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