Annotation of imach096d/src/imach.c, revision 1.10
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
11: reach the Maximum Likelihood of the parameters involved in the model.
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.
25: hPijx is the probability to be
26: observed in state i at age x+h conditional to the observed state i at age
27: x. The delay 'h' can be split into an exact number (nh*stepm) of
28: unobserved intermediate states. This elementary transition (by month or
29: quarter trimester, semester or year) is model as a multinomial logistic.
30: The hPx matrix is simply the matrix product of nh*stepm elementary matrices
31: and the contribution of each individual to the likelihood is simply hPijx.
32:
33: Also this programme outputs the covariance matrix of the parameters but also
34: of the life expectancies. It also computes the prevalence limits.
35:
36: Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).
37: Institut national d'études démographiques, Paris.
38: This software have been partly granted by Euro-REVES, a concerted action
39: from the European Union.
40: It is copyrighted identically to a GNU software product, ie programme and
41: software can be distributed freely for non commercial use. Latest version
42: can be accessed at http://euroreves.ined.fr/imach .
43: **********************************************************************/
44:
45: #include <math.h>
46: #include <stdio.h>
47: #include <stdlib.h>
48: #include <unistd.h>
49:
50: #define MAXLINE 256
51: #define FILENAMELENGTH 80
52: /*#define DEBUG*/
53: #define windows
1.5 lievre 54: #define GLOCK_ERROR_NOPATH -1 /* empty path */
55: #define GLOCK_ERROR_GETCWD -2 /* cannot get cwd */
56:
1.2 lievre 57: #define MAXPARM 30 /* Maximum number of parameters for the optimization */
58: #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */
59:
60: #define NINTERVMAX 8
61: #define NLSTATEMAX 8 /* Maximum number of live states (for func) */
62: #define NDEATHMAX 8 /* Maximum number of dead states (for func) */
63: #define NCOVMAX 8 /* Maximum number of covariates */
1.3 lievre 64: #define MAXN 20000
1.2 lievre 65: #define YEARM 12. /* Number of months per year */
66: #define AGESUP 130
67: #define AGEBASE 40
68:
69:
70: int nvar;
1.8 lievre 71: int cptcovn, cptcovage=0, cptcoveff=0,cptcov;
1.2 lievre 72: int npar=NPARMAX;
73: int nlstate=2; /* Number of live states */
74: int ndeath=1; /* Number of dead states */
75: int ncovmodel, ncov; /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
76:
77: int *wav; /* Number of waves for this individuual 0 is possible */
78: int maxwav; /* Maxim number of waves */
1.8 lievre 79: int jmin, jmax; /* min, max spacing between 2 waves */
1.2 lievre 80: int mle, weightopt;
81: int **mw; /* mw[mi][i] is number of the mi wave for this individual */
82: int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
1.8 lievre 83: double jmean; /* Mean space between 2 waves */
1.2 lievre 84: double **oldm, **newm, **savm; /* Working pointers to matrices */
85: double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
86: FILE *fic,*ficpar, *ficparo,*ficres, *ficrespl, *ficrespij, *ficrest;
87: FILE *ficgp, *fichtm;
88: FILE *ficreseij;
89: char filerese[FILENAMELENGTH];
90: FILE *ficresvij;
91: char fileresv[FILENAMELENGTH];
92: FILE *ficresvpl;
93: char fileresvpl[FILENAMELENGTH];
94:
95: #define NR_END 1
96: #define FREE_ARG char*
97: #define FTOL 1.0e-10
98:
99: #define NRANSI
100: #define ITMAX 200
101:
102: #define TOL 2.0e-4
103:
104: #define CGOLD 0.3819660
105: #define ZEPS 1.0e-10
106: #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);
107:
108: #define GOLD 1.618034
109: #define GLIMIT 100.0
110: #define TINY 1.0e-20
111:
112: static double maxarg1,maxarg2;
113: #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
114: #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
115:
116: #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
117: #define rint(a) floor(a+0.5)
118:
119: static double sqrarg;
120: #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
121: #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}
122:
123: int imx;
124: int stepm;
125: /* Stepm, step in month: minimum step interpolation*/
126:
127: int m,nb;
1.6 lievre 128: int *num, firstpass=0, lastpass=4,*cod, *ncodemax, *Tage;
1.2 lievre 129: double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
130: double **pmmij;
131:
132: double *weight;
133: int **s; /* Status */
134: double *agedc, **covar, idx;
1.7 lievre 135: int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;
1.2 lievre 136:
137: double ftol=FTOL; /* Tolerance for computing Max Likelihood */
138: double ftolhess; /* Tolerance for computing hessian */
139:
1.7 lievre 140: /**************** split *************************/
1.5 lievre 141: static int split( char *path, char *dirc, char *name )
142: {
143: char *s; /* pointer */
144: int l1, l2; /* length counters */
145:
146: l1 = strlen( path ); /* length of path */
147: if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
148: s = strrchr( path, '\\' ); /* find last / */
149: if ( s == NULL ) { /* no directory, so use current */
150: #if defined(__bsd__) /* get current working directory */
151: extern char *getwd( );
152:
153: if ( getwd( dirc ) == NULL ) {
154: #else
155: extern char *getcwd( );
156:
157: if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {
158: #endif
159: return( GLOCK_ERROR_GETCWD );
160: }
161: strcpy( name, path ); /* we've got it */
162: } else { /* strip direcotry from path */
163: s++; /* after this, the filename */
164: l2 = strlen( s ); /* length of filename */
165: if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
166: strcpy( name, s ); /* save file name */
167: strncpy( dirc, path, l1 - l2 ); /* now the directory */
168: dirc[l1-l2] = 0; /* add zero */
169: }
170: l1 = strlen( dirc ); /* length of directory */
171: if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; }
172: return( 0 ); /* we're done */
173: }
174:
175:
1.2 lievre 176: /******************************************/
177:
178: void replace(char *s, char*t)
179: {
180: int i;
181: int lg=20;
182: i=0;
183: lg=strlen(t);
184: for(i=0; i<= lg; i++) {
185: (s[i] = t[i]);
186: if (t[i]== '\\') s[i]='/';
187: }
188: }
189:
190: int nbocc(char *s, char occ)
191: {
192: int i,j=0;
193: int lg=20;
194: i=0;
195: lg=strlen(s);
196: for(i=0; i<= lg; i++) {
197: if (s[i] == occ ) j++;
198: }
199: return j;
200: }
201:
202: void cutv(char *u,char *v, char*t, char occ)
203: {
1.6 lievre 204: int i,lg,j,p=0;
1.2 lievre 205: i=0;
206: for(j=0; j<=strlen(t)-1; j++) {
1.3 lievre 207: if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;
1.2 lievre 208: }
209:
210: lg=strlen(t);
211: for(j=0; j<p; j++) {
212: (u[j] = t[j]);
213: }
1.6 lievre 214: u[p]='\0';
1.2 lievre 215:
216: for(j=0; j<= lg; j++) {
217: if (j>=(p+1))(v[j-p-1] = t[j]);
218: }
219: }
220:
221: /********************** nrerror ********************/
222:
223: void nrerror(char error_text[])
224: {
225: fprintf(stderr,"ERREUR ...\n");
226: fprintf(stderr,"%s\n",error_text);
227: exit(1);
228: }
229: /*********************** vector *******************/
230: double *vector(int nl, int nh)
231: {
232: double *v;
233: v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
234: if (!v) nrerror("allocation failure in vector");
235: return v-nl+NR_END;
236: }
237:
238: /************************ free vector ******************/
239: void free_vector(double*v, int nl, int nh)
240: {
241: free((FREE_ARG)(v+nl-NR_END));
242: }
243:
244: /************************ivector *******************************/
245: int *ivector(long nl,long nh)
246: {
247: int *v;
248: v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
249: if (!v) nrerror("allocation failure in ivector");
250: return v-nl+NR_END;
251: }
252:
253: /******************free ivector **************************/
254: void free_ivector(int *v, long nl, long nh)
255: {
256: free((FREE_ARG)(v+nl-NR_END));
257: }
258:
259: /******************* imatrix *******************************/
260: int **imatrix(long nrl, long nrh, long ncl, long nch)
261: /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */
262: {
263: long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;
264: int **m;
265:
266: /* allocate pointers to rows */
267: m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));
268: if (!m) nrerror("allocation failure 1 in matrix()");
269: m += NR_END;
270: m -= nrl;
271:
272:
273: /* allocate rows and set pointers to them */
274: m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));
275: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
276: m[nrl] += NR_END;
277: m[nrl] -= ncl;
278:
279: for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;
280:
281: /* return pointer to array of pointers to rows */
282: return m;
283: }
284:
285: /****************** free_imatrix *************************/
286: void free_imatrix(m,nrl,nrh,ncl,nch)
287: int **m;
288: long nch,ncl,nrh,nrl;
289: /* free an int matrix allocated by imatrix() */
290: {
291: free((FREE_ARG) (m[nrl]+ncl-NR_END));
292: free((FREE_ARG) (m+nrl-NR_END));
293: }
294:
295: /******************* matrix *******************************/
296: double **matrix(long nrl, long nrh, long ncl, long nch)
297: {
298: long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
299: double **m;
300:
301: m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
302: if (!m) nrerror("allocation failure 1 in matrix()");
303: m += NR_END;
304: m -= nrl;
305:
306: m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
307: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
308: m[nrl] += NR_END;
309: m[nrl] -= ncl;
310:
311: for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
312: return m;
313: }
314:
315: /*************************free matrix ************************/
316: void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
317: {
318: free((FREE_ARG)(m[nrl]+ncl-NR_END));
319: free((FREE_ARG)(m+nrl-NR_END));
320: }
321:
322: /******************* ma3x *******************************/
323: double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
324: {
325: long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
326: double ***m;
327:
328: m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
329: if (!m) nrerror("allocation failure 1 in matrix()");
330: m += NR_END;
331: m -= nrl;
332:
333: m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
334: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
335: m[nrl] += NR_END;
336: m[nrl] -= ncl;
337:
338: for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
339:
340: m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
341: if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
342: m[nrl][ncl] += NR_END;
343: m[nrl][ncl] -= nll;
344: for (j=ncl+1; j<=nch; j++)
345: m[nrl][j]=m[nrl][j-1]+nlay;
346:
347: for (i=nrl+1; i<=nrh; i++) {
348: m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
349: for (j=ncl+1; j<=nch; j++)
350: m[i][j]=m[i][j-1]+nlay;
351: }
352: return m;
353: }
354:
355: /*************************free ma3x ************************/
356: void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
357: {
358: free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
359: free((FREE_ARG)(m[nrl]+ncl-NR_END));
360: free((FREE_ARG)(m+nrl-NR_END));
361: }
362:
363: /***************** f1dim *************************/
364: extern int ncom;
365: extern double *pcom,*xicom;
366: extern double (*nrfunc)(double []);
367:
368: double f1dim(double x)
369: {
370: int j;
371: double f;
372: double *xt;
373:
374: xt=vector(1,ncom);
375: for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];
376: f=(*nrfunc)(xt);
377: free_vector(xt,1,ncom);
378: return f;
379: }
380:
381: /*****************brent *************************/
382: double brent(double ax, double bx, double cx, double (*f)(double), double tol, double *xmin)
383: {
384: int iter;
385: double a,b,d,etemp;
386: double fu,fv,fw,fx;
387: double ftemp;
388: double p,q,r,tol1,tol2,u,v,w,x,xm;
389: double e=0.0;
390:
391: a=(ax < cx ? ax : cx);
392: b=(ax > cx ? ax : cx);
393: x=w=v=bx;
394: fw=fv=fx=(*f)(x);
395: for (iter=1;iter<=ITMAX;iter++) {
396: xm=0.5*(a+b);
397: tol2=2.0*(tol1=tol*fabs(x)+ZEPS);
398: /* if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
399: printf(".");fflush(stdout);
400: #ifdef DEBUG
401: printf("br %d,x=%.10e xm=%.10e b=%.10e a=%.10e tol=%.10e tol1=%.10e tol2=%.10e x-xm=%.10e fx=%.12e fu=%.12e,fw=%.12e,ftemp=%.12e,ftol=%.12e\n",iter,x,xm,b,a,tol,tol1,tol2,(x-xm),fx,fu,fw,ftemp,ftol);
402: /* if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
403: #endif
404: if (fabs(x-xm) <= (tol2-0.5*(b-a))){
405: *xmin=x;
406: return fx;
407: }
408: ftemp=fu;
409: if (fabs(e) > tol1) {
410: r=(x-w)*(fx-fv);
411: q=(x-v)*(fx-fw);
412: p=(x-v)*q-(x-w)*r;
413: q=2.0*(q-r);
414: if (q > 0.0) p = -p;
415: q=fabs(q);
416: etemp=e;
417: e=d;
418: if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))
419: d=CGOLD*(e=(x >= xm ? a-x : b-x));
420: else {
421: d=p/q;
422: u=x+d;
423: if (u-a < tol2 || b-u < tol2)
424: d=SIGN(tol1,xm-x);
425: }
426: } else {
427: d=CGOLD*(e=(x >= xm ? a-x : b-x));
428: }
429: u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));
430: fu=(*f)(u);
431: if (fu <= fx) {
432: if (u >= x) a=x; else b=x;
433: SHFT(v,w,x,u)
434: SHFT(fv,fw,fx,fu)
435: } else {
436: if (u < x) a=u; else b=u;
437: if (fu <= fw || w == x) {
438: v=w;
439: w=u;
440: fv=fw;
441: fw=fu;
442: } else if (fu <= fv || v == x || v == w) {
443: v=u;
444: fv=fu;
445: }
446: }
447: }
448: nrerror("Too many iterations in brent");
449: *xmin=x;
450: return fx;
451: }
452:
453: /****************** mnbrak ***********************/
454:
455: void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,
456: double (*func)(double))
457: {
458: double ulim,u,r,q, dum;
459: double fu;
460:
461: *fa=(*func)(*ax);
462: *fb=(*func)(*bx);
463: if (*fb > *fa) {
464: SHFT(dum,*ax,*bx,dum)
465: SHFT(dum,*fb,*fa,dum)
466: }
467: *cx=(*bx)+GOLD*(*bx-*ax);
468: *fc=(*func)(*cx);
469: while (*fb > *fc) {
470: r=(*bx-*ax)*(*fb-*fc);
471: q=(*bx-*cx)*(*fb-*fa);
472: u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/
473: (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r));
474: ulim=(*bx)+GLIMIT*(*cx-*bx);
475: if ((*bx-u)*(u-*cx) > 0.0) {
476: fu=(*func)(u);
477: } else if ((*cx-u)*(u-ulim) > 0.0) {
478: fu=(*func)(u);
479: if (fu < *fc) {
480: SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))
481: SHFT(*fb,*fc,fu,(*func)(u))
482: }
483: } else if ((u-ulim)*(ulim-*cx) >= 0.0) {
484: u=ulim;
485: fu=(*func)(u);
486: } else {
487: u=(*cx)+GOLD*(*cx-*bx);
488: fu=(*func)(u);
489: }
490: SHFT(*ax,*bx,*cx,u)
491: SHFT(*fa,*fb,*fc,fu)
492: }
493: }
494:
495: /*************** linmin ************************/
496:
497: int ncom;
498: double *pcom,*xicom;
499: double (*nrfunc)(double []);
500:
501: void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))
502: {
503: double brent(double ax, double bx, double cx,
504: double (*f)(double), double tol, double *xmin);
505: double f1dim(double x);
506: void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,
507: double *fc, double (*func)(double));
508: int j;
509: double xx,xmin,bx,ax;
510: double fx,fb,fa;
511:
512: ncom=n;
513: pcom=vector(1,n);
514: xicom=vector(1,n);
515: nrfunc=func;
516: for (j=1;j<=n;j++) {
517: pcom[j]=p[j];
518: xicom[j]=xi[j];
519: }
520: ax=0.0;
521: xx=1.0;
522: mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim);
523: *fret=brent(ax,xx,bx,f1dim,TOL,&xmin);
524: #ifdef DEBUG
525: printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
526: #endif
527: for (j=1;j<=n;j++) {
528: xi[j] *= xmin;
529: p[j] += xi[j];
530: }
531: free_vector(xicom,1,n);
532: free_vector(pcom,1,n);
533: }
534:
535: /*************** powell ************************/
536: void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,
537: double (*func)(double []))
538: {
539: void linmin(double p[], double xi[], int n, double *fret,
540: double (*func)(double []));
541: int i,ibig,j;
542: double del,t,*pt,*ptt,*xit;
543: double fp,fptt;
544: double *xits;
545: pt=vector(1,n);
546: ptt=vector(1,n);
547: xit=vector(1,n);
548: xits=vector(1,n);
549: *fret=(*func)(p);
550: for (j=1;j<=n;j++) pt[j]=p[j];
551: for (*iter=1;;++(*iter)) {
552: fp=(*fret);
553: ibig=0;
554: del=0.0;
555: printf("\nPowell iter=%d -2*LL=%.12f",*iter,*fret);
556: for (i=1;i<=n;i++)
557: printf(" %d %.12f",i, p[i]);
558: printf("\n");
559: for (i=1;i<=n;i++) {
560: for (j=1;j<=n;j++) xit[j]=xi[j][i];
561: fptt=(*fret);
562: #ifdef DEBUG
563: printf("fret=%lf \n",*fret);
564: #endif
565: printf("%d",i);fflush(stdout);
566: linmin(p,xit,n,fret,func);
567: if (fabs(fptt-(*fret)) > del) {
568: del=fabs(fptt-(*fret));
569: ibig=i;
570: }
571: #ifdef DEBUG
572: printf("%d %.12e",i,(*fret));
573: for (j=1;j<=n;j++) {
574: xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
575: printf(" x(%d)=%.12e",j,xit[j]);
576: }
577: for(j=1;j<=n;j++)
578: printf(" p=%.12e",p[j]);
579: printf("\n");
580: #endif
581: }
582: if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {
583: #ifdef DEBUG
584: int k[2],l;
585: k[0]=1;
586: k[1]=-1;
587: printf("Max: %.12e",(*func)(p));
588: for (j=1;j<=n;j++)
589: printf(" %.12e",p[j]);
590: printf("\n");
591: for(l=0;l<=1;l++) {
592: for (j=1;j<=n;j++) {
593: ptt[j]=p[j]+(p[j]-pt[j])*k[l];
594: printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
595: }
596: printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
597: }
598: #endif
599:
600:
601: free_vector(xit,1,n);
602: free_vector(xits,1,n);
603: free_vector(ptt,1,n);
604: free_vector(pt,1,n);
605: return;
606: }
607: if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");
608: for (j=1;j<=n;j++) {
609: ptt[j]=2.0*p[j]-pt[j];
610: xit[j]=p[j]-pt[j];
611: pt[j]=p[j];
612: }
613: fptt=(*func)(ptt);
614: if (fptt < fp) {
615: t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt);
616: if (t < 0.0) {
617: linmin(p,xit,n,fret,func);
618: for (j=1;j<=n;j++) {
619: xi[j][ibig]=xi[j][n];
620: xi[j][n]=xit[j];
621: }
622: #ifdef DEBUG
623: printf("Direction changed last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
624: for(j=1;j<=n;j++)
625: printf(" %.12e",xit[j]);
626: printf("\n");
627: #endif
628: }
629: }
630: }
631: }
632:
633: /**** Prevalence limit ****************/
634:
635: double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)
636: {
637: /* Computes the prevalence limit in each live state at age x by left multiplying the unit
638: matrix by transitions matrix until convergence is reached */
639:
640: int i, ii,j,k;
641: double min, max, maxmin, maxmax,sumnew=0.;
642: double **matprod2();
643: double **out, cov[NCOVMAX], **pmij();
644: double **newm;
645: double agefin, delaymax=50 ; /* Max number of years to converge */
646:
647: for (ii=1;ii<=nlstate+ndeath;ii++)
648: for (j=1;j<=nlstate+ndeath;j++){
649: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
650: }
1.6 lievre 651:
652: cov[1]=1.;
653:
654: /* Even if hstepm = 1, at least one multiplication by the unit matrix */
1.2 lievre 655: for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
656: newm=savm;
657: /* Covariates have to be included here again */
1.6 lievre 658: cov[2]=agefin;
659:
660: for (k=1; k<=cptcovn;k++) {
1.7 lievre 661: cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
662: /*printf("ij=%d Tvar[k]=%d nbcode=%d cov=%lf\n",ij, Tvar[k],nbcode[Tvar[k]][codtab[ij][Tvar[k]]],cov[2+k]);*/
1.6 lievre 663: }
664: for (k=1; k<=cptcovage;k++)
665: cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
1.7 lievre 666: for (k=1; k<=cptcovprod;k++)
667: cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
668:
669: /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
670: /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
671:
1.2 lievre 672: out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);
673:
674: savm=oldm;
675: oldm=newm;
676: maxmax=0.;
677: for(j=1;j<=nlstate;j++){
678: min=1.;
679: max=0.;
680: for(i=1; i<=nlstate; i++) {
681: sumnew=0;
682: for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
683: prlim[i][j]= newm[i][j]/(1-sumnew);
684: max=FMAX(max,prlim[i][j]);
685: min=FMIN(min,prlim[i][j]);
686: }
687: maxmin=max-min;
688: maxmax=FMAX(maxmax,maxmin);
689: }
690: if(maxmax < ftolpl){
691: return prlim;
692: }
693: }
694: }
695:
696: /*************** transition probabilities **********/
697:
698: double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
699: {
700: double s1, s2;
701: /*double t34;*/
702: int i,j,j1, nc, ii, jj;
703:
704: for(i=1; i<= nlstate; i++){
705: for(j=1; j<i;j++){
706: for (nc=1, s2=0.;nc <=ncovmodel; nc++){
707: /*s2 += param[i][j][nc]*cov[nc];*/
708: s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
709: /*printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2);*/
710: }
711: ps[i][j]=s2;
712: /*printf("s1=%.17e, s2=%.17e\n",s1,s2);*/
713: }
714: for(j=i+1; j<=nlstate+ndeath;j++){
715: for (nc=1, s2=0.;nc <=ncovmodel; nc++){
716: s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
717: /*printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2);*/
718: }
719: ps[i][j]=s2;
720: }
721: }
722: for(i=1; i<= nlstate; i++){
723: s1=0;
724: for(j=1; j<i; j++)
725: s1+=exp(ps[i][j]);
726: for(j=i+1; j<=nlstate+ndeath; j++)
727: s1+=exp(ps[i][j]);
728: ps[i][i]=1./(s1+1.);
729: for(j=1; j<i; j++)
730: ps[i][j]= exp(ps[i][j])*ps[i][i];
731: for(j=i+1; j<=nlstate+ndeath; j++)
732: ps[i][j]= exp(ps[i][j])*ps[i][i];
733: /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
734: } /* end i */
735:
736: for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
737: for(jj=1; jj<= nlstate+ndeath; jj++){
738: ps[ii][jj]=0;
739: ps[ii][ii]=1;
740: }
741: }
742:
743: /* for(ii=1; ii<= nlstate+ndeath; ii++){
744: for(jj=1; jj<= nlstate+ndeath; jj++){
745: printf("%lf ",ps[ii][jj]);
746: }
747: printf("\n ");
748: }
749: printf("\n ");printf("%lf ",cov[2]);*/
750: /*
751: for(i=1; i<= npar; i++) printf("%f ",x[i]);
752: goto end;*/
753: return ps;
754: }
755:
756: /**************** Product of 2 matrices ******************/
757:
758: double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)
759: {
760: /* Computes the matric product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
761: b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
762: /* in, b, out are matrice of pointers which should have been initialized
763: before: only the contents of out is modified. The function returns
764: a pointer to pointers identical to out */
765: long i, j, k;
766: for(i=nrl; i<= nrh; i++)
767: for(k=ncolol; k<=ncoloh; k++)
768: for(j=ncl,out[i][k]=0.; j<=nch; j++)
769: out[i][k] +=in[i][j]*b[j][k];
770:
771: return out;
772: }
773:
774:
775: /************* Higher Matrix Product ***************/
776:
777: double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
778: {
779: /* Computes the transition matrix starting at age 'age' over 'nhstepm*hstepm*stepm' month
780: duration (i.e. until
781: age (in years) age+nhstepm*stepm/12) by multiplying nhstepm*hstepm matrices.
782: Output is stored in matrix po[i][j][h] for h every 'hstepm' step
783: (typically every 2 years instead of every month which is too big).
784: Model is determined by parameters x and covariates have to be
785: included manually here.
786:
787: */
788:
789: int i, j, d, h, k;
790: double **out, cov[NCOVMAX];
791: double **newm;
792:
793: /* Hstepm could be zero and should return the unit matrix */
794: for (i=1;i<=nlstate+ndeath;i++)
795: for (j=1;j<=nlstate+ndeath;j++){
796: oldm[i][j]=(i==j ? 1.0 : 0.0);
797: po[i][j][0]=(i==j ? 1.0 : 0.0);
798: }
799: /* Even if hstepm = 1, at least one multiplication by the unit matrix */
800: for(h=1; h <=nhstepm; h++){
801: for(d=1; d <=hstepm; d++){
802: newm=savm;
803: /* Covariates have to be included here again */
804: cov[1]=1.;
805: cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
1.7 lievre 806: for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
807: for (k=1; k<=cptcovage;k++)
808: cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
809: for (k=1; k<=cptcovprod;k++)
810: cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
811:
812:
1.2 lievre 813: /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
814: /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
815: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,
816: pmij(pmmij,cov,ncovmodel,x,nlstate));
817: savm=oldm;
818: oldm=newm;
819: }
820: for(i=1; i<=nlstate+ndeath; i++)
821: for(j=1;j<=nlstate+ndeath;j++) {
822: po[i][j][h]=newm[i][j];
823: /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);
824: */
825: }
826: } /* end h */
827: return po;
828: }
829:
830:
831: /*************** log-likelihood *************/
832: double func( double *x)
833: {
1.6 lievre 834: int i, ii, j, k, mi, d, kk;
1.2 lievre 835: double l, ll[NLSTATEMAX], cov[NCOVMAX];
836: double **out;
837: double sw; /* Sum of weights */
838: double lli; /* Individual log likelihood */
839: long ipmx;
840: /*extern weight */
841: /* We are differentiating ll according to initial status */
842: /* for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
843: /*for(i=1;i<imx;i++)
1.8 lievre 844: printf(" %d\n",s[4][i]);
1.2 lievre 845: */
1.6 lievre 846: cov[1]=1.;
1.2 lievre 847:
848: for(k=1; k<=nlstate; k++) ll[k]=0.;
849: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1.6 lievre 850: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
1.8 lievre 851: for(mi=1; mi<= wav[i]-1; mi++){
1.2 lievre 852: for (ii=1;ii<=nlstate+ndeath;ii++)
853: for (j=1;j<=nlstate+ndeath;j++) oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1.8 lievre 854: for(d=0; d<dh[mi][i]; d++){
855: newm=savm;
856: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
857: for (kk=1; kk<=cptcovage;kk++) {
858: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
859: }
860:
861: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
862: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
863: savm=oldm;
864: oldm=newm;
865:
866:
1.2 lievre 867: } /* end mult */
1.8 lievre 868:
1.2 lievre 869: lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);
870: /* printf(" %f ",out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/
871: ipmx +=1;
872: sw += weight[i];
873: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
874: } /* end of wave */
875: } /* end of individual */
876:
877: for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
878: /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
879: l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
880: return -l;
881: }
882:
883:
884: /*********** Maximum Likelihood Estimation ***************/
885:
886: void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
887: {
888: int i,j, iter;
889: double **xi,*delti;
890: double fret;
891: xi=matrix(1,npar,1,npar);
892: for (i=1;i<=npar;i++)
893: for (j=1;j<=npar;j++)
894: xi[i][j]=(i==j ? 1.0 : 0.0);
895: printf("Powell\n");
896: powell(p,xi,npar,ftol,&iter,&fret,func);
897:
898: printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));
899: fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f ",iter,func(p));
900:
901: }
902:
903: /**** Computes Hessian and covariance matrix ***/
904: void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
905: {
906: double **a,**y,*x,pd;
907: double **hess;
908: int i, j,jk;
909: int *indx;
910:
911: double hessii(double p[], double delta, int theta, double delti[]);
912: double hessij(double p[], double delti[], int i, int j);
913: void lubksb(double **a, int npar, int *indx, double b[]) ;
914: void ludcmp(double **a, int npar, int *indx, double *d) ;
915:
916:
917: hess=matrix(1,npar,1,npar);
918:
919: printf("\nCalculation of the hessian matrix. Wait...\n");
920: for (i=1;i<=npar;i++){
921: printf("%d",i);fflush(stdout);
922: hess[i][i]=hessii(p,ftolhess,i,delti);
923: /*printf(" %f ",p[i]);*/
924: }
925:
926: for (i=1;i<=npar;i++) {
927: for (j=1;j<=npar;j++) {
928: if (j>i) {
929: printf(".%d%d",i,j);fflush(stdout);
930: hess[i][j]=hessij(p,delti,i,j);
931: hess[j][i]=hess[i][j];
932: }
933: }
934: }
935: printf("\n");
936:
937: printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
938:
939: a=matrix(1,npar,1,npar);
940: y=matrix(1,npar,1,npar);
941: x=vector(1,npar);
942: indx=ivector(1,npar);
943: for (i=1;i<=npar;i++)
944: for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
945: ludcmp(a,npar,indx,&pd);
946:
947: for (j=1;j<=npar;j++) {
948: for (i=1;i<=npar;i++) x[i]=0;
949: x[j]=1;
950: lubksb(a,npar,indx,x);
951: for (i=1;i<=npar;i++){
952: matcov[i][j]=x[i];
953: }
954: }
955:
956: printf("\n#Hessian matrix#\n");
957: for (i=1;i<=npar;i++) {
958: for (j=1;j<=npar;j++) {
959: printf("%.3e ",hess[i][j]);
960: }
961: printf("\n");
962: }
963:
964: /* Recompute Inverse */
965: for (i=1;i<=npar;i++)
966: for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];
967: ludcmp(a,npar,indx,&pd);
968:
969: /* printf("\n#Hessian matrix recomputed#\n");
970:
971: for (j=1;j<=npar;j++) {
972: for (i=1;i<=npar;i++) x[i]=0;
973: x[j]=1;
974: lubksb(a,npar,indx,x);
975: for (i=1;i<=npar;i++){
976: y[i][j]=x[i];
977: printf("%.3e ",y[i][j]);
978: }
979: printf("\n");
980: }
981: */
982:
983: free_matrix(a,1,npar,1,npar);
984: free_matrix(y,1,npar,1,npar);
985: free_vector(x,1,npar);
986: free_ivector(indx,1,npar);
987: free_matrix(hess,1,npar,1,npar);
988:
989:
990: }
991:
992: /*************** hessian matrix ****************/
993: double hessii( double x[], double delta, int theta, double delti[])
994: {
995: int i;
996: int l=1, lmax=20;
997: double k1,k2;
998: double p2[NPARMAX+1];
999: double res;
1000: double delt, delts, nkhi=10.,nkhif=1., khi=1.e-4;
1001: double fx;
1002: int k=0,kmax=10;
1003: double l1;
1004:
1005: fx=func(x);
1006: for (i=1;i<=npar;i++) p2[i]=x[i];
1007: for(l=0 ; l <=lmax; l++){
1008: l1=pow(10,l);
1009: delts=delt;
1010: for(k=1 ; k <kmax; k=k+1){
1011: delt = delta*(l1*k);
1012: p2[theta]=x[theta] +delt;
1013: k1=func(p2)-fx;
1014: p2[theta]=x[theta]-delt;
1015: k2=func(p2)-fx;
1016: /*res= (k1-2.0*fx+k2)/delt/delt; */
1017: res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */
1018:
1019: #ifdef DEBUG
1020: 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);
1021: #endif
1022: /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
1023: if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
1024: k=kmax;
1025: }
1026: else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
1027: k=kmax; l=lmax*10.;
1028: }
1029: else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){
1030: delts=delt;
1031: }
1032: }
1033: }
1034: delti[theta]=delts;
1.3 lievre 1035: return res;
1036:
1.2 lievre 1037: }
1038:
1039: double hessij( double x[], double delti[], int thetai,int thetaj)
1040: {
1041: int i;
1042: int l=1, l1, lmax=20;
1043: double k1,k2,k3,k4,res,fx;
1044: double p2[NPARMAX+1];
1045: int k;
1046:
1047: fx=func(x);
1048: for (k=1; k<=2; k++) {
1049: for (i=1;i<=npar;i++) p2[i]=x[i];
1050: p2[thetai]=x[thetai]+delti[thetai]/k;
1051: p2[thetaj]=x[thetaj]+delti[thetaj]/k;
1052: k1=func(p2)-fx;
1053:
1054: p2[thetai]=x[thetai]+delti[thetai]/k;
1055: p2[thetaj]=x[thetaj]-delti[thetaj]/k;
1056: k2=func(p2)-fx;
1057:
1058: p2[thetai]=x[thetai]-delti[thetai]/k;
1059: p2[thetaj]=x[thetaj]+delti[thetaj]/k;
1060: k3=func(p2)-fx;
1061:
1062: p2[thetai]=x[thetai]-delti[thetai]/k;
1063: p2[thetaj]=x[thetaj]-delti[thetaj]/k;
1064: k4=func(p2)-fx;
1065: res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */
1066: #ifdef DEBUG
1067: 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);
1068: #endif
1069: }
1070: return res;
1071: }
1072:
1073: /************** Inverse of matrix **************/
1074: void ludcmp(double **a, int n, int *indx, double *d)
1075: {
1076: int i,imax,j,k;
1077: double big,dum,sum,temp;
1078: double *vv;
1079:
1080: vv=vector(1,n);
1081: *d=1.0;
1082: for (i=1;i<=n;i++) {
1083: big=0.0;
1084: for (j=1;j<=n;j++)
1085: if ((temp=fabs(a[i][j])) > big) big=temp;
1086: if (big == 0.0) nrerror("Singular matrix in routine ludcmp");
1087: vv[i]=1.0/big;
1088: }
1089: for (j=1;j<=n;j++) {
1090: for (i=1;i<j;i++) {
1091: sum=a[i][j];
1092: for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];
1093: a[i][j]=sum;
1094: }
1095: big=0.0;
1096: for (i=j;i<=n;i++) {
1097: sum=a[i][j];
1098: for (k=1;k<j;k++)
1099: sum -= a[i][k]*a[k][j];
1100: a[i][j]=sum;
1101: if ( (dum=vv[i]*fabs(sum)) >= big) {
1102: big=dum;
1103: imax=i;
1104: }
1105: }
1106: if (j != imax) {
1107: for (k=1;k<=n;k++) {
1108: dum=a[imax][k];
1109: a[imax][k]=a[j][k];
1110: a[j][k]=dum;
1111: }
1112: *d = -(*d);
1113: vv[imax]=vv[j];
1114: }
1115: indx[j]=imax;
1116: if (a[j][j] == 0.0) a[j][j]=TINY;
1117: if (j != n) {
1118: dum=1.0/(a[j][j]);
1119: for (i=j+1;i<=n;i++) a[i][j] *= dum;
1120: }
1121: }
1122: free_vector(vv,1,n); /* Doesn't work */
1123: ;
1124: }
1125:
1126: void lubksb(double **a, int n, int *indx, double b[])
1127: {
1128: int i,ii=0,ip,j;
1129: double sum;
1130:
1131: for (i=1;i<=n;i++) {
1132: ip=indx[i];
1133: sum=b[ip];
1134: b[ip]=b[i];
1135: if (ii)
1136: for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];
1137: else if (sum) ii=i;
1138: b[i]=sum;
1139: }
1140: for (i=n;i>=1;i--) {
1141: sum=b[i];
1142: for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];
1143: b[i]=sum/a[i][i];
1144: }
1145: }
1146:
1147: /************ Frequencies ********************/
1148: void freqsummary(char fileres[], int agemin, int agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax)
1149: { /* Some frequencies */
1150:
1151: int i, m, jk, k1, i1, j1, bool, z1,z2,j;
1152: double ***freq; /* Frequencies */
1153: double *pp;
1154: double pos;
1155: FILE *ficresp;
1156: char fileresp[FILENAMELENGTH];
1157:
1158: pp=vector(1,nlstate);
1159:
1160: strcpy(fileresp,"p");
1161: strcat(fileresp,fileres);
1162: if((ficresp=fopen(fileresp,"w"))==NULL) {
1163: printf("Problem with prevalence resultfile: %s\n", fileresp);
1164: exit(0);
1165: }
1166: freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);
1167: j1=0;
1168:
1.7 lievre 1169: j=cptcoveff;
1.2 lievre 1170: if (cptcovn<1) {j=1;ncodemax[1]=1;}
1171:
1172: for(k1=1; k1<=j;k1++){
1173: for(i1=1; i1<=ncodemax[k1];i1++){
1174: j1++;
1.8 lievre 1175: /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
1176: scanf("%d", i);*/
1.2 lievre 1177: for (i=-1; i<=nlstate+ndeath; i++)
1178: for (jk=-1; jk<=nlstate+ndeath; jk++)
1179: for(m=agemin; m <= agemax+3; m++)
1180: freq[i][jk][m]=0;
1181:
1182: for (i=1; i<=imx; i++) {
1183: bool=1;
1184: if (cptcovn>0) {
1.7 lievre 1185: for (z1=1; z1<=cptcoveff; z1++)
1.8 lievre 1186: if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])
1187: bool=0;
1.2 lievre 1188: }
1189: if (bool==1) {
1190: for(m=firstpass; m<=lastpass-1; m++){
1191: if(agev[m][i]==0) agev[m][i]=agemax+1;
1192: if(agev[m][i]==1) agev[m][i]=agemax+2;
1193: freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
1194: freq[s[m][i]][s[m+1][i]][(int) agemax+3] += weight[i];
1195: }
1196: }
1197: }
1198: if (cptcovn>0) {
1.7 lievre 1199: fprintf(ficresp, "\n#********** Variable ");
1200: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
1201: fprintf(ficresp, "**********\n#");
1.8 lievre 1202: }
1.2 lievre 1203: for(i=1; i<=nlstate;i++)
1204: fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
1205: fprintf(ficresp, "\n");
1206:
1207: for(i=(int)agemin; i <= (int)agemax+3; i++){
1208: if(i==(int)agemax+3)
1209: printf("Total");
1210: else
1211: printf("Age %d", i);
1212: for(jk=1; jk <=nlstate ; jk++){
1213: for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
1214: pp[jk] += freq[jk][m][i];
1215: }
1216: for(jk=1; jk <=nlstate ; jk++){
1217: for(m=-1, pos=0; m <=0 ; m++)
1218: pos += freq[jk][m][i];
1219: if(pp[jk]>=1.e-10)
1220: printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
1221: else
1222: printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
1223: }
1224: for(jk=1; jk <=nlstate ; jk++){
1225: for(m=1, pp[jk]=0; m <=nlstate+ndeath; m++)
1226: pp[jk] += freq[jk][m][i];
1227: }
1228: for(jk=1,pos=0; jk <=nlstate ; jk++)
1229: pos += pp[jk];
1230: for(jk=1; jk <=nlstate ; jk++){
1231: if(pos>=1.e-5)
1232: printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
1233: else
1234: printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
1235: if( i <= (int) agemax){
1236: if(pos>=1.e-5)
1237: fprintf(ficresp," %d %.5f %.0f %.0f",i,pp[jk]/pos, pp[jk],pos);
1238: else
1239: fprintf(ficresp," %d NaNq %.0f %.0f",i,pp[jk],pos);
1240: }
1241: }
1242: for(jk=-1; jk <=nlstate+ndeath; jk++)
1243: for(m=-1; m <=nlstate+ndeath; m++)
1244: if(freq[jk][m][i] !=0 ) printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
1245: if(i <= (int) agemax)
1246: fprintf(ficresp,"\n");
1247: printf("\n");
1248: }
1249: }
1250: }
1251:
1252: fclose(ficresp);
1253: free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);
1254: free_vector(pp,1,nlstate);
1255:
1256: } /* End of Freq */
1257:
1258: /************* Waves Concatenation ***************/
1259:
1260: void concatwav(int wav[], int **dh, int **mw, int **s, double *agedc, double **agev, int firstpass, int lastpass, int imx, int nlstate, int stepm)
1261: {
1262: /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
1263: Death is a valid wave (if date is known).
1264: mw[mi][i] is the mi (mi=1 to wav[i]) effective wave of individual i
1265: dh[m][i] of dh[mw[mi][i][i] is the delay between two effective waves m=mw[mi][i]
1266: and mw[mi+1][i]. dh depends on stepm.
1267: */
1268:
1269: int i, mi, m;
1.8 lievre 1270: /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
1271: double sum=0., jmean=0.;*/
1.2 lievre 1272:
1.8 lievre 1273: int j, k=0,jk, ju, jl;
1274: double sum=0.;
1275: jmin=1e+5;
1276: jmax=-1;
1277: jmean=0.;
1.2 lievre 1278: for(i=1; i<=imx; i++){
1279: mi=0;
1280: m=firstpass;
1281: while(s[m][i] <= nlstate){
1282: if(s[m][i]>=1)
1283: mw[++mi][i]=m;
1284: if(m >=lastpass)
1285: break;
1286: else
1287: m++;
1288: }/* end while */
1289: if (s[m][i] > nlstate){
1290: mi++; /* Death is another wave */
1291: /* if(mi==0) never been interviewed correctly before death */
1292: /* Only death is a correct wave */
1293: mw[mi][i]=m;
1294: }
1295:
1296: wav[i]=mi;
1297: if(mi==0)
1298: printf("Warning, no any valid information for:%d line=%d\n",num[i],i);
1299: }
1300:
1301: for(i=1; i<=imx; i++){
1302: for(mi=1; mi<wav[i];mi++){
1303: if (stepm <=0)
1304: dh[mi][i]=1;
1305: else{
1306: if (s[mw[mi+1][i]][i] > nlstate) {
1.10 ! lievre 1307: if (agedc[i] < 2*AGESUP) {
1.2 lievre 1308: j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);
1.8 lievre 1309: if(j==0) j=1; /* Survives at least one month after exam */
1310: k=k+1;
1311: if (j >= jmax) jmax=j;
1312: else if (j <= jmin)jmin=j;
1313: sum=sum+j;
1.10 ! lievre 1314: if (j<0) printf("j=%d num=%d ",j,i);
! 1315: }
1.2 lievre 1316: }
1317: else{
1318: j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
1319: k=k+1;
1320: if (j >= jmax) jmax=j;
1321: else if (j <= jmin)jmin=j;
1322: sum=sum+j;
1323: }
1324: jk= j/stepm;
1325: jl= j -jk*stepm;
1326: ju= j -(jk+1)*stepm;
1327: if(jl <= -ju)
1328: dh[mi][i]=jk;
1329: else
1330: dh[mi][i]=jk+1;
1331: if(dh[mi][i]==0)
1332: dh[mi][i]=1; /* At least one step */
1333: }
1334: }
1335: }
1.8 lievre 1336: jmean=sum/k;
1337: printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);
1.2 lievre 1338: }
1339: /*********** Tricode ****************************/
1340: void tricode(int *Tvar, int **nbcode, int imx)
1341: {
1.7 lievre 1342: int Ndum[20],ij=1, k, j, i;
1.2 lievre 1343: int cptcode=0;
1.7 lievre 1344: cptcoveff=0;
1345:
1346: for (k=0; k<19; k++) Ndum[k]=0;
1.2 lievre 1347: for (k=1; k<=7; k++) ncodemax[k]=0;
1.6 lievre 1348:
1.7 lievre 1349: for (j=1; j<=(cptcovn+2*cptcovprod); j++) {
1.2 lievre 1350: for (i=1; i<=imx; i++) {
1351: ij=(int)(covar[Tvar[j]][i]);
1352: Ndum[ij]++;
1.8 lievre 1353: /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
1.2 lievre 1354: if (ij > cptcode) cptcode=ij;
1355: }
1.7 lievre 1356:
1.2 lievre 1357: for (i=0; i<=cptcode; i++) {
1358: if(Ndum[i]!=0) ncodemax[j]++;
1359: }
1360: ij=1;
1.7 lievre 1361:
1.8 lievre 1362:
1.2 lievre 1363: for (i=1; i<=ncodemax[j]; i++) {
1.7 lievre 1364: for (k=0; k<=19; k++) {
1.2 lievre 1365: if (Ndum[k] != 0) {
1366: nbcode[Tvar[j]][ij]=k;
1367: ij++;
1368: }
1369: if (ij > ncodemax[j]) break;
1370: }
1371: }
1.7 lievre 1372: }
1.8 lievre 1373:
1374: for (k=0; k<19; k++) Ndum[k]=0;
1375:
1376: for (i=1; i<=ncovmodel; i++) {
1.7 lievre 1377: ij=Tvar[i];
1378: Ndum[ij]++;
1379: }
1.8 lievre 1380:
1.7 lievre 1381: ij=1;
1.8 lievre 1382: for (i=1; i<=10; i++) {
1.7 lievre 1383: if((Ndum[i]!=0) && (i<=ncov)){
1.8 lievre 1384: Tvaraff[ij]=i;
1385: ij++;
1.7 lievre 1386: }
1387: }
1388:
1.8 lievre 1389: cptcoveff=ij-1;
1.6 lievre 1390: }
1.2 lievre 1391:
1392: /*********** Health Expectancies ****************/
1393:
1394: void evsij(char fileres[], double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int ij)
1395: {
1396: /* Health expectancies */
1397: int i, j, nhstepm, hstepm, h;
1398: double age, agelim,hf;
1399: double ***p3mat;
1400:
1401: fprintf(ficreseij,"# Health expectancies\n");
1402: fprintf(ficreseij,"# Age");
1403: for(i=1; i<=nlstate;i++)
1404: for(j=1; j<=nlstate;j++)
1405: fprintf(ficreseij," %1d-%1d",i,j);
1406: fprintf(ficreseij,"\n");
1407:
1408: hstepm=1*YEARM; /* Every j years of age (in month) */
1409: hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */
1410:
1411: agelim=AGESUP;
1412: for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
1413: /* nhstepm age range expressed in number of stepm */
1414: nhstepm=(int) rint((agelim-age)*YEARM/stepm);
1415: /* Typically if 20 years = 20*12/6=40 stepm */
1416: if (stepm >= YEARM) hstepm=1;
1417: nhstepm = nhstepm/hstepm;/* Expressed in hstepm, typically 40/4=10 */
1418: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
1419: /* Computed by stepm unit matrices, product of hstepm matrices, stored
1420: in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
1421: hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);
1422:
1423:
1424: for(i=1; i<=nlstate;i++)
1425: for(j=1; j<=nlstate;j++)
1426: for (h=0, eij[i][j][(int)age]=0; h<=nhstepm; h++){
1427: eij[i][j][(int)age] +=p3mat[i][j][h];
1428: }
1429:
1430: hf=1;
1431: if (stepm >= YEARM) hf=stepm/YEARM;
1432: fprintf(ficreseij,"%.0f",age );
1433: for(i=1; i<=nlstate;i++)
1434: for(j=1; j<=nlstate;j++){
1435: fprintf(ficreseij," %.4f", hf*eij[i][j][(int)age]);
1436: }
1437: fprintf(ficreseij,"\n");
1438: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
1439: }
1440: }
1441:
1442: /************ Variance ******************/
1443: 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)
1444: {
1445: /* Variance of health expectancies */
1446: /* double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
1447: double **newm;
1448: double **dnewm,**doldm;
1449: int i, j, nhstepm, hstepm, h;
1450: int k, cptcode;
1451: double *xp;
1452: double **gp, **gm;
1453: double ***gradg, ***trgradg;
1454: double ***p3mat;
1455: double age,agelim;
1456: int theta;
1457:
1458: fprintf(ficresvij,"# Covariances of life expectancies\n");
1459: fprintf(ficresvij,"# Age");
1460: for(i=1; i<=nlstate;i++)
1461: for(j=1; j<=nlstate;j++)
1462: fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);
1463: fprintf(ficresvij,"\n");
1464:
1465: xp=vector(1,npar);
1466: dnewm=matrix(1,nlstate,1,npar);
1467: doldm=matrix(1,nlstate,1,nlstate);
1468:
1469: hstepm=1*YEARM; /* Every year of age */
1470: hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */
1471: agelim = AGESUP;
1472: for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
1473: nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
1474: if (stepm >= YEARM) hstepm=1;
1475: nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
1476: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
1477: gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
1478: gp=matrix(0,nhstepm,1,nlstate);
1479: gm=matrix(0,nhstepm,1,nlstate);
1480:
1481: for(theta=1; theta <=npar; theta++){
1482: for(i=1; i<=npar; i++){ /* Computes gradient */
1483: xp[i] = x[i] + (i==theta ?delti[theta]:0);
1484: }
1485: hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
1486: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
1487: for(j=1; j<= nlstate; j++){
1488: for(h=0; h<=nhstepm; h++){
1489: for(i=1, gp[h][j]=0.;i<=nlstate;i++)
1490: gp[h][j] += prlim[i][i]*p3mat[i][j][h];
1491: }
1492: }
1493:
1494: for(i=1; i<=npar; i++) /* Computes gradient */
1495: xp[i] = x[i] - (i==theta ?delti[theta]:0);
1496: hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
1497: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
1498: for(j=1; j<= nlstate; j++){
1499: for(h=0; h<=nhstepm; h++){
1500: for(i=1, gm[h][j]=0.;i<=nlstate;i++)
1501: gm[h][j] += prlim[i][i]*p3mat[i][j][h];
1502: }
1503: }
1504: for(j=1; j<= nlstate; j++)
1505: for(h=0; h<=nhstepm; h++){
1506: gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
1507: }
1508: } /* End theta */
1509:
1510: trgradg =ma3x(0,nhstepm,1,nlstate,1,npar);
1511:
1512: for(h=0; h<=nhstepm; h++)
1513: for(j=1; j<=nlstate;j++)
1514: for(theta=1; theta <=npar; theta++)
1515: trgradg[h][j][theta]=gradg[h][theta][j];
1516:
1517: for(i=1;i<=nlstate;i++)
1518: for(j=1;j<=nlstate;j++)
1519: vareij[i][j][(int)age] =0.;
1520: for(h=0;h<=nhstepm;h++){
1521: for(k=0;k<=nhstepm;k++){
1522: matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
1523: matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
1524: for(i=1;i<=nlstate;i++)
1525: for(j=1;j<=nlstate;j++)
1526: vareij[i][j][(int)age] += doldm[i][j];
1527: }
1528: }
1529: h=1;
1530: if (stepm >= YEARM) h=stepm/YEARM;
1531: fprintf(ficresvij,"%.0f ",age );
1532: for(i=1; i<=nlstate;i++)
1533: for(j=1; j<=nlstate;j++){
1534: fprintf(ficresvij," %.4f", h*vareij[i][j][(int)age]);
1535: }
1536: fprintf(ficresvij,"\n");
1537: free_matrix(gp,0,nhstepm,1,nlstate);
1538: free_matrix(gm,0,nhstepm,1,nlstate);
1539: free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
1540: free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
1541: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
1542: } /* End age */
1543:
1544: free_vector(xp,1,npar);
1545: free_matrix(doldm,1,nlstate,1,npar);
1546: free_matrix(dnewm,1,nlstate,1,nlstate);
1547:
1548: }
1549:
1550: /************ Variance of prevlim ******************/
1551: 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)
1552: {
1553: /* Variance of prevalence limit */
1554: /* double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
1555: double **newm;
1556: double **dnewm,**doldm;
1557: int i, j, nhstepm, hstepm;
1558: int k, cptcode;
1559: double *xp;
1560: double *gp, *gm;
1561: double **gradg, **trgradg;
1562: double age,agelim;
1563: int theta;
1564:
1565: fprintf(ficresvpl,"# Standard deviation of prevalences limit\n");
1566: fprintf(ficresvpl,"# Age");
1567: for(i=1; i<=nlstate;i++)
1568: fprintf(ficresvpl," %1d-%1d",i,i);
1569: fprintf(ficresvpl,"\n");
1570:
1571: xp=vector(1,npar);
1572: dnewm=matrix(1,nlstate,1,npar);
1573: doldm=matrix(1,nlstate,1,nlstate);
1574:
1575: hstepm=1*YEARM; /* Every year of age */
1576: hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */
1577: agelim = AGESUP;
1578: for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
1579: nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
1580: if (stepm >= YEARM) hstepm=1;
1581: nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
1582: gradg=matrix(1,npar,1,nlstate);
1583: gp=vector(1,nlstate);
1584: gm=vector(1,nlstate);
1585:
1586: for(theta=1; theta <=npar; theta++){
1587: for(i=1; i<=npar; i++){ /* Computes gradient */
1588: xp[i] = x[i] + (i==theta ?delti[theta]:0);
1589: }
1590: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
1591: for(i=1;i<=nlstate;i++)
1592: gp[i] = prlim[i][i];
1593:
1594: for(i=1; i<=npar; i++) /* Computes gradient */
1595: xp[i] = x[i] - (i==theta ?delti[theta]:0);
1596: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
1597: for(i=1;i<=nlstate;i++)
1598: gm[i] = prlim[i][i];
1599:
1600: for(i=1;i<=nlstate;i++)
1601: gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
1602: } /* End theta */
1603:
1604: trgradg =matrix(1,nlstate,1,npar);
1605:
1606: for(j=1; j<=nlstate;j++)
1607: for(theta=1; theta <=npar; theta++)
1608: trgradg[j][theta]=gradg[theta][j];
1609:
1610: for(i=1;i<=nlstate;i++)
1611: varpl[i][(int)age] =0.;
1612: matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
1613: matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
1614: for(i=1;i<=nlstate;i++)
1615: varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
1616:
1617: fprintf(ficresvpl,"%.0f ",age );
1618: for(i=1; i<=nlstate;i++)
1619: fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
1620: fprintf(ficresvpl,"\n");
1621: free_vector(gp,1,nlstate);
1622: free_vector(gm,1,nlstate);
1623: free_matrix(gradg,1,npar,1,nlstate);
1624: free_matrix(trgradg,1,nlstate,1,npar);
1625: } /* End age */
1626:
1627: free_vector(xp,1,npar);
1628: free_matrix(doldm,1,nlstate,1,npar);
1629: free_matrix(dnewm,1,nlstate,1,nlstate);
1630:
1631: }
1632:
1633:
1634:
1635: /***********************************************/
1636: /**************** Main Program *****************/
1637: /***********************************************/
1638:
1639: /*int main(int argc, char *argv[])*/
1640: int main()
1641: {
1642:
1.8 lievre 1643: int i,j, k, n=MAXN,iter,m,size,cptcode, cptcod;
1.2 lievre 1644: double agedeb, agefin,hf;
1645: double agemin=1.e20, agemax=-1.e20;
1646:
1647: double fret;
1648: double **xi,tmp,delta;
1649:
1650: double dum; /* Dummy variable */
1651: double ***p3mat;
1652: int *indx;
1653: char line[MAXLINE], linepar[MAXLINE];
1654: char title[MAXLINE];
1.9 lievre 1655: char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH], filerespl[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH];
1.2 lievre 1656: char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH];
1657: char filerest[FILENAMELENGTH];
1658: char fileregp[FILENAMELENGTH];
1659: char path[80],pathc[80],pathcd[80],pathtot[80],model[20];
1660: int firstobs=1, lastobs=10;
1661: int sdeb, sfin; /* Status at beginning and end */
1662: int c, h , cpt,l;
1663: int ju,jl, mi;
1.7 lievre 1664: int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;
1.2 lievre 1665: int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,**adl,*tab;
1666:
1667: int hstepm, nhstepm;
1668: double bage, fage, age, agelim, agebase;
1669: double ftolpl=FTOL;
1670: double **prlim;
1671: double *severity;
1672: double ***param; /* Matrix of parameters */
1673: double *p;
1674: double **matcov; /* Matrix of covariance */
1675: double ***delti3; /* Scale */
1676: double *delti; /* Scale */
1677: double ***eij, ***vareij;
1678: double **varpl; /* Variances of prevalence limits by age */
1679: double *epj, vepp;
1.10 ! lievre 1680: char version[80]="Imach version 64b, May 2001, INED-EUROREVES ";
1.2 lievre 1681: char *alph[]={"a","a","b","c","d","e"}, str[4];
1.5 lievre 1682:
1.2 lievre 1683: char z[1]="c", occ;
1684: #include <sys/time.h>
1685: #include <time.h>
1686: char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];
1687: /* long total_usecs;
1688: struct timeval start_time, end_time;
1689:
1690: gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */
1691:
1692:
1.9 lievre 1693: printf("\nIMACH, Version 0.64b");
1.2 lievre 1694: printf("\nEnter the parameter file name: ");
1695:
1696: #ifdef windows
1697: scanf("%s",pathtot);
1.5 lievre 1698: getcwd(pathcd, size);
1699: /*cygwin_split_path(pathtot,path,optionfile);
1700: printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/
1701: /* cutv(path,optionfile,pathtot,'\\');*/
1702:
1703: split(pathtot, path,optionfile);
1.2 lievre 1704: chdir(path);
1705: replace(pathc,path);
1706: #endif
1707: #ifdef unix
1708: scanf("%s",optionfile);
1709: #endif
1710:
1711: /*-------- arguments in the command line --------*/
1712:
1713: strcpy(fileres,"r");
1714: strcat(fileres, optionfile);
1715:
1716: /*---------arguments file --------*/
1717:
1718: if((ficpar=fopen(optionfile,"r"))==NULL) {
1719: printf("Problem with optionfile %s\n",optionfile);
1720: goto end;
1721: }
1722:
1723: strcpy(filereso,"o");
1724: strcat(filereso,fileres);
1725: if((ficparo=fopen(filereso,"w"))==NULL) {
1726: printf("Problem with Output resultfile: %s\n", filereso);goto end;
1727: }
1728:
1729: /* Reads comments: lines beginning with '#' */
1730: while((c=getc(ficpar))=='#' && c!= EOF){
1731: ungetc(c,ficpar);
1732: fgets(line, MAXLINE, ficpar);
1733: puts(line);
1734: fputs(line,ficparo);
1735: }
1736: ungetc(c,ficpar);
1737:
1738: 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);
1739: 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);
1740: 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);
1741:
1.8 lievre 1742: covar=matrix(0,NCOVMAX,1,n);
1743: cptcovn=0;
1744: if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;
1.2 lievre 1745:
1746: ncovmodel=2+cptcovn;
1747: nvar=ncovmodel-1; /* Suppressing age as a basic covariate */
1748:
1749: /* Read guess parameters */
1750: /* Reads comments: lines beginning with '#' */
1751: while((c=getc(ficpar))=='#' && c!= EOF){
1752: ungetc(c,ficpar);
1753: fgets(line, MAXLINE, ficpar);
1754: puts(line);
1755: fputs(line,ficparo);
1756: }
1757: ungetc(c,ficpar);
1758:
1759: param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
1760: for(i=1; i <=nlstate; i++)
1761: for(j=1; j <=nlstate+ndeath-1; j++){
1762: fscanf(ficpar,"%1d%1d",&i1,&j1);
1763: fprintf(ficparo,"%1d%1d",i1,j1);
1764: printf("%1d%1d",i,j);
1765: for(k=1; k<=ncovmodel;k++){
1766: fscanf(ficpar," %lf",¶m[i][j][k]);
1767: printf(" %lf",param[i][j][k]);
1768: fprintf(ficparo," %lf",param[i][j][k]);
1769: }
1770: fscanf(ficpar,"\n");
1771: printf("\n");
1772: fprintf(ficparo,"\n");
1773: }
1774:
1775: npar= (nlstate+ndeath-1)*nlstate*ncovmodel;
1776: p=param[1][1];
1777:
1778: /* Reads comments: lines beginning with '#' */
1779: while((c=getc(ficpar))=='#' && c!= EOF){
1780: ungetc(c,ficpar);
1781: fgets(line, MAXLINE, ficpar);
1782: puts(line);
1783: fputs(line,ficparo);
1784: }
1785: ungetc(c,ficpar);
1786:
1787: delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
1788: delti=vector(1,npar); /* Scale of each paramater (output from hesscov) */
1789: for(i=1; i <=nlstate; i++){
1790: for(j=1; j <=nlstate+ndeath-1; j++){
1791: fscanf(ficpar,"%1d%1d",&i1,&j1);
1792: printf("%1d%1d",i,j);
1793: fprintf(ficparo,"%1d%1d",i1,j1);
1794: for(k=1; k<=ncovmodel;k++){
1795: fscanf(ficpar,"%le",&delti3[i][j][k]);
1796: printf(" %le",delti3[i][j][k]);
1797: fprintf(ficparo," %le",delti3[i][j][k]);
1798: }
1799: fscanf(ficpar,"\n");
1800: printf("\n");
1801: fprintf(ficparo,"\n");
1802: }
1803: }
1804: delti=delti3[1][1];
1805:
1806: /* Reads comments: lines beginning with '#' */
1807: while((c=getc(ficpar))=='#' && c!= EOF){
1808: ungetc(c,ficpar);
1809: fgets(line, MAXLINE, ficpar);
1810: puts(line);
1811: fputs(line,ficparo);
1812: }
1813: ungetc(c,ficpar);
1814:
1815: matcov=matrix(1,npar,1,npar);
1816: for(i=1; i <=npar; i++){
1817: fscanf(ficpar,"%s",&str);
1818: printf("%s",str);
1819: fprintf(ficparo,"%s",str);
1820: for(j=1; j <=i; j++){
1821: fscanf(ficpar," %le",&matcov[i][j]);
1822: printf(" %.5le",matcov[i][j]);
1823: fprintf(ficparo," %.5le",matcov[i][j]);
1824: }
1825: fscanf(ficpar,"\n");
1826: printf("\n");
1827: fprintf(ficparo,"\n");
1828: }
1829: for(i=1; i <=npar; i++)
1830: for(j=i+1;j<=npar;j++)
1831: matcov[i][j]=matcov[j][i];
1832:
1833: printf("\n");
1834:
1835:
1836: /*-------- data file ----------*/
1837: if((ficres =fopen(fileres,"w"))==NULL) {
1838: printf("Problem with resultfile: %s\n", fileres);goto end;
1839: }
1840: fprintf(ficres,"#%s\n",version);
1841:
1842: if((fic=fopen(datafile,"r"))==NULL) {
1843: printf("Problem with datafile: %s\n", datafile);goto end;
1844: }
1845:
1846: n= lastobs;
1847: severity = vector(1,maxwav);
1848: outcome=imatrix(1,maxwav+1,1,n);
1849: num=ivector(1,n);
1850: moisnais=vector(1,n);
1851: annais=vector(1,n);
1852: moisdc=vector(1,n);
1853: andc=vector(1,n);
1854: agedc=vector(1,n);
1855: cod=ivector(1,n);
1856: weight=vector(1,n);
1857: for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */
1858: mint=matrix(1,maxwav,1,n);
1859: anint=matrix(1,maxwav,1,n);
1860: s=imatrix(1,maxwav+1,1,n);
1861: adl=imatrix(1,maxwav+1,1,n);
1862: tab=ivector(1,NCOVMAX);
1.3 lievre 1863: ncodemax=ivector(1,8);
1.2 lievre 1864:
1865: i=1;
1866: while (fgets(line, MAXLINE, fic) != NULL) {
1867: if ((i >= firstobs) && (i <=lastobs)) {
1868:
1869: for (j=maxwav;j>=1;j--){
1870: cutv(stra, strb,line,' '); s[j][i]=atoi(strb);
1871: strcpy(line,stra);
1872: cutv(stra, strb,line,'/'); anint[j][i]=(double)(atoi(strb)); strcpy(line,stra);
1873: cutv(stra, strb,line,' '); mint[j][i]=(double)(atoi(strb)); strcpy(line,stra);
1874: }
1875:
1876: cutv(stra, strb,line,'/'); andc[i]=(double)(atoi(strb)); strcpy(line,stra);
1877: cutv(stra, strb,line,' '); moisdc[i]=(double)(atoi(strb)); strcpy(line,stra);
1878:
1879: cutv(stra, strb,line,'/'); annais[i]=(double)(atoi(strb)); strcpy(line,stra);
1880: cutv(stra, strb,line,' '); moisnais[i]=(double)(atoi(strb)); strcpy(line,stra);
1881:
1882: cutv(stra, strb,line,' '); weight[i]=(double)(atoi(strb)); strcpy(line,stra);
1883: for (j=ncov;j>=1;j--){
1884: cutv(stra, strb,line,' '); covar[j][i]=(double)(atoi(strb)); strcpy(line,stra);
1885: }
1886: num[i]=atol(stra);
1887:
1.5 lievre 1888: /*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 1889:
1890: i=i+1;
1891: }
1892: }
1.3 lievre 1893:
1.2 lievre 1894: /*scanf("%d",i);*/
1.3 lievre 1895: imx=i-1; /* Number of individuals */
1.2 lievre 1896:
1897: /* Calculation of the number of parameter from char model*/
1.7 lievre 1898: Tvar=ivector(1,15);
1899: Tprod=ivector(1,15);
1900: Tvaraff=ivector(1,15);
1901: Tvard=imatrix(1,15,1,2);
1.6 lievre 1902: Tage=ivector(1,15);
1.2 lievre 1903:
1904: if (strlen(model) >1){
1.7 lievre 1905: j=0, j1=0, k1=1, k2=1;
1.2 lievre 1906: j=nbocc(model,'+');
1.6 lievre 1907: j1=nbocc(model,'*');
1.2 lievre 1908: cptcovn=j+1;
1.7 lievre 1909: cptcovprod=j1;
1.3 lievre 1910:
1.8 lievre 1911:
1.2 lievre 1912: strcpy(modelsav,model);
1.8 lievre 1913: if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){
1914: printf("Error. Non available option model=%s ",model);
1915: goto end;
1916: }
1917:
1918: for(i=(j+1); i>=1;i--){
1919: cutv(stra,strb,modelsav,'+');
1920: if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav);
1921: /* printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/
1922: /*scanf("%d",i);*/
1923: if (strchr(strb,'*')) {
1924: cutv(strd,strc,strb,'*');
1925: if (strcmp(strc,"age")==0) {
1.7 lievre 1926: cptcovprod--;
1.8 lievre 1927: cutv(strb,stre,strd,'V');
1928: Tvar[i]=atoi(stre);
1929: cptcovage++;
1930: Tage[cptcovage]=i;
1931: /*printf("stre=%s ", stre);*/
1.7 lievre 1932: }
1.8 lievre 1933: else if (strcmp(strd,"age")==0) {
1.7 lievre 1934: cptcovprod--;
1.8 lievre 1935: cutv(strb,stre,strc,'V');
1936: Tvar[i]=atoi(stre);
1937: cptcovage++;
1938: Tage[cptcovage]=i;
1.7 lievre 1939: }
1940: else {
1.8 lievre 1941: cutv(strb,stre,strc,'V');
1942: Tvar[i]=ncov+k1;
1943: cutv(strb,strc,strd,'V');
1944: Tprod[k1]=i;
1945: Tvard[k1][1]=atoi(strc);
1946: Tvard[k1][2]=atoi(stre);
1947: Tvar[cptcovn+k2]=Tvard[k1][1];
1948: Tvar[cptcovn+k2+1]=Tvard[k1][2];
1.7 lievre 1949: for (k=1; k<=lastobs;k++)
1.8 lievre 1950: covar[ncov+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];
1951: k1++;
1952: k2=k2+2;
1.7 lievre 1953: }
1.2 lievre 1954: }
1.8 lievre 1955: else {
1956: /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/
1957: /* scanf("%d",i);*/
1958: cutv(strd,strc,strb,'V');
1959: Tvar[i]=atoi(strc);
1960: }
1961: strcpy(modelsav,stra);
1962: /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);
1963: scanf("%d",i);*/
1.2 lievre 1964: }
1.8 lievre 1965: }
1966:
1967: /*printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);
1968: printf("cptcovprod=%d ", cptcovprod);
1969: scanf("%d ",i);*/
1.2 lievre 1970: fclose(fic);
1971:
1.7 lievre 1972: /* if(mle==1){*/
1.2 lievre 1973: if (weightopt != 1) { /* Maximisation without weights*/
1974: for(i=1;i<=n;i++) weight[i]=1.0;
1975: }
1976: /*-calculation of age at interview from date of interview and age at death -*/
1977: agev=matrix(1,maxwav,1,imx);
1978:
1979: for (i=1; i<=imx; i++) {
1980: agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);
1981: for(m=1; (m<= maxwav); m++){
1982: if(s[m][i] >0){
1983: if (s[m][i] == nlstate+1) {
1984: if(agedc[i]>0)
1985: if(moisdc[i]!=99 && andc[i]!=9999)
1986: agev[m][i]=agedc[i];
1.8 lievre 1987: else {
1988: if (andc[i]!=9999){
1.2 lievre 1989: printf("Warning negative age at death: %d line:%d\n",num[i],i);
1990: agev[m][i]=-1;
1.8 lievre 1991: }
1.2 lievre 1992: }
1993: }
1994: else if(s[m][i] !=9){ /* Should no more exist */
1995: agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);
1.3 lievre 1996: if(mint[m][i]==99 || anint[m][i]==9999)
1.2 lievre 1997: agev[m][i]=1;
1998: else if(agev[m][i] <agemin){
1999: agemin=agev[m][i];
2000: /*printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], agemin);*/
2001: }
2002: else if(agev[m][i] >agemax){
2003: agemax=agev[m][i];
2004: /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/
2005: }
2006: /*agev[m][i]=anint[m][i]-annais[i];*/
2007: /* agev[m][i] = age[i]+2*m;*/
2008: }
2009: else { /* =9 */
2010: agev[m][i]=1;
2011: s[m][i]=-1;
2012: }
2013: }
2014: else /*= 0 Unknown */
2015: agev[m][i]=1;
2016: }
2017:
2018: }
2019: for (i=1; i<=imx; i++) {
2020: for(m=1; (m<= maxwav); m++){
2021: if (s[m][i] > (nlstate+ndeath)) {
2022: printf("Error: Wrong value in nlstate or ndeath\n");
2023: goto end;
2024: }
2025: }
2026: }
2027:
2028: printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);
2029:
2030: free_vector(severity,1,maxwav);
2031: free_imatrix(outcome,1,maxwav+1,1,n);
2032: free_vector(moisnais,1,n);
2033: free_vector(annais,1,n);
2034: free_matrix(mint,1,maxwav,1,n);
2035: free_matrix(anint,1,maxwav,1,n);
2036: free_vector(moisdc,1,n);
2037: free_vector(andc,1,n);
2038:
2039:
2040: wav=ivector(1,imx);
2041: dh=imatrix(1,lastpass-firstpass+1,1,imx);
2042: mw=imatrix(1,lastpass-firstpass+1,1,imx);
2043:
2044: /* Concatenates waves */
2045: concatwav(wav, dh, mw, s, agedc, agev, firstpass, lastpass, imx, nlstate, stepm);
2046:
2047:
1.6 lievre 2048: Tcode=ivector(1,100);
1.8 lievre 2049: nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);
1.7 lievre 2050: ncodemax[1]=1;
2051: if (cptcovn > 0) tricode(Tvar,nbcode,imx);
2052:
1.2 lievre 2053: codtab=imatrix(1,100,1,10);
2054: h=0;
1.7 lievre 2055: m=pow(2,cptcoveff);
1.2 lievre 2056:
1.7 lievre 2057: for(k=1;k<=cptcoveff; k++){
1.2 lievre 2058: for(i=1; i <=(m/pow(2,k));i++){
2059: for(j=1; j <= ncodemax[k]; j++){
1.7 lievre 2060: for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){
1.2 lievre 2061: h++;
2062: if (h>m) h=1;codtab[h][k]=j;
2063: }
2064: }
2065: }
2066: }
2067:
1.7 lievre 2068:
2069: /*for(i=1; i <=m ;i++){
1.2 lievre 2070: for(k=1; k <=cptcovn; k++){
1.7 lievre 2071: printf("i=%d k=%d %d %d",i,k,codtab[i][k], cptcoveff);
1.2 lievre 2072: }
2073: printf("\n");
1.6 lievre 2074: }
2075: scanf("%d",i);*/
1.2 lievre 2076:
2077: /* Calculates basic frequencies. Computes observed prevalence at single age
2078: and prints on file fileres'p'. */
1.7 lievre 2079: freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax);
1.2 lievre 2080:
2081: pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
2082: oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
2083: newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
2084: savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
2085: oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */
2086:
2087: /* For Powell, parameters are in a vector p[] starting at p[1]
2088: so we point p on param[1][1] so that p[1] maps on param[1][1][1] */
2089: p=param[1][1]; /* *(*(*(param +1)+1)+0) */
1.7 lievre 2090:
2091: if(mle==1){
1.2 lievre 2092: mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);
1.7 lievre 2093: }
1.2 lievre 2094:
2095: /*--------- results files --------------*/
2096: 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);
2097:
2098: jk=1;
2099: fprintf(ficres,"# Parameters\n");
2100: printf("# Parameters\n");
2101: for(i=1,jk=1; i <=nlstate; i++){
2102: for(k=1; k <=(nlstate+ndeath); k++){
2103: if (k != i)
2104: {
2105: printf("%d%d ",i,k);
2106: fprintf(ficres,"%1d%1d ",i,k);
2107: for(j=1; j <=ncovmodel; j++){
2108: printf("%f ",p[jk]);
2109: fprintf(ficres,"%f ",p[jk]);
2110: jk++;
2111: }
2112: printf("\n");
2113: fprintf(ficres,"\n");
2114: }
2115: }
2116: }
1.7 lievre 2117: if(mle==1){
1.2 lievre 2118: /* Computing hessian and covariance matrix */
2119: ftolhess=ftol; /* Usually correct */
2120: hesscov(matcov, p, npar, delti, ftolhess, func);
1.7 lievre 2121: }
1.2 lievre 2122: fprintf(ficres,"# Scales\n");
2123: printf("# Scales\n");
2124: for(i=1,jk=1; i <=nlstate; i++){
2125: for(j=1; j <=nlstate+ndeath; j++){
2126: if (j!=i) {
2127: fprintf(ficres,"%1d%1d",i,j);
2128: printf("%1d%1d",i,j);
2129: for(k=1; k<=ncovmodel;k++){
2130: printf(" %.5e",delti[jk]);
2131: fprintf(ficres," %.5e",delti[jk]);
2132: jk++;
2133: }
2134: printf("\n");
2135: fprintf(ficres,"\n");
2136: }
2137: }
2138: }
2139:
2140: k=1;
2141: fprintf(ficres,"# Covariance\n");
2142: printf("# Covariance\n");
2143: for(i=1;i<=npar;i++){
2144: /* if (k>nlstate) k=1;
2145: i1=(i-1)/(ncovmodel*nlstate)+1;
2146: fprintf(ficres,"%s%d%d",alph[k],i1,tab[i]);
2147: printf("%s%d%d",alph[k],i1,tab[i]);*/
2148: fprintf(ficres,"%3d",i);
2149: printf("%3d",i);
2150: for(j=1; j<=i;j++){
2151: fprintf(ficres," %.5e",matcov[i][j]);
2152: printf(" %.5e",matcov[i][j]);
2153: }
2154: fprintf(ficres,"\n");
2155: printf("\n");
2156: k++;
2157: }
2158:
2159: while((c=getc(ficpar))=='#' && c!= EOF){
2160: ungetc(c,ficpar);
2161: fgets(line, MAXLINE, ficpar);
2162: puts(line);
2163: fputs(line,ficparo);
2164: }
2165: ungetc(c,ficpar);
2166:
2167: fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf\n",&agemin,&agemax, &bage, &fage);
2168:
2169: if (fage <= 2) {
2170: bage = agemin;
2171: fage = agemax;
2172: }
2173:
2174: fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");
2175: fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemax,bage,fage);
1.7 lievre 2176:
2177:
1.2 lievre 2178: /*------------ gnuplot -------------*/
2179: chdir(pathcd);
2180: if((ficgp=fopen("graph.plt","w"))==NULL) {
1.5 lievre 2181: printf("Problem with file graph.gp");goto end;
1.2 lievre 2182: }
2183: #ifdef windows
2184: fprintf(ficgp,"cd \"%s\" \n",pathc);
2185: #endif
1.7 lievre 2186: m=pow(2,cptcoveff);
1.2 lievre 2187:
2188: /* 1eme*/
2189: for (cpt=1; cpt<= nlstate ; cpt ++) {
2190: for (k1=1; k1<= m ; k1 ++) {
2191:
2192: #ifdef windows
2193: 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);
2194: #endif
2195: #ifdef unix
2196: fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nplot [%.f:%.f] \"vpl%s\" u 1:2 \"\%%lf",agemin,fage,fileres);
2197: #endif
2198:
2199: for (i=1; i<= nlstate ; i ++) {
2200: if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
2201: else fprintf(ficgp," \%%*lf (\%%*lf)");
2202: }
2203: fprintf(ficgp,"\" t\"Stationary prevalence\" w l 0,\"vpl%s\" every :::%d::%d u 1:($2+2*$3) \"\%%lf",fileres,k1-1,k1-1);
2204: for (i=1; i<= nlstate ; i ++) {
2205: if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
2206: else fprintf(ficgp," \%%*lf (\%%*lf)");
2207: }
2208: fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"vpl%s\" every :::%d::%d u 1:($2-2*$3) \"\%%lf",fileres,k1-1,k1-1);
2209: for (i=1; i<= nlstate ; i ++) {
2210: if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
2211: else fprintf(ficgp," \%%*lf (\%%*lf)");
2212: }
2213: fprintf(ficgp,"\" t\"\" w l 1,\"p%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",fileres,k1-1,k1-1,2+4*(cpt-1));
2214: #ifdef unix
2215: fprintf(ficgp,"\nset ter gif small size 400,300");
2216: #endif
2217: fprintf(ficgp,"\nset out \"v%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);
2218: }
2219: }
2220: /*2 eme*/
2221:
2222: for (k1=1; k1<= m ; k1 ++) {
2223: fprintf(ficgp,"set ylabel \"Years\" \nset ter gif small size 400,300\nplot [%.f:%.f] ",agemin,fage);
2224:
2225: for (i=1; i<= nlstate+1 ; i ++) {
2226: k=2*i;
2227: fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:2 \"\%%lf",fileres,k1-1,k1-1);
2228: for (j=1; j<= nlstate+1 ; j ++) {
2229: if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
2230: else fprintf(ficgp," \%%*lf (\%%*lf)");
2231: }
2232: if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");
2233: else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);
2234: fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",fileres,k1-1,k1-1);
2235: for (j=1; j<= nlstate+1 ; j ++) {
2236: if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
2237: else fprintf(ficgp," \%%*lf (\%%*lf)");
2238: }
2239: fprintf(ficgp,"\" t\"\" w l 0,");
2240: fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",fileres,k1-1,k1-1);
2241: for (j=1; j<= nlstate+1 ; j ++) {
2242: if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
2243: else fprintf(ficgp," \%%*lf (\%%*lf)");
2244: }
2245: if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");
2246: else fprintf(ficgp,"\" t\"\" w l 0,");
2247: }
2248: fprintf(ficgp,"\nset out \"e%s%d.gif\" \nreplot\n\n",strtok(optionfile, "."),k1);
2249: }
2250:
2251: /*3eme*/
2252:
1.5 lievre 2253: for (k1=1; k1<= m ; k1 ++) {
1.2 lievre 2254: for (cpt=1; cpt<= nlstate ; cpt ++) {
2255: k=2+nlstate*(cpt-1);
2256: 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);
2257: for (i=1; i< nlstate ; i ++) {
2258: 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);
2259: }
2260: fprintf(ficgp,"\nset out \"exp%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);
2261: }
1.5 lievre 2262: }
1.2 lievre 2263:
2264: /* CV preval stat */
1.5 lievre 2265: for (k1=1; k1<= m ; k1 ++) {
1.2 lievre 2266: for (cpt=1; cpt<nlstate ; cpt ++) {
2267: k=3;
2268: 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/($%d",agemin,agemax,fileres,k1,k+cpt+1,k+1);
2269: for (i=1; i< nlstate ; i ++)
2270: fprintf(ficgp,"+$%d",k+i+1);
2271: fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);
2272:
2273: l=3+(nlstate+ndeath)*cpt;
2274: fprintf(ficgp,",\"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",fileres,k1,l+cpt+1,l+1);
2275: for (i=1; i< nlstate ; i ++) {
2276: l=3+(nlstate+ndeath)*cpt;
2277: fprintf(ficgp,"+$%d",l+i+1);
2278: }
2279: fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);
2280: fprintf(ficgp,"set out \"p%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);
2281: }
2282: }
1.5 lievre 2283:
1.2 lievre 2284: /* proba elementaires */
1.5 lievre 2285: for(i=1,jk=1; i <=nlstate; i++){
1.2 lievre 2286: for(k=1; k <=(nlstate+ndeath); k++){
2287: if (k != i) {
2288: for(j=1; j <=ncovmodel; j++){
1.5 lievre 2289: /*fprintf(ficgp,"%s%1d%1d=%f ",alph[j],i,k,p[jk]);*/
2290: /*fprintf(ficgp,"%s",alph[1]);*/
2291: fprintf(ficgp,"p%d=%f ",jk,p[jk]);
1.2 lievre 2292: jk++;
2293: fprintf(ficgp,"\n");
2294: }
2295: }
2296: }
1.5 lievre 2297: }
2298:
1.2 lievre 2299: for(jk=1; jk <=m; jk++) {
2300: fprintf(ficgp,"\nset ter gif small size 400,300\nset log y\nplot [%.f:%.f] ",agemin,agemax);
1.5 lievre 2301: i=1;
2302: for(k2=1; k2<=nlstate; k2++) {
2303: k3=i;
2304: for(k=1; k<=(nlstate+ndeath); k++) {
2305: if (k != k2){
2306: fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
1.7 lievre 2307: ij=1;
2308: for(j=3; j <=ncovmodel; j++) {
2309: if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
2310: fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
2311: ij++;
2312: }
2313: else
1.6 lievre 2314: fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
1.7 lievre 2315: }
2316: fprintf(ficgp,")/(1");
1.6 lievre 2317:
2318: for(k1=1; k1 <=nlstate; k1++){
2319: fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);
1.7 lievre 2320: ij=1;
2321: for(j=3; j <=ncovmodel; j++){
2322: if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
2323: fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
2324: ij++;
2325: }
2326: else
1.6 lievre 2327: fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
1.7 lievre 2328: }
1.6 lievre 2329: fprintf(ficgp,")");
1.5 lievre 2330: }
2331: fprintf(ficgp,") t \"p%d%d\" ", k2,k);
2332: if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");
1.6 lievre 2333: i=i+ncovmodel;
1.5 lievre 2334: }
2335: }
2336: }
1.6 lievre 2337: fprintf(ficgp,"\nset out \"pe%s%d.gif\" \nreplot\n\n",strtok(optionfile, "."),jk);
2338: }
1.5 lievre 2339:
2340: fclose(ficgp);
2341:
2342: chdir(path);
1.2 lievre 2343: free_matrix(agev,1,maxwav,1,imx);
2344: free_ivector(wav,1,imx);
2345: free_imatrix(dh,1,lastpass-firstpass+1,1,imx);
2346: free_imatrix(mw,1,lastpass-firstpass+1,1,imx);
2347:
2348: free_imatrix(s,1,maxwav+1,1,n);
2349:
2350:
2351: free_ivector(num,1,n);
2352: free_vector(agedc,1,n);
2353: free_vector(weight,1,n);
2354: /*free_matrix(covar,1,NCOVMAX,1,n);*/
2355: fclose(ficparo);
2356: fclose(ficres);
1.7 lievre 2357: /* }*/
1.2 lievre 2358:
2359: /*________fin mle=1_________*/
2360:
2361:
2362:
2363: /* No more information from the sample is required now */
2364: /* Reads comments: lines beginning with '#' */
2365: while((c=getc(ficpar))=='#' && c!= EOF){
2366: ungetc(c,ficpar);
2367: fgets(line, MAXLINE, ficpar);
2368: puts(line);
2369: fputs(line,ficparo);
2370: }
2371: ungetc(c,ficpar);
2372:
2373: fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf\n",&agemin,&agemax, &bage, &fage);
2374: printf("agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemax, bage, fage);
2375: fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemax,bage,fage);
2376: /*--------- index.htm --------*/
2377:
1.9 lievre 2378: strcpy(optionfilehtm,optionfile);
2379: strcat(optionfilehtm,".htm");
2380: if((fichtm=fopen(optionfilehtm,"w"))==NULL) {
2381: printf("Problem with %s \n",optionfilehtm);goto end;
1.2 lievre 2382: }
2383:
1.9 lievre 2384: fprintf(fichtm,"<body><ul> <font size=\"6\">Imach, Version 0.64b </font> <hr size=\"2\" color=\"#EC5E5E\">
1.8 lievre 2385: Titre=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>
2386: Total number of observations=%d <br>
2387: Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>
2388: <hr size=\"2\" color=\"#EC5E5E\">
2389: <li>Outputs files<br><br>\n
1.2 lievre 2390: - Observed prevalence in each state: <a href=\"p%s\">p%s</a> <br>\n
2391: - Estimated parameters and the covariance matrix: <a href=\"%s\">%s</a> <br>
2392: - Stationary prevalence in each state: <a href=\"pl%s\">pl%s</a> <br>
2393: - Transition probabilities: <a href=\"pij%s\">pij%s</a><br>
2394: - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>
2395: - Life expectancies by age and initial health status: <a href=\"e%s\">e%s</a> <br>
2396: - Variances of life expectancies by age and initial health status: <a href=\"v%s\">v%s</a><br>
2397: - Health expectancies with their variances: <a href=\"t%s\">t%s</a> <br>
1.8 lievre 2398: - Standard deviation of stationary prevalences: <a href=\"vpl%s\">vpl%s</a> <br><br>",title,datafile,firstpass,lastpass,stepm, weightopt,model,imx,jmin,jmax,jmean,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres);
1.2 lievre 2399:
1.8 lievre 2400: fprintf(fichtm," <li>Graphs</li><p>");
1.2 lievre 2401:
1.7 lievre 2402: m=cptcoveff;
1.2 lievre 2403: if (cptcovn < 1) {m=1;ncodemax[1]=1;}
2404:
2405: j1=0;
2406: for(k1=1; k1<=m;k1++){
2407: for(i1=1; i1<=ncodemax[k1];i1++){
2408: j1++;
2409: if (cptcovn > 0) {
1.8 lievre 2410: fprintf(fichtm,"<hr size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
1.7 lievre 2411: for (cpt=1; cpt<=cptcoveff;cpt++)
2412: fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[j1][cpt]]);
1.8 lievre 2413: fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
1.2 lievre 2414: }
2415: fprintf(fichtm,"<br>- Probabilities: pe%s%d.gif<br>
2416: <img src=\"pe%s%d.gif\">",strtok(optionfile, "."),j1,strtok(optionfile, "."),j1);
2417: for(cpt=1; cpt<nlstate;cpt++){
2418: fprintf(fichtm,"<br>- Prevalence of disability : p%s%d%d.gif<br>
2419: <img src=\"p%s%d%d.gif\">",strtok(optionfile, "."),cpt,j1,strtok(optionfile, "."),cpt,j1);
2420: }
2421: for(cpt=1; cpt<=nlstate;cpt++) {
2422: fprintf(fichtm,"<br>- Observed and stationary prevalence (with confident
2423: interval) in state (%d): v%s%d%d.gif <br>
2424: <img src=\"v%s%d%d.gif\">",cpt,strtok(optionfile, "."),cpt,j1,strtok(optionfile, "."),cpt,j1);
2425: }
2426: for(cpt=1; cpt<=nlstate;cpt++) {
2427: fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): exp%s%d%d.gif <br>
1.5 lievre 2428: <img src=\"exp%s%d%d.gif\">",cpt,strtok(optionfile, "."),cpt,j1,strtok(optionfile, "."),cpt,j1);
1.2 lievre 2429: }
2430: fprintf(fichtm,"\n<br>- Total life expectancy by age and
2431: health expectancies in states (1) and (2): e%s%d.gif<br>
2432: <img src=\"e%s%d.gif\">",strtok(optionfile, "."),j1,strtok(optionfile, "."),j1);
2433: fprintf(fichtm,"\n</body>");
2434: }
2435: }
2436: fclose(fichtm);
2437:
2438: /*--------------- Prevalence limit --------------*/
2439:
2440: strcpy(filerespl,"pl");
2441: strcat(filerespl,fileres);
2442: if((ficrespl=fopen(filerespl,"w"))==NULL) {
2443: printf("Problem with Prev limit resultfile: %s\n", filerespl);goto end;
2444: }
2445: printf("Computing prevalence limit: result on file '%s' \n", filerespl);
2446: fprintf(ficrespl,"#Prevalence limit\n");
2447: fprintf(ficrespl,"#Age ");
2448: for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);
2449: fprintf(ficrespl,"\n");
2450:
2451: prlim=matrix(1,nlstate,1,nlstate);
2452: pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
2453: oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
2454: newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
2455: savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
2456: oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */
2457: k=0;
2458: agebase=agemin;
2459: agelim=agemax;
2460: ftolpl=1.e-10;
1.7 lievre 2461: i1=cptcoveff;
1.2 lievre 2462: if (cptcovn < 1){i1=1;}
2463:
2464: for(cptcov=1;cptcov<=i1;cptcov++){
2465: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
2466: k=k+1;
2467: /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/
1.6 lievre 2468: fprintf(ficrespl,"\n#******");
1.7 lievre 2469: for(j=1;j<=cptcoveff;j++)
2470: fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
1.2 lievre 2471: fprintf(ficrespl,"******\n");
2472:
2473: for (age=agebase; age<=agelim; age++){
2474: prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
2475: fprintf(ficrespl,"%.0f",age );
2476: for(i=1; i<=nlstate;i++)
2477: fprintf(ficrespl," %.5f", prlim[i][i]);
2478: fprintf(ficrespl,"\n");
2479: }
2480: }
2481: }
2482: fclose(ficrespl);
2483: /*------------- h Pij x at various ages ------------*/
2484:
2485: strcpy(filerespij,"pij"); strcat(filerespij,fileres);
2486: if((ficrespij=fopen(filerespij,"w"))==NULL) {
2487: printf("Problem with Pij resultfile: %s\n", filerespij);goto end;
2488: }
2489: printf("Computing pij: result on file '%s' \n", filerespij);
2490:
2491: stepsize=(int) (stepm+YEARM-1)/YEARM;
2492: if (stepm<=24) stepsize=2;
2493:
2494: agelim=AGESUP;
2495: hstepm=stepsize*YEARM; /* Every year of age */
2496: hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */
2497:
2498: k=0;
2499: for(cptcov=1;cptcov<=i1;cptcov++){
2500: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
2501: k=k+1;
2502: fprintf(ficrespij,"\n#****** ");
1.7 lievre 2503: for(j=1;j<=cptcoveff;j++)
2504: fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
1.2 lievre 2505: fprintf(ficrespij,"******\n");
2506:
2507: for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */
2508: nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
2509: nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
2510: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
2511: oldm=oldms;savm=savms;
2512: hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
2513: fprintf(ficrespij,"# Age");
2514: for(i=1; i<=nlstate;i++)
2515: for(j=1; j<=nlstate+ndeath;j++)
2516: fprintf(ficrespij," %1d-%1d",i,j);
2517: fprintf(ficrespij,"\n");
2518: for (h=0; h<=nhstepm; h++){
2519: fprintf(ficrespij,"%d %.0f %.0f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );
2520: for(i=1; i<=nlstate;i++)
2521: for(j=1; j<=nlstate+ndeath;j++)
2522: fprintf(ficrespij," %.5f", p3mat[i][j][h]);
2523: fprintf(ficrespij,"\n");
2524: }
2525: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
2526: fprintf(ficrespij,"\n");
2527: }
2528: }
2529: }
2530:
2531: fclose(ficrespij);
2532:
2533: /*---------- Health expectancies and variances ------------*/
2534:
2535: strcpy(filerest,"t");
2536: strcat(filerest,fileres);
2537: if((ficrest=fopen(filerest,"w"))==NULL) {
2538: printf("Problem with total LE resultfile: %s\n", filerest);goto end;
2539: }
2540: printf("Computing Total LEs with variances: file '%s' \n", filerest);
2541:
2542:
2543: strcpy(filerese,"e");
2544: strcat(filerese,fileres);
2545: if((ficreseij=fopen(filerese,"w"))==NULL) {
2546: printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
2547: }
2548: printf("Computing Health Expectancies: result on file '%s' \n", filerese);
2549:
2550: strcpy(fileresv,"v");
2551: strcat(fileresv,fileres);
2552: if((ficresvij=fopen(fileresv,"w"))==NULL) {
2553: printf("Problem with variance resultfile: %s\n", fileresv);exit(0);
2554: }
2555: printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
2556:
2557: k=0;
2558: for(cptcov=1;cptcov<=i1;cptcov++){
2559: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
2560: k=k+1;
2561: fprintf(ficrest,"\n#****** ");
1.7 lievre 2562: for(j=1;j<=cptcoveff;j++)
2563: fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
1.2 lievre 2564: fprintf(ficrest,"******\n");
2565:
2566: fprintf(ficreseij,"\n#****** ");
1.7 lievre 2567: for(j=1;j<=cptcoveff;j++)
1.2 lievre 2568: fprintf(ficreseij,"V%d=%d ",j,nbcode[j][codtab[k][j]]);
2569: fprintf(ficreseij,"******\n");
2570:
2571: fprintf(ficresvij,"\n#****** ");
1.7 lievre 2572: for(j=1;j<=cptcoveff;j++)
1.2 lievre 2573: fprintf(ficresvij,"V%d=%d ",j,nbcode[j][codtab[k][j]]);
2574: fprintf(ficresvij,"******\n");
2575:
2576: eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
2577: oldm=oldms;savm=savms;
2578: evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k);
2579: vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
2580: oldm=oldms;savm=savms;
2581: varevsij(fileres, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);
2582:
2583: fprintf(ficrest,"#Total LEs with variances: e.. (std) ");
2584: for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);
2585: fprintf(ficrest,"\n");
2586:
2587: hf=1;
2588: if (stepm >= YEARM) hf=stepm/YEARM;
2589: epj=vector(1,nlstate+1);
2590: for(age=bage; age <=fage ;age++){
2591: prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
2592: fprintf(ficrest," %.0f",age);
2593: for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){
2594: for(i=1, epj[j]=0.;i <=nlstate;i++) {
2595: epj[j] += prlim[i][i]*hf*eij[i][j][(int)age];
2596: }
2597: epj[nlstate+1] +=epj[j];
2598: }
2599: for(i=1, vepp=0.;i <=nlstate;i++)
2600: for(j=1;j <=nlstate;j++)
2601: vepp += vareij[i][j][(int)age];
2602: fprintf(ficrest," %.2f (%.2f)", epj[nlstate+1],hf*sqrt(vepp));
2603: for(j=1;j <=nlstate;j++){
2604: fprintf(ficrest," %.2f (%.2f)", epj[j],hf*sqrt(vareij[j][j][(int)age]));
2605: }
2606: fprintf(ficrest,"\n");
2607: }
2608: }
2609: }
2610:
2611: fclose(ficreseij);
2612: fclose(ficresvij);
2613: fclose(ficrest);
2614: fclose(ficpar);
2615: free_vector(epj,1,nlstate+1);
1.5 lievre 2616: /* scanf("%d ",i); */
1.2 lievre 2617:
2618: /*------- Variance limit prevalence------*/
2619:
2620: strcpy(fileresvpl,"vpl");
2621: strcat(fileresvpl,fileres);
2622: if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {
2623: printf("Problem with variance prev lim resultfile: %s\n", fileresvpl);
2624: exit(0);
2625: }
2626: printf("Computing Variance-covariance of Prevalence limit: file '%s' \n", fileresvpl);
2627:
2628: k=0;
2629: for(cptcov=1;cptcov<=i1;cptcov++){
2630: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
2631: k=k+1;
2632: fprintf(ficresvpl,"\n#****** ");
1.7 lievre 2633: for(j=1;j<=cptcoveff;j++)
2634: fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
1.2 lievre 2635: fprintf(ficresvpl,"******\n");
2636:
2637: varpl=matrix(1,nlstate,(int) bage, (int) fage);
2638: oldm=oldms;savm=savms;
2639: varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);
2640: }
2641: }
2642:
2643: fclose(ficresvpl);
2644:
2645: /*---------- End : free ----------------*/
2646: free_matrix(varpl,1,nlstate,(int) bage, (int)fage);
2647:
2648: free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);
2649: free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
2650:
2651:
2652: free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);
2653: free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);
2654: free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);
2655: free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);
2656:
2657: free_matrix(matcov,1,npar,1,npar);
2658: free_vector(delti,1,npar);
2659:
2660: free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
2661:
2662: printf("End of Imach\n");
2663: /* gettimeofday(&end_time, (struct timezone*)0);*/ /* after time */
2664:
2665: /* 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);*/
2666: /*printf("Total time was %d uSec.\n", total_usecs);*/
2667: /*------ End -----------*/
2668:
2669: end:
2670: #ifdef windows
2671: chdir(pathcd);
2672: #endif
1.8 lievre 2673: /*system("wgnuplot graph.plt");*/
2674: system("../gp37mgw/wgnuplot graph.plt");
1.2 lievre 2675:
2676: #ifdef windows
2677: while (z[0] != 'q') {
2678: chdir(pathcd);
2679: printf("\nType e to edit output files, c to start again, and q for exiting: ");
2680: scanf("%s",z);
2681: if (z[0] == 'c') system("./imach");
2682: else if (z[0] == 'e') {
2683: chdir(path);
1.10 ! lievre 2684: system(optionfilehtm);
1.2 lievre 2685: }
2686: else if (z[0] == 'q') exit(0);
2687: }
2688: #endif
2689: }
2690:
2691:
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