Annotation of imach/src/imach.c, revision 1.48
1.48 ! brouard 1: /* $Id: imach.c,v 1.47 2002/06/10 13:12:01 brouard Exp $
1.24 lievre 2: Interpolated Markov Chain
1.22 brouard 3:
4: Short summary of the programme:
5:
6: This program computes Healthy Life Expectancies from
7: cross-longitudinal data. Cross-longitudinal data consist in: -1- a
8: first survey ("cross") where individuals from different ages are
9: interviewed on their health status or degree of disability (in the
10: case of a health survey which is our main interest) -2- at least a
11: second wave of interviews ("longitudinal") which measure each change
12: (if any) in individual health status. Health expectancies are
13: computed from the time spent in each health state according to a
14: model. More health states you consider, more time is necessary to reach the
15: Maximum Likelihood of the parameters involved in the model. The
16: simplest model is the multinomial logistic model where pij is the
1.39 lievre 17: probability to be observed in state j at the second wave
1.22 brouard 18: conditional to be observed in state i at the first wave. Therefore
19: the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where
20: 'age' is age and 'sex' is a covariate. If you want to have a more
21: complex model than "constant and age", you should modify the program
22: where the markup *Covariates have to be included here again* invites
23: you to do it. More covariates you add, slower the
24: convergence.
25:
26: The advantage of this computer programme, compared to a simple
27: multinomial logistic model, is clear when the delay between waves is not
28: identical for each individual. Also, if a individual missed an
29: intermediate interview, the information is lost, but taken into
30: account using an interpolation or extrapolation.
31:
32: hPijx is the probability to be observed in state i at age x+h
33: conditional to the observed state i at age x. The delay 'h' can be
34: split into an exact number (nh*stepm) of unobserved intermediate
35: states. This elementary transition (by month or quarter trimester,
36: semester or year) is model as a multinomial logistic. The hPx
37: matrix is simply the matrix product of nh*stepm elementary matrices
38: and the contribution of each individual to the likelihood is simply
39: hPijx.
1.2 lievre 40:
41: Also this programme outputs the covariance matrix of the parameters but also
42: of the life expectancies. It also computes the prevalence limits.
43:
44: Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).
45: Institut national d'études démographiques, Paris.
46: This software have been partly granted by Euro-REVES, a concerted action
47: from the European Union.
48: It is copyrighted identically to a GNU software product, ie programme and
49: software can be distributed freely for non commercial use. Latest version
50: can be accessed at http://euroreves.ined.fr/imach .
51: **********************************************************************/
52:
53: #include <math.h>
54: #include <stdio.h>
55: #include <stdlib.h>
56: #include <unistd.h>
57:
58: #define MAXLINE 256
1.42 brouard 59: #define GNUPLOTPROGRAM "gnuplot"
1.35 lievre 60: /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
1.2 lievre 61: #define FILENAMELENGTH 80
62: /*#define DEBUG*/
63: #define windows
1.5 lievre 64: #define GLOCK_ERROR_NOPATH -1 /* empty path */
65: #define GLOCK_ERROR_GETCWD -2 /* cannot get cwd */
66:
1.2 lievre 67: #define MAXPARM 30 /* Maximum number of parameters for the optimization */
68: #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */
69:
70: #define NINTERVMAX 8
71: #define NLSTATEMAX 8 /* Maximum number of live states (for func) */
72: #define NDEATHMAX 8 /* Maximum number of dead states (for func) */
73: #define NCOVMAX 8 /* Maximum number of covariates */
1.3 lievre 74: #define MAXN 20000
1.2 lievre 75: #define YEARM 12. /* Number of months per year */
76: #define AGESUP 130
77: #define AGEBASE 40
1.47 brouard 78: #ifdef windows
79: #define DIRSEPARATOR '\\'
80: #else
81: #define DIRSEPARATOR '/'
82: #endif
1.2 lievre 83:
1.48 ! brouard 84: char version[80]="Imach version 0.8h, May 2002, INED-EUROREVES ";
1.21 lievre 85: int erreur; /* Error number */
1.2 lievre 86: int nvar;
1.8 lievre 87: int cptcovn, cptcovage=0, cptcoveff=0,cptcov;
1.2 lievre 88: int npar=NPARMAX;
89: int nlstate=2; /* Number of live states */
90: int ndeath=1; /* Number of dead states */
1.34 brouard 91: int ncovmodel, ncovcol; /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
1.15 lievre 92: int popbased=0;
1.2 lievre 93:
94: int *wav; /* Number of waves for this individuual 0 is possible */
95: int maxwav; /* Maxim number of waves */
1.8 lievre 96: int jmin, jmax; /* min, max spacing between 2 waves */
1.2 lievre 97: int mle, weightopt;
98: int **mw; /* mw[mi][i] is number of the mi wave for this individual */
99: int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
1.8 lievre 100: double jmean; /* Mean space between 2 waves */
1.2 lievre 101: double **oldm, **newm, **savm; /* Working pointers to matrices */
102: double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
1.27 lievre 103: FILE *fic,*ficpar, *ficparo,*ficres, *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
1.46 brouard 104: FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
1.47 brouard 105: FILE *fichtm; /* Html File */
1.2 lievre 106: FILE *ficreseij;
1.47 brouard 107: char filerese[FILENAMELENGTH];
108: FILE *ficresvij;
109: char fileresv[FILENAMELENGTH];
110: FILE *ficresvpl;
111: char fileresvpl[FILENAMELENGTH];
112: char title[MAXLINE];
113: char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH], filerespl[FILENAMELENGTH];
114: char optionfilext[10], optionfilefiname[FILENAMELENGTH], plotcmd[FILENAMELENGTH];
115:
116: char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
117:
118: char filerest[FILENAMELENGTH];
119: char fileregp[FILENAMELENGTH];
120: char popfile[FILENAMELENGTH];
121:
122: char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH];
1.2 lievre 123:
124: #define NR_END 1
125: #define FREE_ARG char*
126: #define FTOL 1.0e-10
127:
128: #define NRANSI
129: #define ITMAX 200
130:
131: #define TOL 2.0e-4
132:
133: #define CGOLD 0.3819660
134: #define ZEPS 1.0e-10
135: #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);
136:
137: #define GOLD 1.618034
138: #define GLIMIT 100.0
139: #define TINY 1.0e-20
140:
141: static double maxarg1,maxarg2;
142: #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
143: #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
1.25 lievre 144:
1.2 lievre 145: #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
146: #define rint(a) floor(a+0.5)
147:
148: static double sqrarg;
149: #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
150: #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}
151:
152: int imx;
153: int stepm;
154: /* Stepm, step in month: minimum step interpolation*/
155:
1.36 brouard 156: int estepm;
157: /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
158:
1.2 lievre 159: int m,nb;
1.6 lievre 160: int *num, firstpass=0, lastpass=4,*cod, *ncodemax, *Tage;
1.2 lievre 161: double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
1.13 lievre 162: double **pmmij, ***probs, ***mobaverage;
1.19 lievre 163: double dateintmean=0;
1.2 lievre 164:
165: double *weight;
166: int **s; /* Status */
167: double *agedc, **covar, idx;
1.7 lievre 168: int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;
1.2 lievre 169:
170: double ftol=FTOL; /* Tolerance for computing Max Likelihood */
171: double ftolhess; /* Tolerance for computing hessian */
172:
1.7 lievre 173: /**************** split *************************/
1.22 brouard 174: static int split( char *path, char *dirc, char *name, char *ext, char *finame )
1.5 lievre 175: {
176: char *s; /* pointer */
177: int l1, l2; /* length counters */
178:
179: l1 = strlen( path ); /* length of path */
180: if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
1.47 brouard 181: s = strrchr( path, DIRSEPARATOR ); /* find last / */
1.5 lievre 182: if ( s == NULL ) { /* no directory, so use current */
183: #if defined(__bsd__) /* get current working directory */
184: extern char *getwd( );
185:
186: if ( getwd( dirc ) == NULL ) {
187: #else
188: extern char *getcwd( );
189:
190: if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {
191: #endif
192: return( GLOCK_ERROR_GETCWD );
193: }
194: strcpy( name, path ); /* we've got it */
195: } else { /* strip direcotry from path */
196: s++; /* after this, the filename */
197: l2 = strlen( s ); /* length of filename */
198: if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
199: strcpy( name, s ); /* save file name */
200: strncpy( dirc, path, l1 - l2 ); /* now the directory */
201: dirc[l1-l2] = 0; /* add zero */
202: }
203: l1 = strlen( dirc ); /* length of directory */
1.22 brouard 204: #ifdef windows
1.5 lievre 205: if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; }
1.22 brouard 206: #else
207: if ( dirc[l1-1] != '/' ) { dirc[l1] = '/'; dirc[l1+1] = 0; }
208: #endif
209: s = strrchr( name, '.' ); /* find last / */
210: s++;
211: strcpy(ext,s); /* save extension */
212: l1= strlen( name);
213: l2= strlen( s)+1;
214: strncpy( finame, name, l1-l2);
215: finame[l1-l2]= 0;
1.5 lievre 216: return( 0 ); /* we're done */
217: }
218:
219:
1.2 lievre 220: /******************************************/
221:
222: void replace(char *s, char*t)
223: {
224: int i;
225: int lg=20;
226: i=0;
227: lg=strlen(t);
228: for(i=0; i<= lg; i++) {
229: (s[i] = t[i]);
230: if (t[i]== '\\') s[i]='/';
231: }
232: }
233:
234: int nbocc(char *s, char occ)
235: {
236: int i,j=0;
237: int lg=20;
238: i=0;
239: lg=strlen(s);
240: for(i=0; i<= lg; i++) {
241: if (s[i] == occ ) j++;
242: }
243: return j;
244: }
245:
246: void cutv(char *u,char *v, char*t, char occ)
247: {
1.6 lievre 248: int i,lg,j,p=0;
1.2 lievre 249: i=0;
250: for(j=0; j<=strlen(t)-1; j++) {
1.3 lievre 251: if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;
1.2 lievre 252: }
253:
254: lg=strlen(t);
255: for(j=0; j<p; j++) {
256: (u[j] = t[j]);
257: }
1.6 lievre 258: u[p]='\0';
1.2 lievre 259:
260: for(j=0; j<= lg; j++) {
261: if (j>=(p+1))(v[j-p-1] = t[j]);
262: }
263: }
264:
265: /********************** nrerror ********************/
266:
267: void nrerror(char error_text[])
268: {
269: fprintf(stderr,"ERREUR ...\n");
270: fprintf(stderr,"%s\n",error_text);
271: exit(1);
272: }
273: /*********************** vector *******************/
274: double *vector(int nl, int nh)
275: {
276: double *v;
277: v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
278: if (!v) nrerror("allocation failure in vector");
279: return v-nl+NR_END;
280: }
281:
282: /************************ free vector ******************/
283: void free_vector(double*v, int nl, int nh)
284: {
285: free((FREE_ARG)(v+nl-NR_END));
286: }
287:
288: /************************ivector *******************************/
289: int *ivector(long nl,long nh)
290: {
291: int *v;
292: v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
293: if (!v) nrerror("allocation failure in ivector");
294: return v-nl+NR_END;
295: }
296:
297: /******************free ivector **************************/
298: void free_ivector(int *v, long nl, long nh)
299: {
300: free((FREE_ARG)(v+nl-NR_END));
301: }
302:
303: /******************* imatrix *******************************/
304: int **imatrix(long nrl, long nrh, long ncl, long nch)
305: /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */
306: {
307: long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;
308: int **m;
309:
310: /* allocate pointers to rows */
311: m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));
312: if (!m) nrerror("allocation failure 1 in matrix()");
313: m += NR_END;
314: m -= nrl;
315:
316:
317: /* allocate rows and set pointers to them */
318: m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));
319: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
320: m[nrl] += NR_END;
321: m[nrl] -= ncl;
322:
323: for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;
324:
325: /* return pointer to array of pointers to rows */
326: return m;
327: }
328:
329: /****************** free_imatrix *************************/
330: void free_imatrix(m,nrl,nrh,ncl,nch)
331: int **m;
332: long nch,ncl,nrh,nrl;
333: /* free an int matrix allocated by imatrix() */
334: {
335: free((FREE_ARG) (m[nrl]+ncl-NR_END));
336: free((FREE_ARG) (m+nrl-NR_END));
337: }
338:
339: /******************* matrix *******************************/
340: double **matrix(long nrl, long nrh, long ncl, long nch)
341: {
342: long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
343: double **m;
344:
345: m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
346: if (!m) nrerror("allocation failure 1 in matrix()");
347: m += NR_END;
348: m -= nrl;
349:
350: m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
351: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
352: m[nrl] += NR_END;
353: m[nrl] -= ncl;
354:
355: for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
356: return m;
357: }
358:
359: /*************************free matrix ************************/
360: void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
361: {
362: free((FREE_ARG)(m[nrl]+ncl-NR_END));
363: free((FREE_ARG)(m+nrl-NR_END));
364: }
365:
366: /******************* ma3x *******************************/
367: double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
368: {
369: long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
370: double ***m;
371:
372: m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
373: if (!m) nrerror("allocation failure 1 in matrix()");
374: m += NR_END;
375: m -= nrl;
376:
377: m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
378: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
379: m[nrl] += NR_END;
380: m[nrl] -= ncl;
381:
382: for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
383:
384: m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
385: if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
386: m[nrl][ncl] += NR_END;
387: m[nrl][ncl] -= nll;
388: for (j=ncl+1; j<=nch; j++)
389: m[nrl][j]=m[nrl][j-1]+nlay;
390:
391: for (i=nrl+1; i<=nrh; i++) {
392: m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
393: for (j=ncl+1; j<=nch; j++)
394: m[i][j]=m[i][j-1]+nlay;
395: }
396: return m;
397: }
398:
399: /*************************free ma3x ************************/
400: void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
401: {
402: free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
403: free((FREE_ARG)(m[nrl]+ncl-NR_END));
404: free((FREE_ARG)(m+nrl-NR_END));
405: }
406:
407: /***************** f1dim *************************/
408: extern int ncom;
409: extern double *pcom,*xicom;
410: extern double (*nrfunc)(double []);
411:
412: double f1dim(double x)
413: {
414: int j;
415: double f;
416: double *xt;
417:
418: xt=vector(1,ncom);
419: for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];
420: f=(*nrfunc)(xt);
421: free_vector(xt,1,ncom);
422: return f;
423: }
424:
425: /*****************brent *************************/
426: double brent(double ax, double bx, double cx, double (*f)(double), double tol, double *xmin)
427: {
428: int iter;
429: double a,b,d,etemp;
430: double fu,fv,fw,fx;
431: double ftemp;
432: double p,q,r,tol1,tol2,u,v,w,x,xm;
433: double e=0.0;
434:
435: a=(ax < cx ? ax : cx);
436: b=(ax > cx ? ax : cx);
437: x=w=v=bx;
438: fw=fv=fx=(*f)(x);
439: for (iter=1;iter<=ITMAX;iter++) {
440: xm=0.5*(a+b);
441: tol2=2.0*(tol1=tol*fabs(x)+ZEPS);
442: /* if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
443: printf(".");fflush(stdout);
444: #ifdef DEBUG
445: 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);
446: /* if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
447: #endif
448: if (fabs(x-xm) <= (tol2-0.5*(b-a))){
449: *xmin=x;
450: return fx;
451: }
452: ftemp=fu;
453: if (fabs(e) > tol1) {
454: r=(x-w)*(fx-fv);
455: q=(x-v)*(fx-fw);
456: p=(x-v)*q-(x-w)*r;
457: q=2.0*(q-r);
458: if (q > 0.0) p = -p;
459: q=fabs(q);
460: etemp=e;
461: e=d;
462: if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))
463: d=CGOLD*(e=(x >= xm ? a-x : b-x));
464: else {
465: d=p/q;
466: u=x+d;
467: if (u-a < tol2 || b-u < tol2)
468: d=SIGN(tol1,xm-x);
469: }
470: } else {
471: d=CGOLD*(e=(x >= xm ? a-x : b-x));
472: }
473: u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));
474: fu=(*f)(u);
475: if (fu <= fx) {
476: if (u >= x) a=x; else b=x;
477: SHFT(v,w,x,u)
478: SHFT(fv,fw,fx,fu)
479: } else {
480: if (u < x) a=u; else b=u;
481: if (fu <= fw || w == x) {
482: v=w;
483: w=u;
484: fv=fw;
485: fw=fu;
486: } else if (fu <= fv || v == x || v == w) {
487: v=u;
488: fv=fu;
489: }
490: }
491: }
492: nrerror("Too many iterations in brent");
493: *xmin=x;
494: return fx;
495: }
496:
497: /****************** mnbrak ***********************/
498:
499: void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,
500: double (*func)(double))
501: {
502: double ulim,u,r,q, dum;
503: double fu;
504:
505: *fa=(*func)(*ax);
506: *fb=(*func)(*bx);
507: if (*fb > *fa) {
508: SHFT(dum,*ax,*bx,dum)
509: SHFT(dum,*fb,*fa,dum)
510: }
511: *cx=(*bx)+GOLD*(*bx-*ax);
512: *fc=(*func)(*cx);
513: while (*fb > *fc) {
514: r=(*bx-*ax)*(*fb-*fc);
515: q=(*bx-*cx)*(*fb-*fa);
516: u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/
517: (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r));
518: ulim=(*bx)+GLIMIT*(*cx-*bx);
519: if ((*bx-u)*(u-*cx) > 0.0) {
520: fu=(*func)(u);
521: } else if ((*cx-u)*(u-ulim) > 0.0) {
522: fu=(*func)(u);
523: if (fu < *fc) {
524: SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))
525: SHFT(*fb,*fc,fu,(*func)(u))
526: }
527: } else if ((u-ulim)*(ulim-*cx) >= 0.0) {
528: u=ulim;
529: fu=(*func)(u);
530: } else {
531: u=(*cx)+GOLD*(*cx-*bx);
532: fu=(*func)(u);
533: }
534: SHFT(*ax,*bx,*cx,u)
535: SHFT(*fa,*fb,*fc,fu)
536: }
537: }
538:
539: /*************** linmin ************************/
540:
541: int ncom;
542: double *pcom,*xicom;
543: double (*nrfunc)(double []);
544:
545: void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))
546: {
547: double brent(double ax, double bx, double cx,
548: double (*f)(double), double tol, double *xmin);
549: double f1dim(double x);
550: void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,
551: double *fc, double (*func)(double));
552: int j;
553: double xx,xmin,bx,ax;
554: double fx,fb,fa;
555:
556: ncom=n;
557: pcom=vector(1,n);
558: xicom=vector(1,n);
559: nrfunc=func;
560: for (j=1;j<=n;j++) {
561: pcom[j]=p[j];
562: xicom[j]=xi[j];
563: }
564: ax=0.0;
565: xx=1.0;
566: mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim);
567: *fret=brent(ax,xx,bx,f1dim,TOL,&xmin);
568: #ifdef DEBUG
569: printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
570: #endif
571: for (j=1;j<=n;j++) {
572: xi[j] *= xmin;
573: p[j] += xi[j];
574: }
575: free_vector(xicom,1,n);
576: free_vector(pcom,1,n);
577: }
578:
579: /*************** powell ************************/
580: void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,
581: double (*func)(double []))
582: {
583: void linmin(double p[], double xi[], int n, double *fret,
584: double (*func)(double []));
585: int i,ibig,j;
586: double del,t,*pt,*ptt,*xit;
587: double fp,fptt;
588: double *xits;
589: pt=vector(1,n);
590: ptt=vector(1,n);
591: xit=vector(1,n);
592: xits=vector(1,n);
593: *fret=(*func)(p);
594: for (j=1;j<=n;j++) pt[j]=p[j];
595: for (*iter=1;;++(*iter)) {
596: fp=(*fret);
597: ibig=0;
598: del=0.0;
599: printf("\nPowell iter=%d -2*LL=%.12f",*iter,*fret);
600: for (i=1;i<=n;i++)
601: printf(" %d %.12f",i, p[i]);
602: printf("\n");
603: for (i=1;i<=n;i++) {
604: for (j=1;j<=n;j++) xit[j]=xi[j][i];
605: fptt=(*fret);
606: #ifdef DEBUG
607: printf("fret=%lf \n",*fret);
608: #endif
609: printf("%d",i);fflush(stdout);
610: linmin(p,xit,n,fret,func);
611: if (fabs(fptt-(*fret)) > del) {
612: del=fabs(fptt-(*fret));
613: ibig=i;
614: }
615: #ifdef DEBUG
616: printf("%d %.12e",i,(*fret));
617: for (j=1;j<=n;j++) {
618: xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
619: printf(" x(%d)=%.12e",j,xit[j]);
620: }
621: for(j=1;j<=n;j++)
622: printf(" p=%.12e",p[j]);
623: printf("\n");
624: #endif
625: }
626: if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {
627: #ifdef DEBUG
628: int k[2],l;
629: k[0]=1;
630: k[1]=-1;
631: printf("Max: %.12e",(*func)(p));
632: for (j=1;j<=n;j++)
633: printf(" %.12e",p[j]);
634: printf("\n");
635: for(l=0;l<=1;l++) {
636: for (j=1;j<=n;j++) {
637: ptt[j]=p[j]+(p[j]-pt[j])*k[l];
638: printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
639: }
640: printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
641: }
642: #endif
643:
644:
645: free_vector(xit,1,n);
646: free_vector(xits,1,n);
647: free_vector(ptt,1,n);
648: free_vector(pt,1,n);
649: return;
650: }
651: if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");
652: for (j=1;j<=n;j++) {
653: ptt[j]=2.0*p[j]-pt[j];
654: xit[j]=p[j]-pt[j];
655: pt[j]=p[j];
656: }
657: fptt=(*func)(ptt);
658: if (fptt < fp) {
659: t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt);
660: if (t < 0.0) {
661: linmin(p,xit,n,fret,func);
662: for (j=1;j<=n;j++) {
663: xi[j][ibig]=xi[j][n];
664: xi[j][n]=xit[j];
665: }
666: #ifdef DEBUG
667: printf("Direction changed last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
668: for(j=1;j<=n;j++)
669: printf(" %.12e",xit[j]);
670: printf("\n");
671: #endif
672: }
673: }
674: }
675: }
676:
677: /**** Prevalence limit ****************/
678:
679: double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)
680: {
681: /* Computes the prevalence limit in each live state at age x by left multiplying the unit
682: matrix by transitions matrix until convergence is reached */
683:
684: int i, ii,j,k;
685: double min, max, maxmin, maxmax,sumnew=0.;
686: double **matprod2();
687: double **out, cov[NCOVMAX], **pmij();
688: double **newm;
689: double agefin, delaymax=50 ; /* Max number of years to converge */
690:
691: for (ii=1;ii<=nlstate+ndeath;ii++)
692: for (j=1;j<=nlstate+ndeath;j++){
693: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
694: }
1.6 lievre 695:
696: cov[1]=1.;
697:
698: /* Even if hstepm = 1, at least one multiplication by the unit matrix */
1.2 lievre 699: for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
700: newm=savm;
701: /* Covariates have to be included here again */
1.6 lievre 702: cov[2]=agefin;
703:
704: for (k=1; k<=cptcovn;k++) {
1.7 lievre 705: cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
1.35 lievre 706: /* 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]]);*/
1.6 lievre 707: }
1.35 lievre 708: for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
1.7 lievre 709: for (k=1; k<=cptcovprod;k++)
710: cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
711:
712: /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
713: /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
1.35 lievre 714: /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
1.2 lievre 715: out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);
716:
717: savm=oldm;
718: oldm=newm;
719: maxmax=0.;
720: for(j=1;j<=nlstate;j++){
721: min=1.;
722: max=0.;
723: for(i=1; i<=nlstate; i++) {
724: sumnew=0;
725: for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
726: prlim[i][j]= newm[i][j]/(1-sumnew);
727: max=FMAX(max,prlim[i][j]);
728: min=FMIN(min,prlim[i][j]);
729: }
730: maxmin=max-min;
731: maxmax=FMAX(maxmax,maxmin);
732: }
733: if(maxmax < ftolpl){
734: return prlim;
735: }
736: }
737: }
738:
1.12 lievre 739: /*************** transition probabilities ***************/
1.2 lievre 740:
741: double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
742: {
743: double s1, s2;
744: /*double t34;*/
745: int i,j,j1, nc, ii, jj;
746:
747: for(i=1; i<= nlstate; i++){
748: for(j=1; j<i;j++){
749: for (nc=1, s2=0.;nc <=ncovmodel; nc++){
750: /*s2 += param[i][j][nc]*cov[nc];*/
751: s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
752: /*printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2);*/
753: }
754: ps[i][j]=s2;
755: /*printf("s1=%.17e, s2=%.17e\n",s1,s2);*/
756: }
757: for(j=i+1; j<=nlstate+ndeath;j++){
758: for (nc=1, s2=0.;nc <=ncovmodel; nc++){
759: s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
760: /*printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2);*/
761: }
1.22 brouard 762: ps[i][j]=s2;
1.2 lievre 763: }
764: }
1.12 lievre 765: /*ps[3][2]=1;*/
766:
1.2 lievre 767: for(i=1; i<= nlstate; i++){
768: s1=0;
769: for(j=1; j<i; j++)
770: s1+=exp(ps[i][j]);
771: for(j=i+1; j<=nlstate+ndeath; j++)
772: s1+=exp(ps[i][j]);
773: ps[i][i]=1./(s1+1.);
774: for(j=1; j<i; j++)
775: ps[i][j]= exp(ps[i][j])*ps[i][i];
776: for(j=i+1; j<=nlstate+ndeath; j++)
777: ps[i][j]= exp(ps[i][j])*ps[i][i];
778: /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
779: } /* end i */
780:
781: for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
782: for(jj=1; jj<= nlstate+ndeath; jj++){
783: ps[ii][jj]=0;
784: ps[ii][ii]=1;
785: }
786: }
787:
1.12 lievre 788:
1.2 lievre 789: /* for(ii=1; ii<= nlstate+ndeath; ii++){
790: for(jj=1; jj<= nlstate+ndeath; jj++){
791: printf("%lf ",ps[ii][jj]);
792: }
793: printf("\n ");
794: }
795: printf("\n ");printf("%lf ",cov[2]);*/
796: /*
797: for(i=1; i<= npar; i++) printf("%f ",x[i]);
798: goto end;*/
799: return ps;
800: }
801:
802: /**************** Product of 2 matrices ******************/
803:
804: double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)
805: {
1.13 lievre 806: /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
1.2 lievre 807: b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
808: /* in, b, out are matrice of pointers which should have been initialized
809: before: only the contents of out is modified. The function returns
810: a pointer to pointers identical to out */
811: long i, j, k;
812: for(i=nrl; i<= nrh; i++)
813: for(k=ncolol; k<=ncoloh; k++)
814: for(j=ncl,out[i][k]=0.; j<=nch; j++)
815: out[i][k] +=in[i][j]*b[j][k];
816:
817: return out;
818: }
819:
820:
821: /************* Higher Matrix Product ***************/
822:
823: double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
824: {
825: /* Computes the transition matrix starting at age 'age' over 'nhstepm*hstepm*stepm' month
826: duration (i.e. until
827: age (in years) age+nhstepm*stepm/12) by multiplying nhstepm*hstepm matrices.
828: Output is stored in matrix po[i][j][h] for h every 'hstepm' step
829: (typically every 2 years instead of every month which is too big).
830: Model is determined by parameters x and covariates have to be
831: included manually here.
832:
833: */
834:
835: int i, j, d, h, k;
836: double **out, cov[NCOVMAX];
837: double **newm;
838:
839: /* Hstepm could be zero and should return the unit matrix */
840: for (i=1;i<=nlstate+ndeath;i++)
841: for (j=1;j<=nlstate+ndeath;j++){
842: oldm[i][j]=(i==j ? 1.0 : 0.0);
843: po[i][j][0]=(i==j ? 1.0 : 0.0);
844: }
845: /* Even if hstepm = 1, at least one multiplication by the unit matrix */
846: for(h=1; h <=nhstepm; h++){
847: for(d=1; d <=hstepm; d++){
848: newm=savm;
849: /* Covariates have to be included here again */
850: cov[1]=1.;
851: cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
1.7 lievre 852: for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
1.12 lievre 853: for (k=1; k<=cptcovage;k++)
1.7 lievre 854: cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
1.12 lievre 855: for (k=1; k<=cptcovprod;k++)
1.7 lievre 856: cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
857:
858:
1.2 lievre 859: /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
860: /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
861: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,
862: pmij(pmmij,cov,ncovmodel,x,nlstate));
863: savm=oldm;
864: oldm=newm;
865: }
866: for(i=1; i<=nlstate+ndeath; i++)
867: for(j=1;j<=nlstate+ndeath;j++) {
868: po[i][j][h]=newm[i][j];
869: /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);
870: */
871: }
872: } /* end h */
873: return po;
874: }
875:
876:
877: /*************** log-likelihood *************/
878: double func( double *x)
879: {
1.6 lievre 880: int i, ii, j, k, mi, d, kk;
1.2 lievre 881: double l, ll[NLSTATEMAX], cov[NCOVMAX];
882: double **out;
883: double sw; /* Sum of weights */
884: double lli; /* Individual log likelihood */
885: long ipmx;
886: /*extern weight */
887: /* We are differentiating ll according to initial status */
888: /* for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
889: /*for(i=1;i<imx;i++)
1.8 lievre 890: printf(" %d\n",s[4][i]);
1.2 lievre 891: */
1.6 lievre 892: cov[1]=1.;
1.2 lievre 893:
894: for(k=1; k<=nlstate; k++) ll[k]=0.;
895: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1.6 lievre 896: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
1.8 lievre 897: for(mi=1; mi<= wav[i]-1; mi++){
1.2 lievre 898: for (ii=1;ii<=nlstate+ndeath;ii++)
899: for (j=1;j<=nlstate+ndeath;j++) oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1.8 lievre 900: for(d=0; d<dh[mi][i]; d++){
901: newm=savm;
902: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
903: for (kk=1; kk<=cptcovage;kk++) {
904: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
905: }
906:
907: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
908: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
909: savm=oldm;
910: oldm=newm;
911:
912:
1.2 lievre 913: } /* end mult */
1.8 lievre 914:
1.2 lievre 915: lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);
916: /* printf(" %f ",out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/
917: ipmx +=1;
918: sw += weight[i];
919: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
920: } /* end of wave */
921: } /* end of individual */
922:
923: for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
924: /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
925: l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
926: return -l;
927: }
928:
929:
930: /*********** Maximum Likelihood Estimation ***************/
931:
932: void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
933: {
934: int i,j, iter;
935: double **xi,*delti;
936: double fret;
937: xi=matrix(1,npar,1,npar);
938: for (i=1;i<=npar;i++)
939: for (j=1;j<=npar;j++)
940: xi[i][j]=(i==j ? 1.0 : 0.0);
941: printf("Powell\n");
942: powell(p,xi,npar,ftol,&iter,&fret,func);
943:
944: printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));
1.21 lievre 945: fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
1.2 lievre 946:
947: }
948:
949: /**** Computes Hessian and covariance matrix ***/
950: void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
951: {
952: double **a,**y,*x,pd;
953: double **hess;
954: int i, j,jk;
955: int *indx;
956:
957: double hessii(double p[], double delta, int theta, double delti[]);
958: double hessij(double p[], double delti[], int i, int j);
959: void lubksb(double **a, int npar, int *indx, double b[]) ;
960: void ludcmp(double **a, int npar, int *indx, double *d) ;
961:
962: hess=matrix(1,npar,1,npar);
963:
964: printf("\nCalculation of the hessian matrix. Wait...\n");
965: for (i=1;i<=npar;i++){
966: printf("%d",i);fflush(stdout);
967: hess[i][i]=hessii(p,ftolhess,i,delti);
968: /*printf(" %f ",p[i]);*/
1.12 lievre 969: /*printf(" %lf ",hess[i][i]);*/
1.2 lievre 970: }
1.12 lievre 971:
1.2 lievre 972: for (i=1;i<=npar;i++) {
973: for (j=1;j<=npar;j++) {
974: if (j>i) {
975: printf(".%d%d",i,j);fflush(stdout);
976: hess[i][j]=hessij(p,delti,i,j);
1.12 lievre 977: hess[j][i]=hess[i][j];
978: /*printf(" %lf ",hess[i][j]);*/
1.2 lievre 979: }
980: }
981: }
982: printf("\n");
983:
984: printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
985:
986: a=matrix(1,npar,1,npar);
987: y=matrix(1,npar,1,npar);
988: x=vector(1,npar);
989: indx=ivector(1,npar);
990: for (i=1;i<=npar;i++)
991: for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
992: ludcmp(a,npar,indx,&pd);
993:
994: for (j=1;j<=npar;j++) {
995: for (i=1;i<=npar;i++) x[i]=0;
996: x[j]=1;
997: lubksb(a,npar,indx,x);
998: for (i=1;i<=npar;i++){
999: matcov[i][j]=x[i];
1000: }
1001: }
1002:
1003: printf("\n#Hessian matrix#\n");
1004: for (i=1;i<=npar;i++) {
1005: for (j=1;j<=npar;j++) {
1006: printf("%.3e ",hess[i][j]);
1007: }
1008: printf("\n");
1009: }
1010:
1011: /* Recompute Inverse */
1012: for (i=1;i<=npar;i++)
1013: for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];
1014: ludcmp(a,npar,indx,&pd);
1015:
1016: /* printf("\n#Hessian matrix recomputed#\n");
1017:
1018: for (j=1;j<=npar;j++) {
1019: for (i=1;i<=npar;i++) x[i]=0;
1020: x[j]=1;
1021: lubksb(a,npar,indx,x);
1022: for (i=1;i<=npar;i++){
1023: y[i][j]=x[i];
1024: printf("%.3e ",y[i][j]);
1025: }
1026: printf("\n");
1027: }
1028: */
1029:
1030: free_matrix(a,1,npar,1,npar);
1031: free_matrix(y,1,npar,1,npar);
1032: free_vector(x,1,npar);
1033: free_ivector(indx,1,npar);
1034: free_matrix(hess,1,npar,1,npar);
1035:
1036:
1037: }
1038:
1039: /*************** hessian matrix ****************/
1040: double hessii( double x[], double delta, int theta, double delti[])
1041: {
1042: int i;
1043: int l=1, lmax=20;
1044: double k1,k2;
1045: double p2[NPARMAX+1];
1046: double res;
1047: double delt, delts, nkhi=10.,nkhif=1., khi=1.e-4;
1048: double fx;
1049: int k=0,kmax=10;
1050: double l1;
1051:
1052: fx=func(x);
1053: for (i=1;i<=npar;i++) p2[i]=x[i];
1054: for(l=0 ; l <=lmax; l++){
1055: l1=pow(10,l);
1056: delts=delt;
1057: for(k=1 ; k <kmax; k=k+1){
1058: delt = delta*(l1*k);
1059: p2[theta]=x[theta] +delt;
1060: k1=func(p2)-fx;
1061: p2[theta]=x[theta]-delt;
1062: k2=func(p2)-fx;
1063: /*res= (k1-2.0*fx+k2)/delt/delt; */
1064: res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */
1065:
1066: #ifdef DEBUG
1067: 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);
1068: #endif
1069: /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
1070: if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
1071: k=kmax;
1072: }
1073: else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
1074: k=kmax; l=lmax*10.;
1075: }
1076: else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){
1077: delts=delt;
1078: }
1079: }
1080: }
1081: delti[theta]=delts;
1.12 lievre 1082: return res;
1.3 lievre 1083:
1.2 lievre 1084: }
1085:
1086: double hessij( double x[], double delti[], int thetai,int thetaj)
1087: {
1088: int i;
1089: int l=1, l1, lmax=20;
1090: double k1,k2,k3,k4,res,fx;
1091: double p2[NPARMAX+1];
1092: int k;
1093:
1094: fx=func(x);
1095: for (k=1; k<=2; k++) {
1096: for (i=1;i<=npar;i++) p2[i]=x[i];
1097: p2[thetai]=x[thetai]+delti[thetai]/k;
1098: p2[thetaj]=x[thetaj]+delti[thetaj]/k;
1099: k1=func(p2)-fx;
1100:
1101: p2[thetai]=x[thetai]+delti[thetai]/k;
1102: p2[thetaj]=x[thetaj]-delti[thetaj]/k;
1103: k2=func(p2)-fx;
1104:
1105: p2[thetai]=x[thetai]-delti[thetai]/k;
1106: p2[thetaj]=x[thetaj]+delti[thetaj]/k;
1107: k3=func(p2)-fx;
1108:
1109: p2[thetai]=x[thetai]-delti[thetai]/k;
1110: p2[thetaj]=x[thetaj]-delti[thetaj]/k;
1111: k4=func(p2)-fx;
1112: res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */
1113: #ifdef DEBUG
1114: 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);
1115: #endif
1116: }
1117: return res;
1118: }
1119:
1120: /************** Inverse of matrix **************/
1121: void ludcmp(double **a, int n, int *indx, double *d)
1122: {
1123: int i,imax,j,k;
1124: double big,dum,sum,temp;
1125: double *vv;
1126:
1127: vv=vector(1,n);
1128: *d=1.0;
1129: for (i=1;i<=n;i++) {
1130: big=0.0;
1131: for (j=1;j<=n;j++)
1132: if ((temp=fabs(a[i][j])) > big) big=temp;
1133: if (big == 0.0) nrerror("Singular matrix in routine ludcmp");
1134: vv[i]=1.0/big;
1135: }
1136: for (j=1;j<=n;j++) {
1137: for (i=1;i<j;i++) {
1138: sum=a[i][j];
1139: for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];
1140: a[i][j]=sum;
1141: }
1142: big=0.0;
1143: for (i=j;i<=n;i++) {
1144: sum=a[i][j];
1145: for (k=1;k<j;k++)
1146: sum -= a[i][k]*a[k][j];
1147: a[i][j]=sum;
1148: if ( (dum=vv[i]*fabs(sum)) >= big) {
1149: big=dum;
1150: imax=i;
1151: }
1152: }
1153: if (j != imax) {
1154: for (k=1;k<=n;k++) {
1155: dum=a[imax][k];
1156: a[imax][k]=a[j][k];
1157: a[j][k]=dum;
1158: }
1159: *d = -(*d);
1160: vv[imax]=vv[j];
1161: }
1162: indx[j]=imax;
1163: if (a[j][j] == 0.0) a[j][j]=TINY;
1164: if (j != n) {
1165: dum=1.0/(a[j][j]);
1166: for (i=j+1;i<=n;i++) a[i][j] *= dum;
1167: }
1168: }
1169: free_vector(vv,1,n); /* Doesn't work */
1170: ;
1171: }
1172:
1173: void lubksb(double **a, int n, int *indx, double b[])
1174: {
1175: int i,ii=0,ip,j;
1176: double sum;
1177:
1178: for (i=1;i<=n;i++) {
1179: ip=indx[i];
1180: sum=b[ip];
1181: b[ip]=b[i];
1182: if (ii)
1183: for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];
1184: else if (sum) ii=i;
1185: b[i]=sum;
1186: }
1187: for (i=n;i>=1;i--) {
1188: sum=b[i];
1189: for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];
1190: b[i]=sum/a[i][i];
1191: }
1192: }
1193:
1194: /************ Frequencies ********************/
1.26 lievre 1195: void freqsummary(char fileres[], int agemin, int agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax,double **mint,double **anint, double dateprev1,double dateprev2,double jprev1, double mprev1,double anprev1,double jprev2, double mprev2,double anprev2)
1.2 lievre 1196: { /* Some frequencies */
1.35 lievre 1197:
1.18 lievre 1198: int i, m, jk, k1,i1, j1, bool, z1,z2,j;
1.2 lievre 1199: double ***freq; /* Frequencies */
1200: double *pp;
1.19 lievre 1201: double pos, k2, dateintsum=0,k2cpt=0;
1.2 lievre 1202: FILE *ficresp;
1203: char fileresp[FILENAMELENGTH];
1.35 lievre 1204:
1.2 lievre 1205: pp=vector(1,nlstate);
1.19 lievre 1206: probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
1.2 lievre 1207: strcpy(fileresp,"p");
1208: strcat(fileresp,fileres);
1209: if((ficresp=fopen(fileresp,"w"))==NULL) {
1210: printf("Problem with prevalence resultfile: %s\n", fileresp);
1211: exit(0);
1212: }
1213: freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);
1214: j1=0;
1.35 lievre 1215:
1.7 lievre 1216: j=cptcoveff;
1.2 lievre 1217: if (cptcovn<1) {j=1;ncodemax[1]=1;}
1.35 lievre 1218:
1.2 lievre 1219: for(k1=1; k1<=j;k1++){
1.35 lievre 1220: for(i1=1; i1<=ncodemax[k1];i1++){
1221: j1++;
1222: /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
1223: scanf("%d", i);*/
1224: for (i=-1; i<=nlstate+ndeath; i++)
1225: for (jk=-1; jk<=nlstate+ndeath; jk++)
1226: for(m=agemin; m <= agemax+3; m++)
1227: freq[i][jk][m]=0;
1228:
1229: dateintsum=0;
1230: k2cpt=0;
1231: for (i=1; i<=imx; i++) {
1232: bool=1;
1233: if (cptcovn>0) {
1234: for (z1=1; z1<=cptcoveff; z1++)
1235: if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])
1236: bool=0;
1237: }
1238: if (bool==1) {
1239: for(m=firstpass; m<=lastpass; m++){
1240: k2=anint[m][i]+(mint[m][i]/12.);
1241: if ((k2>=dateprev1) && (k2<=dateprev2)) {
1242: if(agev[m][i]==0) agev[m][i]=agemax+1;
1243: if(agev[m][i]==1) agev[m][i]=agemax+2;
1244: if (m<lastpass) {
1245: freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
1246: freq[s[m][i]][s[m+1][i]][(int) agemax+3] += weight[i];
1247: }
1248:
1249: if ((agev[m][i]>1) && (agev[m][i]< (agemax+3))) {
1250: dateintsum=dateintsum+k2;
1251: k2cpt++;
1252: }
1253: }
1254: }
1255: }
1256: }
1.26 lievre 1257:
1.35 lievre 1258: fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);
1.26 lievre 1259:
1.35 lievre 1260: if (cptcovn>0) {
1261: fprintf(ficresp, "\n#********** Variable ");
1262: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
1263: fprintf(ficresp, "**********\n#");
1264: }
1265: for(i=1; i<=nlstate;i++)
1266: fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
1267: fprintf(ficresp, "\n");
1268:
1269: for(i=(int)agemin; i <= (int)agemax+3; i++){
1270: if(i==(int)agemax+3)
1271: printf("Total");
1272: else
1273: printf("Age %d", i);
1274: for(jk=1; jk <=nlstate ; jk++){
1275: for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
1276: pp[jk] += freq[jk][m][i];
1277: }
1278: for(jk=1; jk <=nlstate ; jk++){
1279: for(m=-1, pos=0; m <=0 ; m++)
1280: pos += freq[jk][m][i];
1281: if(pp[jk]>=1.e-10)
1282: printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
1283: else
1284: printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
1285: }
1.14 lievre 1286:
1.35 lievre 1287: for(jk=1; jk <=nlstate ; jk++){
1288: for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
1289: pp[jk] += freq[jk][m][i];
1290: }
1.14 lievre 1291:
1.35 lievre 1292: for(jk=1,pos=0; jk <=nlstate ; jk++)
1293: pos += pp[jk];
1294: for(jk=1; jk <=nlstate ; jk++){
1295: if(pos>=1.e-5)
1296: printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
1297: else
1298: printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
1299: if( i <= (int) agemax){
1300: if(pos>=1.e-5){
1301: fprintf(ficresp," %d %.5f %.0f %.0f",i,pp[jk]/pos, pp[jk],pos);
1302: probs[i][jk][j1]= pp[jk]/pos;
1303: /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/
1304: }
1305: else
1306: fprintf(ficresp," %d NaNq %.0f %.0f",i,pp[jk],pos);
1307: }
1.13 lievre 1308: }
1.35 lievre 1309:
1310: for(jk=-1; jk <=nlstate+ndeath; jk++)
1311: for(m=-1; m <=nlstate+ndeath; m++)
1312: if(freq[jk][m][i] !=0 ) printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
1313: if(i <= (int) agemax)
1314: fprintf(ficresp,"\n");
1315: printf("\n");
1.2 lievre 1316: }
1317: }
1.35 lievre 1318: }
1.19 lievre 1319: dateintmean=dateintsum/k2cpt;
1.2 lievre 1320:
1321: fclose(ficresp);
1322: free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);
1323: free_vector(pp,1,nlstate);
1.35 lievre 1324:
1.19 lievre 1325: /* End of Freq */
1326: }
1.2 lievre 1327:
1.15 lievre 1328: /************ Prevalence ********************/
1.28 lievre 1329: void prevalence(int agemin, float agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax,double **mint,double **anint, double dateprev1,double dateprev2, double calagedate)
1.15 lievre 1330: { /* Some frequencies */
1331:
1332: int i, m, jk, k1, i1, j1, bool, z1,z2,j;
1333: double ***freq; /* Frequencies */
1334: double *pp;
1.18 lievre 1335: double pos, k2;
1.15 lievre 1336:
1337: pp=vector(1,nlstate);
1.19 lievre 1338: probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
1.15 lievre 1339:
1340: freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);
1341: j1=0;
1342:
1343: j=cptcoveff;
1344: if (cptcovn<1) {j=1;ncodemax[1]=1;}
1345:
1.42 brouard 1346: for(k1=1; k1<=j;k1++){
1.15 lievre 1347: for(i1=1; i1<=ncodemax[k1];i1++){
1348: j1++;
1.42 brouard 1349:
1.15 lievre 1350: for (i=-1; i<=nlstate+ndeath; i++)
1351: for (jk=-1; jk<=nlstate+ndeath; jk++)
1352: for(m=agemin; m <= agemax+3; m++)
1.19 lievre 1353: freq[i][jk][m]=0;
1.28 lievre 1354:
1.15 lievre 1355: for (i=1; i<=imx; i++) {
1356: bool=1;
1357: if (cptcovn>0) {
1358: for (z1=1; z1<=cptcoveff; z1++)
1359: if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])
1360: bool=0;
1.28 lievre 1361: }
1.19 lievre 1362: if (bool==1) {
1363: for(m=firstpass; m<=lastpass; m++){
1364: k2=anint[m][i]+(mint[m][i]/12.);
1365: if ((k2>=dateprev1) && (k2<=dateprev2)) {
1.18 lievre 1366: if(agev[m][i]==0) agev[m][i]=agemax+1;
1367: if(agev[m][i]==1) agev[m][i]=agemax+2;
1.42 brouard 1368: if (m<lastpass) {
1369: if (calagedate>0)
1370: freq[s[m][i]][s[m+1][i]][(int)(agev[m][i]+1-((int)calagedate %12)/12.)] += weight[i];
1371: else
1372: freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
1373: freq[s[m][i]][s[m+1][i]][(int)(agemax+3)] += weight[i];
1374: }
1.18 lievre 1375: }
1.15 lievre 1376: }
1377: }
1378: }
1.42 brouard 1379: for(i=(int)agemin; i <= (int)agemax+3; i++){
1380: for(jk=1; jk <=nlstate ; jk++){
1381: for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
1382: pp[jk] += freq[jk][m][i];
1383: }
1384: for(jk=1; jk <=nlstate ; jk++){
1385: for(m=-1, pos=0; m <=0 ; m++)
1.15 lievre 1386: pos += freq[jk][m][i];
1387: }
1388:
1.42 brouard 1389: for(jk=1; jk <=nlstate ; jk++){
1390: for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
1391: pp[jk] += freq[jk][m][i];
1392: }
1393:
1394: for(jk=1,pos=0; jk <=nlstate ; jk++) pos += pp[jk];
1395:
1396: for(jk=1; jk <=nlstate ; jk++){
1397: if( i <= (int) agemax){
1398: if(pos>=1.e-5){
1399: probs[i][jk][j1]= pp[jk]/pos;
1400: }
1401: }
1.18 lievre 1402: }
1.42 brouard 1403:
1404: }
1.15 lievre 1405: }
1406: }
1.41 lievre 1407:
1.15 lievre 1408:
1409: free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);
1410: free_vector(pp,1,nlstate);
1411:
1412: } /* End of Freq */
1.19 lievre 1413:
1.2 lievre 1414: /************* Waves Concatenation ***************/
1415:
1416: void concatwav(int wav[], int **dh, int **mw, int **s, double *agedc, double **agev, int firstpass, int lastpass, int imx, int nlstate, int stepm)
1417: {
1418: /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
1419: Death is a valid wave (if date is known).
1420: mw[mi][i] is the mi (mi=1 to wav[i]) effective wave of individual i
1421: dh[m][i] of dh[mw[mi][i][i] is the delay between two effective waves m=mw[mi][i]
1422: and mw[mi+1][i]. dh depends on stepm.
1423: */
1424:
1425: int i, mi, m;
1.8 lievre 1426: /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
1427: double sum=0., jmean=0.;*/
1.2 lievre 1428:
1.11 lievre 1429: int j, k=0,jk, ju, jl;
1430: double sum=0.;
1431: jmin=1e+5;
1432: jmax=-1;
1433: jmean=0.;
1.2 lievre 1434: for(i=1; i<=imx; i++){
1435: mi=0;
1436: m=firstpass;
1437: while(s[m][i] <= nlstate){
1438: if(s[m][i]>=1)
1439: mw[++mi][i]=m;
1440: if(m >=lastpass)
1441: break;
1442: else
1443: m++;
1444: }/* end while */
1445: if (s[m][i] > nlstate){
1446: mi++; /* Death is another wave */
1447: /* if(mi==0) never been interviewed correctly before death */
1448: /* Only death is a correct wave */
1449: mw[mi][i]=m;
1450: }
1451:
1452: wav[i]=mi;
1453: if(mi==0)
1454: printf("Warning, no any valid information for:%d line=%d\n",num[i],i);
1455: }
1456:
1457: for(i=1; i<=imx; i++){
1458: for(mi=1; mi<wav[i];mi++){
1459: if (stepm <=0)
1460: dh[mi][i]=1;
1461: else{
1462: if (s[mw[mi+1][i]][i] > nlstate) {
1.10 lievre 1463: if (agedc[i] < 2*AGESUP) {
1.2 lievre 1464: j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);
1.8 lievre 1465: if(j==0) j=1; /* Survives at least one month after exam */
1466: k=k+1;
1467: if (j >= jmax) jmax=j;
1.11 lievre 1468: if (j <= jmin) jmin=j;
1.8 lievre 1469: sum=sum+j;
1.30 lievre 1470: /*if (j<0) printf("j=%d num=%d \n",j,i); */
1.10 lievre 1471: }
1.2 lievre 1472: }
1473: else{
1474: j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
1475: k=k+1;
1476: if (j >= jmax) jmax=j;
1477: else if (j <= jmin)jmin=j;
1.30 lievre 1478: /* if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
1.2 lievre 1479: sum=sum+j;
1480: }
1481: jk= j/stepm;
1482: jl= j -jk*stepm;
1483: ju= j -(jk+1)*stepm;
1484: if(jl <= -ju)
1485: dh[mi][i]=jk;
1486: else
1487: dh[mi][i]=jk+1;
1488: if(dh[mi][i]==0)
1489: dh[mi][i]=1; /* At least one step */
1490: }
1491: }
1492: }
1.8 lievre 1493: jmean=sum/k;
1494: printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);
1.12 lievre 1495: }
1.2 lievre 1496: /*********** Tricode ****************************/
1497: void tricode(int *Tvar, int **nbcode, int imx)
1498: {
1.7 lievre 1499: int Ndum[20],ij=1, k, j, i;
1.2 lievre 1500: int cptcode=0;
1.7 lievre 1501: cptcoveff=0;
1502:
1503: for (k=0; k<19; k++) Ndum[k]=0;
1.2 lievre 1504: for (k=1; k<=7; k++) ncodemax[k]=0;
1.6 lievre 1505:
1.7 lievre 1506: for (j=1; j<=(cptcovn+2*cptcovprod); j++) {
1.2 lievre 1507: for (i=1; i<=imx; i++) {
1508: ij=(int)(covar[Tvar[j]][i]);
1509: Ndum[ij]++;
1.8 lievre 1510: /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
1.2 lievre 1511: if (ij > cptcode) cptcode=ij;
1512: }
1.7 lievre 1513:
1.2 lievre 1514: for (i=0; i<=cptcode; i++) {
1515: if(Ndum[i]!=0) ncodemax[j]++;
1516: }
1517: ij=1;
1.7 lievre 1518:
1.8 lievre 1519:
1.2 lievre 1520: for (i=1; i<=ncodemax[j]; i++) {
1.7 lievre 1521: for (k=0; k<=19; k++) {
1.2 lievre 1522: if (Ndum[k] != 0) {
1523: nbcode[Tvar[j]][ij]=k;
1.39 lievre 1524:
1.2 lievre 1525: ij++;
1526: }
1527: if (ij > ncodemax[j]) break;
1528: }
1529: }
1.7 lievre 1530: }
1.8 lievre 1531:
1532: for (k=0; k<19; k++) Ndum[k]=0;
1533:
1.12 lievre 1534: for (i=1; i<=ncovmodel-2; i++) {
1.7 lievre 1535: ij=Tvar[i];
1536: Ndum[ij]++;
1537: }
1.8 lievre 1538:
1.7 lievre 1539: ij=1;
1.8 lievre 1540: for (i=1; i<=10; i++) {
1.34 brouard 1541: if((Ndum[i]!=0) && (i<=ncovcol)){
1.8 lievre 1542: Tvaraff[ij]=i;
1543: ij++;
1.7 lievre 1544: }
1545: }
1546:
1.8 lievre 1547: cptcoveff=ij-1;
1.6 lievre 1548: }
1.2 lievre 1549:
1550: /*********** Health Expectancies ****************/
1551:
1.41 lievre 1552: 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 )
1553:
1.2 lievre 1554: {
1555: /* Health expectancies */
1.41 lievre 1556: int i, j, nhstepm, hstepm, h, nstepm, k, cptj;
1.35 lievre 1557: double age, agelim, hf;
1.41 lievre 1558: double ***p3mat,***varhe;
1559: double **dnewm,**doldm;
1560: double *xp;
1561: double **gp, **gm;
1562: double ***gradg, ***trgradg;
1563: int theta;
1564:
1565: varhe=ma3x(1,nlstate*2,1,nlstate*2,(int) bage, (int) fage);
1566: xp=vector(1,npar);
1567: dnewm=matrix(1,nlstate*2,1,npar);
1568: doldm=matrix(1,nlstate*2,1,nlstate*2);
1.2 lievre 1569:
1570: fprintf(ficreseij,"# Health expectancies\n");
1571: fprintf(ficreseij,"# Age");
1572: for(i=1; i<=nlstate;i++)
1573: for(j=1; j<=nlstate;j++)
1.41 lievre 1574: fprintf(ficreseij," %1d-%1d (SE)",i,j);
1.2 lievre 1575: fprintf(ficreseij,"\n");
1576:
1.36 brouard 1577: if(estepm < stepm){
1578: printf ("Problem %d lower than %d\n",estepm, stepm);
1579: }
1580: else hstepm=estepm;
1581: /* We compute the life expectancy from trapezoids spaced every estepm months
1582: * This is mainly to measure the difference between two models: for example
1583: * if stepm=24 months pijx are given only every 2 years and by summing them
1584: * we are calculating an estimate of the Life Expectancy assuming a linear
1585: * progression inbetween and thus overestimating or underestimating according
1586: * to the curvature of the survival function. If, for the same date, we
1587: * estimate the model with stepm=1 month, we can keep estepm to 24 months
1588: * to compare the new estimate of Life expectancy with the same linear
1589: * hypothesis. A more precise result, taking into account a more precise
1590: * curvature will be obtained if estepm is as small as stepm. */
1591:
1592: /* For example we decided to compute the life expectancy with the smallest unit */
1.31 brouard 1593: /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
1594: nhstepm is the number of hstepm from age to agelim
1595: nstepm is the number of stepm from age to agelin.
1596: Look at hpijx to understand the reason of that which relies in memory size
1.36 brouard 1597: and note for a fixed period like estepm months */
1.31 brouard 1598: /* We decided (b) to get a life expectancy respecting the most precise curvature of the
1.32 brouard 1599: survival function given by stepm (the optimization length). Unfortunately it
1.31 brouard 1600: means that if the survival funtion is printed only each two years of age and if
1601: you sum them up and add 1 year (area under the trapezoids) you won't get the same
1602: results. So we changed our mind and took the option of the best precision.
1603: */
1.36 brouard 1604: hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
1.2 lievre 1605:
1606: agelim=AGESUP;
1607: for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
1608: /* nhstepm age range expressed in number of stepm */
1.31 brouard 1609: nstepm=(int) rint((agelim-age)*YEARM/stepm);
1610: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
1.33 brouard 1611: /* if (stepm >= YEARM) hstepm=1;*/
1.31 brouard 1612: nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
1.2 lievre 1613: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
1.41 lievre 1614: gradg=ma3x(0,nhstepm,1,npar,1,nlstate*2);
1615: gp=matrix(0,nhstepm,1,nlstate*2);
1616: gm=matrix(0,nhstepm,1,nlstate*2);
1617:
1.2 lievre 1618: /* Computed by stepm unit matrices, product of hstepm matrices, stored
1619: in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
1620: hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);
1.41 lievre 1621:
1622:
1623: hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
1624:
1625: /* Computing Variances of health expectancies */
1626:
1627: for(theta=1; theta <=npar; theta++){
1628: for(i=1; i<=npar; i++){
1629: xp[i] = x[i] + (i==theta ?delti[theta]:0);
1630: }
1631: hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
1.39 lievre 1632:
1.41 lievre 1633: cptj=0;
1634: for(j=1; j<= nlstate; j++){
1635: for(i=1; i<=nlstate; i++){
1636: cptj=cptj+1;
1637: for(h=0, gp[h][cptj]=0.; h<=nhstepm-1; h++){
1638: gp[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;
1639: }
1640: }
1641: }
1642:
1643:
1644: for(i=1; i<=npar; i++)
1645: xp[i] = x[i] - (i==theta ?delti[theta]:0);
1646: hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
1647:
1648: cptj=0;
1649: for(j=1; j<= nlstate; j++){
1650: for(i=1;i<=nlstate;i++){
1651: cptj=cptj+1;
1652: for(h=0, gm[h][cptj]=0.; h<=nhstepm-1; h++){
1653: gm[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;
1654: }
1655: }
1656: }
1657: for(j=1; j<= nlstate*2; j++)
1658: for(h=0; h<=nhstepm-1; h++){
1659: gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
1660: }
1661: }
1662:
1663: /* End theta */
1664:
1665: trgradg =ma3x(0,nhstepm,1,nlstate*2,1,npar);
1666:
1667: for(h=0; h<=nhstepm-1; h++)
1668: for(j=1; j<=nlstate*2;j++)
1669: for(theta=1; theta <=npar; theta++)
1.46 brouard 1670: trgradg[h][j][theta]=gradg[h][theta][j];
1671:
1.41 lievre 1672:
1673: for(i=1;i<=nlstate*2;i++)
1674: for(j=1;j<=nlstate*2;j++)
1675: varhe[i][j][(int)age] =0.;
1676:
1.43 brouard 1677: printf("%d|",(int)age);fflush(stdout);
1.46 brouard 1678: for(h=0;h<=nhstepm-1;h++){
1.41 lievre 1679: for(k=0;k<=nhstepm-1;k++){
1680: matprod2(dnewm,trgradg[h],1,nlstate*2,1,npar,1,npar,matcov);
1681: matprod2(doldm,dnewm,1,nlstate*2,1,npar,1,nlstate*2,gradg[k]);
1682: for(i=1;i<=nlstate*2;i++)
1683: for(j=1;j<=nlstate*2;j++)
1684: varhe[i][j][(int)age] += doldm[i][j]*hf*hf;
1685: }
1686: }
1687: /* Computing expectancies */
1.2 lievre 1688: for(i=1; i<=nlstate;i++)
1689: for(j=1; j<=nlstate;j++)
1.29 lievre 1690: for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
1.31 brouard 1691: eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
1.41 lievre 1692:
1693: /* 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]);*/
1694:
1.2 lievre 1695: }
1.41 lievre 1696:
1.29 lievre 1697: fprintf(ficreseij,"%3.0f",age );
1.41 lievre 1698: cptj=0;
1.29 lievre 1699: for(i=1; i<=nlstate;i++)
1700: for(j=1; j<=nlstate;j++){
1.41 lievre 1701: cptj++;
1702: fprintf(ficreseij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[cptj][cptj][(int)age]) );
1.2 lievre 1703: }
1704: fprintf(ficreseij,"\n");
1.41 lievre 1705:
1706: free_matrix(gm,0,nhstepm,1,nlstate*2);
1707: free_matrix(gp,0,nhstepm,1,nlstate*2);
1708: free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*2);
1709: free_ma3x(trgradg,0,nhstepm,1,nlstate*2,1,npar);
1.2 lievre 1710: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
1711: }
1.47 brouard 1712: printf("\n");
1713:
1.41 lievre 1714: free_vector(xp,1,npar);
1715: free_matrix(dnewm,1,nlstate*2,1,npar);
1716: free_matrix(doldm,1,nlstate*2,1,nlstate*2);
1717: free_ma3x(varhe,1,nlstate*2,1,nlstate*2,(int) bage, (int)fage);
1.2 lievre 1718: }
1719:
1720: /************ Variance ******************/
1.36 brouard 1721: void varevsij(char fileres[], 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)
1.2 lievre 1722: {
1723: /* Variance of health expectancies */
1724: /* double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
1725: double **newm;
1726: double **dnewm,**doldm;
1.36 brouard 1727: int i, j, nhstepm, hstepm, h, nstepm ;
1.2 lievre 1728: int k, cptcode;
1.12 lievre 1729: double *xp;
1.2 lievre 1730: double **gp, **gm;
1731: double ***gradg, ***trgradg;
1732: double ***p3mat;
1.35 lievre 1733: double age,agelim, hf;
1.2 lievre 1734: int theta;
1735:
1.43 brouard 1736: 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");
1.2 lievre 1737: fprintf(ficresvij,"# Age");
1738: for(i=1; i<=nlstate;i++)
1739: for(j=1; j<=nlstate;j++)
1740: fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);
1741: fprintf(ficresvij,"\n");
1742:
1743: xp=vector(1,npar);
1744: dnewm=matrix(1,nlstate,1,npar);
1745: doldm=matrix(1,nlstate,1,nlstate);
1746:
1.36 brouard 1747: if(estepm < stepm){
1748: printf ("Problem %d lower than %d\n",estepm, stepm);
1749: }
1750: else hstepm=estepm;
1751: /* For example we decided to compute the life expectancy with the smallest unit */
1.35 lievre 1752: /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
1753: nhstepm is the number of hstepm from age to agelim
1754: nstepm is the number of stepm from age to agelin.
1755: Look at hpijx to understand the reason of that which relies in memory size
1756: and note for a fixed period like k years */
1757: /* We decided (b) to get a life expectancy respecting the most precise curvature of the
1758: survival function given by stepm (the optimization length). Unfortunately it
1759: means that if the survival funtion is printed only each two years of age and if
1760: you sum them up and add 1 year (area under the trapezoids) you won't get the same
1761: results. So we changed our mind and took the option of the best precision.
1762: */
1.36 brouard 1763: hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
1.2 lievre 1764: agelim = AGESUP;
1765: for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
1.35 lievre 1766: nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
1767: nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
1.2 lievre 1768: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
1769: gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
1770: gp=matrix(0,nhstepm,1,nlstate);
1771: gm=matrix(0,nhstepm,1,nlstate);
1772:
1773: for(theta=1; theta <=npar; theta++){
1774: for(i=1; i<=npar; i++){ /* Computes gradient */
1775: xp[i] = x[i] + (i==theta ?delti[theta]:0);
1776: }
1777: hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
1778: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
1.14 lievre 1779:
1780: if (popbased==1) {
1781: for(i=1; i<=nlstate;i++)
1782: prlim[i][i]=probs[(int)age][i][ij];
1783: }
1.26 lievre 1784:
1.2 lievre 1785: for(j=1; j<= nlstate; j++){
1786: for(h=0; h<=nhstepm; h++){
1787: for(i=1, gp[h][j]=0.;i<=nlstate;i++)
1788: gp[h][j] += prlim[i][i]*p3mat[i][j][h];
1789: }
1790: }
1791:
1792: for(i=1; i<=npar; i++) /* Computes gradient */
1793: xp[i] = x[i] - (i==theta ?delti[theta]:0);
1794: hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
1795: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
1.26 lievre 1796:
1.14 lievre 1797: if (popbased==1) {
1798: for(i=1; i<=nlstate;i++)
1799: prlim[i][i]=probs[(int)age][i][ij];
1800: }
1801:
1.2 lievre 1802: for(j=1; j<= nlstate; j++){
1803: for(h=0; h<=nhstepm; h++){
1804: for(i=1, gm[h][j]=0.;i<=nlstate;i++)
1805: gm[h][j] += prlim[i][i]*p3mat[i][j][h];
1806: }
1807: }
1.14 lievre 1808:
1.2 lievre 1809: for(j=1; j<= nlstate; j++)
1810: for(h=0; h<=nhstepm; h++){
1811: gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
1812: }
1813: } /* End theta */
1814:
1815: trgradg =ma3x(0,nhstepm,1,nlstate,1,npar);
1816:
1817: for(h=0; h<=nhstepm; h++)
1818: for(j=1; j<=nlstate;j++)
1819: for(theta=1; theta <=npar; theta++)
1820: trgradg[h][j][theta]=gradg[h][theta][j];
1821:
1.35 lievre 1822: hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
1.2 lievre 1823: for(i=1;i<=nlstate;i++)
1824: for(j=1;j<=nlstate;j++)
1825: vareij[i][j][(int)age] =0.;
1.35 lievre 1826:
1.2 lievre 1827: for(h=0;h<=nhstepm;h++){
1828: for(k=0;k<=nhstepm;k++){
1829: matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
1830: matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
1831: for(i=1;i<=nlstate;i++)
1832: for(j=1;j<=nlstate;j++)
1.35 lievre 1833: vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
1.2 lievre 1834: }
1835: }
1.35 lievre 1836:
1.2 lievre 1837: fprintf(ficresvij,"%.0f ",age );
1838: for(i=1; i<=nlstate;i++)
1839: for(j=1; j<=nlstate;j++){
1.35 lievre 1840: fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
1.2 lievre 1841: }
1842: fprintf(ficresvij,"\n");
1843: free_matrix(gp,0,nhstepm,1,nlstate);
1844: free_matrix(gm,0,nhstepm,1,nlstate);
1845: free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
1846: free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
1847: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
1848: } /* End age */
1.26 lievre 1849:
1.2 lievre 1850: free_vector(xp,1,npar);
1851: free_matrix(doldm,1,nlstate,1,npar);
1852: free_matrix(dnewm,1,nlstate,1,nlstate);
1853:
1854: }
1855:
1856: /************ Variance of prevlim ******************/
1857: 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)
1858: {
1859: /* Variance of prevalence limit */
1860: /* double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
1861: double **newm;
1862: double **dnewm,**doldm;
1863: int i, j, nhstepm, hstepm;
1864: int k, cptcode;
1865: double *xp;
1866: double *gp, *gm;
1867: double **gradg, **trgradg;
1868: double age,agelim;
1869: int theta;
1870:
1.43 brouard 1871: fprintf(ficresvpl,"# Standard deviation of prevalence's limit\n");
1.2 lievre 1872: fprintf(ficresvpl,"# Age");
1873: for(i=1; i<=nlstate;i++)
1874: fprintf(ficresvpl," %1d-%1d",i,i);
1875: fprintf(ficresvpl,"\n");
1876:
1877: xp=vector(1,npar);
1878: dnewm=matrix(1,nlstate,1,npar);
1879: doldm=matrix(1,nlstate,1,nlstate);
1880:
1881: hstepm=1*YEARM; /* Every year of age */
1882: hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */
1883: agelim = AGESUP;
1884: for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
1885: nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
1886: if (stepm >= YEARM) hstepm=1;
1887: nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
1888: gradg=matrix(1,npar,1,nlstate);
1889: gp=vector(1,nlstate);
1890: gm=vector(1,nlstate);
1891:
1892: for(theta=1; theta <=npar; theta++){
1893: for(i=1; i<=npar; i++){ /* Computes gradient */
1894: xp[i] = x[i] + (i==theta ?delti[theta]:0);
1895: }
1896: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
1897: for(i=1;i<=nlstate;i++)
1898: gp[i] = prlim[i][i];
1899:
1900: for(i=1; i<=npar; i++) /* Computes gradient */
1901: xp[i] = x[i] - (i==theta ?delti[theta]:0);
1902: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
1903: for(i=1;i<=nlstate;i++)
1904: gm[i] = prlim[i][i];
1905:
1906: for(i=1;i<=nlstate;i++)
1907: gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
1908: } /* End theta */
1909:
1910: trgradg =matrix(1,nlstate,1,npar);
1911:
1912: for(j=1; j<=nlstate;j++)
1913: for(theta=1; theta <=npar; theta++)
1914: trgradg[j][theta]=gradg[theta][j];
1915:
1916: for(i=1;i<=nlstate;i++)
1917: varpl[i][(int)age] =0.;
1918: matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
1919: matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
1920: for(i=1;i<=nlstate;i++)
1921: varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
1922:
1923: fprintf(ficresvpl,"%.0f ",age );
1924: for(i=1; i<=nlstate;i++)
1925: fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
1926: fprintf(ficresvpl,"\n");
1927: free_vector(gp,1,nlstate);
1928: free_vector(gm,1,nlstate);
1929: free_matrix(gradg,1,npar,1,nlstate);
1930: free_matrix(trgradg,1,nlstate,1,npar);
1931: } /* End age */
1932:
1933: free_vector(xp,1,npar);
1934: free_matrix(doldm,1,nlstate,1,npar);
1935: free_matrix(dnewm,1,nlstate,1,nlstate);
1936:
1937: }
1938:
1.13 lievre 1939: /************ Variance of one-step probabilities ******************/
1.47 brouard 1940: void varprob(char optionfilefiname[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij, int *Tvar, int **nbcode, int *ncodemax)
1.13 lievre 1941: {
1.47 brouard 1942: int i, j, i1, k1, l1;
1943: int k2, l2, j1, z1;
1.46 brouard 1944: int k=0,l, cptcode;
1.47 brouard 1945: int first=1;
1946: double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2;
1.13 lievre 1947: double **dnewm,**doldm;
1948: double *xp;
1949: double *gp, *gm;
1950: double **gradg, **trgradg;
1.47 brouard 1951: double **mu;
1.13 lievre 1952: double age,agelim, cov[NCOVMAX];
1.47 brouard 1953: double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
1.13 lievre 1954: int theta;
1955: char fileresprob[FILENAMELENGTH];
1.46 brouard 1956: char fileresprobcov[FILENAMELENGTH];
1957: char fileresprobcor[FILENAMELENGTH];
1.13 lievre 1958:
1.47 brouard 1959: double ***varpij;
1960:
1.13 lievre 1961: strcpy(fileresprob,"prob");
1962: strcat(fileresprob,fileres);
1963: if((ficresprob=fopen(fileresprob,"w"))==NULL) {
1964: printf("Problem with resultfile: %s\n", fileresprob);
1965: }
1.46 brouard 1966: strcpy(fileresprobcov,"probcov");
1967: strcat(fileresprobcov,fileres);
1968: if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
1969: printf("Problem with resultfile: %s\n", fileresprobcov);
1970: }
1971: strcpy(fileresprobcor,"probcor");
1972: strcat(fileresprobcor,fileres);
1973: if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
1974: printf("Problem with resultfile: %s\n", fileresprobcor);
1975: }
1.41 lievre 1976: printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
1.46 brouard 1977: printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
1978: printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
1.13 lievre 1979:
1.46 brouard 1980: fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
1.41 lievre 1981: fprintf(ficresprob,"# Age");
1.46 brouard 1982: fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
1983: fprintf(ficresprobcov,"# Age");
1984: fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
1985: fprintf(ficresprobcov,"# Age");
1.47 brouard 1986:
1987:
1.41 lievre 1988: for(i=1; i<=nlstate;i++)
1.46 brouard 1989: for(j=1; j<=(nlstate+ndeath);j++){
1.41 lievre 1990: fprintf(ficresprob," p%1d-%1d (SE)",i,j);
1.46 brouard 1991: fprintf(ficresprobcov," p%1d-%1d ",i,j);
1992: fprintf(ficresprobcor," p%1d-%1d ",i,j);
1993: }
1.41 lievre 1994: fprintf(ficresprob,"\n");
1.46 brouard 1995: fprintf(ficresprobcov,"\n");
1996: fprintf(ficresprobcor,"\n");
1.13 lievre 1997: xp=vector(1,npar);
1.47 brouard 1998: dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
1999: doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
2000: mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
2001: varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
2002: first=1;
2003: if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {
2004: printf("Problem with gnuplot file: %s\n", optionfilegnuplot);
2005: exit(0);
2006: }
2007: else{
2008: fprintf(ficgp,"\n# Routine varprob");
2009: }
2010: if((fichtm=fopen(optionfilehtm,"a"))==NULL) {
2011: printf("Problem with html file: %s\n", optionfilehtm);
2012: exit(0);
2013: }
2014: else{
2015: fprintf(fichtm,"\n<H2> Computing matrix of variance-covariance of step probabilities</h2>\n");
2016: fprintf(fichtm,"\n<br> We 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");
2017: 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");
2018:
2019: }
1.13 lievre 2020: cov[1]=1;
1.39 lievre 2021: j=cptcoveff;
2022: if (cptcovn<1) {j=1;ncodemax[1]=1;}
2023: j1=0;
2024: for(k1=1; k1<=1;k1++){
2025: for(i1=1; i1<=ncodemax[k1];i1++){
2026: j1++;
2027:
2028: if (cptcovn>0) {
2029: fprintf(ficresprob, "\n#********** Variable ");
1.46 brouard 2030: fprintf(ficresprobcov, "\n#********** Variable ");
1.47 brouard 2031: fprintf(ficgp, "\n#********** Variable ");
2032: fprintf(fichtm, "\n<h4>********** Variable</h4>\n ");
1.46 brouard 2033: fprintf(ficresprobcor, "\n#********** Variable ");
1.39 lievre 2034: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
2035: fprintf(ficresprob, "**********\n#");
1.46 brouard 2036: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
2037: fprintf(ficresprobcov, "**********\n#");
2038: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
1.47 brouard 2039: fprintf(ficgp, "**********\n#");
2040: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, "# V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
2041: fprintf(ficgp, "**********\n#");
2042: for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
2043: fprintf(fichtm, "**********\n#");
1.39 lievre 2044: }
1.13 lievre 2045:
1.39 lievre 2046: for (age=bage; age<=fage; age ++){
2047: cov[2]=age;
2048: for (k=1; k<=cptcovn;k++) {
2049: cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];
1.13 lievre 2050: }
1.39 lievre 2051: for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
2052: for (k=1; k<=cptcovprod;k++)
2053: cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
2054:
1.47 brouard 2055: gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
2056: trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
2057: gp=vector(1,(nlstate)*(nlstate+ndeath));
2058: gm=vector(1,(nlstate)*(nlstate+ndeath));
1.39 lievre 2059:
2060: for(theta=1; theta <=npar; theta++){
2061: for(i=1; i<=npar; i++)
2062: xp[i] = x[i] + (i==theta ?delti[theta]:0);
2063:
2064: pmij(pmmij,cov,ncovmodel,xp,nlstate);
2065:
2066: k=0;
1.47 brouard 2067: for(i=1; i<= (nlstate); i++){
1.39 lievre 2068: for(j=1; j<=(nlstate+ndeath);j++){
2069: k=k+1;
2070: gp[k]=pmmij[i][j];
2071: }
2072: }
2073:
2074: for(i=1; i<=npar; i++)
2075: xp[i] = x[i] - (i==theta ?delti[theta]:0);
1.13 lievre 2076:
1.39 lievre 2077: pmij(pmmij,cov,ncovmodel,xp,nlstate);
2078: k=0;
1.47 brouard 2079: for(i=1; i<=(nlstate); i++){
1.39 lievre 2080: for(j=1; j<=(nlstate+ndeath);j++){
2081: k=k+1;
2082: gm[k]=pmmij[i][j];
2083: }
2084: }
2085:
1.47 brouard 2086: for(i=1; i<= (nlstate)*(nlstate+ndeath); i++)
1.39 lievre 2087: gradg[theta][i]=(gp[i]-gm[i])/2./delti[theta];
1.13 lievre 2088: }
2089:
1.47 brouard 2090: for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
1.39 lievre 2091: for(theta=1; theta <=npar; theta++)
2092: trgradg[j][theta]=gradg[theta][j];
2093:
1.47 brouard 2094: matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov);
2095: matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);
1.39 lievre 2096:
2097: pmij(pmmij,cov,ncovmodel,x,nlstate);
2098:
2099: k=0;
1.47 brouard 2100: for(i=1; i<=(nlstate); i++){
1.39 lievre 2101: for(j=1; j<=(nlstate+ndeath);j++){
2102: k=k+1;
1.47 brouard 2103: mu[k][(int) age]=pmmij[i][j];
1.39 lievre 2104: }
1.13 lievre 2105: }
1.47 brouard 2106: for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
2107: for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
2108: varpij[i][j][(int)age] = doldm[i][j];
2109:
1.46 brouard 2110: /*printf("\n%d ",(int)age);
1.47 brouard 2111: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
1.13 lievre 2112: printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
2113: }*/
2114:
1.39 lievre 2115: fprintf(ficresprob,"\n%d ",(int)age);
1.46 brouard 2116: fprintf(ficresprobcov,"\n%d ",(int)age);
2117: fprintf(ficresprobcor,"\n%d ",(int)age);
1.13 lievre 2118:
1.47 brouard 2119: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)
2120: fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));
1.46 brouard 2121: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
1.47 brouard 2122: fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);
2123: fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
1.46 brouard 2124: }
2125: i=0;
2126: for (k=1; k<=(nlstate);k++){
2127: for (l=1; l<=(nlstate+ndeath);l++){
2128: i=i++;
2129: fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
2130: fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
2131: for (j=1; j<=i;j++){
1.47 brouard 2132: fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);
2133: fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));
1.46 brouard 2134: }
2135: }
1.47 brouard 2136: }/* end of loop for state */
2137: } /* end of loop for age */
2138: /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
2139: for (k1=1; k1<=(nlstate);k1++){
2140: for (l1=1; l1<=(nlstate+ndeath);l1++){
2141: if(l1==k1) continue;
2142: i=(k1-1)*(nlstate+ndeath)+l1;
2143: for (k2=1; k2<=(nlstate);k2++){
2144: for (l2=1; l2<=(nlstate+ndeath);l2++){
2145: if(l2==k2) continue;
2146: j=(k2-1)*(nlstate+ndeath)+l2;
2147: if(j<=i) continue;
2148: for (age=bage; age<=fage; age ++){
2149: if ((int)age %5==0){
2150: v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;
2151: v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;
2152: cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;
2153: mu1=mu[i][(int) age]/stepm*YEARM ;
2154: mu2=mu[j][(int) age]/stepm*YEARM;
2155: /* Computing eigen value of matrix of covariance */
2156: lc1=(v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12));
2157: lc2=(v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12));
2158: printf("Var %.4e %.4e cov %.4e Eigen %.3e %.3e\n",v1,v2,cv12,lc1,lc2);
2159: /* Eigen vectors */
2160: v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
2161: v21=sqrt(1.-v11*v11);
2162: v12=-v21;
2163: v22=v11;
2164: /*printf(fignu*/
2165: /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */
2166: /* mu2+ v21*lc1*cost + v21*lc2*sin(t) */
2167: if(first==1){
2168: first=0;
2169: fprintf(ficgp,"\nset parametric;set nolabel");
2170: fprintf(ficgp,"\nset log y;set log x; set xlabel \"p%1d%1d (year-1)\";set ylabel \"p%1d%1d (year-1)\"",k2,l2,k1,l1);
2171: fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
2172: fprintf(fichtm,"\n<br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup> :<a href=\"varpijgr%s%1d%1d-%1d%1d.png\">varpijgr%s%1d%1d-%1d%1d.png</A>, ",k2,l2,k1,l1,optionfilefiname,k2,l2,k1,l1,optionfilefiname,k2,l2,k1,l1);
2173: fprintf(fichtm,"\n<br><img src=\"varpijgr%s%1d%1d-%1d%1d.png\">, ",optionfilefiname,k2,l2,k1,l1);
2174: fprintf(ficgp,"\nset out \"varpijgr%s%1d%1d-%1d%1d.png\"",optionfilefiname,k2,l2,k1,l1);
2175: fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu2,mu1);
2176: fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k2,l2,k1,l1);
2177: 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)) t \"%d\"",\
2178: mu2,std,v21,sqrt(lc1),v21,sqrt(lc2), \
2179: mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),(int) age);
2180: }else{
2181: first=0;
2182: fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k2,l2,k1,l1);
2183: fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu2,mu1);
2184: 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)) t \"%d\"",\
2185: mu2,std,v21,sqrt(lc1),v21,sqrt(lc2), \
2186: mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),(int) age);
2187: }/* if first */
2188: } /* age mod 5 */
2189: } /* end loop age */
2190: fprintf(ficgp,"\nset out \"varpijgr%s%1d%1d-%1d%1d.png\";replot;",optionfilefiname,k2,l2,k1,l1);
2191: first=1;
2192: } /*l12 */
2193: } /* k12 */
2194: } /*l1 */
2195: }/* k1 */
2196: } /* loop covariates */
2197: free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
1.13 lievre 2198: free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
2199: free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
1.47 brouard 2200: free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
1.13 lievre 2201: free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
2202: free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
1.39 lievre 2203: }
2204: free_vector(xp,1,npar);
2205: fclose(ficresprob);
1.46 brouard 2206: fclose(ficresprobcov);
2207: fclose(ficresprobcor);
1.47 brouard 2208: fclose(ficgp);
2209: fclose(fichtm);
1.13 lievre 2210: }
1.2 lievre 2211:
1.45 lievre 2212:
1.25 lievre 2213: /******************* Printing html file ***********/
1.35 lievre 2214: void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \
1.43 brouard 2215: int lastpass, int stepm, int weightopt, char model[],\
1.47 brouard 2216: int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
2217: int popforecast, int estepm ,\
1.43 brouard 2218: double jprev1, double mprev1,double anprev1, \
2219: double jprev2, double mprev2,double anprev2){
1.25 lievre 2220: int jj1, k1, i1, cpt;
2221: /*char optionfilehtm[FILENAMELENGTH];*/
1.47 brouard 2222: if((fichtm=fopen(optionfilehtm,"a"))==NULL) {
1.25 lievre 2223: printf("Problem with %s \n",optionfilehtm), exit(0);
2224: }
2225:
1.43 brouard 2226: fprintf(fichtm,"<ul><li>Result files (first order: no variance)<br>\n
2227: - Observed prevalence in each state (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"p%s\">p%s</a> <br>\n
2228: - Estimated transition probabilities over %d (stepm) months: <a href=\"pij%s\">pij%s</a><br>\n
2229: - Stable prevalence in each health state: <a href=\"pl%s\">pl%s</a> <br>\n
2230: - Life expectancies by age and initial health status (estepm=%2d months):
2231: <a href=\"e%s\">e%s</a> <br>\n</li>", \
2232: jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,fileres,fileres,stepm,fileres,fileres,fileres,fileres,estepm,fileres,fileres);
2233:
2234: fprintf(fichtm,"\n<li> Result files (second order: variances)<br>\n
2235: - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n
2236: - Variance of one-step probabilities: <a href=\"prob%s\">prob%s</a> <br>\n
1.46 brouard 2237: - Variance-covariance of one-step probabilities: <a href=\"probcov%s\">probcov%s</a> <br>\n
2238: - Correlation matrix of one-step probabilities: <a href=\"probcor%s\">probcor%s</a> <br>\n
1.43 brouard 2239: - Variances and covariances of life expectancies by age and initial health status (estepm=%d months): <a href=\"v%s\">v%s</a><br>\n
2240: - Health expectancies with their variances (no covariance): <a href=\"t%s\">t%s</a> <br>\n
1.46 brouard 2241: - Standard deviation of stable prevalences: <a href=\"vpl%s\">vpl%s</a> <br>\n",rfileres,rfileres,fileres,fileres,fileres,fileres,fileres,fileres, estepm, fileres,fileres,fileres,fileres,fileres,fileres);
1.35 lievre 2242:
2243: if(popforecast==1) fprintf(fichtm,"\n
2244: - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n
2245: - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n
2246: <br>",fileres,fileres,fileres,fileres);
2247: else
2248: 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);
1.25 lievre 2249: fprintf(fichtm," <li>Graphs</li><p>");
2250:
2251: m=cptcoveff;
2252: if (cptcovn < 1) {m=1;ncodemax[1]=1;}
2253:
2254: jj1=0;
2255: for(k1=1; k1<=m;k1++){
2256: for(i1=1; i1<=ncodemax[k1];i1++){
1.45 lievre 2257: jj1++;
2258: if (cptcovn > 0) {
2259: fprintf(fichtm,"<hr size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
2260: for (cpt=1; cpt<=cptcoveff;cpt++)
2261: fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
2262: fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
2263: }
2264: /* Pij */
2265: fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months before: pe%s%d1.png<br>
2266: <img src=\"pe%s%d1.png\">",stepm,strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);
2267: /* Quasi-incidences */
2268: fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months before but expressed in per year i.e. quasi incidences if stepm is small and probabilities too: pe%s%d2.png<br>
2269: <img src=\"pe%s%d2.png\">",stepm,strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);
1.43 brouard 2270: /* Stable prevalence in each health state */
1.25 lievre 2271: for(cpt=1; cpt<nlstate;cpt++){
1.43 brouard 2272: fprintf(fichtm,"<br>- Stable prevalence in each health state : p%s%d%d.png<br>
1.42 brouard 2273: <img src=\"p%s%d%d.png\">",strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);
1.25 lievre 2274: }
2275: for(cpt=1; cpt<=nlstate;cpt++) {
2276: fprintf(fichtm,"<br>- Observed and stationary prevalence (with confident
1.42 brouard 2277: interval) in state (%d): v%s%d%d.png <br>
2278: <img src=\"v%s%d%d.png\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);
1.25 lievre 2279: }
2280: for(cpt=1; cpt<=nlstate;cpt++) {
1.42 brouard 2281: fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): exp%s%d%d.png <br>
2282: <img src=\"exp%s%d%d.png\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);
1.25 lievre 2283: }
2284: fprintf(fichtm,"\n<br>- Total life expectancy by age and
1.42 brouard 2285: health expectancies in states (1) and (2): e%s%d.png<br>
2286: <img src=\"e%s%d.png\">",strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);
1.25 lievre 2287: }
1.45 lievre 2288: }
1.25 lievre 2289: fclose(fichtm);
2290: }
2291:
2292: /******************* Gnuplot file **************/
1.47 brouard 2293: void printinggnuplot(char fileres[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
1.25 lievre 2294:
2295: int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;
1.43 brouard 2296: int ng;
1.47 brouard 2297: if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {
1.25 lievre 2298: printf("Problem with file %s",optionfilegnuplot);
2299: }
2300:
2301: #ifdef windows
2302: fprintf(ficgp,"cd \"%s\" \n",pathc);
2303: #endif
2304: m=pow(2,cptcoveff);
2305:
2306: /* 1eme*/
2307: for (cpt=1; cpt<= nlstate ; cpt ++) {
2308: for (k1=1; k1<= m ; k1 ++) {
2309:
2310: #ifdef windows
1.43 brouard 2311: fprintf(ficgp,"\nset out \"v%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);
1.42 brouard 2312: fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] \"vpl%s\" every :::%d::%d u 1:2 \"\%%lf",ageminpar,fage,fileres,k1-1,k1-1);
1.25 lievre 2313: #endif
2314: #ifdef unix
1.43 brouard 2315: fprintf(ficgp,"\nset out \"v%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);
1.35 lievre 2316: fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nplot [%.f:%.f] \"vpl%s\" u 1:2 \"\%%lf",ageminpar,fage,fileres);
1.25 lievre 2317: #endif
2318:
2319: for (i=1; i<= nlstate ; i ++) {
2320: if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
2321: else fprintf(ficgp," \%%*lf (\%%*lf)");
2322: }
2323: fprintf(ficgp,"\" t\"Stationary prevalence\" w l 0,\"vpl%s\" every :::%d::%d u 1:($2+2*$3) \"\%%lf",fileres,k1-1,k1-1);
2324: for (i=1; i<= nlstate ; i ++) {
2325: if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
2326: else fprintf(ficgp," \%%*lf (\%%*lf)");
2327: }
2328: fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"vpl%s\" every :::%d::%d u 1:($2-2*$3) \"\%%lf",fileres,k1-1,k1-1);
2329: for (i=1; i<= nlstate ; i ++) {
2330: if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
2331: else fprintf(ficgp," \%%*lf (\%%*lf)");
2332: }
2333: fprintf(ficgp,"\" t\"\" w l 1,\"p%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",fileres,k1-1,k1-1,2+4*(cpt-1));
2334: #ifdef unix
1.42 brouard 2335: fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65\n");
1.25 lievre 2336: #endif
2337: }
2338: }
2339: /*2 eme*/
2340:
2341: for (k1=1; k1<= m ; k1 ++) {
1.43 brouard 2342: fprintf(ficgp,"\nset out \"e%s%d.png\" \n",strtok(optionfile, "."),k1);
1.42 brouard 2343: fprintf(ficgp,"set ylabel \"Years\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] ",ageminpar,fage);
1.25 lievre 2344:
2345: for (i=1; i<= nlstate+1 ; i ++) {
2346: k=2*i;
2347: fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:2 \"\%%lf",fileres,k1-1,k1-1);
2348: for (j=1; j<= nlstate+1 ; j ++) {
2349: if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
2350: else fprintf(ficgp," \%%*lf (\%%*lf)");
2351: }
2352: if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");
2353: else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);
2354: fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",fileres,k1-1,k1-1);
2355: for (j=1; j<= nlstate+1 ; j ++) {
2356: if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
2357: else fprintf(ficgp," \%%*lf (\%%*lf)");
2358: }
2359: fprintf(ficgp,"\" t\"\" w l 0,");
2360: fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",fileres,k1-1,k1-1);
2361: for (j=1; j<= nlstate+1 ; j ++) {
2362: if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
2363: else fprintf(ficgp," \%%*lf (\%%*lf)");
2364: }
2365: if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");
2366: else fprintf(ficgp,"\" t\"\" w l 0,");
2367: }
2368: }
2369:
2370: /*3eme*/
2371:
2372: for (k1=1; k1<= m ; k1 ++) {
2373: for (cpt=1; cpt<= nlstate ; cpt ++) {
1.41 lievre 2374: k=2+nlstate*(2*cpt-2);
1.43 brouard 2375: fprintf(ficgp,"\nset out \"exp%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);
1.42 brouard 2376: fprintf(ficgp,"set ter png small\nset size 0.65,0.65\nplot [%.f:%.f] \"e%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,fileres,k1-1,k1-1,k,cpt);
1.41 lievre 2377: /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
2378: for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
2379: fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
2380: fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
2381: for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
2382: fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
2383:
2384: */
1.25 lievre 2385: for (i=1; i< nlstate ; i ++) {
1.41 lievre 2386: fprintf(ficgp," ,\"e%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",fileres,k1-1,k1-1,k+2*i,cpt,i+1);
2387:
1.25 lievre 2388: }
2389: }
1.42 brouard 2390: }
1.25 lievre 2391:
2392: /* CV preval stat */
2393: for (k1=1; k1<= m ; k1 ++) {
2394: for (cpt=1; cpt<nlstate ; cpt ++) {
2395: k=3;
1.43 brouard 2396: fprintf(ficgp,"\nset out \"p%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);
1.42 brouard 2397: fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] \"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",ageminpar,agemaxpar,fileres,k1,k+cpt+1,k+1);
1.25 lievre 2398:
2399: for (i=1; i< nlstate ; i ++)
2400: fprintf(ficgp,"+$%d",k+i+1);
2401: fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);
2402:
2403: l=3+(nlstate+ndeath)*cpt;
2404: fprintf(ficgp,",\"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",fileres,k1,l+cpt+1,l+1);
2405: for (i=1; i< nlstate ; i ++) {
2406: l=3+(nlstate+ndeath)*cpt;
2407: fprintf(ficgp,"+$%d",l+i+1);
2408: }
2409: fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);
2410: }
2411: }
2412:
2413: /* proba elementaires */
2414: for(i=1,jk=1; i <=nlstate; i++){
2415: for(k=1; k <=(nlstate+ndeath); k++){
2416: if (k != i) {
2417: for(j=1; j <=ncovmodel; j++){
2418:
2419: fprintf(ficgp,"p%d=%f ",jk,p[jk]);
2420: jk++;
2421: fprintf(ficgp,"\n");
2422: }
2423: }
2424: }
1.42 brouard 2425: }
1.25 lievre 2426:
1.43 brouard 2427: for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/
2428: for(jk=1; jk <=m; jk++) {
2429: fprintf(ficgp,"\nset out \"pe%s%d%d.png\" \n",strtok(optionfile, "."),jk,ng);
2430: if (ng==2)
2431: fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
2432: else
2433: fprintf(ficgp,"\nset title \"Probability\"\n");
2434: fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65\nset log y\nplot [%.f:%.f] ",ageminpar,agemaxpar);
2435: i=1;
2436: for(k2=1; k2<=nlstate; k2++) {
2437: k3=i;
2438: for(k=1; k<=(nlstate+ndeath); k++) {
2439: if (k != k2){
2440: if(ng==2)
1.46 brouard 2441: fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);
1.42 brouard 2442: else
1.43 brouard 2443: fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
1.42 brouard 2444: ij=1;
1.43 brouard 2445: for(j=3; j <=ncovmodel; j++) {
1.42 brouard 2446: if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
1.43 brouard 2447: fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
1.42 brouard 2448: ij++;
2449: }
2450: else
1.43 brouard 2451: fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
1.42 brouard 2452: }
1.43 brouard 2453: fprintf(ficgp,")/(1");
2454:
2455: for(k1=1; k1 <=nlstate; k1++){
2456: fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);
2457: ij=1;
2458: for(j=3; j <=ncovmodel; j++){
2459: if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
2460: fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
2461: ij++;
2462: }
2463: else
2464: fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
2465: }
2466: fprintf(ficgp,")");
2467: }
2468: fprintf(ficgp,") t \"p%d%d\" ", k2,k);
2469: if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");
2470: i=i+ncovmodel;
1.42 brouard 2471: }
2472: }
1.25 lievre 2473: }
2474: }
2475: }
1.47 brouard 2476: fclose(ficgp);
1.25 lievre 2477: } /* end gnuplot */
2478:
2479:
2480: /*************** Moving average **************/
1.35 lievre 2481: void movingaverage(double agedeb, double fage,double ageminpar, double ***mobaverage){
1.25 lievre 2482:
2483: int i, cpt, cptcod;
1.35 lievre 2484: for (agedeb=ageminpar; agedeb<=fage; agedeb++)
1.25 lievre 2485: for (i=1; i<=nlstate;i++)
2486: for (cptcod=1;cptcod<=ncodemax[cptcov];cptcod++)
2487: mobaverage[(int)agedeb][i][cptcod]=0.;
2488:
1.35 lievre 2489: for (agedeb=ageminpar+4; agedeb<=fage; agedeb++){
1.25 lievre 2490: for (i=1; i<=nlstate;i++){
2491: for (cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
2492: for (cpt=0;cpt<=4;cpt++){
2493: mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]+probs[(int)agedeb-cpt][i][cptcod];
2494: }
2495: mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]/5;
2496: }
2497: }
2498: }
2499:
2500: }
2501:
1.27 lievre 2502:
2503: /************** Forecasting ******************/
1.35 lievre 2504: prevforecast(char fileres[], double anproj1,double mproj1,double jproj1,double ageminpar, double agemax,double dateprev1, double dateprev2, int mobilav, double agedeb, double fage, int popforecast, char popfile[], double anproj2,double p[], int i2){
1.27 lievre 2505:
2506: int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;
2507: int *popage;
2508: double calagedate, agelim, kk1, kk2, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
2509: double *popeffectif,*popcount;
2510: double ***p3mat;
2511: char fileresf[FILENAMELENGTH];
2512:
2513: agelim=AGESUP;
2514: calagedate=(anproj1+mproj1/12.+jproj1/365.-dateintmean)*YEARM;
1.28 lievre 2515:
1.35 lievre 2516: prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);
1.28 lievre 2517:
1.27 lievre 2518:
2519: strcpy(fileresf,"f");
2520: strcat(fileresf,fileres);
2521: if((ficresf=fopen(fileresf,"w"))==NULL) {
2522: printf("Problem with forecast resultfile: %s\n", fileresf);
2523: }
2524: printf("Computing forecasting: result on file '%s' \n", fileresf);
2525:
2526: if (cptcoveff==0) ncodemax[cptcoveff]=1;
2527:
2528: if (mobilav==1) {
2529: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
1.35 lievre 2530: movingaverage(agedeb, fage, ageminpar, mobaverage);
1.27 lievre 2531: }
2532:
2533: stepsize=(int) (stepm+YEARM-1)/YEARM;
2534: if (stepm<=12) stepsize=1;
2535:
2536: agelim=AGESUP;
2537:
2538: hstepm=1;
2539: hstepm=hstepm/stepm;
2540: yp1=modf(dateintmean,&yp);
2541: anprojmean=yp;
2542: yp2=modf((yp1*12),&yp);
2543: mprojmean=yp;
2544: yp1=modf((yp2*30.5),&yp);
2545: jprojmean=yp;
2546: if(jprojmean==0) jprojmean=1;
2547: if(mprojmean==0) jprojmean=1;
2548:
2549: fprintf(ficresf,"# Estimated date of observed prevalence: %.lf/%.lf/%.lf ",jprojmean,mprojmean,anprojmean);
2550:
2551: for(cptcov=1;cptcov<=i2;cptcov++){
2552: for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
2553: k=k+1;
2554: fprintf(ficresf,"\n#******");
2555: for(j=1;j<=cptcoveff;j++) {
2556: fprintf(ficresf," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
2557: }
2558: fprintf(ficresf,"******\n");
2559: fprintf(ficresf,"# StartingAge FinalAge");
2560: for(j=1; j<=nlstate+ndeath;j++) fprintf(ficresf," P.%d",j);
2561:
2562:
2563: for (cpt=0; cpt<=(anproj2-anproj1);cpt++) {
2564: fprintf(ficresf,"\n");
2565: fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+cpt);
1.28 lievre 2566:
1.35 lievre 2567: for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){
1.27 lievre 2568: nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);
2569: nhstepm = nhstepm/hstepm;
2570:
2571: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
2572: oldm=oldms;savm=savms;
2573: hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
2574:
2575: for (h=0; h<=nhstepm; h++){
2576: if (h==(int) (calagedate+YEARM*cpt)) {
1.35 lievre 2577: fprintf(ficresf,"\n %.f %.f ",anproj1+cpt,agedeb+h*hstepm/YEARM*stepm);
1.27 lievre 2578: }
2579: for(j=1; j<=nlstate+ndeath;j++) {
2580: kk1=0.;kk2=0;
2581: for(i=1; i<=nlstate;i++) {
2582: if (mobilav==1)
2583: kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];
2584: else {
2585: kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];
2586: }
2587:
2588: }
2589: if (h==(int)(calagedate+12*cpt)){
2590: fprintf(ficresf," %.3f", kk1);
2591:
2592: }
2593: }
2594: }
2595: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
2596: }
2597: }
2598: }
2599: }
2600:
2601: if (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
2602:
2603: fclose(ficresf);
2604: }
2605: /************** Forecasting ******************/
1.35 lievre 2606: 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){
1.27 lievre 2607:
2608: int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;
2609: int *popage;
2610: double calagedate, agelim, kk1, kk2, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
2611: double *popeffectif,*popcount;
2612: double ***p3mat,***tabpop,***tabpopprev;
2613: char filerespop[FILENAMELENGTH];
2614:
1.28 lievre 2615: tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
2616: tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
2617: agelim=AGESUP;
2618: calagedate=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;
1.27 lievre 2619:
1.35 lievre 2620: prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);
1.28 lievre 2621:
2622:
1.27 lievre 2623: strcpy(filerespop,"pop");
2624: strcat(filerespop,fileres);
2625: if((ficrespop=fopen(filerespop,"w"))==NULL) {
2626: printf("Problem with forecast resultfile: %s\n", filerespop);
2627: }
2628: printf("Computing forecasting: result on file '%s' \n", filerespop);
2629:
2630: if (cptcoveff==0) ncodemax[cptcoveff]=1;
2631:
2632: if (mobilav==1) {
2633: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
1.35 lievre 2634: movingaverage(agedeb, fage, ageminpar, mobaverage);
1.27 lievre 2635: }
2636:
2637: stepsize=(int) (stepm+YEARM-1)/YEARM;
2638: if (stepm<=12) stepsize=1;
2639:
2640: agelim=AGESUP;
2641:
2642: hstepm=1;
2643: hstepm=hstepm/stepm;
2644:
2645: if (popforecast==1) {
2646: if((ficpop=fopen(popfile,"r"))==NULL) {
2647: printf("Problem with population file : %s\n",popfile);exit(0);
2648: }
2649: popage=ivector(0,AGESUP);
2650: popeffectif=vector(0,AGESUP);
2651: popcount=vector(0,AGESUP);
2652:
2653: i=1;
2654: while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;
2655:
2656: imx=i;
2657: for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];
2658: }
2659:
2660: for(cptcov=1;cptcov<=i2;cptcov++){
2661: for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
2662: k=k+1;
2663: fprintf(ficrespop,"\n#******");
2664: for(j=1;j<=cptcoveff;j++) {
2665: fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
2666: }
2667: fprintf(ficrespop,"******\n");
1.28 lievre 2668: fprintf(ficrespop,"# Age");
1.27 lievre 2669: for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);
2670: if (popforecast==1) fprintf(ficrespop," [Population]");
2671:
2672: for (cpt=0; cpt<=0;cpt++) {
1.28 lievre 2673: fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);
1.27 lievre 2674:
1.35 lievre 2675: for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){
1.27 lievre 2676: nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);
2677: nhstepm = nhstepm/hstepm;
2678:
2679: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
2680: oldm=oldms;savm=savms;
2681: hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
2682:
2683: for (h=0; h<=nhstepm; h++){
2684: if (h==(int) (calagedate+YEARM*cpt)) {
1.28 lievre 2685: fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
1.27 lievre 2686: }
2687: for(j=1; j<=nlstate+ndeath;j++) {
2688: kk1=0.;kk2=0;
2689: for(i=1; i<=nlstate;i++) {
2690: if (mobilav==1)
2691: kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];
2692: else {
2693: kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];
2694: }
2695: }
2696: if (h==(int)(calagedate+12*cpt)){
2697: tabpop[(int)(agedeb)][j][cptcod]=kk1;
2698: /*fprintf(ficrespop," %.3f", kk1);
2699: if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/
2700: }
2701: }
2702: for(i=1; i<=nlstate;i++){
2703: kk1=0.;
2704: for(j=1; j<=nlstate;j++){
1.28 lievre 2705: kk1= kk1+tabpop[(int)(agedeb)][j][cptcod];
1.27 lievre 2706: }
2707: tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedate+12*cpt)*hstepm/YEARM*stepm-1)];
2708: }
2709:
1.28 lievre 2710: if (h==(int)(calagedate+12*cpt)) for(j=1; j<=nlstate;j++)
2711: fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);
1.27 lievre 2712: }
2713: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
2714: }
2715: }
2716:
2717: /******/
2718:
1.28 lievre 2719: for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) {
2720: fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);
1.35 lievre 2721: for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){
1.27 lievre 2722: nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);
2723: nhstepm = nhstepm/hstepm;
2724:
2725: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
2726: oldm=oldms;savm=savms;
2727: hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
2728: for (h=0; h<=nhstepm; h++){
2729: if (h==(int) (calagedate+YEARM*cpt)) {
1.28 lievre 2730: fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
1.27 lievre 2731: }
2732: for(j=1; j<=nlstate+ndeath;j++) {
2733: kk1=0.;kk2=0;
2734: for(i=1; i<=nlstate;i++) {
2735: kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];
2736: }
1.28 lievre 2737: if (h==(int)(calagedate+12*cpt)) fprintf(ficresf," %15.2f", kk1);
1.27 lievre 2738: }
2739: }
2740: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
2741: }
2742: }
2743: }
2744: }
2745:
2746: if (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
2747:
2748: if (popforecast==1) {
2749: free_ivector(popage,0,AGESUP);
2750: free_vector(popeffectif,0,AGESUP);
2751: free_vector(popcount,0,AGESUP);
2752: }
2753: free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
2754: free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
2755: fclose(ficrespop);
2756: }
2757:
1.2 lievre 2758: /***********************************************/
2759: /**************** Main Program *****************/
2760: /***********************************************/
2761:
1.22 brouard 2762: int main(int argc, char *argv[])
1.2 lievre 2763: {
2764:
1.8 lievre 2765: int i,j, k, n=MAXN,iter,m,size,cptcode, cptcod;
1.2 lievre 2766: double agedeb, agefin,hf;
1.35 lievre 2767: double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;
1.2 lievre 2768:
2769: double fret;
2770: double **xi,tmp,delta;
2771:
2772: double dum; /* Dummy variable */
2773: double ***p3mat;
2774: int *indx;
2775: char line[MAXLINE], linepar[MAXLINE];
2776: char path[80],pathc[80],pathcd[80],pathtot[80],model[20];
2777: int firstobs=1, lastobs=10;
2778: int sdeb, sfin; /* Status at beginning and end */
2779: int c, h , cpt,l;
2780: int ju,jl, mi;
1.7 lievre 2781: int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;
1.14 lievre 2782: int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,**adl,*tab;
1.19 lievre 2783: int mobilav=0,popforecast=0;
1.2 lievre 2784: int hstepm, nhstepm;
1.41 lievre 2785: double jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,jpyram, mpyram,anpyram,jpyram1, mpyram1,anpyram1, calagedate;
1.14 lievre 2786:
1.2 lievre 2787: double bage, fage, age, agelim, agebase;
2788: double ftolpl=FTOL;
2789: double **prlim;
2790: double *severity;
2791: double ***param; /* Matrix of parameters */
2792: double *p;
2793: double **matcov; /* Matrix of covariance */
2794: double ***delti3; /* Scale */
2795: double *delti; /* Scale */
2796: double ***eij, ***vareij;
2797: double **varpl; /* Variances of prevalence limits by age */
2798: double *epj, vepp;
1.16 lievre 2799: double kk1, kk2;
1.27 lievre 2800: double dateprev1, dateprev2,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2;
2801:
1.13 lievre 2802:
1.2 lievre 2803: char *alph[]={"a","a","b","c","d","e"}, str[4];
1.5 lievre 2804:
1.13 lievre 2805:
1.2 lievre 2806: char z[1]="c", occ;
2807: #include <sys/time.h>
2808: #include <time.h>
2809: char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];
1.19 lievre 2810:
1.2 lievre 2811: /* long total_usecs;
2812: struct timeval start_time, end_time;
2813:
2814: gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */
1.35 lievre 2815: getcwd(pathcd, size);
1.2 lievre 2816:
1.22 brouard 2817: printf("\n%s",version);
2818: if(argc <=1){
2819: printf("\nEnter the parameter file name: ");
2820: scanf("%s",pathtot);
2821: }
2822: else{
2823: strcpy(pathtot,argv[1]);
2824: }
2825: /*if(getcwd(pathcd, 80)!= NULL)printf ("Error pathcd\n");*/
1.5 lievre 2826: /*cygwin_split_path(pathtot,path,optionfile);
2827: printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/
2828: /* cutv(path,optionfile,pathtot,'\\');*/
2829:
1.22 brouard 2830: split(pathtot,path,optionfile,optionfilext,optionfilefiname);
2831: printf("pathtot=%s, path=%s, optionfile=%s optionfilext=%s optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
1.2 lievre 2832: chdir(path);
2833: replace(pathc,path);
2834:
2835: /*-------- arguments in the command line --------*/
2836:
2837: strcpy(fileres,"r");
1.22 brouard 2838: strcat(fileres, optionfilefiname);
2839: strcat(fileres,".txt"); /* Other files have txt extension */
1.2 lievre 2840:
2841: /*---------arguments file --------*/
2842:
2843: if((ficpar=fopen(optionfile,"r"))==NULL) {
2844: printf("Problem with optionfile %s\n",optionfile);
2845: goto end;
2846: }
2847:
2848: strcpy(filereso,"o");
2849: strcat(filereso,fileres);
2850: if((ficparo=fopen(filereso,"w"))==NULL) {
2851: printf("Problem with Output resultfile: %s\n", filereso);goto end;
2852: }
2853:
2854: /* Reads comments: lines beginning with '#' */
2855: while((c=getc(ficpar))=='#' && c!= EOF){
2856: ungetc(c,ficpar);
2857: fgets(line, MAXLINE, ficpar);
2858: puts(line);
2859: fputs(line,ficparo);
2860: }
2861: ungetc(c,ficpar);
2862:
1.34 brouard 2863: 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\nmodel=%s\n",title, datafile, &lastobs, &firstpass,&lastpass,&ftol, &stepm, &ncovcol, &nlstate,&ndeath, &maxwav, &mle, &weightopt,model);
2864: 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);
2865: 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);
1.14 lievre 2866: while((c=getc(ficpar))=='#' && c!= EOF){
2867: ungetc(c,ficpar);
2868: fgets(line, MAXLINE, ficpar);
2869: puts(line);
2870: fputs(line,ficparo);
2871: }
2872: ungetc(c,ficpar);
2873:
1.19 lievre 2874:
1.8 lievre 2875: covar=matrix(0,NCOVMAX,1,n);
2876: cptcovn=0;
2877: if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;
1.2 lievre 2878:
2879: ncovmodel=2+cptcovn;
2880: nvar=ncovmodel-1; /* Suppressing age as a basic covariate */
2881:
2882: /* Read guess parameters */
2883: /* Reads comments: lines beginning with '#' */
2884: while((c=getc(ficpar))=='#' && c!= EOF){
2885: ungetc(c,ficpar);
2886: fgets(line, MAXLINE, ficpar);
2887: puts(line);
2888: fputs(line,ficparo);
2889: }
2890: ungetc(c,ficpar);
2891:
2892: param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
2893: for(i=1; i <=nlstate; i++)
2894: for(j=1; j <=nlstate+ndeath-1; j++){
2895: fscanf(ficpar,"%1d%1d",&i1,&j1);
2896: fprintf(ficparo,"%1d%1d",i1,j1);
2897: printf("%1d%1d",i,j);
2898: for(k=1; k<=ncovmodel;k++){
2899: fscanf(ficpar," %lf",¶m[i][j][k]);
2900: printf(" %lf",param[i][j][k]);
2901: fprintf(ficparo," %lf",param[i][j][k]);
2902: }
2903: fscanf(ficpar,"\n");
2904: printf("\n");
2905: fprintf(ficparo,"\n");
2906: }
2907:
1.12 lievre 2908: npar= (nlstate+ndeath-1)*nlstate*ncovmodel;
2909:
1.2 lievre 2910: p=param[1][1];
2911:
2912: /* Reads comments: lines beginning with '#' */
2913: while((c=getc(ficpar))=='#' && c!= EOF){
2914: ungetc(c,ficpar);
2915: fgets(line, MAXLINE, ficpar);
2916: puts(line);
2917: fputs(line,ficparo);
2918: }
2919: ungetc(c,ficpar);
2920:
2921: delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
2922: delti=vector(1,npar); /* Scale of each paramater (output from hesscov) */
2923: for(i=1; i <=nlstate; i++){
2924: for(j=1; j <=nlstate+ndeath-1; j++){
2925: fscanf(ficpar,"%1d%1d",&i1,&j1);
2926: printf("%1d%1d",i,j);
2927: fprintf(ficparo,"%1d%1d",i1,j1);
2928: for(k=1; k<=ncovmodel;k++){
2929: fscanf(ficpar,"%le",&delti3[i][j][k]);
2930: printf(" %le",delti3[i][j][k]);
2931: fprintf(ficparo," %le",delti3[i][j][k]);
2932: }
2933: fscanf(ficpar,"\n");
2934: printf("\n");
2935: fprintf(ficparo,"\n");
2936: }
2937: }
2938: delti=delti3[1][1];
2939:
2940: /* Reads comments: lines beginning with '#' */
2941: while((c=getc(ficpar))=='#' && c!= EOF){
2942: ungetc(c,ficpar);
2943: fgets(line, MAXLINE, ficpar);
2944: puts(line);
2945: fputs(line,ficparo);
2946: }
2947: ungetc(c,ficpar);
2948:
2949: matcov=matrix(1,npar,1,npar);
2950: for(i=1; i <=npar; i++){
2951: fscanf(ficpar,"%s",&str);
2952: printf("%s",str);
2953: fprintf(ficparo,"%s",str);
2954: for(j=1; j <=i; j++){
2955: fscanf(ficpar," %le",&matcov[i][j]);
2956: printf(" %.5le",matcov[i][j]);
2957: fprintf(ficparo," %.5le",matcov[i][j]);
2958: }
2959: fscanf(ficpar,"\n");
2960: printf("\n");
2961: fprintf(ficparo,"\n");
2962: }
2963: for(i=1; i <=npar; i++)
2964: for(j=i+1;j<=npar;j++)
2965: matcov[i][j]=matcov[j][i];
2966:
2967: printf("\n");
2968:
2969:
1.29 lievre 2970: /*-------- Rewriting paramater file ----------*/
2971: strcpy(rfileres,"r"); /* "Rparameterfile */
2972: strcat(rfileres,optionfilefiname); /* Parameter file first name*/
2973: strcat(rfileres,"."); /* */
2974: strcat(rfileres,optionfilext); /* Other files have txt extension */
2975: if((ficres =fopen(rfileres,"w"))==NULL) {
2976: printf("Problem writing new parameter file: %s\n", fileres);goto end;
1.2 lievre 2977: }
2978: fprintf(ficres,"#%s\n",version);
2979:
1.29 lievre 2980: /*-------- data file ----------*/
1.2 lievre 2981: if((fic=fopen(datafile,"r"))==NULL) {
2982: printf("Problem with datafile: %s\n", datafile);goto end;
2983: }
2984:
2985: n= lastobs;
2986: severity = vector(1,maxwav);
2987: outcome=imatrix(1,maxwav+1,1,n);
2988: num=ivector(1,n);
2989: moisnais=vector(1,n);
2990: annais=vector(1,n);
2991: moisdc=vector(1,n);
2992: andc=vector(1,n);
2993: agedc=vector(1,n);
2994: cod=ivector(1,n);
2995: weight=vector(1,n);
2996: for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */
2997: mint=matrix(1,maxwav,1,n);
2998: anint=matrix(1,maxwav,1,n);
2999: s=imatrix(1,maxwav+1,1,n);
3000: adl=imatrix(1,maxwav+1,1,n);
3001: tab=ivector(1,NCOVMAX);
1.3 lievre 3002: ncodemax=ivector(1,8);
1.2 lievre 3003:
1.12 lievre 3004: i=1;
1.2 lievre 3005: while (fgets(line, MAXLINE, fic) != NULL) {
3006: if ((i >= firstobs) && (i <=lastobs)) {
3007:
3008: for (j=maxwav;j>=1;j--){
3009: cutv(stra, strb,line,' '); s[j][i]=atoi(strb);
3010: strcpy(line,stra);
3011: cutv(stra, strb,line,'/'); anint[j][i]=(double)(atoi(strb)); strcpy(line,stra);
3012: cutv(stra, strb,line,' '); mint[j][i]=(double)(atoi(strb)); strcpy(line,stra);
3013: }
3014:
3015: cutv(stra, strb,line,'/'); andc[i]=(double)(atoi(strb)); strcpy(line,stra);
3016: cutv(stra, strb,line,' '); moisdc[i]=(double)(atoi(strb)); strcpy(line,stra);
3017:
3018: cutv(stra, strb,line,'/'); annais[i]=(double)(atoi(strb)); strcpy(line,stra);
3019: cutv(stra, strb,line,' '); moisnais[i]=(double)(atoi(strb)); strcpy(line,stra);
3020:
3021: cutv(stra, strb,line,' '); weight[i]=(double)(atoi(strb)); strcpy(line,stra);
1.34 brouard 3022: for (j=ncovcol;j>=1;j--){
1.2 lievre 3023: cutv(stra, strb,line,' '); covar[j][i]=(double)(atoi(strb)); strcpy(line,stra);
3024: }
3025: num[i]=atol(stra);
1.12 lievre 3026:
3027: /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){
3028: printf("%d %.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;}*/
1.2 lievre 3029:
3030: i=i+1;
3031: }
3032: }
1.12 lievre 3033: /* printf("ii=%d", ij);
3034: scanf("%d",i);*/
3035: imx=i-1; /* Number of individuals */
1.3 lievre 3036:
1.12 lievre 3037: /* for (i=1; i<=imx; i++){
3038: if ((s[1][i]==3) && (s[2][i]==2)) s[2][i]=3;
3039: if ((s[2][i]==3) && (s[3][i]==2)) s[3][i]=3;
3040: if ((s[3][i]==3) && (s[4][i]==2)) s[4][i]=3;
1.35 lievre 3041: }*/
1.39 lievre 3042: /* for (i=1; i<=imx; i++){
1.35 lievre 3043: if (s[4][i]==9) s[4][i]=-1;
1.39 lievre 3044: printf("%d %.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]));}*/
3045:
1.35 lievre 3046:
1.2 lievre 3047: /* Calculation of the number of parameter from char model*/
1.7 lievre 3048: Tvar=ivector(1,15);
3049: Tprod=ivector(1,15);
3050: Tvaraff=ivector(1,15);
3051: Tvard=imatrix(1,15,1,2);
1.6 lievre 3052: Tage=ivector(1,15);
1.2 lievre 3053:
3054: if (strlen(model) >1){
1.7 lievre 3055: j=0, j1=0, k1=1, k2=1;
1.2 lievre 3056: j=nbocc(model,'+');
1.6 lievre 3057: j1=nbocc(model,'*');
1.2 lievre 3058: cptcovn=j+1;
1.7 lievre 3059: cptcovprod=j1;
1.3 lievre 3060:
1.2 lievre 3061: strcpy(modelsav,model);
1.8 lievre 3062: if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){
3063: printf("Error. Non available option model=%s ",model);
3064: goto end;
3065: }
3066:
3067: for(i=(j+1); i>=1;i--){
3068: cutv(stra,strb,modelsav,'+');
3069: if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav);
3070: /* printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/
3071: /*scanf("%d",i);*/
3072: if (strchr(strb,'*')) {
3073: cutv(strd,strc,strb,'*');
3074: if (strcmp(strc,"age")==0) {
1.7 lievre 3075: cptcovprod--;
1.8 lievre 3076: cutv(strb,stre,strd,'V');
3077: Tvar[i]=atoi(stre);
3078: cptcovage++;
3079: Tage[cptcovage]=i;
3080: /*printf("stre=%s ", stre);*/
1.7 lievre 3081: }
1.8 lievre 3082: else if (strcmp(strd,"age")==0) {
1.7 lievre 3083: cptcovprod--;
1.8 lievre 3084: cutv(strb,stre,strc,'V');
3085: Tvar[i]=atoi(stre);
3086: cptcovage++;
3087: Tage[cptcovage]=i;
1.7 lievre 3088: }
3089: else {
1.8 lievre 3090: cutv(strb,stre,strc,'V');
1.34 brouard 3091: Tvar[i]=ncovcol+k1;
1.8 lievre 3092: cutv(strb,strc,strd,'V');
3093: Tprod[k1]=i;
3094: Tvard[k1][1]=atoi(strc);
3095: Tvard[k1][2]=atoi(stre);
3096: Tvar[cptcovn+k2]=Tvard[k1][1];
3097: Tvar[cptcovn+k2+1]=Tvard[k1][2];
1.7 lievre 3098: for (k=1; k<=lastobs;k++)
1.34 brouard 3099: covar[ncovcol+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];
1.8 lievre 3100: k1++;
3101: k2=k2+2;
1.7 lievre 3102: }
1.2 lievre 3103: }
1.8 lievre 3104: else {
3105: /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/
3106: /* scanf("%d",i);*/
3107: cutv(strd,strc,strb,'V');
3108: Tvar[i]=atoi(strc);
3109: }
3110: strcpy(modelsav,stra);
3111: /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);
3112: scanf("%d",i);*/
1.2 lievre 3113: }
1.8 lievre 3114: }
3115:
1.35 lievre 3116: /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);
1.8 lievre 3117: printf("cptcovprod=%d ", cptcovprod);
3118: scanf("%d ",i);*/
1.2 lievre 3119: fclose(fic);
3120:
1.7 lievre 3121: /* if(mle==1){*/
1.2 lievre 3122: if (weightopt != 1) { /* Maximisation without weights*/
3123: for(i=1;i<=n;i++) weight[i]=1.0;
3124: }
3125: /*-calculation of age at interview from date of interview and age at death -*/
3126: agev=matrix(1,maxwav,1,imx);
1.12 lievre 3127:
1.35 lievre 3128: for (i=1; i<=imx; i++) {
3129: for(m=2; (m<= maxwav); m++) {
1.12 lievre 3130: if ((mint[m][i]== 99) && (s[m][i] <= nlstate)){
3131: anint[m][i]=9999;
3132: s[m][i]=-1;
3133: }
1.35 lievre 3134: if(moisdc[i]==99 && andc[i]==9999 & s[m][i]>nlstate) s[m][i]=-1;
3135: }
3136: }
3137:
1.2 lievre 3138: for (i=1; i<=imx; i++) {
3139: agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);
3140: for(m=1; (m<= maxwav); m++){
3141: if(s[m][i] >0){
1.35 lievre 3142: if (s[m][i] >= nlstate+1) {
1.2 lievre 3143: if(agedc[i]>0)
3144: if(moisdc[i]!=99 && andc[i]!=9999)
1.35 lievre 3145: agev[m][i]=agedc[i];
3146: /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/
3147: else {
1.8 lievre 3148: if (andc[i]!=9999){
1.2 lievre 3149: printf("Warning negative age at death: %d line:%d\n",num[i],i);
3150: agev[m][i]=-1;
1.8 lievre 3151: }
1.2 lievre 3152: }
3153: }
3154: else if(s[m][i] !=9){ /* Should no more exist */
3155: agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);
1.3 lievre 3156: if(mint[m][i]==99 || anint[m][i]==9999)
1.2 lievre 3157: agev[m][i]=1;
3158: else if(agev[m][i] <agemin){
3159: agemin=agev[m][i];
3160: /*printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], agemin);*/
3161: }
3162: else if(agev[m][i] >agemax){
3163: agemax=agev[m][i];
3164: /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/
3165: }
3166: /*agev[m][i]=anint[m][i]-annais[i];*/
3167: /* agev[m][i] = age[i]+2*m;*/
3168: }
3169: else { /* =9 */
3170: agev[m][i]=1;
3171: s[m][i]=-1;
3172: }
3173: }
3174: else /*= 0 Unknown */
3175: agev[m][i]=1;
3176: }
3177:
3178: }
3179: for (i=1; i<=imx; i++) {
3180: for(m=1; (m<= maxwav); m++){
3181: if (s[m][i] > (nlstate+ndeath)) {
3182: printf("Error: Wrong value in nlstate or ndeath\n");
3183: goto end;
3184: }
3185: }
3186: }
3187:
3188: printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);
3189:
3190: free_vector(severity,1,maxwav);
3191: free_imatrix(outcome,1,maxwav+1,1,n);
3192: free_vector(moisnais,1,n);
3193: free_vector(annais,1,n);
1.17 lievre 3194: /* free_matrix(mint,1,maxwav,1,n);
3195: free_matrix(anint,1,maxwav,1,n);*/
1.2 lievre 3196: free_vector(moisdc,1,n);
3197: free_vector(andc,1,n);
3198:
3199:
3200: wav=ivector(1,imx);
3201: dh=imatrix(1,lastpass-firstpass+1,1,imx);
3202: mw=imatrix(1,lastpass-firstpass+1,1,imx);
3203:
3204: /* Concatenates waves */
3205: concatwav(wav, dh, mw, s, agedc, agev, firstpass, lastpass, imx, nlstate, stepm);
3206:
3207:
1.6 lievre 3208: Tcode=ivector(1,100);
1.8 lievre 3209: nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);
1.7 lievre 3210: ncodemax[1]=1;
3211: if (cptcovn > 0) tricode(Tvar,nbcode,imx);
3212:
1.2 lievre 3213: codtab=imatrix(1,100,1,10);
3214: h=0;
1.7 lievre 3215: m=pow(2,cptcoveff);
1.2 lievre 3216:
1.7 lievre 3217: for(k=1;k<=cptcoveff; k++){
1.2 lievre 3218: for(i=1; i <=(m/pow(2,k));i++){
3219: for(j=1; j <= ncodemax[k]; j++){
1.7 lievre 3220: for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){
1.2 lievre 3221: h++;
1.35 lievre 3222: if (h>m) h=1;codtab[h][k]=j;codtab[h][Tvar[k]]=j;
3223: /* printf("h=%d k=%d j=%d codtab[h][k]=%d tvar[k]=%d \n",h, k,j,codtab[h][k],Tvar[k]);*/
1.2 lievre 3224: }
3225: }
3226: }
3227: }
1.35 lievre 3228: /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]);
3229: codtab[1][2]=1;codtab[2][2]=2; */
3230: /* for(i=1; i <=m ;i++){
3231: for(k=1; k <=cptcovn; k++){
3232: printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);
3233: }
3234: printf("\n");
3235: }
3236: scanf("%d",i);*/
1.2 lievre 3237:
3238: /* Calculates basic frequencies. Computes observed prevalence at single age
3239: and prints on file fileres'p'. */
1.18 lievre 3240:
1.19 lievre 3241:
1.18 lievre 3242:
1.19 lievre 3243: pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
1.2 lievre 3244: oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
3245: newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
3246: savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
3247: oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */
1.12 lievre 3248:
1.2 lievre 3249: /* For Powell, parameters are in a vector p[] starting at p[1]
3250: so we point p on param[1][1] so that p[1] maps on param[1][1][1] */
3251: p=param[1][1]; /* *(*(*(param +1)+1)+0) */
1.7 lievre 3252:
3253: if(mle==1){
1.2 lievre 3254: mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);
1.7 lievre 3255: }
1.2 lievre 3256:
3257: /*--------- results files --------------*/
1.34 brouard 3258: 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);
1.19 lievre 3259:
1.16 lievre 3260:
1.2 lievre 3261: jk=1;
1.34 brouard 3262: fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
3263: printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
1.2 lievre 3264: for(i=1,jk=1; i <=nlstate; i++){
3265: for(k=1; k <=(nlstate+ndeath); k++){
3266: if (k != i)
3267: {
3268: printf("%d%d ",i,k);
3269: fprintf(ficres,"%1d%1d ",i,k);
3270: for(j=1; j <=ncovmodel; j++){
3271: printf("%f ",p[jk]);
3272: fprintf(ficres,"%f ",p[jk]);
3273: jk++;
3274: }
3275: printf("\n");
3276: fprintf(ficres,"\n");
3277: }
3278: }
3279: }
1.7 lievre 3280: if(mle==1){
1.2 lievre 3281: /* Computing hessian and covariance matrix */
3282: ftolhess=ftol; /* Usually correct */
3283: hesscov(matcov, p, npar, delti, ftolhess, func);
1.7 lievre 3284: }
1.34 brouard 3285: fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");
3286: printf("# Scales (for hessian or gradient estimation)\n");
1.2 lievre 3287: for(i=1,jk=1; i <=nlstate; i++){
3288: for(j=1; j <=nlstate+ndeath; j++){
3289: if (j!=i) {
3290: fprintf(ficres,"%1d%1d",i,j);
3291: printf("%1d%1d",i,j);
3292: for(k=1; k<=ncovmodel;k++){
3293: printf(" %.5e",delti[jk]);
3294: fprintf(ficres," %.5e",delti[jk]);
3295: jk++;
3296: }
3297: printf("\n");
3298: fprintf(ficres,"\n");
3299: }
3300: }
1.18 lievre 3301: }
1.2 lievre 3302:
3303: k=1;
1.34 brouard 3304: 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");
3305: 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");
1.2 lievre 3306: for(i=1;i<=npar;i++){
3307: /* if (k>nlstate) k=1;
3308: i1=(i-1)/(ncovmodel*nlstate)+1;
3309: fprintf(ficres,"%s%d%d",alph[k],i1,tab[i]);
3310: printf("%s%d%d",alph[k],i1,tab[i]);*/
3311: fprintf(ficres,"%3d",i);
3312: printf("%3d",i);
3313: for(j=1; j<=i;j++){
3314: fprintf(ficres," %.5e",matcov[i][j]);
3315: printf(" %.5e",matcov[i][j]);
3316: }
3317: fprintf(ficres,"\n");
3318: printf("\n");
3319: k++;
3320: }
3321:
3322: while((c=getc(ficpar))=='#' && c!= EOF){
3323: ungetc(c,ficpar);
3324: fgets(line, MAXLINE, ficpar);
3325: puts(line);
3326: fputs(line,ficparo);
3327: }
3328: ungetc(c,ficpar);
1.36 brouard 3329: estepm=0;
3330: fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm);
3331: if (estepm==0 || estepm < stepm) estepm=stepm;
1.2 lievre 3332: if (fage <= 2) {
1.35 lievre 3333: bage = ageminpar;
1.28 lievre 3334: fage = agemaxpar;
1.2 lievre 3335: }
1.22 brouard 3336:
3337: fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");
1.36 brouard 3338: fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
3339: fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
1.19 lievre 3340:
3341: while((c=getc(ficpar))=='#' && c!= EOF){
3342: ungetc(c,ficpar);
3343: fgets(line, MAXLINE, ficpar);
3344: puts(line);
3345: fputs(line,ficparo);
3346: }
3347: ungetc(c,ficpar);
3348:
1.25 lievre 3349: fscanf(ficpar,"begin-prev-date=%lf/%lf/%lf end-prev-date=%lf/%lf/%lf\n",&jprev1, &mprev1,&anprev1,&jprev2, &mprev2,&anprev2);
3350: fprintf(ficparo,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);
3351: fprintf(ficres,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);
1.19 lievre 3352:
3353: while((c=getc(ficpar))=='#' && c!= EOF){
3354: ungetc(c,ficpar);
3355: fgets(line, MAXLINE, ficpar);
3356: puts(line);
3357: fputs(line,ficparo);
3358: }
3359: ungetc(c,ficpar);
3360:
1.7 lievre 3361:
1.19 lievre 3362: dateprev1=anprev1+mprev1/12.+jprev1/365.;
3363: dateprev2=anprev2+mprev2/12.+jprev2/365.;
3364:
3365: fscanf(ficpar,"pop_based=%d\n",&popbased);
1.28 lievre 3366: fprintf(ficparo,"pop_based=%d\n",popbased);
3367: fprintf(ficres,"pop_based=%d\n",popbased);
3368:
3369: while((c=getc(ficpar))=='#' && c!= EOF){
3370: ungetc(c,ficpar);
3371: fgets(line, MAXLINE, ficpar);
3372: puts(line);
3373: fputs(line,ficparo);
3374: }
3375: ungetc(c,ficpar);
1.19 lievre 3376:
1.28 lievre 3377: fscanf(ficpar,"starting-proj-date=%lf/%lf/%lf final-proj-date=%lf/%lf/%lf mov_average=%d\n",&jproj1,&mproj1,&anproj1,&jproj2,&mproj2,&anproj2,&mobilav);
3378: fprintf(ficparo,"starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mov_average=%d\n",jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilav);
3379: fprintf(ficres,"starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mov_average=%d\n",jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilav);
3380:
3381:
3382: while((c=getc(ficpar))=='#' && c!= EOF){
1.19 lievre 3383: ungetc(c,ficpar);
3384: fgets(line, MAXLINE, ficpar);
3385: puts(line);
3386: fputs(line,ficparo);
3387: }
3388: ungetc(c,ficpar);
1.28 lievre 3389:
3390: fscanf(ficpar,"popforecast=%d popfile=%s popfiledate=%lf/%lf/%lf last-popfiledate=%lf/%lf/%lf\n",&popforecast,popfile,&jpyram,&mpyram,&anpyram,&jpyram1,&mpyram1,&anpyram1);
3391: fprintf(ficparo,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);
3392: fprintf(ficres,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);
1.19 lievre 3393:
1.26 lievre 3394: freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);
1.19 lievre 3395:
1.25 lievre 3396: /*------------ gnuplot -------------*/
1.47 brouard 3397: strcpy(optionfilegnuplot,optionfilefiname);
3398: strcat(optionfilegnuplot,".gp");
3399: if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {
3400: printf("Problem with file %s",optionfilegnuplot);
3401: }
3402: fclose(ficgp);
3403: printinggnuplot(fileres, ageminpar,agemaxpar,fage, pathc,p);
3404: /*--------- index.htm --------*/
3405:
3406: strcpy(optionfilehtm,optionfile);
3407: strcat(optionfilehtm,".htm");
3408: if((fichtm=fopen(optionfilehtm,"w"))==NULL) {
3409: printf("Problem with %s \n",optionfilehtm), exit(0);
3410: }
3411:
3412: fprintf(fichtm,"<body> <font size=\"2\">%s </font> <hr size=\"2\" color=\"#EC5E5E\"> \n
3413: Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n
3414: \n
3415: Total number of observations=%d <br>\n
3416: Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n
3417: <hr size=\"2\" color=\"#EC5E5E\">
3418: <ul><li>Parameter files<br>\n
3419: - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n
3420: - Gnuplot file name: <a href=\"%s\">%s</a><br></ul>\n",version,title,datafile,firstpass,lastpass,stepm, weightopt,model,imx,jmin,jmax,jmean,fileres,fileres,optionfilegnuplot,optionfilegnuplot);
3421: fclose(fichtm);
3422:
3423: printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,model,imx,jmin,jmax,jmean,rfileres,popforecast,estepm,jprev1,mprev1,anprev1,jprev2,mprev2,anprev2);
1.25 lievre 3424:
3425: /*------------ free_vector -------------*/
3426: chdir(path);
1.2 lievre 3427:
1.25 lievre 3428: free_ivector(wav,1,imx);
3429: free_imatrix(dh,1,lastpass-firstpass+1,1,imx);
3430: free_imatrix(mw,1,lastpass-firstpass+1,1,imx);
3431: free_ivector(num,1,n);
3432: free_vector(agedc,1,n);
3433: /*free_matrix(covar,1,NCOVMAX,1,n);*/
3434: fclose(ficparo);
3435: fclose(ficres);
1.28 lievre 3436:
1.2 lievre 3437:
3438: /*--------------- Prevalence limit --------------*/
3439:
3440: strcpy(filerespl,"pl");
3441: strcat(filerespl,fileres);
3442: if((ficrespl=fopen(filerespl,"w"))==NULL) {
3443: printf("Problem with Prev limit resultfile: %s\n", filerespl);goto end;
3444: }
3445: printf("Computing prevalence limit: result on file '%s' \n", filerespl);
3446: fprintf(ficrespl,"#Prevalence limit\n");
3447: fprintf(ficrespl,"#Age ");
3448: for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);
3449: fprintf(ficrespl,"\n");
3450:
3451: prlim=matrix(1,nlstate,1,nlstate);
3452: pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
3453: oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
3454: newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
3455: savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
3456: oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */
3457: k=0;
1.35 lievre 3458: agebase=ageminpar;
1.28 lievre 3459: agelim=agemaxpar;
1.2 lievre 3460: ftolpl=1.e-10;
1.7 lievre 3461: i1=cptcoveff;
1.2 lievre 3462: if (cptcovn < 1){i1=1;}
3463:
3464: for(cptcov=1;cptcov<=i1;cptcov++){
3465: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
3466: k=k+1;
3467: /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/
1.6 lievre 3468: fprintf(ficrespl,"\n#******");
1.7 lievre 3469: for(j=1;j<=cptcoveff;j++)
3470: fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
1.2 lievre 3471: fprintf(ficrespl,"******\n");
3472:
3473: for (age=agebase; age<=agelim; age++){
3474: prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
3475: fprintf(ficrespl,"%.0f",age );
3476: for(i=1; i<=nlstate;i++)
3477: fprintf(ficrespl," %.5f", prlim[i][i]);
3478: fprintf(ficrespl,"\n");
3479: }
3480: }
3481: }
3482: fclose(ficrespl);
1.13 lievre 3483:
1.2 lievre 3484: /*------------- h Pij x at various ages ------------*/
3485:
3486: strcpy(filerespij,"pij"); strcat(filerespij,fileres);
3487: if((ficrespij=fopen(filerespij,"w"))==NULL) {
3488: printf("Problem with Pij resultfile: %s\n", filerespij);goto end;
3489: }
3490: printf("Computing pij: result on file '%s' \n", filerespij);
3491:
3492: stepsize=(int) (stepm+YEARM-1)/YEARM;
1.13 lievre 3493: /*if (stepm<=24) stepsize=2;*/
1.2 lievre 3494:
3495: agelim=AGESUP;
3496: hstepm=stepsize*YEARM; /* Every year of age */
3497: hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */
3498:
3499: k=0;
3500: for(cptcov=1;cptcov<=i1;cptcov++){
3501: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
3502: k=k+1;
3503: fprintf(ficrespij,"\n#****** ");
1.7 lievre 3504: for(j=1;j<=cptcoveff;j++)
3505: fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
1.2 lievre 3506: fprintf(ficrespij,"******\n");
3507:
3508: for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */
3509: nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
3510: nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
3511: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3512: oldm=oldms;savm=savms;
3513: hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
3514: fprintf(ficrespij,"# Age");
3515: for(i=1; i<=nlstate;i++)
3516: for(j=1; j<=nlstate+ndeath;j++)
3517: fprintf(ficrespij," %1d-%1d",i,j);
3518: fprintf(ficrespij,"\n");
1.40 lievre 3519: for (h=0; h<=nhstepm; h++){
1.2 lievre 3520: fprintf(ficrespij,"%d %.0f %.0f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );
3521: for(i=1; i<=nlstate;i++)
3522: for(j=1; j<=nlstate+ndeath;j++)
3523: fprintf(ficrespij," %.5f", p3mat[i][j][h]);
3524: fprintf(ficrespij,"\n");
1.40 lievre 3525: }
1.2 lievre 3526: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3527: fprintf(ficrespij,"\n");
3528: }
3529: }
3530: }
3531:
1.47 brouard 3532: varprob(optionfilefiname, matcov, p, delti, nlstate, (int) bage, (int) fage,k,Tvar,nbcode, ncodemax);
1.13 lievre 3533:
1.2 lievre 3534: fclose(ficrespij);
3535:
1.27 lievre 3536:
3537: /*---------- Forecasting ------------------*/
1.32 brouard 3538: if((stepm == 1) && (strcmp(model,".")==0)){
1.27 lievre 3539: prevforecast(fileres, anproj1,mproj1,jproj1, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anproj2,p, i1);
1.32 brouard 3540: if (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);
1.41 lievre 3541: }
1.21 lievre 3542: else{
3543: erreur=108;
1.32 brouard 3544: 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);
1.21 lievre 3545: }
1.26 lievre 3546:
1.27 lievre 3547:
1.2 lievre 3548: /*---------- Health expectancies and variances ------------*/
3549:
3550: strcpy(filerest,"t");
3551: strcat(filerest,fileres);
3552: if((ficrest=fopen(filerest,"w"))==NULL) {
3553: printf("Problem with total LE resultfile: %s\n", filerest);goto end;
3554: }
3555: printf("Computing Total LEs with variances: file '%s' \n", filerest);
3556:
3557:
3558: strcpy(filerese,"e");
3559: strcat(filerese,fileres);
3560: if((ficreseij=fopen(filerese,"w"))==NULL) {
3561: printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
3562: }
3563: printf("Computing Health Expectancies: result on file '%s' \n", filerese);
3564:
3565: strcpy(fileresv,"v");
3566: strcat(fileresv,fileres);
3567: if((ficresvij=fopen(fileresv,"w"))==NULL) {
3568: printf("Problem with variance resultfile: %s\n", fileresv);exit(0);
3569: }
3570: printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
1.41 lievre 3571: calagedate=-1;
3572: prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);
1.2 lievre 3573:
3574: k=0;
3575: for(cptcov=1;cptcov<=i1;cptcov++){
3576: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
3577: k=k+1;
3578: fprintf(ficrest,"\n#****** ");
1.7 lievre 3579: for(j=1;j<=cptcoveff;j++)
3580: fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
1.2 lievre 3581: fprintf(ficrest,"******\n");
3582:
3583: fprintf(ficreseij,"\n#****** ");
1.7 lievre 3584: for(j=1;j<=cptcoveff;j++)
1.35 lievre 3585: fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
1.2 lievre 3586: fprintf(ficreseij,"******\n");
3587:
3588: fprintf(ficresvij,"\n#****** ");
1.7 lievre 3589: for(j=1;j<=cptcoveff;j++)
1.35 lievre 3590: fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
1.2 lievre 3591: fprintf(ficresvij,"******\n");
3592:
3593: eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
3594: oldm=oldms;savm=savms;
1.41 lievre 3595: evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov);
3596:
1.2 lievre 3597: vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
3598: oldm=oldms;savm=savms;
1.36 brouard 3599: varevsij(fileres, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm);
1.26 lievre 3600:
3601:
3602:
1.2 lievre 3603: fprintf(ficrest,"#Total LEs with variances: e.. (std) ");
3604: for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);
3605: fprintf(ficrest,"\n");
1.26 lievre 3606:
1.2 lievre 3607: epj=vector(1,nlstate+1);
3608: for(age=bage; age <=fage ;age++){
3609: prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
1.14 lievre 3610: if (popbased==1) {
3611: for(i=1; i<=nlstate;i++)
3612: prlim[i][i]=probs[(int)age][i][k];
3613: }
3614:
1.33 brouard 3615: fprintf(ficrest," %4.0f",age);
1.2 lievre 3616: for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){
3617: for(i=1, epj[j]=0.;i <=nlstate;i++) {
1.33 brouard 3618: epj[j] += prlim[i][i]*eij[i][j][(int)age];
1.41 lievre 3619: /* printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/
1.2 lievre 3620: }
3621: epj[nlstate+1] +=epj[j];
3622: }
1.41 lievre 3623:
1.2 lievre 3624: for(i=1, vepp=0.;i <=nlstate;i++)
3625: for(j=1;j <=nlstate;j++)
3626: vepp += vareij[i][j][(int)age];
1.38 lievre 3627: fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));
1.2 lievre 3628: for(j=1;j <=nlstate;j++){
1.38 lievre 3629: fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));
1.2 lievre 3630: }
3631: fprintf(ficrest,"\n");
3632: }
3633: }
3634: }
1.41 lievre 3635: free_matrix(mint,1,maxwav,1,n);
3636: free_matrix(anint,1,maxwav,1,n); free_imatrix(s,1,maxwav+1,1,n);
3637: free_vector(weight,1,n);
1.27 lievre 3638: fclose(ficreseij);
3639: fclose(ficresvij);
1.2 lievre 3640: fclose(ficrest);
3641: fclose(ficpar);
3642: free_vector(epj,1,nlstate+1);
1.26 lievre 3643:
1.2 lievre 3644: /*------- Variance limit prevalence------*/
3645:
1.27 lievre 3646: strcpy(fileresvpl,"vpl");
1.2 lievre 3647: strcat(fileresvpl,fileres);
3648: if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {
3649: printf("Problem with variance prev lim resultfile: %s\n", fileresvpl);
3650: exit(0);
3651: }
3652: printf("Computing Variance-covariance of Prevalence limit: file '%s' \n", fileresvpl);
3653:
1.27 lievre 3654: k=0;
3655: for(cptcov=1;cptcov<=i1;cptcov++){
3656: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
3657: k=k+1;
3658: fprintf(ficresvpl,"\n#****** ");
3659: for(j=1;j<=cptcoveff;j++)
3660: fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
3661: fprintf(ficresvpl,"******\n");
3662:
3663: varpl=matrix(1,nlstate,(int) bage, (int) fage);
3664: oldm=oldms;savm=savms;
1.2 lievre 3665: varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);
1.27 lievre 3666: }
1.2 lievre 3667: }
3668:
3669: fclose(ficresvpl);
3670:
3671: /*---------- End : free ----------------*/
3672: free_matrix(varpl,1,nlstate,(int) bage, (int)fage);
3673:
3674: free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);
3675: free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
3676:
3677:
3678: free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);
3679: free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);
3680: free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);
3681: free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);
1.13 lievre 3682:
1.2 lievre 3683: free_matrix(matcov,1,npar,1,npar);
3684: free_vector(delti,1,npar);
1.26 lievre 3685: free_matrix(agev,1,maxwav,1,imx);
1.2 lievre 3686: free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
1.47 brouard 3687:
3688: fprintf(fichtm,"\n</body>");
3689: fclose(fichtm);
3690: fclose(ficgp);
3691:
1.2 lievre 3692:
1.21 lievre 3693: if(erreur >0)
1.34 brouard 3694: printf("End of Imach with error or warning %d\n",erreur);
1.21 lievre 3695: else printf("End of Imach\n");
1.2 lievre 3696: /* gettimeofday(&end_time, (struct timezone*)0);*/ /* after time */
3697:
3698: /* 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);*/
3699: /*printf("Total time was %d uSec.\n", total_usecs);*/
3700: /*------ End -----------*/
1.12 lievre 3701:
1.2 lievre 3702:
3703: end:
3704: #ifdef windows
1.22 brouard 3705: /* chdir(pathcd);*/
1.2 lievre 3706: #endif
1.22 brouard 3707: /*system("wgnuplot graph.plt");*/
3708: /*system("../gp37mgw/wgnuplot graph.plt");*/
3709: /*system("cd ../gp37mgw");*/
3710: /* system("..\\gp37mgw\\wgnuplot graph.plt");*/
3711: strcpy(plotcmd,GNUPLOTPROGRAM);
3712: strcat(plotcmd," ");
3713: strcat(plotcmd,optionfilegnuplot);
3714: system(plotcmd);
1.2 lievre 3715:
3716: #ifdef windows
3717: while (z[0] != 'q') {
1.35 lievre 3718: /* chdir(path); */
3719: printf("\nType e to edit output files, g to graph again, c to start again, and q for exiting: ");
1.2 lievre 3720: scanf("%s",z);
3721: if (z[0] == 'c') system("./imach");
1.35 lievre 3722: else if (z[0] == 'e') system(optionfilehtm);
3723: else if (z[0] == 'g') system(plotcmd);
1.2 lievre 3724: else if (z[0] == 'q') exit(0);
3725: }
3726: #endif
3727: }
3728:
3729:
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