Annotation of imach/src/imach.c, revision 1.46
1.46 ! brouard 1: /* $Id: imach.c,v 1.45 2002/05/24 16:34:18 lievre Exp $
1.24 lievre 2: Interpolated Markov Chain
1.22 brouard 3:
4: Short summary of the programme:
5:
6: This program computes Healthy Life Expectancies from
7: cross-longitudinal data. Cross-longitudinal data consist in: -1- a
8: first survey ("cross") where individuals from different ages are
9: interviewed on their health status or degree of disability (in the
10: case of a health survey which is our main interest) -2- at least a
11: second wave of interviews ("longitudinal") which measure each change
12: (if any) in individual health status. Health expectancies are
13: computed from the time spent in each health state according to a
14: model. More health states you consider, more time is necessary to reach the
15: Maximum Likelihood of the parameters involved in the model. The
16: simplest model is the multinomial logistic model where pij is the
1.39 lievre 17: probability to be observed in state j at the second wave
1.22 brouard 18: conditional to be observed in state i at the first wave. Therefore
19: the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where
20: 'age' is age and 'sex' is a covariate. If you want to have a more
21: complex model than "constant and age", you should modify the program
22: where the markup *Covariates have to be included here again* invites
23: you to do it. More covariates you add, slower the
24: convergence.
25:
26: The advantage of this computer programme, compared to a simple
27: multinomial logistic model, is clear when the delay between waves is not
28: identical for each individual. Also, if a individual missed an
29: intermediate interview, the information is lost, but taken into
30: account using an interpolation or extrapolation.
31:
32: hPijx is the probability to be observed in state i at age x+h
33: conditional to the observed state i at age x. The delay 'h' can be
34: split into an exact number (nh*stepm) of unobserved intermediate
35: states. This elementary transition (by month or quarter trimester,
36: semester or year) is model as a multinomial logistic. The hPx
37: matrix is simply the matrix product of nh*stepm elementary matrices
38: and the contribution of each individual to the likelihood is simply
39: hPijx.
1.2 lievre 40:
41: Also this programme outputs the covariance matrix of the parameters but also
42: of the life expectancies. It also computes the prevalence limits.
43:
44: Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).
45: Institut national d'études démographiques, Paris.
46: This software have been partly granted by Euro-REVES, a concerted action
47: from the European Union.
48: It is copyrighted identically to a GNU software product, ie programme and
49: software can be distributed freely for non commercial use. Latest version
50: can be accessed at http://euroreves.ined.fr/imach .
51: **********************************************************************/
52:
53: #include <math.h>
54: #include <stdio.h>
55: #include <stdlib.h>
56: #include <unistd.h>
57:
58: #define MAXLINE 256
1.42 brouard 59: #define GNUPLOTPROGRAM "gnuplot"
1.35 lievre 60: /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
1.2 lievre 61: #define FILENAMELENGTH 80
62: /*#define DEBUG*/
63: #define windows
1.5 lievre 64: #define GLOCK_ERROR_NOPATH -1 /* empty path */
65: #define GLOCK_ERROR_GETCWD -2 /* cannot get cwd */
66:
1.2 lievre 67: #define MAXPARM 30 /* Maximum number of parameters for the optimization */
68: #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */
69:
70: #define NINTERVMAX 8
71: #define NLSTATEMAX 8 /* Maximum number of live states (for func) */
72: #define NDEATHMAX 8 /* Maximum number of dead states (for func) */
73: #define NCOVMAX 8 /* Maximum number of covariates */
1.3 lievre 74: #define MAXN 20000
1.2 lievre 75: #define YEARM 12. /* Number of months per year */
76: #define AGESUP 130
77: #define AGEBASE 40
78:
79:
1.21 lievre 80: int erreur; /* Error number */
1.2 lievre 81: int nvar;
1.8 lievre 82: int cptcovn, cptcovage=0, cptcoveff=0,cptcov;
1.2 lievre 83: int npar=NPARMAX;
84: int nlstate=2; /* Number of live states */
85: int ndeath=1; /* Number of dead states */
1.34 brouard 86: int ncovmodel, ncovcol; /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
1.15 lievre 87: int popbased=0;
1.2 lievre 88:
89: int *wav; /* Number of waves for this individuual 0 is possible */
90: int maxwav; /* Maxim number of waves */
1.8 lievre 91: int jmin, jmax; /* min, max spacing between 2 waves */
1.2 lievre 92: int mle, weightopt;
93: int **mw; /* mw[mi][i] is number of the mi wave for this individual */
94: int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
1.8 lievre 95: double jmean; /* Mean space between 2 waves */
1.2 lievre 96: double **oldm, **newm, **savm; /* Working pointers to matrices */
97: double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
1.27 lievre 98: FILE *fic,*ficpar, *ficparo,*ficres, *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
1.46 ! brouard 99: FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
1.2 lievre 100: FILE *ficreseij;
101: char filerese[FILENAMELENGTH];
102: FILE *ficresvij;
103: char fileresv[FILENAMELENGTH];
104: FILE *ficresvpl;
105: char fileresvpl[FILENAMELENGTH];
106:
107: #define NR_END 1
108: #define FREE_ARG char*
109: #define FTOL 1.0e-10
110:
111: #define NRANSI
112: #define ITMAX 200
113:
114: #define TOL 2.0e-4
115:
116: #define CGOLD 0.3819660
117: #define ZEPS 1.0e-10
118: #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);
119:
120: #define GOLD 1.618034
121: #define GLIMIT 100.0
122: #define TINY 1.0e-20
123:
124: static double maxarg1,maxarg2;
125: #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
126: #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
1.25 lievre 127:
1.2 lievre 128: #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
129: #define rint(a) floor(a+0.5)
130:
131: static double sqrarg;
132: #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
133: #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}
134:
135: int imx;
136: int stepm;
137: /* Stepm, step in month: minimum step interpolation*/
138:
1.36 brouard 139: int estepm;
140: /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
141:
1.2 lievre 142: int m,nb;
1.6 lievre 143: int *num, firstpass=0, lastpass=4,*cod, *ncodemax, *Tage;
1.2 lievre 144: double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
1.13 lievre 145: double **pmmij, ***probs, ***mobaverage;
1.19 lievre 146: double dateintmean=0;
1.2 lievre 147:
148: double *weight;
149: int **s; /* Status */
150: double *agedc, **covar, idx;
1.7 lievre 151: int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;
1.2 lievre 152:
153: double ftol=FTOL; /* Tolerance for computing Max Likelihood */
154: double ftolhess; /* Tolerance for computing hessian */
155:
1.7 lievre 156: /**************** split *************************/
1.22 brouard 157: static int split( char *path, char *dirc, char *name, char *ext, char *finame )
1.5 lievre 158: {
159: char *s; /* pointer */
160: int l1, l2; /* length counters */
161:
162: l1 = strlen( path ); /* length of path */
163: if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
1.22 brouard 164: #ifdef windows
1.5 lievre 165: s = strrchr( path, '\\' ); /* find last / */
1.22 brouard 166: #else
167: s = strrchr( path, '/' ); /* find last / */
168: #endif
1.5 lievre 169: if ( s == NULL ) { /* no directory, so use current */
170: #if defined(__bsd__) /* get current working directory */
171: extern char *getwd( );
172:
173: if ( getwd( dirc ) == NULL ) {
174: #else
175: extern char *getcwd( );
176:
177: if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {
178: #endif
179: return( GLOCK_ERROR_GETCWD );
180: }
181: strcpy( name, path ); /* we've got it */
182: } else { /* strip direcotry from path */
183: s++; /* after this, the filename */
184: l2 = strlen( s ); /* length of filename */
185: if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
186: strcpy( name, s ); /* save file name */
187: strncpy( dirc, path, l1 - l2 ); /* now the directory */
188: dirc[l1-l2] = 0; /* add zero */
189: }
190: l1 = strlen( dirc ); /* length of directory */
1.22 brouard 191: #ifdef windows
1.5 lievre 192: if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; }
1.22 brouard 193: #else
194: if ( dirc[l1-1] != '/' ) { dirc[l1] = '/'; dirc[l1+1] = 0; }
195: #endif
196: s = strrchr( name, '.' ); /* find last / */
197: s++;
198: strcpy(ext,s); /* save extension */
199: l1= strlen( name);
200: l2= strlen( s)+1;
201: strncpy( finame, name, l1-l2);
202: finame[l1-l2]= 0;
1.5 lievre 203: return( 0 ); /* we're done */
204: }
205:
206:
1.2 lievre 207: /******************************************/
208:
209: void replace(char *s, char*t)
210: {
211: int i;
212: int lg=20;
213: i=0;
214: lg=strlen(t);
215: for(i=0; i<= lg; i++) {
216: (s[i] = t[i]);
217: if (t[i]== '\\') s[i]='/';
218: }
219: }
220:
221: int nbocc(char *s, char occ)
222: {
223: int i,j=0;
224: int lg=20;
225: i=0;
226: lg=strlen(s);
227: for(i=0; i<= lg; i++) {
228: if (s[i] == occ ) j++;
229: }
230: return j;
231: }
232:
233: void cutv(char *u,char *v, char*t, char occ)
234: {
1.6 lievre 235: int i,lg,j,p=0;
1.2 lievre 236: i=0;
237: for(j=0; j<=strlen(t)-1; j++) {
1.3 lievre 238: if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;
1.2 lievre 239: }
240:
241: lg=strlen(t);
242: for(j=0; j<p; j++) {
243: (u[j] = t[j]);
244: }
1.6 lievre 245: u[p]='\0';
1.2 lievre 246:
247: for(j=0; j<= lg; j++) {
248: if (j>=(p+1))(v[j-p-1] = t[j]);
249: }
250: }
251:
252: /********************** nrerror ********************/
253:
254: void nrerror(char error_text[])
255: {
256: fprintf(stderr,"ERREUR ...\n");
257: fprintf(stderr,"%s\n",error_text);
258: exit(1);
259: }
260: /*********************** vector *******************/
261: double *vector(int nl, int nh)
262: {
263: double *v;
264: v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
265: if (!v) nrerror("allocation failure in vector");
266: return v-nl+NR_END;
267: }
268:
269: /************************ free vector ******************/
270: void free_vector(double*v, int nl, int nh)
271: {
272: free((FREE_ARG)(v+nl-NR_END));
273: }
274:
275: /************************ivector *******************************/
276: int *ivector(long nl,long nh)
277: {
278: int *v;
279: v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
280: if (!v) nrerror("allocation failure in ivector");
281: return v-nl+NR_END;
282: }
283:
284: /******************free ivector **************************/
285: void free_ivector(int *v, long nl, long nh)
286: {
287: free((FREE_ARG)(v+nl-NR_END));
288: }
289:
290: /******************* imatrix *******************************/
291: int **imatrix(long nrl, long nrh, long ncl, long nch)
292: /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */
293: {
294: long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;
295: int **m;
296:
297: /* allocate pointers to rows */
298: m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));
299: if (!m) nrerror("allocation failure 1 in matrix()");
300: m += NR_END;
301: m -= nrl;
302:
303:
304: /* allocate rows and set pointers to them */
305: m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));
306: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
307: m[nrl] += NR_END;
308: m[nrl] -= ncl;
309:
310: for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;
311:
312: /* return pointer to array of pointers to rows */
313: return m;
314: }
315:
316: /****************** free_imatrix *************************/
317: void free_imatrix(m,nrl,nrh,ncl,nch)
318: int **m;
319: long nch,ncl,nrh,nrl;
320: /* free an int matrix allocated by imatrix() */
321: {
322: free((FREE_ARG) (m[nrl]+ncl-NR_END));
323: free((FREE_ARG) (m+nrl-NR_END));
324: }
325:
326: /******************* matrix *******************************/
327: double **matrix(long nrl, long nrh, long ncl, long nch)
328: {
329: long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
330: double **m;
331:
332: m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
333: if (!m) nrerror("allocation failure 1 in matrix()");
334: m += NR_END;
335: m -= nrl;
336:
337: m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
338: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
339: m[nrl] += NR_END;
340: m[nrl] -= ncl;
341:
342: for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
343: return m;
344: }
345:
346: /*************************free matrix ************************/
347: void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
348: {
349: free((FREE_ARG)(m[nrl]+ncl-NR_END));
350: free((FREE_ARG)(m+nrl-NR_END));
351: }
352:
353: /******************* ma3x *******************************/
354: double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
355: {
356: long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
357: double ***m;
358:
359: m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
360: if (!m) nrerror("allocation failure 1 in matrix()");
361: m += NR_END;
362: m -= nrl;
363:
364: m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
365: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
366: m[nrl] += NR_END;
367: m[nrl] -= ncl;
368:
369: for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
370:
371: m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
372: if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
373: m[nrl][ncl] += NR_END;
374: m[nrl][ncl] -= nll;
375: for (j=ncl+1; j<=nch; j++)
376: m[nrl][j]=m[nrl][j-1]+nlay;
377:
378: for (i=nrl+1; i<=nrh; i++) {
379: m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
380: for (j=ncl+1; j<=nch; j++)
381: m[i][j]=m[i][j-1]+nlay;
382: }
383: return m;
384: }
385:
386: /*************************free ma3x ************************/
387: void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
388: {
389: free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
390: free((FREE_ARG)(m[nrl]+ncl-NR_END));
391: free((FREE_ARG)(m+nrl-NR_END));
392: }
393:
394: /***************** f1dim *************************/
395: extern int ncom;
396: extern double *pcom,*xicom;
397: extern double (*nrfunc)(double []);
398:
399: double f1dim(double x)
400: {
401: int j;
402: double f;
403: double *xt;
404:
405: xt=vector(1,ncom);
406: for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];
407: f=(*nrfunc)(xt);
408: free_vector(xt,1,ncom);
409: return f;
410: }
411:
412: /*****************brent *************************/
413: double brent(double ax, double bx, double cx, double (*f)(double), double tol, double *xmin)
414: {
415: int iter;
416: double a,b,d,etemp;
417: double fu,fv,fw,fx;
418: double ftemp;
419: double p,q,r,tol1,tol2,u,v,w,x,xm;
420: double e=0.0;
421:
422: a=(ax < cx ? ax : cx);
423: b=(ax > cx ? ax : cx);
424: x=w=v=bx;
425: fw=fv=fx=(*f)(x);
426: for (iter=1;iter<=ITMAX;iter++) {
427: xm=0.5*(a+b);
428: tol2=2.0*(tol1=tol*fabs(x)+ZEPS);
429: /* if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
430: printf(".");fflush(stdout);
431: #ifdef DEBUG
432: 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);
433: /* if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
434: #endif
435: if (fabs(x-xm) <= (tol2-0.5*(b-a))){
436: *xmin=x;
437: return fx;
438: }
439: ftemp=fu;
440: if (fabs(e) > tol1) {
441: r=(x-w)*(fx-fv);
442: q=(x-v)*(fx-fw);
443: p=(x-v)*q-(x-w)*r;
444: q=2.0*(q-r);
445: if (q > 0.0) p = -p;
446: q=fabs(q);
447: etemp=e;
448: e=d;
449: if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))
450: d=CGOLD*(e=(x >= xm ? a-x : b-x));
451: else {
452: d=p/q;
453: u=x+d;
454: if (u-a < tol2 || b-u < tol2)
455: d=SIGN(tol1,xm-x);
456: }
457: } else {
458: d=CGOLD*(e=(x >= xm ? a-x : b-x));
459: }
460: u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));
461: fu=(*f)(u);
462: if (fu <= fx) {
463: if (u >= x) a=x; else b=x;
464: SHFT(v,w,x,u)
465: SHFT(fv,fw,fx,fu)
466: } else {
467: if (u < x) a=u; else b=u;
468: if (fu <= fw || w == x) {
469: v=w;
470: w=u;
471: fv=fw;
472: fw=fu;
473: } else if (fu <= fv || v == x || v == w) {
474: v=u;
475: fv=fu;
476: }
477: }
478: }
479: nrerror("Too many iterations in brent");
480: *xmin=x;
481: return fx;
482: }
483:
484: /****************** mnbrak ***********************/
485:
486: void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,
487: double (*func)(double))
488: {
489: double ulim,u,r,q, dum;
490: double fu;
491:
492: *fa=(*func)(*ax);
493: *fb=(*func)(*bx);
494: if (*fb > *fa) {
495: SHFT(dum,*ax,*bx,dum)
496: SHFT(dum,*fb,*fa,dum)
497: }
498: *cx=(*bx)+GOLD*(*bx-*ax);
499: *fc=(*func)(*cx);
500: while (*fb > *fc) {
501: r=(*bx-*ax)*(*fb-*fc);
502: q=(*bx-*cx)*(*fb-*fa);
503: u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/
504: (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r));
505: ulim=(*bx)+GLIMIT*(*cx-*bx);
506: if ((*bx-u)*(u-*cx) > 0.0) {
507: fu=(*func)(u);
508: } else if ((*cx-u)*(u-ulim) > 0.0) {
509: fu=(*func)(u);
510: if (fu < *fc) {
511: SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))
512: SHFT(*fb,*fc,fu,(*func)(u))
513: }
514: } else if ((u-ulim)*(ulim-*cx) >= 0.0) {
515: u=ulim;
516: fu=(*func)(u);
517: } else {
518: u=(*cx)+GOLD*(*cx-*bx);
519: fu=(*func)(u);
520: }
521: SHFT(*ax,*bx,*cx,u)
522: SHFT(*fa,*fb,*fc,fu)
523: }
524: }
525:
526: /*************** linmin ************************/
527:
528: int ncom;
529: double *pcom,*xicom;
530: double (*nrfunc)(double []);
531:
532: void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))
533: {
534: double brent(double ax, double bx, double cx,
535: double (*f)(double), double tol, double *xmin);
536: double f1dim(double x);
537: void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,
538: double *fc, double (*func)(double));
539: int j;
540: double xx,xmin,bx,ax;
541: double fx,fb,fa;
542:
543: ncom=n;
544: pcom=vector(1,n);
545: xicom=vector(1,n);
546: nrfunc=func;
547: for (j=1;j<=n;j++) {
548: pcom[j]=p[j];
549: xicom[j]=xi[j];
550: }
551: ax=0.0;
552: xx=1.0;
553: mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim);
554: *fret=brent(ax,xx,bx,f1dim,TOL,&xmin);
555: #ifdef DEBUG
556: printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
557: #endif
558: for (j=1;j<=n;j++) {
559: xi[j] *= xmin;
560: p[j] += xi[j];
561: }
562: free_vector(xicom,1,n);
563: free_vector(pcom,1,n);
564: }
565:
566: /*************** powell ************************/
567: void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,
568: double (*func)(double []))
569: {
570: void linmin(double p[], double xi[], int n, double *fret,
571: double (*func)(double []));
572: int i,ibig,j;
573: double del,t,*pt,*ptt,*xit;
574: double fp,fptt;
575: double *xits;
576: pt=vector(1,n);
577: ptt=vector(1,n);
578: xit=vector(1,n);
579: xits=vector(1,n);
580: *fret=(*func)(p);
581: for (j=1;j<=n;j++) pt[j]=p[j];
582: for (*iter=1;;++(*iter)) {
583: fp=(*fret);
584: ibig=0;
585: del=0.0;
586: printf("\nPowell iter=%d -2*LL=%.12f",*iter,*fret);
587: for (i=1;i<=n;i++)
588: printf(" %d %.12f",i, p[i]);
589: printf("\n");
590: for (i=1;i<=n;i++) {
591: for (j=1;j<=n;j++) xit[j]=xi[j][i];
592: fptt=(*fret);
593: #ifdef DEBUG
594: printf("fret=%lf \n",*fret);
595: #endif
596: printf("%d",i);fflush(stdout);
597: linmin(p,xit,n,fret,func);
598: if (fabs(fptt-(*fret)) > del) {
599: del=fabs(fptt-(*fret));
600: ibig=i;
601: }
602: #ifdef DEBUG
603: printf("%d %.12e",i,(*fret));
604: for (j=1;j<=n;j++) {
605: xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
606: printf(" x(%d)=%.12e",j,xit[j]);
607: }
608: for(j=1;j<=n;j++)
609: printf(" p=%.12e",p[j]);
610: printf("\n");
611: #endif
612: }
613: if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {
614: #ifdef DEBUG
615: int k[2],l;
616: k[0]=1;
617: k[1]=-1;
618: printf("Max: %.12e",(*func)(p));
619: for (j=1;j<=n;j++)
620: printf(" %.12e",p[j]);
621: printf("\n");
622: for(l=0;l<=1;l++) {
623: for (j=1;j<=n;j++) {
624: ptt[j]=p[j]+(p[j]-pt[j])*k[l];
625: printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
626: }
627: printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
628: }
629: #endif
630:
631:
632: free_vector(xit,1,n);
633: free_vector(xits,1,n);
634: free_vector(ptt,1,n);
635: free_vector(pt,1,n);
636: return;
637: }
638: if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");
639: for (j=1;j<=n;j++) {
640: ptt[j]=2.0*p[j]-pt[j];
641: xit[j]=p[j]-pt[j];
642: pt[j]=p[j];
643: }
644: fptt=(*func)(ptt);
645: if (fptt < fp) {
646: t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt);
647: if (t < 0.0) {
648: linmin(p,xit,n,fret,func);
649: for (j=1;j<=n;j++) {
650: xi[j][ibig]=xi[j][n];
651: xi[j][n]=xit[j];
652: }
653: #ifdef DEBUG
654: printf("Direction changed last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
655: for(j=1;j<=n;j++)
656: printf(" %.12e",xit[j]);
657: printf("\n");
658: #endif
659: }
660: }
661: }
662: }
663:
664: /**** Prevalence limit ****************/
665:
666: double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)
667: {
668: /* Computes the prevalence limit in each live state at age x by left multiplying the unit
669: matrix by transitions matrix until convergence is reached */
670:
671: int i, ii,j,k;
672: double min, max, maxmin, maxmax,sumnew=0.;
673: double **matprod2();
674: double **out, cov[NCOVMAX], **pmij();
675: double **newm;
676: double agefin, delaymax=50 ; /* Max number of years to converge */
677:
678: for (ii=1;ii<=nlstate+ndeath;ii++)
679: for (j=1;j<=nlstate+ndeath;j++){
680: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
681: }
1.6 lievre 682:
683: cov[1]=1.;
684:
685: /* Even if hstepm = 1, at least one multiplication by the unit matrix */
1.2 lievre 686: for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
687: newm=savm;
688: /* Covariates have to be included here again */
1.6 lievre 689: cov[2]=agefin;
690:
691: for (k=1; k<=cptcovn;k++) {
1.7 lievre 692: cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
1.35 lievre 693: /* printf("ij=%d k=%d Tvar[k]=%d nbcode=%d cov=%lf codtab[ij][Tvar[k]]=%d \n",ij,k, Tvar[k],nbcode[Tvar[k]][codtab[ij][Tvar[k]]],cov[2+k], codtab[ij][Tvar[k]]);*/
1.6 lievre 694: }
1.35 lievre 695: for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
1.7 lievre 696: for (k=1; k<=cptcovprod;k++)
697: cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
698:
699: /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
700: /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
1.35 lievre 701: /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
1.2 lievre 702: out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);
703:
704: savm=oldm;
705: oldm=newm;
706: maxmax=0.;
707: for(j=1;j<=nlstate;j++){
708: min=1.;
709: max=0.;
710: for(i=1; i<=nlstate; i++) {
711: sumnew=0;
712: for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
713: prlim[i][j]= newm[i][j]/(1-sumnew);
714: max=FMAX(max,prlim[i][j]);
715: min=FMIN(min,prlim[i][j]);
716: }
717: maxmin=max-min;
718: maxmax=FMAX(maxmax,maxmin);
719: }
720: if(maxmax < ftolpl){
721: return prlim;
722: }
723: }
724: }
725:
1.12 lievre 726: /*************** transition probabilities ***************/
1.2 lievre 727:
728: double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
729: {
730: double s1, s2;
731: /*double t34;*/
732: int i,j,j1, nc, ii, jj;
733:
734: for(i=1; i<= nlstate; i++){
735: for(j=1; j<i;j++){
736: for (nc=1, s2=0.;nc <=ncovmodel; nc++){
737: /*s2 += param[i][j][nc]*cov[nc];*/
738: s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
739: /*printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2);*/
740: }
741: ps[i][j]=s2;
742: /*printf("s1=%.17e, s2=%.17e\n",s1,s2);*/
743: }
744: for(j=i+1; j<=nlstate+ndeath;j++){
745: for (nc=1, s2=0.;nc <=ncovmodel; nc++){
746: s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
747: /*printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2);*/
748: }
1.22 brouard 749: ps[i][j]=s2;
1.2 lievre 750: }
751: }
1.12 lievre 752: /*ps[3][2]=1;*/
753:
1.2 lievre 754: for(i=1; i<= nlstate; i++){
755: s1=0;
756: for(j=1; j<i; j++)
757: s1+=exp(ps[i][j]);
758: for(j=i+1; j<=nlstate+ndeath; j++)
759: s1+=exp(ps[i][j]);
760: ps[i][i]=1./(s1+1.);
761: for(j=1; j<i; j++)
762: ps[i][j]= exp(ps[i][j])*ps[i][i];
763: for(j=i+1; j<=nlstate+ndeath; j++)
764: ps[i][j]= exp(ps[i][j])*ps[i][i];
765: /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
766: } /* end i */
767:
768: for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
769: for(jj=1; jj<= nlstate+ndeath; jj++){
770: ps[ii][jj]=0;
771: ps[ii][ii]=1;
772: }
773: }
774:
1.12 lievre 775:
1.2 lievre 776: /* for(ii=1; ii<= nlstate+ndeath; ii++){
777: for(jj=1; jj<= nlstate+ndeath; jj++){
778: printf("%lf ",ps[ii][jj]);
779: }
780: printf("\n ");
781: }
782: printf("\n ");printf("%lf ",cov[2]);*/
783: /*
784: for(i=1; i<= npar; i++) printf("%f ",x[i]);
785: goto end;*/
786: return ps;
787: }
788:
789: /**************** Product of 2 matrices ******************/
790:
791: double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)
792: {
1.13 lievre 793: /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
1.2 lievre 794: b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
795: /* in, b, out are matrice of pointers which should have been initialized
796: before: only the contents of out is modified. The function returns
797: a pointer to pointers identical to out */
798: long i, j, k;
799: for(i=nrl; i<= nrh; i++)
800: for(k=ncolol; k<=ncoloh; k++)
801: for(j=ncl,out[i][k]=0.; j<=nch; j++)
802: out[i][k] +=in[i][j]*b[j][k];
803:
804: return out;
805: }
806:
807:
808: /************* Higher Matrix Product ***************/
809:
810: double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
811: {
812: /* Computes the transition matrix starting at age 'age' over 'nhstepm*hstepm*stepm' month
813: duration (i.e. until
814: age (in years) age+nhstepm*stepm/12) by multiplying nhstepm*hstepm matrices.
815: Output is stored in matrix po[i][j][h] for h every 'hstepm' step
816: (typically every 2 years instead of every month which is too big).
817: Model is determined by parameters x and covariates have to be
818: included manually here.
819:
820: */
821:
822: int i, j, d, h, k;
823: double **out, cov[NCOVMAX];
824: double **newm;
825:
826: /* Hstepm could be zero and should return the unit matrix */
827: for (i=1;i<=nlstate+ndeath;i++)
828: for (j=1;j<=nlstate+ndeath;j++){
829: oldm[i][j]=(i==j ? 1.0 : 0.0);
830: po[i][j][0]=(i==j ? 1.0 : 0.0);
831: }
832: /* Even if hstepm = 1, at least one multiplication by the unit matrix */
833: for(h=1; h <=nhstepm; h++){
834: for(d=1; d <=hstepm; d++){
835: newm=savm;
836: /* Covariates have to be included here again */
837: cov[1]=1.;
838: cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
1.7 lievre 839: for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
1.12 lievre 840: for (k=1; k<=cptcovage;k++)
1.7 lievre 841: cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
1.12 lievre 842: for (k=1; k<=cptcovprod;k++)
1.7 lievre 843: cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
844:
845:
1.2 lievre 846: /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
847: /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
848: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,
849: pmij(pmmij,cov,ncovmodel,x,nlstate));
850: savm=oldm;
851: oldm=newm;
852: }
853: for(i=1; i<=nlstate+ndeath; i++)
854: for(j=1;j<=nlstate+ndeath;j++) {
855: po[i][j][h]=newm[i][j];
856: /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);
857: */
858: }
859: } /* end h */
860: return po;
861: }
862:
863:
864: /*************** log-likelihood *************/
865: double func( double *x)
866: {
1.6 lievre 867: int i, ii, j, k, mi, d, kk;
1.2 lievre 868: double l, ll[NLSTATEMAX], cov[NCOVMAX];
869: double **out;
870: double sw; /* Sum of weights */
871: double lli; /* Individual log likelihood */
872: long ipmx;
873: /*extern weight */
874: /* We are differentiating ll according to initial status */
875: /* for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
876: /*for(i=1;i<imx;i++)
1.8 lievre 877: printf(" %d\n",s[4][i]);
1.2 lievre 878: */
1.6 lievre 879: cov[1]=1.;
1.2 lievre 880:
881: for(k=1; k<=nlstate; k++) ll[k]=0.;
882: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1.6 lievre 883: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
1.8 lievre 884: for(mi=1; mi<= wav[i]-1; mi++){
1.2 lievre 885: for (ii=1;ii<=nlstate+ndeath;ii++)
886: for (j=1;j<=nlstate+ndeath;j++) oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1.8 lievre 887: for(d=0; d<dh[mi][i]; d++){
888: newm=savm;
889: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
890: for (kk=1; kk<=cptcovage;kk++) {
891: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
892: }
893:
894: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
895: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
896: savm=oldm;
897: oldm=newm;
898:
899:
1.2 lievre 900: } /* end mult */
1.8 lievre 901:
1.2 lievre 902: lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);
903: /* printf(" %f ",out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/
904: ipmx +=1;
905: sw += weight[i];
906: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
907: } /* end of wave */
908: } /* end of individual */
909:
910: for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
911: /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
912: l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
913: return -l;
914: }
915:
916:
917: /*********** Maximum Likelihood Estimation ***************/
918:
919: void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
920: {
921: int i,j, iter;
922: double **xi,*delti;
923: double fret;
924: xi=matrix(1,npar,1,npar);
925: for (i=1;i<=npar;i++)
926: for (j=1;j<=npar;j++)
927: xi[i][j]=(i==j ? 1.0 : 0.0);
928: printf("Powell\n");
929: powell(p,xi,npar,ftol,&iter,&fret,func);
930:
931: printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));
1.21 lievre 932: fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
1.2 lievre 933:
934: }
935:
936: /**** Computes Hessian and covariance matrix ***/
937: void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
938: {
939: double **a,**y,*x,pd;
940: double **hess;
941: int i, j,jk;
942: int *indx;
943:
944: double hessii(double p[], double delta, int theta, double delti[]);
945: double hessij(double p[], double delti[], int i, int j);
946: void lubksb(double **a, int npar, int *indx, double b[]) ;
947: void ludcmp(double **a, int npar, int *indx, double *d) ;
948:
949: hess=matrix(1,npar,1,npar);
950:
951: printf("\nCalculation of the hessian matrix. Wait...\n");
952: for (i=1;i<=npar;i++){
953: printf("%d",i);fflush(stdout);
954: hess[i][i]=hessii(p,ftolhess,i,delti);
955: /*printf(" %f ",p[i]);*/
1.12 lievre 956: /*printf(" %lf ",hess[i][i]);*/
1.2 lievre 957: }
1.12 lievre 958:
1.2 lievre 959: for (i=1;i<=npar;i++) {
960: for (j=1;j<=npar;j++) {
961: if (j>i) {
962: printf(".%d%d",i,j);fflush(stdout);
963: hess[i][j]=hessij(p,delti,i,j);
1.12 lievre 964: hess[j][i]=hess[i][j];
965: /*printf(" %lf ",hess[i][j]);*/
1.2 lievre 966: }
967: }
968: }
969: printf("\n");
970:
971: printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
972:
973: a=matrix(1,npar,1,npar);
974: y=matrix(1,npar,1,npar);
975: x=vector(1,npar);
976: indx=ivector(1,npar);
977: for (i=1;i<=npar;i++)
978: for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
979: ludcmp(a,npar,indx,&pd);
980:
981: for (j=1;j<=npar;j++) {
982: for (i=1;i<=npar;i++) x[i]=0;
983: x[j]=1;
984: lubksb(a,npar,indx,x);
985: for (i=1;i<=npar;i++){
986: matcov[i][j]=x[i];
987: }
988: }
989:
990: printf("\n#Hessian matrix#\n");
991: for (i=1;i<=npar;i++) {
992: for (j=1;j<=npar;j++) {
993: printf("%.3e ",hess[i][j]);
994: }
995: printf("\n");
996: }
997:
998: /* Recompute Inverse */
999: for (i=1;i<=npar;i++)
1000: for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];
1001: ludcmp(a,npar,indx,&pd);
1002:
1003: /* printf("\n#Hessian matrix recomputed#\n");
1004:
1005: for (j=1;j<=npar;j++) {
1006: for (i=1;i<=npar;i++) x[i]=0;
1007: x[j]=1;
1008: lubksb(a,npar,indx,x);
1009: for (i=1;i<=npar;i++){
1010: y[i][j]=x[i];
1011: printf("%.3e ",y[i][j]);
1012: }
1013: printf("\n");
1014: }
1015: */
1016:
1017: free_matrix(a,1,npar,1,npar);
1018: free_matrix(y,1,npar,1,npar);
1019: free_vector(x,1,npar);
1020: free_ivector(indx,1,npar);
1021: free_matrix(hess,1,npar,1,npar);
1022:
1023:
1024: }
1025:
1026: /*************** hessian matrix ****************/
1027: double hessii( double x[], double delta, int theta, double delti[])
1028: {
1029: int i;
1030: int l=1, lmax=20;
1031: double k1,k2;
1032: double p2[NPARMAX+1];
1033: double res;
1034: double delt, delts, nkhi=10.,nkhif=1., khi=1.e-4;
1035: double fx;
1036: int k=0,kmax=10;
1037: double l1;
1038:
1039: fx=func(x);
1040: for (i=1;i<=npar;i++) p2[i]=x[i];
1041: for(l=0 ; l <=lmax; l++){
1042: l1=pow(10,l);
1043: delts=delt;
1044: for(k=1 ; k <kmax; k=k+1){
1045: delt = delta*(l1*k);
1046: p2[theta]=x[theta] +delt;
1047: k1=func(p2)-fx;
1048: p2[theta]=x[theta]-delt;
1049: k2=func(p2)-fx;
1050: /*res= (k1-2.0*fx+k2)/delt/delt; */
1051: res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */
1052:
1053: #ifdef DEBUG
1054: 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);
1055: #endif
1056: /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
1057: if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
1058: k=kmax;
1059: }
1060: else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
1061: k=kmax; l=lmax*10.;
1062: }
1063: else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){
1064: delts=delt;
1065: }
1066: }
1067: }
1068: delti[theta]=delts;
1.12 lievre 1069: return res;
1.3 lievre 1070:
1.2 lievre 1071: }
1072:
1073: double hessij( double x[], double delti[], int thetai,int thetaj)
1074: {
1075: int i;
1076: int l=1, l1, lmax=20;
1077: double k1,k2,k3,k4,res,fx;
1078: double p2[NPARMAX+1];
1079: int k;
1080:
1081: fx=func(x);
1082: for (k=1; k<=2; k++) {
1083: for (i=1;i<=npar;i++) p2[i]=x[i];
1084: p2[thetai]=x[thetai]+delti[thetai]/k;
1085: p2[thetaj]=x[thetaj]+delti[thetaj]/k;
1086: k1=func(p2)-fx;
1087:
1088: p2[thetai]=x[thetai]+delti[thetai]/k;
1089: p2[thetaj]=x[thetaj]-delti[thetaj]/k;
1090: k2=func(p2)-fx;
1091:
1092: p2[thetai]=x[thetai]-delti[thetai]/k;
1093: p2[thetaj]=x[thetaj]+delti[thetaj]/k;
1094: k3=func(p2)-fx;
1095:
1096: p2[thetai]=x[thetai]-delti[thetai]/k;
1097: p2[thetaj]=x[thetaj]-delti[thetaj]/k;
1098: k4=func(p2)-fx;
1099: res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */
1100: #ifdef DEBUG
1101: 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);
1102: #endif
1103: }
1104: return res;
1105: }
1106:
1107: /************** Inverse of matrix **************/
1108: void ludcmp(double **a, int n, int *indx, double *d)
1109: {
1110: int i,imax,j,k;
1111: double big,dum,sum,temp;
1112: double *vv;
1113:
1114: vv=vector(1,n);
1115: *d=1.0;
1116: for (i=1;i<=n;i++) {
1117: big=0.0;
1118: for (j=1;j<=n;j++)
1119: if ((temp=fabs(a[i][j])) > big) big=temp;
1120: if (big == 0.0) nrerror("Singular matrix in routine ludcmp");
1121: vv[i]=1.0/big;
1122: }
1123: for (j=1;j<=n;j++) {
1124: for (i=1;i<j;i++) {
1125: sum=a[i][j];
1126: for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];
1127: a[i][j]=sum;
1128: }
1129: big=0.0;
1130: for (i=j;i<=n;i++) {
1131: sum=a[i][j];
1132: for (k=1;k<j;k++)
1133: sum -= a[i][k]*a[k][j];
1134: a[i][j]=sum;
1135: if ( (dum=vv[i]*fabs(sum)) >= big) {
1136: big=dum;
1137: imax=i;
1138: }
1139: }
1140: if (j != imax) {
1141: for (k=1;k<=n;k++) {
1142: dum=a[imax][k];
1143: a[imax][k]=a[j][k];
1144: a[j][k]=dum;
1145: }
1146: *d = -(*d);
1147: vv[imax]=vv[j];
1148: }
1149: indx[j]=imax;
1150: if (a[j][j] == 0.0) a[j][j]=TINY;
1151: if (j != n) {
1152: dum=1.0/(a[j][j]);
1153: for (i=j+1;i<=n;i++) a[i][j] *= dum;
1154: }
1155: }
1156: free_vector(vv,1,n); /* Doesn't work */
1157: ;
1158: }
1159:
1160: void lubksb(double **a, int n, int *indx, double b[])
1161: {
1162: int i,ii=0,ip,j;
1163: double sum;
1164:
1165: for (i=1;i<=n;i++) {
1166: ip=indx[i];
1167: sum=b[ip];
1168: b[ip]=b[i];
1169: if (ii)
1170: for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];
1171: else if (sum) ii=i;
1172: b[i]=sum;
1173: }
1174: for (i=n;i>=1;i--) {
1175: sum=b[i];
1176: for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];
1177: b[i]=sum/a[i][i];
1178: }
1179: }
1180:
1181: /************ Frequencies ********************/
1.26 lievre 1182: void freqsummary(char fileres[], int agemin, int agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax,double **mint,double **anint, double dateprev1,double dateprev2,double jprev1, double mprev1,double anprev1,double jprev2, double mprev2,double anprev2)
1.2 lievre 1183: { /* Some frequencies */
1.35 lievre 1184:
1.18 lievre 1185: int i, m, jk, k1,i1, j1, bool, z1,z2,j;
1.2 lievre 1186: double ***freq; /* Frequencies */
1187: double *pp;
1.19 lievre 1188: double pos, k2, dateintsum=0,k2cpt=0;
1.2 lievre 1189: FILE *ficresp;
1190: char fileresp[FILENAMELENGTH];
1.35 lievre 1191:
1.2 lievre 1192: pp=vector(1,nlstate);
1.19 lievre 1193: probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
1.2 lievre 1194: strcpy(fileresp,"p");
1195: strcat(fileresp,fileres);
1196: if((ficresp=fopen(fileresp,"w"))==NULL) {
1197: printf("Problem with prevalence resultfile: %s\n", fileresp);
1198: exit(0);
1199: }
1200: freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);
1201: j1=0;
1.35 lievre 1202:
1.7 lievre 1203: j=cptcoveff;
1.2 lievre 1204: if (cptcovn<1) {j=1;ncodemax[1]=1;}
1.35 lievre 1205:
1.2 lievre 1206: for(k1=1; k1<=j;k1++){
1.35 lievre 1207: for(i1=1; i1<=ncodemax[k1];i1++){
1208: j1++;
1209: /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
1210: scanf("%d", i);*/
1211: for (i=-1; i<=nlstate+ndeath; i++)
1212: for (jk=-1; jk<=nlstate+ndeath; jk++)
1213: for(m=agemin; m <= agemax+3; m++)
1214: freq[i][jk][m]=0;
1215:
1216: dateintsum=0;
1217: k2cpt=0;
1218: for (i=1; i<=imx; i++) {
1219: bool=1;
1220: if (cptcovn>0) {
1221: for (z1=1; z1<=cptcoveff; z1++)
1222: if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])
1223: bool=0;
1224: }
1225: if (bool==1) {
1226: for(m=firstpass; m<=lastpass; m++){
1227: k2=anint[m][i]+(mint[m][i]/12.);
1228: if ((k2>=dateprev1) && (k2<=dateprev2)) {
1229: if(agev[m][i]==0) agev[m][i]=agemax+1;
1230: if(agev[m][i]==1) agev[m][i]=agemax+2;
1231: if (m<lastpass) {
1232: freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
1233: freq[s[m][i]][s[m+1][i]][(int) agemax+3] += weight[i];
1234: }
1235:
1236: if ((agev[m][i]>1) && (agev[m][i]< (agemax+3))) {
1237: dateintsum=dateintsum+k2;
1238: k2cpt++;
1239: }
1240: }
1241: }
1242: }
1243: }
1.26 lievre 1244:
1.35 lievre 1245: fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);
1.26 lievre 1246:
1.35 lievre 1247: if (cptcovn>0) {
1248: fprintf(ficresp, "\n#********** Variable ");
1249: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
1250: fprintf(ficresp, "**********\n#");
1251: }
1252: for(i=1; i<=nlstate;i++)
1253: fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
1254: fprintf(ficresp, "\n");
1255:
1256: for(i=(int)agemin; i <= (int)agemax+3; i++){
1257: if(i==(int)agemax+3)
1258: printf("Total");
1259: else
1260: printf("Age %d", i);
1261: for(jk=1; jk <=nlstate ; jk++){
1262: for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
1263: pp[jk] += freq[jk][m][i];
1264: }
1265: for(jk=1; jk <=nlstate ; jk++){
1266: for(m=-1, pos=0; m <=0 ; m++)
1267: pos += freq[jk][m][i];
1268: if(pp[jk]>=1.e-10)
1269: printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
1270: else
1271: printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
1272: }
1.14 lievre 1273:
1.35 lievre 1274: for(jk=1; jk <=nlstate ; jk++){
1275: for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
1276: pp[jk] += freq[jk][m][i];
1277: }
1.14 lievre 1278:
1.35 lievre 1279: for(jk=1,pos=0; jk <=nlstate ; jk++)
1280: pos += pp[jk];
1281: for(jk=1; jk <=nlstate ; jk++){
1282: if(pos>=1.e-5)
1283: printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
1284: else
1285: printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
1286: if( i <= (int) agemax){
1287: if(pos>=1.e-5){
1288: fprintf(ficresp," %d %.5f %.0f %.0f",i,pp[jk]/pos, pp[jk],pos);
1289: probs[i][jk][j1]= pp[jk]/pos;
1290: /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/
1291: }
1292: else
1293: fprintf(ficresp," %d NaNq %.0f %.0f",i,pp[jk],pos);
1294: }
1.13 lievre 1295: }
1.35 lievre 1296:
1297: for(jk=-1; jk <=nlstate+ndeath; jk++)
1298: for(m=-1; m <=nlstate+ndeath; m++)
1299: if(freq[jk][m][i] !=0 ) printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
1300: if(i <= (int) agemax)
1301: fprintf(ficresp,"\n");
1302: printf("\n");
1.2 lievre 1303: }
1304: }
1.35 lievre 1305: }
1.19 lievre 1306: dateintmean=dateintsum/k2cpt;
1.2 lievre 1307:
1308: fclose(ficresp);
1309: free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);
1310: free_vector(pp,1,nlstate);
1.35 lievre 1311:
1.19 lievre 1312: /* End of Freq */
1313: }
1.2 lievre 1314:
1.15 lievre 1315: /************ Prevalence ********************/
1.28 lievre 1316: void prevalence(int agemin, float agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax,double **mint,double **anint, double dateprev1,double dateprev2, double calagedate)
1.15 lievre 1317: { /* Some frequencies */
1318:
1319: int i, m, jk, k1, i1, j1, bool, z1,z2,j;
1320: double ***freq; /* Frequencies */
1321: double *pp;
1.18 lievre 1322: double pos, k2;
1.15 lievre 1323:
1324: pp=vector(1,nlstate);
1.19 lievre 1325: probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
1.15 lievre 1326:
1327: freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);
1328: j1=0;
1329:
1330: j=cptcoveff;
1331: if (cptcovn<1) {j=1;ncodemax[1]=1;}
1332:
1.42 brouard 1333: for(k1=1; k1<=j;k1++){
1.15 lievre 1334: for(i1=1; i1<=ncodemax[k1];i1++){
1335: j1++;
1.42 brouard 1336:
1.15 lievre 1337: for (i=-1; i<=nlstate+ndeath; i++)
1338: for (jk=-1; jk<=nlstate+ndeath; jk++)
1339: for(m=agemin; m <= agemax+3; m++)
1.19 lievre 1340: freq[i][jk][m]=0;
1.28 lievre 1341:
1.15 lievre 1342: for (i=1; i<=imx; i++) {
1343: bool=1;
1344: if (cptcovn>0) {
1345: for (z1=1; z1<=cptcoveff; z1++)
1346: if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])
1347: bool=0;
1.28 lievre 1348: }
1.19 lievre 1349: if (bool==1) {
1350: for(m=firstpass; m<=lastpass; m++){
1351: k2=anint[m][i]+(mint[m][i]/12.);
1352: if ((k2>=dateprev1) && (k2<=dateprev2)) {
1.18 lievre 1353: if(agev[m][i]==0) agev[m][i]=agemax+1;
1354: if(agev[m][i]==1) agev[m][i]=agemax+2;
1.42 brouard 1355: if (m<lastpass) {
1356: if (calagedate>0)
1357: freq[s[m][i]][s[m+1][i]][(int)(agev[m][i]+1-((int)calagedate %12)/12.)] += weight[i];
1358: else
1359: freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
1360: freq[s[m][i]][s[m+1][i]][(int)(agemax+3)] += weight[i];
1361: }
1.18 lievre 1362: }
1.15 lievre 1363: }
1364: }
1365: }
1.42 brouard 1366: for(i=(int)agemin; i <= (int)agemax+3; i++){
1367: for(jk=1; jk <=nlstate ; jk++){
1368: for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
1369: pp[jk] += freq[jk][m][i];
1370: }
1371: for(jk=1; jk <=nlstate ; jk++){
1372: for(m=-1, pos=0; m <=0 ; m++)
1.15 lievre 1373: pos += freq[jk][m][i];
1374: }
1375:
1.42 brouard 1376: for(jk=1; jk <=nlstate ; jk++){
1377: for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
1378: pp[jk] += freq[jk][m][i];
1379: }
1380:
1381: for(jk=1,pos=0; jk <=nlstate ; jk++) pos += pp[jk];
1382:
1383: for(jk=1; jk <=nlstate ; jk++){
1384: if( i <= (int) agemax){
1385: if(pos>=1.e-5){
1386: probs[i][jk][j1]= pp[jk]/pos;
1387: }
1388: }
1.18 lievre 1389: }
1.42 brouard 1390:
1391: }
1.15 lievre 1392: }
1393: }
1.41 lievre 1394:
1.15 lievre 1395:
1396: free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);
1397: free_vector(pp,1,nlstate);
1398:
1399: } /* End of Freq */
1.19 lievre 1400:
1.2 lievre 1401: /************* Waves Concatenation ***************/
1402:
1403: void concatwav(int wav[], int **dh, int **mw, int **s, double *agedc, double **agev, int firstpass, int lastpass, int imx, int nlstate, int stepm)
1404: {
1405: /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
1406: Death is a valid wave (if date is known).
1407: mw[mi][i] is the mi (mi=1 to wav[i]) effective wave of individual i
1408: dh[m][i] of dh[mw[mi][i][i] is the delay between two effective waves m=mw[mi][i]
1409: and mw[mi+1][i]. dh depends on stepm.
1410: */
1411:
1412: int i, mi, m;
1.8 lievre 1413: /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
1414: double sum=0., jmean=0.;*/
1.2 lievre 1415:
1.11 lievre 1416: int j, k=0,jk, ju, jl;
1417: double sum=0.;
1418: jmin=1e+5;
1419: jmax=-1;
1420: jmean=0.;
1.2 lievre 1421: for(i=1; i<=imx; i++){
1422: mi=0;
1423: m=firstpass;
1424: while(s[m][i] <= nlstate){
1425: if(s[m][i]>=1)
1426: mw[++mi][i]=m;
1427: if(m >=lastpass)
1428: break;
1429: else
1430: m++;
1431: }/* end while */
1432: if (s[m][i] > nlstate){
1433: mi++; /* Death is another wave */
1434: /* if(mi==0) never been interviewed correctly before death */
1435: /* Only death is a correct wave */
1436: mw[mi][i]=m;
1437: }
1438:
1439: wav[i]=mi;
1440: if(mi==0)
1441: printf("Warning, no any valid information for:%d line=%d\n",num[i],i);
1442: }
1443:
1444: for(i=1; i<=imx; i++){
1445: for(mi=1; mi<wav[i];mi++){
1446: if (stepm <=0)
1447: dh[mi][i]=1;
1448: else{
1449: if (s[mw[mi+1][i]][i] > nlstate) {
1.10 lievre 1450: if (agedc[i] < 2*AGESUP) {
1.2 lievre 1451: j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);
1.8 lievre 1452: if(j==0) j=1; /* Survives at least one month after exam */
1453: k=k+1;
1454: if (j >= jmax) jmax=j;
1.11 lievre 1455: if (j <= jmin) jmin=j;
1.8 lievre 1456: sum=sum+j;
1.30 lievre 1457: /*if (j<0) printf("j=%d num=%d \n",j,i); */
1.10 lievre 1458: }
1.2 lievre 1459: }
1460: else{
1461: j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
1462: k=k+1;
1463: if (j >= jmax) jmax=j;
1464: else if (j <= jmin)jmin=j;
1.30 lievre 1465: /* if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
1.2 lievre 1466: sum=sum+j;
1467: }
1468: jk= j/stepm;
1469: jl= j -jk*stepm;
1470: ju= j -(jk+1)*stepm;
1471: if(jl <= -ju)
1472: dh[mi][i]=jk;
1473: else
1474: dh[mi][i]=jk+1;
1475: if(dh[mi][i]==0)
1476: dh[mi][i]=1; /* At least one step */
1477: }
1478: }
1479: }
1.8 lievre 1480: jmean=sum/k;
1481: printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);
1.12 lievre 1482: }
1.2 lievre 1483: /*********** Tricode ****************************/
1484: void tricode(int *Tvar, int **nbcode, int imx)
1485: {
1.7 lievre 1486: int Ndum[20],ij=1, k, j, i;
1.2 lievre 1487: int cptcode=0;
1.7 lievre 1488: cptcoveff=0;
1489:
1490: for (k=0; k<19; k++) Ndum[k]=0;
1.2 lievre 1491: for (k=1; k<=7; k++) ncodemax[k]=0;
1.6 lievre 1492:
1.7 lievre 1493: for (j=1; j<=(cptcovn+2*cptcovprod); j++) {
1.2 lievre 1494: for (i=1; i<=imx; i++) {
1495: ij=(int)(covar[Tvar[j]][i]);
1496: Ndum[ij]++;
1.8 lievre 1497: /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
1.2 lievre 1498: if (ij > cptcode) cptcode=ij;
1499: }
1.7 lievre 1500:
1.2 lievre 1501: for (i=0; i<=cptcode; i++) {
1502: if(Ndum[i]!=0) ncodemax[j]++;
1503: }
1504: ij=1;
1.7 lievre 1505:
1.8 lievre 1506:
1.2 lievre 1507: for (i=1; i<=ncodemax[j]; i++) {
1.7 lievre 1508: for (k=0; k<=19; k++) {
1.2 lievre 1509: if (Ndum[k] != 0) {
1510: nbcode[Tvar[j]][ij]=k;
1.39 lievre 1511:
1.2 lievre 1512: ij++;
1513: }
1514: if (ij > ncodemax[j]) break;
1515: }
1516: }
1.7 lievre 1517: }
1.8 lievre 1518:
1519: for (k=0; k<19; k++) Ndum[k]=0;
1520:
1.12 lievre 1521: for (i=1; i<=ncovmodel-2; i++) {
1.7 lievre 1522: ij=Tvar[i];
1523: Ndum[ij]++;
1524: }
1.8 lievre 1525:
1.7 lievre 1526: ij=1;
1.8 lievre 1527: for (i=1; i<=10; i++) {
1.34 brouard 1528: if((Ndum[i]!=0) && (i<=ncovcol)){
1.8 lievre 1529: Tvaraff[ij]=i;
1530: ij++;
1.7 lievre 1531: }
1532: }
1533:
1.8 lievre 1534: cptcoveff=ij-1;
1.6 lievre 1535: }
1.2 lievre 1536:
1537: /*********** Health Expectancies ****************/
1538:
1.41 lievre 1539: 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 )
1540:
1.2 lievre 1541: {
1542: /* Health expectancies */
1.41 lievre 1543: int i, j, nhstepm, hstepm, h, nstepm, k, cptj;
1.35 lievre 1544: double age, agelim, hf;
1.41 lievre 1545: double ***p3mat,***varhe;
1546: double **dnewm,**doldm;
1547: double *xp;
1548: double **gp, **gm;
1549: double ***gradg, ***trgradg;
1550: int theta;
1551:
1552: varhe=ma3x(1,nlstate*2,1,nlstate*2,(int) bage, (int) fage);
1553: xp=vector(1,npar);
1554: dnewm=matrix(1,nlstate*2,1,npar);
1555: doldm=matrix(1,nlstate*2,1,nlstate*2);
1.2 lievre 1556:
1557: fprintf(ficreseij,"# Health expectancies\n");
1558: fprintf(ficreseij,"# Age");
1559: for(i=1; i<=nlstate;i++)
1560: for(j=1; j<=nlstate;j++)
1.41 lievre 1561: fprintf(ficreseij," %1d-%1d (SE)",i,j);
1.2 lievre 1562: fprintf(ficreseij,"\n");
1563:
1.36 brouard 1564: if(estepm < stepm){
1565: printf ("Problem %d lower than %d\n",estepm, stepm);
1566: }
1567: else hstepm=estepm;
1568: /* We compute the life expectancy from trapezoids spaced every estepm months
1569: * This is mainly to measure the difference between two models: for example
1570: * if stepm=24 months pijx are given only every 2 years and by summing them
1571: * we are calculating an estimate of the Life Expectancy assuming a linear
1572: * progression inbetween and thus overestimating or underestimating according
1573: * to the curvature of the survival function. If, for the same date, we
1574: * estimate the model with stepm=1 month, we can keep estepm to 24 months
1575: * to compare the new estimate of Life expectancy with the same linear
1576: * hypothesis. A more precise result, taking into account a more precise
1577: * curvature will be obtained if estepm is as small as stepm. */
1578:
1579: /* For example we decided to compute the life expectancy with the smallest unit */
1.31 brouard 1580: /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
1581: nhstepm is the number of hstepm from age to agelim
1582: nstepm is the number of stepm from age to agelin.
1583: Look at hpijx to understand the reason of that which relies in memory size
1.36 brouard 1584: and note for a fixed period like estepm months */
1.31 brouard 1585: /* We decided (b) to get a life expectancy respecting the most precise curvature of the
1.32 brouard 1586: survival function given by stepm (the optimization length). Unfortunately it
1.31 brouard 1587: means that if the survival funtion is printed only each two years of age and if
1588: you sum them up and add 1 year (area under the trapezoids) you won't get the same
1589: results. So we changed our mind and took the option of the best precision.
1590: */
1.36 brouard 1591: hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
1.2 lievre 1592:
1593: agelim=AGESUP;
1594: for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
1595: /* nhstepm age range expressed in number of stepm */
1.31 brouard 1596: nstepm=(int) rint((agelim-age)*YEARM/stepm);
1597: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
1.33 brouard 1598: /* if (stepm >= YEARM) hstepm=1;*/
1.31 brouard 1599: nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
1.2 lievre 1600: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
1.41 lievre 1601: gradg=ma3x(0,nhstepm,1,npar,1,nlstate*2);
1602: gp=matrix(0,nhstepm,1,nlstate*2);
1603: gm=matrix(0,nhstepm,1,nlstate*2);
1604:
1.2 lievre 1605: /* Computed by stepm unit matrices, product of hstepm matrices, stored
1606: in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
1607: hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);
1.41 lievre 1608:
1609:
1610: hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
1611:
1612: /* Computing Variances of health expectancies */
1613:
1614: for(theta=1; theta <=npar; theta++){
1615: for(i=1; i<=npar; i++){
1616: xp[i] = x[i] + (i==theta ?delti[theta]:0);
1617: }
1618: hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
1.39 lievre 1619:
1.41 lievre 1620: cptj=0;
1621: for(j=1; j<= nlstate; j++){
1622: for(i=1; i<=nlstate; i++){
1623: cptj=cptj+1;
1624: for(h=0, gp[h][cptj]=0.; h<=nhstepm-1; h++){
1625: gp[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;
1626: }
1627: }
1628: }
1629:
1630:
1631: for(i=1; i<=npar; i++)
1632: xp[i] = x[i] - (i==theta ?delti[theta]:0);
1633: hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
1634:
1635: cptj=0;
1636: for(j=1; j<= nlstate; j++){
1637: for(i=1;i<=nlstate;i++){
1638: cptj=cptj+1;
1639: for(h=0, gm[h][cptj]=0.; h<=nhstepm-1; h++){
1640: gm[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;
1641: }
1642: }
1643: }
1644: for(j=1; j<= nlstate*2; j++)
1645: for(h=0; h<=nhstepm-1; h++){
1646: gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
1647: }
1648: }
1649:
1650: /* End theta */
1651:
1652: trgradg =ma3x(0,nhstepm,1,nlstate*2,1,npar);
1653:
1654: for(h=0; h<=nhstepm-1; h++)
1655: for(j=1; j<=nlstate*2;j++)
1656: for(theta=1; theta <=npar; theta++)
1.46 ! brouard 1657: trgradg[h][j][theta]=gradg[h][theta][j];
! 1658:
1.41 lievre 1659:
1660: for(i=1;i<=nlstate*2;i++)
1661: for(j=1;j<=nlstate*2;j++)
1662: varhe[i][j][(int)age] =0.;
1663:
1.43 brouard 1664: printf("%d|",(int)age);fflush(stdout);
1.46 ! brouard 1665: for(h=0;h<=nhstepm-1;h++){
1.41 lievre 1666: for(k=0;k<=nhstepm-1;k++){
1667: matprod2(dnewm,trgradg[h],1,nlstate*2,1,npar,1,npar,matcov);
1668: matprod2(doldm,dnewm,1,nlstate*2,1,npar,1,nlstate*2,gradg[k]);
1669: for(i=1;i<=nlstate*2;i++)
1670: for(j=1;j<=nlstate*2;j++)
1671: varhe[i][j][(int)age] += doldm[i][j]*hf*hf;
1672: }
1673: }
1674:
1675:
1676: /* Computing expectancies */
1.2 lievre 1677: for(i=1; i<=nlstate;i++)
1678: for(j=1; j<=nlstate;j++)
1.29 lievre 1679: for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
1.31 brouard 1680: eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
1.41 lievre 1681:
1682: /* 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]);*/
1683:
1.2 lievre 1684: }
1.41 lievre 1685:
1.29 lievre 1686: fprintf(ficreseij,"%3.0f",age );
1.41 lievre 1687: cptj=0;
1.29 lievre 1688: for(i=1; i<=nlstate;i++)
1689: for(j=1; j<=nlstate;j++){
1.41 lievre 1690: cptj++;
1691: fprintf(ficreseij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[cptj][cptj][(int)age]) );
1.2 lievre 1692: }
1693: fprintf(ficreseij,"\n");
1.41 lievre 1694:
1695: free_matrix(gm,0,nhstepm,1,nlstate*2);
1696: free_matrix(gp,0,nhstepm,1,nlstate*2);
1697: free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*2);
1698: free_ma3x(trgradg,0,nhstepm,1,nlstate*2,1,npar);
1.2 lievre 1699: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
1700: }
1.41 lievre 1701: free_vector(xp,1,npar);
1702: free_matrix(dnewm,1,nlstate*2,1,npar);
1703: free_matrix(doldm,1,nlstate*2,1,nlstate*2);
1704: free_ma3x(varhe,1,nlstate*2,1,nlstate*2,(int) bage, (int)fage);
1.2 lievre 1705: }
1706:
1707: /************ Variance ******************/
1.36 brouard 1708: void varevsij(char fileres[], double ***vareij, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij, int estepm)
1.2 lievre 1709: {
1710: /* Variance of health expectancies */
1711: /* double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
1712: double **newm;
1713: double **dnewm,**doldm;
1.36 brouard 1714: int i, j, nhstepm, hstepm, h, nstepm ;
1.2 lievre 1715: int k, cptcode;
1.12 lievre 1716: double *xp;
1.2 lievre 1717: double **gp, **gm;
1718: double ***gradg, ***trgradg;
1719: double ***p3mat;
1.35 lievre 1720: double age,agelim, hf;
1.2 lievre 1721: int theta;
1722:
1.43 brouard 1723: fprintf(ficresvij,"# Variance and covariance of health expectancies e.j \n# (weighted average of eij where weights are the stable prevalence in health states i\n");
1.2 lievre 1724: fprintf(ficresvij,"# Age");
1725: for(i=1; i<=nlstate;i++)
1726: for(j=1; j<=nlstate;j++)
1727: fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);
1728: fprintf(ficresvij,"\n");
1729:
1730: xp=vector(1,npar);
1731: dnewm=matrix(1,nlstate,1,npar);
1732: doldm=matrix(1,nlstate,1,nlstate);
1733:
1.36 brouard 1734: if(estepm < stepm){
1735: printf ("Problem %d lower than %d\n",estepm, stepm);
1736: }
1737: else hstepm=estepm;
1738: /* For example we decided to compute the life expectancy with the smallest unit */
1.35 lievre 1739: /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
1740: nhstepm is the number of hstepm from age to agelim
1741: nstepm is the number of stepm from age to agelin.
1742: Look at hpijx to understand the reason of that which relies in memory size
1743: and note for a fixed period like k years */
1744: /* We decided (b) to get a life expectancy respecting the most precise curvature of the
1745: survival function given by stepm (the optimization length). Unfortunately it
1746: means that if the survival funtion is printed only each two years of age and if
1747: you sum them up and add 1 year (area under the trapezoids) you won't get the same
1748: results. So we changed our mind and took the option of the best precision.
1749: */
1.36 brouard 1750: hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
1.2 lievre 1751: agelim = AGESUP;
1752: for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
1.35 lievre 1753: nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
1754: nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
1.2 lievre 1755: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
1756: gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
1757: gp=matrix(0,nhstepm,1,nlstate);
1758: gm=matrix(0,nhstepm,1,nlstate);
1759:
1760: for(theta=1; theta <=npar; theta++){
1761: for(i=1; i<=npar; i++){ /* Computes gradient */
1762: xp[i] = x[i] + (i==theta ?delti[theta]:0);
1763: }
1764: hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
1765: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
1.14 lievre 1766:
1767: if (popbased==1) {
1768: for(i=1; i<=nlstate;i++)
1769: prlim[i][i]=probs[(int)age][i][ij];
1770: }
1.26 lievre 1771:
1.2 lievre 1772: for(j=1; j<= nlstate; j++){
1773: for(h=0; h<=nhstepm; h++){
1774: for(i=1, gp[h][j]=0.;i<=nlstate;i++)
1775: gp[h][j] += prlim[i][i]*p3mat[i][j][h];
1776: }
1777: }
1778:
1779: for(i=1; i<=npar; i++) /* Computes gradient */
1780: xp[i] = x[i] - (i==theta ?delti[theta]:0);
1781: hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
1782: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
1.26 lievre 1783:
1.14 lievre 1784: if (popbased==1) {
1785: for(i=1; i<=nlstate;i++)
1786: prlim[i][i]=probs[(int)age][i][ij];
1787: }
1788:
1.2 lievre 1789: for(j=1; j<= nlstate; j++){
1790: for(h=0; h<=nhstepm; h++){
1791: for(i=1, gm[h][j]=0.;i<=nlstate;i++)
1792: gm[h][j] += prlim[i][i]*p3mat[i][j][h];
1793: }
1794: }
1.14 lievre 1795:
1.2 lievre 1796: for(j=1; j<= nlstate; j++)
1797: for(h=0; h<=nhstepm; h++){
1798: gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
1799: }
1800: } /* End theta */
1801:
1802: trgradg =ma3x(0,nhstepm,1,nlstate,1,npar);
1803:
1804: for(h=0; h<=nhstepm; h++)
1805: for(j=1; j<=nlstate;j++)
1806: for(theta=1; theta <=npar; theta++)
1807: trgradg[h][j][theta]=gradg[h][theta][j];
1808:
1.35 lievre 1809: hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
1.2 lievre 1810: for(i=1;i<=nlstate;i++)
1811: for(j=1;j<=nlstate;j++)
1812: vareij[i][j][(int)age] =0.;
1.35 lievre 1813:
1.2 lievre 1814: for(h=0;h<=nhstepm;h++){
1815: for(k=0;k<=nhstepm;k++){
1816: matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
1817: matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
1818: for(i=1;i<=nlstate;i++)
1819: for(j=1;j<=nlstate;j++)
1.35 lievre 1820: vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
1.2 lievre 1821: }
1822: }
1.35 lievre 1823:
1.2 lievre 1824: fprintf(ficresvij,"%.0f ",age );
1825: for(i=1; i<=nlstate;i++)
1826: for(j=1; j<=nlstate;j++){
1.35 lievre 1827: fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
1.2 lievre 1828: }
1829: fprintf(ficresvij,"\n");
1830: free_matrix(gp,0,nhstepm,1,nlstate);
1831: free_matrix(gm,0,nhstepm,1,nlstate);
1832: free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
1833: free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
1834: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
1835: } /* End age */
1.26 lievre 1836:
1.2 lievre 1837: free_vector(xp,1,npar);
1838: free_matrix(doldm,1,nlstate,1,npar);
1839: free_matrix(dnewm,1,nlstate,1,nlstate);
1840:
1841: }
1842:
1843: /************ Variance of prevlim ******************/
1844: 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)
1845: {
1846: /* Variance of prevalence limit */
1847: /* double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
1848: double **newm;
1849: double **dnewm,**doldm;
1850: int i, j, nhstepm, hstepm;
1851: int k, cptcode;
1852: double *xp;
1853: double *gp, *gm;
1854: double **gradg, **trgradg;
1855: double age,agelim;
1856: int theta;
1857:
1.43 brouard 1858: fprintf(ficresvpl,"# Standard deviation of prevalence's limit\n");
1.2 lievre 1859: fprintf(ficresvpl,"# Age");
1860: for(i=1; i<=nlstate;i++)
1861: fprintf(ficresvpl," %1d-%1d",i,i);
1862: fprintf(ficresvpl,"\n");
1863:
1864: xp=vector(1,npar);
1865: dnewm=matrix(1,nlstate,1,npar);
1866: doldm=matrix(1,nlstate,1,nlstate);
1867:
1868: hstepm=1*YEARM; /* Every year of age */
1869: hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */
1870: agelim = AGESUP;
1871: for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
1872: nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
1873: if (stepm >= YEARM) hstepm=1;
1874: nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
1875: gradg=matrix(1,npar,1,nlstate);
1876: gp=vector(1,nlstate);
1877: gm=vector(1,nlstate);
1878:
1879: for(theta=1; theta <=npar; theta++){
1880: for(i=1; i<=npar; i++){ /* Computes gradient */
1881: xp[i] = x[i] + (i==theta ?delti[theta]:0);
1882: }
1883: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
1884: for(i=1;i<=nlstate;i++)
1885: gp[i] = prlim[i][i];
1886:
1887: for(i=1; i<=npar; i++) /* Computes gradient */
1888: xp[i] = x[i] - (i==theta ?delti[theta]:0);
1889: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
1890: for(i=1;i<=nlstate;i++)
1891: gm[i] = prlim[i][i];
1892:
1893: for(i=1;i<=nlstate;i++)
1894: gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
1895: } /* End theta */
1896:
1897: trgradg =matrix(1,nlstate,1,npar);
1898:
1899: for(j=1; j<=nlstate;j++)
1900: for(theta=1; theta <=npar; theta++)
1901: trgradg[j][theta]=gradg[theta][j];
1902:
1903: for(i=1;i<=nlstate;i++)
1904: varpl[i][(int)age] =0.;
1905: matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
1906: matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
1907: for(i=1;i<=nlstate;i++)
1908: varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
1909:
1910: fprintf(ficresvpl,"%.0f ",age );
1911: for(i=1; i<=nlstate;i++)
1912: fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
1913: fprintf(ficresvpl,"\n");
1914: free_vector(gp,1,nlstate);
1915: free_vector(gm,1,nlstate);
1916: free_matrix(gradg,1,npar,1,nlstate);
1917: free_matrix(trgradg,1,nlstate,1,npar);
1918: } /* End age */
1919:
1920: free_vector(xp,1,npar);
1921: free_matrix(doldm,1,nlstate,1,npar);
1922: free_matrix(dnewm,1,nlstate,1,nlstate);
1923:
1924: }
1925:
1.13 lievre 1926: /************ Variance of one-step probabilities ******************/
1.39 lievre 1927: void varprob(char fileres[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij, int *Tvar, int **nbcode, int *ncodemax)
1.13 lievre 1928: {
1.39 lievre 1929: int i, j, i1, k1, j1, z1;
1.46 ! brouard 1930: int k=0,l, cptcode;
1.13 lievre 1931: double **dnewm,**doldm;
1932: double *xp;
1933: double *gp, *gm;
1934: double **gradg, **trgradg;
1935: double age,agelim, cov[NCOVMAX];
1936: int theta;
1937: char fileresprob[FILENAMELENGTH];
1.46 ! brouard 1938: char fileresprobcov[FILENAMELENGTH];
! 1939: char fileresprobcor[FILENAMELENGTH];
1.13 lievre 1940:
1941: strcpy(fileresprob,"prob");
1942: strcat(fileresprob,fileres);
1943: if((ficresprob=fopen(fileresprob,"w"))==NULL) {
1944: printf("Problem with resultfile: %s\n", fileresprob);
1945: }
1.46 ! brouard 1946: strcpy(fileresprobcov,"probcov");
! 1947: strcat(fileresprobcov,fileres);
! 1948: if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
! 1949: printf("Problem with resultfile: %s\n", fileresprobcov);
! 1950: }
! 1951: strcpy(fileresprobcor,"probcor");
! 1952: strcat(fileresprobcor,fileres);
! 1953: if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
! 1954: printf("Problem with resultfile: %s\n", fileresprobcor);
! 1955: }
1.41 lievre 1956: printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
1.46 ! brouard 1957: printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
! 1958: printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
1.13 lievre 1959:
1.46 ! brouard 1960: fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
1.41 lievre 1961: fprintf(ficresprob,"# Age");
1.46 ! brouard 1962: fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
! 1963: fprintf(ficresprobcov,"# Age");
! 1964: fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
! 1965: fprintf(ficresprobcov,"# Age");
1.41 lievre 1966: for(i=1; i<=nlstate;i++)
1.46 ! brouard 1967: for(j=1; j<=(nlstate+ndeath);j++){
1.41 lievre 1968: fprintf(ficresprob," p%1d-%1d (SE)",i,j);
1.46 ! brouard 1969: fprintf(ficresprobcov," p%1d-%1d ",i,j);
! 1970: fprintf(ficresprobcor," p%1d-%1d ",i,j);
! 1971: }
1.41 lievre 1972: fprintf(ficresprob,"\n");
1.46 ! brouard 1973: fprintf(ficresprobcov,"\n");
! 1974: fprintf(ficresprobcor,"\n");
1.13 lievre 1975: xp=vector(1,npar);
1976: dnewm=matrix(1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
1977: doldm=matrix(1,(nlstate+ndeath)*(nlstate+ndeath),1,(nlstate+ndeath)*(nlstate+ndeath));
1978:
1979: cov[1]=1;
1.39 lievre 1980: j=cptcoveff;
1981: if (cptcovn<1) {j=1;ncodemax[1]=1;}
1982: j1=0;
1983: for(k1=1; k1<=1;k1++){
1984: for(i1=1; i1<=ncodemax[k1];i1++){
1985: j1++;
1986:
1987: if (cptcovn>0) {
1988: fprintf(ficresprob, "\n#********** Variable ");
1.46 ! brouard 1989: fprintf(ficresprobcov, "\n#********** Variable ");
! 1990: fprintf(ficresprobcor, "\n#********** Variable ");
1.39 lievre 1991: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
1992: fprintf(ficresprob, "**********\n#");
1.46 ! brouard 1993: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
! 1994: fprintf(ficresprobcov, "**********\n#");
! 1995: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
! 1996: fprintf(ficresprobcor, "**********\n#");
1.39 lievre 1997: }
1.13 lievre 1998:
1.39 lievre 1999: for (age=bage; age<=fage; age ++){
2000: cov[2]=age;
2001: for (k=1; k<=cptcovn;k++) {
2002: cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];
1.13 lievre 2003: }
1.39 lievre 2004: for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
2005: for (k=1; k<=cptcovprod;k++)
2006: cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
2007:
2008: gradg=matrix(1,npar,1,9);
2009: trgradg=matrix(1,9,1,npar);
2010: gp=vector(1,(nlstate+ndeath)*(nlstate+ndeath));
2011: gm=vector(1,(nlstate+ndeath)*(nlstate+ndeath));
2012:
2013: for(theta=1; theta <=npar; theta++){
2014: for(i=1; i<=npar; i++)
2015: xp[i] = x[i] + (i==theta ?delti[theta]:0);
2016:
2017: pmij(pmmij,cov,ncovmodel,xp,nlstate);
2018:
2019: k=0;
2020: for(i=1; i<= (nlstate+ndeath); i++){
2021: for(j=1; j<=(nlstate+ndeath);j++){
2022: k=k+1;
2023: gp[k]=pmmij[i][j];
2024: }
2025: }
2026:
2027: for(i=1; i<=npar; i++)
2028: xp[i] = x[i] - (i==theta ?delti[theta]:0);
1.13 lievre 2029:
1.39 lievre 2030: pmij(pmmij,cov,ncovmodel,xp,nlstate);
2031: k=0;
2032: for(i=1; i<=(nlstate+ndeath); i++){
2033: for(j=1; j<=(nlstate+ndeath);j++){
2034: k=k+1;
2035: gm[k]=pmmij[i][j];
2036: }
2037: }
2038:
2039: for(i=1; i<= (nlstate+ndeath)*(nlstate+ndeath); i++)
2040: gradg[theta][i]=(gp[i]-gm[i])/2./delti[theta];
1.13 lievre 2041: }
2042:
1.39 lievre 2043: for(j=1; j<=(nlstate+ndeath)*(nlstate+ndeath);j++)
2044: for(theta=1; theta <=npar; theta++)
2045: trgradg[j][theta]=gradg[theta][j];
2046:
2047: matprod2(dnewm,trgradg,1,9,1,npar,1,npar,matcov);
2048: matprod2(doldm,dnewm,1,9,1,npar,1,9,gradg);
2049:
2050: pmij(pmmij,cov,ncovmodel,x,nlstate);
2051:
2052: k=0;
2053: for(i=1; i<=(nlstate+ndeath); i++){
2054: for(j=1; j<=(nlstate+ndeath);j++){
2055: k=k+1;
2056: gm[k]=pmmij[i][j];
2057: }
1.13 lievre 2058: }
2059:
1.46 ! brouard 2060: /*printf("\n%d ",(int)age);
1.13 lievre 2061: for (i=1; i<=(nlstate+ndeath)*(nlstate+ndeath-1);i++){
2062: printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
2063: }*/
2064:
1.39 lievre 2065: fprintf(ficresprob,"\n%d ",(int)age);
1.46 ! brouard 2066: fprintf(ficresprobcov,"\n%d ",(int)age);
! 2067: fprintf(ficresprobcor,"\n%d ",(int)age);
1.13 lievre 2068:
1.39 lievre 2069: for (i=1; i<=(nlstate+ndeath)*(nlstate+ndeath-1);i++)
1.46 ! brouard 2070: fprintf(ficresprob,"%12.3e (%12.3e) ",gm[i],sqrt(doldm[i][j]));
! 2071: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
! 2072: fprintf(ficresprobcov,"%12.3e ",gm[i]);
! 2073: fprintf(ficresprobcor,"%12.3e ",gm[i]);
! 2074: }
! 2075: i=0;
! 2076: for (k=1; k<=(nlstate);k++){
! 2077: for (l=1; l<=(nlstate+ndeath);l++){
! 2078: i=i++;
! 2079: fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
! 2080: fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
! 2081: for (j=1; j<=i;j++){
! 2082: fprintf(ficresprobcov," %12.3e",doldm[i][j]);
! 2083: fprintf(ficresprobcor," %12.3e",doldm[i][j]/sqrt(doldm[i][i])/sqrt(doldm[j][j]));
! 2084: }
! 2085: }
! 2086: }
1.39 lievre 2087: }
2088: }
1.13 lievre 2089: free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
2090: free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
2091: free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
2092: free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
1.39 lievre 2093: }
2094: free_vector(xp,1,npar);
2095: fclose(ficresprob);
1.46 ! brouard 2096: fclose(ficresprobcov);
! 2097: fclose(ficresprobcor);
1.13 lievre 2098: }
1.2 lievre 2099:
1.45 lievre 2100:
1.25 lievre 2101: /******************* Printing html file ***********/
1.35 lievre 2102: void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \
1.43 brouard 2103: int lastpass, int stepm, int weightopt, char model[],\
2104: int imx,int jmin, int jmax, double jmeanint,char optionfile[], \
2105: char optionfilehtm[],char rfileres[], char optionfilegnuplot[],\
1.45 lievre 2106: char version[], int popforecast, int estepm ,\
1.43 brouard 2107: double jprev1, double mprev1,double anprev1, \
2108: double jprev2, double mprev2,double anprev2){
1.25 lievre 2109: int jj1, k1, i1, cpt;
2110: FILE *fichtm;
2111: /*char optionfilehtm[FILENAMELENGTH];*/
2112:
2113: strcpy(optionfilehtm,optionfile);
2114: strcat(optionfilehtm,".htm");
2115: if((fichtm=fopen(optionfilehtm,"w"))==NULL) {
2116: printf("Problem with %s \n",optionfilehtm), exit(0);
2117: }
2118:
1.43 brouard 2119: fprintf(fichtm,"<body> <font size=\"2\">%s </font> <hr size=\"2\" color=\"#EC5E5E\"> \n
1.35 lievre 2120: Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n
2121: \n
2122: Total number of observations=%d <br>\n
2123: Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n
1.43 brouard 2124: <hr size=\"2\" color=\"#EC5E5E\">
2125: <ul><li>Parameter files<br>\n
1.35 lievre 2126: - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n
1.43 brouard 2127: - Gnuplot file name: <a href=\"%s\">%s</a><br></ul>\n",version,title,datafile,firstpass,lastpass,stepm, weightopt,model,imx,jmin,jmax,jmean,fileres,fileres,optionfilegnuplot,optionfilegnuplot);
2128:
2129: fprintf(fichtm,"<ul><li>Result files (first order: no variance)<br>\n
2130: - 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
2131: - Estimated transition probabilities over %d (stepm) months: <a href=\"pij%s\">pij%s</a><br>\n
2132: - Stable prevalence in each health state: <a href=\"pl%s\">pl%s</a> <br>\n
2133: - Life expectancies by age and initial health status (estepm=%2d months):
2134: <a href=\"e%s\">e%s</a> <br>\n</li>", \
2135: jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,fileres,fileres,stepm,fileres,fileres,fileres,fileres,estepm,fileres,fileres);
2136:
2137: fprintf(fichtm,"\n<li> Result files (second order: variances)<br>\n
2138: - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n
2139: - Variance of one-step probabilities: <a href=\"prob%s\">prob%s</a> <br>\n
1.46 ! brouard 2140: - Variance-covariance of one-step probabilities: <a href=\"probcov%s\">probcov%s</a> <br>\n
! 2141: - Correlation matrix of one-step probabilities: <a href=\"probcor%s\">probcor%s</a> <br>\n
1.43 brouard 2142: - Variances and covariances of life expectancies by age and initial health status (estepm=%d months): <a href=\"v%s\">v%s</a><br>\n
2143: - Health expectancies with their variances (no covariance): <a href=\"t%s\">t%s</a> <br>\n
1.46 ! brouard 2144: - Standard deviation of stable prevalences: <a href=\"vpl%s\">vpl%s</a> <br>\n",rfileres,rfileres,fileres,fileres,fileres,fileres,fileres,fileres, estepm, fileres,fileres,fileres,fileres,fileres,fileres);
1.35 lievre 2145:
2146: if(popforecast==1) fprintf(fichtm,"\n
2147: - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n
2148: - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n
2149: <br>",fileres,fileres,fileres,fileres);
2150: else
2151: fprintf(fichtm,"\n No population forecast: popforecast = %d (instead of 1) or stepm = %d (instead of 1) or model=%s (instead of .)<br><br></li>\n",popforecast, stepm, model);
1.25 lievre 2152: fprintf(fichtm," <li>Graphs</li><p>");
2153:
2154: m=cptcoveff;
2155: if (cptcovn < 1) {m=1;ncodemax[1]=1;}
2156:
2157: jj1=0;
2158: for(k1=1; k1<=m;k1++){
2159: for(i1=1; i1<=ncodemax[k1];i1++){
1.45 lievre 2160: jj1++;
2161: if (cptcovn > 0) {
2162: fprintf(fichtm,"<hr size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
2163: for (cpt=1; cpt<=cptcoveff;cpt++)
2164: fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
2165: fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
2166: }
2167: /* Pij */
2168: 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>
2169: <img src=\"pe%s%d1.png\">",stepm,strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);
2170: /* Quasi-incidences */
2171: 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>
2172: <img src=\"pe%s%d2.png\">",stepm,strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);
1.43 brouard 2173: /* Stable prevalence in each health state */
1.25 lievre 2174: for(cpt=1; cpt<nlstate;cpt++){
1.43 brouard 2175: fprintf(fichtm,"<br>- Stable prevalence in each health state : p%s%d%d.png<br>
1.42 brouard 2176: <img src=\"p%s%d%d.png\">",strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);
1.25 lievre 2177: }
2178: for(cpt=1; cpt<=nlstate;cpt++) {
2179: fprintf(fichtm,"<br>- Observed and stationary prevalence (with confident
1.42 brouard 2180: interval) in state (%d): v%s%d%d.png <br>
2181: <img src=\"v%s%d%d.png\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);
1.25 lievre 2182: }
2183: for(cpt=1; cpt<=nlstate;cpt++) {
1.42 brouard 2184: fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): exp%s%d%d.png <br>
2185: <img src=\"exp%s%d%d.png\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);
1.25 lievre 2186: }
2187: fprintf(fichtm,"\n<br>- Total life expectancy by age and
1.42 brouard 2188: health expectancies in states (1) and (2): e%s%d.png<br>
2189: <img src=\"e%s%d.png\">",strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);
1.25 lievre 2190: fprintf(fichtm,"\n</body>");
2191: }
1.45 lievre 2192: }
1.25 lievre 2193: fclose(fichtm);
2194: }
2195:
2196: /******************* Gnuplot file **************/
1.35 lievre 2197: void printinggnuplot(char fileres[],char optionfilefiname[],char optionfile[],char optionfilegnuplot[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
1.25 lievre 2198:
2199: int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;
1.43 brouard 2200: int ng;
1.25 lievre 2201: strcpy(optionfilegnuplot,optionfilefiname);
1.46 ! brouard 2202: strcat(optionfilegnuplot,".gp");
1.25 lievre 2203: if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {
2204: printf("Problem with file %s",optionfilegnuplot);
2205: }
2206:
2207: #ifdef windows
2208: fprintf(ficgp,"cd \"%s\" \n",pathc);
2209: #endif
2210: m=pow(2,cptcoveff);
2211:
2212: /* 1eme*/
2213: for (cpt=1; cpt<= nlstate ; cpt ++) {
2214: for (k1=1; k1<= m ; k1 ++) {
2215:
2216: #ifdef windows
1.43 brouard 2217: fprintf(ficgp,"\nset out \"v%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);
1.42 brouard 2218: fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] \"vpl%s\" every :::%d::%d u 1:2 \"\%%lf",ageminpar,fage,fileres,k1-1,k1-1);
1.25 lievre 2219: #endif
2220: #ifdef unix
1.43 brouard 2221: fprintf(ficgp,"\nset out \"v%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);
1.35 lievre 2222: fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nplot [%.f:%.f] \"vpl%s\" u 1:2 \"\%%lf",ageminpar,fage,fileres);
1.25 lievre 2223: #endif
2224:
2225: for (i=1; i<= nlstate ; i ++) {
2226: if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
2227: else fprintf(ficgp," \%%*lf (\%%*lf)");
2228: }
2229: fprintf(ficgp,"\" t\"Stationary prevalence\" w l 0,\"vpl%s\" every :::%d::%d u 1:($2+2*$3) \"\%%lf",fileres,k1-1,k1-1);
2230: for (i=1; i<= nlstate ; i ++) {
2231: if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
2232: else fprintf(ficgp," \%%*lf (\%%*lf)");
2233: }
2234: fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"vpl%s\" every :::%d::%d u 1:($2-2*$3) \"\%%lf",fileres,k1-1,k1-1);
2235: for (i=1; i<= nlstate ; i ++) {
2236: if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
2237: else fprintf(ficgp," \%%*lf (\%%*lf)");
2238: }
2239: fprintf(ficgp,"\" t\"\" w l 1,\"p%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",fileres,k1-1,k1-1,2+4*(cpt-1));
2240: #ifdef unix
1.42 brouard 2241: fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65\n");
1.25 lievre 2242: #endif
2243: }
2244: }
2245: /*2 eme*/
2246:
2247: for (k1=1; k1<= m ; k1 ++) {
1.43 brouard 2248: fprintf(ficgp,"\nset out \"e%s%d.png\" \n",strtok(optionfile, "."),k1);
1.42 brouard 2249: fprintf(ficgp,"set ylabel \"Years\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] ",ageminpar,fage);
1.25 lievre 2250:
2251: for (i=1; i<= nlstate+1 ; i ++) {
2252: k=2*i;
2253: fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:2 \"\%%lf",fileres,k1-1,k1-1);
2254: for (j=1; j<= nlstate+1 ; j ++) {
2255: if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
2256: else fprintf(ficgp," \%%*lf (\%%*lf)");
2257: }
2258: if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");
2259: else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);
2260: fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",fileres,k1-1,k1-1);
2261: for (j=1; j<= nlstate+1 ; j ++) {
2262: if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
2263: else fprintf(ficgp," \%%*lf (\%%*lf)");
2264: }
2265: fprintf(ficgp,"\" t\"\" w l 0,");
2266: fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",fileres,k1-1,k1-1);
2267: for (j=1; j<= nlstate+1 ; j ++) {
2268: if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
2269: else fprintf(ficgp," \%%*lf (\%%*lf)");
2270: }
2271: if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");
2272: else fprintf(ficgp,"\" t\"\" w l 0,");
2273: }
2274: }
2275:
2276: /*3eme*/
2277:
2278: for (k1=1; k1<= m ; k1 ++) {
2279: for (cpt=1; cpt<= nlstate ; cpt ++) {
1.41 lievre 2280: k=2+nlstate*(2*cpt-2);
1.43 brouard 2281: fprintf(ficgp,"\nset out \"exp%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);
1.42 brouard 2282: fprintf(ficgp,"set ter png small\nset size 0.65,0.65\nplot [%.f:%.f] \"e%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,fileres,k1-1,k1-1,k,cpt);
1.41 lievre 2283: /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
2284: for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
2285: fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
2286: fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
2287: for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
2288: fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
2289:
2290: */
1.25 lievre 2291: for (i=1; i< nlstate ; i ++) {
1.41 lievre 2292: 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);
2293:
1.25 lievre 2294: }
2295: }
1.42 brouard 2296: }
1.25 lievre 2297:
2298: /* CV preval stat */
2299: for (k1=1; k1<= m ; k1 ++) {
2300: for (cpt=1; cpt<nlstate ; cpt ++) {
2301: k=3;
1.43 brouard 2302: fprintf(ficgp,"\nset out \"p%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);
1.42 brouard 2303: fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] \"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",ageminpar,agemaxpar,fileres,k1,k+cpt+1,k+1);
1.25 lievre 2304:
2305: for (i=1; i< nlstate ; i ++)
2306: fprintf(ficgp,"+$%d",k+i+1);
2307: fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);
2308:
2309: l=3+(nlstate+ndeath)*cpt;
2310: fprintf(ficgp,",\"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",fileres,k1,l+cpt+1,l+1);
2311: for (i=1; i< nlstate ; i ++) {
2312: l=3+(nlstate+ndeath)*cpt;
2313: fprintf(ficgp,"+$%d",l+i+1);
2314: }
2315: fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);
2316: }
2317: }
2318:
2319: /* proba elementaires */
2320: for(i=1,jk=1; i <=nlstate; i++){
2321: for(k=1; k <=(nlstate+ndeath); k++){
2322: if (k != i) {
2323: for(j=1; j <=ncovmodel; j++){
2324:
2325: fprintf(ficgp,"p%d=%f ",jk,p[jk]);
2326: jk++;
2327: fprintf(ficgp,"\n");
2328: }
2329: }
2330: }
1.42 brouard 2331: }
1.25 lievre 2332:
1.43 brouard 2333: for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/
2334: for(jk=1; jk <=m; jk++) {
2335: fprintf(ficgp,"\nset out \"pe%s%d%d.png\" \n",strtok(optionfile, "."),jk,ng);
2336: if (ng==2)
2337: fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
2338: else
2339: fprintf(ficgp,"\nset title \"Probability\"\n");
2340: fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65\nset log y\nplot [%.f:%.f] ",ageminpar,agemaxpar);
2341: i=1;
2342: for(k2=1; k2<=nlstate; k2++) {
2343: k3=i;
2344: for(k=1; k<=(nlstate+ndeath); k++) {
2345: if (k != k2){
2346: if(ng==2)
1.46 ! brouard 2347: fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);
1.42 brouard 2348: else
1.43 brouard 2349: fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
1.42 brouard 2350: ij=1;
1.43 brouard 2351: for(j=3; j <=ncovmodel; j++) {
1.42 brouard 2352: if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
1.43 brouard 2353: fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
1.42 brouard 2354: ij++;
2355: }
2356: else
1.43 brouard 2357: fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
1.42 brouard 2358: }
1.43 brouard 2359: fprintf(ficgp,")/(1");
2360:
2361: for(k1=1; k1 <=nlstate; k1++){
2362: fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);
2363: ij=1;
2364: for(j=3; j <=ncovmodel; j++){
2365: if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
2366: fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
2367: ij++;
2368: }
2369: else
2370: fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
2371: }
2372: fprintf(ficgp,")");
2373: }
2374: fprintf(ficgp,") t \"p%d%d\" ", k2,k);
2375: if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");
2376: i=i+ncovmodel;
1.42 brouard 2377: }
2378: }
1.25 lievre 2379: }
2380: }
2381: }
1.42 brouard 2382: fclose(ficgp);
1.25 lievre 2383: } /* end gnuplot */
2384:
2385:
2386: /*************** Moving average **************/
1.35 lievre 2387: void movingaverage(double agedeb, double fage,double ageminpar, double ***mobaverage){
1.25 lievre 2388:
2389: int i, cpt, cptcod;
1.35 lievre 2390: for (agedeb=ageminpar; agedeb<=fage; agedeb++)
1.25 lievre 2391: for (i=1; i<=nlstate;i++)
2392: for (cptcod=1;cptcod<=ncodemax[cptcov];cptcod++)
2393: mobaverage[(int)agedeb][i][cptcod]=0.;
2394:
1.35 lievre 2395: for (agedeb=ageminpar+4; agedeb<=fage; agedeb++){
1.25 lievre 2396: for (i=1; i<=nlstate;i++){
2397: for (cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
2398: for (cpt=0;cpt<=4;cpt++){
2399: mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]+probs[(int)agedeb-cpt][i][cptcod];
2400: }
2401: mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]/5;
2402: }
2403: }
2404: }
2405:
2406: }
2407:
1.27 lievre 2408:
2409: /************** Forecasting ******************/
1.35 lievre 2410: prevforecast(char fileres[], double anproj1,double mproj1,double jproj1,double ageminpar, double agemax,double dateprev1, double dateprev2, int mobilav, double agedeb, double fage, int popforecast, char popfile[], double anproj2,double p[], int i2){
1.27 lievre 2411:
2412: int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;
2413: int *popage;
2414: double calagedate, agelim, kk1, kk2, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
2415: double *popeffectif,*popcount;
2416: double ***p3mat;
2417: char fileresf[FILENAMELENGTH];
2418:
2419: agelim=AGESUP;
2420: calagedate=(anproj1+mproj1/12.+jproj1/365.-dateintmean)*YEARM;
1.28 lievre 2421:
1.35 lievre 2422: prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);
1.28 lievre 2423:
1.27 lievre 2424:
2425: strcpy(fileresf,"f");
2426: strcat(fileresf,fileres);
2427: if((ficresf=fopen(fileresf,"w"))==NULL) {
2428: printf("Problem with forecast resultfile: %s\n", fileresf);
2429: }
2430: printf("Computing forecasting: result on file '%s' \n", fileresf);
2431:
2432: if (cptcoveff==0) ncodemax[cptcoveff]=1;
2433:
2434: if (mobilav==1) {
2435: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
1.35 lievre 2436: movingaverage(agedeb, fage, ageminpar, mobaverage);
1.27 lievre 2437: }
2438:
2439: stepsize=(int) (stepm+YEARM-1)/YEARM;
2440: if (stepm<=12) stepsize=1;
2441:
2442: agelim=AGESUP;
2443:
2444: hstepm=1;
2445: hstepm=hstepm/stepm;
2446: yp1=modf(dateintmean,&yp);
2447: anprojmean=yp;
2448: yp2=modf((yp1*12),&yp);
2449: mprojmean=yp;
2450: yp1=modf((yp2*30.5),&yp);
2451: jprojmean=yp;
2452: if(jprojmean==0) jprojmean=1;
2453: if(mprojmean==0) jprojmean=1;
2454:
2455: fprintf(ficresf,"# Estimated date of observed prevalence: %.lf/%.lf/%.lf ",jprojmean,mprojmean,anprojmean);
2456:
2457: for(cptcov=1;cptcov<=i2;cptcov++){
2458: for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
2459: k=k+1;
2460: fprintf(ficresf,"\n#******");
2461: for(j=1;j<=cptcoveff;j++) {
2462: fprintf(ficresf," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
2463: }
2464: fprintf(ficresf,"******\n");
2465: fprintf(ficresf,"# StartingAge FinalAge");
2466: for(j=1; j<=nlstate+ndeath;j++) fprintf(ficresf," P.%d",j);
2467:
2468:
2469: for (cpt=0; cpt<=(anproj2-anproj1);cpt++) {
2470: fprintf(ficresf,"\n");
2471: fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+cpt);
1.28 lievre 2472:
1.35 lievre 2473: for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){
1.27 lievre 2474: nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);
2475: nhstepm = nhstepm/hstepm;
2476:
2477: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
2478: oldm=oldms;savm=savms;
2479: hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
2480:
2481: for (h=0; h<=nhstepm; h++){
2482: if (h==(int) (calagedate+YEARM*cpt)) {
1.35 lievre 2483: fprintf(ficresf,"\n %.f %.f ",anproj1+cpt,agedeb+h*hstepm/YEARM*stepm);
1.27 lievre 2484: }
2485: for(j=1; j<=nlstate+ndeath;j++) {
2486: kk1=0.;kk2=0;
2487: for(i=1; i<=nlstate;i++) {
2488: if (mobilav==1)
2489: kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];
2490: else {
2491: kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];
2492: }
2493:
2494: }
2495: if (h==(int)(calagedate+12*cpt)){
2496: fprintf(ficresf," %.3f", kk1);
2497:
2498: }
2499: }
2500: }
2501: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
2502: }
2503: }
2504: }
2505: }
2506:
2507: if (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
2508:
2509: fclose(ficresf);
2510: }
2511: /************** Forecasting ******************/
1.35 lievre 2512: populforecast(char fileres[], double anpyram,double mpyram,double jpyram,double ageminpar, double agemax,double dateprev1, double dateprev2, int mobilav, double agedeb, double fage, int popforecast, char popfile[], double anpyram1,double p[], int i2){
1.27 lievre 2513:
2514: int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;
2515: int *popage;
2516: double calagedate, agelim, kk1, kk2, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
2517: double *popeffectif,*popcount;
2518: double ***p3mat,***tabpop,***tabpopprev;
2519: char filerespop[FILENAMELENGTH];
2520:
1.28 lievre 2521: tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
2522: tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
2523: agelim=AGESUP;
2524: calagedate=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;
1.27 lievre 2525:
1.35 lievre 2526: prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);
1.28 lievre 2527:
2528:
1.27 lievre 2529: strcpy(filerespop,"pop");
2530: strcat(filerespop,fileres);
2531: if((ficrespop=fopen(filerespop,"w"))==NULL) {
2532: printf("Problem with forecast resultfile: %s\n", filerespop);
2533: }
2534: printf("Computing forecasting: result on file '%s' \n", filerespop);
2535:
2536: if (cptcoveff==0) ncodemax[cptcoveff]=1;
2537:
2538: if (mobilav==1) {
2539: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
1.35 lievre 2540: movingaverage(agedeb, fage, ageminpar, mobaverage);
1.27 lievre 2541: }
2542:
2543: stepsize=(int) (stepm+YEARM-1)/YEARM;
2544: if (stepm<=12) stepsize=1;
2545:
2546: agelim=AGESUP;
2547:
2548: hstepm=1;
2549: hstepm=hstepm/stepm;
2550:
2551: if (popforecast==1) {
2552: if((ficpop=fopen(popfile,"r"))==NULL) {
2553: printf("Problem with population file : %s\n",popfile);exit(0);
2554: }
2555: popage=ivector(0,AGESUP);
2556: popeffectif=vector(0,AGESUP);
2557: popcount=vector(0,AGESUP);
2558:
2559: i=1;
2560: while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;
2561:
2562: imx=i;
2563: for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];
2564: }
2565:
2566: for(cptcov=1;cptcov<=i2;cptcov++){
2567: for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
2568: k=k+1;
2569: fprintf(ficrespop,"\n#******");
2570: for(j=1;j<=cptcoveff;j++) {
2571: fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
2572: }
2573: fprintf(ficrespop,"******\n");
1.28 lievre 2574: fprintf(ficrespop,"# Age");
1.27 lievre 2575: for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);
2576: if (popforecast==1) fprintf(ficrespop," [Population]");
2577:
2578: for (cpt=0; cpt<=0;cpt++) {
1.28 lievre 2579: fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);
1.27 lievre 2580:
1.35 lievre 2581: for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){
1.27 lievre 2582: nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);
2583: nhstepm = nhstepm/hstepm;
2584:
2585: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
2586: oldm=oldms;savm=savms;
2587: hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
2588:
2589: for (h=0; h<=nhstepm; h++){
2590: if (h==(int) (calagedate+YEARM*cpt)) {
1.28 lievre 2591: fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
1.27 lievre 2592: }
2593: for(j=1; j<=nlstate+ndeath;j++) {
2594: kk1=0.;kk2=0;
2595: for(i=1; i<=nlstate;i++) {
2596: if (mobilav==1)
2597: kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];
2598: else {
2599: kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];
2600: }
2601: }
2602: if (h==(int)(calagedate+12*cpt)){
2603: tabpop[(int)(agedeb)][j][cptcod]=kk1;
2604: /*fprintf(ficrespop," %.3f", kk1);
2605: if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/
2606: }
2607: }
2608: for(i=1; i<=nlstate;i++){
2609: kk1=0.;
2610: for(j=1; j<=nlstate;j++){
1.28 lievre 2611: kk1= kk1+tabpop[(int)(agedeb)][j][cptcod];
1.27 lievre 2612: }
2613: tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedate+12*cpt)*hstepm/YEARM*stepm-1)];
2614: }
2615:
1.28 lievre 2616: if (h==(int)(calagedate+12*cpt)) for(j=1; j<=nlstate;j++)
2617: fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);
1.27 lievre 2618: }
2619: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
2620: }
2621: }
2622:
2623: /******/
2624:
1.28 lievre 2625: for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) {
2626: fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);
1.35 lievre 2627: for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){
1.27 lievre 2628: nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);
2629: nhstepm = nhstepm/hstepm;
2630:
2631: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
2632: oldm=oldms;savm=savms;
2633: hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
2634: for (h=0; h<=nhstepm; h++){
2635: if (h==(int) (calagedate+YEARM*cpt)) {
1.28 lievre 2636: fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
1.27 lievre 2637: }
2638: for(j=1; j<=nlstate+ndeath;j++) {
2639: kk1=0.;kk2=0;
2640: for(i=1; i<=nlstate;i++) {
2641: kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];
2642: }
1.28 lievre 2643: if (h==(int)(calagedate+12*cpt)) fprintf(ficresf," %15.2f", kk1);
1.27 lievre 2644: }
2645: }
2646: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
2647: }
2648: }
2649: }
2650: }
2651:
2652: if (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
2653:
2654: if (popforecast==1) {
2655: free_ivector(popage,0,AGESUP);
2656: free_vector(popeffectif,0,AGESUP);
2657: free_vector(popcount,0,AGESUP);
2658: }
2659: free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
2660: free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
2661: fclose(ficrespop);
2662: }
2663:
1.2 lievre 2664: /***********************************************/
2665: /**************** Main Program *****************/
2666: /***********************************************/
2667:
1.22 brouard 2668: int main(int argc, char *argv[])
1.2 lievre 2669: {
2670:
1.8 lievre 2671: int i,j, k, n=MAXN,iter,m,size,cptcode, cptcod;
1.2 lievre 2672: double agedeb, agefin,hf;
1.35 lievre 2673: double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;
1.2 lievre 2674:
2675: double fret;
2676: double **xi,tmp,delta;
2677:
2678: double dum; /* Dummy variable */
2679: double ***p3mat;
2680: int *indx;
2681: char line[MAXLINE], linepar[MAXLINE];
2682: char title[MAXLINE];
1.25 lievre 2683: char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH], filerespl[FILENAMELENGTH];
2684: char optionfilext[10], optionfilefiname[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilegnuplot[FILENAMELENGTH], plotcmd[FILENAMELENGTH];
1.22 brouard 2685:
1.29 lievre 2686: char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
1.22 brouard 2687:
1.2 lievre 2688: char filerest[FILENAMELENGTH];
2689: char fileregp[FILENAMELENGTH];
1.16 lievre 2690: char popfile[FILENAMELENGTH];
1.2 lievre 2691: char path[80],pathc[80],pathcd[80],pathtot[80],model[20];
2692: int firstobs=1, lastobs=10;
2693: int sdeb, sfin; /* Status at beginning and end */
2694: int c, h , cpt,l;
2695: int ju,jl, mi;
1.7 lievre 2696: int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;
1.14 lievre 2697: int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,**adl,*tab;
1.19 lievre 2698: int mobilav=0,popforecast=0;
1.2 lievre 2699: int hstepm, nhstepm;
1.41 lievre 2700: double jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,jpyram, mpyram,anpyram,jpyram1, mpyram1,anpyram1, calagedate;
1.14 lievre 2701:
1.2 lievre 2702: double bage, fage, age, agelim, agebase;
2703: double ftolpl=FTOL;
2704: double **prlim;
2705: double *severity;
2706: double ***param; /* Matrix of parameters */
2707: double *p;
2708: double **matcov; /* Matrix of covariance */
2709: double ***delti3; /* Scale */
2710: double *delti; /* Scale */
2711: double ***eij, ***vareij;
2712: double **varpl; /* Variances of prevalence limits by age */
2713: double *epj, vepp;
1.16 lievre 2714: double kk1, kk2;
1.27 lievre 2715: double dateprev1, dateprev2,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2;
2716:
1.13 lievre 2717:
1.46 ! brouard 2718: char version[80]="Imach version 0.8g, May 2002, INED-EUROREVES ";
1.2 lievre 2719: char *alph[]={"a","a","b","c","d","e"}, str[4];
1.5 lievre 2720:
1.13 lievre 2721:
1.2 lievre 2722: char z[1]="c", occ;
2723: #include <sys/time.h>
2724: #include <time.h>
2725: char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];
1.19 lievre 2726:
1.2 lievre 2727: /* long total_usecs;
2728: struct timeval start_time, end_time;
2729:
2730: gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */
1.35 lievre 2731: getcwd(pathcd, size);
1.2 lievre 2732:
1.22 brouard 2733: printf("\n%s",version);
2734: if(argc <=1){
2735: printf("\nEnter the parameter file name: ");
2736: scanf("%s",pathtot);
2737: }
2738: else{
2739: strcpy(pathtot,argv[1]);
2740: }
2741: /*if(getcwd(pathcd, 80)!= NULL)printf ("Error pathcd\n");*/
1.5 lievre 2742: /*cygwin_split_path(pathtot,path,optionfile);
2743: printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/
2744: /* cutv(path,optionfile,pathtot,'\\');*/
2745:
1.22 brouard 2746: split(pathtot,path,optionfile,optionfilext,optionfilefiname);
2747: printf("pathtot=%s, path=%s, optionfile=%s optionfilext=%s optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
1.2 lievre 2748: chdir(path);
2749: replace(pathc,path);
2750:
2751: /*-------- arguments in the command line --------*/
2752:
2753: strcpy(fileres,"r");
1.22 brouard 2754: strcat(fileres, optionfilefiname);
2755: strcat(fileres,".txt"); /* Other files have txt extension */
1.2 lievre 2756:
2757: /*---------arguments file --------*/
2758:
2759: if((ficpar=fopen(optionfile,"r"))==NULL) {
2760: printf("Problem with optionfile %s\n",optionfile);
2761: goto end;
2762: }
2763:
2764: strcpy(filereso,"o");
2765: strcat(filereso,fileres);
2766: if((ficparo=fopen(filereso,"w"))==NULL) {
2767: printf("Problem with Output resultfile: %s\n", filereso);goto end;
2768: }
2769:
2770: /* Reads comments: lines beginning with '#' */
2771: while((c=getc(ficpar))=='#' && c!= EOF){
2772: ungetc(c,ficpar);
2773: fgets(line, MAXLINE, ficpar);
2774: puts(line);
2775: fputs(line,ficparo);
2776: }
2777: ungetc(c,ficpar);
2778:
1.34 brouard 2779: fscanf(ficpar,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%lf stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n",title, datafile, &lastobs, &firstpass,&lastpass,&ftol, &stepm, &ncovcol, &nlstate,&ndeath, &maxwav, &mle, &weightopt,model);
2780: 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);
2781: fprintf(ficparo,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol,nlstate,ndeath,maxwav, mle, weightopt,model);
1.14 lievre 2782: while((c=getc(ficpar))=='#' && c!= EOF){
2783: ungetc(c,ficpar);
2784: fgets(line, MAXLINE, ficpar);
2785: puts(line);
2786: fputs(line,ficparo);
2787: }
2788: ungetc(c,ficpar);
2789:
1.19 lievre 2790:
1.8 lievre 2791: covar=matrix(0,NCOVMAX,1,n);
2792: cptcovn=0;
2793: if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;
1.2 lievre 2794:
2795: ncovmodel=2+cptcovn;
2796: nvar=ncovmodel-1; /* Suppressing age as a basic covariate */
2797:
2798: /* Read guess parameters */
2799: /* Reads comments: lines beginning with '#' */
2800: while((c=getc(ficpar))=='#' && c!= EOF){
2801: ungetc(c,ficpar);
2802: fgets(line, MAXLINE, ficpar);
2803: puts(line);
2804: fputs(line,ficparo);
2805: }
2806: ungetc(c,ficpar);
2807:
2808: param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
2809: for(i=1; i <=nlstate; i++)
2810: for(j=1; j <=nlstate+ndeath-1; j++){
2811: fscanf(ficpar,"%1d%1d",&i1,&j1);
2812: fprintf(ficparo,"%1d%1d",i1,j1);
2813: printf("%1d%1d",i,j);
2814: for(k=1; k<=ncovmodel;k++){
2815: fscanf(ficpar," %lf",¶m[i][j][k]);
2816: printf(" %lf",param[i][j][k]);
2817: fprintf(ficparo," %lf",param[i][j][k]);
2818: }
2819: fscanf(ficpar,"\n");
2820: printf("\n");
2821: fprintf(ficparo,"\n");
2822: }
2823:
1.12 lievre 2824: npar= (nlstate+ndeath-1)*nlstate*ncovmodel;
2825:
1.2 lievre 2826: p=param[1][1];
2827:
2828: /* Reads comments: lines beginning with '#' */
2829: while((c=getc(ficpar))=='#' && c!= EOF){
2830: ungetc(c,ficpar);
2831: fgets(line, MAXLINE, ficpar);
2832: puts(line);
2833: fputs(line,ficparo);
2834: }
2835: ungetc(c,ficpar);
2836:
2837: delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
2838: delti=vector(1,npar); /* Scale of each paramater (output from hesscov) */
2839: for(i=1; i <=nlstate; i++){
2840: for(j=1; j <=nlstate+ndeath-1; j++){
2841: fscanf(ficpar,"%1d%1d",&i1,&j1);
2842: printf("%1d%1d",i,j);
2843: fprintf(ficparo,"%1d%1d",i1,j1);
2844: for(k=1; k<=ncovmodel;k++){
2845: fscanf(ficpar,"%le",&delti3[i][j][k]);
2846: printf(" %le",delti3[i][j][k]);
2847: fprintf(ficparo," %le",delti3[i][j][k]);
2848: }
2849: fscanf(ficpar,"\n");
2850: printf("\n");
2851: fprintf(ficparo,"\n");
2852: }
2853: }
2854: delti=delti3[1][1];
2855:
2856: /* Reads comments: lines beginning with '#' */
2857: while((c=getc(ficpar))=='#' && c!= EOF){
2858: ungetc(c,ficpar);
2859: fgets(line, MAXLINE, ficpar);
2860: puts(line);
2861: fputs(line,ficparo);
2862: }
2863: ungetc(c,ficpar);
2864:
2865: matcov=matrix(1,npar,1,npar);
2866: for(i=1; i <=npar; i++){
2867: fscanf(ficpar,"%s",&str);
2868: printf("%s",str);
2869: fprintf(ficparo,"%s",str);
2870: for(j=1; j <=i; j++){
2871: fscanf(ficpar," %le",&matcov[i][j]);
2872: printf(" %.5le",matcov[i][j]);
2873: fprintf(ficparo," %.5le",matcov[i][j]);
2874: }
2875: fscanf(ficpar,"\n");
2876: printf("\n");
2877: fprintf(ficparo,"\n");
2878: }
2879: for(i=1; i <=npar; i++)
2880: for(j=i+1;j<=npar;j++)
2881: matcov[i][j]=matcov[j][i];
2882:
2883: printf("\n");
2884:
2885:
1.29 lievre 2886: /*-------- Rewriting paramater file ----------*/
2887: strcpy(rfileres,"r"); /* "Rparameterfile */
2888: strcat(rfileres,optionfilefiname); /* Parameter file first name*/
2889: strcat(rfileres,"."); /* */
2890: strcat(rfileres,optionfilext); /* Other files have txt extension */
2891: if((ficres =fopen(rfileres,"w"))==NULL) {
2892: printf("Problem writing new parameter file: %s\n", fileres);goto end;
1.2 lievre 2893: }
2894: fprintf(ficres,"#%s\n",version);
2895:
1.29 lievre 2896: /*-------- data file ----------*/
1.2 lievre 2897: if((fic=fopen(datafile,"r"))==NULL) {
2898: printf("Problem with datafile: %s\n", datafile);goto end;
2899: }
2900:
2901: n= lastobs;
2902: severity = vector(1,maxwav);
2903: outcome=imatrix(1,maxwav+1,1,n);
2904: num=ivector(1,n);
2905: moisnais=vector(1,n);
2906: annais=vector(1,n);
2907: moisdc=vector(1,n);
2908: andc=vector(1,n);
2909: agedc=vector(1,n);
2910: cod=ivector(1,n);
2911: weight=vector(1,n);
2912: for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */
2913: mint=matrix(1,maxwav,1,n);
2914: anint=matrix(1,maxwav,1,n);
2915: s=imatrix(1,maxwav+1,1,n);
2916: adl=imatrix(1,maxwav+1,1,n);
2917: tab=ivector(1,NCOVMAX);
1.3 lievre 2918: ncodemax=ivector(1,8);
1.2 lievre 2919:
1.12 lievre 2920: i=1;
1.2 lievre 2921: while (fgets(line, MAXLINE, fic) != NULL) {
2922: if ((i >= firstobs) && (i <=lastobs)) {
2923:
2924: for (j=maxwav;j>=1;j--){
2925: cutv(stra, strb,line,' '); s[j][i]=atoi(strb);
2926: strcpy(line,stra);
2927: cutv(stra, strb,line,'/'); anint[j][i]=(double)(atoi(strb)); strcpy(line,stra);
2928: cutv(stra, strb,line,' '); mint[j][i]=(double)(atoi(strb)); strcpy(line,stra);
2929: }
2930:
2931: cutv(stra, strb,line,'/'); andc[i]=(double)(atoi(strb)); strcpy(line,stra);
2932: cutv(stra, strb,line,' '); moisdc[i]=(double)(atoi(strb)); strcpy(line,stra);
2933:
2934: cutv(stra, strb,line,'/'); annais[i]=(double)(atoi(strb)); strcpy(line,stra);
2935: cutv(stra, strb,line,' '); moisnais[i]=(double)(atoi(strb)); strcpy(line,stra);
2936:
2937: cutv(stra, strb,line,' '); weight[i]=(double)(atoi(strb)); strcpy(line,stra);
1.34 brouard 2938: for (j=ncovcol;j>=1;j--){
1.2 lievre 2939: cutv(stra, strb,line,' '); covar[j][i]=(double)(atoi(strb)); strcpy(line,stra);
2940: }
2941: num[i]=atol(stra);
1.12 lievre 2942:
2943: /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){
2944: printf("%d %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]),weight[i], (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]), (mint[2][i]), (anint[2][i]), (s[2][i]), (mint[3][i]), (anint[3][i]), (s[3][i]), (mint[4][i]), (anint[4][i]), (s[4][i])); ij=ij+1;}*/
1.2 lievre 2945:
2946: i=i+1;
2947: }
2948: }
1.12 lievre 2949: /* printf("ii=%d", ij);
2950: scanf("%d",i);*/
2951: imx=i-1; /* Number of individuals */
1.3 lievre 2952:
1.12 lievre 2953: /* for (i=1; i<=imx; i++){
2954: if ((s[1][i]==3) && (s[2][i]==2)) s[2][i]=3;
2955: if ((s[2][i]==3) && (s[3][i]==2)) s[3][i]=3;
2956: if ((s[3][i]==3) && (s[4][i]==2)) s[4][i]=3;
1.35 lievre 2957: }*/
1.39 lievre 2958: /* for (i=1; i<=imx; i++){
1.35 lievre 2959: if (s[4][i]==9) s[4][i]=-1;
1.39 lievre 2960: 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]));}*/
2961:
1.35 lievre 2962:
1.2 lievre 2963: /* Calculation of the number of parameter from char model*/
1.7 lievre 2964: Tvar=ivector(1,15);
2965: Tprod=ivector(1,15);
2966: Tvaraff=ivector(1,15);
2967: Tvard=imatrix(1,15,1,2);
1.6 lievre 2968: Tage=ivector(1,15);
1.2 lievre 2969:
2970: if (strlen(model) >1){
1.7 lievre 2971: j=0, j1=0, k1=1, k2=1;
1.2 lievre 2972: j=nbocc(model,'+');
1.6 lievre 2973: j1=nbocc(model,'*');
1.2 lievre 2974: cptcovn=j+1;
1.7 lievre 2975: cptcovprod=j1;
1.3 lievre 2976:
1.2 lievre 2977: strcpy(modelsav,model);
1.8 lievre 2978: if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){
2979: printf("Error. Non available option model=%s ",model);
2980: goto end;
2981: }
2982:
2983: for(i=(j+1); i>=1;i--){
2984: cutv(stra,strb,modelsav,'+');
2985: if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav);
2986: /* printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/
2987: /*scanf("%d",i);*/
2988: if (strchr(strb,'*')) {
2989: cutv(strd,strc,strb,'*');
2990: if (strcmp(strc,"age")==0) {
1.7 lievre 2991: cptcovprod--;
1.8 lievre 2992: cutv(strb,stre,strd,'V');
2993: Tvar[i]=atoi(stre);
2994: cptcovage++;
2995: Tage[cptcovage]=i;
2996: /*printf("stre=%s ", stre);*/
1.7 lievre 2997: }
1.8 lievre 2998: else if (strcmp(strd,"age")==0) {
1.7 lievre 2999: cptcovprod--;
1.8 lievre 3000: cutv(strb,stre,strc,'V');
3001: Tvar[i]=atoi(stre);
3002: cptcovage++;
3003: Tage[cptcovage]=i;
1.7 lievre 3004: }
3005: else {
1.8 lievre 3006: cutv(strb,stre,strc,'V');
1.34 brouard 3007: Tvar[i]=ncovcol+k1;
1.8 lievre 3008: cutv(strb,strc,strd,'V');
3009: Tprod[k1]=i;
3010: Tvard[k1][1]=atoi(strc);
3011: Tvard[k1][2]=atoi(stre);
3012: Tvar[cptcovn+k2]=Tvard[k1][1];
3013: Tvar[cptcovn+k2+1]=Tvard[k1][2];
1.7 lievre 3014: for (k=1; k<=lastobs;k++)
1.34 brouard 3015: covar[ncovcol+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];
1.8 lievre 3016: k1++;
3017: k2=k2+2;
1.7 lievre 3018: }
1.2 lievre 3019: }
1.8 lievre 3020: else {
3021: /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/
3022: /* scanf("%d",i);*/
3023: cutv(strd,strc,strb,'V');
3024: Tvar[i]=atoi(strc);
3025: }
3026: strcpy(modelsav,stra);
3027: /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);
3028: scanf("%d",i);*/
1.2 lievre 3029: }
1.8 lievre 3030: }
3031:
1.35 lievre 3032: /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);
1.8 lievre 3033: printf("cptcovprod=%d ", cptcovprod);
3034: scanf("%d ",i);*/
1.2 lievre 3035: fclose(fic);
3036:
1.7 lievre 3037: /* if(mle==1){*/
1.2 lievre 3038: if (weightopt != 1) { /* Maximisation without weights*/
3039: for(i=1;i<=n;i++) weight[i]=1.0;
3040: }
3041: /*-calculation of age at interview from date of interview and age at death -*/
3042: agev=matrix(1,maxwav,1,imx);
1.12 lievre 3043:
1.35 lievre 3044: for (i=1; i<=imx; i++) {
3045: for(m=2; (m<= maxwav); m++) {
1.12 lievre 3046: if ((mint[m][i]== 99) && (s[m][i] <= nlstate)){
3047: anint[m][i]=9999;
3048: s[m][i]=-1;
3049: }
1.35 lievre 3050: if(moisdc[i]==99 && andc[i]==9999 & s[m][i]>nlstate) s[m][i]=-1;
3051: }
3052: }
3053:
1.2 lievre 3054: for (i=1; i<=imx; i++) {
3055: agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);
3056: for(m=1; (m<= maxwav); m++){
3057: if(s[m][i] >0){
1.35 lievre 3058: if (s[m][i] >= nlstate+1) {
1.2 lievre 3059: if(agedc[i]>0)
3060: if(moisdc[i]!=99 && andc[i]!=9999)
1.35 lievre 3061: agev[m][i]=agedc[i];
3062: /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/
3063: else {
1.8 lievre 3064: if (andc[i]!=9999){
1.2 lievre 3065: printf("Warning negative age at death: %d line:%d\n",num[i],i);
3066: agev[m][i]=-1;
1.8 lievre 3067: }
1.2 lievre 3068: }
3069: }
3070: else if(s[m][i] !=9){ /* Should no more exist */
3071: agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);
1.3 lievre 3072: if(mint[m][i]==99 || anint[m][i]==9999)
1.2 lievre 3073: agev[m][i]=1;
3074: else if(agev[m][i] <agemin){
3075: agemin=agev[m][i];
3076: /*printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], agemin);*/
3077: }
3078: else if(agev[m][i] >agemax){
3079: agemax=agev[m][i];
3080: /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/
3081: }
3082: /*agev[m][i]=anint[m][i]-annais[i];*/
3083: /* agev[m][i] = age[i]+2*m;*/
3084: }
3085: else { /* =9 */
3086: agev[m][i]=1;
3087: s[m][i]=-1;
3088: }
3089: }
3090: else /*= 0 Unknown */
3091: agev[m][i]=1;
3092: }
3093:
3094: }
3095: for (i=1; i<=imx; i++) {
3096: for(m=1; (m<= maxwav); m++){
3097: if (s[m][i] > (nlstate+ndeath)) {
3098: printf("Error: Wrong value in nlstate or ndeath\n");
3099: goto end;
3100: }
3101: }
3102: }
3103:
3104: printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);
3105:
3106: free_vector(severity,1,maxwav);
3107: free_imatrix(outcome,1,maxwav+1,1,n);
3108: free_vector(moisnais,1,n);
3109: free_vector(annais,1,n);
1.17 lievre 3110: /* free_matrix(mint,1,maxwav,1,n);
3111: free_matrix(anint,1,maxwav,1,n);*/
1.2 lievre 3112: free_vector(moisdc,1,n);
3113: free_vector(andc,1,n);
3114:
3115:
3116: wav=ivector(1,imx);
3117: dh=imatrix(1,lastpass-firstpass+1,1,imx);
3118: mw=imatrix(1,lastpass-firstpass+1,1,imx);
3119:
3120: /* Concatenates waves */
3121: concatwav(wav, dh, mw, s, agedc, agev, firstpass, lastpass, imx, nlstate, stepm);
3122:
3123:
1.6 lievre 3124: Tcode=ivector(1,100);
1.8 lievre 3125: nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);
1.7 lievre 3126: ncodemax[1]=1;
3127: if (cptcovn > 0) tricode(Tvar,nbcode,imx);
3128:
1.2 lievre 3129: codtab=imatrix(1,100,1,10);
3130: h=0;
1.7 lievre 3131: m=pow(2,cptcoveff);
1.2 lievre 3132:
1.7 lievre 3133: for(k=1;k<=cptcoveff; k++){
1.2 lievre 3134: for(i=1; i <=(m/pow(2,k));i++){
3135: for(j=1; j <= ncodemax[k]; j++){
1.7 lievre 3136: for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){
1.2 lievre 3137: h++;
1.35 lievre 3138: if (h>m) h=1;codtab[h][k]=j;codtab[h][Tvar[k]]=j;
3139: /* printf("h=%d k=%d j=%d codtab[h][k]=%d tvar[k]=%d \n",h, k,j,codtab[h][k],Tvar[k]);*/
1.2 lievre 3140: }
3141: }
3142: }
3143: }
1.35 lievre 3144: /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]);
3145: codtab[1][2]=1;codtab[2][2]=2; */
3146: /* for(i=1; i <=m ;i++){
3147: for(k=1; k <=cptcovn; k++){
3148: printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);
3149: }
3150: printf("\n");
3151: }
3152: scanf("%d",i);*/
1.2 lievre 3153:
3154: /* Calculates basic frequencies. Computes observed prevalence at single age
3155: and prints on file fileres'p'. */
1.18 lievre 3156:
1.19 lievre 3157:
1.18 lievre 3158:
1.19 lievre 3159: pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
1.2 lievre 3160: oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
3161: newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
3162: savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
3163: oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */
1.12 lievre 3164:
1.2 lievre 3165: /* For Powell, parameters are in a vector p[] starting at p[1]
3166: so we point p on param[1][1] so that p[1] maps on param[1][1][1] */
3167: p=param[1][1]; /* *(*(*(param +1)+1)+0) */
1.7 lievre 3168:
3169: if(mle==1){
1.2 lievre 3170: mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);
1.7 lievre 3171: }
1.2 lievre 3172:
3173: /*--------- results files --------------*/
1.34 brouard 3174: fprintf(ficres,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle= 0 weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate, ndeath, maxwav, weightopt,model);
1.19 lievre 3175:
1.16 lievre 3176:
1.2 lievre 3177: jk=1;
1.34 brouard 3178: fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
3179: printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
1.2 lievre 3180: for(i=1,jk=1; i <=nlstate; i++){
3181: for(k=1; k <=(nlstate+ndeath); k++){
3182: if (k != i)
3183: {
3184: printf("%d%d ",i,k);
3185: fprintf(ficres,"%1d%1d ",i,k);
3186: for(j=1; j <=ncovmodel; j++){
3187: printf("%f ",p[jk]);
3188: fprintf(ficres,"%f ",p[jk]);
3189: jk++;
3190: }
3191: printf("\n");
3192: fprintf(ficres,"\n");
3193: }
3194: }
3195: }
1.7 lievre 3196: if(mle==1){
1.2 lievre 3197: /* Computing hessian and covariance matrix */
3198: ftolhess=ftol; /* Usually correct */
3199: hesscov(matcov, p, npar, delti, ftolhess, func);
1.7 lievre 3200: }
1.34 brouard 3201: fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");
3202: printf("# Scales (for hessian or gradient estimation)\n");
1.2 lievre 3203: for(i=1,jk=1; i <=nlstate; i++){
3204: for(j=1; j <=nlstate+ndeath; j++){
3205: if (j!=i) {
3206: fprintf(ficres,"%1d%1d",i,j);
3207: printf("%1d%1d",i,j);
3208: for(k=1; k<=ncovmodel;k++){
3209: printf(" %.5e",delti[jk]);
3210: fprintf(ficres," %.5e",delti[jk]);
3211: jk++;
3212: }
3213: printf("\n");
3214: fprintf(ficres,"\n");
3215: }
3216: }
1.18 lievre 3217: }
1.2 lievre 3218:
3219: k=1;
1.34 brouard 3220: 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");
3221: printf("# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n# ...\n# 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n");
1.2 lievre 3222: for(i=1;i<=npar;i++){
3223: /* if (k>nlstate) k=1;
3224: i1=(i-1)/(ncovmodel*nlstate)+1;
3225: fprintf(ficres,"%s%d%d",alph[k],i1,tab[i]);
3226: printf("%s%d%d",alph[k],i1,tab[i]);*/
3227: fprintf(ficres,"%3d",i);
3228: printf("%3d",i);
3229: for(j=1; j<=i;j++){
3230: fprintf(ficres," %.5e",matcov[i][j]);
3231: printf(" %.5e",matcov[i][j]);
3232: }
3233: fprintf(ficres,"\n");
3234: printf("\n");
3235: k++;
3236: }
3237:
3238: while((c=getc(ficpar))=='#' && c!= EOF){
3239: ungetc(c,ficpar);
3240: fgets(line, MAXLINE, ficpar);
3241: puts(line);
3242: fputs(line,ficparo);
3243: }
3244: ungetc(c,ficpar);
1.36 brouard 3245: estepm=0;
3246: fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm);
3247: if (estepm==0 || estepm < stepm) estepm=stepm;
1.2 lievre 3248: if (fage <= 2) {
1.35 lievre 3249: bage = ageminpar;
1.28 lievre 3250: fage = agemaxpar;
1.2 lievre 3251: }
1.22 brouard 3252:
3253: fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");
1.36 brouard 3254: fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
3255: fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
1.19 lievre 3256:
3257: while((c=getc(ficpar))=='#' && c!= EOF){
3258: ungetc(c,ficpar);
3259: fgets(line, MAXLINE, ficpar);
3260: puts(line);
3261: fputs(line,ficparo);
3262: }
3263: ungetc(c,ficpar);
3264:
1.25 lievre 3265: fscanf(ficpar,"begin-prev-date=%lf/%lf/%lf end-prev-date=%lf/%lf/%lf\n",&jprev1, &mprev1,&anprev1,&jprev2, &mprev2,&anprev2);
3266: fprintf(ficparo,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);
3267: fprintf(ficres,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);
1.19 lievre 3268:
3269: while((c=getc(ficpar))=='#' && c!= EOF){
3270: ungetc(c,ficpar);
3271: fgets(line, MAXLINE, ficpar);
3272: puts(line);
3273: fputs(line,ficparo);
3274: }
3275: ungetc(c,ficpar);
3276:
1.7 lievre 3277:
1.19 lievre 3278: dateprev1=anprev1+mprev1/12.+jprev1/365.;
3279: dateprev2=anprev2+mprev2/12.+jprev2/365.;
3280:
3281: fscanf(ficpar,"pop_based=%d\n",&popbased);
1.28 lievre 3282: fprintf(ficparo,"pop_based=%d\n",popbased);
3283: fprintf(ficres,"pop_based=%d\n",popbased);
3284:
3285: while((c=getc(ficpar))=='#' && c!= EOF){
3286: ungetc(c,ficpar);
3287: fgets(line, MAXLINE, ficpar);
3288: puts(line);
3289: fputs(line,ficparo);
3290: }
3291: ungetc(c,ficpar);
1.19 lievre 3292:
1.28 lievre 3293: fscanf(ficpar,"starting-proj-date=%lf/%lf/%lf final-proj-date=%lf/%lf/%lf mov_average=%d\n",&jproj1,&mproj1,&anproj1,&jproj2,&mproj2,&anproj2,&mobilav);
3294: fprintf(ficparo,"starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mov_average=%d\n",jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilav);
3295: fprintf(ficres,"starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mov_average=%d\n",jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilav);
3296:
3297:
3298: while((c=getc(ficpar))=='#' && c!= EOF){
1.19 lievre 3299: ungetc(c,ficpar);
3300: fgets(line, MAXLINE, ficpar);
3301: puts(line);
3302: fputs(line,ficparo);
3303: }
3304: ungetc(c,ficpar);
1.28 lievre 3305:
3306: fscanf(ficpar,"popforecast=%d popfile=%s popfiledate=%lf/%lf/%lf last-popfiledate=%lf/%lf/%lf\n",&popforecast,popfile,&jpyram,&mpyram,&anpyram,&jpyram1,&mpyram1,&anpyram1);
3307: fprintf(ficparo,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);
3308: fprintf(ficres,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);
1.19 lievre 3309:
1.26 lievre 3310: freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);
1.19 lievre 3311:
1.25 lievre 3312: /*------------ gnuplot -------------*/
1.35 lievre 3313: printinggnuplot(fileres,optionfilefiname,optionfile,optionfilegnuplot, ageminpar,agemaxpar,fage, pathc,p);
1.25 lievre 3314:
3315: /*------------ free_vector -------------*/
3316: chdir(path);
1.2 lievre 3317:
1.25 lievre 3318: free_ivector(wav,1,imx);
3319: free_imatrix(dh,1,lastpass-firstpass+1,1,imx);
3320: free_imatrix(mw,1,lastpass-firstpass+1,1,imx);
3321: free_ivector(num,1,n);
3322: free_vector(agedc,1,n);
3323: /*free_matrix(covar,1,NCOVMAX,1,n);*/
3324: fclose(ficparo);
3325: fclose(ficres);
1.28 lievre 3326:
1.2 lievre 3327: /*--------- index.htm --------*/
3328:
1.45 lievre 3329: printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,model,imx,jmin,jmax,jmean,optionfile,optionfilehtm,rfileres,optionfilegnuplot,version,popforecast,estepm,jprev1,mprev1,anprev1,jprev2,mprev2,anprev2);
1.2 lievre 3330:
1.25 lievre 3331:
1.2 lievre 3332: /*--------------- Prevalence limit --------------*/
3333:
3334: strcpy(filerespl,"pl");
3335: strcat(filerespl,fileres);
3336: if((ficrespl=fopen(filerespl,"w"))==NULL) {
3337: printf("Problem with Prev limit resultfile: %s\n", filerespl);goto end;
3338: }
3339: printf("Computing prevalence limit: result on file '%s' \n", filerespl);
3340: fprintf(ficrespl,"#Prevalence limit\n");
3341: fprintf(ficrespl,"#Age ");
3342: for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);
3343: fprintf(ficrespl,"\n");
3344:
3345: prlim=matrix(1,nlstate,1,nlstate);
3346: pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
3347: oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
3348: newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
3349: savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
3350: oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */
3351: k=0;
1.35 lievre 3352: agebase=ageminpar;
1.28 lievre 3353: agelim=agemaxpar;
1.2 lievre 3354: ftolpl=1.e-10;
1.7 lievre 3355: i1=cptcoveff;
1.2 lievre 3356: if (cptcovn < 1){i1=1;}
3357:
3358: for(cptcov=1;cptcov<=i1;cptcov++){
3359: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
3360: k=k+1;
3361: /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/
1.6 lievre 3362: fprintf(ficrespl,"\n#******");
1.7 lievre 3363: for(j=1;j<=cptcoveff;j++)
3364: fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
1.2 lievre 3365: fprintf(ficrespl,"******\n");
3366:
3367: for (age=agebase; age<=agelim; age++){
3368: prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
3369: fprintf(ficrespl,"%.0f",age );
3370: for(i=1; i<=nlstate;i++)
3371: fprintf(ficrespl," %.5f", prlim[i][i]);
3372: fprintf(ficrespl,"\n");
3373: }
3374: }
3375: }
3376: fclose(ficrespl);
1.13 lievre 3377:
1.2 lievre 3378: /*------------- h Pij x at various ages ------------*/
3379:
3380: strcpy(filerespij,"pij"); strcat(filerespij,fileres);
3381: if((ficrespij=fopen(filerespij,"w"))==NULL) {
3382: printf("Problem with Pij resultfile: %s\n", filerespij);goto end;
3383: }
3384: printf("Computing pij: result on file '%s' \n", filerespij);
3385:
3386: stepsize=(int) (stepm+YEARM-1)/YEARM;
1.13 lievre 3387: /*if (stepm<=24) stepsize=2;*/
1.2 lievre 3388:
3389: agelim=AGESUP;
3390: hstepm=stepsize*YEARM; /* Every year of age */
3391: hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */
3392:
3393: k=0;
3394: for(cptcov=1;cptcov<=i1;cptcov++){
3395: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
3396: k=k+1;
3397: fprintf(ficrespij,"\n#****** ");
1.7 lievre 3398: for(j=1;j<=cptcoveff;j++)
3399: fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
1.2 lievre 3400: fprintf(ficrespij,"******\n");
3401:
3402: for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */
3403: nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
3404: nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
3405: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3406: oldm=oldms;savm=savms;
3407: hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
3408: fprintf(ficrespij,"# Age");
3409: for(i=1; i<=nlstate;i++)
3410: for(j=1; j<=nlstate+ndeath;j++)
3411: fprintf(ficrespij," %1d-%1d",i,j);
3412: fprintf(ficrespij,"\n");
1.40 lievre 3413: for (h=0; h<=nhstepm; h++){
1.2 lievre 3414: fprintf(ficrespij,"%d %.0f %.0f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );
3415: for(i=1; i<=nlstate;i++)
3416: for(j=1; j<=nlstate+ndeath;j++)
3417: fprintf(ficrespij," %.5f", p3mat[i][j][h]);
3418: fprintf(ficrespij,"\n");
1.40 lievre 3419: }
1.2 lievre 3420: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3421: fprintf(ficrespij,"\n");
3422: }
3423: }
3424: }
3425:
1.39 lievre 3426: varprob(fileres, matcov, p, delti, nlstate, (int) bage, (int) fage,k,Tvar,nbcode, ncodemax);
1.13 lievre 3427:
1.2 lievre 3428: fclose(ficrespij);
3429:
1.27 lievre 3430:
3431: /*---------- Forecasting ------------------*/
1.32 brouard 3432: if((stepm == 1) && (strcmp(model,".")==0)){
1.27 lievre 3433: prevforecast(fileres, anproj1,mproj1,jproj1, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anproj2,p, i1);
1.32 brouard 3434: if (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);
1.41 lievre 3435: }
1.21 lievre 3436: else{
3437: erreur=108;
1.32 brouard 3438: printf("Warning %d!! You can only forecast the prevalences if the optimization\n has been performed with stepm = 1 (month) instead of %d or model=. instead of '%s'\n", erreur, stepm, model);
1.21 lievre 3439: }
1.26 lievre 3440:
1.27 lievre 3441:
1.2 lievre 3442: /*---------- Health expectancies and variances ------------*/
3443:
3444: strcpy(filerest,"t");
3445: strcat(filerest,fileres);
3446: if((ficrest=fopen(filerest,"w"))==NULL) {
3447: printf("Problem with total LE resultfile: %s\n", filerest);goto end;
3448: }
3449: printf("Computing Total LEs with variances: file '%s' \n", filerest);
3450:
3451:
3452: strcpy(filerese,"e");
3453: strcat(filerese,fileres);
3454: if((ficreseij=fopen(filerese,"w"))==NULL) {
3455: printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
3456: }
3457: printf("Computing Health Expectancies: result on file '%s' \n", filerese);
3458:
3459: strcpy(fileresv,"v");
3460: strcat(fileresv,fileres);
3461: if((ficresvij=fopen(fileresv,"w"))==NULL) {
3462: printf("Problem with variance resultfile: %s\n", fileresv);exit(0);
3463: }
3464: printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
1.41 lievre 3465: calagedate=-1;
3466: prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);
1.2 lievre 3467:
3468: k=0;
3469: for(cptcov=1;cptcov<=i1;cptcov++){
3470: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
3471: k=k+1;
3472: fprintf(ficrest,"\n#****** ");
1.7 lievre 3473: for(j=1;j<=cptcoveff;j++)
3474: fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
1.2 lievre 3475: fprintf(ficrest,"******\n");
3476:
3477: fprintf(ficreseij,"\n#****** ");
1.7 lievre 3478: for(j=1;j<=cptcoveff;j++)
1.35 lievre 3479: fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
1.2 lievre 3480: fprintf(ficreseij,"******\n");
3481:
3482: fprintf(ficresvij,"\n#****** ");
1.7 lievre 3483: for(j=1;j<=cptcoveff;j++)
1.35 lievre 3484: fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
1.2 lievre 3485: fprintf(ficresvij,"******\n");
3486:
3487: eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
3488: oldm=oldms;savm=savms;
1.41 lievre 3489: evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov);
3490:
1.2 lievre 3491: vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
3492: oldm=oldms;savm=savms;
1.36 brouard 3493: varevsij(fileres, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm);
1.26 lievre 3494:
3495:
3496:
1.2 lievre 3497: fprintf(ficrest,"#Total LEs with variances: e.. (std) ");
3498: for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);
3499: fprintf(ficrest,"\n");
1.26 lievre 3500:
1.2 lievre 3501: epj=vector(1,nlstate+1);
3502: for(age=bage; age <=fage ;age++){
3503: prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
1.14 lievre 3504: if (popbased==1) {
3505: for(i=1; i<=nlstate;i++)
3506: prlim[i][i]=probs[(int)age][i][k];
3507: }
3508:
1.33 brouard 3509: fprintf(ficrest," %4.0f",age);
1.2 lievre 3510: for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){
3511: for(i=1, epj[j]=0.;i <=nlstate;i++) {
1.33 brouard 3512: epj[j] += prlim[i][i]*eij[i][j][(int)age];
1.41 lievre 3513: /* printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/
1.2 lievre 3514: }
3515: epj[nlstate+1] +=epj[j];
3516: }
1.41 lievre 3517:
1.2 lievre 3518: for(i=1, vepp=0.;i <=nlstate;i++)
3519: for(j=1;j <=nlstate;j++)
3520: vepp += vareij[i][j][(int)age];
1.38 lievre 3521: fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));
1.2 lievre 3522: for(j=1;j <=nlstate;j++){
1.38 lievre 3523: fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));
1.2 lievre 3524: }
3525: fprintf(ficrest,"\n");
3526: }
3527: }
3528: }
1.41 lievre 3529: free_matrix(mint,1,maxwav,1,n);
3530: free_matrix(anint,1,maxwav,1,n); free_imatrix(s,1,maxwav+1,1,n);
3531: free_vector(weight,1,n);
1.27 lievre 3532: fclose(ficreseij);
3533: fclose(ficresvij);
1.2 lievre 3534: fclose(ficrest);
3535: fclose(ficpar);
3536: free_vector(epj,1,nlstate+1);
1.26 lievre 3537:
1.2 lievre 3538: /*------- Variance limit prevalence------*/
3539:
1.27 lievre 3540: strcpy(fileresvpl,"vpl");
1.2 lievre 3541: strcat(fileresvpl,fileres);
3542: if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {
3543: printf("Problem with variance prev lim resultfile: %s\n", fileresvpl);
3544: exit(0);
3545: }
3546: printf("Computing Variance-covariance of Prevalence limit: file '%s' \n", fileresvpl);
3547:
1.27 lievre 3548: k=0;
3549: for(cptcov=1;cptcov<=i1;cptcov++){
3550: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
3551: k=k+1;
3552: fprintf(ficresvpl,"\n#****** ");
3553: for(j=1;j<=cptcoveff;j++)
3554: fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
3555: fprintf(ficresvpl,"******\n");
3556:
3557: varpl=matrix(1,nlstate,(int) bage, (int) fage);
3558: oldm=oldms;savm=savms;
1.2 lievre 3559: varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);
1.27 lievre 3560: }
1.2 lievre 3561: }
3562:
3563: fclose(ficresvpl);
3564:
3565: /*---------- End : free ----------------*/
3566: free_matrix(varpl,1,nlstate,(int) bage, (int)fage);
3567:
3568: free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);
3569: free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
3570:
3571:
3572: free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);
3573: free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);
3574: free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);
3575: free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);
1.13 lievre 3576:
1.2 lievre 3577: free_matrix(matcov,1,npar,1,npar);
3578: free_vector(delti,1,npar);
1.26 lievre 3579: free_matrix(agev,1,maxwav,1,imx);
1.2 lievre 3580: free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
3581:
1.21 lievre 3582: if(erreur >0)
1.34 brouard 3583: printf("End of Imach with error or warning %d\n",erreur);
1.21 lievre 3584: else printf("End of Imach\n");
1.2 lievre 3585: /* gettimeofday(&end_time, (struct timezone*)0);*/ /* after time */
3586:
3587: /* 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);*/
3588: /*printf("Total time was %d uSec.\n", total_usecs);*/
3589: /*------ End -----------*/
1.12 lievre 3590:
1.2 lievre 3591:
3592: end:
3593: #ifdef windows
1.22 brouard 3594: /* chdir(pathcd);*/
1.2 lievre 3595: #endif
1.22 brouard 3596: /*system("wgnuplot graph.plt");*/
3597: /*system("../gp37mgw/wgnuplot graph.plt");*/
3598: /*system("cd ../gp37mgw");*/
3599: /* system("..\\gp37mgw\\wgnuplot graph.plt");*/
3600: strcpy(plotcmd,GNUPLOTPROGRAM);
3601: strcat(plotcmd," ");
3602: strcat(plotcmd,optionfilegnuplot);
3603: system(plotcmd);
1.2 lievre 3604:
3605: #ifdef windows
3606: while (z[0] != 'q') {
1.35 lievre 3607: /* chdir(path); */
3608: printf("\nType e to edit output files, g to graph again, c to start again, and q for exiting: ");
1.2 lievre 3609: scanf("%s",z);
3610: if (z[0] == 'c') system("./imach");
1.35 lievre 3611: else if (z[0] == 'e') system(optionfilehtm);
3612: else if (z[0] == 'g') system(plotcmd);
1.2 lievre 3613: else if (z[0] == 'q') exit(0);
3614: }
3615: #endif
3616: }
3617:
3618:
FreeBSD-CVSweb <freebsd-cvsweb@FreeBSD.org>
![[BACK]](/icons/small/back.gif){kind=icon}
Return to imach.c CVS log ![[TXT]](/icons/small/text.gif){kind=icon}
![[DIR]](/icons/small/dir.gif){kind=icon}
Up to [Local Repository] / imach / src