Annotation of imach/src/imach.c, revision 1.4
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
54:
55: #define MAXPARM 30 /* Maximum number of parameters for the optimization */
56: #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */
57:
58: #define NINTERVMAX 8
59: #define NLSTATEMAX 8 /* Maximum number of live states (for func) */
60: #define NDEATHMAX 8 /* Maximum number of dead states (for func) */
61: #define NCOVMAX 8 /* Maximum number of covariates */
1.3 lievre 62: #define MAXN 20000
1.2 lievre 63: #define YEARM 12. /* Number of months per year */
64: #define AGESUP 130
65: #define AGEBASE 40
66:
67:
68: int nvar;
69: static int cptcov;
70: int cptcovn;
71: int npar=NPARMAX;
72: int nlstate=2; /* Number of live states */
73: int ndeath=1; /* Number of dead states */
74: int ncovmodel, ncov; /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
75:
76: int *wav; /* Number of waves for this individuual 0 is possible */
77: int maxwav; /* Maxim number of waves */
78: int mle, weightopt;
79: int **mw; /* mw[mi][i] is number of the mi wave for this individual */
80: int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
81: double **oldm, **newm, **savm; /* Working pointers to matrices */
82: double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
83: FILE *fic,*ficpar, *ficparo,*ficres, *ficrespl, *ficrespij, *ficrest;
84: FILE *ficgp, *fichtm;
85: FILE *ficreseij;
86: char filerese[FILENAMELENGTH];
87: FILE *ficresvij;
88: char fileresv[FILENAMELENGTH];
89: FILE *ficresvpl;
90: char fileresvpl[FILENAMELENGTH];
91:
92:
93:
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;
128: int *num, firstpass=0, lastpass=4,*cod, *ncodemax;
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;
135: int **nbcode, *Tcode, *Tvar, **codtab;
136:
137: double ftol=FTOL; /* Tolerance for computing Max Likelihood */
138: double ftolhess; /* Tolerance for computing hessian */
139:
140:
141: /******************************************/
142:
143: void replace(char *s, char*t)
144: {
145: int i;
146: int lg=20;
147: i=0;
148: lg=strlen(t);
149: for(i=0; i<= lg; i++) {
150: (s[i] = t[i]);
151: if (t[i]== '\\') s[i]='/';
152: }
153: }
154:
155: int nbocc(char *s, char occ)
156: {
157: int i,j=0;
158: int lg=20;
159: i=0;
160: lg=strlen(s);
161: for(i=0; i<= lg; i++) {
162: if (s[i] == occ ) j++;
163: }
164: return j;
165: }
166:
167: void cutv(char *u,char *v, char*t, char occ)
168: {
169: int i,lg,j,p;
170: i=0;
171: for(j=0; j<=strlen(t)-1; j++) {
1.3 lievre 172: if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;
1.2 lievre 173: }
174:
175: lg=strlen(t);
176: for(j=0; j<p; j++) {
177: (u[j] = t[j]);
178: u[p]='\0';
179: }
180:
181: for(j=0; j<= lg; j++) {
182: if (j>=(p+1))(v[j-p-1] = t[j]);
183: }
184: }
185:
186: /********************** nrerror ********************/
187:
188: void nrerror(char error_text[])
189: {
190: fprintf(stderr,"ERREUR ...\n");
191: fprintf(stderr,"%s\n",error_text);
192: exit(1);
193: }
194: /*********************** vector *******************/
195: double *vector(int nl, int nh)
196: {
197: double *v;
198: v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
199: if (!v) nrerror("allocation failure in vector");
200: return v-nl+NR_END;
201: }
202:
203: /************************ free vector ******************/
204: void free_vector(double*v, int nl, int nh)
205: {
206: free((FREE_ARG)(v+nl-NR_END));
207: }
208:
209: /************************ivector *******************************/
210: int *ivector(long nl,long nh)
211: {
212: int *v;
213: v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
214: if (!v) nrerror("allocation failure in ivector");
215: return v-nl+NR_END;
216: }
217:
218: /******************free ivector **************************/
219: void free_ivector(int *v, long nl, long nh)
220: {
221: free((FREE_ARG)(v+nl-NR_END));
222: }
223:
224: /******************* imatrix *******************************/
225: int **imatrix(long nrl, long nrh, long ncl, long nch)
226: /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */
227: {
228: long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;
229: int **m;
230:
231: /* allocate pointers to rows */
232: m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));
233: if (!m) nrerror("allocation failure 1 in matrix()");
234: m += NR_END;
235: m -= nrl;
236:
237:
238: /* allocate rows and set pointers to them */
239: m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));
240: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
241: m[nrl] += NR_END;
242: m[nrl] -= ncl;
243:
244: for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;
245:
246: /* return pointer to array of pointers to rows */
247: return m;
248: }
249:
250: /****************** free_imatrix *************************/
251: void free_imatrix(m,nrl,nrh,ncl,nch)
252: int **m;
253: long nch,ncl,nrh,nrl;
254: /* free an int matrix allocated by imatrix() */
255: {
256: free((FREE_ARG) (m[nrl]+ncl-NR_END));
257: free((FREE_ARG) (m+nrl-NR_END));
258: }
259:
260: /******************* matrix *******************************/
261: double **matrix(long nrl, long nrh, long ncl, long nch)
262: {
263: long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
264: double **m;
265:
266: m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
267: if (!m) nrerror("allocation failure 1 in matrix()");
268: m += NR_END;
269: m -= nrl;
270:
271: m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
272: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
273: m[nrl] += NR_END;
274: m[nrl] -= ncl;
275:
276: for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
277: return m;
278: }
279:
280: /*************************free matrix ************************/
281: void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
282: {
283: free((FREE_ARG)(m[nrl]+ncl-NR_END));
284: free((FREE_ARG)(m+nrl-NR_END));
285: }
286:
287: /******************* ma3x *******************************/
288: double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
289: {
290: long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
291: double ***m;
292:
293: m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
294: if (!m) nrerror("allocation failure 1 in matrix()");
295: m += NR_END;
296: m -= nrl;
297:
298: m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
299: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
300: m[nrl] += NR_END;
301: m[nrl] -= ncl;
302:
303: for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
304:
305: m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
306: if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
307: m[nrl][ncl] += NR_END;
308: m[nrl][ncl] -= nll;
309: for (j=ncl+1; j<=nch; j++)
310: m[nrl][j]=m[nrl][j-1]+nlay;
311:
312: for (i=nrl+1; i<=nrh; i++) {
313: m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
314: for (j=ncl+1; j<=nch; j++)
315: m[i][j]=m[i][j-1]+nlay;
316: }
317: return m;
318: }
319:
320: /*************************free ma3x ************************/
321: void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
322: {
323: free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
324: free((FREE_ARG)(m[nrl]+ncl-NR_END));
325: free((FREE_ARG)(m+nrl-NR_END));
326: }
327:
328: /***************** f1dim *************************/
329: extern int ncom;
330: extern double *pcom,*xicom;
331: extern double (*nrfunc)(double []);
332:
333: double f1dim(double x)
334: {
335: int j;
336: double f;
337: double *xt;
338:
339: xt=vector(1,ncom);
340: for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];
341: f=(*nrfunc)(xt);
342: free_vector(xt,1,ncom);
343: return f;
344: }
345:
346: /*****************brent *************************/
347: double brent(double ax, double bx, double cx, double (*f)(double), double tol, double *xmin)
348: {
349: int iter;
350: double a,b,d,etemp;
351: double fu,fv,fw,fx;
352: double ftemp;
353: double p,q,r,tol1,tol2,u,v,w,x,xm;
354: double e=0.0;
355:
356: a=(ax < cx ? ax : cx);
357: b=(ax > cx ? ax : cx);
358: x=w=v=bx;
359: fw=fv=fx=(*f)(x);
360: for (iter=1;iter<=ITMAX;iter++) {
361: xm=0.5*(a+b);
362: tol2=2.0*(tol1=tol*fabs(x)+ZEPS);
363: /* if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
364: printf(".");fflush(stdout);
365: #ifdef DEBUG
366: 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);
367: /* if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
368: #endif
369: if (fabs(x-xm) <= (tol2-0.5*(b-a))){
370: *xmin=x;
371: return fx;
372: }
373: ftemp=fu;
374: if (fabs(e) > tol1) {
375: r=(x-w)*(fx-fv);
376: q=(x-v)*(fx-fw);
377: p=(x-v)*q-(x-w)*r;
378: q=2.0*(q-r);
379: if (q > 0.0) p = -p;
380: q=fabs(q);
381: etemp=e;
382: e=d;
383: if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))
384: d=CGOLD*(e=(x >= xm ? a-x : b-x));
385: else {
386: d=p/q;
387: u=x+d;
388: if (u-a < tol2 || b-u < tol2)
389: d=SIGN(tol1,xm-x);
390: }
391: } else {
392: d=CGOLD*(e=(x >= xm ? a-x : b-x));
393: }
394: u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));
395: fu=(*f)(u);
396: if (fu <= fx) {
397: if (u >= x) a=x; else b=x;
398: SHFT(v,w,x,u)
399: SHFT(fv,fw,fx,fu)
400: } else {
401: if (u < x) a=u; else b=u;
402: if (fu <= fw || w == x) {
403: v=w;
404: w=u;
405: fv=fw;
406: fw=fu;
407: } else if (fu <= fv || v == x || v == w) {
408: v=u;
409: fv=fu;
410: }
411: }
412: }
413: nrerror("Too many iterations in brent");
414: *xmin=x;
415: return fx;
416: }
417:
418: /****************** mnbrak ***********************/
419:
420: void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,
421: double (*func)(double))
422: {
423: double ulim,u,r,q, dum;
424: double fu;
425:
426: *fa=(*func)(*ax);
427: *fb=(*func)(*bx);
428: if (*fb > *fa) {
429: SHFT(dum,*ax,*bx,dum)
430: SHFT(dum,*fb,*fa,dum)
431: }
432: *cx=(*bx)+GOLD*(*bx-*ax);
433: *fc=(*func)(*cx);
434: while (*fb > *fc) {
435: r=(*bx-*ax)*(*fb-*fc);
436: q=(*bx-*cx)*(*fb-*fa);
437: u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/
438: (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r));
439: ulim=(*bx)+GLIMIT*(*cx-*bx);
440: if ((*bx-u)*(u-*cx) > 0.0) {
441: fu=(*func)(u);
442: } else if ((*cx-u)*(u-ulim) > 0.0) {
443: fu=(*func)(u);
444: if (fu < *fc) {
445: SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))
446: SHFT(*fb,*fc,fu,(*func)(u))
447: }
448: } else if ((u-ulim)*(ulim-*cx) >= 0.0) {
449: u=ulim;
450: fu=(*func)(u);
451: } else {
452: u=(*cx)+GOLD*(*cx-*bx);
453: fu=(*func)(u);
454: }
455: SHFT(*ax,*bx,*cx,u)
456: SHFT(*fa,*fb,*fc,fu)
457: }
458: }
459:
460: /*************** linmin ************************/
461:
462: int ncom;
463: double *pcom,*xicom;
464: double (*nrfunc)(double []);
465:
466: void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))
467: {
468: double brent(double ax, double bx, double cx,
469: double (*f)(double), double tol, double *xmin);
470: double f1dim(double x);
471: void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,
472: double *fc, double (*func)(double));
473: int j;
474: double xx,xmin,bx,ax;
475: double fx,fb,fa;
476:
477: ncom=n;
478: pcom=vector(1,n);
479: xicom=vector(1,n);
480: nrfunc=func;
481: for (j=1;j<=n;j++) {
482: pcom[j]=p[j];
483: xicom[j]=xi[j];
484: }
485: ax=0.0;
486: xx=1.0;
487: mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim);
488: *fret=brent(ax,xx,bx,f1dim,TOL,&xmin);
489: #ifdef DEBUG
490: printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
491: #endif
492: for (j=1;j<=n;j++) {
493: xi[j] *= xmin;
494: p[j] += xi[j];
495: }
496: free_vector(xicom,1,n);
497: free_vector(pcom,1,n);
498: }
499:
500: /*************** powell ************************/
501: void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,
502: double (*func)(double []))
503: {
504: void linmin(double p[], double xi[], int n, double *fret,
505: double (*func)(double []));
506: int i,ibig,j;
507: double del,t,*pt,*ptt,*xit;
508: double fp,fptt;
509: double *xits;
510: pt=vector(1,n);
511: ptt=vector(1,n);
512: xit=vector(1,n);
513: xits=vector(1,n);
514: *fret=(*func)(p);
515: for (j=1;j<=n;j++) pt[j]=p[j];
516: for (*iter=1;;++(*iter)) {
517: fp=(*fret);
518: ibig=0;
519: del=0.0;
520: printf("\nPowell iter=%d -2*LL=%.12f",*iter,*fret);
521: for (i=1;i<=n;i++)
522: printf(" %d %.12f",i, p[i]);
523: printf("\n");
524: for (i=1;i<=n;i++) {
525: for (j=1;j<=n;j++) xit[j]=xi[j][i];
526: fptt=(*fret);
527: #ifdef DEBUG
528: printf("fret=%lf \n",*fret);
529: #endif
530: printf("%d",i);fflush(stdout);
531: linmin(p,xit,n,fret,func);
532: if (fabs(fptt-(*fret)) > del) {
533: del=fabs(fptt-(*fret));
534: ibig=i;
535: }
536: #ifdef DEBUG
537: printf("%d %.12e",i,(*fret));
538: for (j=1;j<=n;j++) {
539: xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
540: printf(" x(%d)=%.12e",j,xit[j]);
541: }
542: for(j=1;j<=n;j++)
543: printf(" p=%.12e",p[j]);
544: printf("\n");
545: #endif
546: }
547: if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {
548: #ifdef DEBUG
549: int k[2],l;
550: k[0]=1;
551: k[1]=-1;
552: printf("Max: %.12e",(*func)(p));
553: for (j=1;j<=n;j++)
554: printf(" %.12e",p[j]);
555: printf("\n");
556: for(l=0;l<=1;l++) {
557: for (j=1;j<=n;j++) {
558: ptt[j]=p[j]+(p[j]-pt[j])*k[l];
559: printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
560: }
561: printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
562: }
563: #endif
564:
565:
566: free_vector(xit,1,n);
567: free_vector(xits,1,n);
568: free_vector(ptt,1,n);
569: free_vector(pt,1,n);
570: return;
571: }
572: if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");
573: for (j=1;j<=n;j++) {
574: ptt[j]=2.0*p[j]-pt[j];
575: xit[j]=p[j]-pt[j];
576: pt[j]=p[j];
577: }
578: fptt=(*func)(ptt);
579: if (fptt < fp) {
580: t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt);
581: if (t < 0.0) {
582: linmin(p,xit,n,fret,func);
583: for (j=1;j<=n;j++) {
584: xi[j][ibig]=xi[j][n];
585: xi[j][n]=xit[j];
586: }
587: #ifdef DEBUG
588: printf("Direction changed last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
589: for(j=1;j<=n;j++)
590: printf(" %.12e",xit[j]);
591: printf("\n");
592: #endif
593: }
594: }
595: }
596: }
597:
598: /**** Prevalence limit ****************/
599:
600: double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)
601: {
602: /* Computes the prevalence limit in each live state at age x by left multiplying the unit
603: matrix by transitions matrix until convergence is reached */
604:
605: int i, ii,j,k;
606: double min, max, maxmin, maxmax,sumnew=0.;
607: double **matprod2();
608: double **out, cov[NCOVMAX], **pmij();
609: double **newm;
610: double agefin, delaymax=50 ; /* Max number of years to converge */
611:
612: for (ii=1;ii<=nlstate+ndeath;ii++)
613: for (j=1;j<=nlstate+ndeath;j++){
614: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
615: }
616: /* Even if hstepm = 1, at least one multiplication by the unit matrix */
617: for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
618: newm=savm;
619: /* Covariates have to be included here again */
620: cov[1]=1.;
621: cov[2]=agefin;
622: if (cptcovn>0){
623: for (k=1; k<=cptcovn;k++) {cov[2+k]=nbcode[Tvar[k]][codtab[ij][k]];/*printf("Tcode[ij]=%d nbcode=%d\n",Tcode[ij],nbcode[k][Tcode[ij]]);*/}
624: }
625: out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);
626:
627: savm=oldm;
628: oldm=newm;
629: maxmax=0.;
630: for(j=1;j<=nlstate;j++){
631: min=1.;
632: max=0.;
633: for(i=1; i<=nlstate; i++) {
634: sumnew=0;
635: for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
636: prlim[i][j]= newm[i][j]/(1-sumnew);
637: max=FMAX(max,prlim[i][j]);
638: min=FMIN(min,prlim[i][j]);
639: }
640: maxmin=max-min;
641: maxmax=FMAX(maxmax,maxmin);
642: }
643: if(maxmax < ftolpl){
644: return prlim;
645: }
646: }
647: }
648:
649: /*************** transition probabilities **********/
650:
651: double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
652: {
653: double s1, s2;
654: /*double t34;*/
655: int i,j,j1, nc, ii, jj;
656:
657: for(i=1; i<= nlstate; i++){
658: for(j=1; j<i;j++){
659: for (nc=1, s2=0.;nc <=ncovmodel; nc++){
660: /*s2 += param[i][j][nc]*cov[nc];*/
661: s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
662: /*printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2);*/
663: }
664: ps[i][j]=s2;
665: /*printf("s1=%.17e, s2=%.17e\n",s1,s2);*/
666: }
667: for(j=i+1; j<=nlstate+ndeath;j++){
668: for (nc=1, s2=0.;nc <=ncovmodel; nc++){
669: s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
670: /*printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2);*/
671: }
672: ps[i][j]=s2;
673: }
674: }
675: for(i=1; i<= nlstate; i++){
676: s1=0;
677: for(j=1; j<i; j++)
678: s1+=exp(ps[i][j]);
679: for(j=i+1; j<=nlstate+ndeath; j++)
680: s1+=exp(ps[i][j]);
681: ps[i][i]=1./(s1+1.);
682: for(j=1; j<i; j++)
683: ps[i][j]= exp(ps[i][j])*ps[i][i];
684: for(j=i+1; j<=nlstate+ndeath; j++)
685: ps[i][j]= exp(ps[i][j])*ps[i][i];
686: /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
687: } /* end i */
688:
689: for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
690: for(jj=1; jj<= nlstate+ndeath; jj++){
691: ps[ii][jj]=0;
692: ps[ii][ii]=1;
693: }
694: }
695:
696: /* for(ii=1; ii<= nlstate+ndeath; ii++){
697: for(jj=1; jj<= nlstate+ndeath; jj++){
698: printf("%lf ",ps[ii][jj]);
699: }
700: printf("\n ");
701: }
702: printf("\n ");printf("%lf ",cov[2]);*/
703: /*
704: for(i=1; i<= npar; i++) printf("%f ",x[i]);
705: goto end;*/
706: return ps;
707: }
708:
709: /**************** Product of 2 matrices ******************/
710:
711: double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)
712: {
713: /* Computes the matric product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
714: b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
715: /* in, b, out are matrice of pointers which should have been initialized
716: before: only the contents of out is modified. The function returns
717: a pointer to pointers identical to out */
718: long i, j, k;
719: for(i=nrl; i<= nrh; i++)
720: for(k=ncolol; k<=ncoloh; k++)
721: for(j=ncl,out[i][k]=0.; j<=nch; j++)
722: out[i][k] +=in[i][j]*b[j][k];
723:
724: return out;
725: }
726:
727:
728: /************* Higher Matrix Product ***************/
729:
730: double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
731: {
732: /* Computes the transition matrix starting at age 'age' over 'nhstepm*hstepm*stepm' month
733: duration (i.e. until
734: age (in years) age+nhstepm*stepm/12) by multiplying nhstepm*hstepm matrices.
735: Output is stored in matrix po[i][j][h] for h every 'hstepm' step
736: (typically every 2 years instead of every month which is too big).
737: Model is determined by parameters x and covariates have to be
738: included manually here.
739:
740: */
741:
742: int i, j, d, h, k;
743: double **out, cov[NCOVMAX];
744: double **newm;
745:
746: /* Hstepm could be zero and should return the unit matrix */
747: for (i=1;i<=nlstate+ndeath;i++)
748: for (j=1;j<=nlstate+ndeath;j++){
749: oldm[i][j]=(i==j ? 1.0 : 0.0);
750: po[i][j][0]=(i==j ? 1.0 : 0.0);
751: }
752: /* Even if hstepm = 1, at least one multiplication by the unit matrix */
753: for(h=1; h <=nhstepm; h++){
754: for(d=1; d <=hstepm; d++){
755: newm=savm;
756: /* Covariates have to be included here again */
757: cov[1]=1.;
758: cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
759: if (cptcovn>0){
760: for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][k]];
761: }
762: /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
763: /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
764: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,
765: pmij(pmmij,cov,ncovmodel,x,nlstate));
766: savm=oldm;
767: oldm=newm;
768: }
769: for(i=1; i<=nlstate+ndeath; i++)
770: for(j=1;j<=nlstate+ndeath;j++) {
771: po[i][j][h]=newm[i][j];
772: /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);
773: */
774: }
775: } /* end h */
776: return po;
777: }
778:
779:
780: /*************** log-likelihood *************/
781: double func( double *x)
782: {
783: int i, ii, j, k, mi, d;
784: double l, ll[NLSTATEMAX], cov[NCOVMAX];
785: double **out;
786: double sw; /* Sum of weights */
787: double lli; /* Individual log likelihood */
788: long ipmx;
789: /*extern weight */
790: /* We are differentiating ll according to initial status */
791: /* for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
792: /*for(i=1;i<imx;i++)
793: printf(" %d\n",s[4][i]);
794: */
795:
796: for(k=1; k<=nlstate; k++) ll[k]=0.;
797: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
798: for(mi=1; mi<= wav[i]-1; mi++){
799: for (ii=1;ii<=nlstate+ndeath;ii++)
800: for (j=1;j<=nlstate+ndeath;j++) oldm[ii][j]=(ii==j ? 1.0 : 0.0);
801: for(d=0; d<dh[mi][i]; d++){
802: newm=savm;
803: cov[1]=1.;
804: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
805: if (cptcovn>0){
1.3 lievre 806: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[1+k-1][i];
1.2 lievre 807: }
808: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
809: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
810: savm=oldm;
811: oldm=newm;
1.3 lievre 812:
813:
1.2 lievre 814: } /* end mult */
815:
816: lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);
817: /* printf(" %f ",out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/
818: ipmx +=1;
819: sw += weight[i];
820: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
821: } /* end of wave */
822: } /* end of individual */
823:
824: for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
825: /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
826: l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
827: return -l;
828: }
829:
830:
831: /*********** Maximum Likelihood Estimation ***************/
832:
833: void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
834: {
835: int i,j, iter;
836: double **xi,*delti;
837: double fret;
838: xi=matrix(1,npar,1,npar);
839: for (i=1;i<=npar;i++)
840: for (j=1;j<=npar;j++)
841: xi[i][j]=(i==j ? 1.0 : 0.0);
842: printf("Powell\n");
843: powell(p,xi,npar,ftol,&iter,&fret,func);
844:
845: printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));
846: fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f ",iter,func(p));
847:
848: }
849:
850: /**** Computes Hessian and covariance matrix ***/
851: void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
852: {
853: double **a,**y,*x,pd;
854: double **hess;
855: int i, j,jk;
856: int *indx;
857:
858: double hessii(double p[], double delta, int theta, double delti[]);
859: double hessij(double p[], double delti[], int i, int j);
860: void lubksb(double **a, int npar, int *indx, double b[]) ;
861: void ludcmp(double **a, int npar, int *indx, double *d) ;
862:
863:
864: hess=matrix(1,npar,1,npar);
865:
866: printf("\nCalculation of the hessian matrix. Wait...\n");
867: for (i=1;i<=npar;i++){
868: printf("%d",i);fflush(stdout);
869: hess[i][i]=hessii(p,ftolhess,i,delti);
870: /*printf(" %f ",p[i]);*/
871: }
872:
873: for (i=1;i<=npar;i++) {
874: for (j=1;j<=npar;j++) {
875: if (j>i) {
876: printf(".%d%d",i,j);fflush(stdout);
877: hess[i][j]=hessij(p,delti,i,j);
878: hess[j][i]=hess[i][j];
879: }
880: }
881: }
882: printf("\n");
883:
884: printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
885:
886: a=matrix(1,npar,1,npar);
887: y=matrix(1,npar,1,npar);
888: x=vector(1,npar);
889: indx=ivector(1,npar);
890: for (i=1;i<=npar;i++)
891: for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
892: ludcmp(a,npar,indx,&pd);
893:
894: for (j=1;j<=npar;j++) {
895: for (i=1;i<=npar;i++) x[i]=0;
896: x[j]=1;
897: lubksb(a,npar,indx,x);
898: for (i=1;i<=npar;i++){
899: matcov[i][j]=x[i];
900: }
901: }
902:
903: printf("\n#Hessian matrix#\n");
904: for (i=1;i<=npar;i++) {
905: for (j=1;j<=npar;j++) {
906: printf("%.3e ",hess[i][j]);
907: }
908: printf("\n");
909: }
910:
911: /* Recompute Inverse */
912: for (i=1;i<=npar;i++)
913: for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];
914: ludcmp(a,npar,indx,&pd);
915:
916: /* printf("\n#Hessian matrix recomputed#\n");
917:
918: for (j=1;j<=npar;j++) {
919: for (i=1;i<=npar;i++) x[i]=0;
920: x[j]=1;
921: lubksb(a,npar,indx,x);
922: for (i=1;i<=npar;i++){
923: y[i][j]=x[i];
924: printf("%.3e ",y[i][j]);
925: }
926: printf("\n");
927: }
928: */
929:
930: free_matrix(a,1,npar,1,npar);
931: free_matrix(y,1,npar,1,npar);
932: free_vector(x,1,npar);
933: free_ivector(indx,1,npar);
934: free_matrix(hess,1,npar,1,npar);
935:
936:
937: }
938:
939: /*************** hessian matrix ****************/
940: double hessii( double x[], double delta, int theta, double delti[])
941: {
942: int i;
943: int l=1, lmax=20;
944: double k1,k2;
945: double p2[NPARMAX+1];
946: double res;
947: double delt, delts, nkhi=10.,nkhif=1., khi=1.e-4;
948: double fx;
949: int k=0,kmax=10;
950: double l1;
951:
952: fx=func(x);
953: for (i=1;i<=npar;i++) p2[i]=x[i];
954: for(l=0 ; l <=lmax; l++){
955: l1=pow(10,l);
956: delts=delt;
957: for(k=1 ; k <kmax; k=k+1){
958: delt = delta*(l1*k);
959: p2[theta]=x[theta] +delt;
960: k1=func(p2)-fx;
961: p2[theta]=x[theta]-delt;
962: k2=func(p2)-fx;
963: /*res= (k1-2.0*fx+k2)/delt/delt; */
964: res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */
965:
966: #ifdef DEBUG
967: 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);
968: #endif
969: /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
970: if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
971: k=kmax;
972: }
973: else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
974: k=kmax; l=lmax*10.;
975: }
976: else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){
977: delts=delt;
978: }
979: }
980: }
981: delti[theta]=delts;
1.3 lievre 982: return res;
983:
1.2 lievre 984: }
985:
986: double hessij( double x[], double delti[], int thetai,int thetaj)
987: {
988: int i;
989: int l=1, l1, lmax=20;
990: double k1,k2,k3,k4,res,fx;
991: double p2[NPARMAX+1];
992: int k;
993:
994: fx=func(x);
995: for (k=1; k<=2; k++) {
996: for (i=1;i<=npar;i++) p2[i]=x[i];
997: p2[thetai]=x[thetai]+delti[thetai]/k;
998: p2[thetaj]=x[thetaj]+delti[thetaj]/k;
999: k1=func(p2)-fx;
1000:
1001: p2[thetai]=x[thetai]+delti[thetai]/k;
1002: p2[thetaj]=x[thetaj]-delti[thetaj]/k;
1003: k2=func(p2)-fx;
1004:
1005: p2[thetai]=x[thetai]-delti[thetai]/k;
1006: p2[thetaj]=x[thetaj]+delti[thetaj]/k;
1007: k3=func(p2)-fx;
1008:
1009: p2[thetai]=x[thetai]-delti[thetai]/k;
1010: p2[thetaj]=x[thetaj]-delti[thetaj]/k;
1011: k4=func(p2)-fx;
1012: res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */
1013: #ifdef DEBUG
1014: 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);
1015: #endif
1016: }
1017: return res;
1018: }
1019:
1020: /************** Inverse of matrix **************/
1021: void ludcmp(double **a, int n, int *indx, double *d)
1022: {
1023: int i,imax,j,k;
1024: double big,dum,sum,temp;
1025: double *vv;
1026:
1027: vv=vector(1,n);
1028: *d=1.0;
1029: for (i=1;i<=n;i++) {
1030: big=0.0;
1031: for (j=1;j<=n;j++)
1032: if ((temp=fabs(a[i][j])) > big) big=temp;
1033: if (big == 0.0) nrerror("Singular matrix in routine ludcmp");
1034: vv[i]=1.0/big;
1035: }
1036: for (j=1;j<=n;j++) {
1037: for (i=1;i<j;i++) {
1038: sum=a[i][j];
1039: for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];
1040: a[i][j]=sum;
1041: }
1042: big=0.0;
1043: for (i=j;i<=n;i++) {
1044: sum=a[i][j];
1045: for (k=1;k<j;k++)
1046: sum -= a[i][k]*a[k][j];
1047: a[i][j]=sum;
1048: if ( (dum=vv[i]*fabs(sum)) >= big) {
1049: big=dum;
1050: imax=i;
1051: }
1052: }
1053: if (j != imax) {
1054: for (k=1;k<=n;k++) {
1055: dum=a[imax][k];
1056: a[imax][k]=a[j][k];
1057: a[j][k]=dum;
1058: }
1059: *d = -(*d);
1060: vv[imax]=vv[j];
1061: }
1062: indx[j]=imax;
1063: if (a[j][j] == 0.0) a[j][j]=TINY;
1064: if (j != n) {
1065: dum=1.0/(a[j][j]);
1066: for (i=j+1;i<=n;i++) a[i][j] *= dum;
1067: }
1068: }
1069: free_vector(vv,1,n); /* Doesn't work */
1070: ;
1071: }
1072:
1073: void lubksb(double **a, int n, int *indx, double b[])
1074: {
1075: int i,ii=0,ip,j;
1076: double sum;
1077:
1078: for (i=1;i<=n;i++) {
1079: ip=indx[i];
1080: sum=b[ip];
1081: b[ip]=b[i];
1082: if (ii)
1083: for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];
1084: else if (sum) ii=i;
1085: b[i]=sum;
1086: }
1087: for (i=n;i>=1;i--) {
1088: sum=b[i];
1089: for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];
1090: b[i]=sum/a[i][i];
1091: }
1092: }
1093:
1094: /************ Frequencies ********************/
1095: void freqsummary(char fileres[], int agemin, int agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax)
1096: { /* Some frequencies */
1097:
1098: int i, m, jk, k1, i1, j1, bool, z1,z2,j;
1099: double ***freq; /* Frequencies */
1100: double *pp;
1101: double pos;
1102: FILE *ficresp;
1103: char fileresp[FILENAMELENGTH];
1104:
1105: pp=vector(1,nlstate);
1106:
1107: strcpy(fileresp,"p");
1108: strcat(fileresp,fileres);
1109: if((ficresp=fopen(fileresp,"w"))==NULL) {
1110: printf("Problem with prevalence resultfile: %s\n", fileresp);
1111: exit(0);
1112: }
1113: freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);
1114: j1=0;
1115:
1116: j=cptcovn;
1117: if (cptcovn<1) {j=1;ncodemax[1]=1;}
1118:
1119: for(k1=1; k1<=j;k1++){
1120: for(i1=1; i1<=ncodemax[k1];i1++){
1121: j1++;
1122:
1123: for (i=-1; i<=nlstate+ndeath; i++)
1124: for (jk=-1; jk<=nlstate+ndeath; jk++)
1125: for(m=agemin; m <= agemax+3; m++)
1126: freq[i][jk][m]=0;
1127:
1128: for (i=1; i<=imx; i++) {
1129: bool=1;
1130: if (cptcovn>0) {
1131: for (z1=1; z1<=cptcovn; z1++)
1132: if (covar[Tvar[z1]][i]!= nbcode[Tvar[z1]][codtab[j1][z1]]) bool=0;
1133: }
1134: if (bool==1) {
1135: for(m=firstpass; m<=lastpass-1; m++){
1136: if(agev[m][i]==0) agev[m][i]=agemax+1;
1137: if(agev[m][i]==1) agev[m][i]=agemax+2;
1138: freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
1139: freq[s[m][i]][s[m+1][i]][(int) agemax+3] += weight[i];
1140: }
1141: }
1142: }
1143: if (cptcovn>0) {
1144: fprintf(ficresp, "\n#Variable");
1145: for (z1=1; z1<=cptcovn; z1++) fprintf(ficresp, " V%d=%d",Tvar[z1],nbcode[Tvar[z1]][codtab[j1][z1]]);
1146: }
1147: fprintf(ficresp, "\n#");
1148: for(i=1; i<=nlstate;i++)
1149: fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
1150: fprintf(ficresp, "\n");
1151:
1152: for(i=(int)agemin; i <= (int)agemax+3; i++){
1153: if(i==(int)agemax+3)
1154: printf("Total");
1155: else
1156: printf("Age %d", i);
1157: for(jk=1; jk <=nlstate ; jk++){
1158: for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
1159: pp[jk] += freq[jk][m][i];
1160: }
1161: for(jk=1; jk <=nlstate ; jk++){
1162: for(m=-1, pos=0; m <=0 ; m++)
1163: pos += freq[jk][m][i];
1164: if(pp[jk]>=1.e-10)
1165: printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
1166: else
1167: printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
1168: }
1169: for(jk=1; jk <=nlstate ; jk++){
1170: for(m=1, pp[jk]=0; m <=nlstate+ndeath; m++)
1171: pp[jk] += freq[jk][m][i];
1172: }
1173: for(jk=1,pos=0; jk <=nlstate ; jk++)
1174: pos += pp[jk];
1175: for(jk=1; jk <=nlstate ; jk++){
1176: if(pos>=1.e-5)
1177: printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
1178: else
1179: printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
1180: if( i <= (int) agemax){
1181: if(pos>=1.e-5)
1182: fprintf(ficresp," %d %.5f %.0f %.0f",i,pp[jk]/pos, pp[jk],pos);
1183: else
1184: fprintf(ficresp," %d NaNq %.0f %.0f",i,pp[jk],pos);
1185: }
1186: }
1187: for(jk=-1; jk <=nlstate+ndeath; jk++)
1188: for(m=-1; m <=nlstate+ndeath; m++)
1189: if(freq[jk][m][i] !=0 ) printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
1190: if(i <= (int) agemax)
1191: fprintf(ficresp,"\n");
1192: printf("\n");
1193: }
1194: }
1195: }
1196:
1197: fclose(ficresp);
1198: free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);
1199: free_vector(pp,1,nlstate);
1200:
1201: } /* End of Freq */
1202:
1203: /************* Waves Concatenation ***************/
1204:
1205: void concatwav(int wav[], int **dh, int **mw, int **s, double *agedc, double **agev, int firstpass, int lastpass, int imx, int nlstate, int stepm)
1206: {
1207: /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
1208: Death is a valid wave (if date is known).
1209: mw[mi][i] is the mi (mi=1 to wav[i]) effective wave of individual i
1210: dh[m][i] of dh[mw[mi][i][i] is the delay between two effective waves m=mw[mi][i]
1211: and mw[mi+1][i]. dh depends on stepm.
1212: */
1213:
1214: int i, mi, m;
1215: int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
1216: float sum=0.;
1217:
1218: for(i=1; i<=imx; i++){
1219: mi=0;
1220: m=firstpass;
1221: while(s[m][i] <= nlstate){
1222: if(s[m][i]>=1)
1223: mw[++mi][i]=m;
1224: if(m >=lastpass)
1225: break;
1226: else
1227: m++;
1228: }/* end while */
1229: if (s[m][i] > nlstate){
1230: mi++; /* Death is another wave */
1231: /* if(mi==0) never been interviewed correctly before death */
1232: /* Only death is a correct wave */
1233: mw[mi][i]=m;
1234: }
1235:
1236: wav[i]=mi;
1237: if(mi==0)
1238: printf("Warning, no any valid information for:%d line=%d\n",num[i],i);
1239: }
1240:
1241: for(i=1; i<=imx; i++){
1242: for(mi=1; mi<wav[i];mi++){
1243: if (stepm <=0)
1244: dh[mi][i]=1;
1245: else{
1246: if (s[mw[mi+1][i]][i] > nlstate) {
1247: j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);
1248: if(j=0) j=1; /* Survives at least one month after exam */
1249: }
1250: else{
1251: j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
1252: k=k+1;
1253: if (j >= jmax) jmax=j;
1254: else if (j <= jmin)jmin=j;
1255: sum=sum+j;
1256: }
1257: jk= j/stepm;
1258: jl= j -jk*stepm;
1259: ju= j -(jk+1)*stepm;
1260: if(jl <= -ju)
1261: dh[mi][i]=jk;
1262: else
1263: dh[mi][i]=jk+1;
1264: if(dh[mi][i]==0)
1265: dh[mi][i]=1; /* At least one step */
1266: }
1267: }
1268: }
1269: printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,sum/k);
1270: }
1271: /*********** Tricode ****************************/
1272: void tricode(int *Tvar, int **nbcode, int imx)
1273: {
1274: int Ndum[80],ij, k, j, i;
1275: int cptcode=0;
1276: for (k=0; k<79; k++) Ndum[k]=0;
1277: for (k=1; k<=7; k++) ncodemax[k]=0;
1278:
1279: for (j=1; j<=cptcovn; j++) {
1280: for (i=1; i<=imx; i++) {
1281: ij=(int)(covar[Tvar[j]][i]);
1282: Ndum[ij]++;
1283: if (ij > cptcode) cptcode=ij;
1284: }
1285: /*printf("cptcode=%d cptcovn=%d ",cptcode,cptcovn);*/
1286: for (i=0; i<=cptcode; i++) {
1287: if(Ndum[i]!=0) ncodemax[j]++;
1288: }
1289:
1290: ij=1;
1291: for (i=1; i<=ncodemax[j]; i++) {
1292: for (k=0; k<=79; k++) {
1293: if (Ndum[k] != 0) {
1294: nbcode[Tvar[j]][ij]=k;
1295: ij++;
1296: }
1297: if (ij > ncodemax[j]) break;
1298: }
1299: }
1300: }
1301:
1302: }
1303:
1304: /*********** Health Expectancies ****************/
1305:
1306: void evsij(char fileres[], double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int ij)
1307: {
1308: /* Health expectancies */
1309: int i, j, nhstepm, hstepm, h;
1310: double age, agelim,hf;
1311: double ***p3mat;
1312:
1313: fprintf(ficreseij,"# Health expectancies\n");
1314: fprintf(ficreseij,"# Age");
1315: for(i=1; i<=nlstate;i++)
1316: for(j=1; j<=nlstate;j++)
1317: fprintf(ficreseij," %1d-%1d",i,j);
1318: fprintf(ficreseij,"\n");
1319:
1320: hstepm=1*YEARM; /* Every j years of age (in month) */
1321: hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */
1322:
1323: agelim=AGESUP;
1324: for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
1325: /* nhstepm age range expressed in number of stepm */
1326: nhstepm=(int) rint((agelim-age)*YEARM/stepm);
1327: /* Typically if 20 years = 20*12/6=40 stepm */
1328: if (stepm >= YEARM) hstepm=1;
1329: nhstepm = nhstepm/hstepm;/* Expressed in hstepm, typically 40/4=10 */
1330: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
1331: /* Computed by stepm unit matrices, product of hstepm matrices, stored
1332: in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
1333: hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);
1334:
1335:
1336: for(i=1; i<=nlstate;i++)
1337: for(j=1; j<=nlstate;j++)
1338: for (h=0, eij[i][j][(int)age]=0; h<=nhstepm; h++){
1339: eij[i][j][(int)age] +=p3mat[i][j][h];
1340: }
1341:
1342: hf=1;
1343: if (stepm >= YEARM) hf=stepm/YEARM;
1344: fprintf(ficreseij,"%.0f",age );
1345: for(i=1; i<=nlstate;i++)
1346: for(j=1; j<=nlstate;j++){
1347: fprintf(ficreseij," %.4f", hf*eij[i][j][(int)age]);
1348: }
1349: fprintf(ficreseij,"\n");
1350: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
1351: }
1352: }
1353:
1354: /************ Variance ******************/
1355: 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)
1356: {
1357: /* Variance of health expectancies */
1358: /* double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
1359: double **newm;
1360: double **dnewm,**doldm;
1361: int i, j, nhstepm, hstepm, h;
1362: int k, cptcode;
1363: double *xp;
1364: double **gp, **gm;
1365: double ***gradg, ***trgradg;
1366: double ***p3mat;
1367: double age,agelim;
1368: int theta;
1369:
1370: fprintf(ficresvij,"# Covariances of life expectancies\n");
1371: fprintf(ficresvij,"# Age");
1372: for(i=1; i<=nlstate;i++)
1373: for(j=1; j<=nlstate;j++)
1374: fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);
1375: fprintf(ficresvij,"\n");
1376:
1377: xp=vector(1,npar);
1378: dnewm=matrix(1,nlstate,1,npar);
1379: doldm=matrix(1,nlstate,1,nlstate);
1380:
1381: hstepm=1*YEARM; /* Every year of age */
1382: hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */
1383: agelim = AGESUP;
1384: for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
1385: nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
1386: if (stepm >= YEARM) hstepm=1;
1387: nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
1388: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
1389: gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
1390: gp=matrix(0,nhstepm,1,nlstate);
1391: gm=matrix(0,nhstepm,1,nlstate);
1392:
1393: for(theta=1; theta <=npar; theta++){
1394: for(i=1; i<=npar; i++){ /* Computes gradient */
1395: xp[i] = x[i] + (i==theta ?delti[theta]:0);
1396: }
1397: hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
1398: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
1399: for(j=1; j<= nlstate; j++){
1400: for(h=0; h<=nhstepm; h++){
1401: for(i=1, gp[h][j]=0.;i<=nlstate;i++)
1402: gp[h][j] += prlim[i][i]*p3mat[i][j][h];
1403: }
1404: }
1405:
1406: for(i=1; i<=npar; i++) /* Computes gradient */
1407: xp[i] = x[i] - (i==theta ?delti[theta]:0);
1408: hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
1409: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
1410: for(j=1; j<= nlstate; j++){
1411: for(h=0; h<=nhstepm; h++){
1412: for(i=1, gm[h][j]=0.;i<=nlstate;i++)
1413: gm[h][j] += prlim[i][i]*p3mat[i][j][h];
1414: }
1415: }
1416: for(j=1; j<= nlstate; j++)
1417: for(h=0; h<=nhstepm; h++){
1418: gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
1419: }
1420: } /* End theta */
1421:
1422: trgradg =ma3x(0,nhstepm,1,nlstate,1,npar);
1423:
1424: for(h=0; h<=nhstepm; h++)
1425: for(j=1; j<=nlstate;j++)
1426: for(theta=1; theta <=npar; theta++)
1427: trgradg[h][j][theta]=gradg[h][theta][j];
1428:
1429: for(i=1;i<=nlstate;i++)
1430: for(j=1;j<=nlstate;j++)
1431: vareij[i][j][(int)age] =0.;
1432: for(h=0;h<=nhstepm;h++){
1433: for(k=0;k<=nhstepm;k++){
1434: matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
1435: matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
1436: for(i=1;i<=nlstate;i++)
1437: for(j=1;j<=nlstate;j++)
1438: vareij[i][j][(int)age] += doldm[i][j];
1439: }
1440: }
1441: h=1;
1442: if (stepm >= YEARM) h=stepm/YEARM;
1443: fprintf(ficresvij,"%.0f ",age );
1444: for(i=1; i<=nlstate;i++)
1445: for(j=1; j<=nlstate;j++){
1446: fprintf(ficresvij," %.4f", h*vareij[i][j][(int)age]);
1447: }
1448: fprintf(ficresvij,"\n");
1449: free_matrix(gp,0,nhstepm,1,nlstate);
1450: free_matrix(gm,0,nhstepm,1,nlstate);
1451: free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
1452: free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
1453: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
1454: } /* End age */
1455:
1456: free_vector(xp,1,npar);
1457: free_matrix(doldm,1,nlstate,1,npar);
1458: free_matrix(dnewm,1,nlstate,1,nlstate);
1459:
1460: }
1461:
1462: /************ Variance of prevlim ******************/
1463: 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)
1464: {
1465: /* Variance of prevalence limit */
1466: /* double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
1467: double **newm;
1468: double **dnewm,**doldm;
1469: int i, j, nhstepm, hstepm;
1470: int k, cptcode;
1471: double *xp;
1472: double *gp, *gm;
1473: double **gradg, **trgradg;
1474: double age,agelim;
1475: int theta;
1476:
1477: fprintf(ficresvpl,"# Standard deviation of prevalences limit\n");
1478: fprintf(ficresvpl,"# Age");
1479: for(i=1; i<=nlstate;i++)
1480: fprintf(ficresvpl," %1d-%1d",i,i);
1481: fprintf(ficresvpl,"\n");
1482:
1483: xp=vector(1,npar);
1484: dnewm=matrix(1,nlstate,1,npar);
1485: doldm=matrix(1,nlstate,1,nlstate);
1486:
1487: hstepm=1*YEARM; /* Every year of age */
1488: hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */
1489: agelim = AGESUP;
1490: for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
1491: nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
1492: if (stepm >= YEARM) hstepm=1;
1493: nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
1494: gradg=matrix(1,npar,1,nlstate);
1495: gp=vector(1,nlstate);
1496: gm=vector(1,nlstate);
1497:
1498: for(theta=1; theta <=npar; theta++){
1499: for(i=1; i<=npar; i++){ /* Computes gradient */
1500: xp[i] = x[i] + (i==theta ?delti[theta]:0);
1501: }
1502: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
1503: for(i=1;i<=nlstate;i++)
1504: gp[i] = prlim[i][i];
1505:
1506: for(i=1; i<=npar; i++) /* Computes gradient */
1507: xp[i] = x[i] - (i==theta ?delti[theta]:0);
1508: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
1509: for(i=1;i<=nlstate;i++)
1510: gm[i] = prlim[i][i];
1511:
1512: for(i=1;i<=nlstate;i++)
1513: gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
1514: } /* End theta */
1515:
1516: trgradg =matrix(1,nlstate,1,npar);
1517:
1518: for(j=1; j<=nlstate;j++)
1519: for(theta=1; theta <=npar; theta++)
1520: trgradg[j][theta]=gradg[theta][j];
1521:
1522: for(i=1;i<=nlstate;i++)
1523: varpl[i][(int)age] =0.;
1524: matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
1525: matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
1526: for(i=1;i<=nlstate;i++)
1527: varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
1528:
1529: fprintf(ficresvpl,"%.0f ",age );
1530: for(i=1; i<=nlstate;i++)
1531: fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
1532: fprintf(ficresvpl,"\n");
1533: free_vector(gp,1,nlstate);
1534: free_vector(gm,1,nlstate);
1535: free_matrix(gradg,1,npar,1,nlstate);
1536: free_matrix(trgradg,1,nlstate,1,npar);
1537: } /* End age */
1538:
1539: free_vector(xp,1,npar);
1540: free_matrix(doldm,1,nlstate,1,npar);
1541: free_matrix(dnewm,1,nlstate,1,nlstate);
1542:
1543: }
1544:
1545:
1546:
1547: /***********************************************/
1548: /**************** Main Program *****************/
1549: /***********************************************/
1550:
1551: /*int main(int argc, char *argv[])*/
1552: int main()
1553: {
1554:
1555: int i,j, k, n=MAXN,iter,m,size,cptcode, aaa, cptcod;
1556: double agedeb, agefin,hf;
1557: double agemin=1.e20, agemax=-1.e20;
1558:
1559: double fret;
1560: double **xi,tmp,delta;
1561:
1562: double dum; /* Dummy variable */
1563: double ***p3mat;
1564: int *indx;
1565: char line[MAXLINE], linepar[MAXLINE];
1566: char title[MAXLINE];
1567: char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH], filerespl[FILENAMELENGTH];
1568: char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH];
1569: char filerest[FILENAMELENGTH];
1570: char fileregp[FILENAMELENGTH];
1571: char path[80],pathc[80],pathcd[80],pathtot[80],model[20];
1572: int firstobs=1, lastobs=10;
1573: int sdeb, sfin; /* Status at beginning and end */
1574: int c, h , cpt,l;
1575: int ju,jl, mi;
1576: int i1,j1, k1,jk,aa,bb, stepsize;
1577: int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,**adl,*tab;
1578:
1579: int hstepm, nhstepm;
1580: double bage, fage, age, agelim, agebase;
1581: double ftolpl=FTOL;
1582: double **prlim;
1583: double *severity;
1584: double ***param; /* Matrix of parameters */
1585: double *p;
1586: double **matcov; /* Matrix of covariance */
1587: double ***delti3; /* Scale */
1588: double *delti; /* Scale */
1589: double ***eij, ***vareij;
1590: double **varpl; /* Variances of prevalence limits by age */
1591: double *epj, vepp;
1.4 ! lievre 1592: char version[80]="Imach version 0.64, May 2000, INED-EUROREVES ";
1.2 lievre 1593: char *alph[]={"a","a","b","c","d","e"}, str[4];
1594: char z[1]="c", occ;
1595: #include <sys/time.h>
1596: #include <time.h>
1597: char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];
1598: /* long total_usecs;
1599: struct timeval start_time, end_time;
1600:
1601: gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */
1602:
1603:
1.4 ! lievre 1604: printf("\nIMACH, Version 0.64a");
1.2 lievre 1605: printf("\nEnter the parameter file name: ");
1606:
1607: #ifdef windows
1608: scanf("%s",pathtot);
1.4 ! lievre 1609: cygwin_split_path(pathtot,path,optionfile);
! 1610: printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);
! 1611: chdir(path);
! 1612:
! 1613: /*size=30;
! 1614: getcwd(pathcd, size);
! 1615: printf("pathcd=%s, path=%s, optionfile=%s\n",pathcd,path,optionfile);
1.2 lievre 1616: cutv(path,optionfile,pathtot,'\\');
1617: chdir(path);
1618: replace(pathc,path);
1.4 ! lievre 1619: printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);
! 1620: */
1.2 lievre 1621: #endif
1622: #ifdef unix
1623: scanf("%s",optionfile);
1624: #endif
1625:
1626: /*-------- arguments in the command line --------*/
1627:
1628: strcpy(fileres,"r");
1629: strcat(fileres, optionfile);
1630:
1631: /*---------arguments file --------*/
1632:
1633: if((ficpar=fopen(optionfile,"r"))==NULL) {
1634: printf("Problem with optionfile %s\n",optionfile);
1635: goto end;
1636: }
1637:
1638: strcpy(filereso,"o");
1639: strcat(filereso,fileres);
1640: if((ficparo=fopen(filereso,"w"))==NULL) {
1641: printf("Problem with Output resultfile: %s\n", filereso);goto end;
1642: }
1643:
1644: /* Reads comments: lines beginning with '#' */
1645: while((c=getc(ficpar))=='#' && c!= EOF){
1646: ungetc(c,ficpar);
1647: fgets(line, MAXLINE, ficpar);
1648: puts(line);
1649: fputs(line,ficparo);
1650: }
1651: ungetc(c,ficpar);
1652:
1653: 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);
1654: 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);
1655: 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);
1656:
1657: covar=matrix(1,NCOVMAX,1,n);
1658: if (strlen(model)<=1) cptcovn=0;
1659: else {
1660: j=0;
1661: j=nbocc(model,'+');
1662: cptcovn=j+1;
1663: }
1664:
1665: ncovmodel=2+cptcovn;
1666: nvar=ncovmodel-1; /* Suppressing age as a basic covariate */
1667:
1668: /* Read guess parameters */
1669: /* Reads comments: lines beginning with '#' */
1670: while((c=getc(ficpar))=='#' && c!= EOF){
1671: ungetc(c,ficpar);
1672: fgets(line, MAXLINE, ficpar);
1673: puts(line);
1674: fputs(line,ficparo);
1675: }
1676: ungetc(c,ficpar);
1677:
1678: param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
1679: for(i=1; i <=nlstate; i++)
1680: for(j=1; j <=nlstate+ndeath-1; j++){
1681: fscanf(ficpar,"%1d%1d",&i1,&j1);
1682: fprintf(ficparo,"%1d%1d",i1,j1);
1683: printf("%1d%1d",i,j);
1684: for(k=1; k<=ncovmodel;k++){
1685: fscanf(ficpar," %lf",¶m[i][j][k]);
1686: printf(" %lf",param[i][j][k]);
1687: fprintf(ficparo," %lf",param[i][j][k]);
1688: }
1689: fscanf(ficpar,"\n");
1690: printf("\n");
1691: fprintf(ficparo,"\n");
1692: }
1693:
1694: npar= (nlstate+ndeath-1)*nlstate*ncovmodel;
1695: p=param[1][1];
1696:
1697: /* Reads comments: lines beginning with '#' */
1698: while((c=getc(ficpar))=='#' && c!= EOF){
1699: ungetc(c,ficpar);
1700: fgets(line, MAXLINE, ficpar);
1701: puts(line);
1702: fputs(line,ficparo);
1703: }
1704: ungetc(c,ficpar);
1705:
1706: delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
1707: delti=vector(1,npar); /* Scale of each paramater (output from hesscov) */
1708: for(i=1; i <=nlstate; i++){
1709: for(j=1; j <=nlstate+ndeath-1; j++){
1710: fscanf(ficpar,"%1d%1d",&i1,&j1);
1711: printf("%1d%1d",i,j);
1712: fprintf(ficparo,"%1d%1d",i1,j1);
1713: for(k=1; k<=ncovmodel;k++){
1714: fscanf(ficpar,"%le",&delti3[i][j][k]);
1715: printf(" %le",delti3[i][j][k]);
1716: fprintf(ficparo," %le",delti3[i][j][k]);
1717: }
1718: fscanf(ficpar,"\n");
1719: printf("\n");
1720: fprintf(ficparo,"\n");
1721: }
1722: }
1723: delti=delti3[1][1];
1724:
1725: /* Reads comments: lines beginning with '#' */
1726: while((c=getc(ficpar))=='#' && c!= EOF){
1727: ungetc(c,ficpar);
1728: fgets(line, MAXLINE, ficpar);
1729: puts(line);
1730: fputs(line,ficparo);
1731: }
1732: ungetc(c,ficpar);
1733:
1734: matcov=matrix(1,npar,1,npar);
1735: for(i=1; i <=npar; i++){
1736: fscanf(ficpar,"%s",&str);
1737: printf("%s",str);
1738: fprintf(ficparo,"%s",str);
1739: for(j=1; j <=i; j++){
1740: fscanf(ficpar," %le",&matcov[i][j]);
1741: printf(" %.5le",matcov[i][j]);
1742: fprintf(ficparo," %.5le",matcov[i][j]);
1743: }
1744: fscanf(ficpar,"\n");
1745: printf("\n");
1746: fprintf(ficparo,"\n");
1747: }
1748: for(i=1; i <=npar; i++)
1749: for(j=i+1;j<=npar;j++)
1750: matcov[i][j]=matcov[j][i];
1751:
1752: printf("\n");
1753:
1754:
1755: if(mle==1){
1756: /*-------- data file ----------*/
1757: if((ficres =fopen(fileres,"w"))==NULL) {
1758: printf("Problem with resultfile: %s\n", fileres);goto end;
1759: }
1760: fprintf(ficres,"#%s\n",version);
1761:
1762: if((fic=fopen(datafile,"r"))==NULL) {
1763: printf("Problem with datafile: %s\n", datafile);goto end;
1764: }
1765:
1766: n= lastobs;
1767: severity = vector(1,maxwav);
1768: outcome=imatrix(1,maxwav+1,1,n);
1769: num=ivector(1,n);
1770: moisnais=vector(1,n);
1771: annais=vector(1,n);
1772: moisdc=vector(1,n);
1773: andc=vector(1,n);
1774: agedc=vector(1,n);
1775: cod=ivector(1,n);
1776: weight=vector(1,n);
1777: for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */
1778: mint=matrix(1,maxwav,1,n);
1779: anint=matrix(1,maxwav,1,n);
1780: s=imatrix(1,maxwav+1,1,n);
1781: adl=imatrix(1,maxwav+1,1,n);
1782: tab=ivector(1,NCOVMAX);
1.3 lievre 1783: ncodemax=ivector(1,8);
1.2 lievre 1784:
1785: i=1;
1786: while (fgets(line, MAXLINE, fic) != NULL) {
1787: if ((i >= firstobs) && (i <=lastobs)) {
1788:
1789: for (j=maxwav;j>=1;j--){
1790: cutv(stra, strb,line,' '); s[j][i]=atoi(strb);
1791: strcpy(line,stra);
1792: cutv(stra, strb,line,'/'); anint[j][i]=(double)(atoi(strb)); strcpy(line,stra);
1793: cutv(stra, strb,line,' '); mint[j][i]=(double)(atoi(strb)); strcpy(line,stra);
1794: }
1795:
1796: cutv(stra, strb,line,'/'); andc[i]=(double)(atoi(strb)); strcpy(line,stra);
1797: cutv(stra, strb,line,' '); moisdc[i]=(double)(atoi(strb)); strcpy(line,stra);
1798:
1799: cutv(stra, strb,line,'/'); annais[i]=(double)(atoi(strb)); strcpy(line,stra);
1800: cutv(stra, strb,line,' '); moisnais[i]=(double)(atoi(strb)); strcpy(line,stra);
1801:
1802: cutv(stra, strb,line,' '); weight[i]=(double)(atoi(strb)); strcpy(line,stra);
1803: for (j=ncov;j>=1;j--){
1804: cutv(stra, strb,line,' '); covar[j][i]=(double)(atoi(strb)); strcpy(line,stra);
1805: }
1806: num[i]=atol(stra);
1807:
1.3 lievre 1808: /*printf("%d %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.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]), (mint[5][i]), (anint[5][i]), (s[5][i]), (mint[6][i]), (anint[6][i]), (s[6][i]));*/
1.2 lievre 1809:
1810: i=i+1;
1811: }
1812: }
1.3 lievre 1813:
1.2 lievre 1814: /*scanf("%d",i);*/
1.3 lievre 1815: imx=i-1; /* Number of individuals */
1.2 lievre 1816:
1817: /* Calculation of the number of parameter from char model*/
1818: Tvar=ivector(1,8);
1819:
1820: if (strlen(model) >1){
1821: j=0;
1822: j=nbocc(model,'+');
1823: cptcovn=j+1;
1.3 lievre 1824:
1.2 lievre 1825: strcpy(modelsav,model);
1826: if (j==0) {
1827: cutv(stra,strb,modelsav,'V'); Tvar[1]=atoi(strb);
1828: }
1829: else {
1830: for(i=j; i>=1;i--){
1831: cutv(stra,strb,modelsav,'+');
1832: if (strchr(strb,'*')) {
1833: cutv(strd,strc,strb,'*');
1834: cutv(strb,stre,strc,'V');Tvar[i+1]=ncov+1;
1835: cutv(strb,strc,strd,'V');
1836: for (k=1; k<=lastobs;k++)
1837: covar[ncov+1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];
1838: }
1.3 lievre 1839: else {cutv(strd,strc,strb,'V');
1840: Tvar[i+1]=atoi(strc);
1.2 lievre 1841: }
1.3 lievre 1842: strcpy(modelsav,stra);
1.2 lievre 1843: }
1.3 lievre 1844: cutv(strd,strc,stra,'V');
1.2 lievre 1845: Tvar[1]=atoi(strc);
1846: }
1847: }
1.3 lievre 1848: /*printf("tvar=%d ",Tvar[1]);
1849: scanf("%d ",i);*/
1.2 lievre 1850: fclose(fic);
1851:
1852: if (weightopt != 1) { /* Maximisation without weights*/
1853: for(i=1;i<=n;i++) weight[i]=1.0;
1854: }
1855: /*-calculation of age at interview from date of interview and age at death -*/
1856: agev=matrix(1,maxwav,1,imx);
1857:
1858: for (i=1; i<=imx; i++) {
1859: agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);
1860: for(m=1; (m<= maxwav); m++){
1861: if(s[m][i] >0){
1862: if (s[m][i] == nlstate+1) {
1863: if(agedc[i]>0)
1864: if(moisdc[i]!=99 && andc[i]!=9999)
1865: agev[m][i]=agedc[i];
1866: else{
1867: printf("Warning negative age at death: %d line:%d\n",num[i],i);
1868: agev[m][i]=-1;
1869: }
1870: }
1871: else if(s[m][i] !=9){ /* Should no more exist */
1872: agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);
1.3 lievre 1873: if(mint[m][i]==99 || anint[m][i]==9999)
1.2 lievre 1874: agev[m][i]=1;
1875: else if(agev[m][i] <agemin){
1876: agemin=agev[m][i];
1877: /*printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], agemin);*/
1878: }
1879: else if(agev[m][i] >agemax){
1880: agemax=agev[m][i];
1881: /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/
1882: }
1883: /*agev[m][i]=anint[m][i]-annais[i];*/
1884: /* agev[m][i] = age[i]+2*m;*/
1885: }
1886: else { /* =9 */
1887: agev[m][i]=1;
1888: s[m][i]=-1;
1889: }
1890: }
1891: else /*= 0 Unknown */
1892: agev[m][i]=1;
1893: }
1894:
1895: }
1896: for (i=1; i<=imx; i++) {
1897: for(m=1; (m<= maxwav); m++){
1898: if (s[m][i] > (nlstate+ndeath)) {
1899: printf("Error: Wrong value in nlstate or ndeath\n");
1900: goto end;
1901: }
1902: }
1903: }
1904:
1905: printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);
1906:
1907: free_vector(severity,1,maxwav);
1908: free_imatrix(outcome,1,maxwav+1,1,n);
1909: free_vector(moisnais,1,n);
1910: free_vector(annais,1,n);
1911: free_matrix(mint,1,maxwav,1,n);
1912: free_matrix(anint,1,maxwav,1,n);
1913: free_vector(moisdc,1,n);
1914: free_vector(andc,1,n);
1915:
1916:
1917: wav=ivector(1,imx);
1918: dh=imatrix(1,lastpass-firstpass+1,1,imx);
1919: mw=imatrix(1,lastpass-firstpass+1,1,imx);
1920:
1921: /* Concatenates waves */
1922: concatwav(wav, dh, mw, s, agedc, agev, firstpass, lastpass, imx, nlstate, stepm);
1923:
1924:
1925: Tcode=ivector(1,100);
1926: nbcode=imatrix(1,nvar,1,8);
1927: ncodemax[1]=1;
1928: if (cptcovn > 0) tricode(Tvar,nbcode,imx);
1929:
1930: codtab=imatrix(1,100,1,10);
1931: h=0;
1932: m=pow(2,cptcovn);
1933:
1934: for(k=1;k<=cptcovn; k++){
1935: for(i=1; i <=(m/pow(2,k));i++){
1936: for(j=1; j <= ncodemax[k]; j++){
1937: for(cpt=1; cpt <=(m/pow(2,cptcovn+1-k)); cpt++){
1938: h++;
1939: if (h>m) h=1;codtab[h][k]=j;
1940: }
1941: }
1942: }
1943: }
1944:
1945: /*for(i=1; i <=m ;i++){
1946: for(k=1; k <=cptcovn; k++){
1947: printf("i=%d k=%d %d ",i,k,codtab[i][k]);
1948: }
1949: printf("\n");
1.3 lievre 1950: }*/
1951: /*scanf("%d",i);*/
1.2 lievre 1952:
1953: /* Calculates basic frequencies. Computes observed prevalence at single age
1954: and prints on file fileres'p'. */
1955: freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax);
1956:
1.3 lievre 1957:
1958: /*scanf("%d ",i);*/
1959:
1960:
1.2 lievre 1961: pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
1962: oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
1963: newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
1964: savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
1965: oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */
1966:
1967: /* For Powell, parameters are in a vector p[] starting at p[1]
1968: so we point p on param[1][1] so that p[1] maps on param[1][1][1] */
1969: p=param[1][1]; /* *(*(*(param +1)+1)+0) */
1.3 lievre 1970:
1.2 lievre 1971: mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);
1972:
1973:
1974: /*--------- results files --------------*/
1975: 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);
1976:
1977: jk=1;
1978: fprintf(ficres,"# Parameters\n");
1979: printf("# Parameters\n");
1980: for(i=1,jk=1; i <=nlstate; i++){
1981: for(k=1; k <=(nlstate+ndeath); k++){
1982: if (k != i)
1983: {
1984: printf("%d%d ",i,k);
1985: fprintf(ficres,"%1d%1d ",i,k);
1986: for(j=1; j <=ncovmodel; j++){
1987: printf("%f ",p[jk]);
1988: fprintf(ficres,"%f ",p[jk]);
1989: jk++;
1990: }
1991: printf("\n");
1992: fprintf(ficres,"\n");
1993: }
1994: }
1995: }
1996:
1997: /* Computing hessian and covariance matrix */
1998: ftolhess=ftol; /* Usually correct */
1999: hesscov(matcov, p, npar, delti, ftolhess, func);
2000: fprintf(ficres,"# Scales\n");
2001: printf("# Scales\n");
2002: for(i=1,jk=1; i <=nlstate; i++){
2003: for(j=1; j <=nlstate+ndeath; j++){
2004: if (j!=i) {
2005: fprintf(ficres,"%1d%1d",i,j);
2006: printf("%1d%1d",i,j);
2007: for(k=1; k<=ncovmodel;k++){
2008: printf(" %.5e",delti[jk]);
2009: fprintf(ficres," %.5e",delti[jk]);
2010: jk++;
2011: }
2012: printf("\n");
2013: fprintf(ficres,"\n");
2014: }
2015: }
2016: }
2017:
2018: k=1;
2019: fprintf(ficres,"# Covariance\n");
2020: printf("# Covariance\n");
2021: for(i=1;i<=npar;i++){
2022: /* if (k>nlstate) k=1;
2023: i1=(i-1)/(ncovmodel*nlstate)+1;
2024: fprintf(ficres,"%s%d%d",alph[k],i1,tab[i]);
2025: printf("%s%d%d",alph[k],i1,tab[i]);*/
2026: fprintf(ficres,"%3d",i);
2027: printf("%3d",i);
2028: for(j=1; j<=i;j++){
2029: fprintf(ficres," %.5e",matcov[i][j]);
2030: printf(" %.5e",matcov[i][j]);
2031: }
2032: fprintf(ficres,"\n");
2033: printf("\n");
2034: k++;
2035: }
2036:
2037: while((c=getc(ficpar))=='#' && c!= EOF){
2038: ungetc(c,ficpar);
2039: fgets(line, MAXLINE, ficpar);
2040: puts(line);
2041: fputs(line,ficparo);
2042: }
2043: ungetc(c,ficpar);
2044:
2045: fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf\n",&agemin,&agemax, &bage, &fage);
2046:
2047: if (fage <= 2) {
2048: bage = agemin;
2049: fage = agemax;
2050: }
2051:
2052: fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");
2053: fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemax,bage,fage);
2054: /*------------ gnuplot -------------*/
2055: chdir(pathcd);
2056: if((ficgp=fopen("graph.plt","w"))==NULL) {
1.4 ! lievre 2057: printf("Problem with file graph.plt");goto end;
1.2 lievre 2058: }
2059: #ifdef windows
2060: fprintf(ficgp,"cd \"%s\" \n",pathc);
2061: #endif
2062: m=pow(2,cptcovn);
2063:
2064: /* 1eme*/
2065: for (cpt=1; cpt<= nlstate ; cpt ++) {
2066: for (k1=1; k1<= m ; k1 ++) {
2067:
2068: #ifdef windows
2069: 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);
2070: #endif
2071: #ifdef unix
2072: fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nplot [%.f:%.f] \"vpl%s\" u 1:2 \"\%%lf",agemin,fage,fileres);
2073: #endif
2074:
2075: for (i=1; i<= nlstate ; i ++) {
2076: if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
2077: else fprintf(ficgp," \%%*lf (\%%*lf)");
2078: }
2079: fprintf(ficgp,"\" t\"Stationary prevalence\" w l 0,\"vpl%s\" every :::%d::%d u 1:($2+2*$3) \"\%%lf",fileres,k1-1,k1-1);
2080: for (i=1; i<= nlstate ; i ++) {
2081: if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
2082: else fprintf(ficgp," \%%*lf (\%%*lf)");
2083: }
2084: fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"vpl%s\" every :::%d::%d u 1:($2-2*$3) \"\%%lf",fileres,k1-1,k1-1);
2085: for (i=1; i<= nlstate ; i ++) {
2086: if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
2087: else fprintf(ficgp," \%%*lf (\%%*lf)");
2088: }
2089: fprintf(ficgp,"\" t\"\" w l 1,\"p%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",fileres,k1-1,k1-1,2+4*(cpt-1));
2090: #ifdef unix
2091: fprintf(ficgp,"\nset ter gif small size 400,300");
2092: #endif
2093: fprintf(ficgp,"\nset out \"v%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);
2094: }
2095: }
2096: /*2 eme*/
2097:
2098: for (k1=1; k1<= m ; k1 ++) {
2099: fprintf(ficgp,"set ylabel \"Years\" \nset ter gif small size 400,300\nplot [%.f:%.f] ",agemin,fage);
2100:
2101: for (i=1; i<= nlstate+1 ; i ++) {
2102: k=2*i;
2103: fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:2 \"\%%lf",fileres,k1-1,k1-1);
2104: for (j=1; j<= nlstate+1 ; j ++) {
2105: if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
2106: else fprintf(ficgp," \%%*lf (\%%*lf)");
2107: }
2108: if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");
2109: else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);
2110: fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",fileres,k1-1,k1-1);
2111: for (j=1; j<= nlstate+1 ; j ++) {
2112: if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
2113: else fprintf(ficgp," \%%*lf (\%%*lf)");
2114: }
2115: fprintf(ficgp,"\" t\"\" w l 0,");
2116: fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",fileres,k1-1,k1-1);
2117: for (j=1; j<= nlstate+1 ; j ++) {
2118: if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
2119: else fprintf(ficgp," \%%*lf (\%%*lf)");
2120: }
2121: if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");
2122: else fprintf(ficgp,"\" t\"\" w l 0,");
2123: }
2124: fprintf(ficgp,"\nset out \"e%s%d.gif\" \nreplot\n\n",strtok(optionfile, "."),k1);
2125: }
2126:
2127: /*3eme*/
2128:
1.3 lievre 2129: for (k1=1; k1<= m ; k1 ++) {
1.2 lievre 2130: for (cpt=1; cpt<= nlstate ; cpt ++) {
2131: k=2+nlstate*(cpt-1);
2132: 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);
2133: for (i=1; i< nlstate ; i ++) {
2134: 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);
2135: }
2136: fprintf(ficgp,"\nset out \"exp%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);
2137: }
1.3 lievre 2138: }
1.2 lievre 2139:
2140: /* CV preval stat */
1.3 lievre 2141: for (k1=1; k1<= m ; k1 ++) {
1.2 lievre 2142: for (cpt=1; cpt<nlstate ; cpt ++) {
2143: k=3;
2144: 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/($%d",agemin,agemax,fileres,k1,k+cpt+1,k+1);
2145: for (i=1; i< nlstate ; i ++)
2146: fprintf(ficgp,"+$%d",k+i+1);
2147: fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);
2148:
2149: l=3+(nlstate+ndeath)*cpt;
2150: fprintf(ficgp,",\"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",fileres,k1,l+cpt+1,l+1);
2151: for (i=1; i< nlstate ; i ++) {
2152: l=3+(nlstate+ndeath)*cpt;
2153: fprintf(ficgp,"+$%d",l+i+1);
2154: }
2155: fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);
2156: fprintf(ficgp,"set out \"p%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);
2157: }
2158: }
1.3 lievre 2159:
1.2 lievre 2160: /* proba elementaires */
2161: for(i=1,jk=1; i <=nlstate; i++){
2162: for(k=1; k <=(nlstate+ndeath); k++){
2163: if (k != i) {
2164: /* fprintf(ficgp,"%1d%1d ",i,k);*/
2165: for(j=1; j <=ncovmodel; j++){
2166: fprintf(ficgp,"%s%1d%1d=%f ",alph[j],i,k,p[jk]);
2167: jk++;
2168: fprintf(ficgp,"\n");
2169: }
2170: }
2171: }
2172: }
2173: for(jk=1; jk <=m; jk++) {
2174: fprintf(ficgp,"\nset ter gif small size 400,300\nset log y\nplot [%.f:%.f] ",agemin,agemax);
2175: for(i=1; i <=nlstate; i++) {
2176: for(k=1; k <=(nlstate+ndeath); k++){
2177: if (k != i) {
2178: fprintf(ficgp," exp(a%d%d+b%d%d*x",i,k,i,k);
2179: for(j=3; j <=ncovmodel; j++)
2180: fprintf(ficgp,"+%s%d%d*%d",alph[j],i,k,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
2181: fprintf(ficgp,")/(1");
2182: for(k1=1; k1 <=(nlstate+ndeath); k1++)
2183: if (k1 != i) {
2184: fprintf(ficgp,"+exp(a%d%d+b%d%d*x",i,k1,i,k1);
2185: for(j=3; j <=ncovmodel; j++)
2186: fprintf(ficgp,"+%s%d%d*%d",alph[j],i,k,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
2187: fprintf(ficgp,")");
2188: }
2189: fprintf(ficgp,") t \"p%d%d\" ", i,k);
2190: if ((i+k)!= (nlstate*2+ndeath)) fprintf(ficgp,",");
2191: }
2192: }
2193: }
2194: fprintf(ficgp,"\nset out \"pe%s%d.gif\" \nreplot\n\n",strtok(optionfile, "."),jk);
2195: }
1.3 lievre 2196:
2197: fclose(ficgp);
2198:
2199: chdir(path);
1.2 lievre 2200: free_matrix(agev,1,maxwav,1,imx);
2201: free_ivector(wav,1,imx);
2202: free_imatrix(dh,1,lastpass-firstpass+1,1,imx);
2203: free_imatrix(mw,1,lastpass-firstpass+1,1,imx);
2204:
2205: free_imatrix(s,1,maxwav+1,1,n);
2206:
2207:
2208: free_ivector(num,1,n);
2209: free_vector(agedc,1,n);
2210: free_vector(weight,1,n);
2211: /*free_matrix(covar,1,NCOVMAX,1,n);*/
2212: fclose(ficparo);
2213: fclose(ficres);
2214: }
2215:
2216: /*________fin mle=1_________*/
2217:
2218:
2219:
2220: /* No more information from the sample is required now */
2221: /* Reads comments: lines beginning with '#' */
2222: while((c=getc(ficpar))=='#' && c!= EOF){
2223: ungetc(c,ficpar);
2224: fgets(line, MAXLINE, ficpar);
2225: puts(line);
2226: fputs(line,ficparo);
2227: }
2228: ungetc(c,ficpar);
2229:
1.3 lievre 2230:
1.2 lievre 2231: fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf\n",&agemin,&agemax, &bage, &fage);
2232: printf("agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemax, bage, fage);
2233: fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemax,bage,fage);
2234: /*--------- index.htm --------*/
2235:
2236: if((fichtm=fopen("index.htm","w"))==NULL) {
2237: printf("Problem with index.htm \n");goto end;
2238: }
2239:
2240: fprintf(fichtm,"<body><ul> Imach, Version 0.63<hr> <li>Outputs files<br><br>\n
2241: - Observed prevalence in each state: <a href=\"p%s\">p%s</a> <br>\n
2242: - Estimated parameters and the covariance matrix: <a href=\"%s\">%s</a> <br>
2243: - Stationary prevalence in each state: <a href=\"pl%s\">pl%s</a> <br>
2244: - Transition probabilities: <a href=\"pij%s\">pij%s</a><br>
2245: - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>
2246: - Life expectancies by age and initial health status: <a href=\"e%s\">e%s</a> <br>
2247: - Variances of life expectancies by age and initial health status: <a href=\"v%s\">v%s</a><br>
2248: - Health expectancies with their variances: <a href=\"t%s\">t%s</a> <br>
2249: - Standard deviation of stationary prevalences: <a href=\"vpl%s\">vpl%s</a> <br><br>",fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres);
2250:
2251: fprintf(fichtm," <li>Graphs</li>\n<p>");
2252:
2253: m=cptcovn;
2254: if (cptcovn < 1) {m=1;ncodemax[1]=1;}
2255:
2256: j1=0;
2257: for(k1=1; k1<=m;k1++){
2258: for(i1=1; i1<=ncodemax[k1];i1++){
2259: j1++;
2260: if (cptcovn > 0) {
2261: fprintf(fichtm,"<hr>************ Results for covariates");
2262: for (cpt=1; cpt<=cptcovn;cpt++)
2263: fprintf(fichtm," V%d=%d ",Tvar[cpt],nbcode[Tvar[cpt]][codtab[j1][cpt]]);
2264: fprintf(fichtm," ************\n<hr>");
2265: }
2266: fprintf(fichtm,"<br>- Probabilities: pe%s%d.gif<br>
2267: <img src=\"pe%s%d.gif\">",strtok(optionfile, "."),j1,strtok(optionfile, "."),j1);
2268: for(cpt=1; cpt<nlstate;cpt++){
2269: fprintf(fichtm,"<br>- Prevalence of disability : p%s%d%d.gif<br>
2270: <img src=\"p%s%d%d.gif\">",strtok(optionfile, "."),cpt,j1,strtok(optionfile, "."),cpt,j1);
2271: }
2272: for(cpt=1; cpt<=nlstate;cpt++) {
2273: fprintf(fichtm,"<br>- Observed and stationary prevalence (with confident
2274: interval) in state (%d): v%s%d%d.gif <br>
2275: <img src=\"v%s%d%d.gif\">",cpt,strtok(optionfile, "."),cpt,j1,strtok(optionfile, "."),cpt,j1);
2276: }
2277: for(cpt=1; cpt<=nlstate;cpt++) {
2278: fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): exp%s%d%d.gif <br>
1.3 lievre 2279: <img src=\"ex%s%d%d.gif\">",cpt,strtok(optionfile, "."),cpt,j1,strtok(optionfile, "."),cpt,j1);
1.2 lievre 2280: }
2281: fprintf(fichtm,"\n<br>- Total life expectancy by age and
2282: health expectancies in states (1) and (2): e%s%d.gif<br>
2283: <img src=\"e%s%d.gif\">",strtok(optionfile, "."),j1,strtok(optionfile, "."),j1);
2284: fprintf(fichtm,"\n</body>");
2285: }
2286: }
2287: fclose(fichtm);
2288:
2289: /*--------------- Prevalence limit --------------*/
2290:
2291: strcpy(filerespl,"pl");
2292: strcat(filerespl,fileres);
2293: if((ficrespl=fopen(filerespl,"w"))==NULL) {
2294: printf("Problem with Prev limit resultfile: %s\n", filerespl);goto end;
2295: }
2296: printf("Computing prevalence limit: result on file '%s' \n", filerespl);
2297: fprintf(ficrespl,"#Prevalence limit\n");
2298: fprintf(ficrespl,"#Age ");
2299: for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);
2300: fprintf(ficrespl,"\n");
2301:
2302: prlim=matrix(1,nlstate,1,nlstate);
2303: pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
2304: oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
2305: newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
2306: savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
2307: oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */
2308: k=0;
2309: agebase=agemin;
2310: agelim=agemax;
2311: ftolpl=1.e-10;
2312: i1=cptcovn;
2313: if (cptcovn < 1){i1=1;}
2314:
2315: for(cptcov=1;cptcov<=i1;cptcov++){
2316: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
2317: k=k+1;
2318: /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/
2319: fprintf(ficrespl,"\n#****** ");
2320: for(j=1;j<=cptcovn;j++)
2321: fprintf(ficrespl,"V%d=%d ",Tvar[j],nbcode[Tvar[j]][codtab[k][j]]);
2322: fprintf(ficrespl,"******\n");
2323:
2324: for (age=agebase; age<=agelim; age++){
2325: prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
2326: fprintf(ficrespl,"%.0f",age );
2327: for(i=1; i<=nlstate;i++)
2328: fprintf(ficrespl," %.5f", prlim[i][i]);
2329: fprintf(ficrespl,"\n");
2330: }
2331: }
2332: }
2333: fclose(ficrespl);
2334: /*------------- h Pij x at various ages ------------*/
2335:
2336: strcpy(filerespij,"pij"); strcat(filerespij,fileres);
2337: if((ficrespij=fopen(filerespij,"w"))==NULL) {
2338: printf("Problem with Pij resultfile: %s\n", filerespij);goto end;
2339: }
2340: printf("Computing pij: result on file '%s' \n", filerespij);
2341:
2342: stepsize=(int) (stepm+YEARM-1)/YEARM;
2343: if (stepm<=24) stepsize=2;
2344:
2345: agelim=AGESUP;
2346: hstepm=stepsize*YEARM; /* Every year of age */
2347: hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */
2348:
2349: k=0;
2350: for(cptcov=1;cptcov<=i1;cptcov++){
2351: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
2352: k=k+1;
2353: fprintf(ficrespij,"\n#****** ");
2354: for(j=1;j<=cptcovn;j++)
2355: fprintf(ficrespij,"V%d=%d ",Tvar[j],nbcode[Tvar[j]][codtab[k][j]]);
2356: fprintf(ficrespij,"******\n");
2357:
2358: for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */
2359: nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
2360: nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
2361: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
2362: oldm=oldms;savm=savms;
2363: hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
2364: fprintf(ficrespij,"# Age");
2365: for(i=1; i<=nlstate;i++)
2366: for(j=1; j<=nlstate+ndeath;j++)
2367: fprintf(ficrespij," %1d-%1d",i,j);
2368: fprintf(ficrespij,"\n");
2369: for (h=0; h<=nhstepm; h++){
2370: fprintf(ficrespij,"%d %.0f %.0f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );
2371: for(i=1; i<=nlstate;i++)
2372: for(j=1; j<=nlstate+ndeath;j++)
2373: fprintf(ficrespij," %.5f", p3mat[i][j][h]);
2374: fprintf(ficrespij,"\n");
2375: }
2376: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
2377: fprintf(ficrespij,"\n");
2378: }
2379: }
2380: }
2381:
2382: fclose(ficrespij);
2383:
2384: /*---------- Health expectancies and variances ------------*/
2385:
2386: strcpy(filerest,"t");
2387: strcat(filerest,fileres);
2388: if((ficrest=fopen(filerest,"w"))==NULL) {
2389: printf("Problem with total LE resultfile: %s\n", filerest);goto end;
2390: }
2391: printf("Computing Total LEs with variances: file '%s' \n", filerest);
2392:
2393:
2394: strcpy(filerese,"e");
2395: strcat(filerese,fileres);
2396: if((ficreseij=fopen(filerese,"w"))==NULL) {
2397: printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
2398: }
2399: printf("Computing Health Expectancies: result on file '%s' \n", filerese);
2400:
2401: strcpy(fileresv,"v");
2402: strcat(fileresv,fileres);
2403: if((ficresvij=fopen(fileresv,"w"))==NULL) {
2404: printf("Problem with variance resultfile: %s\n", fileresv);exit(0);
2405: }
2406: printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
2407:
2408: k=0;
2409: for(cptcov=1;cptcov<=i1;cptcov++){
2410: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
2411: k=k+1;
2412: fprintf(ficrest,"\n#****** ");
2413: for(j=1;j<=cptcovn;j++)
2414: fprintf(ficrest,"V%d=%d ",Tvar[j],nbcode[Tvar[j]][codtab[k][j]]);
2415: fprintf(ficrest,"******\n");
2416:
2417: fprintf(ficreseij,"\n#****** ");
2418: for(j=1;j<=cptcovn;j++)
2419: fprintf(ficreseij,"V%d=%d ",j,nbcode[j][codtab[k][j]]);
2420: fprintf(ficreseij,"******\n");
2421:
2422: fprintf(ficresvij,"\n#****** ");
2423: for(j=1;j<=cptcovn;j++)
2424: fprintf(ficresvij,"V%d=%d ",j,nbcode[j][codtab[k][j]]);
2425: fprintf(ficresvij,"******\n");
2426:
2427: eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
2428: oldm=oldms;savm=savms;
2429: evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k);
2430: vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
2431: oldm=oldms;savm=savms;
2432: varevsij(fileres, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);
2433:
2434: fprintf(ficrest,"#Total LEs with variances: e.. (std) ");
2435: for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);
2436: fprintf(ficrest,"\n");
2437:
2438: hf=1;
2439: if (stepm >= YEARM) hf=stepm/YEARM;
2440: epj=vector(1,nlstate+1);
2441: for(age=bage; age <=fage ;age++){
2442: prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
2443: fprintf(ficrest," %.0f",age);
2444: for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){
2445: for(i=1, epj[j]=0.;i <=nlstate;i++) {
2446: epj[j] += prlim[i][i]*hf*eij[i][j][(int)age];
2447: }
2448: epj[nlstate+1] +=epj[j];
2449: }
2450: for(i=1, vepp=0.;i <=nlstate;i++)
2451: for(j=1;j <=nlstate;j++)
2452: vepp += vareij[i][j][(int)age];
2453: fprintf(ficrest," %.2f (%.2f)", epj[nlstate+1],hf*sqrt(vepp));
2454: for(j=1;j <=nlstate;j++){
2455: fprintf(ficrest," %.2f (%.2f)", epj[j],hf*sqrt(vareij[j][j][(int)age]));
2456: }
2457: fprintf(ficrest,"\n");
2458: }
2459: }
2460: }
2461:
2462: fclose(ficreseij);
2463: fclose(ficresvij);
2464: fclose(ficrest);
2465: fclose(ficpar);
2466: free_vector(epj,1,nlstate+1);
1.3 lievre 2467: /*scanf("%d ",i); */
1.2 lievre 2468:
2469: /*------- Variance limit prevalence------*/
2470:
2471: strcpy(fileresvpl,"vpl");
2472: strcat(fileresvpl,fileres);
2473: if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {
2474: printf("Problem with variance prev lim resultfile: %s\n", fileresvpl);
2475: exit(0);
2476: }
2477: printf("Computing Variance-covariance of Prevalence limit: file '%s' \n", fileresvpl);
2478:
2479: k=0;
2480: for(cptcov=1;cptcov<=i1;cptcov++){
2481: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
2482: k=k+1;
2483: fprintf(ficresvpl,"\n#****** ");
2484: for(j=1;j<=cptcovn;j++)
2485: fprintf(ficresvpl,"V%d=%d ",Tvar[j],nbcode[Tvar[j]][codtab[k][j]]);
2486: fprintf(ficresvpl,"******\n");
2487:
2488: varpl=matrix(1,nlstate,(int) bage, (int) fage);
2489: oldm=oldms;savm=savms;
2490: varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);
2491: }
2492: }
2493:
2494: fclose(ficresvpl);
2495:
2496: /*---------- End : free ----------------*/
2497: free_matrix(varpl,1,nlstate,(int) bage, (int)fage);
2498:
2499: free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);
2500: free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
2501:
2502:
2503: free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);
2504: free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);
2505: free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);
2506: free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);
2507:
2508: free_matrix(matcov,1,npar,1,npar);
2509: free_vector(delti,1,npar);
2510:
2511: free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
2512:
2513: printf("End of Imach\n");
2514: /* gettimeofday(&end_time, (struct timezone*)0);*/ /* after time */
2515:
2516: /* 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);*/
2517: /*printf("Total time was %d uSec.\n", total_usecs);*/
2518: /*------ End -----------*/
2519:
2520: end:
2521: #ifdef windows
2522: chdir(pathcd);
2523: #endif
1.3 lievre 2524: system("wgnuplot graph.plt");
1.2 lievre 2525:
2526: #ifdef windows
2527: while (z[0] != 'q') {
2528: chdir(pathcd);
2529: printf("\nType e to edit output files, c to start again, and q for exiting: ");
2530: scanf("%s",z);
2531: if (z[0] == 'c') system("./imach");
2532: else if (z[0] == 'e') {
2533: chdir(path);
2534: system("index.htm");
2535: }
2536: else if (z[0] == 'q') exit(0);
2537: }
2538: #endif
2539: }
2540:
2541:
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