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 Likekilhood 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 win*/
54:
55: #define MAXPARM 30 /* Maximum number of parameters for the optimization */
56: #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncov */
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 */
62: #define MAXN 20000
63: #define YEARM 12. /* Number of months per year */
64: #define AGESUP 130
65: #define AGEBASE 40
66:
67:
68: int nvar;
69:
70: int npar=NPARMAX;
71: int nlstate=2; /* Number of live states */
72: int ndeath=1; /* Number of dead states */
73: int ncov; /* Total number of covariables including constant a12*1 +b12*x ncov=2 */
74:
75: int *wav; /* Number of waves for this individuual 0 is possible */
76: int maxwav; /* Maxim number of waves */
77: int mle, weightopt;
78: int **mw; /* mw[mi][i] is number of the mi wave for this individual */
79: int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
80: double **oldm, **newm, **savm; /* Working pointers to matrices */
81: double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
82: FILE *fic,*ficpar, *ficparo,*ficres, *ficrespl, *ficrespij, *ficrest;
83: FILE *ficgp, *fichtm;
84:
85: #define NR_END 1
86: #define FREE_ARG char*
87: #define FTOL 1.0e-10
88:
89: #define NRANSI
90: #define ITMAX 200
91:
92: #define TOL 2.0e-4
93:
94: #define CGOLD 0.3819660
95: #define ZEPS 1.0e-10
96: #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);
97:
98: #define GOLD 1.618034
99: #define GLIMIT 100.0
100: #define TINY 1.0e-20
101:
102: static double maxarg1,maxarg2;
103: #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
104: #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
105:
106: #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
107: #define rint(a) floor(a+0.5)
108:
109: static double sqrarg;
110: #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
111: #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}
112:
113: int imx;
114: int stepm;
115: /* Stepm, step in month: minimum step interpolation*/
116:
117: int m,nb;
118: int *num, firstpass=0, lastpass=2,*cod;
119: double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
120: double **pmmij;
121:
122: double *weight;
123: int **s; /* Status */
124: double *agedc, **covar, idx;
125:
126:
127: double ftol=FTOL; /* Tolerance for computing Max Likelihood */
128: double ftolhess; /* Tolerance for computing hessian */
129:
130:
131: /******************************************/
132:
133: void replace(char *s, char*t)
134: {
135: int i;
136: int lg=20;
137: i=0;
138: lg=strlen(t);
139: for(i=0; i<= lg; i++) {
140: (s[i] = t[i]);
141: if (t[i]== '\\') s[i]='/';
142: }
143: }
144: void cut(char *u,char *v, char*t)
145: {
146: int i,lg,j,p;
147: i=0;
148: for(j=0; j<=strlen(t); j++) {
149: if(t[j]=='\\') p=j;
150: }
151:
152: lg=strlen(t);
153: for(j=0; j<p; j++) {
154: (u[j] = t[j]);
155: u[p]='\0';
156: }
157:
158: for(j=0; j<= lg; j++) {
159: if (j>=(p+1))(v[j-p-1] = t[j]);
160: }
161: }
162:
163: /********************** nrerror ********************/
164:
165: void nrerror(char error_text[])
166: {
167: fprintf(stderr,"ERREUR ...\n");
168: fprintf(stderr,"%s\n",error_text);
169: exit(1);
170: }
171: /*********************** vector *******************/
172: double *vector(int nl, int nh)
173: {
174: double *v;
175: v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
176: if (!v) nrerror("allocation failure in vector");
177: return v-nl+NR_END;
178: }
179:
180: /************************ free vector ******************/
181: void free_vector(double*v, int nl, int nh)
182: {
183: free((FREE_ARG)(v+nl-NR_END));
184: }
185:
186: /************************ivector *******************************/
187: int *ivector(long nl,long nh)
188: {
189: int *v;
190: v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
191: if (!v) nrerror("allocation failure in ivector");
192: return v-nl+NR_END;
193: }
194:
195: /******************free ivector **************************/
196: void free_ivector(int *v, long nl, long nh)
197: {
198: free((FREE_ARG)(v+nl-NR_END));
199: }
200:
201: /******************* imatrix *******************************/
202: int **imatrix(long nrl, long nrh, long ncl, long nch)
203: /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */
204: {
205: long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;
206: int **m;
207:
208: /* allocate pointers to rows */
209: m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));
210: if (!m) nrerror("allocation failure 1 in matrix()");
211: m += NR_END;
212: m -= nrl;
213:
214:
215: /* allocate rows and set pointers to them */
216: m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));
217: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
218: m[nrl] += NR_END;
219: m[nrl] -= ncl;
220:
221: for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;
222:
223: /* return pointer to array of pointers to rows */
224: return m;
225: }
226:
227: /****************** free_imatrix *************************/
228: void free_imatrix(m,nrl,nrh,ncl,nch)
229: int **m;
230: long nch,ncl,nrh,nrl;
231: /* free an int matrix allocated by imatrix() */
232: {
233: free((FREE_ARG) (m[nrl]+ncl-NR_END));
234: free((FREE_ARG) (m+nrl-NR_END));
235: }
236:
237: /******************* matrix *******************************/
238: double **matrix(long nrl, long nrh, long ncl, long nch)
239: {
240: long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
241: double **m;
242:
243: m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
244: if (!m) nrerror("allocation failure 1 in matrix()");
245: m += NR_END;
246: m -= nrl;
247:
248: m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
249: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
250: m[nrl] += NR_END;
251: m[nrl] -= ncl;
252:
253: for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
254: return m;
255: }
256:
257: /*************************free matrix ************************/
258: void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
259: {
260: free((FREE_ARG)(m[nrl]+ncl-NR_END));
261: free((FREE_ARG)(m+nrl-NR_END));
262: }
263:
264: /******************* ma3x *******************************/
265: double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
266: {
267: long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
268: double ***m;
269:
270: m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
271: if (!m) nrerror("allocation failure 1 in matrix()");
272: m += NR_END;
273: m -= nrl;
274:
275: m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
276: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
277: m[nrl] += NR_END;
278: m[nrl] -= ncl;
279:
280: for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
281:
282: m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
283: if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
284: m[nrl][ncl] += NR_END;
285: m[nrl][ncl] -= nll;
286: for (j=ncl+1; j<=nch; j++)
287: m[nrl][j]=m[nrl][j-1]+nlay;
288:
289: for (i=nrl+1; i<=nrh; i++) {
290: m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
291: for (j=ncl+1; j<=nch; j++)
292: m[i][j]=m[i][j-1]+nlay;
293: }
294: return m;
295: }
296:
297: /*************************free ma3x ************************/
298: void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
299: {
300: free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
301: free((FREE_ARG)(m[nrl]+ncl-NR_END));
302: free((FREE_ARG)(m+nrl-NR_END));
303: }
304:
305: /***************** f1dim *************************/
306: extern int ncom;
307: extern double *pcom,*xicom;
308: extern double (*nrfunc)(double []);
309:
310: double f1dim(double x)
311: {
312: int j;
313: double f;
314: double *xt;
315:
316: xt=vector(1,ncom);
317: for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];
318: f=(*nrfunc)(xt);
319: free_vector(xt,1,ncom);
320: return f;
321: }
322:
323: /*****************brent *************************/
324: double brent(double ax, double bx, double cx, double (*f)(double), double tol, double *xmin)
325: {
326: int iter;
327: double a,b,d,etemp;
328: double fu,fv,fw,fx;
329: double ftemp;
330: double p,q,r,tol1,tol2,u,v,w,x,xm;
331: double e=0.0;
332:
333: a=(ax < cx ? ax : cx);
334: b=(ax > cx ? ax : cx);
335: x=w=v=bx;
336: fw=fv=fx=(*f)(x);
337: for (iter=1;iter<=ITMAX;iter++) {
338: xm=0.5*(a+b);
339: tol2=2.0*(tol1=tol*fabs(x)+ZEPS);
340: /* if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
341: printf(".");fflush(stdout);
342: #ifdef DEBUG
343: 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);
344: /* if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
345: #endif
346: if (fabs(x-xm) <= (tol2-0.5*(b-a))){
347: *xmin=x;
348: return fx;
349: }
350: ftemp=fu;
351: if (fabs(e) > tol1) {
352: r=(x-w)*(fx-fv);
353: q=(x-v)*(fx-fw);
354: p=(x-v)*q-(x-w)*r;
355: q=2.0*(q-r);
356: if (q > 0.0) p = -p;
357: q=fabs(q);
358: etemp=e;
359: e=d;
360: if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))
361: d=CGOLD*(e=(x >= xm ? a-x : b-x));
362: else {
363: d=p/q;
364: u=x+d;
365: if (u-a < tol2 || b-u < tol2)
366: d=SIGN(tol1,xm-x);
367: }
368: } else {
369: d=CGOLD*(e=(x >= xm ? a-x : b-x));
370: }
371: u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));
372: fu=(*f)(u);
373: if (fu <= fx) {
374: if (u >= x) a=x; else b=x;
375: SHFT(v,w,x,u)
376: SHFT(fv,fw,fx,fu)
377: } else {
378: if (u < x) a=u; else b=u;
379: if (fu <= fw || w == x) {
380: v=w;
381: w=u;
382: fv=fw;
383: fw=fu;
384: } else if (fu <= fv || v == x || v == w) {
385: v=u;
386: fv=fu;
387: }
388: }
389: }
390: nrerror("Too many iterations in brent");
391: *xmin=x;
392: return fx;
393: }
394:
395: /****************** mnbrak ***********************/
396:
397: void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,
398: double (*func)(double))
399: {
400: double ulim,u,r,q, dum;
401: double fu;
402:
403: *fa=(*func)(*ax);
404: *fb=(*func)(*bx);
405: if (*fb > *fa) {
406: SHFT(dum,*ax,*bx,dum)
407: SHFT(dum,*fb,*fa,dum)
408: }
409: *cx=(*bx)+GOLD*(*bx-*ax);
410: *fc=(*func)(*cx);
411: while (*fb > *fc) {
412: r=(*bx-*ax)*(*fb-*fc);
413: q=(*bx-*cx)*(*fb-*fa);
414: u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/
415: (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r));
416: ulim=(*bx)+GLIMIT*(*cx-*bx);
417: if ((*bx-u)*(u-*cx) > 0.0) {
418: fu=(*func)(u);
419: } else if ((*cx-u)*(u-ulim) > 0.0) {
420: fu=(*func)(u);
421: if (fu < *fc) {
422: SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))
423: SHFT(*fb,*fc,fu,(*func)(u))
424: }
425: } else if ((u-ulim)*(ulim-*cx) >= 0.0) {
426: u=ulim;
427: fu=(*func)(u);
428: } else {
429: u=(*cx)+GOLD*(*cx-*bx);
430: fu=(*func)(u);
431: }
432: SHFT(*ax,*bx,*cx,u)
433: SHFT(*fa,*fb,*fc,fu)
434: }
435: }
436:
437: /*************** linmin ************************/
438:
439: int ncom;
440: double *pcom,*xicom;
441: double (*nrfunc)(double []);
442:
443: void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))
444: {
445: double brent(double ax, double bx, double cx,
446: double (*f)(double), double tol, double *xmin);
447: double f1dim(double x);
448: void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,
449: double *fc, double (*func)(double));
450: int j;
451: double xx,xmin,bx,ax;
452: double fx,fb,fa;
453:
454: ncom=n;
455: pcom=vector(1,n);
456: xicom=vector(1,n);
457: nrfunc=func;
458: for (j=1;j<=n;j++) {
459: pcom[j]=p[j];
460: xicom[j]=xi[j];
461: }
462: ax=0.0;
463: xx=1.0;
464: mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim);
465: *fret=brent(ax,xx,bx,f1dim,TOL,&xmin);
466: #ifdef DEBUG
467: printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
468: #endif
469: for (j=1;j<=n;j++) {
470: xi[j] *= xmin;
471: p[j] += xi[j];
472: }
473: free_vector(xicom,1,n);
474: free_vector(pcom,1,n);
475: }
476:
477: /*************** powell ************************/
478: void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,
479: double (*func)(double []))
480:
481: {
482:
483:
484: void linmin(double p[], double xi[], int n, double *fret,
485: double (*func)(double []));
486: int i,ibig,j;
487: double del,t,*pt,*ptt,*xit;
488: double fp,fptt;
489: double *xits;
490: pt=vector(1,n);
491: ptt=vector(1,n);
492: xit=vector(1,n);
493: xits=vector(1,n);
494: *fret=(*func)(p);
495: for (j=1;j<=n;j++) pt[j]=p[j];
496: for (*iter=1;;++(*iter)) {
497: fp=(*fret);
498: ibig=0;
499: del=0.0;
500: printf("\nPowell iter=%d -2*LL=%.12f",*iter,*fret);
501: for (i=1;i<=n;i++)
502: printf(" %d %.12f",i, p[i]);
503: printf("\n");
504: for (i=1;i<=n;i++) {
505: for (j=1;j<=n;j++) xit[j]=xi[j][i];
506: fptt=(*fret);
507: #ifdef DEBUG
508: printf("fret=%lf \n",*fret);
509: #endif
510: printf("%d",i);fflush(stdout);
511: linmin(p,xit,n,fret,func);
512: if (fabs(fptt-(*fret)) > del) {
513: del=fabs(fptt-(*fret));
514: ibig=i;
515: }
516: #ifdef DEBUG
517: printf("%d %.12e",i,(*fret));
518: for (j=1;j<=n;j++) {
519: xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
520: printf(" x(%d)=%.12e",j,xit[j]);
521: }
522: for(j=1;j<=n;j++)
523: printf(" p=%.12e",p[j]);
524: printf("\n");
525: #endif
526: }
527: if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {
528: #ifdef DEBUG
529: int k[2],l;
530: k[0]=1;
531: k[1]=-1;
532: printf("Max: %.12e",(*func)(p));
533: for (j=1;j<=n;j++)
534: printf(" %.12e",p[j]);
535: printf("\n");
536: for(l=0;l<=1;l++) {
537: for (j=1;j<=n;j++) {
538: ptt[j]=p[j]+(p[j]-pt[j])*k[l];
539: printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
540: }
541: printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
542: }
543: #endif
544:
545:
546: free_vector(xit,1,n);
547: free_vector(xits,1,n);
548: free_vector(ptt,1,n);
549: free_vector(pt,1,n);
550: return;
551: }
552: if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");
553: for (j=1;j<=n;j++) {
554: ptt[j]=2.0*p[j]-pt[j];
555: xit[j]=p[j]-pt[j];
556: pt[j]=p[j];
557: }
558: fptt=(*func)(ptt);
559: if (fptt < fp) {
560: t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt);
561: if (t < 0.0) {
562: linmin(p,xit,n,fret,func);
563: for (j=1;j<=n;j++) {
564: xi[j][ibig]=xi[j][n];
565: xi[j][n]=xit[j];
566: }
567: #ifdef DEBUG
568: printf("Direction changed last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
569: for(j=1;j<=n;j++)
570: printf(" %.12e",xit[j]);
571: printf("\n");
572: #endif
573: }
574: }
575: }
576: }
577:
578: /**** Prevalence limit ****************/
579:
580: double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl)
581: {
582: /* Computes the prevalence limit in each live state at age x by left multiplying the unit
583: matrix by transitions matrix until convergence is reached */
584:
585: int i, ii,j,k;
586: double min, max, maxmin, maxmax,sumnew=0.;
587: double **matprod2();
588: double **out, cov[NCOVMAX], **pmij();
589: double **newm;
590: double agefin, delaymax=50 ; /* Max number of years to converge */
591:
592: for (ii=1;ii<=nlstate+ndeath;ii++)
593: for (j=1;j<=nlstate+ndeath;j++){
594: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
595: }
596: /* Even if hstepm = 1, at least one multiplication by the unit matrix */
597: for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
598: newm=savm;
599: /* Covariates have to be included here again */
600: cov[1]=1.;
601: cov[2]=agefin;
602: out=matprod2(newm, pmij(pmmij,cov,ncov,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);
603: /* printf("age=%f agefin=%f po=%f pn=%f\n",age,agefin,oldm[1][1],newm[1][1]);*/
604:
605: savm=oldm;
606: oldm=newm;
607: maxmax=0.;
608: for(j=1;j<=nlstate;j++){
609: min=1.;
610: max=0.;
611: for(i=1; i<=nlstate; i++) {
612: sumnew=0;
613: for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
614: prlim[i][j]= newm[i][j]/(1-sumnew);
615: max=FMAX(max,prlim[i][j]);
616: min=FMIN(min,prlim[i][j]);
617: }
618: maxmin=max-min;
619: maxmax=FMAX(maxmax,maxmin);
620: }
621: if(maxmax < ftolpl){
622: return prlim;
623: }
624: }
625: }
626:
627: /*************** transition probabilities **********/
628:
629: double **pmij(double **ps, double *cov, int ncov, double *x, int nlstate )
630: {
631: double s1, s2;
632: /*double t34;*/
633: int i,j,j1, nc, ii, jj;
634:
635: for(i=1; i<= nlstate; i++){
636: for(j=1; j<i;j++){
637: for (nc=1, s2=0.;nc <=ncov; nc++){
638: /*s2 += param[i][j][nc]*cov[nc];*/
639: s2 += x[(i-1)*nlstate*ncov+(j-1)*ncov+nc+(i-1)*(ndeath-1)*ncov]*cov[nc];
640: /*printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2);*/
641: }
642: ps[i][j]=s2;
643: /*printf("s1=%.17e, s2=%.17e\n",s1,s2);*/
644: }
645: for(j=i+1; j<=nlstate+ndeath;j++){
646: for (nc=1, s2=0.;nc <=ncov; nc++){
647: s2 += x[(i-1)*nlstate*ncov+(j-2)*ncov+nc+(i-1)*(ndeath-1)*ncov]*cov[nc];
648: /*printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2);*/
649: }
650: ps[i][j]=s2;
651: }
652: }
653: for(i=1; i<= nlstate; i++){
654: s1=0;
655: for(j=1; j<i; j++)
656: s1+=exp(ps[i][j]);
657: for(j=i+1; j<=nlstate+ndeath; j++)
658: s1+=exp(ps[i][j]);
659: ps[i][i]=1./(s1+1.);
660: for(j=1; j<i; j++)
661: ps[i][j]= exp(ps[i][j])*ps[i][i];
662: for(j=i+1; j<=nlstate+ndeath; j++)
663: ps[i][j]= exp(ps[i][j])*ps[i][i];
664: /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
665: } /* end i */
666:
667: for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
668: for(jj=1; jj<= nlstate+ndeath; jj++){
669: ps[ii][jj]=0;
670: ps[ii][ii]=1;
671: }
672: }
673:
674: /* for(ii=1; ii<= nlstate+ndeath; ii++){
675: for(jj=1; jj<= nlstate+ndeath; jj++){
676: printf("%lf ",ps[ii][jj]);
677: }
678: printf("\n ");
679: }
680: printf("\n ");printf("%lf ",cov[2]);*/
681: /*
682: for(i=1; i<= npar; i++) printf("%f ",x[i]);
683: goto end;*/
684: return ps;
685: }
686:
687: /**************** Product of 2 matrices ******************/
688:
689: double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)
690: {
691: /* Computes the matric product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
692: b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
693: /* in, b, out are matrice of pointers which should have been initialized
694: before: only the contents of out is modified. The function returns
695: a pointer to pointers identical to out */
696: long i, j, k;
697: for(i=nrl; i<= nrh; i++)
698: for(k=ncolol; k<=ncoloh; k++)
699: for(j=ncl,out[i][k]=0.; j<=nch; j++)
700: out[i][k] +=in[i][j]*b[j][k];
701:
702: return out;
703: }
704:
705:
706: /************* Higher Matrix Product ***************/
707:
708: double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm )
709: {
710: /* Computes the transition matrix starting at age 'age' over 'nhstepm*hstepm*stepm' month
711: duration (i.e. until
712: age (in years) age+nhstepm*stepm/12) by multiplying nhstepm*hstepm matrices.
713: Output is stored in matrix po[i][j][h] for h every 'hstepm' step
714: (typically every 2 years instead of every month which is too big).
715: Model is determined by parameters x and covariates have to be
716: included manually here.
717:
718: */
719:
720: int i, j, d, h;
721: double **out, cov[NCOVMAX];
722: double **newm;
723:
724: /* Hstepm could be zero and should return the unit matrix */
725: for (i=1;i<=nlstate+ndeath;i++)
726: for (j=1;j<=nlstate+ndeath;j++){
727: oldm[i][j]=(i==j ? 1.0 : 0.0);
728: po[i][j][0]=(i==j ? 1.0 : 0.0);
729: }
730: /* Even if hstepm = 1, at least one multiplication by the unit matrix */
731: for(h=1; h <=nhstepm; h++){
732: for(d=1; d <=hstepm; d++){
733: newm=savm;
734: /* Covariates have to be included here again */
735: cov[1]=1.;
736: cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
737: /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
738: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,
739: pmij(pmmij,cov,ncov,x,nlstate));
740: savm=oldm;
741: oldm=newm;
742: }
743: for(i=1; i<=nlstate+ndeath; i++)
744: for(j=1;j<=nlstate+ndeath;j++) {
745: po[i][j][h]=newm[i][j];
746: /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);
747: */
748: }
749: } /* end h */
750: return po;
751: }
752:
753:
754: /*************** log-likelihood *************/
755: double func( double *x)
756: {
757: int i, ii, j, k, mi, d;
758: double l, ll[NLSTATEMAX], cov[NCOVMAX];
759: double **out;
760: double sw; /* Sum of weights */
761: double lli; /* Individual log likelihood */
762: long ipmx;
763: /*extern weight */
764: /* We are differentiating ll according to initial status */
765: /* for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
766: /*for(i=1;i<imx;i++)
767: printf(" %d\n",s[4][i]);
768: */
769:
770: for(k=1; k<=nlstate; k++) ll[k]=0.;
771: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
772: for(mi=1; mi<= wav[i]-1; mi++){
773: for (ii=1;ii<=nlstate+ndeath;ii++)
774: for (j=1;j<=nlstate+ndeath;j++) oldm[ii][j]=(ii==j ? 1.0 : 0.0);
775: for(d=0; d<dh[mi][i]; d++){
776: newm=savm;
777: cov[1]=1.;
778: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
779: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
780: 1,nlstate+ndeath,pmij(pmmij,cov,ncov,x,nlstate));
781: savm=oldm;
782: oldm=newm;
783:
784:
785: } /* end mult */
786:
787: lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);
788: /* printf(" %f ",out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/
789: ipmx +=1;
790: sw += weight[i];
791: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
792: } /* end of wave */
793: } /* end of individual */
794:
795: for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
796: /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
797: l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
798: return -l;
799: }
800:
801:
802: /*********** Maximum Likelihood Estimation ***************/
803:
804: void mlikeli(FILE *ficres,double p[], int npar, int ncov, int nlstate, double ftol, double (*func)(double []))
805: {
806: int i,j, iter;
807: double **xi,*delti;
808: double fret;
809: xi=matrix(1,npar,1,npar);
810: for (i=1;i<=npar;i++)
811: for (j=1;j<=npar;j++)
812: xi[i][j]=(i==j ? 1.0 : 0.0);
813: printf("Powell\n");
814: powell(p,xi,npar,ftol,&iter,&fret,func);
815:
816: printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));
817: fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f ",iter,func(p));
818:
819: }
820:
821: /**** Computes Hessian and covariance matrix ***/
822: void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
823: {
824: double **a,**y,*x,pd;
825: double **hess;
826: int i, j,jk;
827: int *indx;
828:
829: double hessii(double p[], double delta, int theta, double delti[]);
830: double hessij(double p[], double delti[], int i, int j);
831: void lubksb(double **a, int npar, int *indx, double b[]) ;
832: void ludcmp(double **a, int npar, int *indx, double *d) ;
833:
834:
835: hess=matrix(1,npar,1,npar);
836:
837: printf("\nCalculation of the hessian matrix. Wait...\n");
838: for (i=1;i<=npar;i++){
839: printf("%d",i);fflush(stdout);
840: hess[i][i]=hessii(p,ftolhess,i,delti);
841: /*printf(" %f ",p[i]);*/
842: }
843:
844: for (i=1;i<=npar;i++) {
845: for (j=1;j<=npar;j++) {
846: if (j>i) {
847: printf(".%d%d",i,j);fflush(stdout);
848: hess[i][j]=hessij(p,delti,i,j);
849: hess[j][i]=hess[i][j];
850: }
851: }
852: }
853: printf("\n");
854:
855: printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
856:
857: a=matrix(1,npar,1,npar);
858: y=matrix(1,npar,1,npar);
859: x=vector(1,npar);
860: indx=ivector(1,npar);
861: for (i=1;i<=npar;i++)
862: for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
863: ludcmp(a,npar,indx,&pd);
864:
865: for (j=1;j<=npar;j++) {
866: for (i=1;i<=npar;i++) x[i]=0;
867: x[j]=1;
868: lubksb(a,npar,indx,x);
869: for (i=1;i<=npar;i++){
870: matcov[i][j]=x[i];
871: }
872: }
873:
874: printf("\n#Hessian matrix#\n");
875: for (i=1;i<=npar;i++) {
876: for (j=1;j<=npar;j++) {
877: printf("%.3e ",hess[i][j]);
878: }
879: printf("\n");
880: }
881:
882: /* Recompute Inverse */
883: for (i=1;i<=npar;i++)
884: for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];
885: ludcmp(a,npar,indx,&pd);
886:
887: /* printf("\n#Hessian matrix recomputed#\n");
888:
889: for (j=1;j<=npar;j++) {
890: for (i=1;i<=npar;i++) x[i]=0;
891: x[j]=1;
892: lubksb(a,npar,indx,x);
893: for (i=1;i<=npar;i++){
894: y[i][j]=x[i];
895: printf("%.3e ",y[i][j]);
896: }
897: printf("\n");
898: }
899: */
900:
901: free_matrix(a,1,npar,1,npar);
902: free_matrix(y,1,npar,1,npar);
903: free_vector(x,1,npar);
904: free_ivector(indx,1,npar);
905: free_matrix(hess,1,npar,1,npar);
906:
907:
908: }
909:
910: /*************** hessian matrix ****************/
911: double hessii( double x[], double delta, int theta, double delti[])
912: {
913: int i;
914: int l=1, lmax=20;
915: double k1,k2;
916: double p2[NPARMAX+1];
917: double res;
918: double delt, delts, nkhi=10.,nkhif=1., khi=1.e-4;
919: double fx;
920: int k=0,kmax=10;
921: double l1;
922:
923: fx=func(x);
924: for (i=1;i<=npar;i++) p2[i]=x[i];
925: for(l=0 ; l <=lmax; l++){
926: l1=pow(10,l);
927: delts=delt;
928: for(k=1 ; k <kmax; k=k+1){
929: delt = delta*(l1*k);
930: p2[theta]=x[theta] +delt;
931: k1=func(p2)-fx;
932: p2[theta]=x[theta]-delt;
933: k2=func(p2)-fx;
934: /*res= (k1-2.0*fx+k2)/delt/delt; */
935: res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */
936:
937: #ifdef DEBUG
938: 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);
939: #endif
940: /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
941: if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
942: k=kmax;
943: }
944: else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
945: k=kmax; l=lmax*10.;
946: }
947: else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){
948: delts=delt;
949: }
950: }
951: }
952: delti[theta]=delts;
953: return res;
954:
955: }
956:
957: double hessij( double x[], double delti[], int thetai,int thetaj)
958: {
959: int i;
960: int l=1, l1, lmax=20;
961: double k1,k2,k3,k4,res,fx;
962: double p2[NPARMAX+1];
963: int k;
964:
965: fx=func(x);
966: for (k=1; k<=2; k++) {
967: for (i=1;i<=npar;i++) p2[i]=x[i];
968: p2[thetai]=x[thetai]+delti[thetai]/k;
969: p2[thetaj]=x[thetaj]+delti[thetaj]/k;
970: k1=func(p2)-fx;
971:
972: p2[thetai]=x[thetai]+delti[thetai]/k;
973: p2[thetaj]=x[thetaj]-delti[thetaj]/k;
974: k2=func(p2)-fx;
975:
976: p2[thetai]=x[thetai]-delti[thetai]/k;
977: p2[thetaj]=x[thetaj]+delti[thetaj]/k;
978: k3=func(p2)-fx;
979:
980: p2[thetai]=x[thetai]-delti[thetai]/k;
981: p2[thetaj]=x[thetaj]-delti[thetaj]/k;
982: k4=func(p2)-fx;
983: res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */
984: #ifdef DEBUG
985: 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);
986: #endif
987: }
988: return res;
989: }
990:
991: /************** Inverse of matrix **************/
992: void ludcmp(double **a, int n, int *indx, double *d)
993: {
994: int i,imax,j,k;
995: double big,dum,sum,temp;
996: double *vv;
997:
998: vv=vector(1,n);
999: *d=1.0;
1000: for (i=1;i<=n;i++) {
1001: big=0.0;
1002: for (j=1;j<=n;j++)
1003: if ((temp=fabs(a[i][j])) > big) big=temp;
1004: if (big == 0.0) nrerror("Singular matrix in routine ludcmp");
1005: vv[i]=1.0/big;
1006: }
1007: for (j=1;j<=n;j++) {
1008: for (i=1;i<j;i++) {
1009: sum=a[i][j];
1010: for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];
1011: a[i][j]=sum;
1012: }
1013: big=0.0;
1014: for (i=j;i<=n;i++) {
1015: sum=a[i][j];
1016: for (k=1;k<j;k++)
1017: sum -= a[i][k]*a[k][j];
1018: a[i][j]=sum;
1019: if ( (dum=vv[i]*fabs(sum)) >= big) {
1020: big=dum;
1021: imax=i;
1022: }
1023: }
1024: if (j != imax) {
1025: for (k=1;k<=n;k++) {
1026: dum=a[imax][k];
1027: a[imax][k]=a[j][k];
1028: a[j][k]=dum;
1029: }
1030: *d = -(*d);
1031: vv[imax]=vv[j];
1032: }
1033: indx[j]=imax;
1034: if (a[j][j] == 0.0) a[j][j]=TINY;
1035: if (j != n) {
1036: dum=1.0/(a[j][j]);
1037: for (i=j+1;i<=n;i++) a[i][j] *= dum;
1038: }
1039: }
1040: free_vector(vv,1,n); /* Doesn't work */
1041: ;
1042: }
1043:
1044: void lubksb(double **a, int n, int *indx, double b[])
1045: {
1046: int i,ii=0,ip,j;
1047: double sum;
1048:
1049: for (i=1;i<=n;i++) {
1050: ip=indx[i];
1051: sum=b[ip];
1052: b[ip]=b[i];
1053: if (ii)
1054: for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];
1055: else if (sum) ii=i;
1056: b[i]=sum;
1057: }
1058: for (i=n;i>=1;i--) {
1059: sum=b[i];
1060: for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];
1061: b[i]=sum/a[i][i];
1062: }
1063: }
1064:
1065: /************ Frequencies ********************/
1066: void freqsummary(char fileres[], int agemin, int agemax, int **s, double **agev, int nlstate, int imx)
1067: { /* Some frequencies */
1068:
1069: int i, m, jk;
1070: double ***freq; /* Frequencies */
1071: double *pp;
1072: double pos;
1073: FILE *ficresp;
1074: char fileresp[FILENAMELENGTH];
1075:
1076: pp=vector(1,nlstate);
1077:
1078: strcpy(fileresp,"p");
1079: strcat(fileresp,fileres);
1080: if((ficresp=fopen(fileresp,"w"))==NULL) {
1081: printf("Problem with prevalence resultfile: %s\n", fileresp);
1082: exit(0);
1083: }
1084:
1085: freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);
1086: for (i=-1; i<=nlstate+ndeath; i++)
1087: for (jk=-1; jk<=nlstate+ndeath; jk++)
1088: for(m=agemin; m <= agemax+3; m++)
1089: freq[i][jk][m]=0;
1090:
1091: for (i=1; i<=imx; i++) {
1092: for(m=firstpass; m<= lastpass-1; m++){
1093: if(agev[m][i]==0) agev[m][i]=agemax+1;
1094: if(agev[m][i]==1) agev[m][i]=agemax+2;
1095: freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
1096: freq[s[m][i]][s[m+1][i]][(int) agemax+3] += weight[i];
1097: }
1098: }
1099:
1100: fprintf(ficresp, "#");
1101: for(i=1; i<=nlstate;i++)
1102: fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
1103: fprintf(ficresp, "\n");
1104:
1105: for(i=(int)agemin; i <= (int)agemax+3; i++){
1106: if(i==(int)agemax+3)
1107: printf("Total");
1108: else
1109: printf("Age %d", i);
1110: for(jk=1; jk <=nlstate ; jk++){
1111: for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
1112: pp[jk] += freq[jk][m][i];
1113: }
1114: for(jk=1; jk <=nlstate ; jk++){
1115: for(m=-1, pos=0; m <=0 ; m++)
1116: pos += freq[jk][m][i];
1117: if(pp[jk]>=1.e-10)
1118: printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
1119: else
1120: printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
1121: }
1122: for(jk=1; jk <=nlstate ; jk++){
1123: for(m=1, pp[jk]=0; m <=nlstate+ndeath; m++)
1124: pp[jk] += freq[jk][m][i];
1125: }
1126: for(jk=1,pos=0; jk <=nlstate ; jk++)
1127: pos += pp[jk];
1128: for(jk=1; jk <=nlstate ; jk++){
1129: if(pos>=1.e-5)
1130: printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
1131: else
1132: printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
1133: if( i <= (int) agemax){
1134: if(pos>=1.e-5)
1135: fprintf(ficresp," %d %.5f %.0f %.0f",i,pp[jk]/pos, pp[jk],pos);
1136: else
1137: fprintf(ficresp," %d NaNq %.0f %.0f",i,pp[jk],pos);
1138: }
1139: }
1140: for(jk=-1; jk <=nlstate+ndeath; jk++)
1141: for(m=-1; m <=nlstate+ndeath; m++)
1142: if(freq[jk][m][i] !=0 ) printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
1143: if(i <= (int) agemax)
1144: fprintf(ficresp,"\n");
1145: printf("\n");
1146: }
1147:
1148: fclose(ficresp);
1149: free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);
1150: free_vector(pp,1,nlstate);
1151:
1152: } /* End of Freq */
1153:
1154: /************* Waves Concatenation ***************/
1155:
1156: void concatwav(int wav[], int **dh, int **mw, int **s, double *agedc, double **agev, int firstpass, int lastpass, int imx, int nlstate, int stepm)
1157: {
1158: /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
1159: Death is a valid wave (if date is known).
1160: mw[mi][i] is the mi (mi=1 to wav[i]) effective wave of individual i
1161: dh[m][i] of dh[mw[mi][i][i] is the delay between two effective waves m=mw[mi][i]
1162: and mw[mi+1][i]. dh depends on stepm.
1163: */
1164:
1165: int i, mi, m;
1166: int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
1167: float sum=0.;
1168:
1169: for(i=1; i<=imx; i++){
1170: mi=0;
1171: m=firstpass;
1172: while(s[m][i] <= nlstate){
1173: if(s[m][i]>=1)
1174: mw[++mi][i]=m;
1175: if(m >=lastpass)
1176: break;
1177: else
1178: m++;
1179: }/* end while */
1180: if (s[m][i] > nlstate){
1181: mi++; /* Death is another wave */
1182: /* if(mi==0) never been interviewed correctly before death */
1183: /* Only death is a correct wave */
1184: mw[mi][i]=m;
1185: }
1186:
1187: wav[i]=mi;
1188: if(mi==0)
1189: printf("Warning, no any valid information for:%d line=%d\n",num[i],i);
1190: }
1191:
1192: for(i=1; i<=imx; i++){
1193: for(mi=1; mi<wav[i];mi++){
1194: if (stepm <=0)
1195: dh[mi][i]=1;
1196: else{
1197: if (s[mw[mi+1][i]][i] > nlstate) {
1198: j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);
1199: if(j=0) j=1; /* Survives at least one month after exam */
1200: }
1201: else{
1202: j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
1203: k=k+1;
1204: if (j >= jmax) jmax=j;
1205: else if (j <= jmin)jmin=j;
1206: sum=sum+j;
1207: }
1208: jk= j/stepm;
1209: jl= j -jk*stepm;
1210: ju= j -(jk+1)*stepm;
1211: if(jl <= -ju)
1212: dh[mi][i]=jk;
1213: else
1214: dh[mi][i]=jk+1;
1215: if(dh[mi][i]==0)
1216: dh[mi][i]=1; /* At least one step */
1217: }
1218: }
1219: }
1220: printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,sum/k);
1221: }
1222:
1223: /*********** Health Expectancies ****************/
1224:
1225: void evsij(char fileres[], double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm)
1226: {
1227: /* Health expectancies */
1228: int i, j, nhstepm, hstepm, h;
1229: double age, agelim,hf;
1230: double ***p3mat;
1231:
1232: FILE *ficreseij;
1233: char filerese[FILENAMELENGTH];
1234:
1235: strcpy(filerese,"e");
1236: strcat(filerese,fileres);
1237: if((ficreseij=fopen(filerese,"w"))==NULL) {
1238: printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
1239: }
1240: printf("Computing Health Expectancies: result on file '%s' \n", filerese);
1241:
1242: fprintf(ficreseij,"# Health expectancies\n");
1243: fprintf(ficreseij,"# Age");
1244: for(i=1; i<=nlstate;i++)
1245: for(j=1; j<=nlstate;j++)
1246: fprintf(ficreseij," %1d-%1d",i,j);
1247: fprintf(ficreseij,"\n");
1248:
1249: hstepm=1*YEARM; /* Every j years of age (in month) */
1250: hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */
1251:
1252: agelim=AGESUP;
1253: for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
1254: /* nhstepm age range expressed in number of stepm */
1255: nhstepm=(int) rint((agelim-age)*YEARM/stepm);
1256: /* Typically if 20 years = 20*12/6=40 stepm */
1257: if (stepm >= YEARM) hstepm=1;
1258: nhstepm = nhstepm/hstepm;/* Expressed in hstepm, typically 40/4=10 */
1259: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
1260: /* Computed by stepm unit matrices, product of hstepm matrices, stored
1261: in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
1262: hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm);
1263:
1264:
1265: for(i=1; i<=nlstate;i++)
1266: for(j=1; j<=nlstate;j++)
1267: for (h=0, eij[i][j][(int)age]=0; h<=nhstepm; h++){
1268: eij[i][j][(int)age] +=p3mat[i][j][h];
1269: }
1270:
1271: hf=1;
1272: if (stepm >= YEARM) hf=stepm/YEARM;
1273: fprintf(ficreseij,"%.0f",age );
1274: for(i=1; i<=nlstate;i++)
1275: for(j=1; j<=nlstate;j++){
1276: fprintf(ficreseij," %.4f", hf*eij[i][j][(int)age]);
1277: }
1278: fprintf(ficreseij,"\n");
1279: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
1280: }
1281: fclose(ficreseij);
1282: }
1283:
1284: /************ Variance ******************/
1285: 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)
1286: {
1287: /* Variance of health expectancies */
1288: /* double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
1289: double **newm;
1290: double **dnewm,**doldm;
1291: int i, j, nhstepm, hstepm, h;
1292: int k;
1293: FILE *ficresvij;
1294: char fileresv[FILENAMELENGTH];
1295: double *xp;
1296: double **gp, **gm;
1297: double ***gradg, ***trgradg;
1298: double ***p3mat;
1299: double age,agelim;
1300: int theta;
1301:
1302: strcpy(fileresv,"v");
1303: strcat(fileresv,fileres);
1304: if((ficresvij=fopen(fileresv,"w"))==NULL) {
1305: printf("Problem with variance resultfile: %s\n", fileresv);exit(0);
1306: }
1307: printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
1308:
1309:
1310: fprintf(ficresvij,"# Covariances of life expectancies\n");
1311: fprintf(ficresvij,"# Age");
1312: for(i=1; i<=nlstate;i++)
1313: for(j=1; j<=nlstate;j++)
1314: fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);
1315: fprintf(ficresvij,"\n");
1316:
1317: xp=vector(1,npar);
1318: dnewm=matrix(1,nlstate,1,npar);
1319: doldm=matrix(1,nlstate,1,nlstate);
1320:
1321: hstepm=1*YEARM; /* Every year of age */
1322: hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */
1323: agelim = AGESUP;
1324: for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
1325: nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
1326: if (stepm >= YEARM) hstepm=1;
1327: nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
1328: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
1329: gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
1330: gp=matrix(0,nhstepm,1,nlstate);
1331: gm=matrix(0,nhstepm,1,nlstate);
1332:
1333: for(theta=1; theta <=npar; theta++){
1334: for(i=1; i<=npar; i++){ /* Computes gradient */
1335: xp[i] = x[i] + (i==theta ?delti[theta]:0);
1336: }
1337: hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm);
1338: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl);
1339: for(j=1; j<= nlstate; j++){
1340: for(h=0; h<=nhstepm; h++){
1341: for(i=1, gp[h][j]=0.;i<=nlstate;i++)
1342: gp[h][j] += prlim[i][i]*p3mat[i][j][h];
1343: }
1344: }
1345:
1346: for(i=1; i<=npar; i++) /* Computes gradient */
1347: xp[i] = x[i] - (i==theta ?delti[theta]:0);
1348: hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm);
1349: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl);
1350: for(j=1; j<= nlstate; j++){
1351: for(h=0; h<=nhstepm; h++){
1352: for(i=1, gm[h][j]=0.;i<=nlstate;i++)
1353: gm[h][j] += prlim[i][i]*p3mat[i][j][h];
1354: }
1355: }
1356: for(j=1; j<= nlstate; j++)
1357: for(h=0; h<=nhstepm; h++){
1358: gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
1359: }
1360: } /* End theta */
1361:
1362: trgradg =ma3x(0,nhstepm,1,nlstate,1,npar);
1363:
1364: for(h=0; h<=nhstepm; h++)
1365: for(j=1; j<=nlstate;j++)
1366: for(theta=1; theta <=npar; theta++)
1367: trgradg[h][j][theta]=gradg[h][theta][j];
1368:
1369: for(i=1;i<=nlstate;i++)
1370: for(j=1;j<=nlstate;j++)
1371: vareij[i][j][(int)age] =0.;
1372: for(h=0;h<=nhstepm;h++){
1373: for(k=0;k<=nhstepm;k++){
1374: matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
1375: matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
1376: for(i=1;i<=nlstate;i++)
1377: for(j=1;j<=nlstate;j++)
1378: vareij[i][j][(int)age] += doldm[i][j];
1379: }
1380: }
1381: h=1;
1382: if (stepm >= YEARM) h=stepm/YEARM;
1383: fprintf(ficresvij,"%.0f ",age );
1384: for(i=1; i<=nlstate;i++)
1385: for(j=1; j<=nlstate;j++){
1386: fprintf(ficresvij," %.4f", h*vareij[i][j][(int)age]);
1387: }
1388: fprintf(ficresvij,"\n");
1389: free_matrix(gp,0,nhstepm,1,nlstate);
1390: free_matrix(gm,0,nhstepm,1,nlstate);
1391: free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
1392: free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
1393: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
1394: } /* End age */
1395: fclose(ficresvij);
1396: free_vector(xp,1,npar);
1397: free_matrix(doldm,1,nlstate,1,npar);
1398: free_matrix(dnewm,1,nlstate,1,nlstate);
1399:
1400: }
1401:
1402: /************ Variance of prevlim ******************/
1403: 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)
1404: {
1405: /* Variance of health expectancies */
1406: /* double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
1407: double **newm;
1408: double **dnewm,**doldm;
1409: int i, j, nhstepm, hstepm;
1410: int k;
1411: FILE *ficresvpl;
1412: char fileresvpl[FILENAMELENGTH];
1413: double *xp;
1414: double *gp, *gm;
1415: double **gradg, **trgradg;
1416: double age,agelim;
1417: int theta;
1418:
1419: strcpy(fileresvpl,"vpl");
1420: strcat(fileresvpl,fileres);
1421: if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {
1422: printf("Problem with variance prev lim resultfile: %s\n", fileresvpl);
1423: exit(0);
1424: }
1425: printf("Computing Variance-covariance of Prevalence limit: file '%s' \n", fileresvpl);
1426:
1427:
1428: fprintf(ficresvpl,"# Standard deviation of prevalences limit\n");
1429: fprintf(ficresvpl,"# Age");
1430: for(i=1; i<=nlstate;i++)
1431: fprintf(ficresvpl," %1d-%1d",i,i);
1432: fprintf(ficresvpl,"\n");
1433:
1434: xp=vector(1,npar);
1435: dnewm=matrix(1,nlstate,1,npar);
1436: doldm=matrix(1,nlstate,1,nlstate);
1437:
1438: hstepm=1*YEARM; /* Every year of age */
1439: hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */
1440: agelim = AGESUP;
1441: for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
1442: nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
1443: if (stepm >= YEARM) hstepm=1;
1444: nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
1445: gradg=matrix(1,npar,1,nlstate);
1446: gp=vector(1,nlstate);
1447: gm=vector(1,nlstate);
1448:
1449: for(theta=1; theta <=npar; theta++){
1450: for(i=1; i<=npar; i++){ /* Computes gradient */
1451: xp[i] = x[i] + (i==theta ?delti[theta]:0);
1452: }
1453: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl);
1454: for(i=1;i<=nlstate;i++)
1455: gp[i] = prlim[i][i];
1456:
1457: for(i=1; i<=npar; i++) /* Computes gradient */
1458: xp[i] = x[i] - (i==theta ?delti[theta]:0);
1459: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl);
1460: for(i=1;i<=nlstate;i++)
1461: gm[i] = prlim[i][i];
1462:
1463: for(i=1;i<=nlstate;i++)
1464: gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
1465: } /* End theta */
1466:
1467: trgradg =matrix(1,nlstate,1,npar);
1468:
1469: for(j=1; j<=nlstate;j++)
1470: for(theta=1; theta <=npar; theta++)
1471: trgradg[j][theta]=gradg[theta][j];
1472:
1473: for(i=1;i<=nlstate;i++)
1474: varpl[i][(int)age] =0.;
1475: matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
1476: matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
1477: for(i=1;i<=nlstate;i++)
1478: varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
1479:
1480: fprintf(ficresvpl,"%.0f ",age );
1481: for(i=1; i<=nlstate;i++)
1482: fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
1483: fprintf(ficresvpl,"\n");
1484: free_vector(gp,1,nlstate);
1485: free_vector(gm,1,nlstate);
1486: free_matrix(gradg,1,npar,1,nlstate);
1487: free_matrix(trgradg,1,nlstate,1,npar);
1488: } /* End age */
1489: fclose(ficresvpl);
1490: free_vector(xp,1,npar);
1491: free_matrix(doldm,1,nlstate,1,npar);
1492: free_matrix(dnewm,1,nlstate,1,nlstate);
1493:
1494: }
1495:
1496:
1497:
1498: /***********************************************/
1499: /**************** Main Program *****************/
1500: /***********************************************/
1501:
1502: /*int main(int argc, char *argv[])*/
1503: int main()
1504: {
1505:
1506: int i,j, k, n=MAXN,iter,m,size;
1507: double agedeb, agefin,hf;
1508: double agemin=1.e20, agemax=-1.e20;
1509:
1510: double fret;
1511: double **xi,tmp,delta;
1512:
1513: double dum; /* Dummy variable */
1514: double ***p3mat;
1515: int *indx;
1516: char line[MAXLINE], linepar[MAXLINE];
1517: char title[MAXLINE];
1518: char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH], filerespl[FILENAMELENGTH];
1519: char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH];
1520: char filerest[FILENAMELENGTH];
1521: char fileregp[FILENAMELENGTH];
1522: char path[80],pathc[80],pathcd[80],pathtot[80];
1523: int firstobs=1, lastobs=10;
1524: int sdeb, sfin; /* Status at beginning and end */
1525: int c, h , cpt,l;
1526: int ju,jl, mi;
1527: int i1,j1, k1,jk,aa,bb, stepsize;
1528: int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,**adl,*tab;
1529:
1530: int hstepm, nhstepm;
1531: double bage, fage, age, agelim, agebase;
1532: double ftolpl=FTOL;
1533: double **prlim;
1534: double *severity;
1535: double ***param; /* Matrix of parameters */
1536: double *p;
1537: double **matcov; /* Matrix of covariance */
1538: double ***delti3; /* Scale */
1539: double *delti; /* Scale */
1540: double ***eij, ***vareij;
1541: double **varpl; /* Variances of prevalence limits by age */
1542: double *epj, vepp;
1543: char version[80]="Imach version 0.64, May 2000, INED-EUROREVES ";
1544: char *alph[]={"a","a","b","c","d","e"}, str[4];
1545: char z[1]="c";
1546: #include <sys/time.h>
1547: #include <time.h>
1548:
1549: /* long total_usecs;
1550: struct timeval start_time, end_time;
1551:
1552: gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */
1553:
1554:
1555: printf("\nIMACH, Version 0.64");
1556: printf("\nEnter the parameter file name: ");
1557: #define windows 1
1558: #ifdef windows
1559: scanf("%s",pathtot);
1560: getcwd(pathcd, size);
1561: cut(path,optionfile,pathtot);
1562: chdir(path);
1563: replace(pathc,path);
1564: #endif
1565: #ifdef unix
1566: scanf("%s",optionfile);
1567: #endif
1568:
1569: /*-------- arguments in the command line --------*/
1570:
1571: strcpy(fileres,"r");
1572: strcat(fileres, optionfile);
1573:
1574: /*---------arguments file --------*/
1575:
1576: if((ficpar=fopen(optionfile,"r"))==NULL) {
1577: printf("Problem with optionfile %s\n",optionfile);
1578: goto end;
1579: }
1580:
1581: strcpy(filereso,"o");
1582: strcat(filereso,fileres);
1583: if((ficparo=fopen(filereso,"w"))==NULL) {
1584: printf("Problem with Output resultfile: %s\n", filereso);goto end;
1585: }
1586:
1587: /*--------- index.htm --------*/
1588:
1589: if((fichtm=fopen("index.htm","w"))==NULL) {
1590: printf("Problem with index.htm \n");goto end;
1591: }
1592:
1593: fprintf(fichtm,"<body><ul><li>Outputs files<br><br>\n
1594: - Observed prevalence in each state: <a href=\"p%s\">p%s</a> <br>\n
1595: - Estimated parameters and the covariance matrix: <a href=\"%s\">%s</a> <br>
1596: - Stationary prevalence in each state: <a href=\"pl%s\">pl%s</a> <br>
1597: - Transition probabilities: <a href=\"pij%s\">pij%s</a><br>
1598: - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>
1599: - Life expectancies by age and initial health status: <a href=\"e%s\">e%s</a> <br>
1600: - Variances of life expectancies by age and initial health status: <a href=\"v%s\">v%s</a><br>
1601: - Health expectancies with their variances: <a href=\"t%s\">t%s</a> <br>
1602: - 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);
1603:
1604: fprintf(fichtm," <li>Graphs<br> <br>");
1605:
1606: for(cpt=1; cpt<nlstate;cpt++)
1607: fprintf(fichtm,"- Prevalence of disability: p%s1.gif<br>
1608: <img src=\"p%s1.gif\"><br>",strtok(optionfile, "."),strtok(optionfile, "."),cpt);
1609: for(cpt=1; cpt<=nlstate;cpt++)
1610: fprintf(fichtm,"- Observed and stationary prevalence (with confident
1611: interval) in state (%d): v%s%d.gif <br>
1612: <img src=\"v%s%d.gif\"><br>",cpt,strtok(optionfile, "."),cpt,strtok(optionfile, "."),cpt);
1613:
1614: for(cpt=1; cpt<=nlstate;cpt++)
1615: fprintf(fichtm,"- Health life expectancies by age and initial health state (%d): exp%s%d.gif <br>
1616: <img src=\"ex%s%d.gif\"><br>",cpt,strtok(optionfile, "."),cpt,strtok(optionfile, "."),cpt);
1617:
1618: fprintf(fichtm,"- Total life expectancy by age and
1619: health expectancies in states (1) and (2): e%s.gif<br>
1620: <img src=\"e%s.gif\"></li> </ul></body>",strtok(optionfile, "."),strtok(optionfile, "."));
1621:
1622:
1623: fclose(fichtm);
1624:
1625: /* Reads comments: lines beginning with '#' */
1626: while((c=getc(ficpar))=='#' && c!= EOF){
1627: ungetc(c,ficpar);
1628: fgets(line, MAXLINE, ficpar);
1629: puts(line);
1630: fputs(line,ficparo);
1631: }
1632: ungetc(c,ficpar);
1633:
1634: 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\n",title, datafile, &lastobs, &firstpass,&lastpass,&ftol, &stepm, &ncov, &nlstate,&ndeath, &maxwav, &mle, &weightopt);
1635: 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\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncov, nlstate,ndeath, maxwav, mle, weightopt);
1636: 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\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncov,nlstate,ndeath,maxwav, mle, weightopt);
1637:
1638: nvar=ncov-1; /* Suppressing age as a basic covariate */
1639:
1640: /* Read guess parameters */
1641: /* Reads comments: lines beginning with '#' */
1642: while((c=getc(ficpar))=='#' && c!= EOF){
1643: ungetc(c,ficpar);
1644: fgets(line, MAXLINE, ficpar);
1645: puts(line);
1646: fputs(line,ficparo);
1647: }
1648: ungetc(c,ficpar);
1649:
1650: param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncov);
1651: for(i=1; i <=nlstate; i++)
1652: for(j=1; j <=nlstate+ndeath-1; j++){
1653: fscanf(ficpar,"%1d%1d",&i1,&j1);
1654: fprintf(ficparo,"%1d%1d",i1,j1);
1655: printf("%1d%1d",i,j);
1656: for(k=1; k<=ncov;k++){
1657: fscanf(ficpar," %lf",¶m[i][j][k]);
1658: printf(" %lf",param[i][j][k]);
1659: fprintf(ficparo," %lf",param[i][j][k]);
1660: }
1661: fscanf(ficpar,"\n");
1662: printf("\n");
1663: fprintf(ficparo,"\n");
1664: }
1665:
1666: npar= (nlstate+ndeath-1)*nlstate*ncov;
1667: p=param[1][1];
1668:
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: delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncov);
1679: delti=vector(1,npar); /* Scale of each paramater (output from hesscov) */
1680: for(i=1; i <=nlstate; i++){
1681: for(j=1; j <=nlstate+ndeath-1; j++){
1682: fscanf(ficpar,"%1d%1d",&i1,&j1);
1683: printf("%1d%1d",i,j);
1684: fprintf(ficparo,"%1d%1d",i1,j1);
1685: for(k=1; k<=ncov;k++){
1686: fscanf(ficpar,"%le",&delti3[i][j][k]);
1687: printf(" %le",delti3[i][j][k]);
1688: fprintf(ficparo," %le",delti3[i][j][k]);
1689: }
1690: fscanf(ficpar,"\n");
1691: printf("\n");
1692: fprintf(ficparo,"\n");
1693: }
1694: }
1695: delti=delti3[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: matcov=matrix(1,npar,1,npar);
1707: for(i=1; i <=npar; i++){
1708: fscanf(ficpar,"%s",&str);
1709: printf("%s",str);
1710: fprintf(ficparo,"%s",str);
1711: for(j=1; j <=i; j++){
1712: fscanf(ficpar," %le",&matcov[i][j]);
1713: printf(" %.5le",matcov[i][j]);
1714: fprintf(ficparo," %.5le",matcov[i][j]);
1715: }
1716: fscanf(ficpar,"\n");
1717: printf("\n");
1718: fprintf(ficparo,"\n");
1719: }
1720: for(i=1; i <=npar; i++)
1721: for(j=i+1;j<=npar;j++)
1722: matcov[i][j]=matcov[j][i];
1723:
1724: printf("\n");
1725:
1726:
1727: if(mle==1){
1728: /*-------- data file ----------*/
1729: if((ficres =fopen(fileres,"w"))==NULL) {
1730: printf("Problem with resultfile: %s\n", fileres);goto end;
1731: }
1732: fprintf(ficres,"#%s\n",version);
1733:
1734: if((fic=fopen(datafile,"r"))==NULL) {
1735: printf("Problem with datafile: %s\n", datafile);goto end;
1736: }
1737:
1738: n= lastobs;
1739: severity = vector(1,maxwav);
1740: outcome=imatrix(1,maxwav+1,1,n);
1741: num=ivector(1,n);
1742: moisnais=vector(1,n);
1743: annais=vector(1,n);
1744: moisdc=vector(1,n);
1745: andc=vector(1,n);
1746: agedc=vector(1,n);
1747: cod=ivector(1,n);
1748: weight=vector(1,n);
1749: for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */
1750: mint=matrix(1,maxwav,1,n);
1751: anint=matrix(1,maxwav,1,n);
1752: covar=matrix(1,NCOVMAX,1,n);
1753: s=imatrix(1,maxwav+1,1,n);
1754: adl=imatrix(1,maxwav+1,1,n);
1755: tab=ivector(1,NCOVMAX);
1756: i=1;
1757: while (fgets(line, MAXLINE, fic) != NULL) {
1758: if ((i >= firstobs) && (i <lastobs)) {
1759: sscanf(line,"%d %lf %lf %lf %lf/%lf %lf/%lf %lf/%lf %d %lf/%lf %d %lf/%lf %d %lf/%lf %d", &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]);
1760: i=i+1;
1761: }
1762: }
1763: imx=i-1; /* Number of individuals */
1764:
1765: fclose(fic);
1766:
1767: if (weightopt != 1) { /* Maximisation without weights*/
1768: for(i=1;i<=n;i++) weight[i]=1.0;
1769: }
1770: /*-calculation of age at interview from date of interview and age at death -*/
1771: agev=matrix(1,maxwav,1,imx);
1772:
1773: for (i=1; i<=imx; i++) {
1774: agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);
1775: for(m=1; (m<= maxwav); m++){
1776: if(s[m][i] >0){
1777: if (s[m][i] == nlstate+1) {
1778: if(agedc[i]>0)
1779: agev[m][i]=agedc[i];
1780: else{
1781: printf("Warning negative age at death: %d line:%d\n",num[i],i);
1782: agev[m][i]=-1;
1783: }
1784: }
1785: else if(s[m][i] !=9){ /* Should no more exist */
1786: agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);
1787: if(mint[m][i]==99 || anint[m][i]==9999)
1788: agev[m][i]=1;
1789: else if(agev[m][i] <agemin){
1790: agemin=agev[m][i];
1791: /*printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], agemin);*/
1792: }
1793: else if(agev[m][i] >agemax){
1794: agemax=agev[m][i];
1795: /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/
1796: }
1797: /*agev[m][i]=anint[m][i]-annais[i];*/
1798: /* agev[m][i] = age[i]+2*m;*/
1799: }
1800: else { /* =9 */
1801: agev[m][i]=1;
1802: s[m][i]=-1;
1803: }
1804: }
1805: else /*= 0 Unknown */
1806: agev[m][i]=1;
1807: }
1808:
1809: }
1810: for (i=1; i<=imx; i++) {
1811: for(m=1; (m<= maxwav); m++){
1812: if (s[m][i] > (nlstate+ndeath)) {
1813: printf("Error: Wrong value in nlstate or ndeath\n");
1814: goto end;
1815: }
1816: }
1817: }
1818:
1819: printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);
1820:
1821: free_vector(severity,1,maxwav);
1822: free_imatrix(outcome,1,maxwav+1,1,n);
1823: free_vector(moisnais,1,n);
1824: free_vector(annais,1,n);
1825: free_matrix(mint,1,maxwav,1,n);
1826: free_matrix(anint,1,maxwav,1,n);
1827: free_vector(moisdc,1,n);
1828: free_vector(andc,1,n);
1829:
1830:
1831: wav=ivector(1,imx);
1832: dh=imatrix(1,lastpass-firstpass+1,1,imx);
1833: mw=imatrix(1,lastpass-firstpass+1,1,imx);
1834:
1835: /* Concatenates waves */
1836: concatwav(wav, dh, mw, s, agedc, agev, firstpass, lastpass, imx, nlstate, stepm);
1837:
1838: /* Calculates basic frequencies. Computes observed prevalence at single age
1839: and prints on file fileres'p'. */
1840: freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx);
1841:
1842: pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
1843: oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
1844: newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
1845: savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
1846: oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */
1847:
1848: /* For Powell, parameters are in a vector p[] starting at p[1]
1849: so we point p on param[1][1] so that p[1] maps on param[1][1][1] */
1850: p=param[1][1]; /* *(*(*(param +1)+1)+0) */
1851:
1852: mlikeli(ficres,p, npar, ncov, nlstate, ftol, func);
1853:
1854:
1855: /*--------- results files --------------*/
1856: 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\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncov, nlstate, ndeath, maxwav, mle,weightopt);
1857:
1858: jk=1;
1859: fprintf(ficres,"# Parameters\n");
1860: printf("# Parameters\n");
1861: for(i=1,jk=1; i <=nlstate; i++){
1862: for(k=1; k <=(nlstate+ndeath); k++){
1863: if (k != i)
1864: {
1865: printf("%d%d ",i,k);
1866: fprintf(ficres,"%1d%1d ",i,k);
1867: for(j=1; j <=ncov; j++){
1868: printf("%f ",p[jk]);
1869: fprintf(ficres,"%f ",p[jk]);
1870: jk++;
1871: }
1872: printf("\n");
1873: fprintf(ficres,"\n");
1874: }
1875: }
1876: }
1877:
1878: /* Computing hessian and covariance matrix */
1879: ftolhess=ftol; /* Usually correct */
1880: hesscov(matcov, p, npar, delti, ftolhess, func);
1881: fprintf(ficres,"# Scales\n");
1882: printf("# Scales\n");
1883: for(i=1,jk=1; i <=nlstate; i++){
1884: for(j=1; j <=nlstate+ndeath; j++){
1885: if (j!=i) {
1886: fprintf(ficres,"%1d%1d",i,j);
1887: printf("%1d%1d",i,j);
1888: for(k=1; k<=ncov;k++){
1889: printf(" %.5e",delti[jk]);
1890: fprintf(ficres," %.5e",delti[jk]);
1891: jk++;
1892: }
1893: printf("\n");
1894: fprintf(ficres,"\n");
1895: }
1896: }
1897: }
1898:
1899: k=1;
1900: fprintf(ficres,"# Covariance\n");
1901: printf("# Covariance\n");
1902: for(i=1;i<=npar;i++){
1903: /* if (k>nlstate) k=1;
1904: i1=(i-1)/(ncov*nlstate)+1;
1905: fprintf(ficres,"%s%d%d",alph[k],i1,tab[i]);
1906: printf("%s%d%d",alph[k],i1,tab[i]);*/
1907: fprintf(ficres,"%3d",i);
1908: printf("%3d",i);
1909: for(j=1; j<=i;j++){
1910: fprintf(ficres," %.5e",matcov[i][j]);
1911: printf(" %.5e",matcov[i][j]);
1912: }
1913: fprintf(ficres,"\n");
1914: printf("\n");
1915: k++;
1916: }
1917:
1918: while((c=getc(ficpar))=='#' && c!= EOF){
1919: ungetc(c,ficpar);
1920: fgets(line, MAXLINE, ficpar);
1921: puts(line);
1922: fputs(line,ficparo);
1923: }
1924: ungetc(c,ficpar);
1925:
1926: fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf\n",&agemin,&agemax, &bage, &fage);
1927:
1928: if (fage <= 2) {
1929: bage = agemin;
1930: fage = agemax;
1931: }
1932:
1933: fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");
1934: fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemax,bage,fage);
1935: /*------------ gnuplot -------------*/
1936: chdir(pathcd);
1937: if((ficgp=fopen("graph.gp","w"))==NULL) {
1938: printf("Problem with file graph.gp");goto end;
1939: }
1940: #ifdef windows
1941: fprintf(ficgp,"cd \"%s\" \n",pathc);
1942: #endif
1943: /* 1eme*/
1944:
1945: for (cpt=1; cpt<= nlstate ; cpt ++) {
1946: #ifdef windows
1947: fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter gif small size 400,300\nplot [%.f:%.f] \"vpl%s\" u 1:%d \"\%%lf",agemin,fage,fileres,cpt*2);
1948: #endif
1949: #ifdef unix
1950: fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nplot [%.f:%.f] \"vpl%s\" u 1:%d \"\%%lf",agemin,fage,fileres,cpt*2);
1951: #endif
1952: for (i=1; i<= nlstate ; i ++) fprintf(ficgp," \%%lf (\%%lf)");
1953: fprintf(ficgp,"\" t\"Stationary prevalence\" w l 0,\"vpl%s\" u 1:($%d+2*$%d) \"\%%lf",fileres,2*cpt,cpt*2+1);
1954: for (i=1; i<= nlstate ; i ++) fprintf(ficgp," \%%lf (\%%lf)");
1955: fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"vpl%s\" u 1:($%d-2*$%d) \"\%%lf",fileres,2*cpt,2*cpt+1);
1956: for (i=1; i<= nlstate ; i ++) fprintf(ficgp," \%%lf (\%%lf)");
1957: fprintf(ficgp,"\" t\"\" w l 1,\"p%s\" u 1:($%d) t\"Observed prevalence \" w l 2",fileres,2+4*(cpt-1));
1958: #ifdef unix
1959: fprintf(ficgp,"\nset ter gif small size 400,300");
1960: #endif
1961: fprintf(ficgp,"\nset out \"v%s%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt);
1962:
1963: }
1964: /*2 eme*/
1965:
1966: fprintf(ficgp,"set ylabel \"Years\" \nset ter gif small size 400,300\nplot [%.f:%.f] ",agemin,fage);
1967: for (i=1; i<= nlstate+1 ; i ++) {
1968: k=2*i;
1969: fprintf(ficgp,"\"t%s\" u 1:%d \"\%%lf \%%lf (\%%lf) \%%lf (\%%lf)",fileres,k);
1970: for (j=1; j< nlstate ; j ++) fprintf(ficgp," \%%lf (\%%lf)");
1971: if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");
1972: else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);
1973: fprintf(ficgp,"\"t%s\" u 1:($%d-2*$%d) \"\%%lf \%%lf (\%%lf) \%%lf (\%%lf)",fileres,k,k+1);
1974: for (j=1; j< nlstate ; j ++) fprintf(ficgp," \%%lf (\%%lf)");
1975: fprintf(ficgp,"\" t\"\" w l 0,");
1976: fprintf(ficgp,"\"t%s\" u 1:($%d+2*$%d) \"\%%lf \%%lf (\%%lf) \%%lf (\%%lf)",fileres,k,k+1);
1977: for (j=1; j< nlstate ; j ++) fprintf(ficgp," \%%lf (\%%lf)");
1978: if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");
1979: else fprintf(ficgp,"\" t\"\" w l 0,");
1980: }
1981: fprintf(ficgp,"\nset out \"e%s.gif\" \nreplot\n\n",strtok(optionfile, "."));
1982:
1983: /*3eme*/
1984: for (cpt=1; cpt<= nlstate ; cpt ++) {
1985: k=2+nlstate*(cpt-1);
1986: fprintf(ficgp,"set ter gif small size 400,300\nplot [%.f:%.f] \"e%s\" u 1:%d t \"e%d1\" w l",agemin,fage,fileres,k,cpt);
1987: for (i=1; i< nlstate ; i ++) {
1988: fprintf(ficgp,",\"e%s\" u 1:%d t \"e%d%d\" w l",fileres,k+1,cpt,i+1);
1989: }
1990: fprintf(ficgp,"\nset out \"ex%s%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt);
1991: }
1992:
1993: /* CV preval stat */
1994: for (cpt=1; cpt<nlstate ; cpt ++) {
1995: k=3;
1996: fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter gif small size 400,300\nplot [%.f:%.f] \"pij%s\" u 2:($%d/($%d",agemin,agemax,fileres,k+cpt,k);
1997: for (i=1; i< nlstate ; i ++)
1998: fprintf(ficgp,"+$%d",k+i);
1999: fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);
2000:
2001: l=3+(nlstate+ndeath)*cpt;
2002: fprintf(ficgp,",\"pij%s\" u 2:($%d/($%d",fileres,l+cpt,l);
2003:
2004: for (i=1; i< nlstate ; i ++) {
2005: l=3+(nlstate+ndeath)*cpt;
2006: fprintf(ficgp,"+$%d",l+i);
2007: }
2008: fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);
2009:
2010:
2011: fprintf(ficgp,"set out \"p%s%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt);
2012: }
2013:
2014:
2015: fclose(ficgp);
2016:
2017: chdir(path);
2018: free_matrix(agev,1,maxwav,1,imx);
2019: free_ivector(wav,1,imx);
2020: free_imatrix(dh,1,lastpass-firstpass+1,1,imx);
2021: free_imatrix(mw,1,lastpass-firstpass+1,1,imx);
2022:
2023: free_imatrix(s,1,maxwav+1,1,n);
2024:
2025:
2026: free_ivector(num,1,n);
2027: free_vector(agedc,1,n);
2028: free_vector(weight,1,n);
2029: free_matrix(covar,1,NCOVMAX,1,n);
2030: fclose(ficparo);
2031: fclose(ficres);
2032: }
2033:
2034: /*________fin mle=1_________*/
2035:
2036:
2037:
2038: /* No more information from the sample is required now */
2039: /* Reads comments: lines beginning with '#' */
2040: while((c=getc(ficpar))=='#' && c!= EOF){
2041: ungetc(c,ficpar);
2042: fgets(line, MAXLINE, ficpar);
2043: puts(line);
2044: fputs(line,ficparo);
2045: }
2046: ungetc(c,ficpar);
2047:
2048: fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf\n",&agemin,&agemax, &bage, &fage);
2049: printf("agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemax, bage, fage);
2050: fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemax,bage,fage);
2051:
2052: /*--------------- Prevalence limit --------------*/
2053:
2054: strcpy(filerespl,"pl");
2055: strcat(filerespl,fileres);
2056: if((ficrespl=fopen(filerespl,"w"))==NULL) {
2057: printf("Problem with Prev limit resultfile: %s\n", filerespl);goto end;
2058: }
2059: printf("Computing prevalence limit: result on file '%s' \n", filerespl);
2060: fprintf(ficrespl,"#Prevalence limit\n");
2061: fprintf(ficrespl,"#Age ");
2062: for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);
2063: fprintf(ficrespl,"\n");
2064:
2065: prlim=matrix(1,nlstate,1,nlstate);
2066: pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
2067: oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
2068: newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
2069: savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
2070: oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */
2071:
2072: agebase=agemin;
2073: agelim=agemax;
2074: ftolpl=1.e-10;
2075: for (age=agebase; age<=agelim; age++){
2076: prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl);
2077: fprintf(ficrespl,"%.0f",age );
2078: for(i=1; i<=nlstate;i++)
2079: fprintf(ficrespl," %.5f", prlim[i][i]);
2080: fprintf(ficrespl,"\n");
2081: }
2082: fclose(ficrespl);
2083:
2084: /*------------- h Pij x at various ages ------------*/
2085:
2086: strcpy(filerespij,"pij"); strcat(filerespij,fileres);
2087: if((ficrespij=fopen(filerespij,"w"))==NULL) {
2088: printf("Problem with Pij resultfile: %s\n", filerespij);goto end;
2089: }
2090: printf("Computing pij: result on file '%s' \n", filerespij);
2091: stepsize=(int) (stepm+YEARM-1)/YEARM;
2092: if (stepm<=24) stepsize=2;
2093:
2094: agelim=AGESUP;
2095: hstepm=stepsize*YEARM; /* Every year of age */
2096: hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */
2097: for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */
2098: nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
2099: nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
2100: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
2101: oldm=oldms;savm=savms;
2102: hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm);
2103: fprintf(ficrespij,"# Age");
2104: for(i=1; i<=nlstate;i++)
2105: for(j=1; j<=nlstate+ndeath;j++)
2106: fprintf(ficrespij," %1d-%1d",i,j);
2107: fprintf(ficrespij,"\n");
2108: for (h=0; h<=nhstepm; h++){
2109: fprintf(ficrespij,"%.0f %.0f",agedeb, agedeb+ h*hstepm/YEARM*stepm );
2110: for(i=1; i<=nlstate;i++)
2111: for(j=1; j<=nlstate+ndeath;j++)
2112: fprintf(ficrespij," %.5f", p3mat[i][j][h]);
2113: fprintf(ficrespij,"\n");
2114: }
2115: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
2116: fprintf(ficrespij,"\n");
2117: }
2118: fclose(ficrespij);
2119:
2120: /*---------- Health expectancies and variances ------------*/
2121:
2122: eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
2123: oldm=oldms;savm=savms;
2124: evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm);
2125:
2126: vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
2127: oldm=oldms;savm=savms;
2128: varevsij(fileres, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl);
2129:
2130: strcpy(filerest,"t");
2131: strcat(filerest,fileres);
2132: if((ficrest=fopen(filerest,"w"))==NULL) {
2133: printf("Problem with total LE resultfile: %s\n", filerest);goto end;
2134: }
2135: printf("Computing Total LEs with variances: file '%s' \n", filerest);
2136: fprintf(ficrest,"#Total LEs with variances: e.. (std) ");
2137: for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);
2138: fprintf(ficrest,"\n");
2139:
2140: hf=1;
2141: if (stepm >= YEARM) hf=stepm/YEARM;
2142: epj=vector(1,nlstate+1);
2143: for(age=bage; age <=fage ;age++){
2144: prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl);
2145: fprintf(ficrest," %.0f",age);
2146: for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){
2147: for(i=1, epj[j]=0.;i <=nlstate;i++) {
2148: epj[j] += prlim[i][i]*hf*eij[i][j][(int)age];
2149: }
2150: epj[nlstate+1] +=epj[j];
2151: }
2152: for(i=1, vepp=0.;i <=nlstate;i++)
2153: for(j=1;j <=nlstate;j++)
2154: vepp += vareij[i][j][(int)age];
2155: fprintf(ficrest," %.2f (%.2f)", epj[nlstate+1],hf*sqrt(vepp));
2156: for(j=1;j <=nlstate;j++){
2157: fprintf(ficrest," %.2f (%.2f)", epj[j],hf*sqrt(vareij[j][j][(int)age]));
2158: }
2159: fprintf(ficrest,"\n");
2160: }
2161: fclose(ficrest);
2162: fclose(ficpar);
2163: free_vector(epj,1,nlstate+1);
2164:
2165: /*------- Variance limit prevalence------*/
2166:
2167: varpl=matrix(1,nlstate,(int) bage, (int) fage);
2168: oldm=oldms;savm=savms;
2169: varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl);
2170:
2171:
2172: free_matrix(varpl,1,nlstate,(int) bage, (int)fage);
2173:
2174: free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);
2175: free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
2176:
2177:
2178: free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);
2179: free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);
2180: free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);
2181: free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);
2182:
2183: free_matrix(matcov,1,npar,1,npar);
2184: free_vector(delti,1,npar);
2185:
2186: free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncov);
2187:
2188: printf("End of Imach\n");
2189: /* gettimeofday(&end_time, (struct timezone*)0);*/ /* after time */
2190:
2191: /* 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);*/
2192: /*printf("Total time was %d uSec.\n", total_usecs);*/
2193: /*------ End -----------*/
2194:
2195: end:
2196: #ifdef windows
2197: chdir(pathcd);
2198: #endif
2199: system("gnuplot graph.gp");
2200:
2201: #ifdef windows
2202: while (z[0] != 'q') {
2203: chdir(pathcd);
2204: printf("\nType e to edit output files, c to start again, and q for exiting: ");
2205: scanf("%s",z);
2206: if (z[0] == 'c') system("./imach");
2207: else if (z[0] == 'e') {
2208: chdir(path);
2209: system("index.htm");
2210: }
2211: else if (z[0] == 'q') exit(0);
2212: }
2213: #endif
2214: }
2215:
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