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,*ficpop;
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,double **mint,double **anint, int boolprev, double dateprev1,double dateprev2)
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, k2;
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: if (boolprev==1){
1196: for(m=fprev1; m<=lprev1; m++){
1197: if(agev[m][i]==0) agev[m][i]=agemax+1;
1198: if(agev[m][i]==1) agev[m][i]=agemax+2;
1199: freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
1200: freq[s[m][i]][s[m+1][i]][(int) agemax+3] += weight[i];
1201: }
1202: }
1203: else {
1204: for(m=firstpass; m<=lastpass; m++){
1205: k2=anint[m][i]+(mint[m][i]/12.);
1206: if ((k2>=dateprev1) && (k2<=dateprev2)) {
1207: if(agev[m][i]==0) agev[m][i]=agemax+1;
1208: if(agev[m][i]==1) agev[m][i]=agemax+2;
1209: freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
1210: freq[s[m][i]][s[m+1][i]][(int) agemax+3] += weight[i];
1211: }
1212: }
1213: }
1214: }
1215: }
1216: if (cptcovn>0) {
1217: fprintf(ficresp, "\n#********** Variable ");
1218: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
1219: fprintf(ficresp, "**********\n#");
1220: }
1221: for(i=1; i<=nlstate;i++)
1222: fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
1223: fprintf(ficresp, "\n");
1224:
1225: for(i=(int)agemin; i <= (int)agemax+3; i++){
1226: if(i==(int)agemax+3)
1227: printf("Total");
1228: else
1229: printf("Age %d", i);
1230: for(jk=1; jk <=nlstate ; jk++){
1231: for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
1232: pp[jk] += freq[jk][m][i];
1233: }
1234: for(jk=1; jk <=nlstate ; jk++){
1235: for(m=-1, pos=0; m <=0 ; m++)
1236: pos += freq[jk][m][i];
1237: if(pp[jk]>=1.e-10)
1238: printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
1239: else
1240: printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
1241: }
1242:
1243: for(jk=1; jk <=nlstate ; jk++){
1244: for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
1245: pp[jk] += freq[jk][m][i];
1246: }
1247:
1248: for(jk=1,pos=0; jk <=nlstate ; jk++)
1249: pos += pp[jk];
1250: for(jk=1; jk <=nlstate ; jk++){
1251: if(pos>=1.e-5)
1252: printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
1253: else
1254: printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
1255: if( i <= (int) agemax){
1256: if(pos>=1.e-5){
1257: fprintf(ficresp," %d %.5f %.0f %.0f",i,pp[jk]/pos, pp[jk],pos);
1258: probs[i][jk][j1]= pp[jk]/pos;
1259: /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/
1260: }
1261: else
1262: fprintf(ficresp," %d NaNq %.0f %.0f",i,pp[jk],pos);
1263: }
1264: }
1265: for(jk=-1; jk <=nlstate+ndeath; jk++)
1266: for(m=-1; m <=nlstate+ndeath; m++)
1267: if(freq[jk][m][i] !=0 ) printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
1268: if(i <= (int) agemax)
1269: fprintf(ficresp,"\n");
1270: printf("\n");
1271: }
1272: }
1273: }
1274:
1275: fclose(ficresp);
1276: free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);
1277: free_vector(pp,1,nlstate);
1278:
1279: } /* End of Freq */
1280:
1281: /************ Prevalence ********************/
1282: void prevalence(int agemin, int agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax, int fprev1,int lprev1, double **mint,double **anint,int boolprev, double dateprev1, double dateprev2)
1283: { /* Some frequencies */
1284:
1285: int i, m, jk, k1, i1, j1, bool, z1,z2,j;
1286: double ***freq; /* Frequencies */
1287: double *pp;
1288: double pos, k2;
1289:
1290: pp=vector(1,nlstate);
1291: probs= ma3x(1,130 ,1,8, 1,8);
1292:
1293: freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);
1294: j1=0;
1295:
1296: j=cptcoveff;
1297: if (cptcovn<1) {j=1;ncodemax[1]=1;}
1298:
1299: for(k1=1; k1<=j;k1++){
1300: for(i1=1; i1<=ncodemax[k1];i1++){
1301: j1++;
1302:
1303: for (i=-1; i<=nlstate+ndeath; i++)
1304: for (jk=-1; jk<=nlstate+ndeath; jk++)
1305: for(m=agemin; m <= agemax+3; m++)
1306: freq[i][jk][m]=0;
1307:
1308: for (i=1; i<=imx; i++) {
1309: bool=1;
1310: if (cptcovn>0) {
1311: for (z1=1; z1<=cptcoveff; z1++)
1312: if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])
1313: bool=0;
1314: }
1315: if (bool==1) {
1316: if (boolprev==1){
1317: for(m=fprev1; m<=lprev1; m++){
1318: if(agev[m][i]==0) agev[m][i]=agemax+1;
1319: if(agev[m][i]==1) agev[m][i]=agemax+2;
1320: freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
1321: freq[s[m][i]][s[m+1][i]][(int) agemax+3] += weight[i];
1322: }
1323: }
1324: else {
1325: for(m=firstpass; m<=lastpass; m++){
1326: k2=anint[m][i]+(mint[m][i]/12.);
1327: if ((k2>=dateprev1) && (k2<=dateprev2)) {
1328: if(agev[m][i]==0) agev[m][i]=agemax+1;
1329: if(agev[m][i]==1) agev[m][i]=agemax+2;
1330: freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
1331: freq[s[m][i]][s[m+1][i]][(int) agemax+3] += weight[i];
1332: }
1333: }
1334: }
1335: }
1336: }
1337: for(i=(int)agemin; i <= (int)agemax+3; i++){
1338: for(jk=1; jk <=nlstate ; jk++){
1339: for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
1340: pp[jk] += freq[jk][m][i];
1341: }
1342: for(jk=1; jk <=nlstate ; jk++){
1343: for(m=-1, pos=0; m <=0 ; m++)
1344: pos += freq[jk][m][i];
1345: }
1346:
1347: for(jk=1; jk <=nlstate ; jk++){
1348: for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
1349: pp[jk] += freq[jk][m][i];
1350: }
1351:
1352: for(jk=1,pos=0; jk <=nlstate ; jk++) pos += pp[jk];
1353:
1354: for(jk=1; jk <=nlstate ; jk++){
1355: if( i <= (int) agemax){
1356: if(pos>=1.e-5){
1357: probs[i][jk][j1]= pp[jk]/pos;
1358: }
1359: }
1360: }
1361:
1362: }
1363: }
1364: }
1365:
1366:
1367: free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);
1368: free_vector(pp,1,nlstate);
1369:
1370: } /* End of Freq */
1371: /************* Waves Concatenation ***************/
1372:
1373: void concatwav(int wav[], int **dh, int **mw, int **s, double *agedc, double **agev, int firstpass, int lastpass, int imx, int nlstate, int stepm)
1374: {
1375: /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
1376: Death is a valid wave (if date is known).
1377: mw[mi][i] is the mi (mi=1 to wav[i]) effective wave of individual i
1378: dh[m][i] of dh[mw[mi][i][i] is the delay between two effective waves m=mw[mi][i]
1379: and mw[mi+1][i]. dh depends on stepm.
1380: */
1381:
1382: int i, mi, m;
1383: /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
1384: double sum=0., jmean=0.;*/
1385:
1386: int j, k=0,jk, ju, jl;
1387: double sum=0.;
1388: jmin=1e+5;
1389: jmax=-1;
1390: jmean=0.;
1391: for(i=1; i<=imx; i++){
1392: mi=0;
1393: m=firstpass;
1394: while(s[m][i] <= nlstate){
1395: if(s[m][i]>=1)
1396: mw[++mi][i]=m;
1397: if(m >=lastpass)
1398: break;
1399: else
1400: m++;
1401: }/* end while */
1402: if (s[m][i] > nlstate){
1403: mi++; /* Death is another wave */
1404: /* if(mi==0) never been interviewed correctly before death */
1405: /* Only death is a correct wave */
1406: mw[mi][i]=m;
1407: }
1408:
1409: wav[i]=mi;
1410: if(mi==0)
1411: printf("Warning, no any valid information for:%d line=%d\n",num[i],i);
1412: }
1413:
1414: for(i=1; i<=imx; i++){
1415: for(mi=1; mi<wav[i];mi++){
1416: if (stepm <=0)
1417: dh[mi][i]=1;
1418: else{
1419: if (s[mw[mi+1][i]][i] > nlstate) {
1420: if (agedc[i] < 2*AGESUP) {
1421: j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);
1422: if(j==0) j=1; /* Survives at least one month after exam */
1423: k=k+1;
1424: if (j >= jmax) jmax=j;
1425: if (j <= jmin) jmin=j;
1426: sum=sum+j;
1427: /* if (j<10) printf("j=%d num=%d ",j,i); */
1428: }
1429: }
1430: else{
1431: j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
1432: k=k+1;
1433: if (j >= jmax) jmax=j;
1434: else if (j <= jmin)jmin=j;
1435: /* if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
1436: sum=sum+j;
1437: }
1438: jk= j/stepm;
1439: jl= j -jk*stepm;
1440: ju= j -(jk+1)*stepm;
1441: if(jl <= -ju)
1442: dh[mi][i]=jk;
1443: else
1444: dh[mi][i]=jk+1;
1445: if(dh[mi][i]==0)
1446: dh[mi][i]=1; /* At least one step */
1447: }
1448: }
1449: }
1450: jmean=sum/k;
1451: printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);
1452: }
1453: /*********** Tricode ****************************/
1454: void tricode(int *Tvar, int **nbcode, int imx)
1455: {
1456: int Ndum[20],ij=1, k, j, i;
1457: int cptcode=0;
1458: cptcoveff=0;
1459:
1460: for (k=0; k<19; k++) Ndum[k]=0;
1461: for (k=1; k<=7; k++) ncodemax[k]=0;
1462:
1463: for (j=1; j<=(cptcovn+2*cptcovprod); j++) {
1464: for (i=1; i<=imx; i++) {
1465: ij=(int)(covar[Tvar[j]][i]);
1466: Ndum[ij]++;
1467: /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
1468: if (ij > cptcode) cptcode=ij;
1469: }
1470:
1471: for (i=0; i<=cptcode; i++) {
1472: if(Ndum[i]!=0) ncodemax[j]++;
1473: }
1474: ij=1;
1475:
1476:
1477: for (i=1; i<=ncodemax[j]; i++) {
1478: for (k=0; k<=19; k++) {
1479: if (Ndum[k] != 0) {
1480: nbcode[Tvar[j]][ij]=k;
1481: ij++;
1482: }
1483: if (ij > ncodemax[j]) break;
1484: }
1485: }
1486: }
1487:
1488: for (k=0; k<19; k++) Ndum[k]=0;
1489:
1490: for (i=1; i<=ncovmodel-2; i++) {
1491: ij=Tvar[i];
1492: Ndum[ij]++;
1493: }
1494:
1495: ij=1;
1496: for (i=1; i<=10; i++) {
1497: if((Ndum[i]!=0) && (i<=ncov)){
1498: Tvaraff[ij]=i;
1499: ij++;
1500: }
1501: }
1502:
1503: cptcoveff=ij-1;
1504: }
1505:
1506: /*********** Health Expectancies ****************/
1507:
1508: void evsij(char fileres[], double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int ij)
1509: {
1510: /* Health expectancies */
1511: int i, j, nhstepm, hstepm, h;
1512: double age, agelim,hf;
1513: double ***p3mat;
1514:
1515: fprintf(ficreseij,"# Health expectancies\n");
1516: fprintf(ficreseij,"# Age");
1517: for(i=1; i<=nlstate;i++)
1518: for(j=1; j<=nlstate;j++)
1519: fprintf(ficreseij," %1d-%1d",i,j);
1520: fprintf(ficreseij,"\n");
1521:
1522: hstepm=1*YEARM; /* Every j years of age (in month) */
1523: hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */
1524:
1525: agelim=AGESUP;
1526: for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
1527: /* nhstepm age range expressed in number of stepm */
1528: nhstepm=(int) rint((agelim-age)*YEARM/stepm);
1529: /* Typically if 20 years = 20*12/6=40 stepm */
1530: if (stepm >= YEARM) hstepm=1;
1531: nhstepm = nhstepm/hstepm;/* Expressed in hstepm, typically 40/4=10 */
1532: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
1533: /* Computed by stepm unit matrices, product of hstepm matrices, stored
1534: in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
1535: hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);
1536:
1537:
1538: for(i=1; i<=nlstate;i++)
1539: for(j=1; j<=nlstate;j++)
1540: for (h=0, eij[i][j][(int)age]=0; h<=nhstepm; h++){
1541: eij[i][j][(int)age] +=p3mat[i][j][h];
1542: }
1543:
1544: hf=1;
1545: if (stepm >= YEARM) hf=stepm/YEARM;
1546: fprintf(ficreseij,"%.0f",age );
1547: for(i=1; i<=nlstate;i++)
1548: for(j=1; j<=nlstate;j++){
1549: fprintf(ficreseij," %.4f", hf*eij[i][j][(int)age]);
1550: }
1551: fprintf(ficreseij,"\n");
1552: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
1553: }
1554: }
1555:
1556: /************ Variance ******************/
1557: 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)
1558: {
1559: /* Variance of health expectancies */
1560: /* double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
1561: double **newm;
1562: double **dnewm,**doldm;
1563: int i, j, nhstepm, hstepm, h;
1564: int k, cptcode;
1565: double *xp;
1566: double **gp, **gm;
1567: double ***gradg, ***trgradg;
1568: double ***p3mat;
1569: double age,agelim;
1570: int theta;
1571:
1572: fprintf(ficresvij,"# Covariances of life expectancies\n");
1573: fprintf(ficresvij,"# Age");
1574: for(i=1; i<=nlstate;i++)
1575: for(j=1; j<=nlstate;j++)
1576: fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);
1577: fprintf(ficresvij,"\n");
1578:
1579: xp=vector(1,npar);
1580: dnewm=matrix(1,nlstate,1,npar);
1581: doldm=matrix(1,nlstate,1,nlstate);
1582:
1583: hstepm=1*YEARM; /* Every year of age */
1584: hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */
1585: agelim = AGESUP;
1586: for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
1587: nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
1588: if (stepm >= YEARM) hstepm=1;
1589: nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
1590: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
1591: gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
1592: gp=matrix(0,nhstepm,1,nlstate);
1593: gm=matrix(0,nhstepm,1,nlstate);
1594:
1595: for(theta=1; theta <=npar; theta++){
1596: for(i=1; i<=npar; i++){ /* Computes gradient */
1597: xp[i] = x[i] + (i==theta ?delti[theta]:0);
1598: }
1599: hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
1600: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
1601:
1602: if (popbased==1) {
1603: for(i=1; i<=nlstate;i++)
1604: prlim[i][i]=probs[(int)age][i][ij];
1605: }
1606:
1607: for(j=1; j<= nlstate; j++){
1608: for(h=0; h<=nhstepm; h++){
1609: for(i=1, gp[h][j]=0.;i<=nlstate;i++)
1610: gp[h][j] += prlim[i][i]*p3mat[i][j][h];
1611: }
1612: }
1613:
1614: for(i=1; i<=npar; i++) /* Computes gradient */
1615: xp[i] = x[i] - (i==theta ?delti[theta]:0);
1616: hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
1617: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
1618:
1619: if (popbased==1) {
1620: for(i=1; i<=nlstate;i++)
1621: prlim[i][i]=probs[(int)age][i][ij];
1622: }
1623:
1624: for(j=1; j<= nlstate; j++){
1625: for(h=0; h<=nhstepm; h++){
1626: for(i=1, gm[h][j]=0.;i<=nlstate;i++)
1627: gm[h][j] += prlim[i][i]*p3mat[i][j][h];
1628: }
1629: }
1630:
1631: for(j=1; j<= nlstate; j++)
1632: for(h=0; h<=nhstepm; h++){
1633: gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
1634: }
1635: } /* End theta */
1636:
1637: trgradg =ma3x(0,nhstepm,1,nlstate,1,npar);
1638:
1639: for(h=0; h<=nhstepm; h++)
1640: for(j=1; j<=nlstate;j++)
1641: for(theta=1; theta <=npar; theta++)
1642: trgradg[h][j][theta]=gradg[h][theta][j];
1643:
1644: for(i=1;i<=nlstate;i++)
1645: for(j=1;j<=nlstate;j++)
1646: vareij[i][j][(int)age] =0.;
1647: for(h=0;h<=nhstepm;h++){
1648: for(k=0;k<=nhstepm;k++){
1649: matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
1650: matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
1651: for(i=1;i<=nlstate;i++)
1652: for(j=1;j<=nlstate;j++)
1653: vareij[i][j][(int)age] += doldm[i][j];
1654: }
1655: }
1656: h=1;
1657: if (stepm >= YEARM) h=stepm/YEARM;
1658: fprintf(ficresvij,"%.0f ",age );
1659: for(i=1; i<=nlstate;i++)
1660: for(j=1; j<=nlstate;j++){
1661: fprintf(ficresvij," %.4f", h*vareij[i][j][(int)age]);
1662: }
1663: fprintf(ficresvij,"\n");
1664: free_matrix(gp,0,nhstepm,1,nlstate);
1665: free_matrix(gm,0,nhstepm,1,nlstate);
1666: free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
1667: free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
1668: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
1669: } /* End age */
1670:
1671: free_vector(xp,1,npar);
1672: free_matrix(doldm,1,nlstate,1,npar);
1673: free_matrix(dnewm,1,nlstate,1,nlstate);
1674:
1675: }
1676:
1677: /************ Variance of prevlim ******************/
1678: 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)
1679: {
1680: /* Variance of prevalence limit */
1681: /* double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
1682: double **newm;
1683: double **dnewm,**doldm;
1684: int i, j, nhstepm, hstepm;
1685: int k, cptcode;
1686: double *xp;
1687: double *gp, *gm;
1688: double **gradg, **trgradg;
1689: double age,agelim;
1690: int theta;
1691:
1692: fprintf(ficresvpl,"# Standard deviation of prevalences limit\n");
1693: fprintf(ficresvpl,"# Age");
1694: for(i=1; i<=nlstate;i++)
1695: fprintf(ficresvpl," %1d-%1d",i,i);
1696: fprintf(ficresvpl,"\n");
1697:
1698: xp=vector(1,npar);
1699: dnewm=matrix(1,nlstate,1,npar);
1700: doldm=matrix(1,nlstate,1,nlstate);
1701:
1702: hstepm=1*YEARM; /* Every year of age */
1703: hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */
1704: agelim = AGESUP;
1705: for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
1706: nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
1707: if (stepm >= YEARM) hstepm=1;
1708: nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
1709: gradg=matrix(1,npar,1,nlstate);
1710: gp=vector(1,nlstate);
1711: gm=vector(1,nlstate);
1712:
1713: for(theta=1; theta <=npar; theta++){
1714: for(i=1; i<=npar; i++){ /* Computes gradient */
1715: xp[i] = x[i] + (i==theta ?delti[theta]:0);
1716: }
1717: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
1718: for(i=1;i<=nlstate;i++)
1719: gp[i] = prlim[i][i];
1720:
1721: for(i=1; i<=npar; i++) /* Computes gradient */
1722: xp[i] = x[i] - (i==theta ?delti[theta]:0);
1723: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
1724: for(i=1;i<=nlstate;i++)
1725: gm[i] = prlim[i][i];
1726:
1727: for(i=1;i<=nlstate;i++)
1728: gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
1729: } /* End theta */
1730:
1731: trgradg =matrix(1,nlstate,1,npar);
1732:
1733: for(j=1; j<=nlstate;j++)
1734: for(theta=1; theta <=npar; theta++)
1735: trgradg[j][theta]=gradg[theta][j];
1736:
1737: for(i=1;i<=nlstate;i++)
1738: varpl[i][(int)age] =0.;
1739: matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
1740: matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
1741: for(i=1;i<=nlstate;i++)
1742: varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
1743:
1744: fprintf(ficresvpl,"%.0f ",age );
1745: for(i=1; i<=nlstate;i++)
1746: fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
1747: fprintf(ficresvpl,"\n");
1748: free_vector(gp,1,nlstate);
1749: free_vector(gm,1,nlstate);
1750: free_matrix(gradg,1,npar,1,nlstate);
1751: free_matrix(trgradg,1,nlstate,1,npar);
1752: } /* End age */
1753:
1754: free_vector(xp,1,npar);
1755: free_matrix(doldm,1,nlstate,1,npar);
1756: free_matrix(dnewm,1,nlstate,1,nlstate);
1757:
1758: }
1759:
1760: /************ Variance of one-step probabilities ******************/
1761: void varprob(char fileres[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij)
1762: {
1763: int i, j;
1764: int k=0, cptcode;
1765: double **dnewm,**doldm;
1766: double *xp;
1767: double *gp, *gm;
1768: double **gradg, **trgradg;
1769: double age,agelim, cov[NCOVMAX];
1770: int theta;
1771: char fileresprob[FILENAMELENGTH];
1772:
1773: strcpy(fileresprob,"prob");
1774: strcat(fileresprob,fileres);
1775: if((ficresprob=fopen(fileresprob,"w"))==NULL) {
1776: printf("Problem with resultfile: %s\n", fileresprob);
1777: }
1778: printf("Computing variance of one-step probabilities: result on file '%s' \n",fileresprob);
1779:
1780:
1781: xp=vector(1,npar);
1782: dnewm=matrix(1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
1783: doldm=matrix(1,(nlstate+ndeath)*(nlstate+ndeath),1,(nlstate+ndeath)*(nlstate+ndeath));
1784:
1785: cov[1]=1;
1786: for (age=bage; age<=fage; age ++){
1787: cov[2]=age;
1788: gradg=matrix(1,npar,1,9);
1789: trgradg=matrix(1,9,1,npar);
1790: gp=vector(1,(nlstate+ndeath)*(nlstate+ndeath));
1791: gm=vector(1,(nlstate+ndeath)*(nlstate+ndeath));
1792:
1793: for(theta=1; theta <=npar; theta++){
1794: for(i=1; i<=npar; i++)
1795: xp[i] = x[i] + (i==theta ?delti[theta]:0);
1796:
1797: pmij(pmmij,cov,ncovmodel,xp,nlstate);
1798:
1799: k=0;
1800: for(i=1; i<= (nlstate+ndeath); i++){
1801: for(j=1; j<=(nlstate+ndeath);j++){
1802: k=k+1;
1803: gp[k]=pmmij[i][j];
1804: }
1805: }
1806:
1807: for(i=1; i<=npar; i++)
1808: xp[i] = x[i] - (i==theta ?delti[theta]:0);
1809:
1810:
1811: pmij(pmmij,cov,ncovmodel,xp,nlstate);
1812: k=0;
1813: for(i=1; i<=(nlstate+ndeath); i++){
1814: for(j=1; j<=(nlstate+ndeath);j++){
1815: k=k+1;
1816: gm[k]=pmmij[i][j];
1817: }
1818: }
1819:
1820: for(i=1; i<= (nlstate+ndeath)*(nlstate+ndeath); i++)
1821: gradg[theta][i]=(gp[i]-gm[i])/2./delti[theta];
1822: }
1823:
1824: for(j=1; j<=(nlstate+ndeath)*(nlstate+ndeath);j++)
1825: for(theta=1; theta <=npar; theta++)
1826: trgradg[j][theta]=gradg[theta][j];
1827:
1828: matprod2(dnewm,trgradg,1,9,1,npar,1,npar,matcov);
1829: matprod2(doldm,dnewm,1,9,1,npar,1,9,gradg);
1830:
1831: pmij(pmmij,cov,ncovmodel,x,nlstate);
1832:
1833: k=0;
1834: for(i=1; i<=(nlstate+ndeath); i++){
1835: for(j=1; j<=(nlstate+ndeath);j++){
1836: k=k+1;
1837: gm[k]=pmmij[i][j];
1838: }
1839: }
1840:
1841: /*printf("\n%d ",(int)age);
1842: for (i=1; i<=(nlstate+ndeath)*(nlstate+ndeath-1);i++){
1843:
1844:
1845: printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
1846: }*/
1847:
1848: fprintf(ficresprob,"\n%d ",(int)age);
1849:
1850: for (i=1; i<=(nlstate+ndeath)*(nlstate+ndeath-1);i++){
1851: if (i== 2) fprintf(ficresprob,"%.3e %.3e ",gm[i],doldm[i][i]);
1852: if (i== 4) fprintf(ficresprob,"%.3e %.3e ",gm[i],doldm[i][i]);
1853: }
1854:
1855: free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
1856: free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
1857: free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
1858: free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
1859: }
1860: free_vector(xp,1,npar);
1861: fclose(ficresprob);
1862: exit(0);
1863: }
1864:
1865: /***********************************************/
1866: /**************** Main Program *****************/
1867: /***********************************************/
1868:
1869: /*int main(int argc, char *argv[])*/
1870: int main()
1871: {
1872:
1873: int i,j, k, n=MAXN,iter,m,size,cptcode, cptcod;
1874: double agedeb, agefin,hf;
1875: double agemin=1.e20, agemax=-1.e20;
1876:
1877: double fret;
1878: double **xi,tmp,delta;
1879:
1880: double dum; /* Dummy variable */
1881: double ***p3mat;
1882: int *indx;
1883: char line[MAXLINE], linepar[MAXLINE];
1884: char title[MAXLINE];
1885: char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH], filerespl[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH];
1886: char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], fileresf[FILENAMELENGTH];
1887: char filerest[FILENAMELENGTH];
1888: char fileregp[FILENAMELENGTH];
1889: char popfile[FILENAMELENGTH];
1890: char path[80],pathc[80],pathcd[80],pathtot[80],model[20];
1891: int firstobs=1, lastobs=10;
1892: int sdeb, sfin; /* Status at beginning and end */
1893: int c, h , cpt,l;
1894: int ju,jl, mi;
1895: int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;
1896: int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,**adl,*tab;
1897: int mobilav=0, fprev, lprev ,fprevfore=1, lprevfore=1,nforecast,popforecast=0;
1898: int hstepm, nhstepm;
1899: int *popage,boolprev=0;/*boolprev=0 if date and zero if wave*/
1900:
1901: double bage, fage, age, agelim, agebase;
1902: double ftolpl=FTOL;
1903: double **prlim;
1904: double *severity;
1905: double ***param; /* Matrix of parameters */
1906: double *p;
1907: double **matcov; /* Matrix of covariance */
1908: double ***delti3; /* Scale */
1909: double *delti; /* Scale */
1910: double ***eij, ***vareij;
1911: double **varpl; /* Variances of prevalence limits by age */
1912: double *epj, vepp;
1913: double kk1, kk2;
1914: double *popeffectif,*popcount;
1915: double dateprev1, dateprev2;
1916:
1917: char version[80]="Imach version 64b, May 2001, INED-EUROREVES ";
1918: char *alph[]={"a","a","b","c","d","e"}, str[4];
1919:
1920:
1921: char z[1]="c", occ;
1922: #include <sys/time.h>
1923: #include <time.h>
1924: char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];
1925: char strfprev[10], strlprev[10];
1926: char strfprevfore[10], strlprevfore[10];
1927: /* long total_usecs;
1928: struct timeval start_time, end_time;
1929:
1930: gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */
1931:
1932:
1933: printf("\nIMACH, Version 0.7");
1934: printf("\nEnter the parameter file name: ");
1935:
1936: #ifdef windows
1937: scanf("%s",pathtot);
1938: getcwd(pathcd, size);
1939: /*cygwin_split_path(pathtot,path,optionfile);
1940: printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/
1941: /* cutv(path,optionfile,pathtot,'\\');*/
1942:
1943: split(pathtot, path,optionfile);
1944: chdir(path);
1945: replace(pathc,path);
1946: #endif
1947: #ifdef unix
1948: scanf("%s",optionfile);
1949: #endif
1950:
1951: /*-------- arguments in the command line --------*/
1952:
1953: strcpy(fileres,"r");
1954: strcat(fileres, optionfile);
1955:
1956: /*---------arguments file --------*/
1957:
1958: if((ficpar=fopen(optionfile,"r"))==NULL) {
1959: printf("Problem with optionfile %s\n",optionfile);
1960: goto end;
1961: }
1962:
1963: strcpy(filereso,"o");
1964: strcat(filereso,fileres);
1965: if((ficparo=fopen(filereso,"w"))==NULL) {
1966: printf("Problem with Output resultfile: %s\n", filereso);goto end;
1967: }
1968:
1969: /* Reads comments: lines beginning with '#' */
1970: while((c=getc(ficpar))=='#' && c!= EOF){
1971: ungetc(c,ficpar);
1972: fgets(line, MAXLINE, ficpar);
1973: puts(line);
1974: fputs(line,ficparo);
1975: }
1976: ungetc(c,ficpar);
1977:
1978: 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);
1979: 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);
1980: 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);
1981: while((c=getc(ficpar))=='#' && c!= EOF){
1982: ungetc(c,ficpar);
1983: fgets(line, MAXLINE, ficpar);
1984: puts(line);
1985: fputs(line,ficparo);
1986: }
1987: ungetc(c,ficpar);
1988:
1989: fscanf(ficpar,"fprevalence=%s lprevalence=%s pop_based=%d\n",strfprev,strlprev,&popbased);
1990: fprintf(ficparo,"fprevalence=%s lprevalence=%s pop_based=%d\n",strfprev,strlprev,popbased);
1991:
1992: /* printf("%s %s",strfprev,strlprev);
1993: exit(0);*/
1994: while((c=getc(ficpar))=='#' && c!= EOF){
1995: ungetc(c,ficpar);
1996: fgets(line, MAXLINE, ficpar);
1997: puts(line);
1998: fputs(line,ficparo);
1999: }
2000: ungetc(c,ficpar);
2001:
2002: fscanf(ficpar,"fprevalence=%s lprevalence=%s nforecast=%d mob_average=%d\n",strfprevfore,strlprevfore,&nforecast,&mobilav);
2003: fprintf(ficparo,"fprevalence=%s lprevalence=%s nforecast=%d mob_average=%d\n",strfprevfore,strlprevfore,nforecast,mobilav);
2004:
2005:
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: fscanf(ficpar,"popforecast=%d popfile=%s\n",&popforecast,popfile);
2015:
2016: covar=matrix(0,NCOVMAX,1,n);
2017: cptcovn=0;
2018: if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;
2019:
2020: ncovmodel=2+cptcovn;
2021: nvar=ncovmodel-1; /* Suppressing age as a basic covariate */
2022:
2023: /* Read guess parameters */
2024: /* Reads comments: lines beginning with '#' */
2025: while((c=getc(ficpar))=='#' && c!= EOF){
2026: ungetc(c,ficpar);
2027: fgets(line, MAXLINE, ficpar);
2028: puts(line);
2029: fputs(line,ficparo);
2030: }
2031: ungetc(c,ficpar);
2032:
2033: param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
2034: for(i=1; i <=nlstate; i++)
2035: for(j=1; j <=nlstate+ndeath-1; j++){
2036: fscanf(ficpar,"%1d%1d",&i1,&j1);
2037: fprintf(ficparo,"%1d%1d",i1,j1);
2038: printf("%1d%1d",i,j);
2039: for(k=1; k<=ncovmodel;k++){
2040: fscanf(ficpar," %lf",¶m[i][j][k]);
2041: printf(" %lf",param[i][j][k]);
2042: fprintf(ficparo," %lf",param[i][j][k]);
2043: }
2044: fscanf(ficpar,"\n");
2045: printf("\n");
2046: fprintf(ficparo,"\n");
2047: }
2048:
2049: npar= (nlstate+ndeath-1)*nlstate*ncovmodel;
2050:
2051: p=param[1][1];
2052:
2053: /* Reads comments: lines beginning with '#' */
2054: while((c=getc(ficpar))=='#' && c!= EOF){
2055: ungetc(c,ficpar);
2056: fgets(line, MAXLINE, ficpar);
2057: puts(line);
2058: fputs(line,ficparo);
2059: }
2060: ungetc(c,ficpar);
2061:
2062: delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
2063: delti=vector(1,npar); /* Scale of each paramater (output from hesscov) */
2064: for(i=1; i <=nlstate; i++){
2065: for(j=1; j <=nlstate+ndeath-1; j++){
2066: fscanf(ficpar,"%1d%1d",&i1,&j1);
2067: printf("%1d%1d",i,j);
2068: fprintf(ficparo,"%1d%1d",i1,j1);
2069: for(k=1; k<=ncovmodel;k++){
2070: fscanf(ficpar,"%le",&delti3[i][j][k]);
2071: printf(" %le",delti3[i][j][k]);
2072: fprintf(ficparo," %le",delti3[i][j][k]);
2073: }
2074: fscanf(ficpar,"\n");
2075: printf("\n");
2076: fprintf(ficparo,"\n");
2077: }
2078: }
2079: delti=delti3[1][1];
2080:
2081: /* Reads comments: lines beginning with '#' */
2082: while((c=getc(ficpar))=='#' && c!= EOF){
2083: ungetc(c,ficpar);
2084: fgets(line, MAXLINE, ficpar);
2085: puts(line);
2086: fputs(line,ficparo);
2087: }
2088: ungetc(c,ficpar);
2089:
2090: matcov=matrix(1,npar,1,npar);
2091: for(i=1; i <=npar; i++){
2092: fscanf(ficpar,"%s",&str);
2093: printf("%s",str);
2094: fprintf(ficparo,"%s",str);
2095: for(j=1; j <=i; j++){
2096: fscanf(ficpar," %le",&matcov[i][j]);
2097: printf(" %.5le",matcov[i][j]);
2098: fprintf(ficparo," %.5le",matcov[i][j]);
2099: }
2100: fscanf(ficpar,"\n");
2101: printf("\n");
2102: fprintf(ficparo,"\n");
2103: }
2104: for(i=1; i <=npar; i++)
2105: for(j=i+1;j<=npar;j++)
2106: matcov[i][j]=matcov[j][i];
2107:
2108: printf("\n");
2109:
2110:
2111: /*-------- data file ----------*/
2112: if((ficres =fopen(fileres,"w"))==NULL) {
2113: printf("Problem with resultfile: %s\n", fileres);goto end;
2114: }
2115: fprintf(ficres,"#%s\n",version);
2116:
2117: if((fic=fopen(datafile,"r"))==NULL) {
2118: printf("Problem with datafile: %s\n", datafile);goto end;
2119: }
2120:
2121: n= lastobs;
2122: severity = vector(1,maxwav);
2123: outcome=imatrix(1,maxwav+1,1,n);
2124: num=ivector(1,n);
2125: moisnais=vector(1,n);
2126: annais=vector(1,n);
2127: moisdc=vector(1,n);
2128: andc=vector(1,n);
2129: agedc=vector(1,n);
2130: cod=ivector(1,n);
2131: weight=vector(1,n);
2132: for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */
2133: mint=matrix(1,maxwav,1,n);
2134: anint=matrix(1,maxwav,1,n);
2135: s=imatrix(1,maxwav+1,1,n);
2136: adl=imatrix(1,maxwav+1,1,n);
2137: tab=ivector(1,NCOVMAX);
2138: ncodemax=ivector(1,8);
2139:
2140: i=1;
2141: while (fgets(line, MAXLINE, fic) != NULL) {
2142: if ((i >= firstobs) && (i <=lastobs)) {
2143:
2144: for (j=maxwav;j>=1;j--){
2145: cutv(stra, strb,line,' '); s[j][i]=atoi(strb);
2146: strcpy(line,stra);
2147: cutv(stra, strb,line,'/'); anint[j][i]=(double)(atoi(strb)); strcpy(line,stra);
2148: cutv(stra, strb,line,' '); mint[j][i]=(double)(atoi(strb)); strcpy(line,stra);
2149: }
2150:
2151: cutv(stra, strb,line,'/'); andc[i]=(double)(atoi(strb)); strcpy(line,stra);
2152: cutv(stra, strb,line,' '); moisdc[i]=(double)(atoi(strb)); strcpy(line,stra);
2153:
2154: cutv(stra, strb,line,'/'); annais[i]=(double)(atoi(strb)); strcpy(line,stra);
2155: cutv(stra, strb,line,' '); moisnais[i]=(double)(atoi(strb)); strcpy(line,stra);
2156:
2157: cutv(stra, strb,line,' '); weight[i]=(double)(atoi(strb)); strcpy(line,stra);
2158: for (j=ncov;j>=1;j--){
2159: cutv(stra, strb,line,' '); covar[j][i]=(double)(atoi(strb)); strcpy(line,stra);
2160: }
2161: num[i]=atol(stra);
2162:
2163: /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){
2164: 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;}*/
2165:
2166: i=i+1;
2167: }
2168: }
2169: /* printf("ii=%d", ij);
2170: scanf("%d",i);*/
2171: imx=i-1; /* Number of individuals */
2172:
2173: /* for (i=1; i<=imx; i++){
2174: if ((s[1][i]==3) && (s[2][i]==2)) s[2][i]=3;
2175: if ((s[2][i]==3) && (s[3][i]==2)) s[3][i]=3;
2176: if ((s[3][i]==3) && (s[4][i]==2)) s[4][i]=3;
2177: }
2178: 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]));*/
2179:
2180: /* Calculation of the number of parameter from char model*/
2181: Tvar=ivector(1,15);
2182: Tprod=ivector(1,15);
2183: Tvaraff=ivector(1,15);
2184: Tvard=imatrix(1,15,1,2);
2185: Tage=ivector(1,15);
2186:
2187: if (strlen(model) >1){
2188: j=0, j1=0, k1=1, k2=1;
2189: j=nbocc(model,'+');
2190: j1=nbocc(model,'*');
2191: cptcovn=j+1;
2192: cptcovprod=j1;
2193:
2194:
2195: strcpy(modelsav,model);
2196: if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){
2197: printf("Error. Non available option model=%s ",model);
2198: goto end;
2199: }
2200:
2201: for(i=(j+1); i>=1;i--){
2202: cutv(stra,strb,modelsav,'+');
2203: if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav);
2204: /* printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/
2205: /*scanf("%d",i);*/
2206: if (strchr(strb,'*')) {
2207: cutv(strd,strc,strb,'*');
2208: if (strcmp(strc,"age")==0) {
2209: cptcovprod--;
2210: cutv(strb,stre,strd,'V');
2211: Tvar[i]=atoi(stre);
2212: cptcovage++;
2213: Tage[cptcovage]=i;
2214: /*printf("stre=%s ", stre);*/
2215: }
2216: else if (strcmp(strd,"age")==0) {
2217: cptcovprod--;
2218: cutv(strb,stre,strc,'V');
2219: Tvar[i]=atoi(stre);
2220: cptcovage++;
2221: Tage[cptcovage]=i;
2222: }
2223: else {
2224: cutv(strb,stre,strc,'V');
2225: Tvar[i]=ncov+k1;
2226: cutv(strb,strc,strd,'V');
2227: Tprod[k1]=i;
2228: Tvard[k1][1]=atoi(strc);
2229: Tvard[k1][2]=atoi(stre);
2230: Tvar[cptcovn+k2]=Tvard[k1][1];
2231: Tvar[cptcovn+k2+1]=Tvard[k1][2];
2232: for (k=1; k<=lastobs;k++)
2233: covar[ncov+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];
2234: k1++;
2235: k2=k2+2;
2236: }
2237: }
2238: else {
2239: /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/
2240: /* scanf("%d",i);*/
2241: cutv(strd,strc,strb,'V');
2242: Tvar[i]=atoi(strc);
2243: }
2244: strcpy(modelsav,stra);
2245: /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);
2246: scanf("%d",i);*/
2247: }
2248: }
2249:
2250: /*printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);
2251: printf("cptcovprod=%d ", cptcovprod);
2252: scanf("%d ",i);*/
2253: fclose(fic);
2254:
2255: /* if(mle==1){*/
2256: if (weightopt != 1) { /* Maximisation without weights*/
2257: for(i=1;i<=n;i++) weight[i]=1.0;
2258: }
2259: /*-calculation of age at interview from date of interview and age at death -*/
2260: agev=matrix(1,maxwav,1,imx);
2261:
2262: for (i=1; i<=imx; i++)
2263: for(m=2; (m<= maxwav); m++)
2264: if ((mint[m][i]== 99) && (s[m][i] <= nlstate)){
2265: anint[m][i]=9999;
2266: s[m][i]=-1;
2267: }
2268:
2269: for (i=1; i<=imx; i++) {
2270: agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);
2271: for(m=1; (m<= maxwav); m++){
2272: if(s[m][i] >0){
2273: if (s[m][i] == nlstate+1) {
2274: if(agedc[i]>0)
2275: if(moisdc[i]!=99 && andc[i]!=9999)
2276: agev[m][i]=agedc[i];
2277: else {
2278: if (andc[i]!=9999){
2279: printf("Warning negative age at death: %d line:%d\n",num[i],i);
2280: agev[m][i]=-1;
2281: }
2282: }
2283: }
2284: else if(s[m][i] !=9){ /* Should no more exist */
2285: agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);
2286: if(mint[m][i]==99 || anint[m][i]==9999)
2287: agev[m][i]=1;
2288: else if(agev[m][i] <agemin){
2289: agemin=agev[m][i];
2290: /*printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], agemin);*/
2291: }
2292: else if(agev[m][i] >agemax){
2293: agemax=agev[m][i];
2294: /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/
2295: }
2296: /*agev[m][i]=anint[m][i]-annais[i];*/
2297: /* agev[m][i] = age[i]+2*m;*/
2298: }
2299: else { /* =9 */
2300: agev[m][i]=1;
2301: s[m][i]=-1;
2302: }
2303: }
2304: else /*= 0 Unknown */
2305: agev[m][i]=1;
2306: }
2307:
2308: }
2309: for (i=1; i<=imx; i++) {
2310: for(m=1; (m<= maxwav); m++){
2311: if (s[m][i] > (nlstate+ndeath)) {
2312: printf("Error: Wrong value in nlstate or ndeath\n");
2313: goto end;
2314: }
2315: }
2316: }
2317:
2318: printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);
2319:
2320: free_vector(severity,1,maxwav);
2321: free_imatrix(outcome,1,maxwav+1,1,n);
2322: free_vector(moisnais,1,n);
2323: free_vector(annais,1,n);
2324: /* free_matrix(mint,1,maxwav,1,n);
2325: free_matrix(anint,1,maxwav,1,n);*/
2326: free_vector(moisdc,1,n);
2327: free_vector(andc,1,n);
2328:
2329:
2330: wav=ivector(1,imx);
2331: dh=imatrix(1,lastpass-firstpass+1,1,imx);
2332: mw=imatrix(1,lastpass-firstpass+1,1,imx);
2333:
2334: /* Concatenates waves */
2335: concatwav(wav, dh, mw, s, agedc, agev, firstpass, lastpass, imx, nlstate, stepm);
2336:
2337:
2338: Tcode=ivector(1,100);
2339: nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);
2340: ncodemax[1]=1;
2341: if (cptcovn > 0) tricode(Tvar,nbcode,imx);
2342:
2343: codtab=imatrix(1,100,1,10);
2344: h=0;
2345: m=pow(2,cptcoveff);
2346:
2347: for(k=1;k<=cptcoveff; k++){
2348: for(i=1; i <=(m/pow(2,k));i++){
2349: for(j=1; j <= ncodemax[k]; j++){
2350: for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){
2351: h++;
2352: if (h>m) h=1;codtab[h][k]=j;
2353: }
2354: }
2355: }
2356: }
2357:
2358: /* Calculates basic frequencies. Computes observed prevalence at single age
2359: and prints on file fileres'p'. */
2360:
2361: if ((nbocc(strfprev,'/')==1) && (nbocc(strlprev,'/')==1)){
2362: boolprev=0;
2363: cutv(stra,strb,strfprev,'/');
2364: dateprev1=(double)(atoi(strb)+atoi(stra)/12.);
2365: cutv(stra,strb,strlprev,'/');
2366: dateprev2=(double)(atoi(strb)+atoi(stra)/12.);
2367: }
2368:
2369: else if ((nbocc(strfprev,'/')==0) &&(nbocc(strlprev,'/')==0)){
2370: boolprev=1;
2371: fprev=atoi(strfprev); lprev=atoi(strlprev);
2372: }
2373: else {
2374: printf("Error in statement lprevalence or fprevalence\n");
2375: goto end;
2376: }
2377:
2378: freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax, fprev, lprev,mint,anint,boolprev,dateprev1,dateprev2);
2379:
2380: pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
2381: oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
2382: newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
2383: savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
2384: oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */
2385:
2386: /* For Powell, parameters are in a vector p[] starting at p[1]
2387: so we point p on param[1][1] so that p[1] maps on param[1][1][1] */
2388: p=param[1][1]; /* *(*(*(param +1)+1)+0) */
2389:
2390: if(mle==1){
2391: mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);
2392: }
2393:
2394: /*--------- results files --------------*/
2395: fprintf(ficres,"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);
2396: fprintf(ficres,"fprevalence=%s lprevalence=%s pop_based=%d\n",strfprev,strlprev,popbased);
2397: fprintf(ficres,"fprevalence=%s lprevalence=%s nforecast=%d mob_average=%d\n",strfprevfore,strlprevfore,nforecast,mobilav);
2398:
2399: jk=1;
2400: fprintf(ficres,"# Parameters\n");
2401: printf("# Parameters\n");
2402: for(i=1,jk=1; i <=nlstate; i++){
2403: for(k=1; k <=(nlstate+ndeath); k++){
2404: if (k != i)
2405: {
2406: printf("%d%d ",i,k);
2407: fprintf(ficres,"%1d%1d ",i,k);
2408: for(j=1; j <=ncovmodel; j++){
2409: printf("%f ",p[jk]);
2410: fprintf(ficres,"%f ",p[jk]);
2411: jk++;
2412: }
2413: printf("\n");
2414: fprintf(ficres,"\n");
2415: }
2416: }
2417: }
2418: if(mle==1){
2419: /* Computing hessian and covariance matrix */
2420: ftolhess=ftol; /* Usually correct */
2421: hesscov(matcov, p, npar, delti, ftolhess, func);
2422: }
2423: fprintf(ficres,"# Scales\n");
2424: printf("# Scales\n");
2425: for(i=1,jk=1; i <=nlstate; i++){
2426: for(j=1; j <=nlstate+ndeath; j++){
2427: if (j!=i) {
2428: fprintf(ficres,"%1d%1d",i,j);
2429: printf("%1d%1d",i,j);
2430: for(k=1; k<=ncovmodel;k++){
2431: printf(" %.5e",delti[jk]);
2432: fprintf(ficres," %.5e",delti[jk]);
2433: jk++;
2434: }
2435: printf("\n");
2436: fprintf(ficres,"\n");
2437: }
2438: }
2439: }
2440:
2441: k=1;
2442: fprintf(ficres,"# Covariance\n");
2443: printf("# Covariance\n");
2444: for(i=1;i<=npar;i++){
2445: /* if (k>nlstate) k=1;
2446: i1=(i-1)/(ncovmodel*nlstate)+1;
2447: fprintf(ficres,"%s%d%d",alph[k],i1,tab[i]);
2448: printf("%s%d%d",alph[k],i1,tab[i]);*/
2449: fprintf(ficres,"%3d",i);
2450: printf("%3d",i);
2451: for(j=1; j<=i;j++){
2452: fprintf(ficres," %.5e",matcov[i][j]);
2453: printf(" %.5e",matcov[i][j]);
2454: }
2455: fprintf(ficres,"\n");
2456: printf("\n");
2457: k++;
2458: }
2459:
2460: while((c=getc(ficpar))=='#' && c!= EOF){
2461: ungetc(c,ficpar);
2462: fgets(line, MAXLINE, ficpar);
2463: puts(line);
2464: fputs(line,ficparo);
2465: }
2466: ungetc(c,ficpar);
2467:
2468: fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf\n",&agemin,&agemax, &bage, &fage);
2469:
2470: if (fage <= 2) {
2471: bage = agemin;
2472: fage = agemax;
2473: }
2474:
2475: fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");
2476: fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemax,bage,fage);
2477:
2478:
2479: /*------------ gnuplot -------------*/
2480: chdir(pathcd);
2481: if((ficgp=fopen("graph.plt","w"))==NULL) {
2482: printf("Problem with file graph.gp");goto end;
2483: }
2484: #ifdef windows
2485: fprintf(ficgp,"cd \"%s\" \n",pathc);
2486: #endif
2487: m=pow(2,cptcoveff);
2488:
2489: /* 1eme*/
2490: for (cpt=1; cpt<= nlstate ; cpt ++) {
2491: for (k1=1; k1<= m ; k1 ++) {
2492:
2493: #ifdef windows
2494: 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);
2495: #endif
2496: #ifdef unix
2497: fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nplot [%.f:%.f] \"vpl%s\" u 1:2 \"\%%lf",agemin,fage,fileres);
2498: #endif
2499:
2500: for (i=1; i<= nlstate ; i ++) {
2501: if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
2502: else fprintf(ficgp," \%%*lf (\%%*lf)");
2503: }
2504: fprintf(ficgp,"\" t\"Stationary prevalence\" w l 0,\"vpl%s\" every :::%d::%d u 1:($2+2*$3) \"\%%lf",fileres,k1-1,k1-1);
2505: for (i=1; i<= nlstate ; i ++) {
2506: if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
2507: else fprintf(ficgp," \%%*lf (\%%*lf)");
2508: }
2509: fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"vpl%s\" every :::%d::%d u 1:($2-2*$3) \"\%%lf",fileres,k1-1,k1-1);
2510: for (i=1; i<= nlstate ; i ++) {
2511: if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
2512: else fprintf(ficgp," \%%*lf (\%%*lf)");
2513: }
2514: fprintf(ficgp,"\" t\"\" w l 1,\"p%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",fileres,k1-1,k1-1,2+4*(cpt-1));
2515: #ifdef unix
2516: fprintf(ficgp,"\nset ter gif small size 400,300");
2517: #endif
2518: fprintf(ficgp,"\nset out \"v%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);
2519: }
2520: }
2521: /*2 eme*/
2522:
2523: for (k1=1; k1<= m ; k1 ++) {
2524: fprintf(ficgp,"set ylabel \"Years\" \nset ter gif small size 400,300\nplot [%.f:%.f] ",agemin,fage);
2525:
2526: for (i=1; i<= nlstate+1 ; i ++) {
2527: k=2*i;
2528: fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:2 \"\%%lf",fileres,k1-1,k1-1);
2529: for (j=1; j<= nlstate+1 ; j ++) {
2530: if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
2531: else fprintf(ficgp," \%%*lf (\%%*lf)");
2532: }
2533: if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");
2534: else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);
2535: fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",fileres,k1-1,k1-1);
2536: for (j=1; j<= nlstate+1 ; j ++) {
2537: if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
2538: else fprintf(ficgp," \%%*lf (\%%*lf)");
2539: }
2540: fprintf(ficgp,"\" t\"\" w l 0,");
2541: fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",fileres,k1-1,k1-1);
2542: for (j=1; j<= nlstate+1 ; j ++) {
2543: if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
2544: else fprintf(ficgp," \%%*lf (\%%*lf)");
2545: }
2546: if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");
2547: else fprintf(ficgp,"\" t\"\" w l 0,");
2548: }
2549: fprintf(ficgp,"\nset out \"e%s%d.gif\" \nreplot\n\n",strtok(optionfile, "."),k1);
2550: }
2551:
2552: /*3eme*/
2553:
2554: for (k1=1; k1<= m ; k1 ++) {
2555: for (cpt=1; cpt<= nlstate ; cpt ++) {
2556: k=2+nlstate*(cpt-1);
2557: 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);
2558: for (i=1; i< nlstate ; i ++) {
2559: 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);
2560: }
2561: fprintf(ficgp,"\nset out \"exp%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);
2562: }
2563: }
2564:
2565: /* CV preval stat */
2566: for (k1=1; k1<= m ; k1 ++) {
2567: for (cpt=1; cpt<nlstate ; cpt ++) {
2568: k=3;
2569: 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/($%d",agemin,agemax,fileres,k1,k+cpt+1,k+1);
2570: for (i=1; i< nlstate ; i ++)
2571: fprintf(ficgp,"+$%d",k+i+1);
2572: fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);
2573:
2574: l=3+(nlstate+ndeath)*cpt;
2575: fprintf(ficgp,",\"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",fileres,k1,l+cpt+1,l+1);
2576: for (i=1; i< nlstate ; i ++) {
2577: l=3+(nlstate+ndeath)*cpt;
2578: fprintf(ficgp,"+$%d",l+i+1);
2579: }
2580: fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);
2581: fprintf(ficgp,"set out \"p%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);
2582: }
2583: }
2584:
2585: /* proba elementaires */
2586: for(i=1,jk=1; i <=nlstate; i++){
2587: for(k=1; k <=(nlstate+ndeath); k++){
2588: if (k != i) {
2589: for(j=1; j <=ncovmodel; j++){
2590: /*fprintf(ficgp,"%s%1d%1d=%f ",alph[j],i,k,p[jk]);*/
2591: /*fprintf(ficgp,"%s",alph[1]);*/
2592: fprintf(ficgp,"p%d=%f ",jk,p[jk]);
2593: jk++;
2594: fprintf(ficgp,"\n");
2595: }
2596: }
2597: }
2598: }
2599:
2600: for(jk=1; jk <=m; jk++) {
2601: fprintf(ficgp,"\nset ter gif small size 400,300\nset log y\nplot [%.f:%.f] ",agemin,agemax);
2602: i=1;
2603: for(k2=1; k2<=nlstate; k2++) {
2604: k3=i;
2605: for(k=1; k<=(nlstate+ndeath); k++) {
2606: if (k != k2){
2607: fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
2608: ij=1;
2609: for(j=3; j <=ncovmodel; j++) {
2610: if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
2611: fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
2612: ij++;
2613: }
2614: else
2615: fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
2616: }
2617: fprintf(ficgp,")/(1");
2618:
2619: for(k1=1; k1 <=nlstate; k1++){
2620: fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);
2621: ij=1;
2622: for(j=3; j <=ncovmodel; j++){
2623: if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
2624: fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
2625: ij++;
2626: }
2627: else
2628: fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
2629: }
2630: fprintf(ficgp,")");
2631: }
2632: fprintf(ficgp,") t \"p%d%d\" ", k2,k);
2633: if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");
2634: i=i+ncovmodel;
2635: }
2636: }
2637: }
2638: fprintf(ficgp,"\nset out \"pe%s%d.gif\" \nreplot\n\n",strtok(optionfile, "."),jk);
2639: }
2640:
2641: fclose(ficgp);
2642:
2643: chdir(path);
2644:
2645: free_ivector(wav,1,imx);
2646: free_imatrix(dh,1,lastpass-firstpass+1,1,imx);
2647: free_imatrix(mw,1,lastpass-firstpass+1,1,imx);
2648: free_ivector(num,1,n);
2649: free_vector(agedc,1,n);
2650: /*free_matrix(covar,1,NCOVMAX,1,n);*/
2651: fclose(ficparo);
2652: fclose(ficres);
2653: /* }*/
2654:
2655: /*________fin mle=1_________*/
2656:
2657:
2658:
2659: /* No more information from the sample is required now */
2660: /* Reads comments: lines beginning with '#' */
2661: while((c=getc(ficpar))=='#' && c!= EOF){
2662: ungetc(c,ficpar);
2663: fgets(line, MAXLINE, ficpar);
2664: puts(line);
2665: fputs(line,ficparo);
2666: }
2667: ungetc(c,ficpar);
2668:
2669: fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf\n",&agemin,&agemax, &bage, &fage);
2670: printf("agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemax, bage, fage);
2671: fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemax,bage,fage);
2672: /*--------- index.htm --------*/
2673:
2674: strcpy(optionfilehtm,optionfile);
2675: strcat(optionfilehtm,".htm");
2676: if((fichtm=fopen(optionfilehtm,"w"))==NULL) {
2677: printf("Problem with %s \n",optionfilehtm);goto end;
2678: }
2679:
2680: fprintf(fichtm,"<body><ul> <font size=\"6\">Imach, Version 0.7 </font> <hr size=\"2\" color=\"#EC5E5E\">
2681: Titre=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>
2682: Total number of observations=%d <br>
2683: Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>
2684: <hr size=\"2\" color=\"#EC5E5E\">
2685: <li>Outputs files<br><br>\n
2686: - Observed prevalence in each state: <a href=\"p%s\">p%s</a> <br>\n
2687: - Estimated parameters and the covariance matrix: <a href=\"%s\">%s</a> <br>
2688: - Stationary prevalence in each state: <a href=\"pl%s\">pl%s</a> <br>
2689: - Transition probabilities: <a href=\"pij%s\">pij%s</a><br>
2690: - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>
2691: - Life expectancies by age and initial health status: <a href=\"e%s\">e%s</a> <br>
2692: - Variances of life expectancies by age and initial health status: <a href=\"v%s\">v%s</a><br>
2693: - Health expectancies with their variances: <a href=\"t%s\">t%s</a> <br>
2694: - Standard deviation of stationary prevalences: <a href=\"vpl%s\">vpl%s</a> <br>
2695: - Prevalences and population forecasting: <a href=\"f%s\">f%s</a> <br>
2696: <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);
2697:
2698: fprintf(fichtm," <li>Graphs</li><p>");
2699:
2700: m=cptcoveff;
2701: if (cptcovn < 1) {m=1;ncodemax[1]=1;}
2702:
2703: j1=0;
2704: for(k1=1; k1<=m;k1++){
2705: for(i1=1; i1<=ncodemax[k1];i1++){
2706: j1++;
2707: if (cptcovn > 0) {
2708: fprintf(fichtm,"<hr size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
2709: for (cpt=1; cpt<=cptcoveff;cpt++)
2710: fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[j1][cpt]]);
2711: fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
2712: }
2713: fprintf(fichtm,"<br>- Probabilities: pe%s%d.gif<br>
2714: <img src=\"pe%s%d.gif\">",strtok(optionfile, "."),j1,strtok(optionfile, "."),j1);
2715: for(cpt=1; cpt<nlstate;cpt++){
2716: fprintf(fichtm,"<br>- Prevalence of disability : p%s%d%d.gif<br>
2717: <img src=\"p%s%d%d.gif\">",strtok(optionfile, "."),cpt,j1,strtok(optionfile, "."),cpt,j1);
2718: }
2719: for(cpt=1; cpt<=nlstate;cpt++) {
2720: fprintf(fichtm,"<br>- Observed and stationary prevalence (with confident
2721: interval) in state (%d): v%s%d%d.gif <br>
2722: <img src=\"v%s%d%d.gif\">",cpt,strtok(optionfile, "."),cpt,j1,strtok(optionfile, "."),cpt,j1);
2723: }
2724: for(cpt=1; cpt<=nlstate;cpt++) {
2725: fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): exp%s%d%d.gif <br>
2726: <img src=\"exp%s%d%d.gif\">",cpt,strtok(optionfile, "."),cpt,j1,strtok(optionfile, "."),cpt,j1);
2727: }
2728: fprintf(fichtm,"\n<br>- Total life expectancy by age and
2729: health expectancies in states (1) and (2): e%s%d.gif<br>
2730: <img src=\"e%s%d.gif\">",strtok(optionfile, "."),j1,strtok(optionfile, "."),j1);
2731: fprintf(fichtm,"\n</body>");
2732: }
2733: }
2734: fclose(fichtm);
2735:
2736: /*--------------- Prevalence limit --------------*/
2737:
2738: strcpy(filerespl,"pl");
2739: strcat(filerespl,fileres);
2740: if((ficrespl=fopen(filerespl,"w"))==NULL) {
2741: printf("Problem with Prev limit resultfile: %s\n", filerespl);goto end;
2742: }
2743: printf("Computing prevalence limit: result on file '%s' \n", filerespl);
2744: fprintf(ficrespl,"#Prevalence limit\n");
2745: fprintf(ficrespl,"#Age ");
2746: for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);
2747: fprintf(ficrespl,"\n");
2748:
2749: prlim=matrix(1,nlstate,1,nlstate);
2750: pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
2751: oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
2752: newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
2753: savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
2754: oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */
2755: k=0;
2756: agebase=agemin;
2757: agelim=agemax;
2758: ftolpl=1.e-10;
2759: i1=cptcoveff;
2760: if (cptcovn < 1){i1=1;}
2761:
2762: for(cptcov=1;cptcov<=i1;cptcov++){
2763: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
2764: k=k+1;
2765: /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/
2766: fprintf(ficrespl,"\n#******");
2767: for(j=1;j<=cptcoveff;j++)
2768: fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
2769: fprintf(ficrespl,"******\n");
2770:
2771: for (age=agebase; age<=agelim; age++){
2772: prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
2773: fprintf(ficrespl,"%.0f",age );
2774: for(i=1; i<=nlstate;i++)
2775: fprintf(ficrespl," %.5f", prlim[i][i]);
2776: fprintf(ficrespl,"\n");
2777: }
2778: }
2779: }
2780: fclose(ficrespl);
2781:
2782: /*------------- h Pij x at various ages ------------*/
2783:
2784: strcpy(filerespij,"pij"); strcat(filerespij,fileres);
2785: if((ficrespij=fopen(filerespij,"w"))==NULL) {
2786: printf("Problem with Pij resultfile: %s\n", filerespij);goto end;
2787: }
2788: printf("Computing pij: result on file '%s' \n", filerespij);
2789:
2790: stepsize=(int) (stepm+YEARM-1)/YEARM;
2791: /*if (stepm<=24) stepsize=2;*/
2792:
2793: agelim=AGESUP;
2794: hstepm=stepsize*YEARM; /* Every year of age */
2795: hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */
2796:
2797: k=0;
2798: for(cptcov=1;cptcov<=i1;cptcov++){
2799: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
2800: k=k+1;
2801: fprintf(ficrespij,"\n#****** ");
2802: for(j=1;j<=cptcoveff;j++)
2803: fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
2804: fprintf(ficrespij,"******\n");
2805:
2806: for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */
2807: nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
2808: nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
2809: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
2810: oldm=oldms;savm=savms;
2811: hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
2812: fprintf(ficrespij,"# Age");
2813: for(i=1; i<=nlstate;i++)
2814: for(j=1; j<=nlstate+ndeath;j++)
2815: fprintf(ficrespij," %1d-%1d",i,j);
2816: fprintf(ficrespij,"\n");
2817: for (h=0; h<=nhstepm; h++){
2818: fprintf(ficrespij,"%d %.0f %.0f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );
2819: for(i=1; i<=nlstate;i++)
2820: for(j=1; j<=nlstate+ndeath;j++)
2821: fprintf(ficrespij," %.5f", p3mat[i][j][h]);
2822: fprintf(ficrespij,"\n");
2823: }
2824: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
2825: fprintf(ficrespij,"\n");
2826: }
2827: }
2828: }
2829:
2830: /* varprob(fileres, matcov, p, delti, nlstate, (int) bage, (int) fage,k);*/
2831:
2832: fclose(ficrespij);
2833:
2834: /*---------- Forecasting ------------------*/
2835:
2836: strcpy(fileresf,"f");
2837: strcat(fileresf,fileres);
2838: if((ficresf=fopen(fileresf,"w"))==NULL) {
2839: printf("Problem with forecast resultfile: %s\n", fileresf);goto end;
2840: }
2841: printf("Computing forecasting: result on file '%s' \n", fileresf);
2842:
2843: if ((nbocc(strfprevfore,'/')==1) && (nbocc(strlprevfore,'/')==1)){
2844: boolprev=0;
2845: cutv(stra,strb,strfprevfore,'/');
2846: dateprev1=(double)(atoi(strb)+atoi(stra)/12.);
2847: cutv(stra,strb,strlprevfore,'/');
2848: dateprev2=(double)(atoi(strb)+atoi(stra)/12.);
2849: }
2850:
2851: else if ((nbocc(strfprevfore,'/')==0) &&(nbocc(strlprevfore,'/')==0)){
2852: boolprev=1;
2853: fprev=atoi(strfprevfore); lprev=atoi(strlprevfore);
2854: }
2855: else {
2856: printf("Error in statement lprevalence or fprevalence\n");
2857: goto end;
2858: }
2859:
2860: prevalence(agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax, fprevfore, lprevfore,mint,anint,boolprev,dateprev1,dateprev2);
2861:
2862: free_matrix(mint,1,maxwav,1,n);
2863: free_matrix(anint,1,maxwav,1,n);
2864: free_matrix(agev,1,maxwav,1,imx);
2865: /* Mobile average */
2866:
2867: if (cptcoveff==0) ncodemax[cptcoveff]=1;
2868:
2869: if (mobilav==1) {
2870: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
2871: for (agedeb=bage+3; agedeb<=fage-2; agedeb++)
2872: for (i=1; i<=nlstate;i++)
2873: for (cptcod=1;cptcod<=ncodemax[cptcov];cptcod++)
2874: mobaverage[(int)agedeb][i][cptcod]=0.;
2875:
2876: for (agedeb=bage+4; agedeb<=fage; agedeb++){
2877: for (i=1; i<=nlstate;i++){
2878: for (cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
2879: for (cpt=0;cpt<=4;cpt++){
2880: mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]+probs[(int)agedeb-cpt][i][cptcod];
2881: }
2882: mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]/5;
2883: }
2884: }
2885: }
2886: }
2887:
2888: stepsize=(int) (stepm+YEARM-1)/YEARM;
2889: if (stepm<=12) stepsize=1;
2890:
2891: agelim=AGESUP;
2892: hstepm=stepsize*YEARM; /* Every year of age */
2893: hstepm=hstepm/stepm; /* Typically 2 years, = 2 years/6 months = 4 */
2894:
2895: if (popforecast==1) {
2896: if((ficpop=fopen(popfile,"r"))==NULL) {
2897: printf("Problem with population file : %s\n",popfile);goto end;
2898: }
2899: popage=ivector(0,AGESUP);
2900: popeffectif=vector(0,AGESUP);
2901: popcount=vector(0,AGESUP);
2902:
2903: i=1;
2904: while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF)
2905: {
2906: i=i+1;
2907: }
2908: imx=i;
2909:
2910: for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];
2911: }
2912:
2913: for(cptcov=1;cptcov<=i1;cptcov++){
2914: for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
2915: k=k+1;
2916: fprintf(ficresf,"\n#****** ");
2917: for(j=1;j<=cptcoveff;j++) {
2918: fprintf(ficresf,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
2919: }
2920: fprintf(ficresf,"******\n");
2921: fprintf(ficresf,"# StartingAge FinalAge Horizon(in years)");
2922: for(j=1; j<=nlstate+ndeath;j++) fprintf(ficresf," P.%d",j);
2923: if (popforecast==1) fprintf(ficresf," [Population]");
2924:
2925: for (agedeb=fage; agedeb>=bage; agedeb--){
2926: fprintf(ficresf,"\n%.f %.f 0",agedeb, agedeb);
2927: if (mobilav==1) {
2928: for(j=1; j<=nlstate;j++)
2929: fprintf(ficresf," %.3f",mobaverage[(int)agedeb][j][cptcod]);
2930: }
2931: else {
2932: for(j=1; j<=nlstate;j++)
2933: fprintf(ficresf," %.3f",probs[(int)agedeb][j][cptcod]);
2934: }
2935:
2936: for(j=1; j<=ndeath;j++) fprintf(ficresf," 0.00000");
2937: if (popforecast==1) fprintf(ficresf," [%.f] ",popeffectif[(int)agedeb]);
2938: }
2939:
2940: for (cpt=1; cpt<=nforecast;cpt++) {
2941: fprintf(ficresf,"\n");
2942: for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */
2943: nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);
2944: nhstepm = nhstepm/hstepm;
2945: /*printf("agedeb=%.lf stepm=%d hstepm=%d nhstepm=%d \n",agedeb,stepm,hstepm,nhstepm);*/
2946:
2947: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
2948: oldm=oldms;savm=savms;
2949: hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
2950:
2951: for (h=0; h<=nhstepm; h++){
2952:
2953: if (h*hstepm/YEARM*stepm==cpt)
2954: fprintf(ficresf,"\n%.f %.f %.f",agedeb, agedeb+ h*hstepm/YEARM*stepm, h*hstepm/YEARM*stepm);
2955:
2956:
2957: for(j=1; j<=nlstate+ndeath;j++) {
2958: kk1=0.;kk2=0;
2959: for(i=1; i<=nlstate;i++) {
2960: if (mobilav==1)
2961: kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb][i][cptcod];
2962: else kk1=kk1+p3mat[i][j][h]*probs[(int)agedeb][i][cptcod];
2963: if (popforecast==1) kk2=kk1*popeffectif[(int)agedeb];
2964: }
2965: if (h*hstepm/YEARM*stepm==cpt) {
2966: fprintf(ficresf," %.3f", kk1);
2967: if (popforecast==1) fprintf(ficresf," [%.f]", kk2);
2968: }
2969: }
2970: }
2971: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
2972:
2973: }
2974: }
2975: }
2976: }
2977: if (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
2978: if (popforecast==1) {
2979: free_ivector(popage,0,AGESUP);
2980: free_vector(popeffectif,0,AGESUP);
2981: free_vector(popcount,0,AGESUP);
2982: }
2983: free_imatrix(s,1,maxwav+1,1,n);
2984: free_vector(weight,1,n);
2985: fclose(ficresf);
2986: /*---------- Health expectancies and variances ------------*/
2987:
2988: strcpy(filerest,"t");
2989: strcat(filerest,fileres);
2990: if((ficrest=fopen(filerest,"w"))==NULL) {
2991: printf("Problem with total LE resultfile: %s\n", filerest);goto end;
2992: }
2993: printf("Computing Total LEs with variances: file '%s' \n", filerest);
2994:
2995:
2996: strcpy(filerese,"e");
2997: strcat(filerese,fileres);
2998: if((ficreseij=fopen(filerese,"w"))==NULL) {
2999: printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
3000: }
3001: printf("Computing Health Expectancies: result on file '%s' \n", filerese);
3002:
3003: strcpy(fileresv,"v");
3004: strcat(fileresv,fileres);
3005: if((ficresvij=fopen(fileresv,"w"))==NULL) {
3006: printf("Problem with variance resultfile: %s\n", fileresv);exit(0);
3007: }
3008: printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
3009:
3010: k=0;
3011: for(cptcov=1;cptcov<=i1;cptcov++){
3012: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
3013: k=k+1;
3014: fprintf(ficrest,"\n#****** ");
3015: for(j=1;j<=cptcoveff;j++)
3016: fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
3017: fprintf(ficrest,"******\n");
3018:
3019: fprintf(ficreseij,"\n#****** ");
3020: for(j=1;j<=cptcoveff;j++)
3021: fprintf(ficreseij,"V%d=%d ",j,nbcode[j][codtab[k][j]]);
3022: fprintf(ficreseij,"******\n");
3023:
3024: fprintf(ficresvij,"\n#****** ");
3025: for(j=1;j<=cptcoveff;j++)
3026: fprintf(ficresvij,"V%d=%d ",j,nbcode[j][codtab[k][j]]);
3027: fprintf(ficresvij,"******\n");
3028:
3029: eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
3030: oldm=oldms;savm=savms;
3031: evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k);
3032: vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
3033: oldm=oldms;savm=savms;
3034: varevsij(fileres, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);
3035:
3036: fprintf(ficrest,"#Total LEs with variances: e.. (std) ");
3037: for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);
3038: fprintf(ficrest,"\n");
3039:
3040: hf=1;
3041: if (stepm >= YEARM) hf=stepm/YEARM;
3042: epj=vector(1,nlstate+1);
3043: for(age=bage; age <=fage ;age++){
3044: prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
3045: if (popbased==1) {
3046: for(i=1; i<=nlstate;i++)
3047: prlim[i][i]=probs[(int)age][i][k];
3048: }
3049:
3050: fprintf(ficrest," %.0f",age);
3051: for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){
3052: for(i=1, epj[j]=0.;i <=nlstate;i++) {
3053: epj[j] += prlim[i][i]*hf*eij[i][j][(int)age];
3054: }
3055: epj[nlstate+1] +=epj[j];
3056: }
3057: for(i=1, vepp=0.;i <=nlstate;i++)
3058: for(j=1;j <=nlstate;j++)
3059: vepp += vareij[i][j][(int)age];
3060: fprintf(ficrest," %.2f (%.2f)", epj[nlstate+1],hf*sqrt(vepp));
3061: for(j=1;j <=nlstate;j++){
3062: fprintf(ficrest," %.2f (%.2f)", epj[j],hf*sqrt(vareij[j][j][(int)age]));
3063: }
3064: fprintf(ficrest,"\n");
3065: }
3066: }
3067: }
3068:
3069:
3070:
3071:
3072: fclose(ficreseij);
3073: fclose(ficresvij);
3074: fclose(ficrest);
3075: fclose(ficpar);
3076: free_vector(epj,1,nlstate+1);
3077: /* scanf("%d ",i); */
3078:
3079: /*------- Variance limit prevalence------*/
3080:
3081: strcpy(fileresvpl,"vpl");
3082: strcat(fileresvpl,fileres);
3083: if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {
3084: printf("Problem with variance prev lim resultfile: %s\n", fileresvpl);
3085: exit(0);
3086: }
3087: printf("Computing Variance-covariance of Prevalence limit: file '%s' \n", fileresvpl);
3088:
3089: k=0;
3090: for(cptcov=1;cptcov<=i1;cptcov++){
3091: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
3092: k=k+1;
3093: fprintf(ficresvpl,"\n#****** ");
3094: for(j=1;j<=cptcoveff;j++)
3095: fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
3096: fprintf(ficresvpl,"******\n");
3097:
3098: varpl=matrix(1,nlstate,(int) bage, (int) fage);
3099: oldm=oldms;savm=savms;
3100: varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);
3101: }
3102: }
3103:
3104: fclose(ficresvpl);
3105:
3106: /*---------- End : free ----------------*/
3107: free_matrix(varpl,1,nlstate,(int) bage, (int)fage);
3108:
3109: free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);
3110: free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
3111:
3112:
3113: free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);
3114: free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);
3115: free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);
3116: free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);
3117:
3118: free_matrix(matcov,1,npar,1,npar);
3119: free_vector(delti,1,npar);
3120:
3121: free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
3122:
3123: printf("End of Imach\n");
3124: /* gettimeofday(&end_time, (struct timezone*)0);*/ /* after time */
3125:
3126: /* 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);*/
3127: /*printf("Total time was %d uSec.\n", total_usecs);*/
3128: /*------ End -----------*/
3129:
3130:
3131: end:
3132: #ifdef windows
3133: chdir(pathcd);
3134: #endif
3135:
3136: system("..\\gp37mgw\\wgnuplot graph.plt");
3137:
3138: #ifdef windows
3139: while (z[0] != 'q') {
3140: chdir(pathcd);
3141: printf("\nType e to edit output files, c to start again, and q for exiting: ");
3142: scanf("%s",z);
3143: if (z[0] == 'c') system("./imach");
3144: else if (z[0] == 'e') {
3145: chdir(path);
3146: system(optionfilehtm);
3147: }
3148: else if (z[0] == 'q') exit(0);
3149: }
3150: #endif
3151: }
3152:
3153:
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