlstate+ndeath;j++){
1573: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1574: savm[ii][j]=(ii==j ? 1.0 : 0.0);
1575: }
1576: for(d=0; d<dh[mi][i]; d++){
1577: newm=savm;
1578: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
1579: for (kk=1; kk<=cptcovage;kk++) {
1580: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
1581: }
1582: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1583: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1584: savm=oldm;
1585: oldm=newm;
1586: } /* end mult */
1587:
1588: s1=s[mw[mi][i]][i];
1589: s2=s[mw[mi+1][i]][i];
1590: bbh=(double)bh[mi][i]/(double)stepm;
1591: /* bias is positive if real duration
1592: * is higher than the multiple of stepm and negative otherwise.
1593: */
1594: if( s2 > nlstate && (mle <5) ){ /* Jackson */
1595: lli=log(out[s1][s2] - savm[s1][s2]);
1596: } else if (mle==1){
1597: lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
1598: } else if(mle==2){
1599: 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 */
1600: } else if(mle==3){ /* exponential inter-extrapolation */
1601: 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 */
1602: } else if (mle==4){ /* mle=4 no inter-extrapolation */
1603: lli=log(out[s1][s2]); /* Original formula */
1604: } else{ /* ml>=5 no inter-extrapolation no jackson =0.8a */
1605: lli=log(out[s1][s2]); /* Original formula */
1606: } /* End of if */
1607: ipmx +=1;
1608: sw += weight[i];
1609: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1610: /* 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]); */
1611: if(globpr){
1612: fprintf(ficresilk,"%9d %6d %1d %1d %1d %1d %3d %10.6f %6.4f\
1613: %10.6f %10.6f %10.6f ", \
1614: num[i],i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],
1615: 2*weight[i]*lli,out[s1][s2],savm[s1][s2]);
1616: for(k=1,llt=0.,l=0.; k<=nlstate; k++){
1617: llt +=ll[k]*gipmx/gsw;
1618: fprintf(ficresilk," %10.6f",-ll[k]*gipmx/gsw);
1619: }
1620: fprintf(ficresilk," %10.6f\n", -llt);
1621: }
1622: } /* end of wave */
1623: } /* end of individual */
1624: for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
1625: /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
1626: l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
1627: if(globpr==0){ /* First time we count the contributions and weights */
1628: gipmx=ipmx;
1629: gsw=sw;
1630: }
1631: return -l;
1632: }
1633:
1634:
1635: /*************** function likelione ***********/
1636: void likelione(FILE *ficres,double p[], int npar, int nlstate, int *globpri, long *ipmx, double *sw, double *fretone, double (*funcone)(double []))
1637: {
1638: /* This routine should help understanding what is done with
1639: the selection of individuals/waves and
1640: to check the exact contribution to the likelihood.
1641: Plotting could be done.
1642: */
1643: int k;
1644:
1645: if(*globpri !=0){ /* Just counts and sums, no printings */
1646: strcpy(fileresilk,"ilk");
1647: strcat(fileresilk,fileres);
1648: if((ficresilk=fopen(fileresilk,"w"))==NULL) {
1649: printf("Problem with resultfile: %s\n", fileresilk);
1650: fprintf(ficlog,"Problem with resultfile: %s\n", fileresilk);
1651: }
1652: 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");
1653: fprintf(ficresilk, "#num_i i s1 s2 mi mw dh likeli weight 2wlli out sav ");
1654: /* i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],2*weight[i]*lli,out[s1][s2],savm[s1][s2]); */
1655: for(k=1; k<=nlstate; k++)
1656: fprintf(ficresilk," -2*gipw/gsw*weight*ll[%d]++",k);
1657: fprintf(ficresilk," -2*gipw/gsw*weight*ll(total)\n");
1658: }
1659:
1660: *fretone=(*funcone)(p);
1661: if(*globpri !=0){
1662: fclose(ficresilk);
1663: fprintf(fichtm,"\n<br>File of contributions to the likelihood: <a href=\"%s\">%s</a><br>\n",subdirf(fileresilk),subdirf(fileresilk));
1664: fflush(fichtm);
1665: }
1666: return;
1667: }
1668:
1669:
1670: /*********** Maximum Likelihood Estimation ***************/
1671:
1672: void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
1673: {
1674: int i,j, iter;
1675: double **xi;
1676: double fret;
1677: double fretone; /* Only one call to likelihood */
1678: /* char filerespow[FILENAMELENGTH];*/
1679: xi=matrix(1,npar,1,npar);
1680: for (i=1;i<=npar;i++)
1681: for (j=1;j<=npar;j++)
1682: xi[i][j]=(i==j ? 1.0 : 0.0);
1683: printf("Powell\n"); fprintf(ficlog,"Powell\n");
1684: strcpy(filerespow,"pow");
1685: strcat(filerespow,fileres);
1686: if((ficrespow=fopen(filerespow,"w"))==NULL) {
1687: printf("Problem with resultfile: %s\n", filerespow);
1688: fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
1689: }
1690: fprintf(ficrespow,"# Powell\n# iter -2*LL");
1691: for (i=1;i<=nlstate;i++)
1692: for(j=1;j<=nlstate+ndeath;j++)
1693: if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
1694: fprintf(ficrespow,"\n");
1695:
1696: powell(p,xi,npar,ftol,&iter,&fret,func);
1697:
1698: free_matrix(xi,1,npar,1,npar);
1699: fclose(ficrespow);
1700: printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));
1701: fprintf(ficlog,"\n#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
1702: fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
1703:
1704: }
1705:
1706: /**** Computes Hessian and covariance matrix ***/
1707: void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
1708: {
1709: double **a,**y,*x,pd;
1710: double **hess;
1711: int i, j,jk;
1712: int *indx;
1713:
1714: double hessii(double p[], double delta, int theta, double delti[],double (*func)(double []),int npar);
1715: double hessij(double p[], double delti[], int i, int j,double (*func)(double []),int npar);
1716: void lubksb(double **a, int npar, int *indx, double b[]) ;
1717: void ludcmp(double **a, int npar, int *indx, double *d) ;
1718: double gompertz(double p[]);
1719: hess=matrix(1,npar,1,npar);
1720:
1721: printf("\nCalculation of the hessian matrix. Wait...\n");
1722: fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
1723: for (i=1;i<=npar;i++){
1724: printf("%d",i);fflush(stdout);
1725: fprintf(ficlog,"%d",i);fflush(ficlog);
1726:
1727: hess[i][i]=hessii(p,ftolhess,i,delti,func,npar);
1728:
1729: /* printf(" %f ",p[i]);
1730: printf(" %lf %lf %lf",hess[i][i],ftolhess,delti[i]);*/
1731: }
1732:
1733: for (i=1;i<=npar;i++) {
1734: for (j=1;j<=npar;j++) {
1735: if (j>i) {
1736: printf(".%d%d",i,j);fflush(stdout);
1737: fprintf(ficlog,".%d%d",i,j);fflush(ficlog);
1738: hess[i][j]=hessij(p,delti,i,j,func,npar);
1739:
1740: hess[j][i]=hess[i][j];
1741: /*printf(" %lf ",hess[i][j]);*/
1742: }
1743: }
1744: }
1745: printf("\n");
1746: fprintf(ficlog,"\n");
1747:
1748: printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
1749: fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
1750:
1751: a=matrix(1,npar,1,npar);
1752: y=matrix(1,npar,1,npar);
1753: x=vector(1,npar);
1754: indx=ivector(1,npar);
1755: for (i=1;i<=npar;i++)
1756: for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
1757: ludcmp(a,npar,indx,&pd);
1758:
1759: for (j=1;j<=npar;j++) {
1760: for (i=1;i<=npar;i++) x[i]=0;
1761: x[j]=1;
1762: lubksb(a,npar,indx,x);
1763: for (i=1;i<=npar;i++){
1764: matcov[i][j]=x[i];
1765: }
1766: }
1767:
1768: printf("\n#Hessian matrix#\n");
1769: fprintf(ficlog,"\n#Hessian matrix#\n");
1770: for (i=1;i<=npar;i++) {
1771: for (j=1;j<=npar;j++) {
1772: printf("%.3e ",hess[i][j]);
1773: fprintf(ficlog,"%.3e ",hess[i][j]);
1774: }
1775: printf("\n");
1776: fprintf(ficlog,"\n");
1777: }
1778:
1779: /* Recompute Inverse */
1780: for (i=1;i<=npar;i++)
1781: for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];
1782: ludcmp(a,npar,indx,&pd);
1783:
1784: /* printf("\n#Hessian matrix recomputed#\n");
1785:
1786: for (j=1;j<=npar;j++) {
1787: for (i=1;i<=npar;i++) x[i]=0;
1788: x[j]=1;
1789: lubksb(a,npar,indx,x);
1790: for (i=1;i<=npar;i++){
1791: y[i][j]=x[i];
1792: printf("%.3e ",y[i][j]);
1793: fprintf(ficlog,"%.3e ",y[i][j]);
1794: }
1795: printf("\n");
1796: fprintf(ficlog,"\n");
1797: }
1798: */
1799:
1800: free_matrix(a,1,npar,1,npar);
1801: free_matrix(y,1,npar,1,npar);
1802: free_vector(x,1,npar);
1803: free_ivector(indx,1,npar);
1804: free_matrix(hess,1,npar,1,npar);
1805:
1806:
1807: }
1808:
1809: /*************** hessian matrix ****************/
1810: double hessii(double x[], double delta, int theta, double delti[], double (*func)(double []), int npar)
1811: {
1812: int i;
1813: int l=1, lmax=20;
1814: double k1,k2;
1815: double p2[NPARMAX+1];
1816: double res;
1817: double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4;
1818: double fx;
1819: int k=0,kmax=10;
1820: double l1;
1821:
1822: fx=func(x);
1823: for (i=1;i<=npar;i++) p2[i]=x[i];
1824: for(l=0 ; l <=lmax; l++){
1825: l1=pow(10,l);
1826: delts=delt;
1827: for(k=1 ; k <kmax; k=k+1){
1828: delt = delta*(l1*k);
1829: p2[theta]=x[theta] +delt;
1830: k1=func(p2)-fx;
1831: p2[theta]=x[theta]-delt;
1832: k2=func(p2)-fx;
1833: /*res= (k1-2.0*fx+k2)/delt/delt; */
1834: res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */
1835:
1836: #ifdef DEBUG
1837: 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);
1838: 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);
1839: #endif
1840: /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
1841: if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
1842: k=kmax;
1843: }
1844: else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
1845: k=kmax; l=lmax*10.;
1846: }
1847: else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){
1848: delts=delt;
1849: }
1850: }
1851: }
1852: delti[theta]=delts;
1853: return res;
1854:
1855: }
1856:
1857: double hessij( double x[], double delti[], int thetai,int thetaj,double (*func)(double []),int npar)
1858: {
1859: int i;
1860: int l=1, l1, lmax=20;
1861: double k1,k2,k3,k4,res,fx;
1862: double p2[NPARMAX+1];
1863: int k;
1864:
1865: fx=func(x);
1866: for (k=1; k<=2; k++) {
1867: for (i=1;i<=npar;i++) p2[i]=x[i];
1868: p2[thetai]=x[thetai]+delti[thetai]/k;
1869: p2[thetaj]=x[thetaj]+delti[thetaj]/k;
1870: k1=func(p2)-fx;
1871:
1872: p2[thetai]=x[thetai]+delti[thetai]/k;
1873: p2[thetaj]=x[thetaj]-delti[thetaj]/k;
1874: k2=func(p2)-fx;
1875:
1876: p2[thetai]=x[thetai]-delti[thetai]/k;
1877: p2[thetaj]=x[thetaj]+delti[thetaj]/k;
1878: k3=func(p2)-fx;
1879:
1880: p2[thetai]=x[thetai]-delti[thetai]/k;
1881: p2[thetaj]=x[thetaj]-delti[thetaj]/k;
1882: k4=func(p2)-fx;
1883: res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */
1884: #ifdef DEBUG
1885: 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);
1886: 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);
1887: #endif
1888: }
1889: return res;
1890: }
1891:
1892: /************** Inverse of matrix **************/
1893: void ludcmp(double **a, int n, int *indx, double *d)
1894: {
1895: int i,imax,j,k;
1896: double big,dum,sum,temp;
1897: double *vv;
1898:
1899: vv=vector(1,n);
1900: *d=1.0;
1901: for (i=1;i<=n;i++) {
1902: big=0.0;
1903: for (j=1;j<=n;j++)
1904: if ((temp=fabs(a[i][j])) > big) big=temp;
1905: if (big == 0.0) nrerror("Singular matrix in routine ludcmp");
1906: vv[i]=1.0/big;
1907: }
1908: for (j=1;j<=n;j++) {
1909: for (i=1;i<j;i++) {
1910: sum=a[i][j];
1911: for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];
1912: a[i][j]=sum;
1913: }
1914: big=0.0;
1915: for (i=j;i<=n;i++) {
1916: sum=a[i][j];
1917: for (k=1;k<j;k++)
1918: sum -= a[i][k]*a[k][j];
1919: a[i][j]=sum;
1920: if ( (dum=vv[i]*fabs(sum)) >= big) {
1921: big=dum;
1922: imax=i;
1923: }
1924: }
1925: if (j != imax) {
1926: for (k=1;k<=n;k++) {
1927: dum=a[imax][k];
1928: a[imax][k]=a[j][k];
1929: a[j][k]=dum;
1930: }
1931: *d = -(*d);
1932: vv[imax]=vv[j];
1933: }
1934: indx[j]=imax;
1935: if (a[j][j] == 0.0) a[j][j]=TINY;
1936: if (j != n) {
1937: dum=1.0/(a[j][j]);
1938: for (i=j+1;i<=n;i++) a[i][j] *= dum;
1939: }
1940: }
1941: free_vector(vv,1,n); /* Doesn't work */
1942: ;
1943: }
1944:
1945: void lubksb(double **a, int n, int *indx, double b[])
1946: {
1947: int i,ii=0,ip,j;
1948: double sum;
1949:
1950: for (i=1;i<=n;i++) {
1951: ip=indx[i];
1952: sum=b[ip];
1953: b[ip]=b[i];
1954: if (ii)
1955: for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];
1956: else if (sum) ii=i;
1957: b[i]=sum;
1958: }
1959: for (i=n;i>=1;i--) {
1960: sum=b[i];
1961: for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];
1962: b[i]=sum/a[i][i];
1963: }
1964: }
1965:
1966: void pstamp(FILE *fichier)
1967: {
1968: fprintf(fichier,"# %s.%s\n#%s\n#%s\n# %s", optionfilefiname,optionfilext,version,fullversion,strstart);
1969: }
1970:
1971: /************ Frequencies ********************/
1972: 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[])
1973: { /* Some frequencies */
1974:
1975: int i, m, jk, k1,i1, j1, bool, z1,z2,j;
1976: int first;
1977: double ***freq; /* Frequencies */
1978: double *pp, **prop;
1979: double pos,posprop, k2, dateintsum=0,k2cpt=0;
1980: char fileresp[FILENAMELENGTH];
1981:
1982: pp=vector(1,nlstate);
1983: prop=matrix(1,nlstate,iagemin,iagemax+3);
1984: strcpy(fileresp,"p");
1985: strcat(fileresp,fileres);
1986: if((ficresp=fopen(fileresp,"w"))==NULL) {
1987: printf("Problem with prevalence resultfile: %s\n", fileresp);
1988: fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
1989: exit(0);
1990: }
1991: freq= ma3x(-5,nlstate+ndeath,-5,nlstate+ndeath,iagemin,iagemax+3);
1992: j1=0;
1993:
1994: j=cptcoveff;
1995: if (cptcovn<1) {j=1;ncodemax[1]=1;}
1996:
1997: first=1;
1998:
1999: for(k1=1; k1<=j;k1++){
2000: for(i1=1; i1<=ncodemax[k1];i1++){
2001: j1++;
2002: /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
2003: scanf("%d", i);*/
2004: for (i=-5; i<=nlstate+ndeath; i++)
2005: for (jk=-5; jk<=nlstate+ndeath; jk++)
2006: for(m=iagemin; m <= iagemax+3; m++)
2007: freq[i][jk][m]=0;
2008:
2009: for (i=1; i<=nlstate; i++)
2010: for(m=iagemin; m <= iagemax+3; m++)
2011: prop[i][m]=0;
2012:
2013: dateintsum=0;
2014: k2cpt=0;
2015: for (i=1; i<=imx; i++) {
2016: bool=1;
2017: if (cptcovn>0) {
2018: for (z1=1; z1<=cptcoveff; z1++)
2019: if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])
2020: bool=0;
2021: }
2022: if (bool==1){
2023: for(m=firstpass; m<=lastpass; m++){
2024: k2=anint[m][i]+(mint[m][i]/12.);
2025: /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/
2026: if(agev[m][i]==0) agev[m][i]=iagemax+1;
2027: if(agev[m][i]==1) agev[m][i]=iagemax+2;
2028: if (s[m][i]>0 && s[m][i]<=nlstate) prop[s[m][i]][(int)agev[m][i]] += weight[i];
2029: if (m<lastpass) {
2030: freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
2031: freq[s[m][i]][s[m+1][i]][iagemax+3] += weight[i];
2032: }
2033:
2034: if ((agev[m][i]>1) && (agev[m][i]< (iagemax+3))) {
2035: dateintsum=dateintsum+k2;
2036: k2cpt++;
2037: }
2038: /*}*/
2039: }
2040: }
2041: }
2042:
2043: /* fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
2044: pstamp(ficresp);
2045: if (cptcovn>0) {
2046: fprintf(ficresp, "\n#********** Variable ");
2047: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
2048: fprintf(ficresp, "**********\n#");
2049: }
2050: for(i=1; i<=nlstate;i++)
2051: fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
2052: fprintf(ficresp, "\n");
2053:
2054: for(i=iagemin; i <= iagemax+3; i++){
2055: if(i==iagemax+3){
2056: fprintf(ficlog,"Total");
2057: }else{
2058: if(first==1){
2059: first=0;
2060: printf("See log file for details...\n");
2061: }
2062: fprintf(ficlog,"Age %d", i);
2063: }
2064: for(jk=1; jk <=nlstate ; jk++){
2065: for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
2066: pp[jk] += freq[jk][m][i];
2067: }
2068: for(jk=1; jk <=nlstate ; jk++){
2069: for(m=-1, pos=0; m <=0 ; m++)
2070: pos += freq[jk][m][i];
2071: if(pp[jk]>=1.e-10){
2072: if(first==1){
2073: printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
2074: }
2075: fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
2076: }else{
2077: if(first==1)
2078: printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
2079: fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
2080: }
2081: }
2082:
2083: for(jk=1; jk <=nlstate ; jk++){
2084: for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
2085: pp[jk] += freq[jk][m][i];
2086: }
2087: for(jk=1,pos=0,posprop=0; jk <=nlstate ; jk++){
2088: pos += pp[jk];
2089: posprop += prop[jk][i];
2090: }
2091: for(jk=1; jk <=nlstate ; jk++){
2092: if(pos>=1.e-5){
2093: if(first==1)
2094: printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
2095: fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
2096: }else{
2097: if(first==1)
2098: printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
2099: fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
2100: }
2101: if( i <= iagemax){
2102: if(pos>=1.e-5){
2103: fprintf(ficresp," %d %.5f %.0f %.0f",i,prop[jk][i]/posprop, prop[jk][i],posprop);
2104: /*probs[i][jk][j1]= pp[jk]/pos;*/
2105: /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/
2106: }
2107: else
2108: fprintf(ficresp," %d NaNq %.0f %.0f",i,prop[jk][i],posprop);
2109: }
2110: }
2111:
2112: for(jk=-1; jk <=nlstate+ndeath; jk++)
2113: for(m=-1; m <=nlstate+ndeath; m++)
2114: if(freq[jk][m][i] !=0 ) {
2115: if(first==1)
2116: printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
2117: fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
2118: }
2119: if(i <= iagemax)
2120: fprintf(ficresp,"\n");
2121: if(first==1)
2122: printf("Others in log...\n");
2123: fprintf(ficlog,"\n");
2124: }
2125: }
2126: }
2127: dateintmean=dateintsum/k2cpt;
2128:
2129: fclose(ficresp);
2130: free_ma3x(freq,-5,nlstate+ndeath,-5,nlstate+ndeath, iagemin, iagemax+3);
2131: free_vector(pp,1,nlstate);
2132: free_matrix(prop,1,nlstate,iagemin, iagemax+3);
2133: /* End of Freq */
2134: }
2135:
2136: /************ Prevalence ********************/
2137: 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)
2138: {
2139: /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
2140: in each health status at the date of interview (if between dateprev1 and dateprev2).
2141: We still use firstpass and lastpass as another selection.
2142: */
2143:
2144: int i, m, jk, k1, i1, j1, bool, z1,z2,j;
2145: double ***freq; /* Frequencies */
2146: double *pp, **prop;
2147: double pos,posprop;
2148: double y2; /* in fractional years */
2149: int iagemin, iagemax;
2150:
2151: iagemin= (int) agemin;
2152: iagemax= (int) agemax;
2153: /*pp=vector(1,nlstate);*/
2154: prop=matrix(1,nlstate,iagemin,iagemax+3);
2155: /* freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
2156: j1=0;
2157:
2158: j=cptcoveff;
2159: if (cptcovn<1) {j=1;ncodemax[1]=1;}
2160:
2161: for(k1=1; k1<=j;k1++){
2162: for(i1=1; i1<=ncodemax[k1];i1++){
2163: j1++;
2164:
2165: for (i=1; i<=nlstate; i++)
2166: for(m=iagemin; m <= iagemax+3; m++)
2167: prop[i][m]=0.0;
2168:
2169: for (i=1; i<=imx; i++) { /* Each individual */
2170: bool=1;
2171: if (cptcovn>0) {
2172: for (z1=1; z1<=cptcoveff; z1++)
2173: if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])
2174: bool=0;
2175: }
2176: if (bool==1) {
2177: for(m=firstpass; m<=lastpass; m++){/* Other selection (we can limit to certain interviews*/
2178: y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
2179: if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
2180: if(agev[m][i]==0) agev[m][i]=iagemax+1;
2181: if(agev[m][i]==1) agev[m][i]=iagemax+2;
2182: 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);
2183: if (s[m][i]>0 && s[m][i]<=nlstate) {
2184: /*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]]);*/
2185: prop[s[m][i]][(int)agev[m][i]] += weight[i];
2186: prop[s[m][i]][iagemax+3] += weight[i];
2187: }
2188: }
2189: } /* end selection of waves */
2190: }
2191: }
2192: for(i=iagemin; i <= iagemax+3; i++){
2193:
2194: for(jk=1,posprop=0; jk <=nlstate ; jk++) {
2195: posprop += prop[jk][i];
2196: }
2197:
2198: for(jk=1; jk <=nlstate ; jk++){
2199: if( i <= iagemax){
2200: if(posprop>=1.e-5){
2201: probs[i][jk][j1]= prop[jk][i]/posprop;
2202: }
2203: }
2204: }/* end jk */
2205: }/* end i */
2206: } /* end i1 */
2207: } /* end k1 */
2208:
2209: /* free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
2210: /*free_vector(pp,1,nlstate);*/
2211: free_matrix(prop,1,nlstate, iagemin,iagemax+3);
2212: } /* End of prevalence */
2213:
2214: /************* Waves Concatenation ***************/
2215:
2216: 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)
2217: {
2218: /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
2219: Death is a valid wave (if date is known).
2220: mw[mi][i] is the mi (mi=1 to wav[i]) effective wave of individual i
2221: dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
2222: and mw[mi+1][i]. dh depends on stepm.
2223: */
2224:
2225: int i, mi, m;
2226: /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
2227: double sum=0., jmean=0.;*/
2228: int first;
2229: int j, k=0,jk, ju, jl;
2230: double sum=0.;
2231: first=0;
2232: jmin=1e+5;
2233: jmax=-1;
2234: jmean=0.;
2235: for(i=1; i<=imx; i++){
2236: mi=0;
2237: m=firstpass;
2238: while(s[m][i] <= nlstate){
2239: if(s[m][i]>=1 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5)
2240: mw[++mi][i]=m;
2241: if(m >=lastpass)
2242: break;
2243: else
2244: m++;
2245: }/* end while */
2246: if (s[m][i] > nlstate){
2247: mi++; /* Death is another wave */
2248: /* if(mi==0) never been interviewed correctly before death */
2249: /* Only death is a correct wave */
2250: mw[mi][i]=m;
2251: }
2252:
2253: wav[i]=mi;
2254: if(mi==0){
2255: nbwarn++;
2256: if(first==0){
2257: printf("Warning! No valid information for individual %ld line=%d (skipped) and may be others, see log file\n",num[i],i);
2258: first=1;
2259: }
2260: if(first==1){
2261: fprintf(ficlog,"Warning! No valid information for individual %ld line=%d (skipped)\n",num[i],i);
2262: }
2263: } /* end mi==0 */
2264: } /* End individuals */
2265:
2266: for(i=1; i<=imx; i++){
2267: for(mi=1; mi<wav[i];mi++){
2268: if (stepm <=0)
2269: dh[mi][i]=1;
2270: else{
2271: if (s[mw[mi+1][i]][i] > nlstate) { /* A death */
2272: if (agedc[i] < 2*AGESUP) {
2273: j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);
2274: if(j==0) j=1; /* Survives at least one month after exam */
2275: else if(j<0){
2276: nberr++;
2277: 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]);
2278: j=1; /* Temporary Dangerous patch */
2279: 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);
2280: 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]);
2281: 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);
2282: }
2283: k=k+1;
2284: if (j >= jmax){
2285: jmax=j;
2286: ijmax=i;
2287: }
2288: if (j <= jmin){
2289: jmin=j;
2290: ijmin=i;
2291: }
2292: sum=sum+j;
2293: /*if (j<0) printf("j=%d num=%d \n",j,i);*/
2294: /* printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
2295: }
2296: }
2297: else{
2298: j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
2299: /* 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]); */
2300:
2301: k=k+1;
2302: if (j >= jmax) {
2303: jmax=j;
2304: ijmax=i;
2305: }
2306: else if (j <= jmin){
2307: jmin=j;
2308: ijmin=i;
2309: }
2310: /* if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
2311: /*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]);*/
2312: if(j<0){
2313: nberr++;
2314: 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]);
2315: 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]);
2316: }
2317: sum=sum+j;
2318: }
2319: jk= j/stepm;
2320: jl= j -jk*stepm;
2321: ju= j -(jk+1)*stepm;
2322: if(mle <=1){ /* only if we use a the linear-interpoloation pseudo-likelihood */
2323: if(jl==0){
2324: dh[mi][i]=jk;
2325: bh[mi][i]=0;
2326: }else{ /* We want a negative bias in order to only have interpolation ie
2327: * at the price of an extra matrix product in likelihood */
2328: dh[mi][i]=jk+1;
2329: bh[mi][i]=ju;
2330: }
2331: }else{
2332: if(jl <= -ju){
2333: dh[mi][i]=jk;
2334: bh[mi][i]=jl; /* bias is positive if real duration
2335: * is higher than the multiple of stepm and negative otherwise.
2336: */
2337: }
2338: else{
2339: dh[mi][i]=jk+1;
2340: bh[mi][i]=ju;
2341: }
2342: if(dh[mi][i]==0){
2343: dh[mi][i]=1; /* At least one step */
2344: bh[mi][i]=ju; /* At least one step */
2345: /* 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);*/
2346: }
2347: } /* end if mle */
2348: }
2349: } /* end wave */
2350: }
2351: jmean=sum/k;
2352: 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);
2353: fprintf(ficlog,"Delay (in months) between two waves Min=%d (for indiviudal %ld) Max=%d (%ld) Mean=%f\n\n ",jmin, ijmin, jmax, ijmax, jmean);
2354: }
2355:
2356: /*********** Tricode ****************************/
2357: void tricode(int *Tvar, int **nbcode, int imx)
2358: {
2359:
2360: int Ndum[20],ij=1, k, j, i, maxncov=19;
2361: int cptcode=0;
2362: cptcoveff=0;
2363:
2364: for (k=0; k<maxncov; k++) Ndum[k]=0;
2365: for (k=1; k<=7; k++) ncodemax[k]=0;
2366:
2367: for (j=1; j<=(cptcovn+2*cptcovprod); j++) {
2368: for (i=1; i<=imx; i++) { /*reads the data file to get the maximum
2369: modality*/
2370: ij=(int)(covar[Tvar[j]][i]); /* ij is the modality of this individual*/
2371: Ndum[ij]++; /*store the modality */
2372: /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
2373: if (ij > cptcode) cptcode=ij; /* getting the maximum of covariable
2374: Tvar[j]. If V=sex and male is 0 and
2375: female is 1, then cptcode=1.*/
2376: }
2377:
2378: for (i=0; i<=cptcode; i++) {
2379: if(Ndum[i]!=0) ncodemax[j]++; /* Nomber of modalities of the j th covariates. In fact ncodemax[j]=2 (dichotom. variables) but it can be more */
2380: }
2381:
2382: ij=1;
2383: for (i=1; i<=ncodemax[j]; i++) {
2384: for (k=0; k<= maxncov; k++) {
2385: if (Ndum[k] != 0) {
2386: nbcode[Tvar[j]][ij]=k;
2387: /* store the modality in an array. k is a modality. If we have model=V1+V1*sex then: nbcode[1][1]=0 ; nbcode[1][2]=1; nbcode[2][1]=0 ; nbcode[2][2]=1; */
2388:
2389: ij++;
2390: }
2391: if (ij > ncodemax[j]) break;
2392: }
2393: }
2394: }
2395:
2396: for (k=0; k< maxncov; k++) Ndum[k]=0;
2397:
2398: for (i=1; i<=ncovmodel-2; i++) {
2399: /* Listing of all covariables in statement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/
2400: ij=Tvar[i];
2401: Ndum[ij]++;
2402: }
2403:
2404: ij=1;
2405: for (i=1; i<= maxncov; i++) {
2406: if((Ndum[i]!=0) && (i<=ncovcol)){
2407: Tvaraff[ij]=i; /*For printing */
2408: ij++;
2409: }
2410: }
2411:
2412: cptcoveff=ij-1; /*Number of simple covariates*/
2413: }
2414:
2415: /*********** Health Expectancies ****************/
2416:
2417: void evsij(char fileres[], double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int cij, int estepm,char strstart[] )
2418:
2419: {
2420: /* Health expectancies, no variances */
2421: int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2;
2422: double age, agelim, hf;
2423: double ***p3mat;
2424: double eip;
2425:
2426: pstamp(ficreseij);
2427: fprintf(ficreseij,"# (a) Life expectancies by health status at initial age and (b) health expectancies by health status at initial age\n");
2428: fprintf(ficreseij,"# Age");
2429: for(i=1; i<=nlstate;i++){
2430: for(j=1; j<=nlstate;j++){
2431: fprintf(ficreseij," e%1d%1d ",i,j);
2432: }
2433: fprintf(ficreseij," e%1d. ",i);
2434: }
2435: fprintf(ficreseij,"\n");
2436:
2437:
2438: if(estepm < stepm){
2439: printf ("Problem %d lower than %d\n",estepm, stepm);
2440: }
2441: else hstepm=estepm;
2442: /* We compute the life expectancy from trapezoids spaced every estepm months
2443: * This is mainly to measure the difference between two models: for example
2444: * if stepm=24 months pijx are given only every 2 years and by summing them
2445: * we are calculating an estimate of the Life Expectancy assuming a linear
2446: * progression in between and thus overestimating or underestimating according
2447: * to the curvature of the survival function. If, for the same date, we
2448: * estimate the model with stepm=1 month, we can keep estepm to 24 months
2449: * to compare the new estimate of Life expectancy with the same linear
2450: * hypothesis. A more precise result, taking into account a more precise
2451: * curvature will be obtained if estepm is as small as stepm. */
2452:
2453: /* For example we decided to compute the life expectancy with the smallest unit */
2454: /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
2455: nhstepm is the number of hstepm from age to agelim
2456: nstepm is the number of stepm from age to agelin.
2457: Look at hpijx to understand the reason of that which relies in memory size
2458: and note for a fixed period like estepm months */
2459: /* We decided (b) to get a life expectancy respecting the most precise curvature of the
2460: survival function given by stepm (the optimization length). Unfortunately it
2461: means that if the survival funtion is printed only each two years of age and if
2462: you sum them up and add 1 year (area under the trapezoids) you won't get the same
2463: results. So we changed our mind and took the option of the best precision.
2464: */
2465: hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
2466:
2467: agelim=AGESUP;
2468: /* nhstepm age range expressed in number of stepm */
2469: nstepm=(int) rint((agelim-age)*YEARM/stepm);
2470: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
2471: /* if (stepm >= YEARM) hstepm=1;*/
2472: nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
2473: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
2474:
2475: for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
2476: /* Computed by stepm unit matrices, product of hstepm matrices, stored
2477: in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
2478:
2479: hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, cij);
2480:
2481: hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
2482:
2483: /* Computing Variances of health expectancies */
2484: /* Gradient is computed with plus gp and minus gm. Code is duplicated in order to
2485: decrease memory allocation */
2486: printf("%d|",(int)age);fflush(stdout);
2487: fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
2488: /* Computing expectancies */
2489: for(i=1; i<=nlstate;i++)
2490: for(j=1; j<=nlstate;j++)
2491: for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
2492: eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
2493:
2494: /* 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]);*/
2495:
2496: }
2497:
2498: fprintf(ficreseij,"%3.0f",age );
2499: for(i=1; i<=nlstate;i++){
2500: eip=0;
2501: for(j=1; j<=nlstate;j++){
2502: eip +=eij[i][j][(int)age];
2503: fprintf(ficreseij,"%9.4f", eij[i][j][(int)age] );
2504: }
2505: fprintf(ficreseij,"%9.4f", eip );
2506: }
2507: fprintf(ficreseij,"\n");
2508:
2509: }
2510: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
2511: printf("\n");
2512: fprintf(ficlog,"\n");
2513:
2514: }
2515:
2516: void cvevsij(char fileres[], 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[] )
2517:
2518: {
2519: /* Covariances of health expectancies eij and of total life expectancies according
2520: to initial status i, ei. .
2521: */
2522: int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2, ij, ji;
2523: double age, agelim, hf;
2524: double ***p3matp, ***p3matm, ***varhe;
2525: double **dnewm,**doldm;
2526: double *xp, *xm;
2527: double **gp, **gm;
2528: double ***gradg, ***trgradg;
2529: int theta;
2530:
2531: double eip, vip;
2532:
2533: varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage);
2534: xp=vector(1,npar);
2535: xm=vector(1,npar);
2536: dnewm=matrix(1,nlstate*nlstate,1,npar);
2537: doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate);
2538:
2539: pstamp(ficresstdeij);
2540: fprintf(ficresstdeij,"# Health expectancies with standard errors\n");
2541: fprintf(ficresstdeij,"# Age");
2542: for(i=1; i<=nlstate;i++){
2543: for(j=1; j<=nlstate;j++)
2544: fprintf(ficresstdeij," e%1d%1d (SE)",i,j);
2545: fprintf(ficresstdeij," e%1d. ",i);
2546: }
2547: fprintf(ficresstdeij,"\n");
2548:
2549: pstamp(ficrescveij);
2550: fprintf(ficrescveij,"# Subdiagonal matrix of covariances of health expectancies by age: cov(eij,ekl)\n");
2551: fprintf(ficrescveij,"# Age");
2552: for(i=1; i<=nlstate;i++)
2553: for(j=1; j<=nlstate;j++){
2554: cptj= (j-1)*nlstate+i;
2555: for(i2=1; i2<=nlstate;i2++)
2556: for(j2=1; j2<=nlstate;j2++){
2557: cptj2= (j2-1)*nlstate+i2;
2558: if(cptj2 <= cptj)
2559: fprintf(ficrescveij," %1d%1d,%1d%1d",i,j,i2,j2);
2560: }
2561: }
2562: fprintf(ficrescveij,"\n");
2563:
2564: if(estepm < stepm){
2565: printf ("Problem %d lower than %d\n",estepm, stepm);
2566: }
2567: else hstepm=estepm;
2568: /* We compute the life expectancy from trapezoids spaced every estepm months
2569: * This is mainly to measure the difference between two models: for example
2570: * if stepm=24 months pijx are given only every 2 years and by summing them
2571: * we are calculating an estimate of the Life Expectancy assuming a linear
2572: * progression in between and thus overestimating or underestimating according
2573: * to the curvature of the survival function. If, for the same date, we
2574: * estimate the model with stepm=1 month, we can keep estepm to 24 months
2575: * to compare the new estimate of Life expectancy with the same linear
2576: * hypothesis. A more precise result, taking into account a more precise
2577: * curvature will be obtained if estepm is as small as stepm. */
2578:
2579: /* For example we decided to compute the life expectancy with the smallest unit */
2580: /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
2581: nhstepm is the number of hstepm from age to agelim
2582: nstepm is the number of stepm from age to agelin.
2583: Look at hpijx to understand the reason of that which relies in memory size
2584: and note for a fixed period like estepm months */
2585: /* We decided (b) to get a life expectancy respecting the most precise curvature of the
2586: survival function given by stepm (the optimization length). Unfortunately it
2587: means that if the survival funtion is printed only each two years of age and if
2588: you sum them up and add 1 year (area under the trapezoids) you won't get the same
2589: results. So we changed our mind and took the option of the best precision.
2590: */
2591: hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
2592:
2593: /* If stepm=6 months */
2594: /* nhstepm age range expressed in number of stepm */
2595: agelim=AGESUP;
2596: nstepm=(int) rint((agelim-age)*YEARM/stepm);
2597: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
2598: /* if (stepm >= YEARM) hstepm=1;*/
2599: nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
2600:
2601: p3matp=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
2602: p3matm=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
2603: gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);
2604: trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar);
2605: gp=matrix(0,nhstepm,1,nlstate*nlstate);
2606: gm=matrix(0,nhstepm,1,nlstate*nlstate);
2607:
2608: for (age=bage; age<=fage; age ++){
2609:
2610: /* Computed by stepm unit matrices, product of hstepm matrices, stored
2611: in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
2612:
2613: hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
2614:
2615: /* Computing Variances of health expectancies */
2616: /* Gradient is computed with plus gp and minus gm. Code is duplicated in order to
2617: decrease memory allocation */
2618: for(theta=1; theta <=npar; theta++){
2619: for(i=1; i<=npar; i++){
2620: xp[i] = x[i] + (i==theta ?delti[theta]:0);
2621: xm[i] = x[i] - (i==theta ?delti[theta]:0);
2622: }
2623: hpxij(p3matp,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, cij);
2624: hpxij(p3matm,nhstepm,age,hstepm,xm,nlstate,stepm,oldm,savm, cij);
2625:
2626: for(j=1; j<= nlstate; j++){
2627: for(i=1; i<=nlstate; i++){
2628: for(h=0; h<=nhstepm-1; h++){
2629: gp[h][(j-1)*nlstate + i] = (p3matp[i][j][h]+p3matp[i][j][h+1])/2.;
2630: gm[h][(j-1)*nlstate + i] = (p3matm[i][j][h]+p3matm[i][j][h+1])/2.;
2631: }
2632: }
2633: }
2634:
2635: for(ij=1; ij<= nlstate*nlstate; ij++)
2636: for(h=0; h<=nhstepm-1; h++){
2637: gradg[h][theta][ij]= (gp[h][ij]-gm[h][ij])/2./delti[theta];
2638: }
2639: }/* End theta */
2640:
2641:
2642: for(h=0; h<=nhstepm-1; h++)
2643: for(j=1; j<=nlstate*nlstate;j++)
2644: for(theta=1; theta <=npar; theta++)
2645: trgradg[h][j][theta]=gradg[h][theta][j];
2646:
2647:
2648: for(ij=1;ij<=nlstate*nlstate;ij++)
2649: for(ji=1;ji<=nlstate*nlstate;ji++)
2650: varhe[ij][ji][(int)age] =0.;
2651:
2652: printf("%d|",(int)age);fflush(stdout);
2653: fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
2654: for(h=0;h<=nhstepm-1;h++){
2655: for(k=0;k<=nhstepm-1;k++){
2656: matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov);
2657: matprod2(doldm,dnewm,1,nlstate*nlstate,1,npar,1,nlstate*nlstate,gradg[k]);
2658: for(ij=1;ij<=nlstate*nlstate;ij++)
2659: for(ji=1;ji<=nlstate*nlstate;ji++)
2660: varhe[ij][ji][(int)age] += doldm[ij][ji]*hf*hf;
2661: }
2662: }
2663: /* Computing expectancies */
2664: hpxij(p3matm,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, cij);
2665: for(i=1; i<=nlstate;i++)
2666: for(j=1; j<=nlstate;j++)
2667: for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
2668: eij[i][j][(int)age] += (p3matm[i][j][h]+p3matm[i][j][h+1])/2.0*hf;
2669:
2670: /* 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]);*/
2671:
2672: }
2673:
2674: fprintf(ficresstdeij,"%3.0f",age );
2675: for(i=1; i<=nlstate;i++){
2676: eip=0.;
2677: vip=0.;
2678: for(j=1; j<=nlstate;j++){
2679: eip += eij[i][j][(int)age];
2680: for(k=1; k<=nlstate;k++) /* Sum on j and k of cov(eij,eik) */
2681: vip += varhe[(j-1)*nlstate+i][(k-1)*nlstate+i][(int)age];
2682: fprintf(ficresstdeij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[(j-1)*nlstate+i][(j-1)*nlstate+i][(int)age]) );
2683: }
2684: fprintf(ficresstdeij," %9.4f (%.4f)", eip, sqrt(vip));
2685: }
2686: fprintf(ficresstdeij,"\n");
2687:
2688: fprintf(ficrescveij,"%3.0f",age );
2689: for(i=1; i<=nlstate;i++)
2690: for(j=1; j<=nlstate;j++){
2691: cptj= (j-1)*nlstate+i;
2692: for(i2=1; i2<=nlstate;i2++)
2693: for(j2=1; j2<=nlstate;j2++){
2694: cptj2= (j2-1)*nlstate+i2;
2695: if(cptj2 <= cptj)
2696: fprintf(ficrescveij," %.4f", varhe[cptj][cptj2][(int)age]);
2697: }
2698: }
2699: fprintf(ficrescveij,"\n");
2700:
2701: }
2702: free_matrix(gm,0,nhstepm,1,nlstate*nlstate);
2703: free_matrix(gp,0,nhstepm,1,nlstate*nlstate);
2704: free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*nlstate);
2705: free_ma3x(trgradg,0,nhstepm,1,nlstate*nlstate,1,npar);
2706: free_ma3x(p3matm,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
2707: free_ma3x(p3matp,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
2708: printf("\n");
2709: fprintf(ficlog,"\n");
2710:
2711: free_vector(xm,1,npar);
2712: free_vector(xp,1,npar);
2713: free_matrix(dnewm,1,nlstate*nlstate,1,npar);
2714: free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate);
2715: free_ma3x(varhe,1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int)fage);
2716: }
2717:
2718: /************ Variance ******************/
2719: 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[])
2720: {
2721: /* Variance of health expectancies */
2722: /* double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
2723: /* double **newm;*/
2724: double **dnewm,**doldm;
2725: double **dnewmp,**doldmp;
2726: int i, j, nhstepm, hstepm, h, nstepm ;
2727: int k, cptcode;
2728: double *xp;
2729: double **gp, **gm; /* for var eij */
2730: double ***gradg, ***trgradg; /*for var eij */
2731: double **gradgp, **trgradgp; /* for var p point j */
2732: double *gpp, *gmp; /* for var p point j */
2733: double **varppt; /* for var p point j nlstate to nlstate+ndeath */
2734: double ***p3mat;
2735: double age,agelim, hf;
2736: double ***mobaverage;
2737: int theta;
2738: char digit[4];
2739: char digitp[25];
2740:
2741: char fileresprobmorprev[FILENAMELENGTH];
2742:
2743: if(popbased==1){
2744: if(mobilav!=0)
2745: strcpy(digitp,"-populbased-mobilav-");
2746: else strcpy(digitp,"-populbased-nomobil-");
2747: }
2748: else
2749: strcpy(digitp,"-stablbased-");
2750:
2751: if (mobilav!=0) {
2752: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
2753: if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
2754: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
2755: printf(" Error in movingaverage mobilav=%d\n",mobilav);
2756: }
2757: }
2758:
2759: strcpy(fileresprobmorprev,"prmorprev");
2760: sprintf(digit,"%-d",ij);
2761: /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
2762: strcat(fileresprobmorprev,digit); /* Tvar to be done */
2763: strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
2764: strcat(fileresprobmorprev,fileres);
2765: if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
2766: printf("Problem with resultfile: %s\n", fileresprobmorprev);
2767: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
2768: }
2769: printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
2770:
2771: fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
2772: pstamp(ficresprobmorprev);
2773: 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);
2774: fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
2775: for(j=nlstate+1; j<=(nlstate+ndeath);j++){
2776: fprintf(ficresprobmorprev," p.%-d SE",j);
2777: for(i=1; i<=nlstate;i++)
2778: fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
2779: }
2780: fprintf(ficresprobmorprev,"\n");
2781: fprintf(ficgp,"\n# Routine varevsij");
2782: /* fprintf(fichtm, "#Local time at start: %s", strstart);*/
2783: 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");
2784: fprintf(fichtm,"\n<br>%s <br>\n",digitp);
2785: /* } */
2786: varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
2787: pstamp(ficresvij);
2788: fprintf(ficresvij,"# Variance and covariance of health expectancies e.j \n# (weighted average of eij where weights are ");
2789: if(popbased==1)
2790: fprintf(ficresvij,"the age specific prevalence observed in the population i.e cross-sectionally\n in each health state (popbased=1)");
2791: else
2792: fprintf(ficresvij,"the age specific period (stable) prevalences in each health state \n");
2793: fprintf(ficresvij,"# Age");
2794: for(i=1; i<=nlstate;i++)
2795: for(j=1; j<=nlstate;j++)
2796: fprintf(ficresvij," Cov(e.%1d, e.%1d)",i,j);
2797: fprintf(ficresvij,"\n");
2798:
2799: xp=vector(1,npar);
2800: dnewm=matrix(1,nlstate,1,npar);
2801: doldm=matrix(1,nlstate,1,nlstate);
2802: dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
2803: doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
2804:
2805: gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
2806: gpp=vector(nlstate+1,nlstate+ndeath);
2807: gmp=vector(nlstate+1,nlstate+ndeath);
2808: trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
2809:
2810: if(estepm < stepm){
2811: printf ("Problem %d lower than %d\n",estepm, stepm);
2812: }
2813: else hstepm=estepm;
2814: /* For example we decided to compute the life expectancy with the smallest unit */
2815: /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
2816: nhstepm is the number of hstepm from age to agelim
2817: nstepm is the number of stepm from age to agelin.
2818: Look at hpijx to understand the reason of that which relies in memory size
2819: and note for a fixed period like k years */
2820: /* We decided (b) to get a life expectancy respecting the most precise curvature of the
2821: survival function given by stepm (the optimization length). Unfortunately it
2822: means that if the survival funtion is printed every two years of age and if
2823: you sum them up and add 1 year (area under the trapezoids) you won't get the same
2824: results. So we changed our mind and took the option of the best precision.
2825: */
2826: hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
2827: agelim = AGESUP;
2828: for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
2829: nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
2830: nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
2831: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
2832: gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
2833: gp=matrix(0,nhstepm,1,nlstate);
2834: gm=matrix(0,nhstepm,1,nlstate);
2835:
2836:
2837: for(theta=1; theta <=npar; theta++){
2838: for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
2839: xp[i] = x[i] + (i==theta ?delti[theta]:0);
2840: }
2841: hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
2842: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
2843:
2844: if (popbased==1) {
2845: if(mobilav ==0){
2846: for(i=1; i<=nlstate;i++)
2847: prlim[i][i]=probs[(int)age][i][ij];
2848: }else{ /* mobilav */
2849: for(i=1; i<=nlstate;i++)
2850: prlim[i][i]=mobaverage[(int)age][i][ij];
2851: }
2852: }
2853:
2854: for(j=1; j<= nlstate; j++){
2855: for(h=0; h<=nhstepm; h++){
2856: for(i=1, gp[h][j]=0.;i<=nlstate;i++)
2857: gp[h][j] += prlim[i][i]*p3mat[i][j][h];
2858: }
2859: }
2860: /* This for computing probability of death (h=1 means
2861: computed over hstepm matrices product = hstepm*stepm months)
2862: as a weighted average of prlim.
2863: */
2864: for(j=nlstate+1;j<=nlstate+ndeath;j++){
2865: for(i=1,gpp[j]=0.; i<= nlstate; i++)
2866: gpp[j] += prlim[i][i]*p3mat[i][j][1];
2867: }
2868: /* end probability of death */
2869:
2870: for(i=1; i<=npar; i++) /* Computes gradient x - delta */
2871: xp[i] = x[i] - (i==theta ?delti[theta]:0);
2872: hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
2873: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
2874:
2875: if (popbased==1) {
2876: if(mobilav ==0){
2877: for(i=1; i<=nlstate;i++)
2878: prlim[i][i]=probs[(int)age][i][ij];
2879: }else{ /* mobilav */
2880: for(i=1; i<=nlstate;i++)
2881: prlim[i][i]=mobaverage[(int)age][i][ij];
2882: }
2883: }
2884:
2885: for(j=1; j<= nlstate; j++){
2886: for(h=0; h<=nhstepm; h++){
2887: for(i=1, gm[h][j]=0.;i<=nlstate;i++)
2888: gm[h][j] += prlim[i][i]*p3mat[i][j][h];
2889: }
2890: }
2891: /* This for computing probability of death (h=1 means
2892: computed over hstepm matrices product = hstepm*stepm months)
2893: as a weighted average of prlim.
2894: */
2895: for(j=nlstate+1;j<=nlstate+ndeath;j++){
2896: for(i=1,gmp[j]=0.; i<= nlstate; i++)
2897: gmp[j] += prlim[i][i]*p3mat[i][j][1];
2898: }
2899: /* end probability of death */
2900:
2901: for(j=1; j<= nlstate; j++) /* vareij */
2902: for(h=0; h<=nhstepm; h++){
2903: gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
2904: }
2905:
2906: for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
2907: gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
2908: }
2909:
2910: } /* End theta */
2911:
2912: trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
2913:
2914: for(h=0; h<=nhstepm; h++) /* veij */
2915: for(j=1; j<=nlstate;j++)
2916: for(theta=1; theta <=npar; theta++)
2917: trgradg[h][j][theta]=gradg[h][theta][j];
2918:
2919: for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
2920: for(theta=1; theta <=npar; theta++)
2921: trgradgp[j][theta]=gradgp[theta][j];
2922:
2923:
2924: hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
2925: for(i=1;i<=nlstate;i++)
2926: for(j=1;j<=nlstate;j++)
2927: vareij[i][j][(int)age] =0.;
2928:
2929: for(h=0;h<=nhstepm;h++){
2930: for(k=0;k<=nhstepm;k++){
2931: matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
2932: matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
2933: for(i=1;i<=nlstate;i++)
2934: for(j=1;j<=nlstate;j++)
2935: vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
2936: }
2937: }
2938:
2939: /* pptj */
2940: matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
2941: matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
2942: for(j=nlstate+1;j<=nlstate+ndeath;j++)
2943: for(i=nlstate+1;i<=nlstate+ndeath;i++)
2944: varppt[j][i]=doldmp[j][i];
2945: /* end ppptj */
2946: /* x centered again */
2947: hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);
2948: prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);
2949:
2950: if (popbased==1) {
2951: if(mobilav ==0){
2952: for(i=1; i<=nlstate;i++)
2953: prlim[i][i]=probs[(int)age][i][ij];
2954: }else{ /* mobilav */
2955: for(i=1; i<=nlstate;i++)
2956: prlim[i][i]=mobaverage[(int)age][i][ij];
2957: }
2958: }
2959:
2960: /* This for computing probability of death (h=1 means
2961: computed over hstepm (estepm) matrices product = hstepm*stepm months)
2962: as a weighted average of prlim.
2963: */
2964: for(j=nlstate+1;j<=nlstate+ndeath;j++){
2965: for(i=1,gmp[j]=0.;i<= nlstate; i++)
2966: gmp[j] += prlim[i][i]*p3mat[i][j][1];
2967: }
2968: /* end probability of death */
2969:
2970: fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
2971: for(j=nlstate+1; j<=(nlstate+ndeath);j++){
2972: fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
2973: for(i=1; i<=nlstate;i++){
2974: fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
2975: }
2976: }
2977: fprintf(ficresprobmorprev,"\n");
2978:
2979: fprintf(ficresvij,"%.0f ",age );
2980: for(i=1; i<=nlstate;i++)
2981: for(j=1; j<=nlstate;j++){
2982: fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
2983: }
2984: fprintf(ficresvij,"\n");
2985: free_matrix(gp,0,nhstepm,1,nlstate);
2986: free_matrix(gm,0,nhstepm,1,nlstate);
2987: free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
2988: free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
2989: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
2990: } /* End age */
2991: free_vector(gpp,nlstate+1,nlstate+ndeath);
2992: free_vector(gmp,nlstate+1,nlstate+ndeath);
2993: free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
2994: free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
2995: fprintf(ficgp,"\nset noparametric;set nolabel; set ter png small;set size 0.65, 0.65");
2996: /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */
2997: fprintf(ficgp,"\n set log y; set nolog x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
2998: /* fprintf(ficgp,"\n plot \"%s\" u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm); */
2999: /* fprintf(ficgp,"\n replot \"%s\" u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm); */
3000: /* fprintf(ficgp,"\n replot \"%s\" u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm); */
3001: fprintf(ficgp,"\n plot \"%s\" u 1:($3) not w l 1 ",subdirf(fileresprobmorprev));
3002: fprintf(ficgp,"\n replot \"%s\" u 1:(($3+1.96*$4)) t \"95\%% interval\" w l 2 ",subdirf(fileresprobmorprev));
3003: fprintf(ficgp,"\n replot \"%s\" u 1:(($3-1.96*$4)) not w l 2 ",subdirf(fileresprobmorprev));
3004: fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",subdirf(fileresprobmorprev),subdirf(fileresprobmorprev));
3005: 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);
3006: /* 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);
3007: */
3008: /* fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.png\";replot;",digitp,optionfilefiname,digit); */
3009: fprintf(ficgp,"\nset out \"%s%s.png\";replot;\n",subdirf3(optionfilefiname,"varmuptjgr",digitp),digit);
3010:
3011: free_vector(xp,1,npar);
3012: free_matrix(doldm,1,nlstate,1,nlstate);
3013: free_matrix(dnewm,1,nlstate,1,npar);
3014: free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
3015: free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
3016: free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
3017: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
3018: fclose(ficresprobmorprev);
3019: fflush(ficgp);
3020: fflush(fichtm);
3021: } /* end varevsij */
3022:
3023: /************ Variance of prevlim ******************/
3024: 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[])
3025: {
3026: /* Variance of prevalence limit */
3027: /* double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
3028: double **newm;
3029: double **dnewm,**doldm;
3030: int i, j, nhstepm, hstepm;
3031: int k, cptcode;
3032: double *xp;
3033: double *gp, *gm;
3034: double **gradg, **trgradg;
3035: double age,agelim;
3036: int theta;
3037:
3038: pstamp(ficresvpl);
3039: fprintf(ficresvpl,"# Standard deviation of period (stable) prevalences \n");
3040: fprintf(ficresvpl,"# Age");
3041: for(i=1; i<=nlstate;i++)
3042: fprintf(ficresvpl," %1d-%1d",i,i);
3043: fprintf(ficresvpl,"\n");
3044:
3045: xp=vector(1,npar);
3046: dnewm=matrix(1,nlstate,1,npar);
3047: doldm=matrix(1,nlstate,1,nlstate);
3048:
3049: hstepm=1*YEARM; /* Every year of age */
3050: hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */
3051: agelim = AGESUP;
3052: for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
3053: nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
3054: if (stepm >= YEARM) hstepm=1;
3055: nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
3056: gradg=matrix(1,npar,1,nlstate);
3057: gp=vector(1,nlstate);
3058: gm=vector(1,nlstate);
3059:
3060: for(theta=1; theta <=npar; theta++){
3061: for(i=1; i<=npar; i++){ /* Computes gradient */
3062: xp[i] = x[i] + (i==theta ?delti[theta]:0);
3063: }
3064: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
3065: for(i=1;i<=nlstate;i++)
3066: gp[i] = prlim[i][i];
3067:
3068: for(i=1; i<=npar; i++) /* Computes gradient */
3069: xp[i] = x[i] - (i==theta ?delti[theta]:0);
3070: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
3071: for(i=1;i<=nlstate;i++)
3072: gm[i] = prlim[i][i];
3073:
3074: for(i=1;i<=nlstate;i++)
3075: gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
3076: } /* End theta */
3077:
3078: trgradg =matrix(1,nlstate,1,npar);
3079:
3080: for(j=1; j<=nlstate;j++)
3081: for(theta=1; theta <=npar; theta++)
3082: trgradg[j][theta]=gradg[theta][j];
3083:
3084: for(i=1;i<=nlstate;i++)
3085: varpl[i][(int)age] =0.;
3086: matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
3087: matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
3088: for(i=1;i<=nlstate;i++)
3089: varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
3090:
3091: fprintf(ficresvpl,"%.0f ",age );
3092: for(i=1; i<=nlstate;i++)
3093: fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
3094: fprintf(ficresvpl,"\n");
3095: free_vector(gp,1,nlstate);
3096: free_vector(gm,1,nlstate);
3097: free_matrix(gradg,1,npar,1,nlstate);
3098: free_matrix(trgradg,1,nlstate,1,npar);
3099: } /* End age */
3100:
3101: free_vector(xp,1,npar);
3102: free_matrix(doldm,1,nlstate,1,npar);
3103: free_matrix(dnewm,1,nlstate,1,nlstate);
3104:
3105: }
3106:
3107: /************ Variance of one-step probabilities ******************/
3108: 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[])
3109: {
3110: int i, j=0, i1, k1, l1, t, tj;
3111: int k2, l2, j1, z1;
3112: int k=0,l, cptcode;
3113: int first=1, first1;
3114: double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
3115: double **dnewm,**doldm;
3116: double *xp;
3117: double *gp, *gm;
3118: double **gradg, **trgradg;
3119: double **mu;
3120: double age,agelim, cov[NCOVMAX];
3121: double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
3122: int theta;
3123: char fileresprob[FILENAMELENGTH];
3124: char fileresprobcov[FILENAMELENGTH];
3125: char fileresprobcor[FILENAMELENGTH];
3126:
3127: double ***varpij;
3128:
3129: strcpy(fileresprob,"prob");
3130: strcat(fileresprob,fileres);
3131: if((ficresprob=fopen(fileresprob,"w"))==NULL) {
3132: printf("Problem with resultfile: %s\n", fileresprob);
3133: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
3134: }
3135: strcpy(fileresprobcov,"probcov");
3136: strcat(fileresprobcov,fileres);
3137: if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
3138: printf("Problem with resultfile: %s\n", fileresprobcov);
3139: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
3140: }
3141: strcpy(fileresprobcor,"probcor");
3142: strcat(fileresprobcor,fileres);
3143: if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
3144: printf("Problem with resultfile: %s\n", fileresprobcor);
3145: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
3146: }
3147: printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
3148: fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
3149: printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
3150: fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
3151: printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
3152: fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
3153: pstamp(ficresprob);
3154: fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
3155: fprintf(ficresprob,"# Age");
3156: pstamp(ficresprobcov);
3157: fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
3158: fprintf(ficresprobcov,"# Age");
3159: pstamp(ficresprobcor);
3160: fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
3161: fprintf(ficresprobcor,"# Age");
3162:
3163:
3164: for(i=1; i<=nlstate;i++)
3165: for(j=1; j<=(nlstate+ndeath);j++){
3166: fprintf(ficresprob," p%1d-%1d (SE)",i,j);
3167: fprintf(ficresprobcov," p%1d-%1d ",i,j);
3168: fprintf(ficresprobcor," p%1d-%1d ",i,j);
3169: }
3170: /* fprintf(ficresprob,"\n");
3171: fprintf(ficresprobcov,"\n");
3172: fprintf(ficresprobcor,"\n");
3173: */
3174: xp=vector(1,npar);
3175: dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
3176: doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
3177: mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
3178: varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
3179: first=1;
3180: fprintf(ficgp,"\n# Routine varprob");
3181: fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
3182: fprintf(fichtm,"\n");
3183:
3184: fprintf(fichtm,"\n<li><h4> <a href=\"%s\">Matrix of variance-covariance of pairs of step probabilities (drawings)</a></h4></li>\n",optionfilehtmcov);
3185: fprintf(fichtmcov,"\n<h4>Matrix of variance-covariance of pairs of step probabilities</h4>\n\
3186: file %s<br>\n",optionfilehtmcov);
3187: fprintf(fichtmcov,"\nEllipsoids of confidence centered on point (p<inf>ij</inf>, p<inf>kl</inf>) are estimated\
3188: and drawn. It helps understanding how is the covariance between two incidences.\
3189: They are expressed in year<sup>-1</sup> in order to be less dependent of stepm.<br>\n");
3190: 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. \
3191: It can be understood this way: if pij and pkl where uncorrelated the (2x2) matrix of covariance \
3192: would have been (1/(var pij), 0 , 0, 1/(var pkl)), and the confidence interval would be 2 \
3193: standard deviations wide on each axis. <br>\
3194: Now, if both incidences are correlated (usual case) we diagonalised the inverse of the covariance matrix\
3195: and made the appropriate rotation to look at the uncorrelated principal directions.<br>\
3196: To be simple, these graphs help to understand the significativity of each parameter in relation to a second other one.<br> \n");
3197:
3198: cov[1]=1;
3199: tj=cptcoveff;
3200: if (cptcovn<1) {tj=1;ncodemax[1]=1;}
3201: j1=0;
3202: for(t=1; t<=tj;t++){
3203: for(i1=1; i1<=ncodemax[t];i1++){
3204: j1++;
3205: if (cptcovn>0) {
3206: fprintf(ficresprob, "\n#********** Variable ");
3207: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
3208: fprintf(ficresprob, "**********\n#\n");
3209: fprintf(ficresprobcov, "\n#********** Variable ");
3210: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
3211: fprintf(ficresprobcov, "**********\n#\n");
3212:
3213: fprintf(ficgp, "\n#********** Variable ");
3214: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
3215: fprintf(ficgp, "**********\n#\n");
3216:
3217:
3218: fprintf(fichtmcov, "\n<hr size=\"2\" color=\"#EC5E5E\">********** Variable ");
3219: for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
3220: fprintf(fichtmcov, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
3221:
3222: fprintf(ficresprobcor, "\n#********** Variable ");
3223: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
3224: fprintf(ficresprobcor, "**********\n#");
3225: }
3226:
3227: for (age=bage; age<=fage; age ++){
3228: cov[2]=age;
3229: for (k=1; k<=cptcovn;k++) {
3230: cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];
3231: }
3232: for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
3233: for (k=1; k<=cptcovprod;k++)
3234: cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
3235:
3236: gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
3237: trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
3238: gp=vector(1,(nlstate)*(nlstate+ndeath));
3239: gm=vector(1,(nlstate)*(nlstate+ndeath));
3240:
3241: for(theta=1; theta <=npar; theta++){
3242: for(i=1; i<=npar; i++)
3243: xp[i] = x[i] + (i==theta ?delti[theta]:(double)0);
3244:
3245: pmij(pmmij,cov,ncovmodel,xp,nlstate);
3246:
3247: k=0;
3248: for(i=1; i<= (nlstate); i++){
3249: for(j=1; j<=(nlstate+ndeath);j++){
3250: k=k+1;
3251: gp[k]=pmmij[i][j];
3252: }
3253: }
3254:
3255: for(i=1; i<=npar; i++)
3256: xp[i] = x[i] - (i==theta ?delti[theta]:(double)0);
3257:
3258: pmij(pmmij,cov,ncovmodel,xp,nlstate);
3259: k=0;
3260: for(i=1; i<=(nlstate); i++){
3261: for(j=1; j<=(nlstate+ndeath);j++){
3262: k=k+1;
3263: gm[k]=pmmij[i][j];
3264: }
3265: }
3266:
3267: for(i=1; i<= (nlstate)*(nlstate+ndeath); i++)
3268: gradg[theta][i]=(gp[i]-gm[i])/(double)2./delti[theta];
3269: }
3270:
3271: for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
3272: for(theta=1; theta <=npar; theta++)
3273: trgradg[j][theta]=gradg[theta][j];
3274:
3275: matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov);
3276: matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);
3277: free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
3278: free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
3279: free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
3280: free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
3281:
3282: pmij(pmmij,cov,ncovmodel,x,nlstate);
3283:
3284: k=0;
3285: for(i=1; i<=(nlstate); i++){
3286: for(j=1; j<=(nlstate+ndeath);j++){
3287: k=k+1;
3288: mu[k][(int) age]=pmmij[i][j];
3289: }
3290: }
3291: for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
3292: for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
3293: varpij[i][j][(int)age] = doldm[i][j];
3294:
3295: /*printf("\n%d ",(int)age);
3296: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
3297: printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
3298: fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
3299: }*/
3300:
3301: fprintf(ficresprob,"\n%d ",(int)age);
3302: fprintf(ficresprobcov,"\n%d ",(int)age);
3303: fprintf(ficresprobcor,"\n%d ",(int)age);
3304:
3305: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)
3306: fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));
3307: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
3308: fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);
3309: fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
3310: }
3311: i=0;
3312: for (k=1; k<=(nlstate);k++){
3313: for (l=1; l<=(nlstate+ndeath);l++){
3314: i=i++;
3315: fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
3316: fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
3317: for (j=1; j<=i;j++){
3318: fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);
3319: fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));
3320: }
3321: }
3322: }/* end of loop for state */
3323: } /* end of loop for age */
3324:
3325: /* Confidence intervalle of pij */
3326: /*
3327: fprintf(ficgp,"\nset noparametric;unset label");
3328: fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");
3329: fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
3330: 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);
3331: fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);
3332: fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);
3333: fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);
3334: */
3335:
3336: /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
3337: first1=1;
3338: for (k2=1; k2<=(nlstate);k2++){
3339: for (l2=1; l2<=(nlstate+ndeath);l2++){
3340: if(l2==k2) continue;
3341: j=(k2-1)*(nlstate+ndeath)+l2;
3342: for (k1=1; k1<=(nlstate);k1++){
3343: for (l1=1; l1<=(nlstate+ndeath);l1++){
3344: if(l1==k1) continue;
3345: i=(k1-1)*(nlstate+ndeath)+l1;
3346: if(i<=j) continue;
3347: for (age=bage; age<=fage; age ++){
3348: if ((int)age %5==0){
3349: v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;
3350: v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;
3351: cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;
3352: mu1=mu[i][(int) age]/stepm*YEARM ;
3353: mu2=mu[j][(int) age]/stepm*YEARM;
3354: c12=cv12/sqrt(v1*v2);
3355: /* Computing eigen value of matrix of covariance */
3356: lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
3357: lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
3358: /* Eigen vectors */
3359: v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
3360: /*v21=sqrt(1.-v11*v11); *//* error */
3361: v21=(lc1-v1)/cv12*v11;
3362: v12=-v21;
3363: v22=v11;
3364: tnalp=v21/v11;
3365: if(first1==1){
3366: first1=0;
3367: 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);
3368: }
3369: 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);
3370: /*printf(fignu*/
3371: /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */
3372: /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */
3373: if(first==1){
3374: first=0;
3375: fprintf(ficgp,"\nset parametric;unset label");
3376: 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);
3377: fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
3378: fprintf(fichtmcov,"\n<br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup>\
3379: :<a href=\"%s%d%1d%1d-%1d%1d.png\">\
3380: %s%d%1d%1d-%1d%1d.png</A>, ",k1,l1,k2,l2,\
3381: subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2,\
3382: subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
3383: fprintf(fichtmcov,"\n<br><img src=\"%s%d%1d%1d-%1d%1d.png\"> ",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
3384: fprintf(fichtmcov,"\n<br> Correlation at age %d (%.3f),",(int) age, c12);
3385: fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\"",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
3386: fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
3387: fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
3388: 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",\
3389: mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
3390: mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
3391: }else{
3392: first=0;
3393: fprintf(fichtmcov," %d (%.3f),",(int) age, c12);
3394: fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
3395: fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
3396: 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",\
3397: mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
3398: mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
3399: }/* if first */
3400: } /* age mod 5 */
3401: } /* end loop age */
3402: fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\";replot;",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
3403: first=1;
3404: } /*l12 */
3405: } /* k12 */
3406: } /*l1 */
3407: }/* k1 */
3408: } /* loop covariates */
3409: }
3410: free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
3411: free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
3412: free_matrix(doldm,1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
3413: free_matrix(dnewm,1,(nlstate)*(nlstate+ndeath),1,npar);
3414: free_vector(xp,1,npar);
3415: fclose(ficresprob);
3416: fclose(ficresprobcov);
3417: fclose(ficresprobcor);
3418: fflush(ficgp);
3419: fflush(fichtmcov);
3420: }
3421:
3422:
3423: /******************* Printing html file ***********/
3424: void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \
3425: int lastpass, int stepm, int weightopt, char model[],\
3426: int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
3427: int popforecast, int estepm ,\
3428: double jprev1, double mprev1,double anprev1, \
3429: double jprev2, double mprev2,double anprev2){
3430: int jj1, k1, i1, cpt;
3431:
3432: fprintf(fichtm,"<ul><li><a href='#firstorder'>Result files (first order: no variance)</a>\n \
3433: <li><a href='#secondorder'>Result files (second order (variance)</a>\n \
3434: </ul>");
3435: fprintf(fichtm,"<ul><li><h4><a name='firstorder'>Result files (first order: no variance)</a></h4>\n \
3436: - Observed prevalence in each state (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"%s\">%s</a> <br>\n ",
3437: jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirf2(fileres,"p"),subdirf2(fileres,"p"));
3438: fprintf(fichtm,"\
3439: - Estimated transition probabilities over %d (stepm) months: <a href=\"%s\">%s</a><br>\n ",
3440: stepm,subdirf2(fileres,"pij"),subdirf2(fileres,"pij"));
3441: fprintf(fichtm,"\
3442: - Period (stable) prevalence in each health state: <a href=\"%s\">%s</a> <br>\n",
3443: subdirf2(fileres,"pl"),subdirf2(fileres,"pl"));
3444: fprintf(fichtm,"\
3445: - (a) Life expectancies by health status at initial age, (b) health expectancies by health status at initial age: ei., eij (estepm=%2d months): \
3446: <a href=\"%s\">%s</a> <br>\n</li>",
3447: estepm,subdirf2(fileres,"e"),subdirf2(fileres,"e"));
3448:
3449:
3450: fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
3451:
3452: m=cptcoveff;
3453: if (cptcovn < 1) {m=1;ncodemax[1]=1;}
3454:
3455: jj1=0;
3456: for(k1=1; k1<=m;k1++){
3457: for(i1=1; i1<=ncodemax[k1];i1++){
3458: jj1++;
3459: if (cptcovn > 0) {
3460: fprintf(fichtm,"<hr size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
3461: for (cpt=1; cpt<=cptcoveff;cpt++)
3462: fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
3463: fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
3464: }
3465: /* Pij */
3466: fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i, %d (stepm) months before: <a href=\"%s%d1.png\">%s%d1.png</a><br> \
3467: <img src=\"%s%d1.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);
3468: /* Quasi-incidences */
3469: fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months\
3470: before but expressed in per year i.e. quasi incidences if stepm is small and probabilities too: <a href=\"%s%d2.png\">%s%d2.png</a><br> \
3471: <img src=\"%s%d2.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);
3472: /* Period (stable) prevalence in each health state */
3473: for(cpt=1; cpt<nlstate;cpt++){
3474: fprintf(fichtm,"<br>- Period (stable) prevalence in each health state : <a href=\"%s%d%d.png\">%s%d%d.png</a><br> \
3475: <img src=\"%s%d%d.png\">",subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1);
3476: }
3477: for(cpt=1; cpt<=nlstate;cpt++) {
3478: fprintf(fichtm,"\n<br>- Life expectancy by health state (%d) at initial age and its decomposition into health expectancies : <a href=\"%s%d%d.png\">%s%d%d.png</a> <br> \
3479: <img src=\"%s%d%d.png\">",cpt,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1);
3480: }
3481: } /* end i1 */
3482: }/* End k1 */
3483: fprintf(fichtm,"</ul>");
3484:
3485:
3486: fprintf(fichtm,"\
3487: \n<br><li><h4> <a name='secondorder'>Result files (second order: variances)</a></h4>\n\
3488: - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n", rfileres,rfileres);
3489:
3490: fprintf(fichtm," - Variance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
3491: subdirf2(fileres,"prob"),subdirf2(fileres,"prob"));
3492: fprintf(fichtm,"\
3493: - Variance-covariance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
3494: subdirf2(fileres,"probcov"),subdirf2(fileres,"probcov"));
3495:
3496: fprintf(fichtm,"\
3497: - Correlation matrix of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
3498: subdirf2(fileres,"probcor"),subdirf2(fileres,"probcor"));
3499: fprintf(fichtm,"\
3500: - 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): \
3501: <a href=\"%s\">%s</a> <br>\n</li>",
3502: estepm,subdirf2(fileres,"cve"),subdirf2(fileres,"cve"));
3503: fprintf(fichtm,"\
3504: - (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): \
3505: <a href=\"%s\">%s</a> <br>\n</li>",
3506: estepm,subdirf2(fileres,"stde"),subdirf2(fileres,"stde"));
3507: fprintf(fichtm,"\
3508: - Variances and covariances of health expectancies by age. Status (i) based health expectancies (in state j), eij 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",
3509: estepm, subdirf2(fileres,"v"),subdirf2(fileres,"v"));
3510: fprintf(fichtm,"\
3511: - Total life expectancy and total health expectancies to be spent in each health state e<sup>.j</sup> with their standard errors: <a href=\"%s\">%s</a> <br>\n",
3512: subdirf2(fileres,"t"),subdirf2(fileres,"t"));
3513: fprintf(fichtm,"\
3514: - Standard deviation of period (stable) prevalences: <a href=\"%s\">%s</a> <br>\n",\
3515: subdirf2(fileres,"vpl"),subdirf2(fileres,"vpl"));
3516:
3517: /* if(popforecast==1) fprintf(fichtm,"\n */
3518: /* - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n */
3519: /* - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n */
3520: /* <br>",fileres,fileres,fileres,fileres); */
3521: /* else */
3522: /* 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); */
3523: fflush(fichtm);
3524: fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
3525:
3526: m=cptcoveff;
3527: if (cptcovn < 1) {m=1;ncodemax[1]=1;}
3528:
3529: jj1=0;
3530: for(k1=1; k1<=m;k1++){
3531: for(i1=1; i1<=ncodemax[k1];i1++){
3532: jj1++;
3533: if (cptcovn > 0) {
3534: fprintf(fichtm,"<hr size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
3535: for (cpt=1; cpt<=cptcoveff;cpt++)
3536: fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
3537: fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
3538: }
3539: for(cpt=1; cpt<=nlstate;cpt++) {
3540: fprintf(fichtm,"<br>- Observed (cross-sectional) and period (incidence based) \
3541: prevalence (with 95%% confidence interval) in state (%d): %s%d%d.png <br>\
3542: <img src=\"%s%d%d.png\">",cpt,subdirf2(optionfilefiname,"v"),cpt,jj1,subdirf2(optionfilefiname,"v"),cpt,jj1);
3543: }
3544: fprintf(fichtm,"\n<br>- Total life expectancy by age and \
3545: health expectancies in states (1) and (2): %s%d.png<br>\
3546: <img src=\"%s%d.png\">",subdirf2(optionfilefiname,"e"),jj1,subdirf2(optionfilefiname,"e"),jj1);
3547: } /* end i1 */
3548: }/* End k1 */
3549: fprintf(fichtm,"</ul>");
3550: fflush(fichtm);
3551: }
3552:
3553: /******************* Gnuplot file **************/
3554: void printinggnuplot(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
3555:
3556: char dirfileres[132],optfileres[132];
3557: int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;
3558: int ng;
3559: /* if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) { */
3560: /* printf("Problem with file %s",optionfilegnuplot); */
3561: /* fprintf(ficlog,"Problem with file %s",optionfilegnuplot); */
3562: /* } */
3563:
3564: /*#ifdef windows */
3565: fprintf(ficgp,"cd \"%s\" \n",pathc);
3566: /*#endif */
3567: m=pow(2,cptcoveff);
3568:
3569: strcpy(dirfileres,optionfilefiname);
3570: strcpy(optfileres,"vpl");
3571: /* 1eme*/
3572: for (cpt=1; cpt<= nlstate ; cpt ++) {
3573: for (k1=1; k1<= m ; k1 ++) {
3574: fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"v"),cpt,k1);
3575: fprintf(ficgp,"\n#set out \"v%s%d%d.png\" \n",optionfilefiname,cpt,k1);
3576: fprintf(ficgp,"set xlabel \"Age\" \n\
3577: set ylabel \"Probability\" \n\
3578: set ter png small\n\
3579: set size 0.65,0.65\n\
3580: plot [%.f:%.f] \"%s\" every :::%d::%d u 1:2 \"\%%lf",ageminpar,fage,subdirf2(fileres,"vpl"),k1-1,k1-1);
3581:
3582: for (i=1; i<= nlstate ; i ++) {
3583: if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
3584: else fprintf(ficgp," \%%*lf (\%%*lf)");
3585: }
3586: fprintf(ficgp,"\" t\"Period (stable) prevalence\" w l 0,\"%s\" every :::%d::%d u 1:($2+1.96*$3) \"\%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1);
3587: for (i=1; i<= nlstate ; i ++) {
3588: if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
3589: else fprintf(ficgp," \%%*lf (\%%*lf)");
3590: }
3591: fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"%s\" every :::%d::%d u 1:($2-1.96*$3) \"\%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1);
3592: for (i=1; i<= nlstate ; i ++) {
3593: if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
3594: else fprintf(ficgp," \%%*lf (\%%*lf)");
3595: }
3596: fprintf(ficgp,"\" t\"\" w l 1,\"%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",subdirf2(fileres,"p"),k1-1,k1-1,2+4*(cpt-1));
3597: }
3598: }
3599: /*2 eme*/
3600:
3601: for (k1=1; k1<= m ; k1 ++) {
3602: fprintf(ficgp,"\nset out \"%s%d.png\" \n",subdirf2(optionfilefiname,"e"),k1);
3603: fprintf(ficgp,"set ylabel \"Years\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] ",ageminpar,fage);
3604:
3605: for (i=1; i<= nlstate+1 ; i ++) {
3606: k=2*i;
3607: fprintf(ficgp,"\"%s\" every :::%d::%d u 1:2 \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
3608: for (j=1; j<= nlstate+1 ; j ++) {
3609: if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
3610: else fprintf(ficgp," \%%*lf (\%%*lf)");
3611: }
3612: if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");
3613: else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);
3614: fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
3615: for (j=1; j<= nlstate+1 ; j ++) {
3616: if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
3617: else fprintf(ficgp," \%%*lf (\%%*lf)");
3618: }
3619: fprintf(ficgp,"\" t\"\" w l 0,");
3620: fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
3621: for (j=1; j<= nlstate+1 ; j ++) {
3622: if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
3623: else fprintf(ficgp," \%%*lf (\%%*lf)");
3624: }
3625: if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");
3626: else fprintf(ficgp,"\" t\"\" w l 0,");
3627: }
3628: }
3629:
3630: /*3eme*/
3631:
3632: for (k1=1; k1<= m ; k1 ++) {
3633: for (cpt=1; cpt<= nlstate ; cpt ++) {
3634: /* k=2+nlstate*(2*cpt-2); */
3635: k=2+(nlstate+1)*(cpt-1);
3636: fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"exp"),cpt,k1);
3637: fprintf(ficgp,"set ter png small\n\
3638: set size 0.65,0.65\n\
3639: plot [%.f:%.f] \"%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,subdirf2(fileres,"e"),k1-1,k1-1,k,cpt);
3640: /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
3641: for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
3642: fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
3643: fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
3644: for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
3645: fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
3646:
3647: */
3648: for (i=1; i< nlstate ; i ++) {
3649: 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);
3650: /* 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);*/
3651:
3652: }
3653: fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d.\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+nlstate,cpt);
3654: }
3655: }
3656:
3657: /* CV preval stable (period) */
3658: for (k1=1; k1<= m ; k1 ++) {
3659: for (cpt=1; cpt<=nlstate ; cpt ++) {
3660: k=3;
3661: fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"p"),cpt,k1);
3662: fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\
3663: set ter png small\nset size 0.65,0.65\n\
3664: unset log y\n\
3665: plot [%.f:%.f] \"%s\" u ($1==%d ? ($3):1/0):($%d/($%d",ageminpar,agemaxpar,subdirf2(fileres,"pij"),k1,k+cpt+1,k+1);
3666:
3667: for (i=1; i< nlstate ; i ++)
3668: fprintf(ficgp,"+$%d",k+i+1);
3669: fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);
3670:
3671: l=3+(nlstate+ndeath)*cpt;
3672: fprintf(ficgp,",\"%s\" u ($1==%d ? ($3):1/0):($%d/($%d",subdirf2(fileres,"pij"),k1,l+cpt+1,l+1);
3673: for (i=1; i< nlstate ; i ++) {
3674: l=3+(nlstate+ndeath)*cpt;
3675: fprintf(ficgp,"+$%d",l+i+1);
3676: }
3677: fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);
3678: }
3679: }
3680:
3681: /* proba elementaires */
3682: for(i=1,jk=1; i <=nlstate; i++){
3683: for(k=1; k <=(nlstate+ndeath); k++){
3684: if (k != i) {
3685: for(j=1; j <=ncovmodel; j++){
3686: fprintf(ficgp,"p%d=%f ",jk,p[jk]);
3687: jk++;
3688: fprintf(ficgp,"\n");
3689: }
3690: }
3691: }
3692: }
3693:
3694: for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/
3695: for(jk=1; jk <=m; jk++) {
3696: fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"pe"),jk,ng);
3697: if (ng==2)
3698: fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
3699: else
3700: fprintf(ficgp,"\nset title \"Probability\"\n");
3701: fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65\nset log y\nplot [%.f:%.f] ",ageminpar,agemaxpar);
3702: i=1;
3703: for(k2=1; k2<=nlstate; k2++) {
3704: k3=i;
3705: for(k=1; k<=(nlstate+ndeath); k++) {
3706: if (k != k2){
3707: if(ng==2)
3708: fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);
3709: else
3710: fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
3711: ij=1;
3712: for(j=3; j <=ncovmodel; j++) {
3713: if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
3714: fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
3715: ij++;
3716: }
3717: else
3718: fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
3719: }
3720: fprintf(ficgp,")/(1");
3721:
3722: for(k1=1; k1 <=nlstate; k1++){
3723: fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);
3724: ij=1;
3725: for(j=3; j <=ncovmodel; j++){
3726: if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
3727: fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
3728: ij++;
3729: }
3730: else
3731: fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
3732: }
3733: fprintf(ficgp,")");
3734: }
3735: fprintf(ficgp,") t \"p%d%d\" ", k2,k);
3736: if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");
3737: i=i+ncovmodel;
3738: }
3739: } /* end k */
3740: } /* end k2 */
3741: } /* end jk */
3742: } /* end ng */
3743: fflush(ficgp);
3744: } /* end gnuplot */
3745:
3746:
3747: /*************** Moving average **************/
3748: int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav){
3749:
3750: int i, cpt, cptcod;
3751: int modcovmax =1;
3752: int mobilavrange, mob;
3753: double age;
3754:
3755: modcovmax=2*cptcoveff;/* Max number of modalities. We suppose
3756: a covariate has 2 modalities */
3757: if (cptcovn<1) modcovmax=1; /* At least 1 pass */
3758:
3759: if(mobilav==1||mobilav ==3 ||mobilav==5 ||mobilav== 7){
3760: if(mobilav==1) mobilavrange=5; /* default */
3761: else mobilavrange=mobilav;
3762: for (age=bage; age<=fage; age++)
3763: for (i=1; i<=nlstate;i++)
3764: for (cptcod=1;cptcod<=modcovmax;cptcod++)
3765: mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
3766: /* We keep the original values on the extreme ages bage, fage and for
3767: fage+1 and bage-1 we use a 3 terms moving average; for fage+2 bage+2
3768: we use a 5 terms etc. until the borders are no more concerned.
3769: */
3770: for (mob=3;mob <=mobilavrange;mob=mob+2){
3771: for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){
3772: for (i=1; i<=nlstate;i++){
3773: for (cptcod=1;cptcod<=modcovmax;cptcod++){
3774: mobaverage[(int)age][i][cptcod] =probs[(int)age][i][cptcod];
3775: for (cpt=1;cpt<=(mob-1)/2;cpt++){
3776: mobaverage[(int)age][i][cptcod] +=probs[(int)age-cpt][i][cptcod];
3777: mobaverage[(int)age][i][cptcod] +=probs[(int)age+cpt][i][cptcod];
3778: }
3779: mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/mob;
3780: }
3781: }
3782: }/* end age */
3783: }/* end mob */
3784: }else return -1;
3785: return 0;
3786: }/* End movingaverage */
3787:
3788:
3789: /************** Forecasting ******************/
3790: 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){
3791: /* proj1, year, month, day of starting projection
3792: agemin, agemax range of age
3793: dateprev1 dateprev2 range of dates during which prevalence is computed
3794: anproj2 year of en of projection (same day and month as proj1).
3795: */
3796: int yearp, stepsize, hstepm, nhstepm, j, k, c, cptcod, i, h, i1;
3797: int *popage;
3798: double agec; /* generic age */
3799: double agelim, ppij, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
3800: double *popeffectif,*popcount;
3801: double ***p3mat;
3802: double ***mobaverage;
3803: char fileresf[FILENAMELENGTH];
3804:
3805: agelim=AGESUP;
3806: prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
3807:
3808: strcpy(fileresf,"f");
3809: strcat(fileresf,fileres);
3810: if((ficresf=fopen(fileresf,"w"))==NULL) {
3811: printf("Problem with forecast resultfile: %s\n", fileresf);
3812: fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);
3813: }
3814: printf("Computing forecasting: result on file '%s' \n", fileresf);
3815: fprintf(ficlog,"Computing forecasting: result on file '%s' \n", fileresf);
3816:
3817: if (cptcoveff==0) ncodemax[cptcoveff]=1;
3818:
3819: if (mobilav!=0) {
3820: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
3821: if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
3822: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
3823: printf(" Error in movingaverage mobilav=%d\n",mobilav);
3824: }
3825: }
3826:
3827: stepsize=(int) (stepm+YEARM-1)/YEARM;
3828: if (stepm<=12) stepsize=1;
3829: if(estepm < stepm){
3830: printf ("Problem %d lower than %d\n",estepm, stepm);
3831: }
3832: else hstepm=estepm;
3833:
3834: hstepm=hstepm/stepm;
3835: yp1=modf(dateintmean,&yp);/* extracts integral of datemean in yp and
3836: fractional in yp1 */
3837: anprojmean=yp;
3838: yp2=modf((yp1*12),&yp);
3839: mprojmean=yp;
3840: yp1=modf((yp2*30.5),&yp);
3841: jprojmean=yp;
3842: if(jprojmean==0) jprojmean=1;
3843: if(mprojmean==0) jprojmean=1;
3844:
3845: i1=cptcoveff;
3846: if (cptcovn < 1){i1=1;}
3847:
3848: fprintf(ficresf,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2);
3849:
3850: fprintf(ficresf,"#****** Routine prevforecast **\n");
3851:
3852: /* if (h==(int)(YEARM*yearp)){ */
3853: for(cptcov=1, k=0;cptcov<=i1;cptcov++){
3854: for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
3855: k=k+1;
3856: fprintf(ficresf,"\n#******");
3857: for(j=1;j<=cptcoveff;j++) {
3858: 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]]);
3859: }
3860: fprintf(ficresf,"******\n");
3861: fprintf(ficresf,"# Covariate valuofcovar yearproj age");
3862: for(j=1; j<=nlstate+ndeath;j++){
3863: for(i=1; i<=nlstate;i++)
3864: fprintf(ficresf," p%d%d",i,j);
3865: fprintf(ficresf," p.%d",j);
3866: }
3867: for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) {
3868: fprintf(ficresf,"\n");
3869: fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+yearp);
3870:
3871: for (agec=fage; agec>=(ageminpar-1); agec--){
3872: nhstepm=(int) rint((agelim-agec)*YEARM/stepm);
3873: nhstepm = nhstepm/hstepm;
3874: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3875: oldm=oldms;savm=savms;
3876: hpxij(p3mat,nhstepm,agec,hstepm,p,nlstate,stepm,oldm,savm, k);
3877:
3878: for (h=0; h<=nhstepm; h++){
3879: if (h*hstepm/YEARM*stepm ==yearp) {
3880: fprintf(ficresf,"\n");
3881: for(j=1;j<=cptcoveff;j++)
3882: fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
3883: fprintf(ficresf,"%.f %.f ",anproj1+yearp,agec+h*hstepm/YEARM*stepm);
3884: }
3885: for(j=1; j<=nlstate+ndeath;j++) {
3886: ppij=0.;
3887: for(i=1; i<=nlstate;i++) {
3888: if (mobilav==1)
3889: ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][i][cptcod];
3890: else {
3891: ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][cptcod];
3892: }
3893: if (h*hstepm/YEARM*stepm== yearp) {
3894: fprintf(ficresf," %.3f", p3mat[i][j][h]);
3895: }
3896: } /* end i */
3897: if (h*hstepm/YEARM*stepm==yearp) {
3898: fprintf(ficresf," %.3f", ppij);
3899: }
3900: }/* end j */
3901: } /* end h */
3902: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3903: } /* end agec */
3904: } /* end yearp */
3905: } /* end cptcod */
3906: } /* end cptcov */
3907:
3908: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
3909:
3910: fclose(ficresf);
3911: }
3912:
3913: /************** Forecasting *****not tested NB*************/
3914: 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){
3915:
3916: int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;
3917: int *popage;
3918: double calagedatem, agelim, kk1, kk2;
3919: double *popeffectif,*popcount;
3920: double ***p3mat,***tabpop,***tabpopprev;
3921: double ***mobaverage;
3922: char filerespop[FILENAMELENGTH];
3923:
3924: tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
3925: tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
3926: agelim=AGESUP;
3927: calagedatem=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;
3928:
3929: prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
3930:
3931:
3932: strcpy(filerespop,"pop");
3933: strcat(filerespop,fileres);
3934: if((ficrespop=fopen(filerespop,"w"))==NULL) {
3935: printf("Problem with forecast resultfile: %s\n", filerespop);
3936: fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop);
3937: }
3938: printf("Computing forecasting: result on file '%s' \n", filerespop);
3939: fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop);
3940:
3941: if (cptcoveff==0) ncodemax[cptcoveff]=1;
3942:
3943: if (mobilav!=0) {
3944: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
3945: if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
3946: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
3947: printf(" Error in movingaverage mobilav=%d\n",mobilav);
3948: }
3949: }
3950:
3951: stepsize=(int) (stepm+YEARM-1)/YEARM;
3952: if (stepm<=12) stepsize=1;
3953:
3954: agelim=AGESUP;
3955:
3956: hstepm=1;
3957: hstepm=hstepm/stepm;
3958:
3959: if (popforecast==1) {
3960: if((ficpop=fopen(popfile,"r"))==NULL) {
3961: printf("Problem with population file : %s\n",popfile);exit(0);
3962: fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0);
3963: }
3964: popage=ivector(0,AGESUP);
3965: popeffectif=vector(0,AGESUP);
3966: popcount=vector(0,AGESUP);
3967:
3968: i=1;
3969: while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;
3970:
3971: imx=i;
3972: for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];
3973: }
3974:
3975: for(cptcov=1,k=0;cptcov<=i2;cptcov++){
3976: for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
3977: k=k+1;
3978: fprintf(ficrespop,"\n#******");
3979: for(j=1;j<=cptcoveff;j++) {
3980: fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
3981: }
3982: fprintf(ficrespop,"******\n");
3983: fprintf(ficrespop,"# Age");
3984: for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);
3985: if (popforecast==1) fprintf(ficrespop," [Population]");
3986:
3987: for (cpt=0; cpt<=0;cpt++) {
3988: fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);
3989:
3990: for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){
3991: nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);
3992: nhstepm = nhstepm/hstepm;
3993:
3994: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3995: oldm=oldms;savm=savms;
3996: hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
3997:
3998: for (h=0; h<=nhstepm; h++){
3999: if (h==(int) (calagedatem+YEARM*cpt)) {
4000: fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
4001: }
4002: for(j=1; j<=nlstate+ndeath;j++) {
4003: kk1=0.;kk2=0;
4004: for(i=1; i<=nlstate;i++) {
4005: if (mobilav==1)
4006: kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];
4007: else {
4008: kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];
4009: }
4010: }
4011: if (h==(int)(calagedatem+12*cpt)){
4012: tabpop[(int)(agedeb)][j][cptcod]=kk1;
4013: /*fprintf(ficrespop," %.3f", kk1);
4014: if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/
4015: }
4016: }
4017: for(i=1; i<=nlstate;i++){
4018: kk1=0.;
4019: for(j=1; j<=nlstate;j++){
4020: kk1= kk1+tabpop[(int)(agedeb)][j][cptcod];
4021: }
4022: tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedatem+12*cpt)*hstepm/YEARM*stepm-1)];
4023: }
4024:
4025: if (h==(int)(calagedatem+12*cpt)) for(j=1; j<=nlstate;j++)
4026: fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);
4027: }
4028: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4029: }
4030: }
4031:
4032: /******/
4033:
4034: for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) {
4035: fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);
4036: for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){
4037: nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);
4038: nhstepm = nhstepm/hstepm;
4039:
4040: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4041: oldm=oldms;savm=savms;
4042: hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
4043: for (h=0; h<=nhstepm; h++){
4044: if (h==(int) (calagedatem+YEARM*cpt)) {
4045: fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
4046: }
4047: for(j=1; j<=nlstate+ndeath;j++) {
4048: kk1=0.;kk2=0;
4049: for(i=1; i<=nlstate;i++) {
4050: kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];
4051: }
4052: if (h==(int)(calagedatem+12*cpt)) fprintf(ficresf," %15.2f", kk1);
4053: }
4054: }
4055: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4056: }
4057: }
4058: }
4059: }
4060:
4061: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
4062:
4063: if (popforecast==1) {
4064: free_ivector(popage,0,AGESUP);
4065: free_vector(popeffectif,0,AGESUP);
4066: free_vector(popcount,0,AGESUP);
4067: }
4068: free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
4069: free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
4070: fclose(ficrespop);
4071: } /* End of popforecast */
4072:
4073: int fileappend(FILE *fichier, char *optionfich)
4074: {
4075: if((fichier=fopen(optionfich,"a"))==NULL) {
4076: printf("Problem with file: %s\n", optionfich);
4077: fprintf(ficlog,"Problem with file: %s\n", optionfich);
4078: return (0);
4079: }
4080: fflush(fichier);
4081: return (1);
4082: }
4083:
4084:
4085: /**************** function prwizard **********************/
4086: void prwizard(int ncovmodel, int nlstate, int ndeath, char model[], FILE *ficparo)
4087: {
4088:
4089: /* Wizard to print covariance matrix template */
4090:
4091: char ca[32], cb[32], cc[32];
4092: int i,j, k, l, li, lj, lk, ll, jj, npar, itimes;
4093: int numlinepar;
4094:
4095: printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
4096: fprintf(ficparo,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
4097: for(i=1; i <=nlstate; i++){
4098: jj=0;
4099: for(j=1; j <=nlstate+ndeath; j++){
4100: if(j==i) continue;
4101: jj++;
4102: /*ca[0]= k+'a'-1;ca[1]='\0';*/
4103: printf("%1d%1d",i,j);
4104: fprintf(ficparo,"%1d%1d",i,j);
4105: for(k=1; k<=ncovmodel;k++){
4106: /* printf(" %lf",param[i][j][k]); */
4107: /* fprintf(ficparo," %lf",param[i][j][k]); */
4108: printf(" 0.");
4109: fprintf(ficparo," 0.");
4110: }
4111: printf("\n");
4112: fprintf(ficparo,"\n");
4113: }
4114: }
4115: printf("# Scales (for hessian or gradient estimation)\n");
4116: fprintf(ficparo,"# Scales (for hessian or gradient estimation)\n");
4117: npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/
4118: for(i=1; i <=nlstate; i++){
4119: jj=0;
4120: for(j=1; j <=nlstate+ndeath; j++){
4121: if(j==i) continue;
4122: jj++;
4123: fprintf(ficparo,"%1d%1d",i,j);
4124: printf("%1d%1d",i,j);
4125: fflush(stdout);
4126: for(k=1; k<=ncovmodel;k++){
4127: /* printf(" %le",delti3[i][j][k]); */
4128: /* fprintf(ficparo," %le",delti3[i][j][k]); */
4129: printf(" 0.");
4130: fprintf(ficparo," 0.");
4131: }
4132: numlinepar++;
4133: printf("\n");
4134: fprintf(ficparo,"\n");
4135: }
4136: }
4137: printf("# Covariance matrix\n");
4138: /* # 121 Var(a12)\n\ */
4139: /* # 122 Cov(b12,a12) Var(b12)\n\ */
4140: /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
4141: /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
4142: /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
4143: /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
4144: /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
4145: /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
4146: fflush(stdout);
4147: fprintf(ficparo,"# Covariance matrix\n");
4148: /* # 121 Var(a12)\n\ */
4149: /* # 122 Cov(b12,a12) Var(b12)\n\ */
4150: /* # ...\n\ */
4151: /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
4152:
4153: for(itimes=1;itimes<=2;itimes++){
4154: jj=0;
4155: for(i=1; i <=nlstate; i++){
4156: for(j=1; j <=nlstate+ndeath; j++){
4157: if(j==i) continue;
4158: for(k=1; k<=ncovmodel;k++){
4159: jj++;
4160: ca[0]= k+'a'-1;ca[1]='\0';
4161: if(itimes==1){
4162: printf("#%1d%1d%d",i,j,k);
4163: fprintf(ficparo,"#%1d%1d%d",i,j,k);
4164: }else{
4165: printf("%1d%1d%d",i,j,k);
4166: fprintf(ficparo,"%1d%1d%d",i,j,k);
4167: /* printf(" %.5le",matcov[i][j]); */
4168: }
4169: ll=0;
4170: for(li=1;li <=nlstate; li++){
4171: for(lj=1;lj <=nlstate+ndeath; lj++){
4172: if(lj==li) continue;
4173: for(lk=1;lk<=ncovmodel;lk++){
4174: ll++;
4175: if(ll<=jj){
4176: cb[0]= lk +'a'-1;cb[1]='\0';
4177: if(ll<jj){
4178: if(itimes==1){
4179: printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
4180: fprintf(ficparo," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
4181: }else{
4182: printf(" 0.");
4183: fprintf(ficparo," 0.");
4184: }
4185: }else{
4186: if(itimes==1){
4187: printf(" Var(%s%1d%1d)",ca,i,j);
4188: fprintf(ficparo," Var(%s%1d%1d)",ca,i,j);
4189: }else{
4190: printf(" 0.");
4191: fprintf(ficparo," 0.");
4192: }
4193: }
4194: }
4195: } /* end lk */
4196: } /* end lj */
4197: } /* end li */
4198: printf("\n");
4199: fprintf(ficparo,"\n");
4200: numlinepar++;
4201: } /* end k*/
4202: } /*end j */
4203: } /* end i */
4204: } /* end itimes */
4205:
4206: } /* end of prwizard */
4207: /******************* Gompertz Likelihood ******************************/
4208: double gompertz(double x[])
4209: {
4210: double A,B,L=0.0,sump=0.,num=0.;
4211: int i,n=0; /* n is the size of the sample */
4212:
4213: for (i=0;i<=imx-1 ; i++) {
4214: sump=sump+weight[i];
4215: /* sump=sump+1;*/
4216: num=num+1;
4217: }
4218:
4219:
4220: /* for (i=0; i<=imx; i++)
4221: 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]);*/
4222:
4223: for (i=1;i<=imx ; i++)
4224: {
4225: if (cens[i] == 1 && wav[i]>1)
4226: A=-x[1]/(x[2])*(exp(x[2]*(agecens[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)));
4227:
4228: if (cens[i] == 0 && wav[i]>1)
4229: A=-x[1]/(x[2])*(exp(x[2]*(agedc[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)))
4230: +log(x[1]/YEARM)+x[2]*(agedc[i]-agegomp)+log(YEARM);
4231:
4232: /*if (wav[i] > 1 && agecens[i] > 15) {*/ /* ??? */
4233: if (wav[i] > 1 ) { /* ??? */
4234: L=L+A*weight[i];
4235: /* 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]);*/
4236: }
4237: }
4238:
4239: /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/
4240:
4241: return -2*L*num/sump;
4242: }
4243:
4244: /******************* Printing html file ***********/
4245: void printinghtmlmort(char fileres[], char title[], char datafile[], int firstpass, \
4246: int lastpass, int stepm, int weightopt, char model[],\
4247: int imx, double p[],double **matcov,double agemortsup){
4248: int i,k;
4249:
4250: fprintf(fichtm,"<ul><li><h4>Result files </h4>\n Force of mortality. Parameters of the Gompertz fit (with confidence interval in brackets):<br>");
4251: fprintf(fichtm," mu(age) =%lf*exp(%lf*(age-%d)) per year<br><br>",p[1],p[2],agegomp);
4252: for (i=1;i<=2;i++)
4253: 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]));
4254: fprintf(fichtm,"<br><br><img src=\"graphmort.png\">");
4255: fprintf(fichtm,"</ul>");
4256:
4257: fprintf(fichtm,"<ul><li><h4>Life table</h4>\n <br>");
4258:
4259: 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>");
4260:
4261: for (k=agegomp;k<(agemortsup-2);k++)
4262: 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]);
4263:
4264:
4265: fflush(fichtm);
4266: }
4267:
4268: /******************* Gnuplot file **************/
4269: void printinggnuplotmort(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
4270:
4271: char dirfileres[132],optfileres[132];
4272: int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;
4273: int ng;
4274:
4275:
4276: /*#ifdef windows */
4277: fprintf(ficgp,"cd \"%s\" \n",pathc);
4278: /*#endif */
4279:
4280:
4281: strcpy(dirfileres,optionfilefiname);
4282: strcpy(optfileres,"vpl");
4283: fprintf(ficgp,"set out \"graphmort.png\"\n ");
4284: fprintf(ficgp,"set xlabel \"Age\"\n set ylabel \"Force of mortality (per year)\" \n ");
4285: fprintf(ficgp, "set ter png small\n set log y\n");
4286: fprintf(ficgp, "set size 0.65,0.65\n");
4287: fprintf(ficgp,"plot [%d:100] %lf*exp(%lf*(x-%d))",agegomp,p[1],p[2],agegomp);
4288:
4289: }
4290:
4291:
4292:
4293:
4294:
4295: /***********************************************/
4296: /**************** Main Program *****************/
4297: /***********************************************/
4298:
4299: int main(int argc, char *argv[])
4300: {
4301: int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav);
4302: int i,j, k, n=MAXN,iter,m,size=100,cptcode, cptcod;
4303: int linei, month, year,iout;
4304: int jj, ll, li, lj, lk, imk;
4305: int numlinepar=0; /* Current linenumber of parameter file */
4306: int itimes;
4307: int NDIM=2;
4308:
4309: char ca[32], cb[32], cc[32];
4310: char dummy[]=" ";
4311: /* FILE *fichtm; *//* Html File */
4312: /* FILE *ficgp;*/ /*Gnuplot File */
4313: struct stat info;
4314: double agedeb, agefin,hf;
4315: double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;
4316:
4317: double fret;
4318: double **xi,tmp,delta;
4319:
4320: double dum; /* Dummy variable */
4321: double ***p3mat;
4322: double ***mobaverage;
4323: int *indx;
4324: char line[MAXLINE], linepar[MAXLINE];
4325: char path[MAXLINE],pathc[MAXLINE],pathcd[MAXLINE],pathtot[MAXLINE],model[MAXLINE];
4326: char pathr[MAXLINE], pathimach[MAXLINE];
4327: char **bp, *tok, *val; /* pathtot */
4328: int firstobs=1, lastobs=10;
4329: int sdeb, sfin; /* Status at beginning and end */
4330: int c, h , cpt,l;
4331: int ju,jl, mi;
4332: int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;
4333: int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,*tab;
4334: int mobilavproj=0 , prevfcast=0 ; /* moving average of prev, If prevfcast=1 prevalence projection */
4335: int mobilav=0,popforecast=0;
4336: int hstepm, nhstepm;
4337: int agemortsup;
4338: float sumlpop=0.;
4339: double jprev1=1, mprev1=1,anprev1=2000,jprev2=1, mprev2=1,anprev2=2000;
4340: double jpyram=1, mpyram=1,anpyram=2000,jpyram1=1, mpyram1=1,anpyram1=2000;
4341:
4342: double bage, fage, age, agelim, agebase;
4343: double ftolpl=FTOL;
4344: double **prlim;
4345: double *severity;
4346: double ***param; /* Matrix of parameters */
4347: double *p;
4348: double **matcov; /* Matrix of covariance */
4349: double ***delti3; /* Scale */
4350: double *delti; /* Scale */
4351: double ***eij, ***vareij;
4352: double **varpl; /* Variances of prevalence limits by age */
4353: double *epj, vepp;
4354: double kk1, kk2;
4355: double dateprev1, dateprev2,jproj1=1,mproj1=1,anproj1=2000,jproj2=1,mproj2=1,anproj2=2000;
4356: double **ximort;
4357: char *alph[]={"a","a","b","c","d","e"}, str[4];
4358: int *dcwave;
4359:
4360: char z[1]="c", occ;
4361:
4362: char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];
4363: char *strt, strtend[80];
4364: char *stratrunc;
4365: int lstra;
4366:
4367: long total_usecs;
4368:
4369: /* setlocale (LC_ALL, ""); */
4370: /* bindtextdomain (PACKAGE, LOCALEDIR); */
4371: /* textdomain (PACKAGE); */
4372: /* setlocale (LC_CTYPE, ""); */
4373: /* setlocale (LC_MESSAGES, ""); */
4374:
4375: /* gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */
4376: (void) gettimeofday(&start_time,&tzp);
4377: curr_time=start_time;
4378: tm = *localtime(&start_time.tv_sec);
4379: tmg = *gmtime(&start_time.tv_sec);
4380: strcpy(strstart,asctime(&tm));
4381:
4382: /* printf("Localtime (at start)=%s",strstart); */
4383: /* tp.tv_sec = tp.tv_sec +86400; */
4384: /* tm = *localtime(&start_time.tv_sec); */
4385: /* tmg.tm_year=tmg.tm_year +dsign*dyear; */
4386: /* tmg.tm_mon=tmg.tm_mon +dsign*dmonth; */
4387: /* tmg.tm_hour=tmg.tm_hour + 1; */
4388: /* tp.tv_sec = mktime(&tmg); */
4389: /* strt=asctime(&tmg); */
4390: /* printf("Time(after) =%s",strstart); */
4391: /* (void) time (&time_value);
4392: * printf("time=%d,t-=%d\n",time_value,time_value-86400);
4393: * tm = *localtime(&time_value);
4394: * strstart=asctime(&tm);
4395: * printf("tim_value=%d,asctime=%s\n",time_value,strstart);
4396: */
4397:
4398: nberr=0; /* Number of errors and warnings */
4399: nbwarn=0;
4400: getcwd(pathcd, size);
4401:
4402: printf("\n%s\n%s",version,fullversion);
4403: if(argc <=1){
4404: printf("\nEnter the parameter file name: ");
4405: fgets(pathr,FILENAMELENGTH,stdin);
4406: i=strlen(pathr);
4407: if(pathr[i-1]=='\n')
4408: pathr[i-1]='\0';
4409: for (tok = pathr; tok != NULL; ){
4410: printf("Pathr |%s|\n",pathr);
4411: while ((val = strsep(&tok, "\"" )) != NULL && *val == '\0');
4412: printf("val= |%s| pathr=%s\n",val,pathr);
4413: strcpy (pathtot, val);
4414: if(pathr[0] == '\0') break; /* Un peu sale */
4415: }
4416: }
4417: else{
4418: strcpy(pathtot,argv[1]);
4419: }
4420: /*if(getcwd(pathcd, MAXLINE)!= NULL)printf ("Error pathcd\n");*/
4421: /*cygwin_split_path(pathtot,path,optionfile);
4422: printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/
4423: /* cutv(path,optionfile,pathtot,'\\');*/
4424:
4425: /* Split argv[0], imach program to get pathimach */
4426: printf("\nargv[0]=%s argv[1]=%s, \n",argv[0],argv[1]);
4427: split(argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
4428: printf("\nargv[0]=%s pathimach=%s, \noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
4429: /* strcpy(pathimach,argv[0]); */
4430: /* Split argv[1]=pathtot, parameter file name to get path, optionfile, extension and name */
4431: split(pathtot,path,optionfile,optionfilext,optionfilefiname);
4432: printf("\npathtot=%s,\npath=%s,\noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
4433: chdir(path);
4434: strcpy(command,"mkdir ");
4435: strcat(command,optionfilefiname);
4436: if((outcmd=system(command)) != 0){
4437: printf("Problem creating directory or it already exists %s%s, err=%d\n",path,optionfilefiname,outcmd);
4438: /* fprintf(ficlog,"Problem creating directory %s%s\n",path,optionfilefiname); */
4439: /* fclose(ficlog); */
4440: /* exit(1); */
4441: }
4442: /* if((imk=mkdir(optionfilefiname))<0){ */
4443: /* perror("mkdir"); */
4444: /* } */
4445:
4446: /*-------- arguments in the command line --------*/
4447:
4448: /* Log file */
4449: strcat(filelog, optionfilefiname);
4450: strcat(filelog,".log"); /* */
4451: if((ficlog=fopen(filelog,"w"))==NULL) {
4452: printf("Problem with logfile %s\n",filelog);
4453: goto end;
4454: }
4455: fprintf(ficlog,"Log filename:%s\n",filelog);
4456: fprintf(ficlog,"\n%s\n%s",version,fullversion);
4457: fprintf(ficlog,"\nEnter the parameter file name: \n");
4458: fprintf(ficlog,"pathimach=%s\npathtot=%s\n\
4459: path=%s \n\
4460: optionfile=%s\n\
4461: optionfilext=%s\n\
4462: optionfilefiname=%s\n",pathimach,pathtot,path,optionfile,optionfilext,optionfilefiname);
4463:
4464: printf("Local time (at start):%s",strstart);
4465: fprintf(ficlog,"Local time (at start): %s",strstart);
4466: fflush(ficlog);
4467: /* (void) gettimeofday(&curr_time,&tzp); */
4468: /* printf("Elapsed time %d\n", asc_diff_time(curr_time.tv_sec-start_time.tv_sec,tmpout)); */
4469:
4470: /* */
4471: strcpy(fileres,"r");
4472: strcat(fileres, optionfilefiname);
4473: strcat(fileres,".txt"); /* Other files have txt extension */
4474:
4475: /*---------arguments file --------*/
4476:
4477: if((ficpar=fopen(optionfile,"r"))==NULL) {
4478: printf("Problem with optionfile %s\n",optionfile);
4479: fprintf(ficlog,"Problem with optionfile %s\n",optionfile);
4480: fflush(ficlog);
4481: goto end;
4482: }
4483:
4484:
4485:
4486: strcpy(filereso,"o");
4487: strcat(filereso,fileres);
4488: if((ficparo=fopen(filereso,"w"))==NULL) { /* opened on subdirectory */
4489: printf("Problem with Output resultfile: %s\n", filereso);
4490: fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso);
4491: fflush(ficlog);
4492: goto end;
4493: }
4494:
4495: /* Reads comments: lines beginning with '#' */
4496: numlinepar=0;
4497: while((c=getc(ficpar))=='#' && c!= EOF){
4498: ungetc(c,ficpar);
4499: fgets(line, MAXLINE, ficpar);
4500: numlinepar++;
4501: puts(line);
4502: fputs(line,ficparo);
4503: fputs(line,ficlog);
4504: }
4505: ungetc(c,ficpar);
4506:
4507: 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);
4508: numlinepar++;
4509: 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);
4510: 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);
4511: 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);
4512: fflush(ficlog);
4513: while((c=getc(ficpar))=='#' && c!= EOF){
4514: ungetc(c,ficpar);
4515: fgets(line, MAXLINE, ficpar);
4516: numlinepar++;
4517: puts(line);
4518: fputs(line,ficparo);
4519: fputs(line,ficlog);
4520: }
4521: ungetc(c,ficpar);
4522:
4523:
4524: covar=matrix(0,NCOVMAX,1,n);
4525: cptcovn=0; /*Number of covariates, i.e. number of '+' in model statement*/
4526: if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;
4527:
4528: ncovmodel=2+cptcovn; /*Number of variables = cptcovn + intercept + age */
4529: nvar=ncovmodel-1; /* Suppressing age as a basic covariate */
4530: npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/
4531:
4532: delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
4533: delti=delti3[1][1];
4534: /*delti=vector(1,npar); *//* Scale of each paramater (output from hesscov)*/
4535: if(mle==-1){ /* Print a wizard for help writing covariance matrix */
4536: prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
4537: printf(" You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
4538: fprintf(ficlog," You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
4539: free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
4540: fclose (ficparo);
4541: fclose (ficlog);
4542: exit(0);
4543: }
4544: else if(mle==-3) {
4545: prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
4546: printf(" You choose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
4547: fprintf(ficlog," You choose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
4548: param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
4549: matcov=matrix(1,npar,1,npar);
4550: }
4551: else{
4552: /* Read guess parameters */
4553: /* Reads comments: lines beginning with '#' */
4554: while((c=getc(ficpar))=='#' && c!= EOF){
4555: ungetc(c,ficpar);
4556: fgets(line, MAXLINE, ficpar);
4557: numlinepar++;
4558: puts(line);
4559: fputs(line,ficparo);
4560: fputs(line,ficlog);
4561: }
4562: ungetc(c,ficpar);
4563:
4564: param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
4565: for(i=1; i <=nlstate; i++){
4566: j=0;
4567: for(jj=1; jj <=nlstate+ndeath; jj++){
4568: if(jj==i) continue;
4569: j++;
4570: fscanf(ficpar,"%1d%1d",&i1,&j1);
4571: if ((i1 != i) && (j1 != j)){
4572: printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n",numlinepar, i,j, i1, j1);
4573: exit(1);
4574: }
4575: fprintf(ficparo,"%1d%1d",i1,j1);
4576: if(mle==1)
4577: printf("%1d%1d",i,j);
4578: fprintf(ficlog,"%1d%1d",i,j);
4579: for(k=1; k<=ncovmodel;k++){
4580: fscanf(ficpar," %lf",¶m[i][j][k]);
4581: if(mle==1){
4582: printf(" %lf",param[i][j][k]);
4583: fprintf(ficlog," %lf",param[i][j][k]);
4584: }
4585: else
4586: fprintf(ficlog," %lf",param[i][j][k]);
4587: fprintf(ficparo," %lf",param[i][j][k]);
4588: }
4589: fscanf(ficpar,"\n");
4590: numlinepar++;
4591: if(mle==1)
4592: printf("\n");
4593: fprintf(ficlog,"\n");
4594: fprintf(ficparo,"\n");
4595: }
4596: }
4597: fflush(ficlog);
4598:
4599: p=param[1][1];
4600:
4601: /* Reads comments: lines beginning with '#' */
4602: while((c=getc(ficpar))=='#' && c!= EOF){
4603: ungetc(c,ficpar);
4604: fgets(line, MAXLINE, ficpar);
4605: numlinepar++;
4606: puts(line);
4607: fputs(line,ficparo);
4608: fputs(line,ficlog);
4609: }
4610: ungetc(c,ficpar);
4611:
4612: for(i=1; i <=nlstate; i++){
4613: for(j=1; j <=nlstate+ndeath-1; j++){
4614: fscanf(ficpar,"%1d%1d",&i1,&j1);
4615: if ((i1-i)*(j1-j)!=0){
4616: printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n",numlinepar, i,j, i1, j1);
4617: exit(1);
4618: }
4619: printf("%1d%1d",i,j);
4620: fprintf(ficparo,"%1d%1d",i1,j1);
4621: fprintf(ficlog,"%1d%1d",i1,j1);
4622: for(k=1; k<=ncovmodel;k++){
4623: fscanf(ficpar,"%le",&delti3[i][j][k]);
4624: printf(" %le",delti3[i][j][k]);
4625: fprintf(ficparo," %le",delti3[i][j][k]);
4626: fprintf(ficlog," %le",delti3[i][j][k]);
4627: }
4628: fscanf(ficpar,"\n");
4629: numlinepar++;
4630: printf("\n");
4631: fprintf(ficparo,"\n");
4632: fprintf(ficlog,"\n");
4633: }
4634: }
4635: fflush(ficlog);
4636:
4637: delti=delti3[1][1];
4638:
4639:
4640: /* free_ma3x(delti3,1,nlstate,1,nlstate+ndeath-1,1,ncovmodel); */ /* Hasn't to to freed here otherwise delti is no more allocated */
4641:
4642: /* Reads comments: lines beginning with '#' */
4643: while((c=getc(ficpar))=='#' && c!= EOF){
4644: ungetc(c,ficpar);
4645: fgets(line, MAXLINE, ficpar);
4646: numlinepar++;
4647: puts(line);
4648: fputs(line,ficparo);
4649: fputs(line,ficlog);
4650: }
4651: ungetc(c,ficpar);
4652:
4653: matcov=matrix(1,npar,1,npar);
4654: for(i=1; i <=npar; i++){
4655: fscanf(ficpar,"%s",&str);
4656: if(mle==1)
4657: printf("%s",str);
4658: fprintf(ficlog,"%s",str);
4659: fprintf(ficparo,"%s",str);
4660: for(j=1; j <=i; j++){
4661: fscanf(ficpar," %le",&matcov[i][j]);
4662: if(mle==1){
4663: printf(" %.5le",matcov[i][j]);
4664: }
4665: fprintf(ficlog," %.5le",matcov[i][j]);
4666: fprintf(ficparo," %.5le",matcov[i][j]);
4667: }
4668: fscanf(ficpar,"\n");
4669: numlinepar++;
4670: if(mle==1)
4671: printf("\n");
4672: fprintf(ficlog,"\n");
4673: fprintf(ficparo,"\n");
4674: }
4675: for(i=1; i <=npar; i++)
4676: for(j=i+1;j<=npar;j++)
4677: matcov[i][j]=matcov[j][i];
4678:
4679: if(mle==1)
4680: printf("\n");
4681: fprintf(ficlog,"\n");
4682:
4683: fflush(ficlog);
4684:
4685: /*-------- Rewriting parameter file ----------*/
4686: strcpy(rfileres,"r"); /* "Rparameterfile */
4687: strcat(rfileres,optionfilefiname); /* Parameter file first name*/
4688: strcat(rfileres,"."); /* */
4689: strcat(rfileres,optionfilext); /* Other files have txt extension */
4690: if((ficres =fopen(rfileres,"w"))==NULL) {
4691: printf("Problem writing new parameter file: %s\n", fileres);goto end;
4692: fprintf(ficlog,"Problem writing new parameter file: %s\n", fileres);goto end;
4693: }
4694: fprintf(ficres,"#%s\n",version);
4695: } /* End of mle != -3 */
4696:
4697: /*-------- data file ----------*/
4698: if((fic=fopen(datafile,"r"))==NULL) {
4699: printf("Problem while opening datafile: %s\n", datafile);goto end;
4700: fprintf(ficlog,"Problem while opening datafile: %s\n", datafile);goto end;
4701: }
4702:
4703: n= lastobs;
4704: severity = vector(1,maxwav);
4705: outcome=imatrix(1,maxwav+1,1,n);
4706: num=lvector(1,n);
4707: moisnais=vector(1,n);
4708: annais=vector(1,n);
4709: moisdc=vector(1,n);
4710: andc=vector(1,n);
4711: agedc=vector(1,n);
4712: cod=ivector(1,n);
4713: weight=vector(1,n);
4714: for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */
4715: mint=matrix(1,maxwav,1,n);
4716: anint=matrix(1,maxwav,1,n);
4717: s=imatrix(1,maxwav+1,1,n);
4718: tab=ivector(1,NCOVMAX);
4719: ncodemax=ivector(1,8);
4720:
4721: i=1;
4722: linei=0;
4723: while ((fgets(line, MAXLINE, fic) != NULL) &&((i >= firstobs) && (i <=lastobs))) {
4724: linei=linei+1;
4725: for(j=strlen(line); j>=0;j--){ /* Untabifies line */
4726: if(line[j] == '\t')
4727: line[j] = ' ';
4728: }
4729: for(j=strlen(line)-1; (line[j]==' ')||(line[j]==10)||(line[j]==13);j--){
4730: ;
4731: };
4732: line[j+1]=0; /* Trims blanks at end of line */
4733: if(line[0]=='#'){
4734: fprintf(ficlog,"Comment line\n%s\n",line);
4735: printf("Comment line\n%s\n",line);
4736: continue;
4737: }
4738:
4739: for (j=maxwav;j>=1;j--){
4740: cutv(stra, strb,line,' ');
4741: errno=0;
4742: lval=strtol(strb,&endptr,10);
4743: /* if (errno == ERANGE && (lval == LONG_MAX || lval == LONG_MIN))*/
4744: if( strb[0]=='\0' || (*endptr != '\0')){
4745: printf("Error reading data around '%d' at line number %d %s 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);
4746: exit(1);
4747: }
4748: s[j][i]=lval;
4749:
4750: strcpy(line,stra);
4751: cutv(stra, strb,line,' ');
4752: if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){
4753: }
4754: else if(iout=sscanf(strb,"%s.") != 0){
4755: month=99;
4756: year=9999;
4757: }else{
4758: printf("Error reading data around '%s' at line number %ld %s for individual %d, '%s'\nShould be a date of interview (mm/yyyy or .) at wave %d. Exiting.\n",strb, linei,i, line,j);
4759: exit(1);
4760: }
4761: anint[j][i]= (double) year;
4762: mint[j][i]= (double)month;
4763: strcpy(line,stra);
4764: } /* ENd Waves */
4765:
4766: cutv(stra, strb,line,' ');
4767: if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){
4768: }
4769: else if(iout=sscanf(strb,"%s.",dummy) != 0){
4770: month=99;
4771: year=9999;
4772: }else{
4773: printf("Error reading data around '%s' at line number %ld %s for individual %d, '%s'\nShould be a date of death (mm/yyyy or .). Exiting.\n",strb, linei,i,line);
4774: exit(1);
4775: }
4776: andc[i]=(double) year;
4777: moisdc[i]=(double) month;
4778: strcpy(line,stra);
4779:
4780: cutv(stra, strb,line,' ');
4781: if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){
4782: }
4783: else if(iout=sscanf(strb,"%s.") != 0){
4784: month=99;
4785: year=9999;
4786: }else{
4787: printf("Error reading data around '%s' at line number %ld %s for individual %d, '%s'\nShould be a date of birth (mm/yyyy or .). Exiting.\n",strb, linei,i,line,j);
4788: exit(1);
4789: }
4790: annais[i]=(double)(year);
4791: moisnais[i]=(double)(month);
4792: strcpy(line,stra);
4793:
4794: cutv(stra, strb,line,' ');
4795: errno=0;
4796: lval=strtol(strb,&endptr,10);
4797: if( strb[0]=='\0' || (*endptr != '\0')){
4798: printf("Error reading data around '%d' at line number %ld %s for individual %d\nShould be a weight. Exiting.\n",lval, i,line,linei);
4799: exit(1);
4800: }
4801: weight[i]=(double)(lval);
4802: strcpy(line,stra);
4803:
4804: for (j=ncovcol;j>=1;j--){
4805: cutv(stra, strb,line,' ');
4806: errno=0;
4807: lval=strtol(strb,&endptr,10);
4808: if( strb[0]=='\0' || (*endptr != '\0')){
4809: printf("Error reading data around '%d' at line number %ld %s for individual %d, '%s'\nShould be a covar (meaning 0 for the reference or 1). Exiting.\n",lval, linei,i, line);
4810: exit(1);
4811: }
4812: if(lval <-1 || lval >1){
4813: printf("Error reading data around '%d' at line number %ld %s for individual %d, '%s'\nShould be a value of the %d covar (meaning 0 for the reference or 1. IMaCh does not build design variables, do it your self). Exiting.\n",lval,linei, i,line,j);
4814: exit(1);
4815: }
4816: covar[j][i]=(double)(lval);
4817: strcpy(line,stra);
4818: }
4819: lstra=strlen(stra);
4820:
4821: if(lstra > 9){ /* More than 2**32 or max of what printf can write with %ld */
4822: stratrunc = &(stra[lstra-9]);
4823: num[i]=atol(stratrunc);
4824: }
4825: else
4826: num[i]=atol(stra);
4827: /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){
4828: 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;}*/
4829:
4830: i=i+1;
4831: } /* End loop reading data */
4832: fclose(fic);
4833: /* printf("ii=%d", ij);
4834: scanf("%d",i);*/
4835: imx=i-1; /* Number of individuals */
4836:
4837: /* for (i=1; i<=imx; i++){
4838: if ((s[1][i]==3) && (s[2][i]==2)) s[2][i]=3;
4839: if ((s[2][i]==3) && (s[3][i]==2)) s[3][i]=3;
4840: if ((s[3][i]==3) && (s[4][i]==2)) s[4][i]=3;
4841: }*/
4842: /* for (i=1; i<=imx; i++){
4843: if (s[4][i]==9) s[4][i]=-1;
4844: 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]));}*/
4845:
4846: /* for (i=1; i<=imx; i++) */
4847:
4848: /*if ((s[3][i]==3) || (s[4][i]==3)) weight[i]=0.08;
4849: else weight[i]=1;*/
4850:
4851: /* Calculation of the number of parameters from char model */
4852: Tvar=ivector(1,15); /* stores the number n of the covariates in Vm+Vn at 1 and m at 2 */
4853: Tprod=ivector(1,15);
4854: Tvaraff=ivector(1,15);
4855: Tvard=imatrix(1,15,1,2);
4856: Tage=ivector(1,15);
4857:
4858: if (strlen(model) >1){ /* If there is at least 1 covariate */
4859: j=0, j1=0, k1=1, k2=1;
4860: j=nbocc(model,'+'); /* j=Number of '+' */
4861: j1=nbocc(model,'*'); /* j1=Number of '*' */
4862: cptcovn=j+1;
4863: cptcovprod=j1; /*Number of products */
4864:
4865: strcpy(modelsav,model);
4866: if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){
4867: printf("Error. Non available option model=%s ",model);
4868: fprintf(ficlog,"Error. Non available option model=%s ",model);
4869: goto end;
4870: }
4871:
4872: /* This loop fills the array Tvar from the string 'model'.*/
4873:
4874: for(i=(j+1); i>=1;i--){
4875: cutv(stra,strb,modelsav,'+'); /* keeps in strb after the last + */
4876: if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyzes it */
4877: /* printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/
4878: /*scanf("%d",i);*/
4879: if (strchr(strb,'*')) { /* Model includes a product */
4880: cutv(strd,strc,strb,'*'); /* strd*strc Vm*Vn (if not *age)*/
4881: if (strcmp(strc,"age")==0) { /* Vn*age */
4882: cptcovprod--;
4883: cutv(strb,stre,strd,'V');
4884: Tvar[i]=atoi(stre); /* computes n in Vn and stores in Tvar*/
4885: cptcovage++;
4886: Tage[cptcovage]=i;
4887: /*printf("stre=%s ", stre);*/
4888: }
4889: else if (strcmp(strd,"age")==0) { /* or age*Vn */
4890: cptcovprod--;
4891: cutv(strb,stre,strc,'V');
4892: Tvar[i]=atoi(stre);
4893: cptcovage++;
4894: Tage[cptcovage]=i;
4895: }
4896: else { /* Age is not in the model */
4897: cutv(strb,stre,strc,'V'); /* strc= Vn, stre is n*/
4898: Tvar[i]=ncovcol+k1;
4899: cutv(strb,strc,strd,'V'); /* strd was Vm, strc is m */
4900: Tprod[k1]=i;
4901: Tvard[k1][1]=atoi(strc); /* m*/
4902: Tvard[k1][2]=atoi(stre); /* n */
4903: Tvar[cptcovn+k2]=Tvard[k1][1];
4904: Tvar[cptcovn+k2+1]=Tvard[k1][2];
4905: for (k=1; k<=lastobs;k++)
4906: covar[ncovcol+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];
4907: k1++;
4908: k2=k2+2;
4909: }
4910: }
4911: else { /* no more sum */
4912: /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/
4913: /* scanf("%d",i);*/
4914: cutv(strd,strc,strb,'V');
4915: Tvar[i]=atoi(strc);
4916: }
4917: strcpy(modelsav,stra);
4918: /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);
4919: scanf("%d",i);*/
4920: } /* end of loop + */
4921: } /* end model */
4922:
4923: /*The number n of Vn is stored in Tvar. cptcovage =number of age covariate. Tage gives the position of age. cptcovprod= number of products.
4924: If model=V1+V1*age then Tvar[1]=1 Tvar[2]=1 cptcovage=1 Tage[1]=2 cptcovprod=0*/
4925:
4926: /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);
4927: printf("cptcovprod=%d ", cptcovprod);
4928: fprintf(ficlog,"cptcovprod=%d ", cptcovprod);
4929:
4930: scanf("%d ",i);*/
4931:
4932: /* if(mle==1){*/
4933: if (weightopt != 1) { /* Maximisation without weights*/
4934: for(i=1;i<=n;i++) weight[i]=1.0;
4935: }
4936: /*-calculation of age at interview from date of interview and age at death -*/
4937: agev=matrix(1,maxwav,1,imx);
4938:
4939: for (i=1; i<=imx; i++) {
4940: for(m=2; (m<= maxwav); m++) {
4941: if (((int)mint[m][i]== 99) && (s[m][i] <= nlstate)){
4942: anint[m][i]=9999;
4943: s[m][i]=-1;
4944: }
4945: if((int)moisdc[i]==99 && (int)andc[i]==9999 && s[m][i]>nlstate){
4946: nberr++;
4947: 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);
4948: 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);
4949: s[m][i]=-1;
4950: }
4951: if((int)moisdc[i]==99 && (int)andc[i]!=9999 && s[m][i]>nlstate){
4952: nberr++;
4953: 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]);
4954: 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]);
4955: s[m][i]=-1; /* We prefer to skip it (and to skip it in version 0.8a1 too */
4956: }
4957: }
4958: }
4959:
4960: for (i=1; i<=imx; i++) {
4961: agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);
4962: for(m=firstpass; (m<= lastpass); m++){
4963: if(s[m][i] >0 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5){
4964: if (s[m][i] >= nlstate+1) {
4965: if(agedc[i]>0)
4966: if((int)moisdc[i]!=99 && (int)andc[i]!=9999)
4967: agev[m][i]=agedc[i];
4968: /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/
4969: else {
4970: if ((int)andc[i]!=9999){
4971: nbwarn++;
4972: printf("Warning negative age at death: %ld line:%d\n",num[i],i);
4973: fprintf(ficlog,"Warning negative age at death: %ld line:%d\n",num[i],i);
4974: agev[m][i]=-1;
4975: }
4976: }
4977: }
4978: else if(s[m][i] !=9){ /* Standard case, age in fractional
4979: years but with the precision of a month */
4980: agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);
4981: if((int)mint[m][i]==99 || (int)anint[m][i]==9999)
4982: agev[m][i]=1;
4983: else if(agev[m][i] <agemin){
4984: agemin=agev[m][i];
4985: /*printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], agemin);*/
4986: }
4987: else if(agev[m][i] >agemax){
4988: agemax=agev[m][i];
4989: /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/
4990: }
4991: /*agev[m][i]=anint[m][i]-annais[i];*/
4992: /* agev[m][i] = age[i]+2*m;*/
4993: }
4994: else { /* =9 */
4995: agev[m][i]=1;
4996: s[m][i]=-1;
4997: }
4998: }
4999: else /*= 0 Unknown */
5000: agev[m][i]=1;
5001: }
5002:
5003: }
5004: for (i=1; i<=imx; i++) {
5005: for(m=firstpass; (m<=lastpass); m++){
5006: if (s[m][i] > (nlstate+ndeath)) {
5007: nberr++;
5008: 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);
5009: 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);
5010: goto end;
5011: }
5012: }
5013: }
5014:
5015: /*for (i=1; i<=imx; i++){
5016: for (m=firstpass; (m<lastpass); m++){
5017: printf("%ld %d %.lf %d %d\n", num[i],(covar[1][i]),agev[m][i],s[m][i],s[m+1][i]);
5018: }
5019:
5020: }*/
5021:
5022:
5023: printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);
5024: fprintf(ficlog,"Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);
5025:
5026: agegomp=(int)agemin;
5027: free_vector(severity,1,maxwav);
5028: free_imatrix(outcome,1,maxwav+1,1,n);
5029: free_vector(moisnais,1,n);
5030: free_vector(annais,1,n);
5031: /* free_matrix(mint,1,maxwav,1,n);
5032: free_matrix(anint,1,maxwav,1,n);*/
5033: free_vector(moisdc,1,n);
5034: free_vector(andc,1,n);
5035:
5036:
5037: wav=ivector(1,imx);
5038: dh=imatrix(1,lastpass-firstpass+1,1,imx);
5039: bh=imatrix(1,lastpass-firstpass+1,1,imx);
5040: mw=imatrix(1,lastpass-firstpass+1,1,imx);
5041:
5042: /* Concatenates waves */
5043: concatwav(wav, dh, bh, mw, s, agedc, agev, firstpass, lastpass, imx, nlstate, stepm);
5044:
5045: /* Routine tricode is to calculate cptcoveff (real number of unique covariates) and to associate covariable number and modality */
5046:
5047: Tcode=ivector(1,100);
5048: nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);
5049: ncodemax[1]=1;
5050: if (cptcovn > 0) tricode(Tvar,nbcode,imx);
5051:
5052: codtab=imatrix(1,100,1,10); /* Cross tabulation to get the order of
5053: the estimations*/
5054: h=0;
5055: m=pow(2,cptcoveff);
5056:
5057: for(k=1;k<=cptcoveff; k++){
5058: for(i=1; i <=(m/pow(2,k));i++){
5059: for(j=1; j <= ncodemax[k]; j++){
5060: for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){
5061: h++;
5062: if (h>m) h=1;codtab[h][k]=j;codtab[h][Tvar[k]]=j;
5063: /* printf("h=%d k=%d j=%d codtab[h][k]=%d tvar[k]=%d \n",h, k,j,codtab[h][k],Tvar[k]);*/
5064: }
5065: }
5066: }
5067: }
5068: /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]);
5069: codtab[1][2]=1;codtab[2][2]=2; */
5070: /* for(i=1; i <=m ;i++){
5071: for(k=1; k <=cptcovn; k++){
5072: printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);
5073: }
5074: printf("\n");
5075: }
5076: scanf("%d",i);*/
5077:
5078: /*------------ gnuplot -------------*/
5079: strcpy(optionfilegnuplot,optionfilefiname);
5080: if(mle==-3)
5081: strcat(optionfilegnuplot,"-mort");
5082: strcat(optionfilegnuplot,".gp");
5083:
5084: if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {
5085: printf("Problem with file %s",optionfilegnuplot);
5086: }
5087: else{
5088: fprintf(ficgp,"\n# %s\n", version);
5089: fprintf(ficgp,"# %s\n", optionfilegnuplot);
5090: fprintf(ficgp,"set missing 'NaNq'\n");
5091: }
5092: /* fclose(ficgp);*/
5093: /*--------- index.htm --------*/
5094:
5095: strcpy(optionfilehtm,optionfilefiname); /* Main html file */
5096: if(mle==-3)
5097: strcat(optionfilehtm,"-mort");
5098: strcat(optionfilehtm,".htm");
5099: if((fichtm=fopen(optionfilehtm,"w"))==NULL) {
5100: printf("Problem with %s \n",optionfilehtm), exit(0);
5101: }
5102:
5103: strcpy(optionfilehtmcov,optionfilefiname); /* Only for matrix of covariance */
5104: strcat(optionfilehtmcov,"-cov.htm");
5105: if((fichtmcov=fopen(optionfilehtmcov,"w"))==NULL) {
5106: printf("Problem with %s \n",optionfilehtmcov), exit(0);
5107: }
5108: else{
5109: fprintf(fichtmcov,"<body>\n<title>IMaCh Cov %s</title>\n <font size=\"2\">%s <br> %s</font> \
5110: <hr size=\"2\" color=\"#EC5E5E\"> \n\
5111: Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n",\
5112: fileres,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);
5113: }
5114:
5115: fprintf(fichtm,"<body>\n<title>IMaCh %s</title>\n <font size=\"2\">%s <br> %s</font> \
5116: <hr size=\"2\" color=\"#EC5E5E\"> \n\
5117: Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n\
5118: \n\
5119: <hr size=\"2\" color=\"#EC5E5E\">\
5120: <ul><li><h4>Parameter files</h4>\n\
5121: - Parameter file: <a href=\"%s.%s\">%s.%s</a><br>\n\
5122: - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n\
5123: - Log file of the run: <a href=\"%s\">%s</a><br>\n\
5124: - Gnuplot file name: <a href=\"%s\">%s</a><br>\n\
5125: - Date and time at start: %s</ul>\n",\
5126: fileres,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model,\
5127: optionfilefiname,optionfilext,optionfilefiname,optionfilext,\
5128: fileres,fileres,\
5129: filelog,filelog,optionfilegnuplot,optionfilegnuplot,strstart);
5130: fflush(fichtm);
5131:
5132: strcpy(pathr,path);
5133: strcat(pathr,optionfilefiname);
5134: chdir(optionfilefiname); /* Move to directory named optionfile */
5135:
5136: /* Calculates basic frequencies. Computes observed prevalence at single age
5137: and prints on file fileres'p'. */
5138: freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint,strstart);
5139:
5140: fprintf(fichtm,"\n");
5141: fprintf(fichtm,"<br>Total number of observations=%d <br>\n\
5142: Youngest age at first (selected) pass %.2f, oldest age %.2f<br>\n\
5143: Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n",\
5144: imx,agemin,agemax,jmin,jmax,jmean);
5145: pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
5146: oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
5147: newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
5148: savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
5149: oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */
5150:
5151:
5152: /* For Powell, parameters are in a vector p[] starting at p[1]
5153: so we point p on param[1][1] so that p[1] maps on param[1][1][1] */
5154: p=param[1][1]; /* *(*(*(param +1)+1)+0) */
5155:
5156: globpr=0; /* To get the number ipmx of contributions and the sum of weights*/
5157:
5158: if (mle==-3){
5159: ximort=matrix(1,NDIM,1,NDIM);
5160: cens=ivector(1,n);
5161: ageexmed=vector(1,n);
5162: agecens=vector(1,n);
5163: dcwave=ivector(1,n);
5164:
5165: for (i=1; i<=imx; i++){
5166: dcwave[i]=-1;
5167: for (m=firstpass; m<=lastpass; m++)
5168: if (s[m][i]>nlstate) {
5169: dcwave[i]=m;
5170: /* printf("i=%d j=%d s=%d dcwave=%d\n",i,j, s[j][i],dcwave[i]);*/
5171: break;
5172: }
5173: }
5174:
5175: for (i=1; i<=imx; i++) {
5176: if (wav[i]>0){
5177: ageexmed[i]=agev[mw[1][i]][i];
5178: j=wav[i];
5179: agecens[i]=1.;
5180:
5181: if (ageexmed[i]> 1 && wav[i] > 0){
5182: agecens[i]=agev[mw[j][i]][i];
5183: cens[i]= 1;
5184: }else if (ageexmed[i]< 1)
5185: cens[i]= -1;
5186: if (agedc[i]< AGESUP && agedc[i]>1 && dcwave[i]>firstpass && dcwave[i]<=lastpass)
5187: cens[i]=0 ;
5188: }
5189: else cens[i]=-1;
5190: }
5191:
5192: for (i=1;i<=NDIM;i++) {
5193: for (j=1;j<=NDIM;j++)
5194: ximort[i][j]=(i == j ? 1.0 : 0.0);
5195: }
5196:
5197: p[1]=0.0268; p[NDIM]=0.083;
5198: /*printf("%lf %lf", p[1], p[2]);*/
5199:
5200:
5201: printf("Powell\n"); fprintf(ficlog,"Powell\n");
5202: strcpy(filerespow,"pow-mort");
5203: strcat(filerespow,fileres);
5204: if((ficrespow=fopen(filerespow,"w"))==NULL) {
5205: printf("Problem with resultfile: %s\n", filerespow);
5206: fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
5207: }
5208: fprintf(ficrespow,"# Powell\n# iter -2*LL");
5209: /* for (i=1;i<=nlstate;i++)
5210: for(j=1;j<=nlstate+ndeath;j++)
5211: if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
5212: */
5213: fprintf(ficrespow,"\n");
5214:
5215: powell(p,ximort,NDIM,ftol,&iter,&fret,gompertz);
5216: fclose(ficrespow);
5217:
5218: hesscov(matcov, p, NDIM, delti, 1e-4, gompertz);
5219:
5220: for(i=1; i <=NDIM; i++)
5221: for(j=i+1;j<=NDIM;j++)
5222: matcov[i][j]=matcov[j][i];
5223:
5224: printf("\nCovariance matrix\n ");
5225: for(i=1; i <=NDIM; i++) {
5226: for(j=1;j<=NDIM;j++){
5227: printf("%f ",matcov[i][j]);
5228: }
5229: printf("\n ");
5230: }
5231:
5232: printf("iter=%d MLE=%f Eq=%lf*exp(%lf*(age-%d))\n",iter,-gompertz(p),p[1],p[2],agegomp);
5233: for (i=1;i<=NDIM;i++)
5234: printf("%f [%f ; %f]\n",p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
5235:
5236: lsurv=vector(1,AGESUP);
5237: lpop=vector(1,AGESUP);
5238: tpop=vector(1,AGESUP);
5239: lsurv[agegomp]=100000;
5240:
5241: for (k=agegomp;k<=AGESUP;k++) {
5242: agemortsup=k;
5243: if (p[1]*exp(p[2]*(k-agegomp))>1) break;
5244: }
5245:
5246: for (k=agegomp;k<agemortsup;k++)
5247: lsurv[k+1]=lsurv[k]-lsurv[k]*(p[1]*exp(p[2]*(k-agegomp)));
5248:
5249: for (k=agegomp;k<agemortsup;k++){
5250: lpop[k]=(lsurv[k]+lsurv[k+1])/2.;
5251: sumlpop=sumlpop+lpop[k];
5252: }
5253:
5254: tpop[agegomp]=sumlpop;
5255: for (k=agegomp;k<(agemortsup-3);k++){
5256: /* tpop[k+1]=2;*/
5257: tpop[k+1]=tpop[k]-lpop[k];
5258: }
5259:
5260:
5261: printf("\nAge lx qx dx Lx Tx e(x)\n");
5262: for (k=agegomp;k<(agemortsup-2);k++)
5263: 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]);
5264:
5265:
5266: replace_back_to_slash(pathc,path); /* Even gnuplot wants a / */
5267: printinggnuplotmort(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
5268:
5269: printinghtmlmort(fileres,title,datafile, firstpass, lastpass, \
5270: stepm, weightopt,\
5271: model,imx,p,matcov,agemortsup);
5272:
5273: free_vector(lsurv,1,AGESUP);
5274: free_vector(lpop,1,AGESUP);
5275: free_vector(tpop,1,AGESUP);
5276: } /* Endof if mle==-3 */
5277:
5278: else{ /* For mle >=1 */
5279:
5280: likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
5281: printf("First Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
5282: for (k=1; k<=npar;k++)
5283: printf(" %d %8.5f",k,p[k]);
5284: printf("\n");
5285: globpr=1; /* to print the contributions */
5286: likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
5287: printf("Second Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
5288: for (k=1; k<=npar;k++)
5289: printf(" %d %8.5f",k,p[k]);
5290: printf("\n");
5291: if(mle>=1){ /* Could be 1 or 2 */
5292: mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);
5293: }
5294:
5295: /*--------- results files --------------*/
5296: 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);
5297:
5298:
5299: fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
5300: printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
5301: fprintf(ficlog,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
5302: for(i=1,jk=1; i <=nlstate; i++){
5303: for(k=1; k <=(nlstate+ndeath); k++){
5304: if (k != i) {
5305: printf("%d%d ",i,k);
5306: fprintf(ficlog,"%d%d ",i,k);
5307: fprintf(ficres,"%1d%1d ",i,k);
5308: for(j=1; j <=ncovmodel; j++){
5309: printf("%f ",p[jk]);
5310: fprintf(ficlog,"%f ",p[jk]);
5311: fprintf(ficres,"%f ",p[jk]);
5312: jk++;
5313: }
5314: printf("\n");
5315: fprintf(ficlog,"\n");
5316: fprintf(ficres,"\n");
5317: }
5318: }
5319: }
5320: if(mle!=0){
5321: /* Computing hessian and covariance matrix */
5322: ftolhess=ftol; /* Usually correct */
5323: hesscov(matcov, p, npar, delti, ftolhess, func);
5324: }
5325: fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");
5326: printf("# Scales (for hessian or gradient estimation)\n");
5327: fprintf(ficlog,"# Scales (for hessian or gradient estimation)\n");
5328: for(i=1,jk=1; i <=nlstate; i++){
5329: for(j=1; j <=nlstate+ndeath; j++){
5330: if (j!=i) {
5331: fprintf(ficres,"%1d%1d",i,j);
5332: printf("%1d%1d",i,j);
5333: fprintf(ficlog,"%1d%1d",i,j);
5334: for(k=1; k<=ncovmodel;k++){
5335: printf(" %.5e",delti[jk]);
5336: fprintf(ficlog," %.5e",delti[jk]);
5337: fprintf(ficres," %.5e",delti[jk]);
5338: jk++;
5339: }
5340: printf("\n");
5341: fprintf(ficlog,"\n");
5342: fprintf(ficres,"\n");
5343: }
5344: }
5345: }
5346:
5347: 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");
5348: if(mle>=1)
5349: 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");
5350: 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");
5351: /* # 121 Var(a12)\n\ */
5352: /* # 122 Cov(b12,a12) Var(b12)\n\ */
5353: /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
5354: /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
5355: /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
5356: /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
5357: /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
5358: /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
5359:
5360:
5361: /* Just to have a covariance matrix which will be more understandable
5362: even is we still don't want to manage dictionary of variables
5363: */
5364: for(itimes=1;itimes<=2;itimes++){
5365: jj=0;
5366: for(i=1; i <=nlstate; i++){
5367: for(j=1; j <=nlstate+ndeath; j++){
5368: if(j==i) continue;
5369: for(k=1; k<=ncovmodel;k++){
5370: jj++;
5371: ca[0]= k+'a'-1;ca[1]='\0';
5372: if(itimes==1){
5373: if(mle>=1)
5374: printf("#%1d%1d%d",i,j,k);
5375: fprintf(ficlog,"#%1d%1d%d",i,j,k);
5376: fprintf(ficres,"#%1d%1d%d",i,j,k);
5377: }else{
5378: if(mle>=1)
5379: printf("%1d%1d%d",i,j,k);
5380: fprintf(ficlog,"%1d%1d%d",i,j,k);
5381: fprintf(ficres,"%1d%1d%d",i,j,k);
5382: }
5383: ll=0;
5384: for(li=1;li <=nlstate; li++){
5385: for(lj=1;lj <=nlstate+ndeath; lj++){
5386: if(lj==li) continue;
5387: for(lk=1;lk<=ncovmodel;lk++){
5388: ll++;
5389: if(ll<=jj){
5390: cb[0]= lk +'a'-1;cb[1]='\0';
5391: if(ll<jj){
5392: if(itimes==1){
5393: if(mle>=1)
5394: printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
5395: fprintf(ficlog," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
5396: fprintf(ficres," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
5397: }else{
5398: if(mle>=1)
5399: printf(" %.5e",matcov[jj][ll]);
5400: fprintf(ficlog," %.5e",matcov[jj][ll]);
5401: fprintf(ficres," %.5e",matcov[jj][ll]);
5402: }
5403: }else{
5404: if(itimes==1){
5405: if(mle>=1)
5406: printf(" Var(%s%1d%1d)",ca,i,j);
5407: fprintf(ficlog," Var(%s%1d%1d)",ca,i,j);
5408: fprintf(ficres," Var(%s%1d%1d)",ca,i,j);
5409: }else{
5410: if(mle>=1)
5411: printf(" %.5e",matcov[jj][ll]);
5412: fprintf(ficlog," %.5e",matcov[jj][ll]);
5413: fprintf(ficres," %.5e",matcov[jj][ll]);
5414: }
5415: }
5416: }
5417: } /* end lk */
5418: } /* end lj */
5419: } /* end li */
5420: if(mle>=1)
5421: printf("\n");
5422: fprintf(ficlog,"\n");
5423: fprintf(ficres,"\n");
5424: numlinepar++;
5425: } /* end k*/
5426: } /*end j */
5427: } /* end i */
5428: } /* end itimes */
5429:
5430: fflush(ficlog);
5431: fflush(ficres);
5432:
5433: while((c=getc(ficpar))=='#' && c!= EOF){
5434: ungetc(c,ficpar);
5435: fgets(line, MAXLINE, ficpar);
5436: puts(line);
5437: fputs(line,ficparo);
5438: }
5439: ungetc(c,ficpar);
5440:
5441: estepm=0;
5442: fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm);
5443: if (estepm==0 || estepm < stepm) estepm=stepm;
5444: if (fage <= 2) {
5445: bage = ageminpar;
5446: fage = agemaxpar;
5447: }
5448:
5449: fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");
5450: fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
5451: fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
5452:
5453: while((c=getc(ficpar))=='#' && c!= EOF){
5454: ungetc(c,ficpar);
5455: fgets(line, MAXLINE, ficpar);
5456: puts(line);
5457: fputs(line,ficparo);
5458: }
5459: ungetc(c,ficpar);
5460:
5461: 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);
5462: 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);
5463: 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);
5464: printf("begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
5465: 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);
5466:
5467: while((c=getc(ficpar))=='#' && c!= EOF){
5468: ungetc(c,ficpar);
5469: fgets(line, MAXLINE, ficpar);
5470: puts(line);
5471: fputs(line,ficparo);
5472: }
5473: ungetc(c,ficpar);
5474:
5475:
5476: dateprev1=anprev1+(mprev1-1)/12.+(jprev1-1)/365.;
5477: dateprev2=anprev2+(mprev2-1)/12.+(jprev2-1)/365.;
5478:
5479: fscanf(ficpar,"pop_based=%d\n",&popbased);
5480: fprintf(ficparo,"pop_based=%d\n",popbased);
5481: fprintf(ficres,"pop_based=%d\n",popbased);
5482:
5483: while((c=getc(ficpar))=='#' && c!= EOF){
5484: ungetc(c,ficpar);
5485: fgets(line, MAXLINE, ficpar);
5486: puts(line);
5487: fputs(line,ficparo);
5488: }
5489: ungetc(c,ficpar);
5490:
5491: 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);
5492: 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);
5493: 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);
5494: 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);
5495: 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);
5496: /* day and month of proj2 are not used but only year anproj2.*/
5497:
5498:
5499:
5500: /* freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint);*/
5501: /*,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
5502:
5503: replace_back_to_slash(pathc,path); /* Even gnuplot wants a / */
5504: printinggnuplot(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
5505:
5506: printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,\
5507: model,imx,jmin,jmax,jmean,rfileres,popforecast,estepm,\
5508: jprev1,mprev1,anprev1,jprev2,mprev2,anprev2);
5509:
5510: /*------------ free_vector -------------*/
5511: /* chdir(path); */
5512:
5513: free_ivector(wav,1,imx);
5514: free_imatrix(dh,1,lastpass-firstpass+1,1,imx);
5515: free_imatrix(bh,1,lastpass-firstpass+1,1,imx);
5516: free_imatrix(mw,1,lastpass-firstpass+1,1,imx);
5517: free_lvector(num,1,n);
5518: free_vector(agedc,1,n);
5519: /*free_matrix(covar,0,NCOVMAX,1,n);*/
5520: /*free_matrix(covar,1,NCOVMAX,1,n);*/
5521: fclose(ficparo);
5522: fclose(ficres);
5523:
5524:
5525: /*--------------- Prevalence limit (period or stable prevalence) --------------*/
5526:
5527: strcpy(filerespl,"pl");
5528: strcat(filerespl,fileres);
5529: if((ficrespl=fopen(filerespl,"w"))==NULL) {
5530: printf("Problem with period (stable) prevalence resultfile: %s\n", filerespl);goto end;
5531: fprintf(ficlog,"Problem with period (stable) prevalence resultfile: %s\n", filerespl);goto end;
5532: }
5533: printf("Computing period (stable) prevalence: result on file '%s' \n", filerespl);
5534: fprintf(ficlog,"Computing period (stable) prevalence: result on file '%s' \n", filerespl);
5535: pstamp(ficrespl);
5536: fprintf(ficrespl,"# Period (stable) prevalence \n");
5537: fprintf(ficrespl,"#Age ");
5538: for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);
5539: fprintf(ficrespl,"\n");
5540:
5541: prlim=matrix(1,nlstate,1,nlstate);
5542:
5543: agebase=ageminpar;
5544: agelim=agemaxpar;
5545: ftolpl=1.e-10;
5546: i1=cptcoveff;
5547: if (cptcovn < 1){i1=1;}
5548:
5549: for(cptcov=1,k=0;cptcov<=i1;cptcov++){
5550: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
5551: k=k+1;
5552: /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/
5553: fprintf(ficrespl,"\n#******");
5554: printf("\n#******");
5555: fprintf(ficlog,"\n#******");
5556: for(j=1;j<=cptcoveff;j++) {
5557: fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
5558: printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
5559: fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
5560: }
5561: fprintf(ficrespl,"******\n");
5562: printf("******\n");
5563: fprintf(ficlog,"******\n");
5564:
5565: for (age=agebase; age<=agelim; age++){
5566: prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
5567: fprintf(ficrespl,"%.0f ",age );
5568: for(j=1;j<=cptcoveff;j++)
5569: fprintf(ficrespl,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
5570: for(i=1; i<=nlstate;i++)
5571: fprintf(ficrespl," %.5f", prlim[i][i]);
5572: fprintf(ficrespl,"\n");
5573: }
5574: }
5575: }
5576: fclose(ficrespl);
5577:
5578: /*------------- h Pij x at various ages ------------*/
5579:
5580: strcpy(filerespij,"pij"); strcat(filerespij,fileres);
5581: if((ficrespij=fopen(filerespij,"w"))==NULL) {
5582: printf("Problem with Pij resultfile: %s\n", filerespij);goto end;
5583: fprintf(ficlog,"Problem with Pij resultfile: %s\n", filerespij);goto end;
5584: }
5585: printf("Computing pij: result on file '%s' \n", filerespij);
5586: fprintf(ficlog,"Computing pij: result on file '%s' \n", filerespij);
5587:
5588: stepsize=(int) (stepm+YEARM-1)/YEARM;
5589: /*if (stepm<=24) stepsize=2;*/
5590:
5591: agelim=AGESUP;
5592: hstepm=stepsize*YEARM; /* Every year of age */
5593: hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */
5594:
5595: /* hstepm=1; aff par mois*/
5596: pstamp(ficrespij);
5597: fprintf(ficrespij,"#****** h Pij x Probability to be in state j at age x+h being in i at x ");
5598: for(cptcov=1,k=0;cptcov<=i1;cptcov++){
5599: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
5600: k=k+1;
5601: fprintf(ficrespij,"\n#****** ");
5602: for(j=1;j<=cptcoveff;j++)
5603: fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
5604: fprintf(ficrespij,"******\n");
5605:
5606: for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */
5607: nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
5608: nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
5609:
5610: /* nhstepm=nhstepm*YEARM; aff par mois*/
5611:
5612: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
5613: oldm=oldms;savm=savms;
5614: hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
5615: fprintf(ficrespij,"# Cov Agex agex+h hpijx with i,j=");
5616: for(i=1; i<=nlstate;i++)
5617: for(j=1; j<=nlstate+ndeath;j++)
5618: fprintf(ficrespij," %1d-%1d",i,j);
5619: fprintf(ficrespij,"\n");
5620: for (h=0; h<=nhstepm; h++){
5621: fprintf(ficrespij,"%d %3.f %3.f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );
5622: for(i=1; i<=nlstate;i++)
5623: for(j=1; j<=nlstate+ndeath;j++)
5624: fprintf(ficrespij," %.5f", p3mat[i][j][h]);
5625: fprintf(ficrespij,"\n");
5626: }
5627: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
5628: fprintf(ficrespij,"\n");
5629: }
5630: }
5631: }
5632:
5633: varprob(optionfilefiname, matcov, p, delti, nlstate, bage, fage,k,Tvar,nbcode, ncodemax,strstart);
5634:
5635: fclose(ficrespij);
5636:
5637: probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
5638: for(i=1;i<=AGESUP;i++)
5639: for(j=1;j<=NCOVMAX;j++)
5640: for(k=1;k<=NCOVMAX;k++)
5641: probs[i][j][k]=0.;
5642:
5643: /*---------- Forecasting ------------------*/
5644: /*if((stepm == 1) && (strcmp(model,".")==0)){*/
5645: if(prevfcast==1){
5646: /* if(stepm ==1){*/
5647: prevforecast(fileres, anproj1, mproj1, jproj1, agemin, agemax, dateprev1, dateprev2, mobilavproj, bage, fage, firstpass, lastpass, anproj2, p, cptcoveff);
5648: /* (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);*/
5649: /* } */
5650: /* else{ */
5651: /* erreur=108; */
5652: /* 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); */
5653: /* 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); */
5654: /* } */
5655: }
5656:
5657:
5658: /*---------- Health expectancies and variances ------------*/
5659:
5660: strcpy(filerest,"t");
5661: strcat(filerest,fileres);
5662: if((ficrest=fopen(filerest,"w"))==NULL) {
5663: printf("Problem with total LE resultfile: %s\n", filerest);goto end;
5664: fprintf(ficlog,"Problem with total LE resultfile: %s\n", filerest);goto end;
5665: }
5666: printf("Computing Total Life expectancies with their standard errors: file '%s' \n", filerest);
5667: fprintf(ficlog,"Computing Total Life expectancies with their standard errors: file '%s' \n", filerest);
5668:
5669:
5670: strcpy(filerese,"e");
5671: strcat(filerese,fileres);
5672: if((ficreseij=fopen(filerese,"w"))==NULL) {
5673: printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
5674: fprintf(ficlog,"Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
5675: }
5676: printf("Computing Health Expectancies: result on file '%s' \n", filerese);
5677: fprintf(ficlog,"Computing Health Expectancies: result on file '%s' \n", filerese);
5678:
5679: strcpy(fileresstde,"stde");
5680: strcat(fileresstde,fileres);
5681: if((ficresstdeij=fopen(fileresstde,"w"))==NULL) {
5682: printf("Problem with Health Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
5683: fprintf(ficlog,"Problem with Health Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
5684: }
5685: printf("Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde);
5686: fprintf(ficlog,"Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde);
5687:
5688: strcpy(filerescve,"cve");
5689: strcat(filerescve,fileres);
5690: if((ficrescveij=fopen(filerescve,"w"))==NULL) {
5691: printf("Problem with Covar. Health Exp. resultfile: %s\n", filerescve); exit(0);
5692: fprintf(ficlog,"Problem with Covar. Health Exp. resultfile: %s\n", filerescve); exit(0);
5693: }
5694: printf("Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve);
5695: fprintf(ficlog,"Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve);
5696:
5697: strcpy(fileresv,"v");
5698: strcat(fileresv,fileres);
5699: if((ficresvij=fopen(fileresv,"w"))==NULL) {
5700: printf("Problem with variance resultfile: %s\n", fileresv);exit(0);
5701: fprintf(ficlog,"Problem with variance resultfile: %s\n", fileresv);exit(0);
5702: }
5703: printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
5704: fprintf(ficlog,"Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
5705:
5706: /* Computes prevalence between agemin (i.e minimal age computed) and no more ageminpar */
5707: prevalence(probs, agemin, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
5708: /* 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",\
5709: ageminpar, agemax, s[lastpass][imx], agev[lastpass][imx], nlstate, imx, mint[lastpass][imx],anint[lastpass][imx], dateprev1, dateprev2, firstpass, lastpass);
5710: */
5711:
5712: if (mobilav!=0) {
5713: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
5714: if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
5715: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
5716: printf(" Error in movingaverage mobilav=%d\n",mobilav);
5717: }
5718: }
5719:
5720: for(cptcov=1,k=0;cptcov<=i1;cptcov++){
5721: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
5722: k=k+1;
5723: fprintf(ficrest,"\n#****** ");
5724: for(j=1;j<=cptcoveff;j++)
5725: fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
5726: fprintf(ficrest,"******\n");
5727:
5728: fprintf(ficreseij,"\n#****** ");
5729: fprintf(ficresstdeij,"\n#****** ");
5730: fprintf(ficrescveij,"\n#****** ");
5731: for(j=1;j<=cptcoveff;j++) {
5732: fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
5733: fprintf(ficresstdeij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
5734: fprintf(ficrescveij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
5735: }
5736: fprintf(ficreseij,"******\n");
5737: fprintf(ficresstdeij,"******\n");
5738: fprintf(ficrescveij,"******\n");
5739:
5740: fprintf(ficresvij,"\n#****** ");
5741: for(j=1;j<=cptcoveff;j++)
5742: fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
5743: fprintf(ficresvij,"******\n");
5744:
5745: eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
5746: oldm=oldms;savm=savms;
5747: evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, strstart);
5748: cvevsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov, strstart);
5749:
5750: vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
5751: oldm=oldms;savm=savms;
5752: varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,0, mobilav, strstart);
5753: if(popbased==1){
5754: varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,popbased,mobilav, strstart);
5755: }
5756:
5757: pstamp(ficrest);
5758: fprintf(ficrest,"# Total life expectancy with std error and decomposition into time to be expected in each health state\n# Age ( e.. (std) ");
5759: for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);
5760: fprintf(ficrest,"\n");
5761:
5762: epj=vector(1,nlstate+1);
5763: for(age=bage; age <=fage ;age++){
5764: prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
5765: if (popbased==1) {
5766: if(mobilav ==0){
5767: for(i=1; i<=nlstate;i++)
5768: prlim[i][i]=probs[(int)age][i][k];
5769: }else{ /* mobilav */
5770: for(i=1; i<=nlstate;i++)
5771: prlim[i][i]=mobaverage[(int)age][i][k];
5772: }
5773: }
5774:
5775: fprintf(ficrest," %4.0f",age);
5776: for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){
5777: for(i=1, epj[j]=0.;i <=nlstate;i++) {
5778: epj[j] += prlim[i][i]*eij[i][j][(int)age];
5779: /* printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/
5780: }
5781: epj[nlstate+1] +=epj[j];
5782: }
5783:
5784: for(i=1, vepp=0.;i <=nlstate;i++)
5785: for(j=1;j <=nlstate;j++)
5786: vepp += vareij[i][j][(int)age];
5787: fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));
5788: for(j=1;j <=nlstate;j++){
5789: fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));
5790: }
5791: fprintf(ficrest,"\n");
5792: }
5793: free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
5794: free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);
5795: free_vector(epj,1,nlstate+1);
5796: }
5797: }
5798: free_vector(weight,1,n);
5799: free_imatrix(Tvard,1,15,1,2);
5800: free_imatrix(s,1,maxwav+1,1,n);
5801: free_matrix(anint,1,maxwav,1,n);
5802: free_matrix(mint,1,maxwav,1,n);
5803: free_ivector(cod,1,n);
5804: free_ivector(tab,1,NCOVMAX);
5805: fclose(ficreseij);
5806: fclose(ficresstdeij);
5807: fclose(ficrescveij);
5808: fclose(ficresvij);
5809: fclose(ficrest);
5810: fclose(ficpar);
5811:
5812: /*------- Variance of period (stable) prevalence------*/
5813:
5814: strcpy(fileresvpl,"vpl");
5815: strcat(fileresvpl,fileres);
5816: if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {
5817: printf("Problem with variance of period (stable) prevalence resultfile: %s\n", fileresvpl);
5818: exit(0);
5819: }
5820: printf("Computing Variance-covariance of period (stable) prevalence: file '%s' \n", fileresvpl);
5821:
5822: for(cptcov=1,k=0;cptcov<=i1;cptcov++){
5823: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
5824: k=k+1;
5825: fprintf(ficresvpl,"\n#****** ");
5826: for(j=1;j<=cptcoveff;j++)
5827: fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
5828: fprintf(ficresvpl,"******\n");
5829:
5830: varpl=matrix(1,nlstate,(int) bage, (int) fage);
5831: oldm=oldms;savm=savms;
5832: varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k,strstart);
5833: free_matrix(varpl,1,nlstate,(int) bage, (int)fage);
5834: }
5835: }
5836:
5837: fclose(ficresvpl);
5838:
5839: /*---------- End : free ----------------*/
5840: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
5841: free_ma3x(probs,1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
5842:
5843: } /* mle==-3 arrives here for freeing */
5844: free_matrix(prlim,1,nlstate,1,nlstate);
5845: free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);
5846: free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);
5847: free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);
5848: free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);
5849: free_matrix(covar,0,NCOVMAX,1,n);
5850: free_matrix(matcov,1,npar,1,npar);
5851: /*free_vector(delti,1,npar);*/
5852: free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
5853: free_matrix(agev,1,maxwav,1,imx);
5854: free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
5855:
5856: free_ivector(ncodemax,1,8);
5857: free_ivector(Tvar,1,15);
5858: free_ivector(Tprod,1,15);
5859: free_ivector(Tvaraff,1,15);
5860: free_ivector(Tage,1,15);
5861: free_ivector(Tcode,1,100);
5862:
5863: free_imatrix(nbcode,0,NCOVMAX,0,NCOVMAX);
5864: free_imatrix(codtab,1,100,1,10);
5865: fflush(fichtm);
5866: fflush(ficgp);
5867:
5868:
5869: if((nberr >0) || (nbwarn>0)){
5870: printf("End of Imach with %d errors and/or %d warnings\n",nberr,nbwarn);
5871: fprintf(ficlog,"End of Imach with %d errors and/or warnings %d\n",nberr,nbwarn);
5872: }else{
5873: printf("End of Imach\n");
5874: fprintf(ficlog,"End of Imach\n");
5875: }
5876: printf("See log file on %s\n",filelog);
5877: /* gettimeofday(&end_time, (struct timezone*)0);*/ /* after time */
5878: (void) gettimeofday(&end_time,&tzp);
5879: tm = *localtime(&end_time.tv_sec);
5880: tmg = *gmtime(&end_time.tv_sec);
5881: strcpy(strtend,asctime(&tm));
5882: printf("Local time at start %s\nLocal time at end %s",strstart, strtend);
5883: fprintf(ficlog,"Local time at start %s\nLocal time at end %s\n",strstart, strtend);
5884: printf("Total time used %s\n", asc_diff_time(end_time.tv_sec -start_time.tv_sec,tmpout));
5885:
5886: printf("Total time was %d Sec.\n", end_time.tv_sec -start_time.tv_sec);
5887: fprintf(ficlog,"Total time used %s\n", asc_diff_time(end_time.tv_sec -start_time.tv_sec,tmpout));
5888: fprintf(ficlog,"Total time was %d Sec.\n", end_time.tv_sec -start_time.tv_sec);
5889: /* printf("Total time was %d uSec.\n", total_usecs);*/
5890: /* if(fileappend(fichtm,optionfilehtm)){ */
5891: fprintf(fichtm,"<br>Local time at start %s<br>Local time at end %s<br>",strstart, strtend);
5892: fclose(fichtm);
5893: fclose(fichtmcov);
5894: fclose(ficgp);
5895: fclose(ficlog);
5896: /*------ End -----------*/
5897:
5898: chdir(path);
5899: /*strcat(plotcmd,CHARSEPARATOR);*/
5900: sprintf(plotcmd,"gnuplot");
5901: #ifndef UNIX
5902: sprintf(plotcmd,"\"%sgnuplot.exe\"",pathimach);
5903: #endif
5904: if(!stat(plotcmd,&info)){
5905: printf("Error gnuplot program not found: %s\n",plotcmd);fflush(stdout);
5906: if(!stat(getenv("GNUPLOTBIN"),&info)){
5907: printf("Error gnuplot program not found: %s Environment GNUPLOTBIN not set.\n",plotcmd);fflush(stdout);
5908: }else
5909: strcpy(pplotcmd,plotcmd);
5910: #ifdef UNIX
5911: strcpy(plotcmd,GNUPLOTPROGRAM);
5912: if(!stat(plotcmd,&info)){
5913: printf("Error gnuplot program not found: %s\n",plotcmd);fflush(stdout);
5914: }else
5915: strcpy(pplotcmd,plotcmd);
5916: #endif
5917: }else
5918: strcpy(pplotcmd,plotcmd);
5919:
5920: sprintf(plotcmd,"%s %s",pplotcmd, optionfilegnuplot);
5921: printf("Starting graphs with: %s\n",plotcmd);fflush(stdout);
5922:
5923: if((outcmd=system(plotcmd)) != 0){
5924: printf("\n Problem with gnuplot\n");
5925: }
5926: printf(" Wait...");
5927: while (z[0] != 'q') {
5928: /* chdir(path); */
5929: printf("\nType e to edit output files, g to graph again and q for exiting: ");
5930: scanf("%s",z);
5931: /* if (z[0] == 'c') system("./imach"); */
5932: if (z[0] == 'e') {
5933: printf("Starting browser with: %s",optionfilehtm);fflush(stdout);
5934: system(optionfilehtm);
5935: }
5936: else if (z[0] == 'g') system(plotcmd);
5937: else if (z[0] == 'q') exit(0);
5938: }
5939: end:
5940: while (z[0] != 'q') {
5941: printf("\nType q for exiting: ");
5942: scanf("%s",z);
5943: }
5944: }
5945:
5946:
5947:
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