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