Annotation of imach096d/src/imach.c, revision 1.14
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 */
1.14 ! lievre 76: int popbased=0, fprev,lprev;
1.2 lievre 77:
78: int *wav; /* Number of waves for this individuual 0 is possible */
79: int maxwav; /* Maxim number of waves */
1.8 lievre 80: int jmin, jmax; /* min, max spacing between 2 waves */
1.2 lievre 81: int mle, weightopt;
82: int **mw; /* mw[mi][i] is number of the mi wave for this individual */
83: int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
1.8 lievre 84: double jmean; /* Mean space between 2 waves */
1.2 lievre 85: double **oldm, **newm, **savm; /* Working pointers to matrices */
86: double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
1.13 lievre 87: FILE *fic,*ficpar, *ficparo,*ficres, *ficrespl, *ficrespij, *ficrest,*ficresf;
88: FILE *ficgp, *fichtm,*ficresprob;
1.2 lievre 89: FILE *ficreseij;
90: char filerese[FILENAMELENGTH];
91: FILE *ficresvij;
92: char fileresv[FILENAMELENGTH];
93: FILE *ficresvpl;
94: char fileresvpl[FILENAMELENGTH];
95:
96: #define NR_END 1
97: #define FREE_ARG char*
98: #define FTOL 1.0e-10
99:
100: #define NRANSI
101: #define ITMAX 200
102:
103: #define TOL 2.0e-4
104:
105: #define CGOLD 0.3819660
106: #define ZEPS 1.0e-10
107: #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);
108:
109: #define GOLD 1.618034
110: #define GLIMIT 100.0
111: #define TINY 1.0e-20
112:
113: static double maxarg1,maxarg2;
114: #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
115: #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
116:
117: #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
118: #define rint(a) floor(a+0.5)
119:
120: static double sqrarg;
121: #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
122: #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}
123:
124: int imx;
125: int stepm;
126: /* Stepm, step in month: minimum step interpolation*/
127:
128: int m,nb;
1.6 lievre 129: int *num, firstpass=0, lastpass=4,*cod, *ncodemax, *Tage;
1.2 lievre 130: double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
1.13 lievre 131: double **pmmij, ***probs, ***mobaverage;
1.2 lievre 132:
133: double *weight;
134: int **s; /* Status */
135: double *agedc, **covar, idx;
1.7 lievre 136: int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;
1.2 lievre 137:
138: double ftol=FTOL; /* Tolerance for computing Max Likelihood */
139: double ftolhess; /* Tolerance for computing hessian */
140:
1.7 lievre 141: /**************** split *************************/
1.5 lievre 142: static int split( char *path, char *dirc, char *name )
143: {
144: char *s; /* pointer */
145: int l1, l2; /* length counters */
146:
147: l1 = strlen( path ); /* length of path */
148: if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
149: s = strrchr( path, '\\' ); /* find last / */
150: if ( s == NULL ) { /* no directory, so use current */
151: #if defined(__bsd__) /* get current working directory */
152: extern char *getwd( );
153:
154: if ( getwd( dirc ) == NULL ) {
155: #else
156: extern char *getcwd( );
157:
158: if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {
159: #endif
160: return( GLOCK_ERROR_GETCWD );
161: }
162: strcpy( name, path ); /* we've got it */
163: } else { /* strip direcotry from path */
164: s++; /* after this, the filename */
165: l2 = strlen( s ); /* length of filename */
166: if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
167: strcpy( name, s ); /* save file name */
168: strncpy( dirc, path, l1 - l2 ); /* now the directory */
169: dirc[l1-l2] = 0; /* add zero */
170: }
171: l1 = strlen( dirc ); /* length of directory */
172: if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; }
173: return( 0 ); /* we're done */
174: }
175:
176:
1.2 lievre 177: /******************************************/
178:
179: void replace(char *s, char*t)
180: {
181: int i;
182: int lg=20;
183: i=0;
184: lg=strlen(t);
185: for(i=0; i<= lg; i++) {
186: (s[i] = t[i]);
187: if (t[i]== '\\') s[i]='/';
188: }
189: }
190:
191: int nbocc(char *s, char occ)
192: {
193: int i,j=0;
194: int lg=20;
195: i=0;
196: lg=strlen(s);
197: for(i=0; i<= lg; i++) {
198: if (s[i] == occ ) j++;
199: }
200: return j;
201: }
202:
203: void cutv(char *u,char *v, char*t, char occ)
204: {
1.6 lievre 205: int i,lg,j,p=0;
1.2 lievre 206: i=0;
207: for(j=0; j<=strlen(t)-1; j++) {
1.3 lievre 208: if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;
1.2 lievre 209: }
210:
211: lg=strlen(t);
212: for(j=0; j<p; j++) {
213: (u[j] = t[j]);
214: }
1.6 lievre 215: u[p]='\0';
1.2 lievre 216:
217: for(j=0; j<= lg; j++) {
218: if (j>=(p+1))(v[j-p-1] = t[j]);
219: }
220: }
221:
222: /********************** nrerror ********************/
223:
224: void nrerror(char error_text[])
225: {
226: fprintf(stderr,"ERREUR ...\n");
227: fprintf(stderr,"%s\n",error_text);
228: exit(1);
229: }
230: /*********************** vector *******************/
231: double *vector(int nl, int nh)
232: {
233: double *v;
234: v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
235: if (!v) nrerror("allocation failure in vector");
236: return v-nl+NR_END;
237: }
238:
239: /************************ free vector ******************/
240: void free_vector(double*v, int nl, int nh)
241: {
242: free((FREE_ARG)(v+nl-NR_END));
243: }
244:
245: /************************ivector *******************************/
246: int *ivector(long nl,long nh)
247: {
248: int *v;
249: v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
250: if (!v) nrerror("allocation failure in ivector");
251: return v-nl+NR_END;
252: }
253:
254: /******************free ivector **************************/
255: void free_ivector(int *v, long nl, long nh)
256: {
257: free((FREE_ARG)(v+nl-NR_END));
258: }
259:
260: /******************* imatrix *******************************/
261: int **imatrix(long nrl, long nrh, long ncl, long nch)
262: /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */
263: {
264: long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;
265: int **m;
266:
267: /* allocate pointers to rows */
268: m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));
269: if (!m) nrerror("allocation failure 1 in matrix()");
270: m += NR_END;
271: m -= nrl;
272:
273:
274: /* allocate rows and set pointers to them */
275: m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));
276: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
277: m[nrl] += NR_END;
278: m[nrl] -= ncl;
279:
280: for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;
281:
282: /* return pointer to array of pointers to rows */
283: return m;
284: }
285:
286: /****************** free_imatrix *************************/
287: void free_imatrix(m,nrl,nrh,ncl,nch)
288: int **m;
289: long nch,ncl,nrh,nrl;
290: /* free an int matrix allocated by imatrix() */
291: {
292: free((FREE_ARG) (m[nrl]+ncl-NR_END));
293: free((FREE_ARG) (m+nrl-NR_END));
294: }
295:
296: /******************* matrix *******************************/
297: double **matrix(long nrl, long nrh, long ncl, long nch)
298: {
299: long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
300: double **m;
301:
302: m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
303: if (!m) nrerror("allocation failure 1 in matrix()");
304: m += NR_END;
305: m -= nrl;
306:
307: m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
308: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
309: m[nrl] += NR_END;
310: m[nrl] -= ncl;
311:
312: for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
313: return m;
314: }
315:
316: /*************************free matrix ************************/
317: void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
318: {
319: free((FREE_ARG)(m[nrl]+ncl-NR_END));
320: free((FREE_ARG)(m+nrl-NR_END));
321: }
322:
323: /******************* ma3x *******************************/
324: double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
325: {
326: long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
327: double ***m;
328:
329: m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
330: if (!m) nrerror("allocation failure 1 in matrix()");
331: m += NR_END;
332: m -= nrl;
333:
334: m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
335: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
336: m[nrl] += NR_END;
337: m[nrl] -= ncl;
338:
339: for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
340:
341: m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
342: if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
343: m[nrl][ncl] += NR_END;
344: m[nrl][ncl] -= nll;
345: for (j=ncl+1; j<=nch; j++)
346: m[nrl][j]=m[nrl][j-1]+nlay;
347:
348: for (i=nrl+1; i<=nrh; i++) {
349: m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
350: for (j=ncl+1; j<=nch; j++)
351: m[i][j]=m[i][j-1]+nlay;
352: }
353: return m;
354: }
355:
356: /*************************free ma3x ************************/
357: void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
358: {
359: free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
360: free((FREE_ARG)(m[nrl]+ncl-NR_END));
361: free((FREE_ARG)(m+nrl-NR_END));
362: }
363:
364: /***************** f1dim *************************/
365: extern int ncom;
366: extern double *pcom,*xicom;
367: extern double (*nrfunc)(double []);
368:
369: double f1dim(double x)
370: {
371: int j;
372: double f;
373: double *xt;
374:
375: xt=vector(1,ncom);
376: for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];
377: f=(*nrfunc)(xt);
378: free_vector(xt,1,ncom);
379: return f;
380: }
381:
382: /*****************brent *************************/
383: double brent(double ax, double bx, double cx, double (*f)(double), double tol, double *xmin)
384: {
385: int iter;
386: double a,b,d,etemp;
387: double fu,fv,fw,fx;
388: double ftemp;
389: double p,q,r,tol1,tol2,u,v,w,x,xm;
390: double e=0.0;
391:
392: a=(ax < cx ? ax : cx);
393: b=(ax > cx ? ax : cx);
394: x=w=v=bx;
395: fw=fv=fx=(*f)(x);
396: for (iter=1;iter<=ITMAX;iter++) {
397: xm=0.5*(a+b);
398: tol2=2.0*(tol1=tol*fabs(x)+ZEPS);
399: /* if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
400: printf(".");fflush(stdout);
401: #ifdef DEBUG
402: 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);
403: /* if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
404: #endif
405: if (fabs(x-xm) <= (tol2-0.5*(b-a))){
406: *xmin=x;
407: return fx;
408: }
409: ftemp=fu;
410: if (fabs(e) > tol1) {
411: r=(x-w)*(fx-fv);
412: q=(x-v)*(fx-fw);
413: p=(x-v)*q-(x-w)*r;
414: q=2.0*(q-r);
415: if (q > 0.0) p = -p;
416: q=fabs(q);
417: etemp=e;
418: e=d;
419: if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))
420: d=CGOLD*(e=(x >= xm ? a-x : b-x));
421: else {
422: d=p/q;
423: u=x+d;
424: if (u-a < tol2 || b-u < tol2)
425: d=SIGN(tol1,xm-x);
426: }
427: } else {
428: d=CGOLD*(e=(x >= xm ? a-x : b-x));
429: }
430: u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));
431: fu=(*f)(u);
432: if (fu <= fx) {
433: if (u >= x) a=x; else b=x;
434: SHFT(v,w,x,u)
435: SHFT(fv,fw,fx,fu)
436: } else {
437: if (u < x) a=u; else b=u;
438: if (fu <= fw || w == x) {
439: v=w;
440: w=u;
441: fv=fw;
442: fw=fu;
443: } else if (fu <= fv || v == x || v == w) {
444: v=u;
445: fv=fu;
446: }
447: }
448: }
449: nrerror("Too many iterations in brent");
450: *xmin=x;
451: return fx;
452: }
453:
454: /****************** mnbrak ***********************/
455:
456: void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,
457: double (*func)(double))
458: {
459: double ulim,u,r,q, dum;
460: double fu;
461:
462: *fa=(*func)(*ax);
463: *fb=(*func)(*bx);
464: if (*fb > *fa) {
465: SHFT(dum,*ax,*bx,dum)
466: SHFT(dum,*fb,*fa,dum)
467: }
468: *cx=(*bx)+GOLD*(*bx-*ax);
469: *fc=(*func)(*cx);
470: while (*fb > *fc) {
471: r=(*bx-*ax)*(*fb-*fc);
472: q=(*bx-*cx)*(*fb-*fa);
473: u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/
474: (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r));
475: ulim=(*bx)+GLIMIT*(*cx-*bx);
476: if ((*bx-u)*(u-*cx) > 0.0) {
477: fu=(*func)(u);
478: } else if ((*cx-u)*(u-ulim) > 0.0) {
479: fu=(*func)(u);
480: if (fu < *fc) {
481: SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))
482: SHFT(*fb,*fc,fu,(*func)(u))
483: }
484: } else if ((u-ulim)*(ulim-*cx) >= 0.0) {
485: u=ulim;
486: fu=(*func)(u);
487: } else {
488: u=(*cx)+GOLD*(*cx-*bx);
489: fu=(*func)(u);
490: }
491: SHFT(*ax,*bx,*cx,u)
492: SHFT(*fa,*fb,*fc,fu)
493: }
494: }
495:
496: /*************** linmin ************************/
497:
498: int ncom;
499: double *pcom,*xicom;
500: double (*nrfunc)(double []);
501:
502: void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))
503: {
504: double brent(double ax, double bx, double cx,
505: double (*f)(double), double tol, double *xmin);
506: double f1dim(double x);
507: void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,
508: double *fc, double (*func)(double));
509: int j;
510: double xx,xmin,bx,ax;
511: double fx,fb,fa;
512:
513: ncom=n;
514: pcom=vector(1,n);
515: xicom=vector(1,n);
516: nrfunc=func;
517: for (j=1;j<=n;j++) {
518: pcom[j]=p[j];
519: xicom[j]=xi[j];
520: }
521: ax=0.0;
522: xx=1.0;
523: mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim);
524: *fret=brent(ax,xx,bx,f1dim,TOL,&xmin);
525: #ifdef DEBUG
526: printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
527: #endif
528: for (j=1;j<=n;j++) {
529: xi[j] *= xmin;
530: p[j] += xi[j];
531: }
532: free_vector(xicom,1,n);
533: free_vector(pcom,1,n);
534: }
535:
536: /*************** powell ************************/
537: void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,
538: double (*func)(double []))
539: {
540: void linmin(double p[], double xi[], int n, double *fret,
541: double (*func)(double []));
542: int i,ibig,j;
543: double del,t,*pt,*ptt,*xit;
544: double fp,fptt;
545: double *xits;
546: pt=vector(1,n);
547: ptt=vector(1,n);
548: xit=vector(1,n);
549: xits=vector(1,n);
550: *fret=(*func)(p);
551: for (j=1;j<=n;j++) pt[j]=p[j];
552: for (*iter=1;;++(*iter)) {
553: fp=(*fret);
554: ibig=0;
555: del=0.0;
556: printf("\nPowell iter=%d -2*LL=%.12f",*iter,*fret);
557: for (i=1;i<=n;i++)
558: printf(" %d %.12f",i, p[i]);
559: printf("\n");
560: for (i=1;i<=n;i++) {
561: for (j=1;j<=n;j++) xit[j]=xi[j][i];
562: fptt=(*fret);
563: #ifdef DEBUG
564: printf("fret=%lf \n",*fret);
565: #endif
566: printf("%d",i);fflush(stdout);
567: linmin(p,xit,n,fret,func);
568: if (fabs(fptt-(*fret)) > del) {
569: del=fabs(fptt-(*fret));
570: ibig=i;
571: }
572: #ifdef DEBUG
573: printf("%d %.12e",i,(*fret));
574: for (j=1;j<=n;j++) {
575: xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
576: printf(" x(%d)=%.12e",j,xit[j]);
577: }
578: for(j=1;j<=n;j++)
579: printf(" p=%.12e",p[j]);
580: printf("\n");
581: #endif
582: }
583: if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {
584: #ifdef DEBUG
585: int k[2],l;
586: k[0]=1;
587: k[1]=-1;
588: printf("Max: %.12e",(*func)(p));
589: for (j=1;j<=n;j++)
590: printf(" %.12e",p[j]);
591: printf("\n");
592: for(l=0;l<=1;l++) {
593: for (j=1;j<=n;j++) {
594: ptt[j]=p[j]+(p[j]-pt[j])*k[l];
595: printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
596: }
597: printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
598: }
599: #endif
600:
601:
602: free_vector(xit,1,n);
603: free_vector(xits,1,n);
604: free_vector(ptt,1,n);
605: free_vector(pt,1,n);
606: return;
607: }
608: if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");
609: for (j=1;j<=n;j++) {
610: ptt[j]=2.0*p[j]-pt[j];
611: xit[j]=p[j]-pt[j];
612: pt[j]=p[j];
613: }
614: fptt=(*func)(ptt);
615: if (fptt < fp) {
616: t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt);
617: if (t < 0.0) {
618: linmin(p,xit,n,fret,func);
619: for (j=1;j<=n;j++) {
620: xi[j][ibig]=xi[j][n];
621: xi[j][n]=xit[j];
622: }
623: #ifdef DEBUG
624: printf("Direction changed last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
625: for(j=1;j<=n;j++)
626: printf(" %.12e",xit[j]);
627: printf("\n");
628: #endif
629: }
630: }
631: }
632: }
633:
634: /**** Prevalence limit ****************/
635:
636: double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)
637: {
638: /* Computes the prevalence limit in each live state at age x by left multiplying the unit
639: matrix by transitions matrix until convergence is reached */
640:
641: int i, ii,j,k;
642: double min, max, maxmin, maxmax,sumnew=0.;
643: double **matprod2();
644: double **out, cov[NCOVMAX], **pmij();
645: double **newm;
646: double agefin, delaymax=50 ; /* Max number of years to converge */
647:
648: for (ii=1;ii<=nlstate+ndeath;ii++)
649: for (j=1;j<=nlstate+ndeath;j++){
650: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
651: }
1.6 lievre 652:
653: cov[1]=1.;
654:
655: /* Even if hstepm = 1, at least one multiplication by the unit matrix */
1.2 lievre 656: for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
657: newm=savm;
658: /* Covariates have to be included here again */
1.6 lievre 659: cov[2]=agefin;
660:
661: for (k=1; k<=cptcovn;k++) {
1.7 lievre 662: cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
663: /*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 664: }
665: for (k=1; k<=cptcovage;k++)
666: cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
1.7 lievre 667: for (k=1; k<=cptcovprod;k++)
668: cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
669:
670: /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
671: /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
672:
1.2 lievre 673: out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);
674:
675: savm=oldm;
676: oldm=newm;
677: maxmax=0.;
678: for(j=1;j<=nlstate;j++){
679: min=1.;
680: max=0.;
681: for(i=1; i<=nlstate; i++) {
682: sumnew=0;
683: for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
684: prlim[i][j]= newm[i][j]/(1-sumnew);
685: max=FMAX(max,prlim[i][j]);
686: min=FMIN(min,prlim[i][j]);
687: }
688: maxmin=max-min;
689: maxmax=FMAX(maxmax,maxmin);
690: }
691: if(maxmax < ftolpl){
692: return prlim;
693: }
694: }
695: }
696:
1.12 lievre 697: /*************** transition probabilities ***************/
1.2 lievre 698:
699: double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
700: {
701: double s1, s2;
702: /*double t34;*/
703: int i,j,j1, nc, ii, jj;
704:
705: for(i=1; i<= nlstate; i++){
706: for(j=1; j<i;j++){
707: for (nc=1, s2=0.;nc <=ncovmodel; nc++){
708: /*s2 += param[i][j][nc]*cov[nc];*/
709: s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
710: /*printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2);*/
711: }
712: ps[i][j]=s2;
713: /*printf("s1=%.17e, s2=%.17e\n",s1,s2);*/
714: }
715: for(j=i+1; j<=nlstate+ndeath;j++){
716: for (nc=1, s2=0.;nc <=ncovmodel; nc++){
717: s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
718: /*printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2);*/
719: }
1.12 lievre 720: ps[i][j]=(s2);
1.2 lievre 721: }
722: }
1.12 lievre 723: /*ps[3][2]=1;*/
724:
1.2 lievre 725: for(i=1; i<= nlstate; i++){
726: s1=0;
727: for(j=1; j<i; j++)
728: s1+=exp(ps[i][j]);
729: for(j=i+1; j<=nlstate+ndeath; j++)
730: s1+=exp(ps[i][j]);
731: ps[i][i]=1./(s1+1.);
732: for(j=1; j<i; j++)
733: ps[i][j]= exp(ps[i][j])*ps[i][i];
734: for(j=i+1; j<=nlstate+ndeath; j++)
735: ps[i][j]= exp(ps[i][j])*ps[i][i];
736: /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
737: } /* end i */
738:
739: for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
740: for(jj=1; jj<= nlstate+ndeath; jj++){
741: ps[ii][jj]=0;
742: ps[ii][ii]=1;
743: }
744: }
745:
1.12 lievre 746:
1.2 lievre 747: /* for(ii=1; ii<= nlstate+ndeath; ii++){
748: for(jj=1; jj<= nlstate+ndeath; jj++){
749: printf("%lf ",ps[ii][jj]);
750: }
751: printf("\n ");
752: }
753: printf("\n ");printf("%lf ",cov[2]);*/
754: /*
755: for(i=1; i<= npar; i++) printf("%f ",x[i]);
756: goto end;*/
757: return ps;
758: }
759:
760: /**************** Product of 2 matrices ******************/
761:
762: double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)
763: {
1.13 lievre 764: /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
1.2 lievre 765: b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
766: /* in, b, out are matrice of pointers which should have been initialized
767: before: only the contents of out is modified. The function returns
768: a pointer to pointers identical to out */
769: long i, j, k;
770: for(i=nrl; i<= nrh; i++)
771: for(k=ncolol; k<=ncoloh; k++)
772: for(j=ncl,out[i][k]=0.; j<=nch; j++)
773: out[i][k] +=in[i][j]*b[j][k];
774:
775: return out;
776: }
777:
778:
779: /************* Higher Matrix Product ***************/
780:
781: double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
782: {
783: /* Computes the transition matrix starting at age 'age' over 'nhstepm*hstepm*stepm' month
784: duration (i.e. until
785: age (in years) age+nhstepm*stepm/12) by multiplying nhstepm*hstepm matrices.
786: Output is stored in matrix po[i][j][h] for h every 'hstepm' step
787: (typically every 2 years instead of every month which is too big).
788: Model is determined by parameters x and covariates have to be
789: included manually here.
790:
791: */
792:
793: int i, j, d, h, k;
794: double **out, cov[NCOVMAX];
795: double **newm;
796:
797: /* Hstepm could be zero and should return the unit matrix */
798: for (i=1;i<=nlstate+ndeath;i++)
799: for (j=1;j<=nlstate+ndeath;j++){
800: oldm[i][j]=(i==j ? 1.0 : 0.0);
801: po[i][j][0]=(i==j ? 1.0 : 0.0);
802: }
803: /* Even if hstepm = 1, at least one multiplication by the unit matrix */
804: for(h=1; h <=nhstepm; h++){
805: for(d=1; d <=hstepm; d++){
806: newm=savm;
807: /* Covariates have to be included here again */
808: cov[1]=1.;
809: cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
1.7 lievre 810: for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
1.12 lievre 811: for (k=1; k<=cptcovage;k++)
1.7 lievre 812: cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
1.12 lievre 813: for (k=1; k<=cptcovprod;k++)
1.7 lievre 814: cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
815:
816:
1.2 lievre 817: /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
818: /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
819: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,
820: pmij(pmmij,cov,ncovmodel,x,nlstate));
821: savm=oldm;
822: oldm=newm;
823: }
824: for(i=1; i<=nlstate+ndeath; i++)
825: for(j=1;j<=nlstate+ndeath;j++) {
826: po[i][j][h]=newm[i][j];
827: /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);
828: */
829: }
830: } /* end h */
831: return po;
832: }
833:
834:
835: /*************** log-likelihood *************/
836: double func( double *x)
837: {
1.6 lievre 838: int i, ii, j, k, mi, d, kk;
1.2 lievre 839: double l, ll[NLSTATEMAX], cov[NCOVMAX];
840: double **out;
841: double sw; /* Sum of weights */
842: double lli; /* Individual log likelihood */
843: long ipmx;
844: /*extern weight */
845: /* We are differentiating ll according to initial status */
846: /* for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
847: /*for(i=1;i<imx;i++)
1.8 lievre 848: printf(" %d\n",s[4][i]);
1.2 lievre 849: */
1.6 lievre 850: cov[1]=1.;
1.2 lievre 851:
852: for(k=1; k<=nlstate; k++) ll[k]=0.;
853: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1.6 lievre 854: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
1.8 lievre 855: for(mi=1; mi<= wav[i]-1; mi++){
1.2 lievre 856: for (ii=1;ii<=nlstate+ndeath;ii++)
857: for (j=1;j<=nlstate+ndeath;j++) oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1.8 lievre 858: for(d=0; d<dh[mi][i]; d++){
859: newm=savm;
860: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
861: for (kk=1; kk<=cptcovage;kk++) {
862: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
863: }
864:
865: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
866: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
867: savm=oldm;
868: oldm=newm;
869:
870:
1.2 lievre 871: } /* end mult */
1.8 lievre 872:
1.2 lievre 873: lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);
874: /* printf(" %f ",out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/
875: ipmx +=1;
876: sw += weight[i];
877: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
878: } /* end of wave */
879: } /* end of individual */
880:
881: for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
882: /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
883: l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
884: return -l;
885: }
886:
887:
888: /*********** Maximum Likelihood Estimation ***************/
889:
890: void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
891: {
892: int i,j, iter;
893: double **xi,*delti;
894: double fret;
895: xi=matrix(1,npar,1,npar);
896: for (i=1;i<=npar;i++)
897: for (j=1;j<=npar;j++)
898: xi[i][j]=(i==j ? 1.0 : 0.0);
899: printf("Powell\n");
900: powell(p,xi,npar,ftol,&iter,&fret,func);
901:
902: printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));
903: fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f ",iter,func(p));
904:
905: }
906:
907: /**** Computes Hessian and covariance matrix ***/
908: void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
909: {
910: double **a,**y,*x,pd;
911: double **hess;
912: int i, j,jk;
913: int *indx;
914:
915: double hessii(double p[], double delta, int theta, double delti[]);
916: double hessij(double p[], double delti[], int i, int j);
917: void lubksb(double **a, int npar, int *indx, double b[]) ;
918: void ludcmp(double **a, int npar, int *indx, double *d) ;
919:
920: hess=matrix(1,npar,1,npar);
921:
922: printf("\nCalculation of the hessian matrix. Wait...\n");
923: for (i=1;i<=npar;i++){
924: printf("%d",i);fflush(stdout);
925: hess[i][i]=hessii(p,ftolhess,i,delti);
926: /*printf(" %f ",p[i]);*/
1.12 lievre 927: /*printf(" %lf ",hess[i][i]);*/
1.2 lievre 928: }
1.12 lievre 929:
1.2 lievre 930: for (i=1;i<=npar;i++) {
931: for (j=1;j<=npar;j++) {
932: if (j>i) {
933: printf(".%d%d",i,j);fflush(stdout);
934: hess[i][j]=hessij(p,delti,i,j);
1.12 lievre 935: hess[j][i]=hess[i][j];
936: /*printf(" %lf ",hess[i][j]);*/
1.2 lievre 937: }
938: }
939: }
940: printf("\n");
941:
942: printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
943:
944: a=matrix(1,npar,1,npar);
945: y=matrix(1,npar,1,npar);
946: x=vector(1,npar);
947: indx=ivector(1,npar);
948: for (i=1;i<=npar;i++)
949: for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
950: ludcmp(a,npar,indx,&pd);
951:
952: for (j=1;j<=npar;j++) {
953: for (i=1;i<=npar;i++) x[i]=0;
954: x[j]=1;
955: lubksb(a,npar,indx,x);
956: for (i=1;i<=npar;i++){
957: matcov[i][j]=x[i];
958: }
959: }
960:
961: printf("\n#Hessian matrix#\n");
962: for (i=1;i<=npar;i++) {
963: for (j=1;j<=npar;j++) {
964: printf("%.3e ",hess[i][j]);
965: }
966: printf("\n");
967: }
968:
969: /* Recompute Inverse */
970: for (i=1;i<=npar;i++)
971: for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];
972: ludcmp(a,npar,indx,&pd);
973:
974: /* printf("\n#Hessian matrix recomputed#\n");
975:
976: for (j=1;j<=npar;j++) {
977: for (i=1;i<=npar;i++) x[i]=0;
978: x[j]=1;
979: lubksb(a,npar,indx,x);
980: for (i=1;i<=npar;i++){
981: y[i][j]=x[i];
982: printf("%.3e ",y[i][j]);
983: }
984: printf("\n");
985: }
986: */
987:
988: free_matrix(a,1,npar,1,npar);
989: free_matrix(y,1,npar,1,npar);
990: free_vector(x,1,npar);
991: free_ivector(indx,1,npar);
992: free_matrix(hess,1,npar,1,npar);
993:
994:
995: }
996:
997: /*************** hessian matrix ****************/
998: double hessii( double x[], double delta, int theta, double delti[])
999: {
1000: int i;
1001: int l=1, lmax=20;
1002: double k1,k2;
1003: double p2[NPARMAX+1];
1004: double res;
1005: double delt, delts, nkhi=10.,nkhif=1., khi=1.e-4;
1006: double fx;
1007: int k=0,kmax=10;
1008: double l1;
1009:
1010: fx=func(x);
1011: for (i=1;i<=npar;i++) p2[i]=x[i];
1012: for(l=0 ; l <=lmax; l++){
1013: l1=pow(10,l);
1014: delts=delt;
1015: for(k=1 ; k <kmax; k=k+1){
1016: delt = delta*(l1*k);
1017: p2[theta]=x[theta] +delt;
1018: k1=func(p2)-fx;
1019: p2[theta]=x[theta]-delt;
1020: k2=func(p2)-fx;
1021: /*res= (k1-2.0*fx+k2)/delt/delt; */
1022: res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */
1023:
1024: #ifdef DEBUG
1025: 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);
1026: #endif
1027: /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
1028: if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
1029: k=kmax;
1030: }
1031: else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
1032: k=kmax; l=lmax*10.;
1033: }
1034: else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){
1035: delts=delt;
1036: }
1037: }
1038: }
1039: delti[theta]=delts;
1.12 lievre 1040: return res;
1.3 lievre 1041:
1.2 lievre 1042: }
1043:
1044: double hessij( double x[], double delti[], int thetai,int thetaj)
1045: {
1046: int i;
1047: int l=1, l1, lmax=20;
1048: double k1,k2,k3,k4,res,fx;
1049: double p2[NPARMAX+1];
1050: int k;
1051:
1052: fx=func(x);
1053: for (k=1; k<=2; k++) {
1054: for (i=1;i<=npar;i++) p2[i]=x[i];
1055: p2[thetai]=x[thetai]+delti[thetai]/k;
1056: p2[thetaj]=x[thetaj]+delti[thetaj]/k;
1057: k1=func(p2)-fx;
1058:
1059: p2[thetai]=x[thetai]+delti[thetai]/k;
1060: p2[thetaj]=x[thetaj]-delti[thetaj]/k;
1061: k2=func(p2)-fx;
1062:
1063: p2[thetai]=x[thetai]-delti[thetai]/k;
1064: p2[thetaj]=x[thetaj]+delti[thetaj]/k;
1065: k3=func(p2)-fx;
1066:
1067: p2[thetai]=x[thetai]-delti[thetai]/k;
1068: p2[thetaj]=x[thetaj]-delti[thetaj]/k;
1069: k4=func(p2)-fx;
1070: res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */
1071: #ifdef DEBUG
1072: 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);
1073: #endif
1074: }
1075: return res;
1076: }
1077:
1078: /************** Inverse of matrix **************/
1079: void ludcmp(double **a, int n, int *indx, double *d)
1080: {
1081: int i,imax,j,k;
1082: double big,dum,sum,temp;
1083: double *vv;
1084:
1085: vv=vector(1,n);
1086: *d=1.0;
1087: for (i=1;i<=n;i++) {
1088: big=0.0;
1089: for (j=1;j<=n;j++)
1090: if ((temp=fabs(a[i][j])) > big) big=temp;
1091: if (big == 0.0) nrerror("Singular matrix in routine ludcmp");
1092: vv[i]=1.0/big;
1093: }
1094: for (j=1;j<=n;j++) {
1095: for (i=1;i<j;i++) {
1096: sum=a[i][j];
1097: for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];
1098: a[i][j]=sum;
1099: }
1100: big=0.0;
1101: for (i=j;i<=n;i++) {
1102: sum=a[i][j];
1103: for (k=1;k<j;k++)
1104: sum -= a[i][k]*a[k][j];
1105: a[i][j]=sum;
1106: if ( (dum=vv[i]*fabs(sum)) >= big) {
1107: big=dum;
1108: imax=i;
1109: }
1110: }
1111: if (j != imax) {
1112: for (k=1;k<=n;k++) {
1113: dum=a[imax][k];
1114: a[imax][k]=a[j][k];
1115: a[j][k]=dum;
1116: }
1117: *d = -(*d);
1118: vv[imax]=vv[j];
1119: }
1120: indx[j]=imax;
1121: if (a[j][j] == 0.0) a[j][j]=TINY;
1122: if (j != n) {
1123: dum=1.0/(a[j][j]);
1124: for (i=j+1;i<=n;i++) a[i][j] *= dum;
1125: }
1126: }
1127: free_vector(vv,1,n); /* Doesn't work */
1128: ;
1129: }
1130:
1131: void lubksb(double **a, int n, int *indx, double b[])
1132: {
1133: int i,ii=0,ip,j;
1134: double sum;
1135:
1136: for (i=1;i<=n;i++) {
1137: ip=indx[i];
1138: sum=b[ip];
1139: b[ip]=b[i];
1140: if (ii)
1141: for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];
1142: else if (sum) ii=i;
1143: b[i]=sum;
1144: }
1145: for (i=n;i>=1;i--) {
1146: sum=b[i];
1147: for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];
1148: b[i]=sum/a[i][i];
1149: }
1150: }
1151:
1152: /************ Frequencies ********************/
1153: void freqsummary(char fileres[], int agemin, int agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax)
1154: { /* Some frequencies */
1155:
1156: int i, m, jk, k1, i1, j1, bool, z1,z2,j;
1157: double ***freq; /* Frequencies */
1158: double *pp;
1159: double pos;
1160: FILE *ficresp;
1161: char fileresp[FILENAMELENGTH];
1162:
1163: pp=vector(1,nlstate);
1.13 lievre 1164: probs= ma3x(1,130 ,1,8, 1,8);
1.2 lievre 1165: strcpy(fileresp,"p");
1166: strcat(fileresp,fileres);
1167: if((ficresp=fopen(fileresp,"w"))==NULL) {
1168: printf("Problem with prevalence resultfile: %s\n", fileresp);
1169: exit(0);
1170: }
1171: freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);
1172: j1=0;
1173:
1.7 lievre 1174: j=cptcoveff;
1.2 lievre 1175: if (cptcovn<1) {j=1;ncodemax[1]=1;}
1176:
1177: for(k1=1; k1<=j;k1++){
1178: for(i1=1; i1<=ncodemax[k1];i1++){
1179: j1++;
1.8 lievre 1180: /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
1181: scanf("%d", i);*/
1.2 lievre 1182: for (i=-1; i<=nlstate+ndeath; i++)
1183: for (jk=-1; jk<=nlstate+ndeath; jk++)
1184: for(m=agemin; m <= agemax+3; m++)
1185: freq[i][jk][m]=0;
1186:
1187: for (i=1; i<=imx; i++) {
1188: bool=1;
1189: if (cptcovn>0) {
1.7 lievre 1190: for (z1=1; z1<=cptcoveff; z1++)
1.8 lievre 1191: if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])
1192: bool=0;
1.2 lievre 1193: }
1194: if (bool==1) {
1.14 ! lievre 1195: for(m=fprev; m<=lprev; m++){
1.2 lievre 1196: if(agev[m][i]==0) agev[m][i]=agemax+1;
1197: if(agev[m][i]==1) agev[m][i]=agemax+2;
1198: freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
1199: freq[s[m][i]][s[m+1][i]][(int) agemax+3] += weight[i];
1200: }
1201: }
1202: }
1203: if (cptcovn>0) {
1.7 lievre 1204: fprintf(ficresp, "\n#********** Variable ");
1205: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
1206: fprintf(ficresp, "**********\n#");
1.8 lievre 1207: }
1.2 lievre 1208: for(i=1; i<=nlstate;i++)
1209: fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
1210: fprintf(ficresp, "\n");
1211:
1212: for(i=(int)agemin; i <= (int)agemax+3; i++){
1213: if(i==(int)agemax+3)
1214: printf("Total");
1215: else
1216: printf("Age %d", i);
1217: for(jk=1; jk <=nlstate ; jk++){
1218: for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
1.14 ! lievre 1219: pp[jk] += freq[jk][m][i];
1.2 lievre 1220: }
1221: for(jk=1; jk <=nlstate ; jk++){
1222: for(m=-1, pos=0; m <=0 ; m++)
1223: pos += freq[jk][m][i];
1224: if(pp[jk]>=1.e-10)
1225: printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
1226: else
1227: printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
1228: }
1.14 ! lievre 1229:
! 1230: for(jk=1; jk <=nlstate ; jk++){
! 1231: for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
1.2 lievre 1232: pp[jk] += freq[jk][m][i];
1.14 ! lievre 1233: }
! 1234:
1.2 lievre 1235: for(jk=1,pos=0; jk <=nlstate ; jk++)
1236: pos += pp[jk];
1237: for(jk=1; jk <=nlstate ; jk++){
1238: if(pos>=1.e-5)
1239: printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
1240: else
1241: printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
1242: if( i <= (int) agemax){
1.13 lievre 1243: if(pos>=1.e-5){
1.2 lievre 1244: fprintf(ficresp," %d %.5f %.0f %.0f",i,pp[jk]/pos, pp[jk],pos);
1.13 lievre 1245: probs[i][jk][j1]= pp[jk]/pos;
1246: /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/
1247: }
1.2 lievre 1248: else
1249: fprintf(ficresp," %d NaNq %.0f %.0f",i,pp[jk],pos);
1250: }
1251: }
1252: for(jk=-1; jk <=nlstate+ndeath; jk++)
1253: for(m=-1; m <=nlstate+ndeath; m++)
1254: if(freq[jk][m][i] !=0 ) printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
1255: if(i <= (int) agemax)
1256: fprintf(ficresp,"\n");
1257: printf("\n");
1258: }
1259: }
1260: }
1261:
1262: fclose(ficresp);
1263: free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);
1264: free_vector(pp,1,nlstate);
1265:
1266: } /* End of Freq */
1267:
1268: /************* Waves Concatenation ***************/
1269:
1270: void concatwav(int wav[], int **dh, int **mw, int **s, double *agedc, double **agev, int firstpass, int lastpass, int imx, int nlstate, int stepm)
1271: {
1272: /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
1273: Death is a valid wave (if date is known).
1274: mw[mi][i] is the mi (mi=1 to wav[i]) effective wave of individual i
1275: dh[m][i] of dh[mw[mi][i][i] is the delay between two effective waves m=mw[mi][i]
1276: and mw[mi+1][i]. dh depends on stepm.
1277: */
1278:
1279: int i, mi, m;
1.8 lievre 1280: /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
1281: double sum=0., jmean=0.;*/
1.2 lievre 1282:
1.11 lievre 1283: int j, k=0,jk, ju, jl;
1284: double sum=0.;
1285: jmin=1e+5;
1286: jmax=-1;
1287: jmean=0.;
1.2 lievre 1288: for(i=1; i<=imx; i++){
1289: mi=0;
1290: m=firstpass;
1291: while(s[m][i] <= nlstate){
1292: if(s[m][i]>=1)
1293: mw[++mi][i]=m;
1294: if(m >=lastpass)
1295: break;
1296: else
1297: m++;
1298: }/* end while */
1299: if (s[m][i] > nlstate){
1300: mi++; /* Death is another wave */
1301: /* if(mi==0) never been interviewed correctly before death */
1302: /* Only death is a correct wave */
1303: mw[mi][i]=m;
1304: }
1305:
1306: wav[i]=mi;
1307: if(mi==0)
1308: printf("Warning, no any valid information for:%d line=%d\n",num[i],i);
1309: }
1310:
1311: for(i=1; i<=imx; i++){
1312: for(mi=1; mi<wav[i];mi++){
1313: if (stepm <=0)
1314: dh[mi][i]=1;
1315: else{
1316: if (s[mw[mi+1][i]][i] > nlstate) {
1.10 lievre 1317: if (agedc[i] < 2*AGESUP) {
1.2 lievre 1318: j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);
1.8 lievre 1319: if(j==0) j=1; /* Survives at least one month after exam */
1320: k=k+1;
1321: if (j >= jmax) jmax=j;
1.11 lievre 1322: if (j <= jmin) jmin=j;
1.8 lievre 1323: sum=sum+j;
1.12 lievre 1324: /* if (j<10) printf("j=%d num=%d ",j,i); */
1.10 lievre 1325: }
1.2 lievre 1326: }
1327: else{
1328: j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
1329: k=k+1;
1330: if (j >= jmax) jmax=j;
1331: else if (j <= jmin)jmin=j;
1.12 lievre 1332: /* if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
1.2 lievre 1333: sum=sum+j;
1334: }
1335: jk= j/stepm;
1336: jl= j -jk*stepm;
1337: ju= j -(jk+1)*stepm;
1338: if(jl <= -ju)
1339: dh[mi][i]=jk;
1340: else
1341: dh[mi][i]=jk+1;
1342: if(dh[mi][i]==0)
1343: dh[mi][i]=1; /* At least one step */
1344: }
1345: }
1346: }
1.8 lievre 1347: jmean=sum/k;
1348: printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);
1.12 lievre 1349: }
1.2 lievre 1350: /*********** Tricode ****************************/
1351: void tricode(int *Tvar, int **nbcode, int imx)
1352: {
1.7 lievre 1353: int Ndum[20],ij=1, k, j, i;
1.2 lievre 1354: int cptcode=0;
1.7 lievre 1355: cptcoveff=0;
1356:
1357: for (k=0; k<19; k++) Ndum[k]=0;
1.2 lievre 1358: for (k=1; k<=7; k++) ncodemax[k]=0;
1.6 lievre 1359:
1.7 lievre 1360: for (j=1; j<=(cptcovn+2*cptcovprod); j++) {
1.2 lievre 1361: for (i=1; i<=imx; i++) {
1362: ij=(int)(covar[Tvar[j]][i]);
1363: Ndum[ij]++;
1.8 lievre 1364: /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
1.2 lievre 1365: if (ij > cptcode) cptcode=ij;
1366: }
1.7 lievre 1367:
1.2 lievre 1368: for (i=0; i<=cptcode; i++) {
1369: if(Ndum[i]!=0) ncodemax[j]++;
1370: }
1371: ij=1;
1.7 lievre 1372:
1.8 lievre 1373:
1.2 lievre 1374: for (i=1; i<=ncodemax[j]; i++) {
1.7 lievre 1375: for (k=0; k<=19; k++) {
1.2 lievre 1376: if (Ndum[k] != 0) {
1377: nbcode[Tvar[j]][ij]=k;
1378: ij++;
1379: }
1380: if (ij > ncodemax[j]) break;
1381: }
1382: }
1.7 lievre 1383: }
1.8 lievre 1384:
1385: for (k=0; k<19; k++) Ndum[k]=0;
1386:
1.12 lievre 1387: for (i=1; i<=ncovmodel-2; i++) {
1.7 lievre 1388: ij=Tvar[i];
1389: Ndum[ij]++;
1390: }
1.8 lievre 1391:
1.7 lievre 1392: ij=1;
1.8 lievre 1393: for (i=1; i<=10; i++) {
1.7 lievre 1394: if((Ndum[i]!=0) && (i<=ncov)){
1.8 lievre 1395: Tvaraff[ij]=i;
1396: ij++;
1.7 lievre 1397: }
1398: }
1399:
1.8 lievre 1400: cptcoveff=ij-1;
1.6 lievre 1401: }
1.2 lievre 1402:
1403: /*********** Health Expectancies ****************/
1404:
1405: void evsij(char fileres[], double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int ij)
1406: {
1407: /* Health expectancies */
1408: int i, j, nhstepm, hstepm, h;
1409: double age, agelim,hf;
1410: double ***p3mat;
1411:
1412: fprintf(ficreseij,"# Health expectancies\n");
1413: fprintf(ficreseij,"# Age");
1414: for(i=1; i<=nlstate;i++)
1415: for(j=1; j<=nlstate;j++)
1416: fprintf(ficreseij," %1d-%1d",i,j);
1417: fprintf(ficreseij,"\n");
1418:
1419: hstepm=1*YEARM; /* Every j years of age (in month) */
1420: hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */
1421:
1422: agelim=AGESUP;
1423: for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
1424: /* nhstepm age range expressed in number of stepm */
1425: nhstepm=(int) rint((agelim-age)*YEARM/stepm);
1426: /* Typically if 20 years = 20*12/6=40 stepm */
1427: if (stepm >= YEARM) hstepm=1;
1428: nhstepm = nhstepm/hstepm;/* Expressed in hstepm, typically 40/4=10 */
1429: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
1430: /* Computed by stepm unit matrices, product of hstepm matrices, stored
1431: in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
1432: hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);
1433:
1434:
1435: for(i=1; i<=nlstate;i++)
1436: for(j=1; j<=nlstate;j++)
1437: for (h=0, eij[i][j][(int)age]=0; h<=nhstepm; h++){
1438: eij[i][j][(int)age] +=p3mat[i][j][h];
1439: }
1440:
1441: hf=1;
1442: if (stepm >= YEARM) hf=stepm/YEARM;
1443: fprintf(ficreseij,"%.0f",age );
1444: for(i=1; i<=nlstate;i++)
1445: for(j=1; j<=nlstate;j++){
1446: fprintf(ficreseij," %.4f", hf*eij[i][j][(int)age]);
1447: }
1448: fprintf(ficreseij,"\n");
1449: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
1450: }
1451: }
1452:
1453: /************ Variance ******************/
1454: 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)
1455: {
1456: /* Variance of health expectancies */
1457: /* double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
1458: double **newm;
1459: double **dnewm,**doldm;
1460: int i, j, nhstepm, hstepm, h;
1461: int k, cptcode;
1.12 lievre 1462: double *xp;
1.2 lievre 1463: double **gp, **gm;
1464: double ***gradg, ***trgradg;
1465: double ***p3mat;
1466: double age,agelim;
1467: int theta;
1468:
1469: fprintf(ficresvij,"# Covariances of life expectancies\n");
1470: fprintf(ficresvij,"# Age");
1471: for(i=1; i<=nlstate;i++)
1472: for(j=1; j<=nlstate;j++)
1473: fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);
1474: fprintf(ficresvij,"\n");
1475:
1476: xp=vector(1,npar);
1477: dnewm=matrix(1,nlstate,1,npar);
1478: doldm=matrix(1,nlstate,1,nlstate);
1479:
1480: hstepm=1*YEARM; /* Every year of age */
1481: hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */
1482: agelim = AGESUP;
1483: for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
1484: nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
1485: if (stepm >= YEARM) hstepm=1;
1486: nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
1487: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
1488: gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
1489: gp=matrix(0,nhstepm,1,nlstate);
1490: gm=matrix(0,nhstepm,1,nlstate);
1491:
1492: for(theta=1; theta <=npar; theta++){
1493: for(i=1; i<=npar; i++){ /* Computes gradient */
1494: xp[i] = x[i] + (i==theta ?delti[theta]:0);
1495: }
1496: hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
1497: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
1.14 ! lievre 1498:
! 1499: if (popbased==1) {
! 1500: for(i=1; i<=nlstate;i++)
! 1501: prlim[i][i]=probs[(int)age][i][ij];
! 1502: }
! 1503:
1.2 lievre 1504: for(j=1; j<= nlstate; j++){
1505: for(h=0; h<=nhstepm; h++){
1506: for(i=1, gp[h][j]=0.;i<=nlstate;i++)
1507: gp[h][j] += prlim[i][i]*p3mat[i][j][h];
1508: }
1509: }
1510:
1511: for(i=1; i<=npar; i++) /* Computes gradient */
1512: xp[i] = x[i] - (i==theta ?delti[theta]:0);
1513: hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
1514: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
1.14 ! lievre 1515:
! 1516: if (popbased==1) {
! 1517: for(i=1; i<=nlstate;i++)
! 1518: prlim[i][i]=probs[(int)age][i][ij];
! 1519: }
! 1520:
1.2 lievre 1521: for(j=1; j<= nlstate; j++){
1522: for(h=0; h<=nhstepm; h++){
1523: for(i=1, gm[h][j]=0.;i<=nlstate;i++)
1524: gm[h][j] += prlim[i][i]*p3mat[i][j][h];
1525: }
1526: }
1.14 ! lievre 1527:
1.2 lievre 1528: for(j=1; j<= nlstate; j++)
1529: for(h=0; h<=nhstepm; h++){
1530: gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
1531: }
1532: } /* End theta */
1533:
1534: trgradg =ma3x(0,nhstepm,1,nlstate,1,npar);
1535:
1536: for(h=0; h<=nhstepm; h++)
1537: for(j=1; j<=nlstate;j++)
1538: for(theta=1; theta <=npar; theta++)
1539: trgradg[h][j][theta]=gradg[h][theta][j];
1540:
1541: for(i=1;i<=nlstate;i++)
1542: for(j=1;j<=nlstate;j++)
1543: vareij[i][j][(int)age] =0.;
1544: for(h=0;h<=nhstepm;h++){
1545: for(k=0;k<=nhstepm;k++){
1546: matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
1547: matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
1548: for(i=1;i<=nlstate;i++)
1549: for(j=1;j<=nlstate;j++)
1550: vareij[i][j][(int)age] += doldm[i][j];
1551: }
1552: }
1553: h=1;
1554: if (stepm >= YEARM) h=stepm/YEARM;
1555: fprintf(ficresvij,"%.0f ",age );
1556: for(i=1; i<=nlstate;i++)
1557: for(j=1; j<=nlstate;j++){
1558: fprintf(ficresvij," %.4f", h*vareij[i][j][(int)age]);
1559: }
1560: fprintf(ficresvij,"\n");
1561: free_matrix(gp,0,nhstepm,1,nlstate);
1562: free_matrix(gm,0,nhstepm,1,nlstate);
1563: free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
1564: free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
1565: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
1566: } /* End age */
1567:
1568: free_vector(xp,1,npar);
1569: free_matrix(doldm,1,nlstate,1,npar);
1570: free_matrix(dnewm,1,nlstate,1,nlstate);
1571:
1572: }
1573:
1574: /************ Variance of prevlim ******************/
1575: 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)
1576: {
1577: /* Variance of prevalence limit */
1578: /* double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
1579: double **newm;
1580: double **dnewm,**doldm;
1581: int i, j, nhstepm, hstepm;
1582: int k, cptcode;
1583: double *xp;
1584: double *gp, *gm;
1585: double **gradg, **trgradg;
1586: double age,agelim;
1587: int theta;
1588:
1589: fprintf(ficresvpl,"# Standard deviation of prevalences limit\n");
1590: fprintf(ficresvpl,"# Age");
1591: for(i=1; i<=nlstate;i++)
1592: fprintf(ficresvpl," %1d-%1d",i,i);
1593: fprintf(ficresvpl,"\n");
1594:
1595: xp=vector(1,npar);
1596: dnewm=matrix(1,nlstate,1,npar);
1597: doldm=matrix(1,nlstate,1,nlstate);
1598:
1599: hstepm=1*YEARM; /* Every year of age */
1600: hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */
1601: agelim = AGESUP;
1602: for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
1603: nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
1604: if (stepm >= YEARM) hstepm=1;
1605: nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
1606: gradg=matrix(1,npar,1,nlstate);
1607: gp=vector(1,nlstate);
1608: gm=vector(1,nlstate);
1609:
1610: for(theta=1; theta <=npar; theta++){
1611: for(i=1; i<=npar; i++){ /* Computes gradient */
1612: xp[i] = x[i] + (i==theta ?delti[theta]:0);
1613: }
1614: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
1615: for(i=1;i<=nlstate;i++)
1616: gp[i] = prlim[i][i];
1617:
1618: for(i=1; i<=npar; i++) /* Computes gradient */
1619: xp[i] = x[i] - (i==theta ?delti[theta]:0);
1620: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
1621: for(i=1;i<=nlstate;i++)
1622: gm[i] = prlim[i][i];
1623:
1624: for(i=1;i<=nlstate;i++)
1625: gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
1626: } /* End theta */
1627:
1628: trgradg =matrix(1,nlstate,1,npar);
1629:
1630: for(j=1; j<=nlstate;j++)
1631: for(theta=1; theta <=npar; theta++)
1632: trgradg[j][theta]=gradg[theta][j];
1633:
1634: for(i=1;i<=nlstate;i++)
1635: varpl[i][(int)age] =0.;
1636: matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
1637: matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
1638: for(i=1;i<=nlstate;i++)
1639: varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
1640:
1641: fprintf(ficresvpl,"%.0f ",age );
1642: for(i=1; i<=nlstate;i++)
1643: fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
1644: fprintf(ficresvpl,"\n");
1645: free_vector(gp,1,nlstate);
1646: free_vector(gm,1,nlstate);
1647: free_matrix(gradg,1,npar,1,nlstate);
1648: free_matrix(trgradg,1,nlstate,1,npar);
1649: } /* End age */
1650:
1651: free_vector(xp,1,npar);
1652: free_matrix(doldm,1,nlstate,1,npar);
1653: free_matrix(dnewm,1,nlstate,1,nlstate);
1654:
1655: }
1656:
1.13 lievre 1657: /************ Variance of one-step probabilities ******************/
1658: void varprob(char fileres[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij)
1659: {
1660: int i, j;
1661: int k=0, cptcode;
1662: double **dnewm,**doldm;
1663: double *xp;
1664: double *gp, *gm;
1665: double **gradg, **trgradg;
1666: double age,agelim, cov[NCOVMAX];
1667: int theta;
1668: char fileresprob[FILENAMELENGTH];
1669:
1670: strcpy(fileresprob,"prob");
1671: strcat(fileresprob,fileres);
1672: if((ficresprob=fopen(fileresprob,"w"))==NULL) {
1673: printf("Problem with resultfile: %s\n", fileresprob);
1674: }
1675: printf("Computing variance of one-step probabilities: result on file '%s' \n",fileresprob);
1676:
1.2 lievre 1677:
1.13 lievre 1678: xp=vector(1,npar);
1679: dnewm=matrix(1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
1680: doldm=matrix(1,(nlstate+ndeath)*(nlstate+ndeath),1,(nlstate+ndeath)*(nlstate+ndeath));
1681:
1682: cov[1]=1;
1683: for (age=bage; age<=fage; age ++){
1684: cov[2]=age;
1685: gradg=matrix(1,npar,1,9);
1686: trgradg=matrix(1,9,1,npar);
1687: gp=vector(1,(nlstate+ndeath)*(nlstate+ndeath));
1688: gm=vector(1,(nlstate+ndeath)*(nlstate+ndeath));
1689:
1690: for(theta=1; theta <=npar; theta++){
1691: for(i=1; i<=npar; i++)
1692: xp[i] = x[i] + (i==theta ?delti[theta]:0);
1693:
1694: pmij(pmmij,cov,ncovmodel,xp,nlstate);
1695:
1696: k=0;
1697: for(i=1; i<= (nlstate+ndeath); i++){
1698: for(j=1; j<=(nlstate+ndeath);j++){
1699: k=k+1;
1700: gp[k]=pmmij[i][j];
1701: }
1702: }
1703:
1704: for(i=1; i<=npar; i++)
1705: xp[i] = x[i] - (i==theta ?delti[theta]:0);
1706:
1707:
1708: pmij(pmmij,cov,ncovmodel,xp,nlstate);
1709: k=0;
1710: for(i=1; i<=(nlstate+ndeath); i++){
1711: for(j=1; j<=(nlstate+ndeath);j++){
1712: k=k+1;
1713: gm[k]=pmmij[i][j];
1714: }
1715: }
1716:
1717: for(i=1; i<= (nlstate+ndeath)*(nlstate+ndeath); i++)
1718: gradg[theta][i]=(gp[i]-gm[i])/2./delti[theta];
1719: }
1720:
1721: for(j=1; j<=(nlstate+ndeath)*(nlstate+ndeath);j++)
1722: for(theta=1; theta <=npar; theta++)
1723: trgradg[j][theta]=gradg[theta][j];
1724:
1725: matprod2(dnewm,trgradg,1,9,1,npar,1,npar,matcov);
1726: matprod2(doldm,dnewm,1,9,1,npar,1,9,gradg);
1727:
1728: pmij(pmmij,cov,ncovmodel,x,nlstate);
1729:
1730: k=0;
1731: for(i=1; i<=(nlstate+ndeath); i++){
1732: for(j=1; j<=(nlstate+ndeath);j++){
1733: k=k+1;
1734: gm[k]=pmmij[i][j];
1735: }
1736: }
1737:
1738: /*printf("\n%d ",(int)age);
1739: for (i=1; i<=(nlstate+ndeath)*(nlstate+ndeath-1);i++){
1740:
1741:
1742: printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
1743: }*/
1744:
1745: fprintf(ficresprob,"\n%d ",(int)age);
1746:
1747: for (i=1; i<=(nlstate+ndeath)*(nlstate+ndeath-1);i++){
1748: if (i== 2) fprintf(ficresprob,"%.3e %.3e ",gm[i],doldm[i][i]);
1749: if (i== 4) fprintf(ficresprob,"%.3e %.3e ",gm[i],doldm[i][i]);
1750: }
1751:
1752: free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
1753: free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
1754: free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
1755: free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
1756: }
1757: free_vector(xp,1,npar);
1758: fclose(ficresprob);
1759: exit(0);
1760: }
1.2 lievre 1761:
1762: /***********************************************/
1763: /**************** Main Program *****************/
1764: /***********************************************/
1765:
1766: /*int main(int argc, char *argv[])*/
1767: int main()
1768: {
1769:
1.8 lievre 1770: int i,j, k, n=MAXN,iter,m,size,cptcode, cptcod;
1.2 lievre 1771: double agedeb, agefin,hf;
1772: double agemin=1.e20, agemax=-1.e20;
1773:
1774: double fret;
1775: double **xi,tmp,delta;
1776:
1777: double dum; /* Dummy variable */
1778: double ***p3mat;
1779: int *indx;
1780: char line[MAXLINE], linepar[MAXLINE];
1781: char title[MAXLINE];
1.9 lievre 1782: char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH], filerespl[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH];
1.13 lievre 1783: char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], fileresf[FILENAMELENGTH];
1.2 lievre 1784: char filerest[FILENAMELENGTH];
1785: char fileregp[FILENAMELENGTH];
1786: char path[80],pathc[80],pathcd[80],pathtot[80],model[20];
1787: int firstobs=1, lastobs=10;
1788: int sdeb, sfin; /* Status at beginning and end */
1789: int c, h , cpt,l;
1790: int ju,jl, mi;
1.7 lievre 1791: int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;
1.14 ! lievre 1792: int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,**adl,*tab;
! 1793: int mobilav=0, fprevfore=1, lprevfore=1;
1.2 lievre 1794: int hstepm, nhstepm;
1.14 ! lievre 1795:
1.2 lievre 1796: double bage, fage, age, agelim, agebase;
1797: double ftolpl=FTOL;
1798: double **prlim;
1799: double *severity;
1800: double ***param; /* Matrix of parameters */
1801: double *p;
1802: double **matcov; /* Matrix of covariance */
1803: double ***delti3; /* Scale */
1804: double *delti; /* Scale */
1805: double ***eij, ***vareij;
1806: double **varpl; /* Variances of prevalence limits by age */
1807: double *epj, vepp;
1.13 lievre 1808: double kk1;
1809:
1.10 lievre 1810: char version[80]="Imach version 64b, May 2001, INED-EUROREVES ";
1.2 lievre 1811: char *alph[]={"a","a","b","c","d","e"}, str[4];
1.5 lievre 1812:
1.13 lievre 1813:
1.2 lievre 1814: char z[1]="c", occ;
1815: #include <sys/time.h>
1816: #include <time.h>
1817: char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];
1818: /* long total_usecs;
1819: struct timeval start_time, end_time;
1820:
1821: gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */
1822:
1823:
1.9 lievre 1824: printf("\nIMACH, Version 0.64b");
1.2 lievre 1825: printf("\nEnter the parameter file name: ");
1826:
1827: #ifdef windows
1828: scanf("%s",pathtot);
1.5 lievre 1829: getcwd(pathcd, size);
1830: /*cygwin_split_path(pathtot,path,optionfile);
1831: printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/
1832: /* cutv(path,optionfile,pathtot,'\\');*/
1833:
1834: split(pathtot, path,optionfile);
1.2 lievre 1835: chdir(path);
1836: replace(pathc,path);
1837: #endif
1838: #ifdef unix
1839: scanf("%s",optionfile);
1840: #endif
1841:
1842: /*-------- arguments in the command line --------*/
1843:
1844: strcpy(fileres,"r");
1845: strcat(fileres, optionfile);
1846:
1847: /*---------arguments file --------*/
1848:
1849: if((ficpar=fopen(optionfile,"r"))==NULL) {
1850: printf("Problem with optionfile %s\n",optionfile);
1851: goto end;
1852: }
1853:
1854: strcpy(filereso,"o");
1855: strcat(filereso,fileres);
1856: if((ficparo=fopen(filereso,"w"))==NULL) {
1857: printf("Problem with Output resultfile: %s\n", filereso);goto end;
1858: }
1859:
1860: /* Reads comments: lines beginning with '#' */
1861: while((c=getc(ficpar))=='#' && c!= EOF){
1862: ungetc(c,ficpar);
1863: fgets(line, MAXLINE, ficpar);
1864: puts(line);
1865: fputs(line,ficparo);
1866: }
1867: ungetc(c,ficpar);
1868:
1869: 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);
1870: 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);
1871: fprintf(ficparo,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncov=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncov,nlstate,ndeath,maxwav, mle, weightopt,model);
1.14 ! lievre 1872: while((c=getc(ficpar))=='#' && c!= EOF){
! 1873: ungetc(c,ficpar);
! 1874: fgets(line, MAXLINE, ficpar);
! 1875: puts(line);
! 1876: fputs(line,ficparo);
! 1877: }
! 1878: ungetc(c,ficpar);
! 1879:
! 1880: fscanf(ficpar,"fprevalence=%d lprevalence=%d pop_based=%d\n",&fprev,&lprev,&popbased);
! 1881: while((c=getc(ficpar))=='#' && c!= EOF){
! 1882: ungetc(c,ficpar);
! 1883: fgets(line, MAXLINE, ficpar);
! 1884: puts(line);
! 1885: fputs(line,ficparo);
! 1886: }
! 1887: ungetc(c,ficpar);
! 1888:
! 1889: fscanf(ficpar,"fprevalence=%d lprevalence=%d mob_average=%d\n",&fprevfore,&lprevfore,&mobilav);
! 1890:
1.8 lievre 1891: covar=matrix(0,NCOVMAX,1,n);
1892: cptcovn=0;
1893: if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;
1.2 lievre 1894:
1895: ncovmodel=2+cptcovn;
1896: nvar=ncovmodel-1; /* Suppressing age as a basic covariate */
1897:
1898: /* Read guess parameters */
1899: /* Reads comments: lines beginning with '#' */
1900: while((c=getc(ficpar))=='#' && c!= EOF){
1901: ungetc(c,ficpar);
1902: fgets(line, MAXLINE, ficpar);
1903: puts(line);
1904: fputs(line,ficparo);
1905: }
1906: ungetc(c,ficpar);
1907:
1908: param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
1909: for(i=1; i <=nlstate; i++)
1910: for(j=1; j <=nlstate+ndeath-1; j++){
1911: fscanf(ficpar,"%1d%1d",&i1,&j1);
1912: fprintf(ficparo,"%1d%1d",i1,j1);
1913: printf("%1d%1d",i,j);
1914: for(k=1; k<=ncovmodel;k++){
1915: fscanf(ficpar," %lf",¶m[i][j][k]);
1916: printf(" %lf",param[i][j][k]);
1917: fprintf(ficparo," %lf",param[i][j][k]);
1918: }
1919: fscanf(ficpar,"\n");
1920: printf("\n");
1921: fprintf(ficparo,"\n");
1922: }
1923:
1.12 lievre 1924: npar= (nlstate+ndeath-1)*nlstate*ncovmodel;
1925:
1.2 lievre 1926: p=param[1][1];
1927:
1928: /* Reads comments: lines beginning with '#' */
1929: while((c=getc(ficpar))=='#' && c!= EOF){
1930: ungetc(c,ficpar);
1931: fgets(line, MAXLINE, ficpar);
1932: puts(line);
1933: fputs(line,ficparo);
1934: }
1935: ungetc(c,ficpar);
1936:
1937: delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
1938: delti=vector(1,npar); /* Scale of each paramater (output from hesscov) */
1939: for(i=1; i <=nlstate; i++){
1940: for(j=1; j <=nlstate+ndeath-1; j++){
1941: fscanf(ficpar,"%1d%1d",&i1,&j1);
1942: printf("%1d%1d",i,j);
1943: fprintf(ficparo,"%1d%1d",i1,j1);
1944: for(k=1; k<=ncovmodel;k++){
1945: fscanf(ficpar,"%le",&delti3[i][j][k]);
1946: printf(" %le",delti3[i][j][k]);
1947: fprintf(ficparo," %le",delti3[i][j][k]);
1948: }
1949: fscanf(ficpar,"\n");
1950: printf("\n");
1951: fprintf(ficparo,"\n");
1952: }
1953: }
1954: delti=delti3[1][1];
1955:
1956: /* Reads comments: lines beginning with '#' */
1957: while((c=getc(ficpar))=='#' && c!= EOF){
1958: ungetc(c,ficpar);
1959: fgets(line, MAXLINE, ficpar);
1960: puts(line);
1961: fputs(line,ficparo);
1962: }
1963: ungetc(c,ficpar);
1964:
1965: matcov=matrix(1,npar,1,npar);
1966: for(i=1; i <=npar; i++){
1967: fscanf(ficpar,"%s",&str);
1968: printf("%s",str);
1969: fprintf(ficparo,"%s",str);
1970: for(j=1; j <=i; j++){
1971: fscanf(ficpar," %le",&matcov[i][j]);
1972: printf(" %.5le",matcov[i][j]);
1973: fprintf(ficparo," %.5le",matcov[i][j]);
1974: }
1975: fscanf(ficpar,"\n");
1976: printf("\n");
1977: fprintf(ficparo,"\n");
1978: }
1979: for(i=1; i <=npar; i++)
1980: for(j=i+1;j<=npar;j++)
1981: matcov[i][j]=matcov[j][i];
1982:
1983: printf("\n");
1984:
1985:
1986: /*-------- data file ----------*/
1987: if((ficres =fopen(fileres,"w"))==NULL) {
1988: printf("Problem with resultfile: %s\n", fileres);goto end;
1989: }
1990: fprintf(ficres,"#%s\n",version);
1991:
1992: if((fic=fopen(datafile,"r"))==NULL) {
1993: printf("Problem with datafile: %s\n", datafile);goto end;
1994: }
1995:
1996: n= lastobs;
1997: severity = vector(1,maxwav);
1998: outcome=imatrix(1,maxwav+1,1,n);
1999: num=ivector(1,n);
2000: moisnais=vector(1,n);
2001: annais=vector(1,n);
2002: moisdc=vector(1,n);
2003: andc=vector(1,n);
2004: agedc=vector(1,n);
2005: cod=ivector(1,n);
2006: weight=vector(1,n);
2007: for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */
2008: mint=matrix(1,maxwav,1,n);
2009: anint=matrix(1,maxwav,1,n);
2010: s=imatrix(1,maxwav+1,1,n);
2011: adl=imatrix(1,maxwav+1,1,n);
2012: tab=ivector(1,NCOVMAX);
1.3 lievre 2013: ncodemax=ivector(1,8);
1.2 lievre 2014:
1.12 lievre 2015: i=1;
1.2 lievre 2016: while (fgets(line, MAXLINE, fic) != NULL) {
2017: if ((i >= firstobs) && (i <=lastobs)) {
2018:
2019: for (j=maxwav;j>=1;j--){
2020: cutv(stra, strb,line,' '); s[j][i]=atoi(strb);
2021: strcpy(line,stra);
2022: cutv(stra, strb,line,'/'); anint[j][i]=(double)(atoi(strb)); strcpy(line,stra);
2023: cutv(stra, strb,line,' '); mint[j][i]=(double)(atoi(strb)); strcpy(line,stra);
2024: }
2025:
2026: cutv(stra, strb,line,'/'); andc[i]=(double)(atoi(strb)); strcpy(line,stra);
2027: cutv(stra, strb,line,' '); moisdc[i]=(double)(atoi(strb)); strcpy(line,stra);
2028:
2029: cutv(stra, strb,line,'/'); annais[i]=(double)(atoi(strb)); strcpy(line,stra);
2030: cutv(stra, strb,line,' '); moisnais[i]=(double)(atoi(strb)); strcpy(line,stra);
2031:
2032: cutv(stra, strb,line,' '); weight[i]=(double)(atoi(strb)); strcpy(line,stra);
2033: for (j=ncov;j>=1;j--){
2034: cutv(stra, strb,line,' '); covar[j][i]=(double)(atoi(strb)); strcpy(line,stra);
2035: }
2036: num[i]=atol(stra);
1.12 lievre 2037:
2038: /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){
2039: 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 2040:
2041: i=i+1;
2042: }
2043: }
1.12 lievre 2044: /* printf("ii=%d", ij);
2045: scanf("%d",i);*/
2046: imx=i-1; /* Number of individuals */
1.3 lievre 2047:
1.12 lievre 2048: /* for (i=1; i<=imx; i++){
2049: if ((s[1][i]==3) && (s[2][i]==2)) s[2][i]=3;
2050: if ((s[2][i]==3) && (s[3][i]==2)) s[3][i]=3;
2051: if ((s[3][i]==3) && (s[4][i]==2)) s[4][i]=3;
1.14 ! lievre 2052: }
! 2053: 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 2054:
2055: /* Calculation of the number of parameter from char model*/
1.7 lievre 2056: Tvar=ivector(1,15);
2057: Tprod=ivector(1,15);
2058: Tvaraff=ivector(1,15);
2059: Tvard=imatrix(1,15,1,2);
1.6 lievre 2060: Tage=ivector(1,15);
1.2 lievre 2061:
2062: if (strlen(model) >1){
1.7 lievre 2063: j=0, j1=0, k1=1, k2=1;
1.2 lievre 2064: j=nbocc(model,'+');
1.6 lievre 2065: j1=nbocc(model,'*');
1.2 lievre 2066: cptcovn=j+1;
1.7 lievre 2067: cptcovprod=j1;
1.3 lievre 2068:
1.8 lievre 2069:
1.2 lievre 2070: strcpy(modelsav,model);
1.8 lievre 2071: if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){
2072: printf("Error. Non available option model=%s ",model);
2073: goto end;
2074: }
2075:
2076: for(i=(j+1); i>=1;i--){
2077: cutv(stra,strb,modelsav,'+');
2078: if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav);
2079: /* printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/
2080: /*scanf("%d",i);*/
2081: if (strchr(strb,'*')) {
2082: cutv(strd,strc,strb,'*');
2083: if (strcmp(strc,"age")==0) {
1.7 lievre 2084: cptcovprod--;
1.8 lievre 2085: cutv(strb,stre,strd,'V');
2086: Tvar[i]=atoi(stre);
2087: cptcovage++;
2088: Tage[cptcovage]=i;
2089: /*printf("stre=%s ", stre);*/
1.7 lievre 2090: }
1.8 lievre 2091: else if (strcmp(strd,"age")==0) {
1.7 lievre 2092: cptcovprod--;
1.8 lievre 2093: cutv(strb,stre,strc,'V');
2094: Tvar[i]=atoi(stre);
2095: cptcovage++;
2096: Tage[cptcovage]=i;
1.7 lievre 2097: }
2098: else {
1.8 lievre 2099: cutv(strb,stre,strc,'V');
2100: Tvar[i]=ncov+k1;
2101: cutv(strb,strc,strd,'V');
2102: Tprod[k1]=i;
2103: Tvard[k1][1]=atoi(strc);
2104: Tvard[k1][2]=atoi(stre);
2105: Tvar[cptcovn+k2]=Tvard[k1][1];
2106: Tvar[cptcovn+k2+1]=Tvard[k1][2];
1.7 lievre 2107: for (k=1; k<=lastobs;k++)
1.8 lievre 2108: covar[ncov+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];
2109: k1++;
2110: k2=k2+2;
1.7 lievre 2111: }
1.2 lievre 2112: }
1.8 lievre 2113: else {
2114: /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/
2115: /* scanf("%d",i);*/
2116: cutv(strd,strc,strb,'V');
2117: Tvar[i]=atoi(strc);
2118: }
2119: strcpy(modelsav,stra);
2120: /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);
2121: scanf("%d",i);*/
1.2 lievre 2122: }
1.8 lievre 2123: }
2124:
2125: /*printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);
2126: printf("cptcovprod=%d ", cptcovprod);
2127: scanf("%d ",i);*/
1.2 lievre 2128: fclose(fic);
2129:
1.7 lievre 2130: /* if(mle==1){*/
1.2 lievre 2131: if (weightopt != 1) { /* Maximisation without weights*/
2132: for(i=1;i<=n;i++) weight[i]=1.0;
2133: }
2134: /*-calculation of age at interview from date of interview and age at death -*/
2135: agev=matrix(1,maxwav,1,imx);
1.12 lievre 2136:
2137: for (i=1; i<=imx; i++)
2138: for(m=2; (m<= maxwav); m++)
2139: if ((mint[m][i]== 99) && (s[m][i] <= nlstate)){
2140: anint[m][i]=9999;
2141: s[m][i]=-1;
2142: }
1.2 lievre 2143:
2144: for (i=1; i<=imx; i++) {
2145: agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);
2146: for(m=1; (m<= maxwav); m++){
2147: if(s[m][i] >0){
2148: if (s[m][i] == nlstate+1) {
2149: if(agedc[i]>0)
2150: if(moisdc[i]!=99 && andc[i]!=9999)
2151: agev[m][i]=agedc[i];
1.8 lievre 2152: else {
2153: if (andc[i]!=9999){
1.2 lievre 2154: printf("Warning negative age at death: %d line:%d\n",num[i],i);
2155: agev[m][i]=-1;
1.8 lievre 2156: }
1.2 lievre 2157: }
2158: }
2159: else if(s[m][i] !=9){ /* Should no more exist */
2160: agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);
1.3 lievre 2161: if(mint[m][i]==99 || anint[m][i]==9999)
1.2 lievre 2162: agev[m][i]=1;
2163: else if(agev[m][i] <agemin){
2164: agemin=agev[m][i];
2165: /*printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], agemin);*/
2166: }
2167: else if(agev[m][i] >agemax){
2168: agemax=agev[m][i];
2169: /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/
2170: }
2171: /*agev[m][i]=anint[m][i]-annais[i];*/
2172: /* agev[m][i] = age[i]+2*m;*/
2173: }
2174: else { /* =9 */
2175: agev[m][i]=1;
2176: s[m][i]=-1;
2177: }
2178: }
2179: else /*= 0 Unknown */
2180: agev[m][i]=1;
2181: }
2182:
2183: }
2184: for (i=1; i<=imx; i++) {
2185: for(m=1; (m<= maxwav); m++){
2186: if (s[m][i] > (nlstate+ndeath)) {
2187: printf("Error: Wrong value in nlstate or ndeath\n");
2188: goto end;
2189: }
2190: }
2191: }
2192:
2193: printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);
2194:
2195: free_vector(severity,1,maxwav);
2196: free_imatrix(outcome,1,maxwav+1,1,n);
2197: free_vector(moisnais,1,n);
2198: free_vector(annais,1,n);
2199: free_matrix(mint,1,maxwav,1,n);
2200: free_matrix(anint,1,maxwav,1,n);
2201: free_vector(moisdc,1,n);
2202: free_vector(andc,1,n);
2203:
2204:
2205: wav=ivector(1,imx);
2206: dh=imatrix(1,lastpass-firstpass+1,1,imx);
2207: mw=imatrix(1,lastpass-firstpass+1,1,imx);
2208:
2209: /* Concatenates waves */
2210: concatwav(wav, dh, mw, s, agedc, agev, firstpass, lastpass, imx, nlstate, stepm);
2211:
2212:
1.6 lievre 2213: Tcode=ivector(1,100);
1.8 lievre 2214: nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);
1.7 lievre 2215: ncodemax[1]=1;
2216: if (cptcovn > 0) tricode(Tvar,nbcode,imx);
2217:
1.2 lievre 2218: codtab=imatrix(1,100,1,10);
2219: h=0;
1.7 lievre 2220: m=pow(2,cptcoveff);
1.2 lievre 2221:
1.7 lievre 2222: for(k=1;k<=cptcoveff; k++){
1.2 lievre 2223: for(i=1; i <=(m/pow(2,k));i++){
2224: for(j=1; j <= ncodemax[k]; j++){
1.7 lievre 2225: for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){
1.2 lievre 2226: h++;
2227: if (h>m) h=1;codtab[h][k]=j;
2228: }
2229: }
2230: }
2231: }
2232:
1.7 lievre 2233:
2234: /*for(i=1; i <=m ;i++){
1.2 lievre 2235: for(k=1; k <=cptcovn; k++){
1.7 lievre 2236: printf("i=%d k=%d %d %d",i,k,codtab[i][k], cptcoveff);
1.2 lievre 2237: }
2238: printf("\n");
1.6 lievre 2239: }
2240: scanf("%d",i);*/
1.2 lievre 2241:
2242: /* Calculates basic frequencies. Computes observed prevalence at single age
2243: and prints on file fileres'p'. */
1.7 lievre 2244: freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax);
1.2 lievre 2245:
2246: pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
2247: oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
2248: newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
2249: savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
2250: oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */
1.12 lievre 2251:
1.2 lievre 2252: /* For Powell, parameters are in a vector p[] starting at p[1]
2253: so we point p on param[1][1] so that p[1] maps on param[1][1][1] */
2254: p=param[1][1]; /* *(*(*(param +1)+1)+0) */
1.7 lievre 2255:
2256: if(mle==1){
1.2 lievre 2257: mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);
1.7 lievre 2258: }
1.2 lievre 2259:
2260: /*--------- results files --------------*/
2261: 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);
2262:
2263: jk=1;
2264: fprintf(ficres,"# Parameters\n");
2265: printf("# Parameters\n");
2266: for(i=1,jk=1; i <=nlstate; i++){
2267: for(k=1; k <=(nlstate+ndeath); k++){
2268: if (k != i)
2269: {
2270: printf("%d%d ",i,k);
2271: fprintf(ficres,"%1d%1d ",i,k);
2272: for(j=1; j <=ncovmodel; j++){
2273: printf("%f ",p[jk]);
2274: fprintf(ficres,"%f ",p[jk]);
2275: jk++;
2276: }
2277: printf("\n");
2278: fprintf(ficres,"\n");
2279: }
2280: }
2281: }
1.7 lievre 2282: if(mle==1){
1.2 lievre 2283: /* Computing hessian and covariance matrix */
2284: ftolhess=ftol; /* Usually correct */
2285: hesscov(matcov, p, npar, delti, ftolhess, func);
1.7 lievre 2286: }
1.2 lievre 2287: fprintf(ficres,"# Scales\n");
2288: printf("# Scales\n");
2289: for(i=1,jk=1; i <=nlstate; i++){
2290: for(j=1; j <=nlstate+ndeath; j++){
2291: if (j!=i) {
2292: fprintf(ficres,"%1d%1d",i,j);
2293: printf("%1d%1d",i,j);
2294: for(k=1; k<=ncovmodel;k++){
2295: printf(" %.5e",delti[jk]);
2296: fprintf(ficres," %.5e",delti[jk]);
2297: jk++;
2298: }
2299: printf("\n");
2300: fprintf(ficres,"\n");
2301: }
2302: }
2303: }
2304:
2305: k=1;
2306: fprintf(ficres,"# Covariance\n");
2307: printf("# Covariance\n");
2308: for(i=1;i<=npar;i++){
2309: /* if (k>nlstate) k=1;
2310: i1=(i-1)/(ncovmodel*nlstate)+1;
2311: fprintf(ficres,"%s%d%d",alph[k],i1,tab[i]);
2312: printf("%s%d%d",alph[k],i1,tab[i]);*/
2313: fprintf(ficres,"%3d",i);
2314: printf("%3d",i);
2315: for(j=1; j<=i;j++){
2316: fprintf(ficres," %.5e",matcov[i][j]);
2317: printf(" %.5e",matcov[i][j]);
2318: }
2319: fprintf(ficres,"\n");
2320: printf("\n");
2321: k++;
2322: }
2323:
2324: while((c=getc(ficpar))=='#' && c!= EOF){
2325: ungetc(c,ficpar);
2326: fgets(line, MAXLINE, ficpar);
2327: puts(line);
2328: fputs(line,ficparo);
2329: }
2330: ungetc(c,ficpar);
2331:
2332: fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf\n",&agemin,&agemax, &bage, &fage);
2333:
2334: if (fage <= 2) {
2335: bage = agemin;
2336: fage = agemax;
2337: }
2338:
2339: fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");
2340: fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemax,bage,fage);
1.7 lievre 2341:
2342:
1.2 lievre 2343: /*------------ gnuplot -------------*/
2344: chdir(pathcd);
2345: if((ficgp=fopen("graph.plt","w"))==NULL) {
1.5 lievre 2346: printf("Problem with file graph.gp");goto end;
1.2 lievre 2347: }
2348: #ifdef windows
2349: fprintf(ficgp,"cd \"%s\" \n",pathc);
2350: #endif
1.7 lievre 2351: m=pow(2,cptcoveff);
1.2 lievre 2352:
2353: /* 1eme*/
2354: for (cpt=1; cpt<= nlstate ; cpt ++) {
2355: for (k1=1; k1<= m ; k1 ++) {
2356:
2357: #ifdef windows
2358: 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);
2359: #endif
2360: #ifdef unix
2361: fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nplot [%.f:%.f] \"vpl%s\" u 1:2 \"\%%lf",agemin,fage,fileres);
2362: #endif
2363:
2364: for (i=1; i<= nlstate ; i ++) {
2365: if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
2366: else fprintf(ficgp," \%%*lf (\%%*lf)");
2367: }
2368: fprintf(ficgp,"\" t\"Stationary prevalence\" w l 0,\"vpl%s\" every :::%d::%d u 1:($2+2*$3) \"\%%lf",fileres,k1-1,k1-1);
2369: for (i=1; i<= nlstate ; i ++) {
2370: if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
2371: else fprintf(ficgp," \%%*lf (\%%*lf)");
2372: }
2373: fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"vpl%s\" every :::%d::%d u 1:($2-2*$3) \"\%%lf",fileres,k1-1,k1-1);
2374: for (i=1; i<= nlstate ; i ++) {
2375: if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
2376: else fprintf(ficgp," \%%*lf (\%%*lf)");
2377: }
2378: fprintf(ficgp,"\" t\"\" w l 1,\"p%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",fileres,k1-1,k1-1,2+4*(cpt-1));
2379: #ifdef unix
2380: fprintf(ficgp,"\nset ter gif small size 400,300");
2381: #endif
2382: fprintf(ficgp,"\nset out \"v%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);
2383: }
2384: }
2385: /*2 eme*/
2386:
2387: for (k1=1; k1<= m ; k1 ++) {
2388: fprintf(ficgp,"set ylabel \"Years\" \nset ter gif small size 400,300\nplot [%.f:%.f] ",agemin,fage);
2389:
2390: for (i=1; i<= nlstate+1 ; i ++) {
2391: k=2*i;
2392: fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:2 \"\%%lf",fileres,k1-1,k1-1);
2393: for (j=1; j<= nlstate+1 ; j ++) {
2394: if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
2395: else fprintf(ficgp," \%%*lf (\%%*lf)");
2396: }
2397: if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");
2398: else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);
2399: fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",fileres,k1-1,k1-1);
2400: for (j=1; j<= nlstate+1 ; j ++) {
2401: if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
2402: else fprintf(ficgp," \%%*lf (\%%*lf)");
2403: }
2404: fprintf(ficgp,"\" t\"\" w l 0,");
2405: fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",fileres,k1-1,k1-1);
2406: for (j=1; j<= nlstate+1 ; j ++) {
2407: if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
2408: else fprintf(ficgp," \%%*lf (\%%*lf)");
2409: }
2410: if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");
2411: else fprintf(ficgp,"\" t\"\" w l 0,");
2412: }
2413: fprintf(ficgp,"\nset out \"e%s%d.gif\" \nreplot\n\n",strtok(optionfile, "."),k1);
2414: }
2415:
2416: /*3eme*/
2417:
1.5 lievre 2418: for (k1=1; k1<= m ; k1 ++) {
1.2 lievre 2419: for (cpt=1; cpt<= nlstate ; cpt ++) {
2420: k=2+nlstate*(cpt-1);
2421: 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);
2422: for (i=1; i< nlstate ; i ++) {
2423: 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);
2424: }
2425: fprintf(ficgp,"\nset out \"exp%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);
2426: }
1.5 lievre 2427: }
1.2 lievre 2428:
2429: /* CV preval stat */
1.5 lievre 2430: for (k1=1; k1<= m ; k1 ++) {
1.2 lievre 2431: for (cpt=1; cpt<nlstate ; cpt ++) {
2432: k=3;
2433: 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/($%d",agemin,agemax,fileres,k1,k+cpt+1,k+1);
2434: for (i=1; i< nlstate ; i ++)
2435: fprintf(ficgp,"+$%d",k+i+1);
2436: fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);
2437:
2438: l=3+(nlstate+ndeath)*cpt;
2439: fprintf(ficgp,",\"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",fileres,k1,l+cpt+1,l+1);
2440: for (i=1; i< nlstate ; i ++) {
2441: l=3+(nlstate+ndeath)*cpt;
2442: fprintf(ficgp,"+$%d",l+i+1);
2443: }
2444: fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);
2445: fprintf(ficgp,"set out \"p%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);
2446: }
1.13 lievre 2447: }
1.5 lievre 2448:
1.2 lievre 2449: /* proba elementaires */
1.5 lievre 2450: for(i=1,jk=1; i <=nlstate; i++){
1.2 lievre 2451: for(k=1; k <=(nlstate+ndeath); k++){
2452: if (k != i) {
2453: for(j=1; j <=ncovmodel; j++){
1.5 lievre 2454: /*fprintf(ficgp,"%s%1d%1d=%f ",alph[j],i,k,p[jk]);*/
2455: /*fprintf(ficgp,"%s",alph[1]);*/
2456: fprintf(ficgp,"p%d=%f ",jk,p[jk]);
1.2 lievre 2457: jk++;
2458: fprintf(ficgp,"\n");
2459: }
2460: }
2461: }
1.5 lievre 2462: }
2463:
1.2 lievre 2464: for(jk=1; jk <=m; jk++) {
2465: fprintf(ficgp,"\nset ter gif small size 400,300\nset log y\nplot [%.f:%.f] ",agemin,agemax);
1.5 lievre 2466: i=1;
2467: for(k2=1; k2<=nlstate; k2++) {
2468: k3=i;
2469: for(k=1; k<=(nlstate+ndeath); k++) {
2470: if (k != k2){
2471: fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
1.7 lievre 2472: ij=1;
2473: for(j=3; j <=ncovmodel; j++) {
2474: if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
2475: fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
2476: ij++;
2477: }
2478: else
1.6 lievre 2479: fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
1.7 lievre 2480: }
2481: fprintf(ficgp,")/(1");
1.6 lievre 2482:
2483: for(k1=1; k1 <=nlstate; k1++){
2484: fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);
1.7 lievre 2485: ij=1;
2486: for(j=3; j <=ncovmodel; j++){
2487: if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
2488: fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
2489: ij++;
2490: }
2491: else
1.6 lievre 2492: fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
1.7 lievre 2493: }
1.6 lievre 2494: fprintf(ficgp,")");
1.5 lievre 2495: }
2496: fprintf(ficgp,") t \"p%d%d\" ", k2,k);
2497: if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");
1.6 lievre 2498: i=i+ncovmodel;
1.5 lievre 2499: }
2500: }
2501: }
1.6 lievre 2502: fprintf(ficgp,"\nset out \"pe%s%d.gif\" \nreplot\n\n",strtok(optionfile, "."),jk);
2503: }
1.5 lievre 2504:
2505: fclose(ficgp);
2506:
2507: chdir(path);
1.2 lievre 2508: free_matrix(agev,1,maxwav,1,imx);
2509: free_ivector(wav,1,imx);
2510: free_imatrix(dh,1,lastpass-firstpass+1,1,imx);
2511: free_imatrix(mw,1,lastpass-firstpass+1,1,imx);
2512:
2513: free_imatrix(s,1,maxwav+1,1,n);
2514:
2515:
2516: free_ivector(num,1,n);
2517: free_vector(agedc,1,n);
2518: free_vector(weight,1,n);
2519: /*free_matrix(covar,1,NCOVMAX,1,n);*/
2520: fclose(ficparo);
2521: fclose(ficres);
1.7 lievre 2522: /* }*/
1.2 lievre 2523:
2524: /*________fin mle=1_________*/
2525:
2526:
2527:
2528: /* No more information from the sample is required now */
2529: /* Reads comments: lines beginning with '#' */
2530: while((c=getc(ficpar))=='#' && c!= EOF){
2531: ungetc(c,ficpar);
2532: fgets(line, MAXLINE, ficpar);
2533: puts(line);
2534: fputs(line,ficparo);
2535: }
2536: ungetc(c,ficpar);
2537:
2538: fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf\n",&agemin,&agemax, &bage, &fage);
2539: printf("agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemax, bage, fage);
2540: fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemax,bage,fage);
2541: /*--------- index.htm --------*/
2542:
1.9 lievre 2543: strcpy(optionfilehtm,optionfile);
2544: strcat(optionfilehtm,".htm");
2545: if((fichtm=fopen(optionfilehtm,"w"))==NULL) {
2546: printf("Problem with %s \n",optionfilehtm);goto end;
1.2 lievre 2547: }
2548:
1.9 lievre 2549: fprintf(fichtm,"<body><ul> <font size=\"6\">Imach, Version 0.64b </font> <hr size=\"2\" color=\"#EC5E5E\">
1.8 lievre 2550: Titre=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>
2551: Total number of observations=%d <br>
2552: Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>
2553: <hr size=\"2\" color=\"#EC5E5E\">
2554: <li>Outputs files<br><br>\n
1.2 lievre 2555: - Observed prevalence in each state: <a href=\"p%s\">p%s</a> <br>\n
2556: - Estimated parameters and the covariance matrix: <a href=\"%s\">%s</a> <br>
2557: - Stationary prevalence in each state: <a href=\"pl%s\">pl%s</a> <br>
2558: - Transition probabilities: <a href=\"pij%s\">pij%s</a><br>
2559: - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>
2560: - Life expectancies by age and initial health status: <a href=\"e%s\">e%s</a> <br>
2561: - Variances of life expectancies by age and initial health status: <a href=\"v%s\">v%s</a><br>
2562: - Health expectancies with their variances: <a href=\"t%s\">t%s</a> <br>
1.14 ! lievre 2563: - Standard deviation of stationary prevalences: <a href=\"vpl%s\">vpl%s</a> <br>
! 2564: - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>
! 2565: <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,fileres,fileres);
1.2 lievre 2566:
1.8 lievre 2567: fprintf(fichtm," <li>Graphs</li><p>");
1.2 lievre 2568:
1.7 lievre 2569: m=cptcoveff;
1.2 lievre 2570: if (cptcovn < 1) {m=1;ncodemax[1]=1;}
2571:
2572: j1=0;
2573: for(k1=1; k1<=m;k1++){
2574: for(i1=1; i1<=ncodemax[k1];i1++){
2575: j1++;
2576: if (cptcovn > 0) {
1.8 lievre 2577: fprintf(fichtm,"<hr size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
1.7 lievre 2578: for (cpt=1; cpt<=cptcoveff;cpt++)
2579: fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[j1][cpt]]);
1.8 lievre 2580: fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
1.2 lievre 2581: }
2582: fprintf(fichtm,"<br>- Probabilities: pe%s%d.gif<br>
2583: <img src=\"pe%s%d.gif\">",strtok(optionfile, "."),j1,strtok(optionfile, "."),j1);
2584: for(cpt=1; cpt<nlstate;cpt++){
2585: fprintf(fichtm,"<br>- Prevalence of disability : p%s%d%d.gif<br>
2586: <img src=\"p%s%d%d.gif\">",strtok(optionfile, "."),cpt,j1,strtok(optionfile, "."),cpt,j1);
2587: }
2588: for(cpt=1; cpt<=nlstate;cpt++) {
2589: fprintf(fichtm,"<br>- Observed and stationary prevalence (with confident
2590: interval) in state (%d): v%s%d%d.gif <br>
2591: <img src=\"v%s%d%d.gif\">",cpt,strtok(optionfile, "."),cpt,j1,strtok(optionfile, "."),cpt,j1);
2592: }
2593: for(cpt=1; cpt<=nlstate;cpt++) {
2594: fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): exp%s%d%d.gif <br>
1.5 lievre 2595: <img src=\"exp%s%d%d.gif\">",cpt,strtok(optionfile, "."),cpt,j1,strtok(optionfile, "."),cpt,j1);
1.2 lievre 2596: }
2597: fprintf(fichtm,"\n<br>- Total life expectancy by age and
2598: health expectancies in states (1) and (2): e%s%d.gif<br>
2599: <img src=\"e%s%d.gif\">",strtok(optionfile, "."),j1,strtok(optionfile, "."),j1);
2600: fprintf(fichtm,"\n</body>");
2601: }
2602: }
2603: fclose(fichtm);
2604:
2605: /*--------------- Prevalence limit --------------*/
2606:
2607: strcpy(filerespl,"pl");
2608: strcat(filerespl,fileres);
2609: if((ficrespl=fopen(filerespl,"w"))==NULL) {
2610: printf("Problem with Prev limit resultfile: %s\n", filerespl);goto end;
2611: }
2612: printf("Computing prevalence limit: result on file '%s' \n", filerespl);
2613: fprintf(ficrespl,"#Prevalence limit\n");
2614: fprintf(ficrespl,"#Age ");
2615: for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);
2616: fprintf(ficrespl,"\n");
2617:
2618: prlim=matrix(1,nlstate,1,nlstate);
2619: pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
2620: oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
2621: newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
2622: savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
2623: oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */
2624: k=0;
2625: agebase=agemin;
2626: agelim=agemax;
2627: ftolpl=1.e-10;
1.7 lievre 2628: i1=cptcoveff;
1.2 lievre 2629: if (cptcovn < 1){i1=1;}
2630:
2631: for(cptcov=1;cptcov<=i1;cptcov++){
2632: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
2633: k=k+1;
2634: /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/
1.6 lievre 2635: fprintf(ficrespl,"\n#******");
1.7 lievre 2636: for(j=1;j<=cptcoveff;j++)
2637: fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
1.2 lievre 2638: fprintf(ficrespl,"******\n");
2639:
2640: for (age=agebase; age<=agelim; age++){
2641: prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
2642: fprintf(ficrespl,"%.0f",age );
2643: for(i=1; i<=nlstate;i++)
2644: fprintf(ficrespl," %.5f", prlim[i][i]);
2645: fprintf(ficrespl,"\n");
2646: }
2647: }
2648: }
2649: fclose(ficrespl);
1.13 lievre 2650:
1.2 lievre 2651: /*------------- h Pij x at various ages ------------*/
2652:
2653: strcpy(filerespij,"pij"); strcat(filerespij,fileres);
2654: if((ficrespij=fopen(filerespij,"w"))==NULL) {
2655: printf("Problem with Pij resultfile: %s\n", filerespij);goto end;
2656: }
2657: printf("Computing pij: result on file '%s' \n", filerespij);
2658:
2659: stepsize=(int) (stepm+YEARM-1)/YEARM;
1.13 lievre 2660: /*if (stepm<=24) stepsize=2;*/
1.2 lievre 2661:
2662: agelim=AGESUP;
2663: hstepm=stepsize*YEARM; /* Every year of age */
2664: hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */
2665:
2666: k=0;
2667: for(cptcov=1;cptcov<=i1;cptcov++){
2668: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
2669: k=k+1;
2670: fprintf(ficrespij,"\n#****** ");
1.7 lievre 2671: for(j=1;j<=cptcoveff;j++)
2672: fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
1.2 lievre 2673: fprintf(ficrespij,"******\n");
2674:
2675: for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */
2676: nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
2677: nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
2678: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
2679: oldm=oldms;savm=savms;
2680: hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
2681: fprintf(ficrespij,"# Age");
2682: for(i=1; i<=nlstate;i++)
2683: for(j=1; j<=nlstate+ndeath;j++)
2684: fprintf(ficrespij," %1d-%1d",i,j);
2685: fprintf(ficrespij,"\n");
2686: for (h=0; h<=nhstepm; h++){
2687: fprintf(ficrespij,"%d %.0f %.0f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );
2688: for(i=1; i<=nlstate;i++)
2689: for(j=1; j<=nlstate+ndeath;j++)
2690: fprintf(ficrespij," %.5f", p3mat[i][j][h]);
2691: fprintf(ficrespij,"\n");
2692: }
2693: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
2694: fprintf(ficrespij,"\n");
2695: }
2696: }
2697: }
2698:
1.13 lievre 2699: /* varprob(fileres, matcov, p, delti, nlstate, (int) bage, (int) fage,k);*/
2700:
1.2 lievre 2701: fclose(ficrespij);
2702:
1.13 lievre 2703: /*---------- Forecasting ------------------*/
2704:
2705: strcpy(fileresf,"f");
2706: strcat(fileresf,fileres);
2707: if((ficresf=fopen(fileresf,"w"))==NULL) {
2708: printf("Problem with forecast resultfile: %s\n", fileresf);goto end;
2709: }
2710: printf("Computing forecasting: result on file '%s' \n", fileresf);
2711:
2712: /* Mobile average */
2713:
2714: /* for (agedeb=bage; agedeb<=fage; agedeb++)
2715: for (i=1; i<=nlstate;i++)
2716: for (cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++)
2717: printf("%f %d i=%d j1=%d\n", probs[(int)agedeb][i][cptcod],(int) agedeb,i,cptcod);*/
2718:
2719: if (cptcoveff==0) ncodemax[cptcoveff]=1;
2720:
1.14 ! lievre 2721: if (mobilav==1) {
! 2722: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
! 2723: for (agedeb=bage+3; agedeb<=fage-2; agedeb++)
! 2724: for (i=1; i<=nlstate;i++)
! 2725: for (cptcod=1;cptcod<=ncodemax[cptcov];cptcod++)
! 2726: mobaverage[(int)agedeb][i][cptcod]=0.;
! 2727:
! 2728: for (agedeb=bage+4; agedeb<=fage; agedeb++){
! 2729: for (i=1; i<=nlstate;i++){
! 2730: for (cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
! 2731: for (cpt=0;cpt<=4;cpt++){
! 2732: mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]+probs[(int)agedeb-cpt][i][cptcod];
1.13 lievre 2733: }
2734: mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]/5;
1.14 ! lievre 2735: }
1.13 lievre 2736: }
1.14 ! lievre 2737: }
1.13 lievre 2738: }
2739:
2740: stepsize=(int) (stepm+YEARM-1)/YEARM;
2741: if (stepm<=24) stepsize=2;
2742:
2743: agelim=AGESUP;
2744: hstepm=stepsize*YEARM; /* Every year of age */
2745: hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */
2746: hstepm=12;
2747: k=0;
2748: for(cptcov=1;cptcov<=i1;cptcov++){
2749: for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
2750: k=k+1;
2751: fprintf(ficresf,"\n#****** ");
2752: for(j=1;j<=cptcoveff;j++) {
2753: fprintf(ficresf,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
2754: }
2755:
2756: fprintf(ficresf,"******\n");
2757:
2758: fprintf(ficresf,"# StartingAge FinalAge Horizon(in years)");
2759: for(j=1; j<=nlstate+ndeath;j++) fprintf(ficresf," P.%d",j);
2760:
2761: for (agedeb=fage; agedeb>=bage; agedeb--){
2762: fprintf(ficresf,"\n%d %.f %.f 0 ",k,agedeb, agedeb);
1.14 ! lievre 2763: if (mobilav==1) {
1.13 lievre 2764: for(j=1; j<=nlstate;j++)
1.14 ! lievre 2765: fprintf(ficresf,"%.5f ",mobaverage[(int)agedeb][j][cptcod]);
! 2766: }
! 2767: else {
! 2768: for(j=1; j<=nlstate;j++)
! 2769: fprintf(ficresf,"%.5f ",probs[(int)agedeb][j][cptcod]);
! 2770: }
! 2771:
! 2772: for(j=1; j<=ndeath;j++) fprintf(ficresf,"0.");
1.13 lievre 2773: }
1.14 ! lievre 2774: for (cpt=1; cpt<=NCOVMAX;cpt++)
1.13 lievre 2775: for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */
2776:
2777: nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
2778: nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
2779: /*printf("stepm=%d hstepm=%d nhstepm=%d \n",stepm,hstepm,nhstepm);*/
2780:
2781: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
2782: oldm=oldms;savm=savms;
2783: hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
2784:
2785: for (h=0; h<=nhstepm; h++){
2786:
2787: if (h*hstepm/YEARM*stepm==cpt)
2788: fprintf(ficresf,"\n%d %.f %.f %.f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm, h*hstepm/YEARM*stepm);
2789:
2790: for(j=1; j<=nlstate+ndeath;j++) {
2791: kk1=0.;
2792: for(i=1; i<=nlstate;i++) {
1.14 ! lievre 2793: if (mobilav==1)
! 2794: kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb][i][cptcod];
! 2795: else kk1=kk1+p3mat[i][j][h]*probs[(int)agedeb][i][cptcod];
! 2796: }
! 2797: if (h*hstepm/YEARM*stepm==cpt) fprintf(ficresf," %.5f ", kk1);
1.13 lievre 2798: }
1.14 ! lievre 2799: }
1.13 lievre 2800: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
2801: }
2802: }
1.14 ! lievre 2803: }
! 2804: if (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
1.13 lievre 2805: fclose(ficresf);
1.2 lievre 2806: /*---------- Health expectancies and variances ------------*/
2807:
2808: strcpy(filerest,"t");
2809: strcat(filerest,fileres);
2810: if((ficrest=fopen(filerest,"w"))==NULL) {
2811: printf("Problem with total LE resultfile: %s\n", filerest);goto end;
2812: }
2813: printf("Computing Total LEs with variances: file '%s' \n", filerest);
2814:
2815:
2816: strcpy(filerese,"e");
2817: strcat(filerese,fileres);
2818: if((ficreseij=fopen(filerese,"w"))==NULL) {
2819: printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
2820: }
2821: printf("Computing Health Expectancies: result on file '%s' \n", filerese);
2822:
2823: strcpy(fileresv,"v");
2824: strcat(fileresv,fileres);
2825: if((ficresvij=fopen(fileresv,"w"))==NULL) {
2826: printf("Problem with variance resultfile: %s\n", fileresv);exit(0);
2827: }
2828: printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
2829:
2830: k=0;
2831: for(cptcov=1;cptcov<=i1;cptcov++){
2832: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
2833: k=k+1;
2834: fprintf(ficrest,"\n#****** ");
1.7 lievre 2835: for(j=1;j<=cptcoveff;j++)
2836: fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
1.2 lievre 2837: fprintf(ficrest,"******\n");
2838:
2839: fprintf(ficreseij,"\n#****** ");
1.7 lievre 2840: for(j=1;j<=cptcoveff;j++)
1.2 lievre 2841: fprintf(ficreseij,"V%d=%d ",j,nbcode[j][codtab[k][j]]);
2842: fprintf(ficreseij,"******\n");
2843:
2844: fprintf(ficresvij,"\n#****** ");
1.7 lievre 2845: for(j=1;j<=cptcoveff;j++)
1.2 lievre 2846: fprintf(ficresvij,"V%d=%d ",j,nbcode[j][codtab[k][j]]);
2847: fprintf(ficresvij,"******\n");
2848:
2849: eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
2850: oldm=oldms;savm=savms;
2851: evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k);
2852: vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
2853: oldm=oldms;savm=savms;
2854: varevsij(fileres, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);
2855:
2856: fprintf(ficrest,"#Total LEs with variances: e.. (std) ");
2857: for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);
2858: fprintf(ficrest,"\n");
2859:
2860: hf=1;
2861: if (stepm >= YEARM) hf=stepm/YEARM;
2862: epj=vector(1,nlstate+1);
2863: for(age=bage; age <=fage ;age++){
2864: prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
1.14 ! lievre 2865: if (popbased==1) {
! 2866: for(i=1; i<=nlstate;i++)
! 2867: prlim[i][i]=probs[(int)age][i][k];
! 2868: }
! 2869:
1.2 lievre 2870: fprintf(ficrest," %.0f",age);
2871: for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){
2872: for(i=1, epj[j]=0.;i <=nlstate;i++) {
2873: epj[j] += prlim[i][i]*hf*eij[i][j][(int)age];
2874: }
2875: epj[nlstate+1] +=epj[j];
2876: }
2877: for(i=1, vepp=0.;i <=nlstate;i++)
2878: for(j=1;j <=nlstate;j++)
2879: vepp += vareij[i][j][(int)age];
2880: fprintf(ficrest," %.2f (%.2f)", epj[nlstate+1],hf*sqrt(vepp));
2881: for(j=1;j <=nlstate;j++){
2882: fprintf(ficrest," %.2f (%.2f)", epj[j],hf*sqrt(vareij[j][j][(int)age]));
2883: }
2884: fprintf(ficrest,"\n");
2885: }
2886: }
2887: }
2888:
1.13 lievre 2889:
2890:
2891:
1.2 lievre 2892: fclose(ficreseij);
2893: fclose(ficresvij);
2894: fclose(ficrest);
2895: fclose(ficpar);
2896: free_vector(epj,1,nlstate+1);
1.5 lievre 2897: /* scanf("%d ",i); */
1.2 lievre 2898:
2899: /*------- Variance limit prevalence------*/
2900:
2901: strcpy(fileresvpl,"vpl");
2902: strcat(fileresvpl,fileres);
2903: if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {
2904: printf("Problem with variance prev lim resultfile: %s\n", fileresvpl);
2905: exit(0);
2906: }
2907: printf("Computing Variance-covariance of Prevalence limit: file '%s' \n", fileresvpl);
2908:
2909: k=0;
2910: for(cptcov=1;cptcov<=i1;cptcov++){
2911: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
2912: k=k+1;
2913: fprintf(ficresvpl,"\n#****** ");
1.7 lievre 2914: for(j=1;j<=cptcoveff;j++)
2915: fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
1.2 lievre 2916: fprintf(ficresvpl,"******\n");
2917:
2918: varpl=matrix(1,nlstate,(int) bage, (int) fage);
2919: oldm=oldms;savm=savms;
2920: varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);
2921: }
2922: }
2923:
2924: fclose(ficresvpl);
2925:
2926: /*---------- End : free ----------------*/
2927: free_matrix(varpl,1,nlstate,(int) bage, (int)fage);
2928:
2929: free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);
2930: free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
2931:
2932:
2933: free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);
2934: free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);
2935: free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);
2936: free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);
1.13 lievre 2937:
1.2 lievre 2938: free_matrix(matcov,1,npar,1,npar);
2939: free_vector(delti,1,npar);
2940:
2941: free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
2942:
2943: printf("End of Imach\n");
2944: /* gettimeofday(&end_time, (struct timezone*)0);*/ /* after time */
2945:
2946: /* 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);*/
2947: /*printf("Total time was %d uSec.\n", total_usecs);*/
2948: /*------ End -----------*/
1.12 lievre 2949:
1.2 lievre 2950:
2951: end:
2952: #ifdef windows
2953: chdir(pathcd);
2954: #endif
1.13 lievre 2955:
1.11 lievre 2956: system("..\\gp37mgw\\wgnuplot graph.plt");
1.2 lievre 2957:
2958: #ifdef windows
2959: while (z[0] != 'q') {
2960: chdir(pathcd);
2961: printf("\nType e to edit output files, c to start again, and q for exiting: ");
2962: scanf("%s",z);
2963: if (z[0] == 'c') system("./imach");
2964: else if (z[0] == 'e') {
2965: chdir(path);
1.10 lievre 2966: system(optionfilehtm);
1.2 lievre 2967: }
2968: else if (z[0] == 'q') exit(0);
2969: }
2970: #endif
2971: }
2972:
2973:
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