Annotation of imach/src/imach.c, revision 1.88
1.88 ! brouard 1: /* $Id: imach.c,v 1.87 2003/06/18 12:26:01 brouard Exp $
1.83 lievre 2: $State: Exp $
3: $Log: imach.c,v $
1.88 ! brouard 4: Revision 1.87 2003/06/18 12:26:01 brouard
! 5: Version 0.96
! 6:
1.87 brouard 7: Revision 1.86 2003/06/17 20:04:08 brouard
8: (Module): Change position of html and gnuplot routines and added
9: routine fileappend.
10:
1.86 brouard 11: Revision 1.85 2003/06/17 13:12:43 brouard
12: * imach.c (Repository): Check when date of death was earlier that
13: current date of interview. It may happen when the death was just
14: prior to the death. In this case, dh was negative and likelihood
15: was wrong (infinity). We still send an "Error" but patch by
16: assuming that the date of death was just one stepm after the
17: interview.
18: (Repository): Because some people have very long ID (first column)
19: we changed int to long in num[] and we added a new lvector for
20: memory allocation. But we also truncated to 8 characters (left
21: truncation)
22: (Repository): No more line truncation errors.
23:
1.85 brouard 24: Revision 1.84 2003/06/13 21:44:43 brouard
25: * imach.c (Repository): Replace "freqsummary" at a correct
26: place. It differs from routine "prevalence" which may be called
27: many times. Probs is memory consuming and must be used with
28: parcimony.
1.86 brouard 29: Version 0.95a3 (should output exactly the same maximization than 0.8a2)
1.85 brouard 30:
1.84 brouard 31: Revision 1.83 2003/06/10 13:39:11 lievre
32: *** empty log message ***
33:
1.83 lievre 34: Revision 1.82 2003/06/05 15:57:20 brouard
35: Add log in imach.c and fullversion number is now printed.
36:
1.82 brouard 37: */
38: /*
1.53 brouard 39: Interpolated Markov Chain
40:
41: Short summary of the programme:
42:
43: This program computes Healthy Life Expectancies from
44: cross-longitudinal data. Cross-longitudinal data consist in: -1- a
45: first survey ("cross") where individuals from different ages are
46: interviewed on their health status or degree of disability (in the
47: case of a health survey which is our main interest) -2- at least a
48: second wave of interviews ("longitudinal") which measure each change
49: (if any) in individual health status. Health expectancies are
50: computed from the time spent in each health state according to a
51: model. More health states you consider, more time is necessary to reach the
52: Maximum Likelihood of the parameters involved in the model. The
53: simplest model is the multinomial logistic model where pij is the
54: probability to be observed in state j at the second wave
55: conditional to be observed in state i at the first wave. Therefore
56: the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where
57: 'age' is age and 'sex' is a covariate. If you want to have a more
58: complex model than "constant and age", you should modify the program
59: where the markup *Covariates have to be included here again* invites
60: you to do it. More covariates you add, slower the
61: convergence.
62:
63: The advantage of this computer programme, compared to a simple
64: multinomial logistic model, is clear when the delay between waves is not
65: identical for each individual. Also, if a individual missed an
66: intermediate interview, the information is lost, but taken into
67: account using an interpolation or extrapolation.
68:
69: hPijx is the probability to be observed in state i at age x+h
70: conditional to the observed state i at age x. The delay 'h' can be
71: split into an exact number (nh*stepm) of unobserved intermediate
1.66 brouard 72: states. This elementary transition (by month, quarter,
73: semester or year) is modelled as a multinomial logistic. The hPx
1.53 brouard 74: matrix is simply the matrix product of nh*stepm elementary matrices
75: and the contribution of each individual to the likelihood is simply
76: hPijx.
77:
78: Also this programme outputs the covariance matrix of the parameters but also
1.54 brouard 79: of the life expectancies. It also computes the stable prevalence.
1.53 brouard 80:
81: Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).
82: Institut national d'études démographiques, Paris.
83: This software have been partly granted by Euro-REVES, a concerted action
84: from the European Union.
85: It is copyrighted identically to a GNU software product, ie programme and
86: software can be distributed freely for non commercial use. Latest version
87: can be accessed at http://euroreves.ined.fr/imach .
1.74 brouard 88:
89: Help to debug: LD_PRELOAD=/usr/local/lib/libnjamd.so ./imach foo.imach
90: or better on gdb : set env LD_PRELOAD=/usr/local/lib/libnjamd.so
91:
1.53 brouard 92: **********************************************************************/
1.74 brouard 93: /*
94: main
95: read parameterfile
96: read datafile
97: concatwav
1.84 brouard 98: freqsummary
1.74 brouard 99: if (mle >= 1)
100: mlikeli
101: print results files
102: if mle==1
103: computes hessian
104: read end of parameter file: agemin, agemax, bage, fage, estepm
105: begin-prev-date,...
106: open gnuplot file
107: open html file
108: stable prevalence
109: for age prevalim()
110: h Pij x
111: variance of p varprob
112: forecasting if prevfcast==1 prevforecast call prevalence()
113: health expectancies
114: Variance-covariance of DFLE
115: prevalence()
116: movingaverage()
117: varevsij()
118: if popbased==1 varevsij(,popbased)
119: total life expectancies
120: Variance of stable prevalence
121: end
122: */
123:
124:
125:
1.53 brouard 126:
127: #include <math.h>
128: #include <stdio.h>
129: #include <stdlib.h>
130: #include <unistd.h>
131:
1.86 brouard 132: #include <sys/time.h>
133: #include <time.h>
134: #include "timeval.h"
135:
1.53 brouard 136: #define MAXLINE 256
137: #define GNUPLOTPROGRAM "gnuplot"
138: /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
1.85 brouard 139: #define FILENAMELENGTH 132
1.53 brouard 140: /*#define DEBUG*/
1.85 brouard 141: /*#define windows*/
1.53 brouard 142: #define GLOCK_ERROR_NOPATH -1 /* empty path */
143: #define GLOCK_ERROR_GETCWD -2 /* cannot get cwd */
144:
145: #define MAXPARM 30 /* Maximum number of parameters for the optimization */
146: #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */
147:
148: #define NINTERVMAX 8
149: #define NLSTATEMAX 8 /* Maximum number of live states (for func) */
150: #define NDEATHMAX 8 /* Maximum number of dead states (for func) */
151: #define NCOVMAX 8 /* Maximum number of covariates */
152: #define MAXN 20000
153: #define YEARM 12. /* Number of months per year */
154: #define AGESUP 130
155: #define AGEBASE 40
1.85 brouard 156: #ifdef unix
157: #define DIRSEPARATOR '/'
158: #define ODIRSEPARATOR '\\'
159: #else
1.53 brouard 160: #define DIRSEPARATOR '\\'
161: #define ODIRSEPARATOR '/'
162: #endif
163:
1.88 ! brouard 164: /* $Id: imach.c,v 1.87 2003/06/18 12:26:01 brouard Exp $ */
1.81 brouard 165: /* $State: Exp $ */
1.80 brouard 166:
1.88 ! brouard 167: char version[]="Imach version 0.96a, June 2003, INED-EUROREVES ";
! 168: char fullversion[]="$Revision: 1.87 $ $Date: 2003/06/18 12:26:01 $";
1.53 brouard 169: int erreur; /* Error number */
170: int nvar;
171: int cptcovn=0, cptcovage=0, cptcoveff=0,cptcov;
172: int npar=NPARMAX;
173: int nlstate=2; /* Number of live states */
174: int ndeath=1; /* Number of dead states */
175: int ncovmodel, ncovcol; /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
176: int popbased=0;
177:
178: int *wav; /* Number of waves for this individuual 0 is possible */
179: int maxwav; /* Maxim number of waves */
180: int jmin, jmax; /* min, max spacing between 2 waves */
1.87 brouard 181: int gipmx, gsw; /* Global variables on the number of contributions
182: to the likelihood and the sum of weights (done by funcone)*/
1.53 brouard 183: int mle, weightopt;
184: int **mw; /* mw[mi][i] is number of the mi wave for this individual */
185: int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
1.59 brouard 186: int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between
187: * wave mi and wave mi+1 is not an exact multiple of stepm. */
1.53 brouard 188: double jmean; /* Mean space between 2 waves */
189: double **oldm, **newm, **savm; /* Working pointers to matrices */
190: double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
191: FILE *fic,*ficpar, *ficparo,*ficres, *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
1.76 brouard 192: FILE *ficlog, *ficrespow;
1.85 brouard 193: int globpr; /* Global variable for printing or not */
194: double fretone; /* Only one call to likelihood */
195: long ipmx; /* Number of contributions */
196: double sw; /* Sum of weights */
197: char fileresilk[FILENAMELENGTH]; /* File of individual contributions to the likelihood */
198: FILE *ficresilk;
1.53 brouard 199: FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
200: FILE *ficresprobmorprev;
201: FILE *fichtm; /* Html File */
202: FILE *ficreseij;
203: char filerese[FILENAMELENGTH];
204: FILE *ficresvij;
205: char fileresv[FILENAMELENGTH];
206: FILE *ficresvpl;
207: char fileresvpl[FILENAMELENGTH];
208: char title[MAXLINE];
209: char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH], filerespl[FILENAMELENGTH];
210: char optionfilext[10], optionfilefiname[FILENAMELENGTH], plotcmd[FILENAMELENGTH];
1.88 ! brouard 211: char tmpout[FILENAMELENGTH];
! 212: char command[FILENAMELENGTH];
! 213: int outcmd=0;
1.53 brouard 214:
215: char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
1.88 ! brouard 216: char lfileres[FILENAMELENGTH];
1.53 brouard 217: char filelog[FILENAMELENGTH]; /* Log file */
218: char filerest[FILENAMELENGTH];
219: char fileregp[FILENAMELENGTH];
220: char popfile[FILENAMELENGTH];
221:
222: char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH];
223:
224: #define NR_END 1
225: #define FREE_ARG char*
226: #define FTOL 1.0e-10
227:
228: #define NRANSI
229: #define ITMAX 200
230:
231: #define TOL 2.0e-4
232:
233: #define CGOLD 0.3819660
234: #define ZEPS 1.0e-10
235: #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);
236:
237: #define GOLD 1.618034
238: #define GLIMIT 100.0
239: #define TINY 1.0e-20
240:
241: static double maxarg1,maxarg2;
242: #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
243: #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
244:
245: #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
246: #define rint(a) floor(a+0.5)
247:
248: static double sqrarg;
249: #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
250: #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}
251:
252: int imx;
253: int stepm;
254: /* Stepm, step in month: minimum step interpolation*/
255:
256: int estepm;
257: /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
258:
259: int m,nb;
1.85 brouard 260: long *num;
261: int firstpass=0, lastpass=4,*cod, *ncodemax, *Tage;
1.53 brouard 262: double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
1.55 lievre 263: double **pmmij, ***probs;
1.53 brouard 264: double dateintmean=0;
265:
266: double *weight;
267: int **s; /* Status */
268: double *agedc, **covar, idx;
269: int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;
270:
271: double ftol=FTOL; /* Tolerance for computing Max Likelihood */
272: double ftolhess; /* Tolerance for computing hessian */
273:
274: /**************** split *************************/
275: static int split( char *path, char *dirc, char *name, char *ext, char *finame )
276: {
1.59 brouard 277: char *ss; /* pointer */
278: int l1, l2; /* length counters */
1.53 brouard 279:
1.59 brouard 280: l1 = strlen(path ); /* length of path */
281: if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
282: ss= strrchr( path, DIRSEPARATOR ); /* find last / */
283: if ( ss == NULL ) { /* no directory, so use current */
284: /*if(strrchr(path, ODIRSEPARATOR )==NULL)
285: printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
1.74 brouard 286: /* get current working directory */
287: /* extern char* getcwd ( char *buf , int len);*/
1.59 brouard 288: if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {
289: return( GLOCK_ERROR_GETCWD );
290: }
291: strcpy( name, path ); /* we've got it */
292: } else { /* strip direcotry from path */
293: ss++; /* after this, the filename */
294: l2 = strlen( ss ); /* length of filename */
295: if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
296: strcpy( name, ss ); /* save file name */
297: strncpy( dirc, path, l1 - l2 ); /* now the directory */
298: dirc[l1-l2] = 0; /* add zero */
299: }
300: l1 = strlen( dirc ); /* length of directory */
1.85 brouard 301: /*#ifdef windows
1.59 brouard 302: if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; }
1.53 brouard 303: #else
1.59 brouard 304: if ( dirc[l1-1] != '/' ) { dirc[l1] = '/'; dirc[l1+1] = 0; }
1.53 brouard 305: #endif
1.85 brouard 306: */
1.59 brouard 307: ss = strrchr( name, '.' ); /* find last / */
308: ss++;
309: strcpy(ext,ss); /* save extension */
310: l1= strlen( name);
311: l2= strlen(ss)+1;
312: strncpy( finame, name, l1-l2);
313: finame[l1-l2]= 0;
314: return( 0 ); /* we're done */
1.53 brouard 315: }
316:
317:
318: /******************************************/
319:
320: void replace(char *s, char*t)
321: {
322: int i;
323: int lg=20;
324: i=0;
325: lg=strlen(t);
326: for(i=0; i<= lg; i++) {
327: (s[i] = t[i]);
328: if (t[i]== '\\') s[i]='/';
329: }
330: }
331:
332: int nbocc(char *s, char occ)
333: {
334: int i,j=0;
335: int lg=20;
336: i=0;
337: lg=strlen(s);
338: for(i=0; i<= lg; i++) {
339: if (s[i] == occ ) j++;
340: }
341: return j;
342: }
343:
344: void cutv(char *u,char *v, char*t, char occ)
345: {
346: /* cuts string t into u and v where u is ended by char occ excluding it
347: and v is after occ excluding it too : ex cutv(u,v,"abcdef2ghi2j",2)
348: gives u="abcedf" and v="ghi2j" */
349: int i,lg,j,p=0;
350: i=0;
351: for(j=0; j<=strlen(t)-1; j++) {
352: if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;
353: }
354:
355: lg=strlen(t);
356: for(j=0; j<p; j++) {
357: (u[j] = t[j]);
358: }
359: u[p]='\0';
360:
361: for(j=0; j<= lg; j++) {
362: if (j>=(p+1))(v[j-p-1] = t[j]);
363: }
364: }
365:
366: /********************** nrerror ********************/
367:
368: void nrerror(char error_text[])
369: {
370: fprintf(stderr,"ERREUR ...\n");
371: fprintf(stderr,"%s\n",error_text);
1.59 brouard 372: exit(EXIT_FAILURE);
1.53 brouard 373: }
374: /*********************** vector *******************/
375: double *vector(int nl, int nh)
376: {
377: double *v;
378: v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
379: if (!v) nrerror("allocation failure in vector");
380: return v-nl+NR_END;
381: }
382:
383: /************************ free vector ******************/
384: void free_vector(double*v, int nl, int nh)
385: {
386: free((FREE_ARG)(v+nl-NR_END));
387: }
388:
389: /************************ivector *******************************/
1.85 brouard 390: int *ivector(long nl,long nh)
1.76 brouard 391: {
1.85 brouard 392: int *v;
393: v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
394: if (!v) nrerror("allocation failure in ivector");
1.76 brouard 395: return v-nl+NR_END;
396: }
397:
398: /******************free ivector **************************/
1.85 brouard 399: void free_ivector(int *v, long nl, long nh)
1.76 brouard 400: {
401: free((FREE_ARG)(v+nl-NR_END));
402: }
403:
1.85 brouard 404: /************************lvector *******************************/
405: long *lvector(long nl,long nh)
1.53 brouard 406: {
1.85 brouard 407: long *v;
408: v=(long *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(long)));
1.53 brouard 409: if (!v) nrerror("allocation failure in ivector");
410: return v-nl+NR_END;
411: }
412:
1.85 brouard 413: /******************free lvector **************************/
414: void free_lvector(long *v, long nl, long nh)
1.53 brouard 415: {
416: free((FREE_ARG)(v+nl-NR_END));
417: }
418:
419: /******************* imatrix *******************************/
420: int **imatrix(long nrl, long nrh, long ncl, long nch)
421: /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */
422: {
423: long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;
424: int **m;
425:
426: /* allocate pointers to rows */
427: m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));
428: if (!m) nrerror("allocation failure 1 in matrix()");
429: m += NR_END;
430: m -= nrl;
431:
432:
433: /* allocate rows and set pointers to them */
434: m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));
435: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
436: m[nrl] += NR_END;
437: m[nrl] -= ncl;
438:
439: for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;
440:
441: /* return pointer to array of pointers to rows */
442: return m;
443: }
444:
445: /****************** free_imatrix *************************/
446: void free_imatrix(m,nrl,nrh,ncl,nch)
447: int **m;
448: long nch,ncl,nrh,nrl;
449: /* free an int matrix allocated by imatrix() */
450: {
451: free((FREE_ARG) (m[nrl]+ncl-NR_END));
452: free((FREE_ARG) (m+nrl-NR_END));
453: }
454:
455: /******************* matrix *******************************/
456: double **matrix(long nrl, long nrh, long ncl, long nch)
457: {
458: long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
459: double **m;
460:
461: m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
462: if (!m) nrerror("allocation failure 1 in matrix()");
463: m += NR_END;
464: m -= nrl;
465:
466: m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
467: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
468: m[nrl] += NR_END;
469: m[nrl] -= ncl;
470:
471: for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
472: return m;
1.85 brouard 473: /* print *(*(m+1)+70) or print m[1][70]; print m+1 or print &(m[1])
1.74 brouard 474: */
1.53 brouard 475: }
476:
477: /*************************free matrix ************************/
478: void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
479: {
480: free((FREE_ARG)(m[nrl]+ncl-NR_END));
481: free((FREE_ARG)(m+nrl-NR_END));
482: }
483:
484: /******************* ma3x *******************************/
485: double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
486: {
487: long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
488: double ***m;
489:
490: m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
491: if (!m) nrerror("allocation failure 1 in matrix()");
492: m += NR_END;
493: m -= nrl;
494:
495: m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
496: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
497: m[nrl] += NR_END;
498: m[nrl] -= ncl;
499:
500: for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
501:
502: m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
503: if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
504: m[nrl][ncl] += NR_END;
505: m[nrl][ncl] -= nll;
506: for (j=ncl+1; j<=nch; j++)
507: m[nrl][j]=m[nrl][j-1]+nlay;
508:
509: for (i=nrl+1; i<=nrh; i++) {
510: m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
511: for (j=ncl+1; j<=nch; j++)
512: m[i][j]=m[i][j-1]+nlay;
513: }
1.74 brouard 514: return m;
515: /* gdb: p *(m+1) <=> p m[1] and p (m+1) <=> p (m+1) <=> p &(m[1])
516: &(m[i][j][k]) <=> *((*(m+i) + j)+k)
517: */
1.53 brouard 518: }
519:
520: /*************************free ma3x ************************/
521: void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
522: {
523: free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
524: free((FREE_ARG)(m[nrl]+ncl-NR_END));
525: free((FREE_ARG)(m+nrl-NR_END));
526: }
527:
528: /***************** f1dim *************************/
529: extern int ncom;
530: extern double *pcom,*xicom;
531: extern double (*nrfunc)(double []);
532:
533: double f1dim(double x)
534: {
535: int j;
536: double f;
537: double *xt;
538:
539: xt=vector(1,ncom);
540: for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];
541: f=(*nrfunc)(xt);
542: free_vector(xt,1,ncom);
543: return f;
544: }
545:
546: /*****************brent *************************/
547: double brent(double ax, double bx, double cx, double (*f)(double), double tol, double *xmin)
548: {
549: int iter;
550: double a,b,d,etemp;
551: double fu,fv,fw,fx;
552: double ftemp;
553: double p,q,r,tol1,tol2,u,v,w,x,xm;
554: double e=0.0;
555:
556: a=(ax < cx ? ax : cx);
557: b=(ax > cx ? ax : cx);
558: x=w=v=bx;
559: fw=fv=fx=(*f)(x);
560: for (iter=1;iter<=ITMAX;iter++) {
561: xm=0.5*(a+b);
562: tol2=2.0*(tol1=tol*fabs(x)+ZEPS);
563: /* if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
564: printf(".");fflush(stdout);
565: fprintf(ficlog,".");fflush(ficlog);
566: #ifdef DEBUG
567: 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);
568: 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);
569: /* if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
570: #endif
571: if (fabs(x-xm) <= (tol2-0.5*(b-a))){
572: *xmin=x;
573: return fx;
574: }
575: ftemp=fu;
576: if (fabs(e) > tol1) {
577: r=(x-w)*(fx-fv);
578: q=(x-v)*(fx-fw);
579: p=(x-v)*q-(x-w)*r;
580: q=2.0*(q-r);
581: if (q > 0.0) p = -p;
582: q=fabs(q);
583: etemp=e;
584: e=d;
585: if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))
586: d=CGOLD*(e=(x >= xm ? a-x : b-x));
587: else {
588: d=p/q;
589: u=x+d;
590: if (u-a < tol2 || b-u < tol2)
591: d=SIGN(tol1,xm-x);
592: }
593: } else {
594: d=CGOLD*(e=(x >= xm ? a-x : b-x));
595: }
596: u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));
597: fu=(*f)(u);
598: if (fu <= fx) {
599: if (u >= x) a=x; else b=x;
600: SHFT(v,w,x,u)
601: SHFT(fv,fw,fx,fu)
602: } else {
603: if (u < x) a=u; else b=u;
604: if (fu <= fw || w == x) {
605: v=w;
606: w=u;
607: fv=fw;
608: fw=fu;
609: } else if (fu <= fv || v == x || v == w) {
610: v=u;
611: fv=fu;
612: }
613: }
614: }
615: nrerror("Too many iterations in brent");
616: *xmin=x;
617: return fx;
618: }
619:
620: /****************** mnbrak ***********************/
621:
622: void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,
623: double (*func)(double))
624: {
625: double ulim,u,r,q, dum;
626: double fu;
627:
628: *fa=(*func)(*ax);
629: *fb=(*func)(*bx);
630: if (*fb > *fa) {
631: SHFT(dum,*ax,*bx,dum)
632: SHFT(dum,*fb,*fa,dum)
633: }
634: *cx=(*bx)+GOLD*(*bx-*ax);
635: *fc=(*func)(*cx);
636: while (*fb > *fc) {
637: r=(*bx-*ax)*(*fb-*fc);
638: q=(*bx-*cx)*(*fb-*fa);
639: u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/
640: (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r));
641: ulim=(*bx)+GLIMIT*(*cx-*bx);
642: if ((*bx-u)*(u-*cx) > 0.0) {
643: fu=(*func)(u);
644: } else if ((*cx-u)*(u-ulim) > 0.0) {
645: fu=(*func)(u);
646: if (fu < *fc) {
647: SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))
648: SHFT(*fb,*fc,fu,(*func)(u))
649: }
650: } else if ((u-ulim)*(ulim-*cx) >= 0.0) {
651: u=ulim;
652: fu=(*func)(u);
653: } else {
654: u=(*cx)+GOLD*(*cx-*bx);
655: fu=(*func)(u);
656: }
657: SHFT(*ax,*bx,*cx,u)
658: SHFT(*fa,*fb,*fc,fu)
659: }
660: }
661:
662: /*************** linmin ************************/
663:
664: int ncom;
665: double *pcom,*xicom;
666: double (*nrfunc)(double []);
667:
668: void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))
669: {
670: double brent(double ax, double bx, double cx,
671: double (*f)(double), double tol, double *xmin);
672: double f1dim(double x);
673: void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,
674: double *fc, double (*func)(double));
675: int j;
676: double xx,xmin,bx,ax;
677: double fx,fb,fa;
678:
679: ncom=n;
680: pcom=vector(1,n);
681: xicom=vector(1,n);
682: nrfunc=func;
683: for (j=1;j<=n;j++) {
684: pcom[j]=p[j];
685: xicom[j]=xi[j];
686: }
687: ax=0.0;
688: xx=1.0;
689: mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim);
690: *fret=brent(ax,xx,bx,f1dim,TOL,&xmin);
691: #ifdef DEBUG
692: printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
693: fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
694: #endif
695: for (j=1;j<=n;j++) {
696: xi[j] *= xmin;
697: p[j] += xi[j];
698: }
699: free_vector(xicom,1,n);
700: free_vector(pcom,1,n);
701: }
702:
703: /*************** powell ************************/
704: void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,
705: double (*func)(double []))
706: {
707: void linmin(double p[], double xi[], int n, double *fret,
708: double (*func)(double []));
709: int i,ibig,j;
710: double del,t,*pt,*ptt,*xit;
711: double fp,fptt;
712: double *xits;
713: pt=vector(1,n);
714: ptt=vector(1,n);
715: xit=vector(1,n);
716: xits=vector(1,n);
717: *fret=(*func)(p);
718: for (j=1;j<=n;j++) pt[j]=p[j];
719: for (*iter=1;;++(*iter)) {
720: fp=(*fret);
721: ibig=0;
722: del=0.0;
723: printf("\nPowell iter=%d -2*LL=%.12f",*iter,*fret);
724: fprintf(ficlog,"\nPowell iter=%d -2*LL=%.12f",*iter,*fret);
1.76 brouard 725: fprintf(ficrespow,"%d %.12f",*iter,*fret);
726: for (i=1;i<=n;i++) {
1.53 brouard 727: printf(" %d %.12f",i, p[i]);
1.76 brouard 728: fprintf(ficlog," %d %.12lf",i, p[i]);
729: fprintf(ficrespow," %.12lf", p[i]);
730: }
1.53 brouard 731: printf("\n");
732: fprintf(ficlog,"\n");
1.76 brouard 733: fprintf(ficrespow,"\n");
1.53 brouard 734: for (i=1;i<=n;i++) {
735: for (j=1;j<=n;j++) xit[j]=xi[j][i];
736: fptt=(*fret);
737: #ifdef DEBUG
738: printf("fret=%lf \n",*fret);
739: fprintf(ficlog,"fret=%lf \n",*fret);
740: #endif
741: printf("%d",i);fflush(stdout);
742: fprintf(ficlog,"%d",i);fflush(ficlog);
743: linmin(p,xit,n,fret,func);
744: if (fabs(fptt-(*fret)) > del) {
745: del=fabs(fptt-(*fret));
746: ibig=i;
747: }
748: #ifdef DEBUG
749: printf("%d %.12e",i,(*fret));
750: fprintf(ficlog,"%d %.12e",i,(*fret));
751: for (j=1;j<=n;j++) {
752: xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
753: printf(" x(%d)=%.12e",j,xit[j]);
754: fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
755: }
756: for(j=1;j<=n;j++) {
757: printf(" p=%.12e",p[j]);
758: fprintf(ficlog," p=%.12e",p[j]);
759: }
760: printf("\n");
761: fprintf(ficlog,"\n");
762: #endif
763: }
764: if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {
765: #ifdef DEBUG
766: int k[2],l;
767: k[0]=1;
768: k[1]=-1;
769: printf("Max: %.12e",(*func)(p));
770: fprintf(ficlog,"Max: %.12e",(*func)(p));
771: for (j=1;j<=n;j++) {
772: printf(" %.12e",p[j]);
773: fprintf(ficlog," %.12e",p[j]);
774: }
775: printf("\n");
776: fprintf(ficlog,"\n");
777: for(l=0;l<=1;l++) {
778: for (j=1;j<=n;j++) {
779: ptt[j]=p[j]+(p[j]-pt[j])*k[l];
780: printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
781: fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
782: }
783: printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
784: fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
785: }
786: #endif
787:
788:
789: free_vector(xit,1,n);
790: free_vector(xits,1,n);
791: free_vector(ptt,1,n);
792: free_vector(pt,1,n);
793: return;
794: }
795: if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");
796: for (j=1;j<=n;j++) {
797: ptt[j]=2.0*p[j]-pt[j];
798: xit[j]=p[j]-pt[j];
799: pt[j]=p[j];
800: }
801: fptt=(*func)(ptt);
802: if (fptt < fp) {
803: t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt);
804: if (t < 0.0) {
805: linmin(p,xit,n,fret,func);
806: for (j=1;j<=n;j++) {
807: xi[j][ibig]=xi[j][n];
808: xi[j][n]=xit[j];
809: }
810: #ifdef DEBUG
811: printf("Direction changed last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
812: fprintf(ficlog,"Direction changed last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
813: for(j=1;j<=n;j++){
814: printf(" %.12e",xit[j]);
815: fprintf(ficlog," %.12e",xit[j]);
816: }
817: printf("\n");
818: fprintf(ficlog,"\n");
819: #endif
1.54 brouard 820: }
1.53 brouard 821: }
822: }
823: }
824:
1.54 brouard 825: /**** Prevalence limit (stable prevalence) ****************/
1.53 brouard 826:
827: double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)
828: {
829: /* Computes the prevalence limit in each live state at age x by left multiplying the unit
830: matrix by transitions matrix until convergence is reached */
831:
832: int i, ii,j,k;
833: double min, max, maxmin, maxmax,sumnew=0.;
834: double **matprod2();
835: double **out, cov[NCOVMAX], **pmij();
836: double **newm;
837: double agefin, delaymax=50 ; /* Max number of years to converge */
838:
839: for (ii=1;ii<=nlstate+ndeath;ii++)
840: for (j=1;j<=nlstate+ndeath;j++){
841: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
842: }
843:
844: cov[1]=1.;
845:
846: /* Even if hstepm = 1, at least one multiplication by the unit matrix */
847: for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
848: newm=savm;
849: /* Covariates have to be included here again */
850: cov[2]=agefin;
851:
852: for (k=1; k<=cptcovn;k++) {
853: cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
854: /* 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]]);*/
855: }
856: for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
857: for (k=1; k<=cptcovprod;k++)
858: cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
859:
860: /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
861: /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
862: /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
863: out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);
864:
865: savm=oldm;
866: oldm=newm;
867: maxmax=0.;
868: for(j=1;j<=nlstate;j++){
869: min=1.;
870: max=0.;
871: for(i=1; i<=nlstate; i++) {
872: sumnew=0;
873: for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
874: prlim[i][j]= newm[i][j]/(1-sumnew);
875: max=FMAX(max,prlim[i][j]);
876: min=FMIN(min,prlim[i][j]);
877: }
878: maxmin=max-min;
879: maxmax=FMAX(maxmax,maxmin);
880: }
881: if(maxmax < ftolpl){
882: return prlim;
883: }
884: }
885: }
886:
887: /*************** transition probabilities ***************/
888:
889: double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
890: {
891: double s1, s2;
892: /*double t34;*/
893: int i,j,j1, nc, ii, jj;
894:
895: for(i=1; i<= nlstate; i++){
896: for(j=1; j<i;j++){
897: for (nc=1, s2=0.;nc <=ncovmodel; nc++){
898: /*s2 += param[i][j][nc]*cov[nc];*/
899: s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
900: /*printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2);*/
901: }
902: ps[i][j]=s2;
903: /*printf("s1=%.17e, s2=%.17e\n",s1,s2);*/
904: }
905: for(j=i+1; j<=nlstate+ndeath;j++){
906: for (nc=1, s2=0.;nc <=ncovmodel; nc++){
907: s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
908: /*printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2);*/
909: }
910: ps[i][j]=s2;
911: }
912: }
913: /*ps[3][2]=1;*/
914:
915: for(i=1; i<= nlstate; i++){
916: s1=0;
917: for(j=1; j<i; j++)
918: s1+=exp(ps[i][j]);
919: for(j=i+1; j<=nlstate+ndeath; j++)
920: s1+=exp(ps[i][j]);
921: ps[i][i]=1./(s1+1.);
922: for(j=1; j<i; j++)
923: ps[i][j]= exp(ps[i][j])*ps[i][i];
924: for(j=i+1; j<=nlstate+ndeath; j++)
925: ps[i][j]= exp(ps[i][j])*ps[i][i];
926: /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
927: } /* end i */
928:
929: for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
930: for(jj=1; jj<= nlstate+ndeath; jj++){
931: ps[ii][jj]=0;
932: ps[ii][ii]=1;
933: }
934: }
935:
936:
937: /* for(ii=1; ii<= nlstate+ndeath; ii++){
938: for(jj=1; jj<= nlstate+ndeath; jj++){
939: printf("%lf ",ps[ii][jj]);
940: }
941: printf("\n ");
942: }
943: printf("\n ");printf("%lf ",cov[2]);*/
944: /*
945: for(i=1; i<= npar; i++) printf("%f ",x[i]);
946: goto end;*/
947: return ps;
948: }
949:
950: /**************** Product of 2 matrices ******************/
951:
952: double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)
953: {
954: /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
955: b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
956: /* in, b, out are matrice of pointers which should have been initialized
957: before: only the contents of out is modified. The function returns
958: a pointer to pointers identical to out */
959: long i, j, k;
960: for(i=nrl; i<= nrh; i++)
961: for(k=ncolol; k<=ncoloh; k++)
962: for(j=ncl,out[i][k]=0.; j<=nch; j++)
963: out[i][k] +=in[i][j]*b[j][k];
964:
965: return out;
966: }
967:
968:
969: /************* Higher Matrix Product ***************/
970:
971: double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
972: {
1.66 brouard 973: /* Computes the transition matrix starting at age 'age' over
974: 'nhstepm*hstepm*stepm' months (i.e. until
975: age (in years) age+nhstepm*hstepm*stepm/12) by multiplying
976: nhstepm*hstepm matrices.
1.53 brouard 977: Output is stored in matrix po[i][j][h] for h every 'hstepm' step
1.66 brouard 978: (typically every 2 years instead of every month which is too big
979: for the memory).
1.53 brouard 980: Model is determined by parameters x and covariates have to be
981: included manually here.
982:
983: */
984:
985: int i, j, d, h, k;
986: double **out, cov[NCOVMAX];
987: double **newm;
988:
989: /* Hstepm could be zero and should return the unit matrix */
990: for (i=1;i<=nlstate+ndeath;i++)
991: for (j=1;j<=nlstate+ndeath;j++){
992: oldm[i][j]=(i==j ? 1.0 : 0.0);
993: po[i][j][0]=(i==j ? 1.0 : 0.0);
994: }
995: /* Even if hstepm = 1, at least one multiplication by the unit matrix */
996: for(h=1; h <=nhstepm; h++){
997: for(d=1; d <=hstepm; d++){
998: newm=savm;
999: /* Covariates have to be included here again */
1000: cov[1]=1.;
1001: cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
1002: for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
1003: for (k=1; k<=cptcovage;k++)
1004: cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
1005: for (k=1; k<=cptcovprod;k++)
1006: cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
1007:
1008:
1009: /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
1010: /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
1011: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,
1012: pmij(pmmij,cov,ncovmodel,x,nlstate));
1013: savm=oldm;
1014: oldm=newm;
1015: }
1016: for(i=1; i<=nlstate+ndeath; i++)
1017: for(j=1;j<=nlstate+ndeath;j++) {
1018: po[i][j][h]=newm[i][j];
1019: /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);
1020: */
1021: }
1022: } /* end h */
1023: return po;
1024: }
1025:
1026:
1027: /*************** log-likelihood *************/
1028: double func( double *x)
1029: {
1030: int i, ii, j, k, mi, d, kk;
1031: double l, ll[NLSTATEMAX], cov[NCOVMAX];
1032: double **out;
1033: double sw; /* Sum of weights */
1034: double lli; /* Individual log likelihood */
1.59 brouard 1035: int s1, s2;
1.68 lievre 1036: double bbh, survp;
1.53 brouard 1037: long ipmx;
1038: /*extern weight */
1039: /* We are differentiating ll according to initial status */
1040: /* for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
1041: /*for(i=1;i<imx;i++)
1042: printf(" %d\n",s[4][i]);
1043: */
1044: cov[1]=1.;
1045:
1046: for(k=1; k<=nlstate; k++) ll[k]=0.;
1.61 brouard 1047:
1048: if(mle==1){
1049: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1050: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
1051: for(mi=1; mi<= wav[i]-1; mi++){
1052: for (ii=1;ii<=nlstate+ndeath;ii++)
1053: for (j=1;j<=nlstate+ndeath;j++){
1054: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1055: savm[ii][j]=(ii==j ? 1.0 : 0.0);
1056: }
1057: for(d=0; d<dh[mi][i]; d++){
1058: newm=savm;
1059: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
1060: for (kk=1; kk<=cptcovage;kk++) {
1061: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
1062: }
1063: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1064: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1065: savm=oldm;
1066: oldm=newm;
1067: } /* end mult */
1.53 brouard 1068:
1.61 brouard 1069: /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
1070: /* But now since version 0.9 we anticipate for bias and large stepm.
1071: * If stepm is larger than one month (smallest stepm) and if the exact delay
1072: * (in months) between two waves is not a multiple of stepm, we rounded to
1073: * the nearest (and in case of equal distance, to the lowest) interval but now
1074: * we keep into memory the bias bh[mi][i] and also the previous matrix product
1075: * (i.e to dh[mi][i]-1) saved in 'savm'. The we inter(extra)polate the
1076: * probability in order to take into account the bias as a fraction of the way
1077: * from savm to out if bh is neagtive or even beyond if bh is positive. bh varies
1078: * -stepm/2 to stepm/2 .
1079: * For stepm=1 the results are the same as for previous versions of Imach.
1080: * For stepm > 1 the results are less biased than in previous versions.
1081: */
1082: s1=s[mw[mi][i]][i];
1083: s2=s[mw[mi+1][i]][i];
1.64 lievre 1084: bbh=(double)bh[mi][i]/(double)stepm;
1085: /* bias is positive if real duration
1086: * is higher than the multiple of stepm and negative otherwise.
1087: */
1088: /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
1.71 brouard 1089: if( s2 > nlstate){
1090: /* i.e. if s2 is a death state and if the date of death is known then the contribution
1091: to the likelihood is the probability to die between last step unit time and current
1092: step unit time, which is also the differences between probability to die before dh
1093: and probability to die before dh-stepm .
1094: In version up to 0.92 likelihood was computed
1095: as if date of death was unknown. Death was treated as any other
1096: health state: the date of the interview describes the actual state
1097: and not the date of a change in health state. The former idea was
1098: to consider that at each interview the state was recorded
1099: (healthy, disable or death) and IMaCh was corrected; but when we
1100: introduced the exact date of death then we should have modified
1101: the contribution of an exact death to the likelihood. This new
1102: contribution is smaller and very dependent of the step unit
1103: stepm. It is no more the probability to die between last interview
1104: and month of death but the probability to survive from last
1105: interview up to one month before death multiplied by the
1106: probability to die within a month. Thanks to Chris
1107: Jackson for correcting this bug. Former versions increased
1108: mortality artificially. The bad side is that we add another loop
1109: which slows down the processing. The difference can be up to 10%
1110: lower mortality.
1111: */
1112: lli=log(out[s1][s2] - savm[s1][s2]);
1113: }else{
1114: lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
1115: /* 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 */
1116: }
1.64 lievre 1117: /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
1118: /*if(lli ==000.0)*/
1119: /*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); */
1.71 brouard 1120: ipmx +=1;
1.64 lievre 1121: sw += weight[i];
1122: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1123: } /* end of wave */
1124: } /* end of individual */
1125: } else if(mle==2){
1126: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1127: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
1128: for(mi=1; mi<= wav[i]-1; mi++){
1129: for (ii=1;ii<=nlstate+ndeath;ii++)
1130: for (j=1;j<=nlstate+ndeath;j++){
1131: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1132: savm[ii][j]=(ii==j ? 1.0 : 0.0);
1133: }
1134: for(d=0; d<=dh[mi][i]; d++){
1135: newm=savm;
1136: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
1137: for (kk=1; kk<=cptcovage;kk++) {
1138: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
1139: }
1140: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1141: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1142: savm=oldm;
1143: oldm=newm;
1144: } /* end mult */
1145:
1146: /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
1147: /* But now since version 0.9 we anticipate for bias and large stepm.
1148: * If stepm is larger than one month (smallest stepm) and if the exact delay
1149: * (in months) between two waves is not a multiple of stepm, we rounded to
1150: * the nearest (and in case of equal distance, to the lowest) interval but now
1151: * we keep into memory the bias bh[mi][i] and also the previous matrix product
1152: * (i.e to dh[mi][i]-1) saved in 'savm'. The we inter(extra)polate the
1153: * probability in order to take into account the bias as a fraction of the way
1154: * from savm to out if bh is neagtive or even beyond if bh is positive. bh varies
1155: * -stepm/2 to stepm/2 .
1156: * For stepm=1 the results are the same as for previous versions of Imach.
1157: * For stepm > 1 the results are less biased than in previous versions.
1158: */
1159: s1=s[mw[mi][i]][i];
1160: s2=s[mw[mi+1][i]][i];
1161: bbh=(double)bh[mi][i]/(double)stepm;
1162: /* bias is positive if real duration
1163: * is higher than the multiple of stepm and negative otherwise.
1164: */
1.63 lievre 1165: 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 */
1.64 lievre 1166: /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
1167: /*lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.-+bh)*out[s1][s2])); */ /* exponential interpolation */
1168: /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
1169: /*if(lli ==000.0)*/
1170: /*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); */
1171: ipmx +=1;
1172: sw += weight[i];
1173: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1174: } /* end of wave */
1175: } /* end of individual */
1176: } else if(mle==3){ /* exponential inter-extrapolation */
1177: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1178: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
1179: for(mi=1; mi<= wav[i]-1; mi++){
1180: for (ii=1;ii<=nlstate+ndeath;ii++)
1181: for (j=1;j<=nlstate+ndeath;j++){
1182: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1183: savm[ii][j]=(ii==j ? 1.0 : 0.0);
1184: }
1185: for(d=0; d<dh[mi][i]; d++){
1186: newm=savm;
1187: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
1188: for (kk=1; kk<=cptcovage;kk++) {
1189: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
1190: }
1191: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1192: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1193: savm=oldm;
1194: oldm=newm;
1195: } /* end mult */
1196:
1197: /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
1198: /* But now since version 0.9 we anticipate for bias and large stepm.
1199: * If stepm is larger than one month (smallest stepm) and if the exact delay
1200: * (in months) between two waves is not a multiple of stepm, we rounded to
1201: * the nearest (and in case of equal distance, to the lowest) interval but now
1202: * we keep into memory the bias bh[mi][i] and also the previous matrix product
1203: * (i.e to dh[mi][i]-1) saved in 'savm'. The we inter(extra)polate the
1204: * probability in order to take into account the bias as a fraction of the way
1205: * from savm to out if bh is neagtive or even beyond if bh is positive. bh varies
1206: * -stepm/2 to stepm/2 .
1207: * For stepm=1 the results are the same as for previous versions of Imach.
1208: * For stepm > 1 the results are less biased than in previous versions.
1209: */
1210: s1=s[mw[mi][i]][i];
1211: s2=s[mw[mi+1][i]][i];
1212: bbh=(double)bh[mi][i]/(double)stepm;
1213: /* bias is positive if real duration
1214: * is higher than the multiple of stepm and negative otherwise.
1215: */
1216: /* 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 */
1217: 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 */
1.61 brouard 1218: /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
1219: /*if(lli ==000.0)*/
1220: /*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); */
1221: ipmx +=1;
1222: sw += weight[i];
1223: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1224: } /* end of wave */
1225: } /* end of individual */
1.84 brouard 1226: }else if (mle==4){ /* ml=4 no inter-extrapolation */
1.61 brouard 1227: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1228: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
1229: for(mi=1; mi<= wav[i]-1; mi++){
1230: for (ii=1;ii<=nlstate+ndeath;ii++)
1231: for (j=1;j<=nlstate+ndeath;j++){
1232: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1233: savm[ii][j]=(ii==j ? 1.0 : 0.0);
1234: }
1235: for(d=0; d<dh[mi][i]; d++){
1236: newm=savm;
1237: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
1238: for (kk=1; kk<=cptcovage;kk++) {
1239: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
1240: }
1241:
1242: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1243: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1244: savm=oldm;
1245: oldm=newm;
1246: } /* end mult */
1247:
1.84 brouard 1248: s1=s[mw[mi][i]][i];
1249: s2=s[mw[mi+1][i]][i];
1250: if( s2 > nlstate){
1251: lli=log(out[s1][s2] - savm[s1][s2]);
1252: }else{
1253: lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
1254: }
1255: ipmx +=1;
1256: sw += weight[i];
1257: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1.85 brouard 1258: /* printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]); */
1.84 brouard 1259: } /* end of wave */
1260: } /* end of individual */
1261: }else{ /* ml=5 no inter-extrapolation no jackson =0.8a */
1262: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1263: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
1264: for(mi=1; mi<= wav[i]-1; mi++){
1265: for (ii=1;ii<=nlstate+ndeath;ii++)
1266: for (j=1;j<=nlstate+ndeath;j++){
1267: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1268: savm[ii][j]=(ii==j ? 1.0 : 0.0);
1269: }
1270: for(d=0; d<dh[mi][i]; d++){
1271: newm=savm;
1272: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
1273: for (kk=1; kk<=cptcovage;kk++) {
1274: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
1275: }
1276:
1277: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1278: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1279: savm=oldm;
1280: oldm=newm;
1281: } /* end mult */
1282:
1283: s1=s[mw[mi][i]][i];
1284: s2=s[mw[mi+1][i]][i];
1.61 brouard 1285: lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
1286: ipmx +=1;
1287: sw += weight[i];
1288: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1.84 brouard 1289: /*printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]);*/
1.61 brouard 1290: } /* end of wave */
1291: } /* end of individual */
1292: } /* End of if */
1.53 brouard 1293: for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
1294: /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
1295: l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
1.85 brouard 1296: return -l;
1297: }
1298:
1299: /*************** log-likelihood *************/
1300: double funcone( double *x)
1301: {
1.87 brouard 1302: /* Same as likeli but slower because of a lot of printf and if */
1.85 brouard 1303: int i, ii, j, k, mi, d, kk;
1304: double l, ll[NLSTATEMAX], cov[NCOVMAX];
1305: double **out;
1306: double lli; /* Individual log likelihood */
1.87 brouard 1307: double llt;
1.85 brouard 1308: int s1, s2;
1309: double bbh, survp;
1310: /*extern weight */
1311: /* We are differentiating ll according to initial status */
1312: /* for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
1313: /*for(i=1;i<imx;i++)
1314: printf(" %d\n",s[4][i]);
1315: */
1316: cov[1]=1.;
1317:
1318: for(k=1; k<=nlstate; k++) ll[k]=0.;
1319:
1320: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1321: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
1322: for(mi=1; mi<= wav[i]-1; mi++){
1323: for (ii=1;ii<=nlstate+ndeath;ii++)
1324: for (j=1;j<=nlstate+ndeath;j++){
1325: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1326: savm[ii][j]=(ii==j ? 1.0 : 0.0);
1327: }
1328: for(d=0; d<dh[mi][i]; d++){
1329: newm=savm;
1330: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
1331: for (kk=1; kk<=cptcovage;kk++) {
1332: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
1333: }
1334: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1335: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1336: savm=oldm;
1337: oldm=newm;
1338: } /* end mult */
1339:
1340: s1=s[mw[mi][i]][i];
1341: s2=s[mw[mi+1][i]][i];
1342: bbh=(double)bh[mi][i]/(double)stepm;
1343: /* bias is positive if real duration
1344: * is higher than the multiple of stepm and negative otherwise.
1345: */
1346: if( s2 > nlstate && (mle <5) ){ /* Jackson */
1347: lli=log(out[s1][s2] - savm[s1][s2]);
1348: } else if (mle==1){
1349: lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
1350: } else if(mle==2){
1351: 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 */
1352: } else if(mle==3){ /* exponential inter-extrapolation */
1353: 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 */
1354: } else if (mle==4){ /* mle=4 no inter-extrapolation */
1355: lli=log(out[s1][s2]); /* Original formula */
1356: } else{ /* ml>=5 no inter-extrapolation no jackson =0.8a */
1357: lli=log(out[s1][s2]); /* Original formula */
1358: } /* End of if */
1359: ipmx +=1;
1360: sw += weight[i];
1361: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1362: /* 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]); */
1363: if(globpr){
1.88 ! brouard 1364: fprintf(ficresilk,"%9d %6d %1d %1d %1d %1d %3d %10.6f %6.4f\
1.86 brouard 1365: %10.6f %10.6f %10.6f ", \
1366: num[i],i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],
1367: 2*weight[i]*lli,out[s1][s2],savm[s1][s2]);
1.87 brouard 1368: for(k=1,llt=0.,l=0.; k<=nlstate; k++){
1369: llt +=ll[k]*gipmx/gsw;
1370: fprintf(ficresilk," %10.6f",-ll[k]*gipmx/gsw);
1371: }
1372: fprintf(ficresilk," %10.6f\n", -llt);
1.85 brouard 1373: }
1374: } /* end of wave */
1375: } /* end of individual */
1376: for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
1377: /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
1378: l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
1.87 brouard 1379: if(globpr==0){ /* First time we count the contributions and weights */
1380: gipmx=ipmx;
1381: gsw=sw;
1382: }
1.53 brouard 1383: return -l;
1384: }
1385:
1.88 ! brouard 1386: char *subdirf(char fileres[])
! 1387: {
! 1388:
! 1389: strcpy(tmpout,optionfilefiname);
! 1390: strcat(tmpout,"/"); /* Add to the right */
! 1391: strcat(tmpout,fileres);
! 1392: return tmpout;
! 1393: }
! 1394:
! 1395: char *subdirf2(char fileres[], char *preop)
! 1396: {
! 1397:
! 1398: strcpy(tmpout,optionfilefiname);
! 1399: strcat(tmpout,"/");
! 1400: strcat(tmpout,preop);
! 1401: strcat(tmpout,fileres);
! 1402: return tmpout;
! 1403: }
! 1404: char *subdirf3(char fileres[], char *preop, char *preop2)
! 1405: {
! 1406:
! 1407: strcpy(tmpout,optionfilefiname);
! 1408: strcat(tmpout,"/");
! 1409: strcat(tmpout,preop);
! 1410: strcat(tmpout,preop2);
! 1411: strcat(tmpout,fileres);
! 1412: return tmpout;
! 1413: }
1.53 brouard 1414:
1.87 brouard 1415: void likelione(FILE *ficres,double p[], int npar, int nlstate, int *globpri, long *ipmx, double *sw, double *fretone, double (*funcone)(double []))
1.85 brouard 1416: {
1.87 brouard 1417: /* This routine should help understanding what is done with
1418: the selection of individuals/waves and
1.85 brouard 1419: to check the exact contribution to the likelihood.
1420: Plotting could be done.
1421: */
1422: int k;
1.87 brouard 1423:
1.88 ! brouard 1424: if(*globpri !=0){ /* Just counts and sums, no printings */
1.85 brouard 1425: strcpy(fileresilk,"ilk");
1426: strcat(fileresilk,fileres);
1427: if((ficresilk=fopen(fileresilk,"w"))==NULL) {
1428: printf("Problem with resultfile: %s\n", fileresilk);
1429: fprintf(ficlog,"Problem with resultfile: %s\n", fileresilk);
1430: }
1.87 brouard 1431: 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");
1.88 ! brouard 1432: fprintf(ficresilk, "#num_i i s1 s2 mi mw dh likeli weight 2wlli out sav ");
1.85 brouard 1433: /* i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],2*weight[i]*lli,out[s1][s2],savm[s1][s2]); */
1434: for(k=1; k<=nlstate; k++)
1.87 brouard 1435: fprintf(ficresilk," -2*gipw/gsw*weight*ll[%d]++",k);
1436: fprintf(ficresilk," -2*gipw/gsw*weight*ll(total)\n");
1.85 brouard 1437: }
1438:
1439: *fretone=(*funcone)(p);
1.87 brouard 1440: if(*globpri !=0){
1.85 brouard 1441: fclose(ficresilk);
1.88 ! brouard 1442: fprintf(fichtm,"\n<br>File of contributions to the likelihood: <a href=\"%s\">%s</a><br>\n",subdirf(fileresilk),subdirf(fileresilk));
1.87 brouard 1443: fflush(fichtm);
1444: }
1.85 brouard 1445: return;
1446: }
1447:
1.88 ! brouard 1448:
1.53 brouard 1449: /*********** Maximum Likelihood Estimation ***************/
1450:
1451: void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
1452: {
1453: int i,j, iter;
1.74 brouard 1454: double **xi;
1.53 brouard 1455: double fret;
1.85 brouard 1456: double fretone; /* Only one call to likelihood */
1.76 brouard 1457: char filerespow[FILENAMELENGTH];
1.53 brouard 1458: xi=matrix(1,npar,1,npar);
1459: for (i=1;i<=npar;i++)
1460: for (j=1;j<=npar;j++)
1461: xi[i][j]=(i==j ? 1.0 : 0.0);
1462: printf("Powell\n"); fprintf(ficlog,"Powell\n");
1.76 brouard 1463: strcpy(filerespow,"pow");
1464: strcat(filerespow,fileres);
1465: if((ficrespow=fopen(filerespow,"w"))==NULL) {
1466: printf("Problem with resultfile: %s\n", filerespow);
1467: fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
1468: }
1469: fprintf(ficrespow,"# Powell\n# iter -2*LL");
1470: for (i=1;i<=nlstate;i++)
1471: for(j=1;j<=nlstate+ndeath;j++)
1472: if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
1473: fprintf(ficrespow,"\n");
1.85 brouard 1474:
1.53 brouard 1475: powell(p,xi,npar,ftol,&iter,&fret,func);
1476:
1.76 brouard 1477: fclose(ficrespow);
1478: printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));
1.65 lievre 1479: fprintf(ficlog,"\n#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
1.53 brouard 1480: fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
1481:
1482: }
1483:
1484: /**** Computes Hessian and covariance matrix ***/
1485: void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
1486: {
1487: double **a,**y,*x,pd;
1488: double **hess;
1489: int i, j,jk;
1490: int *indx;
1491:
1492: double hessii(double p[], double delta, int theta, double delti[]);
1493: double hessij(double p[], double delti[], int i, int j);
1494: void lubksb(double **a, int npar, int *indx, double b[]) ;
1495: void ludcmp(double **a, int npar, int *indx, double *d) ;
1496:
1497: hess=matrix(1,npar,1,npar);
1498:
1499: printf("\nCalculation of the hessian matrix. Wait...\n");
1500: fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
1501: for (i=1;i<=npar;i++){
1502: printf("%d",i);fflush(stdout);
1503: fprintf(ficlog,"%d",i);fflush(ficlog);
1504: hess[i][i]=hessii(p,ftolhess,i,delti);
1505: /*printf(" %f ",p[i]);*/
1506: /*printf(" %lf ",hess[i][i]);*/
1507: }
1508:
1509: for (i=1;i<=npar;i++) {
1510: for (j=1;j<=npar;j++) {
1511: if (j>i) {
1512: printf(".%d%d",i,j);fflush(stdout);
1513: fprintf(ficlog,".%d%d",i,j);fflush(ficlog);
1514: hess[i][j]=hessij(p,delti,i,j);
1515: hess[j][i]=hess[i][j];
1516: /*printf(" %lf ",hess[i][j]);*/
1517: }
1518: }
1519: }
1520: printf("\n");
1521: fprintf(ficlog,"\n");
1522:
1523: printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
1524: fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
1525:
1526: a=matrix(1,npar,1,npar);
1527: y=matrix(1,npar,1,npar);
1528: x=vector(1,npar);
1529: indx=ivector(1,npar);
1530: for (i=1;i<=npar;i++)
1531: for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
1532: ludcmp(a,npar,indx,&pd);
1533:
1534: for (j=1;j<=npar;j++) {
1535: for (i=1;i<=npar;i++) x[i]=0;
1536: x[j]=1;
1537: lubksb(a,npar,indx,x);
1538: for (i=1;i<=npar;i++){
1539: matcov[i][j]=x[i];
1540: }
1541: }
1542:
1543: printf("\n#Hessian matrix#\n");
1544: fprintf(ficlog,"\n#Hessian matrix#\n");
1545: for (i=1;i<=npar;i++) {
1546: for (j=1;j<=npar;j++) {
1547: printf("%.3e ",hess[i][j]);
1548: fprintf(ficlog,"%.3e ",hess[i][j]);
1549: }
1550: printf("\n");
1551: fprintf(ficlog,"\n");
1552: }
1553:
1554: /* Recompute Inverse */
1555: for (i=1;i<=npar;i++)
1556: for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];
1557: ludcmp(a,npar,indx,&pd);
1558:
1559: /* printf("\n#Hessian matrix recomputed#\n");
1560:
1561: for (j=1;j<=npar;j++) {
1562: for (i=1;i<=npar;i++) x[i]=0;
1563: x[j]=1;
1564: lubksb(a,npar,indx,x);
1565: for (i=1;i<=npar;i++){
1566: y[i][j]=x[i];
1567: printf("%.3e ",y[i][j]);
1568: fprintf(ficlog,"%.3e ",y[i][j]);
1569: }
1570: printf("\n");
1571: fprintf(ficlog,"\n");
1572: }
1573: */
1574:
1575: free_matrix(a,1,npar,1,npar);
1576: free_matrix(y,1,npar,1,npar);
1577: free_vector(x,1,npar);
1578: free_ivector(indx,1,npar);
1579: free_matrix(hess,1,npar,1,npar);
1580:
1581:
1582: }
1583:
1584: /*************** hessian matrix ****************/
1585: double hessii( double x[], double delta, int theta, double delti[])
1586: {
1587: int i;
1588: int l=1, lmax=20;
1589: double k1,k2;
1590: double p2[NPARMAX+1];
1591: double res;
1592: double delt, delts, nkhi=10.,nkhif=1., khi=1.e-4;
1593: double fx;
1594: int k=0,kmax=10;
1595: double l1;
1596:
1597: fx=func(x);
1598: for (i=1;i<=npar;i++) p2[i]=x[i];
1599: for(l=0 ; l <=lmax; l++){
1600: l1=pow(10,l);
1601: delts=delt;
1602: for(k=1 ; k <kmax; k=k+1){
1603: delt = delta*(l1*k);
1604: p2[theta]=x[theta] +delt;
1605: k1=func(p2)-fx;
1606: p2[theta]=x[theta]-delt;
1607: k2=func(p2)-fx;
1608: /*res= (k1-2.0*fx+k2)/delt/delt; */
1609: res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */
1610:
1611: #ifdef DEBUG
1612: 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);
1613: 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);
1614: #endif
1615: /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
1616: if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
1617: k=kmax;
1618: }
1619: else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
1620: k=kmax; l=lmax*10.;
1621: }
1622: else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){
1623: delts=delt;
1624: }
1625: }
1626: }
1627: delti[theta]=delts;
1628: return res;
1629:
1630: }
1631:
1632: double hessij( double x[], double delti[], int thetai,int thetaj)
1633: {
1634: int i;
1635: int l=1, l1, lmax=20;
1636: double k1,k2,k3,k4,res,fx;
1637: double p2[NPARMAX+1];
1638: int k;
1639:
1640: fx=func(x);
1641: for (k=1; k<=2; k++) {
1642: for (i=1;i<=npar;i++) p2[i]=x[i];
1643: p2[thetai]=x[thetai]+delti[thetai]/k;
1644: p2[thetaj]=x[thetaj]+delti[thetaj]/k;
1645: k1=func(p2)-fx;
1646:
1647: p2[thetai]=x[thetai]+delti[thetai]/k;
1648: p2[thetaj]=x[thetaj]-delti[thetaj]/k;
1649: k2=func(p2)-fx;
1650:
1651: p2[thetai]=x[thetai]-delti[thetai]/k;
1652: p2[thetaj]=x[thetaj]+delti[thetaj]/k;
1653: k3=func(p2)-fx;
1654:
1655: p2[thetai]=x[thetai]-delti[thetai]/k;
1656: p2[thetaj]=x[thetaj]-delti[thetaj]/k;
1657: k4=func(p2)-fx;
1658: res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */
1659: #ifdef DEBUG
1660: 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);
1661: 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);
1662: #endif
1663: }
1664: return res;
1665: }
1666:
1667: /************** Inverse of matrix **************/
1668: void ludcmp(double **a, int n, int *indx, double *d)
1669: {
1670: int i,imax,j,k;
1671: double big,dum,sum,temp;
1672: double *vv;
1673:
1674: vv=vector(1,n);
1675: *d=1.0;
1676: for (i=1;i<=n;i++) {
1677: big=0.0;
1678: for (j=1;j<=n;j++)
1679: if ((temp=fabs(a[i][j])) > big) big=temp;
1680: if (big == 0.0) nrerror("Singular matrix in routine ludcmp");
1681: vv[i]=1.0/big;
1682: }
1683: for (j=1;j<=n;j++) {
1684: for (i=1;i<j;i++) {
1685: sum=a[i][j];
1686: for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];
1687: a[i][j]=sum;
1688: }
1689: big=0.0;
1690: for (i=j;i<=n;i++) {
1691: sum=a[i][j];
1692: for (k=1;k<j;k++)
1693: sum -= a[i][k]*a[k][j];
1694: a[i][j]=sum;
1695: if ( (dum=vv[i]*fabs(sum)) >= big) {
1696: big=dum;
1697: imax=i;
1698: }
1699: }
1700: if (j != imax) {
1701: for (k=1;k<=n;k++) {
1702: dum=a[imax][k];
1703: a[imax][k]=a[j][k];
1704: a[j][k]=dum;
1705: }
1706: *d = -(*d);
1707: vv[imax]=vv[j];
1708: }
1709: indx[j]=imax;
1710: if (a[j][j] == 0.0) a[j][j]=TINY;
1711: if (j != n) {
1712: dum=1.0/(a[j][j]);
1713: for (i=j+1;i<=n;i++) a[i][j] *= dum;
1714: }
1715: }
1716: free_vector(vv,1,n); /* Doesn't work */
1717: ;
1718: }
1719:
1720: void lubksb(double **a, int n, int *indx, double b[])
1721: {
1722: int i,ii=0,ip,j;
1723: double sum;
1724:
1725: for (i=1;i<=n;i++) {
1726: ip=indx[i];
1727: sum=b[ip];
1728: b[ip]=b[i];
1729: if (ii)
1730: for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];
1731: else if (sum) ii=i;
1732: b[i]=sum;
1733: }
1734: for (i=n;i>=1;i--) {
1735: sum=b[i];
1736: for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];
1737: b[i]=sum/a[i][i];
1738: }
1739: }
1740:
1741: /************ Frequencies ********************/
1.84 brouard 1742: 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)
1.53 brouard 1743: { /* Some frequencies */
1744:
1745: int i, m, jk, k1,i1, j1, bool, z1,z2,j;
1746: int first;
1747: double ***freq; /* Frequencies */
1.73 lievre 1748: double *pp, **prop;
1749: double pos,posprop, k2, dateintsum=0,k2cpt=0;
1.53 brouard 1750: FILE *ficresp;
1751: char fileresp[FILENAMELENGTH];
1752:
1753: pp=vector(1,nlstate);
1.74 brouard 1754: prop=matrix(1,nlstate,iagemin,iagemax+3);
1.53 brouard 1755: strcpy(fileresp,"p");
1756: strcat(fileresp,fileres);
1757: if((ficresp=fopen(fileresp,"w"))==NULL) {
1758: printf("Problem with prevalence resultfile: %s\n", fileresp);
1759: fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
1760: exit(0);
1761: }
1.74 brouard 1762: freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);
1.53 brouard 1763: j1=0;
1764:
1765: j=cptcoveff;
1766: if (cptcovn<1) {j=1;ncodemax[1]=1;}
1767:
1768: first=1;
1769:
1770: for(k1=1; k1<=j;k1++){
1771: for(i1=1; i1<=ncodemax[k1];i1++){
1772: j1++;
1773: /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
1774: scanf("%d", i);*/
1775: for (i=-1; i<=nlstate+ndeath; i++)
1776: for (jk=-1; jk<=nlstate+ndeath; jk++)
1.74 brouard 1777: for(m=iagemin; m <= iagemax+3; m++)
1.53 brouard 1778: freq[i][jk][m]=0;
1.73 lievre 1779:
1780: for (i=1; i<=nlstate; i++)
1.74 brouard 1781: for(m=iagemin; m <= iagemax+3; m++)
1.73 lievre 1782: prop[i][m]=0;
1.53 brouard 1783:
1784: dateintsum=0;
1785: k2cpt=0;
1786: for (i=1; i<=imx; i++) {
1787: bool=1;
1788: if (cptcovn>0) {
1789: for (z1=1; z1<=cptcoveff; z1++)
1790: if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])
1791: bool=0;
1792: }
1.58 lievre 1793: if (bool==1){
1.53 brouard 1794: for(m=firstpass; m<=lastpass; m++){
1795: k2=anint[m][i]+(mint[m][i]/12.);
1.84 brouard 1796: /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/
1.74 brouard 1797: if(agev[m][i]==0) agev[m][i]=iagemax+1;
1798: if(agev[m][i]==1) agev[m][i]=iagemax+2;
1.73 lievre 1799: if (s[m][i]>0 && s[m][i]<=nlstate) prop[s[m][i]][(int)agev[m][i]] += weight[i];
1.53 brouard 1800: if (m<lastpass) {
1801: freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
1.74 brouard 1802: freq[s[m][i]][s[m+1][i]][iagemax+3] += weight[i];
1.53 brouard 1803: }
1804:
1.74 brouard 1805: if ((agev[m][i]>1) && (agev[m][i]< (iagemax+3))) {
1.53 brouard 1806: dateintsum=dateintsum+k2;
1807: k2cpt++;
1808: }
1.84 brouard 1809: /*}*/
1.53 brouard 1810: }
1811: }
1812: }
1813:
1.84 brouard 1814: /* fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
1.53 brouard 1815:
1816: if (cptcovn>0) {
1817: fprintf(ficresp, "\n#********** Variable ");
1818: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
1819: fprintf(ficresp, "**********\n#");
1820: }
1821: for(i=1; i<=nlstate;i++)
1822: fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
1823: fprintf(ficresp, "\n");
1824:
1.74 brouard 1825: for(i=iagemin; i <= iagemax+3; i++){
1826: if(i==iagemax+3){
1.53 brouard 1827: fprintf(ficlog,"Total");
1828: }else{
1829: if(first==1){
1830: first=0;
1831: printf("See log file for details...\n");
1832: }
1833: fprintf(ficlog,"Age %d", i);
1834: }
1835: for(jk=1; jk <=nlstate ; jk++){
1836: for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
1837: pp[jk] += freq[jk][m][i];
1838: }
1839: for(jk=1; jk <=nlstate ; jk++){
1840: for(m=-1, pos=0; m <=0 ; m++)
1841: pos += freq[jk][m][i];
1842: if(pp[jk]>=1.e-10){
1843: if(first==1){
1844: printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
1845: }
1846: fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
1847: }else{
1848: if(first==1)
1849: printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
1850: fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
1851: }
1852: }
1853:
1854: for(jk=1; jk <=nlstate ; jk++){
1855: for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
1856: pp[jk] += freq[jk][m][i];
1.73 lievre 1857: }
1858: for(jk=1,pos=0,posprop=0; jk <=nlstate ; jk++){
1859: pos += pp[jk];
1860: posprop += prop[jk][i];
1.53 brouard 1861: }
1862: for(jk=1; jk <=nlstate ; jk++){
1863: if(pos>=1.e-5){
1864: if(first==1)
1865: printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
1866: fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
1867: }else{
1868: if(first==1)
1869: printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
1870: fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
1871: }
1.74 brouard 1872: if( i <= iagemax){
1.53 brouard 1873: if(pos>=1.e-5){
1.73 lievre 1874: fprintf(ficresp," %d %.5f %.0f %.0f",i,prop[jk][i]/posprop, prop[jk][i],posprop);
1.84 brouard 1875: /*probs[i][jk][j1]= pp[jk]/pos;*/
1.53 brouard 1876: /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/
1877: }
1878: else
1.73 lievre 1879: fprintf(ficresp," %d NaNq %.0f %.0f",i,prop[jk][i],posprop);
1.53 brouard 1880: }
1881: }
1882:
1.69 brouard 1883: for(jk=-1; jk <=nlstate+ndeath; jk++)
1884: for(m=-1; m <=nlstate+ndeath; m++)
1.53 brouard 1885: if(freq[jk][m][i] !=0 ) {
1886: if(first==1)
1887: printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
1888: fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
1889: }
1.74 brouard 1890: if(i <= iagemax)
1.53 brouard 1891: fprintf(ficresp,"\n");
1892: if(first==1)
1893: printf("Others in log...\n");
1894: fprintf(ficlog,"\n");
1895: }
1896: }
1897: }
1898: dateintmean=dateintsum/k2cpt;
1899:
1900: fclose(ficresp);
1.74 brouard 1901: free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);
1.53 brouard 1902: free_vector(pp,1,nlstate);
1.74 brouard 1903: free_matrix(prop,1,nlstate,iagemin, iagemax+3);
1.53 brouard 1904: /* End of Freq */
1905: }
1906:
1907: /************ Prevalence ********************/
1.84 brouard 1908: 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)
1.69 brouard 1909: {
1910: /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
1911: in each health status at the date of interview (if between dateprev1 and dateprev2).
1912: We still use firstpass and lastpass as another selection.
1913: */
1.53 brouard 1914:
1915: int i, m, jk, k1, i1, j1, bool, z1,z2,j;
1916: double ***freq; /* Frequencies */
1.73 lievre 1917: double *pp, **prop;
1918: double pos,posprop;
1.69 brouard 1919: double y2; /* in fractional years */
1.74 brouard 1920: int iagemin, iagemax;
1.53 brouard 1921:
1.74 brouard 1922: iagemin= (int) agemin;
1923: iagemax= (int) agemax;
1924: /*pp=vector(1,nlstate);*/
1925: prop=matrix(1,nlstate,iagemin,iagemax+3);
1926: /* freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
1.53 brouard 1927: j1=0;
1928:
1929: j=cptcoveff;
1930: if (cptcovn<1) {j=1;ncodemax[1]=1;}
1931:
1932: for(k1=1; k1<=j;k1++){
1933: for(i1=1; i1<=ncodemax[k1];i1++){
1934: j1++;
1935:
1.73 lievre 1936: for (i=1; i<=nlstate; i++)
1.74 brouard 1937: for(m=iagemin; m <= iagemax+3; m++)
1938: prop[i][m]=0.0;
1.53 brouard 1939:
1.69 brouard 1940: for (i=1; i<=imx; i++) { /* Each individual */
1.53 brouard 1941: bool=1;
1942: if (cptcovn>0) {
1943: for (z1=1; z1<=cptcoveff; z1++)
1944: if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])
1945: bool=0;
1946: }
1947: if (bool==1) {
1.69 brouard 1948: for(m=firstpass; m<=lastpass; m++){/* Other selection (we can limit to certain interviews*/
1949: y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
1950: if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
1.74 brouard 1951: if(agev[m][i]==0) agev[m][i]=iagemax+1;
1952: if(agev[m][i]==1) agev[m][i]=iagemax+2;
1953: 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);
1954: if (s[m][i]>0 && s[m][i]<=nlstate) {
1955: /*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]]);*/
1956: prop[s[m][i]][(int)agev[m][i]] += weight[i];
1957: prop[s[m][i]][iagemax+3] += weight[i];
1958: }
1.53 brouard 1959: }
1.69 brouard 1960: } /* end selection of waves */
1.53 brouard 1961: }
1962: }
1.74 brouard 1963: for(i=iagemin; i <= iagemax+3; i++){
1.53 brouard 1964:
1.74 brouard 1965: for(jk=1,posprop=0; jk <=nlstate ; jk++) {
1966: posprop += prop[jk][i];
1967: }
1968:
1969: for(jk=1; jk <=nlstate ; jk++){
1970: if( i <= iagemax){
1971: if(posprop>=1.e-5){
1972: probs[i][jk][j1]= prop[jk][i]/posprop;
1973: }
1974: }
1975: }/* end jk */
1976: }/* end i */
1.53 brouard 1977: } /* end i1 */
1978: } /* end k1 */
1979:
1.74 brouard 1980: /* free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
1981: /*free_vector(pp,1,nlstate);*/
1982: free_matrix(prop,1,nlstate, iagemin,iagemax+3);
1983: } /* End of prevalence */
1.53 brouard 1984:
1985: /************* Waves Concatenation ***************/
1986:
1.59 brouard 1987: 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)
1.53 brouard 1988: {
1989: /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
1990: Death is a valid wave (if date is known).
1991: mw[mi][i] is the mi (mi=1 to wav[i]) effective wave of individual i
1.59 brouard 1992: dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
1.53 brouard 1993: and mw[mi+1][i]. dh depends on stepm.
1994: */
1995:
1996: int i, mi, m;
1997: /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
1998: double sum=0., jmean=0.;*/
1999: int first;
2000: int j, k=0,jk, ju, jl;
2001: double sum=0.;
2002: first=0;
2003: jmin=1e+5;
2004: jmax=-1;
2005: jmean=0.;
2006: for(i=1; i<=imx; i++){
2007: mi=0;
2008: m=firstpass;
2009: while(s[m][i] <= nlstate){
1.69 brouard 2010: if(s[m][i]>=1)
1.53 brouard 2011: mw[++mi][i]=m;
2012: if(m >=lastpass)
2013: break;
2014: else
2015: m++;
2016: }/* end while */
2017: if (s[m][i] > nlstate){
2018: mi++; /* Death is another wave */
2019: /* if(mi==0) never been interviewed correctly before death */
2020: /* Only death is a correct wave */
2021: mw[mi][i]=m;
2022: }
2023:
2024: wav[i]=mi;
2025: if(mi==0){
2026: if(first==0){
1.85 brouard 2027: printf("Warning! None valid information for:%ld line=%d (skipped) and may be others, see log file\n",num[i],i);
1.53 brouard 2028: first=1;
2029: }
2030: if(first==1){
1.85 brouard 2031: fprintf(ficlog,"Warning! None valid information for:%ld line=%d (skipped)\n",num[i],i);
1.53 brouard 2032: }
2033: } /* end mi==0 */
1.77 brouard 2034: } /* End individuals */
1.53 brouard 2035:
2036: for(i=1; i<=imx; i++){
2037: for(mi=1; mi<wav[i];mi++){
2038: if (stepm <=0)
2039: dh[mi][i]=1;
2040: else{
1.77 brouard 2041: if (s[mw[mi+1][i]][i] > nlstate) { /* A death */
1.53 brouard 2042: if (agedc[i] < 2*AGESUP) {
1.85 brouard 2043: j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);
2044: if(j==0) j=1; /* Survives at least one month after exam */
2045: else if(j<0){
2046: 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]);
2047: j=1; /* Careful Patch */
1.86 brouard 2048: 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);
1.85 brouard 2049: 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]);
2050: 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);
2051: }
2052: k=k+1;
2053: if (j >= jmax) jmax=j;
2054: if (j <= jmin) jmin=j;
2055: sum=sum+j;
2056: /*if (j<0) printf("j=%d num=%d \n",j,i);*/
2057: /* printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
1.53 brouard 2058: }
2059: }
2060: else{
2061: j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
1.68 lievre 2062: /* printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
1.53 brouard 2063: k=k+1;
2064: if (j >= jmax) jmax=j;
2065: else if (j <= jmin)jmin=j;
2066: /* if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
1.73 lievre 2067: /*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]);*/
1.85 brouard 2068: if(j<0){
2069: 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]);
2070: 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]);
2071: }
1.53 brouard 2072: sum=sum+j;
2073: }
2074: jk= j/stepm;
2075: jl= j -jk*stepm;
2076: ju= j -(jk+1)*stepm;
1.85 brouard 2077: if(mle <=1){ /* only if we use a the linear-interpoloation pseudo-likelihood */
1.64 lievre 2078: if(jl==0){
2079: dh[mi][i]=jk;
2080: bh[mi][i]=0;
2081: }else{ /* We want a negative bias in order to only have interpolation ie
2082: * at the price of an extra matrix product in likelihood */
2083: dh[mi][i]=jk+1;
2084: bh[mi][i]=ju;
2085: }
2086: }else{
2087: if(jl <= -ju){
2088: dh[mi][i]=jk;
2089: bh[mi][i]=jl; /* bias is positive if real duration
2090: * is higher than the multiple of stepm and negative otherwise.
2091: */
2092: }
2093: else{
2094: dh[mi][i]=jk+1;
2095: bh[mi][i]=ju;
2096: }
2097: if(dh[mi][i]==0){
2098: dh[mi][i]=1; /* At least one step */
2099: bh[mi][i]=ju; /* At least one step */
1.71 brouard 2100: /* 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);*/
1.64 lievre 2101: }
1.85 brouard 2102: } /* end if mle */
2103: }
1.64 lievre 2104: } /* end wave */
1.53 brouard 2105: }
2106: jmean=sum/k;
2107: printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);
2108: fprintf(ficlog,"Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);
2109: }
2110:
2111: /*********** Tricode ****************************/
2112: void tricode(int *Tvar, int **nbcode, int imx)
2113: {
1.58 lievre 2114:
2115: int Ndum[20],ij=1, k, j, i, maxncov=19;
1.53 brouard 2116: int cptcode=0;
2117: cptcoveff=0;
2118:
1.58 lievre 2119: for (k=0; k<maxncov; k++) Ndum[k]=0;
1.53 brouard 2120: for (k=1; k<=7; k++) ncodemax[k]=0;
2121:
2122: for (j=1; j<=(cptcovn+2*cptcovprod); j++) {
1.58 lievre 2123: for (i=1; i<=imx; i++) { /*reads the data file to get the maximum
2124: modality*/
2125: ij=(int)(covar[Tvar[j]][i]); /* ij is the modality of this individual*/
2126: Ndum[ij]++; /*store the modality */
1.53 brouard 2127: /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
1.58 lievre 2128: if (ij > cptcode) cptcode=ij; /* getting the maximum of covariable
2129: Tvar[j]. If V=sex and male is 0 and
2130: female is 1, then cptcode=1.*/
1.53 brouard 2131: }
2132:
2133: for (i=0; i<=cptcode; i++) {
1.58 lievre 2134: 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 */
1.53 brouard 2135: }
1.58 lievre 2136:
1.53 brouard 2137: ij=1;
2138: for (i=1; i<=ncodemax[j]; i++) {
1.58 lievre 2139: for (k=0; k<= maxncov; k++) {
1.53 brouard 2140: if (Ndum[k] != 0) {
2141: nbcode[Tvar[j]][ij]=k;
1.58 lievre 2142: /* 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; */
1.53 brouard 2143:
2144: ij++;
2145: }
2146: if (ij > ncodemax[j]) break;
2147: }
2148: }
2149: }
2150:
1.58 lievre 2151: for (k=0; k< maxncov; k++) Ndum[k]=0;
1.53 brouard 2152:
1.58 lievre 2153: for (i=1; i<=ncovmodel-2; i++) {
2154: /* Listing of all covariables in staement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/
1.53 brouard 2155: ij=Tvar[i];
1.58 lievre 2156: Ndum[ij]++;
1.53 brouard 2157: }
2158:
2159: ij=1;
1.58 lievre 2160: for (i=1; i<= maxncov; i++) {
1.53 brouard 2161: if((Ndum[i]!=0) && (i<=ncovcol)){
1.58 lievre 2162: Tvaraff[ij]=i; /*For printing */
1.53 brouard 2163: ij++;
2164: }
2165: }
2166:
1.58 lievre 2167: cptcoveff=ij-1; /*Number of simple covariates*/
1.53 brouard 2168: }
2169:
2170: /*********** Health Expectancies ****************/
2171:
2172: 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 )
2173:
2174: {
2175: /* Health expectancies */
2176: int i, j, nhstepm, hstepm, h, nstepm, k, cptj;
2177: double age, agelim, hf;
2178: double ***p3mat,***varhe;
2179: double **dnewm,**doldm;
2180: double *xp;
2181: double **gp, **gm;
2182: double ***gradg, ***trgradg;
2183: int theta;
2184:
1.74 brouard 2185: varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage);
1.53 brouard 2186: xp=vector(1,npar);
1.74 brouard 2187: dnewm=matrix(1,nlstate*nlstate,1,npar);
2188: doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate);
1.53 brouard 2189:
2190: fprintf(ficreseij,"# Health expectancies\n");
2191: fprintf(ficreseij,"# Age");
2192: for(i=1; i<=nlstate;i++)
2193: for(j=1; j<=nlstate;j++)
2194: fprintf(ficreseij," %1d-%1d (SE)",i,j);
2195: fprintf(ficreseij,"\n");
2196:
2197: if(estepm < stepm){
2198: printf ("Problem %d lower than %d\n",estepm, stepm);
2199: }
2200: else hstepm=estepm;
2201: /* We compute the life expectancy from trapezoids spaced every estepm months
2202: * This is mainly to measure the difference between two models: for example
2203: * if stepm=24 months pijx are given only every 2 years and by summing them
2204: * we are calculating an estimate of the Life Expectancy assuming a linear
1.66 brouard 2205: * progression in between and thus overestimating or underestimating according
1.53 brouard 2206: * to the curvature of the survival function. If, for the same date, we
2207: * estimate the model with stepm=1 month, we can keep estepm to 24 months
2208: * to compare the new estimate of Life expectancy with the same linear
2209: * hypothesis. A more precise result, taking into account a more precise
2210: * curvature will be obtained if estepm is as small as stepm. */
2211:
2212: /* For example we decided to compute the life expectancy with the smallest unit */
2213: /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
2214: nhstepm is the number of hstepm from age to agelim
2215: nstepm is the number of stepm from age to agelin.
2216: Look at hpijx to understand the reason of that which relies in memory size
2217: and note for a fixed period like estepm months */
2218: /* We decided (b) to get a life expectancy respecting the most precise curvature of the
2219: survival function given by stepm (the optimization length). Unfortunately it
2220: means that if the survival funtion is printed only each two years of age and if
2221: you sum them up and add 1 year (area under the trapezoids) you won't get the same
2222: results. So we changed our mind and took the option of the best precision.
2223: */
2224: hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
2225:
2226: agelim=AGESUP;
2227: for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
2228: /* nhstepm age range expressed in number of stepm */
2229: nstepm=(int) rint((agelim-age)*YEARM/stepm);
2230: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
2231: /* if (stepm >= YEARM) hstepm=1;*/
2232: nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
2233: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
1.74 brouard 2234: gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);
2235: gp=matrix(0,nhstepm,1,nlstate*nlstate);
2236: gm=matrix(0,nhstepm,1,nlstate*nlstate);
1.53 brouard 2237:
2238: /* Computed by stepm unit matrices, product of hstepm matrices, stored
2239: in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
2240: hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);
2241:
2242:
2243: hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
2244:
2245: /* Computing Variances of health expectancies */
2246:
2247: for(theta=1; theta <=npar; theta++){
2248: for(i=1; i<=npar; i++){
2249: xp[i] = x[i] + (i==theta ?delti[theta]:0);
2250: }
2251: hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
2252:
2253: cptj=0;
2254: for(j=1; j<= nlstate; j++){
2255: for(i=1; i<=nlstate; i++){
2256: cptj=cptj+1;
2257: for(h=0, gp[h][cptj]=0.; h<=nhstepm-1; h++){
2258: gp[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;
2259: }
2260: }
2261: }
2262:
2263:
2264: for(i=1; i<=npar; i++)
2265: xp[i] = x[i] - (i==theta ?delti[theta]:0);
2266: hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
2267:
2268: cptj=0;
2269: for(j=1; j<= nlstate; j++){
2270: for(i=1;i<=nlstate;i++){
2271: cptj=cptj+1;
2272: for(h=0, gm[h][cptj]=0.; h<=nhstepm-1; h++){
1.77 brouard 2273:
1.53 brouard 2274: gm[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;
2275: }
2276: }
2277: }
1.74 brouard 2278: for(j=1; j<= nlstate*nlstate; j++)
1.53 brouard 2279: for(h=0; h<=nhstepm-1; h++){
2280: gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
2281: }
2282: }
2283:
2284: /* End theta */
2285:
1.74 brouard 2286: trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar);
1.53 brouard 2287:
2288: for(h=0; h<=nhstepm-1; h++)
1.74 brouard 2289: for(j=1; j<=nlstate*nlstate;j++)
1.53 brouard 2290: for(theta=1; theta <=npar; theta++)
2291: trgradg[h][j][theta]=gradg[h][theta][j];
2292:
2293:
1.74 brouard 2294: for(i=1;i<=nlstate*nlstate;i++)
2295: for(j=1;j<=nlstate*nlstate;j++)
1.53 brouard 2296: varhe[i][j][(int)age] =0.;
2297:
2298: printf("%d|",(int)age);fflush(stdout);
2299: fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
2300: for(h=0;h<=nhstepm-1;h++){
2301: for(k=0;k<=nhstepm-1;k++){
1.74 brouard 2302: matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov);
2303: matprod2(doldm,dnewm,1,nlstate*nlstate,1,npar,1,nlstate*nlstate,gradg[k]);
2304: for(i=1;i<=nlstate*nlstate;i++)
2305: for(j=1;j<=nlstate*nlstate;j++)
1.53 brouard 2306: varhe[i][j][(int)age] += doldm[i][j]*hf*hf;
2307: }
2308: }
2309: /* Computing expectancies */
2310: for(i=1; i<=nlstate;i++)
2311: for(j=1; j<=nlstate;j++)
2312: for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
2313: eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
2314:
2315: /* 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]);*/
2316:
2317: }
2318:
2319: fprintf(ficreseij,"%3.0f",age );
2320: cptj=0;
2321: for(i=1; i<=nlstate;i++)
2322: for(j=1; j<=nlstate;j++){
2323: cptj++;
2324: fprintf(ficreseij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[cptj][cptj][(int)age]) );
2325: }
2326: fprintf(ficreseij,"\n");
2327:
1.74 brouard 2328: free_matrix(gm,0,nhstepm,1,nlstate*nlstate);
2329: free_matrix(gp,0,nhstepm,1,nlstate*nlstate);
2330: free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*nlstate);
2331: free_ma3x(trgradg,0,nhstepm,1,nlstate*nlstate,1,npar);
1.53 brouard 2332: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
2333: }
2334: printf("\n");
2335: fprintf(ficlog,"\n");
2336:
2337: free_vector(xp,1,npar);
1.74 brouard 2338: free_matrix(dnewm,1,nlstate*nlstate,1,npar);
2339: free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate);
2340: free_ma3x(varhe,1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int)fage);
1.53 brouard 2341: }
2342:
2343: /************ Variance ******************/
2344: 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)
2345: {
2346: /* Variance of health expectancies */
2347: /* double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
2348: /* double **newm;*/
2349: double **dnewm,**doldm;
2350: double **dnewmp,**doldmp;
2351: int i, j, nhstepm, hstepm, h, nstepm ;
2352: int k, cptcode;
2353: double *xp;
2354: double **gp, **gm; /* for var eij */
2355: double ***gradg, ***trgradg; /*for var eij */
2356: double **gradgp, **trgradgp; /* for var p point j */
2357: double *gpp, *gmp; /* for var p point j */
2358: double **varppt; /* for var p point j nlstate to nlstate+ndeath */
2359: double ***p3mat;
2360: double age,agelim, hf;
2361: double ***mobaverage;
2362: int theta;
2363: char digit[4];
1.55 lievre 2364: char digitp[25];
1.53 brouard 2365:
2366: char fileresprobmorprev[FILENAMELENGTH];
2367:
1.55 lievre 2368: if(popbased==1){
1.58 lievre 2369: if(mobilav!=0)
1.55 lievre 2370: strcpy(digitp,"-populbased-mobilav-");
2371: else strcpy(digitp,"-populbased-nomobil-");
2372: }
2373: else
1.53 brouard 2374: strcpy(digitp,"-stablbased-");
1.56 lievre 2375:
1.54 brouard 2376: if (mobilav!=0) {
1.53 brouard 2377: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
1.54 brouard 2378: if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
2379: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
2380: printf(" Error in movingaverage mobilav=%d\n",mobilav);
2381: }
1.53 brouard 2382: }
2383:
2384: strcpy(fileresprobmorprev,"prmorprev");
2385: sprintf(digit,"%-d",ij);
2386: /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
2387: strcat(fileresprobmorprev,digit); /* Tvar to be done */
2388: strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
2389: strcat(fileresprobmorprev,fileres);
2390: if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
2391: printf("Problem with resultfile: %s\n", fileresprobmorprev);
2392: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
2393: }
2394: printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
2395: fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
1.66 brouard 2396: 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);
1.53 brouard 2397: fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
2398: for(j=nlstate+1; j<=(nlstate+ndeath);j++){
2399: fprintf(ficresprobmorprev," p.%-d SE",j);
2400: for(i=1; i<=nlstate;i++)
2401: fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
2402: }
2403: fprintf(ficresprobmorprev,"\n");
1.88 ! brouard 2404: fprintf(ficgp,"\n# Routine varevsij");
1.87 brouard 2405: 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");
2406: fprintf(fichtm,"\n<br>%s <br>\n",digitp);
2407: /* } */
1.53 brouard 2408: varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
2409:
2410: 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");
2411: fprintf(ficresvij,"# Age");
2412: for(i=1; i<=nlstate;i++)
2413: for(j=1; j<=nlstate;j++)
2414: fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);
2415: fprintf(ficresvij,"\n");
2416:
2417: xp=vector(1,npar);
2418: dnewm=matrix(1,nlstate,1,npar);
2419: doldm=matrix(1,nlstate,1,nlstate);
2420: dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
2421: doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
2422:
2423: gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
2424: gpp=vector(nlstate+1,nlstate+ndeath);
2425: gmp=vector(nlstate+1,nlstate+ndeath);
2426: trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
2427:
2428: if(estepm < stepm){
2429: printf ("Problem %d lower than %d\n",estepm, stepm);
2430: }
2431: else hstepm=estepm;
2432: /* For example we decided to compute the life expectancy with the smallest unit */
2433: /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
2434: nhstepm is the number of hstepm from age to agelim
2435: nstepm is the number of stepm from age to agelin.
2436: Look at hpijx to understand the reason of that which relies in memory size
2437: and note for a fixed period like k years */
2438: /* We decided (b) to get a life expectancy respecting the most precise curvature of the
2439: survival function given by stepm (the optimization length). Unfortunately it
1.66 brouard 2440: means that if the survival funtion is printed every two years of age and if
1.53 brouard 2441: you sum them up and add 1 year (area under the trapezoids) you won't get the same
2442: results. So we changed our mind and took the option of the best precision.
2443: */
2444: hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
2445: agelim = AGESUP;
2446: for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
2447: nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
2448: nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
2449: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
2450: gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
2451: gp=matrix(0,nhstepm,1,nlstate);
2452: gm=matrix(0,nhstepm,1,nlstate);
2453:
2454:
2455: for(theta=1; theta <=npar; theta++){
1.66 brouard 2456: for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
1.53 brouard 2457: xp[i] = x[i] + (i==theta ?delti[theta]:0);
2458: }
2459: hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
2460: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
2461:
2462: if (popbased==1) {
1.54 brouard 2463: if(mobilav ==0){
1.53 brouard 2464: for(i=1; i<=nlstate;i++)
2465: prlim[i][i]=probs[(int)age][i][ij];
1.54 brouard 2466: }else{ /* mobilav */
1.53 brouard 2467: for(i=1; i<=nlstate;i++)
2468: prlim[i][i]=mobaverage[(int)age][i][ij];
2469: }
2470: }
2471:
2472: for(j=1; j<= nlstate; j++){
2473: for(h=0; h<=nhstepm; h++){
2474: for(i=1, gp[h][j]=0.;i<=nlstate;i++)
2475: gp[h][j] += prlim[i][i]*p3mat[i][j][h];
2476: }
2477: }
1.66 brouard 2478: /* This for computing probability of death (h=1 means
2479: computed over hstepm matrices product = hstepm*stepm months)
2480: as a weighted average of prlim.
2481: */
1.69 brouard 2482: for(j=nlstate+1;j<=nlstate+ndeath;j++){
1.68 lievre 2483: for(i=1,gpp[j]=0.; i<= nlstate; i++)
1.53 brouard 2484: gpp[j] += prlim[i][i]*p3mat[i][j][1];
2485: }
1.66 brouard 2486: /* end probability of death */
1.53 brouard 2487:
1.66 brouard 2488: for(i=1; i<=npar; i++) /* Computes gradient x - delta */
1.53 brouard 2489: xp[i] = x[i] - (i==theta ?delti[theta]:0);
2490: hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
2491: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
2492:
2493: if (popbased==1) {
1.54 brouard 2494: if(mobilav ==0){
1.53 brouard 2495: for(i=1; i<=nlstate;i++)
2496: prlim[i][i]=probs[(int)age][i][ij];
1.54 brouard 2497: }else{ /* mobilav */
1.53 brouard 2498: for(i=1; i<=nlstate;i++)
2499: prlim[i][i]=mobaverage[(int)age][i][ij];
2500: }
2501: }
2502:
2503: for(j=1; j<= nlstate; j++){
2504: for(h=0; h<=nhstepm; h++){
2505: for(i=1, gm[h][j]=0.;i<=nlstate;i++)
2506: gm[h][j] += prlim[i][i]*p3mat[i][j][h];
2507: }
2508: }
1.66 brouard 2509: /* This for computing probability of death (h=1 means
2510: computed over hstepm matrices product = hstepm*stepm months)
2511: as a weighted average of prlim.
2512: */
1.69 brouard 2513: for(j=nlstate+1;j<=nlstate+ndeath;j++){
1.68 lievre 2514: for(i=1,gmp[j]=0.; i<= nlstate; i++)
2515: gmp[j] += prlim[i][i]*p3mat[i][j][1];
1.53 brouard 2516: }
1.66 brouard 2517: /* end probability of death */
1.53 brouard 2518:
2519: for(j=1; j<= nlstate; j++) /* vareij */
2520: for(h=0; h<=nhstepm; h++){
2521: gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
2522: }
1.68 lievre 2523:
1.53 brouard 2524: for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
2525: gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
2526: }
2527:
2528: } /* End theta */
2529:
2530: trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
2531:
2532: for(h=0; h<=nhstepm; h++) /* veij */
2533: for(j=1; j<=nlstate;j++)
2534: for(theta=1; theta <=npar; theta++)
2535: trgradg[h][j][theta]=gradg[h][theta][j];
2536:
2537: for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
1.69 brouard 2538: for(theta=1; theta <=npar; theta++)
1.53 brouard 2539: trgradgp[j][theta]=gradgp[theta][j];
1.69 brouard 2540:
1.53 brouard 2541:
2542: hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
2543: for(i=1;i<=nlstate;i++)
2544: for(j=1;j<=nlstate;j++)
2545: vareij[i][j][(int)age] =0.;
2546:
2547: for(h=0;h<=nhstepm;h++){
2548: for(k=0;k<=nhstepm;k++){
2549: matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
2550: matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
2551: for(i=1;i<=nlstate;i++)
2552: for(j=1;j<=nlstate;j++)
2553: vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
2554: }
2555: }
1.70 brouard 2556:
1.53 brouard 2557: /* pptj */
2558: matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
2559: matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
1.70 brouard 2560: for(j=nlstate+1;j<=nlstate+ndeath;j++)
2561: for(i=nlstate+1;i<=nlstate+ndeath;i++)
1.53 brouard 2562: varppt[j][i]=doldmp[j][i];
2563: /* end ppptj */
1.66 brouard 2564: /* x centered again */
1.53 brouard 2565: hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);
2566: prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);
2567:
2568: if (popbased==1) {
1.54 brouard 2569: if(mobilav ==0){
1.53 brouard 2570: for(i=1; i<=nlstate;i++)
2571: prlim[i][i]=probs[(int)age][i][ij];
1.54 brouard 2572: }else{ /* mobilav */
1.53 brouard 2573: for(i=1; i<=nlstate;i++)
2574: prlim[i][i]=mobaverage[(int)age][i][ij];
2575: }
2576: }
1.70 brouard 2577:
1.66 brouard 2578: /* This for computing probability of death (h=1 means
2579: computed over hstepm (estepm) matrices product = hstepm*stepm months)
2580: as a weighted average of prlim.
2581: */
1.68 lievre 2582: for(j=nlstate+1;j<=nlstate+ndeath;j++){
2583: for(i=1,gmp[j]=0.;i<= nlstate; i++)
1.53 brouard 2584: gmp[j] += prlim[i][i]*p3mat[i][j][1];
2585: }
1.66 brouard 2586: /* end probability of death */
1.53 brouard 2587:
2588: fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
2589: for(j=nlstate+1; j<=(nlstate+ndeath);j++){
2590: fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
2591: for(i=1; i<=nlstate;i++){
2592: fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
2593: }
2594: }
2595: fprintf(ficresprobmorprev,"\n");
2596:
2597: fprintf(ficresvij,"%.0f ",age );
2598: for(i=1; i<=nlstate;i++)
2599: for(j=1; j<=nlstate;j++){
2600: fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
2601: }
2602: fprintf(ficresvij,"\n");
2603: free_matrix(gp,0,nhstepm,1,nlstate);
2604: free_matrix(gm,0,nhstepm,1,nlstate);
2605: free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
2606: free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
2607: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
2608: } /* End age */
2609: free_vector(gpp,nlstate+1,nlstate+ndeath);
2610: free_vector(gmp,nlstate+1,nlstate+ndeath);
2611: free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
2612: free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
2613: fprintf(ficgp,"\nset noparametric;set nolabel; set ter png small;set size 0.65, 0.65");
2614: /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */
2615: fprintf(ficgp,"\n set log y; set nolog x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
1.67 brouard 2616: /* fprintf(ficgp,"\n plot \"%s\" u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm); */
2617: /* fprintf(ficgp,"\n replot \"%s\" u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm); */
2618: /* fprintf(ficgp,"\n replot \"%s\" u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm); */
1.88 ! brouard 2619: fprintf(ficgp,"\n plot \"%s\" u 1:($3) not w l 1 ",subdirf(fileresprobmorprev));
! 2620: fprintf(ficgp,"\n replot \"%s\" u 1:(($3+1.96*$4)) t \"95\%% interval\" w l 2 ",subdirf(fileresprobmorprev));
! 2621: fprintf(ficgp,"\n replot \"%s\" u 1:(($3-1.96*$4)) not w l 2 ",subdirf(fileresprobmorprev));
! 2622: fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",subdirf(fileresprobmorprev),subdirf(fileresprobmorprev));
! 2623: 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);
1.53 brouard 2624: /* 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);
2625: */
1.88 ! brouard 2626: /* fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.png\";replot;",digitp,optionfilefiname,digit); */
! 2627: fprintf(ficgp,"\nset out \"%s%s.png\";replot;",digitp,subdirf3(optionfilefiname,"varmuptjgr",digitp),digit);
1.53 brouard 2628:
2629: free_vector(xp,1,npar);
2630: free_matrix(doldm,1,nlstate,1,nlstate);
2631: free_matrix(dnewm,1,nlstate,1,npar);
2632: free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
2633: free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
2634: free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
1.55 lievre 2635: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
1.53 brouard 2636: fclose(ficresprobmorprev);
1.88 ! brouard 2637: fflush(ficgp);
! 2638: fflush(fichtm);
1.84 brouard 2639: } /* end varevsij */
1.53 brouard 2640:
2641: /************ Variance of prevlim ******************/
2642: 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)
2643: {
2644: /* Variance of prevalence limit */
1.59 brouard 2645: /* double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
1.53 brouard 2646: double **newm;
2647: double **dnewm,**doldm;
2648: int i, j, nhstepm, hstepm;
2649: int k, cptcode;
2650: double *xp;
2651: double *gp, *gm;
2652: double **gradg, **trgradg;
2653: double age,agelim;
2654: int theta;
2655:
1.54 brouard 2656: fprintf(ficresvpl,"# Standard deviation of stable prevalences \n");
1.53 brouard 2657: fprintf(ficresvpl,"# Age");
2658: for(i=1; i<=nlstate;i++)
2659: fprintf(ficresvpl," %1d-%1d",i,i);
2660: fprintf(ficresvpl,"\n");
2661:
2662: xp=vector(1,npar);
2663: dnewm=matrix(1,nlstate,1,npar);
2664: doldm=matrix(1,nlstate,1,nlstate);
2665:
2666: hstepm=1*YEARM; /* Every year of age */
2667: hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */
2668: agelim = AGESUP;
2669: for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
2670: nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
2671: if (stepm >= YEARM) hstepm=1;
2672: nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
2673: gradg=matrix(1,npar,1,nlstate);
2674: gp=vector(1,nlstate);
2675: gm=vector(1,nlstate);
2676:
2677: for(theta=1; theta <=npar; theta++){
2678: for(i=1; i<=npar; i++){ /* Computes gradient */
2679: xp[i] = x[i] + (i==theta ?delti[theta]:0);
2680: }
2681: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
2682: for(i=1;i<=nlstate;i++)
2683: gp[i] = prlim[i][i];
2684:
2685: for(i=1; i<=npar; i++) /* Computes gradient */
2686: xp[i] = x[i] - (i==theta ?delti[theta]:0);
2687: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
2688: for(i=1;i<=nlstate;i++)
2689: gm[i] = prlim[i][i];
2690:
2691: for(i=1;i<=nlstate;i++)
2692: gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
2693: } /* End theta */
2694:
2695: trgradg =matrix(1,nlstate,1,npar);
2696:
2697: for(j=1; j<=nlstate;j++)
2698: for(theta=1; theta <=npar; theta++)
2699: trgradg[j][theta]=gradg[theta][j];
2700:
2701: for(i=1;i<=nlstate;i++)
2702: varpl[i][(int)age] =0.;
2703: matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
2704: matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
2705: for(i=1;i<=nlstate;i++)
2706: varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
2707:
2708: fprintf(ficresvpl,"%.0f ",age );
2709: for(i=1; i<=nlstate;i++)
2710: fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
2711: fprintf(ficresvpl,"\n");
2712: free_vector(gp,1,nlstate);
2713: free_vector(gm,1,nlstate);
2714: free_matrix(gradg,1,npar,1,nlstate);
2715: free_matrix(trgradg,1,nlstate,1,npar);
2716: } /* End age */
2717:
2718: free_vector(xp,1,npar);
2719: free_matrix(doldm,1,nlstate,1,npar);
2720: free_matrix(dnewm,1,nlstate,1,nlstate);
2721:
2722: }
2723:
2724: /************ Variance of one-step probabilities ******************/
2725: void varprob(char optionfilefiname[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij, int *Tvar, int **nbcode, int *ncodemax)
2726: {
2727: int i, j=0, i1, k1, l1, t, tj;
2728: int k2, l2, j1, z1;
2729: int k=0,l, cptcode;
2730: int first=1, first1;
2731: double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
2732: double **dnewm,**doldm;
2733: double *xp;
2734: double *gp, *gm;
2735: double **gradg, **trgradg;
2736: double **mu;
2737: double age,agelim, cov[NCOVMAX];
2738: double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
2739: int theta;
2740: char fileresprob[FILENAMELENGTH];
2741: char fileresprobcov[FILENAMELENGTH];
2742: char fileresprobcor[FILENAMELENGTH];
2743:
2744: double ***varpij;
2745:
2746: strcpy(fileresprob,"prob");
2747: strcat(fileresprob,fileres);
2748: if((ficresprob=fopen(fileresprob,"w"))==NULL) {
2749: printf("Problem with resultfile: %s\n", fileresprob);
2750: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
2751: }
2752: strcpy(fileresprobcov,"probcov");
2753: strcat(fileresprobcov,fileres);
2754: if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
2755: printf("Problem with resultfile: %s\n", fileresprobcov);
2756: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
2757: }
2758: strcpy(fileresprobcor,"probcor");
2759: strcat(fileresprobcor,fileres);
2760: if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
2761: printf("Problem with resultfile: %s\n", fileresprobcor);
2762: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
2763: }
2764: printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
2765: fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
2766: printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
2767: fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
2768: printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
2769: fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
2770:
2771: fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
2772: fprintf(ficresprob,"# Age");
2773: fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
2774: fprintf(ficresprobcov,"# Age");
2775: fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
2776: fprintf(ficresprobcov,"# Age");
2777:
2778:
2779: for(i=1; i<=nlstate;i++)
2780: for(j=1; j<=(nlstate+ndeath);j++){
2781: fprintf(ficresprob," p%1d-%1d (SE)",i,j);
2782: fprintf(ficresprobcov," p%1d-%1d ",i,j);
2783: fprintf(ficresprobcor," p%1d-%1d ",i,j);
2784: }
1.69 brouard 2785: /* fprintf(ficresprob,"\n");
1.53 brouard 2786: fprintf(ficresprobcov,"\n");
2787: fprintf(ficresprobcor,"\n");
1.69 brouard 2788: */
2789: xp=vector(1,npar);
1.53 brouard 2790: dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
2791: doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
2792: mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
2793: varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
2794: first=1;
1.88 ! brouard 2795: fprintf(ficgp,"\n# Routine varprob");
! 2796: fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
! 2797: fprintf(fichtm,"\n");
! 2798:
! 2799: fprintf(fichtm,"\n<li><h4> Computing matrix of variance-covariance of step probabilities</h4></li>\n");
! 2800: fprintf(fichtm,"\nWe have drawn ellipsoids of confidence around the p<inf>ij</inf>, p<inf>kl</inf> to understand the covariance between two incidences. They are expressed in year<sup>-1</sup> in order to be less dependent of stepm.<br>\n");
! 2801: fprintf(fichtm,"\n<br> We have drawn x'cov<sup>-1</sup>x = 4 where x is the column vector (pij,pkl). It means that if pij and pkl where uncorrelated the (2X2) matrix would have been (1/(var pij), 0 , 0, 1/(var pkl)), and the confidence interval would be 2 standard deviations wide on each axis. <br> When both incidences are correlated we diagonalised the inverse of the covariance matrix and made the appropriate rotation.<br> \n");
1.53 brouard 2802:
2803: cov[1]=1;
2804: tj=cptcoveff;
2805: if (cptcovn<1) {tj=1;ncodemax[1]=1;}
2806: j1=0;
2807: for(t=1; t<=tj;t++){
2808: for(i1=1; i1<=ncodemax[t];i1++){
2809: j1++;
2810: if (cptcovn>0) {
2811: fprintf(ficresprob, "\n#********** Variable ");
2812: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
1.69 brouard 2813: fprintf(ficresprob, "**********\n#\n");
1.53 brouard 2814: fprintf(ficresprobcov, "\n#********** Variable ");
2815: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
1.69 brouard 2816: fprintf(ficresprobcov, "**********\n#\n");
1.53 brouard 2817:
2818: fprintf(ficgp, "\n#********** Variable ");
1.69 brouard 2819: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
2820: fprintf(ficgp, "**********\n#\n");
1.53 brouard 2821:
2822:
2823: fprintf(fichtm, "\n<hr size=\"2\" color=\"#EC5E5E\">********** Variable ");
2824: for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
2825: fprintf(fichtm, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
2826:
2827: fprintf(ficresprobcor, "\n#********** Variable ");
2828: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
1.69 brouard 2829: fprintf(ficresprobcor, "**********\n#");
1.53 brouard 2830: }
2831:
2832: for (age=bage; age<=fage; age ++){
2833: cov[2]=age;
2834: for (k=1; k<=cptcovn;k++) {
2835: cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];
2836: }
2837: for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
2838: for (k=1; k<=cptcovprod;k++)
2839: cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
2840:
2841: gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
2842: trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
2843: gp=vector(1,(nlstate)*(nlstate+ndeath));
2844: gm=vector(1,(nlstate)*(nlstate+ndeath));
2845:
2846: for(theta=1; theta <=npar; theta++){
2847: for(i=1; i<=npar; i++)
1.74 brouard 2848: xp[i] = x[i] + (i==theta ?delti[theta]:(double)0);
1.53 brouard 2849:
2850: pmij(pmmij,cov,ncovmodel,xp,nlstate);
2851:
2852: k=0;
2853: for(i=1; i<= (nlstate); i++){
2854: for(j=1; j<=(nlstate+ndeath);j++){
2855: k=k+1;
2856: gp[k]=pmmij[i][j];
2857: }
2858: }
2859:
2860: for(i=1; i<=npar; i++)
1.74 brouard 2861: xp[i] = x[i] - (i==theta ?delti[theta]:(double)0);
1.53 brouard 2862:
2863: pmij(pmmij,cov,ncovmodel,xp,nlstate);
2864: k=0;
2865: for(i=1; i<=(nlstate); i++){
2866: for(j=1; j<=(nlstate+ndeath);j++){
2867: k=k+1;
2868: gm[k]=pmmij[i][j];
2869: }
2870: }
2871:
2872: for(i=1; i<= (nlstate)*(nlstate+ndeath); i++)
1.74 brouard 2873: gradg[theta][i]=(gp[i]-gm[i])/(double)2./delti[theta];
1.53 brouard 2874: }
2875:
2876: for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
2877: for(theta=1; theta <=npar; theta++)
2878: trgradg[j][theta]=gradg[theta][j];
2879:
2880: matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov);
2881: matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);
1.59 brouard 2882: free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
2883: free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
2884: free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
2885: free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
2886:
1.53 brouard 2887: pmij(pmmij,cov,ncovmodel,x,nlstate);
2888:
2889: k=0;
2890: for(i=1; i<=(nlstate); i++){
2891: for(j=1; j<=(nlstate+ndeath);j++){
2892: k=k+1;
2893: mu[k][(int) age]=pmmij[i][j];
2894: }
2895: }
2896: for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
2897: for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
2898: varpij[i][j][(int)age] = doldm[i][j];
2899:
2900: /*printf("\n%d ",(int)age);
1.59 brouard 2901: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
2902: printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
2903: fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
2904: }*/
1.53 brouard 2905:
2906: fprintf(ficresprob,"\n%d ",(int)age);
2907: fprintf(ficresprobcov,"\n%d ",(int)age);
2908: fprintf(ficresprobcor,"\n%d ",(int)age);
2909:
2910: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)
2911: fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));
2912: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
2913: fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);
2914: fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
2915: }
2916: i=0;
2917: for (k=1; k<=(nlstate);k++){
2918: for (l=1; l<=(nlstate+ndeath);l++){
2919: i=i++;
2920: fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
2921: fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
2922: for (j=1; j<=i;j++){
2923: fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);
2924: fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));
2925: }
2926: }
2927: }/* end of loop for state */
2928: } /* end of loop for age */
2929:
2930: /* Confidence intervalle of pij */
2931: /*
1.59 brouard 2932: fprintf(ficgp,"\nset noparametric;unset label");
2933: fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");
2934: fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
2935: 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);
2936: fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);
2937: fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);
2938: fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);
1.53 brouard 2939: */
2940:
2941: /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
2942: first1=1;
2943: for (k2=1; k2<=(nlstate);k2++){
2944: for (l2=1; l2<=(nlstate+ndeath);l2++){
2945: if(l2==k2) continue;
2946: j=(k2-1)*(nlstate+ndeath)+l2;
2947: for (k1=1; k1<=(nlstate);k1++){
2948: for (l1=1; l1<=(nlstate+ndeath);l1++){
2949: if(l1==k1) continue;
2950: i=(k1-1)*(nlstate+ndeath)+l1;
2951: if(i<=j) continue;
2952: for (age=bage; age<=fage; age ++){
2953: if ((int)age %5==0){
2954: v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;
2955: v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;
2956: cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;
2957: mu1=mu[i][(int) age]/stepm*YEARM ;
2958: mu2=mu[j][(int) age]/stepm*YEARM;
2959: c12=cv12/sqrt(v1*v2);
2960: /* Computing eigen value of matrix of covariance */
2961: lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
2962: lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
2963: /* Eigen vectors */
2964: v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
2965: /*v21=sqrt(1.-v11*v11); *//* error */
2966: v21=(lc1-v1)/cv12*v11;
2967: v12=-v21;
2968: v22=v11;
2969: tnalp=v21/v11;
2970: if(first1==1){
2971: first1=0;
2972: 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);
2973: }
2974: 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);
2975: /*printf(fignu*/
2976: /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */
2977: /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */
2978: if(first==1){
2979: first=0;
2980: fprintf(ficgp,"\nset parametric;unset label");
2981: 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);
2982: fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
1.88 ! brouard 2983: fprintf(fichtm,"\n<br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup>\
! 2984: :<a href=\"%s%d%1d%1d-%1d%1d.png\">\
! 2985: %s%d%1d%1d-%1d%1d.png</A>, ",k1,l1,k2,l2,\
! 2986: subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2,\
! 2987: subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
! 2988: fprintf(fichtm,"\n<br><img src=\"%s%d%1d%1d-%1d%1d.png\"> ",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
1.53 brouard 2989: fprintf(fichtm,"\n<br> Correlation at age %d (%.3f),",(int) age, c12);
1.88 ! brouard 2990: fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\"",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
1.53 brouard 2991: fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
2992: fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
2993: 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",\
2994: mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
2995: mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
2996: }else{
2997: first=0;
2998: fprintf(fichtm," %d (%.3f),",(int) age, c12);
2999: fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
3000: fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
3001: 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",\
3002: mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
3003: mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
3004: }/* if first */
3005: } /* age mod 5 */
3006: } /* end loop age */
1.88 ! brouard 3007: fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\";replot;",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
1.53 brouard 3008: first=1;
3009: } /*l12 */
3010: } /* k12 */
3011: } /*l1 */
3012: }/* k1 */
3013: } /* loop covariates */
3014: }
1.59 brouard 3015: free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
3016: free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
1.53 brouard 3017: free_vector(xp,1,npar);
3018: fclose(ficresprob);
3019: fclose(ficresprobcov);
3020: fclose(ficresprobcor);
1.88 ! brouard 3021: /* fclose(ficgp);*/
1.53 brouard 3022: }
3023:
3024:
3025: /******************* Printing html file ***********/
3026: void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \
3027: int lastpass, int stepm, int weightopt, char model[],\
3028: int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
3029: int popforecast, int estepm ,\
3030: double jprev1, double mprev1,double anprev1, \
3031: double jprev2, double mprev2,double anprev2){
3032: int jj1, k1, i1, cpt;
3033: /*char optionfilehtm[FILENAMELENGTH];*/
1.87 brouard 3034: /* if((fichtm=fopen(optionfilehtm,"a"))==NULL) { */
3035: /* printf("Problem with %s \n",optionfilehtm), exit(0); */
3036: /* fprintf(ficlog,"Problem with %s \n",optionfilehtm), exit(0); */
3037: /* } */
1.53 brouard 3038:
1.85 brouard 3039: fprintf(fichtm,"<ul><li><h4>Result files (first order: no variance)</h4>\n \
1.88 ! brouard 3040: - Observed prevalence in each state (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"%s\">%s</a> <br>\n \
! 3041: - Estimated transition probabilities over %d (stepm) months: <a href=\"%s\">%s</a><br>\n \
! 3042: - Stable prevalence in each health state: <a href=\"%s\">%s</a> <br>\n \
1.85 brouard 3043: - Life expectancies by age and initial health status (estepm=%2d months): \
1.88 ! brouard 3044: <a href=\"%s\">%s</a> <br>\n</li>", \
! 3045: jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirf2(fileres,"p"),subdirf2(fileres,"p"),\
! 3046: stepm,subdirf2(fileres,"pij"),subdirf2(fileres,"pij"),\
! 3047: subdirf2(fileres,"pl"),subdirf2(fileres,"pl"),\
! 3048: estepm,subdirf2(fileres,"e"),subdirf2(fileres,"e"));
1.53 brouard 3049:
3050: fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
3051:
3052: m=cptcoveff;
3053: if (cptcovn < 1) {m=1;ncodemax[1]=1;}
3054:
3055: jj1=0;
3056: for(k1=1; k1<=m;k1++){
3057: for(i1=1; i1<=ncodemax[k1];i1++){
3058: jj1++;
3059: if (cptcovn > 0) {
3060: fprintf(fichtm,"<hr size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
3061: for (cpt=1; cpt<=cptcoveff;cpt++)
3062: fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
3063: fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
3064: }
3065: /* Pij */
1.88 ! brouard 3066: 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> \
! 3067: <img src=\"%s%d1.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);
1.53 brouard 3068: /* Quasi-incidences */
1.85 brouard 3069: fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months\
1.88 ! brouard 3070: before but expressed in per year i.e. quasi incidences if stepm is small and probabilities too: %s%d2.png<br> \
! 3071: <img src=\"%s%d2.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);
1.53 brouard 3072: /* Stable prevalence in each health state */
3073: for(cpt=1; cpt<nlstate;cpt++){
1.85 brouard 3074: fprintf(fichtm,"<br>- Stable prevalence in each health state : p%s%d%d.png<br> \
1.88 ! brouard 3075: <img src=\"%s%d%d.png\">",subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1);
1.53 brouard 3076: }
3077: for(cpt=1; cpt<=nlstate;cpt++) {
1.88 ! brouard 3078: fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): %s%d%d.png <br> \
! 3079: <img src=\"%s%d%d.png\">",cpt,subdirf2(optionfilefiname,"exo"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1);
1.53 brouard 3080: }
1.85 brouard 3081: fprintf(fichtm,"\n<br>- Total life expectancy by age and \
1.88 ! brouard 3082: health expectancies in states (1) and (2): %s%d.png<br>\
! 3083: <img src=\"%s%d.png\">",subdirf2(optionfilefiname,"e"),jj1,subdirf2(optionfilefiname,"e"),jj1);
1.53 brouard 3084: } /* end i1 */
3085: }/* End k1 */
3086: fprintf(fichtm,"</ul>");
3087:
3088:
1.85 brouard 3089: fprintf(fichtm,"\n<br><li><h4> Result files (second order: variances)</h4>\n\
3090: - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n\
1.88 ! brouard 3091: - Variance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n\
! 3092: - Variance-covariance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n\
! 3093: - Correlation matrix of one-step probabilities: <a href=\"%s\">%s</a> <br>\n\
! 3094: - Variances and covariances of life expectancies by age and initial health status (estepm=%d months): <a href=\"%s\">%s</a><br>\n\
! 3095: - Health expectancies with their variances (no covariance): <a href=\"%s\">%s</a> <br>\n\
! 3096: - Standard deviation of stable prevalences: <a href=\"%s\">%s</a> <br>\n",\
! 3097: rfileres,rfileres,\
! 3098: subdirf2(fileres,"prob"),subdirf2(fileres,"prob"),\
! 3099: subdirf2(fileres,"probcov"),subdirf2(fileres,"probcov"),\
! 3100: subdirf2(fileres,"probcor"),subdirf2(fileres,"probcor"),\
! 3101: estepm, subdirf2(fileres,"v"),subdirf2(fileres,"v"),\
! 3102: subdirf2(fileres,"t"),subdirf2(fileres,"t"),\
! 3103: subdirf2(fileres,"vpl"),subdirf2(fileres,"vpl"));
1.53 brouard 3104:
1.76 brouard 3105: /* if(popforecast==1) fprintf(fichtm,"\n */
3106: /* - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n */
3107: /* - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n */
3108: /* <br>",fileres,fileres,fileres,fileres); */
3109: /* else */
3110: /* 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); */
1.53 brouard 3111: fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
3112:
3113: m=cptcoveff;
3114: if (cptcovn < 1) {m=1;ncodemax[1]=1;}
3115:
3116: jj1=0;
3117: for(k1=1; k1<=m;k1++){
3118: for(i1=1; i1<=ncodemax[k1];i1++){
3119: jj1++;
3120: if (cptcovn > 0) {
3121: fprintf(fichtm,"<hr size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
3122: for (cpt=1; cpt<=cptcoveff;cpt++)
3123: fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
3124: fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
3125: }
3126: for(cpt=1; cpt<=nlstate;cpt++) {
1.85 brouard 3127: fprintf(fichtm,"<br>- Observed and period prevalence (with confident\
1.88 ! brouard 3128: interval) in state (%d): %s%d%d.png <br>\
! 3129: <img src=\"%s%d%d.png\">",cpt,subdirf2(optionfilefiname,"pe"),cpt,jj1,subdirf2(optionfilefiname,"pe"),cpt,jj1);
1.53 brouard 3130: }
3131: } /* end i1 */
3132: }/* End k1 */
3133: fprintf(fichtm,"</ul>");
1.87 brouard 3134: fflush(fichtm);
1.53 brouard 3135: }
3136:
3137: /******************* Gnuplot file **************/
1.88 ! brouard 3138: void printinggnuplot(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char path[], double p[]){
1.53 brouard 3139:
1.88 ! brouard 3140: char dirfileres[132],optfileres[132];
1.53 brouard 3141: int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;
3142: int ng;
1.88 ! brouard 3143: /* if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) { */
! 3144: /* printf("Problem with file %s",optionfilegnuplot); */
! 3145: /* fprintf(ficlog,"Problem with file %s",optionfilegnuplot); */
! 3146: /* } */
1.53 brouard 3147:
1.54 brouard 3148: /*#ifdef windows */
1.88 ! brouard 3149: fprintf(ficgp,"cd \"%s\" \n",path);
1.54 brouard 3150: /*#endif */
1.88 ! brouard 3151: m=pow(2,cptcoveff);
! 3152:
! 3153: strcpy(dirfileres,optionfilefiname);
! 3154: strcpy(optfileres,"vpl");
1.53 brouard 3155: /* 1eme*/
3156: for (cpt=1; cpt<= nlstate ; cpt ++) {
3157: for (k1=1; k1<= m ; k1 ++) {
1.88 ! brouard 3158: fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"v"),cpt,k1);
! 3159: fprintf(ficgp,"\n#set out \"v%s%d%d.png\" \n",optionfilefiname,cpt,k1);
! 3160: fprintf(ficgp,"set xlabel \"Age\" \n\
! 3161: set ylabel \"Probability\" \n\
! 3162: set ter png small\n\
! 3163: set size 0.65,0.65\n\
! 3164: plot [%.f:%.f] \"%s\" every :::%d::%d u 1:2 \"\%%lf",ageminpar,fage,subdirf2(fileres,"vpl"),k1-1,k1-1);
1.53 brouard 3165:
3166: for (i=1; i<= nlstate ; i ++) {
3167: if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
3168: else fprintf(ficgp," \%%*lf (\%%*lf)");
3169: }
1.88 ! brouard 3170: 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);
1.53 brouard 3171: for (i=1; i<= nlstate ; i ++) {
3172: if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
3173: else fprintf(ficgp," \%%*lf (\%%*lf)");
3174: }
1.88 ! brouard 3175: fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"%s\" every :::%d::%d u 1:($2-1.96*$3) \"\%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1);
1.53 brouard 3176: for (i=1; i<= nlstate ; i ++) {
3177: if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
3178: else fprintf(ficgp," \%%*lf (\%%*lf)");
3179: }
1.88 ! brouard 3180: fprintf(ficgp,"\" t\"\" w l 1,\"%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",subdirf2(fileres,"p"),k1-1,k1-1,2+4*(cpt-1));
1.53 brouard 3181: }
3182: }
3183: /*2 eme*/
3184:
3185: for (k1=1; k1<= m ; k1 ++) {
1.88 ! brouard 3186: fprintf(ficgp,"\nset out \"%s%d.png\" \n",subdirf2(optionfilefiname,"e"),k1);
1.53 brouard 3187: fprintf(ficgp,"set ylabel \"Years\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] ",ageminpar,fage);
3188:
3189: for (i=1; i<= nlstate+1 ; i ++) {
3190: k=2*i;
1.88 ! brouard 3191: fprintf(ficgp,"\"%s\" every :::%d::%d u 1:2 \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
1.53 brouard 3192: for (j=1; j<= nlstate+1 ; j ++) {
3193: if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
3194: else fprintf(ficgp," \%%*lf (\%%*lf)");
3195: }
3196: if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");
3197: else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);
1.88 ! brouard 3198: fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
1.53 brouard 3199: for (j=1; j<= nlstate+1 ; j ++) {
3200: if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
3201: else fprintf(ficgp," \%%*lf (\%%*lf)");
3202: }
3203: fprintf(ficgp,"\" t\"\" w l 0,");
1.88 ! brouard 3204: fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
1.53 brouard 3205: for (j=1; j<= nlstate+1 ; j ++) {
3206: if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
3207: else fprintf(ficgp," \%%*lf (\%%*lf)");
3208: }
3209: if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");
3210: else fprintf(ficgp,"\" t\"\" w l 0,");
3211: }
3212: }
3213:
3214: /*3eme*/
3215:
3216: for (k1=1; k1<= m ; k1 ++) {
3217: for (cpt=1; cpt<= nlstate ; cpt ++) {
3218: k=2+nlstate*(2*cpt-2);
1.88 ! brouard 3219: fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"exp"),cpt,k1);
! 3220: fprintf(ficgp,"set ter png small\n\
! 3221: set size 0.65,0.65\n\
! 3222: plot [%.f:%.f] \"%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,subdirf2(fileres,"e"),k1-1,k1-1,k,cpt);
1.53 brouard 3223: /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
3224: for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
3225: fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
3226: fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
3227: for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
3228: fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
3229:
3230: */
3231: for (i=1; i< nlstate ; i ++) {
1.88 ! brouard 3232: 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);
1.53 brouard 3233:
3234: }
3235: }
3236: }
3237:
1.76 brouard 3238: /* CV preval stable (period) */
1.53 brouard 3239: for (k1=1; k1<= m ; k1 ++) {
1.76 brouard 3240: for (cpt=1; cpt<=nlstate ; cpt ++) {
1.53 brouard 3241: k=3;
1.88 ! brouard 3242: fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"p"),cpt,k1);
! 3243: fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\
! 3244: set ter png small\nset size 0.65,0.65\n\
! 3245: plot [%.f:%.f] \"%s\" u ($1==%d ? ($3):1/0):($%d/($%d",ageminpar,agemaxpar,subdirf2(fileres,"pij"),k1,k+cpt+1,k+1);
1.53 brouard 3246:
1.83 lievre 3247: for (i=1; i< nlstate ; i ++)
1.53 brouard 3248: fprintf(ficgp,"+$%d",k+i+1);
3249: fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);
3250:
3251: l=3+(nlstate+ndeath)*cpt;
1.88 ! brouard 3252: fprintf(ficgp,",\"%s\" u ($1==%d ? ($3):1/0):($%d/($%d",subdirf2(fileres,"pij"),k1,l+cpt+1,l+1);
1.53 brouard 3253: for (i=1; i< nlstate ; i ++) {
3254: l=3+(nlstate+ndeath)*cpt;
3255: fprintf(ficgp,"+$%d",l+i+1);
3256: }
3257: fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);
3258: }
3259: }
3260:
3261: /* proba elementaires */
3262: for(i=1,jk=1; i <=nlstate; i++){
3263: for(k=1; k <=(nlstate+ndeath); k++){
3264: if (k != i) {
3265: for(j=1; j <=ncovmodel; j++){
3266: fprintf(ficgp,"p%d=%f ",jk,p[jk]);
3267: jk++;
3268: fprintf(ficgp,"\n");
3269: }
3270: }
3271: }
3272: }
3273:
3274: for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/
3275: for(jk=1; jk <=m; jk++) {
1.88 ! brouard 3276: fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"pe"),jk,ng);
1.53 brouard 3277: if (ng==2)
3278: fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
3279: else
3280: fprintf(ficgp,"\nset title \"Probability\"\n");
3281: fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65\nset log y\nplot [%.f:%.f] ",ageminpar,agemaxpar);
3282: i=1;
3283: for(k2=1; k2<=nlstate; k2++) {
3284: k3=i;
3285: for(k=1; k<=(nlstate+ndeath); k++) {
3286: if (k != k2){
3287: if(ng==2)
3288: fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);
3289: else
3290: fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
3291: ij=1;
3292: for(j=3; j <=ncovmodel; j++) {
3293: if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
3294: fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
3295: ij++;
3296: }
3297: else
3298: fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
3299: }
3300: fprintf(ficgp,")/(1");
3301:
3302: for(k1=1; k1 <=nlstate; k1++){
3303: fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);
3304: ij=1;
3305: for(j=3; j <=ncovmodel; j++){
3306: if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
3307: fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
3308: ij++;
3309: }
3310: else
3311: fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
3312: }
3313: fprintf(ficgp,")");
3314: }
3315: fprintf(ficgp,") t \"p%d%d\" ", k2,k);
3316: if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");
3317: i=i+ncovmodel;
3318: }
3319: } /* end k */
3320: } /* end k2 */
3321: } /* end jk */
3322: } /* end ng */
1.88 ! brouard 3323: fflush(ficgp);
1.53 brouard 3324: } /* end gnuplot */
3325:
3326:
3327: /*************** Moving average **************/
1.54 brouard 3328: int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav){
1.53 brouard 3329:
3330: int i, cpt, cptcod;
1.58 lievre 3331: int modcovmax =1;
1.54 brouard 3332: int mobilavrange, mob;
1.53 brouard 3333: double age;
1.58 lievre 3334:
3335: modcovmax=2*cptcoveff;/* Max number of modalities. We suppose
3336: a covariate has 2 modalities */
3337: if (cptcovn<1) modcovmax=1; /* At least 1 pass */
3338:
1.54 brouard 3339: if(mobilav==1||mobilav ==3 ||mobilav==5 ||mobilav== 7){
3340: if(mobilav==1) mobilavrange=5; /* default */
3341: else mobilavrange=mobilav;
3342: for (age=bage; age<=fage; age++)
3343: for (i=1; i<=nlstate;i++)
1.58 lievre 3344: for (cptcod=1;cptcod<=modcovmax;cptcod++)
1.54 brouard 3345: mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
3346: /* We keep the original values on the extreme ages bage, fage and for
3347: fage+1 and bage-1 we use a 3 terms moving average; for fage+2 bage+2
3348: we use a 5 terms etc. until the borders are no more concerned.
3349: */
3350: for (mob=3;mob <=mobilavrange;mob=mob+2){
3351: for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){
3352: for (i=1; i<=nlstate;i++){
1.58 lievre 3353: for (cptcod=1;cptcod<=modcovmax;cptcod++){
1.54 brouard 3354: mobaverage[(int)age][i][cptcod] =probs[(int)age][i][cptcod];
3355: for (cpt=1;cpt<=(mob-1)/2;cpt++){
3356: mobaverage[(int)age][i][cptcod] +=probs[(int)age-cpt][i][cptcod];
3357: mobaverage[(int)age][i][cptcod] +=probs[(int)age+cpt][i][cptcod];
3358: }
3359: mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/mob;
3360: }
1.53 brouard 3361: }
1.54 brouard 3362: }/* end age */
3363: }/* end mob */
3364: }else return -1;
3365: return 0;
3366: }/* End movingaverage */
1.53 brouard 3367:
3368:
3369: /************** Forecasting ******************/
1.70 brouard 3370: prevforecast(char fileres[], double anproj1, double mproj1, double jproj1, double ageminpar, double agemax, double dateprev1, double dateprev2, int mobilav, double bage, double fage, int firstpass, int lastpass, double anproj2, double p[], int cptcoveff){
1.69 brouard 3371: /* proj1, year, month, day of starting projection
3372: agemin, agemax range of age
3373: dateprev1 dateprev2 range of dates during which prevalence is computed
1.70 brouard 3374: anproj2 year of en of projection (same day and month as proj1).
1.69 brouard 3375: */
1.73 lievre 3376: int yearp, stepsize, hstepm, nhstepm, j, k, c, cptcod, i, h, i1;
1.53 brouard 3377: int *popage;
1.70 brouard 3378: double agec; /* generic age */
3379: double agelim, ppij, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
1.53 brouard 3380: double *popeffectif,*popcount;
3381: double ***p3mat;
1.55 lievre 3382: double ***mobaverage;
1.53 brouard 3383: char fileresf[FILENAMELENGTH];
3384:
1.69 brouard 3385: agelim=AGESUP;
1.84 brouard 3386: prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
1.53 brouard 3387:
3388: strcpy(fileresf,"f");
3389: strcat(fileresf,fileres);
3390: if((ficresf=fopen(fileresf,"w"))==NULL) {
3391: printf("Problem with forecast resultfile: %s\n", fileresf);
3392: fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);
3393: }
3394: printf("Computing forecasting: result on file '%s' \n", fileresf);
3395: fprintf(ficlog,"Computing forecasting: result on file '%s' \n", fileresf);
3396:
3397: if (cptcoveff==0) ncodemax[cptcoveff]=1;
3398:
1.54 brouard 3399: if (mobilav!=0) {
1.53 brouard 3400: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
1.54 brouard 3401: if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
3402: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
3403: printf(" Error in movingaverage mobilav=%d\n",mobilav);
3404: }
1.53 brouard 3405: }
3406:
3407: stepsize=(int) (stepm+YEARM-1)/YEARM;
3408: if (stepm<=12) stepsize=1;
1.74 brouard 3409: if(estepm < stepm){
3410: printf ("Problem %d lower than %d\n",estepm, stepm);
3411: }
3412: else hstepm=estepm;
3413:
1.53 brouard 3414: hstepm=hstepm/stepm;
1.69 brouard 3415: yp1=modf(dateintmean,&yp);/* extracts integral of datemean in yp and
3416: fractional in yp1 */
1.53 brouard 3417: anprojmean=yp;
3418: yp2=modf((yp1*12),&yp);
3419: mprojmean=yp;
3420: yp1=modf((yp2*30.5),&yp);
3421: jprojmean=yp;
3422: if(jprojmean==0) jprojmean=1;
3423: if(mprojmean==0) jprojmean=1;
1.73 lievre 3424:
3425: i1=cptcoveff;
3426: if (cptcovn < 1){i1=1;}
1.53 brouard 3427:
1.70 brouard 3428: fprintf(ficresf,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2);
1.53 brouard 3429:
1.70 brouard 3430: fprintf(ficresf,"#****** Routine prevforecast **\n");
1.73 lievre 3431:
1.75 brouard 3432: /* if (h==(int)(YEARM*yearp)){ */
1.73 lievre 3433: for(cptcov=1, k=0;cptcov<=i1;cptcov++){
1.53 brouard 3434: for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
3435: k=k+1;
3436: fprintf(ficresf,"\n#******");
3437: for(j=1;j<=cptcoveff;j++) {
1.70 brouard 3438: 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]]);
1.53 brouard 3439: }
3440: fprintf(ficresf,"******\n");
1.70 brouard 3441: fprintf(ficresf,"# Covariate valuofcovar yearproj age");
3442: for(j=1; j<=nlstate+ndeath;j++){
3443: for(i=1; i<=nlstate;i++)
3444: fprintf(ficresf," p%d%d",i,j);
3445: fprintf(ficresf," p.%d",j);
3446: }
1.74 brouard 3447: for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) {
1.53 brouard 3448: fprintf(ficresf,"\n");
1.70 brouard 3449: fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+yearp);
1.53 brouard 3450:
1.71 brouard 3451: for (agec=fage; agec>=(ageminpar-1); agec--){
1.70 brouard 3452: nhstepm=(int) rint((agelim-agec)*YEARM/stepm);
1.53 brouard 3453: nhstepm = nhstepm/hstepm;
3454: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3455: oldm=oldms;savm=savms;
1.70 brouard 3456: hpxij(p3mat,nhstepm,agec,hstepm,p,nlstate,stepm,oldm,savm, k);
1.53 brouard 3457:
3458: for (h=0; h<=nhstepm; h++){
1.75 brouard 3459: if (h*hstepm/YEARM*stepm ==yearp) {
1.69 brouard 3460: fprintf(ficresf,"\n");
3461: for(j=1;j<=cptcoveff;j++)
3462: fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
1.70 brouard 3463: fprintf(ficresf,"%.f %.f ",anproj1+yearp,agec+h*hstepm/YEARM*stepm);
1.53 brouard 3464: }
3465: for(j=1; j<=nlstate+ndeath;j++) {
1.70 brouard 3466: ppij=0.;
1.71 brouard 3467: for(i=1; i<=nlstate;i++) {
1.53 brouard 3468: if (mobilav==1)
1.71 brouard 3469: ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][i][cptcod];
1.53 brouard 3470: else {
1.71 brouard 3471: ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][cptcod];
1.53 brouard 3472: }
1.75 brouard 3473: if (h*hstepm/YEARM*stepm== yearp) {
1.70 brouard 3474: fprintf(ficresf," %.3f", p3mat[i][j][h]);
1.75 brouard 3475: }
3476: } /* end i */
3477: if (h*hstepm/YEARM*stepm==yearp) {
1.70 brouard 3478: fprintf(ficresf," %.3f", ppij);
1.53 brouard 3479: }
1.75 brouard 3480: }/* end j */
3481: } /* end h */
1.53 brouard 3482: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
1.75 brouard 3483: } /* end agec */
3484: } /* end yearp */
3485: } /* end cptcod */
3486: } /* end cptcov */
1.53 brouard 3487:
1.54 brouard 3488: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
1.53 brouard 3489:
3490: fclose(ficresf);
3491: }
1.70 brouard 3492:
3493: /************** Forecasting *****not tested NB*************/
1.53 brouard 3494: 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){
3495:
3496: int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;
3497: int *popage;
1.69 brouard 3498: double calagedatem, agelim, kk1, kk2;
1.53 brouard 3499: double *popeffectif,*popcount;
3500: double ***p3mat,***tabpop,***tabpopprev;
1.55 lievre 3501: double ***mobaverage;
1.53 brouard 3502: char filerespop[FILENAMELENGTH];
3503:
3504: tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
3505: tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
3506: agelim=AGESUP;
1.69 brouard 3507: calagedatem=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;
1.53 brouard 3508:
1.84 brouard 3509: prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
1.53 brouard 3510:
3511:
3512: strcpy(filerespop,"pop");
3513: strcat(filerespop,fileres);
3514: if((ficrespop=fopen(filerespop,"w"))==NULL) {
3515: printf("Problem with forecast resultfile: %s\n", filerespop);
3516: fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop);
3517: }
3518: printf("Computing forecasting: result on file '%s' \n", filerespop);
3519: fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop);
3520:
3521: if (cptcoveff==0) ncodemax[cptcoveff]=1;
3522:
1.54 brouard 3523: if (mobilav!=0) {
1.53 brouard 3524: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
1.54 brouard 3525: if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
3526: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
3527: printf(" Error in movingaverage mobilav=%d\n",mobilav);
3528: }
1.53 brouard 3529: }
3530:
3531: stepsize=(int) (stepm+YEARM-1)/YEARM;
3532: if (stepm<=12) stepsize=1;
3533:
3534: agelim=AGESUP;
3535:
3536: hstepm=1;
3537: hstepm=hstepm/stepm;
3538:
3539: if (popforecast==1) {
3540: if((ficpop=fopen(popfile,"r"))==NULL) {
3541: printf("Problem with population file : %s\n",popfile);exit(0);
3542: fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0);
3543: }
3544: popage=ivector(0,AGESUP);
3545: popeffectif=vector(0,AGESUP);
3546: popcount=vector(0,AGESUP);
3547:
3548: i=1;
3549: while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;
3550:
3551: imx=i;
3552: for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];
3553: }
3554:
1.69 brouard 3555: for(cptcov=1,k=0;cptcov<=i2;cptcov++){
1.53 brouard 3556: for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
3557: k=k+1;
3558: fprintf(ficrespop,"\n#******");
3559: for(j=1;j<=cptcoveff;j++) {
3560: fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
3561: }
3562: fprintf(ficrespop,"******\n");
3563: fprintf(ficrespop,"# Age");
3564: for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);
3565: if (popforecast==1) fprintf(ficrespop," [Population]");
3566:
3567: for (cpt=0; cpt<=0;cpt++) {
3568: fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);
3569:
1.69 brouard 3570: for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){
1.53 brouard 3571: nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);
3572: nhstepm = nhstepm/hstepm;
3573:
3574: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3575: oldm=oldms;savm=savms;
3576: hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
3577:
3578: for (h=0; h<=nhstepm; h++){
1.69 brouard 3579: if (h==(int) (calagedatem+YEARM*cpt)) {
1.53 brouard 3580: fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
3581: }
3582: for(j=1; j<=nlstate+ndeath;j++) {
3583: kk1=0.;kk2=0;
3584: for(i=1; i<=nlstate;i++) {
3585: if (mobilav==1)
3586: kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];
3587: else {
3588: kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];
3589: }
3590: }
1.69 brouard 3591: if (h==(int)(calagedatem+12*cpt)){
1.53 brouard 3592: tabpop[(int)(agedeb)][j][cptcod]=kk1;
3593: /*fprintf(ficrespop," %.3f", kk1);
3594: if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/
3595: }
3596: }
3597: for(i=1; i<=nlstate;i++){
3598: kk1=0.;
3599: for(j=1; j<=nlstate;j++){
3600: kk1= kk1+tabpop[(int)(agedeb)][j][cptcod];
3601: }
1.69 brouard 3602: tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedatem+12*cpt)*hstepm/YEARM*stepm-1)];
1.53 brouard 3603: }
3604:
1.69 brouard 3605: if (h==(int)(calagedatem+12*cpt)) for(j=1; j<=nlstate;j++)
1.53 brouard 3606: fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);
3607: }
3608: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3609: }
3610: }
3611:
3612: /******/
3613:
3614: for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) {
3615: fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);
1.69 brouard 3616: for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){
1.53 brouard 3617: nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);
3618: nhstepm = nhstepm/hstepm;
3619:
3620: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3621: oldm=oldms;savm=savms;
3622: hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
3623: for (h=0; h<=nhstepm; h++){
1.69 brouard 3624: if (h==(int) (calagedatem+YEARM*cpt)) {
1.53 brouard 3625: fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
3626: }
3627: for(j=1; j<=nlstate+ndeath;j++) {
3628: kk1=0.;kk2=0;
3629: for(i=1; i<=nlstate;i++) {
3630: kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];
3631: }
1.69 brouard 3632: if (h==(int)(calagedatem+12*cpt)) fprintf(ficresf," %15.2f", kk1);
1.53 brouard 3633: }
3634: }
3635: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3636: }
3637: }
3638: }
3639: }
3640:
1.54 brouard 3641: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
1.53 brouard 3642:
3643: if (popforecast==1) {
3644: free_ivector(popage,0,AGESUP);
3645: free_vector(popeffectif,0,AGESUP);
3646: free_vector(popcount,0,AGESUP);
3647: }
3648: free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
3649: free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
3650: fclose(ficrespop);
1.84 brouard 3651: } /* End of popforecast */
1.53 brouard 3652:
1.87 brouard 3653: int fileappend(FILE *fichier, char *optionfich)
1.86 brouard 3654: {
1.87 brouard 3655: if((fichier=fopen(optionfich,"a"))==NULL) {
3656: printf("Problem with file: %s\n", optionfich);
3657: fprintf(ficlog,"Problem with file: %s\n", optionfich);
3658: return (0);
1.86 brouard 3659: }
1.87 brouard 3660: fflush(fichier);
3661: return (1);
1.86 brouard 3662: }
1.88 ! brouard 3663: void prwizard(int ncovmodel, int nlstate, int ndeath, char model[], FILE *ficparo)
! 3664: {
! 3665:
! 3666: char ca[32], cb[32], cc[32];
! 3667: int i,j, k, l, li, lj, lk, ll, jj, npar, itimes;
! 3668: int numlinepar;
! 3669:
! 3670: printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
! 3671: fprintf(ficparo,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
! 3672: for(i=1; i <=nlstate; i++){
! 3673: jj=0;
! 3674: for(j=1; j <=nlstate+ndeath; j++){
! 3675: if(j==i) continue;
! 3676: jj++;
! 3677: /*ca[0]= k+'a'-1;ca[1]='\0';*/
! 3678: printf("%1d%1d",i,j);
! 3679: fprintf(ficparo,"%1d%1d",i,j);
! 3680: for(k=1; k<=ncovmodel;k++){
! 3681: /* printf(" %lf",param[i][j][k]); */
! 3682: /* fprintf(ficparo," %lf",param[i][j][k]); */
! 3683: printf(" 0.");
! 3684: fprintf(ficparo," 0.");
! 3685: }
! 3686: printf("\n");
! 3687: fprintf(ficparo,"\n");
! 3688: }
! 3689: }
! 3690: printf("# Scales (for hessian or gradient estimation)\n");
! 3691: fprintf(ficparo,"# Scales (for hessian or gradient estimation)\n");
! 3692: npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/
! 3693: for(i=1; i <=nlstate; i++){
! 3694: jj=0;
! 3695: for(j=1; j <=nlstate+ndeath; j++){
! 3696: if(j==i) continue;
! 3697: jj++;
! 3698: fprintf(ficparo,"%1d%1d",i,j);
! 3699: printf("%1d%1d",i,j);
! 3700: fflush(stdout);
! 3701: for(k=1; k<=ncovmodel;k++){
! 3702: /* printf(" %le",delti3[i][j][k]); */
! 3703: /* fprintf(ficparo," %le",delti3[i][j][k]); */
! 3704: printf(" 0.");
! 3705: fprintf(ficparo," 0.");
! 3706: }
! 3707: numlinepar++;
! 3708: printf("\n");
! 3709: fprintf(ficparo,"\n");
! 3710: }
! 3711: }
! 3712: printf("# Covariance matrix\n");
! 3713: /* # 121 Var(a12)\n\ */
! 3714: /* # 122 Cov(b12,a12) Var(b12)\n\ */
! 3715: /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
! 3716: /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
! 3717: /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
! 3718: /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
! 3719: /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
! 3720: /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
! 3721: fflush(stdout);
! 3722: fprintf(ficparo,"# Covariance matrix\n");
! 3723: /* # 121 Var(a12)\n\ */
! 3724: /* # 122 Cov(b12,a12) Var(b12)\n\ */
! 3725: /* # ...\n\ */
! 3726: /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
! 3727:
! 3728: for(itimes=1;itimes<=2;itimes++){
! 3729: jj=0;
! 3730: for(i=1; i <=nlstate; i++){
! 3731: for(j=1; j <=nlstate+ndeath; j++){
! 3732: if(j==i) continue;
! 3733: for(k=1; k<=ncovmodel;k++){
! 3734: jj++;
! 3735: ca[0]= k+'a'-1;ca[1]='\0';
! 3736: if(itimes==1){
! 3737: printf("#%1d%1d%d",i,j,k);
! 3738: fprintf(ficparo,"#%1d%1d%d",i,j,k);
! 3739: }else{
! 3740: printf("%1d%1d%d",i,j,k);
! 3741: fprintf(ficparo,"%1d%1d%d",i,j,k);
! 3742: /* printf(" %.5le",matcov[i][j]); */
! 3743: }
! 3744: ll=0;
! 3745: for(li=1;li <=nlstate; li++){
! 3746: for(lj=1;lj <=nlstate+ndeath; lj++){
! 3747: if(lj==li) continue;
! 3748: for(lk=1;lk<=ncovmodel;lk++){
! 3749: ll++;
! 3750: if(ll<=jj){
! 3751: cb[0]= lk +'a'-1;cb[1]='\0';
! 3752: if(ll<jj){
! 3753: if(itimes==1){
! 3754: printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
! 3755: fprintf(ficparo," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
! 3756: }else{
! 3757: printf(" 0.");
! 3758: fprintf(ficparo," 0.");
! 3759: }
! 3760: }else{
! 3761: if(itimes==1){
! 3762: printf(" Var(%s%1d%1d)",ca,i,j);
! 3763: fprintf(ficparo," Var(%s%1d%1d)",ca,i,j);
! 3764: }else{
! 3765: printf(" 0.");
! 3766: fprintf(ficparo," 0.");
! 3767: }
! 3768: }
! 3769: }
! 3770: } /* end lk */
! 3771: } /* end lj */
! 3772: } /* end li */
! 3773: printf("\n");
! 3774: fprintf(ficparo,"\n");
! 3775: numlinepar++;
! 3776: } /* end k*/
! 3777: } /*end j */
! 3778: } /* end i */
! 3779: }
! 3780:
! 3781: } /* end of prwizard */
! 3782:
1.53 brouard 3783: /***********************************************/
3784: /**************** Main Program *****************/
3785: /***********************************************/
3786:
3787: int main(int argc, char *argv[])
3788: {
1.61 brouard 3789: int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav);
1.74 brouard 3790: int i,j, k, n=MAXN,iter,m,size=100,cptcode, cptcod;
1.88 ! brouard 3791: int jj, imk;
1.85 brouard 3792: int numlinepar=0; /* Current linenumber of parameter file */
1.87 brouard 3793: /* FILE *fichtm; *//* Html File */
3794: /* FILE *ficgp;*/ /*Gnuplot File */
1.53 brouard 3795: double agedeb, agefin,hf;
3796: double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;
3797:
3798: double fret;
3799: double **xi,tmp,delta;
3800:
3801: double dum; /* Dummy variable */
3802: double ***p3mat;
3803: double ***mobaverage;
3804: int *indx;
3805: char line[MAXLINE], linepar[MAXLINE];
1.88 ! brouard 3806: char path[MAXLINE],pathc[MAXLINE],pathcd[MAXLINE],pathtot[MAXLINE],model[MAXLINE];
! 3807: char pathr[MAXLINE];
1.53 brouard 3808: int firstobs=1, lastobs=10;
3809: int sdeb, sfin; /* Status at beginning and end */
3810: int c, h , cpt,l;
3811: int ju,jl, mi;
3812: int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;
1.59 brouard 3813: int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,*tab;
1.69 brouard 3814: int mobilavproj=0 , prevfcast=0 ; /* moving average of prev, If prevfcast=1 prevalence projection */
1.53 brouard 3815: int mobilav=0,popforecast=0;
3816: int hstepm, nhstepm;
1.74 brouard 3817: double jprev1=1, mprev1=1,anprev1=2000,jprev2=1, mprev2=1,anprev2=2000;
3818: double jpyram=1, mpyram=1,anpyram=2000,jpyram1=1, mpyram1=1,anpyram1=2000;
1.53 brouard 3819:
3820: double bage, fage, age, agelim, agebase;
3821: double ftolpl=FTOL;
3822: double **prlim;
3823: double *severity;
3824: double ***param; /* Matrix of parameters */
3825: double *p;
3826: double **matcov; /* Matrix of covariance */
3827: double ***delti3; /* Scale */
3828: double *delti; /* Scale */
3829: double ***eij, ***vareij;
3830: double **varpl; /* Variances of prevalence limits by age */
3831: double *epj, vepp;
3832: double kk1, kk2;
1.74 brouard 3833: double dateprev1, dateprev2,jproj1=1,mproj1=1,anproj1=2000,jproj2=1,mproj2=1,anproj2=2000;
1.53 brouard 3834:
3835: char *alph[]={"a","a","b","c","d","e"}, str[4];
3836:
3837:
3838: char z[1]="c", occ;
1.86 brouard 3839:
1.53 brouard 3840: char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];
1.88 ! brouard 3841: char strstart[80], *strt, strtend[80];
1.85 brouard 3842: char *stratrunc;
3843: int lstra;
3844:
3845: long total_usecs;
3846: struct timeval start_time, end_time, curr_time;
3847: struct timezone tzp;
3848: extern int gettimeofday();
3849: struct tm tmg, tm, *gmtime(), *localtime();
3850: long time_value;
3851: extern long time();
1.53 brouard 3852:
1.85 brouard 3853: /* gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */
3854: (void) gettimeofday(&start_time,&tzp);
3855: tm = *localtime(&start_time.tv_sec);
3856: tmg = *gmtime(&start_time.tv_sec);
1.88 ! brouard 3857: strcpy(strstart,asctime(&tm));
1.86 brouard 3858:
1.88 ! brouard 3859: /* printf("Localtime (at start)=%s",strstart); */
1.85 brouard 3860: /* tp.tv_sec = tp.tv_sec +86400; */
3861: /* tm = *localtime(&start_time.tv_sec); */
3862: /* tmg.tm_year=tmg.tm_year +dsign*dyear; */
3863: /* tmg.tm_mon=tmg.tm_mon +dsign*dmonth; */
3864: /* tmg.tm_hour=tmg.tm_hour + 1; */
3865: /* tp.tv_sec = mktime(&tmg); */
3866: /* strt=asctime(&tmg); */
1.88 ! brouard 3867: /* printf("Time(after) =%s",strstart); */
1.85 brouard 3868: /* (void) time (&time_value);
3869: * printf("time=%d,t-=%d\n",time_value,time_value-86400);
3870: * tm = *localtime(&time_value);
1.88 ! brouard 3871: * strstart=asctime(&tm);
! 3872: * printf("tim_value=%d,asctime=%s\n",time_value,strstart);
1.85 brouard 3873: */
3874:
1.53 brouard 3875: getcwd(pathcd, size);
3876:
1.81 brouard 3877: printf("\n%s\n%s",version,fullversion);
1.53 brouard 3878: if(argc <=1){
3879: printf("\nEnter the parameter file name: ");
3880: scanf("%s",pathtot);
3881: }
3882: else{
3883: strcpy(pathtot,argv[1]);
3884: }
1.88 ! brouard 3885: /*if(getcwd(pathcd, MAXLINE)!= NULL)printf ("Error pathcd\n");*/
1.53 brouard 3886: /*cygwin_split_path(pathtot,path,optionfile);
3887: printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/
3888: /* cutv(path,optionfile,pathtot,'\\');*/
3889:
3890: split(pathtot,path,optionfile,optionfilext,optionfilefiname);
1.85 brouard 3891: printf("pathtot=%s,\npath=%s,\noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
1.53 brouard 3892: chdir(path);
1.88 ! brouard 3893: strcpy(command,"mkdir ");
! 3894: strcat(command,optionfilefiname);
! 3895: if((outcmd=system(command)) != 0){
! 3896: printf("Problem creating directory or it already exists %s%s, err=%d\n",path,optionfilefiname,outcmd);
! 3897: /* fprintf(ficlog,"Problem creating directory %s%s\n",path,optionfilefiname); */
! 3898: /* fclose(ficlog); */
! 3899: /* exit(1); */
! 3900: }
! 3901: /* if((imk=mkdir(optionfilefiname))<0){ */
! 3902: /* perror("mkdir"); */
! 3903: /* } */
1.53 brouard 3904:
1.59 brouard 3905: /*-------- arguments in the command line --------*/
1.53 brouard 3906:
3907: /* Log file */
3908: strcat(filelog, optionfilefiname);
3909: strcat(filelog,".log"); /* */
3910: if((ficlog=fopen(filelog,"w"))==NULL) {
3911: printf("Problem with logfile %s\n",filelog);
3912: goto end;
3913: }
3914: fprintf(ficlog,"Log filename:%s\n",filelog);
1.85 brouard 3915: fprintf(ficlog,"\n%s\n%s",version,fullversion);
1.53 brouard 3916: fprintf(ficlog,"\nEnter the parameter file name: ");
1.88 ! brouard 3917: fprintf(ficlog,"pathtot=%s\n\
! 3918: path=%s \n\
! 3919: optionfile=%s\n\
! 3920: optionfilext=%s\n\
! 3921: optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
1.86 brouard 3922:
1.88 ! brouard 3923: printf("Localtime (at start):%s",strstart);
! 3924: fprintf(ficlog,"Localtime (at start): %s",strstart);
1.53 brouard 3925: fflush(ficlog);
3926:
3927: /* */
3928: strcpy(fileres,"r");
3929: strcat(fileres, optionfilefiname);
3930: strcat(fileres,".txt"); /* Other files have txt extension */
3931:
3932: /*---------arguments file --------*/
3933:
3934: if((ficpar=fopen(optionfile,"r"))==NULL) {
3935: printf("Problem with optionfile %s\n",optionfile);
3936: fprintf(ficlog,"Problem with optionfile %s\n",optionfile);
1.85 brouard 3937: fflush(ficlog);
1.53 brouard 3938: goto end;
3939: }
3940:
1.88 ! brouard 3941:
! 3942:
1.53 brouard 3943: strcpy(filereso,"o");
3944: strcat(filereso,fileres);
1.88 ! brouard 3945: if((ficparo=fopen(filereso,"w"))==NULL) { /* opened on subdirectory */
1.53 brouard 3946: printf("Problem with Output resultfile: %s\n", filereso);
3947: fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso);
1.85 brouard 3948: fflush(ficlog);
1.53 brouard 3949: goto end;
3950: }
3951:
3952: /* Reads comments: lines beginning with '#' */
1.85 brouard 3953: numlinepar=0;
1.53 brouard 3954: while((c=getc(ficpar))=='#' && c!= EOF){
3955: ungetc(c,ficpar);
3956: fgets(line, MAXLINE, ficpar);
1.85 brouard 3957: numlinepar++;
1.53 brouard 3958: puts(line);
3959: fputs(line,ficparo);
1.85 brouard 3960: fputs(line,ficlog);
1.53 brouard 3961: }
3962: ungetc(c,ficpar);
3963:
3964: 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);
1.85 brouard 3965: numlinepar++;
1.53 brouard 3966: 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);
3967: 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);
1.85 brouard 3968: 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);
3969: fflush(ficlog);
1.59 brouard 3970: while((c=getc(ficpar))=='#' && c!= EOF){
1.53 brouard 3971: ungetc(c,ficpar);
3972: fgets(line, MAXLINE, ficpar);
1.85 brouard 3973: numlinepar++;
1.53 brouard 3974: puts(line);
3975: fputs(line,ficparo);
1.85 brouard 3976: fputs(line,ficlog);
1.53 brouard 3977: }
3978: ungetc(c,ficpar);
1.85 brouard 3979:
1.53 brouard 3980:
3981: covar=matrix(0,NCOVMAX,1,n);
1.58 lievre 3982: cptcovn=0; /*Number of covariates, i.e. number of '+' in model statement*/
1.53 brouard 3983: if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;
3984:
1.58 lievre 3985: ncovmodel=2+cptcovn; /*Number of variables = cptcovn + intercept + age */
1.53 brouard 3986: nvar=ncovmodel-1; /* Suppressing age as a basic covariate */
1.88 ! brouard 3987:
! 3988: if(mle==-1){ /* Print a wizard for help writing covariance matrix */
! 3989: prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
! 3990: printf(" You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
! 3991: fprintf(ficlog," You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
! 3992: fclose (ficparo);
! 3993: fclose (ficlog);
! 3994: exit(0);
! 3995: }
1.53 brouard 3996: /* Read guess parameters */
3997: /* Reads comments: lines beginning with '#' */
3998: while((c=getc(ficpar))=='#' && c!= EOF){
3999: ungetc(c,ficpar);
4000: fgets(line, MAXLINE, ficpar);
1.85 brouard 4001: numlinepar++;
1.53 brouard 4002: puts(line);
4003: fputs(line,ficparo);
1.85 brouard 4004: fputs(line,ficlog);
1.53 brouard 4005: }
4006: ungetc(c,ficpar);
1.85 brouard 4007:
1.53 brouard 4008: param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
1.85 brouard 4009: for(i=1; i <=nlstate; i++){
4010: j=0;
4011: for(jj=1; jj <=nlstate+ndeath; jj++){
4012: if(jj==i) continue;
4013: j++;
1.53 brouard 4014: fscanf(ficpar,"%1d%1d",&i1,&j1);
1.85 brouard 4015: if ((i1 != i) && (j1 != j)){
4016: printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n",numlinepar, i,j, i1, j1);
4017: exit(1);
4018: }
1.53 brouard 4019: fprintf(ficparo,"%1d%1d",i1,j1);
4020: if(mle==1)
4021: printf("%1d%1d",i,j);
4022: fprintf(ficlog,"%1d%1d",i,j);
4023: for(k=1; k<=ncovmodel;k++){
4024: fscanf(ficpar," %lf",¶m[i][j][k]);
4025: if(mle==1){
4026: printf(" %lf",param[i][j][k]);
4027: fprintf(ficlog," %lf",param[i][j][k]);
4028: }
4029: else
4030: fprintf(ficlog," %lf",param[i][j][k]);
4031: fprintf(ficparo," %lf",param[i][j][k]);
4032: }
4033: fscanf(ficpar,"\n");
1.85 brouard 4034: numlinepar++;
1.53 brouard 4035: if(mle==1)
4036: printf("\n");
4037: fprintf(ficlog,"\n");
4038: fprintf(ficparo,"\n");
4039: }
1.85 brouard 4040: }
4041: fflush(ficlog);
4042:
1.59 brouard 4043: npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/
1.53 brouard 4044:
4045: p=param[1][1];
4046:
4047: /* Reads comments: lines beginning with '#' */
4048: while((c=getc(ficpar))=='#' && c!= EOF){
4049: ungetc(c,ficpar);
4050: fgets(line, MAXLINE, ficpar);
1.85 brouard 4051: numlinepar++;
1.53 brouard 4052: puts(line);
4053: fputs(line,ficparo);
1.85 brouard 4054: fputs(line,ficlog);
1.53 brouard 4055: }
4056: ungetc(c,ficpar);
4057:
4058: delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
1.74 brouard 4059: /* delti=vector(1,npar); *//* Scale of each paramater (output from hesscov) */
1.53 brouard 4060: for(i=1; i <=nlstate; i++){
4061: for(j=1; j <=nlstate+ndeath-1; j++){
4062: fscanf(ficpar,"%1d%1d",&i1,&j1);
1.85 brouard 4063: if ((i1-i)*(j1-j)!=0){
4064: printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n",numlinepar, i,j, i1, j1);
4065: exit(1);
4066: }
1.53 brouard 4067: printf("%1d%1d",i,j);
4068: fprintf(ficparo,"%1d%1d",i1,j1);
1.85 brouard 4069: fprintf(ficlog,"%1d%1d",i1,j1);
1.53 brouard 4070: for(k=1; k<=ncovmodel;k++){
4071: fscanf(ficpar,"%le",&delti3[i][j][k]);
4072: printf(" %le",delti3[i][j][k]);
4073: fprintf(ficparo," %le",delti3[i][j][k]);
1.85 brouard 4074: fprintf(ficlog," %le",delti3[i][j][k]);
1.53 brouard 4075: }
4076: fscanf(ficpar,"\n");
1.85 brouard 4077: numlinepar++;
1.53 brouard 4078: printf("\n");
4079: fprintf(ficparo,"\n");
1.85 brouard 4080: fprintf(ficlog,"\n");
1.53 brouard 4081: }
4082: }
1.85 brouard 4083: fflush(ficlog);
4084:
1.53 brouard 4085: delti=delti3[1][1];
1.74 brouard 4086:
4087:
4088: /* free_ma3x(delti3,1,nlstate,1,nlstate+ndeath-1,1,ncovmodel); */ /* Hasn't to to freed here otherwise delti is no more allocated */
1.53 brouard 4089:
4090: /* Reads comments: lines beginning with '#' */
4091: while((c=getc(ficpar))=='#' && c!= EOF){
4092: ungetc(c,ficpar);
4093: fgets(line, MAXLINE, ficpar);
1.85 brouard 4094: numlinepar++;
1.53 brouard 4095: puts(line);
4096: fputs(line,ficparo);
1.85 brouard 4097: fputs(line,ficlog);
1.53 brouard 4098: }
4099: ungetc(c,ficpar);
4100:
4101: matcov=matrix(1,npar,1,npar);
4102: for(i=1; i <=npar; i++){
4103: fscanf(ficpar,"%s",&str);
4104: if(mle==1)
4105: printf("%s",str);
4106: fprintf(ficlog,"%s",str);
4107: fprintf(ficparo,"%s",str);
4108: for(j=1; j <=i; j++){
4109: fscanf(ficpar," %le",&matcov[i][j]);
4110: if(mle==1){
4111: printf(" %.5le",matcov[i][j]);
4112: }
1.85 brouard 4113: fprintf(ficlog," %.5le",matcov[i][j]);
1.53 brouard 4114: fprintf(ficparo," %.5le",matcov[i][j]);
4115: }
4116: fscanf(ficpar,"\n");
1.85 brouard 4117: numlinepar++;
1.53 brouard 4118: if(mle==1)
4119: printf("\n");
4120: fprintf(ficlog,"\n");
4121: fprintf(ficparo,"\n");
4122: }
4123: for(i=1; i <=npar; i++)
4124: for(j=i+1;j<=npar;j++)
4125: matcov[i][j]=matcov[j][i];
4126:
4127: if(mle==1)
4128: printf("\n");
4129: fprintf(ficlog,"\n");
4130:
1.85 brouard 4131: fflush(ficlog);
1.53 brouard 4132:
1.59 brouard 4133: /*-------- Rewriting paramater file ----------*/
4134: strcpy(rfileres,"r"); /* "Rparameterfile */
4135: strcat(rfileres,optionfilefiname); /* Parameter file first name*/
4136: strcat(rfileres,"."); /* */
4137: strcat(rfileres,optionfilext); /* Other files have txt extension */
4138: if((ficres =fopen(rfileres,"w"))==NULL) {
4139: printf("Problem writing new parameter file: %s\n", fileres);goto end;
4140: fprintf(ficlog,"Problem writing new parameter file: %s\n", fileres);goto end;
4141: }
4142: fprintf(ficres,"#%s\n",version);
1.53 brouard 4143:
1.59 brouard 4144: /*-------- data file ----------*/
4145: if((fic=fopen(datafile,"r"))==NULL) {
4146: printf("Problem with datafile: %s\n", datafile);goto end;
4147: fprintf(ficlog,"Problem with datafile: %s\n", datafile);goto end;
4148: }
4149:
4150: n= lastobs;
4151: severity = vector(1,maxwav);
4152: outcome=imatrix(1,maxwav+1,1,n);
1.85 brouard 4153: num=lvector(1,n);
1.59 brouard 4154: moisnais=vector(1,n);
4155: annais=vector(1,n);
4156: moisdc=vector(1,n);
4157: andc=vector(1,n);
4158: agedc=vector(1,n);
4159: cod=ivector(1,n);
4160: weight=vector(1,n);
4161: for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */
4162: mint=matrix(1,maxwav,1,n);
4163: anint=matrix(1,maxwav,1,n);
4164: s=imatrix(1,maxwav+1,1,n);
4165: tab=ivector(1,NCOVMAX);
4166: ncodemax=ivector(1,8);
4167:
4168: i=1;
4169: while (fgets(line, MAXLINE, fic) != NULL) {
4170: if ((i >= firstobs) && (i <=lastobs)) {
1.53 brouard 4171:
1.59 brouard 4172: for (j=maxwav;j>=1;j--){
4173: cutv(stra, strb,line,' '); s[j][i]=atoi(strb);
4174: strcpy(line,stra);
4175: cutv(stra, strb,line,'/'); anint[j][i]=(double)(atoi(strb)); strcpy(line,stra);
4176: cutv(stra, strb,line,' '); mint[j][i]=(double)(atoi(strb)); strcpy(line,stra);
4177: }
1.53 brouard 4178:
1.59 brouard 4179: cutv(stra, strb,line,'/'); andc[i]=(double)(atoi(strb)); strcpy(line,stra);
4180: cutv(stra, strb,line,' '); moisdc[i]=(double)(atoi(strb)); strcpy(line,stra);
1.53 brouard 4181:
1.59 brouard 4182: cutv(stra, strb,line,'/'); annais[i]=(double)(atoi(strb)); strcpy(line,stra);
4183: cutv(stra, strb,line,' '); moisnais[i]=(double)(atoi(strb)); strcpy(line,stra);
1.53 brouard 4184:
1.59 brouard 4185: cutv(stra, strb,line,' '); weight[i]=(double)(atoi(strb)); strcpy(line,stra);
4186: for (j=ncovcol;j>=1;j--){
4187: cutv(stra, strb,line,' '); covar[j][i]=(double)(atoi(strb)); strcpy(line,stra);
4188: }
1.85 brouard 4189: lstra=strlen(stra);
4190: if(lstra > 9){ /* More than 2**32 or max of what printf can write with %ld */
4191: stratrunc = &(stra[lstra-9]);
4192: num[i]=atol(stratrunc);
4193: }
4194: else
4195: num[i]=atol(stra);
1.53 brouard 4196:
1.59 brouard 4197: /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){
1.85 brouard 4198: 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;}*/
1.53 brouard 4199:
1.59 brouard 4200: i=i+1;
4201: }
4202: }
4203: /* printf("ii=%d", ij);
4204: scanf("%d",i);*/
1.53 brouard 4205: imx=i-1; /* Number of individuals */
4206:
4207: /* for (i=1; i<=imx; i++){
4208: if ((s[1][i]==3) && (s[2][i]==2)) s[2][i]=3;
4209: if ((s[2][i]==3) && (s[3][i]==2)) s[3][i]=3;
4210: if ((s[3][i]==3) && (s[4][i]==2)) s[4][i]=3;
4211: }*/
4212: /* for (i=1; i<=imx; i++){
4213: if (s[4][i]==9) s[4][i]=-1;
1.85 brouard 4214: 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]));}*/
1.53 brouard 4215:
1.71 brouard 4216: for (i=1; i<=imx; i++)
1.53 brouard 4217:
1.71 brouard 4218: /*if ((s[3][i]==3) || (s[4][i]==3)) weight[i]=0.08;
4219: else weight[i]=1;*/
4220:
1.53 brouard 4221: /* Calculation of the number of parameter from char model*/
4222: Tvar=ivector(1,15); /* stores the number n of the covariates in Vm+Vn at 1 and m at 2 */
4223: Tprod=ivector(1,15);
4224: Tvaraff=ivector(1,15);
4225: Tvard=imatrix(1,15,1,2);
4226: Tage=ivector(1,15);
4227:
1.58 lievre 4228: if (strlen(model) >1){ /* If there is at least 1 covariate */
1.53 brouard 4229: j=0, j1=0, k1=1, k2=1;
1.58 lievre 4230: j=nbocc(model,'+'); /* j=Number of '+' */
4231: j1=nbocc(model,'*'); /* j1=Number of '*' */
4232: cptcovn=j+1;
4233: cptcovprod=j1; /*Number of products */
1.53 brouard 4234:
4235: strcpy(modelsav,model);
4236: if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){
4237: printf("Error. Non available option model=%s ",model);
4238: fprintf(ficlog,"Error. Non available option model=%s ",model);
4239: goto end;
4240: }
4241:
1.59 brouard 4242: /* This loop fills the array Tvar from the string 'model'.*/
1.58 lievre 4243:
1.53 brouard 4244: for(i=(j+1); i>=1;i--){
4245: cutv(stra,strb,modelsav,'+'); /* keeps in strb after the last + */
1.59 brouard 4246: if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyzes it */
1.53 brouard 4247: /* printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/
4248: /*scanf("%d",i);*/
4249: if (strchr(strb,'*')) { /* Model includes a product */
4250: cutv(strd,strc,strb,'*'); /* strd*strc Vm*Vn (if not *age)*/
4251: if (strcmp(strc,"age")==0) { /* Vn*age */
4252: cptcovprod--;
4253: cutv(strb,stre,strd,'V');
4254: Tvar[i]=atoi(stre); /* computes n in Vn and stores in Tvar*/
4255: cptcovage++;
4256: Tage[cptcovage]=i;
4257: /*printf("stre=%s ", stre);*/
4258: }
4259: else if (strcmp(strd,"age")==0) { /* or age*Vn */
4260: cptcovprod--;
4261: cutv(strb,stre,strc,'V');
4262: Tvar[i]=atoi(stre);
4263: cptcovage++;
4264: Tage[cptcovage]=i;
4265: }
4266: else { /* Age is not in the model */
4267: cutv(strb,stre,strc,'V'); /* strc= Vn, stre is n*/
4268: Tvar[i]=ncovcol+k1;
4269: cutv(strb,strc,strd,'V'); /* strd was Vm, strc is m */
4270: Tprod[k1]=i;
4271: Tvard[k1][1]=atoi(strc); /* m*/
4272: Tvard[k1][2]=atoi(stre); /* n */
4273: Tvar[cptcovn+k2]=Tvard[k1][1];
4274: Tvar[cptcovn+k2+1]=Tvard[k1][2];
4275: for (k=1; k<=lastobs;k++)
4276: covar[ncovcol+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];
4277: k1++;
4278: k2=k2+2;
4279: }
4280: }
4281: else { /* no more sum */
4282: /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/
4283: /* scanf("%d",i);*/
4284: cutv(strd,strc,strb,'V');
4285: Tvar[i]=atoi(strc);
4286: }
4287: strcpy(modelsav,stra);
4288: /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);
4289: scanf("%d",i);*/
4290: } /* end of loop + */
4291: } /* end model */
4292:
1.58 lievre 4293: /*The number n of Vn is stored in Tvar. cptcovage =number of age covariate. Tage gives the position of age. cptcovprod= number of products.
4294: If model=V1+V1*age then Tvar[1]=1 Tvar[2]=1 cptcovage=1 Tage[1]=2 cptcovprod=0*/
4295:
1.53 brouard 4296: /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);
4297: printf("cptcovprod=%d ", cptcovprod);
4298: fprintf(ficlog,"cptcovprod=%d ", cptcovprod);
1.58 lievre 4299:
4300: scanf("%d ",i);
4301: fclose(fic);*/
1.53 brouard 4302:
4303: /* if(mle==1){*/
1.59 brouard 4304: if (weightopt != 1) { /* Maximisation without weights*/
4305: for(i=1;i<=n;i++) weight[i]=1.0;
4306: }
1.53 brouard 4307: /*-calculation of age at interview from date of interview and age at death -*/
1.59 brouard 4308: agev=matrix(1,maxwav,1,imx);
1.53 brouard 4309:
1.59 brouard 4310: for (i=1; i<=imx; i++) {
4311: for(m=2; (m<= maxwav); m++) {
1.76 brouard 4312: if (((int)mint[m][i]== 99) && (s[m][i] <= nlstate)){
1.59 brouard 4313: anint[m][i]=9999;
4314: s[m][i]=-1;
4315: }
1.76 brouard 4316: if((int)moisdc[i]==99 && (int)andc[i]==9999 && s[m][i]>nlstate){
1.85 brouard 4317: 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);
4318: 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);
1.76 brouard 4319: s[m][i]=-1;
4320: }
4321: if((int)moisdc[i]==99 && (int)andc[i]!=9999 && s[m][i]>nlstate){
1.85 brouard 4322: 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]);
4323: 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]);
1.84 brouard 4324: s[m][i]=-1; /* We prefer to skip it (and to skip it in version 0.8a1 too */
1.76 brouard 4325: }
1.53 brouard 4326: }
1.59 brouard 4327: }
1.53 brouard 4328:
1.59 brouard 4329: for (i=1; i<=imx; i++) {
4330: agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);
1.71 brouard 4331: for(m=firstpass; (m<= lastpass); m++){
1.69 brouard 4332: if(s[m][i] >0){
1.59 brouard 4333: if (s[m][i] >= nlstate+1) {
4334: if(agedc[i]>0)
1.76 brouard 4335: if((int)moisdc[i]!=99 && (int)andc[i]!=9999)
1.69 brouard 4336: agev[m][i]=agedc[i];
1.59 brouard 4337: /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/
4338: else {
1.76 brouard 4339: if ((int)andc[i]!=9999){
1.85 brouard 4340: printf("Warning negative age at death: %ld line:%d\n",num[i],i);
4341: fprintf(ficlog,"Warning negative age at death: %ld line:%d\n",num[i],i);
1.59 brouard 4342: agev[m][i]=-1;
1.53 brouard 4343: }
4344: }
1.70 brouard 4345: }
1.69 brouard 4346: else if(s[m][i] !=9){ /* Standard case, age in fractional
4347: years but with the precision of a
4348: month */
1.59 brouard 4349: agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);
1.76 brouard 4350: if((int)mint[m][i]==99 || (int)anint[m][i]==9999)
1.59 brouard 4351: agev[m][i]=1;
4352: else if(agev[m][i] <agemin){
4353: agemin=agev[m][i];
4354: /*printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], agemin);*/
1.53 brouard 4355: }
1.59 brouard 4356: else if(agev[m][i] >agemax){
4357: agemax=agev[m][i];
4358: /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/
1.53 brouard 4359: }
1.59 brouard 4360: /*agev[m][i]=anint[m][i]-annais[i];*/
4361: /* agev[m][i] = age[i]+2*m;*/
1.53 brouard 4362: }
1.59 brouard 4363: else { /* =9 */
1.53 brouard 4364: agev[m][i]=1;
1.59 brouard 4365: s[m][i]=-1;
4366: }
1.53 brouard 4367: }
1.59 brouard 4368: else /*= 0 Unknown */
4369: agev[m][i]=1;
4370: }
1.53 brouard 4371:
1.59 brouard 4372: }
4373: for (i=1; i<=imx; i++) {
1.71 brouard 4374: for(m=firstpass; (m<=lastpass); m++){
1.59 brouard 4375: if (s[m][i] > (nlstate+ndeath)) {
4376: 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);
4377: 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);
4378: goto end;
1.53 brouard 4379: }
4380: }
1.59 brouard 4381: }
1.53 brouard 4382:
1.71 brouard 4383: /*for (i=1; i<=imx; i++){
4384: for (m=firstpass; (m<lastpass); m++){
1.85 brouard 4385: printf("%ld %d %.lf %d %d\n", num[i],(covar[1][i]),agev[m][i],s[m][i],s[m+1][i]);
1.71 brouard 4386: }
4387:
4388: }*/
4389:
1.59 brouard 4390: printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);
4391: fprintf(ficlog,"Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);
4392:
4393: free_vector(severity,1,maxwav);
4394: free_imatrix(outcome,1,maxwav+1,1,n);
4395: free_vector(moisnais,1,n);
4396: free_vector(annais,1,n);
4397: /* free_matrix(mint,1,maxwav,1,n);
4398: free_matrix(anint,1,maxwav,1,n);*/
4399: free_vector(moisdc,1,n);
4400: free_vector(andc,1,n);
1.53 brouard 4401:
4402:
1.59 brouard 4403: wav=ivector(1,imx);
4404: dh=imatrix(1,lastpass-firstpass+1,1,imx);
4405: bh=imatrix(1,lastpass-firstpass+1,1,imx);
4406: mw=imatrix(1,lastpass-firstpass+1,1,imx);
1.69 brouard 4407:
1.59 brouard 4408: /* Concatenates waves */
4409: concatwav(wav, dh, bh, mw, s, agedc, agev, firstpass, lastpass, imx, nlstate, stepm);
1.53 brouard 4410:
1.59 brouard 4411: /* Routine tricode is to calculate cptcoveff (real number of unique covariates) and to associate covariable number and modality */
1.53 brouard 4412:
1.59 brouard 4413: Tcode=ivector(1,100);
4414: nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);
4415: ncodemax[1]=1;
4416: if (cptcovn > 0) tricode(Tvar,nbcode,imx);
1.53 brouard 4417:
1.59 brouard 4418: codtab=imatrix(1,100,1,10); /* Cross tabulation to get the order of
4419: the estimations*/
4420: h=0;
4421: m=pow(2,cptcoveff);
1.53 brouard 4422:
1.59 brouard 4423: for(k=1;k<=cptcoveff; k++){
4424: for(i=1; i <=(m/pow(2,k));i++){
4425: for(j=1; j <= ncodemax[k]; j++){
4426: for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){
4427: h++;
4428: if (h>m) h=1;codtab[h][k]=j;codtab[h][Tvar[k]]=j;
4429: /* printf("h=%d k=%d j=%d codtab[h][k]=%d tvar[k]=%d \n",h, k,j,codtab[h][k],Tvar[k]);*/
4430: }
4431: }
4432: }
4433: }
4434: /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]);
4435: codtab[1][2]=1;codtab[2][2]=2; */
4436: /* for(i=1; i <=m ;i++){
4437: for(k=1; k <=cptcovn; k++){
4438: printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);
4439: }
4440: printf("\n");
1.53 brouard 4441: }
1.59 brouard 4442: scanf("%d",i);*/
1.53 brouard 4443:
1.86 brouard 4444: /*------------ gnuplot -------------*/
4445: strcpy(optionfilegnuplot,optionfilefiname);
4446: strcat(optionfilegnuplot,".gp");
4447: if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {
4448: printf("Problem with file %s",optionfilegnuplot);
4449: }
4450: else{
4451: fprintf(ficgp,"\n# %s\n", version);
4452: fprintf(ficgp,"# %s\n", optionfilegnuplot);
4453: fprintf(ficgp,"set missing 'NaNq'\n");
4454: }
1.88 ! brouard 4455: /* fclose(ficgp);*/
1.86 brouard 4456: /*--------- index.htm --------*/
4457:
1.87 brouard 4458: strcpy(optionfilehtm,optionfilefiname);
1.86 brouard 4459: strcat(optionfilehtm,".htm");
4460: if((fichtm=fopen(optionfilehtm,"w"))==NULL) {
4461: printf("Problem with %s \n",optionfilehtm), exit(0);
4462: }
4463:
1.87 brouard 4464: fprintf(fichtm,"<body>\n<title>IMaCh %s</title>\n <font size=\"2\">%s <br> %s</font> \
1.86 brouard 4465: <hr size=\"2\" color=\"#EC5E5E\"> \n\
4466: Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n\
4467: \n\
4468: <hr size=\"2\" color=\"#EC5E5E\">\
4469: <ul><li><h4>Parameter files</h4>\n\
4470: - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n\
4471: - Log file of the run: <a href=\"%s\">%s</a><br>\n\
1.87 brouard 4472: - Gnuplot file name: <a href=\"%s\">%s</a><br>\n\
1.86 brouard 4473: - Date and time at start: %s</ul>\n",\
1.87 brouard 4474: fileres,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt,\
1.86 brouard 4475: model,fileres,fileres,\
1.88 ! brouard 4476: filelog,filelog,optionfilegnuplot,optionfilegnuplot,strstart);
1.87 brouard 4477: /*fclose(fichtm);*/
4478: fflush(fichtm);
1.86 brouard 4479:
1.88 ! brouard 4480: strcpy(pathr,path);
! 4481: strcat(pathr,optionfilefiname);
! 4482: chdir(optionfilefiname); /* Move to directory named optionfile */
! 4483: strcpy(lfileres,fileres);
! 4484: strcat(lfileres,"/");
! 4485: strcat(lfileres,optionfilefiname);
! 4486:
! 4487: /* replace(pathc,path);*/
! 4488:
1.59 brouard 4489: /* Calculates basic frequencies. Computes observed prevalence at single age
4490: and prints on file fileres'p'. */
1.84 brouard 4491: freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint);
1.53 brouard 4492:
1.88 ! brouard 4493: fprintf(fichtm,"\n");
! 4494: fprintf(fichtm,"<br>Total number of observations=%d <br>\n\
1.86 brouard 4495: Youngest age at first (selected) pass %.2f, oldest age %.2f<br>\n\
4496: Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n",\
1.88 ! brouard 4497: imx,agemin,agemax,jmin,jmax,jmean);
! 4498: pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
1.60 brouard 4499: oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
4500: newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
4501: savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
4502: oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */
1.53 brouard 4503:
4504:
1.59 brouard 4505: /* For Powell, parameters are in a vector p[] starting at p[1]
4506: so we point p on param[1][1] so that p[1] maps on param[1][1][1] */
4507: p=param[1][1]; /* *(*(*(param +1)+1)+0) */
1.53 brouard 4508:
1.86 brouard 4509: globpr=0; /* To get the number ipmx of contributions and the sum of weights*/
1.85 brouard 4510: likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
4511: printf("First Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
4512: for (k=1; k<=npar;k++)
4513: printf(" %d %8.5f",k,p[k]);
4514: printf("\n");
4515: globpr=1; /* to print the contributions */
4516: likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
4517: printf("Second Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
4518: for (k=1; k<=npar;k++)
4519: printf(" %d %8.5f",k,p[k]);
4520: printf("\n");
1.61 brouard 4521: if(mle>=1){ /* Could be 1 or 2 */
1.53 brouard 4522: mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);
1.59 brouard 4523: }
1.53 brouard 4524:
1.59 brouard 4525: /*--------- results files --------------*/
4526: 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);
1.53 brouard 4527:
4528:
1.59 brouard 4529: jk=1;
4530: fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
4531: printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
4532: fprintf(ficlog,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
4533: for(i=1,jk=1; i <=nlstate; i++){
4534: for(k=1; k <=(nlstate+ndeath); k++){
4535: if (k != i)
4536: {
4537: printf("%d%d ",i,k);
4538: fprintf(ficlog,"%d%d ",i,k);
4539: fprintf(ficres,"%1d%1d ",i,k);
4540: for(j=1; j <=ncovmodel; j++){
4541: printf("%f ",p[jk]);
4542: fprintf(ficlog,"%f ",p[jk]);
4543: fprintf(ficres,"%f ",p[jk]);
4544: jk++;
4545: }
4546: printf("\n");
4547: fprintf(ficlog,"\n");
4548: fprintf(ficres,"\n");
4549: }
4550: }
4551: }
1.84 brouard 4552: if(mle!=0){
1.59 brouard 4553: /* Computing hessian and covariance matrix */
4554: ftolhess=ftol; /* Usually correct */
4555: hesscov(matcov, p, npar, delti, ftolhess, func);
4556: }
4557: fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");
4558: printf("# Scales (for hessian or gradient estimation)\n");
4559: fprintf(ficlog,"# Scales (for hessian or gradient estimation)\n");
4560: for(i=1,jk=1; i <=nlstate; i++){
4561: for(j=1; j <=nlstate+ndeath; j++){
4562: if (j!=i) {
4563: fprintf(ficres,"%1d%1d",i,j);
4564: printf("%1d%1d",i,j);
4565: fprintf(ficlog,"%1d%1d",i,j);
4566: for(k=1; k<=ncovmodel;k++){
4567: printf(" %.5e",delti[jk]);
4568: fprintf(ficlog," %.5e",delti[jk]);
4569: fprintf(ficres," %.5e",delti[jk]);
4570: jk++;
4571: }
4572: printf("\n");
4573: fprintf(ficlog,"\n");
4574: fprintf(ficres,"\n");
4575: }
4576: }
4577: }
1.53 brouard 4578:
1.59 brouard 4579: 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");
4580: if(mle==1)
4581: 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");
4582: 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");
4583: for(i=1,k=1;i<=npar;i++){
4584: /* if (k>nlstate) k=1;
4585: i1=(i-1)/(ncovmodel*nlstate)+1;
4586: fprintf(ficres,"%s%d%d",alph[k],i1,tab[i]);
4587: printf("%s%d%d",alph[k],i1,tab[i]);
4588: */
4589: fprintf(ficres,"%3d",i);
4590: if(mle==1)
4591: printf("%3d",i);
4592: fprintf(ficlog,"%3d",i);
4593: for(j=1; j<=i;j++){
4594: fprintf(ficres," %.5e",matcov[i][j]);
4595: if(mle==1)
4596: printf(" %.5e",matcov[i][j]);
4597: fprintf(ficlog," %.5e",matcov[i][j]);
4598: }
4599: fprintf(ficres,"\n");
4600: if(mle==1)
4601: printf("\n");
4602: fprintf(ficlog,"\n");
4603: k++;
4604: }
1.53 brouard 4605:
1.59 brouard 4606: while((c=getc(ficpar))=='#' && c!= EOF){
4607: ungetc(c,ficpar);
4608: fgets(line, MAXLINE, ficpar);
4609: puts(line);
4610: fputs(line,ficparo);
4611: }
4612: ungetc(c,ficpar);
4613:
4614: estepm=0;
4615: fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm);
4616: if (estepm==0 || estepm < stepm) estepm=stepm;
4617: if (fage <= 2) {
4618: bage = ageminpar;
4619: fage = agemaxpar;
4620: }
1.53 brouard 4621:
1.59 brouard 4622: fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");
4623: fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
4624: fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
1.53 brouard 4625:
1.59 brouard 4626: while((c=getc(ficpar))=='#' && c!= EOF){
4627: ungetc(c,ficpar);
4628: fgets(line, MAXLINE, ficpar);
4629: puts(line);
4630: fputs(line,ficparo);
4631: }
4632: ungetc(c,ficpar);
1.53 brouard 4633:
1.59 brouard 4634: 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);
4635: 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);
4636: 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);
1.69 brouard 4637: printf("begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
4638: 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);
1.53 brouard 4639:
1.59 brouard 4640: while((c=getc(ficpar))=='#' && c!= EOF){
4641: ungetc(c,ficpar);
4642: fgets(line, MAXLINE, ficpar);
4643: puts(line);
4644: fputs(line,ficparo);
4645: }
4646: ungetc(c,ficpar);
1.53 brouard 4647:
4648:
1.70 brouard 4649: dateprev1=anprev1+(mprev1-1)/12.+(jprev1-1)/365.;
4650: dateprev2=anprev2+(mprev2-1)/12.+(jprev2-1)/365.;
1.53 brouard 4651:
4652: fscanf(ficpar,"pop_based=%d\n",&popbased);
4653: fprintf(ficparo,"pop_based=%d\n",popbased);
4654: fprintf(ficres,"pop_based=%d\n",popbased);
4655:
4656: while((c=getc(ficpar))=='#' && c!= EOF){
4657: ungetc(c,ficpar);
4658: fgets(line, MAXLINE, ficpar);
4659: puts(line);
4660: fputs(line,ficparo);
4661: }
4662: ungetc(c,ficpar);
4663:
1.69 brouard 4664: 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);
1.70 brouard 4665: 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);
1.71 brouard 4666: 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);
4667: 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);
4668: 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);
1.69 brouard 4669: /* day and month of proj2 are not used but only year anproj2.*/
1.53 brouard 4670:
1.59 brouard 4671: while((c=getc(ficpar))=='#' && c!= EOF){
1.53 brouard 4672: ungetc(c,ficpar);
4673: fgets(line, MAXLINE, ficpar);
4674: puts(line);
4675: fputs(line,ficparo);
4676: }
4677: ungetc(c,ficpar);
4678:
4679: fscanf(ficpar,"popforecast=%d popfile=%s popfiledate=%lf/%lf/%lf last-popfiledate=%lf/%lf/%lf\n",&popforecast,popfile,&jpyram,&mpyram,&anpyram,&jpyram1,&mpyram1,&anpyram1);
4680: fprintf(ficparo,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);
4681: fprintf(ficres,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);
4682:
1.86 brouard 4683: /* freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint);*/
1.84 brouard 4684: /*,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
1.58 lievre 4685:
1.88 ! brouard 4686: printinggnuplot(fileres, optionfilefiname,ageminpar,agemaxpar,fage, path,p);
1.53 brouard 4687:
1.85 brouard 4688: printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,\
4689: model,imx,jmin,jmax,jmean,rfileres,popforecast,estepm,\
4690: jprev1,mprev1,anprev1,jprev2,mprev2,anprev2);
1.53 brouard 4691:
1.59 brouard 4692: /*------------ free_vector -------------*/
1.88 ! brouard 4693: /* chdir(path); */
1.53 brouard 4694:
1.59 brouard 4695: free_ivector(wav,1,imx);
4696: free_imatrix(dh,1,lastpass-firstpass+1,1,imx);
4697: free_imatrix(bh,1,lastpass-firstpass+1,1,imx);
4698: free_imatrix(mw,1,lastpass-firstpass+1,1,imx);
1.85 brouard 4699: free_lvector(num,1,n);
1.59 brouard 4700: free_vector(agedc,1,n);
1.65 lievre 4701: /*free_matrix(covar,0,NCOVMAX,1,n);*/
1.59 brouard 4702: /*free_matrix(covar,1,NCOVMAX,1,n);*/
4703: fclose(ficparo);
4704: fclose(ficres);
1.53 brouard 4705:
4706:
1.54 brouard 4707: /*--------------- Prevalence limit (stable prevalence) --------------*/
1.53 brouard 4708:
4709: strcpy(filerespl,"pl");
4710: strcat(filerespl,fileres);
4711: if((ficrespl=fopen(filerespl,"w"))==NULL) {
1.54 brouard 4712: printf("Problem with stable prevalence resultfile: %s\n", filerespl);goto end;
4713: fprintf(ficlog,"Problem with stable prevalence resultfile: %s\n", filerespl);goto end;
1.53 brouard 4714: }
1.54 brouard 4715: printf("Computing stable prevalence: result on file '%s' \n", filerespl);
4716: fprintf(ficlog,"Computing stable prevalence: result on file '%s' \n", filerespl);
4717: fprintf(ficrespl,"#Stable prevalence \n");
1.53 brouard 4718: fprintf(ficrespl,"#Age ");
4719: for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);
4720: fprintf(ficrespl,"\n");
4721:
4722: prlim=matrix(1,nlstate,1,nlstate);
1.59 brouard 4723:
1.53 brouard 4724: agebase=ageminpar;
4725: agelim=agemaxpar;
4726: ftolpl=1.e-10;
4727: i1=cptcoveff;
4728: if (cptcovn < 1){i1=1;}
4729:
1.59 brouard 4730: for(cptcov=1,k=0;cptcov<=i1;cptcov++){
1.53 brouard 4731: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
1.59 brouard 4732: k=k+1;
4733: /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/
4734: fprintf(ficrespl,"\n#******");
4735: printf("\n#******");
4736: fprintf(ficlog,"\n#******");
4737: for(j=1;j<=cptcoveff;j++) {
4738: fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
4739: printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
4740: fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
4741: }
4742: fprintf(ficrespl,"******\n");
4743: printf("******\n");
4744: fprintf(ficlog,"******\n");
1.53 brouard 4745:
1.59 brouard 4746: for (age=agebase; age<=agelim; age++){
4747: prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
1.69 brouard 4748: fprintf(ficrespl,"%.0f ",age );
4749: for(j=1;j<=cptcoveff;j++)
4750: fprintf(ficrespl,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
1.59 brouard 4751: for(i=1; i<=nlstate;i++)
1.53 brouard 4752: fprintf(ficrespl," %.5f", prlim[i][i]);
1.59 brouard 4753: fprintf(ficrespl,"\n");
1.53 brouard 4754: }
4755: }
1.59 brouard 4756: }
1.53 brouard 4757: fclose(ficrespl);
4758:
4759: /*------------- h Pij x at various ages ------------*/
4760:
4761: strcpy(filerespij,"pij"); strcat(filerespij,fileres);
4762: if((ficrespij=fopen(filerespij,"w"))==NULL) {
4763: printf("Problem with Pij resultfile: %s\n", filerespij);goto end;
4764: fprintf(ficlog,"Problem with Pij resultfile: %s\n", filerespij);goto end;
4765: }
4766: printf("Computing pij: result on file '%s' \n", filerespij);
4767: fprintf(ficlog,"Computing pij: result on file '%s' \n", filerespij);
4768:
4769: stepsize=(int) (stepm+YEARM-1)/YEARM;
4770: /*if (stepm<=24) stepsize=2;*/
4771:
4772: agelim=AGESUP;
4773: hstepm=stepsize*YEARM; /* Every year of age */
4774: hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */
4775:
4776: /* hstepm=1; aff par mois*/
4777:
1.70 brouard 4778: fprintf(ficrespij,"#****** h Pij x Probability to be in state j at age x+h being in i at x ");
1.59 brouard 4779: for(cptcov=1,k=0;cptcov<=i1;cptcov++){
1.53 brouard 4780: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
4781: k=k+1;
1.59 brouard 4782: fprintf(ficrespij,"\n#****** ");
4783: for(j=1;j<=cptcoveff;j++)
4784: fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
4785: fprintf(ficrespij,"******\n");
1.53 brouard 4786:
1.59 brouard 4787: for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */
4788: nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
4789: nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
4790:
4791: /* nhstepm=nhstepm*YEARM; aff par mois*/
4792:
4793: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4794: oldm=oldms;savm=savms;
4795: hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
1.70 brouard 4796: fprintf(ficrespij,"# Cov Agex agex+h hpijx with i,j=");
1.59 brouard 4797: for(i=1; i<=nlstate;i++)
4798: for(j=1; j<=nlstate+ndeath;j++)
4799: fprintf(ficrespij," %1d-%1d",i,j);
4800: fprintf(ficrespij,"\n");
4801: for (h=0; h<=nhstepm; h++){
1.70 brouard 4802: fprintf(ficrespij,"%d %3.f %3.f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );
1.53 brouard 4803: for(i=1; i<=nlstate;i++)
4804: for(j=1; j<=nlstate+ndeath;j++)
1.59 brouard 4805: fprintf(ficrespij," %.5f", p3mat[i][j][h]);
1.53 brouard 4806: fprintf(ficrespij,"\n");
4807: }
1.59 brouard 4808: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4809: fprintf(ficrespij,"\n");
4810: }
1.53 brouard 4811: }
4812: }
4813:
1.74 brouard 4814: varprob(optionfilefiname, matcov, p, delti, nlstate, bage, fage,k,Tvar,nbcode, ncodemax);
1.53 brouard 4815:
4816: fclose(ficrespij);
4817:
1.84 brouard 4818: probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
1.53 brouard 4819:
4820: /*---------- Forecasting ------------------*/
1.69 brouard 4821: /*if((stepm == 1) && (strcmp(model,".")==0)){*/
4822: if(prevfcast==1){
1.74 brouard 4823: /* if(stepm ==1){*/
1.70 brouard 4824: prevforecast(fileres, anproj1, mproj1, jproj1, agemin, agemax, dateprev1, dateprev2, mobilavproj, bage, fage, firstpass, lastpass, anproj2, p, cptcoveff);
1.74 brouard 4825: /* (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);*/
4826: /* } */
4827: /* else{ */
4828: /* erreur=108; */
4829: /* 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); */
4830: /* 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); */
4831: /* } */
1.69 brouard 4832: }
1.53 brouard 4833:
4834:
4835: /*---------- Health expectancies and variances ------------*/
4836:
4837: strcpy(filerest,"t");
4838: strcat(filerest,fileres);
4839: if((ficrest=fopen(filerest,"w"))==NULL) {
4840: printf("Problem with total LE resultfile: %s\n", filerest);goto end;
4841: fprintf(ficlog,"Problem with total LE resultfile: %s\n", filerest);goto end;
4842: }
4843: printf("Computing Total LEs with variances: file '%s' \n", filerest);
4844: fprintf(ficlog,"Computing Total LEs with variances: file '%s' \n", filerest);
4845:
4846:
4847: strcpy(filerese,"e");
4848: strcat(filerese,fileres);
4849: if((ficreseij=fopen(filerese,"w"))==NULL) {
4850: printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
4851: fprintf(ficlog,"Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
4852: }
4853: printf("Computing Health Expectancies: result on file '%s' \n", filerese);
4854: fprintf(ficlog,"Computing Health Expectancies: result on file '%s' \n", filerese);
1.68 lievre 4855:
1.53 brouard 4856: strcpy(fileresv,"v");
4857: strcat(fileresv,fileres);
4858: if((ficresvij=fopen(fileresv,"w"))==NULL) {
4859: printf("Problem with variance resultfile: %s\n", fileresv);exit(0);
4860: fprintf(ficlog,"Problem with variance resultfile: %s\n", fileresv);exit(0);
4861: }
4862: printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
4863: fprintf(ficlog,"Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
1.58 lievre 4864:
1.74 brouard 4865: /* Computes prevalence between agemin (i.e minimal age computed) and no more ageminpar */
1.84 brouard 4866: prevalence(probs, agemin, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
1.74 brouard 4867: /* 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",\
4868: ageminpar, agemax, s[lastpass][imx], agev[lastpass][imx], nlstate, imx, mint[lastpass][imx],anint[lastpass][imx], dateprev1, dateprev2, firstpass, lastpass);
4869: */
1.58 lievre 4870:
1.54 brouard 4871: if (mobilav!=0) {
1.53 brouard 4872: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
1.54 brouard 4873: if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
4874: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
4875: printf(" Error in movingaverage mobilav=%d\n",mobilav);
4876: }
1.53 brouard 4877: }
4878:
1.59 brouard 4879: for(cptcov=1,k=0;cptcov<=i1;cptcov++){
1.53 brouard 4880: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
4881: k=k+1;
4882: fprintf(ficrest,"\n#****** ");
4883: for(j=1;j<=cptcoveff;j++)
4884: fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
4885: fprintf(ficrest,"******\n");
4886:
4887: fprintf(ficreseij,"\n#****** ");
4888: for(j=1;j<=cptcoveff;j++)
4889: fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
4890: fprintf(ficreseij,"******\n");
4891:
4892: fprintf(ficresvij,"\n#****** ");
4893: for(j=1;j<=cptcoveff;j++)
4894: fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
4895: fprintf(ficresvij,"******\n");
4896:
4897: eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
4898: oldm=oldms;savm=savms;
4899: evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov);
4900:
4901: vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
4902: oldm=oldms;savm=savms;
4903: varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,0, mobilav);
4904: if(popbased==1){
4905: varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,popbased,mobilav);
1.59 brouard 4906: }
1.53 brouard 4907:
4908:
4909: fprintf(ficrest,"#Total LEs with variances: e.. (std) ");
4910: for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);
4911: fprintf(ficrest,"\n");
4912:
4913: epj=vector(1,nlstate+1);
4914: for(age=bage; age <=fage ;age++){
4915: prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
4916: if (popbased==1) {
1.54 brouard 4917: if(mobilav ==0){
1.53 brouard 4918: for(i=1; i<=nlstate;i++)
4919: prlim[i][i]=probs[(int)age][i][k];
1.54 brouard 4920: }else{ /* mobilav */
1.53 brouard 4921: for(i=1; i<=nlstate;i++)
4922: prlim[i][i]=mobaverage[(int)age][i][k];
4923: }
4924: }
4925:
4926: fprintf(ficrest," %4.0f",age);
4927: for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){
4928: for(i=1, epj[j]=0.;i <=nlstate;i++) {
4929: epj[j] += prlim[i][i]*eij[i][j][(int)age];
4930: /* printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/
4931: }
4932: epj[nlstate+1] +=epj[j];
4933: }
4934:
4935: for(i=1, vepp=0.;i <=nlstate;i++)
4936: for(j=1;j <=nlstate;j++)
4937: vepp += vareij[i][j][(int)age];
4938: fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));
4939: for(j=1;j <=nlstate;j++){
4940: fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));
4941: }
4942: fprintf(ficrest,"\n");
4943: }
1.59 brouard 4944: free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
4945: free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);
4946: free_vector(epj,1,nlstate+1);
1.53 brouard 4947: }
4948: }
1.59 brouard 4949: free_vector(weight,1,n);
4950: free_imatrix(Tvard,1,15,1,2);
4951: free_imatrix(s,1,maxwav+1,1,n);
4952: free_matrix(anint,1,maxwav,1,n);
4953: free_matrix(mint,1,maxwav,1,n);
4954: free_ivector(cod,1,n);
4955: free_ivector(tab,1,NCOVMAX);
1.53 brouard 4956: fclose(ficreseij);
4957: fclose(ficresvij);
4958: fclose(ficrest);
4959: fclose(ficpar);
4960:
1.54 brouard 4961: /*------- Variance of stable prevalence------*/
1.53 brouard 4962:
4963: strcpy(fileresvpl,"vpl");
4964: strcat(fileresvpl,fileres);
4965: if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {
1.54 brouard 4966: printf("Problem with variance of stable prevalence resultfile: %s\n", fileresvpl);
1.53 brouard 4967: exit(0);
4968: }
1.54 brouard 4969: printf("Computing Variance-covariance of stable prevalence: file '%s' \n", fileresvpl);
1.53 brouard 4970:
1.59 brouard 4971: for(cptcov=1,k=0;cptcov<=i1;cptcov++){
1.53 brouard 4972: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
4973: k=k+1;
4974: fprintf(ficresvpl,"\n#****** ");
4975: for(j=1;j<=cptcoveff;j++)
4976: fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
4977: fprintf(ficresvpl,"******\n");
4978:
4979: varpl=matrix(1,nlstate,(int) bage, (int) fage);
4980: oldm=oldms;savm=savms;
1.59 brouard 4981: varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);
4982: free_matrix(varpl,1,nlstate,(int) bage, (int)fage);
1.53 brouard 4983: }
1.59 brouard 4984: }
1.53 brouard 4985:
4986: fclose(ficresvpl);
4987:
4988: /*---------- End : free ----------------*/
4989: free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);
4990: free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);
4991: free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);
4992: free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);
1.65 lievre 4993:
4994: free_matrix(covar,0,NCOVMAX,1,n);
1.53 brouard 4995: free_matrix(matcov,1,npar,1,npar);
1.74 brouard 4996: /*free_vector(delti,1,npar);*/
4997: free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
1.53 brouard 4998: free_matrix(agev,1,maxwav,1,imx);
4999: free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
1.54 brouard 5000: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
1.74 brouard 5001: free_ma3x(probs,1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
5002:
1.59 brouard 5003: free_ivector(ncodemax,1,8);
5004: free_ivector(Tvar,1,15);
5005: free_ivector(Tprod,1,15);
5006: free_ivector(Tvaraff,1,15);
5007: free_ivector(Tage,1,15);
5008: free_ivector(Tcode,1,100);
1.53 brouard 5009:
1.88 ! brouard 5010: fflush(fichtm);
! 5011: fflush(ficgp);
1.53 brouard 5012:
5013:
5014: if(erreur >0){
5015: printf("End of Imach with error or warning %d\n",erreur);
5016: fprintf(ficlog,"End of Imach with error or warning %d\n",erreur);
5017: }else{
5018: printf("End of Imach\n");
5019: fprintf(ficlog,"End of Imach\n");
5020: }
5021: printf("See log file on %s\n",filelog);
5022: fclose(ficlog);
5023: /* gettimeofday(&end_time, (struct timezone*)0);*/ /* after time */
1.85 brouard 5024: (void) gettimeofday(&end_time,&tzp);
5025: tm = *localtime(&end_time.tv_sec);
5026: tmg = *gmtime(&end_time.tv_sec);
1.88 ! brouard 5027: strcpy(strtend,asctime(&tm));
! 5028: printf("Localtime at start %s\nLocaltime at end %s",strstart, strtend);
! 5029: fprintf(ficlog,"Localtime at start %s\nLocal time at end %s",strstart, strtend);
1.85 brouard 5030: /* printf("Total time used %d Sec\n", asc_time(end_time.tv_sec -start_time.tv_sec);*/
5031:
5032: printf("Total time was %d Sec. %d uSec.\n", end_time.tv_sec -start_time.tv_sec, end_time.tv_usec -start_time.tv_usec);
5033: fprintf(ficlog,"Total time was %d Sec. %d uSec.\n", end_time.tv_sec -start_time.tv_sec, end_time.tv_usec -start_time.tv_usec);
5034: /* printf("Total time was %d uSec.\n", total_usecs);*/
1.87 brouard 5035: /* if(fileappend(fichtm,optionfilehtm)){ */
1.88 ! brouard 5036: fprintf(fichtm,"<br>Local time at start %s<br>Local time at end %s<br>",strstart, strtend);
1.87 brouard 5037: fclose(fichtm);
1.88 ! brouard 5038: fclose(ficgp);
1.53 brouard 5039: /*------ End -----------*/
5040:
1.59 brouard 5041: end:
1.53 brouard 5042: #ifdef windows
5043: /* chdir(pathcd);*/
5044: #endif
1.88 ! brouard 5045: chdir(path);
1.53 brouard 5046: /*system("wgnuplot graph.plt");*/
5047: /*system("../gp37mgw/wgnuplot graph.plt");*/
5048: /*system("cd ../gp37mgw");*/
5049: /* system("..\\gp37mgw\\wgnuplot graph.plt");*/
1.59 brouard 5050: strcpy(plotcmd,GNUPLOTPROGRAM);
5051: strcat(plotcmd," ");
5052: strcat(plotcmd,optionfilegnuplot);
1.75 brouard 5053: printf("Starting graphs with: %s",plotcmd);fflush(stdout);
1.59 brouard 5054: system(plotcmd);
1.75 brouard 5055: printf(" Wait...");
1.53 brouard 5056:
1.54 brouard 5057: /*#ifdef windows*/
1.53 brouard 5058: while (z[0] != 'q') {
5059: /* chdir(path); */
5060: printf("\nType e to edit output files, g to graph again, c to start again, and q for exiting: ");
5061: scanf("%s",z);
5062: if (z[0] == 'c') system("./imach");
5063: else if (z[0] == 'e') system(optionfilehtm);
5064: else if (z[0] == 'g') system(plotcmd);
5065: else if (z[0] == 'q') exit(0);
5066: }
1.54 brouard 5067: /*#endif */
1.53 brouard 5068: }
1.88 ! brouard 5069:
1.53 brouard 5070:
5071:
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