Annotation of imach096d/src/imach.c, revision 1.52
1.52 ! brouard 1: /* $Id: imach.c,v 1.51 2002/07/19 12:22:25 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 '\\'
1.50 brouard 80: #define ODIRSEPARATOR '/'
1.47 brouard 81: #else
82: #define DIRSEPARATOR '/'
1.50 brouard 83: #define ODIRSEPARATOR '\\'
1.47 brouard 84: #endif
1.2 lievre 85:
1.50 brouard 86: char version[80]="Imach version 0.8i, June 2002, INED-EUROREVES ";
1.21 lievre 87: int erreur; /* Error number */
1.2 lievre 88: int nvar;
1.49 lievre 89: int cptcovn=0, cptcovage=0, cptcoveff=0,cptcov;
1.2 lievre 90: int npar=NPARMAX;
91: int nlstate=2; /* Number of live states */
92: int ndeath=1; /* Number of dead states */
1.34 brouard 93: int ncovmodel, ncovcol; /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
1.15 lievre 94: int popbased=0;
1.2 lievre 95:
96: int *wav; /* Number of waves for this individuual 0 is possible */
97: int maxwav; /* Maxim number of waves */
1.8 lievre 98: int jmin, jmax; /* min, max spacing between 2 waves */
1.2 lievre 99: int mle, weightopt;
100: int **mw; /* mw[mi][i] is number of the mi wave for this individual */
101: int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
1.8 lievre 102: double jmean; /* Mean space between 2 waves */
1.2 lievre 103: double **oldm, **newm, **savm; /* Working pointers to matrices */
104: double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
1.27 lievre 105: FILE *fic,*ficpar, *ficparo,*ficres, *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
1.50 brouard 106: FILE *ficlog;
1.46 brouard 107: FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
1.50 brouard 108: FILE *ficresprobmorprev;
1.47 brouard 109: FILE *fichtm; /* Html File */
1.2 lievre 110: FILE *ficreseij;
1.47 brouard 111: char filerese[FILENAMELENGTH];
112: FILE *ficresvij;
113: char fileresv[FILENAMELENGTH];
114: FILE *ficresvpl;
115: char fileresvpl[FILENAMELENGTH];
116: char title[MAXLINE];
117: char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH], filerespl[FILENAMELENGTH];
118: char optionfilext[10], optionfilefiname[FILENAMELENGTH], plotcmd[FILENAMELENGTH];
119:
120: char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
1.50 brouard 121: char filelog[FILENAMELENGTH]; /* Log file */
1.47 brouard 122: char filerest[FILENAMELENGTH];
123: char fileregp[FILENAMELENGTH];
124: char popfile[FILENAMELENGTH];
125:
126: char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH];
1.2 lievre 127:
128: #define NR_END 1
129: #define FREE_ARG char*
130: #define FTOL 1.0e-10
131:
132: #define NRANSI
133: #define ITMAX 200
134:
135: #define TOL 2.0e-4
136:
137: #define CGOLD 0.3819660
138: #define ZEPS 1.0e-10
139: #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);
140:
141: #define GOLD 1.618034
142: #define GLIMIT 100.0
143: #define TINY 1.0e-20
144:
145: static double maxarg1,maxarg2;
146: #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
147: #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
1.25 lievre 148:
1.2 lievre 149: #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
150: #define rint(a) floor(a+0.5)
151:
152: static double sqrarg;
153: #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
154: #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}
155:
156: int imx;
157: int stepm;
158: /* Stepm, step in month: minimum step interpolation*/
159:
1.36 brouard 160: int estepm;
161: /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
162:
1.2 lievre 163: int m,nb;
1.6 lievre 164: int *num, firstpass=0, lastpass=4,*cod, *ncodemax, *Tage;
1.2 lievre 165: double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
1.13 lievre 166: double **pmmij, ***probs, ***mobaverage;
1.19 lievre 167: double dateintmean=0;
1.2 lievre 168:
169: double *weight;
170: int **s; /* Status */
171: double *agedc, **covar, idx;
1.7 lievre 172: int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;
1.2 lievre 173:
174: double ftol=FTOL; /* Tolerance for computing Max Likelihood */
175: double ftolhess; /* Tolerance for computing hessian */
176:
1.7 lievre 177: /**************** split *************************/
1.22 brouard 178: static int split( char *path, char *dirc, char *name, char *ext, char *finame )
1.5 lievre 179: {
180: char *s; /* pointer */
181: int l1, l2; /* length counters */
182:
183: l1 = strlen( path ); /* length of path */
184: if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
1.50 brouard 185: s= strrchr( path, DIRSEPARATOR ); /* find last / */
1.5 lievre 186: if ( s == NULL ) { /* no directory, so use current */
1.50 brouard 187: /*if(strrchr(path, ODIRSEPARATOR )==NULL)
188: printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
1.5 lievre 189: #if defined(__bsd__) /* get current working directory */
190: extern char *getwd( );
191:
192: if ( getwd( dirc ) == NULL ) {
193: #else
194: extern char *getcwd( );
195:
196: if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {
197: #endif
198: return( GLOCK_ERROR_GETCWD );
199: }
200: strcpy( name, path ); /* we've got it */
201: } else { /* strip direcotry from path */
202: s++; /* after this, the filename */
203: l2 = strlen( s ); /* length of filename */
204: if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
205: strcpy( name, s ); /* save file name */
206: strncpy( dirc, path, l1 - l2 ); /* now the directory */
207: dirc[l1-l2] = 0; /* add zero */
208: }
209: l1 = strlen( dirc ); /* length of directory */
1.22 brouard 210: #ifdef windows
1.5 lievre 211: if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; }
1.22 brouard 212: #else
213: if ( dirc[l1-1] != '/' ) { dirc[l1] = '/'; dirc[l1+1] = 0; }
214: #endif
215: s = strrchr( name, '.' ); /* find last / */
216: s++;
217: strcpy(ext,s); /* save extension */
218: l1= strlen( name);
219: l2= strlen( s)+1;
220: strncpy( finame, name, l1-l2);
221: finame[l1-l2]= 0;
1.5 lievre 222: return( 0 ); /* we're done */
223: }
224:
225:
1.2 lievre 226: /******************************************/
227:
228: void replace(char *s, char*t)
229: {
230: int i;
231: int lg=20;
232: i=0;
233: lg=strlen(t);
234: for(i=0; i<= lg; i++) {
235: (s[i] = t[i]);
236: if (t[i]== '\\') s[i]='/';
237: }
238: }
239:
240: int nbocc(char *s, char occ)
241: {
242: int i,j=0;
243: int lg=20;
244: i=0;
245: lg=strlen(s);
246: for(i=0; i<= lg; i++) {
247: if (s[i] == occ ) j++;
248: }
249: return j;
250: }
251:
252: void cutv(char *u,char *v, char*t, char occ)
253: {
1.50 brouard 254: /* cuts string t into u and v where u is ended by char occ excluding it
255: and v is after occ excluding it too : ex cutv(u,v,"abcdef2ghi2j",2)
256: gives u="abcedf" and v="ghi2j" */
1.6 lievre 257: int i,lg,j,p=0;
1.2 lievre 258: i=0;
259: for(j=0; j<=strlen(t)-1; j++) {
1.3 lievre 260: if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;
1.2 lievre 261: }
262:
263: lg=strlen(t);
264: for(j=0; j<p; j++) {
265: (u[j] = t[j]);
266: }
1.6 lievre 267: u[p]='\0';
1.2 lievre 268:
269: for(j=0; j<= lg; j++) {
270: if (j>=(p+1))(v[j-p-1] = t[j]);
271: }
272: }
273:
274: /********************** nrerror ********************/
275:
276: void nrerror(char error_text[])
277: {
278: fprintf(stderr,"ERREUR ...\n");
279: fprintf(stderr,"%s\n",error_text);
280: exit(1);
281: }
282: /*********************** vector *******************/
283: double *vector(int nl, int nh)
284: {
285: double *v;
286: v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
287: if (!v) nrerror("allocation failure in vector");
288: return v-nl+NR_END;
289: }
290:
291: /************************ free vector ******************/
292: void free_vector(double*v, int nl, int nh)
293: {
294: free((FREE_ARG)(v+nl-NR_END));
295: }
296:
297: /************************ivector *******************************/
298: int *ivector(long nl,long nh)
299: {
300: int *v;
301: v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
302: if (!v) nrerror("allocation failure in ivector");
303: return v-nl+NR_END;
304: }
305:
306: /******************free ivector **************************/
307: void free_ivector(int *v, long nl, long nh)
308: {
309: free((FREE_ARG)(v+nl-NR_END));
310: }
311:
312: /******************* imatrix *******************************/
313: int **imatrix(long nrl, long nrh, long ncl, long nch)
314: /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */
315: {
316: long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;
317: int **m;
318:
319: /* allocate pointers to rows */
320: m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));
321: if (!m) nrerror("allocation failure 1 in matrix()");
322: m += NR_END;
323: m -= nrl;
324:
325:
326: /* allocate rows and set pointers to them */
327: m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));
328: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
329: m[nrl] += NR_END;
330: m[nrl] -= ncl;
331:
332: for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;
333:
334: /* return pointer to array of pointers to rows */
335: return m;
336: }
337:
338: /****************** free_imatrix *************************/
339: void free_imatrix(m,nrl,nrh,ncl,nch)
340: int **m;
341: long nch,ncl,nrh,nrl;
342: /* free an int matrix allocated by imatrix() */
343: {
344: free((FREE_ARG) (m[nrl]+ncl-NR_END));
345: free((FREE_ARG) (m+nrl-NR_END));
346: }
347:
348: /******************* matrix *******************************/
349: double **matrix(long nrl, long nrh, long ncl, long nch)
350: {
351: long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
352: double **m;
353:
354: m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
355: if (!m) nrerror("allocation failure 1 in matrix()");
356: m += NR_END;
357: m -= nrl;
358:
359: m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
360: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
361: m[nrl] += NR_END;
362: m[nrl] -= ncl;
363:
364: for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
365: return m;
366: }
367:
368: /*************************free matrix ************************/
369: void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
370: {
371: free((FREE_ARG)(m[nrl]+ncl-NR_END));
372: free((FREE_ARG)(m+nrl-NR_END));
373: }
374:
375: /******************* ma3x *******************************/
376: double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
377: {
378: long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
379: double ***m;
380:
381: m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
382: if (!m) nrerror("allocation failure 1 in matrix()");
383: m += NR_END;
384: m -= nrl;
385:
386: m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
387: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
388: m[nrl] += NR_END;
389: m[nrl] -= ncl;
390:
391: for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
392:
393: m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
394: if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
395: m[nrl][ncl] += NR_END;
396: m[nrl][ncl] -= nll;
397: for (j=ncl+1; j<=nch; j++)
398: m[nrl][j]=m[nrl][j-1]+nlay;
399:
400: for (i=nrl+1; i<=nrh; i++) {
401: m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
402: for (j=ncl+1; j<=nch; j++)
403: m[i][j]=m[i][j-1]+nlay;
404: }
405: return m;
406: }
407:
408: /*************************free ma3x ************************/
409: void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
410: {
411: free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
412: free((FREE_ARG)(m[nrl]+ncl-NR_END));
413: free((FREE_ARG)(m+nrl-NR_END));
414: }
415:
416: /***************** f1dim *************************/
417: extern int ncom;
418: extern double *pcom,*xicom;
419: extern double (*nrfunc)(double []);
420:
421: double f1dim(double x)
422: {
423: int j;
424: double f;
425: double *xt;
426:
427: xt=vector(1,ncom);
428: for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];
429: f=(*nrfunc)(xt);
430: free_vector(xt,1,ncom);
431: return f;
432: }
433:
434: /*****************brent *************************/
435: double brent(double ax, double bx, double cx, double (*f)(double), double tol, double *xmin)
436: {
437: int iter;
438: double a,b,d,etemp;
439: double fu,fv,fw,fx;
440: double ftemp;
441: double p,q,r,tol1,tol2,u,v,w,x,xm;
442: double e=0.0;
443:
444: a=(ax < cx ? ax : cx);
445: b=(ax > cx ? ax : cx);
446: x=w=v=bx;
447: fw=fv=fx=(*f)(x);
448: for (iter=1;iter<=ITMAX;iter++) {
449: xm=0.5*(a+b);
450: tol2=2.0*(tol1=tol*fabs(x)+ZEPS);
451: /* if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
452: printf(".");fflush(stdout);
1.50 brouard 453: fprintf(ficlog,".");fflush(ficlog);
1.2 lievre 454: #ifdef DEBUG
455: 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);
1.50 brouard 456: fprintf(ficlog,"br %d,x=%.10e xm=%.10e b=%.10e a=%.10e tol=%.10e tol1=%.10e tol2=%.10e x-xm=%.10e fx=%.12e fu=%.12e,fw=%.12e,ftemp=%.12e,ftol=%.12e\n",iter,x,xm,b,a,tol,tol1,tol2,(x-xm),fx,fu,fw,ftemp,ftol);
1.2 lievre 457: /* if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
458: #endif
459: if (fabs(x-xm) <= (tol2-0.5*(b-a))){
460: *xmin=x;
461: return fx;
462: }
463: ftemp=fu;
464: if (fabs(e) > tol1) {
465: r=(x-w)*(fx-fv);
466: q=(x-v)*(fx-fw);
467: p=(x-v)*q-(x-w)*r;
468: q=2.0*(q-r);
469: if (q > 0.0) p = -p;
470: q=fabs(q);
471: etemp=e;
472: e=d;
473: if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))
474: d=CGOLD*(e=(x >= xm ? a-x : b-x));
475: else {
476: d=p/q;
477: u=x+d;
478: if (u-a < tol2 || b-u < tol2)
479: d=SIGN(tol1,xm-x);
480: }
481: } else {
482: d=CGOLD*(e=(x >= xm ? a-x : b-x));
483: }
484: u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));
485: fu=(*f)(u);
486: if (fu <= fx) {
487: if (u >= x) a=x; else b=x;
488: SHFT(v,w,x,u)
489: SHFT(fv,fw,fx,fu)
490: } else {
491: if (u < x) a=u; else b=u;
492: if (fu <= fw || w == x) {
493: v=w;
494: w=u;
495: fv=fw;
496: fw=fu;
497: } else if (fu <= fv || v == x || v == w) {
498: v=u;
499: fv=fu;
500: }
501: }
502: }
503: nrerror("Too many iterations in brent");
504: *xmin=x;
505: return fx;
506: }
507:
508: /****************** mnbrak ***********************/
509:
510: void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,
511: double (*func)(double))
512: {
513: double ulim,u,r,q, dum;
514: double fu;
515:
516: *fa=(*func)(*ax);
517: *fb=(*func)(*bx);
518: if (*fb > *fa) {
519: SHFT(dum,*ax,*bx,dum)
520: SHFT(dum,*fb,*fa,dum)
521: }
522: *cx=(*bx)+GOLD*(*bx-*ax);
523: *fc=(*func)(*cx);
524: while (*fb > *fc) {
525: r=(*bx-*ax)*(*fb-*fc);
526: q=(*bx-*cx)*(*fb-*fa);
527: u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/
528: (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r));
529: ulim=(*bx)+GLIMIT*(*cx-*bx);
530: if ((*bx-u)*(u-*cx) > 0.0) {
531: fu=(*func)(u);
532: } else if ((*cx-u)*(u-ulim) > 0.0) {
533: fu=(*func)(u);
534: if (fu < *fc) {
535: SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))
536: SHFT(*fb,*fc,fu,(*func)(u))
537: }
538: } else if ((u-ulim)*(ulim-*cx) >= 0.0) {
539: u=ulim;
540: fu=(*func)(u);
541: } else {
542: u=(*cx)+GOLD*(*cx-*bx);
543: fu=(*func)(u);
544: }
545: SHFT(*ax,*bx,*cx,u)
546: SHFT(*fa,*fb,*fc,fu)
547: }
548: }
549:
550: /*************** linmin ************************/
551:
552: int ncom;
553: double *pcom,*xicom;
554: double (*nrfunc)(double []);
555:
556: void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))
557: {
558: double brent(double ax, double bx, double cx,
559: double (*f)(double), double tol, double *xmin);
560: double f1dim(double x);
561: void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,
562: double *fc, double (*func)(double));
563: int j;
564: double xx,xmin,bx,ax;
565: double fx,fb,fa;
566:
567: ncom=n;
568: pcom=vector(1,n);
569: xicom=vector(1,n);
570: nrfunc=func;
571: for (j=1;j<=n;j++) {
572: pcom[j]=p[j];
573: xicom[j]=xi[j];
574: }
575: ax=0.0;
576: xx=1.0;
577: mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim);
578: *fret=brent(ax,xx,bx,f1dim,TOL,&xmin);
579: #ifdef DEBUG
580: printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
1.50 brouard 581: fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
1.2 lievre 582: #endif
583: for (j=1;j<=n;j++) {
584: xi[j] *= xmin;
585: p[j] += xi[j];
586: }
587: free_vector(xicom,1,n);
588: free_vector(pcom,1,n);
589: }
590:
591: /*************** powell ************************/
592: void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,
593: double (*func)(double []))
594: {
595: void linmin(double p[], double xi[], int n, double *fret,
596: double (*func)(double []));
597: int i,ibig,j;
598: double del,t,*pt,*ptt,*xit;
599: double fp,fptt;
600: double *xits;
601: pt=vector(1,n);
602: ptt=vector(1,n);
603: xit=vector(1,n);
604: xits=vector(1,n);
605: *fret=(*func)(p);
606: for (j=1;j<=n;j++) pt[j]=p[j];
607: for (*iter=1;;++(*iter)) {
608: fp=(*fret);
609: ibig=0;
610: del=0.0;
611: printf("\nPowell iter=%d -2*LL=%.12f",*iter,*fret);
1.50 brouard 612: fprintf(ficlog,"\nPowell iter=%d -2*LL=%.12f",*iter,*fret);
1.2 lievre 613: for (i=1;i<=n;i++)
614: printf(" %d %.12f",i, p[i]);
1.50 brouard 615: fprintf(ficlog," %d %.12f",i, p[i]);
1.2 lievre 616: printf("\n");
1.50 brouard 617: fprintf(ficlog,"\n");
1.2 lievre 618: for (i=1;i<=n;i++) {
619: for (j=1;j<=n;j++) xit[j]=xi[j][i];
620: fptt=(*fret);
621: #ifdef DEBUG
622: printf("fret=%lf \n",*fret);
1.50 brouard 623: fprintf(ficlog,"fret=%lf \n",*fret);
1.2 lievre 624: #endif
625: printf("%d",i);fflush(stdout);
1.50 brouard 626: fprintf(ficlog,"%d",i);fflush(ficlog);
1.2 lievre 627: linmin(p,xit,n,fret,func);
628: if (fabs(fptt-(*fret)) > del) {
629: del=fabs(fptt-(*fret));
630: ibig=i;
631: }
632: #ifdef DEBUG
633: printf("%d %.12e",i,(*fret));
1.50 brouard 634: fprintf(ficlog,"%d %.12e",i,(*fret));
1.2 lievre 635: for (j=1;j<=n;j++) {
636: xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
637: printf(" x(%d)=%.12e",j,xit[j]);
1.50 brouard 638: fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
1.2 lievre 639: }
1.50 brouard 640: for(j=1;j<=n;j++) {
1.2 lievre 641: printf(" p=%.12e",p[j]);
1.50 brouard 642: fprintf(ficlog," p=%.12e",p[j]);
643: }
1.2 lievre 644: printf("\n");
1.50 brouard 645: fprintf(ficlog,"\n");
1.2 lievre 646: #endif
647: }
648: if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {
649: #ifdef DEBUG
650: int k[2],l;
651: k[0]=1;
652: k[1]=-1;
653: printf("Max: %.12e",(*func)(p));
1.50 brouard 654: fprintf(ficlog,"Max: %.12e",(*func)(p));
655: for (j=1;j<=n;j++) {
1.2 lievre 656: printf(" %.12e",p[j]);
1.50 brouard 657: fprintf(ficlog," %.12e",p[j]);
658: }
1.2 lievre 659: printf("\n");
1.50 brouard 660: fprintf(ficlog,"\n");
1.2 lievre 661: for(l=0;l<=1;l++) {
662: for (j=1;j<=n;j++) {
663: ptt[j]=p[j]+(p[j]-pt[j])*k[l];
664: printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
1.50 brouard 665: fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
1.2 lievre 666: }
667: printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
1.50 brouard 668: fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
1.2 lievre 669: }
670: #endif
671:
672:
673: free_vector(xit,1,n);
674: free_vector(xits,1,n);
675: free_vector(ptt,1,n);
676: free_vector(pt,1,n);
677: return;
678: }
679: if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");
680: for (j=1;j<=n;j++) {
681: ptt[j]=2.0*p[j]-pt[j];
682: xit[j]=p[j]-pt[j];
683: pt[j]=p[j];
684: }
685: fptt=(*func)(ptt);
686: if (fptt < fp) {
687: t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt);
688: if (t < 0.0) {
689: linmin(p,xit,n,fret,func);
690: for (j=1;j<=n;j++) {
691: xi[j][ibig]=xi[j][n];
692: xi[j][n]=xit[j];
693: }
694: #ifdef DEBUG
695: printf("Direction changed last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
1.50 brouard 696: fprintf(ficlog,"Direction changed last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
697: for(j=1;j<=n;j++){
1.2 lievre 698: printf(" %.12e",xit[j]);
1.50 brouard 699: fprintf(ficlog," %.12e",xit[j]);
700: }
1.2 lievre 701: printf("\n");
1.50 brouard 702: fprintf(ficlog,"\n");
1.2 lievre 703: #endif
704: }
705: }
706: }
707: }
708:
709: /**** Prevalence limit ****************/
710:
711: double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)
712: {
713: /* Computes the prevalence limit in each live state at age x by left multiplying the unit
714: matrix by transitions matrix until convergence is reached */
715:
716: int i, ii,j,k;
717: double min, max, maxmin, maxmax,sumnew=0.;
718: double **matprod2();
719: double **out, cov[NCOVMAX], **pmij();
720: double **newm;
721: double agefin, delaymax=50 ; /* Max number of years to converge */
722:
723: for (ii=1;ii<=nlstate+ndeath;ii++)
724: for (j=1;j<=nlstate+ndeath;j++){
725: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
726: }
1.6 lievre 727:
728: cov[1]=1.;
729:
730: /* Even if hstepm = 1, at least one multiplication by the unit matrix */
1.2 lievre 731: for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
732: newm=savm;
733: /* Covariates have to be included here again */
1.6 lievre 734: cov[2]=agefin;
735:
736: for (k=1; k<=cptcovn;k++) {
1.7 lievre 737: cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
1.35 lievre 738: /* 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 739: }
1.35 lievre 740: for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
1.7 lievre 741: for (k=1; k<=cptcovprod;k++)
742: cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
743:
744: /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
745: /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
1.35 lievre 746: /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
1.2 lievre 747: out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);
748:
749: savm=oldm;
750: oldm=newm;
751: maxmax=0.;
752: for(j=1;j<=nlstate;j++){
753: min=1.;
754: max=0.;
755: for(i=1; i<=nlstate; i++) {
756: sumnew=0;
757: for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
758: prlim[i][j]= newm[i][j]/(1-sumnew);
759: max=FMAX(max,prlim[i][j]);
760: min=FMIN(min,prlim[i][j]);
761: }
762: maxmin=max-min;
763: maxmax=FMAX(maxmax,maxmin);
764: }
765: if(maxmax < ftolpl){
766: return prlim;
767: }
768: }
769: }
770:
1.12 lievre 771: /*************** transition probabilities ***************/
1.2 lievre 772:
773: double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
774: {
775: double s1, s2;
776: /*double t34;*/
777: int i,j,j1, nc, ii, jj;
778:
779: for(i=1; i<= nlstate; i++){
780: for(j=1; j<i;j++){
781: for (nc=1, s2=0.;nc <=ncovmodel; nc++){
782: /*s2 += param[i][j][nc]*cov[nc];*/
783: s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
784: /*printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2);*/
785: }
786: ps[i][j]=s2;
787: /*printf("s1=%.17e, s2=%.17e\n",s1,s2);*/
788: }
789: for(j=i+1; j<=nlstate+ndeath;j++){
790: for (nc=1, s2=0.;nc <=ncovmodel; nc++){
791: s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
792: /*printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2);*/
793: }
1.22 brouard 794: ps[i][j]=s2;
1.2 lievre 795: }
796: }
1.12 lievre 797: /*ps[3][2]=1;*/
798:
1.2 lievre 799: for(i=1; i<= nlstate; i++){
800: s1=0;
801: for(j=1; j<i; j++)
802: s1+=exp(ps[i][j]);
803: for(j=i+1; j<=nlstate+ndeath; j++)
804: s1+=exp(ps[i][j]);
805: ps[i][i]=1./(s1+1.);
806: for(j=1; j<i; j++)
807: ps[i][j]= exp(ps[i][j])*ps[i][i];
808: for(j=i+1; j<=nlstate+ndeath; j++)
809: ps[i][j]= exp(ps[i][j])*ps[i][i];
810: /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
811: } /* end i */
812:
813: for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
814: for(jj=1; jj<= nlstate+ndeath; jj++){
815: ps[ii][jj]=0;
816: ps[ii][ii]=1;
817: }
818: }
819:
1.12 lievre 820:
1.2 lievre 821: /* for(ii=1; ii<= nlstate+ndeath; ii++){
822: for(jj=1; jj<= nlstate+ndeath; jj++){
823: printf("%lf ",ps[ii][jj]);
824: }
825: printf("\n ");
826: }
827: printf("\n ");printf("%lf ",cov[2]);*/
828: /*
829: for(i=1; i<= npar; i++) printf("%f ",x[i]);
830: goto end;*/
831: return ps;
832: }
833:
834: /**************** Product of 2 matrices ******************/
835:
836: double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)
837: {
1.13 lievre 838: /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
1.2 lievre 839: b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
840: /* in, b, out are matrice of pointers which should have been initialized
841: before: only the contents of out is modified. The function returns
842: a pointer to pointers identical to out */
843: long i, j, k;
844: for(i=nrl; i<= nrh; i++)
845: for(k=ncolol; k<=ncoloh; k++)
846: for(j=ncl,out[i][k]=0.; j<=nch; j++)
847: out[i][k] +=in[i][j]*b[j][k];
848:
849: return out;
850: }
851:
852:
853: /************* Higher Matrix Product ***************/
854:
855: double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
856: {
857: /* Computes the transition matrix starting at age 'age' over 'nhstepm*hstepm*stepm' month
858: duration (i.e. until
859: age (in years) age+nhstepm*stepm/12) by multiplying nhstepm*hstepm matrices.
860: Output is stored in matrix po[i][j][h] for h every 'hstepm' step
861: (typically every 2 years instead of every month which is too big).
862: Model is determined by parameters x and covariates have to be
863: included manually here.
864:
865: */
866:
867: int i, j, d, h, k;
868: double **out, cov[NCOVMAX];
869: double **newm;
870:
871: /* Hstepm could be zero and should return the unit matrix */
872: for (i=1;i<=nlstate+ndeath;i++)
873: for (j=1;j<=nlstate+ndeath;j++){
874: oldm[i][j]=(i==j ? 1.0 : 0.0);
875: po[i][j][0]=(i==j ? 1.0 : 0.0);
876: }
877: /* Even if hstepm = 1, at least one multiplication by the unit matrix */
878: for(h=1; h <=nhstepm; h++){
879: for(d=1; d <=hstepm; d++){
880: newm=savm;
881: /* Covariates have to be included here again */
882: cov[1]=1.;
883: cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
1.7 lievre 884: for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
1.12 lievre 885: for (k=1; k<=cptcovage;k++)
1.7 lievre 886: cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
1.12 lievre 887: for (k=1; k<=cptcovprod;k++)
1.7 lievre 888: cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
889:
890:
1.2 lievre 891: /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
892: /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
893: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,
894: pmij(pmmij,cov,ncovmodel,x,nlstate));
895: savm=oldm;
896: oldm=newm;
897: }
898: for(i=1; i<=nlstate+ndeath; i++)
899: for(j=1;j<=nlstate+ndeath;j++) {
900: po[i][j][h]=newm[i][j];
901: /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);
902: */
903: }
904: } /* end h */
905: return po;
906: }
907:
908:
909: /*************** log-likelihood *************/
910: double func( double *x)
911: {
1.6 lievre 912: int i, ii, j, k, mi, d, kk;
1.2 lievre 913: double l, ll[NLSTATEMAX], cov[NCOVMAX];
914: double **out;
915: double sw; /* Sum of weights */
916: double lli; /* Individual log likelihood */
917: long ipmx;
918: /*extern weight */
919: /* We are differentiating ll according to initial status */
920: /* for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
921: /*for(i=1;i<imx;i++)
1.8 lievre 922: printf(" %d\n",s[4][i]);
1.2 lievre 923: */
1.6 lievre 924: cov[1]=1.;
1.2 lievre 925:
926: for(k=1; k<=nlstate; k++) ll[k]=0.;
927: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1.6 lievre 928: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
1.8 lievre 929: for(mi=1; mi<= wav[i]-1; mi++){
1.2 lievre 930: for (ii=1;ii<=nlstate+ndeath;ii++)
931: for (j=1;j<=nlstate+ndeath;j++) oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1.8 lievre 932: for(d=0; d<dh[mi][i]; d++){
933: newm=savm;
934: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
935: for (kk=1; kk<=cptcovage;kk++) {
936: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
937: }
938:
939: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
940: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
941: savm=oldm;
942: oldm=newm;
943:
944:
1.2 lievre 945: } /* end mult */
1.8 lievre 946:
1.2 lievre 947: lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);
948: /* printf(" %f ",out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/
949: ipmx +=1;
950: sw += weight[i];
951: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
952: } /* end of wave */
953: } /* end of individual */
954:
955: for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
956: /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
957: l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
958: return -l;
959: }
960:
961:
962: /*********** Maximum Likelihood Estimation ***************/
963:
964: void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
965: {
966: int i,j, iter;
967: double **xi,*delti;
968: double fret;
969: xi=matrix(1,npar,1,npar);
970: for (i=1;i<=npar;i++)
971: for (j=1;j<=npar;j++)
972: xi[i][j]=(i==j ? 1.0 : 0.0);
1.50 brouard 973: printf("Powell\n"); fprintf(ficlog,"Powell\n");
1.2 lievre 974: powell(p,xi,npar,ftol,&iter,&fret,func);
975:
976: printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));
1.50 brouard 977: fprintf(ficlog,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
1.21 lievre 978: fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
1.2 lievre 979:
980: }
981:
982: /**** Computes Hessian and covariance matrix ***/
983: void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
984: {
985: double **a,**y,*x,pd;
986: double **hess;
987: int i, j,jk;
988: int *indx;
989:
990: double hessii(double p[], double delta, int theta, double delti[]);
991: double hessij(double p[], double delti[], int i, int j);
992: void lubksb(double **a, int npar, int *indx, double b[]) ;
993: void ludcmp(double **a, int npar, int *indx, double *d) ;
994:
995: hess=matrix(1,npar,1,npar);
996:
997: printf("\nCalculation of the hessian matrix. Wait...\n");
1.50 brouard 998: fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
1.2 lievre 999: for (i=1;i<=npar;i++){
1000: printf("%d",i);fflush(stdout);
1.50 brouard 1001: fprintf(ficlog,"%d",i);fflush(ficlog);
1.2 lievre 1002: hess[i][i]=hessii(p,ftolhess,i,delti);
1003: /*printf(" %f ",p[i]);*/
1.12 lievre 1004: /*printf(" %lf ",hess[i][i]);*/
1.2 lievre 1005: }
1.12 lievre 1006:
1.2 lievre 1007: for (i=1;i<=npar;i++) {
1008: for (j=1;j<=npar;j++) {
1009: if (j>i) {
1010: printf(".%d%d",i,j);fflush(stdout);
1.50 brouard 1011: fprintf(ficlog,".%d%d",i,j);fflush(ficlog);
1.2 lievre 1012: hess[i][j]=hessij(p,delti,i,j);
1.12 lievre 1013: hess[j][i]=hess[i][j];
1014: /*printf(" %lf ",hess[i][j]);*/
1.2 lievre 1015: }
1016: }
1017: }
1018: printf("\n");
1.50 brouard 1019: fprintf(ficlog,"\n");
1.2 lievre 1020:
1021: printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
1.50 brouard 1022: fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
1.2 lievre 1023:
1024: a=matrix(1,npar,1,npar);
1025: y=matrix(1,npar,1,npar);
1026: x=vector(1,npar);
1027: indx=ivector(1,npar);
1028: for (i=1;i<=npar;i++)
1029: for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
1030: ludcmp(a,npar,indx,&pd);
1031:
1032: for (j=1;j<=npar;j++) {
1033: for (i=1;i<=npar;i++) x[i]=0;
1034: x[j]=1;
1035: lubksb(a,npar,indx,x);
1036: for (i=1;i<=npar;i++){
1037: matcov[i][j]=x[i];
1038: }
1039: }
1040:
1041: printf("\n#Hessian matrix#\n");
1.50 brouard 1042: fprintf(ficlog,"\n#Hessian matrix#\n");
1.2 lievre 1043: for (i=1;i<=npar;i++) {
1044: for (j=1;j<=npar;j++) {
1045: printf("%.3e ",hess[i][j]);
1.50 brouard 1046: fprintf(ficlog,"%.3e ",hess[i][j]);
1.2 lievre 1047: }
1048: printf("\n");
1.50 brouard 1049: fprintf(ficlog,"\n");
1.2 lievre 1050: }
1051:
1052: /* Recompute Inverse */
1053: for (i=1;i<=npar;i++)
1054: for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];
1055: ludcmp(a,npar,indx,&pd);
1056:
1057: /* printf("\n#Hessian matrix recomputed#\n");
1058:
1059: for (j=1;j<=npar;j++) {
1060: for (i=1;i<=npar;i++) x[i]=0;
1061: x[j]=1;
1062: lubksb(a,npar,indx,x);
1063: for (i=1;i<=npar;i++){
1064: y[i][j]=x[i];
1065: printf("%.3e ",y[i][j]);
1.50 brouard 1066: fprintf(ficlog,"%.3e ",y[i][j]);
1.2 lievre 1067: }
1068: printf("\n");
1.50 brouard 1069: fprintf(ficlog,"\n");
1.2 lievre 1070: }
1071: */
1072:
1073: free_matrix(a,1,npar,1,npar);
1074: free_matrix(y,1,npar,1,npar);
1075: free_vector(x,1,npar);
1076: free_ivector(indx,1,npar);
1077: free_matrix(hess,1,npar,1,npar);
1078:
1079:
1080: }
1081:
1082: /*************** hessian matrix ****************/
1083: double hessii( double x[], double delta, int theta, double delti[])
1084: {
1085: int i;
1086: int l=1, lmax=20;
1087: double k1,k2;
1088: double p2[NPARMAX+1];
1089: double res;
1090: double delt, delts, nkhi=10.,nkhif=1., khi=1.e-4;
1091: double fx;
1092: int k=0,kmax=10;
1093: double l1;
1094:
1095: fx=func(x);
1096: for (i=1;i<=npar;i++) p2[i]=x[i];
1097: for(l=0 ; l <=lmax; l++){
1098: l1=pow(10,l);
1099: delts=delt;
1100: for(k=1 ; k <kmax; k=k+1){
1101: delt = delta*(l1*k);
1102: p2[theta]=x[theta] +delt;
1103: k1=func(p2)-fx;
1104: p2[theta]=x[theta]-delt;
1105: k2=func(p2)-fx;
1106: /*res= (k1-2.0*fx+k2)/delt/delt; */
1107: res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */
1108:
1109: #ifdef DEBUG
1110: 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);
1.50 brouard 1111: fprintf(ficlog,"%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx);
1.2 lievre 1112: #endif
1113: /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
1114: if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
1115: k=kmax;
1116: }
1117: else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
1118: k=kmax; l=lmax*10.;
1119: }
1120: else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){
1121: delts=delt;
1122: }
1123: }
1124: }
1125: delti[theta]=delts;
1.12 lievre 1126: return res;
1.3 lievre 1127:
1.2 lievre 1128: }
1129:
1130: double hessij( double x[], double delti[], int thetai,int thetaj)
1131: {
1132: int i;
1133: int l=1, l1, lmax=20;
1134: double k1,k2,k3,k4,res,fx;
1135: double p2[NPARMAX+1];
1136: int k;
1137:
1138: fx=func(x);
1139: for (k=1; k<=2; k++) {
1140: for (i=1;i<=npar;i++) p2[i]=x[i];
1141: p2[thetai]=x[thetai]+delti[thetai]/k;
1142: p2[thetaj]=x[thetaj]+delti[thetaj]/k;
1143: k1=func(p2)-fx;
1144:
1145: p2[thetai]=x[thetai]+delti[thetai]/k;
1146: p2[thetaj]=x[thetaj]-delti[thetaj]/k;
1147: k2=func(p2)-fx;
1148:
1149: p2[thetai]=x[thetai]-delti[thetai]/k;
1150: p2[thetaj]=x[thetaj]+delti[thetaj]/k;
1151: k3=func(p2)-fx;
1152:
1153: p2[thetai]=x[thetai]-delti[thetai]/k;
1154: p2[thetaj]=x[thetaj]-delti[thetaj]/k;
1155: k4=func(p2)-fx;
1156: res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */
1157: #ifdef DEBUG
1158: 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);
1.50 brouard 1159: fprintf(ficlog,"%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);
1.2 lievre 1160: #endif
1161: }
1162: return res;
1163: }
1164:
1165: /************** Inverse of matrix **************/
1166: void ludcmp(double **a, int n, int *indx, double *d)
1167: {
1168: int i,imax,j,k;
1169: double big,dum,sum,temp;
1170: double *vv;
1171:
1172: vv=vector(1,n);
1173: *d=1.0;
1174: for (i=1;i<=n;i++) {
1175: big=0.0;
1176: for (j=1;j<=n;j++)
1177: if ((temp=fabs(a[i][j])) > big) big=temp;
1178: if (big == 0.0) nrerror("Singular matrix in routine ludcmp");
1179: vv[i]=1.0/big;
1180: }
1181: for (j=1;j<=n;j++) {
1182: for (i=1;i<j;i++) {
1183: sum=a[i][j];
1184: for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];
1185: a[i][j]=sum;
1186: }
1187: big=0.0;
1188: for (i=j;i<=n;i++) {
1189: sum=a[i][j];
1190: for (k=1;k<j;k++)
1191: sum -= a[i][k]*a[k][j];
1192: a[i][j]=sum;
1193: if ( (dum=vv[i]*fabs(sum)) >= big) {
1194: big=dum;
1195: imax=i;
1196: }
1197: }
1198: if (j != imax) {
1199: for (k=1;k<=n;k++) {
1200: dum=a[imax][k];
1201: a[imax][k]=a[j][k];
1202: a[j][k]=dum;
1203: }
1204: *d = -(*d);
1205: vv[imax]=vv[j];
1206: }
1207: indx[j]=imax;
1208: if (a[j][j] == 0.0) a[j][j]=TINY;
1209: if (j != n) {
1210: dum=1.0/(a[j][j]);
1211: for (i=j+1;i<=n;i++) a[i][j] *= dum;
1212: }
1213: }
1214: free_vector(vv,1,n); /* Doesn't work */
1215: ;
1216: }
1217:
1218: void lubksb(double **a, int n, int *indx, double b[])
1219: {
1220: int i,ii=0,ip,j;
1221: double sum;
1222:
1223: for (i=1;i<=n;i++) {
1224: ip=indx[i];
1225: sum=b[ip];
1226: b[ip]=b[i];
1227: if (ii)
1228: for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];
1229: else if (sum) ii=i;
1230: b[i]=sum;
1231: }
1232: for (i=n;i>=1;i--) {
1233: sum=b[i];
1234: for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];
1235: b[i]=sum/a[i][i];
1236: }
1237: }
1238:
1239: /************ Frequencies ********************/
1.26 lievre 1240: 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 1241: { /* Some frequencies */
1.35 lievre 1242:
1.18 lievre 1243: int i, m, jk, k1,i1, j1, bool, z1,z2,j;
1.50 brouard 1244: int first;
1.2 lievre 1245: double ***freq; /* Frequencies */
1246: double *pp;
1.19 lievre 1247: double pos, k2, dateintsum=0,k2cpt=0;
1.2 lievre 1248: FILE *ficresp;
1249: char fileresp[FILENAMELENGTH];
1.35 lievre 1250:
1.2 lievre 1251: pp=vector(1,nlstate);
1.19 lievre 1252: probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
1.2 lievre 1253: strcpy(fileresp,"p");
1254: strcat(fileresp,fileres);
1255: if((ficresp=fopen(fileresp,"w"))==NULL) {
1256: printf("Problem with prevalence resultfile: %s\n", fileresp);
1.50 brouard 1257: fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
1.2 lievre 1258: exit(0);
1259: }
1260: freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);
1261: j1=0;
1.35 lievre 1262:
1.7 lievre 1263: j=cptcoveff;
1.2 lievre 1264: if (cptcovn<1) {j=1;ncodemax[1]=1;}
1.50 brouard 1265:
1266: first=1;
1267:
1.2 lievre 1268: for(k1=1; k1<=j;k1++){
1.35 lievre 1269: for(i1=1; i1<=ncodemax[k1];i1++){
1270: j1++;
1271: /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
1272: scanf("%d", i);*/
1273: for (i=-1; i<=nlstate+ndeath; i++)
1274: for (jk=-1; jk<=nlstate+ndeath; jk++)
1275: for(m=agemin; m <= agemax+3; m++)
1276: freq[i][jk][m]=0;
1277:
1278: dateintsum=0;
1279: k2cpt=0;
1280: for (i=1; i<=imx; i++) {
1281: bool=1;
1282: if (cptcovn>0) {
1283: for (z1=1; z1<=cptcoveff; z1++)
1284: if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])
1285: bool=0;
1286: }
1287: if (bool==1) {
1288: for(m=firstpass; m<=lastpass; m++){
1289: k2=anint[m][i]+(mint[m][i]/12.);
1290: if ((k2>=dateprev1) && (k2<=dateprev2)) {
1291: if(agev[m][i]==0) agev[m][i]=agemax+1;
1292: if(agev[m][i]==1) agev[m][i]=agemax+2;
1293: if (m<lastpass) {
1294: freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
1295: freq[s[m][i]][s[m+1][i]][(int) agemax+3] += weight[i];
1296: }
1297:
1298: if ((agev[m][i]>1) && (agev[m][i]< (agemax+3))) {
1299: dateintsum=dateintsum+k2;
1300: k2cpt++;
1301: }
1302: }
1303: }
1304: }
1305: }
1.26 lievre 1306:
1.35 lievre 1307: fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);
1.26 lievre 1308:
1.35 lievre 1309: if (cptcovn>0) {
1310: fprintf(ficresp, "\n#********** Variable ");
1311: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
1312: fprintf(ficresp, "**********\n#");
1313: }
1314: for(i=1; i<=nlstate;i++)
1315: fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
1316: fprintf(ficresp, "\n");
1317:
1318: for(i=(int)agemin; i <= (int)agemax+3; i++){
1.50 brouard 1319: if(i==(int)agemax+3){
1320: fprintf(ficlog,"Total");
1321: }else{
1322: if(first==1){
1323: first=0;
1324: printf("See log file for details...\n");
1325: }
1326: fprintf(ficlog,"Age %d", i);
1327: }
1.35 lievre 1328: for(jk=1; jk <=nlstate ; jk++){
1329: for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
1330: pp[jk] += freq[jk][m][i];
1331: }
1332: for(jk=1; jk <=nlstate ; jk++){
1333: for(m=-1, pos=0; m <=0 ; m++)
1334: pos += freq[jk][m][i];
1.50 brouard 1335: if(pp[jk]>=1.e-10){
1336: if(first==1){
1.35 lievre 1337: printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
1.50 brouard 1338: }
1339: fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
1340: }else{
1341: if(first==1)
1342: printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
1343: fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
1344: }
1.35 lievre 1345: }
1.14 lievre 1346:
1.35 lievre 1347: for(jk=1; jk <=nlstate ; jk++){
1348: for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
1349: pp[jk] += freq[jk][m][i];
1350: }
1.14 lievre 1351:
1.35 lievre 1352: for(jk=1,pos=0; jk <=nlstate ; jk++)
1353: pos += pp[jk];
1354: for(jk=1; jk <=nlstate ; jk++){
1.50 brouard 1355: if(pos>=1.e-5){
1356: if(first==1)
1357: printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
1358: fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
1359: }else{
1360: if(first==1)
1361: printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
1362: fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
1363: }
1.35 lievre 1364: if( i <= (int) agemax){
1365: if(pos>=1.e-5){
1366: fprintf(ficresp," %d %.5f %.0f %.0f",i,pp[jk]/pos, pp[jk],pos);
1367: probs[i][jk][j1]= pp[jk]/pos;
1368: /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/
1369: }
1370: else
1371: fprintf(ficresp," %d NaNq %.0f %.0f",i,pp[jk],pos);
1372: }
1.13 lievre 1373: }
1.35 lievre 1374:
1375: for(jk=-1; jk <=nlstate+ndeath; jk++)
1376: for(m=-1; m <=nlstate+ndeath; m++)
1.50 brouard 1377: if(freq[jk][m][i] !=0 ) {
1378: if(first==1)
1379: printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
1380: fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
1381: }
1.35 lievre 1382: if(i <= (int) agemax)
1383: fprintf(ficresp,"\n");
1.50 brouard 1384: if(first==1)
1385: printf("Others in log...\n");
1386: fprintf(ficlog,"\n");
1.2 lievre 1387: }
1388: }
1.35 lievre 1389: }
1.19 lievre 1390: dateintmean=dateintsum/k2cpt;
1.2 lievre 1391:
1392: fclose(ficresp);
1393: free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);
1394: free_vector(pp,1,nlstate);
1.35 lievre 1395:
1.19 lievre 1396: /* End of Freq */
1397: }
1.2 lievre 1398:
1.15 lievre 1399: /************ Prevalence ********************/
1.28 lievre 1400: 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 1401: { /* Some frequencies */
1402:
1403: int i, m, jk, k1, i1, j1, bool, z1,z2,j;
1404: double ***freq; /* Frequencies */
1405: double *pp;
1.18 lievre 1406: double pos, k2;
1.15 lievre 1407:
1408: pp=vector(1,nlstate);
1.19 lievre 1409: probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
1.15 lievre 1410:
1411: freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);
1412: j1=0;
1413:
1414: j=cptcoveff;
1415: if (cptcovn<1) {j=1;ncodemax[1]=1;}
1416:
1.42 brouard 1417: for(k1=1; k1<=j;k1++){
1.15 lievre 1418: for(i1=1; i1<=ncodemax[k1];i1++){
1419: j1++;
1.42 brouard 1420:
1.15 lievre 1421: for (i=-1; i<=nlstate+ndeath; i++)
1422: for (jk=-1; jk<=nlstate+ndeath; jk++)
1423: for(m=agemin; m <= agemax+3; m++)
1.19 lievre 1424: freq[i][jk][m]=0;
1.28 lievre 1425:
1.15 lievre 1426: for (i=1; i<=imx; i++) {
1427: bool=1;
1428: if (cptcovn>0) {
1429: for (z1=1; z1<=cptcoveff; z1++)
1430: if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])
1431: bool=0;
1.28 lievre 1432: }
1.19 lievre 1433: if (bool==1) {
1434: for(m=firstpass; m<=lastpass; m++){
1435: k2=anint[m][i]+(mint[m][i]/12.);
1436: if ((k2>=dateprev1) && (k2<=dateprev2)) {
1.18 lievre 1437: if(agev[m][i]==0) agev[m][i]=agemax+1;
1438: if(agev[m][i]==1) agev[m][i]=agemax+2;
1.42 brouard 1439: if (m<lastpass) {
1440: if (calagedate>0)
1441: freq[s[m][i]][s[m+1][i]][(int)(agev[m][i]+1-((int)calagedate %12)/12.)] += weight[i];
1442: else
1443: freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
1444: freq[s[m][i]][s[m+1][i]][(int)(agemax+3)] += weight[i];
1445: }
1.18 lievre 1446: }
1.15 lievre 1447: }
1448: }
1449: }
1.42 brouard 1450: for(i=(int)agemin; i <= (int)agemax+3; i++){
1451: for(jk=1; jk <=nlstate ; jk++){
1452: for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
1453: pp[jk] += freq[jk][m][i];
1454: }
1455: for(jk=1; jk <=nlstate ; jk++){
1456: for(m=-1, pos=0; m <=0 ; m++)
1.15 lievre 1457: pos += freq[jk][m][i];
1458: }
1459:
1.42 brouard 1460: for(jk=1; jk <=nlstate ; jk++){
1461: for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
1462: pp[jk] += freq[jk][m][i];
1463: }
1464:
1465: for(jk=1,pos=0; jk <=nlstate ; jk++) pos += pp[jk];
1466:
1467: for(jk=1; jk <=nlstate ; jk++){
1468: if( i <= (int) agemax){
1469: if(pos>=1.e-5){
1470: probs[i][jk][j1]= pp[jk]/pos;
1471: }
1472: }
1.50 brouard 1473: }/* end jk */
1474: }/* end i */
1475: } /* end i1 */
1476: } /* end k1 */
1.41 lievre 1477:
1.15 lievre 1478:
1479: free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);
1480: free_vector(pp,1,nlstate);
1481:
1482: } /* End of Freq */
1.19 lievre 1483:
1.2 lievre 1484: /************* Waves Concatenation ***************/
1485:
1486: void concatwav(int wav[], int **dh, int **mw, int **s, double *agedc, double **agev, int firstpass, int lastpass, int imx, int nlstate, int stepm)
1487: {
1488: /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
1489: Death is a valid wave (if date is known).
1490: mw[mi][i] is the mi (mi=1 to wav[i]) effective wave of individual i
1491: dh[m][i] of dh[mw[mi][i][i] is the delay between two effective waves m=mw[mi][i]
1492: and mw[mi+1][i]. dh depends on stepm.
1493: */
1494:
1495: int i, mi, m;
1.8 lievre 1496: /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
1497: double sum=0., jmean=0.;*/
1.50 brouard 1498: int first;
1.11 lievre 1499: int j, k=0,jk, ju, jl;
1500: double sum=0.;
1.50 brouard 1501: first=0;
1.11 lievre 1502: jmin=1e+5;
1503: jmax=-1;
1504: jmean=0.;
1.2 lievre 1505: for(i=1; i<=imx; i++){
1506: mi=0;
1507: m=firstpass;
1508: while(s[m][i] <= nlstate){
1509: if(s[m][i]>=1)
1510: mw[++mi][i]=m;
1511: if(m >=lastpass)
1512: break;
1513: else
1514: m++;
1515: }/* end while */
1516: if (s[m][i] > nlstate){
1517: mi++; /* Death is another wave */
1518: /* if(mi==0) never been interviewed correctly before death */
1519: /* Only death is a correct wave */
1520: mw[mi][i]=m;
1521: }
1522:
1523: wav[i]=mi;
1.50 brouard 1524: if(mi==0){
1525: if(first==0){
1526: printf("Warning, no any valid information for:%d line=%d and may be others, see log file\n",num[i],i);
1527: first=1;
1528: }
1529: if(first==1){
1530: fprintf(ficlog,"Warning, no any valid information for:%d line=%d\n",num[i],i);
1531: }
1532: } /* end mi==0 */
1.2 lievre 1533: }
1534:
1535: for(i=1; i<=imx; i++){
1536: for(mi=1; mi<wav[i];mi++){
1537: if (stepm <=0)
1538: dh[mi][i]=1;
1539: else{
1540: if (s[mw[mi+1][i]][i] > nlstate) {
1.10 lievre 1541: if (agedc[i] < 2*AGESUP) {
1.2 lievre 1542: j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);
1.8 lievre 1543: if(j==0) j=1; /* Survives at least one month after exam */
1544: k=k+1;
1545: if (j >= jmax) jmax=j;
1.11 lievre 1546: if (j <= jmin) jmin=j;
1.8 lievre 1547: sum=sum+j;
1.30 lievre 1548: /*if (j<0) printf("j=%d num=%d \n",j,i); */
1.10 lievre 1549: }
1.2 lievre 1550: }
1551: else{
1552: j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
1553: k=k+1;
1554: if (j >= jmax) jmax=j;
1555: else if (j <= jmin)jmin=j;
1.30 lievre 1556: /* if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
1.2 lievre 1557: sum=sum+j;
1558: }
1559: jk= j/stepm;
1560: jl= j -jk*stepm;
1561: ju= j -(jk+1)*stepm;
1562: if(jl <= -ju)
1563: dh[mi][i]=jk;
1564: else
1565: dh[mi][i]=jk+1;
1566: if(dh[mi][i]==0)
1567: dh[mi][i]=1; /* At least one step */
1568: }
1569: }
1570: }
1.8 lievre 1571: jmean=sum/k;
1572: printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);
1.50 brouard 1573: fprintf(ficlog,"Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);
1.12 lievre 1574: }
1.50 brouard 1575:
1.2 lievre 1576: /*********** Tricode ****************************/
1577: void tricode(int *Tvar, int **nbcode, int imx)
1578: {
1.7 lievre 1579: int Ndum[20],ij=1, k, j, i;
1.2 lievre 1580: int cptcode=0;
1.7 lievre 1581: cptcoveff=0;
1582:
1583: for (k=0; k<19; k++) Ndum[k]=0;
1.2 lievre 1584: for (k=1; k<=7; k++) ncodemax[k]=0;
1.6 lievre 1585:
1.7 lievre 1586: for (j=1; j<=(cptcovn+2*cptcovprod); j++) {
1.2 lievre 1587: for (i=1; i<=imx; i++) {
1588: ij=(int)(covar[Tvar[j]][i]);
1589: Ndum[ij]++;
1.8 lievre 1590: /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
1.2 lievre 1591: if (ij > cptcode) cptcode=ij;
1592: }
1.7 lievre 1593:
1.2 lievre 1594: for (i=0; i<=cptcode; i++) {
1595: if(Ndum[i]!=0) ncodemax[j]++;
1596: }
1597: ij=1;
1.7 lievre 1598:
1.8 lievre 1599:
1.2 lievre 1600: for (i=1; i<=ncodemax[j]; i++) {
1.7 lievre 1601: for (k=0; k<=19; k++) {
1.2 lievre 1602: if (Ndum[k] != 0) {
1603: nbcode[Tvar[j]][ij]=k;
1.39 lievre 1604:
1.2 lievre 1605: ij++;
1606: }
1607: if (ij > ncodemax[j]) break;
1608: }
1609: }
1.7 lievre 1610: }
1.8 lievre 1611:
1612: for (k=0; k<19; k++) Ndum[k]=0;
1613:
1.12 lievre 1614: for (i=1; i<=ncovmodel-2; i++) {
1.50 brouard 1615: ij=Tvar[i];
1616: Ndum[ij]++;
1617: }
1.8 lievre 1618:
1.7 lievre 1619: ij=1;
1.8 lievre 1620: for (i=1; i<=10; i++) {
1.34 brouard 1621: if((Ndum[i]!=0) && (i<=ncovcol)){
1.8 lievre 1622: Tvaraff[ij]=i;
1623: ij++;
1.7 lievre 1624: }
1625: }
1626:
1.50 brouard 1627: cptcoveff=ij-1;
1.6 lievre 1628: }
1.2 lievre 1629:
1630: /*********** Health Expectancies ****************/
1631:
1.41 lievre 1632: 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 )
1633:
1.2 lievre 1634: {
1635: /* Health expectancies */
1.41 lievre 1636: int i, j, nhstepm, hstepm, h, nstepm, k, cptj;
1.35 lievre 1637: double age, agelim, hf;
1.41 lievre 1638: double ***p3mat,***varhe;
1639: double **dnewm,**doldm;
1640: double *xp;
1641: double **gp, **gm;
1642: double ***gradg, ***trgradg;
1643: int theta;
1644:
1645: varhe=ma3x(1,nlstate*2,1,nlstate*2,(int) bage, (int) fage);
1646: xp=vector(1,npar);
1647: dnewm=matrix(1,nlstate*2,1,npar);
1648: doldm=matrix(1,nlstate*2,1,nlstate*2);
1.2 lievre 1649:
1650: fprintf(ficreseij,"# Health expectancies\n");
1651: fprintf(ficreseij,"# Age");
1652: for(i=1; i<=nlstate;i++)
1653: for(j=1; j<=nlstate;j++)
1.41 lievre 1654: fprintf(ficreseij," %1d-%1d (SE)",i,j);
1.2 lievre 1655: fprintf(ficreseij,"\n");
1656:
1.36 brouard 1657: if(estepm < stepm){
1658: printf ("Problem %d lower than %d\n",estepm, stepm);
1659: }
1660: else hstepm=estepm;
1661: /* We compute the life expectancy from trapezoids spaced every estepm months
1662: * This is mainly to measure the difference between two models: for example
1663: * if stepm=24 months pijx are given only every 2 years and by summing them
1664: * we are calculating an estimate of the Life Expectancy assuming a linear
1665: * progression inbetween and thus overestimating or underestimating according
1666: * to the curvature of the survival function. If, for the same date, we
1667: * estimate the model with stepm=1 month, we can keep estepm to 24 months
1668: * to compare the new estimate of Life expectancy with the same linear
1669: * hypothesis. A more precise result, taking into account a more precise
1670: * curvature will be obtained if estepm is as small as stepm. */
1671:
1672: /* For example we decided to compute the life expectancy with the smallest unit */
1.31 brouard 1673: /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
1674: nhstepm is the number of hstepm from age to agelim
1675: nstepm is the number of stepm from age to agelin.
1676: Look at hpijx to understand the reason of that which relies in memory size
1.36 brouard 1677: and note for a fixed period like estepm months */
1.31 brouard 1678: /* We decided (b) to get a life expectancy respecting the most precise curvature of the
1.32 brouard 1679: survival function given by stepm (the optimization length). Unfortunately it
1.31 brouard 1680: means that if the survival funtion is printed only each two years of age and if
1681: you sum them up and add 1 year (area under the trapezoids) you won't get the same
1682: results. So we changed our mind and took the option of the best precision.
1683: */
1.36 brouard 1684: hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
1.2 lievre 1685:
1686: agelim=AGESUP;
1687: for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
1688: /* nhstepm age range expressed in number of stepm */
1.31 brouard 1689: nstepm=(int) rint((agelim-age)*YEARM/stepm);
1690: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
1.33 brouard 1691: /* if (stepm >= YEARM) hstepm=1;*/
1.31 brouard 1692: nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
1.2 lievre 1693: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
1.41 lievre 1694: gradg=ma3x(0,nhstepm,1,npar,1,nlstate*2);
1695: gp=matrix(0,nhstepm,1,nlstate*2);
1696: gm=matrix(0,nhstepm,1,nlstate*2);
1697:
1.2 lievre 1698: /* Computed by stepm unit matrices, product of hstepm matrices, stored
1699: in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
1700: hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);
1.41 lievre 1701:
1702:
1703: hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
1704:
1705: /* Computing Variances of health expectancies */
1706:
1707: for(theta=1; theta <=npar; theta++){
1708: for(i=1; i<=npar; i++){
1709: xp[i] = x[i] + (i==theta ?delti[theta]:0);
1710: }
1711: hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
1.39 lievre 1712:
1.41 lievre 1713: cptj=0;
1714: for(j=1; j<= nlstate; j++){
1715: for(i=1; i<=nlstate; i++){
1716: cptj=cptj+1;
1717: for(h=0, gp[h][cptj]=0.; h<=nhstepm-1; h++){
1718: gp[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;
1719: }
1720: }
1721: }
1722:
1723:
1724: for(i=1; i<=npar; i++)
1725: xp[i] = x[i] - (i==theta ?delti[theta]:0);
1726: hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
1727:
1728: cptj=0;
1729: for(j=1; j<= nlstate; j++){
1730: for(i=1;i<=nlstate;i++){
1731: cptj=cptj+1;
1732: for(h=0, gm[h][cptj]=0.; h<=nhstepm-1; h++){
1733: gm[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;
1734: }
1735: }
1736: }
1737: for(j=1; j<= nlstate*2; j++)
1738: for(h=0; h<=nhstepm-1; h++){
1739: gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
1740: }
1741: }
1742:
1743: /* End theta */
1744:
1745: trgradg =ma3x(0,nhstepm,1,nlstate*2,1,npar);
1746:
1747: for(h=0; h<=nhstepm-1; h++)
1748: for(j=1; j<=nlstate*2;j++)
1749: for(theta=1; theta <=npar; theta++)
1.46 brouard 1750: trgradg[h][j][theta]=gradg[h][theta][j];
1751:
1.41 lievre 1752:
1753: for(i=1;i<=nlstate*2;i++)
1754: for(j=1;j<=nlstate*2;j++)
1755: varhe[i][j][(int)age] =0.;
1756:
1.43 brouard 1757: printf("%d|",(int)age);fflush(stdout);
1.50 brouard 1758: fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
1.46 brouard 1759: for(h=0;h<=nhstepm-1;h++){
1.41 lievre 1760: for(k=0;k<=nhstepm-1;k++){
1761: matprod2(dnewm,trgradg[h],1,nlstate*2,1,npar,1,npar,matcov);
1762: matprod2(doldm,dnewm,1,nlstate*2,1,npar,1,nlstate*2,gradg[k]);
1763: for(i=1;i<=nlstate*2;i++)
1764: for(j=1;j<=nlstate*2;j++)
1765: varhe[i][j][(int)age] += doldm[i][j]*hf*hf;
1766: }
1767: }
1768: /* Computing expectancies */
1.2 lievre 1769: for(i=1; i<=nlstate;i++)
1770: for(j=1; j<=nlstate;j++)
1.29 lievre 1771: for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
1.31 brouard 1772: eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
1.41 lievre 1773:
1774: /* 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]);*/
1775:
1.2 lievre 1776: }
1.41 lievre 1777:
1.29 lievre 1778: fprintf(ficreseij,"%3.0f",age );
1.41 lievre 1779: cptj=0;
1.29 lievre 1780: for(i=1; i<=nlstate;i++)
1781: for(j=1; j<=nlstate;j++){
1.41 lievre 1782: cptj++;
1783: fprintf(ficreseij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[cptj][cptj][(int)age]) );
1.2 lievre 1784: }
1785: fprintf(ficreseij,"\n");
1.41 lievre 1786:
1787: free_matrix(gm,0,nhstepm,1,nlstate*2);
1788: free_matrix(gp,0,nhstepm,1,nlstate*2);
1789: free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*2);
1790: free_ma3x(trgradg,0,nhstepm,1,nlstate*2,1,npar);
1.2 lievre 1791: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
1792: }
1.47 brouard 1793: printf("\n");
1.50 brouard 1794: fprintf(ficlog,"\n");
1.47 brouard 1795:
1.41 lievre 1796: free_vector(xp,1,npar);
1797: free_matrix(dnewm,1,nlstate*2,1,npar);
1798: free_matrix(doldm,1,nlstate*2,1,nlstate*2);
1799: free_ma3x(varhe,1,nlstate*2,1,nlstate*2,(int) bage, (int)fage);
1.2 lievre 1800: }
1801:
1802: /************ Variance ******************/
1.50 brouard 1803: void varevsij(char optionfilefiname[], double ***vareij, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij, int estepm, int cptcov, int cptcod, int popbased)
1.2 lievre 1804: {
1805: /* Variance of health expectancies */
1806: /* double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
1.50 brouard 1807: /* double **newm;*/
1.2 lievre 1808: double **dnewm,**doldm;
1.50 brouard 1809: double **dnewmp,**doldmp;
1.36 brouard 1810: int i, j, nhstepm, hstepm, h, nstepm ;
1.2 lievre 1811: int k, cptcode;
1.12 lievre 1812: double *xp;
1.50 brouard 1813: double **gp, **gm; /* for var eij */
1814: double ***gradg, ***trgradg; /*for var eij */
1815: double **gradgp, **trgradgp; /* for var p point j */
1816: double *gpp, *gmp; /* for var p point j */
1817: double **varppt; /* for var p point j nlstate to nlstate+ndeath */
1.2 lievre 1818: double ***p3mat;
1.35 lievre 1819: double age,agelim, hf;
1.2 lievre 1820: int theta;
1.50 brouard 1821: char digit[4];
1822: char digitp[16];
1823:
1824: char fileresprobmorprev[FILENAMELENGTH];
1825:
1826: if(popbased==1)
1827: strcpy(digitp,"-populbased-");
1828: else
1829: strcpy(digitp,"-stablbased-");
1830:
1831: strcpy(fileresprobmorprev,"prmorprev");
1832: sprintf(digit,"%-d",ij);
1833: /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
1834: strcat(fileresprobmorprev,digit); /* Tvar to be done */
1835: strcat(fileresprobmorprev,digitp); /* Popbased or not */
1836: strcat(fileresprobmorprev,fileres);
1837: if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
1838: printf("Problem with resultfile: %s\n", fileresprobmorprev);
1839: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
1840: }
1841: printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
1842: fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
1843: fprintf(ficresprobmorprev,"# probabilities of dying during a year and weighted mean w1*p1j+w2*p2j+... stand dev in()\n");
1844: fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
1845: for(j=nlstate+1; j<=(nlstate+ndeath);j++){
1846: fprintf(ficresprobmorprev," p.%-d SE",j);
1847: for(i=1; i<=nlstate;i++)
1848: fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
1849: }
1850: fprintf(ficresprobmorprev,"\n");
1851: if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {
1852: printf("Problem with gnuplot file: %s\n", optionfilegnuplot);
1853: fprintf(ficlog,"Problem with gnuplot file: %s\n", optionfilegnuplot);
1854: exit(0);
1855: }
1856: else{
1857: fprintf(ficgp,"\n# Routine varevsij");
1858: }
1859: if((fichtm=fopen(optionfilehtm,"a"))==NULL) {
1860: printf("Problem with html file: %s\n", optionfilehtm);
1861: fprintf(ficlog,"Problem with html file: %s\n", optionfilehtm);
1862: exit(0);
1863: }
1864: else{
1.52 ! brouard 1865: fprintf(fichtm,"\n<li><h4> Computing probabilities of dying as a weighted average (i.e global mortality independent of initial healh state)</h4></li>\n");
1.50 brouard 1866: }
1867: varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
1.2 lievre 1868:
1.43 brouard 1869: 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 1870: fprintf(ficresvij,"# Age");
1871: for(i=1; i<=nlstate;i++)
1872: for(j=1; j<=nlstate;j++)
1873: fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);
1874: fprintf(ficresvij,"\n");
1875:
1876: xp=vector(1,npar);
1877: dnewm=matrix(1,nlstate,1,npar);
1878: doldm=matrix(1,nlstate,1,nlstate);
1.50 brouard 1879: dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
1880: doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
1881:
1882: gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
1883: gpp=vector(nlstate+1,nlstate+ndeath);
1884: gmp=vector(nlstate+1,nlstate+ndeath);
1885: trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
1.2 lievre 1886:
1.36 brouard 1887: if(estepm < stepm){
1888: printf ("Problem %d lower than %d\n",estepm, stepm);
1889: }
1890: else hstepm=estepm;
1891: /* For example we decided to compute the life expectancy with the smallest unit */
1.35 lievre 1892: /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
1893: nhstepm is the number of hstepm from age to agelim
1894: nstepm is the number of stepm from age to agelin.
1895: Look at hpijx to understand the reason of that which relies in memory size
1896: and note for a fixed period like k years */
1897: /* We decided (b) to get a life expectancy respecting the most precise curvature of the
1898: survival function given by stepm (the optimization length). Unfortunately it
1899: means that if the survival funtion is printed only each two years of age and if
1900: you sum them up and add 1 year (area under the trapezoids) you won't get the same
1901: results. So we changed our mind and took the option of the best precision.
1902: */
1.36 brouard 1903: hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
1.2 lievre 1904: agelim = AGESUP;
1905: for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
1.35 lievre 1906: nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
1907: nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
1.2 lievre 1908: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
1909: gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
1910: gp=matrix(0,nhstepm,1,nlstate);
1911: gm=matrix(0,nhstepm,1,nlstate);
1912:
1.50 brouard 1913:
1.2 lievre 1914: for(theta=1; theta <=npar; theta++){
1915: for(i=1; i<=npar; i++){ /* Computes gradient */
1916: xp[i] = x[i] + (i==theta ?delti[theta]:0);
1917: }
1918: hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
1919: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
1.14 lievre 1920:
1921: if (popbased==1) {
1922: for(i=1; i<=nlstate;i++)
1923: prlim[i][i]=probs[(int)age][i][ij];
1924: }
1.26 lievre 1925:
1.2 lievre 1926: for(j=1; j<= nlstate; j++){
1927: for(h=0; h<=nhstepm; h++){
1928: for(i=1, gp[h][j]=0.;i<=nlstate;i++)
1929: gp[h][j] += prlim[i][i]*p3mat[i][j][h];
1930: }
1931: }
1.50 brouard 1932: /* This for computing forces of mortality (h=1)as a weighted average */
1933: for(j=nlstate+1,gpp[j]=0.;j<=nlstate+ndeath;j++){
1934: for(i=1; i<= nlstate; i++)
1935: gpp[j] += prlim[i][i]*p3mat[i][j][1];
1936: }
1937: /* end force of mortality */
1938:
1.2 lievre 1939: for(i=1; i<=npar; i++) /* Computes gradient */
1940: xp[i] = x[i] - (i==theta ?delti[theta]:0);
1941: hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
1942: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
1.26 lievre 1943:
1.14 lievre 1944: if (popbased==1) {
1945: for(i=1; i<=nlstate;i++)
1946: prlim[i][i]=probs[(int)age][i][ij];
1947: }
1948:
1.2 lievre 1949: for(j=1; j<= nlstate; j++){
1950: for(h=0; h<=nhstepm; h++){
1951: for(i=1, gm[h][j]=0.;i<=nlstate;i++)
1952: gm[h][j] += prlim[i][i]*p3mat[i][j][h];
1953: }
1954: }
1.50 brouard 1955: /* This for computing force of mortality (h=1)as a weighted average */
1956: for(j=nlstate+1,gmp[j]=0.;j<=nlstate+ndeath;j++){
1957: for(i=1; i<= nlstate; i++)
1958: gmp[j] += prlim[i][i]*p3mat[i][j][1];
1959: }
1960: /* end force of mortality */
1.14 lievre 1961:
1.50 brouard 1962: for(j=1; j<= nlstate; j++) /* vareij */
1.2 lievre 1963: for(h=0; h<=nhstepm; h++){
1964: gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
1965: }
1.50 brouard 1966: for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
1967: gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
1968: }
1969:
1.2 lievre 1970: } /* End theta */
1971:
1.50 brouard 1972: trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
1.2 lievre 1973:
1.50 brouard 1974: for(h=0; h<=nhstepm; h++) /* veij */
1.2 lievre 1975: for(j=1; j<=nlstate;j++)
1976: for(theta=1; theta <=npar; theta++)
1977: trgradg[h][j][theta]=gradg[h][theta][j];
1978:
1.50 brouard 1979: for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
1980: for(theta=1; theta <=npar; theta++)
1981: trgradgp[j][theta]=gradgp[theta][j];
1982:
1.35 lievre 1983: hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
1.2 lievre 1984: for(i=1;i<=nlstate;i++)
1985: for(j=1;j<=nlstate;j++)
1986: vareij[i][j][(int)age] =0.;
1.35 lievre 1987:
1.2 lievre 1988: for(h=0;h<=nhstepm;h++){
1989: for(k=0;k<=nhstepm;k++){
1990: matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
1991: matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
1992: for(i=1;i<=nlstate;i++)
1993: for(j=1;j<=nlstate;j++)
1.35 lievre 1994: vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
1.2 lievre 1995: }
1996: }
1.35 lievre 1997:
1.50 brouard 1998: /* pptj */
1999: matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
2000: matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
2001: for(j=nlstate+1;j<=nlstate+ndeath;j++)
2002: for(i=nlstate+1;i<=nlstate+ndeath;i++)
2003: varppt[j][i]=doldmp[j][i];
2004: /* end ppptj */
2005: hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);
2006: prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);
2007:
2008: if (popbased==1) {
2009: for(i=1; i<=nlstate;i++)
2010: prlim[i][i]=probs[(int)age][i][ij];
2011: }
2012:
2013: /* This for computing force of mortality (h=1)as a weighted average */
2014: for(j=nlstate+1,gmp[j]=0.;j<=nlstate+ndeath;j++){
2015: for(i=1; i<= nlstate; i++)
1.52 ! brouard 2016: gmp[j] += prlim[i][i]*p3mat[i][j][1];
1.50 brouard 2017: }
2018: /* end force of mortality */
2019:
2020: fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
2021: for(j=nlstate+1; j<=(nlstate+ndeath);j++){
2022: fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
2023: for(i=1; i<=nlstate;i++){
2024: fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
2025: }
2026: }
2027: fprintf(ficresprobmorprev,"\n");
2028:
1.2 lievre 2029: fprintf(ficresvij,"%.0f ",age );
2030: for(i=1; i<=nlstate;i++)
2031: for(j=1; j<=nlstate;j++){
1.35 lievre 2032: fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
1.2 lievre 2033: }
2034: fprintf(ficresvij,"\n");
2035: free_matrix(gp,0,nhstepm,1,nlstate);
2036: free_matrix(gm,0,nhstepm,1,nlstate);
2037: free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
2038: free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
2039: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
2040: } /* End age */
1.50 brouard 2041: free_vector(gpp,nlstate+1,nlstate+ndeath);
2042: free_vector(gmp,nlstate+1,nlstate+ndeath);
2043: free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
2044: free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
2045: fprintf(ficgp,"\nset noparametric;set nolabel; set ter png small;set size 0.65, 0.65");
2046: /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */
2047: fprintf(ficgp,"\n set log y; set nolog x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
2048: fprintf(ficgp,"\n plot \"%s\" u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm);
2049: fprintf(ficgp,"\n replot \"%s\" u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm);
2050: fprintf(ficgp,"\n replot \"%s\" u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm);
2051: fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",fileresprobmorprev,fileresprobmorprev);
1.52 ! brouard 2052: fprintf(fichtm,"\n<br> Probability is computed over estepm=%d months. <br> <img src=\"varmuptjgr%s%s.png\"> <br>\n", stepm,digitp,digit);
! 2053: /* fprintf(fichtm,"\n<br> Probability is computed over estepm=%d months and then divided by estepm and multiplied by %.0f in order to have the probability to die over a year <br> <img src=\"varmuptjgr%s%s.png\"> <br>\n", stepm,YEARM,digitp,digit);
! 2054: */
1.50 brouard 2055: fprintf(ficgp,"\nset out \"varmuptjgr%s%s.png\";replot;",digitp,digit);
2056:
1.2 lievre 2057: free_vector(xp,1,npar);
1.50 brouard 2058: free_matrix(doldm,1,nlstate,1,nlstate);
2059: free_matrix(dnewm,1,nlstate,1,npar);
2060: free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
2061: free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
2062: free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
2063: fclose(ficresprobmorprev);
2064: fclose(ficgp);
2065: fclose(fichtm);
1.2 lievre 2066:
2067: }
2068:
2069: /************ Variance of prevlim ******************/
2070: 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)
2071: {
2072: /* Variance of prevalence limit */
2073: /* double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
2074: double **newm;
2075: double **dnewm,**doldm;
2076: int i, j, nhstepm, hstepm;
2077: int k, cptcode;
2078: double *xp;
2079: double *gp, *gm;
2080: double **gradg, **trgradg;
2081: double age,agelim;
2082: int theta;
2083:
1.43 brouard 2084: fprintf(ficresvpl,"# Standard deviation of prevalence's limit\n");
1.2 lievre 2085: fprintf(ficresvpl,"# Age");
2086: for(i=1; i<=nlstate;i++)
2087: fprintf(ficresvpl," %1d-%1d",i,i);
2088: fprintf(ficresvpl,"\n");
2089:
2090: xp=vector(1,npar);
2091: dnewm=matrix(1,nlstate,1,npar);
2092: doldm=matrix(1,nlstate,1,nlstate);
2093:
2094: hstepm=1*YEARM; /* Every year of age */
2095: hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */
2096: agelim = AGESUP;
2097: for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
2098: nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
2099: if (stepm >= YEARM) hstepm=1;
2100: nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
2101: gradg=matrix(1,npar,1,nlstate);
2102: gp=vector(1,nlstate);
2103: gm=vector(1,nlstate);
2104:
2105: for(theta=1; theta <=npar; theta++){
2106: for(i=1; i<=npar; i++){ /* Computes gradient */
2107: xp[i] = x[i] + (i==theta ?delti[theta]:0);
2108: }
2109: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
2110: for(i=1;i<=nlstate;i++)
2111: gp[i] = prlim[i][i];
2112:
2113: for(i=1; i<=npar; i++) /* Computes gradient */
2114: xp[i] = x[i] - (i==theta ?delti[theta]:0);
2115: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
2116: for(i=1;i<=nlstate;i++)
2117: gm[i] = prlim[i][i];
2118:
2119: for(i=1;i<=nlstate;i++)
2120: gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
2121: } /* End theta */
2122:
2123: trgradg =matrix(1,nlstate,1,npar);
2124:
2125: for(j=1; j<=nlstate;j++)
2126: for(theta=1; theta <=npar; theta++)
2127: trgradg[j][theta]=gradg[theta][j];
2128:
2129: for(i=1;i<=nlstate;i++)
2130: varpl[i][(int)age] =0.;
2131: matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
2132: matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
2133: for(i=1;i<=nlstate;i++)
2134: varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
2135:
2136: fprintf(ficresvpl,"%.0f ",age );
2137: for(i=1; i<=nlstate;i++)
2138: fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
2139: fprintf(ficresvpl,"\n");
2140: free_vector(gp,1,nlstate);
2141: free_vector(gm,1,nlstate);
2142: free_matrix(gradg,1,npar,1,nlstate);
2143: free_matrix(trgradg,1,nlstate,1,npar);
2144: } /* End age */
2145:
2146: free_vector(xp,1,npar);
2147: free_matrix(doldm,1,nlstate,1,npar);
2148: free_matrix(dnewm,1,nlstate,1,nlstate);
2149:
2150: }
2151:
1.13 lievre 2152: /************ Variance of one-step probabilities ******************/
1.47 brouard 2153: 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 2154: {
1.49 lievre 2155: int i, j=0, i1, k1, l1, t, tj;
1.47 brouard 2156: int k2, l2, j1, z1;
1.46 brouard 2157: int k=0,l, cptcode;
1.50 brouard 2158: int first=1, first1;
1.51 brouard 2159: double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
1.13 lievre 2160: double **dnewm,**doldm;
2161: double *xp;
2162: double *gp, *gm;
2163: double **gradg, **trgradg;
1.47 brouard 2164: double **mu;
1.13 lievre 2165: double age,agelim, cov[NCOVMAX];
1.47 brouard 2166: double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
1.13 lievre 2167: int theta;
2168: char fileresprob[FILENAMELENGTH];
1.46 brouard 2169: char fileresprobcov[FILENAMELENGTH];
2170: char fileresprobcor[FILENAMELENGTH];
1.13 lievre 2171:
1.47 brouard 2172: double ***varpij;
2173:
1.13 lievre 2174: strcpy(fileresprob,"prob");
2175: strcat(fileresprob,fileres);
2176: if((ficresprob=fopen(fileresprob,"w"))==NULL) {
2177: printf("Problem with resultfile: %s\n", fileresprob);
1.50 brouard 2178: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
1.13 lievre 2179: }
1.46 brouard 2180: strcpy(fileresprobcov,"probcov");
2181: strcat(fileresprobcov,fileres);
2182: if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
2183: printf("Problem with resultfile: %s\n", fileresprobcov);
1.50 brouard 2184: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
1.46 brouard 2185: }
2186: strcpy(fileresprobcor,"probcor");
2187: strcat(fileresprobcor,fileres);
2188: if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
2189: printf("Problem with resultfile: %s\n", fileresprobcor);
1.50 brouard 2190: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
1.46 brouard 2191: }
1.41 lievre 2192: printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
1.50 brouard 2193: fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
1.46 brouard 2194: printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
1.50 brouard 2195: fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
1.46 brouard 2196: printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
1.50 brouard 2197: fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
1.13 lievre 2198:
1.46 brouard 2199: fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
1.41 lievre 2200: fprintf(ficresprob,"# Age");
1.46 brouard 2201: fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
2202: fprintf(ficresprobcov,"# Age");
2203: fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
2204: fprintf(ficresprobcov,"# Age");
1.47 brouard 2205:
2206:
1.41 lievre 2207: for(i=1; i<=nlstate;i++)
1.46 brouard 2208: for(j=1; j<=(nlstate+ndeath);j++){
1.41 lievre 2209: fprintf(ficresprob," p%1d-%1d (SE)",i,j);
1.46 brouard 2210: fprintf(ficresprobcov," p%1d-%1d ",i,j);
2211: fprintf(ficresprobcor," p%1d-%1d ",i,j);
2212: }
1.41 lievre 2213: fprintf(ficresprob,"\n");
1.46 brouard 2214: fprintf(ficresprobcov,"\n");
2215: fprintf(ficresprobcor,"\n");
1.13 lievre 2216: xp=vector(1,npar);
1.47 brouard 2217: dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
2218: doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
2219: mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
2220: varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
2221: first=1;
2222: if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {
2223: printf("Problem with gnuplot file: %s\n", optionfilegnuplot);
1.50 brouard 2224: fprintf(ficlog,"Problem with gnuplot file: %s\n", optionfilegnuplot);
1.47 brouard 2225: exit(0);
2226: }
2227: else{
2228: fprintf(ficgp,"\n# Routine varprob");
2229: }
2230: if((fichtm=fopen(optionfilehtm,"a"))==NULL) {
2231: printf("Problem with html file: %s\n", optionfilehtm);
1.50 brouard 2232: fprintf(ficlog,"Problem with html file: %s\n", optionfilehtm);
1.47 brouard 2233: exit(0);
2234: }
2235: else{
1.50 brouard 2236: fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
2237: fprintf(fichtm,"\n");
2238:
1.49 lievre 2239: fprintf(fichtm,"\n<li><h4> Computing matrix of variance-covariance of step probabilities</h4></li>\n");
2240: fprintf(fichtm,"\nWe have drawn ellipsoids of confidence around the p<inf>ij</inf>, p<inf>kl</inf> to understand the covariance between two incidences. They are expressed in year<sup>-1</sup> in order to be less dependent of stepm.<br>\n");
1.47 brouard 2241: 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");
2242:
2243: }
1.49 lievre 2244:
2245:
1.13 lievre 2246: cov[1]=1;
1.49 lievre 2247: tj=cptcoveff;
2248: if (cptcovn<1) {tj=1;ncodemax[1]=1;}
1.39 lievre 2249: j1=0;
1.49 lievre 2250: for(t=1; t<=tj;t++){
2251: for(i1=1; i1<=ncodemax[t];i1++){
2252: j1++;
2253:
2254: if (cptcovn>0) {
2255: fprintf(ficresprob, "\n#********** Variable ");
2256: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
2257: fprintf(ficresprob, "**********\n#");
2258: fprintf(ficresprobcov, "\n#********** Variable ");
2259: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
2260: fprintf(ficresprobcov, "**********\n#");
2261:
2262: fprintf(ficgp, "\n#********** Variable ");
2263: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, "# V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
2264: fprintf(ficgp, "**********\n#");
2265:
2266:
2267: fprintf(fichtm, "\n<hr size=\"2\" color=\"#EC5E5E\">********** Variable ");
2268: for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
2269: fprintf(fichtm, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
2270:
2271: fprintf(ficresprobcor, "\n#********** Variable ");
2272: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
2273: fprintf(ficgp, "**********\n#");
2274: }
2275:
1.39 lievre 2276: for (age=bage; age<=fage; age ++){
2277: cov[2]=age;
2278: for (k=1; k<=cptcovn;k++) {
2279: cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];
1.13 lievre 2280: }
1.39 lievre 2281: for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
2282: for (k=1; k<=cptcovprod;k++)
2283: cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
2284:
1.47 brouard 2285: gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
2286: trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
2287: gp=vector(1,(nlstate)*(nlstate+ndeath));
2288: gm=vector(1,(nlstate)*(nlstate+ndeath));
1.39 lievre 2289:
2290: for(theta=1; theta <=npar; theta++){
2291: for(i=1; i<=npar; i++)
2292: xp[i] = x[i] + (i==theta ?delti[theta]:0);
2293:
2294: pmij(pmmij,cov,ncovmodel,xp,nlstate);
2295:
2296: k=0;
1.47 brouard 2297: for(i=1; i<= (nlstate); i++){
1.39 lievre 2298: for(j=1; j<=(nlstate+ndeath);j++){
2299: k=k+1;
2300: gp[k]=pmmij[i][j];
2301: }
2302: }
2303:
2304: for(i=1; i<=npar; i++)
2305: xp[i] = x[i] - (i==theta ?delti[theta]:0);
1.13 lievre 2306:
1.39 lievre 2307: pmij(pmmij,cov,ncovmodel,xp,nlstate);
2308: k=0;
1.47 brouard 2309: for(i=1; i<=(nlstate); i++){
1.39 lievre 2310: for(j=1; j<=(nlstate+ndeath);j++){
2311: k=k+1;
2312: gm[k]=pmmij[i][j];
2313: }
2314: }
2315:
1.47 brouard 2316: for(i=1; i<= (nlstate)*(nlstate+ndeath); i++)
1.39 lievre 2317: gradg[theta][i]=(gp[i]-gm[i])/2./delti[theta];
1.13 lievre 2318: }
2319:
1.47 brouard 2320: for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
1.39 lievre 2321: for(theta=1; theta <=npar; theta++)
2322: trgradg[j][theta]=gradg[theta][j];
2323:
1.47 brouard 2324: matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov);
2325: matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);
1.39 lievre 2326:
2327: pmij(pmmij,cov,ncovmodel,x,nlstate);
2328:
2329: k=0;
1.47 brouard 2330: for(i=1; i<=(nlstate); i++){
1.39 lievre 2331: for(j=1; j<=(nlstate+ndeath);j++){
2332: k=k+1;
1.47 brouard 2333: mu[k][(int) age]=pmmij[i][j];
1.39 lievre 2334: }
1.13 lievre 2335: }
1.47 brouard 2336: for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
2337: for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
2338: varpij[i][j][(int)age] = doldm[i][j];
2339:
1.46 brouard 2340: /*printf("\n%d ",(int)age);
1.47 brouard 2341: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
1.13 lievre 2342: printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
1.50 brouard 2343: fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
1.13 lievre 2344: }*/
2345:
1.39 lievre 2346: fprintf(ficresprob,"\n%d ",(int)age);
1.46 brouard 2347: fprintf(ficresprobcov,"\n%d ",(int)age);
2348: fprintf(ficresprobcor,"\n%d ",(int)age);
1.13 lievre 2349:
1.47 brouard 2350: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)
2351: fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));
1.46 brouard 2352: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
1.47 brouard 2353: fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);
2354: fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
1.46 brouard 2355: }
2356: i=0;
2357: for (k=1; k<=(nlstate);k++){
2358: for (l=1; l<=(nlstate+ndeath);l++){
2359: i=i++;
2360: fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
2361: fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
2362: for (j=1; j<=i;j++){
1.47 brouard 2363: fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);
2364: fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));
1.46 brouard 2365: }
2366: }
1.47 brouard 2367: }/* end of loop for state */
2368: } /* end of loop for age */
1.50 brouard 2369:
2370: /* Confidence intervalle of pij */
2371: /*
2372: fprintf(ficgp,"\nset noparametric;unset label");
2373: fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");
2374: fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
2375: fprintf(fichtm,"\n<br>Probability with confidence intervals expressed in year<sup>-1</sup> :<a href=\"pijgr%s.png\">pijgr%s.png</A>, ",optionfilefiname,optionfilefiname);
2376: fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);
2377: fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);
2378: fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);
2379: */
2380:
2381: /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
2382: first1=1;
1.51 brouard 2383: for (k2=1; k2<=(nlstate);k2++){
2384: for (l2=1; l2<=(nlstate+ndeath);l2++){
2385: if(l2==k2) continue;
2386: j=(k2-1)*(nlstate+ndeath)+l2;
2387: for (k1=1; k1<=(nlstate);k1++){
2388: for (l1=1; l1<=(nlstate+ndeath);l1++){
2389: if(l1==k1) continue;
2390: i=(k1-1)*(nlstate+ndeath)+l1;
2391: if(i<=j) continue;
1.47 brouard 2392: for (age=bage; age<=fage; age ++){
2393: if ((int)age %5==0){
2394: v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;
2395: v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;
2396: cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;
2397: mu1=mu[i][(int) age]/stepm*YEARM ;
2398: mu2=mu[j][(int) age]/stepm*YEARM;
1.51 brouard 2399: c12=cv12/sqrt(v1*v2);
1.47 brouard 2400: /* Computing eigen value of matrix of covariance */
1.51 brouard 2401: lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
2402: lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
1.47 brouard 2403: /* Eigen vectors */
2404: v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
1.51 brouard 2405: /*v21=sqrt(1.-v11*v11); *//* error */
2406: v21=(lc1-v1)/cv12*v11;
1.47 brouard 2407: v12=-v21;
2408: v22=v11;
1.51 brouard 2409: tnalp=v21/v11;
2410: if(first1==1){
2411: first1=0;
2412: printf("%d %d%d-%d%d mu %.4e %.4e Var %.4e %.4e cor %.3f cov %.4e Eig %.3e %.3e 1stv %.3f %.3f tang %.3f\nOthers in log...\n",(int) age,k1,l1,k2,l2,mu1,mu2,v1,v2,c12,cv12,lc1,lc2,v11,v21,tnalp);
2413: }
2414: fprintf(ficlog,"%d %d%d-%d%d mu %.4e %.4e Var %.4e %.4e cor %.3f cov %.4e Eig %.3e %.3e 1stv %.3f %.3f tan %.3f\n",(int) age,k1,l1,k2,l2,mu1,mu2,v1,v2,c12,cv12,lc1,lc2,v11,v21,tnalp);
1.47 brouard 2415: /*printf(fignu*/
2416: /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */
1.51 brouard 2417: /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */
1.47 brouard 2418: if(first==1){
2419: first=0;
1.51 brouard 2420: fprintf(ficgp,"\nset parametric;unset label");
2421: fprintf(ficgp,"\nset log y;set log x; set xlabel \"p%1d%1d (year-1)\";set ylabel \"p%1d%1d (year-1)\"",k1,l1,k2,l2);
1.47 brouard 2422: fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
1.51 brouard 2423: fprintf(fichtm,"\n<br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup> :<a href=\"varpijgr%s%d%1d%1d-%1d%1d.png\">varpijgr%s%d%1d%1d-%1d%1d.png</A>, ",k1,l1,k2,l2,optionfilefiname, j1,k1,l1,k2,l2,optionfilefiname, j1,k1,l1,k2,l2);
2424: fprintf(fichtm,"\n<br><img src=\"varpijgr%s%d%1d%1d-%1d%1d.png\"> ",optionfilefiname, j1,k1,l1,k2,l2);
1.52 ! brouard 2425: fprintf(fichtm,"\n<br> Correlation at age %d (%.3f),",(int) age, c12);
1.51 brouard 2426: fprintf(ficgp,"\nset out \"varpijgr%s%d%1d%1d-%1d%1d.png\"",optionfilefiname, j1,k1,l1,k2,l2);
2427: fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
2428: fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
2429: fprintf(ficgp,"\nplot [-pi:pi] %11.3e+ %.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)), %11.3e +%.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)) not",\
2430: mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
2431: mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
1.47 brouard 2432: }else{
2433: first=0;
1.52 ! brouard 2434: fprintf(fichtm," %d (%.3f),",(int) age, c12);
1.51 brouard 2435: fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
2436: fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
2437: fprintf(ficgp,"\nreplot %11.3e+ %.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)), %11.3e +%.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)) not",\
2438: mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
2439: mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
1.47 brouard 2440: }/* if first */
2441: } /* age mod 5 */
2442: } /* end loop age */
1.51 brouard 2443: fprintf(ficgp,"\nset out \"varpijgr%s%d%1d%1d-%1d%1d.png\";replot;",optionfilefiname, j1,k1,l1,k2,l2);
1.47 brouard 2444: first=1;
2445: } /*l12 */
2446: } /* k12 */
2447: } /*l1 */
2448: }/* k1 */
2449: } /* loop covariates */
2450: free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
1.13 lievre 2451: free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
2452: free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
1.47 brouard 2453: free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
1.13 lievre 2454: free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
2455: free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
1.39 lievre 2456: }
2457: free_vector(xp,1,npar);
2458: fclose(ficresprob);
1.46 brouard 2459: fclose(ficresprobcov);
2460: fclose(ficresprobcor);
1.47 brouard 2461: fclose(ficgp);
2462: fclose(fichtm);
1.13 lievre 2463: }
1.2 lievre 2464:
1.45 lievre 2465:
1.25 lievre 2466: /******************* Printing html file ***********/
1.35 lievre 2467: void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \
1.43 brouard 2468: int lastpass, int stepm, int weightopt, char model[],\
1.47 brouard 2469: int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
2470: int popforecast, int estepm ,\
1.43 brouard 2471: double jprev1, double mprev1,double anprev1, \
2472: double jprev2, double mprev2,double anprev2){
1.25 lievre 2473: int jj1, k1, i1, cpt;
2474: /*char optionfilehtm[FILENAMELENGTH];*/
1.47 brouard 2475: if((fichtm=fopen(optionfilehtm,"a"))==NULL) {
1.25 lievre 2476: printf("Problem with %s \n",optionfilehtm), exit(0);
1.50 brouard 2477: fprintf(ficlog,"Problem with %s \n",optionfilehtm), exit(0);
1.25 lievre 2478: }
2479:
1.49 lievre 2480: fprintf(fichtm,"<ul><li><h4>Result files (first order: no variance)</h4>\n
1.43 brouard 2481: - 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
2482: - Estimated transition probabilities over %d (stepm) months: <a href=\"pij%s\">pij%s</a><br>\n
2483: - Stable prevalence in each health state: <a href=\"pl%s\">pl%s</a> <br>\n
2484: - Life expectancies by age and initial health status (estepm=%2d months):
2485: <a href=\"e%s\">e%s</a> <br>\n</li>", \
2486: jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,fileres,fileres,stepm,fileres,fileres,fileres,fileres,estepm,fileres,fileres);
2487:
1.50 brouard 2488: fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
2489:
2490: m=cptcoveff;
2491: if (cptcovn < 1) {m=1;ncodemax[1]=1;}
2492:
2493: jj1=0;
2494: for(k1=1; k1<=m;k1++){
2495: for(i1=1; i1<=ncodemax[k1];i1++){
2496: jj1++;
2497: if (cptcovn > 0) {
2498: fprintf(fichtm,"<hr size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
2499: for (cpt=1; cpt<=cptcoveff;cpt++)
2500: fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
2501: fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
2502: }
2503: /* Pij */
2504: 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>
2505: <img src=\"pe%s%d1.png\">",stepm,strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);
2506: /* Quasi-incidences */
2507: 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>
2508: <img src=\"pe%s%d2.png\">",stepm,strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);
2509: /* Stable prevalence in each health state */
2510: for(cpt=1; cpt<nlstate;cpt++){
2511: fprintf(fichtm,"<br>- Stable prevalence in each health state : p%s%d%d.png<br>
2512: <img src=\"p%s%d%d.png\">",strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);
2513: }
2514: for(cpt=1; cpt<=nlstate;cpt++) {
2515: fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): exp%s%d%d.png <br>
2516: <img src=\"exp%s%d%d.png\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);
2517: }
2518: fprintf(fichtm,"\n<br>- Total life expectancy by age and
2519: health expectancies in states (1) and (2): e%s%d.png<br>
2520: <img src=\"e%s%d.png\">",strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);
2521: } /* end i1 */
2522: }/* End k1 */
2523: fprintf(fichtm,"</ul>");
2524:
2525:
1.49 lievre 2526: fprintf(fichtm,"\n<br><li><h4> Result files (second order: variances)</h4>\n
1.43 brouard 2527: - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n
2528: - Variance of one-step probabilities: <a href=\"prob%s\">prob%s</a> <br>\n
1.46 brouard 2529: - Variance-covariance of one-step probabilities: <a href=\"probcov%s\">probcov%s</a> <br>\n
2530: - Correlation matrix of one-step probabilities: <a href=\"probcor%s\">probcor%s</a> <br>\n
1.43 brouard 2531: - Variances and covariances of life expectancies by age and initial health status (estepm=%d months): <a href=\"v%s\">v%s</a><br>\n
2532: - Health expectancies with their variances (no covariance): <a href=\"t%s\">t%s</a> <br>\n
1.46 brouard 2533: - 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 2534:
2535: if(popforecast==1) fprintf(fichtm,"\n
2536: - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n
2537: - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n
2538: <br>",fileres,fileres,fileres,fileres);
2539: else
2540: 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);
1.50 brouard 2541: fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
1.25 lievre 2542:
2543: m=cptcoveff;
2544: if (cptcovn < 1) {m=1;ncodemax[1]=1;}
2545:
2546: jj1=0;
2547: for(k1=1; k1<=m;k1++){
2548: for(i1=1; i1<=ncodemax[k1];i1++){
1.45 lievre 2549: jj1++;
2550: if (cptcovn > 0) {
2551: fprintf(fichtm,"<hr size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
2552: for (cpt=1; cpt<=cptcoveff;cpt++)
2553: fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
2554: fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
2555: }
1.50 brouard 2556: for(cpt=1; cpt<=nlstate;cpt++) {
1.25 lievre 2557: fprintf(fichtm,"<br>- Observed and stationary prevalence (with confident
1.42 brouard 2558: interval) in state (%d): v%s%d%d.png <br>
2559: <img src=\"v%s%d%d.png\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);
1.25 lievre 2560: }
1.50 brouard 2561: } /* end i1 */
2562: }/* End k1 */
2563: fprintf(fichtm,"</ul>");
1.25 lievre 2564: fclose(fichtm);
2565: }
2566:
2567: /******************* Gnuplot file **************/
1.47 brouard 2568: void printinggnuplot(char fileres[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
1.25 lievre 2569:
2570: int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;
1.43 brouard 2571: int ng;
1.47 brouard 2572: if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {
1.25 lievre 2573: printf("Problem with file %s",optionfilegnuplot);
1.50 brouard 2574: fprintf(ficlog,"Problem with file %s",optionfilegnuplot);
1.25 lievre 2575: }
2576:
2577: #ifdef windows
2578: fprintf(ficgp,"cd \"%s\" \n",pathc);
2579: #endif
2580: m=pow(2,cptcoveff);
2581:
2582: /* 1eme*/
2583: for (cpt=1; cpt<= nlstate ; cpt ++) {
2584: for (k1=1; k1<= m ; k1 ++) {
2585:
2586: #ifdef windows
1.43 brouard 2587: fprintf(ficgp,"\nset out \"v%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);
1.42 brouard 2588: 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 2589: #endif
2590: #ifdef unix
1.43 brouard 2591: fprintf(ficgp,"\nset out \"v%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);
1.35 lievre 2592: fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nplot [%.f:%.f] \"vpl%s\" u 1:2 \"\%%lf",ageminpar,fage,fileres);
1.25 lievre 2593: #endif
2594:
2595: for (i=1; i<= nlstate ; i ++) {
2596: if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
2597: else fprintf(ficgp," \%%*lf (\%%*lf)");
2598: }
2599: fprintf(ficgp,"\" t\"Stationary prevalence\" w l 0,\"vpl%s\" every :::%d::%d u 1:($2+2*$3) \"\%%lf",fileres,k1-1,k1-1);
2600: for (i=1; i<= nlstate ; i ++) {
2601: if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
2602: else fprintf(ficgp," \%%*lf (\%%*lf)");
2603: }
2604: fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"vpl%s\" every :::%d::%d u 1:($2-2*$3) \"\%%lf",fileres,k1-1,k1-1);
2605: for (i=1; i<= nlstate ; i ++) {
2606: if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
2607: else fprintf(ficgp," \%%*lf (\%%*lf)");
2608: }
2609: fprintf(ficgp,"\" t\"\" w l 1,\"p%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",fileres,k1-1,k1-1,2+4*(cpt-1));
2610: #ifdef unix
1.42 brouard 2611: fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65\n");
1.25 lievre 2612: #endif
2613: }
2614: }
2615: /*2 eme*/
2616:
2617: for (k1=1; k1<= m ; k1 ++) {
1.43 brouard 2618: fprintf(ficgp,"\nset out \"e%s%d.png\" \n",strtok(optionfile, "."),k1);
1.42 brouard 2619: fprintf(ficgp,"set ylabel \"Years\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] ",ageminpar,fage);
1.25 lievre 2620:
2621: for (i=1; i<= nlstate+1 ; i ++) {
2622: k=2*i;
2623: fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:2 \"\%%lf",fileres,k1-1,k1-1);
2624: for (j=1; j<= nlstate+1 ; j ++) {
2625: if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
2626: else fprintf(ficgp," \%%*lf (\%%*lf)");
2627: }
2628: if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");
2629: else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);
2630: fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",fileres,k1-1,k1-1);
2631: for (j=1; j<= nlstate+1 ; j ++) {
2632: if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
2633: else fprintf(ficgp," \%%*lf (\%%*lf)");
2634: }
2635: fprintf(ficgp,"\" t\"\" w l 0,");
2636: fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",fileres,k1-1,k1-1);
2637: for (j=1; j<= nlstate+1 ; j ++) {
2638: if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
2639: else fprintf(ficgp," \%%*lf (\%%*lf)");
2640: }
2641: if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");
2642: else fprintf(ficgp,"\" t\"\" w l 0,");
2643: }
2644: }
2645:
2646: /*3eme*/
2647:
2648: for (k1=1; k1<= m ; k1 ++) {
2649: for (cpt=1; cpt<= nlstate ; cpt ++) {
1.41 lievre 2650: k=2+nlstate*(2*cpt-2);
1.43 brouard 2651: fprintf(ficgp,"\nset out \"exp%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);
1.42 brouard 2652: fprintf(ficgp,"set ter png small\nset size 0.65,0.65\nplot [%.f:%.f] \"e%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,fileres,k1-1,k1-1,k,cpt);
1.41 lievre 2653: /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
2654: for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
2655: fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
2656: fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
2657: for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
2658: fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
2659:
2660: */
1.25 lievre 2661: for (i=1; i< nlstate ; i ++) {
1.41 lievre 2662: 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);
2663:
1.25 lievre 2664: }
2665: }
1.42 brouard 2666: }
1.25 lievre 2667:
2668: /* CV preval stat */
2669: for (k1=1; k1<= m ; k1 ++) {
2670: for (cpt=1; cpt<nlstate ; cpt ++) {
2671: k=3;
1.43 brouard 2672: fprintf(ficgp,"\nset out \"p%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);
1.42 brouard 2673: 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/($%d",ageminpar,agemaxpar,fileres,k1,k+cpt+1,k+1);
1.25 lievre 2674:
2675: for (i=1; i< nlstate ; i ++)
2676: fprintf(ficgp,"+$%d",k+i+1);
2677: fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);
2678:
2679: l=3+(nlstate+ndeath)*cpt;
2680: fprintf(ficgp,",\"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",fileres,k1,l+cpt+1,l+1);
2681: for (i=1; i< nlstate ; i ++) {
2682: l=3+(nlstate+ndeath)*cpt;
2683: fprintf(ficgp,"+$%d",l+i+1);
2684: }
2685: fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);
2686: }
2687: }
2688:
2689: /* proba elementaires */
2690: for(i=1,jk=1; i <=nlstate; i++){
2691: for(k=1; k <=(nlstate+ndeath); k++){
2692: if (k != i) {
2693: for(j=1; j <=ncovmodel; j++){
2694: fprintf(ficgp,"p%d=%f ",jk,p[jk]);
2695: jk++;
2696: fprintf(ficgp,"\n");
2697: }
2698: }
2699: }
1.42 brouard 2700: }
1.25 lievre 2701:
1.43 brouard 2702: for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/
2703: for(jk=1; jk <=m; jk++) {
2704: fprintf(ficgp,"\nset out \"pe%s%d%d.png\" \n",strtok(optionfile, "."),jk,ng);
2705: if (ng==2)
2706: fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
2707: else
2708: fprintf(ficgp,"\nset title \"Probability\"\n");
2709: fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65\nset log y\nplot [%.f:%.f] ",ageminpar,agemaxpar);
2710: i=1;
2711: for(k2=1; k2<=nlstate; k2++) {
2712: k3=i;
2713: for(k=1; k<=(nlstate+ndeath); k++) {
2714: if (k != k2){
2715: if(ng==2)
1.46 brouard 2716: fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);
1.42 brouard 2717: else
1.43 brouard 2718: fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
1.42 brouard 2719: ij=1;
1.43 brouard 2720: for(j=3; j <=ncovmodel; j++) {
1.42 brouard 2721: if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
1.43 brouard 2722: fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
1.42 brouard 2723: ij++;
2724: }
2725: else
1.43 brouard 2726: fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
1.42 brouard 2727: }
1.43 brouard 2728: fprintf(ficgp,")/(1");
2729:
2730: for(k1=1; k1 <=nlstate; k1++){
2731: fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);
2732: ij=1;
2733: for(j=3; j <=ncovmodel; j++){
2734: if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
2735: fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
2736: ij++;
2737: }
2738: else
2739: fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
2740: }
2741: fprintf(ficgp,")");
2742: }
2743: fprintf(ficgp,") t \"p%d%d\" ", k2,k);
2744: if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");
2745: i=i+ncovmodel;
1.42 brouard 2746: }
1.50 brouard 2747: } /* end k */
2748: } /* end k2 */
2749: } /* end jk */
2750: } /* end ng */
1.47 brouard 2751: fclose(ficgp);
1.25 lievre 2752: } /* end gnuplot */
2753:
2754:
2755: /*************** Moving average **************/
1.35 lievre 2756: void movingaverage(double agedeb, double fage,double ageminpar, double ***mobaverage){
1.25 lievre 2757:
2758: int i, cpt, cptcod;
1.35 lievre 2759: for (agedeb=ageminpar; agedeb<=fage; agedeb++)
1.25 lievre 2760: for (i=1; i<=nlstate;i++)
2761: for (cptcod=1;cptcod<=ncodemax[cptcov];cptcod++)
2762: mobaverage[(int)agedeb][i][cptcod]=0.;
2763:
1.35 lievre 2764: for (agedeb=ageminpar+4; agedeb<=fage; agedeb++){
1.25 lievre 2765: for (i=1; i<=nlstate;i++){
2766: for (cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
2767: for (cpt=0;cpt<=4;cpt++){
2768: mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]+probs[(int)agedeb-cpt][i][cptcod];
2769: }
2770: mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]/5;
2771: }
2772: }
2773: }
2774:
2775: }
2776:
1.27 lievre 2777:
2778: /************** Forecasting ******************/
1.35 lievre 2779: 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 2780:
2781: int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;
2782: int *popage;
2783: double calagedate, agelim, kk1, kk2, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
2784: double *popeffectif,*popcount;
2785: double ***p3mat;
2786: char fileresf[FILENAMELENGTH];
2787:
2788: agelim=AGESUP;
2789: calagedate=(anproj1+mproj1/12.+jproj1/365.-dateintmean)*YEARM;
1.28 lievre 2790:
1.35 lievre 2791: prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);
1.28 lievre 2792:
1.27 lievre 2793:
2794: strcpy(fileresf,"f");
2795: strcat(fileresf,fileres);
2796: if((ficresf=fopen(fileresf,"w"))==NULL) {
2797: printf("Problem with forecast resultfile: %s\n", fileresf);
1.50 brouard 2798: fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);
1.27 lievre 2799: }
2800: printf("Computing forecasting: result on file '%s' \n", fileresf);
1.50 brouard 2801: fprintf(ficlog,"Computing forecasting: result on file '%s' \n", fileresf);
1.27 lievre 2802:
2803: if (cptcoveff==0) ncodemax[cptcoveff]=1;
2804:
2805: if (mobilav==1) {
2806: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
1.35 lievre 2807: movingaverage(agedeb, fage, ageminpar, mobaverage);
1.27 lievre 2808: }
2809:
2810: stepsize=(int) (stepm+YEARM-1)/YEARM;
2811: if (stepm<=12) stepsize=1;
2812:
2813: agelim=AGESUP;
2814:
2815: hstepm=1;
2816: hstepm=hstepm/stepm;
2817: yp1=modf(dateintmean,&yp);
2818: anprojmean=yp;
2819: yp2=modf((yp1*12),&yp);
2820: mprojmean=yp;
2821: yp1=modf((yp2*30.5),&yp);
2822: jprojmean=yp;
2823: if(jprojmean==0) jprojmean=1;
2824: if(mprojmean==0) jprojmean=1;
2825:
2826: fprintf(ficresf,"# Estimated date of observed prevalence: %.lf/%.lf/%.lf ",jprojmean,mprojmean,anprojmean);
2827:
2828: for(cptcov=1;cptcov<=i2;cptcov++){
2829: for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
2830: k=k+1;
2831: fprintf(ficresf,"\n#******");
2832: for(j=1;j<=cptcoveff;j++) {
2833: fprintf(ficresf," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
2834: }
2835: fprintf(ficresf,"******\n");
2836: fprintf(ficresf,"# StartingAge FinalAge");
2837: for(j=1; j<=nlstate+ndeath;j++) fprintf(ficresf," P.%d",j);
2838:
2839:
2840: for (cpt=0; cpt<=(anproj2-anproj1);cpt++) {
2841: fprintf(ficresf,"\n");
2842: fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+cpt);
1.28 lievre 2843:
1.35 lievre 2844: for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){
1.27 lievre 2845: nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);
2846: nhstepm = nhstepm/hstepm;
2847:
2848: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
2849: oldm=oldms;savm=savms;
2850: hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
2851:
2852: for (h=0; h<=nhstepm; h++){
2853: if (h==(int) (calagedate+YEARM*cpt)) {
1.35 lievre 2854: fprintf(ficresf,"\n %.f %.f ",anproj1+cpt,agedeb+h*hstepm/YEARM*stepm);
1.27 lievre 2855: }
2856: for(j=1; j<=nlstate+ndeath;j++) {
2857: kk1=0.;kk2=0;
2858: for(i=1; i<=nlstate;i++) {
2859: if (mobilav==1)
2860: kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];
2861: else {
2862: kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];
2863: }
2864:
2865: }
2866: if (h==(int)(calagedate+12*cpt)){
2867: fprintf(ficresf," %.3f", kk1);
2868:
2869: }
2870: }
2871: }
2872: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
2873: }
2874: }
2875: }
2876: }
2877:
2878: if (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
2879:
2880: fclose(ficresf);
2881: }
2882: /************** Forecasting ******************/
1.35 lievre 2883: 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 2884:
2885: int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;
2886: int *popage;
2887: double calagedate, agelim, kk1, kk2, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
2888: double *popeffectif,*popcount;
2889: double ***p3mat,***tabpop,***tabpopprev;
2890: char filerespop[FILENAMELENGTH];
2891:
1.28 lievre 2892: tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
2893: tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
2894: agelim=AGESUP;
2895: calagedate=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;
1.27 lievre 2896:
1.35 lievre 2897: prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);
1.28 lievre 2898:
2899:
1.27 lievre 2900: strcpy(filerespop,"pop");
2901: strcat(filerespop,fileres);
2902: if((ficrespop=fopen(filerespop,"w"))==NULL) {
2903: printf("Problem with forecast resultfile: %s\n", filerespop);
1.50 brouard 2904: fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop);
1.27 lievre 2905: }
2906: printf("Computing forecasting: result on file '%s' \n", filerespop);
1.50 brouard 2907: fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop);
1.27 lievre 2908:
2909: if (cptcoveff==0) ncodemax[cptcoveff]=1;
2910:
2911: if (mobilav==1) {
2912: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
1.35 lievre 2913: movingaverage(agedeb, fage, ageminpar, mobaverage);
1.27 lievre 2914: }
2915:
2916: stepsize=(int) (stepm+YEARM-1)/YEARM;
2917: if (stepm<=12) stepsize=1;
2918:
2919: agelim=AGESUP;
2920:
2921: hstepm=1;
2922: hstepm=hstepm/stepm;
2923:
2924: if (popforecast==1) {
2925: if((ficpop=fopen(popfile,"r"))==NULL) {
2926: printf("Problem with population file : %s\n",popfile);exit(0);
1.50 brouard 2927: fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0);
1.27 lievre 2928: }
2929: popage=ivector(0,AGESUP);
2930: popeffectif=vector(0,AGESUP);
2931: popcount=vector(0,AGESUP);
2932:
2933: i=1;
2934: while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;
2935:
2936: imx=i;
2937: for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];
2938: }
2939:
2940: for(cptcov=1;cptcov<=i2;cptcov++){
2941: for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
2942: k=k+1;
2943: fprintf(ficrespop,"\n#******");
2944: for(j=1;j<=cptcoveff;j++) {
2945: fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
2946: }
2947: fprintf(ficrespop,"******\n");
1.28 lievre 2948: fprintf(ficrespop,"# Age");
1.27 lievre 2949: for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);
2950: if (popforecast==1) fprintf(ficrespop," [Population]");
2951:
2952: for (cpt=0; cpt<=0;cpt++) {
1.28 lievre 2953: fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);
1.27 lievre 2954:
1.35 lievre 2955: for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){
1.27 lievre 2956: nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);
2957: nhstepm = nhstepm/hstepm;
2958:
2959: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
2960: oldm=oldms;savm=savms;
2961: hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
2962:
2963: for (h=0; h<=nhstepm; h++){
2964: if (h==(int) (calagedate+YEARM*cpt)) {
1.28 lievre 2965: fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
1.27 lievre 2966: }
2967: for(j=1; j<=nlstate+ndeath;j++) {
2968: kk1=0.;kk2=0;
2969: for(i=1; i<=nlstate;i++) {
2970: if (mobilav==1)
2971: kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];
2972: else {
2973: kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];
2974: }
2975: }
2976: if (h==(int)(calagedate+12*cpt)){
2977: tabpop[(int)(agedeb)][j][cptcod]=kk1;
2978: /*fprintf(ficrespop," %.3f", kk1);
2979: if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/
2980: }
2981: }
2982: for(i=1; i<=nlstate;i++){
2983: kk1=0.;
2984: for(j=1; j<=nlstate;j++){
1.28 lievre 2985: kk1= kk1+tabpop[(int)(agedeb)][j][cptcod];
1.27 lievre 2986: }
2987: tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedate+12*cpt)*hstepm/YEARM*stepm-1)];
2988: }
2989:
1.28 lievre 2990: if (h==(int)(calagedate+12*cpt)) for(j=1; j<=nlstate;j++)
2991: fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);
1.27 lievre 2992: }
2993: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
2994: }
2995: }
2996:
2997: /******/
2998:
1.28 lievre 2999: for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) {
3000: fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);
1.35 lievre 3001: for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){
1.27 lievre 3002: nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);
3003: nhstepm = nhstepm/hstepm;
3004:
3005: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3006: oldm=oldms;savm=savms;
3007: hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
3008: for (h=0; h<=nhstepm; h++){
3009: if (h==(int) (calagedate+YEARM*cpt)) {
1.28 lievre 3010: fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
1.27 lievre 3011: }
3012: for(j=1; j<=nlstate+ndeath;j++) {
3013: kk1=0.;kk2=0;
3014: for(i=1; i<=nlstate;i++) {
3015: kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];
3016: }
1.28 lievre 3017: if (h==(int)(calagedate+12*cpt)) fprintf(ficresf," %15.2f", kk1);
1.27 lievre 3018: }
3019: }
3020: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3021: }
3022: }
3023: }
3024: }
3025:
3026: if (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
3027:
3028: if (popforecast==1) {
3029: free_ivector(popage,0,AGESUP);
3030: free_vector(popeffectif,0,AGESUP);
3031: free_vector(popcount,0,AGESUP);
3032: }
3033: free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
3034: free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
3035: fclose(ficrespop);
3036: }
3037:
1.2 lievre 3038: /***********************************************/
3039: /**************** Main Program *****************/
3040: /***********************************************/
3041:
1.22 brouard 3042: int main(int argc, char *argv[])
1.2 lievre 3043: {
3044:
1.8 lievre 3045: int i,j, k, n=MAXN,iter,m,size,cptcode, cptcod;
1.2 lievre 3046: double agedeb, agefin,hf;
1.35 lievre 3047: double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;
1.2 lievre 3048:
3049: double fret;
3050: double **xi,tmp,delta;
3051:
3052: double dum; /* Dummy variable */
3053: double ***p3mat;
3054: int *indx;
3055: char line[MAXLINE], linepar[MAXLINE];
1.50 brouard 3056: char path[80],pathc[80],pathcd[80],pathtot[80],model[80];
1.2 lievre 3057: int firstobs=1, lastobs=10;
3058: int sdeb, sfin; /* Status at beginning and end */
3059: int c, h , cpt,l;
3060: int ju,jl, mi;
1.7 lievre 3061: int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;
1.14 lievre 3062: int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,**adl,*tab;
1.19 lievre 3063: int mobilav=0,popforecast=0;
1.2 lievre 3064: int hstepm, nhstepm;
1.41 lievre 3065: double jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,jpyram, mpyram,anpyram,jpyram1, mpyram1,anpyram1, calagedate;
1.14 lievre 3066:
1.2 lievre 3067: double bage, fage, age, agelim, agebase;
3068: double ftolpl=FTOL;
3069: double **prlim;
3070: double *severity;
3071: double ***param; /* Matrix of parameters */
3072: double *p;
3073: double **matcov; /* Matrix of covariance */
3074: double ***delti3; /* Scale */
3075: double *delti; /* Scale */
3076: double ***eij, ***vareij;
3077: double **varpl; /* Variances of prevalence limits by age */
3078: double *epj, vepp;
1.16 lievre 3079: double kk1, kk2;
1.27 lievre 3080: double dateprev1, dateprev2,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2;
3081:
1.13 lievre 3082:
1.2 lievre 3083: char *alph[]={"a","a","b","c","d","e"}, str[4];
1.5 lievre 3084:
1.13 lievre 3085:
1.2 lievre 3086: char z[1]="c", occ;
3087: #include <sys/time.h>
3088: #include <time.h>
3089: char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];
1.19 lievre 3090:
1.2 lievre 3091: /* long total_usecs;
3092: struct timeval start_time, end_time;
3093:
3094: gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */
1.35 lievre 3095: getcwd(pathcd, size);
1.2 lievre 3096:
1.22 brouard 3097: printf("\n%s",version);
3098: if(argc <=1){
3099: printf("\nEnter the parameter file name: ");
3100: scanf("%s",pathtot);
3101: }
3102: else{
3103: strcpy(pathtot,argv[1]);
3104: }
3105: /*if(getcwd(pathcd, 80)!= NULL)printf ("Error pathcd\n");*/
1.5 lievre 3106: /*cygwin_split_path(pathtot,path,optionfile);
3107: printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/
3108: /* cutv(path,optionfile,pathtot,'\\');*/
3109:
1.22 brouard 3110: split(pathtot,path,optionfile,optionfilext,optionfilefiname);
3111: printf("pathtot=%s, path=%s, optionfile=%s optionfilext=%s optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
1.2 lievre 3112: chdir(path);
3113: replace(pathc,path);
3114:
3115: /*-------- arguments in the command line --------*/
3116:
1.50 brouard 3117: /* Log file */
3118: strcat(filelog, optionfilefiname);
3119: strcat(filelog,".log"); /* */
3120: if((ficlog=fopen(filelog,"w"))==NULL) {
3121: printf("Problem with logfile %s\n",filelog);
3122: goto end;
3123: }
3124: fprintf(ficlog,"Log filename:%s\n",filelog);
3125: fprintf(ficlog,"\n%s",version);
3126: fprintf(ficlog,"\nEnter the parameter file name: ");
3127: fprintf(ficlog,"pathtot=%s, path=%s, optionfile=%s optionfilext=%s optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
3128: fflush(ficlog);
3129:
3130: /* */
1.2 lievre 3131: strcpy(fileres,"r");
1.22 brouard 3132: strcat(fileres, optionfilefiname);
3133: strcat(fileres,".txt"); /* Other files have txt extension */
1.2 lievre 3134:
3135: /*---------arguments file --------*/
3136:
3137: if((ficpar=fopen(optionfile,"r"))==NULL) {
3138: printf("Problem with optionfile %s\n",optionfile);
1.50 brouard 3139: fprintf(ficlog,"Problem with optionfile %s\n",optionfile);
1.2 lievre 3140: goto end;
3141: }
3142:
3143: strcpy(filereso,"o");
3144: strcat(filereso,fileres);
3145: if((ficparo=fopen(filereso,"w"))==NULL) {
1.50 brouard 3146: printf("Problem with Output resultfile: %s\n", filereso);
3147: fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso);
3148: goto end;
1.2 lievre 3149: }
3150:
3151: /* Reads comments: lines beginning with '#' */
3152: while((c=getc(ficpar))=='#' && c!= EOF){
3153: ungetc(c,ficpar);
3154: fgets(line, MAXLINE, ficpar);
3155: puts(line);
3156: fputs(line,ficparo);
3157: }
3158: ungetc(c,ficpar);
3159:
1.50 brouard 3160: fscanf(ficpar,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%lf stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d model=%s\n",title, datafile, &lastobs, &firstpass,&lastpass,&ftol, &stepm, &ncovcol, &nlstate,&ndeath, &maxwav, &mle, &weightopt,model);
1.34 brouard 3161: 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);
3162: 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 3163: while((c=getc(ficpar))=='#' && c!= EOF){
3164: ungetc(c,ficpar);
3165: fgets(line, MAXLINE, ficpar);
3166: puts(line);
3167: fputs(line,ficparo);
3168: }
3169: ungetc(c,ficpar);
3170:
1.19 lievre 3171:
1.8 lievre 3172: covar=matrix(0,NCOVMAX,1,n);
3173: cptcovn=0;
3174: if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;
1.2 lievre 3175:
3176: ncovmodel=2+cptcovn;
3177: nvar=ncovmodel-1; /* Suppressing age as a basic covariate */
3178:
3179: /* Read guess parameters */
3180: /* Reads comments: lines beginning with '#' */
3181: while((c=getc(ficpar))=='#' && c!= EOF){
3182: ungetc(c,ficpar);
3183: fgets(line, MAXLINE, ficpar);
3184: puts(line);
3185: fputs(line,ficparo);
3186: }
3187: ungetc(c,ficpar);
3188:
3189: param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
3190: for(i=1; i <=nlstate; i++)
3191: for(j=1; j <=nlstate+ndeath-1; j++){
3192: fscanf(ficpar,"%1d%1d",&i1,&j1);
3193: fprintf(ficparo,"%1d%1d",i1,j1);
1.50 brouard 3194: if(mle==1)
3195: printf("%1d%1d",i,j);
3196: fprintf(ficlog,"%1d%1d",i,j);
1.2 lievre 3197: for(k=1; k<=ncovmodel;k++){
3198: fscanf(ficpar," %lf",¶m[i][j][k]);
1.50 brouard 3199: if(mle==1){
3200: printf(" %lf",param[i][j][k]);
3201: fprintf(ficlog," %lf",param[i][j][k]);
3202: }
3203: else
3204: fprintf(ficlog," %lf",param[i][j][k]);
1.2 lievre 3205: fprintf(ficparo," %lf",param[i][j][k]);
3206: }
3207: fscanf(ficpar,"\n");
1.50 brouard 3208: if(mle==1)
3209: printf("\n");
3210: fprintf(ficlog,"\n");
1.2 lievre 3211: fprintf(ficparo,"\n");
3212: }
3213:
1.12 lievre 3214: npar= (nlstate+ndeath-1)*nlstate*ncovmodel;
3215:
1.2 lievre 3216: p=param[1][1];
3217:
3218: /* Reads comments: lines beginning with '#' */
3219: while((c=getc(ficpar))=='#' && c!= EOF){
3220: ungetc(c,ficpar);
3221: fgets(line, MAXLINE, ficpar);
3222: puts(line);
3223: fputs(line,ficparo);
3224: }
3225: ungetc(c,ficpar);
3226:
3227: delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
3228: delti=vector(1,npar); /* Scale of each paramater (output from hesscov) */
3229: for(i=1; i <=nlstate; i++){
3230: for(j=1; j <=nlstate+ndeath-1; j++){
3231: fscanf(ficpar,"%1d%1d",&i1,&j1);
3232: printf("%1d%1d",i,j);
3233: fprintf(ficparo,"%1d%1d",i1,j1);
3234: for(k=1; k<=ncovmodel;k++){
3235: fscanf(ficpar,"%le",&delti3[i][j][k]);
3236: printf(" %le",delti3[i][j][k]);
3237: fprintf(ficparo," %le",delti3[i][j][k]);
3238: }
3239: fscanf(ficpar,"\n");
3240: printf("\n");
3241: fprintf(ficparo,"\n");
3242: }
3243: }
3244: delti=delti3[1][1];
3245:
3246: /* Reads comments: lines beginning with '#' */
3247: while((c=getc(ficpar))=='#' && c!= EOF){
3248: ungetc(c,ficpar);
3249: fgets(line, MAXLINE, ficpar);
3250: puts(line);
3251: fputs(line,ficparo);
3252: }
3253: ungetc(c,ficpar);
3254:
3255: matcov=matrix(1,npar,1,npar);
3256: for(i=1; i <=npar; i++){
3257: fscanf(ficpar,"%s",&str);
1.50 brouard 3258: if(mle==1)
3259: printf("%s",str);
3260: fprintf(ficlog,"%s",str);
1.2 lievre 3261: fprintf(ficparo,"%s",str);
3262: for(j=1; j <=i; j++){
3263: fscanf(ficpar," %le",&matcov[i][j]);
1.50 brouard 3264: if(mle==1){
3265: printf(" %.5le",matcov[i][j]);
3266: fprintf(ficlog," %.5le",matcov[i][j]);
3267: }
3268: else
3269: fprintf(ficlog," %.5le",matcov[i][j]);
1.2 lievre 3270: fprintf(ficparo," %.5le",matcov[i][j]);
3271: }
3272: fscanf(ficpar,"\n");
1.50 brouard 3273: if(mle==1)
3274: printf("\n");
3275: fprintf(ficlog,"\n");
1.2 lievre 3276: fprintf(ficparo,"\n");
3277: }
3278: for(i=1; i <=npar; i++)
3279: for(j=i+1;j<=npar;j++)
3280: matcov[i][j]=matcov[j][i];
3281:
1.50 brouard 3282: if(mle==1)
3283: printf("\n");
3284: fprintf(ficlog,"\n");
1.2 lievre 3285:
3286:
1.29 lievre 3287: /*-------- Rewriting paramater file ----------*/
3288: strcpy(rfileres,"r"); /* "Rparameterfile */
3289: strcat(rfileres,optionfilefiname); /* Parameter file first name*/
3290: strcat(rfileres,"."); /* */
3291: strcat(rfileres,optionfilext); /* Other files have txt extension */
3292: if((ficres =fopen(rfileres,"w"))==NULL) {
3293: printf("Problem writing new parameter file: %s\n", fileres);goto end;
1.50 brouard 3294: fprintf(ficlog,"Problem writing new parameter file: %s\n", fileres);goto end;
1.2 lievre 3295: }
3296: fprintf(ficres,"#%s\n",version);
3297:
1.29 lievre 3298: /*-------- data file ----------*/
1.2 lievre 3299: if((fic=fopen(datafile,"r"))==NULL) {
3300: printf("Problem with datafile: %s\n", datafile);goto end;
1.50 brouard 3301: fprintf(ficlog,"Problem with datafile: %s\n", datafile);goto end;
1.2 lievre 3302: }
3303:
3304: n= lastobs;
3305: severity = vector(1,maxwav);
3306: outcome=imatrix(1,maxwav+1,1,n);
3307: num=ivector(1,n);
3308: moisnais=vector(1,n);
3309: annais=vector(1,n);
3310: moisdc=vector(1,n);
3311: andc=vector(1,n);
3312: agedc=vector(1,n);
3313: cod=ivector(1,n);
3314: weight=vector(1,n);
3315: for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */
3316: mint=matrix(1,maxwav,1,n);
3317: anint=matrix(1,maxwav,1,n);
3318: s=imatrix(1,maxwav+1,1,n);
3319: adl=imatrix(1,maxwav+1,1,n);
3320: tab=ivector(1,NCOVMAX);
1.3 lievre 3321: ncodemax=ivector(1,8);
1.2 lievre 3322:
1.12 lievre 3323: i=1;
1.2 lievre 3324: while (fgets(line, MAXLINE, fic) != NULL) {
3325: if ((i >= firstobs) && (i <=lastobs)) {
3326:
3327: for (j=maxwav;j>=1;j--){
3328: cutv(stra, strb,line,' '); s[j][i]=atoi(strb);
3329: strcpy(line,stra);
3330: cutv(stra, strb,line,'/'); anint[j][i]=(double)(atoi(strb)); strcpy(line,stra);
3331: cutv(stra, strb,line,' '); mint[j][i]=(double)(atoi(strb)); strcpy(line,stra);
3332: }
3333:
3334: cutv(stra, strb,line,'/'); andc[i]=(double)(atoi(strb)); strcpy(line,stra);
3335: cutv(stra, strb,line,' '); moisdc[i]=(double)(atoi(strb)); strcpy(line,stra);
3336:
3337: cutv(stra, strb,line,'/'); annais[i]=(double)(atoi(strb)); strcpy(line,stra);
3338: cutv(stra, strb,line,' '); moisnais[i]=(double)(atoi(strb)); strcpy(line,stra);
3339:
3340: cutv(stra, strb,line,' '); weight[i]=(double)(atoi(strb)); strcpy(line,stra);
1.34 brouard 3341: for (j=ncovcol;j>=1;j--){
1.2 lievre 3342: cutv(stra, strb,line,' '); covar[j][i]=(double)(atoi(strb)); strcpy(line,stra);
3343: }
3344: num[i]=atol(stra);
1.12 lievre 3345:
3346: /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){
3347: 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 3348:
3349: i=i+1;
3350: }
3351: }
1.12 lievre 3352: /* printf("ii=%d", ij);
3353: scanf("%d",i);*/
3354: imx=i-1; /* Number of individuals */
1.3 lievre 3355:
1.12 lievre 3356: /* for (i=1; i<=imx; i++){
3357: if ((s[1][i]==3) && (s[2][i]==2)) s[2][i]=3;
3358: if ((s[2][i]==3) && (s[3][i]==2)) s[3][i]=3;
3359: if ((s[3][i]==3) && (s[4][i]==2)) s[4][i]=3;
1.35 lievre 3360: }*/
1.39 lievre 3361: /* for (i=1; i<=imx; i++){
1.35 lievre 3362: if (s[4][i]==9) s[4][i]=-1;
1.39 lievre 3363: 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]));}*/
3364:
1.35 lievre 3365:
1.2 lievre 3366: /* Calculation of the number of parameter from char model*/
1.50 brouard 3367: Tvar=ivector(1,15); /* stores the number n of the covariates in Vm+Vn at 1 and m at 2 */
1.7 lievre 3368: Tprod=ivector(1,15);
3369: Tvaraff=ivector(1,15);
3370: Tvard=imatrix(1,15,1,2);
1.6 lievre 3371: Tage=ivector(1,15);
1.2 lievre 3372:
3373: if (strlen(model) >1){
1.7 lievre 3374: j=0, j1=0, k1=1, k2=1;
1.2 lievre 3375: j=nbocc(model,'+');
1.6 lievre 3376: j1=nbocc(model,'*');
1.2 lievre 3377: cptcovn=j+1;
1.7 lievre 3378: cptcovprod=j1;
1.3 lievre 3379:
1.2 lievre 3380: strcpy(modelsav,model);
1.8 lievre 3381: if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){
3382: printf("Error. Non available option model=%s ",model);
1.50 brouard 3383: fprintf(ficlog,"Error. Non available option model=%s ",model);
1.8 lievre 3384: goto end;
3385: }
3386:
3387: for(i=(j+1); i>=1;i--){
1.50 brouard 3388: cutv(stra,strb,modelsav,'+'); /* keeps in strb after the last + */
3389: if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyze it */
1.8 lievre 3390: /* printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/
3391: /*scanf("%d",i);*/
1.50 brouard 3392: if (strchr(strb,'*')) { /* Model includes a product */
3393: cutv(strd,strc,strb,'*'); /* strd*strc Vm*Vn (if not *age)*/
3394: if (strcmp(strc,"age")==0) { /* Vn*age */
1.7 lievre 3395: cptcovprod--;
1.8 lievre 3396: cutv(strb,stre,strd,'V');
1.50 brouard 3397: Tvar[i]=atoi(stre); /* computes n in Vn and stores in Tvar*/
1.8 lievre 3398: cptcovage++;
3399: Tage[cptcovage]=i;
3400: /*printf("stre=%s ", stre);*/
1.7 lievre 3401: }
1.50 brouard 3402: else if (strcmp(strd,"age")==0) { /* or age*Vn */
1.7 lievre 3403: cptcovprod--;
1.8 lievre 3404: cutv(strb,stre,strc,'V');
3405: Tvar[i]=atoi(stre);
3406: cptcovage++;
3407: Tage[cptcovage]=i;
1.7 lievre 3408: }
1.50 brouard 3409: else { /* Age is not in the model */
3410: cutv(strb,stre,strc,'V'); /* strc= Vn, stre is n*/
1.34 brouard 3411: Tvar[i]=ncovcol+k1;
1.50 brouard 3412: cutv(strb,strc,strd,'V'); /* strd was Vm, strc is m */
1.8 lievre 3413: Tprod[k1]=i;
1.50 brouard 3414: Tvard[k1][1]=atoi(strc); /* m*/
3415: Tvard[k1][2]=atoi(stre); /* n */
1.8 lievre 3416: Tvar[cptcovn+k2]=Tvard[k1][1];
3417: Tvar[cptcovn+k2+1]=Tvard[k1][2];
1.7 lievre 3418: for (k=1; k<=lastobs;k++)
1.34 brouard 3419: covar[ncovcol+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];
1.8 lievre 3420: k1++;
3421: k2=k2+2;
1.7 lievre 3422: }
1.2 lievre 3423: }
1.50 brouard 3424: else { /* no more sum */
1.8 lievre 3425: /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/
3426: /* scanf("%d",i);*/
3427: cutv(strd,strc,strb,'V');
3428: Tvar[i]=atoi(strc);
3429: }
3430: strcpy(modelsav,stra);
3431: /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);
3432: scanf("%d",i);*/
1.50 brouard 3433: } /* end of loop + */
3434: } /* end model */
1.8 lievre 3435:
1.35 lievre 3436: /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);
1.8 lievre 3437: printf("cptcovprod=%d ", cptcovprod);
1.50 brouard 3438: fprintf(ficlog,"cptcovprod=%d ", cptcovprod);
1.8 lievre 3439: scanf("%d ",i);*/
1.2 lievre 3440: fclose(fic);
3441:
1.7 lievre 3442: /* if(mle==1){*/
1.2 lievre 3443: if (weightopt != 1) { /* Maximisation without weights*/
3444: for(i=1;i<=n;i++) weight[i]=1.0;
3445: }
3446: /*-calculation of age at interview from date of interview and age at death -*/
3447: agev=matrix(1,maxwav,1,imx);
1.12 lievre 3448:
1.35 lievre 3449: for (i=1; i<=imx; i++) {
3450: for(m=2; (m<= maxwav); m++) {
1.12 lievre 3451: if ((mint[m][i]== 99) && (s[m][i] <= nlstate)){
3452: anint[m][i]=9999;
3453: s[m][i]=-1;
3454: }
1.35 lievre 3455: if(moisdc[i]==99 && andc[i]==9999 & s[m][i]>nlstate) s[m][i]=-1;
3456: }
3457: }
3458:
1.2 lievre 3459: for (i=1; i<=imx; i++) {
3460: agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);
3461: for(m=1; (m<= maxwav); m++){
3462: if(s[m][i] >0){
1.35 lievre 3463: if (s[m][i] >= nlstate+1) {
1.2 lievre 3464: if(agedc[i]>0)
3465: if(moisdc[i]!=99 && andc[i]!=9999)
1.35 lievre 3466: agev[m][i]=agedc[i];
3467: /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/
3468: else {
1.8 lievre 3469: if (andc[i]!=9999){
1.2 lievre 3470: printf("Warning negative age at death: %d line:%d\n",num[i],i);
1.50 brouard 3471: fprintf(ficlog,"Warning negative age at death: %d line:%d\n",num[i],i);
1.2 lievre 3472: agev[m][i]=-1;
1.8 lievre 3473: }
1.2 lievre 3474: }
3475: }
3476: else if(s[m][i] !=9){ /* Should no more exist */
3477: agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);
1.3 lievre 3478: if(mint[m][i]==99 || anint[m][i]==9999)
1.2 lievre 3479: agev[m][i]=1;
3480: else if(agev[m][i] <agemin){
3481: agemin=agev[m][i];
3482: /*printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], agemin);*/
3483: }
3484: else if(agev[m][i] >agemax){
3485: agemax=agev[m][i];
3486: /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/
3487: }
3488: /*agev[m][i]=anint[m][i]-annais[i];*/
3489: /* agev[m][i] = age[i]+2*m;*/
3490: }
3491: else { /* =9 */
3492: agev[m][i]=1;
3493: s[m][i]=-1;
3494: }
3495: }
3496: else /*= 0 Unknown */
3497: agev[m][i]=1;
3498: }
3499:
3500: }
3501: for (i=1; i<=imx; i++) {
3502: for(m=1; (m<= maxwav); m++){
3503: if (s[m][i] > (nlstate+ndeath)) {
1.50 brouard 3504: printf("Error: on wave %d of individual %d status %d > (nlstate+ndeath)=(%d+%d)=%d\n",m,i,s[m][i],nlstate, ndeath, nlstate+ndeath);
3505: fprintf(ficlog,"Error: on wave %d of individual %d status %d > (nlstate+ndeath)=(%d+%d)=%d\n",m,i,s[m][i],nlstate, ndeath, nlstate+ndeath);
1.2 lievre 3506: goto end;
3507: }
3508: }
3509: }
3510:
3511: printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);
1.50 brouard 3512: fprintf(ficlog,"Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);
1.2 lievre 3513:
3514: free_vector(severity,1,maxwav);
3515: free_imatrix(outcome,1,maxwav+1,1,n);
3516: free_vector(moisnais,1,n);
3517: free_vector(annais,1,n);
1.17 lievre 3518: /* free_matrix(mint,1,maxwav,1,n);
3519: free_matrix(anint,1,maxwav,1,n);*/
1.2 lievre 3520: free_vector(moisdc,1,n);
3521: free_vector(andc,1,n);
3522:
3523:
3524: wav=ivector(1,imx);
3525: dh=imatrix(1,lastpass-firstpass+1,1,imx);
3526: mw=imatrix(1,lastpass-firstpass+1,1,imx);
3527:
3528: /* Concatenates waves */
3529: concatwav(wav, dh, mw, s, agedc, agev, firstpass, lastpass, imx, nlstate, stepm);
3530:
3531:
1.6 lievre 3532: Tcode=ivector(1,100);
1.8 lievre 3533: nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);
1.7 lievre 3534: ncodemax[1]=1;
3535: if (cptcovn > 0) tricode(Tvar,nbcode,imx);
3536:
1.2 lievre 3537: codtab=imatrix(1,100,1,10);
3538: h=0;
1.7 lievre 3539: m=pow(2,cptcoveff);
1.2 lievre 3540:
1.7 lievre 3541: for(k=1;k<=cptcoveff; k++){
1.2 lievre 3542: for(i=1; i <=(m/pow(2,k));i++){
3543: for(j=1; j <= ncodemax[k]; j++){
1.7 lievre 3544: for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){
1.2 lievre 3545: h++;
1.35 lievre 3546: if (h>m) h=1;codtab[h][k]=j;codtab[h][Tvar[k]]=j;
3547: /* 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 3548: }
3549: }
3550: }
3551: }
1.35 lievre 3552: /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]);
3553: codtab[1][2]=1;codtab[2][2]=2; */
3554: /* for(i=1; i <=m ;i++){
3555: for(k=1; k <=cptcovn; k++){
3556: printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);
3557: }
3558: printf("\n");
3559: }
3560: scanf("%d",i);*/
1.2 lievre 3561:
3562: /* Calculates basic frequencies. Computes observed prevalence at single age
3563: and prints on file fileres'p'. */
1.18 lievre 3564:
1.19 lievre 3565:
1.18 lievre 3566:
1.19 lievre 3567: pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
1.2 lievre 3568: oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
3569: newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
3570: savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
3571: oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */
1.12 lievre 3572:
1.2 lievre 3573: /* For Powell, parameters are in a vector p[] starting at p[1]
3574: so we point p on param[1][1] so that p[1] maps on param[1][1][1] */
3575: p=param[1][1]; /* *(*(*(param +1)+1)+0) */
1.7 lievre 3576:
3577: if(mle==1){
1.2 lievre 3578: mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);
1.7 lievre 3579: }
1.2 lievre 3580:
3581: /*--------- results files --------------*/
1.34 brouard 3582: 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 3583:
1.16 lievre 3584:
1.2 lievre 3585: jk=1;
1.34 brouard 3586: fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
3587: printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
1.50 brouard 3588: fprintf(ficlog,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
1.2 lievre 3589: for(i=1,jk=1; i <=nlstate; i++){
3590: for(k=1; k <=(nlstate+ndeath); k++){
3591: if (k != i)
3592: {
3593: printf("%d%d ",i,k);
1.50 brouard 3594: fprintf(ficlog,"%d%d ",i,k);
1.2 lievre 3595: fprintf(ficres,"%1d%1d ",i,k);
3596: for(j=1; j <=ncovmodel; j++){
3597: printf("%f ",p[jk]);
1.50 brouard 3598: fprintf(ficlog,"%f ",p[jk]);
1.2 lievre 3599: fprintf(ficres,"%f ",p[jk]);
3600: jk++;
3601: }
3602: printf("\n");
1.50 brouard 3603: fprintf(ficlog,"\n");
1.2 lievre 3604: fprintf(ficres,"\n");
3605: }
3606: }
3607: }
1.50 brouard 3608: if(mle==1){
3609: /* Computing hessian and covariance matrix */
3610: ftolhess=ftol; /* Usually correct */
3611: hesscov(matcov, p, npar, delti, ftolhess, func);
3612: }
3613: fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");
3614: printf("# Scales (for hessian or gradient estimation)\n");
3615: fprintf(ficlog,"# Scales (for hessian or gradient estimation)\n");
3616: for(i=1,jk=1; i <=nlstate; i++){
3617: for(j=1; j <=nlstate+ndeath; j++){
3618: if (j!=i) {
3619: fprintf(ficres,"%1d%1d",i,j);
3620: printf("%1d%1d",i,j);
3621: fprintf(ficlog,"%1d%1d",i,j);
3622: for(k=1; k<=ncovmodel;k++){
3623: printf(" %.5e",delti[jk]);
3624: fprintf(ficlog," %.5e",delti[jk]);
3625: fprintf(ficres," %.5e",delti[jk]);
3626: jk++;
3627: }
3628: printf("\n");
3629: fprintf(ficlog,"\n");
3630: fprintf(ficres,"\n");
3631: }
3632: }
3633: }
3634:
3635: k=1;
3636: 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");
3637: if(mle==1)
3638: 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");
3639: fprintf(ficlog,"# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n# ...\n# 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n");
3640: for(i=1;i<=npar;i++){
3641: /* if (k>nlstate) k=1;
3642: i1=(i-1)/(ncovmodel*nlstate)+1;
3643: fprintf(ficres,"%s%d%d",alph[k],i1,tab[i]);
3644: printf("%s%d%d",alph[k],i1,tab[i]);*/
3645: fprintf(ficres,"%3d",i);
3646: if(mle==1)
3647: printf("%3d",i);
3648: fprintf(ficlog,"%3d",i);
3649: for(j=1; j<=i;j++){
3650: fprintf(ficres," %.5e",matcov[i][j]);
3651: if(mle==1)
3652: printf(" %.5e",matcov[i][j]);
3653: fprintf(ficlog," %.5e",matcov[i][j]);
1.18 lievre 3654: }
1.50 brouard 3655: fprintf(ficres,"\n");
3656: if(mle==1)
3657: printf("\n");
3658: fprintf(ficlog,"\n");
3659: k++;
3660: }
3661:
3662: while((c=getc(ficpar))=='#' && c!= EOF){
3663: ungetc(c,ficpar);
3664: fgets(line, MAXLINE, ficpar);
3665: puts(line);
3666: fputs(line,ficparo);
3667: }
3668: ungetc(c,ficpar);
3669: estepm=0;
3670: fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm);
3671: if (estepm==0 || estepm < stepm) estepm=stepm;
3672: if (fage <= 2) {
3673: bage = ageminpar;
3674: fage = agemaxpar;
3675: }
3676:
3677: fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");
3678: fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
3679: fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
3680:
3681: while((c=getc(ficpar))=='#' && c!= EOF){
3682: ungetc(c,ficpar);
3683: fgets(line, MAXLINE, ficpar);
3684: puts(line);
3685: fputs(line,ficparo);
3686: }
3687: ungetc(c,ficpar);
1.19 lievre 3688:
1.50 brouard 3689: fscanf(ficpar,"begin-prev-date=%lf/%lf/%lf end-prev-date=%lf/%lf/%lf\n",&jprev1, &mprev1,&anprev1,&jprev2, &mprev2,&anprev2);
3690: fprintf(ficparo,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);
3691: fprintf(ficres,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);
3692:
3693: while((c=getc(ficpar))=='#' && c!= EOF){
3694: ungetc(c,ficpar);
3695: fgets(line, MAXLINE, ficpar);
3696: puts(line);
3697: fputs(line,ficparo);
3698: }
3699: ungetc(c,ficpar);
1.19 lievre 3700:
1.7 lievre 3701:
1.19 lievre 3702: dateprev1=anprev1+mprev1/12.+jprev1/365.;
3703: dateprev2=anprev2+mprev2/12.+jprev2/365.;
3704:
3705: fscanf(ficpar,"pop_based=%d\n",&popbased);
1.28 lievre 3706: fprintf(ficparo,"pop_based=%d\n",popbased);
3707: fprintf(ficres,"pop_based=%d\n",popbased);
3708:
3709: while((c=getc(ficpar))=='#' && c!= EOF){
3710: ungetc(c,ficpar);
3711: fgets(line, MAXLINE, ficpar);
3712: puts(line);
3713: fputs(line,ficparo);
3714: }
3715: ungetc(c,ficpar);
1.19 lievre 3716:
1.28 lievre 3717: 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);
3718: 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);
3719: 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);
3720:
3721:
3722: while((c=getc(ficpar))=='#' && c!= EOF){
1.19 lievre 3723: ungetc(c,ficpar);
3724: fgets(line, MAXLINE, ficpar);
3725: puts(line);
3726: fputs(line,ficparo);
3727: }
3728: ungetc(c,ficpar);
1.28 lievre 3729:
3730: fscanf(ficpar,"popforecast=%d popfile=%s popfiledate=%lf/%lf/%lf last-popfiledate=%lf/%lf/%lf\n",&popforecast,popfile,&jpyram,&mpyram,&anpyram,&jpyram1,&mpyram1,&anpyram1);
3731: fprintf(ficparo,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);
3732: 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 3733:
1.26 lievre 3734: freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);
1.19 lievre 3735:
1.25 lievre 3736: /*------------ gnuplot -------------*/
1.47 brouard 3737: strcpy(optionfilegnuplot,optionfilefiname);
3738: strcat(optionfilegnuplot,".gp");
3739: if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {
3740: printf("Problem with file %s",optionfilegnuplot);
3741: }
3742: fclose(ficgp);
3743: printinggnuplot(fileres, ageminpar,agemaxpar,fage, pathc,p);
3744: /*--------- index.htm --------*/
3745:
3746: strcpy(optionfilehtm,optionfile);
3747: strcat(optionfilehtm,".htm");
3748: if((fichtm=fopen(optionfilehtm,"w"))==NULL) {
3749: printf("Problem with %s \n",optionfilehtm), exit(0);
3750: }
3751:
3752: fprintf(fichtm,"<body> <font size=\"2\">%s </font> <hr size=\"2\" color=\"#EC5E5E\"> \n
3753: Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n
3754: \n
3755: Total number of observations=%d <br>\n
3756: Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n
3757: <hr size=\"2\" color=\"#EC5E5E\">
1.49 lievre 3758: <ul><li><h4>Parameter files</h4>\n
1.47 brouard 3759: - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n
1.50 brouard 3760: - Log file of the run: <a href=\"%s\">%s</a><br>\n
3761: - Gnuplot file name: <a href=\"%s\">%s</a></ul>\n",version,title,datafile,firstpass,lastpass,stepm, weightopt,model,imx,jmin,jmax,jmean,fileres,fileres,filelog,filelog,optionfilegnuplot,optionfilegnuplot);
1.47 brouard 3762: fclose(fichtm);
3763:
3764: 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 3765:
3766: /*------------ free_vector -------------*/
3767: chdir(path);
1.2 lievre 3768:
1.25 lievre 3769: free_ivector(wav,1,imx);
3770: free_imatrix(dh,1,lastpass-firstpass+1,1,imx);
3771: free_imatrix(mw,1,lastpass-firstpass+1,1,imx);
3772: free_ivector(num,1,n);
3773: free_vector(agedc,1,n);
3774: /*free_matrix(covar,1,NCOVMAX,1,n);*/
3775: fclose(ficparo);
3776: fclose(ficres);
1.28 lievre 3777:
1.2 lievre 3778:
3779: /*--------------- Prevalence limit --------------*/
3780:
3781: strcpy(filerespl,"pl");
3782: strcat(filerespl,fileres);
3783: if((ficrespl=fopen(filerespl,"w"))==NULL) {
3784: printf("Problem with Prev limit resultfile: %s\n", filerespl);goto end;
1.50 brouard 3785: fprintf(ficlog,"Problem with Prev limit resultfile: %s\n", filerespl);goto end;
1.2 lievre 3786: }
3787: printf("Computing prevalence limit: result on file '%s' \n", filerespl);
1.50 brouard 3788: fprintf(ficlog,"Computing prevalence limit: result on file '%s' \n", filerespl);
1.2 lievre 3789: fprintf(ficrespl,"#Prevalence limit\n");
3790: fprintf(ficrespl,"#Age ");
3791: for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);
3792: fprintf(ficrespl,"\n");
3793:
3794: prlim=matrix(1,nlstate,1,nlstate);
3795: pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
3796: oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
3797: newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
3798: savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
3799: oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */
3800: k=0;
1.35 lievre 3801: agebase=ageminpar;
1.28 lievre 3802: agelim=agemaxpar;
1.2 lievre 3803: ftolpl=1.e-10;
1.7 lievre 3804: i1=cptcoveff;
1.2 lievre 3805: if (cptcovn < 1){i1=1;}
3806:
3807: for(cptcov=1;cptcov<=i1;cptcov++){
3808: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
3809: k=k+1;
3810: /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/
1.6 lievre 3811: fprintf(ficrespl,"\n#******");
1.50 brouard 3812: printf("\n#******");
3813: fprintf(ficlog,"\n#******");
3814: for(j=1;j<=cptcoveff;j++) {
1.7 lievre 3815: fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
1.50 brouard 3816: printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
3817: fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
3818: }
1.2 lievre 3819: fprintf(ficrespl,"******\n");
1.50 brouard 3820: printf("******\n");
3821: fprintf(ficlog,"******\n");
1.2 lievre 3822:
3823: for (age=agebase; age<=agelim; age++){
3824: prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
3825: fprintf(ficrespl,"%.0f",age );
3826: for(i=1; i<=nlstate;i++)
3827: fprintf(ficrespl," %.5f", prlim[i][i]);
3828: fprintf(ficrespl,"\n");
3829: }
3830: }
3831: }
3832: fclose(ficrespl);
1.13 lievre 3833:
1.2 lievre 3834: /*------------- h Pij x at various ages ------------*/
3835:
3836: strcpy(filerespij,"pij"); strcat(filerespij,fileres);
3837: if((ficrespij=fopen(filerespij,"w"))==NULL) {
3838: printf("Problem with Pij resultfile: %s\n", filerespij);goto end;
1.50 brouard 3839: fprintf(ficlog,"Problem with Pij resultfile: %s\n", filerespij);goto end;
1.2 lievre 3840: }
3841: printf("Computing pij: result on file '%s' \n", filerespij);
1.50 brouard 3842: fprintf(ficlog,"Computing pij: result on file '%s' \n", filerespij);
1.2 lievre 3843:
3844: stepsize=(int) (stepm+YEARM-1)/YEARM;
1.13 lievre 3845: /*if (stepm<=24) stepsize=2;*/
1.2 lievre 3846:
3847: agelim=AGESUP;
3848: hstepm=stepsize*YEARM; /* Every year of age */
3849: hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */
1.49 lievre 3850:
3851: /* hstepm=1; aff par mois*/
3852:
1.2 lievre 3853: k=0;
3854: for(cptcov=1;cptcov<=i1;cptcov++){
3855: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
3856: k=k+1;
3857: fprintf(ficrespij,"\n#****** ");
1.7 lievre 3858: for(j=1;j<=cptcoveff;j++)
3859: fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
1.2 lievre 3860: fprintf(ficrespij,"******\n");
3861:
3862: for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */
3863: nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
3864: nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
1.49 lievre 3865:
3866: /* nhstepm=nhstepm*YEARM; aff par mois*/
3867:
1.2 lievre 3868: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3869: oldm=oldms;savm=savms;
3870: hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
3871: fprintf(ficrespij,"# Age");
3872: for(i=1; i<=nlstate;i++)
3873: for(j=1; j<=nlstate+ndeath;j++)
3874: fprintf(ficrespij," %1d-%1d",i,j);
3875: fprintf(ficrespij,"\n");
1.40 lievre 3876: for (h=0; h<=nhstepm; h++){
1.49 lievre 3877: fprintf(ficrespij,"%d %f %f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );
1.2 lievre 3878: for(i=1; i<=nlstate;i++)
3879: for(j=1; j<=nlstate+ndeath;j++)
3880: fprintf(ficrespij," %.5f", p3mat[i][j][h]);
3881: fprintf(ficrespij,"\n");
1.40 lievre 3882: }
1.2 lievre 3883: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3884: fprintf(ficrespij,"\n");
3885: }
3886: }
3887: }
3888:
1.47 brouard 3889: varprob(optionfilefiname, matcov, p, delti, nlstate, (int) bage, (int) fage,k,Tvar,nbcode, ncodemax);
1.13 lievre 3890:
1.2 lievre 3891: fclose(ficrespij);
3892:
1.27 lievre 3893:
3894: /*---------- Forecasting ------------------*/
1.32 brouard 3895: if((stepm == 1) && (strcmp(model,".")==0)){
1.27 lievre 3896: prevforecast(fileres, anproj1,mproj1,jproj1, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anproj2,p, i1);
1.32 brouard 3897: if (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);
1.41 lievre 3898: }
1.21 lievre 3899: else{
3900: erreur=108;
1.32 brouard 3901: 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);
1.50 brouard 3902: fprintf(ficlog,"Warning %d!! You can only forecast the prevalences if the optimization\n has been performed with stepm = 1 (month) instead of %d or model=. instead of '%s'\n", erreur, stepm, model);
1.21 lievre 3903: }
1.26 lievre 3904:
1.27 lievre 3905:
1.2 lievre 3906: /*---------- Health expectancies and variances ------------*/
3907:
3908: strcpy(filerest,"t");
3909: strcat(filerest,fileres);
3910: if((ficrest=fopen(filerest,"w"))==NULL) {
3911: printf("Problem with total LE resultfile: %s\n", filerest);goto end;
1.50 brouard 3912: fprintf(ficlog,"Problem with total LE resultfile: %s\n", filerest);goto end;
1.2 lievre 3913: }
3914: printf("Computing Total LEs with variances: file '%s' \n", filerest);
1.50 brouard 3915: fprintf(ficlog,"Computing Total LEs with variances: file '%s' \n", filerest);
1.2 lievre 3916:
3917:
3918: strcpy(filerese,"e");
3919: strcat(filerese,fileres);
3920: if((ficreseij=fopen(filerese,"w"))==NULL) {
3921: printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
1.50 brouard 3922: fprintf(ficlog,"Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
1.2 lievre 3923: }
3924: printf("Computing Health Expectancies: result on file '%s' \n", filerese);
1.50 brouard 3925: fprintf(ficlog,"Computing Health Expectancies: result on file '%s' \n", filerese);
1.2 lievre 3926:
1.50 brouard 3927: strcpy(fileresv,"v");
1.2 lievre 3928: strcat(fileresv,fileres);
3929: if((ficresvij=fopen(fileresv,"w"))==NULL) {
3930: printf("Problem with variance resultfile: %s\n", fileresv);exit(0);
1.50 brouard 3931: fprintf(ficlog,"Problem with variance resultfile: %s\n", fileresv);exit(0);
1.2 lievre 3932: }
3933: printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
1.50 brouard 3934: fprintf(ficlog,"Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
1.41 lievre 3935: calagedate=-1;
1.50 brouard 3936: prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);
1.2 lievre 3937:
3938: k=0;
3939: for(cptcov=1;cptcov<=i1;cptcov++){
3940: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
1.50 brouard 3941: k=k+1;
1.2 lievre 3942: fprintf(ficrest,"\n#****** ");
1.7 lievre 3943: for(j=1;j<=cptcoveff;j++)
3944: fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
1.2 lievre 3945: fprintf(ficrest,"******\n");
3946:
3947: fprintf(ficreseij,"\n#****** ");
1.7 lievre 3948: for(j=1;j<=cptcoveff;j++)
1.35 lievre 3949: fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
1.2 lievre 3950: fprintf(ficreseij,"******\n");
3951:
3952: fprintf(ficresvij,"\n#****** ");
1.7 lievre 3953: for(j=1;j<=cptcoveff;j++)
1.35 lievre 3954: fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
1.2 lievre 3955: fprintf(ficresvij,"******\n");
3956:
3957: eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
3958: oldm=oldms;savm=savms;
1.41 lievre 3959: evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov);
3960:
1.2 lievre 3961: vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
3962: oldm=oldms;savm=savms;
1.50 brouard 3963: varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,0);
3964: if(popbased==1){
3965: varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,popbased);
3966: }
1.26 lievre 3967:
3968:
1.2 lievre 3969: fprintf(ficrest,"#Total LEs with variances: e.. (std) ");
3970: for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);
3971: fprintf(ficrest,"\n");
1.26 lievre 3972:
1.2 lievre 3973: epj=vector(1,nlstate+1);
3974: for(age=bage; age <=fage ;age++){
3975: prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
1.14 lievre 3976: if (popbased==1) {
3977: for(i=1; i<=nlstate;i++)
3978: prlim[i][i]=probs[(int)age][i][k];
3979: }
3980:
1.33 brouard 3981: fprintf(ficrest," %4.0f",age);
1.2 lievre 3982: for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){
3983: for(i=1, epj[j]=0.;i <=nlstate;i++) {
1.33 brouard 3984: epj[j] += prlim[i][i]*eij[i][j][(int)age];
1.41 lievre 3985: /* printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/
1.2 lievre 3986: }
3987: epj[nlstate+1] +=epj[j];
3988: }
1.41 lievre 3989:
1.2 lievre 3990: for(i=1, vepp=0.;i <=nlstate;i++)
3991: for(j=1;j <=nlstate;j++)
3992: vepp += vareij[i][j][(int)age];
1.38 lievre 3993: fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));
1.2 lievre 3994: for(j=1;j <=nlstate;j++){
1.38 lievre 3995: fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));
1.2 lievre 3996: }
3997: fprintf(ficrest,"\n");
3998: }
3999: }
4000: }
1.41 lievre 4001: free_matrix(mint,1,maxwav,1,n);
4002: free_matrix(anint,1,maxwav,1,n); free_imatrix(s,1,maxwav+1,1,n);
4003: free_vector(weight,1,n);
1.27 lievre 4004: fclose(ficreseij);
4005: fclose(ficresvij);
1.2 lievre 4006: fclose(ficrest);
4007: fclose(ficpar);
4008: free_vector(epj,1,nlstate+1);
1.26 lievre 4009:
1.2 lievre 4010: /*------- Variance limit prevalence------*/
4011:
1.27 lievre 4012: strcpy(fileresvpl,"vpl");
1.2 lievre 4013: strcat(fileresvpl,fileres);
4014: if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {
4015: printf("Problem with variance prev lim resultfile: %s\n", fileresvpl);
4016: exit(0);
4017: }
4018: printf("Computing Variance-covariance of Prevalence limit: file '%s' \n", fileresvpl);
4019:
1.27 lievre 4020: k=0;
4021: for(cptcov=1;cptcov<=i1;cptcov++){
4022: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
4023: k=k+1;
4024: fprintf(ficresvpl,"\n#****** ");
4025: for(j=1;j<=cptcoveff;j++)
4026: fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
4027: fprintf(ficresvpl,"******\n");
4028:
4029: varpl=matrix(1,nlstate,(int) bage, (int) fage);
4030: oldm=oldms;savm=savms;
1.2 lievre 4031: varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);
1.27 lievre 4032: }
1.2 lievre 4033: }
4034:
4035: fclose(ficresvpl);
4036:
4037: /*---------- End : free ----------------*/
4038: free_matrix(varpl,1,nlstate,(int) bage, (int)fage);
4039:
4040: free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);
4041: free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
4042:
4043:
4044: free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);
4045: free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);
4046: free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);
4047: free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);
1.13 lievre 4048:
1.2 lievre 4049: free_matrix(matcov,1,npar,1,npar);
4050: free_vector(delti,1,npar);
1.26 lievre 4051: free_matrix(agev,1,maxwav,1,imx);
1.2 lievre 4052: free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
1.47 brouard 4053:
4054: fprintf(fichtm,"\n</body>");
4055: fclose(fichtm);
4056: fclose(ficgp);
4057:
1.2 lievre 4058:
1.50 brouard 4059: if(erreur >0){
1.34 brouard 4060: printf("End of Imach with error or warning %d\n",erreur);
1.50 brouard 4061: fprintf(ficlog,"End of Imach with error or warning %d\n",erreur);
4062: }else{
4063: printf("End of Imach\n");
4064: fprintf(ficlog,"End of Imach\n");
4065: }
4066: printf("See log file on %s\n",filelog);
4067: fclose(ficlog);
1.2 lievre 4068: /* gettimeofday(&end_time, (struct timezone*)0);*/ /* after time */
4069:
4070: /* 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);*/
4071: /*printf("Total time was %d uSec.\n", total_usecs);*/
4072: /*------ End -----------*/
1.12 lievre 4073:
1.2 lievre 4074:
4075: end:
4076: #ifdef windows
1.22 brouard 4077: /* chdir(pathcd);*/
1.2 lievre 4078: #endif
1.22 brouard 4079: /*system("wgnuplot graph.plt");*/
4080: /*system("../gp37mgw/wgnuplot graph.plt");*/
4081: /*system("cd ../gp37mgw");*/
4082: /* system("..\\gp37mgw\\wgnuplot graph.plt");*/
4083: strcpy(plotcmd,GNUPLOTPROGRAM);
4084: strcat(plotcmd," ");
4085: strcat(plotcmd,optionfilegnuplot);
4086: system(plotcmd);
1.2 lievre 4087:
4088: #ifdef windows
4089: while (z[0] != 'q') {
1.35 lievre 4090: /* chdir(path); */
4091: printf("\nType e to edit output files, g to graph again, c to start again, and q for exiting: ");
1.2 lievre 4092: scanf("%s",z);
4093: if (z[0] == 'c') system("./imach");
1.35 lievre 4094: else if (z[0] == 'e') system(optionfilehtm);
4095: else if (z[0] == 'g') system(plotcmd);
1.2 lievre 4096: else if (z[0] == 'q') exit(0);
4097: }
4098: #endif
4099: }
4100:
4101:
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