Annotation of imach/src/imach.c, revision 1.13
1.2 lievre 1:
2: /*********************** Imach **************************************
3: This program computes Healthy Life Expectancies from cross-longitudinal
4: data. Cross-longitudinal consist in a first survey ("cross") where
5: individuals from different ages are interviewed on their health status
6: or degree of disability. At least a second wave of interviews
7: ("longitudinal") should measure each new individual health status.
8: Health expectancies are computed from the transistions observed between
9: waves and are computed for each degree of severity of disability (number
10: of life states). More degrees you consider, more time is necessary to
1.11 lievre 11: reach the Maximum Likelihood of the parameters involved in the model.
1.2 lievre 12: The simplest model is the multinomial logistic model where pij is
13: the probabibility to be observed in state j at the second wave conditional
14: to be observed in state i at the first wave. Therefore the model is:
15: log(pij/pii)= aij + bij*age+ cij*sex + etc , where 'age' is age and 'sex'
16: is a covariate. If you want to have a more complex model than "constant and
17: age", you should modify the program where the markup
18: *Covariates have to be included here again* invites you to do it.
19: More covariates you add, less is the speed of the convergence.
20:
21: The advantage that this computer programme claims, comes from that if the
22: delay between waves is not identical for each individual, or if some
23: individual missed an interview, the information is not rounded or lost, but
24: taken into account using an interpolation or extrapolation.
1.12 lievre 25: hPijx is the probability to be
1.2 lievre 26: observed in state i at age x+h conditional to the observed state i at age
27: x. The delay 'h' can be split into an exact number (nh*stepm) of
28: unobserved intermediate states. This elementary transition (by month or
29: quarter trimester, semester or year) is model as a multinomial logistic.
30: The hPx matrix is simply the matrix product of nh*stepm elementary matrices
31: and the contribution of each individual to the likelihood is simply hPijx.
32:
33: Also this programme outputs the covariance matrix of the parameters but also
34: of the life expectancies. It also computes the prevalence limits.
35:
36: Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).
37: Institut national d'études démographiques, Paris.
38: This software have been partly granted by Euro-REVES, a concerted action
39: from the European Union.
40: It is copyrighted identically to a GNU software product, ie programme and
41: software can be distributed freely for non commercial use. Latest version
42: can be accessed at http://euroreves.ined.fr/imach .
43: **********************************************************************/
44:
45: #include <math.h>
46: #include <stdio.h>
47: #include <stdlib.h>
48: #include <unistd.h>
49:
50: #define MAXLINE 256
51: #define FILENAMELENGTH 80
52: /*#define DEBUG*/
53: #define windows
1.5 lievre 54: #define GLOCK_ERROR_NOPATH -1 /* empty path */
55: #define GLOCK_ERROR_GETCWD -2 /* cannot get cwd */
56:
1.2 lievre 57: #define MAXPARM 30 /* Maximum number of parameters for the optimization */
58: #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */
59:
60: #define NINTERVMAX 8
61: #define NLSTATEMAX 8 /* Maximum number of live states (for func) */
62: #define NDEATHMAX 8 /* Maximum number of dead states (for func) */
63: #define NCOVMAX 8 /* Maximum number of covariates */
1.3 lievre 64: #define MAXN 20000
1.2 lievre 65: #define YEARM 12. /* Number of months per year */
66: #define AGESUP 130
67: #define AGEBASE 40
68:
69:
70: int nvar;
1.8 lievre 71: int cptcovn, cptcovage=0, cptcoveff=0,cptcov;
1.2 lievre 72: int npar=NPARMAX;
73: int nlstate=2; /* Number of live states */
74: int ndeath=1; /* Number of dead states */
75: int ncovmodel, ncov; /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
76:
77: int *wav; /* Number of waves for this individuual 0 is possible */
78: int maxwav; /* Maxim number of waves */
1.8 lievre 79: int jmin, jmax; /* min, max spacing between 2 waves */
1.2 lievre 80: int mle, weightopt;
81: int **mw; /* mw[mi][i] is number of the mi wave for this individual */
82: int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
1.8 lievre 83: double jmean; /* Mean space between 2 waves */
1.2 lievre 84: double **oldm, **newm, **savm; /* Working pointers to matrices */
85: double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
1.13 ! lievre 86: FILE *fic,*ficpar, *ficparo,*ficres, *ficrespl, *ficrespij, *ficrest,*ficresf;
! 87: FILE *ficgp, *fichtm,*ficresprob;
1.2 lievre 88: FILE *ficreseij;
89: char filerese[FILENAMELENGTH];
90: FILE *ficresvij;
91: char fileresv[FILENAMELENGTH];
92: FILE *ficresvpl;
93: char fileresvpl[FILENAMELENGTH];
94:
95: #define NR_END 1
96: #define FREE_ARG char*
97: #define FTOL 1.0e-10
98:
99: #define NRANSI
100: #define ITMAX 200
101:
102: #define TOL 2.0e-4
103:
104: #define CGOLD 0.3819660
105: #define ZEPS 1.0e-10
106: #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);
107:
108: #define GOLD 1.618034
109: #define GLIMIT 100.0
110: #define TINY 1.0e-20
111:
112: static double maxarg1,maxarg2;
113: #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
114: #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
115:
116: #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
117: #define rint(a) floor(a+0.5)
118:
119: static double sqrarg;
120: #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
121: #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}
122:
123: int imx;
124: int stepm;
125: /* Stepm, step in month: minimum step interpolation*/
126:
127: int m,nb;
1.6 lievre 128: int *num, firstpass=0, lastpass=4,*cod, *ncodemax, *Tage;
1.2 lievre 129: double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
1.13 ! lievre 130: double **pmmij, ***probs, ***mobaverage;
1.2 lievre 131:
132: double *weight;
133: int **s; /* Status */
134: double *agedc, **covar, idx;
1.7 lievre 135: int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;
1.2 lievre 136:
137: double ftol=FTOL; /* Tolerance for computing Max Likelihood */
138: double ftolhess; /* Tolerance for computing hessian */
139:
1.7 lievre 140: /**************** split *************************/
1.5 lievre 141: static int split( char *path, char *dirc, char *name )
142: {
143: char *s; /* pointer */
144: int l1, l2; /* length counters */
145:
146: l1 = strlen( path ); /* length of path */
147: if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
148: s = strrchr( path, '\\' ); /* find last / */
149: if ( s == NULL ) { /* no directory, so use current */
150: #if defined(__bsd__) /* get current working directory */
151: extern char *getwd( );
152:
153: if ( getwd( dirc ) == NULL ) {
154: #else
155: extern char *getcwd( );
156:
157: if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {
158: #endif
159: return( GLOCK_ERROR_GETCWD );
160: }
161: strcpy( name, path ); /* we've got it */
162: } else { /* strip direcotry from path */
163: s++; /* after this, the filename */
164: l2 = strlen( s ); /* length of filename */
165: if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
166: strcpy( name, s ); /* save file name */
167: strncpy( dirc, path, l1 - l2 ); /* now the directory */
168: dirc[l1-l2] = 0; /* add zero */
169: }
170: l1 = strlen( dirc ); /* length of directory */
171: if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; }
172: return( 0 ); /* we're done */
173: }
174:
175:
1.2 lievre 176: /******************************************/
177:
178: void replace(char *s, char*t)
179: {
180: int i;
181: int lg=20;
182: i=0;
183: lg=strlen(t);
184: for(i=0; i<= lg; i++) {
185: (s[i] = t[i]);
186: if (t[i]== '\\') s[i]='/';
187: }
188: }
189:
190: int nbocc(char *s, char occ)
191: {
192: int i,j=0;
193: int lg=20;
194: i=0;
195: lg=strlen(s);
196: for(i=0; i<= lg; i++) {
197: if (s[i] == occ ) j++;
198: }
199: return j;
200: }
201:
202: void cutv(char *u,char *v, char*t, char occ)
203: {
1.6 lievre 204: int i,lg,j,p=0;
1.2 lievre 205: i=0;
206: for(j=0; j<=strlen(t)-1; j++) {
1.3 lievre 207: if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;
1.2 lievre 208: }
209:
210: lg=strlen(t);
211: for(j=0; j<p; j++) {
212: (u[j] = t[j]);
213: }
1.6 lievre 214: u[p]='\0';
1.2 lievre 215:
216: for(j=0; j<= lg; j++) {
217: if (j>=(p+1))(v[j-p-1] = t[j]);
218: }
219: }
220:
221: /********************** nrerror ********************/
222:
223: void nrerror(char error_text[])
224: {
225: fprintf(stderr,"ERREUR ...\n");
226: fprintf(stderr,"%s\n",error_text);
227: exit(1);
228: }
229: /*********************** vector *******************/
230: double *vector(int nl, int nh)
231: {
232: double *v;
233: v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
234: if (!v) nrerror("allocation failure in vector");
235: return v-nl+NR_END;
236: }
237:
238: /************************ free vector ******************/
239: void free_vector(double*v, int nl, int nh)
240: {
241: free((FREE_ARG)(v+nl-NR_END));
242: }
243:
244: /************************ivector *******************************/
245: int *ivector(long nl,long nh)
246: {
247: int *v;
248: v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
249: if (!v) nrerror("allocation failure in ivector");
250: return v-nl+NR_END;
251: }
252:
253: /******************free ivector **************************/
254: void free_ivector(int *v, long nl, long nh)
255: {
256: free((FREE_ARG)(v+nl-NR_END));
257: }
258:
259: /******************* imatrix *******************************/
260: int **imatrix(long nrl, long nrh, long ncl, long nch)
261: /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */
262: {
263: long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;
264: int **m;
265:
266: /* allocate pointers to rows */
267: m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));
268: if (!m) nrerror("allocation failure 1 in matrix()");
269: m += NR_END;
270: m -= nrl;
271:
272:
273: /* allocate rows and set pointers to them */
274: m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));
275: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
276: m[nrl] += NR_END;
277: m[nrl] -= ncl;
278:
279: for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;
280:
281: /* return pointer to array of pointers to rows */
282: return m;
283: }
284:
285: /****************** free_imatrix *************************/
286: void free_imatrix(m,nrl,nrh,ncl,nch)
287: int **m;
288: long nch,ncl,nrh,nrl;
289: /* free an int matrix allocated by imatrix() */
290: {
291: free((FREE_ARG) (m[nrl]+ncl-NR_END));
292: free((FREE_ARG) (m+nrl-NR_END));
293: }
294:
295: /******************* matrix *******************************/
296: double **matrix(long nrl, long nrh, long ncl, long nch)
297: {
298: long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
299: double **m;
300:
301: m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
302: if (!m) nrerror("allocation failure 1 in matrix()");
303: m += NR_END;
304: m -= nrl;
305:
306: m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
307: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
308: m[nrl] += NR_END;
309: m[nrl] -= ncl;
310:
311: for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
312: return m;
313: }
314:
315: /*************************free matrix ************************/
316: void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
317: {
318: free((FREE_ARG)(m[nrl]+ncl-NR_END));
319: free((FREE_ARG)(m+nrl-NR_END));
320: }
321:
322: /******************* ma3x *******************************/
323: double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
324: {
325: long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+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:
340: m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
341: if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
342: m[nrl][ncl] += NR_END;
343: m[nrl][ncl] -= nll;
344: for (j=ncl+1; j<=nch; j++)
345: m[nrl][j]=m[nrl][j-1]+nlay;
346:
347: for (i=nrl+1; i<=nrh; i++) {
348: m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
349: for (j=ncl+1; j<=nch; j++)
350: m[i][j]=m[i][j-1]+nlay;
351: }
352: return m;
353: }
354:
355: /*************************free ma3x ************************/
356: void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
357: {
358: free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
359: free((FREE_ARG)(m[nrl]+ncl-NR_END));
360: free((FREE_ARG)(m+nrl-NR_END));
361: }
362:
363: /***************** f1dim *************************/
364: extern int ncom;
365: extern double *pcom,*xicom;
366: extern double (*nrfunc)(double []);
367:
368: double f1dim(double x)
369: {
370: int j;
371: double f;
372: double *xt;
373:
374: xt=vector(1,ncom);
375: for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];
376: f=(*nrfunc)(xt);
377: free_vector(xt,1,ncom);
378: return f;
379: }
380:
381: /*****************brent *************************/
382: double brent(double ax, double bx, double cx, double (*f)(double), double tol, double *xmin)
383: {
384: int iter;
385: double a,b,d,etemp;
386: double fu,fv,fw,fx;
387: double ftemp;
388: double p,q,r,tol1,tol2,u,v,w,x,xm;
389: double e=0.0;
390:
391: a=(ax < cx ? ax : cx);
392: b=(ax > cx ? ax : cx);
393: x=w=v=bx;
394: fw=fv=fx=(*f)(x);
395: for (iter=1;iter<=ITMAX;iter++) {
396: xm=0.5*(a+b);
397: tol2=2.0*(tol1=tol*fabs(x)+ZEPS);
398: /* if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
399: printf(".");fflush(stdout);
400: #ifdef DEBUG
401: 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);
402: /* if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
403: #endif
404: if (fabs(x-xm) <= (tol2-0.5*(b-a))){
405: *xmin=x;
406: return fx;
407: }
408: ftemp=fu;
409: if (fabs(e) > tol1) {
410: r=(x-w)*(fx-fv);
411: q=(x-v)*(fx-fw);
412: p=(x-v)*q-(x-w)*r;
413: q=2.0*(q-r);
414: if (q > 0.0) p = -p;
415: q=fabs(q);
416: etemp=e;
417: e=d;
418: if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))
419: d=CGOLD*(e=(x >= xm ? a-x : b-x));
420: else {
421: d=p/q;
422: u=x+d;
423: if (u-a < tol2 || b-u < tol2)
424: d=SIGN(tol1,xm-x);
425: }
426: } else {
427: d=CGOLD*(e=(x >= xm ? a-x : b-x));
428: }
429: u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));
430: fu=(*f)(u);
431: if (fu <= fx) {
432: if (u >= x) a=x; else b=x;
433: SHFT(v,w,x,u)
434: SHFT(fv,fw,fx,fu)
435: } else {
436: if (u < x) a=u; else b=u;
437: if (fu <= fw || w == x) {
438: v=w;
439: w=u;
440: fv=fw;
441: fw=fu;
442: } else if (fu <= fv || v == x || v == w) {
443: v=u;
444: fv=fu;
445: }
446: }
447: }
448: nrerror("Too many iterations in brent");
449: *xmin=x;
450: return fx;
451: }
452:
453: /****************** mnbrak ***********************/
454:
455: void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,
456: double (*func)(double))
457: {
458: double ulim,u,r,q, dum;
459: double fu;
460:
461: *fa=(*func)(*ax);
462: *fb=(*func)(*bx);
463: if (*fb > *fa) {
464: SHFT(dum,*ax,*bx,dum)
465: SHFT(dum,*fb,*fa,dum)
466: }
467: *cx=(*bx)+GOLD*(*bx-*ax);
468: *fc=(*func)(*cx);
469: while (*fb > *fc) {
470: r=(*bx-*ax)*(*fb-*fc);
471: q=(*bx-*cx)*(*fb-*fa);
472: u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/
473: (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r));
474: ulim=(*bx)+GLIMIT*(*cx-*bx);
475: if ((*bx-u)*(u-*cx) > 0.0) {
476: fu=(*func)(u);
477: } else if ((*cx-u)*(u-ulim) > 0.0) {
478: fu=(*func)(u);
479: if (fu < *fc) {
480: SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))
481: SHFT(*fb,*fc,fu,(*func)(u))
482: }
483: } else if ((u-ulim)*(ulim-*cx) >= 0.0) {
484: u=ulim;
485: fu=(*func)(u);
486: } else {
487: u=(*cx)+GOLD*(*cx-*bx);
488: fu=(*func)(u);
489: }
490: SHFT(*ax,*bx,*cx,u)
491: SHFT(*fa,*fb,*fc,fu)
492: }
493: }
494:
495: /*************** linmin ************************/
496:
497: int ncom;
498: double *pcom,*xicom;
499: double (*nrfunc)(double []);
500:
501: void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))
502: {
503: double brent(double ax, double bx, double cx,
504: double (*f)(double), double tol, double *xmin);
505: double f1dim(double x);
506: void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,
507: double *fc, double (*func)(double));
508: int j;
509: double xx,xmin,bx,ax;
510: double fx,fb,fa;
511:
512: ncom=n;
513: pcom=vector(1,n);
514: xicom=vector(1,n);
515: nrfunc=func;
516: for (j=1;j<=n;j++) {
517: pcom[j]=p[j];
518: xicom[j]=xi[j];
519: }
520: ax=0.0;
521: xx=1.0;
522: mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim);
523: *fret=brent(ax,xx,bx,f1dim,TOL,&xmin);
524: #ifdef DEBUG
525: printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
526: #endif
527: for (j=1;j<=n;j++) {
528: xi[j] *= xmin;
529: p[j] += xi[j];
530: }
531: free_vector(xicom,1,n);
532: free_vector(pcom,1,n);
533: }
534:
535: /*************** powell ************************/
536: void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,
537: double (*func)(double []))
538: {
539: void linmin(double p[], double xi[], int n, double *fret,
540: double (*func)(double []));
541: int i,ibig,j;
542: double del,t,*pt,*ptt,*xit;
543: double fp,fptt;
544: double *xits;
545: pt=vector(1,n);
546: ptt=vector(1,n);
547: xit=vector(1,n);
548: xits=vector(1,n);
549: *fret=(*func)(p);
550: for (j=1;j<=n;j++) pt[j]=p[j];
551: for (*iter=1;;++(*iter)) {
552: fp=(*fret);
553: ibig=0;
554: del=0.0;
555: printf("\nPowell iter=%d -2*LL=%.12f",*iter,*fret);
556: for (i=1;i<=n;i++)
557: printf(" %d %.12f",i, p[i]);
558: printf("\n");
559: for (i=1;i<=n;i++) {
560: for (j=1;j<=n;j++) xit[j]=xi[j][i];
561: fptt=(*fret);
562: #ifdef DEBUG
563: printf("fret=%lf \n",*fret);
564: #endif
565: printf("%d",i);fflush(stdout);
566: linmin(p,xit,n,fret,func);
567: if (fabs(fptt-(*fret)) > del) {
568: del=fabs(fptt-(*fret));
569: ibig=i;
570: }
571: #ifdef DEBUG
572: printf("%d %.12e",i,(*fret));
573: for (j=1;j<=n;j++) {
574: xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
575: printf(" x(%d)=%.12e",j,xit[j]);
576: }
577: for(j=1;j<=n;j++)
578: printf(" p=%.12e",p[j]);
579: printf("\n");
580: #endif
581: }
582: if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {
583: #ifdef DEBUG
584: int k[2],l;
585: k[0]=1;
586: k[1]=-1;
587: printf("Max: %.12e",(*func)(p));
588: for (j=1;j<=n;j++)
589: printf(" %.12e",p[j]);
590: printf("\n");
591: for(l=0;l<=1;l++) {
592: for (j=1;j<=n;j++) {
593: ptt[j]=p[j]+(p[j]-pt[j])*k[l];
594: printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
595: }
596: printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
597: }
598: #endif
599:
600:
601: free_vector(xit,1,n);
602: free_vector(xits,1,n);
603: free_vector(ptt,1,n);
604: free_vector(pt,1,n);
605: return;
606: }
607: if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");
608: for (j=1;j<=n;j++) {
609: ptt[j]=2.0*p[j]-pt[j];
610: xit[j]=p[j]-pt[j];
611: pt[j]=p[j];
612: }
613: fptt=(*func)(ptt);
614: if (fptt < fp) {
615: t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt);
616: if (t < 0.0) {
617: linmin(p,xit,n,fret,func);
618: for (j=1;j<=n;j++) {
619: xi[j][ibig]=xi[j][n];
620: xi[j][n]=xit[j];
621: }
622: #ifdef DEBUG
623: printf("Direction changed last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
624: for(j=1;j<=n;j++)
625: printf(" %.12e",xit[j]);
626: printf("\n");
627: #endif
628: }
629: }
630: }
631: }
632:
633: /**** Prevalence limit ****************/
634:
635: double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)
636: {
637: /* Computes the prevalence limit in each live state at age x by left multiplying the unit
638: matrix by transitions matrix until convergence is reached */
639:
640: int i, ii,j,k;
641: double min, max, maxmin, maxmax,sumnew=0.;
642: double **matprod2();
643: double **out, cov[NCOVMAX], **pmij();
644: double **newm;
645: double agefin, delaymax=50 ; /* Max number of years to converge */
646:
647: for (ii=1;ii<=nlstate+ndeath;ii++)
648: for (j=1;j<=nlstate+ndeath;j++){
649: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
650: }
1.6 lievre 651:
652: cov[1]=1.;
653:
654: /* Even if hstepm = 1, at least one multiplication by the unit matrix */
1.2 lievre 655: for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
656: newm=savm;
657: /* Covariates have to be included here again */
1.6 lievre 658: cov[2]=agefin;
659:
660: for (k=1; k<=cptcovn;k++) {
1.7 lievre 661: cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
662: /*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 663: }
664: for (k=1; k<=cptcovage;k++)
665: cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
1.7 lievre 666: for (k=1; k<=cptcovprod;k++)
667: cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
668:
669: /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
670: /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
671:
1.2 lievre 672: out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);
673:
674: savm=oldm;
675: oldm=newm;
676: maxmax=0.;
677: for(j=1;j<=nlstate;j++){
678: min=1.;
679: max=0.;
680: for(i=1; i<=nlstate; i++) {
681: sumnew=0;
682: for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
683: prlim[i][j]= newm[i][j]/(1-sumnew);
684: max=FMAX(max,prlim[i][j]);
685: min=FMIN(min,prlim[i][j]);
686: }
687: maxmin=max-min;
688: maxmax=FMAX(maxmax,maxmin);
689: }
690: if(maxmax < ftolpl){
691: return prlim;
692: }
693: }
694: }
695:
1.12 lievre 696: /*************** transition probabilities ***************/
1.2 lievre 697:
698: double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
699: {
700: double s1, s2;
701: /*double t34;*/
702: int i,j,j1, nc, ii, jj;
703:
704: for(i=1; i<= nlstate; i++){
705: for(j=1; j<i;j++){
706: for (nc=1, s2=0.;nc <=ncovmodel; nc++){
707: /*s2 += param[i][j][nc]*cov[nc];*/
708: s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
709: /*printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2);*/
710: }
711: ps[i][j]=s2;
712: /*printf("s1=%.17e, s2=%.17e\n",s1,s2);*/
713: }
714: for(j=i+1; j<=nlstate+ndeath;j++){
715: for (nc=1, s2=0.;nc <=ncovmodel; nc++){
716: s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
717: /*printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2);*/
718: }
1.12 lievre 719: ps[i][j]=(s2);
1.2 lievre 720: }
721: }
1.12 lievre 722: /*ps[3][2]=1;*/
723:
1.2 lievre 724: for(i=1; i<= nlstate; i++){
725: s1=0;
726: for(j=1; j<i; j++)
727: s1+=exp(ps[i][j]);
728: for(j=i+1; j<=nlstate+ndeath; j++)
729: s1+=exp(ps[i][j]);
730: ps[i][i]=1./(s1+1.);
731: for(j=1; j<i; j++)
732: ps[i][j]= exp(ps[i][j])*ps[i][i];
733: for(j=i+1; j<=nlstate+ndeath; j++)
734: ps[i][j]= exp(ps[i][j])*ps[i][i];
735: /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
736: } /* end i */
737:
738: for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
739: for(jj=1; jj<= nlstate+ndeath; jj++){
740: ps[ii][jj]=0;
741: ps[ii][ii]=1;
742: }
743: }
744:
1.12 lievre 745:
1.2 lievre 746: /* for(ii=1; ii<= nlstate+ndeath; ii++){
747: for(jj=1; jj<= nlstate+ndeath; jj++){
748: printf("%lf ",ps[ii][jj]);
749: }
750: printf("\n ");
751: }
752: printf("\n ");printf("%lf ",cov[2]);*/
753: /*
754: for(i=1; i<= npar; i++) printf("%f ",x[i]);
755: goto end;*/
756: return ps;
757: }
758:
759: /**************** Product of 2 matrices ******************/
760:
761: double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)
762: {
1.13 ! lievre 763: /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
1.2 lievre 764: b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
765: /* in, b, out are matrice of pointers which should have been initialized
766: before: only the contents of out is modified. The function returns
767: a pointer to pointers identical to out */
768: long i, j, k;
769: for(i=nrl; i<= nrh; i++)
770: for(k=ncolol; k<=ncoloh; k++)
771: for(j=ncl,out[i][k]=0.; j<=nch; j++)
772: out[i][k] +=in[i][j]*b[j][k];
773:
774: return out;
775: }
776:
777:
778: /************* Higher Matrix Product ***************/
779:
780: double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
781: {
782: /* Computes the transition matrix starting at age 'age' over 'nhstepm*hstepm*stepm' month
783: duration (i.e. until
784: age (in years) age+nhstepm*stepm/12) by multiplying nhstepm*hstepm matrices.
785: Output is stored in matrix po[i][j][h] for h every 'hstepm' step
786: (typically every 2 years instead of every month which is too big).
787: Model is determined by parameters x and covariates have to be
788: included manually here.
789:
790: */
791:
792: int i, j, d, h, k;
793: double **out, cov[NCOVMAX];
794: double **newm;
795:
796: /* Hstepm could be zero and should return the unit matrix */
797: for (i=1;i<=nlstate+ndeath;i++)
798: for (j=1;j<=nlstate+ndeath;j++){
799: oldm[i][j]=(i==j ? 1.0 : 0.0);
800: po[i][j][0]=(i==j ? 1.0 : 0.0);
801: }
802: /* Even if hstepm = 1, at least one multiplication by the unit matrix */
803: for(h=1; h <=nhstepm; h++){
804: for(d=1; d <=hstepm; d++){
805: newm=savm;
806: /* Covariates have to be included here again */
807: cov[1]=1.;
808: cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
1.7 lievre 809: for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
1.12 lievre 810: for (k=1; k<=cptcovage;k++)
1.7 lievre 811: cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
1.12 lievre 812: for (k=1; k<=cptcovprod;k++)
1.7 lievre 813: cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
814:
815:
1.2 lievre 816: /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
817: /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
818: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,
819: pmij(pmmij,cov,ncovmodel,x,nlstate));
820: savm=oldm;
821: oldm=newm;
822: }
823: for(i=1; i<=nlstate+ndeath; i++)
824: for(j=1;j<=nlstate+ndeath;j++) {
825: po[i][j][h]=newm[i][j];
826: /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);
827: */
828: }
829: } /* end h */
830: return po;
831: }
832:
833:
834: /*************** log-likelihood *************/
835: double func( double *x)
836: {
1.6 lievre 837: int i, ii, j, k, mi, d, kk;
1.2 lievre 838: double l, ll[NLSTATEMAX], cov[NCOVMAX];
839: double **out;
840: double sw; /* Sum of weights */
841: double lli; /* Individual log likelihood */
842: long ipmx;
843: /*extern weight */
844: /* We are differentiating ll according to initial status */
845: /* for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
846: /*for(i=1;i<imx;i++)
1.8 lievre 847: printf(" %d\n",s[4][i]);
1.2 lievre 848: */
1.6 lievre 849: cov[1]=1.;
1.2 lievre 850:
851: for(k=1; k<=nlstate; k++) ll[k]=0.;
852: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1.6 lievre 853: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
1.8 lievre 854: for(mi=1; mi<= wav[i]-1; mi++){
1.2 lievre 855: for (ii=1;ii<=nlstate+ndeath;ii++)
856: for (j=1;j<=nlstate+ndeath;j++) oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1.8 lievre 857: for(d=0; d<dh[mi][i]; d++){
858: newm=savm;
859: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
860: for (kk=1; kk<=cptcovage;kk++) {
861: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
862: }
863:
864: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
865: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
866: savm=oldm;
867: oldm=newm;
868:
869:
1.2 lievre 870: } /* end mult */
1.8 lievre 871:
1.2 lievre 872: lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);
873: /* printf(" %f ",out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/
874: ipmx +=1;
875: sw += weight[i];
876: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
877: } /* end of wave */
878: } /* end of individual */
879:
880: for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
881: /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
882: l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
883: return -l;
884: }
885:
886:
887: /*********** Maximum Likelihood Estimation ***************/
888:
889: void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
890: {
891: int i,j, iter;
892: double **xi,*delti;
893: double fret;
894: xi=matrix(1,npar,1,npar);
895: for (i=1;i<=npar;i++)
896: for (j=1;j<=npar;j++)
897: xi[i][j]=(i==j ? 1.0 : 0.0);
898: printf("Powell\n");
899: powell(p,xi,npar,ftol,&iter,&fret,func);
900:
901: printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));
902: fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f ",iter,func(p));
903:
904: }
905:
906: /**** Computes Hessian and covariance matrix ***/
907: void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
908: {
909: double **a,**y,*x,pd;
910: double **hess;
911: int i, j,jk;
912: int *indx;
913:
914: double hessii(double p[], double delta, int theta, double delti[]);
915: double hessij(double p[], double delti[], int i, int j);
916: void lubksb(double **a, int npar, int *indx, double b[]) ;
917: void ludcmp(double **a, int npar, int *indx, double *d) ;
918:
919: hess=matrix(1,npar,1,npar);
920:
921: printf("\nCalculation of the hessian matrix. Wait...\n");
922: for (i=1;i<=npar;i++){
923: printf("%d",i);fflush(stdout);
924: hess[i][i]=hessii(p,ftolhess,i,delti);
925: /*printf(" %f ",p[i]);*/
1.12 lievre 926: /*printf(" %lf ",hess[i][i]);*/
1.2 lievre 927: }
1.12 lievre 928:
1.2 lievre 929: for (i=1;i<=npar;i++) {
930: for (j=1;j<=npar;j++) {
931: if (j>i) {
932: printf(".%d%d",i,j);fflush(stdout);
933: hess[i][j]=hessij(p,delti,i,j);
1.12 lievre 934: hess[j][i]=hess[i][j];
935: /*printf(" %lf ",hess[i][j]);*/
1.2 lievre 936: }
937: }
938: }
939: printf("\n");
940:
941: printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
942:
943: a=matrix(1,npar,1,npar);
944: y=matrix(1,npar,1,npar);
945: x=vector(1,npar);
946: indx=ivector(1,npar);
947: for (i=1;i<=npar;i++)
948: for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
949: ludcmp(a,npar,indx,&pd);
950:
951: for (j=1;j<=npar;j++) {
952: for (i=1;i<=npar;i++) x[i]=0;
953: x[j]=1;
954: lubksb(a,npar,indx,x);
955: for (i=1;i<=npar;i++){
956: matcov[i][j]=x[i];
957: }
958: }
959:
960: printf("\n#Hessian matrix#\n");
961: for (i=1;i<=npar;i++) {
962: for (j=1;j<=npar;j++) {
963: printf("%.3e ",hess[i][j]);
964: }
965: printf("\n");
966: }
967:
968: /* Recompute Inverse */
969: for (i=1;i<=npar;i++)
970: for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];
971: ludcmp(a,npar,indx,&pd);
972:
973: /* printf("\n#Hessian matrix recomputed#\n");
974:
975: for (j=1;j<=npar;j++) {
976: for (i=1;i<=npar;i++) x[i]=0;
977: x[j]=1;
978: lubksb(a,npar,indx,x);
979: for (i=1;i<=npar;i++){
980: y[i][j]=x[i];
981: printf("%.3e ",y[i][j]);
982: }
983: printf("\n");
984: }
985: */
986:
987: free_matrix(a,1,npar,1,npar);
988: free_matrix(y,1,npar,1,npar);
989: free_vector(x,1,npar);
990: free_ivector(indx,1,npar);
991: free_matrix(hess,1,npar,1,npar);
992:
993:
994: }
995:
996: /*************** hessian matrix ****************/
997: double hessii( double x[], double delta, int theta, double delti[])
998: {
999: int i;
1000: int l=1, lmax=20;
1001: double k1,k2;
1002: double p2[NPARMAX+1];
1003: double res;
1004: double delt, delts, nkhi=10.,nkhif=1., khi=1.e-4;
1005: double fx;
1006: int k=0,kmax=10;
1007: double l1;
1008:
1009: fx=func(x);
1010: for (i=1;i<=npar;i++) p2[i]=x[i];
1011: for(l=0 ; l <=lmax; l++){
1012: l1=pow(10,l);
1013: delts=delt;
1014: for(k=1 ; k <kmax; k=k+1){
1015: delt = delta*(l1*k);
1016: p2[theta]=x[theta] +delt;
1017: k1=func(p2)-fx;
1018: p2[theta]=x[theta]-delt;
1019: k2=func(p2)-fx;
1020: /*res= (k1-2.0*fx+k2)/delt/delt; */
1021: res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */
1022:
1023: #ifdef DEBUG
1024: 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);
1025: #endif
1026: /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
1027: if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
1028: k=kmax;
1029: }
1030: else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
1031: k=kmax; l=lmax*10.;
1032: }
1033: else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){
1034: delts=delt;
1035: }
1036: }
1037: }
1038: delti[theta]=delts;
1.12 lievre 1039: return res;
1.3 lievre 1040:
1.2 lievre 1041: }
1042:
1043: double hessij( double x[], double delti[], int thetai,int thetaj)
1044: {
1045: int i;
1046: int l=1, l1, lmax=20;
1047: double k1,k2,k3,k4,res,fx;
1048: double p2[NPARMAX+1];
1049: int k;
1050:
1051: fx=func(x);
1052: for (k=1; k<=2; k++) {
1053: for (i=1;i<=npar;i++) p2[i]=x[i];
1054: p2[thetai]=x[thetai]+delti[thetai]/k;
1055: p2[thetaj]=x[thetaj]+delti[thetaj]/k;
1056: k1=func(p2)-fx;
1057:
1058: p2[thetai]=x[thetai]+delti[thetai]/k;
1059: p2[thetaj]=x[thetaj]-delti[thetaj]/k;
1060: k2=func(p2)-fx;
1061:
1062: p2[thetai]=x[thetai]-delti[thetai]/k;
1063: p2[thetaj]=x[thetaj]+delti[thetaj]/k;
1064: k3=func(p2)-fx;
1065:
1066: p2[thetai]=x[thetai]-delti[thetai]/k;
1067: p2[thetaj]=x[thetaj]-delti[thetaj]/k;
1068: k4=func(p2)-fx;
1069: res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */
1070: #ifdef DEBUG
1071: 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);
1072: #endif
1073: }
1074: return res;
1075: }
1076:
1077: /************** Inverse of matrix **************/
1078: void ludcmp(double **a, int n, int *indx, double *d)
1079: {
1080: int i,imax,j,k;
1081: double big,dum,sum,temp;
1082: double *vv;
1083:
1084: vv=vector(1,n);
1085: *d=1.0;
1086: for (i=1;i<=n;i++) {
1087: big=0.0;
1088: for (j=1;j<=n;j++)
1089: if ((temp=fabs(a[i][j])) > big) big=temp;
1090: if (big == 0.0) nrerror("Singular matrix in routine ludcmp");
1091: vv[i]=1.0/big;
1092: }
1093: for (j=1;j<=n;j++) {
1094: for (i=1;i<j;i++) {
1095: sum=a[i][j];
1096: for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];
1097: a[i][j]=sum;
1098: }
1099: big=0.0;
1100: for (i=j;i<=n;i++) {
1101: sum=a[i][j];
1102: for (k=1;k<j;k++)
1103: sum -= a[i][k]*a[k][j];
1104: a[i][j]=sum;
1105: if ( (dum=vv[i]*fabs(sum)) >= big) {
1106: big=dum;
1107: imax=i;
1108: }
1109: }
1110: if (j != imax) {
1111: for (k=1;k<=n;k++) {
1112: dum=a[imax][k];
1113: a[imax][k]=a[j][k];
1114: a[j][k]=dum;
1115: }
1116: *d = -(*d);
1117: vv[imax]=vv[j];
1118: }
1119: indx[j]=imax;
1120: if (a[j][j] == 0.0) a[j][j]=TINY;
1121: if (j != n) {
1122: dum=1.0/(a[j][j]);
1123: for (i=j+1;i<=n;i++) a[i][j] *= dum;
1124: }
1125: }
1126: free_vector(vv,1,n); /* Doesn't work */
1127: ;
1128: }
1129:
1130: void lubksb(double **a, int n, int *indx, double b[])
1131: {
1132: int i,ii=0,ip,j;
1133: double sum;
1134:
1135: for (i=1;i<=n;i++) {
1136: ip=indx[i];
1137: sum=b[ip];
1138: b[ip]=b[i];
1139: if (ii)
1140: for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];
1141: else if (sum) ii=i;
1142: b[i]=sum;
1143: }
1144: for (i=n;i>=1;i--) {
1145: sum=b[i];
1146: for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];
1147: b[i]=sum/a[i][i];
1148: }
1149: }
1150:
1151: /************ Frequencies ********************/
1152: void freqsummary(char fileres[], int agemin, int agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax)
1153: { /* Some frequencies */
1154:
1155: int i, m, jk, k1, i1, j1, bool, z1,z2,j;
1156: double ***freq; /* Frequencies */
1157: double *pp;
1158: double pos;
1159: FILE *ficresp;
1160: char fileresp[FILENAMELENGTH];
1161:
1162: pp=vector(1,nlstate);
1.13 ! lievre 1163: probs= ma3x(1,130 ,1,8, 1,8);
1.2 lievre 1164: strcpy(fileresp,"p");
1165: strcat(fileresp,fileres);
1166: if((ficresp=fopen(fileresp,"w"))==NULL) {
1167: printf("Problem with prevalence resultfile: %s\n", fileresp);
1168: exit(0);
1169: }
1170: freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);
1171: j1=0;
1172:
1.7 lievre 1173: j=cptcoveff;
1.2 lievre 1174: if (cptcovn<1) {j=1;ncodemax[1]=1;}
1175:
1176: for(k1=1; k1<=j;k1++){
1177: for(i1=1; i1<=ncodemax[k1];i1++){
1178: j1++;
1.8 lievre 1179: /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
1180: scanf("%d", i);*/
1.2 lievre 1181: for (i=-1; i<=nlstate+ndeath; i++)
1182: for (jk=-1; jk<=nlstate+ndeath; jk++)
1183: for(m=agemin; m <= agemax+3; m++)
1184: freq[i][jk][m]=0;
1185:
1186: for (i=1; i<=imx; i++) {
1187: bool=1;
1188: if (cptcovn>0) {
1.7 lievre 1189: for (z1=1; z1<=cptcoveff; z1++)
1.8 lievre 1190: if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])
1191: bool=0;
1.2 lievre 1192: }
1193: if (bool==1) {
1194: for(m=firstpass; m<=lastpass-1; m++){
1195: if(agev[m][i]==0) agev[m][i]=agemax+1;
1196: if(agev[m][i]==1) agev[m][i]=agemax+2;
1197: freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
1198: freq[s[m][i]][s[m+1][i]][(int) agemax+3] += weight[i];
1199: }
1200: }
1201: }
1202: if (cptcovn>0) {
1.7 lievre 1203: fprintf(ficresp, "\n#********** Variable ");
1204: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
1205: fprintf(ficresp, "**********\n#");
1.8 lievre 1206: }
1.2 lievre 1207: for(i=1; i<=nlstate;i++)
1208: fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
1209: fprintf(ficresp, "\n");
1210:
1211: for(i=(int)agemin; i <= (int)agemax+3; i++){
1212: if(i==(int)agemax+3)
1213: printf("Total");
1214: else
1215: printf("Age %d", i);
1216: for(jk=1; jk <=nlstate ; jk++){
1217: for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
1218: pp[jk] += freq[jk][m][i];
1219: }
1220: for(jk=1; jk <=nlstate ; jk++){
1221: for(m=-1, pos=0; m <=0 ; m++)
1222: pos += freq[jk][m][i];
1223: if(pp[jk]>=1.e-10)
1224: printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
1225: else
1226: printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
1227: }
1228: for(jk=1; jk <=nlstate ; jk++){
1229: for(m=1, pp[jk]=0; m <=nlstate+ndeath; m++)
1230: pp[jk] += freq[jk][m][i];
1231: }
1232: for(jk=1,pos=0; jk <=nlstate ; jk++)
1233: pos += pp[jk];
1234: for(jk=1; jk <=nlstate ; jk++){
1235: if(pos>=1.e-5)
1236: printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
1237: else
1238: printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
1239: if( i <= (int) agemax){
1.13 ! lievre 1240: if(pos>=1.e-5){
1.2 lievre 1241: fprintf(ficresp," %d %.5f %.0f %.0f",i,pp[jk]/pos, pp[jk],pos);
1.13 ! lievre 1242: probs[i][jk][j1]= pp[jk]/pos;
! 1243: /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/
! 1244: }
1.2 lievre 1245: else
1246: fprintf(ficresp," %d NaNq %.0f %.0f",i,pp[jk],pos);
1247: }
1248: }
1249: for(jk=-1; jk <=nlstate+ndeath; jk++)
1250: for(m=-1; m <=nlstate+ndeath; m++)
1251: if(freq[jk][m][i] !=0 ) printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
1252: if(i <= (int) agemax)
1253: fprintf(ficresp,"\n");
1254: printf("\n");
1255: }
1256: }
1257: }
1258:
1259: fclose(ficresp);
1260: free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);
1261: free_vector(pp,1,nlstate);
1262:
1263: } /* End of Freq */
1264:
1265: /************* Waves Concatenation ***************/
1266:
1267: void concatwav(int wav[], int **dh, int **mw, int **s, double *agedc, double **agev, int firstpass, int lastpass, int imx, int nlstate, int stepm)
1268: {
1269: /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
1270: Death is a valid wave (if date is known).
1271: mw[mi][i] is the mi (mi=1 to wav[i]) effective wave of individual i
1272: dh[m][i] of dh[mw[mi][i][i] is the delay between two effective waves m=mw[mi][i]
1273: and mw[mi+1][i]. dh depends on stepm.
1274: */
1275:
1276: int i, mi, m;
1.8 lievre 1277: /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
1278: double sum=0., jmean=0.;*/
1.2 lievre 1279:
1.11 lievre 1280: int j, k=0,jk, ju, jl;
1281: double sum=0.;
1282: jmin=1e+5;
1283: jmax=-1;
1284: jmean=0.;
1.2 lievre 1285: for(i=1; i<=imx; i++){
1286: mi=0;
1287: m=firstpass;
1288: while(s[m][i] <= nlstate){
1289: if(s[m][i]>=1)
1290: mw[++mi][i]=m;
1291: if(m >=lastpass)
1292: break;
1293: else
1294: m++;
1295: }/* end while */
1296: if (s[m][i] > nlstate){
1297: mi++; /* Death is another wave */
1298: /* if(mi==0) never been interviewed correctly before death */
1299: /* Only death is a correct wave */
1300: mw[mi][i]=m;
1301: }
1302:
1303: wav[i]=mi;
1304: if(mi==0)
1305: printf("Warning, no any valid information for:%d line=%d\n",num[i],i);
1306: }
1307:
1308: for(i=1; i<=imx; i++){
1309: for(mi=1; mi<wav[i];mi++){
1310: if (stepm <=0)
1311: dh[mi][i]=1;
1312: else{
1313: if (s[mw[mi+1][i]][i] > nlstate) {
1.10 lievre 1314: if (agedc[i] < 2*AGESUP) {
1.2 lievre 1315: j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);
1.8 lievre 1316: if(j==0) j=1; /* Survives at least one month after exam */
1317: k=k+1;
1318: if (j >= jmax) jmax=j;
1.11 lievre 1319: if (j <= jmin) jmin=j;
1.8 lievre 1320: sum=sum+j;
1.12 lievre 1321: /* if (j<10) printf("j=%d num=%d ",j,i); */
1.10 lievre 1322: }
1.2 lievre 1323: }
1324: else{
1325: j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
1326: k=k+1;
1327: if (j >= jmax) jmax=j;
1328: else if (j <= jmin)jmin=j;
1.12 lievre 1329: /* if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
1.2 lievre 1330: sum=sum+j;
1331: }
1332: jk= j/stepm;
1333: jl= j -jk*stepm;
1334: ju= j -(jk+1)*stepm;
1335: if(jl <= -ju)
1336: dh[mi][i]=jk;
1337: else
1338: dh[mi][i]=jk+1;
1339: if(dh[mi][i]==0)
1340: dh[mi][i]=1; /* At least one step */
1341: }
1342: }
1343: }
1.8 lievre 1344: jmean=sum/k;
1345: printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);
1.12 lievre 1346: }
1.2 lievre 1347: /*********** Tricode ****************************/
1348: void tricode(int *Tvar, int **nbcode, int imx)
1349: {
1.7 lievre 1350: int Ndum[20],ij=1, k, j, i;
1.2 lievre 1351: int cptcode=0;
1.7 lievre 1352: cptcoveff=0;
1353:
1354: for (k=0; k<19; k++) Ndum[k]=0;
1.2 lievre 1355: for (k=1; k<=7; k++) ncodemax[k]=0;
1.6 lievre 1356:
1.7 lievre 1357: for (j=1; j<=(cptcovn+2*cptcovprod); j++) {
1.2 lievre 1358: for (i=1; i<=imx; i++) {
1359: ij=(int)(covar[Tvar[j]][i]);
1360: Ndum[ij]++;
1.8 lievre 1361: /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
1.2 lievre 1362: if (ij > cptcode) cptcode=ij;
1363: }
1.7 lievre 1364:
1.2 lievre 1365: for (i=0; i<=cptcode; i++) {
1366: if(Ndum[i]!=0) ncodemax[j]++;
1367: }
1368: ij=1;
1.7 lievre 1369:
1.8 lievre 1370:
1.2 lievre 1371: for (i=1; i<=ncodemax[j]; i++) {
1.7 lievre 1372: for (k=0; k<=19; k++) {
1.2 lievre 1373: if (Ndum[k] != 0) {
1374: nbcode[Tvar[j]][ij]=k;
1375: ij++;
1376: }
1377: if (ij > ncodemax[j]) break;
1378: }
1379: }
1.7 lievre 1380: }
1.8 lievre 1381:
1382: for (k=0; k<19; k++) Ndum[k]=0;
1383:
1.12 lievre 1384: for (i=1; i<=ncovmodel-2; i++) {
1.7 lievre 1385: ij=Tvar[i];
1386: Ndum[ij]++;
1387: }
1.8 lievre 1388:
1.7 lievre 1389: ij=1;
1.8 lievre 1390: for (i=1; i<=10; i++) {
1.7 lievre 1391: if((Ndum[i]!=0) && (i<=ncov)){
1.8 lievre 1392: Tvaraff[ij]=i;
1393: ij++;
1.7 lievre 1394: }
1395: }
1396:
1.8 lievre 1397: cptcoveff=ij-1;
1.6 lievre 1398: }
1.2 lievre 1399:
1400: /*********** Health Expectancies ****************/
1401:
1402: void evsij(char fileres[], double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int ij)
1403: {
1404: /* Health expectancies */
1405: int i, j, nhstepm, hstepm, h;
1406: double age, agelim,hf;
1407: double ***p3mat;
1408:
1409: fprintf(ficreseij,"# Health expectancies\n");
1410: fprintf(ficreseij,"# Age");
1411: for(i=1; i<=nlstate;i++)
1412: for(j=1; j<=nlstate;j++)
1413: fprintf(ficreseij," %1d-%1d",i,j);
1414: fprintf(ficreseij,"\n");
1415:
1416: hstepm=1*YEARM; /* Every j years of age (in month) */
1417: hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */
1418:
1419: agelim=AGESUP;
1420: for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
1421: /* nhstepm age range expressed in number of stepm */
1422: nhstepm=(int) rint((agelim-age)*YEARM/stepm);
1423: /* Typically if 20 years = 20*12/6=40 stepm */
1424: if (stepm >= YEARM) hstepm=1;
1425: nhstepm = nhstepm/hstepm;/* Expressed in hstepm, typically 40/4=10 */
1426: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
1427: /* Computed by stepm unit matrices, product of hstepm matrices, stored
1428: in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
1429: hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);
1430:
1431:
1432: for(i=1; i<=nlstate;i++)
1433: for(j=1; j<=nlstate;j++)
1434: for (h=0, eij[i][j][(int)age]=0; h<=nhstepm; h++){
1435: eij[i][j][(int)age] +=p3mat[i][j][h];
1436: }
1437:
1438: hf=1;
1439: if (stepm >= YEARM) hf=stepm/YEARM;
1440: fprintf(ficreseij,"%.0f",age );
1441: for(i=1; i<=nlstate;i++)
1442: for(j=1; j<=nlstate;j++){
1443: fprintf(ficreseij," %.4f", hf*eij[i][j][(int)age]);
1444: }
1445: fprintf(ficreseij,"\n");
1446: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
1447: }
1448: }
1449:
1450: /************ Variance ******************/
1451: 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)
1452: {
1453: /* Variance of health expectancies */
1454: /* double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
1455: double **newm;
1456: double **dnewm,**doldm;
1457: int i, j, nhstepm, hstepm, h;
1458: int k, cptcode;
1.12 lievre 1459: double *xp;
1.2 lievre 1460: double **gp, **gm;
1461: double ***gradg, ***trgradg;
1462: double ***p3mat;
1463: double age,agelim;
1464: int theta;
1465:
1466: fprintf(ficresvij,"# Covariances of life expectancies\n");
1467: fprintf(ficresvij,"# Age");
1468: for(i=1; i<=nlstate;i++)
1469: for(j=1; j<=nlstate;j++)
1470: fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);
1471: fprintf(ficresvij,"\n");
1472:
1473: xp=vector(1,npar);
1474: dnewm=matrix(1,nlstate,1,npar);
1475: doldm=matrix(1,nlstate,1,nlstate);
1476:
1477: hstepm=1*YEARM; /* Every year of age */
1478: hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */
1479: agelim = AGESUP;
1480: for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
1481: nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
1482: if (stepm >= YEARM) hstepm=1;
1483: nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
1484: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
1485: gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
1486: gp=matrix(0,nhstepm,1,nlstate);
1487: gm=matrix(0,nhstepm,1,nlstate);
1488:
1489: for(theta=1; theta <=npar; theta++){
1490: for(i=1; i<=npar; i++){ /* Computes gradient */
1491: xp[i] = x[i] + (i==theta ?delti[theta]:0);
1492: }
1493: hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
1494: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
1495: for(j=1; j<= nlstate; j++){
1496: for(h=0; h<=nhstepm; h++){
1497: for(i=1, gp[h][j]=0.;i<=nlstate;i++)
1498: gp[h][j] += prlim[i][i]*p3mat[i][j][h];
1499: }
1500: }
1501:
1502: for(i=1; i<=npar; i++) /* Computes gradient */
1503: xp[i] = x[i] - (i==theta ?delti[theta]:0);
1504: hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
1505: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
1506: for(j=1; j<= nlstate; j++){
1507: for(h=0; h<=nhstepm; h++){
1508: for(i=1, gm[h][j]=0.;i<=nlstate;i++)
1509: gm[h][j] += prlim[i][i]*p3mat[i][j][h];
1510: }
1511: }
1512: for(j=1; j<= nlstate; j++)
1513: for(h=0; h<=nhstepm; h++){
1514: gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
1515: }
1516: } /* End theta */
1517:
1518: trgradg =ma3x(0,nhstepm,1,nlstate,1,npar);
1519:
1520: for(h=0; h<=nhstepm; h++)
1521: for(j=1; j<=nlstate;j++)
1522: for(theta=1; theta <=npar; theta++)
1523: trgradg[h][j][theta]=gradg[h][theta][j];
1524:
1525: for(i=1;i<=nlstate;i++)
1526: for(j=1;j<=nlstate;j++)
1527: vareij[i][j][(int)age] =0.;
1528: for(h=0;h<=nhstepm;h++){
1529: for(k=0;k<=nhstepm;k++){
1530: matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
1531: matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
1532: for(i=1;i<=nlstate;i++)
1533: for(j=1;j<=nlstate;j++)
1534: vareij[i][j][(int)age] += doldm[i][j];
1535: }
1536: }
1537: h=1;
1538: if (stepm >= YEARM) h=stepm/YEARM;
1539: fprintf(ficresvij,"%.0f ",age );
1540: for(i=1; i<=nlstate;i++)
1541: for(j=1; j<=nlstate;j++){
1542: fprintf(ficresvij," %.4f", h*vareij[i][j][(int)age]);
1543: }
1544: fprintf(ficresvij,"\n");
1545: free_matrix(gp,0,nhstepm,1,nlstate);
1546: free_matrix(gm,0,nhstepm,1,nlstate);
1547: free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
1548: free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
1549: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
1550: } /* End age */
1551:
1552: free_vector(xp,1,npar);
1553: free_matrix(doldm,1,nlstate,1,npar);
1554: free_matrix(dnewm,1,nlstate,1,nlstate);
1555:
1556: }
1557:
1558: /************ Variance of prevlim ******************/
1559: 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)
1560: {
1561: /* Variance of prevalence limit */
1562: /* double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
1563: double **newm;
1564: double **dnewm,**doldm;
1565: int i, j, nhstepm, hstepm;
1566: int k, cptcode;
1567: double *xp;
1568: double *gp, *gm;
1569: double **gradg, **trgradg;
1570: double age,agelim;
1571: int theta;
1572:
1573: fprintf(ficresvpl,"# Standard deviation of prevalences limit\n");
1574: fprintf(ficresvpl,"# Age");
1575: for(i=1; i<=nlstate;i++)
1576: fprintf(ficresvpl," %1d-%1d",i,i);
1577: fprintf(ficresvpl,"\n");
1578:
1579: xp=vector(1,npar);
1580: dnewm=matrix(1,nlstate,1,npar);
1581: doldm=matrix(1,nlstate,1,nlstate);
1582:
1583: hstepm=1*YEARM; /* Every year of age */
1584: hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */
1585: agelim = AGESUP;
1586: for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
1587: nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
1588: if (stepm >= YEARM) hstepm=1;
1589: nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
1590: gradg=matrix(1,npar,1,nlstate);
1591: gp=vector(1,nlstate);
1592: gm=vector(1,nlstate);
1593:
1594: for(theta=1; theta <=npar; theta++){
1595: for(i=1; i<=npar; i++){ /* Computes gradient */
1596: xp[i] = x[i] + (i==theta ?delti[theta]:0);
1597: }
1598: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
1599: for(i=1;i<=nlstate;i++)
1600: gp[i] = prlim[i][i];
1601:
1602: for(i=1; i<=npar; i++) /* Computes gradient */
1603: xp[i] = x[i] - (i==theta ?delti[theta]:0);
1604: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
1605: for(i=1;i<=nlstate;i++)
1606: gm[i] = prlim[i][i];
1607:
1608: for(i=1;i<=nlstate;i++)
1609: gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
1610: } /* End theta */
1611:
1612: trgradg =matrix(1,nlstate,1,npar);
1613:
1614: for(j=1; j<=nlstate;j++)
1615: for(theta=1; theta <=npar; theta++)
1616: trgradg[j][theta]=gradg[theta][j];
1617:
1618: for(i=1;i<=nlstate;i++)
1619: varpl[i][(int)age] =0.;
1620: matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
1621: matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
1622: for(i=1;i<=nlstate;i++)
1623: varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
1624:
1625: fprintf(ficresvpl,"%.0f ",age );
1626: for(i=1; i<=nlstate;i++)
1627: fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
1628: fprintf(ficresvpl,"\n");
1629: free_vector(gp,1,nlstate);
1630: free_vector(gm,1,nlstate);
1631: free_matrix(gradg,1,npar,1,nlstate);
1632: free_matrix(trgradg,1,nlstate,1,npar);
1633: } /* End age */
1634:
1635: free_vector(xp,1,npar);
1636: free_matrix(doldm,1,nlstate,1,npar);
1637: free_matrix(dnewm,1,nlstate,1,nlstate);
1638:
1639: }
1640:
1.13 ! lievre 1641: /************ Variance of one-step probabilities ******************/
! 1642: void varprob(char fileres[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij)
! 1643: {
! 1644: int i, j;
! 1645: int k=0, cptcode;
! 1646: double **dnewm,**doldm;
! 1647: double *xp;
! 1648: double *gp, *gm;
! 1649: double **gradg, **trgradg;
! 1650: double age,agelim, cov[NCOVMAX];
! 1651: int theta;
! 1652: char fileresprob[FILENAMELENGTH];
! 1653:
! 1654: strcpy(fileresprob,"prob");
! 1655: strcat(fileresprob,fileres);
! 1656: if((ficresprob=fopen(fileresprob,"w"))==NULL) {
! 1657: printf("Problem with resultfile: %s\n", fileresprob);
! 1658: }
! 1659: printf("Computing variance of one-step probabilities: result on file '%s' \n",fileresprob);
! 1660:
1.2 lievre 1661:
1.13 ! lievre 1662: xp=vector(1,npar);
! 1663: dnewm=matrix(1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
! 1664: doldm=matrix(1,(nlstate+ndeath)*(nlstate+ndeath),1,(nlstate+ndeath)*(nlstate+ndeath));
! 1665:
! 1666: cov[1]=1;
! 1667: for (age=bage; age<=fage; age ++){
! 1668: cov[2]=age;
! 1669: gradg=matrix(1,npar,1,9);
! 1670: trgradg=matrix(1,9,1,npar);
! 1671: gp=vector(1,(nlstate+ndeath)*(nlstate+ndeath));
! 1672: gm=vector(1,(nlstate+ndeath)*(nlstate+ndeath));
! 1673:
! 1674: for(theta=1; theta <=npar; theta++){
! 1675: for(i=1; i<=npar; i++)
! 1676: xp[i] = x[i] + (i==theta ?delti[theta]:0);
! 1677:
! 1678: pmij(pmmij,cov,ncovmodel,xp,nlstate);
! 1679:
! 1680: k=0;
! 1681: for(i=1; i<= (nlstate+ndeath); i++){
! 1682: for(j=1; j<=(nlstate+ndeath);j++){
! 1683: k=k+1;
! 1684: gp[k]=pmmij[i][j];
! 1685: }
! 1686: }
! 1687:
! 1688: for(i=1; i<=npar; i++)
! 1689: xp[i] = x[i] - (i==theta ?delti[theta]:0);
! 1690:
! 1691:
! 1692: pmij(pmmij,cov,ncovmodel,xp,nlstate);
! 1693: k=0;
! 1694: for(i=1; i<=(nlstate+ndeath); i++){
! 1695: for(j=1; j<=(nlstate+ndeath);j++){
! 1696: k=k+1;
! 1697: gm[k]=pmmij[i][j];
! 1698: }
! 1699: }
! 1700:
! 1701: for(i=1; i<= (nlstate+ndeath)*(nlstate+ndeath); i++)
! 1702: gradg[theta][i]=(gp[i]-gm[i])/2./delti[theta];
! 1703: }
! 1704:
! 1705: for(j=1; j<=(nlstate+ndeath)*(nlstate+ndeath);j++)
! 1706: for(theta=1; theta <=npar; theta++)
! 1707: trgradg[j][theta]=gradg[theta][j];
! 1708:
! 1709: matprod2(dnewm,trgradg,1,9,1,npar,1,npar,matcov);
! 1710: matprod2(doldm,dnewm,1,9,1,npar,1,9,gradg);
! 1711:
! 1712: pmij(pmmij,cov,ncovmodel,x,nlstate);
! 1713:
! 1714: k=0;
! 1715: for(i=1; i<=(nlstate+ndeath); i++){
! 1716: for(j=1; j<=(nlstate+ndeath);j++){
! 1717: k=k+1;
! 1718: gm[k]=pmmij[i][j];
! 1719: }
! 1720: }
! 1721:
! 1722: /*printf("\n%d ",(int)age);
! 1723: for (i=1; i<=(nlstate+ndeath)*(nlstate+ndeath-1);i++){
! 1724:
! 1725:
! 1726: printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
! 1727: }*/
! 1728:
! 1729: fprintf(ficresprob,"\n%d ",(int)age);
! 1730:
! 1731: for (i=1; i<=(nlstate+ndeath)*(nlstate+ndeath-1);i++){
! 1732: if (i== 2) fprintf(ficresprob,"%.3e %.3e ",gm[i],doldm[i][i]);
! 1733: if (i== 4) fprintf(ficresprob,"%.3e %.3e ",gm[i],doldm[i][i]);
! 1734: }
! 1735:
! 1736: free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
! 1737: free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
! 1738: free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
! 1739: free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
! 1740: }
! 1741: free_vector(xp,1,npar);
! 1742: fclose(ficresprob);
! 1743: exit(0);
! 1744: }
1.2 lievre 1745:
1746: /***********************************************/
1747: /**************** Main Program *****************/
1748: /***********************************************/
1749:
1750: /*int main(int argc, char *argv[])*/
1751: int main()
1752: {
1753:
1.8 lievre 1754: int i,j, k, n=MAXN,iter,m,size,cptcode, cptcod;
1.2 lievre 1755: double agedeb, agefin,hf;
1756: double agemin=1.e20, agemax=-1.e20;
1757:
1758: double fret;
1759: double **xi,tmp,delta;
1760:
1761: double dum; /* Dummy variable */
1762: double ***p3mat;
1763: int *indx;
1764: char line[MAXLINE], linepar[MAXLINE];
1765: char title[MAXLINE];
1.9 lievre 1766: char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH], filerespl[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH];
1.13 ! lievre 1767: char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], fileresf[FILENAMELENGTH];
1.2 lievre 1768: char filerest[FILENAMELENGTH];
1769: char fileregp[FILENAMELENGTH];
1770: char path[80],pathc[80],pathcd[80],pathtot[80],model[20];
1771: int firstobs=1, lastobs=10;
1772: int sdeb, sfin; /* Status at beginning and end */
1773: int c, h , cpt,l;
1774: int ju,jl, mi;
1.7 lievre 1775: int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;
1.2 lievre 1776: int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,**adl,*tab;
1.12 lievre 1777:
1.2 lievre 1778: int hstepm, nhstepm;
1779: double bage, fage, age, agelim, agebase;
1780: double ftolpl=FTOL;
1781: double **prlim;
1782: double *severity;
1783: double ***param; /* Matrix of parameters */
1784: double *p;
1785: double **matcov; /* Matrix of covariance */
1786: double ***delti3; /* Scale */
1787: double *delti; /* Scale */
1788: double ***eij, ***vareij;
1789: double **varpl; /* Variances of prevalence limits by age */
1790: double *epj, vepp;
1.13 ! lievre 1791: double kk1;
! 1792:
1.10 lievre 1793: char version[80]="Imach version 64b, May 2001, INED-EUROREVES ";
1.2 lievre 1794: char *alph[]={"a","a","b","c","d","e"}, str[4];
1.5 lievre 1795:
1.13 ! lievre 1796:
1.2 lievre 1797: char z[1]="c", occ;
1798: #include <sys/time.h>
1799: #include <time.h>
1800: char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];
1801: /* long total_usecs;
1802: struct timeval start_time, end_time;
1803:
1804: gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */
1805:
1806:
1.9 lievre 1807: printf("\nIMACH, Version 0.64b");
1.2 lievre 1808: printf("\nEnter the parameter file name: ");
1809:
1810: #ifdef windows
1811: scanf("%s",pathtot);
1.5 lievre 1812: getcwd(pathcd, size);
1813: /*cygwin_split_path(pathtot,path,optionfile);
1814: printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/
1815: /* cutv(path,optionfile,pathtot,'\\');*/
1816:
1817: split(pathtot, path,optionfile);
1.2 lievre 1818: chdir(path);
1819: replace(pathc,path);
1820: #endif
1821: #ifdef unix
1822: scanf("%s",optionfile);
1823: #endif
1824:
1825: /*-------- arguments in the command line --------*/
1826:
1827: strcpy(fileres,"r");
1828: strcat(fileres, optionfile);
1829:
1830: /*---------arguments file --------*/
1831:
1832: if((ficpar=fopen(optionfile,"r"))==NULL) {
1833: printf("Problem with optionfile %s\n",optionfile);
1834: goto end;
1835: }
1836:
1837: strcpy(filereso,"o");
1838: strcat(filereso,fileres);
1839: if((ficparo=fopen(filereso,"w"))==NULL) {
1840: printf("Problem with Output resultfile: %s\n", filereso);goto end;
1841: }
1842:
1843: /* Reads comments: lines beginning with '#' */
1844: while((c=getc(ficpar))=='#' && c!= EOF){
1845: ungetc(c,ficpar);
1846: fgets(line, MAXLINE, ficpar);
1847: puts(line);
1848: fputs(line,ficparo);
1849: }
1850: ungetc(c,ficpar);
1851:
1852: 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);
1853: 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);
1854: 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);
1855:
1.8 lievre 1856: covar=matrix(0,NCOVMAX,1,n);
1857: cptcovn=0;
1858: if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;
1.2 lievre 1859:
1860: ncovmodel=2+cptcovn;
1861: nvar=ncovmodel-1; /* Suppressing age as a basic covariate */
1862:
1863: /* Read guess parameters */
1864: /* Reads comments: lines beginning with '#' */
1865: while((c=getc(ficpar))=='#' && c!= EOF){
1866: ungetc(c,ficpar);
1867: fgets(line, MAXLINE, ficpar);
1868: puts(line);
1869: fputs(line,ficparo);
1870: }
1871: ungetc(c,ficpar);
1872:
1873: param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
1874: for(i=1; i <=nlstate; i++)
1875: for(j=1; j <=nlstate+ndeath-1; j++){
1876: fscanf(ficpar,"%1d%1d",&i1,&j1);
1877: fprintf(ficparo,"%1d%1d",i1,j1);
1878: printf("%1d%1d",i,j);
1879: for(k=1; k<=ncovmodel;k++){
1880: fscanf(ficpar," %lf",¶m[i][j][k]);
1881: printf(" %lf",param[i][j][k]);
1882: fprintf(ficparo," %lf",param[i][j][k]);
1883: }
1884: fscanf(ficpar,"\n");
1885: printf("\n");
1886: fprintf(ficparo,"\n");
1887: }
1888:
1.12 lievre 1889: npar= (nlstate+ndeath-1)*nlstate*ncovmodel;
1890:
1.2 lievre 1891: p=param[1][1];
1892:
1893: /* Reads comments: lines beginning with '#' */
1894: while((c=getc(ficpar))=='#' && c!= EOF){
1895: ungetc(c,ficpar);
1896: fgets(line, MAXLINE, ficpar);
1897: puts(line);
1898: fputs(line,ficparo);
1899: }
1900: ungetc(c,ficpar);
1901:
1902: delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
1903: delti=vector(1,npar); /* Scale of each paramater (output from hesscov) */
1904: for(i=1; i <=nlstate; i++){
1905: for(j=1; j <=nlstate+ndeath-1; j++){
1906: fscanf(ficpar,"%1d%1d",&i1,&j1);
1907: printf("%1d%1d",i,j);
1908: fprintf(ficparo,"%1d%1d",i1,j1);
1909: for(k=1; k<=ncovmodel;k++){
1910: fscanf(ficpar,"%le",&delti3[i][j][k]);
1911: printf(" %le",delti3[i][j][k]);
1912: fprintf(ficparo," %le",delti3[i][j][k]);
1913: }
1914: fscanf(ficpar,"\n");
1915: printf("\n");
1916: fprintf(ficparo,"\n");
1917: }
1918: }
1919: delti=delti3[1][1];
1920:
1921: /* Reads comments: lines beginning with '#' */
1922: while((c=getc(ficpar))=='#' && c!= EOF){
1923: ungetc(c,ficpar);
1924: fgets(line, MAXLINE, ficpar);
1925: puts(line);
1926: fputs(line,ficparo);
1927: }
1928: ungetc(c,ficpar);
1929:
1930: matcov=matrix(1,npar,1,npar);
1931: for(i=1; i <=npar; i++){
1932: fscanf(ficpar,"%s",&str);
1933: printf("%s",str);
1934: fprintf(ficparo,"%s",str);
1935: for(j=1; j <=i; j++){
1936: fscanf(ficpar," %le",&matcov[i][j]);
1937: printf(" %.5le",matcov[i][j]);
1938: fprintf(ficparo," %.5le",matcov[i][j]);
1939: }
1940: fscanf(ficpar,"\n");
1941: printf("\n");
1942: fprintf(ficparo,"\n");
1943: }
1944: for(i=1; i <=npar; i++)
1945: for(j=i+1;j<=npar;j++)
1946: matcov[i][j]=matcov[j][i];
1947:
1948: printf("\n");
1949:
1950:
1951: /*-------- data file ----------*/
1952: if((ficres =fopen(fileres,"w"))==NULL) {
1953: printf("Problem with resultfile: %s\n", fileres);goto end;
1954: }
1955: fprintf(ficres,"#%s\n",version);
1956:
1957: if((fic=fopen(datafile,"r"))==NULL) {
1958: printf("Problem with datafile: %s\n", datafile);goto end;
1959: }
1960:
1961: n= lastobs;
1962: severity = vector(1,maxwav);
1963: outcome=imatrix(1,maxwav+1,1,n);
1964: num=ivector(1,n);
1965: moisnais=vector(1,n);
1966: annais=vector(1,n);
1967: moisdc=vector(1,n);
1968: andc=vector(1,n);
1969: agedc=vector(1,n);
1970: cod=ivector(1,n);
1971: weight=vector(1,n);
1972: for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */
1973: mint=matrix(1,maxwav,1,n);
1974: anint=matrix(1,maxwav,1,n);
1975: s=imatrix(1,maxwav+1,1,n);
1976: adl=imatrix(1,maxwav+1,1,n);
1977: tab=ivector(1,NCOVMAX);
1.3 lievre 1978: ncodemax=ivector(1,8);
1.2 lievre 1979:
1.12 lievre 1980: i=1;
1.2 lievre 1981: while (fgets(line, MAXLINE, fic) != NULL) {
1982: if ((i >= firstobs) && (i <=lastobs)) {
1983:
1984: for (j=maxwav;j>=1;j--){
1985: cutv(stra, strb,line,' '); s[j][i]=atoi(strb);
1986: strcpy(line,stra);
1987: cutv(stra, strb,line,'/'); anint[j][i]=(double)(atoi(strb)); strcpy(line,stra);
1988: cutv(stra, strb,line,' '); mint[j][i]=(double)(atoi(strb)); strcpy(line,stra);
1989: }
1990:
1991: cutv(stra, strb,line,'/'); andc[i]=(double)(atoi(strb)); strcpy(line,stra);
1992: cutv(stra, strb,line,' '); moisdc[i]=(double)(atoi(strb)); strcpy(line,stra);
1993:
1994: cutv(stra, strb,line,'/'); annais[i]=(double)(atoi(strb)); strcpy(line,stra);
1995: cutv(stra, strb,line,' '); moisnais[i]=(double)(atoi(strb)); strcpy(line,stra);
1996:
1997: cutv(stra, strb,line,' '); weight[i]=(double)(atoi(strb)); strcpy(line,stra);
1998: for (j=ncov;j>=1;j--){
1999: cutv(stra, strb,line,' '); covar[j][i]=(double)(atoi(strb)); strcpy(line,stra);
2000: }
2001: num[i]=atol(stra);
1.12 lievre 2002:
2003: /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){
2004: 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 2005:
2006: i=i+1;
2007: }
2008: }
1.12 lievre 2009: /* printf("ii=%d", ij);
2010: scanf("%d",i);*/
2011: imx=i-1; /* Number of individuals */
1.3 lievre 2012:
1.12 lievre 2013: /* for (i=1; i<=imx; i++){
2014: if ((s[1][i]==3) && (s[2][i]==2)) s[2][i]=3;
2015: if ((s[2][i]==3) && (s[3][i]==2)) s[3][i]=3;
2016: if ((s[3][i]==3) && (s[4][i]==2)) s[4][i]=3;
2017: }
2018: for (i=1; i<=imx; i++) 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 2019:
2020: /* Calculation of the number of parameter from char model*/
1.7 lievre 2021: Tvar=ivector(1,15);
2022: Tprod=ivector(1,15);
2023: Tvaraff=ivector(1,15);
2024: Tvard=imatrix(1,15,1,2);
1.6 lievre 2025: Tage=ivector(1,15);
1.2 lievre 2026:
2027: if (strlen(model) >1){
1.7 lievre 2028: j=0, j1=0, k1=1, k2=1;
1.2 lievre 2029: j=nbocc(model,'+');
1.6 lievre 2030: j1=nbocc(model,'*');
1.2 lievre 2031: cptcovn=j+1;
1.7 lievre 2032: cptcovprod=j1;
1.3 lievre 2033:
1.8 lievre 2034:
1.2 lievre 2035: strcpy(modelsav,model);
1.8 lievre 2036: if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){
2037: printf("Error. Non available option model=%s ",model);
2038: goto end;
2039: }
2040:
2041: for(i=(j+1); i>=1;i--){
2042: cutv(stra,strb,modelsav,'+');
2043: if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav);
2044: /* printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/
2045: /*scanf("%d",i);*/
2046: if (strchr(strb,'*')) {
2047: cutv(strd,strc,strb,'*');
2048: if (strcmp(strc,"age")==0) {
1.7 lievre 2049: cptcovprod--;
1.8 lievre 2050: cutv(strb,stre,strd,'V');
2051: Tvar[i]=atoi(stre);
2052: cptcovage++;
2053: Tage[cptcovage]=i;
2054: /*printf("stre=%s ", stre);*/
1.7 lievre 2055: }
1.8 lievre 2056: else if (strcmp(strd,"age")==0) {
1.7 lievre 2057: cptcovprod--;
1.8 lievre 2058: cutv(strb,stre,strc,'V');
2059: Tvar[i]=atoi(stre);
2060: cptcovage++;
2061: Tage[cptcovage]=i;
1.7 lievre 2062: }
2063: else {
1.8 lievre 2064: cutv(strb,stre,strc,'V');
2065: Tvar[i]=ncov+k1;
2066: cutv(strb,strc,strd,'V');
2067: Tprod[k1]=i;
2068: Tvard[k1][1]=atoi(strc);
2069: Tvard[k1][2]=atoi(stre);
2070: Tvar[cptcovn+k2]=Tvard[k1][1];
2071: Tvar[cptcovn+k2+1]=Tvard[k1][2];
1.7 lievre 2072: for (k=1; k<=lastobs;k++)
1.8 lievre 2073: covar[ncov+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];
2074: k1++;
2075: k2=k2+2;
1.7 lievre 2076: }
1.2 lievre 2077: }
1.8 lievre 2078: else {
2079: /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/
2080: /* scanf("%d",i);*/
2081: cutv(strd,strc,strb,'V');
2082: Tvar[i]=atoi(strc);
2083: }
2084: strcpy(modelsav,stra);
2085: /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);
2086: scanf("%d",i);*/
1.2 lievre 2087: }
1.8 lievre 2088: }
2089:
2090: /*printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);
2091: printf("cptcovprod=%d ", cptcovprod);
2092: scanf("%d ",i);*/
1.2 lievre 2093: fclose(fic);
2094:
1.7 lievre 2095: /* if(mle==1){*/
1.2 lievre 2096: if (weightopt != 1) { /* Maximisation without weights*/
2097: for(i=1;i<=n;i++) weight[i]=1.0;
2098: }
2099: /*-calculation of age at interview from date of interview and age at death -*/
2100: agev=matrix(1,maxwav,1,imx);
1.12 lievre 2101:
2102: for (i=1; i<=imx; i++)
2103: for(m=2; (m<= maxwav); m++)
2104: if ((mint[m][i]== 99) && (s[m][i] <= nlstate)){
2105: anint[m][i]=9999;
2106: s[m][i]=-1;
2107: }
1.2 lievre 2108:
2109: for (i=1; i<=imx; i++) {
2110: agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);
2111: for(m=1; (m<= maxwav); m++){
2112: if(s[m][i] >0){
2113: if (s[m][i] == nlstate+1) {
2114: if(agedc[i]>0)
2115: if(moisdc[i]!=99 && andc[i]!=9999)
2116: agev[m][i]=agedc[i];
1.8 lievre 2117: else {
2118: if (andc[i]!=9999){
1.2 lievre 2119: printf("Warning negative age at death: %d line:%d\n",num[i],i);
2120: agev[m][i]=-1;
1.8 lievre 2121: }
1.2 lievre 2122: }
2123: }
2124: else if(s[m][i] !=9){ /* Should no more exist */
2125: agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);
1.3 lievre 2126: if(mint[m][i]==99 || anint[m][i]==9999)
1.2 lievre 2127: agev[m][i]=1;
2128: else if(agev[m][i] <agemin){
2129: agemin=agev[m][i];
2130: /*printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], agemin);*/
2131: }
2132: else if(agev[m][i] >agemax){
2133: agemax=agev[m][i];
2134: /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/
2135: }
2136: /*agev[m][i]=anint[m][i]-annais[i];*/
2137: /* agev[m][i] = age[i]+2*m;*/
2138: }
2139: else { /* =9 */
2140: agev[m][i]=1;
2141: s[m][i]=-1;
2142: }
2143: }
2144: else /*= 0 Unknown */
2145: agev[m][i]=1;
2146: }
2147:
2148: }
2149: for (i=1; i<=imx; i++) {
2150: for(m=1; (m<= maxwav); m++){
2151: if (s[m][i] > (nlstate+ndeath)) {
2152: printf("Error: Wrong value in nlstate or ndeath\n");
2153: goto end;
2154: }
2155: }
2156: }
2157:
2158: printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);
2159:
2160: free_vector(severity,1,maxwav);
2161: free_imatrix(outcome,1,maxwav+1,1,n);
2162: free_vector(moisnais,1,n);
2163: free_vector(annais,1,n);
2164: free_matrix(mint,1,maxwav,1,n);
2165: free_matrix(anint,1,maxwav,1,n);
2166: free_vector(moisdc,1,n);
2167: free_vector(andc,1,n);
2168:
2169:
2170: wav=ivector(1,imx);
2171: dh=imatrix(1,lastpass-firstpass+1,1,imx);
2172: mw=imatrix(1,lastpass-firstpass+1,1,imx);
2173:
2174: /* Concatenates waves */
2175: concatwav(wav, dh, mw, s, agedc, agev, firstpass, lastpass, imx, nlstate, stepm);
2176:
2177:
1.6 lievre 2178: Tcode=ivector(1,100);
1.8 lievre 2179: nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);
1.7 lievre 2180: ncodemax[1]=1;
2181: if (cptcovn > 0) tricode(Tvar,nbcode,imx);
2182:
1.2 lievre 2183: codtab=imatrix(1,100,1,10);
2184: h=0;
1.7 lievre 2185: m=pow(2,cptcoveff);
1.2 lievre 2186:
1.7 lievre 2187: for(k=1;k<=cptcoveff; k++){
1.2 lievre 2188: for(i=1; i <=(m/pow(2,k));i++){
2189: for(j=1; j <= ncodemax[k]; j++){
1.7 lievre 2190: for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){
1.2 lievre 2191: h++;
2192: if (h>m) h=1;codtab[h][k]=j;
2193: }
2194: }
2195: }
2196: }
2197:
1.7 lievre 2198:
2199: /*for(i=1; i <=m ;i++){
1.2 lievre 2200: for(k=1; k <=cptcovn; k++){
1.7 lievre 2201: printf("i=%d k=%d %d %d",i,k,codtab[i][k], cptcoveff);
1.2 lievre 2202: }
2203: printf("\n");
1.6 lievre 2204: }
2205: scanf("%d",i);*/
1.2 lievre 2206:
2207: /* Calculates basic frequencies. Computes observed prevalence at single age
2208: and prints on file fileres'p'. */
1.7 lievre 2209: freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax);
1.2 lievre 2210:
2211: pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
2212: oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
2213: newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
2214: savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
2215: oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */
1.12 lievre 2216:
1.2 lievre 2217: /* For Powell, parameters are in a vector p[] starting at p[1]
2218: so we point p on param[1][1] so that p[1] maps on param[1][1][1] */
2219: p=param[1][1]; /* *(*(*(param +1)+1)+0) */
1.7 lievre 2220:
2221: if(mle==1){
1.2 lievre 2222: mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);
1.7 lievre 2223: }
1.2 lievre 2224:
2225: /*--------- results files --------------*/
2226: fprintf(ficres,"\ntitle=%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);
2227:
2228: jk=1;
2229: fprintf(ficres,"# Parameters\n");
2230: printf("# Parameters\n");
2231: for(i=1,jk=1; i <=nlstate; i++){
2232: for(k=1; k <=(nlstate+ndeath); k++){
2233: if (k != i)
2234: {
2235: printf("%d%d ",i,k);
2236: fprintf(ficres,"%1d%1d ",i,k);
2237: for(j=1; j <=ncovmodel; j++){
2238: printf("%f ",p[jk]);
2239: fprintf(ficres,"%f ",p[jk]);
2240: jk++;
2241: }
2242: printf("\n");
2243: fprintf(ficres,"\n");
2244: }
2245: }
2246: }
1.7 lievre 2247: if(mle==1){
1.2 lievre 2248: /* Computing hessian and covariance matrix */
2249: ftolhess=ftol; /* Usually correct */
2250: hesscov(matcov, p, npar, delti, ftolhess, func);
1.7 lievre 2251: }
1.2 lievre 2252: fprintf(ficres,"# Scales\n");
2253: printf("# Scales\n");
2254: for(i=1,jk=1; i <=nlstate; i++){
2255: for(j=1; j <=nlstate+ndeath; j++){
2256: if (j!=i) {
2257: fprintf(ficres,"%1d%1d",i,j);
2258: printf("%1d%1d",i,j);
2259: for(k=1; k<=ncovmodel;k++){
2260: printf(" %.5e",delti[jk]);
2261: fprintf(ficres," %.5e",delti[jk]);
2262: jk++;
2263: }
2264: printf("\n");
2265: fprintf(ficres,"\n");
2266: }
2267: }
2268: }
2269:
2270: k=1;
2271: fprintf(ficres,"# Covariance\n");
2272: printf("# Covariance\n");
2273: for(i=1;i<=npar;i++){
2274: /* if (k>nlstate) k=1;
2275: i1=(i-1)/(ncovmodel*nlstate)+1;
2276: fprintf(ficres,"%s%d%d",alph[k],i1,tab[i]);
2277: printf("%s%d%d",alph[k],i1,tab[i]);*/
2278: fprintf(ficres,"%3d",i);
2279: printf("%3d",i);
2280: for(j=1; j<=i;j++){
2281: fprintf(ficres," %.5e",matcov[i][j]);
2282: printf(" %.5e",matcov[i][j]);
2283: }
2284: fprintf(ficres,"\n");
2285: printf("\n");
2286: k++;
2287: }
2288:
2289: while((c=getc(ficpar))=='#' && c!= EOF){
2290: ungetc(c,ficpar);
2291: fgets(line, MAXLINE, ficpar);
2292: puts(line);
2293: fputs(line,ficparo);
2294: }
2295: ungetc(c,ficpar);
2296:
2297: fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf\n",&agemin,&agemax, &bage, &fage);
2298:
2299: if (fage <= 2) {
2300: bage = agemin;
2301: fage = agemax;
2302: }
2303:
2304: fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");
2305: fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemax,bage,fage);
1.7 lievre 2306:
2307:
1.2 lievre 2308: /*------------ gnuplot -------------*/
2309: chdir(pathcd);
2310: if((ficgp=fopen("graph.plt","w"))==NULL) {
1.5 lievre 2311: printf("Problem with file graph.gp");goto end;
1.2 lievre 2312: }
2313: #ifdef windows
2314: fprintf(ficgp,"cd \"%s\" \n",pathc);
2315: #endif
1.7 lievre 2316: m=pow(2,cptcoveff);
1.2 lievre 2317:
2318: /* 1eme*/
2319: for (cpt=1; cpt<= nlstate ; cpt ++) {
2320: for (k1=1; k1<= m ; k1 ++) {
2321:
2322: #ifdef windows
2323: 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);
2324: #endif
2325: #ifdef unix
2326: fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nplot [%.f:%.f] \"vpl%s\" u 1:2 \"\%%lf",agemin,fage,fileres);
2327: #endif
2328:
2329: for (i=1; i<= nlstate ; i ++) {
2330: if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
2331: else fprintf(ficgp," \%%*lf (\%%*lf)");
2332: }
2333: fprintf(ficgp,"\" t\"Stationary prevalence\" w l 0,\"vpl%s\" every :::%d::%d u 1:($2+2*$3) \"\%%lf",fileres,k1-1,k1-1);
2334: for (i=1; i<= nlstate ; i ++) {
2335: if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
2336: else fprintf(ficgp," \%%*lf (\%%*lf)");
2337: }
2338: fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"vpl%s\" every :::%d::%d u 1:($2-2*$3) \"\%%lf",fileres,k1-1,k1-1);
2339: for (i=1; i<= nlstate ; i ++) {
2340: if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
2341: else fprintf(ficgp," \%%*lf (\%%*lf)");
2342: }
2343: fprintf(ficgp,"\" t\"\" w l 1,\"p%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",fileres,k1-1,k1-1,2+4*(cpt-1));
2344: #ifdef unix
2345: fprintf(ficgp,"\nset ter gif small size 400,300");
2346: #endif
2347: fprintf(ficgp,"\nset out \"v%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);
2348: }
2349: }
2350: /*2 eme*/
2351:
2352: for (k1=1; k1<= m ; k1 ++) {
2353: fprintf(ficgp,"set ylabel \"Years\" \nset ter gif small size 400,300\nplot [%.f:%.f] ",agemin,fage);
2354:
2355: for (i=1; i<= nlstate+1 ; i ++) {
2356: k=2*i;
2357: fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:2 \"\%%lf",fileres,k1-1,k1-1);
2358: for (j=1; j<= nlstate+1 ; j ++) {
2359: if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
2360: else fprintf(ficgp," \%%*lf (\%%*lf)");
2361: }
2362: if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");
2363: else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);
2364: fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",fileres,k1-1,k1-1);
2365: for (j=1; j<= nlstate+1 ; j ++) {
2366: if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
2367: else fprintf(ficgp," \%%*lf (\%%*lf)");
2368: }
2369: fprintf(ficgp,"\" t\"\" w l 0,");
2370: fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",fileres,k1-1,k1-1);
2371: for (j=1; j<= nlstate+1 ; j ++) {
2372: if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
2373: else fprintf(ficgp," \%%*lf (\%%*lf)");
2374: }
2375: if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");
2376: else fprintf(ficgp,"\" t\"\" w l 0,");
2377: }
2378: fprintf(ficgp,"\nset out \"e%s%d.gif\" \nreplot\n\n",strtok(optionfile, "."),k1);
2379: }
2380:
2381: /*3eme*/
2382:
1.5 lievre 2383: for (k1=1; k1<= m ; k1 ++) {
1.2 lievre 2384: for (cpt=1; cpt<= nlstate ; cpt ++) {
2385: k=2+nlstate*(cpt-1);
2386: 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);
2387: for (i=1; i< nlstate ; i ++) {
2388: 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);
2389: }
2390: fprintf(ficgp,"\nset out \"exp%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);
2391: }
1.5 lievre 2392: }
1.2 lievre 2393:
2394: /* CV preval stat */
1.5 lievre 2395: for (k1=1; k1<= m ; k1 ++) {
1.2 lievre 2396: for (cpt=1; cpt<nlstate ; cpt ++) {
2397: k=3;
2398: 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/($%d",agemin,agemax,fileres,k1,k+cpt+1,k+1);
2399: for (i=1; i< nlstate ; i ++)
2400: fprintf(ficgp,"+$%d",k+i+1);
2401: fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);
2402:
2403: l=3+(nlstate+ndeath)*cpt;
2404: fprintf(ficgp,",\"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",fileres,k1,l+cpt+1,l+1);
2405: for (i=1; i< nlstate ; i ++) {
2406: l=3+(nlstate+ndeath)*cpt;
2407: fprintf(ficgp,"+$%d",l+i+1);
2408: }
2409: fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);
2410: fprintf(ficgp,"set out \"p%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);
2411: }
1.13 ! lievre 2412: }
1.5 lievre 2413:
1.2 lievre 2414: /* proba elementaires */
1.5 lievre 2415: for(i=1,jk=1; i <=nlstate; i++){
1.2 lievre 2416: for(k=1; k <=(nlstate+ndeath); k++){
2417: if (k != i) {
2418: for(j=1; j <=ncovmodel; j++){
1.5 lievre 2419: /*fprintf(ficgp,"%s%1d%1d=%f ",alph[j],i,k,p[jk]);*/
2420: /*fprintf(ficgp,"%s",alph[1]);*/
2421: fprintf(ficgp,"p%d=%f ",jk,p[jk]);
1.2 lievre 2422: jk++;
2423: fprintf(ficgp,"\n");
2424: }
2425: }
2426: }
1.5 lievre 2427: }
2428:
1.2 lievre 2429: for(jk=1; jk <=m; jk++) {
2430: fprintf(ficgp,"\nset ter gif small size 400,300\nset log y\nplot [%.f:%.f] ",agemin,agemax);
1.5 lievre 2431: i=1;
2432: for(k2=1; k2<=nlstate; k2++) {
2433: k3=i;
2434: for(k=1; k<=(nlstate+ndeath); k++) {
2435: if (k != k2){
2436: fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
1.7 lievre 2437: ij=1;
2438: for(j=3; j <=ncovmodel; j++) {
2439: if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
2440: fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
2441: ij++;
2442: }
2443: else
1.6 lievre 2444: fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
1.7 lievre 2445: }
2446: fprintf(ficgp,")/(1");
1.6 lievre 2447:
2448: for(k1=1; k1 <=nlstate; k1++){
2449: fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);
1.7 lievre 2450: ij=1;
2451: for(j=3; j <=ncovmodel; j++){
2452: if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
2453: fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
2454: ij++;
2455: }
2456: else
1.6 lievre 2457: fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
1.7 lievre 2458: }
1.6 lievre 2459: fprintf(ficgp,")");
1.5 lievre 2460: }
2461: fprintf(ficgp,") t \"p%d%d\" ", k2,k);
2462: if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");
1.6 lievre 2463: i=i+ncovmodel;
1.5 lievre 2464: }
2465: }
2466: }
1.6 lievre 2467: fprintf(ficgp,"\nset out \"pe%s%d.gif\" \nreplot\n\n",strtok(optionfile, "."),jk);
2468: }
1.5 lievre 2469:
2470: fclose(ficgp);
2471:
2472: chdir(path);
1.2 lievre 2473: free_matrix(agev,1,maxwav,1,imx);
2474: free_ivector(wav,1,imx);
2475: free_imatrix(dh,1,lastpass-firstpass+1,1,imx);
2476: free_imatrix(mw,1,lastpass-firstpass+1,1,imx);
2477:
2478: free_imatrix(s,1,maxwav+1,1,n);
2479:
2480:
2481: free_ivector(num,1,n);
2482: free_vector(agedc,1,n);
2483: free_vector(weight,1,n);
2484: /*free_matrix(covar,1,NCOVMAX,1,n);*/
2485: fclose(ficparo);
2486: fclose(ficres);
1.7 lievre 2487: /* }*/
1.2 lievre 2488:
2489: /*________fin mle=1_________*/
2490:
2491:
2492:
2493: /* No more information from the sample is required now */
2494: /* Reads comments: lines beginning with '#' */
2495: while((c=getc(ficpar))=='#' && c!= EOF){
2496: ungetc(c,ficpar);
2497: fgets(line, MAXLINE, ficpar);
2498: puts(line);
2499: fputs(line,ficparo);
2500: }
2501: ungetc(c,ficpar);
2502:
2503: fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf\n",&agemin,&agemax, &bage, &fage);
2504: printf("agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemax, bage, fage);
2505: fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemax,bage,fage);
2506: /*--------- index.htm --------*/
2507:
1.9 lievre 2508: strcpy(optionfilehtm,optionfile);
2509: strcat(optionfilehtm,".htm");
2510: if((fichtm=fopen(optionfilehtm,"w"))==NULL) {
2511: printf("Problem with %s \n",optionfilehtm);goto end;
1.2 lievre 2512: }
2513:
1.9 lievre 2514: fprintf(fichtm,"<body><ul> <font size=\"6\">Imach, Version 0.64b </font> <hr size=\"2\" color=\"#EC5E5E\">
1.8 lievre 2515: Titre=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>
2516: Total number of observations=%d <br>
2517: Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>
2518: <hr size=\"2\" color=\"#EC5E5E\">
2519: <li>Outputs files<br><br>\n
1.2 lievre 2520: - Observed prevalence in each state: <a href=\"p%s\">p%s</a> <br>\n
2521: - Estimated parameters and the covariance matrix: <a href=\"%s\">%s</a> <br>
2522: - Stationary prevalence in each state: <a href=\"pl%s\">pl%s</a> <br>
2523: - Transition probabilities: <a href=\"pij%s\">pij%s</a><br>
2524: - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>
2525: - Life expectancies by age and initial health status: <a href=\"e%s\">e%s</a> <br>
2526: - Variances of life expectancies by age and initial health status: <a href=\"v%s\">v%s</a><br>
2527: - Health expectancies with their variances: <a href=\"t%s\">t%s</a> <br>
1.8 lievre 2528: - Standard deviation of stationary prevalences: <a href=\"vpl%s\">vpl%s</a> <br><br>",title,datafile,firstpass,lastpass,stepm, weightopt,model,imx,jmin,jmax,jmean,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres);
1.2 lievre 2529:
1.8 lievre 2530: fprintf(fichtm," <li>Graphs</li><p>");
1.2 lievre 2531:
1.7 lievre 2532: m=cptcoveff;
1.2 lievre 2533: if (cptcovn < 1) {m=1;ncodemax[1]=1;}
2534:
2535: j1=0;
2536: for(k1=1; k1<=m;k1++){
2537: for(i1=1; i1<=ncodemax[k1];i1++){
2538: j1++;
2539: if (cptcovn > 0) {
1.8 lievre 2540: fprintf(fichtm,"<hr size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
1.7 lievre 2541: for (cpt=1; cpt<=cptcoveff;cpt++)
2542: fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[j1][cpt]]);
1.8 lievre 2543: fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
1.2 lievre 2544: }
2545: fprintf(fichtm,"<br>- Probabilities: pe%s%d.gif<br>
2546: <img src=\"pe%s%d.gif\">",strtok(optionfile, "."),j1,strtok(optionfile, "."),j1);
2547: for(cpt=1; cpt<nlstate;cpt++){
2548: fprintf(fichtm,"<br>- Prevalence of disability : p%s%d%d.gif<br>
2549: <img src=\"p%s%d%d.gif\">",strtok(optionfile, "."),cpt,j1,strtok(optionfile, "."),cpt,j1);
2550: }
2551: for(cpt=1; cpt<=nlstate;cpt++) {
2552: fprintf(fichtm,"<br>- Observed and stationary prevalence (with confident
2553: interval) in state (%d): v%s%d%d.gif <br>
2554: <img src=\"v%s%d%d.gif\">",cpt,strtok(optionfile, "."),cpt,j1,strtok(optionfile, "."),cpt,j1);
2555: }
2556: for(cpt=1; cpt<=nlstate;cpt++) {
2557: fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): exp%s%d%d.gif <br>
1.5 lievre 2558: <img src=\"exp%s%d%d.gif\">",cpt,strtok(optionfile, "."),cpt,j1,strtok(optionfile, "."),cpt,j1);
1.2 lievre 2559: }
2560: fprintf(fichtm,"\n<br>- Total life expectancy by age and
2561: health expectancies in states (1) and (2): e%s%d.gif<br>
2562: <img src=\"e%s%d.gif\">",strtok(optionfile, "."),j1,strtok(optionfile, "."),j1);
2563: fprintf(fichtm,"\n</body>");
2564: }
2565: }
2566: fclose(fichtm);
2567:
2568: /*--------------- Prevalence limit --------------*/
2569:
2570: strcpy(filerespl,"pl");
2571: strcat(filerespl,fileres);
2572: if((ficrespl=fopen(filerespl,"w"))==NULL) {
2573: printf("Problem with Prev limit resultfile: %s\n", filerespl);goto end;
2574: }
2575: printf("Computing prevalence limit: result on file '%s' \n", filerespl);
2576: fprintf(ficrespl,"#Prevalence limit\n");
2577: fprintf(ficrespl,"#Age ");
2578: for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);
2579: fprintf(ficrespl,"\n");
2580:
2581: prlim=matrix(1,nlstate,1,nlstate);
2582: pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
2583: oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
2584: newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
2585: savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
2586: oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */
2587: k=0;
2588: agebase=agemin;
2589: agelim=agemax;
2590: ftolpl=1.e-10;
1.7 lievre 2591: i1=cptcoveff;
1.2 lievre 2592: if (cptcovn < 1){i1=1;}
2593:
2594: for(cptcov=1;cptcov<=i1;cptcov++){
2595: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
2596: k=k+1;
2597: /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/
1.6 lievre 2598: fprintf(ficrespl,"\n#******");
1.7 lievre 2599: for(j=1;j<=cptcoveff;j++)
2600: fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
1.2 lievre 2601: fprintf(ficrespl,"******\n");
2602:
2603: for (age=agebase; age<=agelim; age++){
2604: prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
2605: fprintf(ficrespl,"%.0f",age );
2606: for(i=1; i<=nlstate;i++)
2607: fprintf(ficrespl," %.5f", prlim[i][i]);
2608: fprintf(ficrespl,"\n");
2609: }
2610: }
2611: }
2612: fclose(ficrespl);
1.13 ! lievre 2613:
1.2 lievre 2614: /*------------- h Pij x at various ages ------------*/
2615:
2616: strcpy(filerespij,"pij"); strcat(filerespij,fileres);
2617: if((ficrespij=fopen(filerespij,"w"))==NULL) {
2618: printf("Problem with Pij resultfile: %s\n", filerespij);goto end;
2619: }
2620: printf("Computing pij: result on file '%s' \n", filerespij);
2621:
2622: stepsize=(int) (stepm+YEARM-1)/YEARM;
1.13 ! lievre 2623: /*if (stepm<=24) stepsize=2;*/
1.2 lievre 2624:
2625: agelim=AGESUP;
2626: hstepm=stepsize*YEARM; /* Every year of age */
2627: hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */
2628:
2629: k=0;
2630: for(cptcov=1;cptcov<=i1;cptcov++){
2631: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
2632: k=k+1;
2633: fprintf(ficrespij,"\n#****** ");
1.7 lievre 2634: for(j=1;j<=cptcoveff;j++)
2635: fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
1.2 lievre 2636: fprintf(ficrespij,"******\n");
2637:
2638: for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */
2639: nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
2640: nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
2641: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
2642: oldm=oldms;savm=savms;
2643: hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
2644: fprintf(ficrespij,"# Age");
2645: for(i=1; i<=nlstate;i++)
2646: for(j=1; j<=nlstate+ndeath;j++)
2647: fprintf(ficrespij," %1d-%1d",i,j);
2648: fprintf(ficrespij,"\n");
2649: for (h=0; h<=nhstepm; h++){
2650: fprintf(ficrespij,"%d %.0f %.0f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );
2651: for(i=1; i<=nlstate;i++)
2652: for(j=1; j<=nlstate+ndeath;j++)
2653: fprintf(ficrespij," %.5f", p3mat[i][j][h]);
2654: fprintf(ficrespij,"\n");
2655: }
2656: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
2657: fprintf(ficrespij,"\n");
2658: }
2659: }
2660: }
2661:
1.13 ! lievre 2662: /* varprob(fileres, matcov, p, delti, nlstate, (int) bage, (int) fage,k);*/
! 2663:
1.2 lievre 2664: fclose(ficrespij);
2665:
1.13 ! lievre 2666: exit(0);
! 2667: /*---------- Forecasting ------------------*/
! 2668:
! 2669: strcpy(fileresf,"f");
! 2670: strcat(fileresf,fileres);
! 2671: if((ficresf=fopen(fileresf,"w"))==NULL) {
! 2672: printf("Problem with forecast resultfile: %s\n", fileresf);goto end;
! 2673: }
! 2674: printf("Computing forecasting: result on file '%s' \n", fileresf);
! 2675:
! 2676: /* Mobile average */
! 2677:
! 2678: /* for (agedeb=bage; agedeb<=fage; agedeb++)
! 2679: for (i=1; i<=nlstate;i++)
! 2680: for (cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++)
! 2681: printf("%f %d i=%d j1=%d\n", probs[(int)agedeb][i][cptcod],(int) agedeb,i,cptcod);*/
! 2682:
! 2683: if (cptcoveff==0) ncodemax[cptcoveff]=1;
! 2684:
! 2685: mobaverage= ma3x(1,130 ,1,8, 1,8);
! 2686: for (agedeb=bage+3; agedeb<=fage-2; agedeb++)
! 2687: for (i=1; i<=nlstate;i++)
! 2688: for (cptcod=1;cptcod<=ncodemax[cptcov];cptcod++)
! 2689: mobaverage[(int)agedeb][i][cptcod]=0.;
! 2690:
! 2691: for (agedeb=bage+4; agedeb<=fage; agedeb++){
! 2692: for (i=1; i<=nlstate;i++){
! 2693: for (cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
! 2694: for (cpt=0;cpt<=4;cpt++){
! 2695: mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]+probs[(int)agedeb-cpt][i][cptcod];
! 2696: }
! 2697: mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]/5;
! 2698: }
! 2699: }
! 2700: }
! 2701:
! 2702: /* if (cptcod==2) printf("m=%f p=%f %d age=%d ",mobaverage[(int)agedeb-2][i][cptcod],probs[(int)agedeb-cpt][i][cptcod],cpt,(int)agedeb-2);*/
! 2703:
! 2704:
! 2705: stepsize=(int) (stepm+YEARM-1)/YEARM;
! 2706: if (stepm<=24) stepsize=2;
! 2707:
! 2708: agelim=AGESUP;
! 2709: hstepm=stepsize*YEARM; /* Every year of age */
! 2710: hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */
! 2711: hstepm=12;
! 2712: k=0;
! 2713: for(cptcov=1;cptcov<=i1;cptcov++){
! 2714: for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
! 2715: k=k+1;
! 2716: fprintf(ficresf,"\n#****** ");
! 2717: for(j=1;j<=cptcoveff;j++) {
! 2718: fprintf(ficresf,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
! 2719: }
! 2720:
! 2721: fprintf(ficresf,"******\n");
! 2722:
! 2723: fprintf(ficresf,"# StartingAge FinalAge Horizon(in years)");
! 2724: for(j=1; j<=nlstate+ndeath;j++) fprintf(ficresf," P.%d",j);
! 2725:
! 2726: for (agedeb=fage; agedeb>=bage; agedeb--){
! 2727: fprintf(ficresf,"\n%d %.f %.f 0 ",k,agedeb, agedeb);
! 2728: for(j=1; j<=nlstate;j++)
! 2729: fprintf(ficresf,"%.3f ",mobaverage[(int)agedeb][j][cptcod]);
! 2730: }
! 2731: for(j=1; j<=ndeath;j++) fprintf(ficresf,"0.");
! 2732:
! 2733: for (cpt=1; cpt<=8;cpt++)
! 2734: for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */
! 2735:
! 2736: nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
! 2737: nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
! 2738: /*printf("stepm=%d hstepm=%d nhstepm=%d \n",stepm,hstepm,nhstepm);*/
! 2739:
! 2740: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
! 2741: oldm=oldms;savm=savms;
! 2742: hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
! 2743:
! 2744: for (h=0; h<=nhstepm; h++){
! 2745:
! 2746: if (h*hstepm/YEARM*stepm==cpt)
! 2747: fprintf(ficresf,"\n%d %.f %.f %.f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm, h*hstepm/YEARM*stepm);
! 2748:
! 2749: for(j=1; j<=nlstate+ndeath;j++) {
! 2750: kk1=0.;
! 2751: for(i=1; i<=nlstate;i++) {
! 2752: /* kk1=kk1+p3mat[i][j][h]*probs[(int)agedeb][i][cptcod];*/
! 2753: kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb][i][cptcod];
! 2754: }
! 2755:
! 2756: if (h*hstepm/YEARM*stepm==cpt)
! 2757: fprintf(ficresf," %.5f ", kk1);
! 2758: }
! 2759: }
! 2760: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
! 2761: }
! 2762: }
! 2763: }
! 2764: fclose(ficresf);
! 2765:
1.2 lievre 2766: /*---------- Health expectancies and variances ------------*/
2767:
2768: strcpy(filerest,"t");
2769: strcat(filerest,fileres);
2770: if((ficrest=fopen(filerest,"w"))==NULL) {
2771: printf("Problem with total LE resultfile: %s\n", filerest);goto end;
2772: }
2773: printf("Computing Total LEs with variances: file '%s' \n", filerest);
2774:
2775:
2776: strcpy(filerese,"e");
2777: strcat(filerese,fileres);
2778: if((ficreseij=fopen(filerese,"w"))==NULL) {
2779: printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
2780: }
2781: printf("Computing Health Expectancies: result on file '%s' \n", filerese);
2782:
2783: strcpy(fileresv,"v");
2784: strcat(fileresv,fileres);
2785: if((ficresvij=fopen(fileresv,"w"))==NULL) {
2786: printf("Problem with variance resultfile: %s\n", fileresv);exit(0);
2787: }
2788: printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
2789:
2790: k=0;
2791: for(cptcov=1;cptcov<=i1;cptcov++){
2792: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
2793: k=k+1;
2794: fprintf(ficrest,"\n#****** ");
1.7 lievre 2795: for(j=1;j<=cptcoveff;j++)
2796: fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
1.2 lievre 2797: fprintf(ficrest,"******\n");
2798:
2799: fprintf(ficreseij,"\n#****** ");
1.7 lievre 2800: for(j=1;j<=cptcoveff;j++)
1.2 lievre 2801: fprintf(ficreseij,"V%d=%d ",j,nbcode[j][codtab[k][j]]);
2802: fprintf(ficreseij,"******\n");
2803:
2804: fprintf(ficresvij,"\n#****** ");
1.7 lievre 2805: for(j=1;j<=cptcoveff;j++)
1.2 lievre 2806: fprintf(ficresvij,"V%d=%d ",j,nbcode[j][codtab[k][j]]);
2807: fprintf(ficresvij,"******\n");
2808:
2809: eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
2810: oldm=oldms;savm=savms;
2811: evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k);
2812: vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
2813: oldm=oldms;savm=savms;
2814: varevsij(fileres, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);
2815:
2816: fprintf(ficrest,"#Total LEs with variances: e.. (std) ");
2817: for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);
2818: fprintf(ficrest,"\n");
2819:
2820: hf=1;
2821: if (stepm >= YEARM) hf=stepm/YEARM;
2822: epj=vector(1,nlstate+1);
2823: for(age=bage; age <=fage ;age++){
2824: prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
2825: fprintf(ficrest," %.0f",age);
2826: for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){
2827: for(i=1, epj[j]=0.;i <=nlstate;i++) {
2828: epj[j] += prlim[i][i]*hf*eij[i][j][(int)age];
2829: }
2830: epj[nlstate+1] +=epj[j];
2831: }
2832: for(i=1, vepp=0.;i <=nlstate;i++)
2833: for(j=1;j <=nlstate;j++)
2834: vepp += vareij[i][j][(int)age];
2835: fprintf(ficrest," %.2f (%.2f)", epj[nlstate+1],hf*sqrt(vepp));
2836: for(j=1;j <=nlstate;j++){
2837: fprintf(ficrest," %.2f (%.2f)", epj[j],hf*sqrt(vareij[j][j][(int)age]));
2838: }
2839: fprintf(ficrest,"\n");
2840: }
2841: }
2842: }
2843:
1.13 ! lievre 2844:
! 2845:
! 2846:
1.2 lievre 2847: fclose(ficreseij);
2848: fclose(ficresvij);
2849: fclose(ficrest);
2850: fclose(ficpar);
2851: free_vector(epj,1,nlstate+1);
1.5 lievre 2852: /* scanf("%d ",i); */
1.2 lievre 2853:
2854: /*------- Variance limit prevalence------*/
2855:
2856: strcpy(fileresvpl,"vpl");
2857: strcat(fileresvpl,fileres);
2858: if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {
2859: printf("Problem with variance prev lim resultfile: %s\n", fileresvpl);
2860: exit(0);
2861: }
2862: printf("Computing Variance-covariance of Prevalence limit: file '%s' \n", fileresvpl);
2863:
2864: k=0;
2865: for(cptcov=1;cptcov<=i1;cptcov++){
2866: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
2867: k=k+1;
2868: fprintf(ficresvpl,"\n#****** ");
1.7 lievre 2869: for(j=1;j<=cptcoveff;j++)
2870: fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
1.2 lievre 2871: fprintf(ficresvpl,"******\n");
2872:
2873: varpl=matrix(1,nlstate,(int) bage, (int) fage);
2874: oldm=oldms;savm=savms;
2875: varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);
2876: }
2877: }
2878:
2879: fclose(ficresvpl);
2880:
2881: /*---------- End : free ----------------*/
2882: free_matrix(varpl,1,nlstate,(int) bage, (int)fage);
2883:
2884: free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);
2885: free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
2886:
2887:
2888: free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);
2889: free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);
2890: free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);
2891: free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);
1.13 ! lievre 2892:
1.2 lievre 2893: free_matrix(matcov,1,npar,1,npar);
2894: free_vector(delti,1,npar);
2895:
2896: free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
2897:
2898: printf("End of Imach\n");
2899: /* gettimeofday(&end_time, (struct timezone*)0);*/ /* after time */
2900:
2901: /* 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);*/
2902: /*printf("Total time was %d uSec.\n", total_usecs);*/
2903: /*------ End -----------*/
1.12 lievre 2904:
1.2 lievre 2905:
2906: end:
2907: #ifdef windows
2908: chdir(pathcd);
2909: #endif
1.13 ! lievre 2910:
1.11 lievre 2911: system("..\\gp37mgw\\wgnuplot graph.plt");
1.2 lievre 2912:
2913: #ifdef windows
2914: while (z[0] != 'q') {
2915: chdir(pathcd);
2916: printf("\nType e to edit output files, c to start again, and q for exiting: ");
2917: scanf("%s",z);
2918: if (z[0] == 'c') system("./imach");
2919: else if (z[0] == 'e') {
2920: chdir(path);
1.10 lievre 2921: system(optionfilehtm);
1.2 lievre 2922: }
2923: else if (z[0] == 'q') exit(0);
2924: }
2925: #endif
2926: }
2927:
2928:
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