Annotation of imach096d/src/imach.c, revision 1.31
1.31 ! brouard 1: /* $Id: imach.c,v 1.30 2002/03/08 16:17:18 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
17: probabibility to be observed in state j at the second wave
18: conditional to be observed in state i at the first wave. Therefore
19: the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where
20: 'age' is age and 'sex' is a covariate. If you want to have a more
21: complex model than "constant and age", you should modify the program
22: where the markup *Covariates have to be included here again* invites
23: you to do it. More covariates you add, slower the
24: convergence.
25:
26: The advantage of this computer programme, compared to a simple
27: multinomial logistic model, is clear when the delay between waves is not
28: identical for each individual. Also, if a individual missed an
29: intermediate interview, the information is lost, but taken into
30: account using an interpolation or extrapolation.
31:
32: hPijx is the probability to be observed in state i at age x+h
33: conditional to the observed state i at age x. The delay 'h' can be
34: split into an exact number (nh*stepm) of unobserved intermediate
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
1.22 brouard 59: #define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"
1.2 lievre 60: #define FILENAMELENGTH 80
61: /*#define DEBUG*/
62: #define windows
1.5 lievre 63: #define GLOCK_ERROR_NOPATH -1 /* empty path */
64: #define GLOCK_ERROR_GETCWD -2 /* cannot get cwd */
65:
1.2 lievre 66: #define MAXPARM 30 /* Maximum number of parameters for the optimization */
67: #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */
68:
69: #define NINTERVMAX 8
70: #define NLSTATEMAX 8 /* Maximum number of live states (for func) */
71: #define NDEATHMAX 8 /* Maximum number of dead states (for func) */
72: #define NCOVMAX 8 /* Maximum number of covariates */
1.3 lievre 73: #define MAXN 20000
1.2 lievre 74: #define YEARM 12. /* Number of months per year */
75: #define AGESUP 130
76: #define AGEBASE 40
77:
78:
1.21 lievre 79: int erreur; /* Error number */
1.2 lievre 80: int nvar;
1.8 lievre 81: int cptcovn, cptcovage=0, cptcoveff=0,cptcov;
1.2 lievre 82: int npar=NPARMAX;
83: int nlstate=2; /* Number of live states */
84: int ndeath=1; /* Number of dead states */
85: int ncovmodel, ncov; /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
1.15 lievre 86: int popbased=0;
1.2 lievre 87:
88: int *wav; /* Number of waves for this individuual 0 is possible */
89: int maxwav; /* Maxim number of waves */
1.8 lievre 90: int jmin, jmax; /* min, max spacing between 2 waves */
1.2 lievre 91: int mle, weightopt;
92: int **mw; /* mw[mi][i] is number of the mi wave for this individual */
93: int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
1.8 lievre 94: double jmean; /* Mean space between 2 waves */
1.2 lievre 95: double **oldm, **newm, **savm; /* Working pointers to matrices */
96: double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
1.27 lievre 97: FILE *fic,*ficpar, *ficparo,*ficres, *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
1.25 lievre 98: FILE *ficgp,*ficresprob,*ficpop;
1.2 lievre 99: FILE *ficreseij;
100: char filerese[FILENAMELENGTH];
101: FILE *ficresvij;
102: char fileresv[FILENAMELENGTH];
103: FILE *ficresvpl;
104: char fileresvpl[FILENAMELENGTH];
105:
106: #define NR_END 1
107: #define FREE_ARG char*
108: #define FTOL 1.0e-10
109:
110: #define NRANSI
111: #define ITMAX 200
112:
113: #define TOL 2.0e-4
114:
115: #define CGOLD 0.3819660
116: #define ZEPS 1.0e-10
117: #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);
118:
119: #define GOLD 1.618034
120: #define GLIMIT 100.0
121: #define TINY 1.0e-20
122:
123: static double maxarg1,maxarg2;
124: #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
125: #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
1.25 lievre 126:
1.2 lievre 127: #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
128: #define rint(a) floor(a+0.5)
129:
130: static double sqrarg;
131: #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
132: #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}
133:
134: int imx;
135: int stepm;
136: /* Stepm, step in month: minimum step interpolation*/
137:
138: int m,nb;
1.6 lievre 139: int *num, firstpass=0, lastpass=4,*cod, *ncodemax, *Tage;
1.2 lievre 140: double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
1.13 lievre 141: double **pmmij, ***probs, ***mobaverage;
1.19 lievre 142: double dateintmean=0;
1.2 lievre 143:
144: double *weight;
145: int **s; /* Status */
146: double *agedc, **covar, idx;
1.7 lievre 147: int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;
1.2 lievre 148:
149: double ftol=FTOL; /* Tolerance for computing Max Likelihood */
150: double ftolhess; /* Tolerance for computing hessian */
151:
1.7 lievre 152: /**************** split *************************/
1.22 brouard 153: static int split( char *path, char *dirc, char *name, char *ext, char *finame )
1.5 lievre 154: {
155: char *s; /* pointer */
156: int l1, l2; /* length counters */
157:
158: l1 = strlen( path ); /* length of path */
159: if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
1.22 brouard 160: #ifdef windows
1.5 lievre 161: s = strrchr( path, '\\' ); /* find last / */
1.22 brouard 162: #else
163: s = strrchr( path, '/' ); /* find last / */
164: #endif
1.5 lievre 165: if ( s == NULL ) { /* no directory, so use current */
166: #if defined(__bsd__) /* get current working directory */
167: extern char *getwd( );
168:
169: if ( getwd( dirc ) == NULL ) {
170: #else
171: extern char *getcwd( );
172:
173: if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {
174: #endif
175: return( GLOCK_ERROR_GETCWD );
176: }
177: strcpy( name, path ); /* we've got it */
178: } else { /* strip direcotry from path */
179: s++; /* after this, the filename */
180: l2 = strlen( s ); /* length of filename */
181: if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
182: strcpy( name, s ); /* save file name */
183: strncpy( dirc, path, l1 - l2 ); /* now the directory */
184: dirc[l1-l2] = 0; /* add zero */
185: }
186: l1 = strlen( dirc ); /* length of directory */
1.22 brouard 187: #ifdef windows
1.5 lievre 188: if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; }
1.22 brouard 189: #else
190: if ( dirc[l1-1] != '/' ) { dirc[l1] = '/'; dirc[l1+1] = 0; }
191: #endif
192: s = strrchr( name, '.' ); /* find last / */
193: s++;
194: strcpy(ext,s); /* save extension */
195: l1= strlen( name);
196: l2= strlen( s)+1;
197: strncpy( finame, name, l1-l2);
198: finame[l1-l2]= 0;
1.5 lievre 199: return( 0 ); /* we're done */
200: }
201:
202:
1.2 lievre 203: /******************************************/
204:
205: void replace(char *s, char*t)
206: {
207: int i;
208: int lg=20;
209: i=0;
210: lg=strlen(t);
211: for(i=0; i<= lg; i++) {
212: (s[i] = t[i]);
213: if (t[i]== '\\') s[i]='/';
214: }
215: }
216:
217: int nbocc(char *s, char occ)
218: {
219: int i,j=0;
220: int lg=20;
221: i=0;
222: lg=strlen(s);
223: for(i=0; i<= lg; i++) {
224: if (s[i] == occ ) j++;
225: }
226: return j;
227: }
228:
229: void cutv(char *u,char *v, char*t, char occ)
230: {
1.6 lievre 231: int i,lg,j,p=0;
1.2 lievre 232: i=0;
233: for(j=0; j<=strlen(t)-1; j++) {
1.3 lievre 234: if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;
1.2 lievre 235: }
236:
237: lg=strlen(t);
238: for(j=0; j<p; j++) {
239: (u[j] = t[j]);
240: }
1.6 lievre 241: u[p]='\0';
1.2 lievre 242:
243: for(j=0; j<= lg; j++) {
244: if (j>=(p+1))(v[j-p-1] = t[j]);
245: }
246: }
247:
248: /********************** nrerror ********************/
249:
250: void nrerror(char error_text[])
251: {
252: fprintf(stderr,"ERREUR ...\n");
253: fprintf(stderr,"%s\n",error_text);
254: exit(1);
255: }
256: /*********************** vector *******************/
257: double *vector(int nl, int nh)
258: {
259: double *v;
260: v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
261: if (!v) nrerror("allocation failure in vector");
262: return v-nl+NR_END;
263: }
264:
265: /************************ free vector ******************/
266: void free_vector(double*v, int nl, int nh)
267: {
268: free((FREE_ARG)(v+nl-NR_END));
269: }
270:
271: /************************ivector *******************************/
272: int *ivector(long nl,long nh)
273: {
274: int *v;
275: v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
276: if (!v) nrerror("allocation failure in ivector");
277: return v-nl+NR_END;
278: }
279:
280: /******************free ivector **************************/
281: void free_ivector(int *v, long nl, long nh)
282: {
283: free((FREE_ARG)(v+nl-NR_END));
284: }
285:
286: /******************* imatrix *******************************/
287: int **imatrix(long nrl, long nrh, long ncl, long nch)
288: /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */
289: {
290: long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;
291: int **m;
292:
293: /* allocate pointers to rows */
294: m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));
295: if (!m) nrerror("allocation failure 1 in matrix()");
296: m += NR_END;
297: m -= nrl;
298:
299:
300: /* allocate rows and set pointers to them */
301: m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));
302: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
303: m[nrl] += NR_END;
304: m[nrl] -= ncl;
305:
306: for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;
307:
308: /* return pointer to array of pointers to rows */
309: return m;
310: }
311:
312: /****************** free_imatrix *************************/
313: void free_imatrix(m,nrl,nrh,ncl,nch)
314: int **m;
315: long nch,ncl,nrh,nrl;
316: /* free an int matrix allocated by imatrix() */
317: {
318: free((FREE_ARG) (m[nrl]+ncl-NR_END));
319: free((FREE_ARG) (m+nrl-NR_END));
320: }
321:
322: /******************* matrix *******************************/
323: double **matrix(long nrl, long nrh, long ncl, long nch)
324: {
325: long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
326: double **m;
327:
328: m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
329: if (!m) nrerror("allocation failure 1 in matrix()");
330: m += NR_END;
331: m -= nrl;
332:
333: m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
334: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
335: m[nrl] += NR_END;
336: m[nrl] -= ncl;
337:
338: for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
339: return m;
340: }
341:
342: /*************************free matrix ************************/
343: void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
344: {
345: free((FREE_ARG)(m[nrl]+ncl-NR_END));
346: free((FREE_ARG)(m+nrl-NR_END));
347: }
348:
349: /******************* ma3x *******************************/
350: double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
351: {
352: long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
353: double ***m;
354:
355: m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
356: if (!m) nrerror("allocation failure 1 in matrix()");
357: m += NR_END;
358: m -= nrl;
359:
360: m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
361: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
362: m[nrl] += NR_END;
363: m[nrl] -= ncl;
364:
365: for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
366:
367: m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
368: if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
369: m[nrl][ncl] += NR_END;
370: m[nrl][ncl] -= nll;
371: for (j=ncl+1; j<=nch; j++)
372: m[nrl][j]=m[nrl][j-1]+nlay;
373:
374: for (i=nrl+1; i<=nrh; i++) {
375: m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
376: for (j=ncl+1; j<=nch; j++)
377: m[i][j]=m[i][j-1]+nlay;
378: }
379: return m;
380: }
381:
382: /*************************free ma3x ************************/
383: void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
384: {
385: free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
386: free((FREE_ARG)(m[nrl]+ncl-NR_END));
387: free((FREE_ARG)(m+nrl-NR_END));
388: }
389:
390: /***************** f1dim *************************/
391: extern int ncom;
392: extern double *pcom,*xicom;
393: extern double (*nrfunc)(double []);
394:
395: double f1dim(double x)
396: {
397: int j;
398: double f;
399: double *xt;
400:
401: xt=vector(1,ncom);
402: for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];
403: f=(*nrfunc)(xt);
404: free_vector(xt,1,ncom);
405: return f;
406: }
407:
408: /*****************brent *************************/
409: double brent(double ax, double bx, double cx, double (*f)(double), double tol, double *xmin)
410: {
411: int iter;
412: double a,b,d,etemp;
413: double fu,fv,fw,fx;
414: double ftemp;
415: double p,q,r,tol1,tol2,u,v,w,x,xm;
416: double e=0.0;
417:
418: a=(ax < cx ? ax : cx);
419: b=(ax > cx ? ax : cx);
420: x=w=v=bx;
421: fw=fv=fx=(*f)(x);
422: for (iter=1;iter<=ITMAX;iter++) {
423: xm=0.5*(a+b);
424: tol2=2.0*(tol1=tol*fabs(x)+ZEPS);
425: /* if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
426: printf(".");fflush(stdout);
427: #ifdef DEBUG
428: 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);
429: /* if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
430: #endif
431: if (fabs(x-xm) <= (tol2-0.5*(b-a))){
432: *xmin=x;
433: return fx;
434: }
435: ftemp=fu;
436: if (fabs(e) > tol1) {
437: r=(x-w)*(fx-fv);
438: q=(x-v)*(fx-fw);
439: p=(x-v)*q-(x-w)*r;
440: q=2.0*(q-r);
441: if (q > 0.0) p = -p;
442: q=fabs(q);
443: etemp=e;
444: e=d;
445: if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))
446: d=CGOLD*(e=(x >= xm ? a-x : b-x));
447: else {
448: d=p/q;
449: u=x+d;
450: if (u-a < tol2 || b-u < tol2)
451: d=SIGN(tol1,xm-x);
452: }
453: } else {
454: d=CGOLD*(e=(x >= xm ? a-x : b-x));
455: }
456: u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));
457: fu=(*f)(u);
458: if (fu <= fx) {
459: if (u >= x) a=x; else b=x;
460: SHFT(v,w,x,u)
461: SHFT(fv,fw,fx,fu)
462: } else {
463: if (u < x) a=u; else b=u;
464: if (fu <= fw || w == x) {
465: v=w;
466: w=u;
467: fv=fw;
468: fw=fu;
469: } else if (fu <= fv || v == x || v == w) {
470: v=u;
471: fv=fu;
472: }
473: }
474: }
475: nrerror("Too many iterations in brent");
476: *xmin=x;
477: return fx;
478: }
479:
480: /****************** mnbrak ***********************/
481:
482: void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,
483: double (*func)(double))
484: {
485: double ulim,u,r,q, dum;
486: double fu;
487:
488: *fa=(*func)(*ax);
489: *fb=(*func)(*bx);
490: if (*fb > *fa) {
491: SHFT(dum,*ax,*bx,dum)
492: SHFT(dum,*fb,*fa,dum)
493: }
494: *cx=(*bx)+GOLD*(*bx-*ax);
495: *fc=(*func)(*cx);
496: while (*fb > *fc) {
497: r=(*bx-*ax)*(*fb-*fc);
498: q=(*bx-*cx)*(*fb-*fa);
499: u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/
500: (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r));
501: ulim=(*bx)+GLIMIT*(*cx-*bx);
502: if ((*bx-u)*(u-*cx) > 0.0) {
503: fu=(*func)(u);
504: } else if ((*cx-u)*(u-ulim) > 0.0) {
505: fu=(*func)(u);
506: if (fu < *fc) {
507: SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))
508: SHFT(*fb,*fc,fu,(*func)(u))
509: }
510: } else if ((u-ulim)*(ulim-*cx) >= 0.0) {
511: u=ulim;
512: fu=(*func)(u);
513: } else {
514: u=(*cx)+GOLD*(*cx-*bx);
515: fu=(*func)(u);
516: }
517: SHFT(*ax,*bx,*cx,u)
518: SHFT(*fa,*fb,*fc,fu)
519: }
520: }
521:
522: /*************** linmin ************************/
523:
524: int ncom;
525: double *pcom,*xicom;
526: double (*nrfunc)(double []);
527:
528: void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))
529: {
530: double brent(double ax, double bx, double cx,
531: double (*f)(double), double tol, double *xmin);
532: double f1dim(double x);
533: void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,
534: double *fc, double (*func)(double));
535: int j;
536: double xx,xmin,bx,ax;
537: double fx,fb,fa;
538:
539: ncom=n;
540: pcom=vector(1,n);
541: xicom=vector(1,n);
542: nrfunc=func;
543: for (j=1;j<=n;j++) {
544: pcom[j]=p[j];
545: xicom[j]=xi[j];
546: }
547: ax=0.0;
548: xx=1.0;
549: mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim);
550: *fret=brent(ax,xx,bx,f1dim,TOL,&xmin);
551: #ifdef DEBUG
552: printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
553: #endif
554: for (j=1;j<=n;j++) {
555: xi[j] *= xmin;
556: p[j] += xi[j];
557: }
558: free_vector(xicom,1,n);
559: free_vector(pcom,1,n);
560: }
561:
562: /*************** powell ************************/
563: void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,
564: double (*func)(double []))
565: {
566: void linmin(double p[], double xi[], int n, double *fret,
567: double (*func)(double []));
568: int i,ibig,j;
569: double del,t,*pt,*ptt,*xit;
570: double fp,fptt;
571: double *xits;
572: pt=vector(1,n);
573: ptt=vector(1,n);
574: xit=vector(1,n);
575: xits=vector(1,n);
576: *fret=(*func)(p);
577: for (j=1;j<=n;j++) pt[j]=p[j];
578: for (*iter=1;;++(*iter)) {
579: fp=(*fret);
580: ibig=0;
581: del=0.0;
582: printf("\nPowell iter=%d -2*LL=%.12f",*iter,*fret);
583: for (i=1;i<=n;i++)
584: printf(" %d %.12f",i, p[i]);
585: printf("\n");
586: for (i=1;i<=n;i++) {
587: for (j=1;j<=n;j++) xit[j]=xi[j][i];
588: fptt=(*fret);
589: #ifdef DEBUG
590: printf("fret=%lf \n",*fret);
591: #endif
592: printf("%d",i);fflush(stdout);
593: linmin(p,xit,n,fret,func);
594: if (fabs(fptt-(*fret)) > del) {
595: del=fabs(fptt-(*fret));
596: ibig=i;
597: }
598: #ifdef DEBUG
599: printf("%d %.12e",i,(*fret));
600: for (j=1;j<=n;j++) {
601: xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
602: printf(" x(%d)=%.12e",j,xit[j]);
603: }
604: for(j=1;j<=n;j++)
605: printf(" p=%.12e",p[j]);
606: printf("\n");
607: #endif
608: }
609: if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {
610: #ifdef DEBUG
611: int k[2],l;
612: k[0]=1;
613: k[1]=-1;
614: printf("Max: %.12e",(*func)(p));
615: for (j=1;j<=n;j++)
616: printf(" %.12e",p[j]);
617: printf("\n");
618: for(l=0;l<=1;l++) {
619: for (j=1;j<=n;j++) {
620: ptt[j]=p[j]+(p[j]-pt[j])*k[l];
621: printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
622: }
623: printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
624: }
625: #endif
626:
627:
628: free_vector(xit,1,n);
629: free_vector(xits,1,n);
630: free_vector(ptt,1,n);
631: free_vector(pt,1,n);
632: return;
633: }
634: if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");
635: for (j=1;j<=n;j++) {
636: ptt[j]=2.0*p[j]-pt[j];
637: xit[j]=p[j]-pt[j];
638: pt[j]=p[j];
639: }
640: fptt=(*func)(ptt);
641: if (fptt < fp) {
642: t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt);
643: if (t < 0.0) {
644: linmin(p,xit,n,fret,func);
645: for (j=1;j<=n;j++) {
646: xi[j][ibig]=xi[j][n];
647: xi[j][n]=xit[j];
648: }
649: #ifdef DEBUG
650: printf("Direction changed last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
651: for(j=1;j<=n;j++)
652: printf(" %.12e",xit[j]);
653: printf("\n");
654: #endif
655: }
656: }
657: }
658: }
659:
660: /**** Prevalence limit ****************/
661:
662: double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)
663: {
664: /* Computes the prevalence limit in each live state at age x by left multiplying the unit
665: matrix by transitions matrix until convergence is reached */
666:
667: int i, ii,j,k;
668: double min, max, maxmin, maxmax,sumnew=0.;
669: double **matprod2();
670: double **out, cov[NCOVMAX], **pmij();
671: double **newm;
672: double agefin, delaymax=50 ; /* Max number of years to converge */
673:
674: for (ii=1;ii<=nlstate+ndeath;ii++)
675: for (j=1;j<=nlstate+ndeath;j++){
676: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
677: }
1.6 lievre 678:
679: cov[1]=1.;
680:
681: /* Even if hstepm = 1, at least one multiplication by the unit matrix */
1.2 lievre 682: for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
683: newm=savm;
684: /* Covariates have to be included here again */
1.6 lievre 685: cov[2]=agefin;
686:
687: for (k=1; k<=cptcovn;k++) {
1.7 lievre 688: cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
689: /*printf("ij=%d Tvar[k]=%d nbcode=%d cov=%lf\n",ij, Tvar[k],nbcode[Tvar[k]][codtab[ij][Tvar[k]]],cov[2+k]);*/
1.6 lievre 690: }
691: for (k=1; k<=cptcovage;k++)
692: cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
1.7 lievre 693: for (k=1; k<=cptcovprod;k++)
694: cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
695:
696: /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
697: /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
698:
1.2 lievre 699: out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);
700:
701: savm=oldm;
702: oldm=newm;
703: maxmax=0.;
704: for(j=1;j<=nlstate;j++){
705: min=1.;
706: max=0.;
707: for(i=1; i<=nlstate; i++) {
708: sumnew=0;
709: for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
710: prlim[i][j]= newm[i][j]/(1-sumnew);
711: max=FMAX(max,prlim[i][j]);
712: min=FMIN(min,prlim[i][j]);
713: }
714: maxmin=max-min;
715: maxmax=FMAX(maxmax,maxmin);
716: }
717: if(maxmax < ftolpl){
718: return prlim;
719: }
720: }
721: }
722:
1.12 lievre 723: /*************** transition probabilities ***************/
1.2 lievre 724:
725: double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
726: {
727: double s1, s2;
728: /*double t34;*/
729: int i,j,j1, nc, ii, jj;
730:
731: for(i=1; i<= nlstate; i++){
732: for(j=1; j<i;j++){
733: for (nc=1, s2=0.;nc <=ncovmodel; nc++){
734: /*s2 += param[i][j][nc]*cov[nc];*/
735: s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
736: /*printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2);*/
737: }
738: ps[i][j]=s2;
739: /*printf("s1=%.17e, s2=%.17e\n",s1,s2);*/
740: }
741: for(j=i+1; j<=nlstate+ndeath;j++){
742: for (nc=1, s2=0.;nc <=ncovmodel; nc++){
743: s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
744: /*printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2);*/
745: }
1.22 brouard 746: ps[i][j]=s2;
1.2 lievre 747: }
748: }
1.12 lievre 749: /*ps[3][2]=1;*/
750:
1.2 lievre 751: for(i=1; i<= nlstate; i++){
752: s1=0;
753: for(j=1; j<i; j++)
754: s1+=exp(ps[i][j]);
755: for(j=i+1; j<=nlstate+ndeath; j++)
756: s1+=exp(ps[i][j]);
757: ps[i][i]=1./(s1+1.);
758: for(j=1; j<i; j++)
759: ps[i][j]= exp(ps[i][j])*ps[i][i];
760: for(j=i+1; j<=nlstate+ndeath; j++)
761: ps[i][j]= exp(ps[i][j])*ps[i][i];
762: /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
763: } /* end i */
764:
765: for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
766: for(jj=1; jj<= nlstate+ndeath; jj++){
767: ps[ii][jj]=0;
768: ps[ii][ii]=1;
769: }
770: }
771:
1.12 lievre 772:
1.2 lievre 773: /* for(ii=1; ii<= nlstate+ndeath; ii++){
774: for(jj=1; jj<= nlstate+ndeath; jj++){
775: printf("%lf ",ps[ii][jj]);
776: }
777: printf("\n ");
778: }
779: printf("\n ");printf("%lf ",cov[2]);*/
780: /*
781: for(i=1; i<= npar; i++) printf("%f ",x[i]);
782: goto end;*/
783: return ps;
784: }
785:
786: /**************** Product of 2 matrices ******************/
787:
788: double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)
789: {
1.13 lievre 790: /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
1.2 lievre 791: b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
792: /* in, b, out are matrice of pointers which should have been initialized
793: before: only the contents of out is modified. The function returns
794: a pointer to pointers identical to out */
795: long i, j, k;
796: for(i=nrl; i<= nrh; i++)
797: for(k=ncolol; k<=ncoloh; k++)
798: for(j=ncl,out[i][k]=0.; j<=nch; j++)
799: out[i][k] +=in[i][j]*b[j][k];
800:
801: return out;
802: }
803:
804:
805: /************* Higher Matrix Product ***************/
806:
807: double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
808: {
809: /* Computes the transition matrix starting at age 'age' over 'nhstepm*hstepm*stepm' month
810: duration (i.e. until
811: age (in years) age+nhstepm*stepm/12) by multiplying nhstepm*hstepm matrices.
812: Output is stored in matrix po[i][j][h] for h every 'hstepm' step
813: (typically every 2 years instead of every month which is too big).
814: Model is determined by parameters x and covariates have to be
815: included manually here.
816:
817: */
818:
819: int i, j, d, h, k;
820: double **out, cov[NCOVMAX];
821: double **newm;
822:
823: /* Hstepm could be zero and should return the unit matrix */
824: for (i=1;i<=nlstate+ndeath;i++)
825: for (j=1;j<=nlstate+ndeath;j++){
826: oldm[i][j]=(i==j ? 1.0 : 0.0);
827: po[i][j][0]=(i==j ? 1.0 : 0.0);
828: }
829: /* Even if hstepm = 1, at least one multiplication by the unit matrix */
830: for(h=1; h <=nhstepm; h++){
831: for(d=1; d <=hstepm; d++){
832: newm=savm;
833: /* Covariates have to be included here again */
834: cov[1]=1.;
835: cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
1.7 lievre 836: for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
1.12 lievre 837: for (k=1; k<=cptcovage;k++)
1.7 lievre 838: cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
1.12 lievre 839: for (k=1; k<=cptcovprod;k++)
1.7 lievre 840: cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
841:
842:
1.2 lievre 843: /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
844: /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
845: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,
846: pmij(pmmij,cov,ncovmodel,x,nlstate));
847: savm=oldm;
848: oldm=newm;
849: }
850: for(i=1; i<=nlstate+ndeath; i++)
851: for(j=1;j<=nlstate+ndeath;j++) {
852: po[i][j][h]=newm[i][j];
853: /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);
854: */
855: }
856: } /* end h */
857: return po;
858: }
859:
860:
861: /*************** log-likelihood *************/
862: double func( double *x)
863: {
1.6 lievre 864: int i, ii, j, k, mi, d, kk;
1.2 lievre 865: double l, ll[NLSTATEMAX], cov[NCOVMAX];
866: double **out;
867: double sw; /* Sum of weights */
868: double lli; /* Individual log likelihood */
869: long ipmx;
870: /*extern weight */
871: /* We are differentiating ll according to initial status */
872: /* for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
873: /*for(i=1;i<imx;i++)
1.8 lievre 874: printf(" %d\n",s[4][i]);
1.2 lievre 875: */
1.6 lievre 876: cov[1]=1.;
1.2 lievre 877:
878: for(k=1; k<=nlstate; k++) ll[k]=0.;
879: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1.6 lievre 880: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
1.8 lievre 881: for(mi=1; mi<= wav[i]-1; mi++){
1.2 lievre 882: for (ii=1;ii<=nlstate+ndeath;ii++)
883: for (j=1;j<=nlstate+ndeath;j++) oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1.8 lievre 884: for(d=0; d<dh[mi][i]; d++){
885: newm=savm;
886: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
887: for (kk=1; kk<=cptcovage;kk++) {
888: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
889: }
890:
891: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
892: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
893: savm=oldm;
894: oldm=newm;
895:
896:
1.2 lievre 897: } /* end mult */
1.8 lievre 898:
1.2 lievre 899: lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);
900: /* printf(" %f ",out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/
901: ipmx +=1;
902: sw += weight[i];
903: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
904: } /* end of wave */
905: } /* end of individual */
906:
907: for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
908: /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
909: l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
910: return -l;
911: }
912:
913:
914: /*********** Maximum Likelihood Estimation ***************/
915:
916: void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
917: {
918: int i,j, iter;
919: double **xi,*delti;
920: double fret;
921: xi=matrix(1,npar,1,npar);
922: for (i=1;i<=npar;i++)
923: for (j=1;j<=npar;j++)
924: xi[i][j]=(i==j ? 1.0 : 0.0);
925: printf("Powell\n");
926: powell(p,xi,npar,ftol,&iter,&fret,func);
927:
928: printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));
1.21 lievre 929: fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
1.2 lievre 930:
931: }
932:
933: /**** Computes Hessian and covariance matrix ***/
934: void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
935: {
936: double **a,**y,*x,pd;
937: double **hess;
938: int i, j,jk;
939: int *indx;
940:
941: double hessii(double p[], double delta, int theta, double delti[]);
942: double hessij(double p[], double delti[], int i, int j);
943: void lubksb(double **a, int npar, int *indx, double b[]) ;
944: void ludcmp(double **a, int npar, int *indx, double *d) ;
945:
946: hess=matrix(1,npar,1,npar);
947:
948: printf("\nCalculation of the hessian matrix. Wait...\n");
949: for (i=1;i<=npar;i++){
950: printf("%d",i);fflush(stdout);
951: hess[i][i]=hessii(p,ftolhess,i,delti);
952: /*printf(" %f ",p[i]);*/
1.12 lievre 953: /*printf(" %lf ",hess[i][i]);*/
1.2 lievre 954: }
1.12 lievre 955:
1.2 lievre 956: for (i=1;i<=npar;i++) {
957: for (j=1;j<=npar;j++) {
958: if (j>i) {
959: printf(".%d%d",i,j);fflush(stdout);
960: hess[i][j]=hessij(p,delti,i,j);
1.12 lievre 961: hess[j][i]=hess[i][j];
962: /*printf(" %lf ",hess[i][j]);*/
1.2 lievre 963: }
964: }
965: }
966: printf("\n");
967:
968: printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
969:
970: a=matrix(1,npar,1,npar);
971: y=matrix(1,npar,1,npar);
972: x=vector(1,npar);
973: indx=ivector(1,npar);
974: for (i=1;i<=npar;i++)
975: for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
976: ludcmp(a,npar,indx,&pd);
977:
978: for (j=1;j<=npar;j++) {
979: for (i=1;i<=npar;i++) x[i]=0;
980: x[j]=1;
981: lubksb(a,npar,indx,x);
982: for (i=1;i<=npar;i++){
983: matcov[i][j]=x[i];
984: }
985: }
986:
987: printf("\n#Hessian matrix#\n");
988: for (i=1;i<=npar;i++) {
989: for (j=1;j<=npar;j++) {
990: printf("%.3e ",hess[i][j]);
991: }
992: printf("\n");
993: }
994:
995: /* Recompute Inverse */
996: for (i=1;i<=npar;i++)
997: for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];
998: ludcmp(a,npar,indx,&pd);
999:
1000: /* printf("\n#Hessian matrix recomputed#\n");
1001:
1002: for (j=1;j<=npar;j++) {
1003: for (i=1;i<=npar;i++) x[i]=0;
1004: x[j]=1;
1005: lubksb(a,npar,indx,x);
1006: for (i=1;i<=npar;i++){
1007: y[i][j]=x[i];
1008: printf("%.3e ",y[i][j]);
1009: }
1010: printf("\n");
1011: }
1012: */
1013:
1014: free_matrix(a,1,npar,1,npar);
1015: free_matrix(y,1,npar,1,npar);
1016: free_vector(x,1,npar);
1017: free_ivector(indx,1,npar);
1018: free_matrix(hess,1,npar,1,npar);
1019:
1020:
1021: }
1022:
1023: /*************** hessian matrix ****************/
1024: double hessii( double x[], double delta, int theta, double delti[])
1025: {
1026: int i;
1027: int l=1, lmax=20;
1028: double k1,k2;
1029: double p2[NPARMAX+1];
1030: double res;
1031: double delt, delts, nkhi=10.,nkhif=1., khi=1.e-4;
1032: double fx;
1033: int k=0,kmax=10;
1034: double l1;
1035:
1036: fx=func(x);
1037: for (i=1;i<=npar;i++) p2[i]=x[i];
1038: for(l=0 ; l <=lmax; l++){
1039: l1=pow(10,l);
1040: delts=delt;
1041: for(k=1 ; k <kmax; k=k+1){
1042: delt = delta*(l1*k);
1043: p2[theta]=x[theta] +delt;
1044: k1=func(p2)-fx;
1045: p2[theta]=x[theta]-delt;
1046: k2=func(p2)-fx;
1047: /*res= (k1-2.0*fx+k2)/delt/delt; */
1048: res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */
1049:
1050: #ifdef DEBUG
1051: 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);
1052: #endif
1053: /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
1054: if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
1055: k=kmax;
1056: }
1057: else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
1058: k=kmax; l=lmax*10.;
1059: }
1060: else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){
1061: delts=delt;
1062: }
1063: }
1064: }
1065: delti[theta]=delts;
1.12 lievre 1066: return res;
1.3 lievre 1067:
1.2 lievre 1068: }
1069:
1070: double hessij( double x[], double delti[], int thetai,int thetaj)
1071: {
1072: int i;
1073: int l=1, l1, lmax=20;
1074: double k1,k2,k3,k4,res,fx;
1075: double p2[NPARMAX+1];
1076: int k;
1077:
1078: fx=func(x);
1079: for (k=1; k<=2; k++) {
1080: for (i=1;i<=npar;i++) p2[i]=x[i];
1081: p2[thetai]=x[thetai]+delti[thetai]/k;
1082: p2[thetaj]=x[thetaj]+delti[thetaj]/k;
1083: k1=func(p2)-fx;
1084:
1085: p2[thetai]=x[thetai]+delti[thetai]/k;
1086: p2[thetaj]=x[thetaj]-delti[thetaj]/k;
1087: k2=func(p2)-fx;
1088:
1089: p2[thetai]=x[thetai]-delti[thetai]/k;
1090: p2[thetaj]=x[thetaj]+delti[thetaj]/k;
1091: k3=func(p2)-fx;
1092:
1093: p2[thetai]=x[thetai]-delti[thetai]/k;
1094: p2[thetaj]=x[thetaj]-delti[thetaj]/k;
1095: k4=func(p2)-fx;
1096: res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */
1097: #ifdef DEBUG
1098: 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);
1099: #endif
1100: }
1101: return res;
1102: }
1103:
1104: /************** Inverse of matrix **************/
1105: void ludcmp(double **a, int n, int *indx, double *d)
1106: {
1107: int i,imax,j,k;
1108: double big,dum,sum,temp;
1109: double *vv;
1110:
1111: vv=vector(1,n);
1112: *d=1.0;
1113: for (i=1;i<=n;i++) {
1114: big=0.0;
1115: for (j=1;j<=n;j++)
1116: if ((temp=fabs(a[i][j])) > big) big=temp;
1117: if (big == 0.0) nrerror("Singular matrix in routine ludcmp");
1118: vv[i]=1.0/big;
1119: }
1120: for (j=1;j<=n;j++) {
1121: for (i=1;i<j;i++) {
1122: sum=a[i][j];
1123: for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];
1124: a[i][j]=sum;
1125: }
1126: big=0.0;
1127: for (i=j;i<=n;i++) {
1128: sum=a[i][j];
1129: for (k=1;k<j;k++)
1130: sum -= a[i][k]*a[k][j];
1131: a[i][j]=sum;
1132: if ( (dum=vv[i]*fabs(sum)) >= big) {
1133: big=dum;
1134: imax=i;
1135: }
1136: }
1137: if (j != imax) {
1138: for (k=1;k<=n;k++) {
1139: dum=a[imax][k];
1140: a[imax][k]=a[j][k];
1141: a[j][k]=dum;
1142: }
1143: *d = -(*d);
1144: vv[imax]=vv[j];
1145: }
1146: indx[j]=imax;
1147: if (a[j][j] == 0.0) a[j][j]=TINY;
1148: if (j != n) {
1149: dum=1.0/(a[j][j]);
1150: for (i=j+1;i<=n;i++) a[i][j] *= dum;
1151: }
1152: }
1153: free_vector(vv,1,n); /* Doesn't work */
1154: ;
1155: }
1156:
1157: void lubksb(double **a, int n, int *indx, double b[])
1158: {
1159: int i,ii=0,ip,j;
1160: double sum;
1161:
1162: for (i=1;i<=n;i++) {
1163: ip=indx[i];
1164: sum=b[ip];
1165: b[ip]=b[i];
1166: if (ii)
1167: for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];
1168: else if (sum) ii=i;
1169: b[i]=sum;
1170: }
1171: for (i=n;i>=1;i--) {
1172: sum=b[i];
1173: for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];
1174: b[i]=sum/a[i][i];
1175: }
1176: }
1177:
1178: /************ Frequencies ********************/
1.26 lievre 1179: 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 1180: { /* Some frequencies */
1181:
1.18 lievre 1182: int i, m, jk, k1,i1, j1, bool, z1,z2,j;
1.2 lievre 1183: double ***freq; /* Frequencies */
1184: double *pp;
1.19 lievre 1185: double pos, k2, dateintsum=0,k2cpt=0;
1.2 lievre 1186: FILE *ficresp;
1187: char fileresp[FILENAMELENGTH];
1.28 lievre 1188:
1.2 lievre 1189: pp=vector(1,nlstate);
1.19 lievre 1190: probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
1.2 lievre 1191: strcpy(fileresp,"p");
1192: strcat(fileresp,fileres);
1193: if((ficresp=fopen(fileresp,"w"))==NULL) {
1194: printf("Problem with prevalence resultfile: %s\n", fileresp);
1195: exit(0);
1196: }
1197: freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);
1198: j1=0;
1199:
1.7 lievre 1200: j=cptcoveff;
1.2 lievre 1201: if (cptcovn<1) {j=1;ncodemax[1]=1;}
1202:
1203: for(k1=1; k1<=j;k1++){
1204: for(i1=1; i1<=ncodemax[k1];i1++){
1205: j1++;
1.8 lievre 1206: /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
1207: scanf("%d", i);*/
1.2 lievre 1208: for (i=-1; i<=nlstate+ndeath; i++)
1209: for (jk=-1; jk<=nlstate+ndeath; jk++)
1210: for(m=agemin; m <= agemax+3; m++)
1211: freq[i][jk][m]=0;
1.19 lievre 1212:
1213: dateintsum=0;
1214: k2cpt=0;
1.2 lievre 1215: for (i=1; i<=imx; i++) {
1216: bool=1;
1217: if (cptcovn>0) {
1.7 lievre 1218: for (z1=1; z1<=cptcoveff; z1++)
1.8 lievre 1219: if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])
1220: bool=0;
1.2 lievre 1221: }
1.18 lievre 1222: if (bool==1) {
1.19 lievre 1223: for(m=firstpass; m<=lastpass; m++){
1224: k2=anint[m][i]+(mint[m][i]/12.);
1225: if ((k2>=dateprev1) && (k2<=dateprev2)) {
1.18 lievre 1226: if(agev[m][i]==0) agev[m][i]=agemax+1;
1227: if(agev[m][i]==1) agev[m][i]=agemax+2;
1228: freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
1229: freq[s[m][i]][s[m+1][i]][(int) agemax+3] += weight[i];
1.19 lievre 1230: if ((agev[m][i]>1) && (agev[m][i]< (agemax+3))) {
1231: dateintsum=dateintsum+k2;
1232: k2cpt++;
1233: }
1234:
1.18 lievre 1235: }
1236: }
1.19 lievre 1237: }
1.2 lievre 1238: }
1.26 lievre 1239:
1240: fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);
1241:
1.2 lievre 1242: if (cptcovn>0) {
1.7 lievre 1243: fprintf(ficresp, "\n#********** Variable ");
1244: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
1245: fprintf(ficresp, "**********\n#");
1.8 lievre 1246: }
1.2 lievre 1247: for(i=1; i<=nlstate;i++)
1248: fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
1249: fprintf(ficresp, "\n");
1250:
1251: for(i=(int)agemin; i <= (int)agemax+3; i++){
1252: if(i==(int)agemax+3)
1253: printf("Total");
1254: else
1255: printf("Age %d", i);
1256: for(jk=1; jk <=nlstate ; jk++){
1257: for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
1.14 lievre 1258: pp[jk] += freq[jk][m][i];
1.2 lievre 1259: }
1260: for(jk=1; jk <=nlstate ; jk++){
1261: for(m=-1, pos=0; m <=0 ; m++)
1262: pos += freq[jk][m][i];
1263: if(pp[jk]>=1.e-10)
1264: printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
1265: else
1266: printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
1267: }
1.14 lievre 1268:
1269: for(jk=1; jk <=nlstate ; jk++){
1270: for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
1.2 lievre 1271: pp[jk] += freq[jk][m][i];
1.14 lievre 1272: }
1273:
1.2 lievre 1274: for(jk=1,pos=0; jk <=nlstate ; jk++)
1275: pos += pp[jk];
1276: for(jk=1; jk <=nlstate ; jk++){
1277: if(pos>=1.e-5)
1278: printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
1279: else
1280: printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
1281: if( i <= (int) agemax){
1.13 lievre 1282: if(pos>=1.e-5){
1.2 lievre 1283: fprintf(ficresp," %d %.5f %.0f %.0f",i,pp[jk]/pos, pp[jk],pos);
1.13 lievre 1284: probs[i][jk][j1]= pp[jk]/pos;
1285: /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/
1286: }
1.2 lievre 1287: else
1288: fprintf(ficresp," %d NaNq %.0f %.0f",i,pp[jk],pos);
1289: }
1290: }
1291: for(jk=-1; jk <=nlstate+ndeath; jk++)
1292: for(m=-1; m <=nlstate+ndeath; m++)
1293: if(freq[jk][m][i] !=0 ) printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
1294: if(i <= (int) agemax)
1295: fprintf(ficresp,"\n");
1296: printf("\n");
1297: }
1298: }
1299: }
1.19 lievre 1300: dateintmean=dateintsum/k2cpt;
1.2 lievre 1301:
1302: fclose(ficresp);
1303: free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);
1304: free_vector(pp,1,nlstate);
1305:
1.19 lievre 1306: /* End of Freq */
1307: }
1.2 lievre 1308:
1.15 lievre 1309: /************ Prevalence ********************/
1.28 lievre 1310: 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 1311: { /* Some frequencies */
1312:
1313: int i, m, jk, k1, i1, j1, bool, z1,z2,j;
1314: double ***freq; /* Frequencies */
1315: double *pp;
1.18 lievre 1316: double pos, k2;
1.15 lievre 1317:
1318: pp=vector(1,nlstate);
1.19 lievre 1319: probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
1.15 lievre 1320:
1321: freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);
1322: j1=0;
1323:
1324: j=cptcoveff;
1325: if (cptcovn<1) {j=1;ncodemax[1]=1;}
1326:
1327: for(k1=1; k1<=j;k1++){
1328: for(i1=1; i1<=ncodemax[k1];i1++){
1329: j1++;
1330:
1331: for (i=-1; i<=nlstate+ndeath; i++)
1332: for (jk=-1; jk<=nlstate+ndeath; jk++)
1333: for(m=agemin; m <= agemax+3; m++)
1.19 lievre 1334: freq[i][jk][m]=0;
1.28 lievre 1335:
1.15 lievre 1336: for (i=1; i<=imx; i++) {
1337: bool=1;
1338: if (cptcovn>0) {
1339: for (z1=1; z1<=cptcoveff; z1++)
1340: if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])
1341: bool=0;
1.28 lievre 1342: }
1.19 lievre 1343: if (bool==1) {
1344: for(m=firstpass; m<=lastpass; m++){
1345: k2=anint[m][i]+(mint[m][i]/12.);
1346: if ((k2>=dateprev1) && (k2<=dateprev2)) {
1.18 lievre 1347: if(agev[m][i]==0) agev[m][i]=agemax+1;
1348: if(agev[m][i]==1) agev[m][i]=agemax+2;
1.20 lievre 1349: freq[s[m][i]][s[m+1][i]][(int)(agev[m][i]+1-((int)calagedate %12)/12.)] += weight[i];
1.28 lievre 1350: /* freq[s[m][i]][s[m+1][i]][(int)(agemax+3+1)] += weight[i]; */
1.18 lievre 1351: }
1.15 lievre 1352: }
1353: }
1354: }
1.18 lievre 1355: for(i=(int)agemin; i <= (int)agemax+3; i++){
1356: for(jk=1; jk <=nlstate ; jk++){
1357: for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
1358: pp[jk] += freq[jk][m][i];
1359: }
1360: for(jk=1; jk <=nlstate ; jk++){
1361: for(m=-1, pos=0; m <=0 ; m++)
1.15 lievre 1362: pos += freq[jk][m][i];
1363: }
1364:
1365: for(jk=1; jk <=nlstate ; jk++){
1366: for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
1367: pp[jk] += freq[jk][m][i];
1368: }
1369:
1370: for(jk=1,pos=0; jk <=nlstate ; jk++) pos += pp[jk];
1371:
1372: for(jk=1; jk <=nlstate ; jk++){
1373: if( i <= (int) agemax){
1374: if(pos>=1.e-5){
1375: probs[i][jk][j1]= pp[jk]/pos;
1376: }
1377: }
1378: }
1379:
1.18 lievre 1380: }
1.15 lievre 1381: }
1382: }
1383:
1384:
1385: free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);
1386: free_vector(pp,1,nlstate);
1387:
1388: } /* End of Freq */
1.19 lievre 1389:
1.2 lievre 1390: /************* Waves Concatenation ***************/
1391:
1392: void concatwav(int wav[], int **dh, int **mw, int **s, double *agedc, double **agev, int firstpass, int lastpass, int imx, int nlstate, int stepm)
1393: {
1394: /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
1395: Death is a valid wave (if date is known).
1396: mw[mi][i] is the mi (mi=1 to wav[i]) effective wave of individual i
1397: dh[m][i] of dh[mw[mi][i][i] is the delay between two effective waves m=mw[mi][i]
1398: and mw[mi+1][i]. dh depends on stepm.
1399: */
1400:
1401: int i, mi, m;
1.8 lievre 1402: /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
1403: double sum=0., jmean=0.;*/
1.2 lievre 1404:
1.11 lievre 1405: int j, k=0,jk, ju, jl;
1406: double sum=0.;
1407: jmin=1e+5;
1408: jmax=-1;
1409: jmean=0.;
1.2 lievre 1410: for(i=1; i<=imx; i++){
1411: mi=0;
1412: m=firstpass;
1413: while(s[m][i] <= nlstate){
1414: if(s[m][i]>=1)
1415: mw[++mi][i]=m;
1416: if(m >=lastpass)
1417: break;
1418: else
1419: m++;
1420: }/* end while */
1421: if (s[m][i] > nlstate){
1422: mi++; /* Death is another wave */
1423: /* if(mi==0) never been interviewed correctly before death */
1424: /* Only death is a correct wave */
1425: mw[mi][i]=m;
1426: }
1427:
1428: wav[i]=mi;
1429: if(mi==0)
1430: printf("Warning, no any valid information for:%d line=%d\n",num[i],i);
1431: }
1432:
1433: for(i=1; i<=imx; i++){
1434: for(mi=1; mi<wav[i];mi++){
1435: if (stepm <=0)
1436: dh[mi][i]=1;
1437: else{
1438: if (s[mw[mi+1][i]][i] > nlstate) {
1.10 lievre 1439: if (agedc[i] < 2*AGESUP) {
1.2 lievre 1440: j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);
1.8 lievre 1441: if(j==0) j=1; /* Survives at least one month after exam */
1442: k=k+1;
1443: if (j >= jmax) jmax=j;
1.11 lievre 1444: if (j <= jmin) jmin=j;
1.8 lievre 1445: sum=sum+j;
1.30 lievre 1446: /*if (j<0) printf("j=%d num=%d \n",j,i); */
1.10 lievre 1447: }
1.2 lievre 1448: }
1449: else{
1450: j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
1451: k=k+1;
1452: if (j >= jmax) jmax=j;
1453: else if (j <= jmin)jmin=j;
1.30 lievre 1454: /* if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
1.2 lievre 1455: sum=sum+j;
1456: }
1457: jk= j/stepm;
1458: jl= j -jk*stepm;
1459: ju= j -(jk+1)*stepm;
1460: if(jl <= -ju)
1461: dh[mi][i]=jk;
1462: else
1463: dh[mi][i]=jk+1;
1464: if(dh[mi][i]==0)
1465: dh[mi][i]=1; /* At least one step */
1466: }
1467: }
1468: }
1.8 lievre 1469: jmean=sum/k;
1470: printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);
1.12 lievre 1471: }
1.2 lievre 1472: /*********** Tricode ****************************/
1473: void tricode(int *Tvar, int **nbcode, int imx)
1474: {
1.7 lievre 1475: int Ndum[20],ij=1, k, j, i;
1.2 lievre 1476: int cptcode=0;
1.7 lievre 1477: cptcoveff=0;
1478:
1479: for (k=0; k<19; k++) Ndum[k]=0;
1.2 lievre 1480: for (k=1; k<=7; k++) ncodemax[k]=0;
1.6 lievre 1481:
1.7 lievre 1482: for (j=1; j<=(cptcovn+2*cptcovprod); j++) {
1.2 lievre 1483: for (i=1; i<=imx; i++) {
1484: ij=(int)(covar[Tvar[j]][i]);
1485: Ndum[ij]++;
1.8 lievre 1486: /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
1.2 lievre 1487: if (ij > cptcode) cptcode=ij;
1488: }
1.7 lievre 1489:
1.2 lievre 1490: for (i=0; i<=cptcode; i++) {
1491: if(Ndum[i]!=0) ncodemax[j]++;
1492: }
1493: ij=1;
1.7 lievre 1494:
1.8 lievre 1495:
1.2 lievre 1496: for (i=1; i<=ncodemax[j]; i++) {
1.7 lievre 1497: for (k=0; k<=19; k++) {
1.2 lievre 1498: if (Ndum[k] != 0) {
1499: nbcode[Tvar[j]][ij]=k;
1500: ij++;
1501: }
1502: if (ij > ncodemax[j]) break;
1503: }
1504: }
1.7 lievre 1505: }
1.8 lievre 1506:
1507: for (k=0; k<19; k++) Ndum[k]=0;
1508:
1.12 lievre 1509: for (i=1; i<=ncovmodel-2; i++) {
1.7 lievre 1510: ij=Tvar[i];
1511: Ndum[ij]++;
1512: }
1.8 lievre 1513:
1.7 lievre 1514: ij=1;
1.8 lievre 1515: for (i=1; i<=10; i++) {
1.7 lievre 1516: if((Ndum[i]!=0) && (i<=ncov)){
1.8 lievre 1517: Tvaraff[ij]=i;
1518: ij++;
1.7 lievre 1519: }
1520: }
1521:
1.8 lievre 1522: cptcoveff=ij-1;
1.6 lievre 1523: }
1.2 lievre 1524:
1525: /*********** Health Expectancies ****************/
1526:
1527: void evsij(char fileres[], double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int ij)
1528: {
1529: /* Health expectancies */
1.31 ! brouard 1530: int i, j, nhstepm, hstepm, h, nstepm, k;
1.2 lievre 1531: double age, agelim,hf;
1532: double ***p3mat;
1533:
1534: fprintf(ficreseij,"# Health expectancies\n");
1535: fprintf(ficreseij,"# Age");
1536: for(i=1; i<=nlstate;i++)
1537: for(j=1; j<=nlstate;j++)
1538: fprintf(ficreseij," %1d-%1d",i,j);
1539: fprintf(ficreseij,"\n");
1540:
1.31 ! brouard 1541: k=1; /* For example stepm=6 months */
! 1542: hstepm=k*YEARM; /* (a) Every k years of age (in months), for example every k=2 years 24 m */
! 1543: hstepm=1; /* or (b) We decided to compute the life expectancy with the smallest unit */
! 1544: /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
! 1545: nhstepm is the number of hstepm from age to agelim
! 1546: nstepm is the number of stepm from age to agelin.
! 1547: Look at hpijx to understand the reason of that which relies in memory size
! 1548: and note for a fixed period like k years */
! 1549: /* We decided (b) to get a life expectancy respecting the most precise curvature of the
! 1550: survival function given par stepm (the optimization length). Unfortunately it
! 1551: means that if the survival funtion is printed only each two years of age and if
! 1552: you sum them up and add 1 year (area under the trapezoids) you won't get the same
! 1553: results. So we changed our mind and took the option of the best precision.
! 1554: */
! 1555: hstepm=hstepm/stepm; /* Typically in stepm units, if k= 2 years, = 2/6 months = 4 */
1.2 lievre 1556:
1557: agelim=AGESUP;
1558: for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
1559: /* nhstepm age range expressed in number of stepm */
1.31 ! brouard 1560: nstepm=(int) rint((agelim-age)*YEARM/stepm);
! 1561: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
! 1562: if (stepm >= YEARM) hstepm=1;
! 1563: nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
1.2 lievre 1564: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
1565: /* Computed by stepm unit matrices, product of hstepm matrices, stored
1566: in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
1567: hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);
1.31 ! brouard 1568: hf=hstepm/YEARM; /* Duration of hstepm expressed in year unit. */
1.2 lievre 1569: for(i=1; i<=nlstate;i++)
1570: for(j=1; j<=nlstate;j++)
1.29 lievre 1571: for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
1.31 ! brouard 1572: eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
! 1573: /* 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]);*/
1.2 lievre 1574: }
1.29 lievre 1575: fprintf(ficreseij,"%3.0f",age );
1576: for(i=1; i<=nlstate;i++)
1577: for(j=1; j<=nlstate;j++){
1.30 lievre 1578: fprintf(ficreseij," %9.4f", eij[i][j][(int)age]);
1.2 lievre 1579: }
1580: fprintf(ficreseij,"\n");
1581: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
1582: }
1583: }
1584:
1585: /************ Variance ******************/
1586: 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)
1587: {
1588: /* Variance of health expectancies */
1589: /* double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
1590: double **newm;
1591: double **dnewm,**doldm;
1592: int i, j, nhstepm, hstepm, h;
1593: int k, cptcode;
1.12 lievre 1594: double *xp;
1.2 lievre 1595: double **gp, **gm;
1596: double ***gradg, ***trgradg;
1597: double ***p3mat;
1598: double age,agelim;
1599: int theta;
1600:
1601: fprintf(ficresvij,"# Covariances of life expectancies\n");
1602: fprintf(ficresvij,"# Age");
1603: for(i=1; i<=nlstate;i++)
1604: for(j=1; j<=nlstate;j++)
1605: fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);
1606: fprintf(ficresvij,"\n");
1607:
1608: xp=vector(1,npar);
1609: dnewm=matrix(1,nlstate,1,npar);
1610: doldm=matrix(1,nlstate,1,nlstate);
1611:
1612: hstepm=1*YEARM; /* Every year of age */
1613: hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */
1614: agelim = AGESUP;
1615: for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
1616: nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
1617: if (stepm >= YEARM) hstepm=1;
1618: nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
1619: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
1620: gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
1621: gp=matrix(0,nhstepm,1,nlstate);
1622: gm=matrix(0,nhstepm,1,nlstate);
1623:
1624: for(theta=1; theta <=npar; theta++){
1625: for(i=1; i<=npar; i++){ /* Computes gradient */
1626: xp[i] = x[i] + (i==theta ?delti[theta]:0);
1627: }
1628: hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
1629: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
1.14 lievre 1630:
1631: if (popbased==1) {
1632: for(i=1; i<=nlstate;i++)
1633: prlim[i][i]=probs[(int)age][i][ij];
1634: }
1.26 lievre 1635:
1.2 lievre 1636: for(j=1; j<= nlstate; j++){
1637: for(h=0; h<=nhstepm; h++){
1638: for(i=1, gp[h][j]=0.;i<=nlstate;i++)
1639: gp[h][j] += prlim[i][i]*p3mat[i][j][h];
1640: }
1641: }
1642:
1643: for(i=1; i<=npar; i++) /* Computes gradient */
1644: xp[i] = x[i] - (i==theta ?delti[theta]:0);
1645: hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
1646: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
1.26 lievre 1647:
1.14 lievre 1648: if (popbased==1) {
1649: for(i=1; i<=nlstate;i++)
1650: prlim[i][i]=probs[(int)age][i][ij];
1651: }
1652:
1.2 lievre 1653: for(j=1; j<= nlstate; j++){
1654: for(h=0; h<=nhstepm; h++){
1655: for(i=1, gm[h][j]=0.;i<=nlstate;i++)
1656: gm[h][j] += prlim[i][i]*p3mat[i][j][h];
1657: }
1658: }
1.14 lievre 1659:
1.2 lievre 1660: for(j=1; j<= nlstate; j++)
1661: for(h=0; h<=nhstepm; h++){
1662: gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
1663: }
1664: } /* End theta */
1665:
1666: trgradg =ma3x(0,nhstepm,1,nlstate,1,npar);
1667:
1668: for(h=0; h<=nhstepm; h++)
1669: for(j=1; j<=nlstate;j++)
1670: for(theta=1; theta <=npar; theta++)
1671: trgradg[h][j][theta]=gradg[h][theta][j];
1672:
1673: for(i=1;i<=nlstate;i++)
1674: for(j=1;j<=nlstate;j++)
1675: vareij[i][j][(int)age] =0.;
1676: for(h=0;h<=nhstepm;h++){
1677: for(k=0;k<=nhstepm;k++){
1678: matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
1679: matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
1680: for(i=1;i<=nlstate;i++)
1681: for(j=1;j<=nlstate;j++)
1682: vareij[i][j][(int)age] += doldm[i][j];
1683: }
1684: }
1685: h=1;
1686: if (stepm >= YEARM) h=stepm/YEARM;
1687: fprintf(ficresvij,"%.0f ",age );
1688: for(i=1; i<=nlstate;i++)
1689: for(j=1; j<=nlstate;j++){
1690: fprintf(ficresvij," %.4f", h*vareij[i][j][(int)age]);
1691: }
1692: fprintf(ficresvij,"\n");
1693: free_matrix(gp,0,nhstepm,1,nlstate);
1694: free_matrix(gm,0,nhstepm,1,nlstate);
1695: free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
1696: free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
1697: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
1698: } /* End age */
1.26 lievre 1699:
1.2 lievre 1700: free_vector(xp,1,npar);
1701: free_matrix(doldm,1,nlstate,1,npar);
1702: free_matrix(dnewm,1,nlstate,1,nlstate);
1703:
1704: }
1705:
1706: /************ Variance of prevlim ******************/
1707: 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)
1708: {
1709: /* Variance of prevalence limit */
1710: /* double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
1711: double **newm;
1712: double **dnewm,**doldm;
1713: int i, j, nhstepm, hstepm;
1714: int k, cptcode;
1715: double *xp;
1716: double *gp, *gm;
1717: double **gradg, **trgradg;
1718: double age,agelim;
1719: int theta;
1720:
1721: fprintf(ficresvpl,"# Standard deviation of prevalences limit\n");
1722: fprintf(ficresvpl,"# Age");
1723: for(i=1; i<=nlstate;i++)
1724: fprintf(ficresvpl," %1d-%1d",i,i);
1725: fprintf(ficresvpl,"\n");
1726:
1727: xp=vector(1,npar);
1728: dnewm=matrix(1,nlstate,1,npar);
1729: doldm=matrix(1,nlstate,1,nlstate);
1730:
1731: hstepm=1*YEARM; /* Every year of age */
1732: hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */
1733: agelim = AGESUP;
1734: for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
1735: nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
1736: if (stepm >= YEARM) hstepm=1;
1737: nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
1738: gradg=matrix(1,npar,1,nlstate);
1739: gp=vector(1,nlstate);
1740: gm=vector(1,nlstate);
1741:
1742: for(theta=1; theta <=npar; theta++){
1743: for(i=1; i<=npar; i++){ /* Computes gradient */
1744: xp[i] = x[i] + (i==theta ?delti[theta]:0);
1745: }
1746: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
1747: for(i=1;i<=nlstate;i++)
1748: gp[i] = prlim[i][i];
1749:
1750: for(i=1; i<=npar; i++) /* Computes gradient */
1751: xp[i] = x[i] - (i==theta ?delti[theta]:0);
1752: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
1753: for(i=1;i<=nlstate;i++)
1754: gm[i] = prlim[i][i];
1755:
1756: for(i=1;i<=nlstate;i++)
1757: gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
1758: } /* End theta */
1759:
1760: trgradg =matrix(1,nlstate,1,npar);
1761:
1762: for(j=1; j<=nlstate;j++)
1763: for(theta=1; theta <=npar; theta++)
1764: trgradg[j][theta]=gradg[theta][j];
1765:
1766: for(i=1;i<=nlstate;i++)
1767: varpl[i][(int)age] =0.;
1768: matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
1769: matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
1770: for(i=1;i<=nlstate;i++)
1771: varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
1772:
1773: fprintf(ficresvpl,"%.0f ",age );
1774: for(i=1; i<=nlstate;i++)
1775: fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
1776: fprintf(ficresvpl,"\n");
1777: free_vector(gp,1,nlstate);
1778: free_vector(gm,1,nlstate);
1779: free_matrix(gradg,1,npar,1,nlstate);
1780: free_matrix(trgradg,1,nlstate,1,npar);
1781: } /* End age */
1782:
1783: free_vector(xp,1,npar);
1784: free_matrix(doldm,1,nlstate,1,npar);
1785: free_matrix(dnewm,1,nlstate,1,nlstate);
1786:
1787: }
1788:
1.13 lievre 1789: /************ Variance of one-step probabilities ******************/
1790: void varprob(char fileres[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij)
1791: {
1792: int i, j;
1793: int k=0, cptcode;
1794: double **dnewm,**doldm;
1795: double *xp;
1796: double *gp, *gm;
1797: double **gradg, **trgradg;
1798: double age,agelim, cov[NCOVMAX];
1799: int theta;
1800: char fileresprob[FILENAMELENGTH];
1801:
1802: strcpy(fileresprob,"prob");
1803: strcat(fileresprob,fileres);
1804: if((ficresprob=fopen(fileresprob,"w"))==NULL) {
1805: printf("Problem with resultfile: %s\n", fileresprob);
1806: }
1807: printf("Computing variance of one-step probabilities: result on file '%s' \n",fileresprob);
1808:
1.2 lievre 1809:
1.13 lievre 1810: xp=vector(1,npar);
1811: dnewm=matrix(1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
1812: doldm=matrix(1,(nlstate+ndeath)*(nlstate+ndeath),1,(nlstate+ndeath)*(nlstate+ndeath));
1813:
1814: cov[1]=1;
1815: for (age=bage; age<=fage; age ++){
1816: cov[2]=age;
1817: gradg=matrix(1,npar,1,9);
1818: trgradg=matrix(1,9,1,npar);
1819: gp=vector(1,(nlstate+ndeath)*(nlstate+ndeath));
1820: gm=vector(1,(nlstate+ndeath)*(nlstate+ndeath));
1821:
1822: for(theta=1; theta <=npar; theta++){
1823: for(i=1; i<=npar; i++)
1824: xp[i] = x[i] + (i==theta ?delti[theta]:0);
1825:
1826: pmij(pmmij,cov,ncovmodel,xp,nlstate);
1827:
1828: k=0;
1829: for(i=1; i<= (nlstate+ndeath); i++){
1830: for(j=1; j<=(nlstate+ndeath);j++){
1831: k=k+1;
1832: gp[k]=pmmij[i][j];
1833: }
1834: }
1835:
1836: for(i=1; i<=npar; i++)
1837: xp[i] = x[i] - (i==theta ?delti[theta]:0);
1838:
1839:
1840: pmij(pmmij,cov,ncovmodel,xp,nlstate);
1841: k=0;
1842: for(i=1; i<=(nlstate+ndeath); i++){
1843: for(j=1; j<=(nlstate+ndeath);j++){
1844: k=k+1;
1845: gm[k]=pmmij[i][j];
1846: }
1847: }
1848:
1849: for(i=1; i<= (nlstate+ndeath)*(nlstate+ndeath); i++)
1850: gradg[theta][i]=(gp[i]-gm[i])/2./delti[theta];
1851: }
1852:
1853: for(j=1; j<=(nlstate+ndeath)*(nlstate+ndeath);j++)
1854: for(theta=1; theta <=npar; theta++)
1855: trgradg[j][theta]=gradg[theta][j];
1856:
1857: matprod2(dnewm,trgradg,1,9,1,npar,1,npar,matcov);
1858: matprod2(doldm,dnewm,1,9,1,npar,1,9,gradg);
1859:
1860: pmij(pmmij,cov,ncovmodel,x,nlstate);
1861:
1862: k=0;
1863: for(i=1; i<=(nlstate+ndeath); i++){
1864: for(j=1; j<=(nlstate+ndeath);j++){
1865: k=k+1;
1866: gm[k]=pmmij[i][j];
1867: }
1868: }
1869:
1870: /*printf("\n%d ",(int)age);
1871: for (i=1; i<=(nlstate+ndeath)*(nlstate+ndeath-1);i++){
1872:
1873:
1874: printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
1875: }*/
1876:
1877: fprintf(ficresprob,"\n%d ",(int)age);
1878:
1879: for (i=1; i<=(nlstate+ndeath)*(nlstate+ndeath-1);i++){
1880: if (i== 2) fprintf(ficresprob,"%.3e %.3e ",gm[i],doldm[i][i]);
1881: if (i== 4) fprintf(ficresprob,"%.3e %.3e ",gm[i],doldm[i][i]);
1882: }
1883:
1884: free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
1885: free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
1886: free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
1887: free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
1888: }
1889: free_vector(xp,1,npar);
1890: fclose(ficresprob);
1.26 lievre 1891:
1.13 lievre 1892: }
1.2 lievre 1893:
1.25 lievre 1894: /******************* Printing html file ***********/
1.29 lievre 1895: void printinghtml(char fileres[], char title[], char datafile[], int firstpass, int lastpass, int stepm, int weightopt, char model[],int imx,int jmin, int jmax, double jmeanint,char optionfile[],char optionfilehtm[],char rfileres[] ){
1.25 lievre 1896: int jj1, k1, i1, cpt;
1897: FILE *fichtm;
1898: /*char optionfilehtm[FILENAMELENGTH];*/
1899:
1900: strcpy(optionfilehtm,optionfile);
1901: strcat(optionfilehtm,".htm");
1902: if((fichtm=fopen(optionfilehtm,"w"))==NULL) {
1903: printf("Problem with %s \n",optionfilehtm), exit(0);
1904: }
1905:
1.31 ! brouard 1906: fprintf(fichtm,"<body><ul> <font size=\"6\">Imach, Version 0.71a </font> <hr size=\"2\" color=\"#EC5E5E\">
1.25 lievre 1907: Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>
1908:
1909: Total number of observations=%d <br>
1910: Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>
1911: <hr size=\"2\" color=\"#EC5E5E\">
1912: <li>Outputs files<br><br>\n
1913: - Observed prevalence in each state: <a href=\"p%s\">p%s</a> <br>\n
1914: - Estimated parameters and the covariance matrix: <a href=\"%s\">%s</a> <br>
1915: - Stationary prevalence in each state: <a href=\"pl%s\">pl%s</a> <br>
1916: - Transition probabilities: <a href=\"pij%s\">pij%s</a><br>
1917: - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>
1918: - Life expectancies by age and initial health status: <a href=\"e%s\">e%s</a> <br>
1919: - Variances of life expectancies by age and initial health status: <a href=\"v%s\">v%s</a><br>
1920: - Health expectancies with their variances: <a href=\"t%s\">t%s</a> <br>
1921: - Standard deviation of stationary prevalences: <a href=\"vpl%s\">vpl%s</a> <br>
1.28 lievre 1922: - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>
1923: - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>
1.29 lievre 1924: <br>",title,datafile,firstpass,lastpass,stepm, weightopt,model,imx,jmin,jmax,jmean,fileres,fileres,rfileres,rfileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres);
1.25 lievre 1925:
1926: fprintf(fichtm," <li>Graphs</li><p>");
1927:
1928: m=cptcoveff;
1929: if (cptcovn < 1) {m=1;ncodemax[1]=1;}
1930:
1931: jj1=0;
1932: for(k1=1; k1<=m;k1++){
1933: for(i1=1; i1<=ncodemax[k1];i1++){
1934: jj1++;
1935: if (cptcovn > 0) {
1936: fprintf(fichtm,"<hr size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
1937: for (cpt=1; cpt<=cptcoveff;cpt++)
1938: fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
1939: fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
1940: }
1941: fprintf(fichtm,"<br>- Probabilities: pe%s%d.gif<br>
1942: <img src=\"pe%s%d.gif\">",strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);
1943: for(cpt=1; cpt<nlstate;cpt++){
1944: fprintf(fichtm,"<br>- Prevalence of disability : p%s%d%d.gif<br>
1945: <img src=\"p%s%d%d.gif\">",strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);
1946: }
1947: for(cpt=1; cpt<=nlstate;cpt++) {
1948: fprintf(fichtm,"<br>- Observed and stationary prevalence (with confident
1949: interval) in state (%d): v%s%d%d.gif <br>
1950: <img src=\"v%s%d%d.gif\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);
1951: }
1952: for(cpt=1; cpt<=nlstate;cpt++) {
1953: fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): exp%s%d%d.gif <br>
1954: <img src=\"exp%s%d%d.gif\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);
1955: }
1956: fprintf(fichtm,"\n<br>- Total life expectancy by age and
1957: health expectancies in states (1) and (2): e%s%d.gif<br>
1958: <img src=\"e%s%d.gif\">",strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);
1959: fprintf(fichtm,"\n</body>");
1960: }
1961: }
1962: fclose(fichtm);
1963: }
1964:
1965: /******************* Gnuplot file **************/
1.28 lievre 1966: void printinggnuplot(char fileres[],char optionfilefiname[],char optionfile[],char optionfilegnuplot[], double agemin, double agemaxpar, double fage , char pathc[], double p[]){
1.25 lievre 1967:
1968: int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;
1969:
1970: strcpy(optionfilegnuplot,optionfilefiname);
1971: strcat(optionfilegnuplot,".plt");
1972: if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {
1973: printf("Problem with file %s",optionfilegnuplot);
1974: }
1975:
1976: #ifdef windows
1977: fprintf(ficgp,"cd \"%s\" \n",pathc);
1978: #endif
1979: m=pow(2,cptcoveff);
1980:
1981: /* 1eme*/
1982: for (cpt=1; cpt<= nlstate ; cpt ++) {
1983: for (k1=1; k1<= m ; k1 ++) {
1984:
1985: #ifdef windows
1986: fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter gif small size 400,300\nplot [%.f:%.f] \"vpl%s\" every :::%d::%d u 1:2 \"\%%lf",agemin,fage,fileres,k1-1,k1-1);
1987: #endif
1988: #ifdef unix
1989: fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nplot [%.f:%.f] \"vpl%s\" u 1:2 \"\%%lf",agemin,fage,fileres);
1990: #endif
1991:
1992: for (i=1; i<= nlstate ; i ++) {
1993: if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
1994: else fprintf(ficgp," \%%*lf (\%%*lf)");
1995: }
1996: fprintf(ficgp,"\" t\"Stationary prevalence\" w l 0,\"vpl%s\" every :::%d::%d u 1:($2+2*$3) \"\%%lf",fileres,k1-1,k1-1);
1997: for (i=1; i<= nlstate ; i ++) {
1998: if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
1999: else fprintf(ficgp," \%%*lf (\%%*lf)");
2000: }
2001: fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"vpl%s\" every :::%d::%d u 1:($2-2*$3) \"\%%lf",fileres,k1-1,k1-1);
2002: for (i=1; i<= nlstate ; i ++) {
2003: if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
2004: else fprintf(ficgp," \%%*lf (\%%*lf)");
2005: }
2006: fprintf(ficgp,"\" t\"\" w l 1,\"p%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",fileres,k1-1,k1-1,2+4*(cpt-1));
2007: #ifdef unix
2008: fprintf(ficgp,"\nset ter gif small size 400,300");
2009: #endif
2010: fprintf(ficgp,"\nset out \"v%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);
2011: }
2012: }
2013: /*2 eme*/
2014:
2015: for (k1=1; k1<= m ; k1 ++) {
2016: fprintf(ficgp,"set ylabel \"Years\" \nset ter gif small size 400,300\nplot [%.f:%.f] ",agemin,fage);
2017:
2018: for (i=1; i<= nlstate+1 ; i ++) {
2019: k=2*i;
2020: fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:2 \"\%%lf",fileres,k1-1,k1-1);
2021: for (j=1; j<= nlstate+1 ; j ++) {
2022: if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
2023: else fprintf(ficgp," \%%*lf (\%%*lf)");
2024: }
2025: if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");
2026: else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);
2027: fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",fileres,k1-1,k1-1);
2028: for (j=1; j<= nlstate+1 ; j ++) {
2029: if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
2030: else fprintf(ficgp," \%%*lf (\%%*lf)");
2031: }
2032: fprintf(ficgp,"\" t\"\" w l 0,");
2033: fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",fileres,k1-1,k1-1);
2034: for (j=1; j<= nlstate+1 ; j ++) {
2035: if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
2036: else fprintf(ficgp," \%%*lf (\%%*lf)");
2037: }
2038: if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");
2039: else fprintf(ficgp,"\" t\"\" w l 0,");
2040: }
2041: fprintf(ficgp,"\nset out \"e%s%d.gif\" \nreplot\n\n",strtok(optionfile, "."),k1);
2042: }
2043:
2044: /*3eme*/
2045:
2046: for (k1=1; k1<= m ; k1 ++) {
2047: for (cpt=1; cpt<= nlstate ; cpt ++) {
2048: k=2+nlstate*(cpt-1);
2049: fprintf(ficgp,"set ter gif small size 400,300\nplot [%.f:%.f] \"e%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",agemin,fage,fileres,k1-1,k1-1,k,cpt);
2050: for (i=1; i< nlstate ; i ++) {
2051: fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",fileres,k1-1,k1-1,k+i,cpt,i+1);
2052: }
2053: fprintf(ficgp,"\nset out \"exp%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);
2054: }
2055: }
2056:
2057: /* CV preval stat */
2058: for (k1=1; k1<= m ; k1 ++) {
2059: for (cpt=1; cpt<nlstate ; cpt ++) {
2060: k=3;
1.28 lievre 2061: fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter gif small size 400,300\nplot [%.f:%.f] \"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",agemin,agemaxpar,fileres,k1,k+cpt+1,k+1);
1.25 lievre 2062:
2063: for (i=1; i< nlstate ; i ++)
2064: fprintf(ficgp,"+$%d",k+i+1);
2065: fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);
2066:
2067: l=3+(nlstate+ndeath)*cpt;
2068: fprintf(ficgp,",\"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",fileres,k1,l+cpt+1,l+1);
2069: for (i=1; i< nlstate ; i ++) {
2070: l=3+(nlstate+ndeath)*cpt;
2071: fprintf(ficgp,"+$%d",l+i+1);
2072: }
2073: fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);
2074: fprintf(ficgp,"set out \"p%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);
2075: }
2076: }
2077:
2078: /* proba elementaires */
2079: for(i=1,jk=1; i <=nlstate; i++){
2080: for(k=1; k <=(nlstate+ndeath); k++){
2081: if (k != i) {
2082: for(j=1; j <=ncovmodel; j++){
2083:
2084: fprintf(ficgp,"p%d=%f ",jk,p[jk]);
2085: jk++;
2086: fprintf(ficgp,"\n");
2087: }
2088: }
2089: }
2090: }
2091:
2092: for(jk=1; jk <=m; jk++) {
1.28 lievre 2093: fprintf(ficgp,"\nset ter gif small size 400,300\nset log y\nplot [%.f:%.f] ",agemin,agemaxpar);
1.25 lievre 2094: i=1;
2095: for(k2=1; k2<=nlstate; k2++) {
2096: k3=i;
2097: for(k=1; k<=(nlstate+ndeath); k++) {
2098: if (k != k2){
2099: fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
2100: ij=1;
2101: for(j=3; j <=ncovmodel; j++) {
2102: if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
2103: fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
2104: ij++;
2105: }
2106: else
2107: fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
2108: }
2109: fprintf(ficgp,")/(1");
2110:
2111: for(k1=1; k1 <=nlstate; k1++){
2112: fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);
2113: ij=1;
2114: for(j=3; j <=ncovmodel; j++){
2115: if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
2116: fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
2117: ij++;
2118: }
2119: else
2120: fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
2121: }
2122: fprintf(ficgp,")");
2123: }
2124: fprintf(ficgp,") t \"p%d%d\" ", k2,k);
2125: if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");
2126: i=i+ncovmodel;
2127: }
2128: }
2129: }
2130: fprintf(ficgp,"\nset out \"pe%s%d.gif\" \nreplot\n\n",strtok(optionfile, "."),jk);
2131: }
2132:
2133: fclose(ficgp);
2134: } /* end gnuplot */
2135:
2136:
2137: /*************** Moving average **************/
2138: void movingaverage(double agedeb, double fage,double agemin, double ***mobaverage){
2139:
2140: int i, cpt, cptcod;
2141: for (agedeb=agemin; agedeb<=fage; agedeb++)
2142: for (i=1; i<=nlstate;i++)
2143: for (cptcod=1;cptcod<=ncodemax[cptcov];cptcod++)
2144: mobaverage[(int)agedeb][i][cptcod]=0.;
2145:
2146: for (agedeb=agemin+4; agedeb<=fage; agedeb++){
2147: for (i=1; i<=nlstate;i++){
2148: for (cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
2149: for (cpt=0;cpt<=4;cpt++){
2150: mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]+probs[(int)agedeb-cpt][i][cptcod];
2151: }
2152: mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]/5;
2153: }
2154: }
2155: }
2156:
2157: }
2158:
1.27 lievre 2159:
2160: /************** Forecasting ******************/
2161: prevforecast(char fileres[], double anproj1,double mproj1,double jproj1,double agemin, double agemax,double dateprev1, double dateprev2, int mobilav, double agedeb, double fage, int popforecast, char popfile[], double anproj2,double p[], int i2){
2162:
2163: int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;
2164: int *popage;
2165: double calagedate, agelim, kk1, kk2, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
2166: double *popeffectif,*popcount;
2167: double ***p3mat;
2168: char fileresf[FILENAMELENGTH];
2169:
2170: agelim=AGESUP;
2171: calagedate=(anproj1+mproj1/12.+jproj1/365.-dateintmean)*YEARM;
1.28 lievre 2172:
1.27 lievre 2173: prevalence(agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);
1.28 lievre 2174:
1.27 lievre 2175:
2176: strcpy(fileresf,"f");
2177: strcat(fileresf,fileres);
2178: if((ficresf=fopen(fileresf,"w"))==NULL) {
2179: printf("Problem with forecast resultfile: %s\n", fileresf);
2180: }
2181: printf("Computing forecasting: result on file '%s' \n", fileresf);
2182:
2183: if (cptcoveff==0) ncodemax[cptcoveff]=1;
2184:
2185: if (mobilav==1) {
2186: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
2187: movingaverage(agedeb, fage, agemin, mobaverage);
2188: }
2189:
2190: stepsize=(int) (stepm+YEARM-1)/YEARM;
2191: if (stepm<=12) stepsize=1;
2192:
2193: agelim=AGESUP;
2194:
2195: hstepm=1;
2196: hstepm=hstepm/stepm;
2197: yp1=modf(dateintmean,&yp);
2198: anprojmean=yp;
2199: yp2=modf((yp1*12),&yp);
2200: mprojmean=yp;
2201: yp1=modf((yp2*30.5),&yp);
2202: jprojmean=yp;
2203: if(jprojmean==0) jprojmean=1;
2204: if(mprojmean==0) jprojmean=1;
2205:
2206: fprintf(ficresf,"# Estimated date of observed prevalence: %.lf/%.lf/%.lf ",jprojmean,mprojmean,anprojmean);
2207:
2208: for(cptcov=1;cptcov<=i2;cptcov++){
2209: for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
2210: k=k+1;
2211: fprintf(ficresf,"\n#******");
2212: for(j=1;j<=cptcoveff;j++) {
2213: fprintf(ficresf," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
2214: }
2215: fprintf(ficresf,"******\n");
2216: fprintf(ficresf,"# StartingAge FinalAge");
2217: for(j=1; j<=nlstate+ndeath;j++) fprintf(ficresf," P.%d",j);
2218:
2219:
2220: for (cpt=0; cpt<=(anproj2-anproj1);cpt++) {
2221: fprintf(ficresf,"\n");
2222: fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+cpt);
1.28 lievre 2223:
1.27 lievre 2224: for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(agemin-((int)calagedate %12)/12.); agedeb--){
2225: nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);
2226: nhstepm = nhstepm/hstepm;
2227:
2228: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
2229: oldm=oldms;savm=savms;
2230: hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
2231:
2232: for (h=0; h<=nhstepm; h++){
2233: if (h==(int) (calagedate+YEARM*cpt)) {
2234: fprintf(ficresf,"\n %.f ",agedeb+h*hstepm/YEARM*stepm);
2235: }
2236: for(j=1; j<=nlstate+ndeath;j++) {
2237: kk1=0.;kk2=0;
2238: for(i=1; i<=nlstate;i++) {
2239: if (mobilav==1)
2240: kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];
2241: else {
2242: kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];
2243: }
2244:
2245: }
2246: if (h==(int)(calagedate+12*cpt)){
2247: fprintf(ficresf," %.3f", kk1);
2248:
2249: }
2250: }
2251: }
2252: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
2253: }
2254: }
2255: }
2256: }
2257:
2258: if (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
2259:
2260: fclose(ficresf);
2261: }
2262: /************** Forecasting ******************/
1.28 lievre 2263: populforecast(char fileres[], double anpyram,double mpyram,double jpyram,double agemin, 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 2264:
2265: int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;
2266: int *popage;
2267: double calagedate, agelim, kk1, kk2, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
2268: double *popeffectif,*popcount;
2269: double ***p3mat,***tabpop,***tabpopprev;
2270: char filerespop[FILENAMELENGTH];
2271:
1.28 lievre 2272: tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
2273: tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
2274: agelim=AGESUP;
2275: calagedate=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;
1.27 lievre 2276:
2277: prevalence(agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);
1.28 lievre 2278:
2279:
1.27 lievre 2280: strcpy(filerespop,"pop");
2281: strcat(filerespop,fileres);
2282: if((ficrespop=fopen(filerespop,"w"))==NULL) {
2283: printf("Problem with forecast resultfile: %s\n", filerespop);
2284: }
2285: printf("Computing forecasting: result on file '%s' \n", filerespop);
2286:
2287: if (cptcoveff==0) ncodemax[cptcoveff]=1;
2288:
2289: if (mobilav==1) {
2290: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
2291: movingaverage(agedeb, fage, agemin, mobaverage);
2292: }
2293:
2294: stepsize=(int) (stepm+YEARM-1)/YEARM;
2295: if (stepm<=12) stepsize=1;
2296:
2297: agelim=AGESUP;
2298:
2299: hstepm=1;
2300: hstepm=hstepm/stepm;
2301:
2302: if (popforecast==1) {
2303: if((ficpop=fopen(popfile,"r"))==NULL) {
2304: printf("Problem with population file : %s\n",popfile);exit(0);
2305: }
2306: popage=ivector(0,AGESUP);
2307: popeffectif=vector(0,AGESUP);
2308: popcount=vector(0,AGESUP);
2309:
2310: i=1;
2311: while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;
2312:
2313: imx=i;
2314: for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];
2315: }
2316:
2317: for(cptcov=1;cptcov<=i2;cptcov++){
2318: for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
2319: k=k+1;
2320: fprintf(ficrespop,"\n#******");
2321: for(j=1;j<=cptcoveff;j++) {
2322: fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
2323: }
2324: fprintf(ficrespop,"******\n");
1.28 lievre 2325: fprintf(ficrespop,"# Age");
1.27 lievre 2326: for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);
2327: if (popforecast==1) fprintf(ficrespop," [Population]");
2328:
2329: for (cpt=0; cpt<=0;cpt++) {
1.28 lievre 2330: fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);
1.27 lievre 2331:
2332: for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(agemin-((int)calagedate %12)/12.); agedeb--){
2333: nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);
2334: nhstepm = nhstepm/hstepm;
2335:
2336: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
2337: oldm=oldms;savm=savms;
2338: hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
2339:
2340: for (h=0; h<=nhstepm; h++){
2341: if (h==(int) (calagedate+YEARM*cpt)) {
1.28 lievre 2342: fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
1.27 lievre 2343: }
2344: for(j=1; j<=nlstate+ndeath;j++) {
2345: kk1=0.;kk2=0;
2346: for(i=1; i<=nlstate;i++) {
2347: if (mobilav==1)
2348: kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];
2349: else {
2350: kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];
2351: }
2352: }
2353: if (h==(int)(calagedate+12*cpt)){
2354: tabpop[(int)(agedeb)][j][cptcod]=kk1;
2355: /*fprintf(ficrespop," %.3f", kk1);
2356: if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/
2357: }
2358: }
2359: for(i=1; i<=nlstate;i++){
2360: kk1=0.;
2361: for(j=1; j<=nlstate;j++){
1.28 lievre 2362: kk1= kk1+tabpop[(int)(agedeb)][j][cptcod];
1.27 lievre 2363: }
2364: tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedate+12*cpt)*hstepm/YEARM*stepm-1)];
2365: }
2366:
1.28 lievre 2367: if (h==(int)(calagedate+12*cpt)) for(j=1; j<=nlstate;j++)
2368: fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);
1.27 lievre 2369: }
2370: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
2371: }
2372: }
2373:
2374: /******/
2375:
1.28 lievre 2376: for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) {
2377: fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);
1.27 lievre 2378: for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(agemin-((int)calagedate %12)/12.); agedeb--){
2379: nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);
2380: nhstepm = nhstepm/hstepm;
2381:
2382: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
2383: oldm=oldms;savm=savms;
2384: hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
2385: for (h=0; h<=nhstepm; h++){
2386: if (h==(int) (calagedate+YEARM*cpt)) {
1.28 lievre 2387: fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
1.27 lievre 2388: }
2389: for(j=1; j<=nlstate+ndeath;j++) {
2390: kk1=0.;kk2=0;
2391: for(i=1; i<=nlstate;i++) {
2392: kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];
2393: }
1.28 lievre 2394: if (h==(int)(calagedate+12*cpt)) fprintf(ficresf," %15.2f", kk1);
1.27 lievre 2395: }
2396: }
2397: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
2398: }
2399: }
2400: }
2401: }
2402:
2403: if (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
2404:
2405: if (popforecast==1) {
2406: free_ivector(popage,0,AGESUP);
2407: free_vector(popeffectif,0,AGESUP);
2408: free_vector(popcount,0,AGESUP);
2409: }
2410: free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
2411: free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
2412: fclose(ficrespop);
2413: }
2414:
1.2 lievre 2415: /***********************************************/
2416: /**************** Main Program *****************/
2417: /***********************************************/
2418:
1.22 brouard 2419: int main(int argc, char *argv[])
1.2 lievre 2420: {
2421:
1.8 lievre 2422: int i,j, k, n=MAXN,iter,m,size,cptcode, cptcod;
1.2 lievre 2423: double agedeb, agefin,hf;
1.28 lievre 2424: double agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;
1.2 lievre 2425:
2426: double fret;
2427: double **xi,tmp,delta;
2428:
2429: double dum; /* Dummy variable */
2430: double ***p3mat;
2431: int *indx;
2432: char line[MAXLINE], linepar[MAXLINE];
2433: char title[MAXLINE];
1.25 lievre 2434: char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH], filerespl[FILENAMELENGTH];
2435: char optionfilext[10], optionfilefiname[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilegnuplot[FILENAMELENGTH], plotcmd[FILENAMELENGTH];
1.22 brouard 2436:
1.29 lievre 2437: char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
1.22 brouard 2438:
1.2 lievre 2439: char filerest[FILENAMELENGTH];
2440: char fileregp[FILENAMELENGTH];
1.16 lievre 2441: char popfile[FILENAMELENGTH];
1.2 lievre 2442: char path[80],pathc[80],pathcd[80],pathtot[80],model[20];
2443: int firstobs=1, lastobs=10;
2444: int sdeb, sfin; /* Status at beginning and end */
2445: int c, h , cpt,l;
2446: int ju,jl, mi;
1.7 lievre 2447: int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;
1.14 lievre 2448: int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,**adl,*tab;
1.19 lievre 2449: int mobilav=0,popforecast=0;
1.2 lievre 2450: int hstepm, nhstepm;
1.28 lievre 2451: double jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,jpyram, mpyram,anpyram,jpyram1, mpyram1,anpyram1;
1.14 lievre 2452:
1.2 lievre 2453: double bage, fage, age, agelim, agebase;
2454: double ftolpl=FTOL;
2455: double **prlim;
2456: double *severity;
2457: double ***param; /* Matrix of parameters */
2458: double *p;
2459: double **matcov; /* Matrix of covariance */
2460: double ***delti3; /* Scale */
2461: double *delti; /* Scale */
2462: double ***eij, ***vareij;
2463: double **varpl; /* Variances of prevalence limits by age */
2464: double *epj, vepp;
1.16 lievre 2465: double kk1, kk2;
1.27 lievre 2466: double dateprev1, dateprev2,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2;
2467:
1.13 lievre 2468:
1.31 ! brouard 2469: char version[80]="Imach version 0.71a, March 2002, INED-EUROREVES ";
1.2 lievre 2470: char *alph[]={"a","a","b","c","d","e"}, str[4];
1.5 lievre 2471:
1.13 lievre 2472:
1.2 lievre 2473: char z[1]="c", occ;
2474: #include <sys/time.h>
2475: #include <time.h>
2476: char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];
1.19 lievre 2477:
1.2 lievre 2478: /* long total_usecs;
2479: struct timeval start_time, end_time;
2480:
2481: gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */
2482:
2483:
1.22 brouard 2484: printf("\n%s",version);
2485: if(argc <=1){
2486: printf("\nEnter the parameter file name: ");
2487: scanf("%s",pathtot);
2488: }
2489: else{
2490: strcpy(pathtot,argv[1]);
2491: }
2492: /*if(getcwd(pathcd, 80)!= NULL)printf ("Error pathcd\n");*/
1.5 lievre 2493: /*cygwin_split_path(pathtot,path,optionfile);
2494: printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/
2495: /* cutv(path,optionfile,pathtot,'\\');*/
2496:
1.22 brouard 2497: split(pathtot,path,optionfile,optionfilext,optionfilefiname);
2498: printf("pathtot=%s, path=%s, optionfile=%s optionfilext=%s optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
1.2 lievre 2499: chdir(path);
2500: replace(pathc,path);
2501:
2502: /*-------- arguments in the command line --------*/
2503:
2504: strcpy(fileres,"r");
1.22 brouard 2505: strcat(fileres, optionfilefiname);
2506: strcat(fileres,".txt"); /* Other files have txt extension */
1.2 lievre 2507:
2508: /*---------arguments file --------*/
2509:
2510: if((ficpar=fopen(optionfile,"r"))==NULL) {
2511: printf("Problem with optionfile %s\n",optionfile);
2512: goto end;
2513: }
2514:
2515: strcpy(filereso,"o");
2516: strcat(filereso,fileres);
2517: if((ficparo=fopen(filereso,"w"))==NULL) {
2518: printf("Problem with Output resultfile: %s\n", filereso);goto end;
2519: }
2520:
2521: /* Reads comments: lines beginning with '#' */
2522: while((c=getc(ficpar))=='#' && c!= EOF){
2523: ungetc(c,ficpar);
2524: fgets(line, MAXLINE, ficpar);
2525: puts(line);
2526: fputs(line,ficparo);
2527: }
2528: ungetc(c,ficpar);
2529:
2530: fscanf(ficpar,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%lf stepm=%d ncov=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n",title, datafile, &lastobs, &firstpass,&lastpass,&ftol, &stepm, &ncov, &nlstate,&ndeath, &maxwav, &mle, &weightopt,model);
2531: printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncov=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncov, nlstate,ndeath, maxwav, mle, weightopt,model);
2532: fprintf(ficparo,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncov=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncov,nlstate,ndeath,maxwav, mle, weightopt,model);
1.14 lievre 2533: while((c=getc(ficpar))=='#' && c!= EOF){
2534: ungetc(c,ficpar);
2535: fgets(line, MAXLINE, ficpar);
2536: puts(line);
2537: fputs(line,ficparo);
2538: }
2539: ungetc(c,ficpar);
2540:
1.19 lievre 2541:
1.8 lievre 2542: covar=matrix(0,NCOVMAX,1,n);
2543: cptcovn=0;
2544: if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;
1.2 lievre 2545:
2546: ncovmodel=2+cptcovn;
2547: nvar=ncovmodel-1; /* Suppressing age as a basic covariate */
2548:
2549: /* Read guess parameters */
2550: /* Reads comments: lines beginning with '#' */
2551: while((c=getc(ficpar))=='#' && c!= EOF){
2552: ungetc(c,ficpar);
2553: fgets(line, MAXLINE, ficpar);
2554: puts(line);
2555: fputs(line,ficparo);
2556: }
2557: ungetc(c,ficpar);
2558:
2559: param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
2560: for(i=1; i <=nlstate; i++)
2561: for(j=1; j <=nlstate+ndeath-1; j++){
2562: fscanf(ficpar,"%1d%1d",&i1,&j1);
2563: fprintf(ficparo,"%1d%1d",i1,j1);
2564: printf("%1d%1d",i,j);
2565: for(k=1; k<=ncovmodel;k++){
2566: fscanf(ficpar," %lf",¶m[i][j][k]);
2567: printf(" %lf",param[i][j][k]);
2568: fprintf(ficparo," %lf",param[i][j][k]);
2569: }
2570: fscanf(ficpar,"\n");
2571: printf("\n");
2572: fprintf(ficparo,"\n");
2573: }
2574:
1.12 lievre 2575: npar= (nlstate+ndeath-1)*nlstate*ncovmodel;
2576:
1.2 lievre 2577: p=param[1][1];
2578:
2579: /* Reads comments: lines beginning with '#' */
2580: while((c=getc(ficpar))=='#' && c!= EOF){
2581: ungetc(c,ficpar);
2582: fgets(line, MAXLINE, ficpar);
2583: puts(line);
2584: fputs(line,ficparo);
2585: }
2586: ungetc(c,ficpar);
2587:
2588: delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
2589: delti=vector(1,npar); /* Scale of each paramater (output from hesscov) */
2590: for(i=1; i <=nlstate; i++){
2591: for(j=1; j <=nlstate+ndeath-1; j++){
2592: fscanf(ficpar,"%1d%1d",&i1,&j1);
2593: printf("%1d%1d",i,j);
2594: fprintf(ficparo,"%1d%1d",i1,j1);
2595: for(k=1; k<=ncovmodel;k++){
2596: fscanf(ficpar,"%le",&delti3[i][j][k]);
2597: printf(" %le",delti3[i][j][k]);
2598: fprintf(ficparo," %le",delti3[i][j][k]);
2599: }
2600: fscanf(ficpar,"\n");
2601: printf("\n");
2602: fprintf(ficparo,"\n");
2603: }
2604: }
2605: delti=delti3[1][1];
2606:
2607: /* Reads comments: lines beginning with '#' */
2608: while((c=getc(ficpar))=='#' && c!= EOF){
2609: ungetc(c,ficpar);
2610: fgets(line, MAXLINE, ficpar);
2611: puts(line);
2612: fputs(line,ficparo);
2613: }
2614: ungetc(c,ficpar);
2615:
2616: matcov=matrix(1,npar,1,npar);
2617: for(i=1; i <=npar; i++){
2618: fscanf(ficpar,"%s",&str);
2619: printf("%s",str);
2620: fprintf(ficparo,"%s",str);
2621: for(j=1; j <=i; j++){
2622: fscanf(ficpar," %le",&matcov[i][j]);
2623: printf(" %.5le",matcov[i][j]);
2624: fprintf(ficparo," %.5le",matcov[i][j]);
2625: }
2626: fscanf(ficpar,"\n");
2627: printf("\n");
2628: fprintf(ficparo,"\n");
2629: }
2630: for(i=1; i <=npar; i++)
2631: for(j=i+1;j<=npar;j++)
2632: matcov[i][j]=matcov[j][i];
2633:
2634: printf("\n");
2635:
2636:
1.29 lievre 2637: /*-------- Rewriting paramater file ----------*/
2638: strcpy(rfileres,"r"); /* "Rparameterfile */
2639: strcat(rfileres,optionfilefiname); /* Parameter file first name*/
2640: strcat(rfileres,"."); /* */
2641: strcat(rfileres,optionfilext); /* Other files have txt extension */
2642: if((ficres =fopen(rfileres,"w"))==NULL) {
2643: printf("Problem writing new parameter file: %s\n", fileres);goto end;
1.2 lievre 2644: }
2645: fprintf(ficres,"#%s\n",version);
2646:
1.29 lievre 2647: /*-------- data file ----------*/
1.2 lievre 2648: if((fic=fopen(datafile,"r"))==NULL) {
2649: printf("Problem with datafile: %s\n", datafile);goto end;
2650: }
2651:
2652: n= lastobs;
2653: severity = vector(1,maxwav);
2654: outcome=imatrix(1,maxwav+1,1,n);
2655: num=ivector(1,n);
2656: moisnais=vector(1,n);
2657: annais=vector(1,n);
2658: moisdc=vector(1,n);
2659: andc=vector(1,n);
2660: agedc=vector(1,n);
2661: cod=ivector(1,n);
2662: weight=vector(1,n);
2663: for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */
2664: mint=matrix(1,maxwav,1,n);
2665: anint=matrix(1,maxwav,1,n);
2666: s=imatrix(1,maxwav+1,1,n);
2667: adl=imatrix(1,maxwav+1,1,n);
2668: tab=ivector(1,NCOVMAX);
1.3 lievre 2669: ncodemax=ivector(1,8);
1.2 lievre 2670:
1.12 lievre 2671: i=1;
1.2 lievre 2672: while (fgets(line, MAXLINE, fic) != NULL) {
2673: if ((i >= firstobs) && (i <=lastobs)) {
2674:
2675: for (j=maxwav;j>=1;j--){
2676: cutv(stra, strb,line,' '); s[j][i]=atoi(strb);
2677: strcpy(line,stra);
2678: cutv(stra, strb,line,'/'); anint[j][i]=(double)(atoi(strb)); strcpy(line,stra);
2679: cutv(stra, strb,line,' '); mint[j][i]=(double)(atoi(strb)); strcpy(line,stra);
2680: }
2681:
2682: cutv(stra, strb,line,'/'); andc[i]=(double)(atoi(strb)); strcpy(line,stra);
2683: cutv(stra, strb,line,' '); moisdc[i]=(double)(atoi(strb)); strcpy(line,stra);
2684:
2685: cutv(stra, strb,line,'/'); annais[i]=(double)(atoi(strb)); strcpy(line,stra);
2686: cutv(stra, strb,line,' '); moisnais[i]=(double)(atoi(strb)); strcpy(line,stra);
2687:
2688: cutv(stra, strb,line,' '); weight[i]=(double)(atoi(strb)); strcpy(line,stra);
2689: for (j=ncov;j>=1;j--){
2690: cutv(stra, strb,line,' '); covar[j][i]=(double)(atoi(strb)); strcpy(line,stra);
2691: }
2692: num[i]=atol(stra);
1.12 lievre 2693:
2694: /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){
2695: 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 2696:
2697: i=i+1;
2698: }
2699: }
1.12 lievre 2700: /* printf("ii=%d", ij);
2701: scanf("%d",i);*/
2702: imx=i-1; /* Number of individuals */
1.3 lievre 2703:
1.12 lievre 2704: /* for (i=1; i<=imx; i++){
2705: if ((s[1][i]==3) && (s[2][i]==2)) s[2][i]=3;
2706: if ((s[2][i]==3) && (s[3][i]==2)) s[3][i]=3;
2707: if ((s[3][i]==3) && (s[4][i]==2)) s[4][i]=3;
1.14 lievre 2708: }
1.19 lievre 2709:
2710: for (i=1; i<=imx; i++)
2711: if (covar[1][i]==0) 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]));*/
1.2 lievre 2712:
2713: /* Calculation of the number of parameter from char model*/
1.7 lievre 2714: Tvar=ivector(1,15);
2715: Tprod=ivector(1,15);
2716: Tvaraff=ivector(1,15);
2717: Tvard=imatrix(1,15,1,2);
1.6 lievre 2718: Tage=ivector(1,15);
1.2 lievre 2719:
2720: if (strlen(model) >1){
1.7 lievre 2721: j=0, j1=0, k1=1, k2=1;
1.2 lievre 2722: j=nbocc(model,'+');
1.6 lievre 2723: j1=nbocc(model,'*');
1.2 lievre 2724: cptcovn=j+1;
1.7 lievre 2725: cptcovprod=j1;
1.3 lievre 2726:
1.8 lievre 2727:
1.2 lievre 2728: strcpy(modelsav,model);
1.8 lievre 2729: if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){
2730: printf("Error. Non available option model=%s ",model);
2731: goto end;
2732: }
2733:
2734: for(i=(j+1); i>=1;i--){
2735: cutv(stra,strb,modelsav,'+');
2736: if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav);
2737: /* printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/
2738: /*scanf("%d",i);*/
2739: if (strchr(strb,'*')) {
2740: cutv(strd,strc,strb,'*');
2741: if (strcmp(strc,"age")==0) {
1.7 lievre 2742: cptcovprod--;
1.8 lievre 2743: cutv(strb,stre,strd,'V');
2744: Tvar[i]=atoi(stre);
2745: cptcovage++;
2746: Tage[cptcovage]=i;
2747: /*printf("stre=%s ", stre);*/
1.7 lievre 2748: }
1.8 lievre 2749: else if (strcmp(strd,"age")==0) {
1.7 lievre 2750: cptcovprod--;
1.8 lievre 2751: cutv(strb,stre,strc,'V');
2752: Tvar[i]=atoi(stre);
2753: cptcovage++;
2754: Tage[cptcovage]=i;
1.7 lievre 2755: }
2756: else {
1.8 lievre 2757: cutv(strb,stre,strc,'V');
2758: Tvar[i]=ncov+k1;
2759: cutv(strb,strc,strd,'V');
2760: Tprod[k1]=i;
2761: Tvard[k1][1]=atoi(strc);
2762: Tvard[k1][2]=atoi(stre);
2763: Tvar[cptcovn+k2]=Tvard[k1][1];
2764: Tvar[cptcovn+k2+1]=Tvard[k1][2];
1.7 lievre 2765: for (k=1; k<=lastobs;k++)
1.8 lievre 2766: covar[ncov+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];
2767: k1++;
2768: k2=k2+2;
1.7 lievre 2769: }
1.2 lievre 2770: }
1.8 lievre 2771: else {
2772: /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/
2773: /* scanf("%d",i);*/
2774: cutv(strd,strc,strb,'V');
2775: Tvar[i]=atoi(strc);
2776: }
2777: strcpy(modelsav,stra);
2778: /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);
2779: scanf("%d",i);*/
1.2 lievre 2780: }
1.8 lievre 2781: }
2782:
2783: /*printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);
2784: printf("cptcovprod=%d ", cptcovprod);
2785: scanf("%d ",i);*/
1.2 lievre 2786: fclose(fic);
2787:
1.7 lievre 2788: /* if(mle==1){*/
1.2 lievre 2789: if (weightopt != 1) { /* Maximisation without weights*/
2790: for(i=1;i<=n;i++) weight[i]=1.0;
2791: }
2792: /*-calculation of age at interview from date of interview and age at death -*/
2793: agev=matrix(1,maxwav,1,imx);
1.12 lievre 2794:
2795: for (i=1; i<=imx; i++)
2796: for(m=2; (m<= maxwav); m++)
2797: if ((mint[m][i]== 99) && (s[m][i] <= nlstate)){
2798: anint[m][i]=9999;
2799: s[m][i]=-1;
2800: }
1.2 lievre 2801:
2802: for (i=1; i<=imx; i++) {
2803: agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);
2804: for(m=1; (m<= maxwav); m++){
2805: if(s[m][i] >0){
2806: if (s[m][i] == nlstate+1) {
2807: if(agedc[i]>0)
2808: if(moisdc[i]!=99 && andc[i]!=9999)
2809: agev[m][i]=agedc[i];
1.8 lievre 2810: else {
2811: if (andc[i]!=9999){
1.2 lievre 2812: printf("Warning negative age at death: %d line:%d\n",num[i],i);
2813: agev[m][i]=-1;
1.8 lievre 2814: }
1.2 lievre 2815: }
2816: }
2817: else if(s[m][i] !=9){ /* Should no more exist */
2818: agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);
1.3 lievre 2819: if(mint[m][i]==99 || anint[m][i]==9999)
1.2 lievre 2820: agev[m][i]=1;
2821: else if(agev[m][i] <agemin){
2822: agemin=agev[m][i];
2823: /*printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], agemin);*/
2824: }
2825: else if(agev[m][i] >agemax){
2826: agemax=agev[m][i];
2827: /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/
2828: }
2829: /*agev[m][i]=anint[m][i]-annais[i];*/
2830: /* agev[m][i] = age[i]+2*m;*/
2831: }
2832: else { /* =9 */
2833: agev[m][i]=1;
2834: s[m][i]=-1;
2835: }
2836: }
2837: else /*= 0 Unknown */
2838: agev[m][i]=1;
2839: }
2840:
2841: }
2842: for (i=1; i<=imx; i++) {
2843: for(m=1; (m<= maxwav); m++){
2844: if (s[m][i] > (nlstate+ndeath)) {
2845: printf("Error: Wrong value in nlstate or ndeath\n");
2846: goto end;
2847: }
2848: }
2849: }
2850:
2851: printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);
2852:
2853: free_vector(severity,1,maxwav);
2854: free_imatrix(outcome,1,maxwav+1,1,n);
2855: free_vector(moisnais,1,n);
2856: free_vector(annais,1,n);
1.17 lievre 2857: /* free_matrix(mint,1,maxwav,1,n);
2858: free_matrix(anint,1,maxwav,1,n);*/
1.2 lievre 2859: free_vector(moisdc,1,n);
2860: free_vector(andc,1,n);
2861:
2862:
2863: wav=ivector(1,imx);
2864: dh=imatrix(1,lastpass-firstpass+1,1,imx);
2865: mw=imatrix(1,lastpass-firstpass+1,1,imx);
2866:
2867: /* Concatenates waves */
2868: concatwav(wav, dh, mw, s, agedc, agev, firstpass, lastpass, imx, nlstate, stepm);
2869:
2870:
1.6 lievre 2871: Tcode=ivector(1,100);
1.8 lievre 2872: nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);
1.7 lievre 2873: ncodemax[1]=1;
2874: if (cptcovn > 0) tricode(Tvar,nbcode,imx);
2875:
1.2 lievre 2876: codtab=imatrix(1,100,1,10);
2877: h=0;
1.7 lievre 2878: m=pow(2,cptcoveff);
1.2 lievre 2879:
1.7 lievre 2880: for(k=1;k<=cptcoveff; k++){
1.2 lievre 2881: for(i=1; i <=(m/pow(2,k));i++){
2882: for(j=1; j <= ncodemax[k]; j++){
1.7 lievre 2883: for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){
1.2 lievre 2884: h++;
2885: if (h>m) h=1;codtab[h][k]=j;
2886: }
2887: }
2888: }
2889: }
1.22 brouard 2890:
2891:
2892: /*for(i=1; i <=m ;i++){
2893: for(k=1; k <=cptcovn; k++){
2894: printf("i=%d k=%d %d %d",i,k,codtab[i][k], cptcoveff);
2895: }
2896: printf("\n");
2897: }
2898: scanf("%d",i);*/
1.2 lievre 2899:
2900: /* Calculates basic frequencies. Computes observed prevalence at single age
2901: and prints on file fileres'p'. */
1.18 lievre 2902:
1.19 lievre 2903:
1.18 lievre 2904:
1.19 lievre 2905: pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
1.2 lievre 2906: oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
2907: newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
2908: savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
2909: oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */
1.12 lievre 2910:
1.2 lievre 2911: /* For Powell, parameters are in a vector p[] starting at p[1]
2912: so we point p on param[1][1] so that p[1] maps on param[1][1][1] */
2913: p=param[1][1]; /* *(*(*(param +1)+1)+0) */
1.7 lievre 2914:
2915: if(mle==1){
1.2 lievre 2916: mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);
1.7 lievre 2917: }
1.2 lievre 2918:
2919: /*--------- results files --------------*/
1.29 lievre 2920: fprintf(ficres,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncov=%d nlstate=%d ndeath=%d maxwav=%d mle= 0 weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncov, nlstate, ndeath, maxwav, weightopt,model);
1.19 lievre 2921:
1.16 lievre 2922:
1.2 lievre 2923: jk=1;
2924: fprintf(ficres,"# Parameters\n");
2925: printf("# Parameters\n");
2926: for(i=1,jk=1; i <=nlstate; i++){
2927: for(k=1; k <=(nlstate+ndeath); k++){
2928: if (k != i)
2929: {
2930: printf("%d%d ",i,k);
2931: fprintf(ficres,"%1d%1d ",i,k);
2932: for(j=1; j <=ncovmodel; j++){
2933: printf("%f ",p[jk]);
2934: fprintf(ficres,"%f ",p[jk]);
2935: jk++;
2936: }
2937: printf("\n");
2938: fprintf(ficres,"\n");
2939: }
2940: }
2941: }
1.7 lievre 2942: if(mle==1){
1.2 lievre 2943: /* Computing hessian and covariance matrix */
2944: ftolhess=ftol; /* Usually correct */
2945: hesscov(matcov, p, npar, delti, ftolhess, func);
1.7 lievre 2946: }
1.2 lievre 2947: fprintf(ficres,"# Scales\n");
2948: printf("# Scales\n");
2949: for(i=1,jk=1; i <=nlstate; i++){
2950: for(j=1; j <=nlstate+ndeath; j++){
2951: if (j!=i) {
2952: fprintf(ficres,"%1d%1d",i,j);
2953: printf("%1d%1d",i,j);
2954: for(k=1; k<=ncovmodel;k++){
2955: printf(" %.5e",delti[jk]);
2956: fprintf(ficres," %.5e",delti[jk]);
2957: jk++;
2958: }
2959: printf("\n");
2960: fprintf(ficres,"\n");
2961: }
2962: }
1.18 lievre 2963: }
1.2 lievre 2964:
2965: k=1;
2966: fprintf(ficres,"# Covariance\n");
2967: printf("# Covariance\n");
2968: for(i=1;i<=npar;i++){
2969: /* if (k>nlstate) k=1;
2970: i1=(i-1)/(ncovmodel*nlstate)+1;
2971: fprintf(ficres,"%s%d%d",alph[k],i1,tab[i]);
2972: printf("%s%d%d",alph[k],i1,tab[i]);*/
2973: fprintf(ficres,"%3d",i);
2974: printf("%3d",i);
2975: for(j=1; j<=i;j++){
2976: fprintf(ficres," %.5e",matcov[i][j]);
2977: printf(" %.5e",matcov[i][j]);
2978: }
2979: fprintf(ficres,"\n");
2980: printf("\n");
2981: k++;
2982: }
2983:
2984: while((c=getc(ficpar))=='#' && c!= EOF){
2985: ungetc(c,ficpar);
2986: fgets(line, MAXLINE, ficpar);
2987: puts(line);
2988: fputs(line,ficparo);
2989: }
2990: ungetc(c,ficpar);
2991:
1.28 lievre 2992: fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf\n",&agemin,&agemaxpar, &bage, &fage);
1.2 lievre 2993:
2994: if (fage <= 2) {
2995: bage = agemin;
1.28 lievre 2996: fage = agemaxpar;
1.2 lievre 2997: }
1.22 brouard 2998:
2999: fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");
1.28 lievre 3000: fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemaxpar,bage,fage);
3001: fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemaxpar,bage,fage);
1.19 lievre 3002:
3003: while((c=getc(ficpar))=='#' && c!= EOF){
3004: ungetc(c,ficpar);
3005: fgets(line, MAXLINE, ficpar);
3006: puts(line);
3007: fputs(line,ficparo);
3008: }
3009: ungetc(c,ficpar);
3010:
1.25 lievre 3011: fscanf(ficpar,"begin-prev-date=%lf/%lf/%lf end-prev-date=%lf/%lf/%lf\n",&jprev1, &mprev1,&anprev1,&jprev2, &mprev2,&anprev2);
3012: fprintf(ficparo,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);
3013: fprintf(ficres,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);
1.19 lievre 3014:
3015: while((c=getc(ficpar))=='#' && c!= EOF){
3016: ungetc(c,ficpar);
3017: fgets(line, MAXLINE, ficpar);
3018: puts(line);
3019: fputs(line,ficparo);
3020: }
3021: ungetc(c,ficpar);
3022:
1.7 lievre 3023:
1.19 lievre 3024: dateprev1=anprev1+mprev1/12.+jprev1/365.;
3025: dateprev2=anprev2+mprev2/12.+jprev2/365.;
3026:
3027: fscanf(ficpar,"pop_based=%d\n",&popbased);
1.28 lievre 3028: fprintf(ficparo,"pop_based=%d\n",popbased);
3029: fprintf(ficres,"pop_based=%d\n",popbased);
3030:
3031: while((c=getc(ficpar))=='#' && c!= EOF){
3032: ungetc(c,ficpar);
3033: fgets(line, MAXLINE, ficpar);
3034: puts(line);
3035: fputs(line,ficparo);
3036: }
3037: ungetc(c,ficpar);
1.19 lievre 3038:
1.28 lievre 3039: 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);
3040: 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);
3041: 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);
3042:
3043:
3044: while((c=getc(ficpar))=='#' && c!= EOF){
1.19 lievre 3045: ungetc(c,ficpar);
3046: fgets(line, MAXLINE, ficpar);
3047: puts(line);
3048: fputs(line,ficparo);
3049: }
3050: ungetc(c,ficpar);
1.28 lievre 3051:
3052: fscanf(ficpar,"popforecast=%d popfile=%s popfiledate=%lf/%lf/%lf last-popfiledate=%lf/%lf/%lf\n",&popforecast,popfile,&jpyram,&mpyram,&anpyram,&jpyram1,&mpyram1,&anpyram1);
3053: fprintf(ficparo,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);
3054: 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 3055:
1.26 lievre 3056: freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);
1.19 lievre 3057:
1.25 lievre 3058: /*------------ gnuplot -------------*/
1.28 lievre 3059: printinggnuplot(fileres,optionfilefiname,optionfile,optionfilegnuplot, agemin,agemaxpar,fage, pathc,p);
1.25 lievre 3060:
3061: /*------------ free_vector -------------*/
3062: chdir(path);
1.2 lievre 3063:
1.25 lievre 3064: free_ivector(wav,1,imx);
3065: free_imatrix(dh,1,lastpass-firstpass+1,1,imx);
3066: free_imatrix(mw,1,lastpass-firstpass+1,1,imx);
3067: free_ivector(num,1,n);
3068: free_vector(agedc,1,n);
3069: /*free_matrix(covar,1,NCOVMAX,1,n);*/
3070: fclose(ficparo);
3071: fclose(ficres);
1.28 lievre 3072:
1.2 lievre 3073: /*--------- index.htm --------*/
3074:
1.29 lievre 3075: printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,model,imx,jmin,jmax,jmean,optionfile,optionfilehtm,rfileres);
1.2 lievre 3076:
1.25 lievre 3077:
1.2 lievre 3078: /*--------------- Prevalence limit --------------*/
3079:
3080: strcpy(filerespl,"pl");
3081: strcat(filerespl,fileres);
3082: if((ficrespl=fopen(filerespl,"w"))==NULL) {
3083: printf("Problem with Prev limit resultfile: %s\n", filerespl);goto end;
3084: }
3085: printf("Computing prevalence limit: result on file '%s' \n", filerespl);
3086: fprintf(ficrespl,"#Prevalence limit\n");
3087: fprintf(ficrespl,"#Age ");
3088: for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);
3089: fprintf(ficrespl,"\n");
3090:
3091: prlim=matrix(1,nlstate,1,nlstate);
3092: pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
3093: oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
3094: newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
3095: savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
3096: oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */
3097: k=0;
3098: agebase=agemin;
1.28 lievre 3099: agelim=agemaxpar;
1.2 lievre 3100: ftolpl=1.e-10;
1.7 lievre 3101: i1=cptcoveff;
1.2 lievre 3102: if (cptcovn < 1){i1=1;}
3103:
3104: for(cptcov=1;cptcov<=i1;cptcov++){
3105: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
3106: k=k+1;
3107: /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/
1.6 lievre 3108: fprintf(ficrespl,"\n#******");
1.7 lievre 3109: for(j=1;j<=cptcoveff;j++)
3110: fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
1.2 lievre 3111: fprintf(ficrespl,"******\n");
3112:
3113: for (age=agebase; age<=agelim; age++){
3114: prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
3115: fprintf(ficrespl,"%.0f",age );
3116: for(i=1; i<=nlstate;i++)
3117: fprintf(ficrespl," %.5f", prlim[i][i]);
3118: fprintf(ficrespl,"\n");
3119: }
3120: }
3121: }
3122: fclose(ficrespl);
1.13 lievre 3123:
1.2 lievre 3124: /*------------- h Pij x at various ages ------------*/
3125:
3126: strcpy(filerespij,"pij"); strcat(filerespij,fileres);
3127: if((ficrespij=fopen(filerespij,"w"))==NULL) {
3128: printf("Problem with Pij resultfile: %s\n", filerespij);goto end;
3129: }
3130: printf("Computing pij: result on file '%s' \n", filerespij);
3131:
3132: stepsize=(int) (stepm+YEARM-1)/YEARM;
1.13 lievre 3133: /*if (stepm<=24) stepsize=2;*/
1.2 lievre 3134:
3135: agelim=AGESUP;
3136: hstepm=stepsize*YEARM; /* Every year of age */
3137: hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */
3138:
3139: k=0;
3140: for(cptcov=1;cptcov<=i1;cptcov++){
3141: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
3142: k=k+1;
3143: fprintf(ficrespij,"\n#****** ");
1.7 lievre 3144: for(j=1;j<=cptcoveff;j++)
3145: fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
1.2 lievre 3146: fprintf(ficrespij,"******\n");
3147:
3148: for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */
3149: nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
3150: nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
3151: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3152: oldm=oldms;savm=savms;
3153: hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
3154: fprintf(ficrespij,"# Age");
3155: for(i=1; i<=nlstate;i++)
3156: for(j=1; j<=nlstate+ndeath;j++)
3157: fprintf(ficrespij," %1d-%1d",i,j);
3158: fprintf(ficrespij,"\n");
3159: for (h=0; h<=nhstepm; h++){
3160: fprintf(ficrespij,"%d %.0f %.0f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );
3161: for(i=1; i<=nlstate;i++)
3162: for(j=1; j<=nlstate+ndeath;j++)
3163: fprintf(ficrespij," %.5f", p3mat[i][j][h]);
3164: fprintf(ficrespij,"\n");
3165: }
3166: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3167: fprintf(ficrespij,"\n");
3168: }
3169: }
3170: }
3171:
1.13 lievre 3172: /* varprob(fileres, matcov, p, delti, nlstate, (int) bage, (int) fage,k);*/
3173:
1.2 lievre 3174: fclose(ficrespij);
3175:
1.27 lievre 3176:
3177: /*---------- Forecasting ------------------*/
1.30 lievre 3178: if((stepm == 1) && (model==".")){
1.27 lievre 3179: prevforecast(fileres, anproj1,mproj1,jproj1, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anproj2,p, i1);
1.28 lievre 3180: if (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);
1.27 lievre 3181: free_matrix(mint,1,maxwav,1,n);
3182: free_matrix(anint,1,maxwav,1,n); free_imatrix(s,1,maxwav+1,1,n);
3183: free_vector(weight,1,n);}
1.21 lievre 3184: else{
3185: erreur=108;
3186: printf("Error %d!! You can only forecast the prevalences if the optimization\n has been performed with stepm = 1 (month) instead of %d\n", erreur, stepm);
3187: }
1.26 lievre 3188:
1.27 lievre 3189:
1.2 lievre 3190: /*---------- Health expectancies and variances ------------*/
3191:
3192: strcpy(filerest,"t");
3193: strcat(filerest,fileres);
3194: if((ficrest=fopen(filerest,"w"))==NULL) {
3195: printf("Problem with total LE resultfile: %s\n", filerest);goto end;
3196: }
3197: printf("Computing Total LEs with variances: file '%s' \n", filerest);
3198:
3199:
3200: strcpy(filerese,"e");
3201: strcat(filerese,fileres);
3202: if((ficreseij=fopen(filerese,"w"))==NULL) {
3203: printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
3204: }
3205: printf("Computing Health Expectancies: result on file '%s' \n", filerese);
3206:
3207: strcpy(fileresv,"v");
3208: strcat(fileresv,fileres);
3209: if((ficresvij=fopen(fileresv,"w"))==NULL) {
3210: printf("Problem with variance resultfile: %s\n", fileresv);exit(0);
3211: }
3212: printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
3213:
3214: k=0;
3215: for(cptcov=1;cptcov<=i1;cptcov++){
3216: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
3217: k=k+1;
3218: fprintf(ficrest,"\n#****** ");
1.7 lievre 3219: for(j=1;j<=cptcoveff;j++)
3220: fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
1.2 lievre 3221: fprintf(ficrest,"******\n");
3222:
3223: fprintf(ficreseij,"\n#****** ");
1.7 lievre 3224: for(j=1;j<=cptcoveff;j++)
1.2 lievre 3225: fprintf(ficreseij,"V%d=%d ",j,nbcode[j][codtab[k][j]]);
3226: fprintf(ficreseij,"******\n");
3227:
3228: fprintf(ficresvij,"\n#****** ");
1.7 lievre 3229: for(j=1;j<=cptcoveff;j++)
1.2 lievre 3230: fprintf(ficresvij,"V%d=%d ",j,nbcode[j][codtab[k][j]]);
3231: fprintf(ficresvij,"******\n");
3232:
3233: eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
3234: oldm=oldms;savm=savms;
3235: evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k);
3236: vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
3237: oldm=oldms;savm=savms;
1.26 lievre 3238: varevsij(fileres, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);
3239:
3240:
3241:
1.2 lievre 3242: fprintf(ficrest,"#Total LEs with variances: e.. (std) ");
3243: for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);
3244: fprintf(ficrest,"\n");
1.26 lievre 3245:
1.2 lievre 3246: hf=1;
3247: if (stepm >= YEARM) hf=stepm/YEARM;
3248: epj=vector(1,nlstate+1);
3249: for(age=bage; age <=fage ;age++){
3250: prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
1.14 lievre 3251: if (popbased==1) {
3252: for(i=1; i<=nlstate;i++)
3253: prlim[i][i]=probs[(int)age][i][k];
3254: }
3255:
1.2 lievre 3256: fprintf(ficrest," %.0f",age);
3257: for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){
3258: for(i=1, epj[j]=0.;i <=nlstate;i++) {
3259: epj[j] += prlim[i][i]*hf*eij[i][j][(int)age];
3260: }
3261: epj[nlstate+1] +=epj[j];
3262: }
3263: for(i=1, vepp=0.;i <=nlstate;i++)
3264: for(j=1;j <=nlstate;j++)
3265: vepp += vareij[i][j][(int)age];
3266: fprintf(ficrest," %.2f (%.2f)", epj[nlstate+1],hf*sqrt(vepp));
3267: for(j=1;j <=nlstate;j++){
3268: fprintf(ficrest," %.2f (%.2f)", epj[j],hf*sqrt(vareij[j][j][(int)age]));
3269: }
3270: fprintf(ficrest,"\n");
3271: }
3272: }
3273: }
1.13 lievre 3274:
1.27 lievre 3275: fclose(ficreseij);
3276: fclose(ficresvij);
1.2 lievre 3277: fclose(ficrest);
3278: fclose(ficpar);
3279: free_vector(epj,1,nlstate+1);
1.26 lievre 3280:
1.2 lievre 3281: /*------- Variance limit prevalence------*/
3282:
1.27 lievre 3283: strcpy(fileresvpl,"vpl");
1.2 lievre 3284: strcat(fileresvpl,fileres);
3285: if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {
3286: printf("Problem with variance prev lim resultfile: %s\n", fileresvpl);
3287: exit(0);
3288: }
3289: printf("Computing Variance-covariance of Prevalence limit: file '%s' \n", fileresvpl);
3290:
1.27 lievre 3291: k=0;
3292: for(cptcov=1;cptcov<=i1;cptcov++){
3293: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
3294: k=k+1;
3295: fprintf(ficresvpl,"\n#****** ");
3296: for(j=1;j<=cptcoveff;j++)
3297: fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
3298: fprintf(ficresvpl,"******\n");
3299:
3300: varpl=matrix(1,nlstate,(int) bage, (int) fage);
3301: oldm=oldms;savm=savms;
1.2 lievre 3302: varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);
1.27 lievre 3303: }
1.2 lievre 3304: }
3305:
3306: fclose(ficresvpl);
3307:
3308: /*---------- End : free ----------------*/
3309: free_matrix(varpl,1,nlstate,(int) bage, (int)fage);
3310:
3311: free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);
3312: free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
3313:
3314:
3315: free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);
3316: free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);
3317: free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);
3318: free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);
1.13 lievre 3319:
1.2 lievre 3320: free_matrix(matcov,1,npar,1,npar);
3321: free_vector(delti,1,npar);
1.26 lievre 3322: free_matrix(agev,1,maxwav,1,imx);
1.2 lievre 3323: free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
3324:
1.21 lievre 3325: if(erreur >0)
3326: printf("End of Imach with error %d\n",erreur);
3327: else printf("End of Imach\n");
1.2 lievre 3328: /* gettimeofday(&end_time, (struct timezone*)0);*/ /* after time */
3329:
3330: /* 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);*/
3331: /*printf("Total time was %d uSec.\n", total_usecs);*/
3332: /*------ End -----------*/
1.12 lievre 3333:
1.2 lievre 3334:
3335: end:
3336: #ifdef windows
1.22 brouard 3337: /* chdir(pathcd);*/
1.2 lievre 3338: #endif
1.22 brouard 3339: /*system("wgnuplot graph.plt");*/
3340: /*system("../gp37mgw/wgnuplot graph.plt");*/
3341: /*system("cd ../gp37mgw");*/
3342: /* system("..\\gp37mgw\\wgnuplot graph.plt");*/
3343: strcpy(plotcmd,GNUPLOTPROGRAM);
3344: strcat(plotcmd," ");
3345: strcat(plotcmd,optionfilegnuplot);
3346: system(plotcmd);
1.2 lievre 3347:
3348: #ifdef windows
3349: while (z[0] != 'q') {
1.22 brouard 3350: chdir(path);
1.2 lievre 3351: printf("\nType e to edit output files, c to start again, and q for exiting: ");
3352: scanf("%s",z);
3353: if (z[0] == 'c') system("./imach");
3354: else if (z[0] == 'e') {
3355: chdir(path);
1.10 lievre 3356: system(optionfilehtm);
1.2 lievre 3357: }
3358: else if (z[0] == 'q') exit(0);
3359: }
3360: #endif
3361: }
3362:
3363:
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