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: #define GLOCK_ERROR_NOPATH -1 /* empty path */
55: #define GLOCK_ERROR_GETCWD -2 /* cannot get cwd */
56:
57: #define MAXPARM 30 /* Maximum number of parameters for the optimization */
58: #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */
59:
60: #define NINTERVMAX 8
61: #define NLSTATEMAX 8 /* Maximum number of live states (for func) */
62: #define NDEATHMAX 8 /* Maximum number of dead states (for func) */
63: #define NCOVMAX 8 /* Maximum number of covariates */
64: #define MAXN 20000
65: #define YEARM 12. /* Number of months per year */
66: #define AGESUP 130
67: #define AGEBASE 40
68:
69:
70: int nvar;
71: int cptcovn, cptcovage=0, cptcoveff=0,cptcov;
72: int npar=NPARMAX;
73: int nlstate=2; /* Number of live states */
74: int ndeath=1; /* Number of dead states */
75: int ncovmodel, ncov; /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
76: int popbased=0;
77:
78: int *wav; /* Number of waves for this individuual 0 is possible */
79: int maxwav; /* Maxim number of waves */
80: int jmin, jmax; /* min, max spacing between 2 waves */
81: int mle, weightopt;
82: int **mw; /* mw[mi][i] is number of the mi wave for this individual */
83: int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
84: double jmean; /* Mean space between 2 waves */
85: double **oldm, **newm, **savm; /* Working pointers to matrices */
86: double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
87: FILE *fic,*ficpar, *ficparo,*ficres, *ficrespl, *ficrespij, *ficrest,*ficresf;
88: FILE *ficgp, *fichtm,*ficresprob;
89: FILE *ficreseij;
90: char filerese[FILENAMELENGTH];
91: FILE *ficresvij;
92: char fileresv[FILENAMELENGTH];
93: FILE *ficresvpl;
94: char fileresvpl[FILENAMELENGTH];
95:
96: #define NR_END 1
97: #define FREE_ARG char*
98: #define FTOL 1.0e-10
99:
100: #define NRANSI
101: #define ITMAX 200
102:
103: #define TOL 2.0e-4
104:
105: #define CGOLD 0.3819660
106: #define ZEPS 1.0e-10
107: #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);
108:
109: #define GOLD 1.618034
110: #define GLIMIT 100.0
111: #define TINY 1.0e-20
112:
113: static double maxarg1,maxarg2;
114: #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
115: #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
116:
117: #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
118: #define rint(a) floor(a+0.5)
119:
120: static double sqrarg;
121: #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
122: #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}
123:
124: int imx;
125: int stepm;
126: /* Stepm, step in month: minimum step interpolation*/
127:
128: int m,nb;
129: int *num, firstpass=0, lastpass=4,*cod, *ncodemax, *Tage;
130: double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
131: double **pmmij, ***probs, ***mobaverage;
132:
133: double *weight;
134: int **s; /* Status */
135: double *agedc, **covar, idx;
136: int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;
137:
138: double ftol=FTOL; /* Tolerance for computing Max Likelihood */
139: double ftolhess; /* Tolerance for computing hessian */
140:
141: /**************** split *************************/
142: static int split( char *path, char *dirc, char *name )
143: {
144: char *s; /* pointer */
145: int l1, l2; /* length counters */
146:
147: l1 = strlen( path ); /* length of path */
148: if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
149: s = strrchr( path, '\\' ); /* find last / */
150: if ( s == NULL ) { /* no directory, so use current */
151: #if defined(__bsd__) /* get current working directory */
152: extern char *getwd( );
153:
154: if ( getwd( dirc ) == NULL ) {
155: #else
156: extern char *getcwd( );
157:
158: if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {
159: #endif
160: return( GLOCK_ERROR_GETCWD );
161: }
162: strcpy( name, path ); /* we've got it */
163: } else { /* strip direcotry from path */
164: s++; /* after this, the filename */
165: l2 = strlen( s ); /* length of filename */
166: if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
167: strcpy( name, s ); /* save file name */
168: strncpy( dirc, path, l1 - l2 ); /* now the directory */
169: dirc[l1-l2] = 0; /* add zero */
170: }
171: l1 = strlen( dirc ); /* length of directory */
172: if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; }
173: return( 0 ); /* we're done */
174: }
175:
176:
177: /******************************************/
178:
179: void replace(char *s, char*t)
180: {
181: int i;
182: int lg=20;
183: i=0;
184: lg=strlen(t);
185: for(i=0; i<= lg; i++) {
186: (s[i] = t[i]);
187: if (t[i]== '\\') s[i]='/';
188: }
189: }
190:
191: int nbocc(char *s, char occ)
192: {
193: int i,j=0;
194: int lg=20;
195: i=0;
196: lg=strlen(s);
197: for(i=0; i<= lg; i++) {
198: if (s[i] == occ ) j++;
199: }
200: return j;
201: }
202:
203: void cutv(char *u,char *v, char*t, char occ)
204: {
205: int i,lg,j,p=0;
206: i=0;
207: for(j=0; j<=strlen(t)-1; j++) {
208: if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;
209: }
210:
211: lg=strlen(t);
212: for(j=0; j<p; j++) {
213: (u[j] = t[j]);
214: }
215: u[p]='\0';
216:
217: for(j=0; j<= lg; j++) {
218: if (j>=(p+1))(v[j-p-1] = t[j]);
219: }
220: }
221:
222: /********************** nrerror ********************/
223:
224: void nrerror(char error_text[])
225: {
226: fprintf(stderr,"ERREUR ...\n");
227: fprintf(stderr,"%s\n",error_text);
228: exit(1);
229: }
230: /*********************** vector *******************/
231: double *vector(int nl, int nh)
232: {
233: double *v;
234: v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
235: if (!v) nrerror("allocation failure in vector");
236: return v-nl+NR_END;
237: }
238:
239: /************************ free vector ******************/
240: void free_vector(double*v, int nl, int nh)
241: {
242: free((FREE_ARG)(v+nl-NR_END));
243: }
244:
245: /************************ivector *******************************/
246: int *ivector(long nl,long nh)
247: {
248: int *v;
249: v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
250: if (!v) nrerror("allocation failure in ivector");
251: return v-nl+NR_END;
252: }
253:
254: /******************free ivector **************************/
255: void free_ivector(int *v, long nl, long nh)
256: {
257: free((FREE_ARG)(v+nl-NR_END));
258: }
259:
260: /******************* imatrix *******************************/
261: int **imatrix(long nrl, long nrh, long ncl, long nch)
262: /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */
263: {
264: long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;
265: int **m;
266:
267: /* allocate pointers to rows */
268: m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));
269: if (!m) nrerror("allocation failure 1 in matrix()");
270: m += NR_END;
271: m -= nrl;
272:
273:
274: /* allocate rows and set pointers to them */
275: m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));
276: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
277: m[nrl] += NR_END;
278: m[nrl] -= ncl;
279:
280: for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;
281:
282: /* return pointer to array of pointers to rows */
283: return m;
284: }
285:
286: /****************** free_imatrix *************************/
287: void free_imatrix(m,nrl,nrh,ncl,nch)
288: int **m;
289: long nch,ncl,nrh,nrl;
290: /* free an int matrix allocated by imatrix() */
291: {
292: free((FREE_ARG) (m[nrl]+ncl-NR_END));
293: free((FREE_ARG) (m+nrl-NR_END));
294: }
295:
296: /******************* matrix *******************************/
297: double **matrix(long nrl, long nrh, long ncl, long nch)
298: {
299: long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
300: double **m;
301:
302: m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
303: if (!m) nrerror("allocation failure 1 in matrix()");
304: m += NR_END;
305: m -= nrl;
306:
307: m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
308: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
309: m[nrl] += NR_END;
310: m[nrl] -= ncl;
311:
312: for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
313: return m;
314: }
315:
316: /*************************free matrix ************************/
317: void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
318: {
319: free((FREE_ARG)(m[nrl]+ncl-NR_END));
320: free((FREE_ARG)(m+nrl-NR_END));
321: }
322:
323: /******************* ma3x *******************************/
324: double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
325: {
326: long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
327: double ***m;
328:
329: m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
330: if (!m) nrerror("allocation failure 1 in matrix()");
331: m += NR_END;
332: m -= nrl;
333:
334: m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
335: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
336: m[nrl] += NR_END;
337: m[nrl] -= ncl;
338:
339: for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
340:
341: m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
342: if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
343: m[nrl][ncl] += NR_END;
344: m[nrl][ncl] -= nll;
345: for (j=ncl+1; j<=nch; j++)
346: m[nrl][j]=m[nrl][j-1]+nlay;
347:
348: for (i=nrl+1; i<=nrh; i++) {
349: m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
350: for (j=ncl+1; j<=nch; j++)
351: m[i][j]=m[i][j-1]+nlay;
352: }
353: return m;
354: }
355:
356: /*************************free ma3x ************************/
357: void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
358: {
359: free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
360: free((FREE_ARG)(m[nrl]+ncl-NR_END));
361: free((FREE_ARG)(m+nrl-NR_END));
362: }
363:
364: /***************** f1dim *************************/
365: extern int ncom;
366: extern double *pcom,*xicom;
367: extern double (*nrfunc)(double []);
368:
369: double f1dim(double x)
370: {
371: int j;
372: double f;
373: double *xt;
374:
375: xt=vector(1,ncom);
376: for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];
377: f=(*nrfunc)(xt);
378: free_vector(xt,1,ncom);
379: return f;
380: }
381:
382: /*****************brent *************************/
383: double brent(double ax, double bx, double cx, double (*f)(double), double tol, double *xmin)
384: {
385: int iter;
386: double a,b,d,etemp;
387: double fu,fv,fw,fx;
388: double ftemp;
389: double p,q,r,tol1,tol2,u,v,w,x,xm;
390: double e=0.0;
391:
392: a=(ax < cx ? ax : cx);
393: b=(ax > cx ? ax : cx);
394: x=w=v=bx;
395: fw=fv=fx=(*f)(x);
396: for (iter=1;iter<=ITMAX;iter++) {
397: xm=0.5*(a+b);
398: tol2=2.0*(tol1=tol*fabs(x)+ZEPS);
399: /* if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
400: printf(".");fflush(stdout);
401: #ifdef DEBUG
402: printf("br %d,x=%.10e xm=%.10e b=%.10e a=%.10e tol=%.10e tol1=%.10e tol2=%.10e x-xm=%.10e fx=%.12e fu=%.12e,fw=%.12e,ftemp=%.12e,ftol=%.12e\n",iter,x,xm,b,a,tol,tol1,tol2,(x-xm),fx,fu,fw,ftemp,ftol);
403: /* if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
404: #endif
405: if (fabs(x-xm) <= (tol2-0.5*(b-a))){
406: *xmin=x;
407: return fx;
408: }
409: ftemp=fu;
410: if (fabs(e) > tol1) {
411: r=(x-w)*(fx-fv);
412: q=(x-v)*(fx-fw);
413: p=(x-v)*q-(x-w)*r;
414: q=2.0*(q-r);
415: if (q > 0.0) p = -p;
416: q=fabs(q);
417: etemp=e;
418: e=d;
419: if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))
420: d=CGOLD*(e=(x >= xm ? a-x : b-x));
421: else {
422: d=p/q;
423: u=x+d;
424: if (u-a < tol2 || b-u < tol2)
425: d=SIGN(tol1,xm-x);
426: }
427: } else {
428: d=CGOLD*(e=(x >= xm ? a-x : b-x));
429: }
430: u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));
431: fu=(*f)(u);
432: if (fu <= fx) {
433: if (u >= x) a=x; else b=x;
434: SHFT(v,w,x,u)
435: SHFT(fv,fw,fx,fu)
436: } else {
437: if (u < x) a=u; else b=u;
438: if (fu <= fw || w == x) {
439: v=w;
440: w=u;
441: fv=fw;
442: fw=fu;
443: } else if (fu <= fv || v == x || v == w) {
444: v=u;
445: fv=fu;
446: }
447: }
448: }
449: nrerror("Too many iterations in brent");
450: *xmin=x;
451: return fx;
452: }
453:
454: /****************** mnbrak ***********************/
455:
456: void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,
457: double (*func)(double))
458: {
459: double ulim,u,r,q, dum;
460: double fu;
461:
462: *fa=(*func)(*ax);
463: *fb=(*func)(*bx);
464: if (*fb > *fa) {
465: SHFT(dum,*ax,*bx,dum)
466: SHFT(dum,*fb,*fa,dum)
467: }
468: *cx=(*bx)+GOLD*(*bx-*ax);
469: *fc=(*func)(*cx);
470: while (*fb > *fc) {
471: r=(*bx-*ax)*(*fb-*fc);
472: q=(*bx-*cx)*(*fb-*fa);
473: u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/
474: (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r));
475: ulim=(*bx)+GLIMIT*(*cx-*bx);
476: if ((*bx-u)*(u-*cx) > 0.0) {
477: fu=(*func)(u);
478: } else if ((*cx-u)*(u-ulim) > 0.0) {
479: fu=(*func)(u);
480: if (fu < *fc) {
481: SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))
482: SHFT(*fb,*fc,fu,(*func)(u))
483: }
484: } else if ((u-ulim)*(ulim-*cx) >= 0.0) {
485: u=ulim;
486: fu=(*func)(u);
487: } else {
488: u=(*cx)+GOLD*(*cx-*bx);
489: fu=(*func)(u);
490: }
491: SHFT(*ax,*bx,*cx,u)
492: SHFT(*fa,*fb,*fc,fu)
493: }
494: }
495:
496: /*************** linmin ************************/
497:
498: int ncom;
499: double *pcom,*xicom;
500: double (*nrfunc)(double []);
501:
502: void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))
503: {
504: double brent(double ax, double bx, double cx,
505: double (*f)(double), double tol, double *xmin);
506: double f1dim(double x);
507: void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,
508: double *fc, double (*func)(double));
509: int j;
510: double xx,xmin,bx,ax;
511: double fx,fb,fa;
512:
513: ncom=n;
514: pcom=vector(1,n);
515: xicom=vector(1,n);
516: nrfunc=func;
517: for (j=1;j<=n;j++) {
518: pcom[j]=p[j];
519: xicom[j]=xi[j];
520: }
521: ax=0.0;
522: xx=1.0;
523: mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim);
524: *fret=brent(ax,xx,bx,f1dim,TOL,&xmin);
525: #ifdef DEBUG
526: printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
527: #endif
528: for (j=1;j<=n;j++) {
529: xi[j] *= xmin;
530: p[j] += xi[j];
531: }
532: free_vector(xicom,1,n);
533: free_vector(pcom,1,n);
534: }
535:
536: /*************** powell ************************/
537: void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,
538: double (*func)(double []))
539: {
540: void linmin(double p[], double xi[], int n, double *fret,
541: double (*func)(double []));
542: int i,ibig,j;
543: double del,t,*pt,*ptt,*xit;
544: double fp,fptt;
545: double *xits;
546: pt=vector(1,n);
547: ptt=vector(1,n);
548: xit=vector(1,n);
549: xits=vector(1,n);
550: *fret=(*func)(p);
551: for (j=1;j<=n;j++) pt[j]=p[j];
552: for (*iter=1;;++(*iter)) {
553: fp=(*fret);
554: ibig=0;
555: del=0.0;
556: printf("\nPowell iter=%d -2*LL=%.12f",*iter,*fret);
557: for (i=1;i<=n;i++)
558: printf(" %d %.12f",i, p[i]);
559: printf("\n");
560: for (i=1;i<=n;i++) {
561: for (j=1;j<=n;j++) xit[j]=xi[j][i];
562: fptt=(*fret);
563: #ifdef DEBUG
564: printf("fret=%lf \n",*fret);
565: #endif
566: printf("%d",i);fflush(stdout);
567: linmin(p,xit,n,fret,func);
568: if (fabs(fptt-(*fret)) > del) {
569: del=fabs(fptt-(*fret));
570: ibig=i;
571: }
572: #ifdef DEBUG
573: printf("%d %.12e",i,(*fret));
574: for (j=1;j<=n;j++) {
575: xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
576: printf(" x(%d)=%.12e",j,xit[j]);
577: }
578: for(j=1;j<=n;j++)
579: printf(" p=%.12e",p[j]);
580: printf("\n");
581: #endif
582: }
583: if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {
584: #ifdef DEBUG
585: int k[2],l;
586: k[0]=1;
587: k[1]=-1;
588: printf("Max: %.12e",(*func)(p));
589: for (j=1;j<=n;j++)
590: printf(" %.12e",p[j]);
591: printf("\n");
592: for(l=0;l<=1;l++) {
593: for (j=1;j<=n;j++) {
594: ptt[j]=p[j]+(p[j]-pt[j])*k[l];
595: printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
596: }
597: printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
598: }
599: #endif
600:
601:
602: free_vector(xit,1,n);
603: free_vector(xits,1,n);
604: free_vector(ptt,1,n);
605: free_vector(pt,1,n);
606: return;
607: }
608: if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");
609: for (j=1;j<=n;j++) {
610: ptt[j]=2.0*p[j]-pt[j];
611: xit[j]=p[j]-pt[j];
612: pt[j]=p[j];
613: }
614: fptt=(*func)(ptt);
615: if (fptt < fp) {
616: t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt);
617: if (t < 0.0) {
618: linmin(p,xit,n,fret,func);
619: for (j=1;j<=n;j++) {
620: xi[j][ibig]=xi[j][n];
621: xi[j][n]=xit[j];
622: }
623: #ifdef DEBUG
624: printf("Direction changed last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
625: for(j=1;j<=n;j++)
626: printf(" %.12e",xit[j]);
627: printf("\n");
628: #endif
629: }
630: }
631: }
632: }
633:
634: /**** Prevalence limit ****************/
635:
636: double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)
637: {
638: /* Computes the prevalence limit in each live state at age x by left multiplying the unit
639: matrix by transitions matrix until convergence is reached */
640:
641: int i, ii,j,k;
642: double min, max, maxmin, maxmax,sumnew=0.;
643: double **matprod2();
644: double **out, cov[NCOVMAX], **pmij();
645: double **newm;
646: double agefin, delaymax=50 ; /* Max number of years to converge */
647:
648: for (ii=1;ii<=nlstate+ndeath;ii++)
649: for (j=1;j<=nlstate+ndeath;j++){
650: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
651: }
652:
653: cov[1]=1.;
654:
655: /* Even if hstepm = 1, at least one multiplication by the unit matrix */
656: for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
657: newm=savm;
658: /* Covariates have to be included here again */
659: cov[2]=agefin;
660:
661: for (k=1; k<=cptcovn;k++) {
662: cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
663: /*printf("ij=%d Tvar[k]=%d nbcode=%d cov=%lf\n",ij, Tvar[k],nbcode[Tvar[k]][codtab[ij][Tvar[k]]],cov[2+k]);*/
664: }
665: for (k=1; k<=cptcovage;k++)
666: cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
667: for (k=1; k<=cptcovprod;k++)
668: cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
669:
670: /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
671: /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
672:
673: out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);
674:
675: savm=oldm;
676: oldm=newm;
677: maxmax=0.;
678: for(j=1;j<=nlstate;j++){
679: min=1.;
680: max=0.;
681: for(i=1; i<=nlstate; i++) {
682: sumnew=0;
683: for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
684: prlim[i][j]= newm[i][j]/(1-sumnew);
685: max=FMAX(max,prlim[i][j]);
686: min=FMIN(min,prlim[i][j]);
687: }
688: maxmin=max-min;
689: maxmax=FMAX(maxmax,maxmin);
690: }
691: if(maxmax < ftolpl){
692: return prlim;
693: }
694: }
695: }
696:
697: /*************** transition probabilities ***************/
698:
699: double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
700: {
701: double s1, s2;
702: /*double t34;*/
703: int i,j,j1, nc, ii, jj;
704:
705: for(i=1; i<= nlstate; i++){
706: for(j=1; j<i;j++){
707: for (nc=1, s2=0.;nc <=ncovmodel; nc++){
708: /*s2 += param[i][j][nc]*cov[nc];*/
709: s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
710: /*printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2);*/
711: }
712: ps[i][j]=s2;
713: /*printf("s1=%.17e, s2=%.17e\n",s1,s2);*/
714: }
715: for(j=i+1; j<=nlstate+ndeath;j++){
716: for (nc=1, s2=0.;nc <=ncovmodel; nc++){
717: s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
718: /*printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2);*/
719: }
720: ps[i][j]=(s2);
721: }
722: }
723: /*ps[3][2]=1;*/
724:
725: for(i=1; i<= nlstate; i++){
726: s1=0;
727: for(j=1; j<i; j++)
728: s1+=exp(ps[i][j]);
729: for(j=i+1; j<=nlstate+ndeath; j++)
730: s1+=exp(ps[i][j]);
731: ps[i][i]=1./(s1+1.);
732: for(j=1; j<i; j++)
733: ps[i][j]= exp(ps[i][j])*ps[i][i];
734: for(j=i+1; j<=nlstate+ndeath; j++)
735: ps[i][j]= exp(ps[i][j])*ps[i][i];
736: /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
737: } /* end i */
738:
739: for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
740: for(jj=1; jj<= nlstate+ndeath; jj++){
741: ps[ii][jj]=0;
742: ps[ii][ii]=1;
743: }
744: }
745:
746:
747: /* for(ii=1; ii<= nlstate+ndeath; ii++){
748: for(jj=1; jj<= nlstate+ndeath; jj++){
749: printf("%lf ",ps[ii][jj]);
750: }
751: printf("\n ");
752: }
753: printf("\n ");printf("%lf ",cov[2]);*/
754: /*
755: for(i=1; i<= npar; i++) printf("%f ",x[i]);
756: goto end;*/
757: return ps;
758: }
759:
760: /**************** Product of 2 matrices ******************/
761:
762: double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)
763: {
764: /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
765: b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
766: /* in, b, out are matrice of pointers which should have been initialized
767: before: only the contents of out is modified. The function returns
768: a pointer to pointers identical to out */
769: long i, j, k;
770: for(i=nrl; i<= nrh; i++)
771: for(k=ncolol; k<=ncoloh; k++)
772: for(j=ncl,out[i][k]=0.; j<=nch; j++)
773: out[i][k] +=in[i][j]*b[j][k];
774:
775: return out;
776: }
777:
778:
779: /************* Higher Matrix Product ***************/
780:
781: double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
782: {
783: /* Computes the transition matrix starting at age 'age' over 'nhstepm*hstepm*stepm' month
784: duration (i.e. until
785: age (in years) age+nhstepm*stepm/12) by multiplying nhstepm*hstepm matrices.
786: Output is stored in matrix po[i][j][h] for h every 'hstepm' step
787: (typically every 2 years instead of every month which is too big).
788: Model is determined by parameters x and covariates have to be
789: included manually here.
790:
791: */
792:
793: int i, j, d, h, k;
794: double **out, cov[NCOVMAX];
795: double **newm;
796:
797: /* Hstepm could be zero and should return the unit matrix */
798: for (i=1;i<=nlstate+ndeath;i++)
799: for (j=1;j<=nlstate+ndeath;j++){
800: oldm[i][j]=(i==j ? 1.0 : 0.0);
801: po[i][j][0]=(i==j ? 1.0 : 0.0);
802: }
803: /* Even if hstepm = 1, at least one multiplication by the unit matrix */
804: for(h=1; h <=nhstepm; h++){
805: for(d=1; d <=hstepm; d++){
806: newm=savm;
807: /* Covariates have to be included here again */
808: cov[1]=1.;
809: cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
810: for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
811: for (k=1; k<=cptcovage;k++)
812: cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
813: for (k=1; k<=cptcovprod;k++)
814: cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
815:
816:
817: /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
818: /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
819: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,
820: pmij(pmmij,cov,ncovmodel,x,nlstate));
821: savm=oldm;
822: oldm=newm;
823: }
824: for(i=1; i<=nlstate+ndeath; i++)
825: for(j=1;j<=nlstate+ndeath;j++) {
826: po[i][j][h]=newm[i][j];
827: /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);
828: */
829: }
830: } /* end h */
831: return po;
832: }
833:
834:
835: /*************** log-likelihood *************/
836: double func( double *x)
837: {
838: int i, ii, j, k, mi, d, kk;
839: double l, ll[NLSTATEMAX], cov[NCOVMAX];
840: double **out;
841: double sw; /* Sum of weights */
842: double lli; /* Individual log likelihood */
843: long ipmx;
844: /*extern weight */
845: /* We are differentiating ll according to initial status */
846: /* for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
847: /*for(i=1;i<imx;i++)
848: printf(" %d\n",s[4][i]);
849: */
850: cov[1]=1.;
851:
852: for(k=1; k<=nlstate; k++) ll[k]=0.;
853: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
854: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
855: for(mi=1; mi<= wav[i]-1; mi++){
856: for (ii=1;ii<=nlstate+ndeath;ii++)
857: for (j=1;j<=nlstate+ndeath;j++) oldm[ii][j]=(ii==j ? 1.0 : 0.0);
858: for(d=0; d<dh[mi][i]; d++){
859: newm=savm;
860: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
861: for (kk=1; kk<=cptcovage;kk++) {
862: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
863: }
864:
865: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
866: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
867: savm=oldm;
868: oldm=newm;
869:
870:
871: } /* end mult */
872:
873: lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);
874: /* printf(" %f ",out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/
875: ipmx +=1;
876: sw += weight[i];
877: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
878: } /* end of wave */
879: } /* end of individual */
880:
881: for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
882: /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
883: l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
884: return -l;
885: }
886:
887:
888: /*********** Maximum Likelihood Estimation ***************/
889:
890: void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
891: {
892: int i,j, iter;
893: double **xi,*delti;
894: double fret;
895: xi=matrix(1,npar,1,npar);
896: for (i=1;i<=npar;i++)
897: for (j=1;j<=npar;j++)
898: xi[i][j]=(i==j ? 1.0 : 0.0);
899: printf("Powell\n");
900: powell(p,xi,npar,ftol,&iter,&fret,func);
901:
902: printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));
903: fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f ",iter,func(p));
904:
905: }
906:
907: /**** Computes Hessian and covariance matrix ***/
908: void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
909: {
910: double **a,**y,*x,pd;
911: double **hess;
912: int i, j,jk;
913: int *indx;
914:
915: double hessii(double p[], double delta, int theta, double delti[]);
916: double hessij(double p[], double delti[], int i, int j);
917: void lubksb(double **a, int npar, int *indx, double b[]) ;
918: void ludcmp(double **a, int npar, int *indx, double *d) ;
919:
920: hess=matrix(1,npar,1,npar);
921:
922: printf("\nCalculation of the hessian matrix. Wait...\n");
923: for (i=1;i<=npar;i++){
924: printf("%d",i);fflush(stdout);
925: hess[i][i]=hessii(p,ftolhess,i,delti);
926: /*printf(" %f ",p[i]);*/
927: /*printf(" %lf ",hess[i][i]);*/
928: }
929:
930: for (i=1;i<=npar;i++) {
931: for (j=1;j<=npar;j++) {
932: if (j>i) {
933: printf(".%d%d",i,j);fflush(stdout);
934: hess[i][j]=hessij(p,delti,i,j);
935: hess[j][i]=hess[i][j];
936: /*printf(" %lf ",hess[i][j]);*/
937: }
938: }
939: }
940: printf("\n");
941:
942: printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
943:
944: a=matrix(1,npar,1,npar);
945: y=matrix(1,npar,1,npar);
946: x=vector(1,npar);
947: indx=ivector(1,npar);
948: for (i=1;i<=npar;i++)
949: for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
950: ludcmp(a,npar,indx,&pd);
951:
952: for (j=1;j<=npar;j++) {
953: for (i=1;i<=npar;i++) x[i]=0;
954: x[j]=1;
955: lubksb(a,npar,indx,x);
956: for (i=1;i<=npar;i++){
957: matcov[i][j]=x[i];
958: }
959: }
960:
961: printf("\n#Hessian matrix#\n");
962: for (i=1;i<=npar;i++) {
963: for (j=1;j<=npar;j++) {
964: printf("%.3e ",hess[i][j]);
965: }
966: printf("\n");
967: }
968:
969: /* Recompute Inverse */
970: for (i=1;i<=npar;i++)
971: for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];
972: ludcmp(a,npar,indx,&pd);
973:
974: /* printf("\n#Hessian matrix recomputed#\n");
975:
976: for (j=1;j<=npar;j++) {
977: for (i=1;i<=npar;i++) x[i]=0;
978: x[j]=1;
979: lubksb(a,npar,indx,x);
980: for (i=1;i<=npar;i++){
981: y[i][j]=x[i];
982: printf("%.3e ",y[i][j]);
983: }
984: printf("\n");
985: }
986: */
987:
988: free_matrix(a,1,npar,1,npar);
989: free_matrix(y,1,npar,1,npar);
990: free_vector(x,1,npar);
991: free_ivector(indx,1,npar);
992: free_matrix(hess,1,npar,1,npar);
993:
994:
995: }
996:
997: /*************** hessian matrix ****************/
998: double hessii( double x[], double delta, int theta, double delti[])
999: {
1000: int i;
1001: int l=1, lmax=20;
1002: double k1,k2;
1003: double p2[NPARMAX+1];
1004: double res;
1005: double delt, delts, nkhi=10.,nkhif=1., khi=1.e-4;
1006: double fx;
1007: int k=0,kmax=10;
1008: double l1;
1009:
1010: fx=func(x);
1011: for (i=1;i<=npar;i++) p2[i]=x[i];
1012: for(l=0 ; l <=lmax; l++){
1013: l1=pow(10,l);
1014: delts=delt;
1015: for(k=1 ; k <kmax; k=k+1){
1016: delt = delta*(l1*k);
1017: p2[theta]=x[theta] +delt;
1018: k1=func(p2)-fx;
1019: p2[theta]=x[theta]-delt;
1020: k2=func(p2)-fx;
1021: /*res= (k1-2.0*fx+k2)/delt/delt; */
1022: res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */
1023:
1024: #ifdef DEBUG
1025: printf("%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx);
1026: #endif
1027: /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
1028: if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
1029: k=kmax;
1030: }
1031: else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
1032: k=kmax; l=lmax*10.;
1033: }
1034: else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){
1035: delts=delt;
1036: }
1037: }
1038: }
1039: delti[theta]=delts;
1040: return res;
1041:
1042: }
1043:
1044: double hessij( double x[], double delti[], int thetai,int thetaj)
1045: {
1046: int i;
1047: int l=1, l1, lmax=20;
1048: double k1,k2,k3,k4,res,fx;
1049: double p2[NPARMAX+1];
1050: int k;
1051:
1052: fx=func(x);
1053: for (k=1; k<=2; k++) {
1054: for (i=1;i<=npar;i++) p2[i]=x[i];
1055: p2[thetai]=x[thetai]+delti[thetai]/k;
1056: p2[thetaj]=x[thetaj]+delti[thetaj]/k;
1057: k1=func(p2)-fx;
1058:
1059: p2[thetai]=x[thetai]+delti[thetai]/k;
1060: p2[thetaj]=x[thetaj]-delti[thetaj]/k;
1061: k2=func(p2)-fx;
1062:
1063: p2[thetai]=x[thetai]-delti[thetai]/k;
1064: p2[thetaj]=x[thetaj]+delti[thetaj]/k;
1065: k3=func(p2)-fx;
1066:
1067: p2[thetai]=x[thetai]-delti[thetai]/k;
1068: p2[thetaj]=x[thetaj]-delti[thetaj]/k;
1069: k4=func(p2)-fx;
1070: res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */
1071: #ifdef DEBUG
1072: printf("%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);
1073: #endif
1074: }
1075: return res;
1076: }
1077:
1078: /************** Inverse of matrix **************/
1079: void ludcmp(double **a, int n, int *indx, double *d)
1080: {
1081: int i,imax,j,k;
1082: double big,dum,sum,temp;
1083: double *vv;
1084:
1085: vv=vector(1,n);
1086: *d=1.0;
1087: for (i=1;i<=n;i++) {
1088: big=0.0;
1089: for (j=1;j<=n;j++)
1090: if ((temp=fabs(a[i][j])) > big) big=temp;
1091: if (big == 0.0) nrerror("Singular matrix in routine ludcmp");
1092: vv[i]=1.0/big;
1093: }
1094: for (j=1;j<=n;j++) {
1095: for (i=1;i<j;i++) {
1096: sum=a[i][j];
1097: for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];
1098: a[i][j]=sum;
1099: }
1100: big=0.0;
1101: for (i=j;i<=n;i++) {
1102: sum=a[i][j];
1103: for (k=1;k<j;k++)
1104: sum -= a[i][k]*a[k][j];
1105: a[i][j]=sum;
1106: if ( (dum=vv[i]*fabs(sum)) >= big) {
1107: big=dum;
1108: imax=i;
1109: }
1110: }
1111: if (j != imax) {
1112: for (k=1;k<=n;k++) {
1113: dum=a[imax][k];
1114: a[imax][k]=a[j][k];
1115: a[j][k]=dum;
1116: }
1117: *d = -(*d);
1118: vv[imax]=vv[j];
1119: }
1120: indx[j]=imax;
1121: if (a[j][j] == 0.0) a[j][j]=TINY;
1122: if (j != n) {
1123: dum=1.0/(a[j][j]);
1124: for (i=j+1;i<=n;i++) a[i][j] *= dum;
1125: }
1126: }
1127: free_vector(vv,1,n); /* Doesn't work */
1128: ;
1129: }
1130:
1131: void lubksb(double **a, int n, int *indx, double b[])
1132: {
1133: int i,ii=0,ip,j;
1134: double sum;
1135:
1136: for (i=1;i<=n;i++) {
1137: ip=indx[i];
1138: sum=b[ip];
1139: b[ip]=b[i];
1140: if (ii)
1141: for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];
1142: else if (sum) ii=i;
1143: b[i]=sum;
1144: }
1145: for (i=n;i>=1;i--) {
1146: sum=b[i];
1147: for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];
1148: b[i]=sum/a[i][i];
1149: }
1150: }
1151:
1152: /************ Frequencies ********************/
1153: void freqsummary(char fileres[], int agemin, int agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax, int fprev1,int lprev1)
1154: { /* Some frequencies */
1155:
1156: int i, m, jk, k1, i1, j1, bool, z1,z2,j;
1157: double ***freq; /* Frequencies */
1158: double *pp;
1159: double pos;
1160: FILE *ficresp;
1161: char fileresp[FILENAMELENGTH];
1162:
1163: pp=vector(1,nlstate);
1164: probs= ma3x(1,130 ,1,8, 1,8);
1165: strcpy(fileresp,"p");
1166: strcat(fileresp,fileres);
1167: if((ficresp=fopen(fileresp,"w"))==NULL) {
1168: printf("Problem with prevalence resultfile: %s\n", fileresp);
1169: exit(0);
1170: }
1171: freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);
1172: j1=0;
1173:
1174: j=cptcoveff;
1175: if (cptcovn<1) {j=1;ncodemax[1]=1;}
1176:
1177: for(k1=1; k1<=j;k1++){
1178: for(i1=1; i1<=ncodemax[k1];i1++){
1179: j1++;
1180: /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
1181: scanf("%d", i);*/
1182: for (i=-1; i<=nlstate+ndeath; i++)
1183: for (jk=-1; jk<=nlstate+ndeath; jk++)
1184: for(m=agemin; m <= agemax+3; m++)
1185: freq[i][jk][m]=0;
1186:
1187: for (i=1; i<=imx; i++) {
1188: bool=1;
1189: if (cptcovn>0) {
1190: for (z1=1; z1<=cptcoveff; z1++)
1191: if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])
1192: bool=0;
1193: }
1194: if (bool==1) {
1195: for(m=fprev1; m<=lprev1; m++){
1196: if(agev[m][i]==0) agev[m][i]=agemax+1;
1197: if(agev[m][i]==1) agev[m][i]=agemax+2;
1198: freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
1199: freq[s[m][i]][s[m+1][i]][(int) agemax+3] += weight[i];
1200: }
1201: }
1202: }
1203: if (cptcovn>0) {
1204: fprintf(ficresp, "\n#********** Variable ");
1205: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
1206: fprintf(ficresp, "**********\n#");
1207: }
1208: for(i=1; i<=nlstate;i++)
1209: fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
1210: fprintf(ficresp, "\n");
1211:
1212: for(i=(int)agemin; i <= (int)agemax+3; i++){
1213: if(i==(int)agemax+3)
1214: printf("Total");
1215: else
1216: printf("Age %d", i);
1217: for(jk=1; jk <=nlstate ; jk++){
1218: for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
1219: pp[jk] += freq[jk][m][i];
1220: }
1221: for(jk=1; jk <=nlstate ; jk++){
1222: for(m=-1, pos=0; m <=0 ; m++)
1223: pos += freq[jk][m][i];
1224: if(pp[jk]>=1.e-10)
1225: printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
1226: else
1227: printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
1228: }
1229:
1230: for(jk=1; jk <=nlstate ; jk++){
1231: for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
1232: pp[jk] += freq[jk][m][i];
1233: }
1234:
1235: for(jk=1,pos=0; jk <=nlstate ; jk++)
1236: pos += pp[jk];
1237: for(jk=1; jk <=nlstate ; jk++){
1238: if(pos>=1.e-5)
1239: printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
1240: else
1241: printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
1242: if( i <= (int) agemax){
1243: if(pos>=1.e-5){
1244: fprintf(ficresp," %d %.5f %.0f %.0f",i,pp[jk]/pos, pp[jk],pos);
1245: probs[i][jk][j1]= pp[jk]/pos;
1246: /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/
1247: }
1248: else
1249: fprintf(ficresp," %d NaNq %.0f %.0f",i,pp[jk],pos);
1250: }
1251: }
1252: for(jk=-1; jk <=nlstate+ndeath; jk++)
1253: for(m=-1; m <=nlstate+ndeath; m++)
1254: if(freq[jk][m][i] !=0 ) printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
1255: if(i <= (int) agemax)
1256: fprintf(ficresp,"\n");
1257: printf("\n");
1258: }
1259: }
1260: }
1261:
1262: fclose(ficresp);
1263: free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);
1264: free_vector(pp,1,nlstate);
1265:
1266: } /* End of Freq */
1267:
1268: /************ Prevalence ********************/
1269: void prevalence(int agemin, int agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax, int fprev1,int lprev1)
1270: { /* Some frequencies */
1271:
1272: int i, m, jk, k1, i1, j1, bool, z1,z2,j;
1273: double ***freq; /* Frequencies */
1274: double *pp;
1275: double pos;
1276:
1277: pp=vector(1,nlstate);
1278: probs= ma3x(1,130 ,1,8, 1,8);
1279:
1280: freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);
1281: j1=0;
1282:
1283: j=cptcoveff;
1284: if (cptcovn<1) {j=1;ncodemax[1]=1;}
1285:
1286: for(k1=1; k1<=j;k1++){
1287: for(i1=1; i1<=ncodemax[k1];i1++){
1288: j1++;
1289:
1290: for (i=-1; i<=nlstate+ndeath; i++)
1291: for (jk=-1; jk<=nlstate+ndeath; jk++)
1292: for(m=agemin; m <= agemax+3; m++)
1293: freq[i][jk][m]=0;
1294:
1295: for (i=1; i<=imx; i++) {
1296: bool=1;
1297: if (cptcovn>0) {
1298: for (z1=1; z1<=cptcoveff; z1++)
1299: if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])
1300: bool=0;
1301: }
1302: if (bool==1) {
1303: for(m=fprev1; m<=lprev1; m++){
1304: if(agev[m][i]==0) agev[m][i]=agemax+1;
1305: if(agev[m][i]==1) agev[m][i]=agemax+2;
1306: freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
1307: freq[s[m][i]][s[m+1][i]][(int) agemax+3] += weight[i];
1308: }
1309: }
1310: }
1311: for(i=(int)agemin; i <= (int)agemax+3; i++){
1312: for(jk=1; jk <=nlstate ; jk++){
1313: for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
1314: pp[jk] += freq[jk][m][i];
1315: }
1316: for(jk=1; jk <=nlstate ; jk++){
1317: for(m=-1, pos=0; m <=0 ; m++)
1318: pos += freq[jk][m][i];
1319: }
1320:
1321: for(jk=1; jk <=nlstate ; jk++){
1322: for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
1323: pp[jk] += freq[jk][m][i];
1324: }
1325:
1326: for(jk=1,pos=0; jk <=nlstate ; jk++) pos += pp[jk];
1327:
1328: for(jk=1; jk <=nlstate ; jk++){
1329: if( i <= (int) agemax){
1330: if(pos>=1.e-5){
1331: probs[i][jk][j1]= pp[jk]/pos;
1332: }
1333: }
1334: }
1335:
1336: }
1337: }
1338: }
1339:
1340:
1341: free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);
1342: free_vector(pp,1,nlstate);
1343:
1344: } /* End of Freq */
1345: /************* Waves Concatenation ***************/
1346:
1347: void concatwav(int wav[], int **dh, int **mw, int **s, double *agedc, double **agev, int firstpass, int lastpass, int imx, int nlstate, int stepm)
1348: {
1349: /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
1350: Death is a valid wave (if date is known).
1351: mw[mi][i] is the mi (mi=1 to wav[i]) effective wave of individual i
1352: dh[m][i] of dh[mw[mi][i][i] is the delay between two effective waves m=mw[mi][i]
1353: and mw[mi+1][i]. dh depends on stepm.
1354: */
1355:
1356: int i, mi, m;
1357: /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
1358: double sum=0., jmean=0.;*/
1359:
1360: int j, k=0,jk, ju, jl;
1361: double sum=0.;
1362: jmin=1e+5;
1363: jmax=-1;
1364: jmean=0.;
1365: for(i=1; i<=imx; i++){
1366: mi=0;
1367: m=firstpass;
1368: while(s[m][i] <= nlstate){
1369: if(s[m][i]>=1)
1370: mw[++mi][i]=m;
1371: if(m >=lastpass)
1372: break;
1373: else
1374: m++;
1375: }/* end while */
1376: if (s[m][i] > nlstate){
1377: mi++; /* Death is another wave */
1378: /* if(mi==0) never been interviewed correctly before death */
1379: /* Only death is a correct wave */
1380: mw[mi][i]=m;
1381: }
1382:
1383: wav[i]=mi;
1384: if(mi==0)
1385: printf("Warning, no any valid information for:%d line=%d\n",num[i],i);
1386: }
1387:
1388: for(i=1; i<=imx; i++){
1389: for(mi=1; mi<wav[i];mi++){
1390: if (stepm <=0)
1391: dh[mi][i]=1;
1392: else{
1393: if (s[mw[mi+1][i]][i] > nlstate) {
1394: if (agedc[i] < 2*AGESUP) {
1395: j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);
1396: if(j==0) j=1; /* Survives at least one month after exam */
1397: k=k+1;
1398: if (j >= jmax) jmax=j;
1399: if (j <= jmin) jmin=j;
1400: sum=sum+j;
1401: /* if (j<10) printf("j=%d num=%d ",j,i); */
1402: }
1403: }
1404: else{
1405: j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
1406: k=k+1;
1407: if (j >= jmax) jmax=j;
1408: else if (j <= jmin)jmin=j;
1409: /* if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
1410: sum=sum+j;
1411: }
1412: jk= j/stepm;
1413: jl= j -jk*stepm;
1414: ju= j -(jk+1)*stepm;
1415: if(jl <= -ju)
1416: dh[mi][i]=jk;
1417: else
1418: dh[mi][i]=jk+1;
1419: if(dh[mi][i]==0)
1420: dh[mi][i]=1; /* At least one step */
1421: }
1422: }
1423: }
1424: jmean=sum/k;
1425: printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);
1426: }
1427: /*********** Tricode ****************************/
1428: void tricode(int *Tvar, int **nbcode, int imx)
1429: {
1430: int Ndum[20],ij=1, k, j, i;
1431: int cptcode=0;
1432: cptcoveff=0;
1433:
1434: for (k=0; k<19; k++) Ndum[k]=0;
1435: for (k=1; k<=7; k++) ncodemax[k]=0;
1436:
1437: for (j=1; j<=(cptcovn+2*cptcovprod); j++) {
1438: for (i=1; i<=imx; i++) {
1439: ij=(int)(covar[Tvar[j]][i]);
1440: Ndum[ij]++;
1441: /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
1442: if (ij > cptcode) cptcode=ij;
1443: }
1444:
1445: for (i=0; i<=cptcode; i++) {
1446: if(Ndum[i]!=0) ncodemax[j]++;
1447: }
1448: ij=1;
1449:
1450:
1451: for (i=1; i<=ncodemax[j]; i++) {
1452: for (k=0; k<=19; k++) {
1453: if (Ndum[k] != 0) {
1454: nbcode[Tvar[j]][ij]=k;
1455: ij++;
1456: }
1457: if (ij > ncodemax[j]) break;
1458: }
1459: }
1460: }
1461:
1462: for (k=0; k<19; k++) Ndum[k]=0;
1463:
1464: for (i=1; i<=ncovmodel-2; i++) {
1465: ij=Tvar[i];
1466: Ndum[ij]++;
1467: }
1468:
1469: ij=1;
1470: for (i=1; i<=10; i++) {
1471: if((Ndum[i]!=0) && (i<=ncov)){
1472: Tvaraff[ij]=i;
1473: ij++;
1474: }
1475: }
1476:
1477: cptcoveff=ij-1;
1478: }
1479:
1480: /*********** Health Expectancies ****************/
1481:
1482: void evsij(char fileres[], double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int ij)
1483: {
1484: /* Health expectancies */
1485: int i, j, nhstepm, hstepm, h;
1486: double age, agelim,hf;
1487: double ***p3mat;
1488:
1489: fprintf(ficreseij,"# Health expectancies\n");
1490: fprintf(ficreseij,"# Age");
1491: for(i=1; i<=nlstate;i++)
1492: for(j=1; j<=nlstate;j++)
1493: fprintf(ficreseij," %1d-%1d",i,j);
1494: fprintf(ficreseij,"\n");
1495:
1496: hstepm=1*YEARM; /* Every j years of age (in month) */
1497: hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */
1498:
1499: agelim=AGESUP;
1500: for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
1501: /* nhstepm age range expressed in number of stepm */
1502: nhstepm=(int) rint((agelim-age)*YEARM/stepm);
1503: /* Typically if 20 years = 20*12/6=40 stepm */
1504: if (stepm >= YEARM) hstepm=1;
1505: nhstepm = nhstepm/hstepm;/* Expressed in hstepm, typically 40/4=10 */
1506: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
1507: /* Computed by stepm unit matrices, product of hstepm matrices, stored
1508: in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
1509: hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);
1510:
1511:
1512: for(i=1; i<=nlstate;i++)
1513: for(j=1; j<=nlstate;j++)
1514: for (h=0, eij[i][j][(int)age]=0; h<=nhstepm; h++){
1515: eij[i][j][(int)age] +=p3mat[i][j][h];
1516: }
1517:
1518: hf=1;
1519: if (stepm >= YEARM) hf=stepm/YEARM;
1520: fprintf(ficreseij,"%.0f",age );
1521: for(i=1; i<=nlstate;i++)
1522: for(j=1; j<=nlstate;j++){
1523: fprintf(ficreseij," %.4f", hf*eij[i][j][(int)age]);
1524: }
1525: fprintf(ficreseij,"\n");
1526: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
1527: }
1528: }
1529:
1530: /************ Variance ******************/
1531: 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)
1532: {
1533: /* Variance of health expectancies */
1534: /* double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
1535: double **newm;
1536: double **dnewm,**doldm;
1537: int i, j, nhstepm, hstepm, h;
1538: int k, cptcode;
1539: double *xp;
1540: double **gp, **gm;
1541: double ***gradg, ***trgradg;
1542: double ***p3mat;
1543: double age,agelim;
1544: int theta;
1545:
1546: fprintf(ficresvij,"# Covariances of life expectancies\n");
1547: fprintf(ficresvij,"# Age");
1548: for(i=1; i<=nlstate;i++)
1549: for(j=1; j<=nlstate;j++)
1550: fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);
1551: fprintf(ficresvij,"\n");
1552:
1553: xp=vector(1,npar);
1554: dnewm=matrix(1,nlstate,1,npar);
1555: doldm=matrix(1,nlstate,1,nlstate);
1556:
1557: hstepm=1*YEARM; /* Every year of age */
1558: hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */
1559: agelim = AGESUP;
1560: for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
1561: nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
1562: if (stepm >= YEARM) hstepm=1;
1563: nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
1564: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
1565: gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
1566: gp=matrix(0,nhstepm,1,nlstate);
1567: gm=matrix(0,nhstepm,1,nlstate);
1568:
1569: for(theta=1; theta <=npar; theta++){
1570: for(i=1; i<=npar; i++){ /* Computes gradient */
1571: xp[i] = x[i] + (i==theta ?delti[theta]:0);
1572: }
1573: hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
1574: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
1575:
1576: if (popbased==1) {
1577: for(i=1; i<=nlstate;i++)
1578: prlim[i][i]=probs[(int)age][i][ij];
1579: }
1580:
1581: for(j=1; j<= nlstate; j++){
1582: for(h=0; h<=nhstepm; h++){
1583: for(i=1, gp[h][j]=0.;i<=nlstate;i++)
1584: gp[h][j] += prlim[i][i]*p3mat[i][j][h];
1585: }
1586: }
1587:
1588: for(i=1; i<=npar; i++) /* Computes gradient */
1589: xp[i] = x[i] - (i==theta ?delti[theta]:0);
1590: hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
1591: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
1592:
1593: if (popbased==1) {
1594: for(i=1; i<=nlstate;i++)
1595: prlim[i][i]=probs[(int)age][i][ij];
1596: }
1597:
1598: for(j=1; j<= nlstate; j++){
1599: for(h=0; h<=nhstepm; h++){
1600: for(i=1, gm[h][j]=0.;i<=nlstate;i++)
1601: gm[h][j] += prlim[i][i]*p3mat[i][j][h];
1602: }
1603: }
1604:
1605: for(j=1; j<= nlstate; j++)
1606: for(h=0; h<=nhstepm; h++){
1607: gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
1608: }
1609: } /* End theta */
1610:
1611: trgradg =ma3x(0,nhstepm,1,nlstate,1,npar);
1612:
1613: for(h=0; h<=nhstepm; h++)
1614: for(j=1; j<=nlstate;j++)
1615: for(theta=1; theta <=npar; theta++)
1616: trgradg[h][j][theta]=gradg[h][theta][j];
1617:
1618: for(i=1;i<=nlstate;i++)
1619: for(j=1;j<=nlstate;j++)
1620: vareij[i][j][(int)age] =0.;
1621: for(h=0;h<=nhstepm;h++){
1622: for(k=0;k<=nhstepm;k++){
1623: matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
1624: matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
1625: for(i=1;i<=nlstate;i++)
1626: for(j=1;j<=nlstate;j++)
1627: vareij[i][j][(int)age] += doldm[i][j];
1628: }
1629: }
1630: h=1;
1631: if (stepm >= YEARM) h=stepm/YEARM;
1632: fprintf(ficresvij,"%.0f ",age );
1633: for(i=1; i<=nlstate;i++)
1634: for(j=1; j<=nlstate;j++){
1635: fprintf(ficresvij," %.4f", h*vareij[i][j][(int)age]);
1636: }
1637: fprintf(ficresvij,"\n");
1638: free_matrix(gp,0,nhstepm,1,nlstate);
1639: free_matrix(gm,0,nhstepm,1,nlstate);
1640: free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
1641: free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
1642: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
1643: } /* End age */
1644:
1645: free_vector(xp,1,npar);
1646: free_matrix(doldm,1,nlstate,1,npar);
1647: free_matrix(dnewm,1,nlstate,1,nlstate);
1648:
1649: }
1650:
1651: /************ Variance of prevlim ******************/
1652: 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)
1653: {
1654: /* Variance of prevalence limit */
1655: /* double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
1656: double **newm;
1657: double **dnewm,**doldm;
1658: int i, j, nhstepm, hstepm;
1659: int k, cptcode;
1660: double *xp;
1661: double *gp, *gm;
1662: double **gradg, **trgradg;
1663: double age,agelim;
1664: int theta;
1665:
1666: fprintf(ficresvpl,"# Standard deviation of prevalences limit\n");
1667: fprintf(ficresvpl,"# Age");
1668: for(i=1; i<=nlstate;i++)
1669: fprintf(ficresvpl," %1d-%1d",i,i);
1670: fprintf(ficresvpl,"\n");
1671:
1672: xp=vector(1,npar);
1673: dnewm=matrix(1,nlstate,1,npar);
1674: doldm=matrix(1,nlstate,1,nlstate);
1675:
1676: hstepm=1*YEARM; /* Every year of age */
1677: hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */
1678: agelim = AGESUP;
1679: for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
1680: nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
1681: if (stepm >= YEARM) hstepm=1;
1682: nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
1683: gradg=matrix(1,npar,1,nlstate);
1684: gp=vector(1,nlstate);
1685: gm=vector(1,nlstate);
1686:
1687: for(theta=1; theta <=npar; theta++){
1688: for(i=1; i<=npar; i++){ /* Computes gradient */
1689: xp[i] = x[i] + (i==theta ?delti[theta]:0);
1690: }
1691: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
1692: for(i=1;i<=nlstate;i++)
1693: gp[i] = prlim[i][i];
1694:
1695: for(i=1; i<=npar; i++) /* Computes gradient */
1696: xp[i] = x[i] - (i==theta ?delti[theta]:0);
1697: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
1698: for(i=1;i<=nlstate;i++)
1699: gm[i] = prlim[i][i];
1700:
1701: for(i=1;i<=nlstate;i++)
1702: gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
1703: } /* End theta */
1704:
1705: trgradg =matrix(1,nlstate,1,npar);
1706:
1707: for(j=1; j<=nlstate;j++)
1708: for(theta=1; theta <=npar; theta++)
1709: trgradg[j][theta]=gradg[theta][j];
1710:
1711: for(i=1;i<=nlstate;i++)
1712: varpl[i][(int)age] =0.;
1713: matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
1714: matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
1715: for(i=1;i<=nlstate;i++)
1716: varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
1717:
1718: fprintf(ficresvpl,"%.0f ",age );
1719: for(i=1; i<=nlstate;i++)
1720: fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
1721: fprintf(ficresvpl,"\n");
1722: free_vector(gp,1,nlstate);
1723: free_vector(gm,1,nlstate);
1724: free_matrix(gradg,1,npar,1,nlstate);
1725: free_matrix(trgradg,1,nlstate,1,npar);
1726: } /* End age */
1727:
1728: free_vector(xp,1,npar);
1729: free_matrix(doldm,1,nlstate,1,npar);
1730: free_matrix(dnewm,1,nlstate,1,nlstate);
1731:
1732: }
1733:
1734: /************ Variance of one-step probabilities ******************/
1735: void varprob(char fileres[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij)
1736: {
1737: int i, j;
1738: int k=0, cptcode;
1739: double **dnewm,**doldm;
1740: double *xp;
1741: double *gp, *gm;
1742: double **gradg, **trgradg;
1743: double age,agelim, cov[NCOVMAX];
1744: int theta;
1745: char fileresprob[FILENAMELENGTH];
1746:
1747: strcpy(fileresprob,"prob");
1748: strcat(fileresprob,fileres);
1749: if((ficresprob=fopen(fileresprob,"w"))==NULL) {
1750: printf("Problem with resultfile: %s\n", fileresprob);
1751: }
1752: printf("Computing variance of one-step probabilities: result on file '%s' \n",fileresprob);
1753:
1754:
1755: xp=vector(1,npar);
1756: dnewm=matrix(1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
1757: doldm=matrix(1,(nlstate+ndeath)*(nlstate+ndeath),1,(nlstate+ndeath)*(nlstate+ndeath));
1758:
1759: cov[1]=1;
1760: for (age=bage; age<=fage; age ++){
1761: cov[2]=age;
1762: gradg=matrix(1,npar,1,9);
1763: trgradg=matrix(1,9,1,npar);
1764: gp=vector(1,(nlstate+ndeath)*(nlstate+ndeath));
1765: gm=vector(1,(nlstate+ndeath)*(nlstate+ndeath));
1766:
1767: for(theta=1; theta <=npar; theta++){
1768: for(i=1; i<=npar; i++)
1769: xp[i] = x[i] + (i==theta ?delti[theta]:0);
1770:
1771: pmij(pmmij,cov,ncovmodel,xp,nlstate);
1772:
1773: k=0;
1774: for(i=1; i<= (nlstate+ndeath); i++){
1775: for(j=1; j<=(nlstate+ndeath);j++){
1776: k=k+1;
1777: gp[k]=pmmij[i][j];
1778: }
1779: }
1780:
1781: for(i=1; i<=npar; i++)
1782: xp[i] = x[i] - (i==theta ?delti[theta]:0);
1783:
1784:
1785: pmij(pmmij,cov,ncovmodel,xp,nlstate);
1786: k=0;
1787: for(i=1; i<=(nlstate+ndeath); i++){
1788: for(j=1; j<=(nlstate+ndeath);j++){
1789: k=k+1;
1790: gm[k]=pmmij[i][j];
1791: }
1792: }
1793:
1794: for(i=1; i<= (nlstate+ndeath)*(nlstate+ndeath); i++)
1795: gradg[theta][i]=(gp[i]-gm[i])/2./delti[theta];
1796: }
1797:
1798: for(j=1; j<=(nlstate+ndeath)*(nlstate+ndeath);j++)
1799: for(theta=1; theta <=npar; theta++)
1800: trgradg[j][theta]=gradg[theta][j];
1801:
1802: matprod2(dnewm,trgradg,1,9,1,npar,1,npar,matcov);
1803: matprod2(doldm,dnewm,1,9,1,npar,1,9,gradg);
1804:
1805: pmij(pmmij,cov,ncovmodel,x,nlstate);
1806:
1807: k=0;
1808: for(i=1; i<=(nlstate+ndeath); i++){
1809: for(j=1; j<=(nlstate+ndeath);j++){
1810: k=k+1;
1811: gm[k]=pmmij[i][j];
1812: }
1813: }
1814:
1815: /*printf("\n%d ",(int)age);
1816: for (i=1; i<=(nlstate+ndeath)*(nlstate+ndeath-1);i++){
1817:
1818:
1819: printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
1820: }*/
1821:
1822: fprintf(ficresprob,"\n%d ",(int)age);
1823:
1824: for (i=1; i<=(nlstate+ndeath)*(nlstate+ndeath-1);i++){
1825: if (i== 2) fprintf(ficresprob,"%.3e %.3e ",gm[i],doldm[i][i]);
1826: if (i== 4) fprintf(ficresprob,"%.3e %.3e ",gm[i],doldm[i][i]);
1827: }
1828:
1829: free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
1830: free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
1831: free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
1832: free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
1833: }
1834: free_vector(xp,1,npar);
1835: fclose(ficresprob);
1836: exit(0);
1837: }
1838:
1839: /***********************************************/
1840: /**************** Main Program *****************/
1841: /***********************************************/
1842:
1843: /*int main(int argc, char *argv[])*/
1844: int main()
1845: {
1846:
1847: int i,j, k, n=MAXN,iter,m,size,cptcode, cptcod;
1848: double agedeb, agefin,hf;
1849: double agemin=1.e20, agemax=-1.e20;
1850:
1851: double fret;
1852: double **xi,tmp,delta;
1853:
1854: double dum; /* Dummy variable */
1855: double ***p3mat;
1856: int *indx;
1857: char line[MAXLINE], linepar[MAXLINE];
1858: char title[MAXLINE];
1859: char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH], filerespl[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH];
1860: char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], fileresf[FILENAMELENGTH];
1861: char filerest[FILENAMELENGTH];
1862: char fileregp[FILENAMELENGTH];
1863: char path[80],pathc[80],pathcd[80],pathtot[80],model[20];
1864: int firstobs=1, lastobs=10;
1865: int sdeb, sfin; /* Status at beginning and end */
1866: int c, h , cpt,l;
1867: int ju,jl, mi;
1868: int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;
1869: int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,**adl,*tab;
1870: int mobilav=0, fprev, lprev ,fprevfore=1, lprevfore=1,nforecast;
1871: int hstepm, nhstepm;
1872:
1873: double bage, fage, age, agelim, agebase;
1874: double ftolpl=FTOL;
1875: double **prlim;
1876: double *severity;
1877: double ***param; /* Matrix of parameters */
1878: double *p;
1879: double **matcov; /* Matrix of covariance */
1880: double ***delti3; /* Scale */
1881: double *delti; /* Scale */
1882: double ***eij, ***vareij;
1883: double **varpl; /* Variances of prevalence limits by age */
1884: double *epj, vepp;
1885: double kk1;
1886:
1887: char version[80]="Imach version 64b, May 2001, INED-EUROREVES ";
1888: char *alph[]={"a","a","b","c","d","e"}, str[4];
1889:
1890:
1891: char z[1]="c", occ;
1892: #include <sys/time.h>
1893: #include <time.h>
1894: char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];
1895: /* long total_usecs;
1896: struct timeval start_time, end_time;
1897:
1898: gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */
1899:
1900:
1901: printf("\nIMACH, Version 0.64b");
1902: printf("\nEnter the parameter file name: ");
1903:
1904: #ifdef windows
1905: scanf("%s",pathtot);
1906: getcwd(pathcd, size);
1907: /*cygwin_split_path(pathtot,path,optionfile);
1908: printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/
1909: /* cutv(path,optionfile,pathtot,'\\');*/
1910:
1911: split(pathtot, path,optionfile);
1912: chdir(path);
1913: replace(pathc,path);
1914: #endif
1915: #ifdef unix
1916: scanf("%s",optionfile);
1917: #endif
1918:
1919: /*-------- arguments in the command line --------*/
1920:
1921: strcpy(fileres,"r");
1922: strcat(fileres, optionfile);
1923:
1924: /*---------arguments file --------*/
1925:
1926: if((ficpar=fopen(optionfile,"r"))==NULL) {
1927: printf("Problem with optionfile %s\n",optionfile);
1928: goto end;
1929: }
1930:
1931: strcpy(filereso,"o");
1932: strcat(filereso,fileres);
1933: if((ficparo=fopen(filereso,"w"))==NULL) {
1934: printf("Problem with Output resultfile: %s\n", filereso);goto end;
1935: }
1936:
1937: /* Reads comments: lines beginning with '#' */
1938: while((c=getc(ficpar))=='#' && c!= EOF){
1939: ungetc(c,ficpar);
1940: fgets(line, MAXLINE, ficpar);
1941: puts(line);
1942: fputs(line,ficparo);
1943: }
1944: ungetc(c,ficpar);
1945:
1946: 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);
1947: 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);
1948: 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);
1949: while((c=getc(ficpar))=='#' && c!= EOF){
1950: ungetc(c,ficpar);
1951: fgets(line, MAXLINE, ficpar);
1952: puts(line);
1953: fputs(line,ficparo);
1954: }
1955: ungetc(c,ficpar);
1956:
1957: fscanf(ficpar,"fprevalence=%d lprevalence=%d pop_based=%d\n",&fprev,&lprev,&popbased);
1958: while((c=getc(ficpar))=='#' && c!= EOF){
1959: ungetc(c,ficpar);
1960: fgets(line, MAXLINE, ficpar);
1961: puts(line);
1962: fputs(line,ficparo);
1963: }
1964: ungetc(c,ficpar);
1965:
1966: fscanf(ficpar,"fprevalence=%d lprevalence=%d nforecast=%d mob_average=%d\n",&fprevfore,&lprevfore,&nforecast,&mobilav);
1967:
1968: covar=matrix(0,NCOVMAX,1,n);
1969: cptcovn=0;
1970: if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;
1971:
1972: ncovmodel=2+cptcovn;
1973: nvar=ncovmodel-1; /* Suppressing age as a basic covariate */
1974:
1975: /* Read guess parameters */
1976: /* Reads comments: lines beginning with '#' */
1977: while((c=getc(ficpar))=='#' && c!= EOF){
1978: ungetc(c,ficpar);
1979: fgets(line, MAXLINE, ficpar);
1980: puts(line);
1981: fputs(line,ficparo);
1982: }
1983: ungetc(c,ficpar);
1984:
1985: param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
1986: for(i=1; i <=nlstate; i++)
1987: for(j=1; j <=nlstate+ndeath-1; j++){
1988: fscanf(ficpar,"%1d%1d",&i1,&j1);
1989: fprintf(ficparo,"%1d%1d",i1,j1);
1990: printf("%1d%1d",i,j);
1991: for(k=1; k<=ncovmodel;k++){
1992: fscanf(ficpar," %lf",¶m[i][j][k]);
1993: printf(" %lf",param[i][j][k]);
1994: fprintf(ficparo," %lf",param[i][j][k]);
1995: }
1996: fscanf(ficpar,"\n");
1997: printf("\n");
1998: fprintf(ficparo,"\n");
1999: }
2000:
2001: npar= (nlstate+ndeath-1)*nlstate*ncovmodel;
2002:
2003: p=param[1][1];
2004:
2005: /* Reads comments: lines beginning with '#' */
2006: while((c=getc(ficpar))=='#' && c!= EOF){
2007: ungetc(c,ficpar);
2008: fgets(line, MAXLINE, ficpar);
2009: puts(line);
2010: fputs(line,ficparo);
2011: }
2012: ungetc(c,ficpar);
2013:
2014: delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
2015: delti=vector(1,npar); /* Scale of each paramater (output from hesscov) */
2016: for(i=1; i <=nlstate; i++){
2017: for(j=1; j <=nlstate+ndeath-1; j++){
2018: fscanf(ficpar,"%1d%1d",&i1,&j1);
2019: printf("%1d%1d",i,j);
2020: fprintf(ficparo,"%1d%1d",i1,j1);
2021: for(k=1; k<=ncovmodel;k++){
2022: fscanf(ficpar,"%le",&delti3[i][j][k]);
2023: printf(" %le",delti3[i][j][k]);
2024: fprintf(ficparo," %le",delti3[i][j][k]);
2025: }
2026: fscanf(ficpar,"\n");
2027: printf("\n");
2028: fprintf(ficparo,"\n");
2029: }
2030: }
2031: delti=delti3[1][1];
2032:
2033: /* Reads comments: lines beginning with '#' */
2034: while((c=getc(ficpar))=='#' && c!= EOF){
2035: ungetc(c,ficpar);
2036: fgets(line, MAXLINE, ficpar);
2037: puts(line);
2038: fputs(line,ficparo);
2039: }
2040: ungetc(c,ficpar);
2041:
2042: matcov=matrix(1,npar,1,npar);
2043: for(i=1; i <=npar; i++){
2044: fscanf(ficpar,"%s",&str);
2045: printf("%s",str);
2046: fprintf(ficparo,"%s",str);
2047: for(j=1; j <=i; j++){
2048: fscanf(ficpar," %le",&matcov[i][j]);
2049: printf(" %.5le",matcov[i][j]);
2050: fprintf(ficparo," %.5le",matcov[i][j]);
2051: }
2052: fscanf(ficpar,"\n");
2053: printf("\n");
2054: fprintf(ficparo,"\n");
2055: }
2056: for(i=1; i <=npar; i++)
2057: for(j=i+1;j<=npar;j++)
2058: matcov[i][j]=matcov[j][i];
2059:
2060: printf("\n");
2061:
2062:
2063: /*-------- data file ----------*/
2064: if((ficres =fopen(fileres,"w"))==NULL) {
2065: printf("Problem with resultfile: %s\n", fileres);goto end;
2066: }
2067: fprintf(ficres,"#%s\n",version);
2068:
2069: if((fic=fopen(datafile,"r"))==NULL) {
2070: printf("Problem with datafile: %s\n", datafile);goto end;
2071: }
2072:
2073: n= lastobs;
2074: severity = vector(1,maxwav);
2075: outcome=imatrix(1,maxwav+1,1,n);
2076: num=ivector(1,n);
2077: moisnais=vector(1,n);
2078: annais=vector(1,n);
2079: moisdc=vector(1,n);
2080: andc=vector(1,n);
2081: agedc=vector(1,n);
2082: cod=ivector(1,n);
2083: weight=vector(1,n);
2084: for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */
2085: mint=matrix(1,maxwav,1,n);
2086: anint=matrix(1,maxwav,1,n);
2087: s=imatrix(1,maxwav+1,1,n);
2088: adl=imatrix(1,maxwav+1,1,n);
2089: tab=ivector(1,NCOVMAX);
2090: ncodemax=ivector(1,8);
2091:
2092: i=1;
2093: while (fgets(line, MAXLINE, fic) != NULL) {
2094: if ((i >= firstobs) && (i <=lastobs)) {
2095:
2096: for (j=maxwav;j>=1;j--){
2097: cutv(stra, strb,line,' '); s[j][i]=atoi(strb);
2098: strcpy(line,stra);
2099: cutv(stra, strb,line,'/'); anint[j][i]=(double)(atoi(strb)); strcpy(line,stra);
2100: cutv(stra, strb,line,' '); mint[j][i]=(double)(atoi(strb)); strcpy(line,stra);
2101: }
2102:
2103: cutv(stra, strb,line,'/'); andc[i]=(double)(atoi(strb)); strcpy(line,stra);
2104: cutv(stra, strb,line,' '); moisdc[i]=(double)(atoi(strb)); strcpy(line,stra);
2105:
2106: cutv(stra, strb,line,'/'); annais[i]=(double)(atoi(strb)); strcpy(line,stra);
2107: cutv(stra, strb,line,' '); moisnais[i]=(double)(atoi(strb)); strcpy(line,stra);
2108:
2109: cutv(stra, strb,line,' '); weight[i]=(double)(atoi(strb)); strcpy(line,stra);
2110: for (j=ncov;j>=1;j--){
2111: cutv(stra, strb,line,' '); covar[j][i]=(double)(atoi(strb)); strcpy(line,stra);
2112: }
2113: num[i]=atol(stra);
2114:
2115: /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){
2116: printf("%d %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]),weight[i], (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]), (mint[2][i]), (anint[2][i]), (s[2][i]), (mint[3][i]), (anint[3][i]), (s[3][i]), (mint[4][i]), (anint[4][i]), (s[4][i])); ij=ij+1;}*/
2117:
2118: i=i+1;
2119: }
2120: }
2121: /* printf("ii=%d", ij);
2122: scanf("%d",i);*/
2123: imx=i-1; /* Number of individuals */
2124:
2125: /* for (i=1; i<=imx; i++){
2126: if ((s[1][i]==3) && (s[2][i]==2)) s[2][i]=3;
2127: if ((s[2][i]==3) && (s[3][i]==2)) s[3][i]=3;
2128: if ((s[3][i]==3) && (s[4][i]==2)) s[4][i]=3;
2129: }
2130: for (i=1; i<=imx; i++) printf("%d %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]), (weight[i]), (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]), (mint[2][i]), (anint[2][i]), (s[2][i]), (mint[3][i]), (anint[3][i]), (s[3][i]), (mint[4][i]), (anint[4][i]), (s[4][i]));*/
2131:
2132: /* Calculation of the number of parameter from char model*/
2133: Tvar=ivector(1,15);
2134: Tprod=ivector(1,15);
2135: Tvaraff=ivector(1,15);
2136: Tvard=imatrix(1,15,1,2);
2137: Tage=ivector(1,15);
2138:
2139: if (strlen(model) >1){
2140: j=0, j1=0, k1=1, k2=1;
2141: j=nbocc(model,'+');
2142: j1=nbocc(model,'*');
2143: cptcovn=j+1;
2144: cptcovprod=j1;
2145:
2146:
2147: strcpy(modelsav,model);
2148: if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){
2149: printf("Error. Non available option model=%s ",model);
2150: goto end;
2151: }
2152:
2153: for(i=(j+1); i>=1;i--){
2154: cutv(stra,strb,modelsav,'+');
2155: if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav);
2156: /* printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/
2157: /*scanf("%d",i);*/
2158: if (strchr(strb,'*')) {
2159: cutv(strd,strc,strb,'*');
2160: if (strcmp(strc,"age")==0) {
2161: cptcovprod--;
2162: cutv(strb,stre,strd,'V');
2163: Tvar[i]=atoi(stre);
2164: cptcovage++;
2165: Tage[cptcovage]=i;
2166: /*printf("stre=%s ", stre);*/
2167: }
2168: else if (strcmp(strd,"age")==0) {
2169: cptcovprod--;
2170: cutv(strb,stre,strc,'V');
2171: Tvar[i]=atoi(stre);
2172: cptcovage++;
2173: Tage[cptcovage]=i;
2174: }
2175: else {
2176: cutv(strb,stre,strc,'V');
2177: Tvar[i]=ncov+k1;
2178: cutv(strb,strc,strd,'V');
2179: Tprod[k1]=i;
2180: Tvard[k1][1]=atoi(strc);
2181: Tvard[k1][2]=atoi(stre);
2182: Tvar[cptcovn+k2]=Tvard[k1][1];
2183: Tvar[cptcovn+k2+1]=Tvard[k1][2];
2184: for (k=1; k<=lastobs;k++)
2185: covar[ncov+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];
2186: k1++;
2187: k2=k2+2;
2188: }
2189: }
2190: else {
2191: /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/
2192: /* scanf("%d",i);*/
2193: cutv(strd,strc,strb,'V');
2194: Tvar[i]=atoi(strc);
2195: }
2196: strcpy(modelsav,stra);
2197: /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);
2198: scanf("%d",i);*/
2199: }
2200: }
2201:
2202: /*printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);
2203: printf("cptcovprod=%d ", cptcovprod);
2204: scanf("%d ",i);*/
2205: fclose(fic);
2206:
2207: /* if(mle==1){*/
2208: if (weightopt != 1) { /* Maximisation without weights*/
2209: for(i=1;i<=n;i++) weight[i]=1.0;
2210: }
2211: /*-calculation of age at interview from date of interview and age at death -*/
2212: agev=matrix(1,maxwav,1,imx);
2213:
2214: for (i=1; i<=imx; i++)
2215: for(m=2; (m<= maxwav); m++)
2216: if ((mint[m][i]== 99) && (s[m][i] <= nlstate)){
2217: anint[m][i]=9999;
2218: s[m][i]=-1;
2219: }
2220:
2221: for (i=1; i<=imx; i++) {
2222: agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);
2223: for(m=1; (m<= maxwav); m++){
2224: if(s[m][i] >0){
2225: if (s[m][i] == nlstate+1) {
2226: if(agedc[i]>0)
2227: if(moisdc[i]!=99 && andc[i]!=9999)
2228: agev[m][i]=agedc[i];
2229: else {
2230: if (andc[i]!=9999){
2231: printf("Warning negative age at death: %d line:%d\n",num[i],i);
2232: agev[m][i]=-1;
2233: }
2234: }
2235: }
2236: else if(s[m][i] !=9){ /* Should no more exist */
2237: agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);
2238: if(mint[m][i]==99 || anint[m][i]==9999)
2239: agev[m][i]=1;
2240: else if(agev[m][i] <agemin){
2241: agemin=agev[m][i];
2242: /*printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], agemin);*/
2243: }
2244: else if(agev[m][i] >agemax){
2245: agemax=agev[m][i];
2246: /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/
2247: }
2248: /*agev[m][i]=anint[m][i]-annais[i];*/
2249: /* agev[m][i] = age[i]+2*m;*/
2250: }
2251: else { /* =9 */
2252: agev[m][i]=1;
2253: s[m][i]=-1;
2254: }
2255: }
2256: else /*= 0 Unknown */
2257: agev[m][i]=1;
2258: }
2259:
2260: }
2261: for (i=1; i<=imx; i++) {
2262: for(m=1; (m<= maxwav); m++){
2263: if (s[m][i] > (nlstate+ndeath)) {
2264: printf("Error: Wrong value in nlstate or ndeath\n");
2265: goto end;
2266: }
2267: }
2268: }
2269:
2270: printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);
2271:
2272: free_vector(severity,1,maxwav);
2273: free_imatrix(outcome,1,maxwav+1,1,n);
2274: free_vector(moisnais,1,n);
2275: free_vector(annais,1,n);
2276: free_matrix(mint,1,maxwav,1,n);
2277: free_matrix(anint,1,maxwav,1,n);
2278: free_vector(moisdc,1,n);
2279: free_vector(andc,1,n);
2280:
2281:
2282: wav=ivector(1,imx);
2283: dh=imatrix(1,lastpass-firstpass+1,1,imx);
2284: mw=imatrix(1,lastpass-firstpass+1,1,imx);
2285:
2286: /* Concatenates waves */
2287: concatwav(wav, dh, mw, s, agedc, agev, firstpass, lastpass, imx, nlstate, stepm);
2288:
2289:
2290: Tcode=ivector(1,100);
2291: nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);
2292: ncodemax[1]=1;
2293: if (cptcovn > 0) tricode(Tvar,nbcode,imx);
2294:
2295: codtab=imatrix(1,100,1,10);
2296: h=0;
2297: m=pow(2,cptcoveff);
2298:
2299: for(k=1;k<=cptcoveff; k++){
2300: for(i=1; i <=(m/pow(2,k));i++){
2301: for(j=1; j <= ncodemax[k]; j++){
2302: for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){
2303: h++;
2304: if (h>m) h=1;codtab[h][k]=j;
2305: }
2306: }
2307: }
2308: }
2309:
2310:
2311: /*for(i=1; i <=m ;i++){
2312: for(k=1; k <=cptcovn; k++){
2313: printf("i=%d k=%d %d %d",i,k,codtab[i][k], cptcoveff);
2314: }
2315: printf("\n");
2316: }
2317: scanf("%d",i);*/
2318:
2319: /* Calculates basic frequencies. Computes observed prevalence at single age
2320: and prints on file fileres'p'. */
2321: freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax, fprev, lprev);
2322:
2323: pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
2324: oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
2325: newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
2326: savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
2327: oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */
2328:
2329: /* For Powell, parameters are in a vector p[] starting at p[1]
2330: so we point p on param[1][1] so that p[1] maps on param[1][1][1] */
2331: p=param[1][1]; /* *(*(*(param +1)+1)+0) */
2332:
2333: if(mle==1){
2334: mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);
2335: }
2336:
2337: /*--------- results files --------------*/
2338: 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);
2339:
2340: jk=1;
2341: fprintf(ficres,"# Parameters\n");
2342: printf("# Parameters\n");
2343: for(i=1,jk=1; i <=nlstate; i++){
2344: for(k=1; k <=(nlstate+ndeath); k++){
2345: if (k != i)
2346: {
2347: printf("%d%d ",i,k);
2348: fprintf(ficres,"%1d%1d ",i,k);
2349: for(j=1; j <=ncovmodel; j++){
2350: printf("%f ",p[jk]);
2351: fprintf(ficres,"%f ",p[jk]);
2352: jk++;
2353: }
2354: printf("\n");
2355: fprintf(ficres,"\n");
2356: }
2357: }
2358: }
2359: if(mle==1){
2360: /* Computing hessian and covariance matrix */
2361: ftolhess=ftol; /* Usually correct */
2362: hesscov(matcov, p, npar, delti, ftolhess, func);
2363: }
2364: fprintf(ficres,"# Scales\n");
2365: printf("# Scales\n");
2366: for(i=1,jk=1; i <=nlstate; i++){
2367: for(j=1; j <=nlstate+ndeath; j++){
2368: if (j!=i) {
2369: fprintf(ficres,"%1d%1d",i,j);
2370: printf("%1d%1d",i,j);
2371: for(k=1; k<=ncovmodel;k++){
2372: printf(" %.5e",delti[jk]);
2373: fprintf(ficres," %.5e",delti[jk]);
2374: jk++;
2375: }
2376: printf("\n");
2377: fprintf(ficres,"\n");
2378: }
2379: }
2380: }
2381:
2382: k=1;
2383: fprintf(ficres,"# Covariance\n");
2384: printf("# Covariance\n");
2385: for(i=1;i<=npar;i++){
2386: /* if (k>nlstate) k=1;
2387: i1=(i-1)/(ncovmodel*nlstate)+1;
2388: fprintf(ficres,"%s%d%d",alph[k],i1,tab[i]);
2389: printf("%s%d%d",alph[k],i1,tab[i]);*/
2390: fprintf(ficres,"%3d",i);
2391: printf("%3d",i);
2392: for(j=1; j<=i;j++){
2393: fprintf(ficres," %.5e",matcov[i][j]);
2394: printf(" %.5e",matcov[i][j]);
2395: }
2396: fprintf(ficres,"\n");
2397: printf("\n");
2398: k++;
2399: }
2400:
2401: while((c=getc(ficpar))=='#' && c!= EOF){
2402: ungetc(c,ficpar);
2403: fgets(line, MAXLINE, ficpar);
2404: puts(line);
2405: fputs(line,ficparo);
2406: }
2407: ungetc(c,ficpar);
2408:
2409: fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf\n",&agemin,&agemax, &bage, &fage);
2410:
2411: if (fage <= 2) {
2412: bage = agemin;
2413: fage = agemax;
2414: }
2415:
2416: fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");
2417: fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemax,bage,fage);
2418:
2419:
2420: /*------------ gnuplot -------------*/
2421: chdir(pathcd);
2422: if((ficgp=fopen("graph.plt","w"))==NULL) {
2423: printf("Problem with file graph.gp");goto end;
2424: }
2425: #ifdef windows
2426: fprintf(ficgp,"cd \"%s\" \n",pathc);
2427: #endif
2428: m=pow(2,cptcoveff);
2429:
2430: /* 1eme*/
2431: for (cpt=1; cpt<= nlstate ; cpt ++) {
2432: for (k1=1; k1<= m ; k1 ++) {
2433:
2434: #ifdef windows
2435: 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);
2436: #endif
2437: #ifdef unix
2438: fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nplot [%.f:%.f] \"vpl%s\" u 1:2 \"\%%lf",agemin,fage,fileres);
2439: #endif
2440:
2441: for (i=1; i<= nlstate ; i ++) {
2442: if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
2443: else fprintf(ficgp," \%%*lf (\%%*lf)");
2444: }
2445: fprintf(ficgp,"\" t\"Stationary prevalence\" w l 0,\"vpl%s\" every :::%d::%d u 1:($2+2*$3) \"\%%lf",fileres,k1-1,k1-1);
2446: for (i=1; i<= nlstate ; i ++) {
2447: if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
2448: else fprintf(ficgp," \%%*lf (\%%*lf)");
2449: }
2450: fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"vpl%s\" every :::%d::%d u 1:($2-2*$3) \"\%%lf",fileres,k1-1,k1-1);
2451: for (i=1; i<= nlstate ; i ++) {
2452: if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
2453: else fprintf(ficgp," \%%*lf (\%%*lf)");
2454: }
2455: fprintf(ficgp,"\" t\"\" w l 1,\"p%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",fileres,k1-1,k1-1,2+4*(cpt-1));
2456: #ifdef unix
2457: fprintf(ficgp,"\nset ter gif small size 400,300");
2458: #endif
2459: fprintf(ficgp,"\nset out \"v%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);
2460: }
2461: }
2462: /*2 eme*/
2463:
2464: for (k1=1; k1<= m ; k1 ++) {
2465: fprintf(ficgp,"set ylabel \"Years\" \nset ter gif small size 400,300\nplot [%.f:%.f] ",agemin,fage);
2466:
2467: for (i=1; i<= nlstate+1 ; i ++) {
2468: k=2*i;
2469: fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:2 \"\%%lf",fileres,k1-1,k1-1);
2470: for (j=1; j<= nlstate+1 ; j ++) {
2471: if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
2472: else fprintf(ficgp," \%%*lf (\%%*lf)");
2473: }
2474: if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");
2475: else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);
2476: fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",fileres,k1-1,k1-1);
2477: for (j=1; j<= nlstate+1 ; j ++) {
2478: if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
2479: else fprintf(ficgp," \%%*lf (\%%*lf)");
2480: }
2481: fprintf(ficgp,"\" t\"\" w l 0,");
2482: fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",fileres,k1-1,k1-1);
2483: for (j=1; j<= nlstate+1 ; j ++) {
2484: if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
2485: else fprintf(ficgp," \%%*lf (\%%*lf)");
2486: }
2487: if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");
2488: else fprintf(ficgp,"\" t\"\" w l 0,");
2489: }
2490: fprintf(ficgp,"\nset out \"e%s%d.gif\" \nreplot\n\n",strtok(optionfile, "."),k1);
2491: }
2492:
2493: /*3eme*/
2494:
2495: for (k1=1; k1<= m ; k1 ++) {
2496: for (cpt=1; cpt<= nlstate ; cpt ++) {
2497: k=2+nlstate*(cpt-1);
2498: 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);
2499: for (i=1; i< nlstate ; i ++) {
2500: 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);
2501: }
2502: fprintf(ficgp,"\nset out \"exp%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);
2503: }
2504: }
2505:
2506: /* CV preval stat */
2507: for (k1=1; k1<= m ; k1 ++) {
2508: for (cpt=1; cpt<nlstate ; cpt ++) {
2509: k=3;
2510: 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/($%d",agemin,agemax,fileres,k1,k+cpt+1,k+1);
2511: for (i=1; i< nlstate ; i ++)
2512: fprintf(ficgp,"+$%d",k+i+1);
2513: fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);
2514:
2515: l=3+(nlstate+ndeath)*cpt;
2516: fprintf(ficgp,",\"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",fileres,k1,l+cpt+1,l+1);
2517: for (i=1; i< nlstate ; i ++) {
2518: l=3+(nlstate+ndeath)*cpt;
2519: fprintf(ficgp,"+$%d",l+i+1);
2520: }
2521: fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);
2522: fprintf(ficgp,"set out \"p%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);
2523: }
2524: }
2525:
2526: /* proba elementaires */
2527: for(i=1,jk=1; i <=nlstate; i++){
2528: for(k=1; k <=(nlstate+ndeath); k++){
2529: if (k != i) {
2530: for(j=1; j <=ncovmodel; j++){
2531: /*fprintf(ficgp,"%s%1d%1d=%f ",alph[j],i,k,p[jk]);*/
2532: /*fprintf(ficgp,"%s",alph[1]);*/
2533: fprintf(ficgp,"p%d=%f ",jk,p[jk]);
2534: jk++;
2535: fprintf(ficgp,"\n");
2536: }
2537: }
2538: }
2539: }
2540:
2541: for(jk=1; jk <=m; jk++) {
2542: fprintf(ficgp,"\nset ter gif small size 400,300\nset log y\nplot [%.f:%.f] ",agemin,agemax);
2543: i=1;
2544: for(k2=1; k2<=nlstate; k2++) {
2545: k3=i;
2546: for(k=1; k<=(nlstate+ndeath); k++) {
2547: if (k != k2){
2548: fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
2549: ij=1;
2550: for(j=3; j <=ncovmodel; j++) {
2551: if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
2552: fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
2553: ij++;
2554: }
2555: else
2556: fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
2557: }
2558: fprintf(ficgp,")/(1");
2559:
2560: for(k1=1; k1 <=nlstate; k1++){
2561: fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);
2562: ij=1;
2563: for(j=3; j <=ncovmodel; j++){
2564: if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
2565: fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
2566: ij++;
2567: }
2568: else
2569: fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
2570: }
2571: fprintf(ficgp,")");
2572: }
2573: fprintf(ficgp,") t \"p%d%d\" ", k2,k);
2574: if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");
2575: i=i+ncovmodel;
2576: }
2577: }
2578: }
2579: fprintf(ficgp,"\nset out \"pe%s%d.gif\" \nreplot\n\n",strtok(optionfile, "."),jk);
2580: }
2581:
2582: fclose(ficgp);
2583:
2584: chdir(path);
2585:
2586: free_ivector(wav,1,imx);
2587: free_imatrix(dh,1,lastpass-firstpass+1,1,imx);
2588: free_imatrix(mw,1,lastpass-firstpass+1,1,imx);
2589: free_ivector(num,1,n);
2590: free_vector(agedc,1,n);
2591: /*free_matrix(covar,1,NCOVMAX,1,n);*/
2592: fclose(ficparo);
2593: fclose(ficres);
2594: /* }*/
2595:
2596: /*________fin mle=1_________*/
2597:
2598:
2599:
2600: /* No more information from the sample is required now */
2601: /* Reads comments: lines beginning with '#' */
2602: while((c=getc(ficpar))=='#' && c!= EOF){
2603: ungetc(c,ficpar);
2604: fgets(line, MAXLINE, ficpar);
2605: puts(line);
2606: fputs(line,ficparo);
2607: }
2608: ungetc(c,ficpar);
2609:
2610: fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf\n",&agemin,&agemax, &bage, &fage);
2611: printf("agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemax, bage, fage);
2612: fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemax,bage,fage);
2613: /*--------- index.htm --------*/
2614:
2615: strcpy(optionfilehtm,optionfile);
2616: strcat(optionfilehtm,".htm");
2617: if((fichtm=fopen(optionfilehtm,"w"))==NULL) {
2618: printf("Problem with %s \n",optionfilehtm);goto end;
2619: }
2620:
2621: fprintf(fichtm,"<body><ul> <font size=\"6\">Imach, Version 0.64b </font> <hr size=\"2\" color=\"#EC5E5E\">
2622: Titre=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>
2623: Total number of observations=%d <br>
2624: Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>
2625: <hr size=\"2\" color=\"#EC5E5E\">
2626: <li>Outputs files<br><br>\n
2627: - Observed prevalence in each state: <a href=\"p%s\">p%s</a> <br>\n
2628: - Estimated parameters and the covariance matrix: <a href=\"%s\">%s</a> <br>
2629: - Stationary prevalence in each state: <a href=\"pl%s\">pl%s</a> <br>
2630: - Transition probabilities: <a href=\"pij%s\">pij%s</a><br>
2631: - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>
2632: - Life expectancies by age and initial health status: <a href=\"e%s\">e%s</a> <br>
2633: - Variances of life expectancies by age and initial health status: <a href=\"v%s\">v%s</a><br>
2634: - Health expectancies with their variances: <a href=\"t%s\">t%s</a> <br>
2635: - Standard deviation of stationary prevalences: <a href=\"vpl%s\">vpl%s</a> <br>
2636: - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>
2637: <br>",title,datafile,firstpass,lastpass,stepm, weightopt,model,imx,jmin,jmax,jmean,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres);
2638:
2639: fprintf(fichtm," <li>Graphs</li><p>");
2640:
2641: m=cptcoveff;
2642: if (cptcovn < 1) {m=1;ncodemax[1]=1;}
2643:
2644: j1=0;
2645: for(k1=1; k1<=m;k1++){
2646: for(i1=1; i1<=ncodemax[k1];i1++){
2647: j1++;
2648: if (cptcovn > 0) {
2649: fprintf(fichtm,"<hr size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
2650: for (cpt=1; cpt<=cptcoveff;cpt++)
2651: fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[j1][cpt]]);
2652: fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
2653: }
2654: fprintf(fichtm,"<br>- Probabilities: pe%s%d.gif<br>
2655: <img src=\"pe%s%d.gif\">",strtok(optionfile, "."),j1,strtok(optionfile, "."),j1);
2656: for(cpt=1; cpt<nlstate;cpt++){
2657: fprintf(fichtm,"<br>- Prevalence of disability : p%s%d%d.gif<br>
2658: <img src=\"p%s%d%d.gif\">",strtok(optionfile, "."),cpt,j1,strtok(optionfile, "."),cpt,j1);
2659: }
2660: for(cpt=1; cpt<=nlstate;cpt++) {
2661: fprintf(fichtm,"<br>- Observed and stationary prevalence (with confident
2662: interval) in state (%d): v%s%d%d.gif <br>
2663: <img src=\"v%s%d%d.gif\">",cpt,strtok(optionfile, "."),cpt,j1,strtok(optionfile, "."),cpt,j1);
2664: }
2665: for(cpt=1; cpt<=nlstate;cpt++) {
2666: fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): exp%s%d%d.gif <br>
2667: <img src=\"exp%s%d%d.gif\">",cpt,strtok(optionfile, "."),cpt,j1,strtok(optionfile, "."),cpt,j1);
2668: }
2669: fprintf(fichtm,"\n<br>- Total life expectancy by age and
2670: health expectancies in states (1) and (2): e%s%d.gif<br>
2671: <img src=\"e%s%d.gif\">",strtok(optionfile, "."),j1,strtok(optionfile, "."),j1);
2672: fprintf(fichtm,"\n</body>");
2673: }
2674: }
2675: fclose(fichtm);
2676:
2677: /*--------------- Prevalence limit --------------*/
2678:
2679: strcpy(filerespl,"pl");
2680: strcat(filerespl,fileres);
2681: if((ficrespl=fopen(filerespl,"w"))==NULL) {
2682: printf("Problem with Prev limit resultfile: %s\n", filerespl);goto end;
2683: }
2684: printf("Computing prevalence limit: result on file '%s' \n", filerespl);
2685: fprintf(ficrespl,"#Prevalence limit\n");
2686: fprintf(ficrespl,"#Age ");
2687: for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);
2688: fprintf(ficrespl,"\n");
2689:
2690: prlim=matrix(1,nlstate,1,nlstate);
2691: pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
2692: oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
2693: newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
2694: savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
2695: oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */
2696: k=0;
2697: agebase=agemin;
2698: agelim=agemax;
2699: ftolpl=1.e-10;
2700: i1=cptcoveff;
2701: if (cptcovn < 1){i1=1;}
2702:
2703: for(cptcov=1;cptcov<=i1;cptcov++){
2704: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
2705: k=k+1;
2706: /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/
2707: fprintf(ficrespl,"\n#******");
2708: for(j=1;j<=cptcoveff;j++)
2709: fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
2710: fprintf(ficrespl,"******\n");
2711:
2712: for (age=agebase; age<=agelim; age++){
2713: prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
2714: fprintf(ficrespl,"%.0f",age );
2715: for(i=1; i<=nlstate;i++)
2716: fprintf(ficrespl," %.5f", prlim[i][i]);
2717: fprintf(ficrespl,"\n");
2718: }
2719: }
2720: }
2721: fclose(ficrespl);
2722:
2723: /*------------- h Pij x at various ages ------------*/
2724:
2725: strcpy(filerespij,"pij"); strcat(filerespij,fileres);
2726: if((ficrespij=fopen(filerespij,"w"))==NULL) {
2727: printf("Problem with Pij resultfile: %s\n", filerespij);goto end;
2728: }
2729: printf("Computing pij: result on file '%s' \n", filerespij);
2730:
2731: stepsize=(int) (stepm+YEARM-1)/YEARM;
2732: /*if (stepm<=24) stepsize=2;*/
2733:
2734: agelim=AGESUP;
2735: hstepm=stepsize*YEARM; /* Every year of age */
2736: hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */
2737:
2738: k=0;
2739: for(cptcov=1;cptcov<=i1;cptcov++){
2740: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
2741: k=k+1;
2742: fprintf(ficrespij,"\n#****** ");
2743: for(j=1;j<=cptcoveff;j++)
2744: fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
2745: fprintf(ficrespij,"******\n");
2746:
2747: for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */
2748: nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
2749: nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
2750: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
2751: oldm=oldms;savm=savms;
2752: hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
2753: fprintf(ficrespij,"# Age");
2754: for(i=1; i<=nlstate;i++)
2755: for(j=1; j<=nlstate+ndeath;j++)
2756: fprintf(ficrespij," %1d-%1d",i,j);
2757: fprintf(ficrespij,"\n");
2758: for (h=0; h<=nhstepm; h++){
2759: fprintf(ficrespij,"%d %.0f %.0f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );
2760: for(i=1; i<=nlstate;i++)
2761: for(j=1; j<=nlstate+ndeath;j++)
2762: fprintf(ficrespij," %.5f", p3mat[i][j][h]);
2763: fprintf(ficrespij,"\n");
2764: }
2765: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
2766: fprintf(ficrespij,"\n");
2767: }
2768: }
2769: }
2770:
2771: /* varprob(fileres, matcov, p, delti, nlstate, (int) bage, (int) fage,k);*/
2772:
2773: fclose(ficrespij);
2774:
2775: /*---------- Forecasting ------------------*/
2776:
2777: strcpy(fileresf,"f");
2778: strcat(fileresf,fileres);
2779: if((ficresf=fopen(fileresf,"w"))==NULL) {
2780: printf("Problem with forecast resultfile: %s\n", fileresf);goto end;
2781: }
2782: printf("Computing forecasting: result on file '%s' \n", fileresf);
2783:
2784: prevalence(agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax, fprevfore, lprevfore);
2785:
2786: free_matrix(agev,1,maxwav,1,imx);
2787: /* Mobile average */
2788:
2789: if (cptcoveff==0) ncodemax[cptcoveff]=1;
2790:
2791: if (mobilav==1) {
2792: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
2793: for (agedeb=bage+3; agedeb<=fage-2; agedeb++)
2794: for (i=1; i<=nlstate;i++)
2795: for (cptcod=1;cptcod<=ncodemax[cptcov];cptcod++)
2796: mobaverage[(int)agedeb][i][cptcod]=0.;
2797:
2798: for (agedeb=bage+4; agedeb<=fage; agedeb++){
2799: for (i=1; i<=nlstate;i++){
2800: for (cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
2801: for (cpt=0;cpt<=4;cpt++){
2802: mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]+probs[(int)agedeb-cpt][i][cptcod];
2803: }
2804: mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]/5;
2805: }
2806: }
2807: }
2808: }
2809:
2810: stepsize=(int) (stepm+YEARM-1)/YEARM;
2811: if (stepm<=12) stepsize=1;
2812:
2813: agelim=AGESUP;
2814: hstepm=stepsize*YEARM; /* Every year of age */
2815: hstepm=hstepm/stepm; /* Typically 2 years, = 2 years/6 months = 4 */
2816:
2817: k=0;
2818: for(cptcov=1;cptcov<=i1;cptcov++){
2819: for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
2820: k=k+1;
2821: fprintf(ficresf,"\n#****** ");
2822: for(j=1;j<=cptcoveff;j++) {
2823: fprintf(ficresf,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
2824: }
2825: fprintf(ficresf,"******\n");
2826: fprintf(ficresf,"# StartingAge FinalAge Horizon(in years)");
2827: for(j=1; j<=nlstate+ndeath;j++) fprintf(ficresf," P.%d",j);
2828:
2829: for (agedeb=fage; agedeb>=bage; agedeb--){
2830: fprintf(ficresf,"\n%d %.f %.f 0 ",k,agedeb, agedeb);
2831: if (mobilav==1) {
2832: for(j=1; j<=nlstate;j++)
2833: fprintf(ficresf," %.5f ",mobaverage[(int)agedeb][j][cptcod]);
2834: }
2835: else {
2836: for(j=1; j<=nlstate;j++)
2837: fprintf(ficresf," %.5f ",probs[(int)agedeb][j][cptcod]);
2838: }
2839: for(j=1; j<=ndeath;j++) fprintf(ficresf," 0.00000");
2840: }
2841: for (cpt=1; cpt<=nforecast;cpt++)
2842: for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */
2843:
2844: nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);
2845: nhstepm = nhstepm/hstepm;
2846: /*printf("agedeb=%.lf stepm=%d hstepm=%d nhstepm=%d \n",agedeb,stepm,hstepm,nhstepm);*/
2847:
2848: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
2849: oldm=oldms;savm=savms;
2850: hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
2851:
2852: for (h=0; h<=nhstepm; h++){
2853:
2854: if (h*hstepm/YEARM*stepm==cpt)
2855: fprintf(ficresf,"\n%d %.f %.f %.f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm, h*hstepm/YEARM*stepm);
2856:
2857:
2858: for(j=1; j<=nlstate+ndeath;j++) {
2859: kk1=0.;
2860: for(i=1; i<=nlstate;i++) {
2861: if (mobilav==1)
2862: kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb][i][cptcod];
2863: else kk1=kk1+p3mat[i][j][h]*probs[(int)agedeb][i][cptcod];
2864: }
2865: if (h*hstepm/YEARM*stepm==cpt) fprintf(ficresf," %.5f ", kk1);
2866: }
2867: }
2868: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
2869: }
2870: }
2871: }
2872: if (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
2873: free_imatrix(s,1,maxwav+1,1,n);
2874: free_vector(weight,1,n);
2875: fclose(ficresf);
2876: /*---------- Health expectancies and variances ------------*/
2877:
2878: strcpy(filerest,"t");
2879: strcat(filerest,fileres);
2880: if((ficrest=fopen(filerest,"w"))==NULL) {
2881: printf("Problem with total LE resultfile: %s\n", filerest);goto end;
2882: }
2883: printf("Computing Total LEs with variances: file '%s' \n", filerest);
2884:
2885:
2886: strcpy(filerese,"e");
2887: strcat(filerese,fileres);
2888: if((ficreseij=fopen(filerese,"w"))==NULL) {
2889: printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
2890: }
2891: printf("Computing Health Expectancies: result on file '%s' \n", filerese);
2892:
2893: strcpy(fileresv,"v");
2894: strcat(fileresv,fileres);
2895: if((ficresvij=fopen(fileresv,"w"))==NULL) {
2896: printf("Problem with variance resultfile: %s\n", fileresv);exit(0);
2897: }
2898: printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
2899:
2900: k=0;
2901: for(cptcov=1;cptcov<=i1;cptcov++){
2902: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
2903: k=k+1;
2904: fprintf(ficrest,"\n#****** ");
2905: for(j=1;j<=cptcoveff;j++)
2906: fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
2907: fprintf(ficrest,"******\n");
2908:
2909: fprintf(ficreseij,"\n#****** ");
2910: for(j=1;j<=cptcoveff;j++)
2911: fprintf(ficreseij,"V%d=%d ",j,nbcode[j][codtab[k][j]]);
2912: fprintf(ficreseij,"******\n");
2913:
2914: fprintf(ficresvij,"\n#****** ");
2915: for(j=1;j<=cptcoveff;j++)
2916: fprintf(ficresvij,"V%d=%d ",j,nbcode[j][codtab[k][j]]);
2917: fprintf(ficresvij,"******\n");
2918:
2919: eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
2920: oldm=oldms;savm=savms;
2921: evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k);
2922: vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
2923: oldm=oldms;savm=savms;
2924: varevsij(fileres, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);
2925:
2926: fprintf(ficrest,"#Total LEs with variances: e.. (std) ");
2927: for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);
2928: fprintf(ficrest,"\n");
2929:
2930: hf=1;
2931: if (stepm >= YEARM) hf=stepm/YEARM;
2932: epj=vector(1,nlstate+1);
2933: for(age=bage; age <=fage ;age++){
2934: prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
2935: if (popbased==1) {
2936: for(i=1; i<=nlstate;i++)
2937: prlim[i][i]=probs[(int)age][i][k];
2938: }
2939:
2940: fprintf(ficrest," %.0f",age);
2941: for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){
2942: for(i=1, epj[j]=0.;i <=nlstate;i++) {
2943: epj[j] += prlim[i][i]*hf*eij[i][j][(int)age];
2944: }
2945: epj[nlstate+1] +=epj[j];
2946: }
2947: for(i=1, vepp=0.;i <=nlstate;i++)
2948: for(j=1;j <=nlstate;j++)
2949: vepp += vareij[i][j][(int)age];
2950: fprintf(ficrest," %.2f (%.2f)", epj[nlstate+1],hf*sqrt(vepp));
2951: for(j=1;j <=nlstate;j++){
2952: fprintf(ficrest," %.2f (%.2f)", epj[j],hf*sqrt(vareij[j][j][(int)age]));
2953: }
2954: fprintf(ficrest,"\n");
2955: }
2956: }
2957: }
2958:
2959:
2960:
2961:
2962: fclose(ficreseij);
2963: fclose(ficresvij);
2964: fclose(ficrest);
2965: fclose(ficpar);
2966: free_vector(epj,1,nlstate+1);
2967: /* scanf("%d ",i); */
2968:
2969: /*------- Variance limit prevalence------*/
2970:
2971: strcpy(fileresvpl,"vpl");
2972: strcat(fileresvpl,fileres);
2973: if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {
2974: printf("Problem with variance prev lim resultfile: %s\n", fileresvpl);
2975: exit(0);
2976: }
2977: printf("Computing Variance-covariance of Prevalence limit: file '%s' \n", fileresvpl);
2978:
2979: k=0;
2980: for(cptcov=1;cptcov<=i1;cptcov++){
2981: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
2982: k=k+1;
2983: fprintf(ficresvpl,"\n#****** ");
2984: for(j=1;j<=cptcoveff;j++)
2985: fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
2986: fprintf(ficresvpl,"******\n");
2987:
2988: varpl=matrix(1,nlstate,(int) bage, (int) fage);
2989: oldm=oldms;savm=savms;
2990: varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);
2991: }
2992: }
2993:
2994: fclose(ficresvpl);
2995:
2996: /*---------- End : free ----------------*/
2997: free_matrix(varpl,1,nlstate,(int) bage, (int)fage);
2998:
2999: free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);
3000: free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
3001:
3002:
3003: free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);
3004: free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);
3005: free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);
3006: free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);
3007:
3008: free_matrix(matcov,1,npar,1,npar);
3009: free_vector(delti,1,npar);
3010:
3011: free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
3012:
3013: printf("End of Imach\n");
3014: /* gettimeofday(&end_time, (struct timezone*)0);*/ /* after time */
3015:
3016: /* 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);*/
3017: /*printf("Total time was %d uSec.\n", total_usecs);*/
3018: /*------ End -----------*/
3019:
3020:
3021: end:
3022: #ifdef windows
3023: chdir(pathcd);
3024: #endif
3025:
3026: system("..\\gp37mgw\\wgnuplot graph.plt");
3027:
3028: #ifdef windows
3029: while (z[0] != 'q') {
3030: chdir(pathcd);
3031: printf("\nType e to edit output files, c to start again, and q for exiting: ");
3032: scanf("%s",z);
3033: if (z[0] == 'c') system("./imach");
3034: else if (z[0] == 'e') {
3035: chdir(path);
3036: system(optionfilehtm);
3037: }
3038: else if (z[0] == 'q') exit(0);
3039: }
3040: #endif
3041: }
3042:
3043:
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