Annotation of imach/src/imach.c, revision 1.70
1.70 ! brouard 1: /* $Id: imach.c,v 1.69 2003/02/04 20:55:29 brouard Exp $
1.53 brouard 2: Interpolated Markov Chain
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
17: probability to be observed in state j at the second wave
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
1.66 brouard 35: states. This elementary transition (by month, quarter,
36: semester or year) is modelled as a multinomial logistic. The hPx
1.53 brouard 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.
40:
41: Also this programme outputs the covariance matrix of the parameters but also
1.54 brouard 42: of the life expectancies. It also computes the stable prevalence.
1.53 brouard 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
59: #define GNUPLOTPROGRAM "gnuplot"
60: /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
61: #define FILENAMELENGTH 80
62: /*#define DEBUG*/
1.55 lievre 63: #define windows
1.53 brouard 64: #define GLOCK_ERROR_NOPATH -1 /* empty path */
65: #define GLOCK_ERROR_GETCWD -2 /* cannot get cwd */
66:
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 */
74: #define MAXN 20000
75: #define YEARM 12. /* Number of months per year */
76: #define AGESUP 130
77: #define AGEBASE 40
78: #ifdef windows
79: #define DIRSEPARATOR '\\'
80: #define ODIRSEPARATOR '/'
81: #else
82: #define DIRSEPARATOR '/'
83: #define ODIRSEPARATOR '\\'
84: #endif
85:
1.70 ! brouard 86: char version[80]="Imach version 0.92, February 2003, INED-EUROREVES ";
1.53 brouard 87: int erreur; /* Error number */
88: int nvar;
89: int cptcovn=0, cptcovage=0, cptcoveff=0,cptcov;
90: int npar=NPARMAX;
91: int nlstate=2; /* Number of live states */
92: int ndeath=1; /* Number of dead states */
93: int ncovmodel, ncovcol; /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
94: int popbased=0;
95:
96: int *wav; /* Number of waves for this individuual 0 is possible */
97: int maxwav; /* Maxim number of waves */
98: int jmin, jmax; /* min, max spacing between 2 waves */
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 */
1.59 brouard 102: int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between
103: * wave mi and wave mi+1 is not an exact multiple of stepm. */
1.53 brouard 104: double jmean; /* Mean space between 2 waves */
105: double **oldm, **newm, **savm; /* Working pointers to matrices */
106: double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
107: FILE *fic,*ficpar, *ficparo,*ficres, *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
108: FILE *ficlog;
109: FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
110: FILE *ficresprobmorprev;
111: FILE *fichtm; /* Html File */
112: FILE *ficreseij;
113: char filerese[FILENAMELENGTH];
114: FILE *ficresvij;
115: char fileresv[FILENAMELENGTH];
116: FILE *ficresvpl;
117: char fileresvpl[FILENAMELENGTH];
118: char title[MAXLINE];
119: char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH], filerespl[FILENAMELENGTH];
120: char optionfilext[10], optionfilefiname[FILENAMELENGTH], plotcmd[FILENAMELENGTH];
121:
122: char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
123: char filelog[FILENAMELENGTH]; /* Log file */
124: char filerest[FILENAMELENGTH];
125: char fileregp[FILENAMELENGTH];
126: char popfile[FILENAMELENGTH];
127:
128: char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH];
129:
130: #define NR_END 1
131: #define FREE_ARG char*
132: #define FTOL 1.0e-10
133:
134: #define NRANSI
135: #define ITMAX 200
136:
137: #define TOL 2.0e-4
138:
139: #define CGOLD 0.3819660
140: #define ZEPS 1.0e-10
141: #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);
142:
143: #define GOLD 1.618034
144: #define GLIMIT 100.0
145: #define TINY 1.0e-20
146:
147: static double maxarg1,maxarg2;
148: #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
149: #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
150:
151: #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
152: #define rint(a) floor(a+0.5)
153:
154: static double sqrarg;
155: #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
156: #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}
157:
158: int imx;
159: int stepm;
160: /* Stepm, step in month: minimum step interpolation*/
161:
162: int estepm;
163: /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
164:
165: int m,nb;
166: int *num, firstpass=0, lastpass=4,*cod, *ncodemax, *Tage;
167: double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
1.55 lievre 168: double **pmmij, ***probs;
1.53 brouard 169: double dateintmean=0;
170:
171: double *weight;
172: int **s; /* Status */
173: double *agedc, **covar, idx;
174: int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;
175:
176: double ftol=FTOL; /* Tolerance for computing Max Likelihood */
177: double ftolhess; /* Tolerance for computing hessian */
178:
179: /**************** split *************************/
180: static int split( char *path, char *dirc, char *name, char *ext, char *finame )
181: {
1.59 brouard 182: char *ss; /* pointer */
183: int l1, l2; /* length counters */
1.53 brouard 184:
1.59 brouard 185: l1 = strlen(path ); /* length of path */
186: if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
187: ss= strrchr( path, DIRSEPARATOR ); /* find last / */
188: if ( ss == NULL ) { /* no directory, so use current */
189: /*if(strrchr(path, ODIRSEPARATOR )==NULL)
190: printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
1.53 brouard 191: #if defined(__bsd__) /* get current working directory */
1.59 brouard 192: extern char *getwd( );
1.53 brouard 193:
1.59 brouard 194: if ( getwd( dirc ) == NULL ) {
1.53 brouard 195: #else
1.59 brouard 196: extern char *getcwd( );
1.53 brouard 197:
1.59 brouard 198: if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {
1.53 brouard 199: #endif
1.59 brouard 200: return( GLOCK_ERROR_GETCWD );
201: }
202: strcpy( name, path ); /* we've got it */
203: } else { /* strip direcotry from path */
204: ss++; /* after this, the filename */
205: l2 = strlen( ss ); /* length of filename */
206: if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
207: strcpy( name, ss ); /* save file name */
208: strncpy( dirc, path, l1 - l2 ); /* now the directory */
209: dirc[l1-l2] = 0; /* add zero */
210: }
211: l1 = strlen( dirc ); /* length of directory */
1.53 brouard 212: #ifdef windows
1.59 brouard 213: if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; }
1.53 brouard 214: #else
1.59 brouard 215: if ( dirc[l1-1] != '/' ) { dirc[l1] = '/'; dirc[l1+1] = 0; }
1.53 brouard 216: #endif
1.59 brouard 217: ss = strrchr( name, '.' ); /* find last / */
218: ss++;
219: strcpy(ext,ss); /* save extension */
220: l1= strlen( name);
221: l2= strlen(ss)+1;
222: strncpy( finame, name, l1-l2);
223: finame[l1-l2]= 0;
224: return( 0 ); /* we're done */
1.53 brouard 225: }
226:
227:
228: /******************************************/
229:
230: void replace(char *s, char*t)
231: {
232: int i;
233: int lg=20;
234: i=0;
235: lg=strlen(t);
236: for(i=0; i<= lg; i++) {
237: (s[i] = t[i]);
238: if (t[i]== '\\') s[i]='/';
239: }
240: }
241:
242: int nbocc(char *s, char occ)
243: {
244: int i,j=0;
245: int lg=20;
246: i=0;
247: lg=strlen(s);
248: for(i=0; i<= lg; i++) {
249: if (s[i] == occ ) j++;
250: }
251: return j;
252: }
253:
254: void cutv(char *u,char *v, char*t, char occ)
255: {
256: /* cuts string t into u and v where u is ended by char occ excluding it
257: and v is after occ excluding it too : ex cutv(u,v,"abcdef2ghi2j",2)
258: gives u="abcedf" and v="ghi2j" */
259: int i,lg,j,p=0;
260: i=0;
261: for(j=0; j<=strlen(t)-1; j++) {
262: if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;
263: }
264:
265: lg=strlen(t);
266: for(j=0; j<p; j++) {
267: (u[j] = t[j]);
268: }
269: u[p]='\0';
270:
271: for(j=0; j<= lg; j++) {
272: if (j>=(p+1))(v[j-p-1] = t[j]);
273: }
274: }
275:
276: /********************** nrerror ********************/
277:
278: void nrerror(char error_text[])
279: {
280: fprintf(stderr,"ERREUR ...\n");
281: fprintf(stderr,"%s\n",error_text);
1.59 brouard 282: exit(EXIT_FAILURE);
1.53 brouard 283: }
284: /*********************** vector *******************/
285: double *vector(int nl, int nh)
286: {
287: double *v;
288: v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
289: if (!v) nrerror("allocation failure in vector");
290: return v-nl+NR_END;
291: }
292:
293: /************************ free vector ******************/
294: void free_vector(double*v, int nl, int nh)
295: {
296: free((FREE_ARG)(v+nl-NR_END));
297: }
298:
299: /************************ivector *******************************/
300: int *ivector(long nl,long nh)
301: {
302: int *v;
303: v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
304: if (!v) nrerror("allocation failure in ivector");
305: return v-nl+NR_END;
306: }
307:
308: /******************free ivector **************************/
309: void free_ivector(int *v, long nl, long nh)
310: {
311: free((FREE_ARG)(v+nl-NR_END));
312: }
313:
314: /******************* imatrix *******************************/
315: int **imatrix(long nrl, long nrh, long ncl, long nch)
316: /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */
317: {
318: long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;
319: int **m;
320:
321: /* allocate pointers to rows */
322: m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));
323: if (!m) nrerror("allocation failure 1 in matrix()");
324: m += NR_END;
325: m -= nrl;
326:
327:
328: /* allocate rows and set pointers to them */
329: m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));
330: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
331: m[nrl] += NR_END;
332: m[nrl] -= ncl;
333:
334: for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;
335:
336: /* return pointer to array of pointers to rows */
337: return m;
338: }
339:
340: /****************** free_imatrix *************************/
341: void free_imatrix(m,nrl,nrh,ncl,nch)
342: int **m;
343: long nch,ncl,nrh,nrl;
344: /* free an int matrix allocated by imatrix() */
345: {
346: free((FREE_ARG) (m[nrl]+ncl-NR_END));
347: free((FREE_ARG) (m+nrl-NR_END));
348: }
349:
350: /******************* matrix *******************************/
351: double **matrix(long nrl, long nrh, long ncl, long nch)
352: {
353: long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
354: double **m;
355:
356: m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
357: if (!m) nrerror("allocation failure 1 in matrix()");
358: m += NR_END;
359: m -= nrl;
360:
361: m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
362: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
363: m[nrl] += NR_END;
364: m[nrl] -= ncl;
365:
366: for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
367: return m;
368: }
369:
370: /*************************free matrix ************************/
371: void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
372: {
373: free((FREE_ARG)(m[nrl]+ncl-NR_END));
374: free((FREE_ARG)(m+nrl-NR_END));
375: }
376:
377: /******************* ma3x *******************************/
378: double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
379: {
380: long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
381: double ***m;
382:
383: m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
384: if (!m) nrerror("allocation failure 1 in matrix()");
385: m += NR_END;
386: m -= nrl;
387:
388: m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
389: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
390: m[nrl] += NR_END;
391: m[nrl] -= ncl;
392:
393: for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
394:
395: m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
396: if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
397: m[nrl][ncl] += NR_END;
398: m[nrl][ncl] -= nll;
399: for (j=ncl+1; j<=nch; j++)
400: m[nrl][j]=m[nrl][j-1]+nlay;
401:
402: for (i=nrl+1; i<=nrh; i++) {
403: m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
404: for (j=ncl+1; j<=nch; j++)
405: m[i][j]=m[i][j-1]+nlay;
406: }
407: return m;
408: }
409:
410: /*************************free ma3x ************************/
411: void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
412: {
413: free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
414: free((FREE_ARG)(m[nrl]+ncl-NR_END));
415: free((FREE_ARG)(m+nrl-NR_END));
416: }
417:
418: /***************** f1dim *************************/
419: extern int ncom;
420: extern double *pcom,*xicom;
421: extern double (*nrfunc)(double []);
422:
423: double f1dim(double x)
424: {
425: int j;
426: double f;
427: double *xt;
428:
429: xt=vector(1,ncom);
430: for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];
431: f=(*nrfunc)(xt);
432: free_vector(xt,1,ncom);
433: return f;
434: }
435:
436: /*****************brent *************************/
437: double brent(double ax, double bx, double cx, double (*f)(double), double tol, double *xmin)
438: {
439: int iter;
440: double a,b,d,etemp;
441: double fu,fv,fw,fx;
442: double ftemp;
443: double p,q,r,tol1,tol2,u,v,w,x,xm;
444: double e=0.0;
445:
446: a=(ax < cx ? ax : cx);
447: b=(ax > cx ? ax : cx);
448: x=w=v=bx;
449: fw=fv=fx=(*f)(x);
450: for (iter=1;iter<=ITMAX;iter++) {
451: xm=0.5*(a+b);
452: tol2=2.0*(tol1=tol*fabs(x)+ZEPS);
453: /* if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
454: printf(".");fflush(stdout);
455: fprintf(ficlog,".");fflush(ficlog);
456: #ifdef DEBUG
457: 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);
458: 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);
459: /* if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
460: #endif
461: if (fabs(x-xm) <= (tol2-0.5*(b-a))){
462: *xmin=x;
463: return fx;
464: }
465: ftemp=fu;
466: if (fabs(e) > tol1) {
467: r=(x-w)*(fx-fv);
468: q=(x-v)*(fx-fw);
469: p=(x-v)*q-(x-w)*r;
470: q=2.0*(q-r);
471: if (q > 0.0) p = -p;
472: q=fabs(q);
473: etemp=e;
474: e=d;
475: if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))
476: d=CGOLD*(e=(x >= xm ? a-x : b-x));
477: else {
478: d=p/q;
479: u=x+d;
480: if (u-a < tol2 || b-u < tol2)
481: d=SIGN(tol1,xm-x);
482: }
483: } else {
484: d=CGOLD*(e=(x >= xm ? a-x : b-x));
485: }
486: u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));
487: fu=(*f)(u);
488: if (fu <= fx) {
489: if (u >= x) a=x; else b=x;
490: SHFT(v,w,x,u)
491: SHFT(fv,fw,fx,fu)
492: } else {
493: if (u < x) a=u; else b=u;
494: if (fu <= fw || w == x) {
495: v=w;
496: w=u;
497: fv=fw;
498: fw=fu;
499: } else if (fu <= fv || v == x || v == w) {
500: v=u;
501: fv=fu;
502: }
503: }
504: }
505: nrerror("Too many iterations in brent");
506: *xmin=x;
507: return fx;
508: }
509:
510: /****************** mnbrak ***********************/
511:
512: void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,
513: double (*func)(double))
514: {
515: double ulim,u,r,q, dum;
516: double fu;
517:
518: *fa=(*func)(*ax);
519: *fb=(*func)(*bx);
520: if (*fb > *fa) {
521: SHFT(dum,*ax,*bx,dum)
522: SHFT(dum,*fb,*fa,dum)
523: }
524: *cx=(*bx)+GOLD*(*bx-*ax);
525: *fc=(*func)(*cx);
526: while (*fb > *fc) {
527: r=(*bx-*ax)*(*fb-*fc);
528: q=(*bx-*cx)*(*fb-*fa);
529: u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/
530: (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r));
531: ulim=(*bx)+GLIMIT*(*cx-*bx);
532: if ((*bx-u)*(u-*cx) > 0.0) {
533: fu=(*func)(u);
534: } else if ((*cx-u)*(u-ulim) > 0.0) {
535: fu=(*func)(u);
536: if (fu < *fc) {
537: SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))
538: SHFT(*fb,*fc,fu,(*func)(u))
539: }
540: } else if ((u-ulim)*(ulim-*cx) >= 0.0) {
541: u=ulim;
542: fu=(*func)(u);
543: } else {
544: u=(*cx)+GOLD*(*cx-*bx);
545: fu=(*func)(u);
546: }
547: SHFT(*ax,*bx,*cx,u)
548: SHFT(*fa,*fb,*fc,fu)
549: }
550: }
551:
552: /*************** linmin ************************/
553:
554: int ncom;
555: double *pcom,*xicom;
556: double (*nrfunc)(double []);
557:
558: void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))
559: {
560: double brent(double ax, double bx, double cx,
561: double (*f)(double), double tol, double *xmin);
562: double f1dim(double x);
563: void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,
564: double *fc, double (*func)(double));
565: int j;
566: double xx,xmin,bx,ax;
567: double fx,fb,fa;
568:
569: ncom=n;
570: pcom=vector(1,n);
571: xicom=vector(1,n);
572: nrfunc=func;
573: for (j=1;j<=n;j++) {
574: pcom[j]=p[j];
575: xicom[j]=xi[j];
576: }
577: ax=0.0;
578: xx=1.0;
579: mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim);
580: *fret=brent(ax,xx,bx,f1dim,TOL,&xmin);
581: #ifdef DEBUG
582: printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
583: fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
584: #endif
585: for (j=1;j<=n;j++) {
586: xi[j] *= xmin;
587: p[j] += xi[j];
588: }
589: free_vector(xicom,1,n);
590: free_vector(pcom,1,n);
591: }
592:
593: /*************** powell ************************/
594: void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,
595: double (*func)(double []))
596: {
597: void linmin(double p[], double xi[], int n, double *fret,
598: double (*func)(double []));
599: int i,ibig,j;
600: double del,t,*pt,*ptt,*xit;
601: double fp,fptt;
602: double *xits;
603: pt=vector(1,n);
604: ptt=vector(1,n);
605: xit=vector(1,n);
606: xits=vector(1,n);
607: *fret=(*func)(p);
608: for (j=1;j<=n;j++) pt[j]=p[j];
609: for (*iter=1;;++(*iter)) {
610: fp=(*fret);
611: ibig=0;
612: del=0.0;
613: printf("\nPowell iter=%d -2*LL=%.12f",*iter,*fret);
614: fprintf(ficlog,"\nPowell iter=%d -2*LL=%.12f",*iter,*fret);
615: for (i=1;i<=n;i++)
616: printf(" %d %.12f",i, p[i]);
617: fprintf(ficlog," %d %.12f",i, p[i]);
618: printf("\n");
619: fprintf(ficlog,"\n");
620: for (i=1;i<=n;i++) {
621: for (j=1;j<=n;j++) xit[j]=xi[j][i];
622: fptt=(*fret);
623: #ifdef DEBUG
624: printf("fret=%lf \n",*fret);
625: fprintf(ficlog,"fret=%lf \n",*fret);
626: #endif
627: printf("%d",i);fflush(stdout);
628: fprintf(ficlog,"%d",i);fflush(ficlog);
629: linmin(p,xit,n,fret,func);
630: if (fabs(fptt-(*fret)) > del) {
631: del=fabs(fptt-(*fret));
632: ibig=i;
633: }
634: #ifdef DEBUG
635: printf("%d %.12e",i,(*fret));
636: fprintf(ficlog,"%d %.12e",i,(*fret));
637: for (j=1;j<=n;j++) {
638: xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
639: printf(" x(%d)=%.12e",j,xit[j]);
640: fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
641: }
642: for(j=1;j<=n;j++) {
643: printf(" p=%.12e",p[j]);
644: fprintf(ficlog," p=%.12e",p[j]);
645: }
646: printf("\n");
647: fprintf(ficlog,"\n");
648: #endif
649: }
650: if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {
651: #ifdef DEBUG
652: int k[2],l;
653: k[0]=1;
654: k[1]=-1;
655: printf("Max: %.12e",(*func)(p));
656: fprintf(ficlog,"Max: %.12e",(*func)(p));
657: for (j=1;j<=n;j++) {
658: printf(" %.12e",p[j]);
659: fprintf(ficlog," %.12e",p[j]);
660: }
661: printf("\n");
662: fprintf(ficlog,"\n");
663: for(l=0;l<=1;l++) {
664: for (j=1;j<=n;j++) {
665: ptt[j]=p[j]+(p[j]-pt[j])*k[l];
666: printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
667: fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
668: }
669: printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
670: fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
671: }
672: #endif
673:
674:
675: free_vector(xit,1,n);
676: free_vector(xits,1,n);
677: free_vector(ptt,1,n);
678: free_vector(pt,1,n);
679: return;
680: }
681: if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");
682: for (j=1;j<=n;j++) {
683: ptt[j]=2.0*p[j]-pt[j];
684: xit[j]=p[j]-pt[j];
685: pt[j]=p[j];
686: }
687: fptt=(*func)(ptt);
688: if (fptt < fp) {
689: t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt);
690: if (t < 0.0) {
691: linmin(p,xit,n,fret,func);
692: for (j=1;j<=n;j++) {
693: xi[j][ibig]=xi[j][n];
694: xi[j][n]=xit[j];
695: }
696: #ifdef DEBUG
697: printf("Direction changed last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
698: fprintf(ficlog,"Direction changed last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
699: for(j=1;j<=n;j++){
700: printf(" %.12e",xit[j]);
701: fprintf(ficlog," %.12e",xit[j]);
702: }
703: printf("\n");
704: fprintf(ficlog,"\n");
705: #endif
1.54 brouard 706: }
1.53 brouard 707: }
708: }
709: }
710:
1.54 brouard 711: /**** Prevalence limit (stable prevalence) ****************/
1.53 brouard 712:
713: double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)
714: {
715: /* Computes the prevalence limit in each live state at age x by left multiplying the unit
716: matrix by transitions matrix until convergence is reached */
717:
718: int i, ii,j,k;
719: double min, max, maxmin, maxmax,sumnew=0.;
720: double **matprod2();
721: double **out, cov[NCOVMAX], **pmij();
722: double **newm;
723: double agefin, delaymax=50 ; /* Max number of years to converge */
724:
725: for (ii=1;ii<=nlstate+ndeath;ii++)
726: for (j=1;j<=nlstate+ndeath;j++){
727: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
728: }
729:
730: cov[1]=1.;
731:
732: /* Even if hstepm = 1, at least one multiplication by the unit matrix */
733: for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
734: newm=savm;
735: /* Covariates have to be included here again */
736: cov[2]=agefin;
737:
738: for (k=1; k<=cptcovn;k++) {
739: cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
740: /* 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]]);*/
741: }
742: for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
743: for (k=1; k<=cptcovprod;k++)
744: cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
745:
746: /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
747: /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
748: /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
749: out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);
750:
751: savm=oldm;
752: oldm=newm;
753: maxmax=0.;
754: for(j=1;j<=nlstate;j++){
755: min=1.;
756: max=0.;
757: for(i=1; i<=nlstate; i++) {
758: sumnew=0;
759: for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
760: prlim[i][j]= newm[i][j]/(1-sumnew);
761: max=FMAX(max,prlim[i][j]);
762: min=FMIN(min,prlim[i][j]);
763: }
764: maxmin=max-min;
765: maxmax=FMAX(maxmax,maxmin);
766: }
767: if(maxmax < ftolpl){
768: return prlim;
769: }
770: }
771: }
772:
773: /*************** transition probabilities ***************/
774:
775: double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
776: {
777: double s1, s2;
778: /*double t34;*/
779: int i,j,j1, nc, ii, jj;
780:
781: for(i=1; i<= nlstate; i++){
782: for(j=1; j<i;j++){
783: for (nc=1, s2=0.;nc <=ncovmodel; nc++){
784: /*s2 += param[i][j][nc]*cov[nc];*/
785: s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
786: /*printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2);*/
787: }
788: ps[i][j]=s2;
789: /*printf("s1=%.17e, s2=%.17e\n",s1,s2);*/
790: }
791: for(j=i+1; j<=nlstate+ndeath;j++){
792: for (nc=1, s2=0.;nc <=ncovmodel; nc++){
793: s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
794: /*printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2);*/
795: }
796: ps[i][j]=s2;
797: }
798: }
799: /*ps[3][2]=1;*/
800:
801: for(i=1; i<= nlstate; i++){
802: s1=0;
803: for(j=1; j<i; j++)
804: s1+=exp(ps[i][j]);
805: for(j=i+1; j<=nlstate+ndeath; j++)
806: s1+=exp(ps[i][j]);
807: ps[i][i]=1./(s1+1.);
808: for(j=1; j<i; j++)
809: ps[i][j]= exp(ps[i][j])*ps[i][i];
810: for(j=i+1; j<=nlstate+ndeath; j++)
811: ps[i][j]= exp(ps[i][j])*ps[i][i];
812: /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
813: } /* end i */
814:
815: for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
816: for(jj=1; jj<= nlstate+ndeath; jj++){
817: ps[ii][jj]=0;
818: ps[ii][ii]=1;
819: }
820: }
821:
822:
823: /* for(ii=1; ii<= nlstate+ndeath; ii++){
824: for(jj=1; jj<= nlstate+ndeath; jj++){
825: printf("%lf ",ps[ii][jj]);
826: }
827: printf("\n ");
828: }
829: printf("\n ");printf("%lf ",cov[2]);*/
830: /*
831: for(i=1; i<= npar; i++) printf("%f ",x[i]);
832: goto end;*/
833: return ps;
834: }
835:
836: /**************** Product of 2 matrices ******************/
837:
838: double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)
839: {
840: /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
841: b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
842: /* in, b, out are matrice of pointers which should have been initialized
843: before: only the contents of out is modified. The function returns
844: a pointer to pointers identical to out */
845: long i, j, k;
846: for(i=nrl; i<= nrh; i++)
847: for(k=ncolol; k<=ncoloh; k++)
848: for(j=ncl,out[i][k]=0.; j<=nch; j++)
849: out[i][k] +=in[i][j]*b[j][k];
850:
851: return out;
852: }
853:
854:
855: /************* Higher Matrix Product ***************/
856:
857: double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
858: {
1.66 brouard 859: /* Computes the transition matrix starting at age 'age' over
860: 'nhstepm*hstepm*stepm' months (i.e. until
861: age (in years) age+nhstepm*hstepm*stepm/12) by multiplying
862: nhstepm*hstepm matrices.
1.53 brouard 863: Output is stored in matrix po[i][j][h] for h every 'hstepm' step
1.66 brouard 864: (typically every 2 years instead of every month which is too big
865: for the memory).
1.53 brouard 866: Model is determined by parameters x and covariates have to be
867: included manually here.
868:
869: */
870:
871: int i, j, d, h, k;
872: double **out, cov[NCOVMAX];
873: double **newm;
874:
875: /* Hstepm could be zero and should return the unit matrix */
876: for (i=1;i<=nlstate+ndeath;i++)
877: for (j=1;j<=nlstate+ndeath;j++){
878: oldm[i][j]=(i==j ? 1.0 : 0.0);
879: po[i][j][0]=(i==j ? 1.0 : 0.0);
880: }
881: /* Even if hstepm = 1, at least one multiplication by the unit matrix */
882: for(h=1; h <=nhstepm; h++){
883: for(d=1; d <=hstepm; d++){
884: newm=savm;
885: /* Covariates have to be included here again */
886: cov[1]=1.;
887: cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
888: for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
889: for (k=1; k<=cptcovage;k++)
890: cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
891: for (k=1; k<=cptcovprod;k++)
892: cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
893:
894:
895: /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
896: /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
897: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,
898: pmij(pmmij,cov,ncovmodel,x,nlstate));
899: savm=oldm;
900: oldm=newm;
901: }
902: for(i=1; i<=nlstate+ndeath; i++)
903: for(j=1;j<=nlstate+ndeath;j++) {
904: po[i][j][h]=newm[i][j];
905: /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);
906: */
907: }
908: } /* end h */
909: return po;
910: }
911:
912:
913: /*************** log-likelihood *************/
914: double func( double *x)
915: {
916: int i, ii, j, k, mi, d, kk;
917: double l, ll[NLSTATEMAX], cov[NCOVMAX];
918: double **out;
919: double sw; /* Sum of weights */
920: double lli; /* Individual log likelihood */
1.59 brouard 921: int s1, s2;
1.68 lievre 922: double bbh, survp;
1.53 brouard 923: long ipmx;
924: /*extern weight */
925: /* We are differentiating ll according to initial status */
926: /* for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
927: /*for(i=1;i<imx;i++)
928: printf(" %d\n",s[4][i]);
929: */
930: cov[1]=1.;
931:
932: for(k=1; k<=nlstate; k++) ll[k]=0.;
1.61 brouard 933:
934: if(mle==1){
935: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
936: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
937: for(mi=1; mi<= wav[i]-1; mi++){
938: for (ii=1;ii<=nlstate+ndeath;ii++)
939: for (j=1;j<=nlstate+ndeath;j++){
940: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
941: savm[ii][j]=(ii==j ? 1.0 : 0.0);
942: }
943: for(d=0; d<dh[mi][i]; d++){
944: newm=savm;
945: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
946: for (kk=1; kk<=cptcovage;kk++) {
947: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
948: }
949: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
950: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
951: savm=oldm;
952: oldm=newm;
953: } /* end mult */
1.53 brouard 954:
1.61 brouard 955: /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
956: /* But now since version 0.9 we anticipate for bias and large stepm.
957: * If stepm is larger than one month (smallest stepm) and if the exact delay
958: * (in months) between two waves is not a multiple of stepm, we rounded to
959: * the nearest (and in case of equal distance, to the lowest) interval but now
960: * we keep into memory the bias bh[mi][i] and also the previous matrix product
961: * (i.e to dh[mi][i]-1) saved in 'savm'. The we inter(extra)polate the
962: * probability in order to take into account the bias as a fraction of the way
963: * from savm to out if bh is neagtive or even beyond if bh is positive. bh varies
964: * -stepm/2 to stepm/2 .
965: * For stepm=1 the results are the same as for previous versions of Imach.
966: * For stepm > 1 the results are less biased than in previous versions.
967: */
968: s1=s[mw[mi][i]][i];
969: s2=s[mw[mi+1][i]][i];
1.64 lievre 970: bbh=(double)bh[mi][i]/(double)stepm;
971: /* bias is positive if real duration
972: * is higher than the multiple of stepm and negative otherwise.
973: */
974: /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
975: lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*(savm[s1][s2])):log((1.+bbh)*out[s1][s2])); /* linear interpolation */
976: /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
977: /*if(lli ==000.0)*/
978: /*printf("bbh= %f lli=%f savm=%f out=%f %d\n",bbh,lli,savm[s1][s2], out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]],i); */
979: ipmx +=1;
980: sw += weight[i];
981: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
982: } /* end of wave */
983: } /* end of individual */
984: } else if(mle==2){
985: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
986: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
987: for(mi=1; mi<= wav[i]-1; mi++){
988: for (ii=1;ii<=nlstate+ndeath;ii++)
989: for (j=1;j<=nlstate+ndeath;j++){
990: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
991: savm[ii][j]=(ii==j ? 1.0 : 0.0);
992: }
993: for(d=0; d<=dh[mi][i]; d++){
994: newm=savm;
995: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
996: for (kk=1; kk<=cptcovage;kk++) {
997: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
998: }
999: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1000: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1001: savm=oldm;
1002: oldm=newm;
1003: } /* end mult */
1004:
1005: /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
1006: /* But now since version 0.9 we anticipate for bias and large stepm.
1007: * If stepm is larger than one month (smallest stepm) and if the exact delay
1008: * (in months) between two waves is not a multiple of stepm, we rounded to
1009: * the nearest (and in case of equal distance, to the lowest) interval but now
1010: * we keep into memory the bias bh[mi][i] and also the previous matrix product
1011: * (i.e to dh[mi][i]-1) saved in 'savm'. The we inter(extra)polate the
1012: * probability in order to take into account the bias as a fraction of the way
1013: * from savm to out if bh is neagtive or even beyond if bh is positive. bh varies
1014: * -stepm/2 to stepm/2 .
1015: * For stepm=1 the results are the same as for previous versions of Imach.
1016: * For stepm > 1 the results are less biased than in previous versions.
1017: */
1018: s1=s[mw[mi][i]][i];
1019: s2=s[mw[mi+1][i]][i];
1020: bbh=(double)bh[mi][i]/(double)stepm;
1021: /* bias is positive if real duration
1022: * is higher than the multiple of stepm and negative otherwise.
1023: */
1.63 lievre 1024: lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*(savm[s1][s2])):log((1.+bbh)*out[s1][s2])); /* linear interpolation */
1.64 lievre 1025: /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
1026: /*lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.-+bh)*out[s1][s2])); */ /* exponential interpolation */
1027: /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
1028: /*if(lli ==000.0)*/
1029: /*printf("bbh= %f lli=%f savm=%f out=%f %d\n",bbh,lli,savm[s1][s2], out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]],i); */
1030: ipmx +=1;
1031: sw += weight[i];
1032: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1033: } /* end of wave */
1034: } /* end of individual */
1035: } else if(mle==3){ /* exponential inter-extrapolation */
1036: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1037: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
1038: for(mi=1; mi<= wav[i]-1; mi++){
1039: for (ii=1;ii<=nlstate+ndeath;ii++)
1040: for (j=1;j<=nlstate+ndeath;j++){
1041: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1042: savm[ii][j]=(ii==j ? 1.0 : 0.0);
1043: }
1044: for(d=0; d<dh[mi][i]; d++){
1045: newm=savm;
1046: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
1047: for (kk=1; kk<=cptcovage;kk++) {
1048: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
1049: }
1050: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1051: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1052: savm=oldm;
1053: oldm=newm;
1054: } /* end mult */
1055:
1056: /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
1057: /* But now since version 0.9 we anticipate for bias and large stepm.
1058: * If stepm is larger than one month (smallest stepm) and if the exact delay
1059: * (in months) between two waves is not a multiple of stepm, we rounded to
1060: * the nearest (and in case of equal distance, to the lowest) interval but now
1061: * we keep into memory the bias bh[mi][i] and also the previous matrix product
1062: * (i.e to dh[mi][i]-1) saved in 'savm'. The we inter(extra)polate the
1063: * probability in order to take into account the bias as a fraction of the way
1064: * from savm to out if bh is neagtive or even beyond if bh is positive. bh varies
1065: * -stepm/2 to stepm/2 .
1066: * For stepm=1 the results are the same as for previous versions of Imach.
1067: * For stepm > 1 the results are less biased than in previous versions.
1068: */
1069: s1=s[mw[mi][i]][i];
1070: s2=s[mw[mi+1][i]][i];
1071: bbh=(double)bh[mi][i]/(double)stepm;
1072: /* bias is positive if real duration
1073: * is higher than the multiple of stepm and negative otherwise.
1074: */
1075: /* lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*(savm[s1][s2])):log((1.+bbh)*out[s1][s2])); */ /* linear interpolation */
1076: lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2])); /* exponential inter-extrapolation */
1.61 brouard 1077: /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
1078: /*if(lli ==000.0)*/
1079: /*printf("bbh= %f lli=%f savm=%f out=%f %d\n",bbh,lli,savm[s1][s2], out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]],i); */
1080: ipmx +=1;
1081: sw += weight[i];
1082: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1083: } /* end of wave */
1084: } /* end of individual */
1.64 lievre 1085: }else{ /* ml=4 no inter-extrapolation */
1.61 brouard 1086: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1087: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
1088: for(mi=1; mi<= wav[i]-1; mi++){
1089: for (ii=1;ii<=nlstate+ndeath;ii++)
1090: for (j=1;j<=nlstate+ndeath;j++){
1091: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1092: savm[ii][j]=(ii==j ? 1.0 : 0.0);
1093: }
1094: for(d=0; d<dh[mi][i]; d++){
1095: newm=savm;
1096: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
1097: for (kk=1; kk<=cptcovage;kk++) {
1098: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
1099: }
1100:
1101: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1102: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1103: savm=oldm;
1104: oldm=newm;
1105: } /* end mult */
1106:
1107: lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
1108: ipmx +=1;
1109: sw += weight[i];
1110: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1111: } /* end of wave */
1112: } /* end of individual */
1113: } /* End of if */
1.53 brouard 1114: for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
1115: /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
1116: l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
1117: return -l;
1118: }
1119:
1120:
1121: /*********** Maximum Likelihood Estimation ***************/
1122:
1123: void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
1124: {
1125: int i,j, iter;
1126: double **xi,*delti;
1127: double fret;
1128: xi=matrix(1,npar,1,npar);
1129: for (i=1;i<=npar;i++)
1130: for (j=1;j<=npar;j++)
1131: xi[i][j]=(i==j ? 1.0 : 0.0);
1132: printf("Powell\n"); fprintf(ficlog,"Powell\n");
1133: powell(p,xi,npar,ftol,&iter,&fret,func);
1134:
1135: printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));
1.65 lievre 1136: fprintf(ficlog,"\n#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
1.53 brouard 1137: fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
1138:
1139: }
1140:
1141: /**** Computes Hessian and covariance matrix ***/
1142: void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
1143: {
1144: double **a,**y,*x,pd;
1145: double **hess;
1146: int i, j,jk;
1147: int *indx;
1148:
1149: double hessii(double p[], double delta, int theta, double delti[]);
1150: double hessij(double p[], double delti[], int i, int j);
1151: void lubksb(double **a, int npar, int *indx, double b[]) ;
1152: void ludcmp(double **a, int npar, int *indx, double *d) ;
1153:
1154: hess=matrix(1,npar,1,npar);
1155:
1156: printf("\nCalculation of the hessian matrix. Wait...\n");
1157: fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
1158: for (i=1;i<=npar;i++){
1159: printf("%d",i);fflush(stdout);
1160: fprintf(ficlog,"%d",i);fflush(ficlog);
1161: hess[i][i]=hessii(p,ftolhess,i,delti);
1162: /*printf(" %f ",p[i]);*/
1163: /*printf(" %lf ",hess[i][i]);*/
1164: }
1165:
1166: for (i=1;i<=npar;i++) {
1167: for (j=1;j<=npar;j++) {
1168: if (j>i) {
1169: printf(".%d%d",i,j);fflush(stdout);
1170: fprintf(ficlog,".%d%d",i,j);fflush(ficlog);
1171: hess[i][j]=hessij(p,delti,i,j);
1172: hess[j][i]=hess[i][j];
1173: /*printf(" %lf ",hess[i][j]);*/
1174: }
1175: }
1176: }
1177: printf("\n");
1178: fprintf(ficlog,"\n");
1179:
1180: printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
1181: fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
1182:
1183: a=matrix(1,npar,1,npar);
1184: y=matrix(1,npar,1,npar);
1185: x=vector(1,npar);
1186: indx=ivector(1,npar);
1187: for (i=1;i<=npar;i++)
1188: for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
1189: ludcmp(a,npar,indx,&pd);
1190:
1191: for (j=1;j<=npar;j++) {
1192: for (i=1;i<=npar;i++) x[i]=0;
1193: x[j]=1;
1194: lubksb(a,npar,indx,x);
1195: for (i=1;i<=npar;i++){
1196: matcov[i][j]=x[i];
1197: }
1198: }
1199:
1200: printf("\n#Hessian matrix#\n");
1201: fprintf(ficlog,"\n#Hessian matrix#\n");
1202: for (i=1;i<=npar;i++) {
1203: for (j=1;j<=npar;j++) {
1204: printf("%.3e ",hess[i][j]);
1205: fprintf(ficlog,"%.3e ",hess[i][j]);
1206: }
1207: printf("\n");
1208: fprintf(ficlog,"\n");
1209: }
1210:
1211: /* Recompute Inverse */
1212: for (i=1;i<=npar;i++)
1213: for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];
1214: ludcmp(a,npar,indx,&pd);
1215:
1216: /* printf("\n#Hessian matrix recomputed#\n");
1217:
1218: for (j=1;j<=npar;j++) {
1219: for (i=1;i<=npar;i++) x[i]=0;
1220: x[j]=1;
1221: lubksb(a,npar,indx,x);
1222: for (i=1;i<=npar;i++){
1223: y[i][j]=x[i];
1224: printf("%.3e ",y[i][j]);
1225: fprintf(ficlog,"%.3e ",y[i][j]);
1226: }
1227: printf("\n");
1228: fprintf(ficlog,"\n");
1229: }
1230: */
1231:
1232: free_matrix(a,1,npar,1,npar);
1233: free_matrix(y,1,npar,1,npar);
1234: free_vector(x,1,npar);
1235: free_ivector(indx,1,npar);
1236: free_matrix(hess,1,npar,1,npar);
1237:
1238:
1239: }
1240:
1241: /*************** hessian matrix ****************/
1242: double hessii( double x[], double delta, int theta, double delti[])
1243: {
1244: int i;
1245: int l=1, lmax=20;
1246: double k1,k2;
1247: double p2[NPARMAX+1];
1248: double res;
1249: double delt, delts, nkhi=10.,nkhif=1., khi=1.e-4;
1250: double fx;
1251: int k=0,kmax=10;
1252: double l1;
1253:
1254: fx=func(x);
1255: for (i=1;i<=npar;i++) p2[i]=x[i];
1256: for(l=0 ; l <=lmax; l++){
1257: l1=pow(10,l);
1258: delts=delt;
1259: for(k=1 ; k <kmax; k=k+1){
1260: delt = delta*(l1*k);
1261: p2[theta]=x[theta] +delt;
1262: k1=func(p2)-fx;
1263: p2[theta]=x[theta]-delt;
1264: k2=func(p2)-fx;
1265: /*res= (k1-2.0*fx+k2)/delt/delt; */
1266: res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */
1267:
1268: #ifdef DEBUG
1269: 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);
1270: 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);
1271: #endif
1272: /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
1273: if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
1274: k=kmax;
1275: }
1276: else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
1277: k=kmax; l=lmax*10.;
1278: }
1279: else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){
1280: delts=delt;
1281: }
1282: }
1283: }
1284: delti[theta]=delts;
1285: return res;
1286:
1287: }
1288:
1289: double hessij( double x[], double delti[], int thetai,int thetaj)
1290: {
1291: int i;
1292: int l=1, l1, lmax=20;
1293: double k1,k2,k3,k4,res,fx;
1294: double p2[NPARMAX+1];
1295: int k;
1296:
1297: fx=func(x);
1298: for (k=1; k<=2; k++) {
1299: for (i=1;i<=npar;i++) p2[i]=x[i];
1300: p2[thetai]=x[thetai]+delti[thetai]/k;
1301: p2[thetaj]=x[thetaj]+delti[thetaj]/k;
1302: k1=func(p2)-fx;
1303:
1304: p2[thetai]=x[thetai]+delti[thetai]/k;
1305: p2[thetaj]=x[thetaj]-delti[thetaj]/k;
1306: k2=func(p2)-fx;
1307:
1308: p2[thetai]=x[thetai]-delti[thetai]/k;
1309: p2[thetaj]=x[thetaj]+delti[thetaj]/k;
1310: k3=func(p2)-fx;
1311:
1312: p2[thetai]=x[thetai]-delti[thetai]/k;
1313: p2[thetaj]=x[thetaj]-delti[thetaj]/k;
1314: k4=func(p2)-fx;
1315: res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */
1316: #ifdef DEBUG
1317: 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);
1318: 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);
1319: #endif
1320: }
1321: return res;
1322: }
1323:
1324: /************** Inverse of matrix **************/
1325: void ludcmp(double **a, int n, int *indx, double *d)
1326: {
1327: int i,imax,j,k;
1328: double big,dum,sum,temp;
1329: double *vv;
1330:
1331: vv=vector(1,n);
1332: *d=1.0;
1333: for (i=1;i<=n;i++) {
1334: big=0.0;
1335: for (j=1;j<=n;j++)
1336: if ((temp=fabs(a[i][j])) > big) big=temp;
1337: if (big == 0.0) nrerror("Singular matrix in routine ludcmp");
1338: vv[i]=1.0/big;
1339: }
1340: for (j=1;j<=n;j++) {
1341: for (i=1;i<j;i++) {
1342: sum=a[i][j];
1343: for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];
1344: a[i][j]=sum;
1345: }
1346: big=0.0;
1347: for (i=j;i<=n;i++) {
1348: sum=a[i][j];
1349: for (k=1;k<j;k++)
1350: sum -= a[i][k]*a[k][j];
1351: a[i][j]=sum;
1352: if ( (dum=vv[i]*fabs(sum)) >= big) {
1353: big=dum;
1354: imax=i;
1355: }
1356: }
1357: if (j != imax) {
1358: for (k=1;k<=n;k++) {
1359: dum=a[imax][k];
1360: a[imax][k]=a[j][k];
1361: a[j][k]=dum;
1362: }
1363: *d = -(*d);
1364: vv[imax]=vv[j];
1365: }
1366: indx[j]=imax;
1367: if (a[j][j] == 0.0) a[j][j]=TINY;
1368: if (j != n) {
1369: dum=1.0/(a[j][j]);
1370: for (i=j+1;i<=n;i++) a[i][j] *= dum;
1371: }
1372: }
1373: free_vector(vv,1,n); /* Doesn't work */
1374: ;
1375: }
1376:
1377: void lubksb(double **a, int n, int *indx, double b[])
1378: {
1379: int i,ii=0,ip,j;
1380: double sum;
1381:
1382: for (i=1;i<=n;i++) {
1383: ip=indx[i];
1384: sum=b[ip];
1385: b[ip]=b[i];
1386: if (ii)
1387: for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];
1388: else if (sum) ii=i;
1389: b[i]=sum;
1390: }
1391: for (i=n;i>=1;i--) {
1392: sum=b[i];
1393: for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];
1394: b[i]=sum/a[i][i];
1395: }
1396: }
1397:
1398: /************ Frequencies ********************/
1.59 brouard 1399: void freqsummary(char fileres[], int agemin, int agemax, int **s, double **agev, int nlstate, int imx, int *Tvaraff, int **nbcode, int *ncodemax,double **mint,double **anint, double dateprev1,double dateprev2,double jprev1, double mprev1,double anprev1,double jprev2, double mprev2,double anprev2)
1.53 brouard 1400: { /* Some frequencies */
1401:
1402: int i, m, jk, k1,i1, j1, bool, z1,z2,j;
1403: int first;
1404: double ***freq; /* Frequencies */
1405: double *pp;
1406: double pos, k2, dateintsum=0,k2cpt=0;
1407: FILE *ficresp;
1408: char fileresp[FILENAMELENGTH];
1409:
1410: pp=vector(1,nlstate);
1411: probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
1412: strcpy(fileresp,"p");
1413: strcat(fileresp,fileres);
1414: if((ficresp=fopen(fileresp,"w"))==NULL) {
1415: printf("Problem with prevalence resultfile: %s\n", fileresp);
1416: fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
1417: exit(0);
1418: }
1.69 brouard 1419: freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);
1.53 brouard 1420: j1=0;
1421:
1422: j=cptcoveff;
1423: if (cptcovn<1) {j=1;ncodemax[1]=1;}
1424:
1425: first=1;
1426:
1427: for(k1=1; k1<=j;k1++){
1428: for(i1=1; i1<=ncodemax[k1];i1++){
1429: j1++;
1430: /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
1431: scanf("%d", i);*/
1432: for (i=-1; i<=nlstate+ndeath; i++)
1433: for (jk=-1; jk<=nlstate+ndeath; jk++)
1434: for(m=agemin; m <= agemax+3; m++)
1435: freq[i][jk][m]=0;
1436:
1437: dateintsum=0;
1438: k2cpt=0;
1439: for (i=1; i<=imx; i++) {
1440: bool=1;
1441: if (cptcovn>0) {
1442: for (z1=1; z1<=cptcoveff; z1++)
1443: if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])
1444: bool=0;
1445: }
1.58 lievre 1446: if (bool==1){
1.53 brouard 1447: for(m=firstpass; m<=lastpass; m++){
1448: k2=anint[m][i]+(mint[m][i]/12.);
1449: if ((k2>=dateprev1) && (k2<=dateprev2)) {
1450: if(agev[m][i]==0) agev[m][i]=agemax+1;
1451: if(agev[m][i]==1) agev[m][i]=agemax+2;
1452: if (m<lastpass) {
1453: freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
1454: freq[s[m][i]][s[m+1][i]][(int) agemax+3] += weight[i];
1455: }
1456:
1457: if ((agev[m][i]>1) && (agev[m][i]< (agemax+3))) {
1458: dateintsum=dateintsum+k2;
1459: k2cpt++;
1460: }
1461: }
1462: }
1463: }
1464: }
1465:
1466: fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);
1467:
1468: if (cptcovn>0) {
1469: fprintf(ficresp, "\n#********** Variable ");
1470: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
1471: fprintf(ficresp, "**********\n#");
1472: }
1473: for(i=1; i<=nlstate;i++)
1474: fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
1475: fprintf(ficresp, "\n");
1476:
1477: for(i=(int)agemin; i <= (int)agemax+3; i++){
1478: if(i==(int)agemax+3){
1479: fprintf(ficlog,"Total");
1480: }else{
1481: if(first==1){
1482: first=0;
1483: printf("See log file for details...\n");
1484: }
1485: fprintf(ficlog,"Age %d", i);
1486: }
1487: for(jk=1; jk <=nlstate ; jk++){
1488: for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
1489: pp[jk] += freq[jk][m][i];
1490: }
1491: for(jk=1; jk <=nlstate ; jk++){
1492: for(m=-1, pos=0; m <=0 ; m++)
1493: pos += freq[jk][m][i];
1494: if(pp[jk]>=1.e-10){
1495: if(first==1){
1496: printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
1497: }
1498: fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
1499: }else{
1500: if(first==1)
1501: printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
1502: fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
1503: }
1504: }
1505:
1506: for(jk=1; jk <=nlstate ; jk++){
1507: for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
1508: pp[jk] += freq[jk][m][i];
1509: }
1510:
1511: for(jk=1,pos=0; jk <=nlstate ; jk++)
1512: pos += pp[jk];
1513: for(jk=1; jk <=nlstate ; jk++){
1514: if(pos>=1.e-5){
1515: if(first==1)
1516: printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
1517: fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
1518: }else{
1519: if(first==1)
1520: printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
1521: fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
1522: }
1523: if( i <= (int) agemax){
1524: if(pos>=1.e-5){
1525: fprintf(ficresp," %d %.5f %.0f %.0f",i,pp[jk]/pos, pp[jk],pos);
1526: probs[i][jk][j1]= pp[jk]/pos;
1527: /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/
1528: }
1529: else
1530: fprintf(ficresp," %d NaNq %.0f %.0f",i,pp[jk],pos);
1531: }
1532: }
1533:
1.69 brouard 1534: for(jk=-1; jk <=nlstate+ndeath; jk++)
1535: for(m=-1; m <=nlstate+ndeath; m++)
1.53 brouard 1536: if(freq[jk][m][i] !=0 ) {
1537: if(first==1)
1538: printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
1539: fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
1540: }
1541: if(i <= (int) agemax)
1542: fprintf(ficresp,"\n");
1543: if(first==1)
1544: printf("Others in log...\n");
1545: fprintf(ficlog,"\n");
1546: }
1547: }
1548: }
1549: dateintmean=dateintsum/k2cpt;
1550:
1551: fclose(ficresp);
1.69 brouard 1552: free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);
1.53 brouard 1553: free_vector(pp,1,nlstate);
1554:
1555: /* End of Freq */
1556: }
1557:
1558: /************ Prevalence ********************/
1.70 ! brouard 1559: 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, int firstpass, int lastpass)
1.69 brouard 1560: {
1561: /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
1562: in each health status at the date of interview (if between dateprev1 and dateprev2).
1563: We still use firstpass and lastpass as another selection.
1564: */
1.53 brouard 1565:
1566: int i, m, jk, k1, i1, j1, bool, z1,z2,j;
1567: double ***freq; /* Frequencies */
1568: double *pp;
1.69 brouard 1569: double pos;
1570: double y2; /* in fractional years */
1.53 brouard 1571:
1572: pp=vector(1,nlstate);
1573:
1.69 brouard 1574: freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);
1.53 brouard 1575: j1=0;
1576:
1577: j=cptcoveff;
1578: if (cptcovn<1) {j=1;ncodemax[1]=1;}
1579:
1580: for(k1=1; k1<=j;k1++){
1581: for(i1=1; i1<=ncodemax[k1];i1++){
1582: j1++;
1583:
1.69 brouard 1584: for (i=-1; i<=nlstate+ndeath; i++)
1585: for (jk=-1; jk<=nlstate+ndeath; jk++)
1.53 brouard 1586: for(m=agemin; m <= agemax+3; m++)
1587: freq[i][jk][m]=0;
1588:
1.69 brouard 1589: for (i=1; i<=imx; i++) { /* Each individual */
1.53 brouard 1590: bool=1;
1591: if (cptcovn>0) {
1592: for (z1=1; z1<=cptcoveff; z1++)
1593: if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])
1594: bool=0;
1595: }
1596: if (bool==1) {
1.69 brouard 1597: for(m=firstpass; m<=lastpass; m++){/* Other selection (we can limit to certain interviews*/
1598: y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
1599: if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
1.53 brouard 1600: if(agev[m][i]==0) agev[m][i]=agemax+1;
1601: if(agev[m][i]==1) agev[m][i]=agemax+2;
1602: if (m<lastpass) {
1.70 ! brouard 1603: freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
1.53 brouard 1604: freq[s[m][i]][s[m+1][i]][(int)(agemax+3)] += weight[i];
1605: }
1606: }
1.69 brouard 1607: } /* end selection of waves */
1.53 brouard 1608: }
1609: }
1610: for(i=(int)agemin; i <= (int)agemax+3; i++){
1611: for(jk=1; jk <=nlstate ; jk++){
1612: for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
1613: pp[jk] += freq[jk][m][i];
1614: }
1615: for(jk=1; jk <=nlstate ; jk++){
1616: for(m=-1, pos=0; m <=0 ; m++)
1617: pos += freq[jk][m][i];
1618: }
1619:
1620: for(jk=1; jk <=nlstate ; jk++){
1621: for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
1622: pp[jk] += freq[jk][m][i];
1623: }
1624:
1625: for(jk=1,pos=0; jk <=nlstate ; jk++) pos += pp[jk];
1626:
1627: for(jk=1; jk <=nlstate ; jk++){
1628: if( i <= (int) agemax){
1629: if(pos>=1.e-5){
1630: probs[i][jk][j1]= pp[jk]/pos;
1631: }
1632: }
1633: }/* end jk */
1634: }/* end i */
1635: } /* end i1 */
1636: } /* end k1 */
1637:
1638:
1.69 brouard 1639: free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);
1.53 brouard 1640: free_vector(pp,1,nlstate);
1641:
1642: } /* End of Freq */
1643:
1644: /************* Waves Concatenation ***************/
1645:
1.59 brouard 1646: void concatwav(int wav[], int **dh, int **bh, int **mw, int **s, double *agedc, double **agev, int firstpass, int lastpass, int imx, int nlstate, int stepm)
1.53 brouard 1647: {
1648: /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
1649: Death is a valid wave (if date is known).
1650: mw[mi][i] is the mi (mi=1 to wav[i]) effective wave of individual i
1.59 brouard 1651: dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
1.53 brouard 1652: and mw[mi+1][i]. dh depends on stepm.
1653: */
1654:
1655: int i, mi, m;
1656: /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
1657: double sum=0., jmean=0.;*/
1658: int first;
1659: int j, k=0,jk, ju, jl;
1660: double sum=0.;
1661: first=0;
1662: jmin=1e+5;
1663: jmax=-1;
1664: jmean=0.;
1665: for(i=1; i<=imx; i++){
1666: mi=0;
1667: m=firstpass;
1668: while(s[m][i] <= nlstate){
1.69 brouard 1669: if(s[m][i]>=1)
1.53 brouard 1670: mw[++mi][i]=m;
1671: if(m >=lastpass)
1672: break;
1673: else
1674: m++;
1675: }/* end while */
1676: if (s[m][i] > nlstate){
1677: mi++; /* Death is another wave */
1678: /* if(mi==0) never been interviewed correctly before death */
1679: /* Only death is a correct wave */
1680: mw[mi][i]=m;
1681: }
1682:
1683: wav[i]=mi;
1684: if(mi==0){
1685: if(first==0){
1686: printf("Warning, no any valid information for:%d line=%d and may be others, see log file\n",num[i],i);
1687: first=1;
1688: }
1689: if(first==1){
1690: fprintf(ficlog,"Warning, no any valid information for:%d line=%d\n",num[i],i);
1691: }
1692: } /* end mi==0 */
1693: }
1694:
1695: for(i=1; i<=imx; i++){
1696: for(mi=1; mi<wav[i];mi++){
1697: if (stepm <=0)
1698: dh[mi][i]=1;
1699: else{
1700: if (s[mw[mi+1][i]][i] > nlstate) {
1701: if (agedc[i] < 2*AGESUP) {
1702: j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);
1703: if(j==0) j=1; /* Survives at least one month after exam */
1704: k=k+1;
1705: if (j >= jmax) jmax=j;
1706: if (j <= jmin) jmin=j;
1707: sum=sum+j;
1708: /*if (j<0) printf("j=%d num=%d \n",j,i); */
1.68 lievre 1709: /* printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
1.53 brouard 1710: }
1711: }
1712: else{
1713: j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
1.68 lievre 1714: /* printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
1.53 brouard 1715: k=k+1;
1716: if (j >= jmax) jmax=j;
1717: else if (j <= jmin)jmin=j;
1718: /* if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
1719: sum=sum+j;
1720: }
1721: jk= j/stepm;
1722: jl= j -jk*stepm;
1723: ju= j -(jk+1)*stepm;
1.64 lievre 1724: if(mle <=1){
1725: if(jl==0){
1726: dh[mi][i]=jk;
1727: bh[mi][i]=0;
1728: }else{ /* We want a negative bias in order to only have interpolation ie
1729: * at the price of an extra matrix product in likelihood */
1730: dh[mi][i]=jk+1;
1731: bh[mi][i]=ju;
1732: }
1733: }else{
1734: if(jl <= -ju){
1735: dh[mi][i]=jk;
1736: bh[mi][i]=jl; /* bias is positive if real duration
1737: * is higher than the multiple of stepm and negative otherwise.
1738: */
1739: }
1740: else{
1741: dh[mi][i]=jk+1;
1742: bh[mi][i]=ju;
1743: }
1744: if(dh[mi][i]==0){
1745: dh[mi][i]=1; /* At least one step */
1746: bh[mi][i]=ju; /* At least one step */
1747: printf(" bh=%d ju=%d jl=%d dh=%d jk=%d stepm=%d %d\n",bh[mi][i],ju,jl,dh[mi][i],jk,stepm,i);
1748: }
1.59 brouard 1749: }
1.64 lievre 1750: } /* end if mle */
1751: } /* end wave */
1.53 brouard 1752: }
1753: jmean=sum/k;
1754: printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);
1755: fprintf(ficlog,"Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);
1756: }
1757:
1758: /*********** Tricode ****************************/
1759: void tricode(int *Tvar, int **nbcode, int imx)
1760: {
1.58 lievre 1761:
1762: int Ndum[20],ij=1, k, j, i, maxncov=19;
1.53 brouard 1763: int cptcode=0;
1764: cptcoveff=0;
1765:
1.58 lievre 1766: for (k=0; k<maxncov; k++) Ndum[k]=0;
1.53 brouard 1767: for (k=1; k<=7; k++) ncodemax[k]=0;
1768:
1769: for (j=1; j<=(cptcovn+2*cptcovprod); j++) {
1.58 lievre 1770: for (i=1; i<=imx; i++) { /*reads the data file to get the maximum
1771: modality*/
1772: ij=(int)(covar[Tvar[j]][i]); /* ij is the modality of this individual*/
1773: Ndum[ij]++; /*store the modality */
1.53 brouard 1774: /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
1.58 lievre 1775: if (ij > cptcode) cptcode=ij; /* getting the maximum of covariable
1776: Tvar[j]. If V=sex and male is 0 and
1777: female is 1, then cptcode=1.*/
1.53 brouard 1778: }
1779:
1780: for (i=0; i<=cptcode; i++) {
1.58 lievre 1781: if(Ndum[i]!=0) ncodemax[j]++; /* Nomber of modalities of the j th covariates. In fact ncodemax[j]=2 (dichotom. variables) but it can be more */
1.53 brouard 1782: }
1.58 lievre 1783:
1.53 brouard 1784: ij=1;
1785: for (i=1; i<=ncodemax[j]; i++) {
1.58 lievre 1786: for (k=0; k<= maxncov; k++) {
1.53 brouard 1787: if (Ndum[k] != 0) {
1788: nbcode[Tvar[j]][ij]=k;
1.58 lievre 1789: /* store the modality in an array. k is a modality. If we have model=V1+V1*sex then: nbcode[1][1]=0 ; nbcode[1][2]=1; nbcode[2][1]=0 ; nbcode[2][2]=1; */
1.53 brouard 1790:
1791: ij++;
1792: }
1793: if (ij > ncodemax[j]) break;
1794: }
1795: }
1796: }
1797:
1.58 lievre 1798: for (k=0; k< maxncov; k++) Ndum[k]=0;
1.53 brouard 1799:
1.58 lievre 1800: for (i=1; i<=ncovmodel-2; i++) {
1801: /* Listing of all covariables in staement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/
1.53 brouard 1802: ij=Tvar[i];
1.58 lievre 1803: Ndum[ij]++;
1.53 brouard 1804: }
1805:
1806: ij=1;
1.58 lievre 1807: for (i=1; i<= maxncov; i++) {
1.53 brouard 1808: if((Ndum[i]!=0) && (i<=ncovcol)){
1.58 lievre 1809: Tvaraff[ij]=i; /*For printing */
1.53 brouard 1810: ij++;
1811: }
1812: }
1813:
1.58 lievre 1814: cptcoveff=ij-1; /*Number of simple covariates*/
1.53 brouard 1815: }
1816:
1817: /*********** Health Expectancies ****************/
1818:
1819: 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 )
1820:
1821: {
1822: /* Health expectancies */
1823: int i, j, nhstepm, hstepm, h, nstepm, k, cptj;
1824: double age, agelim, hf;
1825: double ***p3mat,***varhe;
1826: double **dnewm,**doldm;
1827: double *xp;
1828: double **gp, **gm;
1829: double ***gradg, ***trgradg;
1830: int theta;
1831:
1832: varhe=ma3x(1,nlstate*2,1,nlstate*2,(int) bage, (int) fage);
1833: xp=vector(1,npar);
1834: dnewm=matrix(1,nlstate*2,1,npar);
1835: doldm=matrix(1,nlstate*2,1,nlstate*2);
1836:
1837: fprintf(ficreseij,"# Health expectancies\n");
1838: fprintf(ficreseij,"# Age");
1839: for(i=1; i<=nlstate;i++)
1840: for(j=1; j<=nlstate;j++)
1841: fprintf(ficreseij," %1d-%1d (SE)",i,j);
1842: fprintf(ficreseij,"\n");
1843:
1844: if(estepm < stepm){
1845: printf ("Problem %d lower than %d\n",estepm, stepm);
1846: }
1847: else hstepm=estepm;
1848: /* We compute the life expectancy from trapezoids spaced every estepm months
1849: * This is mainly to measure the difference between two models: for example
1850: * if stepm=24 months pijx are given only every 2 years and by summing them
1851: * we are calculating an estimate of the Life Expectancy assuming a linear
1.66 brouard 1852: * progression in between and thus overestimating or underestimating according
1.53 brouard 1853: * to the curvature of the survival function. If, for the same date, we
1854: * estimate the model with stepm=1 month, we can keep estepm to 24 months
1855: * to compare the new estimate of Life expectancy with the same linear
1856: * hypothesis. A more precise result, taking into account a more precise
1857: * curvature will be obtained if estepm is as small as stepm. */
1858:
1859: /* For example we decided to compute the life expectancy with the smallest unit */
1860: /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
1861: nhstepm is the number of hstepm from age to agelim
1862: nstepm is the number of stepm from age to agelin.
1863: Look at hpijx to understand the reason of that which relies in memory size
1864: and note for a fixed period like estepm months */
1865: /* We decided (b) to get a life expectancy respecting the most precise curvature of the
1866: survival function given by stepm (the optimization length). Unfortunately it
1867: means that if the survival funtion is printed only each two years of age and if
1868: you sum them up and add 1 year (area under the trapezoids) you won't get the same
1869: results. So we changed our mind and took the option of the best precision.
1870: */
1871: hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
1872:
1873: agelim=AGESUP;
1874: for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
1875: /* nhstepm age range expressed in number of stepm */
1876: nstepm=(int) rint((agelim-age)*YEARM/stepm);
1877: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
1878: /* if (stepm >= YEARM) hstepm=1;*/
1879: nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
1880: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
1881: gradg=ma3x(0,nhstepm,1,npar,1,nlstate*2);
1882: gp=matrix(0,nhstepm,1,nlstate*2);
1883: gm=matrix(0,nhstepm,1,nlstate*2);
1884:
1885: /* Computed by stepm unit matrices, product of hstepm matrices, stored
1886: in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
1887: hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);
1888:
1889:
1890: hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
1891:
1892: /* Computing Variances of health expectancies */
1893:
1894: for(theta=1; theta <=npar; theta++){
1895: for(i=1; i<=npar; i++){
1896: xp[i] = x[i] + (i==theta ?delti[theta]:0);
1897: }
1898: hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
1899:
1900: cptj=0;
1901: for(j=1; j<= nlstate; j++){
1902: for(i=1; i<=nlstate; i++){
1903: cptj=cptj+1;
1904: for(h=0, gp[h][cptj]=0.; h<=nhstepm-1; h++){
1905: gp[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;
1906: }
1907: }
1908: }
1909:
1910:
1911: for(i=1; i<=npar; i++)
1912: xp[i] = x[i] - (i==theta ?delti[theta]:0);
1913: hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
1914:
1915: cptj=0;
1916: for(j=1; j<= nlstate; j++){
1917: for(i=1;i<=nlstate;i++){
1918: cptj=cptj+1;
1919: for(h=0, gm[h][cptj]=0.; h<=nhstepm-1; h++){
1920: gm[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;
1921: }
1922: }
1923: }
1924: for(j=1; j<= nlstate*2; j++)
1925: for(h=0; h<=nhstepm-1; h++){
1926: gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
1927: }
1928: }
1929:
1930: /* End theta */
1931:
1932: trgradg =ma3x(0,nhstepm,1,nlstate*2,1,npar);
1933:
1934: for(h=0; h<=nhstepm-1; h++)
1935: for(j=1; j<=nlstate*2;j++)
1936: for(theta=1; theta <=npar; theta++)
1937: trgradg[h][j][theta]=gradg[h][theta][j];
1938:
1939:
1940: for(i=1;i<=nlstate*2;i++)
1941: for(j=1;j<=nlstate*2;j++)
1942: varhe[i][j][(int)age] =0.;
1943:
1944: printf("%d|",(int)age);fflush(stdout);
1945: fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
1946: for(h=0;h<=nhstepm-1;h++){
1947: for(k=0;k<=nhstepm-1;k++){
1948: matprod2(dnewm,trgradg[h],1,nlstate*2,1,npar,1,npar,matcov);
1949: matprod2(doldm,dnewm,1,nlstate*2,1,npar,1,nlstate*2,gradg[k]);
1950: for(i=1;i<=nlstate*2;i++)
1951: for(j=1;j<=nlstate*2;j++)
1952: varhe[i][j][(int)age] += doldm[i][j]*hf*hf;
1953: }
1954: }
1955: /* Computing expectancies */
1956: for(i=1; i<=nlstate;i++)
1957: for(j=1; j<=nlstate;j++)
1958: for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
1959: eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
1960:
1961: /* 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]);*/
1962:
1963: }
1964:
1965: fprintf(ficreseij,"%3.0f",age );
1966: cptj=0;
1967: for(i=1; i<=nlstate;i++)
1968: for(j=1; j<=nlstate;j++){
1969: cptj++;
1970: fprintf(ficreseij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[cptj][cptj][(int)age]) );
1971: }
1972: fprintf(ficreseij,"\n");
1973:
1974: free_matrix(gm,0,nhstepm,1,nlstate*2);
1975: free_matrix(gp,0,nhstepm,1,nlstate*2);
1976: free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*2);
1977: free_ma3x(trgradg,0,nhstepm,1,nlstate*2,1,npar);
1978: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
1979: }
1980: printf("\n");
1981: fprintf(ficlog,"\n");
1982:
1983: free_vector(xp,1,npar);
1984: free_matrix(dnewm,1,nlstate*2,1,npar);
1985: free_matrix(doldm,1,nlstate*2,1,nlstate*2);
1986: free_ma3x(varhe,1,nlstate*2,1,nlstate*2,(int) bage, (int)fage);
1987: }
1988:
1989: /************ Variance ******************/
1990: void varevsij(char optionfilefiname[], double ***vareij, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij, int estepm, int cptcov, int cptcod, int popbased, int mobilav)
1991: {
1992: /* Variance of health expectancies */
1993: /* double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
1994: /* double **newm;*/
1995: double **dnewm,**doldm;
1996: double **dnewmp,**doldmp;
1997: int i, j, nhstepm, hstepm, h, nstepm ;
1998: int k, cptcode;
1999: double *xp;
2000: double **gp, **gm; /* for var eij */
2001: double ***gradg, ***trgradg; /*for var eij */
2002: double **gradgp, **trgradgp; /* for var p point j */
2003: double *gpp, *gmp; /* for var p point j */
2004: double **varppt; /* for var p point j nlstate to nlstate+ndeath */
2005: double ***p3mat;
2006: double age,agelim, hf;
2007: double ***mobaverage;
2008: int theta;
2009: char digit[4];
1.55 lievre 2010: char digitp[25];
1.53 brouard 2011:
2012: char fileresprobmorprev[FILENAMELENGTH];
2013:
1.55 lievre 2014: if(popbased==1){
1.58 lievre 2015: if(mobilav!=0)
1.55 lievre 2016: strcpy(digitp,"-populbased-mobilav-");
2017: else strcpy(digitp,"-populbased-nomobil-");
2018: }
2019: else
1.53 brouard 2020: strcpy(digitp,"-stablbased-");
1.56 lievre 2021:
1.54 brouard 2022: if (mobilav!=0) {
1.53 brouard 2023: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
1.54 brouard 2024: if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
2025: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
2026: printf(" Error in movingaverage mobilav=%d\n",mobilav);
2027: }
1.53 brouard 2028: }
2029:
2030: strcpy(fileresprobmorprev,"prmorprev");
2031: sprintf(digit,"%-d",ij);
2032: /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
2033: strcat(fileresprobmorprev,digit); /* Tvar to be done */
2034: strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
2035: strcat(fileresprobmorprev,fileres);
2036: if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
2037: printf("Problem with resultfile: %s\n", fileresprobmorprev);
2038: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
2039: }
2040: printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
2041: fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
1.66 brouard 2042: fprintf(ficresprobmorprev,"# probabilities of dying before estepm=%d months for people of exact age and weighted probabilities w1*p1j+w2*p2j+... stand dev in()\n",estepm);
1.53 brouard 2043: fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
2044: for(j=nlstate+1; j<=(nlstate+ndeath);j++){
2045: fprintf(ficresprobmorprev," p.%-d SE",j);
2046: for(i=1; i<=nlstate;i++)
2047: fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
2048: }
2049: fprintf(ficresprobmorprev,"\n");
2050: if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {
2051: printf("Problem with gnuplot file: %s\n", optionfilegnuplot);
2052: fprintf(ficlog,"Problem with gnuplot file: %s\n", optionfilegnuplot);
2053: exit(0);
2054: }
2055: else{
2056: fprintf(ficgp,"\n# Routine varevsij");
2057: }
2058: if((fichtm=fopen(optionfilehtm,"a"))==NULL) {
2059: printf("Problem with html file: %s\n", optionfilehtm);
2060: fprintf(ficlog,"Problem with html file: %s\n", optionfilehtm);
2061: exit(0);
2062: }
2063: else{
1.67 brouard 2064: fprintf(fichtm,"\n<li><h4> Computing probabilities of dying over estepm months as a weighted average (i.e global mortality independent of initial healh state)</h4></li>\n");
2065: fprintf(fichtm,"\n<br>%s <br>\n",digitp);
1.53 brouard 2066: }
2067: varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
2068:
2069: 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");
2070: fprintf(ficresvij,"# Age");
2071: for(i=1; i<=nlstate;i++)
2072: for(j=1; j<=nlstate;j++)
2073: fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);
2074: fprintf(ficresvij,"\n");
2075:
2076: xp=vector(1,npar);
2077: dnewm=matrix(1,nlstate,1,npar);
2078: doldm=matrix(1,nlstate,1,nlstate);
2079: dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
2080: doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
2081:
2082: gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
2083: gpp=vector(nlstate+1,nlstate+ndeath);
2084: gmp=vector(nlstate+1,nlstate+ndeath);
2085: trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
2086:
2087: if(estepm < stepm){
2088: printf ("Problem %d lower than %d\n",estepm, stepm);
2089: }
2090: else hstepm=estepm;
2091: /* For example we decided to compute the life expectancy with the smallest unit */
2092: /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
2093: nhstepm is the number of hstepm from age to agelim
2094: nstepm is the number of stepm from age to agelin.
2095: Look at hpijx to understand the reason of that which relies in memory size
2096: and note for a fixed period like k years */
2097: /* We decided (b) to get a life expectancy respecting the most precise curvature of the
2098: survival function given by stepm (the optimization length). Unfortunately it
1.66 brouard 2099: means that if the survival funtion is printed every two years of age and if
1.53 brouard 2100: you sum them up and add 1 year (area under the trapezoids) you won't get the same
2101: results. So we changed our mind and took the option of the best precision.
2102: */
2103: hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
2104: agelim = AGESUP;
2105: for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
2106: nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
2107: nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
2108: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
2109: gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
2110: gp=matrix(0,nhstepm,1,nlstate);
2111: gm=matrix(0,nhstepm,1,nlstate);
2112:
2113:
2114: for(theta=1; theta <=npar; theta++){
1.66 brouard 2115: for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
1.53 brouard 2116: xp[i] = x[i] + (i==theta ?delti[theta]:0);
2117: }
2118: hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
2119: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
2120:
2121: if (popbased==1) {
1.54 brouard 2122: if(mobilav ==0){
1.53 brouard 2123: for(i=1; i<=nlstate;i++)
2124: prlim[i][i]=probs[(int)age][i][ij];
1.54 brouard 2125: }else{ /* mobilav */
1.53 brouard 2126: for(i=1; i<=nlstate;i++)
2127: prlim[i][i]=mobaverage[(int)age][i][ij];
2128: }
2129: }
2130:
2131: for(j=1; j<= nlstate; j++){
2132: for(h=0; h<=nhstepm; h++){
2133: for(i=1, gp[h][j]=0.;i<=nlstate;i++)
2134: gp[h][j] += prlim[i][i]*p3mat[i][j][h];
2135: }
2136: }
1.66 brouard 2137: /* This for computing probability of death (h=1 means
2138: computed over hstepm matrices product = hstepm*stepm months)
2139: as a weighted average of prlim.
2140: */
1.69 brouard 2141: for(j=nlstate+1;j<=nlstate+ndeath;j++){
1.68 lievre 2142: for(i=1,gpp[j]=0.; i<= nlstate; i++)
1.53 brouard 2143: gpp[j] += prlim[i][i]*p3mat[i][j][1];
2144: }
1.66 brouard 2145: /* end probability of death */
1.53 brouard 2146:
1.66 brouard 2147: for(i=1; i<=npar; i++) /* Computes gradient x - delta */
1.53 brouard 2148: xp[i] = x[i] - (i==theta ?delti[theta]:0);
2149: hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
2150: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
2151:
2152: if (popbased==1) {
1.54 brouard 2153: if(mobilav ==0){
1.53 brouard 2154: for(i=1; i<=nlstate;i++)
2155: prlim[i][i]=probs[(int)age][i][ij];
1.54 brouard 2156: }else{ /* mobilav */
1.53 brouard 2157: for(i=1; i<=nlstate;i++)
2158: prlim[i][i]=mobaverage[(int)age][i][ij];
2159: }
2160: }
2161:
2162: for(j=1; j<= nlstate; j++){
2163: for(h=0; h<=nhstepm; h++){
2164: for(i=1, gm[h][j]=0.;i<=nlstate;i++)
2165: gm[h][j] += prlim[i][i]*p3mat[i][j][h];
2166: }
2167: }
1.66 brouard 2168: /* This for computing probability of death (h=1 means
2169: computed over hstepm matrices product = hstepm*stepm months)
2170: as a weighted average of prlim.
2171: */
1.69 brouard 2172: for(j=nlstate+1;j<=nlstate+ndeath;j++){
1.68 lievre 2173: for(i=1,gmp[j]=0.; i<= nlstate; i++)
2174: gmp[j] += prlim[i][i]*p3mat[i][j][1];
1.53 brouard 2175: }
1.66 brouard 2176: /* end probability of death */
1.53 brouard 2177:
2178: for(j=1; j<= nlstate; j++) /* vareij */
2179: for(h=0; h<=nhstepm; h++){
2180: gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
2181: }
1.68 lievre 2182:
1.53 brouard 2183: for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
2184: gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
2185: }
2186:
2187: } /* End theta */
2188:
2189: trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
2190:
2191: for(h=0; h<=nhstepm; h++) /* veij */
2192: for(j=1; j<=nlstate;j++)
2193: for(theta=1; theta <=npar; theta++)
2194: trgradg[h][j][theta]=gradg[h][theta][j];
2195:
2196: for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
1.69 brouard 2197: for(theta=1; theta <=npar; theta++)
1.53 brouard 2198: trgradgp[j][theta]=gradgp[theta][j];
1.69 brouard 2199:
1.53 brouard 2200:
2201: hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
2202: for(i=1;i<=nlstate;i++)
2203: for(j=1;j<=nlstate;j++)
2204: vareij[i][j][(int)age] =0.;
2205:
2206: for(h=0;h<=nhstepm;h++){
2207: for(k=0;k<=nhstepm;k++){
2208: matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
2209: matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
2210: for(i=1;i<=nlstate;i++)
2211: for(j=1;j<=nlstate;j++)
2212: vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
2213: }
2214: }
1.70 ! brouard 2215:
1.53 brouard 2216: /* pptj */
2217: matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
2218: matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
1.70 ! brouard 2219: for(j=nlstate+1;j<=nlstate+ndeath;j++)
! 2220: for(i=nlstate+1;i<=nlstate+ndeath;i++)
1.53 brouard 2221: varppt[j][i]=doldmp[j][i];
2222: /* end ppptj */
1.66 brouard 2223: /* x centered again */
1.53 brouard 2224: hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);
2225: prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);
2226:
2227: if (popbased==1) {
1.54 brouard 2228: if(mobilav ==0){
1.53 brouard 2229: for(i=1; i<=nlstate;i++)
2230: prlim[i][i]=probs[(int)age][i][ij];
1.54 brouard 2231: }else{ /* mobilav */
1.53 brouard 2232: for(i=1; i<=nlstate;i++)
2233: prlim[i][i]=mobaverage[(int)age][i][ij];
2234: }
2235: }
1.70 ! brouard 2236:
1.66 brouard 2237: /* This for computing probability of death (h=1 means
2238: computed over hstepm (estepm) matrices product = hstepm*stepm months)
2239: as a weighted average of prlim.
2240: */
1.68 lievre 2241: for(j=nlstate+1;j<=nlstate+ndeath;j++){
2242: for(i=1,gmp[j]=0.;i<= nlstate; i++)
1.53 brouard 2243: gmp[j] += prlim[i][i]*p3mat[i][j][1];
2244: }
1.66 brouard 2245: /* end probability of death */
1.53 brouard 2246:
2247: fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
2248: for(j=nlstate+1; j<=(nlstate+ndeath);j++){
2249: fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
2250: for(i=1; i<=nlstate;i++){
2251: fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
2252: }
2253: }
2254: fprintf(ficresprobmorprev,"\n");
2255:
2256: fprintf(ficresvij,"%.0f ",age );
2257: for(i=1; i<=nlstate;i++)
2258: for(j=1; j<=nlstate;j++){
2259: fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
2260: }
2261: fprintf(ficresvij,"\n");
2262: free_matrix(gp,0,nhstepm,1,nlstate);
2263: free_matrix(gm,0,nhstepm,1,nlstate);
2264: free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
2265: free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
2266: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
2267: } /* End age */
2268: free_vector(gpp,nlstate+1,nlstate+ndeath);
2269: free_vector(gmp,nlstate+1,nlstate+ndeath);
2270: free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
2271: free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
2272: fprintf(ficgp,"\nset noparametric;set nolabel; set ter png small;set size 0.65, 0.65");
2273: /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */
2274: fprintf(ficgp,"\n set log y; set nolog x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
1.67 brouard 2275: /* fprintf(ficgp,"\n plot \"%s\" u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm); */
2276: /* fprintf(ficgp,"\n replot \"%s\" u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm); */
2277: /* fprintf(ficgp,"\n replot \"%s\" u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm); */
2278: fprintf(ficgp,"\n plot \"%s\" u 1:($3) not w l 1 ",fileresprobmorprev);
2279: fprintf(ficgp,"\n replot \"%s\" u 1:(($3+1.96*$4)) t \"95\%% interval\" w l 2 ",fileresprobmorprev);
2280: fprintf(ficgp,"\n replot \"%s\" u 1:(($3-1.96*$4)) not w l 2 ",fileresprobmorprev);
1.53 brouard 2281: fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",fileresprobmorprev,fileresprobmorprev);
1.66 brouard 2282: fprintf(fichtm,"\n<br> Probability is computed over estepm=%d months. <br> <img src=\"varmuptjgr%s%s.png\"> <br>\n", estepm,digitp,digit);
1.53 brouard 2283: /* 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);
2284: */
2285: fprintf(ficgp,"\nset out \"varmuptjgr%s%s.png\";replot;",digitp,digit);
2286:
2287: free_vector(xp,1,npar);
2288: free_matrix(doldm,1,nlstate,1,nlstate);
2289: free_matrix(dnewm,1,nlstate,1,npar);
2290: free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
2291: free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
2292: free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
1.55 lievre 2293: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
1.53 brouard 2294: fclose(ficresprobmorprev);
2295: fclose(ficgp);
2296: fclose(fichtm);
1.70 ! brouard 2297: }
1.53 brouard 2298:
2299: /************ Variance of prevlim ******************/
2300: 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)
2301: {
2302: /* Variance of prevalence limit */
1.59 brouard 2303: /* double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
1.53 brouard 2304: double **newm;
2305: double **dnewm,**doldm;
2306: int i, j, nhstepm, hstepm;
2307: int k, cptcode;
2308: double *xp;
2309: double *gp, *gm;
2310: double **gradg, **trgradg;
2311: double age,agelim;
2312: int theta;
2313:
1.54 brouard 2314: fprintf(ficresvpl,"# Standard deviation of stable prevalences \n");
1.53 brouard 2315: fprintf(ficresvpl,"# Age");
2316: for(i=1; i<=nlstate;i++)
2317: fprintf(ficresvpl," %1d-%1d",i,i);
2318: fprintf(ficresvpl,"\n");
2319:
2320: xp=vector(1,npar);
2321: dnewm=matrix(1,nlstate,1,npar);
2322: doldm=matrix(1,nlstate,1,nlstate);
2323:
2324: hstepm=1*YEARM; /* Every year of age */
2325: hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */
2326: agelim = AGESUP;
2327: for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
2328: nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
2329: if (stepm >= YEARM) hstepm=1;
2330: nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
2331: gradg=matrix(1,npar,1,nlstate);
2332: gp=vector(1,nlstate);
2333: gm=vector(1,nlstate);
2334:
2335: for(theta=1; theta <=npar; theta++){
2336: for(i=1; i<=npar; i++){ /* Computes gradient */
2337: xp[i] = x[i] + (i==theta ?delti[theta]:0);
2338: }
2339: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
2340: for(i=1;i<=nlstate;i++)
2341: gp[i] = prlim[i][i];
2342:
2343: for(i=1; i<=npar; i++) /* Computes gradient */
2344: xp[i] = x[i] - (i==theta ?delti[theta]:0);
2345: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
2346: for(i=1;i<=nlstate;i++)
2347: gm[i] = prlim[i][i];
2348:
2349: for(i=1;i<=nlstate;i++)
2350: gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
2351: } /* End theta */
2352:
2353: trgradg =matrix(1,nlstate,1,npar);
2354:
2355: for(j=1; j<=nlstate;j++)
2356: for(theta=1; theta <=npar; theta++)
2357: trgradg[j][theta]=gradg[theta][j];
2358:
2359: for(i=1;i<=nlstate;i++)
2360: varpl[i][(int)age] =0.;
2361: matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
2362: matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
2363: for(i=1;i<=nlstate;i++)
2364: varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
2365:
2366: fprintf(ficresvpl,"%.0f ",age );
2367: for(i=1; i<=nlstate;i++)
2368: fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
2369: fprintf(ficresvpl,"\n");
2370: free_vector(gp,1,nlstate);
2371: free_vector(gm,1,nlstate);
2372: free_matrix(gradg,1,npar,1,nlstate);
2373: free_matrix(trgradg,1,nlstate,1,npar);
2374: } /* End age */
2375:
2376: free_vector(xp,1,npar);
2377: free_matrix(doldm,1,nlstate,1,npar);
2378: free_matrix(dnewm,1,nlstate,1,nlstate);
2379:
2380: }
2381:
2382: /************ Variance of one-step probabilities ******************/
2383: void varprob(char optionfilefiname[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij, int *Tvar, int **nbcode, int *ncodemax)
2384: {
2385: int i, j=0, i1, k1, l1, t, tj;
2386: int k2, l2, j1, z1;
2387: int k=0,l, cptcode;
2388: int first=1, first1;
2389: double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
2390: double **dnewm,**doldm;
2391: double *xp;
2392: double *gp, *gm;
2393: double **gradg, **trgradg;
2394: double **mu;
2395: double age,agelim, cov[NCOVMAX];
2396: double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
2397: int theta;
2398: char fileresprob[FILENAMELENGTH];
2399: char fileresprobcov[FILENAMELENGTH];
2400: char fileresprobcor[FILENAMELENGTH];
2401:
2402: double ***varpij;
2403:
2404: strcpy(fileresprob,"prob");
2405: strcat(fileresprob,fileres);
2406: if((ficresprob=fopen(fileresprob,"w"))==NULL) {
2407: printf("Problem with resultfile: %s\n", fileresprob);
2408: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
2409: }
2410: strcpy(fileresprobcov,"probcov");
2411: strcat(fileresprobcov,fileres);
2412: if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
2413: printf("Problem with resultfile: %s\n", fileresprobcov);
2414: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
2415: }
2416: strcpy(fileresprobcor,"probcor");
2417: strcat(fileresprobcor,fileres);
2418: if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
2419: printf("Problem with resultfile: %s\n", fileresprobcor);
2420: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
2421: }
2422: printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
2423: fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
2424: printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
2425: fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
2426: printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
2427: fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
2428:
2429: fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
2430: fprintf(ficresprob,"# Age");
2431: fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
2432: fprintf(ficresprobcov,"# Age");
2433: fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
2434: fprintf(ficresprobcov,"# Age");
2435:
2436:
2437: for(i=1; i<=nlstate;i++)
2438: for(j=1; j<=(nlstate+ndeath);j++){
2439: fprintf(ficresprob," p%1d-%1d (SE)",i,j);
2440: fprintf(ficresprobcov," p%1d-%1d ",i,j);
2441: fprintf(ficresprobcor," p%1d-%1d ",i,j);
2442: }
1.69 brouard 2443: /* fprintf(ficresprob,"\n");
1.53 brouard 2444: fprintf(ficresprobcov,"\n");
2445: fprintf(ficresprobcor,"\n");
1.69 brouard 2446: */
2447: xp=vector(1,npar);
1.53 brouard 2448: dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
2449: doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
2450: mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
2451: varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
2452: first=1;
2453: if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {
2454: printf("Problem with gnuplot file: %s\n", optionfilegnuplot);
2455: fprintf(ficlog,"Problem with gnuplot file: %s\n", optionfilegnuplot);
2456: exit(0);
2457: }
2458: else{
2459: fprintf(ficgp,"\n# Routine varprob");
2460: }
2461: if((fichtm=fopen(optionfilehtm,"a"))==NULL) {
2462: printf("Problem with html file: %s\n", optionfilehtm);
2463: fprintf(ficlog,"Problem with html file: %s\n", optionfilehtm);
2464: exit(0);
2465: }
2466: else{
2467: fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
2468: fprintf(fichtm,"\n");
2469:
2470: fprintf(fichtm,"\n<li><h4> Computing matrix of variance-covariance of step probabilities</h4></li>\n");
2471: 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");
2472: 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");
2473:
2474: }
2475:
2476: cov[1]=1;
2477: tj=cptcoveff;
2478: if (cptcovn<1) {tj=1;ncodemax[1]=1;}
2479: j1=0;
2480: for(t=1; t<=tj;t++){
2481: for(i1=1; i1<=ncodemax[t];i1++){
2482: j1++;
2483: if (cptcovn>0) {
2484: fprintf(ficresprob, "\n#********** Variable ");
2485: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
1.69 brouard 2486: fprintf(ficresprob, "**********\n#\n");
1.53 brouard 2487: fprintf(ficresprobcov, "\n#********** Variable ");
2488: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
1.69 brouard 2489: fprintf(ficresprobcov, "**********\n#\n");
1.53 brouard 2490:
2491: fprintf(ficgp, "\n#********** Variable ");
1.69 brouard 2492: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
2493: fprintf(ficgp, "**********\n#\n");
1.53 brouard 2494:
2495:
2496: fprintf(fichtm, "\n<hr size=\"2\" color=\"#EC5E5E\">********** Variable ");
2497: for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
2498: fprintf(fichtm, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
2499:
2500: fprintf(ficresprobcor, "\n#********** Variable ");
2501: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
1.69 brouard 2502: fprintf(ficresprobcor, "**********\n#");
1.53 brouard 2503: }
2504:
2505: for (age=bage; age<=fage; age ++){
2506: cov[2]=age;
2507: for (k=1; k<=cptcovn;k++) {
2508: cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];
2509: }
2510: for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
2511: for (k=1; k<=cptcovprod;k++)
2512: cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
2513:
2514: gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
2515: trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
2516: gp=vector(1,(nlstate)*(nlstate+ndeath));
2517: gm=vector(1,(nlstate)*(nlstate+ndeath));
2518:
2519: for(theta=1; theta <=npar; theta++){
2520: for(i=1; i<=npar; i++)
2521: xp[i] = x[i] + (i==theta ?delti[theta]:0);
2522:
2523: pmij(pmmij,cov,ncovmodel,xp,nlstate);
2524:
2525: k=0;
2526: for(i=1; i<= (nlstate); i++){
2527: for(j=1; j<=(nlstate+ndeath);j++){
2528: k=k+1;
2529: gp[k]=pmmij[i][j];
2530: }
2531: }
2532:
2533: for(i=1; i<=npar; i++)
2534: xp[i] = x[i] - (i==theta ?delti[theta]:0);
2535:
2536: pmij(pmmij,cov,ncovmodel,xp,nlstate);
2537: k=0;
2538: for(i=1; i<=(nlstate); i++){
2539: for(j=1; j<=(nlstate+ndeath);j++){
2540: k=k+1;
2541: gm[k]=pmmij[i][j];
2542: }
2543: }
2544:
2545: for(i=1; i<= (nlstate)*(nlstate+ndeath); i++)
2546: gradg[theta][i]=(gp[i]-gm[i])/2./delti[theta];
2547: }
2548:
2549: for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
2550: for(theta=1; theta <=npar; theta++)
2551: trgradg[j][theta]=gradg[theta][j];
2552:
2553: matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov);
2554: matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);
1.59 brouard 2555: free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
2556: free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
2557: free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
2558: free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
2559:
1.53 brouard 2560: pmij(pmmij,cov,ncovmodel,x,nlstate);
2561:
2562: k=0;
2563: for(i=1; i<=(nlstate); i++){
2564: for(j=1; j<=(nlstate+ndeath);j++){
2565: k=k+1;
2566: mu[k][(int) age]=pmmij[i][j];
2567: }
2568: }
2569: for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
2570: for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
2571: varpij[i][j][(int)age] = doldm[i][j];
2572:
2573: /*printf("\n%d ",(int)age);
1.59 brouard 2574: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
2575: printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
2576: fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
2577: }*/
1.53 brouard 2578:
2579: fprintf(ficresprob,"\n%d ",(int)age);
2580: fprintf(ficresprobcov,"\n%d ",(int)age);
2581: fprintf(ficresprobcor,"\n%d ",(int)age);
2582:
2583: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)
2584: fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));
2585: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
2586: fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);
2587: fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
2588: }
2589: i=0;
2590: for (k=1; k<=(nlstate);k++){
2591: for (l=1; l<=(nlstate+ndeath);l++){
2592: i=i++;
2593: fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
2594: fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
2595: for (j=1; j<=i;j++){
2596: fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);
2597: fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));
2598: }
2599: }
2600: }/* end of loop for state */
2601: } /* end of loop for age */
2602:
2603: /* Confidence intervalle of pij */
2604: /*
1.59 brouard 2605: fprintf(ficgp,"\nset noparametric;unset label");
2606: fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");
2607: fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
2608: 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);
2609: fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);
2610: fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);
2611: fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);
1.53 brouard 2612: */
2613:
2614: /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
2615: first1=1;
2616: for (k2=1; k2<=(nlstate);k2++){
2617: for (l2=1; l2<=(nlstate+ndeath);l2++){
2618: if(l2==k2) continue;
2619: j=(k2-1)*(nlstate+ndeath)+l2;
2620: for (k1=1; k1<=(nlstate);k1++){
2621: for (l1=1; l1<=(nlstate+ndeath);l1++){
2622: if(l1==k1) continue;
2623: i=(k1-1)*(nlstate+ndeath)+l1;
2624: if(i<=j) continue;
2625: for (age=bage; age<=fage; age ++){
2626: if ((int)age %5==0){
2627: v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;
2628: v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;
2629: cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;
2630: mu1=mu[i][(int) age]/stepm*YEARM ;
2631: mu2=mu[j][(int) age]/stepm*YEARM;
2632: c12=cv12/sqrt(v1*v2);
2633: /* Computing eigen value of matrix of covariance */
2634: lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
2635: lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
2636: /* Eigen vectors */
2637: v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
2638: /*v21=sqrt(1.-v11*v11); *//* error */
2639: v21=(lc1-v1)/cv12*v11;
2640: v12=-v21;
2641: v22=v11;
2642: tnalp=v21/v11;
2643: if(first1==1){
2644: first1=0;
2645: 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);
2646: }
2647: 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);
2648: /*printf(fignu*/
2649: /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */
2650: /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */
2651: if(first==1){
2652: first=0;
2653: fprintf(ficgp,"\nset parametric;unset label");
2654: 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);
2655: fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
2656: 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);
2657: fprintf(fichtm,"\n<br><img src=\"varpijgr%s%d%1d%1d-%1d%1d.png\"> ",optionfilefiname, j1,k1,l1,k2,l2);
2658: fprintf(fichtm,"\n<br> Correlation at age %d (%.3f),",(int) age, c12);
2659: fprintf(ficgp,"\nset out \"varpijgr%s%d%1d%1d-%1d%1d.png\"",optionfilefiname, j1,k1,l1,k2,l2);
2660: fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
2661: fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
2662: 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",\
2663: mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
2664: mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
2665: }else{
2666: first=0;
2667: fprintf(fichtm," %d (%.3f),",(int) age, c12);
2668: fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
2669: fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
2670: 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",\
2671: mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
2672: mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
2673: }/* if first */
2674: } /* age mod 5 */
2675: } /* end loop age */
2676: fprintf(ficgp,"\nset out \"varpijgr%s%d%1d%1d-%1d%1d.png\";replot;",optionfilefiname, j1,k1,l1,k2,l2);
2677: first=1;
2678: } /*l12 */
2679: } /* k12 */
2680: } /*l1 */
2681: }/* k1 */
2682: } /* loop covariates */
2683: }
1.59 brouard 2684: free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
2685: free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
1.53 brouard 2686: free_vector(xp,1,npar);
2687: fclose(ficresprob);
2688: fclose(ficresprobcov);
2689: fclose(ficresprobcor);
2690: fclose(ficgp);
2691: fclose(fichtm);
2692: }
2693:
2694:
2695: /******************* Printing html file ***********/
2696: void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \
2697: int lastpass, int stepm, int weightopt, char model[],\
2698: int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
2699: int popforecast, int estepm ,\
2700: double jprev1, double mprev1,double anprev1, \
2701: double jprev2, double mprev2,double anprev2){
2702: int jj1, k1, i1, cpt;
2703: /*char optionfilehtm[FILENAMELENGTH];*/
2704: if((fichtm=fopen(optionfilehtm,"a"))==NULL) {
2705: printf("Problem with %s \n",optionfilehtm), exit(0);
2706: fprintf(ficlog,"Problem with %s \n",optionfilehtm), exit(0);
2707: }
2708:
2709: fprintf(fichtm,"<ul><li><h4>Result files (first order: no variance)</h4>\n
2710: - 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
2711: - Estimated transition probabilities over %d (stepm) months: <a href=\"pij%s\">pij%s</a><br>\n
2712: - Stable prevalence in each health state: <a href=\"pl%s\">pl%s</a> <br>\n
2713: - Life expectancies by age and initial health status (estepm=%2d months):
2714: <a href=\"e%s\">e%s</a> <br>\n</li>", \
2715: jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,fileres,fileres,stepm,fileres,fileres,fileres,fileres,estepm,fileres,fileres);
2716:
2717: fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
2718:
2719: m=cptcoveff;
2720: if (cptcovn < 1) {m=1;ncodemax[1]=1;}
2721:
2722: jj1=0;
2723: for(k1=1; k1<=m;k1++){
2724: for(i1=1; i1<=ncodemax[k1];i1++){
2725: jj1++;
2726: if (cptcovn > 0) {
2727: fprintf(fichtm,"<hr size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
2728: for (cpt=1; cpt<=cptcoveff;cpt++)
2729: fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
2730: fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
2731: }
2732: /* Pij */
2733: 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>
2734: <img src=\"pe%s%d1.png\">",stepm,strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);
2735: /* Quasi-incidences */
2736: 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>
2737: <img src=\"pe%s%d2.png\">",stepm,strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);
2738: /* Stable prevalence in each health state */
2739: for(cpt=1; cpt<nlstate;cpt++){
2740: fprintf(fichtm,"<br>- Stable prevalence in each health state : p%s%d%d.png<br>
2741: <img src=\"p%s%d%d.png\">",strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);
2742: }
2743: for(cpt=1; cpt<=nlstate;cpt++) {
2744: fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): exp%s%d%d.png <br>
2745: <img src=\"exp%s%d%d.png\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);
2746: }
2747: fprintf(fichtm,"\n<br>- Total life expectancy by age and
2748: health expectancies in states (1) and (2): e%s%d.png<br>
2749: <img src=\"e%s%d.png\">",strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);
2750: } /* end i1 */
2751: }/* End k1 */
2752: fprintf(fichtm,"</ul>");
2753:
2754:
2755: fprintf(fichtm,"\n<br><li><h4> Result files (second order: variances)</h4>\n
2756: - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n
2757: - Variance of one-step probabilities: <a href=\"prob%s\">prob%s</a> <br>\n
2758: - Variance-covariance of one-step probabilities: <a href=\"probcov%s\">probcov%s</a> <br>\n
2759: - Correlation matrix of one-step probabilities: <a href=\"probcor%s\">probcor%s</a> <br>\n
2760: - Variances and covariances of life expectancies by age and initial health status (estepm=%d months): <a href=\"v%s\">v%s</a><br>\n
2761: - Health expectancies with their variances (no covariance): <a href=\"t%s\">t%s</a> <br>\n
2762: - 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);
2763:
2764: if(popforecast==1) fprintf(fichtm,"\n
2765: - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n
2766: - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n
2767: <br>",fileres,fileres,fileres,fileres);
2768: else
2769: 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);
2770: fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
2771:
2772: m=cptcoveff;
2773: if (cptcovn < 1) {m=1;ncodemax[1]=1;}
2774:
2775: jj1=0;
2776: for(k1=1; k1<=m;k1++){
2777: for(i1=1; i1<=ncodemax[k1];i1++){
2778: jj1++;
2779: if (cptcovn > 0) {
2780: fprintf(fichtm,"<hr size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
2781: for (cpt=1; cpt<=cptcoveff;cpt++)
2782: fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
2783: fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
2784: }
2785: for(cpt=1; cpt<=nlstate;cpt++) {
2786: fprintf(fichtm,"<br>- Observed and stationary prevalence (with confident
2787: interval) in state (%d): v%s%d%d.png <br>
2788: <img src=\"v%s%d%d.png\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);
2789: }
2790: } /* end i1 */
2791: }/* End k1 */
2792: fprintf(fichtm,"</ul>");
2793: fclose(fichtm);
2794: }
2795:
2796: /******************* Gnuplot file **************/
2797: void printinggnuplot(char fileres[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
2798:
2799: int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;
2800: int ng;
2801: if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {
2802: printf("Problem with file %s",optionfilegnuplot);
2803: fprintf(ficlog,"Problem with file %s",optionfilegnuplot);
2804: }
2805:
1.54 brouard 2806: /*#ifdef windows */
1.53 brouard 2807: fprintf(ficgp,"cd \"%s\" \n",pathc);
1.54 brouard 2808: /*#endif */
1.53 brouard 2809: m=pow(2,cptcoveff);
2810:
2811: /* 1eme*/
2812: for (cpt=1; cpt<= nlstate ; cpt ++) {
2813: for (k1=1; k1<= m ; k1 ++) {
2814: fprintf(ficgp,"\nset out \"v%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);
2815: 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);
2816:
2817: for (i=1; i<= nlstate ; i ++) {
2818: if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
2819: else fprintf(ficgp," \%%*lf (\%%*lf)");
2820: }
1.69 brouard 2821: fprintf(ficgp,"\" t\"Stable prevalence\" w l 0,\"vpl%s\" every :::%d::%d u 1:($2+1.96*$3) \"\%%lf",fileres,k1-1,k1-1);
1.53 brouard 2822: for (i=1; i<= nlstate ; i ++) {
2823: if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
2824: else fprintf(ficgp," \%%*lf (\%%*lf)");
2825: }
1.69 brouard 2826: fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"vpl%s\" every :::%d::%d u 1:($2-1.96*$3) \"\%%lf",fileres,k1-1,k1-1);
1.53 brouard 2827: for (i=1; i<= nlstate ; i ++) {
2828: if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
2829: else fprintf(ficgp," \%%*lf (\%%*lf)");
2830: }
2831: fprintf(ficgp,"\" t\"\" w l 1,\"p%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",fileres,k1-1,k1-1,2+4*(cpt-1));
2832: }
2833: }
2834: /*2 eme*/
2835:
2836: for (k1=1; k1<= m ; k1 ++) {
2837: fprintf(ficgp,"\nset out \"e%s%d.png\" \n",strtok(optionfile, "."),k1);
2838: fprintf(ficgp,"set ylabel \"Years\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] ",ageminpar,fage);
2839:
2840: for (i=1; i<= nlstate+1 ; i ++) {
2841: k=2*i;
2842: fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:2 \"\%%lf",fileres,k1-1,k1-1);
2843: for (j=1; j<= nlstate+1 ; j ++) {
2844: if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
2845: else fprintf(ficgp," \%%*lf (\%%*lf)");
2846: }
2847: if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");
2848: else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);
2849: fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",fileres,k1-1,k1-1);
2850: for (j=1; j<= nlstate+1 ; j ++) {
2851: if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
2852: else fprintf(ficgp," \%%*lf (\%%*lf)");
2853: }
2854: fprintf(ficgp,"\" t\"\" w l 0,");
2855: fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",fileres,k1-1,k1-1);
2856: for (j=1; j<= nlstate+1 ; j ++) {
2857: if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
2858: else fprintf(ficgp," \%%*lf (\%%*lf)");
2859: }
2860: if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");
2861: else fprintf(ficgp,"\" t\"\" w l 0,");
2862: }
2863: }
2864:
2865: /*3eme*/
2866:
2867: for (k1=1; k1<= m ; k1 ++) {
2868: for (cpt=1; cpt<= nlstate ; cpt ++) {
2869: k=2+nlstate*(2*cpt-2);
2870: fprintf(ficgp,"\nset out \"exp%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);
2871: fprintf(ficgp,"set ter png small\nset size 0.65,0.65\nplot [%.f:%.f] \"e%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,fileres,k1-1,k1-1,k,cpt);
2872: /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
2873: for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
2874: fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
2875: fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
2876: for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
2877: fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
2878:
2879: */
2880: for (i=1; i< nlstate ; i ++) {
2881: 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);
2882:
2883: }
2884: }
2885: }
2886:
2887: /* CV preval stat */
2888: for (k1=1; k1<= m ; k1 ++) {
2889: for (cpt=1; cpt<nlstate ; cpt ++) {
2890: k=3;
2891: fprintf(ficgp,"\nset out \"p%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);
2892: 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/($%d",ageminpar,agemaxpar,fileres,k1,k+cpt+1,k+1);
2893:
2894: for (i=1; i< nlstate ; i ++)
2895: fprintf(ficgp,"+$%d",k+i+1);
2896: fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);
2897:
2898: l=3+(nlstate+ndeath)*cpt;
2899: fprintf(ficgp,",\"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",fileres,k1,l+cpt+1,l+1);
2900: for (i=1; i< nlstate ; i ++) {
2901: l=3+(nlstate+ndeath)*cpt;
2902: fprintf(ficgp,"+$%d",l+i+1);
2903: }
2904: fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);
2905: }
2906: }
2907:
2908: /* proba elementaires */
2909: for(i=1,jk=1; i <=nlstate; i++){
2910: for(k=1; k <=(nlstate+ndeath); k++){
2911: if (k != i) {
2912: for(j=1; j <=ncovmodel; j++){
2913: fprintf(ficgp,"p%d=%f ",jk,p[jk]);
2914: jk++;
2915: fprintf(ficgp,"\n");
2916: }
2917: }
2918: }
2919: }
2920:
2921: for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/
2922: for(jk=1; jk <=m; jk++) {
2923: fprintf(ficgp,"\nset out \"pe%s%d%d.png\" \n",strtok(optionfile, "."),jk,ng);
2924: if (ng==2)
2925: fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
2926: else
2927: fprintf(ficgp,"\nset title \"Probability\"\n");
2928: fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65\nset log y\nplot [%.f:%.f] ",ageminpar,agemaxpar);
2929: i=1;
2930: for(k2=1; k2<=nlstate; k2++) {
2931: k3=i;
2932: for(k=1; k<=(nlstate+ndeath); k++) {
2933: if (k != k2){
2934: if(ng==2)
2935: fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);
2936: else
2937: fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
2938: ij=1;
2939: for(j=3; j <=ncovmodel; j++) {
2940: if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
2941: fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
2942: ij++;
2943: }
2944: else
2945: fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
2946: }
2947: fprintf(ficgp,")/(1");
2948:
2949: for(k1=1; k1 <=nlstate; k1++){
2950: fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);
2951: ij=1;
2952: for(j=3; j <=ncovmodel; j++){
2953: if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
2954: fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
2955: ij++;
2956: }
2957: else
2958: fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
2959: }
2960: fprintf(ficgp,")");
2961: }
2962: fprintf(ficgp,") t \"p%d%d\" ", k2,k);
2963: if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");
2964: i=i+ncovmodel;
2965: }
2966: } /* end k */
2967: } /* end k2 */
2968: } /* end jk */
2969: } /* end ng */
2970: fclose(ficgp);
2971: } /* end gnuplot */
2972:
2973:
2974: /*************** Moving average **************/
1.54 brouard 2975: int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav){
1.53 brouard 2976:
2977: int i, cpt, cptcod;
1.58 lievre 2978: int modcovmax =1;
1.54 brouard 2979: int mobilavrange, mob;
1.53 brouard 2980: double age;
1.58 lievre 2981:
2982: modcovmax=2*cptcoveff;/* Max number of modalities. We suppose
2983: a covariate has 2 modalities */
2984: if (cptcovn<1) modcovmax=1; /* At least 1 pass */
2985:
1.54 brouard 2986: if(mobilav==1||mobilav ==3 ||mobilav==5 ||mobilav== 7){
2987: if(mobilav==1) mobilavrange=5; /* default */
2988: else mobilavrange=mobilav;
2989: for (age=bage; age<=fage; age++)
2990: for (i=1; i<=nlstate;i++)
1.58 lievre 2991: for (cptcod=1;cptcod<=modcovmax;cptcod++)
1.54 brouard 2992: mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
2993: /* We keep the original values on the extreme ages bage, fage and for
2994: fage+1 and bage-1 we use a 3 terms moving average; for fage+2 bage+2
2995: we use a 5 terms etc. until the borders are no more concerned.
2996: */
2997: for (mob=3;mob <=mobilavrange;mob=mob+2){
2998: for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){
2999: for (i=1; i<=nlstate;i++){
1.58 lievre 3000: for (cptcod=1;cptcod<=modcovmax;cptcod++){
1.54 brouard 3001: mobaverage[(int)age][i][cptcod] =probs[(int)age][i][cptcod];
3002: for (cpt=1;cpt<=(mob-1)/2;cpt++){
3003: mobaverage[(int)age][i][cptcod] +=probs[(int)age-cpt][i][cptcod];
3004: mobaverage[(int)age][i][cptcod] +=probs[(int)age+cpt][i][cptcod];
3005: }
3006: mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/mob;
3007: }
1.53 brouard 3008: }
1.54 brouard 3009: }/* end age */
3010: }/* end mob */
3011: }else return -1;
3012: return 0;
3013: }/* End movingaverage */
1.53 brouard 3014:
3015:
3016: /************** Forecasting ******************/
1.70 ! brouard 3017: prevforecast(char fileres[], double anproj1, double mproj1, double jproj1, double ageminpar, double agemax, double dateprev1, double dateprev2, int mobilav, double bage, double fage, int firstpass, int lastpass, double anproj2, double p[], int cptcoveff){
1.69 brouard 3018: /* proj1, year, month, day of starting projection
3019: agemin, agemax range of age
3020: dateprev1 dateprev2 range of dates during which prevalence is computed
1.70 ! brouard 3021: anproj2 year of en of projection (same day and month as proj1).
1.69 brouard 3022: */
1.70 ! brouard 3023: int yearp, stepsize, hstepm, nhstepm, j, k, c, cptcod, i, h;
1.53 brouard 3024: int *popage;
1.70 ! brouard 3025: double agec; /* generic age */
! 3026: double agelim, ppij, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
1.53 brouard 3027: double *popeffectif,*popcount;
3028: double ***p3mat;
1.55 lievre 3029: double ***mobaverage;
1.53 brouard 3030: char fileresf[FILENAMELENGTH];
3031:
1.69 brouard 3032: agelim=AGESUP;
1.70 ! brouard 3033: prevalence(ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
1.53 brouard 3034:
3035: strcpy(fileresf,"f");
3036: strcat(fileresf,fileres);
3037: if((ficresf=fopen(fileresf,"w"))==NULL) {
3038: printf("Problem with forecast resultfile: %s\n", fileresf);
3039: fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);
3040: }
3041: printf("Computing forecasting: result on file '%s' \n", fileresf);
3042: fprintf(ficlog,"Computing forecasting: result on file '%s' \n", fileresf);
3043:
3044: if (cptcoveff==0) ncodemax[cptcoveff]=1;
3045:
1.54 brouard 3046: if (mobilav!=0) {
1.53 brouard 3047: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
1.54 brouard 3048: if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
3049: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
3050: printf(" Error in movingaverage mobilav=%d\n",mobilav);
3051: }
1.53 brouard 3052: }
3053:
3054: stepsize=(int) (stepm+YEARM-1)/YEARM;
3055: if (stepm<=12) stepsize=1;
3056:
3057: hstepm=1;
3058: hstepm=hstepm/stepm;
1.69 brouard 3059: yp1=modf(dateintmean,&yp);/* extracts integral of datemean in yp and
3060: fractional in yp1 */
1.53 brouard 3061: anprojmean=yp;
3062: yp2=modf((yp1*12),&yp);
3063: mprojmean=yp;
3064: yp1=modf((yp2*30.5),&yp);
3065: jprojmean=yp;
3066: if(jprojmean==0) jprojmean=1;
3067: if(mprojmean==0) jprojmean=1;
3068:
1.70 ! brouard 3069: fprintf(ficresf,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2);
1.53 brouard 3070:
1.70 ! brouard 3071: fprintf(ficresf,"#****** Routine prevforecast **\n");
! 3072: for(cptcov=1, k=0;cptcov<=cptcoveff;cptcov++){
1.53 brouard 3073: for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
3074: k=k+1;
3075: fprintf(ficresf,"\n#******");
3076: for(j=1;j<=cptcoveff;j++) {
1.70 ! brouard 3077: fprintf(ficresf," V%d=%d, hpijx=probability over h years, hp.jx is weighted by observed prev ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
1.53 brouard 3078: }
3079: fprintf(ficresf,"******\n");
1.70 ! brouard 3080: fprintf(ficresf,"# Covariate valuofcovar yearproj age");
! 3081: for(j=1; j<=nlstate+ndeath;j++){
! 3082: for(i=1; i<=nlstate;i++)
! 3083: fprintf(ficresf," p%d%d",i,j);
! 3084: fprintf(ficresf," p.%d",j);
! 3085: }
1.69 brouard 3086: for (yearp=0; yearp<=(anproj2-anproj1);yearp++) {
1.53 brouard 3087: fprintf(ficresf,"\n");
1.70 ! brouard 3088: fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+yearp);
1.53 brouard 3089:
1.70 ! brouard 3090: for (agec=fage; agec>=ageminpar; agec--){
! 3091: nhstepm=(int) rint((agelim-agec)*YEARM/stepm);
1.53 brouard 3092: nhstepm = nhstepm/hstepm;
3093: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3094: oldm=oldms;savm=savms;
1.70 ! brouard 3095: hpxij(p3mat,nhstepm,agec,hstepm,p,nlstate,stepm,oldm,savm, k);
1.53 brouard 3096:
3097: for (h=0; h<=nhstepm; h++){
1.70 ! brouard 3098: if (h==(int) (YEARM*yearp)) {
1.69 brouard 3099: fprintf(ficresf,"\n");
3100: for(j=1;j<=cptcoveff;j++)
3101: fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
1.70 ! brouard 3102: fprintf(ficresf,"%.f %.f ",anproj1+yearp,agec+h*hstepm/YEARM*stepm);
1.53 brouard 3103: }
3104: for(j=1; j<=nlstate+ndeath;j++) {
1.70 ! brouard 3105: ppij=0.;
1.53 brouard 3106: for(i=1; i<=nlstate;i++) {
3107: if (mobilav==1)
1.70 ! brouard 3108: ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec+1][i][cptcod];
1.53 brouard 3109: else {
1.70 ! brouard 3110: ppij=ppij+p3mat[i][j][h]*probs[(int)(agec+1)][i][cptcod];
1.53 brouard 3111: }
1.70 ! brouard 3112: if (h==(int)(YEARM*yearp))
! 3113: fprintf(ficresf," %.3f", p3mat[i][j][h]);
1.53 brouard 3114: }
1.70 ! brouard 3115: if (h==(int)(YEARM*yearp)){
! 3116: fprintf(ficresf," %.3f", ppij);
1.53 brouard 3117: }
3118: }
3119: }
3120: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3121: }
3122: }
3123: }
3124: }
3125:
1.54 brouard 3126: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
1.53 brouard 3127:
3128: fclose(ficresf);
3129: }
1.70 ! brouard 3130:
! 3131: /************** Forecasting *****not tested NB*************/
1.53 brouard 3132: 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){
3133:
3134: int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;
3135: int *popage;
1.69 brouard 3136: double calagedatem, agelim, kk1, kk2;
1.53 brouard 3137: double *popeffectif,*popcount;
3138: double ***p3mat,***tabpop,***tabpopprev;
1.55 lievre 3139: double ***mobaverage;
1.53 brouard 3140: char filerespop[FILENAMELENGTH];
3141:
3142: tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
3143: tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
3144: agelim=AGESUP;
1.69 brouard 3145: calagedatem=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;
1.53 brouard 3146:
1.70 ! brouard 3147: prevalence(ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
1.53 brouard 3148:
3149:
3150: strcpy(filerespop,"pop");
3151: strcat(filerespop,fileres);
3152: if((ficrespop=fopen(filerespop,"w"))==NULL) {
3153: printf("Problem with forecast resultfile: %s\n", filerespop);
3154: fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop);
3155: }
3156: printf("Computing forecasting: result on file '%s' \n", filerespop);
3157: fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop);
3158:
3159: if (cptcoveff==0) ncodemax[cptcoveff]=1;
3160:
1.54 brouard 3161: if (mobilav!=0) {
1.53 brouard 3162: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
1.54 brouard 3163: if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
3164: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
3165: printf(" Error in movingaverage mobilav=%d\n",mobilav);
3166: }
1.53 brouard 3167: }
3168:
3169: stepsize=(int) (stepm+YEARM-1)/YEARM;
3170: if (stepm<=12) stepsize=1;
3171:
3172: agelim=AGESUP;
3173:
3174: hstepm=1;
3175: hstepm=hstepm/stepm;
3176:
3177: if (popforecast==1) {
3178: if((ficpop=fopen(popfile,"r"))==NULL) {
3179: printf("Problem with population file : %s\n",popfile);exit(0);
3180: fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0);
3181: }
3182: popage=ivector(0,AGESUP);
3183: popeffectif=vector(0,AGESUP);
3184: popcount=vector(0,AGESUP);
3185:
3186: i=1;
3187: while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;
3188:
3189: imx=i;
3190: for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];
3191: }
3192:
1.69 brouard 3193: for(cptcov=1,k=0;cptcov<=i2;cptcov++){
1.53 brouard 3194: for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
3195: k=k+1;
3196: fprintf(ficrespop,"\n#******");
3197: for(j=1;j<=cptcoveff;j++) {
3198: fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
3199: }
3200: fprintf(ficrespop,"******\n");
3201: fprintf(ficrespop,"# Age");
3202: for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);
3203: if (popforecast==1) fprintf(ficrespop," [Population]");
3204:
3205: for (cpt=0; cpt<=0;cpt++) {
3206: fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);
3207:
1.69 brouard 3208: for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){
1.53 brouard 3209: nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);
3210: nhstepm = nhstepm/hstepm;
3211:
3212: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3213: oldm=oldms;savm=savms;
3214: hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
3215:
3216: for (h=0; h<=nhstepm; h++){
1.69 brouard 3217: if (h==(int) (calagedatem+YEARM*cpt)) {
1.53 brouard 3218: fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
3219: }
3220: for(j=1; j<=nlstate+ndeath;j++) {
3221: kk1=0.;kk2=0;
3222: for(i=1; i<=nlstate;i++) {
3223: if (mobilav==1)
3224: kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];
3225: else {
3226: kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];
3227: }
3228: }
1.69 brouard 3229: if (h==(int)(calagedatem+12*cpt)){
1.53 brouard 3230: tabpop[(int)(agedeb)][j][cptcod]=kk1;
3231: /*fprintf(ficrespop," %.3f", kk1);
3232: if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/
3233: }
3234: }
3235: for(i=1; i<=nlstate;i++){
3236: kk1=0.;
3237: for(j=1; j<=nlstate;j++){
3238: kk1= kk1+tabpop[(int)(agedeb)][j][cptcod];
3239: }
1.69 brouard 3240: tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedatem+12*cpt)*hstepm/YEARM*stepm-1)];
1.53 brouard 3241: }
3242:
1.69 brouard 3243: if (h==(int)(calagedatem+12*cpt)) for(j=1; j<=nlstate;j++)
1.53 brouard 3244: fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);
3245: }
3246: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3247: }
3248: }
3249:
3250: /******/
3251:
3252: for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) {
3253: fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);
1.69 brouard 3254: for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){
1.53 brouard 3255: nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);
3256: nhstepm = nhstepm/hstepm;
3257:
3258: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3259: oldm=oldms;savm=savms;
3260: hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
3261: for (h=0; h<=nhstepm; h++){
1.69 brouard 3262: if (h==(int) (calagedatem+YEARM*cpt)) {
1.53 brouard 3263: fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
3264: }
3265: for(j=1; j<=nlstate+ndeath;j++) {
3266: kk1=0.;kk2=0;
3267: for(i=1; i<=nlstate;i++) {
3268: kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];
3269: }
1.69 brouard 3270: if (h==(int)(calagedatem+12*cpt)) fprintf(ficresf," %15.2f", kk1);
1.53 brouard 3271: }
3272: }
3273: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3274: }
3275: }
3276: }
3277: }
3278:
1.54 brouard 3279: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
1.53 brouard 3280:
3281: if (popforecast==1) {
3282: free_ivector(popage,0,AGESUP);
3283: free_vector(popeffectif,0,AGESUP);
3284: free_vector(popcount,0,AGESUP);
3285: }
3286: free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
3287: free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
3288: fclose(ficrespop);
3289: }
3290:
3291: /***********************************************/
3292: /**************** Main Program *****************/
3293: /***********************************************/
3294:
3295: int main(int argc, char *argv[])
3296: {
1.61 brouard 3297: int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav);
1.53 brouard 3298: int i,j, k, n=MAXN,iter,m,size,cptcode, cptcod;
3299: double agedeb, agefin,hf;
3300: double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;
3301:
3302: double fret;
3303: double **xi,tmp,delta;
3304:
3305: double dum; /* Dummy variable */
3306: double ***p3mat;
3307: double ***mobaverage;
3308: int *indx;
3309: char line[MAXLINE], linepar[MAXLINE];
3310: char path[80],pathc[80],pathcd[80],pathtot[80],model[80];
3311: int firstobs=1, lastobs=10;
3312: int sdeb, sfin; /* Status at beginning and end */
3313: int c, h , cpt,l;
3314: int ju,jl, mi;
3315: int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;
1.59 brouard 3316: int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,*tab;
1.69 brouard 3317: int mobilavproj=0 , prevfcast=0 ; /* moving average of prev, If prevfcast=1 prevalence projection */
1.53 brouard 3318: int mobilav=0,popforecast=0;
3319: int hstepm, nhstepm;
1.70 ! brouard 3320: double jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,jpyram, mpyram,anpyram,jpyram1, mpyram1,anpyram1;
1.53 brouard 3321:
3322: double bage, fage, age, agelim, agebase;
3323: double ftolpl=FTOL;
3324: double **prlim;
3325: double *severity;
3326: double ***param; /* Matrix of parameters */
3327: double *p;
3328: double **matcov; /* Matrix of covariance */
3329: double ***delti3; /* Scale */
3330: double *delti; /* Scale */
3331: double ***eij, ***vareij;
3332: double **varpl; /* Variances of prevalence limits by age */
3333: double *epj, vepp;
3334: double kk1, kk2;
3335: double dateprev1, dateprev2,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2;
3336:
3337: char *alph[]={"a","a","b","c","d","e"}, str[4];
3338:
3339:
3340: char z[1]="c", occ;
3341: #include <sys/time.h>
3342: #include <time.h>
3343: char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];
3344:
3345: /* long total_usecs;
1.59 brouard 3346: struct timeval start_time, end_time;
1.53 brouard 3347:
1.59 brouard 3348: gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */
1.53 brouard 3349: getcwd(pathcd, size);
3350:
3351: printf("\n%s",version);
3352: if(argc <=1){
3353: printf("\nEnter the parameter file name: ");
3354: scanf("%s",pathtot);
3355: }
3356: else{
3357: strcpy(pathtot,argv[1]);
3358: }
3359: /*if(getcwd(pathcd, 80)!= NULL)printf ("Error pathcd\n");*/
3360: /*cygwin_split_path(pathtot,path,optionfile);
3361: printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/
3362: /* cutv(path,optionfile,pathtot,'\\');*/
3363:
3364: split(pathtot,path,optionfile,optionfilext,optionfilefiname);
1.59 brouard 3365: printf("pathtot=%s, path=%s, optionfile=%s optionfilext=%s optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
1.53 brouard 3366: chdir(path);
3367: replace(pathc,path);
3368:
1.59 brouard 3369: /*-------- arguments in the command line --------*/
1.53 brouard 3370:
3371: /* Log file */
3372: strcat(filelog, optionfilefiname);
3373: strcat(filelog,".log"); /* */
3374: if((ficlog=fopen(filelog,"w"))==NULL) {
3375: printf("Problem with logfile %s\n",filelog);
3376: goto end;
3377: }
3378: fprintf(ficlog,"Log filename:%s\n",filelog);
3379: fprintf(ficlog,"\n%s",version);
3380: fprintf(ficlog,"\nEnter the parameter file name: ");
3381: fprintf(ficlog,"pathtot=%s, path=%s, optionfile=%s optionfilext=%s optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
3382: fflush(ficlog);
3383:
3384: /* */
3385: strcpy(fileres,"r");
3386: strcat(fileres, optionfilefiname);
3387: strcat(fileres,".txt"); /* Other files have txt extension */
3388:
3389: /*---------arguments file --------*/
3390:
3391: if((ficpar=fopen(optionfile,"r"))==NULL) {
3392: printf("Problem with optionfile %s\n",optionfile);
3393: fprintf(ficlog,"Problem with optionfile %s\n",optionfile);
3394: goto end;
3395: }
3396:
3397: strcpy(filereso,"o");
3398: strcat(filereso,fileres);
3399: if((ficparo=fopen(filereso,"w"))==NULL) {
3400: printf("Problem with Output resultfile: %s\n", filereso);
3401: fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso);
3402: goto end;
3403: }
3404:
3405: /* Reads comments: lines beginning with '#' */
3406: while((c=getc(ficpar))=='#' && c!= EOF){
3407: ungetc(c,ficpar);
3408: fgets(line, MAXLINE, ficpar);
3409: puts(line);
3410: fputs(line,ficparo);
3411: }
3412: ungetc(c,ficpar);
3413:
3414: 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);
3415: 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);
3416: 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);
1.59 brouard 3417: while((c=getc(ficpar))=='#' && c!= EOF){
1.53 brouard 3418: ungetc(c,ficpar);
3419: fgets(line, MAXLINE, ficpar);
3420: puts(line);
3421: fputs(line,ficparo);
3422: }
3423: ungetc(c,ficpar);
3424:
3425:
3426: covar=matrix(0,NCOVMAX,1,n);
1.58 lievre 3427: cptcovn=0; /*Number of covariates, i.e. number of '+' in model statement*/
1.53 brouard 3428: if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;
3429:
1.58 lievre 3430: ncovmodel=2+cptcovn; /*Number of variables = cptcovn + intercept + age */
1.53 brouard 3431: nvar=ncovmodel-1; /* Suppressing age as a basic covariate */
3432:
3433: /* Read guess parameters */
3434: /* Reads comments: lines beginning with '#' */
3435: while((c=getc(ficpar))=='#' && c!= EOF){
3436: ungetc(c,ficpar);
3437: fgets(line, MAXLINE, ficpar);
3438: puts(line);
3439: fputs(line,ficparo);
3440: }
3441: ungetc(c,ficpar);
3442:
3443: param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
1.59 brouard 3444: for(i=1; i <=nlstate; i++)
1.53 brouard 3445: for(j=1; j <=nlstate+ndeath-1; j++){
3446: fscanf(ficpar,"%1d%1d",&i1,&j1);
3447: fprintf(ficparo,"%1d%1d",i1,j1);
3448: if(mle==1)
3449: printf("%1d%1d",i,j);
3450: fprintf(ficlog,"%1d%1d",i,j);
3451: for(k=1; k<=ncovmodel;k++){
3452: fscanf(ficpar," %lf",¶m[i][j][k]);
3453: if(mle==1){
3454: printf(" %lf",param[i][j][k]);
3455: fprintf(ficlog," %lf",param[i][j][k]);
3456: }
3457: else
3458: fprintf(ficlog," %lf",param[i][j][k]);
3459: fprintf(ficparo," %lf",param[i][j][k]);
3460: }
3461: fscanf(ficpar,"\n");
3462: if(mle==1)
3463: printf("\n");
3464: fprintf(ficlog,"\n");
3465: fprintf(ficparo,"\n");
3466: }
3467:
1.59 brouard 3468: npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/
1.53 brouard 3469:
3470: p=param[1][1];
3471:
3472: /* Reads comments: lines beginning with '#' */
3473: while((c=getc(ficpar))=='#' && c!= EOF){
3474: ungetc(c,ficpar);
3475: fgets(line, MAXLINE, ficpar);
3476: puts(line);
3477: fputs(line,ficparo);
3478: }
3479: ungetc(c,ficpar);
3480:
3481: delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
3482: delti=vector(1,npar); /* Scale of each paramater (output from hesscov) */
3483: for(i=1; i <=nlstate; i++){
3484: for(j=1; j <=nlstate+ndeath-1; j++){
3485: fscanf(ficpar,"%1d%1d",&i1,&j1);
3486: printf("%1d%1d",i,j);
3487: fprintf(ficparo,"%1d%1d",i1,j1);
3488: for(k=1; k<=ncovmodel;k++){
3489: fscanf(ficpar,"%le",&delti3[i][j][k]);
3490: printf(" %le",delti3[i][j][k]);
3491: fprintf(ficparo," %le",delti3[i][j][k]);
3492: }
3493: fscanf(ficpar,"\n");
3494: printf("\n");
3495: fprintf(ficparo,"\n");
3496: }
3497: }
3498: delti=delti3[1][1];
3499:
3500: /* Reads comments: lines beginning with '#' */
3501: while((c=getc(ficpar))=='#' && c!= EOF){
3502: ungetc(c,ficpar);
3503: fgets(line, MAXLINE, ficpar);
3504: puts(line);
3505: fputs(line,ficparo);
3506: }
3507: ungetc(c,ficpar);
3508:
3509: matcov=matrix(1,npar,1,npar);
3510: for(i=1; i <=npar; i++){
3511: fscanf(ficpar,"%s",&str);
3512: if(mle==1)
3513: printf("%s",str);
3514: fprintf(ficlog,"%s",str);
3515: fprintf(ficparo,"%s",str);
3516: for(j=1; j <=i; j++){
3517: fscanf(ficpar," %le",&matcov[i][j]);
3518: if(mle==1){
3519: printf(" %.5le",matcov[i][j]);
3520: fprintf(ficlog," %.5le",matcov[i][j]);
3521: }
3522: else
3523: fprintf(ficlog," %.5le",matcov[i][j]);
3524: fprintf(ficparo," %.5le",matcov[i][j]);
3525: }
3526: fscanf(ficpar,"\n");
3527: if(mle==1)
3528: printf("\n");
3529: fprintf(ficlog,"\n");
3530: fprintf(ficparo,"\n");
3531: }
3532: for(i=1; i <=npar; i++)
3533: for(j=i+1;j<=npar;j++)
3534: matcov[i][j]=matcov[j][i];
3535:
3536: if(mle==1)
3537: printf("\n");
3538: fprintf(ficlog,"\n");
3539:
3540:
1.59 brouard 3541: /*-------- Rewriting paramater file ----------*/
3542: strcpy(rfileres,"r"); /* "Rparameterfile */
3543: strcat(rfileres,optionfilefiname); /* Parameter file first name*/
3544: strcat(rfileres,"."); /* */
3545: strcat(rfileres,optionfilext); /* Other files have txt extension */
3546: if((ficres =fopen(rfileres,"w"))==NULL) {
3547: printf("Problem writing new parameter file: %s\n", fileres);goto end;
3548: fprintf(ficlog,"Problem writing new parameter file: %s\n", fileres);goto end;
3549: }
3550: fprintf(ficres,"#%s\n",version);
1.53 brouard 3551:
1.59 brouard 3552: /*-------- data file ----------*/
3553: if((fic=fopen(datafile,"r"))==NULL) {
3554: printf("Problem with datafile: %s\n", datafile);goto end;
3555: fprintf(ficlog,"Problem with datafile: %s\n", datafile);goto end;
3556: }
3557:
3558: n= lastobs;
3559: severity = vector(1,maxwav);
3560: outcome=imatrix(1,maxwav+1,1,n);
3561: num=ivector(1,n);
3562: moisnais=vector(1,n);
3563: annais=vector(1,n);
3564: moisdc=vector(1,n);
3565: andc=vector(1,n);
3566: agedc=vector(1,n);
3567: cod=ivector(1,n);
3568: weight=vector(1,n);
3569: for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */
3570: mint=matrix(1,maxwav,1,n);
3571: anint=matrix(1,maxwav,1,n);
3572: s=imatrix(1,maxwav+1,1,n);
3573: tab=ivector(1,NCOVMAX);
3574: ncodemax=ivector(1,8);
3575:
3576: i=1;
3577: while (fgets(line, MAXLINE, fic) != NULL) {
3578: if ((i >= firstobs) && (i <=lastobs)) {
1.53 brouard 3579:
1.59 brouard 3580: for (j=maxwav;j>=1;j--){
3581: cutv(stra, strb,line,' '); s[j][i]=atoi(strb);
3582: strcpy(line,stra);
3583: cutv(stra, strb,line,'/'); anint[j][i]=(double)(atoi(strb)); strcpy(line,stra);
3584: cutv(stra, strb,line,' '); mint[j][i]=(double)(atoi(strb)); strcpy(line,stra);
3585: }
1.53 brouard 3586:
1.59 brouard 3587: cutv(stra, strb,line,'/'); andc[i]=(double)(atoi(strb)); strcpy(line,stra);
3588: cutv(stra, strb,line,' '); moisdc[i]=(double)(atoi(strb)); strcpy(line,stra);
1.53 brouard 3589:
1.59 brouard 3590: cutv(stra, strb,line,'/'); annais[i]=(double)(atoi(strb)); strcpy(line,stra);
3591: cutv(stra, strb,line,' '); moisnais[i]=(double)(atoi(strb)); strcpy(line,stra);
1.53 brouard 3592:
1.59 brouard 3593: cutv(stra, strb,line,' '); weight[i]=(double)(atoi(strb)); strcpy(line,stra);
3594: for (j=ncovcol;j>=1;j--){
3595: cutv(stra, strb,line,' '); covar[j][i]=(double)(atoi(strb)); strcpy(line,stra);
3596: }
3597: num[i]=atol(stra);
1.53 brouard 3598:
1.59 brouard 3599: /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){
3600: 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;}*/
1.53 brouard 3601:
1.59 brouard 3602: i=i+1;
3603: }
3604: }
3605: /* printf("ii=%d", ij);
3606: scanf("%d",i);*/
1.53 brouard 3607: imx=i-1; /* Number of individuals */
3608:
3609: /* for (i=1; i<=imx; i++){
3610: if ((s[1][i]==3) && (s[2][i]==2)) s[2][i]=3;
3611: if ((s[2][i]==3) && (s[3][i]==2)) s[3][i]=3;
3612: if ((s[3][i]==3) && (s[4][i]==2)) s[4][i]=3;
3613: }*/
3614: /* for (i=1; i<=imx; i++){
3615: if (s[4][i]==9) s[4][i]=-1;
3616: 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]));}*/
3617:
3618:
3619: /* Calculation of the number of parameter from char model*/
3620: Tvar=ivector(1,15); /* stores the number n of the covariates in Vm+Vn at 1 and m at 2 */
3621: Tprod=ivector(1,15);
3622: Tvaraff=ivector(1,15);
3623: Tvard=imatrix(1,15,1,2);
3624: Tage=ivector(1,15);
3625:
1.58 lievre 3626: if (strlen(model) >1){ /* If there is at least 1 covariate */
1.53 brouard 3627: j=0, j1=0, k1=1, k2=1;
1.58 lievre 3628: j=nbocc(model,'+'); /* j=Number of '+' */
3629: j1=nbocc(model,'*'); /* j1=Number of '*' */
3630: cptcovn=j+1;
3631: cptcovprod=j1; /*Number of products */
1.53 brouard 3632:
3633: strcpy(modelsav,model);
3634: if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){
3635: printf("Error. Non available option model=%s ",model);
3636: fprintf(ficlog,"Error. Non available option model=%s ",model);
3637: goto end;
3638: }
3639:
1.59 brouard 3640: /* This loop fills the array Tvar from the string 'model'.*/
1.58 lievre 3641:
1.53 brouard 3642: for(i=(j+1); i>=1;i--){
3643: cutv(stra,strb,modelsav,'+'); /* keeps in strb after the last + */
1.59 brouard 3644: if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyzes it */
1.53 brouard 3645: /* printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/
3646: /*scanf("%d",i);*/
3647: if (strchr(strb,'*')) { /* Model includes a product */
3648: cutv(strd,strc,strb,'*'); /* strd*strc Vm*Vn (if not *age)*/
3649: if (strcmp(strc,"age")==0) { /* Vn*age */
3650: cptcovprod--;
3651: cutv(strb,stre,strd,'V');
3652: Tvar[i]=atoi(stre); /* computes n in Vn and stores in Tvar*/
3653: cptcovage++;
3654: Tage[cptcovage]=i;
3655: /*printf("stre=%s ", stre);*/
3656: }
3657: else if (strcmp(strd,"age")==0) { /* or age*Vn */
3658: cptcovprod--;
3659: cutv(strb,stre,strc,'V');
3660: Tvar[i]=atoi(stre);
3661: cptcovage++;
3662: Tage[cptcovage]=i;
3663: }
3664: else { /* Age is not in the model */
3665: cutv(strb,stre,strc,'V'); /* strc= Vn, stre is n*/
3666: Tvar[i]=ncovcol+k1;
3667: cutv(strb,strc,strd,'V'); /* strd was Vm, strc is m */
3668: Tprod[k1]=i;
3669: Tvard[k1][1]=atoi(strc); /* m*/
3670: Tvard[k1][2]=atoi(stre); /* n */
3671: Tvar[cptcovn+k2]=Tvard[k1][1];
3672: Tvar[cptcovn+k2+1]=Tvard[k1][2];
3673: for (k=1; k<=lastobs;k++)
3674: covar[ncovcol+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];
3675: k1++;
3676: k2=k2+2;
3677: }
3678: }
3679: else { /* no more sum */
3680: /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/
3681: /* scanf("%d",i);*/
3682: cutv(strd,strc,strb,'V');
3683: Tvar[i]=atoi(strc);
3684: }
3685: strcpy(modelsav,stra);
3686: /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);
3687: scanf("%d",i);*/
3688: } /* end of loop + */
3689: } /* end model */
3690:
1.58 lievre 3691: /*The number n of Vn is stored in Tvar. cptcovage =number of age covariate. Tage gives the position of age. cptcovprod= number of products.
3692: If model=V1+V1*age then Tvar[1]=1 Tvar[2]=1 cptcovage=1 Tage[1]=2 cptcovprod=0*/
3693:
1.53 brouard 3694: /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);
3695: printf("cptcovprod=%d ", cptcovprod);
3696: fprintf(ficlog,"cptcovprod=%d ", cptcovprod);
1.58 lievre 3697:
3698: scanf("%d ",i);
3699: fclose(fic);*/
1.53 brouard 3700:
3701: /* if(mle==1){*/
1.59 brouard 3702: if (weightopt != 1) { /* Maximisation without weights*/
3703: for(i=1;i<=n;i++) weight[i]=1.0;
3704: }
1.53 brouard 3705: /*-calculation of age at interview from date of interview and age at death -*/
1.59 brouard 3706: agev=matrix(1,maxwav,1,imx);
1.53 brouard 3707:
1.59 brouard 3708: for (i=1; i<=imx; i++) {
3709: for(m=2; (m<= maxwav); m++) {
3710: if ((mint[m][i]== 99) && (s[m][i] <= nlstate)){
3711: anint[m][i]=9999;
3712: s[m][i]=-1;
3713: }
3714: if(moisdc[i]==99 && andc[i]==9999 & s[m][i]>nlstate) s[m][i]=-1;
1.53 brouard 3715: }
1.59 brouard 3716: }
1.53 brouard 3717:
1.59 brouard 3718: for (i=1; i<=imx; i++) {
3719: agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);
3720: for(m=1; (m<= maxwav); m++){
1.69 brouard 3721: if(s[m][i] >0){
1.59 brouard 3722: if (s[m][i] >= nlstate+1) {
3723: if(agedc[i]>0)
1.69 brouard 3724: if(moisdc[i]!=99 && andc[i]!=9999)
3725: agev[m][i]=agedc[i];
1.59 brouard 3726: /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/
3727: else {
1.53 brouard 3728: if (andc[i]!=9999){
1.59 brouard 3729: printf("Warning negative age at death: %d line:%d\n",num[i],i);
3730: fprintf(ficlog,"Warning negative age at death: %d line:%d\n",num[i],i);
3731: agev[m][i]=-1;
1.53 brouard 3732: }
3733: }
1.70 ! brouard 3734: }
1.69 brouard 3735: else if(s[m][i] !=9){ /* Standard case, age in fractional
3736: years but with the precision of a
3737: month */
1.59 brouard 3738: agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);
3739: if(mint[m][i]==99 || anint[m][i]==9999)
3740: agev[m][i]=1;
3741: else if(agev[m][i] <agemin){
3742: agemin=agev[m][i];
3743: /*printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], agemin);*/
1.53 brouard 3744: }
1.59 brouard 3745: else if(agev[m][i] >agemax){
3746: agemax=agev[m][i];
3747: /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/
1.53 brouard 3748: }
1.59 brouard 3749: /*agev[m][i]=anint[m][i]-annais[i];*/
3750: /* agev[m][i] = age[i]+2*m;*/
1.53 brouard 3751: }
1.59 brouard 3752: else { /* =9 */
1.53 brouard 3753: agev[m][i]=1;
1.59 brouard 3754: s[m][i]=-1;
3755: }
1.53 brouard 3756: }
1.59 brouard 3757: else /*= 0 Unknown */
3758: agev[m][i]=1;
3759: }
1.53 brouard 3760:
1.59 brouard 3761: }
3762: for (i=1; i<=imx; i++) {
3763: for(m=1; (m<= maxwav); m++){
3764: if (s[m][i] > (nlstate+ndeath)) {
3765: 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);
3766: 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);
3767: goto end;
1.53 brouard 3768: }
3769: }
1.59 brouard 3770: }
1.53 brouard 3771:
1.59 brouard 3772: printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);
3773: fprintf(ficlog,"Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);
3774:
3775: free_vector(severity,1,maxwav);
3776: free_imatrix(outcome,1,maxwav+1,1,n);
3777: free_vector(moisnais,1,n);
3778: free_vector(annais,1,n);
3779: /* free_matrix(mint,1,maxwav,1,n);
3780: free_matrix(anint,1,maxwav,1,n);*/
3781: free_vector(moisdc,1,n);
3782: free_vector(andc,1,n);
1.53 brouard 3783:
3784:
1.59 brouard 3785: wav=ivector(1,imx);
3786: dh=imatrix(1,lastpass-firstpass+1,1,imx);
3787: bh=imatrix(1,lastpass-firstpass+1,1,imx);
3788: mw=imatrix(1,lastpass-firstpass+1,1,imx);
1.69 brouard 3789:
1.59 brouard 3790: /* Concatenates waves */
3791: concatwav(wav, dh, bh, mw, s, agedc, agev, firstpass, lastpass, imx, nlstate, stepm);
1.53 brouard 3792:
1.59 brouard 3793: /* Routine tricode is to calculate cptcoveff (real number of unique covariates) and to associate covariable number and modality */
1.53 brouard 3794:
1.59 brouard 3795: Tcode=ivector(1,100);
3796: nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);
3797: ncodemax[1]=1;
3798: if (cptcovn > 0) tricode(Tvar,nbcode,imx);
1.53 brouard 3799:
1.59 brouard 3800: codtab=imatrix(1,100,1,10); /* Cross tabulation to get the order of
3801: the estimations*/
3802: h=0;
3803: m=pow(2,cptcoveff);
1.53 brouard 3804:
1.59 brouard 3805: for(k=1;k<=cptcoveff; k++){
3806: for(i=1; i <=(m/pow(2,k));i++){
3807: for(j=1; j <= ncodemax[k]; j++){
3808: for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){
3809: h++;
3810: if (h>m) h=1;codtab[h][k]=j;codtab[h][Tvar[k]]=j;
3811: /* printf("h=%d k=%d j=%d codtab[h][k]=%d tvar[k]=%d \n",h, k,j,codtab[h][k],Tvar[k]);*/
3812: }
3813: }
3814: }
3815: }
3816: /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]);
3817: codtab[1][2]=1;codtab[2][2]=2; */
3818: /* for(i=1; i <=m ;i++){
3819: for(k=1; k <=cptcovn; k++){
3820: printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);
3821: }
3822: printf("\n");
1.53 brouard 3823: }
1.59 brouard 3824: scanf("%d",i);*/
1.53 brouard 3825:
1.59 brouard 3826: /* Calculates basic frequencies. Computes observed prevalence at single age
3827: and prints on file fileres'p'. */
1.53 brouard 3828:
1.60 brouard 3829: pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
3830: oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
3831: newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
3832: savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
3833: oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */
1.53 brouard 3834:
3835:
1.59 brouard 3836: /* For Powell, parameters are in a vector p[] starting at p[1]
3837: so we point p on param[1][1] so that p[1] maps on param[1][1][1] */
3838: p=param[1][1]; /* *(*(*(param +1)+1)+0) */
1.53 brouard 3839:
1.61 brouard 3840: if(mle>=1){ /* Could be 1 or 2 */
1.53 brouard 3841: mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);
1.59 brouard 3842: }
1.53 brouard 3843:
1.59 brouard 3844: /*--------- results files --------------*/
3845: fprintf(ficres,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle= 0 weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate, ndeath, maxwav, weightopt,model);
1.53 brouard 3846:
3847:
1.59 brouard 3848: jk=1;
3849: fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
3850: printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
3851: fprintf(ficlog,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
3852: for(i=1,jk=1; i <=nlstate; i++){
3853: for(k=1; k <=(nlstate+ndeath); k++){
3854: if (k != i)
3855: {
3856: printf("%d%d ",i,k);
3857: fprintf(ficlog,"%d%d ",i,k);
3858: fprintf(ficres,"%1d%1d ",i,k);
3859: for(j=1; j <=ncovmodel; j++){
3860: printf("%f ",p[jk]);
3861: fprintf(ficlog,"%f ",p[jk]);
3862: fprintf(ficres,"%f ",p[jk]);
3863: jk++;
3864: }
3865: printf("\n");
3866: fprintf(ficlog,"\n");
3867: fprintf(ficres,"\n");
3868: }
3869: }
3870: }
3871: if(mle==1){
3872: /* Computing hessian and covariance matrix */
3873: ftolhess=ftol; /* Usually correct */
3874: hesscov(matcov, p, npar, delti, ftolhess, func);
3875: }
3876: fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");
3877: printf("# Scales (for hessian or gradient estimation)\n");
3878: fprintf(ficlog,"# Scales (for hessian or gradient estimation)\n");
3879: for(i=1,jk=1; i <=nlstate; i++){
3880: for(j=1; j <=nlstate+ndeath; j++){
3881: if (j!=i) {
3882: fprintf(ficres,"%1d%1d",i,j);
3883: printf("%1d%1d",i,j);
3884: fprintf(ficlog,"%1d%1d",i,j);
3885: for(k=1; k<=ncovmodel;k++){
3886: printf(" %.5e",delti[jk]);
3887: fprintf(ficlog," %.5e",delti[jk]);
3888: fprintf(ficres," %.5e",delti[jk]);
3889: jk++;
3890: }
3891: printf("\n");
3892: fprintf(ficlog,"\n");
3893: fprintf(ficres,"\n");
3894: }
3895: }
3896: }
1.53 brouard 3897:
1.59 brouard 3898: 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");
3899: if(mle==1)
3900: 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");
3901: 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");
3902: for(i=1,k=1;i<=npar;i++){
3903: /* if (k>nlstate) k=1;
3904: i1=(i-1)/(ncovmodel*nlstate)+1;
3905: fprintf(ficres,"%s%d%d",alph[k],i1,tab[i]);
3906: printf("%s%d%d",alph[k],i1,tab[i]);
3907: */
3908: fprintf(ficres,"%3d",i);
3909: if(mle==1)
3910: printf("%3d",i);
3911: fprintf(ficlog,"%3d",i);
3912: for(j=1; j<=i;j++){
3913: fprintf(ficres," %.5e",matcov[i][j]);
3914: if(mle==1)
3915: printf(" %.5e",matcov[i][j]);
3916: fprintf(ficlog," %.5e",matcov[i][j]);
3917: }
3918: fprintf(ficres,"\n");
3919: if(mle==1)
3920: printf("\n");
3921: fprintf(ficlog,"\n");
3922: k++;
3923: }
1.53 brouard 3924:
1.59 brouard 3925: while((c=getc(ficpar))=='#' && c!= EOF){
3926: ungetc(c,ficpar);
3927: fgets(line, MAXLINE, ficpar);
3928: puts(line);
3929: fputs(line,ficparo);
3930: }
3931: ungetc(c,ficpar);
3932:
3933: estepm=0;
3934: fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm);
3935: if (estepm==0 || estepm < stepm) estepm=stepm;
3936: if (fage <= 2) {
3937: bage = ageminpar;
3938: fage = agemaxpar;
3939: }
1.53 brouard 3940:
1.59 brouard 3941: fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");
3942: fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
3943: fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
1.53 brouard 3944:
1.59 brouard 3945: while((c=getc(ficpar))=='#' && c!= EOF){
3946: ungetc(c,ficpar);
3947: fgets(line, MAXLINE, ficpar);
3948: puts(line);
3949: fputs(line,ficparo);
3950: }
3951: ungetc(c,ficpar);
1.53 brouard 3952:
1.59 brouard 3953: fscanf(ficpar,"begin-prev-date=%lf/%lf/%lf end-prev-date=%lf/%lf/%lf mov_average=%d\n",&jprev1, &mprev1,&anprev1,&jprev2, &mprev2,&anprev2,&mobilav);
3954: fprintf(ficparo,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
3955: fprintf(ficres,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
1.69 brouard 3956: printf("begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
3957: fprintf(ficlog,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
1.53 brouard 3958:
1.59 brouard 3959: while((c=getc(ficpar))=='#' && c!= EOF){
3960: ungetc(c,ficpar);
3961: fgets(line, MAXLINE, ficpar);
3962: puts(line);
3963: fputs(line,ficparo);
3964: }
3965: ungetc(c,ficpar);
1.53 brouard 3966:
3967:
1.70 ! brouard 3968: dateprev1=anprev1+(mprev1-1)/12.+(jprev1-1)/365.;
! 3969: dateprev2=anprev2+(mprev2-1)/12.+(jprev2-1)/365.;
1.53 brouard 3970:
3971: fscanf(ficpar,"pop_based=%d\n",&popbased);
3972: fprintf(ficparo,"pop_based=%d\n",popbased);
3973: fprintf(ficres,"pop_based=%d\n",popbased);
3974:
3975: while((c=getc(ficpar))=='#' && c!= EOF){
3976: ungetc(c,ficpar);
3977: fgets(line, MAXLINE, ficpar);
3978: puts(line);
3979: fputs(line,ficparo);
3980: }
3981: ungetc(c,ficpar);
3982:
1.69 brouard 3983: fscanf(ficpar,"prevforecast=%d starting-proj-date=%lf/%lf/%lf final-proj-date=%lf/%lf/%lf mobil_average=%d\n",&prevfcast,&jproj1,&mproj1,&anproj1,&jproj2,&mproj2,&anproj2,&mobilavproj);
1.70 ! brouard 3984: fprintf(ficparo,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
1.69 brouard 3985: printf("prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobilaverage=%d\n",&prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
1.70 ! brouard 3986: fprintf(ficlog,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobilaverage=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
! 3987: fprintf(ficres,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobilaverage=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
1.69 brouard 3988: /* day and month of proj2 are not used but only year anproj2.*/
1.53 brouard 3989:
1.59 brouard 3990: while((c=getc(ficpar))=='#' && c!= EOF){
1.53 brouard 3991: ungetc(c,ficpar);
3992: fgets(line, MAXLINE, ficpar);
3993: puts(line);
3994: fputs(line,ficparo);
3995: }
3996: ungetc(c,ficpar);
3997:
3998: fscanf(ficpar,"popforecast=%d popfile=%s popfiledate=%lf/%lf/%lf last-popfiledate=%lf/%lf/%lf\n",&popforecast,popfile,&jpyram,&mpyram,&anpyram,&jpyram1,&mpyram1,&anpyram1);
3999: fprintf(ficparo,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);
4000: fprintf(ficres,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);
4001:
1.59 brouard 4002: freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);
1.58 lievre 4003:
1.59 brouard 4004: /*------------ gnuplot -------------*/
4005: strcpy(optionfilegnuplot,optionfilefiname);
4006: strcat(optionfilegnuplot,".gp");
4007: if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {
4008: printf("Problem with file %s",optionfilegnuplot);
4009: }
4010: else{
4011: fprintf(ficgp,"\n# %s\n", version);
4012: fprintf(ficgp,"# %s\n", optionfilegnuplot);
4013: fprintf(ficgp,"set missing 'NaNq'\n");
4014: }
4015: fclose(ficgp);
4016: printinggnuplot(fileres, ageminpar,agemaxpar,fage, pathc,p);
4017: /*--------- index.htm --------*/
1.53 brouard 4018:
4019: strcpy(optionfilehtm,optionfile);
4020: strcat(optionfilehtm,".htm");
4021: if((fichtm=fopen(optionfilehtm,"w"))==NULL) {
4022: printf("Problem with %s \n",optionfilehtm), exit(0);
4023: }
4024:
4025: fprintf(fichtm,"<body> <font size=\"2\">%s </font> <hr size=\"2\" color=\"#EC5E5E\"> \n
4026: Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n
4027: \n
4028: Total number of observations=%d <br>\n
4029: Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n
4030: <hr size=\"2\" color=\"#EC5E5E\">
4031: <ul><li><h4>Parameter files</h4>\n
4032: - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n
4033: - Log file of the run: <a href=\"%s\">%s</a><br>\n
4034: - 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);
4035: fclose(fichtm);
4036:
1.59 brouard 4037: printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,model,imx,jmin,jmax,jmean,rfileres,popforecast,estepm,jprev1,mprev1,anprev1,jprev2,mprev2,anprev2);
1.53 brouard 4038:
1.59 brouard 4039: /*------------ free_vector -------------*/
4040: chdir(path);
1.53 brouard 4041:
1.59 brouard 4042: free_ivector(wav,1,imx);
4043: free_imatrix(dh,1,lastpass-firstpass+1,1,imx);
4044: free_imatrix(bh,1,lastpass-firstpass+1,1,imx);
4045: free_imatrix(mw,1,lastpass-firstpass+1,1,imx);
4046: free_ivector(num,1,n);
4047: free_vector(agedc,1,n);
1.65 lievre 4048: /*free_matrix(covar,0,NCOVMAX,1,n);*/
1.59 brouard 4049: /*free_matrix(covar,1,NCOVMAX,1,n);*/
4050: fclose(ficparo);
4051: fclose(ficres);
1.53 brouard 4052:
4053:
1.54 brouard 4054: /*--------------- Prevalence limit (stable prevalence) --------------*/
1.53 brouard 4055:
4056: strcpy(filerespl,"pl");
4057: strcat(filerespl,fileres);
4058: if((ficrespl=fopen(filerespl,"w"))==NULL) {
1.54 brouard 4059: printf("Problem with stable prevalence resultfile: %s\n", filerespl);goto end;
4060: fprintf(ficlog,"Problem with stable prevalence resultfile: %s\n", filerespl);goto end;
1.53 brouard 4061: }
1.54 brouard 4062: printf("Computing stable prevalence: result on file '%s' \n", filerespl);
4063: fprintf(ficlog,"Computing stable prevalence: result on file '%s' \n", filerespl);
4064: fprintf(ficrespl,"#Stable prevalence \n");
1.53 brouard 4065: fprintf(ficrespl,"#Age ");
4066: for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);
4067: fprintf(ficrespl,"\n");
4068:
4069: prlim=matrix(1,nlstate,1,nlstate);
1.59 brouard 4070:
1.53 brouard 4071: agebase=ageminpar;
4072: agelim=agemaxpar;
4073: ftolpl=1.e-10;
4074: i1=cptcoveff;
4075: if (cptcovn < 1){i1=1;}
4076:
1.59 brouard 4077: for(cptcov=1,k=0;cptcov<=i1;cptcov++){
1.53 brouard 4078: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
1.59 brouard 4079: k=k+1;
4080: /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/
4081: fprintf(ficrespl,"\n#******");
4082: printf("\n#******");
4083: fprintf(ficlog,"\n#******");
4084: for(j=1;j<=cptcoveff;j++) {
4085: fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
4086: printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
4087: fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
4088: }
4089: fprintf(ficrespl,"******\n");
4090: printf("******\n");
4091: fprintf(ficlog,"******\n");
1.53 brouard 4092:
1.59 brouard 4093: for (age=agebase; age<=agelim; age++){
4094: prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
1.69 brouard 4095: fprintf(ficrespl,"%.0f ",age );
4096: for(j=1;j<=cptcoveff;j++)
4097: fprintf(ficrespl,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
1.59 brouard 4098: for(i=1; i<=nlstate;i++)
1.53 brouard 4099: fprintf(ficrespl," %.5f", prlim[i][i]);
1.59 brouard 4100: fprintf(ficrespl,"\n");
1.53 brouard 4101: }
4102: }
1.59 brouard 4103: }
1.53 brouard 4104: fclose(ficrespl);
4105:
4106: /*------------- h Pij x at various ages ------------*/
4107:
4108: strcpy(filerespij,"pij"); strcat(filerespij,fileres);
4109: if((ficrespij=fopen(filerespij,"w"))==NULL) {
4110: printf("Problem with Pij resultfile: %s\n", filerespij);goto end;
4111: fprintf(ficlog,"Problem with Pij resultfile: %s\n", filerespij);goto end;
4112: }
4113: printf("Computing pij: result on file '%s' \n", filerespij);
4114: fprintf(ficlog,"Computing pij: result on file '%s' \n", filerespij);
4115:
4116: stepsize=(int) (stepm+YEARM-1)/YEARM;
4117: /*if (stepm<=24) stepsize=2;*/
4118:
4119: agelim=AGESUP;
4120: hstepm=stepsize*YEARM; /* Every year of age */
4121: hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */
4122:
4123: /* hstepm=1; aff par mois*/
4124:
1.70 ! brouard 4125: fprintf(ficrespij,"#****** h Pij x Probability to be in state j at age x+h being in i at x ");
1.59 brouard 4126: for(cptcov=1,k=0;cptcov<=i1;cptcov++){
1.53 brouard 4127: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
4128: k=k+1;
1.59 brouard 4129: fprintf(ficrespij,"\n#****** ");
4130: for(j=1;j<=cptcoveff;j++)
4131: fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
4132: fprintf(ficrespij,"******\n");
1.53 brouard 4133:
1.59 brouard 4134: for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */
4135: nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
4136: nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
4137:
4138: /* nhstepm=nhstepm*YEARM; aff par mois*/
4139:
4140: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4141: oldm=oldms;savm=savms;
4142: hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
1.70 ! brouard 4143: fprintf(ficrespij,"# Cov Agex agex+h hpijx with i,j=");
1.59 brouard 4144: for(i=1; i<=nlstate;i++)
4145: for(j=1; j<=nlstate+ndeath;j++)
4146: fprintf(ficrespij," %1d-%1d",i,j);
4147: fprintf(ficrespij,"\n");
4148: for (h=0; h<=nhstepm; h++){
1.70 ! brouard 4149: fprintf(ficrespij,"%d %3.f %3.f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );
1.53 brouard 4150: for(i=1; i<=nlstate;i++)
4151: for(j=1; j<=nlstate+ndeath;j++)
1.59 brouard 4152: fprintf(ficrespij," %.5f", p3mat[i][j][h]);
1.53 brouard 4153: fprintf(ficrespij,"\n");
4154: }
1.59 brouard 4155: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4156: fprintf(ficrespij,"\n");
4157: }
1.53 brouard 4158: }
4159: }
4160:
4161: varprob(optionfilefiname, matcov, p, delti, nlstate, (int) bage, (int) fage,k,Tvar,nbcode, ncodemax);
4162:
4163: fclose(ficrespij);
4164:
4165:
4166: /*---------- Forecasting ------------------*/
1.69 brouard 4167: /*if((stepm == 1) && (strcmp(model,".")==0)){*/
4168: if(prevfcast==1){
4169: if(stepm ==1){
1.70 ! brouard 4170: prevforecast(fileres, anproj1, mproj1, jproj1, agemin, agemax, dateprev1, dateprev2, mobilavproj, bage, fage, firstpass, lastpass, anproj2, p, cptcoveff);
1.69 brouard 4171: if (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);
4172: }
4173: else{
4174: erreur=108;
4175: 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);
4176: 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);
1.68 lievre 4177: }
1.69 brouard 4178: }
1.53 brouard 4179:
4180:
4181: /*---------- Health expectancies and variances ------------*/
4182:
4183: strcpy(filerest,"t");
4184: strcat(filerest,fileres);
4185: if((ficrest=fopen(filerest,"w"))==NULL) {
4186: printf("Problem with total LE resultfile: %s\n", filerest);goto end;
4187: fprintf(ficlog,"Problem with total LE resultfile: %s\n", filerest);goto end;
4188: }
4189: printf("Computing Total LEs with variances: file '%s' \n", filerest);
4190: fprintf(ficlog,"Computing Total LEs with variances: file '%s' \n", filerest);
4191:
4192:
4193: strcpy(filerese,"e");
4194: strcat(filerese,fileres);
4195: if((ficreseij=fopen(filerese,"w"))==NULL) {
4196: printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
4197: fprintf(ficlog,"Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
4198: }
4199: printf("Computing Health Expectancies: result on file '%s' \n", filerese);
4200: fprintf(ficlog,"Computing Health Expectancies: result on file '%s' \n", filerese);
1.68 lievre 4201:
1.53 brouard 4202: strcpy(fileresv,"v");
4203: strcat(fileresv,fileres);
4204: if((ficresvij=fopen(fileresv,"w"))==NULL) {
4205: printf("Problem with variance resultfile: %s\n", fileresv);exit(0);
4206: fprintf(ficlog,"Problem with variance resultfile: %s\n", fileresv);exit(0);
4207: }
4208: printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
4209: fprintf(ficlog,"Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
1.58 lievre 4210:
1.70 ! brouard 4211: prevalence(ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
1.58 lievre 4212:
1.54 brouard 4213: if (mobilav!=0) {
1.53 brouard 4214: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
1.54 brouard 4215: if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
4216: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
4217: printf(" Error in movingaverage mobilav=%d\n",mobilav);
4218: }
1.53 brouard 4219: }
4220:
1.59 brouard 4221: for(cptcov=1,k=0;cptcov<=i1;cptcov++){
1.53 brouard 4222: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
4223: k=k+1;
4224: fprintf(ficrest,"\n#****** ");
4225: for(j=1;j<=cptcoveff;j++)
4226: fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
4227: fprintf(ficrest,"******\n");
4228:
4229: fprintf(ficreseij,"\n#****** ");
4230: for(j=1;j<=cptcoveff;j++)
4231: fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
4232: fprintf(ficreseij,"******\n");
4233:
4234: fprintf(ficresvij,"\n#****** ");
4235: for(j=1;j<=cptcoveff;j++)
4236: fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
4237: fprintf(ficresvij,"******\n");
4238:
4239: eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
4240: oldm=oldms;savm=savms;
4241: evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov);
4242:
4243: vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
4244: oldm=oldms;savm=savms;
4245: varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,0, mobilav);
4246: if(popbased==1){
4247: varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,popbased,mobilav);
1.59 brouard 4248: }
1.53 brouard 4249:
4250:
4251: fprintf(ficrest,"#Total LEs with variances: e.. (std) ");
4252: for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);
4253: fprintf(ficrest,"\n");
4254:
4255: epj=vector(1,nlstate+1);
4256: for(age=bage; age <=fage ;age++){
4257: prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
4258: if (popbased==1) {
1.54 brouard 4259: if(mobilav ==0){
1.53 brouard 4260: for(i=1; i<=nlstate;i++)
4261: prlim[i][i]=probs[(int)age][i][k];
1.54 brouard 4262: }else{ /* mobilav */
1.53 brouard 4263: for(i=1; i<=nlstate;i++)
4264: prlim[i][i]=mobaverage[(int)age][i][k];
4265: }
4266: }
4267:
4268: fprintf(ficrest," %4.0f",age);
4269: for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){
4270: for(i=1, epj[j]=0.;i <=nlstate;i++) {
4271: epj[j] += prlim[i][i]*eij[i][j][(int)age];
4272: /* printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/
4273: }
4274: epj[nlstate+1] +=epj[j];
4275: }
4276:
4277: for(i=1, vepp=0.;i <=nlstate;i++)
4278: for(j=1;j <=nlstate;j++)
4279: vepp += vareij[i][j][(int)age];
4280: fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));
4281: for(j=1;j <=nlstate;j++){
4282: fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));
4283: }
4284: fprintf(ficrest,"\n");
4285: }
1.59 brouard 4286: free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
4287: free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);
4288: free_vector(epj,1,nlstate+1);
1.53 brouard 4289: }
4290: }
1.59 brouard 4291: free_vector(weight,1,n);
4292: free_imatrix(Tvard,1,15,1,2);
4293: free_imatrix(s,1,maxwav+1,1,n);
4294: free_matrix(anint,1,maxwav,1,n);
4295: free_matrix(mint,1,maxwav,1,n);
4296: free_ivector(cod,1,n);
4297: free_ivector(tab,1,NCOVMAX);
1.53 brouard 4298: fclose(ficreseij);
4299: fclose(ficresvij);
4300: fclose(ficrest);
4301: fclose(ficpar);
4302:
1.54 brouard 4303: /*------- Variance of stable prevalence------*/
1.53 brouard 4304:
4305: strcpy(fileresvpl,"vpl");
4306: strcat(fileresvpl,fileres);
4307: if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {
1.54 brouard 4308: printf("Problem with variance of stable prevalence resultfile: %s\n", fileresvpl);
1.53 brouard 4309: exit(0);
4310: }
1.54 brouard 4311: printf("Computing Variance-covariance of stable prevalence: file '%s' \n", fileresvpl);
1.53 brouard 4312:
1.59 brouard 4313: for(cptcov=1,k=0;cptcov<=i1;cptcov++){
1.53 brouard 4314: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
4315: k=k+1;
4316: fprintf(ficresvpl,"\n#****** ");
4317: for(j=1;j<=cptcoveff;j++)
4318: fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
4319: fprintf(ficresvpl,"******\n");
4320:
4321: varpl=matrix(1,nlstate,(int) bage, (int) fage);
4322: oldm=oldms;savm=savms;
1.59 brouard 4323: varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);
4324: free_matrix(varpl,1,nlstate,(int) bage, (int)fage);
1.53 brouard 4325: }
1.59 brouard 4326: }
1.53 brouard 4327:
4328: fclose(ficresvpl);
4329:
4330: /*---------- End : free ----------------*/
4331: free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);
4332: free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);
4333: free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);
4334: free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);
1.65 lievre 4335:
4336: free_matrix(covar,0,NCOVMAX,1,n);
1.53 brouard 4337: free_matrix(matcov,1,npar,1,npar);
4338: free_vector(delti,1,npar);
4339: free_matrix(agev,1,maxwav,1,imx);
4340: free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
1.54 brouard 4341: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
1.59 brouard 4342: free_ivector(ncodemax,1,8);
4343: free_ivector(Tvar,1,15);
4344: free_ivector(Tprod,1,15);
4345: free_ivector(Tvaraff,1,15);
4346: free_ivector(Tage,1,15);
4347: free_ivector(Tcode,1,100);
1.53 brouard 4348:
4349: fprintf(fichtm,"\n</body>");
4350: fclose(fichtm);
4351: fclose(ficgp);
4352:
4353:
4354: if(erreur >0){
4355: printf("End of Imach with error or warning %d\n",erreur);
4356: fprintf(ficlog,"End of Imach with error or warning %d\n",erreur);
4357: }else{
4358: printf("End of Imach\n");
4359: fprintf(ficlog,"End of Imach\n");
4360: }
4361: printf("See log file on %s\n",filelog);
4362: fclose(ficlog);
4363: /* gettimeofday(&end_time, (struct timezone*)0);*/ /* after time */
4364:
4365: /* 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);*/
4366: /*printf("Total time was %d uSec.\n", total_usecs);*/
4367: /*------ End -----------*/
4368:
1.59 brouard 4369: end:
1.53 brouard 4370: #ifdef windows
4371: /* chdir(pathcd);*/
4372: #endif
4373: /*system("wgnuplot graph.plt");*/
4374: /*system("../gp37mgw/wgnuplot graph.plt");*/
4375: /*system("cd ../gp37mgw");*/
4376: /* system("..\\gp37mgw\\wgnuplot graph.plt");*/
1.59 brouard 4377: strcpy(plotcmd,GNUPLOTPROGRAM);
4378: strcat(plotcmd," ");
4379: strcat(plotcmd,optionfilegnuplot);
4380: printf("Starting: %s\n",plotcmd);fflush(stdout);
4381: system(plotcmd);
1.53 brouard 4382:
1.54 brouard 4383: /*#ifdef windows*/
1.53 brouard 4384: while (z[0] != 'q') {
4385: /* chdir(path); */
4386: printf("\nType e to edit output files, g to graph again, c to start again, and q for exiting: ");
4387: scanf("%s",z);
4388: if (z[0] == 'c') system("./imach");
4389: else if (z[0] == 'e') system(optionfilehtm);
4390: else if (z[0] == 'g') system(plotcmd);
4391: else if (z[0] == 'q') exit(0);
4392: }
1.54 brouard 4393: /*#endif */
1.53 brouard 4394: }
4395:
4396:
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