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 erreur; /* Error number */
71: int nvar;
72: int cptcovn, cptcovage=0, cptcoveff=0,cptcov;
73: int npar=NPARMAX;
74: int nlstate=2; /* Number of live states */
75: int ndeath=1; /* Number of dead states */
76: int ncovmodel, ncov; /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
77: int popbased=0;
78:
79: int *wav; /* Number of waves for this individuual 0 is possible */
80: int maxwav; /* Maxim number of waves */
81: int jmin, jmax; /* min, max spacing between 2 waves */
82: int mle, weightopt;
83: int **mw; /* mw[mi][i] is number of the mi wave for this individual */
84: int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
85: double jmean; /* Mean space between 2 waves */
86: double **oldm, **newm, **savm; /* Working pointers to matrices */
87: double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
88: FILE *fic,*ficpar, *ficparo,*ficres, *ficrespl, *ficrespij, *ficrest,*ficresf;
89: FILE *ficgp, *fichtm,*ficresprob,*ficpop;
90: FILE *ficreseij;
91: char filerese[FILENAMELENGTH];
92: FILE *ficresvij;
93: char fileresv[FILENAMELENGTH];
94: FILE *ficresvpl;
95: char fileresvpl[FILENAMELENGTH];
96:
97: #define NR_END 1
98: #define FREE_ARG char*
99: #define FTOL 1.0e-10
100:
101: #define NRANSI
102: #define ITMAX 200
103:
104: #define TOL 2.0e-4
105:
106: #define CGOLD 0.3819660
107: #define ZEPS 1.0e-10
108: #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);
109:
110: #define GOLD 1.618034
111: #define GLIMIT 100.0
112: #define TINY 1.0e-20
113:
114: static double maxarg1,maxarg2;
115: #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
116: #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
117:
118: #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
119: #define rint(a) floor(a+0.5)
120:
121: static double sqrarg;
122: #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
123: #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}
124:
125: int imx;
126: int stepm;
127: /* Stepm, step in month: minimum step interpolation*/
128:
129: int m,nb;
130: int *num, firstpass=0, lastpass=4,*cod, *ncodemax, *Tage;
131: double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
132: double **pmmij, ***probs, ***mobaverage;
133: double dateintmean=0;
134:
135: double *weight;
136: int **s; /* Status */
137: double *agedc, **covar, idx;
138: int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;
139:
140: double ftol=FTOL; /* Tolerance for computing Max Likelihood */
141: double ftolhess; /* Tolerance for computing hessian */
142:
143: /**************** split *************************/
144: static int split( char *path, char *dirc, char *name )
145: {
146: char *s; /* pointer */
147: int l1, l2; /* length counters */
148:
149: l1 = strlen( path ); /* length of path */
150: if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
151: s = strrchr( path, '\\' ); /* find last / */
152: if ( s == NULL ) { /* no directory, so use current */
153: #if defined(__bsd__) /* get current working directory */
154: extern char *getwd( );
155:
156: if ( getwd( dirc ) == NULL ) {
157: #else
158: extern char *getcwd( );
159:
160: if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {
161: #endif
162: return( GLOCK_ERROR_GETCWD );
163: }
164: strcpy( name, path ); /* we've got it */
165: } else { /* strip direcotry from path */
166: s++; /* after this, the filename */
167: l2 = strlen( s ); /* length of filename */
168: if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
169: strcpy( name, s ); /* save file name */
170: strncpy( dirc, path, l1 - l2 ); /* now the directory */
171: dirc[l1-l2] = 0; /* add zero */
172: }
173: l1 = strlen( dirc ); /* length of directory */
174: if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; }
175: return( 0 ); /* we're done */
176: }
177:
178:
179: /******************************************/
180:
181: void replace(char *s, char*t)
182: {
183: int i;
184: int lg=20;
185: i=0;
186: lg=strlen(t);
187: for(i=0; i<= lg; i++) {
188: (s[i] = t[i]);
189: if (t[i]== '\\') s[i]='/';
190: }
191: }
192:
193: int nbocc(char *s, char occ)
194: {
195: int i,j=0;
196: int lg=20;
197: i=0;
198: lg=strlen(s);
199: for(i=0; i<= lg; i++) {
200: if (s[i] == occ ) j++;
201: }
202: return j;
203: }
204:
205: void cutv(char *u,char *v, char*t, char occ)
206: {
207: int i,lg,j,p=0;
208: i=0;
209: for(j=0; j<=strlen(t)-1; j++) {
210: if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;
211: }
212:
213: lg=strlen(t);
214: for(j=0; j<p; j++) {
215: (u[j] = t[j]);
216: }
217: u[p]='\0';
218:
219: for(j=0; j<= lg; j++) {
220: if (j>=(p+1))(v[j-p-1] = t[j]);
221: }
222: }
223:
224: /********************** nrerror ********************/
225:
226: void nrerror(char error_text[])
227: {
228: fprintf(stderr,"ERREUR ...\n");
229: fprintf(stderr,"%s\n",error_text);
230: exit(1);
231: }
232: /*********************** vector *******************/
233: double *vector(int nl, int nh)
234: {
235: double *v;
236: v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
237: if (!v) nrerror("allocation failure in vector");
238: return v-nl+NR_END;
239: }
240:
241: /************************ free vector ******************/
242: void free_vector(double*v, int nl, int nh)
243: {
244: free((FREE_ARG)(v+nl-NR_END));
245: }
246:
247: /************************ivector *******************************/
248: int *ivector(long nl,long nh)
249: {
250: int *v;
251: v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
252: if (!v) nrerror("allocation failure in ivector");
253: return v-nl+NR_END;
254: }
255:
256: /******************free ivector **************************/
257: void free_ivector(int *v, long nl, long nh)
258: {
259: free((FREE_ARG)(v+nl-NR_END));
260: }
261:
262: /******************* imatrix *******************************/
263: int **imatrix(long nrl, long nrh, long ncl, long nch)
264: /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */
265: {
266: long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;
267: int **m;
268:
269: /* allocate pointers to rows */
270: m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));
271: if (!m) nrerror("allocation failure 1 in matrix()");
272: m += NR_END;
273: m -= nrl;
274:
275:
276: /* allocate rows and set pointers to them */
277: m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));
278: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
279: m[nrl] += NR_END;
280: m[nrl] -= ncl;
281:
282: for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;
283:
284: /* return pointer to array of pointers to rows */
285: return m;
286: }
287:
288: /****************** free_imatrix *************************/
289: void free_imatrix(m,nrl,nrh,ncl,nch)
290: int **m;
291: long nch,ncl,nrh,nrl;
292: /* free an int matrix allocated by imatrix() */
293: {
294: free((FREE_ARG) (m[nrl]+ncl-NR_END));
295: free((FREE_ARG) (m+nrl-NR_END));
296: }
297:
298: /******************* matrix *******************************/
299: double **matrix(long nrl, long nrh, long ncl, long nch)
300: {
301: long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
302: double **m;
303:
304: m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
305: if (!m) nrerror("allocation failure 1 in matrix()");
306: m += NR_END;
307: m -= nrl;
308:
309: m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
310: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
311: m[nrl] += NR_END;
312: m[nrl] -= ncl;
313:
314: for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
315: return m;
316: }
317:
318: /*************************free matrix ************************/
319: void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
320: {
321: free((FREE_ARG)(m[nrl]+ncl-NR_END));
322: free((FREE_ARG)(m+nrl-NR_END));
323: }
324:
325: /******************* ma3x *******************************/
326: double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
327: {
328: long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
329: double ***m;
330:
331: m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
332: if (!m) nrerror("allocation failure 1 in matrix()");
333: m += NR_END;
334: m -= nrl;
335:
336: m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
337: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
338: m[nrl] += NR_END;
339: m[nrl] -= ncl;
340:
341: for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
342:
343: m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
344: if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
345: m[nrl][ncl] += NR_END;
346: m[nrl][ncl] -= nll;
347: for (j=ncl+1; j<=nch; j++)
348: m[nrl][j]=m[nrl][j-1]+nlay;
349:
350: for (i=nrl+1; i<=nrh; i++) {
351: m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
352: for (j=ncl+1; j<=nch; j++)
353: m[i][j]=m[i][j-1]+nlay;
354: }
355: return m;
356: }
357:
358: /*************************free ma3x ************************/
359: void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
360: {
361: free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
362: free((FREE_ARG)(m[nrl]+ncl-NR_END));
363: free((FREE_ARG)(m+nrl-NR_END));
364: }
365:
366: /***************** f1dim *************************/
367: extern int ncom;
368: extern double *pcom,*xicom;
369: extern double (*nrfunc)(double []);
370:
371: double f1dim(double x)
372: {
373: int j;
374: double f;
375: double *xt;
376:
377: xt=vector(1,ncom);
378: for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];
379: f=(*nrfunc)(xt);
380: free_vector(xt,1,ncom);
381: return f;
382: }
383:
384: /*****************brent *************************/
385: double brent(double ax, double bx, double cx, double (*f)(double), double tol, double *xmin)
386: {
387: int iter;
388: double a,b,d,etemp;
389: double fu,fv,fw,fx;
390: double ftemp;
391: double p,q,r,tol1,tol2,u,v,w,x,xm;
392: double e=0.0;
393:
394: a=(ax < cx ? ax : cx);
395: b=(ax > cx ? ax : cx);
396: x=w=v=bx;
397: fw=fv=fx=(*f)(x);
398: for (iter=1;iter<=ITMAX;iter++) {
399: xm=0.5*(a+b);
400: tol2=2.0*(tol1=tol*fabs(x)+ZEPS);
401: /* if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
402: printf(".");fflush(stdout);
403: #ifdef DEBUG
404: 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);
405: /* if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
406: #endif
407: if (fabs(x-xm) <= (tol2-0.5*(b-a))){
408: *xmin=x;
409: return fx;
410: }
411: ftemp=fu;
412: if (fabs(e) > tol1) {
413: r=(x-w)*(fx-fv);
414: q=(x-v)*(fx-fw);
415: p=(x-v)*q-(x-w)*r;
416: q=2.0*(q-r);
417: if (q > 0.0) p = -p;
418: q=fabs(q);
419: etemp=e;
420: e=d;
421: if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))
422: d=CGOLD*(e=(x >= xm ? a-x : b-x));
423: else {
424: d=p/q;
425: u=x+d;
426: if (u-a < tol2 || b-u < tol2)
427: d=SIGN(tol1,xm-x);
428: }
429: } else {
430: d=CGOLD*(e=(x >= xm ? a-x : b-x));
431: }
432: u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));
433: fu=(*f)(u);
434: if (fu <= fx) {
435: if (u >= x) a=x; else b=x;
436: SHFT(v,w,x,u)
437: SHFT(fv,fw,fx,fu)
438: } else {
439: if (u < x) a=u; else b=u;
440: if (fu <= fw || w == x) {
441: v=w;
442: w=u;
443: fv=fw;
444: fw=fu;
445: } else if (fu <= fv || v == x || v == w) {
446: v=u;
447: fv=fu;
448: }
449: }
450: }
451: nrerror("Too many iterations in brent");
452: *xmin=x;
453: return fx;
454: }
455:
456: /****************** mnbrak ***********************/
457:
458: void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,
459: double (*func)(double))
460: {
461: double ulim,u,r,q, dum;
462: double fu;
463:
464: *fa=(*func)(*ax);
465: *fb=(*func)(*bx);
466: if (*fb > *fa) {
467: SHFT(dum,*ax,*bx,dum)
468: SHFT(dum,*fb,*fa,dum)
469: }
470: *cx=(*bx)+GOLD*(*bx-*ax);
471: *fc=(*func)(*cx);
472: while (*fb > *fc) {
473: r=(*bx-*ax)*(*fb-*fc);
474: q=(*bx-*cx)*(*fb-*fa);
475: u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/
476: (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r));
477: ulim=(*bx)+GLIMIT*(*cx-*bx);
478: if ((*bx-u)*(u-*cx) > 0.0) {
479: fu=(*func)(u);
480: } else if ((*cx-u)*(u-ulim) > 0.0) {
481: fu=(*func)(u);
482: if (fu < *fc) {
483: SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))
484: SHFT(*fb,*fc,fu,(*func)(u))
485: }
486: } else if ((u-ulim)*(ulim-*cx) >= 0.0) {
487: u=ulim;
488: fu=(*func)(u);
489: } else {
490: u=(*cx)+GOLD*(*cx-*bx);
491: fu=(*func)(u);
492: }
493: SHFT(*ax,*bx,*cx,u)
494: SHFT(*fa,*fb,*fc,fu)
495: }
496: }
497:
498: /*************** linmin ************************/
499:
500: int ncom;
501: double *pcom,*xicom;
502: double (*nrfunc)(double []);
503:
504: void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))
505: {
506: double brent(double ax, double bx, double cx,
507: double (*f)(double), double tol, double *xmin);
508: double f1dim(double x);
509: void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,
510: double *fc, double (*func)(double));
511: int j;
512: double xx,xmin,bx,ax;
513: double fx,fb,fa;
514:
515: ncom=n;
516: pcom=vector(1,n);
517: xicom=vector(1,n);
518: nrfunc=func;
519: for (j=1;j<=n;j++) {
520: pcom[j]=p[j];
521: xicom[j]=xi[j];
522: }
523: ax=0.0;
524: xx=1.0;
525: mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim);
526: *fret=brent(ax,xx,bx,f1dim,TOL,&xmin);
527: #ifdef DEBUG
528: printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
529: #endif
530: for (j=1;j<=n;j++) {
531: xi[j] *= xmin;
532: p[j] += xi[j];
533: }
534: free_vector(xicom,1,n);
535: free_vector(pcom,1,n);
536: }
537:
538: /*************** powell ************************/
539: void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,
540: double (*func)(double []))
541: {
542: void linmin(double p[], double xi[], int n, double *fret,
543: double (*func)(double []));
544: int i,ibig,j;
545: double del,t,*pt,*ptt,*xit;
546: double fp,fptt;
547: double *xits;
548: pt=vector(1,n);
549: ptt=vector(1,n);
550: xit=vector(1,n);
551: xits=vector(1,n);
552: *fret=(*func)(p);
553: for (j=1;j<=n;j++) pt[j]=p[j];
554: for (*iter=1;;++(*iter)) {
555: fp=(*fret);
556: ibig=0;
557: del=0.0;
558: printf("\nPowell iter=%d -2*LL=%.12f",*iter,*fret);
559: for (i=1;i<=n;i++)
560: printf(" %d %.12f",i, p[i]);
561: printf("\n");
562: for (i=1;i<=n;i++) {
563: for (j=1;j<=n;j++) xit[j]=xi[j][i];
564: fptt=(*fret);
565: #ifdef DEBUG
566: printf("fret=%lf \n",*fret);
567: #endif
568: printf("%d",i);fflush(stdout);
569: linmin(p,xit,n,fret,func);
570: if (fabs(fptt-(*fret)) > del) {
571: del=fabs(fptt-(*fret));
572: ibig=i;
573: }
574: #ifdef DEBUG
575: printf("%d %.12e",i,(*fret));
576: for (j=1;j<=n;j++) {
577: xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
578: printf(" x(%d)=%.12e",j,xit[j]);
579: }
580: for(j=1;j<=n;j++)
581: printf(" p=%.12e",p[j]);
582: printf("\n");
583: #endif
584: }
585: if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {
586: #ifdef DEBUG
587: int k[2],l;
588: k[0]=1;
589: k[1]=-1;
590: printf("Max: %.12e",(*func)(p));
591: for (j=1;j<=n;j++)
592: printf(" %.12e",p[j]);
593: printf("\n");
594: for(l=0;l<=1;l++) {
595: for (j=1;j<=n;j++) {
596: ptt[j]=p[j]+(p[j]-pt[j])*k[l];
597: printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
598: }
599: printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
600: }
601: #endif
602:
603:
604: free_vector(xit,1,n);
605: free_vector(xits,1,n);
606: free_vector(ptt,1,n);
607: free_vector(pt,1,n);
608: return;
609: }
610: if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");
611: for (j=1;j<=n;j++) {
612: ptt[j]=2.0*p[j]-pt[j];
613: xit[j]=p[j]-pt[j];
614: pt[j]=p[j];
615: }
616: fptt=(*func)(ptt);
617: if (fptt < fp) {
618: t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt);
619: if (t < 0.0) {
620: linmin(p,xit,n,fret,func);
621: for (j=1;j<=n;j++) {
622: xi[j][ibig]=xi[j][n];
623: xi[j][n]=xit[j];
624: }
625: #ifdef DEBUG
626: printf("Direction changed last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
627: for(j=1;j<=n;j++)
628: printf(" %.12e",xit[j]);
629: printf("\n");
630: #endif
631: }
632: }
633: }
634: }
635:
636: /**** Prevalence limit ****************/
637:
638: double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)
639: {
640: /* Computes the prevalence limit in each live state at age x by left multiplying the unit
641: matrix by transitions matrix until convergence is reached */
642:
643: int i, ii,j,k;
644: double min, max, maxmin, maxmax,sumnew=0.;
645: double **matprod2();
646: double **out, cov[NCOVMAX], **pmij();
647: double **newm;
648: double agefin, delaymax=50 ; /* Max number of years to converge */
649:
650: for (ii=1;ii<=nlstate+ndeath;ii++)
651: for (j=1;j<=nlstate+ndeath;j++){
652: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
653: }
654:
655: cov[1]=1.;
656:
657: /* Even if hstepm = 1, at least one multiplication by the unit matrix */
658: for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
659: newm=savm;
660: /* Covariates have to be included here again */
661: cov[2]=agefin;
662:
663: for (k=1; k<=cptcovn;k++) {
664: cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
665: /*printf("ij=%d Tvar[k]=%d nbcode=%d cov=%lf\n",ij, Tvar[k],nbcode[Tvar[k]][codtab[ij][Tvar[k]]],cov[2+k]);*/
666: }
667: for (k=1; k<=cptcovage;k++)
668: cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
669: for (k=1; k<=cptcovprod;k++)
670: cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
671:
672: /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
673: /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
674:
675: out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);
676:
677: savm=oldm;
678: oldm=newm;
679: maxmax=0.;
680: for(j=1;j<=nlstate;j++){
681: min=1.;
682: max=0.;
683: for(i=1; i<=nlstate; i++) {
684: sumnew=0;
685: for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
686: prlim[i][j]= newm[i][j]/(1-sumnew);
687: max=FMAX(max,prlim[i][j]);
688: min=FMIN(min,prlim[i][j]);
689: }
690: maxmin=max-min;
691: maxmax=FMAX(maxmax,maxmin);
692: }
693: if(maxmax < ftolpl){
694: return prlim;
695: }
696: }
697: }
698:
699: /*************** transition probabilities ***************/
700:
701: double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
702: {
703: double s1, s2;
704: /*double t34;*/
705: int i,j,j1, nc, ii, jj;
706:
707: for(i=1; i<= nlstate; i++){
708: for(j=1; j<i;j++){
709: for (nc=1, s2=0.;nc <=ncovmodel; nc++){
710: /*s2 += param[i][j][nc]*cov[nc];*/
711: s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
712: /*printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2);*/
713: }
714: ps[i][j]=s2;
715: /*printf("s1=%.17e, s2=%.17e\n",s1,s2);*/
716: }
717: for(j=i+1; j<=nlstate+ndeath;j++){
718: for (nc=1, s2=0.;nc <=ncovmodel; nc++){
719: s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
720: /*printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2);*/
721: }
722: ps[i][j]=(s2);
723: }
724: }
725: /*ps[3][2]=1;*/
726:
727: for(i=1; i<= nlstate; i++){
728: s1=0;
729: for(j=1; j<i; j++)
730: s1+=exp(ps[i][j]);
731: for(j=i+1; j<=nlstate+ndeath; j++)
732: s1+=exp(ps[i][j]);
733: ps[i][i]=1./(s1+1.);
734: for(j=1; j<i; j++)
735: ps[i][j]= exp(ps[i][j])*ps[i][i];
736: for(j=i+1; j<=nlstate+ndeath; j++)
737: ps[i][j]= exp(ps[i][j])*ps[i][i];
738: /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
739: } /* end i */
740:
741: for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
742: for(jj=1; jj<= nlstate+ndeath; jj++){
743: ps[ii][jj]=0;
744: ps[ii][ii]=1;
745: }
746: }
747:
748:
749: /* for(ii=1; ii<= nlstate+ndeath; ii++){
750: for(jj=1; jj<= nlstate+ndeath; jj++){
751: printf("%lf ",ps[ii][jj]);
752: }
753: printf("\n ");
754: }
755: printf("\n ");printf("%lf ",cov[2]);*/
756: /*
757: for(i=1; i<= npar; i++) printf("%f ",x[i]);
758: goto end;*/
759: return ps;
760: }
761:
762: /**************** Product of 2 matrices ******************/
763:
764: double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)
765: {
766: /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
767: b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
768: /* in, b, out are matrice of pointers which should have been initialized
769: before: only the contents of out is modified. The function returns
770: a pointer to pointers identical to out */
771: long i, j, k;
772: for(i=nrl; i<= nrh; i++)
773: for(k=ncolol; k<=ncoloh; k++)
774: for(j=ncl,out[i][k]=0.; j<=nch; j++)
775: out[i][k] +=in[i][j]*b[j][k];
776:
777: return out;
778: }
779:
780:
781: /************* Higher Matrix Product ***************/
782:
783: double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
784: {
785: /* Computes the transition matrix starting at age 'age' over 'nhstepm*hstepm*stepm' month
786: duration (i.e. until
787: age (in years) age+nhstepm*stepm/12) by multiplying nhstepm*hstepm matrices.
788: Output is stored in matrix po[i][j][h] for h every 'hstepm' step
789: (typically every 2 years instead of every month which is too big).
790: Model is determined by parameters x and covariates have to be
791: included manually here.
792:
793: */
794:
795: int i, j, d, h, k;
796: double **out, cov[NCOVMAX];
797: double **newm;
798:
799: /* Hstepm could be zero and should return the unit matrix */
800: for (i=1;i<=nlstate+ndeath;i++)
801: for (j=1;j<=nlstate+ndeath;j++){
802: oldm[i][j]=(i==j ? 1.0 : 0.0);
803: po[i][j][0]=(i==j ? 1.0 : 0.0);
804: }
805: /* Even if hstepm = 1, at least one multiplication by the unit matrix */
806: for(h=1; h <=nhstepm; h++){
807: for(d=1; d <=hstepm; d++){
808: newm=savm;
809: /* Covariates have to be included here again */
810: cov[1]=1.;
811: cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
812: for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
813: for (k=1; k<=cptcovage;k++)
814: cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
815: for (k=1; k<=cptcovprod;k++)
816: cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
817:
818:
819: /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
820: /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
821: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,
822: pmij(pmmij,cov,ncovmodel,x,nlstate));
823: savm=oldm;
824: oldm=newm;
825: }
826: for(i=1; i<=nlstate+ndeath; i++)
827: for(j=1;j<=nlstate+ndeath;j++) {
828: po[i][j][h]=newm[i][j];
829: /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);
830: */
831: }
832: } /* end h */
833: return po;
834: }
835:
836:
837: /*************** log-likelihood *************/
838: double func( double *x)
839: {
840: int i, ii, j, k, mi, d, kk;
841: double l, ll[NLSTATEMAX], cov[NCOVMAX];
842: double **out;
843: double sw; /* Sum of weights */
844: double lli; /* Individual log likelihood */
845: long ipmx;
846: /*extern weight */
847: /* We are differentiating ll according to initial status */
848: /* for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
849: /*for(i=1;i<imx;i++)
850: printf(" %d\n",s[4][i]);
851: */
852: cov[1]=1.;
853:
854: for(k=1; k<=nlstate; k++) ll[k]=0.;
855: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
856: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
857: for(mi=1; mi<= wav[i]-1; mi++){
858: for (ii=1;ii<=nlstate+ndeath;ii++)
859: for (j=1;j<=nlstate+ndeath;j++) oldm[ii][j]=(ii==j ? 1.0 : 0.0);
860: for(d=0; d<dh[mi][i]; d++){
861: newm=savm;
862: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
863: for (kk=1; kk<=cptcovage;kk++) {
864: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
865: }
866:
867: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
868: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
869: savm=oldm;
870: oldm=newm;
871:
872:
873: } /* end mult */
874:
875: lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);
876: /* printf(" %f ",out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/
877: ipmx +=1;
878: sw += weight[i];
879: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
880: } /* end of wave */
881: } /* end of individual */
882:
883: for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
884: /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
885: l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
886: return -l;
887: }
888:
889:
890: /*********** Maximum Likelihood Estimation ***************/
891:
892: void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
893: {
894: int i,j, iter;
895: double **xi,*delti;
896: double fret;
897: xi=matrix(1,npar,1,npar);
898: for (i=1;i<=npar;i++)
899: for (j=1;j<=npar;j++)
900: xi[i][j]=(i==j ? 1.0 : 0.0);
901: printf("Powell\n");
902: powell(p,xi,npar,ftol,&iter,&fret,func);
903:
904: printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));
905: fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
906:
907: }
908:
909: /**** Computes Hessian and covariance matrix ***/
910: void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
911: {
912: double **a,**y,*x,pd;
913: double **hess;
914: int i, j,jk;
915: int *indx;
916:
917: double hessii(double p[], double delta, int theta, double delti[]);
918: double hessij(double p[], double delti[], int i, int j);
919: void lubksb(double **a, int npar, int *indx, double b[]) ;
920: void ludcmp(double **a, int npar, int *indx, double *d) ;
921:
922: hess=matrix(1,npar,1,npar);
923:
924: printf("\nCalculation of the hessian matrix. Wait...\n");
925: for (i=1;i<=npar;i++){
926: printf("%d",i);fflush(stdout);
927: hess[i][i]=hessii(p,ftolhess,i,delti);
928: /*printf(" %f ",p[i]);*/
929: /*printf(" %lf ",hess[i][i]);*/
930: }
931:
932: for (i=1;i<=npar;i++) {
933: for (j=1;j<=npar;j++) {
934: if (j>i) {
935: printf(".%d%d",i,j);fflush(stdout);
936: hess[i][j]=hessij(p,delti,i,j);
937: hess[j][i]=hess[i][j];
938: /*printf(" %lf ",hess[i][j]);*/
939: }
940: }
941: }
942: printf("\n");
943:
944: printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
945:
946: a=matrix(1,npar,1,npar);
947: y=matrix(1,npar,1,npar);
948: x=vector(1,npar);
949: indx=ivector(1,npar);
950: for (i=1;i<=npar;i++)
951: for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
952: ludcmp(a,npar,indx,&pd);
953:
954: for (j=1;j<=npar;j++) {
955: for (i=1;i<=npar;i++) x[i]=0;
956: x[j]=1;
957: lubksb(a,npar,indx,x);
958: for (i=1;i<=npar;i++){
959: matcov[i][j]=x[i];
960: }
961: }
962:
963: printf("\n#Hessian matrix#\n");
964: for (i=1;i<=npar;i++) {
965: for (j=1;j<=npar;j++) {
966: printf("%.3e ",hess[i][j]);
967: }
968: printf("\n");
969: }
970:
971: /* Recompute Inverse */
972: for (i=1;i<=npar;i++)
973: for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];
974: ludcmp(a,npar,indx,&pd);
975:
976: /* printf("\n#Hessian matrix recomputed#\n");
977:
978: for (j=1;j<=npar;j++) {
979: for (i=1;i<=npar;i++) x[i]=0;
980: x[j]=1;
981: lubksb(a,npar,indx,x);
982: for (i=1;i<=npar;i++){
983: y[i][j]=x[i];
984: printf("%.3e ",y[i][j]);
985: }
986: printf("\n");
987: }
988: */
989:
990: free_matrix(a,1,npar,1,npar);
991: free_matrix(y,1,npar,1,npar);
992: free_vector(x,1,npar);
993: free_ivector(indx,1,npar);
994: free_matrix(hess,1,npar,1,npar);
995:
996:
997: }
998:
999: /*************** hessian matrix ****************/
1000: double hessii( double x[], double delta, int theta, double delti[])
1001: {
1002: int i;
1003: int l=1, lmax=20;
1004: double k1,k2;
1005: double p2[NPARMAX+1];
1006: double res;
1007: double delt, delts, nkhi=10.,nkhif=1., khi=1.e-4;
1008: double fx;
1009: int k=0,kmax=10;
1010: double l1;
1011:
1012: fx=func(x);
1013: for (i=1;i<=npar;i++) p2[i]=x[i];
1014: for(l=0 ; l <=lmax; l++){
1015: l1=pow(10,l);
1016: delts=delt;
1017: for(k=1 ; k <kmax; k=k+1){
1018: delt = delta*(l1*k);
1019: p2[theta]=x[theta] +delt;
1020: k1=func(p2)-fx;
1021: p2[theta]=x[theta]-delt;
1022: k2=func(p2)-fx;
1023: /*res= (k1-2.0*fx+k2)/delt/delt; */
1024: res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */
1025:
1026: #ifdef DEBUG
1027: 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);
1028: #endif
1029: /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
1030: if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
1031: k=kmax;
1032: }
1033: else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
1034: k=kmax; l=lmax*10.;
1035: }
1036: else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){
1037: delts=delt;
1038: }
1039: }
1040: }
1041: delti[theta]=delts;
1042: return res;
1043:
1044: }
1045:
1046: double hessij( double x[], double delti[], int thetai,int thetaj)
1047: {
1048: int i;
1049: int l=1, l1, lmax=20;
1050: double k1,k2,k3,k4,res,fx;
1051: double p2[NPARMAX+1];
1052: int k;
1053:
1054: fx=func(x);
1055: for (k=1; k<=2; k++) {
1056: for (i=1;i<=npar;i++) p2[i]=x[i];
1057: p2[thetai]=x[thetai]+delti[thetai]/k;
1058: p2[thetaj]=x[thetaj]+delti[thetaj]/k;
1059: k1=func(p2)-fx;
1060:
1061: p2[thetai]=x[thetai]+delti[thetai]/k;
1062: p2[thetaj]=x[thetaj]-delti[thetaj]/k;
1063: k2=func(p2)-fx;
1064:
1065: p2[thetai]=x[thetai]-delti[thetai]/k;
1066: p2[thetaj]=x[thetaj]+delti[thetaj]/k;
1067: k3=func(p2)-fx;
1068:
1069: p2[thetai]=x[thetai]-delti[thetai]/k;
1070: p2[thetaj]=x[thetaj]-delti[thetaj]/k;
1071: k4=func(p2)-fx;
1072: res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */
1073: #ifdef DEBUG
1074: 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);
1075: #endif
1076: }
1077: return res;
1078: }
1079:
1080: /************** Inverse of matrix **************/
1081: void ludcmp(double **a, int n, int *indx, double *d)
1082: {
1083: int i,imax,j,k;
1084: double big,dum,sum,temp;
1085: double *vv;
1086:
1087: vv=vector(1,n);
1088: *d=1.0;
1089: for (i=1;i<=n;i++) {
1090: big=0.0;
1091: for (j=1;j<=n;j++)
1092: if ((temp=fabs(a[i][j])) > big) big=temp;
1093: if (big == 0.0) nrerror("Singular matrix in routine ludcmp");
1094: vv[i]=1.0/big;
1095: }
1096: for (j=1;j<=n;j++) {
1097: for (i=1;i<j;i++) {
1098: sum=a[i][j];
1099: for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];
1100: a[i][j]=sum;
1101: }
1102: big=0.0;
1103: for (i=j;i<=n;i++) {
1104: sum=a[i][j];
1105: for (k=1;k<j;k++)
1106: sum -= a[i][k]*a[k][j];
1107: a[i][j]=sum;
1108: if ( (dum=vv[i]*fabs(sum)) >= big) {
1109: big=dum;
1110: imax=i;
1111: }
1112: }
1113: if (j != imax) {
1114: for (k=1;k<=n;k++) {
1115: dum=a[imax][k];
1116: a[imax][k]=a[j][k];
1117: a[j][k]=dum;
1118: }
1119: *d = -(*d);
1120: vv[imax]=vv[j];
1121: }
1122: indx[j]=imax;
1123: if (a[j][j] == 0.0) a[j][j]=TINY;
1124: if (j != n) {
1125: dum=1.0/(a[j][j]);
1126: for (i=j+1;i<=n;i++) a[i][j] *= dum;
1127: }
1128: }
1129: free_vector(vv,1,n); /* Doesn't work */
1130: ;
1131: }
1132:
1133: void lubksb(double **a, int n, int *indx, double b[])
1134: {
1135: int i,ii=0,ip,j;
1136: double sum;
1137:
1138: for (i=1;i<=n;i++) {
1139: ip=indx[i];
1140: sum=b[ip];
1141: b[ip]=b[i];
1142: if (ii)
1143: for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];
1144: else if (sum) ii=i;
1145: b[i]=sum;
1146: }
1147: for (i=n;i>=1;i--) {
1148: sum=b[i];
1149: for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];
1150: b[i]=sum/a[i][i];
1151: }
1152: }
1153:
1154: /************ Frequencies ********************/
1155: void freqsummary(char fileres[], int agemin, int agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax,double **mint,double **anint, double dateprev1,double dateprev2)
1156: { /* Some frequencies */
1157:
1158: int i, m, jk, k1,i1, j1, bool, z1,z2,j;
1159: double ***freq; /* Frequencies */
1160: double *pp;
1161: double pos, k2, dateintsum=0,k2cpt=0;
1162: FILE *ficresp;
1163: char fileresp[FILENAMELENGTH];
1164:
1165: pp=vector(1,nlstate);
1166: probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
1167: strcpy(fileresp,"p");
1168: strcat(fileresp,fileres);
1169: if((ficresp=fopen(fileresp,"w"))==NULL) {
1170: printf("Problem with prevalence resultfile: %s\n", fileresp);
1171: exit(0);
1172: }
1173: freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);
1174: j1=0;
1175:
1176: j=cptcoveff;
1177: if (cptcovn<1) {j=1;ncodemax[1]=1;}
1178:
1179: for(k1=1; k1<=j;k1++){
1180: for(i1=1; i1<=ncodemax[k1];i1++){
1181: j1++;
1182: /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
1183: scanf("%d", i);*/
1184: for (i=-1; i<=nlstate+ndeath; i++)
1185: for (jk=-1; jk<=nlstate+ndeath; jk++)
1186: for(m=agemin; m <= agemax+3; m++)
1187: freq[i][jk][m]=0;
1188:
1189: dateintsum=0;
1190: k2cpt=0;
1191: for (i=1; i<=imx; i++) {
1192: bool=1;
1193: if (cptcovn>0) {
1194: for (z1=1; z1<=cptcoveff; z1++)
1195: if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])
1196: bool=0;
1197: }
1198: if (bool==1) {
1199: for(m=firstpass; m<=lastpass; m++){
1200: k2=anint[m][i]+(mint[m][i]/12.);
1201: if ((k2>=dateprev1) && (k2<=dateprev2)) {
1202: if(agev[m][i]==0) agev[m][i]=agemax+1;
1203: if(agev[m][i]==1) agev[m][i]=agemax+2;
1204: freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
1205: freq[s[m][i]][s[m+1][i]][(int) agemax+3] += weight[i];
1206: if ((agev[m][i]>1) && (agev[m][i]< (agemax+3))) {
1207: dateintsum=dateintsum+k2;
1208: k2cpt++;
1209: }
1210:
1211: }
1212: }
1213: }
1214: }
1215: if (cptcovn>0) {
1216: fprintf(ficresp, "\n#********** Variable ");
1217: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
1218: fprintf(ficresp, "**********\n#");
1219: }
1220: for(i=1; i<=nlstate;i++)
1221: fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
1222: fprintf(ficresp, "\n");
1223:
1224: for(i=(int)agemin; i <= (int)agemax+3; i++){
1225: if(i==(int)agemax+3)
1226: printf("Total");
1227: else
1228: printf("Age %d", i);
1229: for(jk=1; jk <=nlstate ; jk++){
1230: for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
1231: pp[jk] += freq[jk][m][i];
1232: }
1233: for(jk=1; jk <=nlstate ; jk++){
1234: for(m=-1, pos=0; m <=0 ; m++)
1235: pos += freq[jk][m][i];
1236: if(pp[jk]>=1.e-10)
1237: printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
1238: else
1239: printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
1240: }
1241:
1242: for(jk=1; jk <=nlstate ; jk++){
1243: for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
1244: pp[jk] += freq[jk][m][i];
1245: }
1246:
1247: for(jk=1,pos=0; jk <=nlstate ; jk++)
1248: pos += pp[jk];
1249: for(jk=1; jk <=nlstate ; jk++){
1250: if(pos>=1.e-5)
1251: printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
1252: else
1253: printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
1254: if( i <= (int) agemax){
1255: if(pos>=1.e-5){
1256: fprintf(ficresp," %d %.5f %.0f %.0f",i,pp[jk]/pos, pp[jk],pos);
1257: probs[i][jk][j1]= pp[jk]/pos;
1258: /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/
1259: }
1260: else
1261: fprintf(ficresp," %d NaNq %.0f %.0f",i,pp[jk],pos);
1262: }
1263: }
1264: for(jk=-1; jk <=nlstate+ndeath; jk++)
1265: for(m=-1; m <=nlstate+ndeath; m++)
1266: if(freq[jk][m][i] !=0 ) printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
1267: if(i <= (int) agemax)
1268: fprintf(ficresp,"\n");
1269: printf("\n");
1270: }
1271: }
1272: }
1273: dateintmean=dateintsum/k2cpt;
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:
1282: /************ Prevalence ********************/
1283: void prevalence(int agemin, int agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax,double **mint,double **anint, double dateprev1,double dateprev2, double calagedate)
1284: { /* Some frequencies */
1285:
1286: int i, m, jk, k1, i1, j1, bool, z1,z2,j;
1287: double ***freq; /* Frequencies */
1288: double *pp;
1289: double pos, k2;
1290:
1291: pp=vector(1,nlstate);
1292: probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
1293:
1294: freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);
1295: j1=0;
1296:
1297: j=cptcoveff;
1298: if (cptcovn<1) {j=1;ncodemax[1]=1;}
1299:
1300: for(k1=1; k1<=j;k1++){
1301: for(i1=1; i1<=ncodemax[k1];i1++){
1302: j1++;
1303:
1304: for (i=-1; i<=nlstate+ndeath; i++)
1305: for (jk=-1; jk<=nlstate+ndeath; jk++)
1306: for(m=agemin; m <= agemax+3; m++)
1307: freq[i][jk][m]=0;
1308:
1309: for (i=1; i<=imx; i++) {
1310: bool=1;
1311: if (cptcovn>0) {
1312: for (z1=1; z1<=cptcoveff; z1++)
1313: if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])
1314: bool=0;
1315: }
1316: if (bool==1) {
1317: for(m=firstpass; m<=lastpass; m++){
1318: k2=anint[m][i]+(mint[m][i]/12.);
1319: if ((k2>=dateprev1) && (k2<=dateprev2)) {
1320: if(agev[m][i]==0) agev[m][i]=agemax+1;
1321: if(agev[m][i]==1) agev[m][i]=agemax+2;
1322: freq[s[m][i]][s[m+1][i]][(int)(agev[m][i]+1-((int)calagedate %12)/12.)] += weight[i];
1323: freq[s[m][i]][s[m+1][i]][(int)(agemax+3+1)] += weight[i];
1324: }
1325: }
1326: }
1327: }
1328:
1329: for(i=(int)agemin; i <= (int)agemax+3; i++){
1330: for(jk=1; jk <=nlstate ; jk++){
1331: for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
1332: pp[jk] += freq[jk][m][i];
1333: }
1334: for(jk=1; jk <=nlstate ; jk++){
1335: for(m=-1, pos=0; m <=0 ; m++)
1336: pos += freq[jk][m][i];
1337: }
1338:
1339: for(jk=1; jk <=nlstate ; jk++){
1340: for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
1341: pp[jk] += freq[jk][m][i];
1342: }
1343:
1344: for(jk=1,pos=0; jk <=nlstate ; jk++) pos += pp[jk];
1345:
1346: for(jk=1; jk <=nlstate ; jk++){
1347: if( i <= (int) agemax){
1348: if(pos>=1.e-5){
1349: probs[i][jk][j1]= pp[jk]/pos;
1350: }
1351: }
1352: }
1353:
1354: }
1355: }
1356: }
1357:
1358:
1359: free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);
1360: free_vector(pp,1,nlstate);
1361:
1362: } /* End of Freq */
1363:
1364: /************* Waves Concatenation ***************/
1365:
1366: void concatwav(int wav[], int **dh, int **mw, int **s, double *agedc, double **agev, int firstpass, int lastpass, int imx, int nlstate, int stepm)
1367: {
1368: /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
1369: Death is a valid wave (if date is known).
1370: mw[mi][i] is the mi (mi=1 to wav[i]) effective wave of individual i
1371: dh[m][i] of dh[mw[mi][i][i] is the delay between two effective waves m=mw[mi][i]
1372: and mw[mi+1][i]. dh depends on stepm.
1373: */
1374:
1375: int i, mi, m;
1376: /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
1377: double sum=0., jmean=0.;*/
1378:
1379: int j, k=0,jk, ju, jl;
1380: double sum=0.;
1381: jmin=1e+5;
1382: jmax=-1;
1383: jmean=0.;
1384: for(i=1; i<=imx; i++){
1385: mi=0;
1386: m=firstpass;
1387: while(s[m][i] <= nlstate){
1388: if(s[m][i]>=1)
1389: mw[++mi][i]=m;
1390: if(m >=lastpass)
1391: break;
1392: else
1393: m++;
1394: }/* end while */
1395: if (s[m][i] > nlstate){
1396: mi++; /* Death is another wave */
1397: /* if(mi==0) never been interviewed correctly before death */
1398: /* Only death is a correct wave */
1399: mw[mi][i]=m;
1400: }
1401:
1402: wav[i]=mi;
1403: if(mi==0)
1404: printf("Warning, no any valid information for:%d line=%d\n",num[i],i);
1405: }
1406:
1407: for(i=1; i<=imx; i++){
1408: for(mi=1; mi<wav[i];mi++){
1409: if (stepm <=0)
1410: dh[mi][i]=1;
1411: else{
1412: if (s[mw[mi+1][i]][i] > nlstate) {
1413: if (agedc[i] < 2*AGESUP) {
1414: j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);
1415: if(j==0) j=1; /* Survives at least one month after exam */
1416: k=k+1;
1417: if (j >= jmax) jmax=j;
1418: if (j <= jmin) jmin=j;
1419: sum=sum+j;
1420: /* if (j<10) printf("j=%d num=%d ",j,i); */
1421: }
1422: }
1423: else{
1424: j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
1425: k=k+1;
1426: if (j >= jmax) jmax=j;
1427: else if (j <= jmin)jmin=j;
1428: /* if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
1429: sum=sum+j;
1430: }
1431: jk= j/stepm;
1432: jl= j -jk*stepm;
1433: ju= j -(jk+1)*stepm;
1434: if(jl <= -ju)
1435: dh[mi][i]=jk;
1436: else
1437: dh[mi][i]=jk+1;
1438: if(dh[mi][i]==0)
1439: dh[mi][i]=1; /* At least one step */
1440: }
1441: }
1442: }
1443: jmean=sum/k;
1444: printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);
1445: }
1446: /*********** Tricode ****************************/
1447: void tricode(int *Tvar, int **nbcode, int imx)
1448: {
1449: int Ndum[20],ij=1, k, j, i;
1450: int cptcode=0;
1451: cptcoveff=0;
1452:
1453: for (k=0; k<19; k++) Ndum[k]=0;
1454: for (k=1; k<=7; k++) ncodemax[k]=0;
1455:
1456: for (j=1; j<=(cptcovn+2*cptcovprod); j++) {
1457: for (i=1; i<=imx; i++) {
1458: ij=(int)(covar[Tvar[j]][i]);
1459: Ndum[ij]++;
1460: /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
1461: if (ij > cptcode) cptcode=ij;
1462: }
1463:
1464: for (i=0; i<=cptcode; i++) {
1465: if(Ndum[i]!=0) ncodemax[j]++;
1466: }
1467: ij=1;
1468:
1469:
1470: for (i=1; i<=ncodemax[j]; i++) {
1471: for (k=0; k<=19; k++) {
1472: if (Ndum[k] != 0) {
1473: nbcode[Tvar[j]][ij]=k;
1474: ij++;
1475: }
1476: if (ij > ncodemax[j]) break;
1477: }
1478: }
1479: }
1480:
1481: for (k=0; k<19; k++) Ndum[k]=0;
1482:
1483: for (i=1; i<=ncovmodel-2; i++) {
1484: ij=Tvar[i];
1485: Ndum[ij]++;
1486: }
1487:
1488: ij=1;
1489: for (i=1; i<=10; i++) {
1490: if((Ndum[i]!=0) && (i<=ncov)){
1491: Tvaraff[ij]=i;
1492: ij++;
1493: }
1494: }
1495:
1496: cptcoveff=ij-1;
1497: }
1498:
1499: /*********** Health Expectancies ****************/
1500:
1501: void evsij(char fileres[], double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int ij)
1502: {
1503: /* Health expectancies */
1504: int i, j, nhstepm, hstepm, h;
1505: double age, agelim,hf;
1506: double ***p3mat;
1507:
1508: fprintf(ficreseij,"# Health expectancies\n");
1509: fprintf(ficreseij,"# Age");
1510: for(i=1; i<=nlstate;i++)
1511: for(j=1; j<=nlstate;j++)
1512: fprintf(ficreseij," %1d-%1d",i,j);
1513: fprintf(ficreseij,"\n");
1514:
1515: hstepm=1*YEARM; /* Every j years of age (in month) */
1516: hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */
1517:
1518: agelim=AGESUP;
1519: for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
1520: /* nhstepm age range expressed in number of stepm */
1521: nhstepm=(int) rint((agelim-age)*YEARM/stepm);
1522: /* Typically if 20 years = 20*12/6=40 stepm */
1523: if (stepm >= YEARM) hstepm=1;
1524: nhstepm = nhstepm/hstepm;/* Expressed in hstepm, typically 40/4=10 */
1525: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
1526: /* Computed by stepm unit matrices, product of hstepm matrices, stored
1527: in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
1528: hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);
1529:
1530:
1531: for(i=1; i<=nlstate;i++)
1532: for(j=1; j<=nlstate;j++)
1533: for (h=0, eij[i][j][(int)age]=0; h<=nhstepm; h++){
1534: eij[i][j][(int)age] +=p3mat[i][j][h];
1535: }
1536:
1537: hf=1;
1538: if (stepm >= YEARM) hf=stepm/YEARM;
1539: fprintf(ficreseij,"%.0f",age );
1540: for(i=1; i<=nlstate;i++)
1541: for(j=1; j<=nlstate;j++){
1542: fprintf(ficreseij," %.4f", hf*eij[i][j][(int)age]);
1543: }
1544: fprintf(ficreseij,"\n");
1545: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
1546: }
1547: }
1548:
1549: /************ Variance ******************/
1550: 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)
1551: {
1552: /* Variance of health expectancies */
1553: /* double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
1554: double **newm;
1555: double **dnewm,**doldm;
1556: int i, j, nhstepm, hstepm, h;
1557: int k, cptcode;
1558: double *xp;
1559: double **gp, **gm;
1560: double ***gradg, ***trgradg;
1561: double ***p3mat;
1562: double age,agelim;
1563: int theta;
1564:
1565: fprintf(ficresvij,"# Covariances of life expectancies\n");
1566: fprintf(ficresvij,"# Age");
1567: for(i=1; i<=nlstate;i++)
1568: for(j=1; j<=nlstate;j++)
1569: fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);
1570: fprintf(ficresvij,"\n");
1571:
1572: xp=vector(1,npar);
1573: dnewm=matrix(1,nlstate,1,npar);
1574: doldm=matrix(1,nlstate,1,nlstate);
1575:
1576: hstepm=1*YEARM; /* Every year of age */
1577: hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */
1578: agelim = AGESUP;
1579: for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
1580: nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
1581: if (stepm >= YEARM) hstepm=1;
1582: nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
1583: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
1584: gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
1585: gp=matrix(0,nhstepm,1,nlstate);
1586: gm=matrix(0,nhstepm,1,nlstate);
1587:
1588: for(theta=1; theta <=npar; theta++){
1589: for(i=1; i<=npar; i++){ /* Computes gradient */
1590: xp[i] = x[i] + (i==theta ?delti[theta]:0);
1591: }
1592: hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
1593: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
1594:
1595: if (popbased==1) {
1596: for(i=1; i<=nlstate;i++)
1597: prlim[i][i]=probs[(int)age][i][ij];
1598: }
1599:
1600: for(j=1; j<= nlstate; j++){
1601: for(h=0; h<=nhstepm; h++){
1602: for(i=1, gp[h][j]=0.;i<=nlstate;i++)
1603: gp[h][j] += prlim[i][i]*p3mat[i][j][h];
1604: }
1605: }
1606:
1607: for(i=1; i<=npar; i++) /* Computes gradient */
1608: xp[i] = x[i] - (i==theta ?delti[theta]:0);
1609: hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
1610: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
1611:
1612: if (popbased==1) {
1613: for(i=1; i<=nlstate;i++)
1614: prlim[i][i]=probs[(int)age][i][ij];
1615: }
1616:
1617: for(j=1; j<= nlstate; j++){
1618: for(h=0; h<=nhstepm; h++){
1619: for(i=1, gm[h][j]=0.;i<=nlstate;i++)
1620: gm[h][j] += prlim[i][i]*p3mat[i][j][h];
1621: }
1622: }
1623:
1624: for(j=1; j<= nlstate; j++)
1625: for(h=0; h<=nhstepm; h++){
1626: gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
1627: }
1628: } /* End theta */
1629:
1630: trgradg =ma3x(0,nhstepm,1,nlstate,1,npar);
1631:
1632: for(h=0; h<=nhstepm; h++)
1633: for(j=1; j<=nlstate;j++)
1634: for(theta=1; theta <=npar; theta++)
1635: trgradg[h][j][theta]=gradg[h][theta][j];
1636:
1637: for(i=1;i<=nlstate;i++)
1638: for(j=1;j<=nlstate;j++)
1639: vareij[i][j][(int)age] =0.;
1640: for(h=0;h<=nhstepm;h++){
1641: for(k=0;k<=nhstepm;k++){
1642: matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
1643: matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
1644: for(i=1;i<=nlstate;i++)
1645: for(j=1;j<=nlstate;j++)
1646: vareij[i][j][(int)age] += doldm[i][j];
1647: }
1648: }
1649: h=1;
1650: if (stepm >= YEARM) h=stepm/YEARM;
1651: fprintf(ficresvij,"%.0f ",age );
1652: for(i=1; i<=nlstate;i++)
1653: for(j=1; j<=nlstate;j++){
1654: fprintf(ficresvij," %.4f", h*vareij[i][j][(int)age]);
1655: }
1656: fprintf(ficresvij,"\n");
1657: free_matrix(gp,0,nhstepm,1,nlstate);
1658: free_matrix(gm,0,nhstepm,1,nlstate);
1659: free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
1660: free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
1661: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
1662: } /* End age */
1663:
1664: free_vector(xp,1,npar);
1665: free_matrix(doldm,1,nlstate,1,npar);
1666: free_matrix(dnewm,1,nlstate,1,nlstate);
1667:
1668: }
1669:
1670: /************ Variance of prevlim ******************/
1671: 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)
1672: {
1673: /* Variance of prevalence limit */
1674: /* double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
1675: double **newm;
1676: double **dnewm,**doldm;
1677: int i, j, nhstepm, hstepm;
1678: int k, cptcode;
1679: double *xp;
1680: double *gp, *gm;
1681: double **gradg, **trgradg;
1682: double age,agelim;
1683: int theta;
1684:
1685: fprintf(ficresvpl,"# Standard deviation of prevalences limit\n");
1686: fprintf(ficresvpl,"# Age");
1687: for(i=1; i<=nlstate;i++)
1688: fprintf(ficresvpl," %1d-%1d",i,i);
1689: fprintf(ficresvpl,"\n");
1690:
1691: xp=vector(1,npar);
1692: dnewm=matrix(1,nlstate,1,npar);
1693: doldm=matrix(1,nlstate,1,nlstate);
1694:
1695: hstepm=1*YEARM; /* Every year of age */
1696: hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */
1697: agelim = AGESUP;
1698: for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
1699: nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
1700: if (stepm >= YEARM) hstepm=1;
1701: nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
1702: gradg=matrix(1,npar,1,nlstate);
1703: gp=vector(1,nlstate);
1704: gm=vector(1,nlstate);
1705:
1706: for(theta=1; theta <=npar; theta++){
1707: for(i=1; i<=npar; i++){ /* Computes gradient */
1708: xp[i] = x[i] + (i==theta ?delti[theta]:0);
1709: }
1710: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
1711: for(i=1;i<=nlstate;i++)
1712: gp[i] = prlim[i][i];
1713:
1714: for(i=1; i<=npar; i++) /* Computes gradient */
1715: xp[i] = x[i] - (i==theta ?delti[theta]:0);
1716: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
1717: for(i=1;i<=nlstate;i++)
1718: gm[i] = prlim[i][i];
1719:
1720: for(i=1;i<=nlstate;i++)
1721: gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
1722: } /* End theta */
1723:
1724: trgradg =matrix(1,nlstate,1,npar);
1725:
1726: for(j=1; j<=nlstate;j++)
1727: for(theta=1; theta <=npar; theta++)
1728: trgradg[j][theta]=gradg[theta][j];
1729:
1730: for(i=1;i<=nlstate;i++)
1731: varpl[i][(int)age] =0.;
1732: matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
1733: matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
1734: for(i=1;i<=nlstate;i++)
1735: varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
1736:
1737: fprintf(ficresvpl,"%.0f ",age );
1738: for(i=1; i<=nlstate;i++)
1739: fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
1740: fprintf(ficresvpl,"\n");
1741: free_vector(gp,1,nlstate);
1742: free_vector(gm,1,nlstate);
1743: free_matrix(gradg,1,npar,1,nlstate);
1744: free_matrix(trgradg,1,nlstate,1,npar);
1745: } /* End age */
1746:
1747: free_vector(xp,1,npar);
1748: free_matrix(doldm,1,nlstate,1,npar);
1749: free_matrix(dnewm,1,nlstate,1,nlstate);
1750:
1751: }
1752:
1753: /************ Variance of one-step probabilities ******************/
1754: void varprob(char fileres[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij)
1755: {
1756: int i, j;
1757: int k=0, cptcode;
1758: double **dnewm,**doldm;
1759: double *xp;
1760: double *gp, *gm;
1761: double **gradg, **trgradg;
1762: double age,agelim, cov[NCOVMAX];
1763: int theta;
1764: char fileresprob[FILENAMELENGTH];
1765:
1766: strcpy(fileresprob,"prob");
1767: strcat(fileresprob,fileres);
1768: if((ficresprob=fopen(fileresprob,"w"))==NULL) {
1769: printf("Problem with resultfile: %s\n", fileresprob);
1770: }
1771: printf("Computing variance of one-step probabilities: result on file '%s' \n",fileresprob);
1772:
1773:
1774: xp=vector(1,npar);
1775: dnewm=matrix(1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
1776: doldm=matrix(1,(nlstate+ndeath)*(nlstate+ndeath),1,(nlstate+ndeath)*(nlstate+ndeath));
1777:
1778: cov[1]=1;
1779: for (age=bage; age<=fage; age ++){
1780: cov[2]=age;
1781: gradg=matrix(1,npar,1,9);
1782: trgradg=matrix(1,9,1,npar);
1783: gp=vector(1,(nlstate+ndeath)*(nlstate+ndeath));
1784: gm=vector(1,(nlstate+ndeath)*(nlstate+ndeath));
1785:
1786: for(theta=1; theta <=npar; theta++){
1787: for(i=1; i<=npar; i++)
1788: xp[i] = x[i] + (i==theta ?delti[theta]:0);
1789:
1790: pmij(pmmij,cov,ncovmodel,xp,nlstate);
1791:
1792: k=0;
1793: for(i=1; i<= (nlstate+ndeath); i++){
1794: for(j=1; j<=(nlstate+ndeath);j++){
1795: k=k+1;
1796: gp[k]=pmmij[i][j];
1797: }
1798: }
1799:
1800: for(i=1; i<=npar; i++)
1801: xp[i] = x[i] - (i==theta ?delti[theta]:0);
1802:
1803:
1804: pmij(pmmij,cov,ncovmodel,xp,nlstate);
1805: k=0;
1806: for(i=1; i<=(nlstate+ndeath); i++){
1807: for(j=1; j<=(nlstate+ndeath);j++){
1808: k=k+1;
1809: gm[k]=pmmij[i][j];
1810: }
1811: }
1812:
1813: for(i=1; i<= (nlstate+ndeath)*(nlstate+ndeath); i++)
1814: gradg[theta][i]=(gp[i]-gm[i])/2./delti[theta];
1815: }
1816:
1817: for(j=1; j<=(nlstate+ndeath)*(nlstate+ndeath);j++)
1818: for(theta=1; theta <=npar; theta++)
1819: trgradg[j][theta]=gradg[theta][j];
1820:
1821: matprod2(dnewm,trgradg,1,9,1,npar,1,npar,matcov);
1822: matprod2(doldm,dnewm,1,9,1,npar,1,9,gradg);
1823:
1824: pmij(pmmij,cov,ncovmodel,x,nlstate);
1825:
1826: k=0;
1827: for(i=1; i<=(nlstate+ndeath); i++){
1828: for(j=1; j<=(nlstate+ndeath);j++){
1829: k=k+1;
1830: gm[k]=pmmij[i][j];
1831: }
1832: }
1833:
1834: /*printf("\n%d ",(int)age);
1835: for (i=1; i<=(nlstate+ndeath)*(nlstate+ndeath-1);i++){
1836:
1837:
1838: printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
1839: }*/
1840:
1841: fprintf(ficresprob,"\n%d ",(int)age);
1842:
1843: for (i=1; i<=(nlstate+ndeath)*(nlstate+ndeath-1);i++){
1844: if (i== 2) fprintf(ficresprob,"%.3e %.3e ",gm[i],doldm[i][i]);
1845: if (i== 4) fprintf(ficresprob,"%.3e %.3e ",gm[i],doldm[i][i]);
1846: }
1847:
1848: free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
1849: free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
1850: free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
1851: free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
1852: }
1853: free_vector(xp,1,npar);
1854: fclose(ficresprob);
1855: exit(0);
1856: }
1857:
1858: /***********************************************/
1859: /**************** Main Program *****************/
1860: /***********************************************/
1861:
1862: /*int main(int argc, char *argv[])*/
1863: int main()
1864: {
1865:
1866: int i,j, k, n=MAXN,iter,m,size,cptcode, cptcod;
1867: double agedeb, agefin,hf;
1868: double agemin=1.e20, agemax=-1.e20;
1869:
1870: double fret;
1871: double **xi,tmp,delta;
1872:
1873: double dum; /* Dummy variable */
1874: double ***p3mat;
1875: int *indx;
1876: char line[MAXLINE], linepar[MAXLINE];
1877: char title[MAXLINE];
1878: char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH], filerespl[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH];
1879: char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], fileresf[FILENAMELENGTH];
1880: char filerest[FILENAMELENGTH];
1881: char fileregp[FILENAMELENGTH];
1882: char popfile[FILENAMELENGTH];
1883: char path[80],pathc[80],pathcd[80],pathtot[80],model[20];
1884: int firstobs=1, lastobs=10;
1885: int sdeb, sfin; /* Status at beginning and end */
1886: int c, h , cpt,l;
1887: int ju,jl, mi;
1888: int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;
1889: int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,**adl,*tab;
1890: int mobilav=0,popforecast=0;
1891: int hstepm, nhstepm;
1892: int *popage;/*boolprev=0 if date and zero if wave*/
1893: double jprev1, mprev1,anprev1,jprev2, mprev2,anprev2;
1894:
1895: double bage, fage, age, agelim, agebase;
1896: double ftolpl=FTOL;
1897: double **prlim;
1898: double *severity;
1899: double ***param; /* Matrix of parameters */
1900: double *p;
1901: double **matcov; /* Matrix of covariance */
1902: double ***delti3; /* Scale */
1903: double *delti; /* Scale */
1904: double ***eij, ***vareij;
1905: double **varpl; /* Variances of prevalence limits by age */
1906: double *epj, vepp;
1907: double kk1, kk2;
1908: double *popeffectif,*popcount;
1909: double dateprev1, dateprev2,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,jprojmean,mprojmean,anprojmean, calagedate;
1910: double yp,yp1,yp2;
1911:
1912: char version[80]="Imach version 64b, May 2001, INED-EUROREVES ";
1913: char *alph[]={"a","a","b","c","d","e"}, str[4];
1914:
1915:
1916: char z[1]="c", occ;
1917: #include <sys/time.h>
1918: #include <time.h>
1919: char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];
1920:
1921: /* long total_usecs;
1922: struct timeval start_time, end_time;
1923:
1924: gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */
1925:
1926:
1927: printf("\nIMACH, Version 0.7");
1928: printf("\nEnter the parameter file name: ");
1929:
1930: #ifdef windows
1931: scanf("%s",pathtot);
1932: getcwd(pathcd, size);
1933: /*cygwin_split_path(pathtot,path,optionfile);
1934: printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/
1935: /* cutv(path,optionfile,pathtot,'\\');*/
1936:
1937: split(pathtot, path,optionfile);
1938: chdir(path);
1939: replace(pathc,path);
1940: #endif
1941: #ifdef unix
1942: scanf("%s",optionfile);
1943: #endif
1944:
1945: /*-------- arguments in the command line --------*/
1946:
1947: strcpy(fileres,"r");
1948: strcat(fileres, optionfile);
1949:
1950: /*---------arguments file --------*/
1951:
1952: if((ficpar=fopen(optionfile,"r"))==NULL) {
1953: printf("Problem with optionfile %s\n",optionfile);
1954: goto end;
1955: }
1956:
1957: strcpy(filereso,"o");
1958: strcat(filereso,fileres);
1959: if((ficparo=fopen(filereso,"w"))==NULL) {
1960: printf("Problem with Output resultfile: %s\n", filereso);goto end;
1961: }
1962:
1963: /* Reads comments: lines beginning with '#' */
1964: while((c=getc(ficpar))=='#' && c!= EOF){
1965: ungetc(c,ficpar);
1966: fgets(line, MAXLINE, ficpar);
1967: puts(line);
1968: fputs(line,ficparo);
1969: }
1970: ungetc(c,ficpar);
1971:
1972: 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);
1973: 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);
1974: 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);
1975: while((c=getc(ficpar))=='#' && c!= EOF){
1976: ungetc(c,ficpar);
1977: fgets(line, MAXLINE, ficpar);
1978: puts(line);
1979: fputs(line,ficparo);
1980: }
1981: ungetc(c,ficpar);
1982:
1983:
1984: covar=matrix(0,NCOVMAX,1,n);
1985: cptcovn=0;
1986: if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;
1987:
1988: ncovmodel=2+cptcovn;
1989: nvar=ncovmodel-1; /* Suppressing age as a basic covariate */
1990:
1991: /* Read guess parameters */
1992: /* Reads comments: lines beginning with '#' */
1993: while((c=getc(ficpar))=='#' && c!= EOF){
1994: ungetc(c,ficpar);
1995: fgets(line, MAXLINE, ficpar);
1996: puts(line);
1997: fputs(line,ficparo);
1998: }
1999: ungetc(c,ficpar);
2000:
2001: param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
2002: for(i=1; i <=nlstate; i++)
2003: for(j=1; j <=nlstate+ndeath-1; j++){
2004: fscanf(ficpar,"%1d%1d",&i1,&j1);
2005: fprintf(ficparo,"%1d%1d",i1,j1);
2006: printf("%1d%1d",i,j);
2007: for(k=1; k<=ncovmodel;k++){
2008: fscanf(ficpar," %lf",¶m[i][j][k]);
2009: printf(" %lf",param[i][j][k]);
2010: fprintf(ficparo," %lf",param[i][j][k]);
2011: }
2012: fscanf(ficpar,"\n");
2013: printf("\n");
2014: fprintf(ficparo,"\n");
2015: }
2016:
2017: npar= (nlstate+ndeath-1)*nlstate*ncovmodel;
2018:
2019: p=param[1][1];
2020:
2021: /* Reads comments: lines beginning with '#' */
2022: while((c=getc(ficpar))=='#' && c!= EOF){
2023: ungetc(c,ficpar);
2024: fgets(line, MAXLINE, ficpar);
2025: puts(line);
2026: fputs(line,ficparo);
2027: }
2028: ungetc(c,ficpar);
2029:
2030: delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
2031: delti=vector(1,npar); /* Scale of each paramater (output from hesscov) */
2032: for(i=1; i <=nlstate; i++){
2033: for(j=1; j <=nlstate+ndeath-1; j++){
2034: fscanf(ficpar,"%1d%1d",&i1,&j1);
2035: printf("%1d%1d",i,j);
2036: fprintf(ficparo,"%1d%1d",i1,j1);
2037: for(k=1; k<=ncovmodel;k++){
2038: fscanf(ficpar,"%le",&delti3[i][j][k]);
2039: printf(" %le",delti3[i][j][k]);
2040: fprintf(ficparo," %le",delti3[i][j][k]);
2041: }
2042: fscanf(ficpar,"\n");
2043: printf("\n");
2044: fprintf(ficparo,"\n");
2045: }
2046: }
2047: delti=delti3[1][1];
2048:
2049: /* Reads comments: lines beginning with '#' */
2050: while((c=getc(ficpar))=='#' && c!= EOF){
2051: ungetc(c,ficpar);
2052: fgets(line, MAXLINE, ficpar);
2053: puts(line);
2054: fputs(line,ficparo);
2055: }
2056: ungetc(c,ficpar);
2057:
2058: matcov=matrix(1,npar,1,npar);
2059: for(i=1; i <=npar; i++){
2060: fscanf(ficpar,"%s",&str);
2061: printf("%s",str);
2062: fprintf(ficparo,"%s",str);
2063: for(j=1; j <=i; j++){
2064: fscanf(ficpar," %le",&matcov[i][j]);
2065: printf(" %.5le",matcov[i][j]);
2066: fprintf(ficparo," %.5le",matcov[i][j]);
2067: }
2068: fscanf(ficpar,"\n");
2069: printf("\n");
2070: fprintf(ficparo,"\n");
2071: }
2072: for(i=1; i <=npar; i++)
2073: for(j=i+1;j<=npar;j++)
2074: matcov[i][j]=matcov[j][i];
2075:
2076: printf("\n");
2077:
2078:
2079: /*-------- data file ----------*/
2080: if((ficres =fopen(fileres,"w"))==NULL) {
2081: printf("Problem with resultfile: %s\n", fileres);goto end;
2082: }
2083: fprintf(ficres,"#%s\n",version);
2084:
2085: if((fic=fopen(datafile,"r"))==NULL) {
2086: printf("Problem with datafile: %s\n", datafile);goto end;
2087: }
2088:
2089: n= lastobs;
2090: severity = vector(1,maxwav);
2091: outcome=imatrix(1,maxwav+1,1,n);
2092: num=ivector(1,n);
2093: moisnais=vector(1,n);
2094: annais=vector(1,n);
2095: moisdc=vector(1,n);
2096: andc=vector(1,n);
2097: agedc=vector(1,n);
2098: cod=ivector(1,n);
2099: weight=vector(1,n);
2100: for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */
2101: mint=matrix(1,maxwav,1,n);
2102: anint=matrix(1,maxwav,1,n);
2103: s=imatrix(1,maxwav+1,1,n);
2104: adl=imatrix(1,maxwav+1,1,n);
2105: tab=ivector(1,NCOVMAX);
2106: ncodemax=ivector(1,8);
2107:
2108: i=1;
2109: while (fgets(line, MAXLINE, fic) != NULL) {
2110: if ((i >= firstobs) && (i <=lastobs)) {
2111:
2112: for (j=maxwav;j>=1;j--){
2113: cutv(stra, strb,line,' '); s[j][i]=atoi(strb);
2114: strcpy(line,stra);
2115: cutv(stra, strb,line,'/'); anint[j][i]=(double)(atoi(strb)); strcpy(line,stra);
2116: cutv(stra, strb,line,' '); mint[j][i]=(double)(atoi(strb)); strcpy(line,stra);
2117: }
2118:
2119: cutv(stra, strb,line,'/'); andc[i]=(double)(atoi(strb)); strcpy(line,stra);
2120: cutv(stra, strb,line,' '); moisdc[i]=(double)(atoi(strb)); strcpy(line,stra);
2121:
2122: cutv(stra, strb,line,'/'); annais[i]=(double)(atoi(strb)); strcpy(line,stra);
2123: cutv(stra, strb,line,' '); moisnais[i]=(double)(atoi(strb)); strcpy(line,stra);
2124:
2125: cutv(stra, strb,line,' '); weight[i]=(double)(atoi(strb)); strcpy(line,stra);
2126: for (j=ncov;j>=1;j--){
2127: cutv(stra, strb,line,' '); covar[j][i]=(double)(atoi(strb)); strcpy(line,stra);
2128: }
2129: num[i]=atol(stra);
2130:
2131: /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){
2132: 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;}*/
2133:
2134: i=i+1;
2135: }
2136: }
2137: /* printf("ii=%d", ij);
2138: scanf("%d",i);*/
2139: imx=i-1; /* Number of individuals */
2140:
2141: /* for (i=1; i<=imx; i++){
2142: if ((s[1][i]==3) && (s[2][i]==2)) s[2][i]=3;
2143: if ((s[2][i]==3) && (s[3][i]==2)) s[3][i]=3;
2144: if ((s[3][i]==3) && (s[4][i]==2)) s[4][i]=3;
2145: }
2146:
2147: for (i=1; i<=imx; i++)
2148: if (covar[1][i]==0) 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]));*/
2149:
2150: /* Calculation of the number of parameter from char model*/
2151: Tvar=ivector(1,15);
2152: Tprod=ivector(1,15);
2153: Tvaraff=ivector(1,15);
2154: Tvard=imatrix(1,15,1,2);
2155: Tage=ivector(1,15);
2156:
2157: if (strlen(model) >1){
2158: j=0, j1=0, k1=1, k2=1;
2159: j=nbocc(model,'+');
2160: j1=nbocc(model,'*');
2161: cptcovn=j+1;
2162: cptcovprod=j1;
2163:
2164:
2165: strcpy(modelsav,model);
2166: if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){
2167: printf("Error. Non available option model=%s ",model);
2168: goto end;
2169: }
2170:
2171: for(i=(j+1); i>=1;i--){
2172: cutv(stra,strb,modelsav,'+');
2173: if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav);
2174: /* printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/
2175: /*scanf("%d",i);*/
2176: if (strchr(strb,'*')) {
2177: cutv(strd,strc,strb,'*');
2178: if (strcmp(strc,"age")==0) {
2179: cptcovprod--;
2180: cutv(strb,stre,strd,'V');
2181: Tvar[i]=atoi(stre);
2182: cptcovage++;
2183: Tage[cptcovage]=i;
2184: /*printf("stre=%s ", stre);*/
2185: }
2186: else if (strcmp(strd,"age")==0) {
2187: cptcovprod--;
2188: cutv(strb,stre,strc,'V');
2189: Tvar[i]=atoi(stre);
2190: cptcovage++;
2191: Tage[cptcovage]=i;
2192: }
2193: else {
2194: cutv(strb,stre,strc,'V');
2195: Tvar[i]=ncov+k1;
2196: cutv(strb,strc,strd,'V');
2197: Tprod[k1]=i;
2198: Tvard[k1][1]=atoi(strc);
2199: Tvard[k1][2]=atoi(stre);
2200: Tvar[cptcovn+k2]=Tvard[k1][1];
2201: Tvar[cptcovn+k2+1]=Tvard[k1][2];
2202: for (k=1; k<=lastobs;k++)
2203: covar[ncov+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];
2204: k1++;
2205: k2=k2+2;
2206: }
2207: }
2208: else {
2209: /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/
2210: /* scanf("%d",i);*/
2211: cutv(strd,strc,strb,'V');
2212: Tvar[i]=atoi(strc);
2213: }
2214: strcpy(modelsav,stra);
2215: /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);
2216: scanf("%d",i);*/
2217: }
2218: }
2219:
2220: /*printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);
2221: printf("cptcovprod=%d ", cptcovprod);
2222: scanf("%d ",i);*/
2223: fclose(fic);
2224:
2225: /* if(mle==1){*/
2226: if (weightopt != 1) { /* Maximisation without weights*/
2227: for(i=1;i<=n;i++) weight[i]=1.0;
2228: }
2229: /*-calculation of age at interview from date of interview and age at death -*/
2230: agev=matrix(1,maxwav,1,imx);
2231:
2232: for (i=1; i<=imx; i++)
2233: for(m=2; (m<= maxwav); m++)
2234: if ((mint[m][i]== 99) && (s[m][i] <= nlstate)){
2235: anint[m][i]=9999;
2236: s[m][i]=-1;
2237: }
2238:
2239: for (i=1; i<=imx; i++) {
2240: agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);
2241: for(m=1; (m<= maxwav); m++){
2242: if(s[m][i] >0){
2243: if (s[m][i] == nlstate+1) {
2244: if(agedc[i]>0)
2245: if(moisdc[i]!=99 && andc[i]!=9999)
2246: agev[m][i]=agedc[i];
2247: else {
2248: if (andc[i]!=9999){
2249: printf("Warning negative age at death: %d line:%d\n",num[i],i);
2250: agev[m][i]=-1;
2251: }
2252: }
2253: }
2254: else if(s[m][i] !=9){ /* Should no more exist */
2255: agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);
2256: if(mint[m][i]==99 || anint[m][i]==9999)
2257: agev[m][i]=1;
2258: else if(agev[m][i] <agemin){
2259: agemin=agev[m][i];
2260: /*printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], agemin);*/
2261: }
2262: else if(agev[m][i] >agemax){
2263: agemax=agev[m][i];
2264: /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/
2265: }
2266: /*agev[m][i]=anint[m][i]-annais[i];*/
2267: /* agev[m][i] = age[i]+2*m;*/
2268: }
2269: else { /* =9 */
2270: agev[m][i]=1;
2271: s[m][i]=-1;
2272: }
2273: }
2274: else /*= 0 Unknown */
2275: agev[m][i]=1;
2276: }
2277:
2278: }
2279: for (i=1; i<=imx; i++) {
2280: for(m=1; (m<= maxwav); m++){
2281: if (s[m][i] > (nlstate+ndeath)) {
2282: printf("Error: Wrong value in nlstate or ndeath\n");
2283: goto end;
2284: }
2285: }
2286: }
2287:
2288: printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);
2289:
2290: free_vector(severity,1,maxwav);
2291: free_imatrix(outcome,1,maxwav+1,1,n);
2292: free_vector(moisnais,1,n);
2293: free_vector(annais,1,n);
2294: /* free_matrix(mint,1,maxwav,1,n);
2295: free_matrix(anint,1,maxwav,1,n);*/
2296: free_vector(moisdc,1,n);
2297: free_vector(andc,1,n);
2298:
2299:
2300: wav=ivector(1,imx);
2301: dh=imatrix(1,lastpass-firstpass+1,1,imx);
2302: mw=imatrix(1,lastpass-firstpass+1,1,imx);
2303:
2304: /* Concatenates waves */
2305: concatwav(wav, dh, mw, s, agedc, agev, firstpass, lastpass, imx, nlstate, stepm);
2306:
2307:
2308: Tcode=ivector(1,100);
2309: nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);
2310: ncodemax[1]=1;
2311: if (cptcovn > 0) tricode(Tvar,nbcode,imx);
2312:
2313: codtab=imatrix(1,100,1,10);
2314: h=0;
2315: m=pow(2,cptcoveff);
2316:
2317: for(k=1;k<=cptcoveff; k++){
2318: for(i=1; i <=(m/pow(2,k));i++){
2319: for(j=1; j <= ncodemax[k]; j++){
2320: for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){
2321: h++;
2322: if (h>m) h=1;codtab[h][k]=j;
2323: }
2324: }
2325: }
2326: }
2327:
2328: /* Calculates basic frequencies. Computes observed prevalence at single age
2329: and prints on file fileres'p'. */
2330:
2331:
2332:
2333: pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
2334: oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
2335: newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
2336: savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
2337: oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */
2338:
2339: /* For Powell, parameters are in a vector p[] starting at p[1]
2340: so we point p on param[1][1] so that p[1] maps on param[1][1][1] */
2341: p=param[1][1]; /* *(*(*(param +1)+1)+0) */
2342:
2343: if(mle==1){
2344: mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);
2345: }
2346:
2347: /*--------- results files --------------*/
2348: 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);
2349:
2350:
2351: jk=1;
2352: fprintf(ficres,"# Parameters\n");
2353: printf("# Parameters\n");
2354: for(i=1,jk=1; i <=nlstate; i++){
2355: for(k=1; k <=(nlstate+ndeath); k++){
2356: if (k != i)
2357: {
2358: printf("%d%d ",i,k);
2359: fprintf(ficres,"%1d%1d ",i,k);
2360: for(j=1; j <=ncovmodel; j++){
2361: printf("%f ",p[jk]);
2362: fprintf(ficres,"%f ",p[jk]);
2363: jk++;
2364: }
2365: printf("\n");
2366: fprintf(ficres,"\n");
2367: }
2368: }
2369: }
2370: if(mle==1){
2371: /* Computing hessian and covariance matrix */
2372: ftolhess=ftol; /* Usually correct */
2373: hesscov(matcov, p, npar, delti, ftolhess, func);
2374: }
2375: fprintf(ficres,"# Scales\n");
2376: printf("# Scales\n");
2377: for(i=1,jk=1; i <=nlstate; i++){
2378: for(j=1; j <=nlstate+ndeath; j++){
2379: if (j!=i) {
2380: fprintf(ficres,"%1d%1d",i,j);
2381: printf("%1d%1d",i,j);
2382: for(k=1; k<=ncovmodel;k++){
2383: printf(" %.5e",delti[jk]);
2384: fprintf(ficres," %.5e",delti[jk]);
2385: jk++;
2386: }
2387: printf("\n");
2388: fprintf(ficres,"\n");
2389: }
2390: }
2391: }
2392:
2393: k=1;
2394: fprintf(ficres,"# Covariance\n");
2395: printf("# Covariance\n");
2396: for(i=1;i<=npar;i++){
2397: /* if (k>nlstate) k=1;
2398: i1=(i-1)/(ncovmodel*nlstate)+1;
2399: fprintf(ficres,"%s%d%d",alph[k],i1,tab[i]);
2400: printf("%s%d%d",alph[k],i1,tab[i]);*/
2401: fprintf(ficres,"%3d",i);
2402: printf("%3d",i);
2403: for(j=1; j<=i;j++){
2404: fprintf(ficres," %.5e",matcov[i][j]);
2405: printf(" %.5e",matcov[i][j]);
2406: }
2407: fprintf(ficres,"\n");
2408: printf("\n");
2409: k++;
2410: }
2411:
2412: while((c=getc(ficpar))=='#' && c!= EOF){
2413: ungetc(c,ficpar);
2414: fgets(line, MAXLINE, ficpar);
2415: puts(line);
2416: fputs(line,ficparo);
2417: }
2418: ungetc(c,ficpar);
2419:
2420: fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf\n",&agemin,&agemax, &bage, &fage);
2421:
2422: if (fage <= 2) {
2423: bage = agemin;
2424: fage = agemax;
2425: }
2426:
2427: fprintf(ficres,"# agemin agemax for life expectancy.\n");
2428:
2429: fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemax,bage,fage);
2430: fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemax,bage,fage);
2431:
2432: while((c=getc(ficpar))=='#' && c!= EOF){
2433: ungetc(c,ficpar);
2434: fgets(line, MAXLINE, ficpar);
2435: puts(line);
2436: fputs(line,ficparo);
2437: }
2438: ungetc(c,ficpar);
2439:
2440: fscanf(ficpar,"begin-prev-date=%lf/%lf/%lf end-prev-date=%lf/%lf/%lf mob_average=%d\n",&jprev1, &mprev1,&anprev1,&jprev2, &mprev2,&anprev2,&mobilav);
2441: fprintf(ficparo,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mob_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
2442: fprintf(ficres,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mob_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
2443:
2444: while((c=getc(ficpar))=='#' && c!= EOF){
2445: ungetc(c,ficpar);
2446: fgets(line, MAXLINE, ficpar);
2447: puts(line);
2448: fputs(line,ficparo);
2449: }
2450: ungetc(c,ficpar);
2451:
2452:
2453: dateprev1=anprev1+mprev1/12.+jprev1/365.;
2454: dateprev2=anprev2+mprev2/12.+jprev2/365.;
2455:
2456: fscanf(ficpar,"pop_based=%d\n",&popbased);
2457: fprintf(ficparo,"pop_based=%d\n",popbased);
2458: fprintf(ficres,"pop_based=%d\n",popbased);
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: fscanf(ficpar,"popforecast=%d popfile=%s starting-proj-date=%lf/%lf/%lf final-proj-date=%lf/%lf/%lf\n",&popforecast,popfile,&jproj1,&mproj1,&anproj1,&jproj2,&mproj2,&anproj2);
2468: fprintf(ficparo,"popforecast=%d popfile=%s starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf\n",popforecast,popfile,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2);
2469: fprintf(ficres,"popforecast=%d popfile=%s starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf\n",popforecast,popfile,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2);
2470:
2471: freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2);
2472:
2473: /*------------ gnuplot -------------*/
2474: chdir(pathcd);
2475: if((ficgp=fopen("graph.plt","w"))==NULL) {
2476: printf("Problem with file graph.gp");goto end;
2477: }
2478: #ifdef windows
2479: fprintf(ficgp,"cd \"%s\" \n",pathc);
2480: #endif
2481: m=pow(2,cptcoveff);
2482:
2483: /* 1eme*/
2484: for (cpt=1; cpt<= nlstate ; cpt ++) {
2485: for (k1=1; k1<= m ; k1 ++) {
2486:
2487: #ifdef windows
2488: 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);
2489: #endif
2490: #ifdef unix
2491: fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nplot [%.f:%.f] \"vpl%s\" u 1:2 \"\%%lf",agemin,fage,fileres);
2492: #endif
2493:
2494: for (i=1; i<= nlstate ; i ++) {
2495: if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
2496: else fprintf(ficgp," \%%*lf (\%%*lf)");
2497: }
2498: fprintf(ficgp,"\" t\"Stationary prevalence\" w l 0,\"vpl%s\" every :::%d::%d u 1:($2+2*$3) \"\%%lf",fileres,k1-1,k1-1);
2499: for (i=1; i<= nlstate ; i ++) {
2500: if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
2501: else fprintf(ficgp," \%%*lf (\%%*lf)");
2502: }
2503: fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"vpl%s\" every :::%d::%d u 1:($2-2*$3) \"\%%lf",fileres,k1-1,k1-1);
2504: for (i=1; i<= nlstate ; i ++) {
2505: if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
2506: else fprintf(ficgp," \%%*lf (\%%*lf)");
2507: }
2508: fprintf(ficgp,"\" t\"\" w l 1,\"p%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",fileres,k1-1,k1-1,2+4*(cpt-1));
2509: #ifdef unix
2510: fprintf(ficgp,"\nset ter gif small size 400,300");
2511: #endif
2512: fprintf(ficgp,"\nset out \"v%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);
2513: }
2514: }
2515: /*2 eme*/
2516:
2517: for (k1=1; k1<= m ; k1 ++) {
2518: fprintf(ficgp,"set ylabel \"Years\" \nset ter gif small size 400,300\nplot [%.f:%.f] ",agemin,fage);
2519:
2520: for (i=1; i<= nlstate+1 ; i ++) {
2521: k=2*i;
2522: fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:2 \"\%%lf",fileres,k1-1,k1-1);
2523: for (j=1; j<= nlstate+1 ; j ++) {
2524: if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
2525: else fprintf(ficgp," \%%*lf (\%%*lf)");
2526: }
2527: if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");
2528: else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);
2529: fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",fileres,k1-1,k1-1);
2530: for (j=1; j<= nlstate+1 ; j ++) {
2531: if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
2532: else fprintf(ficgp," \%%*lf (\%%*lf)");
2533: }
2534: fprintf(ficgp,"\" t\"\" w l 0,");
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: if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");
2541: else fprintf(ficgp,"\" t\"\" w l 0,");
2542: }
2543: fprintf(ficgp,"\nset out \"e%s%d.gif\" \nreplot\n\n",strtok(optionfile, "."),k1);
2544: }
2545:
2546: /*3eme*/
2547:
2548: for (k1=1; k1<= m ; k1 ++) {
2549: for (cpt=1; cpt<= nlstate ; cpt ++) {
2550: k=2+nlstate*(cpt-1);
2551: 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);
2552: for (i=1; i< nlstate ; i ++) {
2553: 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);
2554: }
2555: fprintf(ficgp,"\nset out \"exp%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);
2556: }
2557: }
2558:
2559: /* CV preval stat */
2560: for (k1=1; k1<= m ; k1 ++) {
2561: for (cpt=1; cpt<nlstate ; cpt ++) {
2562: k=3;
2563: 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/($%d",agemin,agemax,fileres,k1,k+cpt+1,k+1);
2564: for (i=1; i< nlstate ; i ++)
2565: fprintf(ficgp,"+$%d",k+i+1);
2566: fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);
2567:
2568: l=3+(nlstate+ndeath)*cpt;
2569: fprintf(ficgp,",\"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",fileres,k1,l+cpt+1,l+1);
2570: for (i=1; i< nlstate ; i ++) {
2571: l=3+(nlstate+ndeath)*cpt;
2572: fprintf(ficgp,"+$%d",l+i+1);
2573: }
2574: fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);
2575: fprintf(ficgp,"set out \"p%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);
2576: }
2577: }
2578:
2579: /* proba elementaires */
2580: for(i=1,jk=1; i <=nlstate; i++){
2581: for(k=1; k <=(nlstate+ndeath); k++){
2582: if (k != i) {
2583: for(j=1; j <=ncovmodel; j++){
2584: /*fprintf(ficgp,"%s%1d%1d=%f ",alph[j],i,k,p[jk]);*/
2585: /*fprintf(ficgp,"%s",alph[1]);*/
2586: fprintf(ficgp,"p%d=%f ",jk,p[jk]);
2587: jk++;
2588: fprintf(ficgp,"\n");
2589: }
2590: }
2591: }
2592: }
2593:
2594: for(jk=1; jk <=m; jk++) {
2595: fprintf(ficgp,"\nset ter gif small size 400,300\nset log y\nplot [%.f:%.f] ",agemin,agemax);
2596: i=1;
2597: for(k2=1; k2<=nlstate; k2++) {
2598: k3=i;
2599: for(k=1; k<=(nlstate+ndeath); k++) {
2600: if (k != k2){
2601: fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
2602: ij=1;
2603: for(j=3; j <=ncovmodel; j++) {
2604: if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
2605: fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
2606: ij++;
2607: }
2608: else
2609: fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
2610: }
2611: fprintf(ficgp,")/(1");
2612:
2613: for(k1=1; k1 <=nlstate; k1++){
2614: fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);
2615: ij=1;
2616: for(j=3; j <=ncovmodel; j++){
2617: if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
2618: fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
2619: ij++;
2620: }
2621: else
2622: fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
2623: }
2624: fprintf(ficgp,")");
2625: }
2626: fprintf(ficgp,") t \"p%d%d\" ", k2,k);
2627: if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");
2628: i=i+ncovmodel;
2629: }
2630: }
2631: }
2632: fprintf(ficgp,"\nset out \"pe%s%d.gif\" \nreplot\n\n",strtok(optionfile, "."),jk);
2633: }
2634:
2635: fclose(ficgp);
2636: /* end gnuplot */
2637:
2638: chdir(path);
2639:
2640: free_ivector(wav,1,imx);
2641: free_imatrix(dh,1,lastpass-firstpass+1,1,imx);
2642: free_imatrix(mw,1,lastpass-firstpass+1,1,imx);
2643: free_ivector(num,1,n);
2644: free_vector(agedc,1,n);
2645: /*free_matrix(covar,1,NCOVMAX,1,n);*/
2646: fclose(ficparo);
2647: fclose(ficres);
2648: /* }*/
2649:
2650: /*________fin mle=1_________*/
2651:
2652:
2653:
2654: /* No more information from the sample is required now */
2655: /* Reads comments: lines beginning with '#' */
2656: while((c=getc(ficpar))=='#' && c!= EOF){
2657: ungetc(c,ficpar);
2658: fgets(line, MAXLINE, ficpar);
2659: puts(line);
2660: fputs(line,ficparo);
2661: }
2662: ungetc(c,ficpar);
2663:
2664: fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf\n",&agemin,&agemax, &bage, &fage);
2665: printf("agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemax, bage, fage);
2666: fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemax,bage,fage);
2667: /*--------- index.htm --------*/
2668:
2669: strcpy(optionfilehtm,optionfile);
2670: strcat(optionfilehtm,".htm");
2671: if((fichtm=fopen(optionfilehtm,"w"))==NULL) {
2672: printf("Problem with %s \n",optionfilehtm);goto end;
2673: }
2674:
2675: fprintf(fichtm,"<body><ul> <font size=\"6\">Imach, Version 0.7 </font> <hr size=\"2\" color=\"#EC5E5E\">
2676: Titre=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>
2677: Total number of observations=%d <br>
2678: Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>
2679: <hr size=\"2\" color=\"#EC5E5E\">
2680: <li>Outputs files<br><br>\n
2681: - Observed prevalence in each state: <a href=\"p%s\">p%s</a> <br>\n
2682: - Estimated parameters and the covariance matrix: <a href=\"%s\">%s</a> <br>
2683: - Stationary prevalence in each state: <a href=\"pl%s\">pl%s</a> <br>
2684: - Transition probabilities: <a href=\"pij%s\">pij%s</a><br>
2685: - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>
2686: - Life expectancies by age and initial health status: <a href=\"e%s\">e%s</a> <br>
2687: - Variances of life expectancies by age and initial health status: <a href=\"v%s\">v%s</a><br>
2688: - Health expectancies with their variances: <a href=\"t%s\">t%s</a> <br>
2689: - Standard deviation of stationary prevalences: <a href=\"vpl%s\">vpl%s</a> <br>
2690: - Prevalences and population forecasting: <a href=\"f%s\">f%s</a> <br>
2691: <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);
2692:
2693: fprintf(fichtm," <li>Graphs</li><p>");
2694:
2695: m=cptcoveff;
2696: if (cptcovn < 1) {m=1;ncodemax[1]=1;}
2697:
2698: j1=0;
2699: for(k1=1; k1<=m;k1++){
2700: for(i1=1; i1<=ncodemax[k1];i1++){
2701: j1++;
2702: if (cptcovn > 0) {
2703: fprintf(fichtm,"<hr size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
2704: for (cpt=1; cpt<=cptcoveff;cpt++)
2705: fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[j1][cpt]]);
2706: fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
2707: }
2708: fprintf(fichtm,"<br>- Probabilities: pe%s%d.gif<br>
2709: <img src=\"pe%s%d.gif\">",strtok(optionfile, "."),j1,strtok(optionfile, "."),j1);
2710: for(cpt=1; cpt<nlstate;cpt++){
2711: fprintf(fichtm,"<br>- Prevalence of disability : p%s%d%d.gif<br>
2712: <img src=\"p%s%d%d.gif\">",strtok(optionfile, "."),cpt,j1,strtok(optionfile, "."),cpt,j1);
2713: }
2714: for(cpt=1; cpt<=nlstate;cpt++) {
2715: fprintf(fichtm,"<br>- Observed and stationary prevalence (with confident
2716: interval) in state (%d): v%s%d%d.gif <br>
2717: <img src=\"v%s%d%d.gif\">",cpt,strtok(optionfile, "."),cpt,j1,strtok(optionfile, "."),cpt,j1);
2718: }
2719: for(cpt=1; cpt<=nlstate;cpt++) {
2720: fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): exp%s%d%d.gif <br>
2721: <img src=\"exp%s%d%d.gif\">",cpt,strtok(optionfile, "."),cpt,j1,strtok(optionfile, "."),cpt,j1);
2722: }
2723: fprintf(fichtm,"\n<br>- Total life expectancy by age and
2724: health expectancies in states (1) and (2): e%s%d.gif<br>
2725: <img src=\"e%s%d.gif\">",strtok(optionfile, "."),j1,strtok(optionfile, "."),j1);
2726: fprintf(fichtm,"\n</body>");
2727: }
2728: }
2729: fclose(fichtm);
2730:
2731: /*--------------- Prevalence limit --------------*/
2732:
2733: strcpy(filerespl,"pl");
2734: strcat(filerespl,fileres);
2735: if((ficrespl=fopen(filerespl,"w"))==NULL) {
2736: printf("Problem with Prev limit resultfile: %s\n", filerespl);goto end;
2737: }
2738: printf("Computing prevalence limit: result on file '%s' \n", filerespl);
2739: fprintf(ficrespl,"#Prevalence limit\n");
2740: fprintf(ficrespl,"#Age ");
2741: for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);
2742: fprintf(ficrespl,"\n");
2743:
2744: prlim=matrix(1,nlstate,1,nlstate);
2745: pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
2746: oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
2747: newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
2748: savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
2749: oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */
2750: k=0;
2751: agebase=agemin;
2752: agelim=agemax;
2753: ftolpl=1.e-10;
2754: i1=cptcoveff;
2755: if (cptcovn < 1){i1=1;}
2756:
2757: for(cptcov=1;cptcov<=i1;cptcov++){
2758: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
2759: k=k+1;
2760: /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/
2761: fprintf(ficrespl,"\n#******");
2762: for(j=1;j<=cptcoveff;j++)
2763: fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
2764: fprintf(ficrespl,"******\n");
2765:
2766: for (age=agebase; age<=agelim; age++){
2767: prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
2768: fprintf(ficrespl,"%.0f",age );
2769: for(i=1; i<=nlstate;i++)
2770: fprintf(ficrespl," %.5f", prlim[i][i]);
2771: fprintf(ficrespl,"\n");
2772: }
2773: }
2774: }
2775: fclose(ficrespl);
2776:
2777: /*------------- h Pij x at various ages ------------*/
2778:
2779: strcpy(filerespij,"pij"); strcat(filerespij,fileres);
2780: if((ficrespij=fopen(filerespij,"w"))==NULL) {
2781: printf("Problem with Pij resultfile: %s\n", filerespij);goto end;
2782: }
2783: printf("Computing pij: result on file '%s' \n", filerespij);
2784:
2785: stepsize=(int) (stepm+YEARM-1)/YEARM;
2786: /*if (stepm<=24) stepsize=2;*/
2787:
2788: agelim=AGESUP;
2789: hstepm=stepsize*YEARM; /* Every year of age */
2790: hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */
2791:
2792: k=0;
2793: for(cptcov=1;cptcov<=i1;cptcov++){
2794: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
2795: k=k+1;
2796: fprintf(ficrespij,"\n#****** ");
2797: for(j=1;j<=cptcoveff;j++)
2798: fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
2799: fprintf(ficrespij,"******\n");
2800:
2801: for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */
2802: nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
2803: nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
2804: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
2805: oldm=oldms;savm=savms;
2806: hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
2807: fprintf(ficrespij,"# Age");
2808: for(i=1; i<=nlstate;i++)
2809: for(j=1; j<=nlstate+ndeath;j++)
2810: fprintf(ficrespij," %1d-%1d",i,j);
2811: fprintf(ficrespij,"\n");
2812: for (h=0; h<=nhstepm; h++){
2813: fprintf(ficrespij,"%d %.0f %.0f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );
2814: for(i=1; i<=nlstate;i++)
2815: for(j=1; j<=nlstate+ndeath;j++)
2816: fprintf(ficrespij," %.5f", p3mat[i][j][h]);
2817: fprintf(ficrespij,"\n");
2818: }
2819: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
2820: fprintf(ficrespij,"\n");
2821: }
2822: }
2823: }
2824:
2825: /* varprob(fileres, matcov, p, delti, nlstate, (int) bage, (int) fage,k);*/
2826:
2827: fclose(ficrespij);
2828:
2829: if(stepm == 1) {
2830: /*---------- Forecasting ------------------*/
2831: calagedate=(anproj1+mproj1/12.+jproj1/365.-dateintmean)*YEARM;
2832:
2833: /*printf("calage= %f", calagedate);*/
2834:
2835: prevalence(agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);
2836:
2837:
2838: strcpy(fileresf,"f");
2839: strcat(fileresf,fileres);
2840: if((ficresf=fopen(fileresf,"w"))==NULL) {
2841: printf("Problem with forecast resultfile: %s\n", fileresf);goto end;
2842: }
2843: printf("Computing forecasting: result on file '%s' \n", fileresf);
2844:
2845: free_matrix(mint,1,maxwav,1,n);
2846: free_matrix(anint,1,maxwav,1,n);
2847: free_matrix(agev,1,maxwav,1,imx);
2848: /* Mobile average */
2849:
2850: if (cptcoveff==0) ncodemax[cptcoveff]=1;
2851:
2852: if (mobilav==1) {
2853: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
2854: for (agedeb=bage+3; agedeb<=fage-2; agedeb++)
2855: for (i=1; i<=nlstate;i++)
2856: for (cptcod=1;cptcod<=ncodemax[cptcov];cptcod++)
2857: mobaverage[(int)agedeb][i][cptcod]=0.;
2858:
2859: for (agedeb=bage+4; agedeb<=fage; agedeb++){
2860: for (i=1; i<=nlstate;i++){
2861: for (cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
2862: for (cpt=0;cpt<=4;cpt++){
2863: mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]+probs[(int)agedeb-cpt][i][cptcod];
2864: }
2865: mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]/5;
2866: }
2867: }
2868: }
2869: }
2870:
2871: stepsize=(int) (stepm+YEARM-1)/YEARM;
2872: if (stepm<=12) stepsize=1;
2873:
2874: agelim=AGESUP;
2875: /*hstepm=stepsize*YEARM; *//* Every year of age */
2876: hstepm=1;
2877: hstepm=hstepm/stepm; /* Typically 2 years, = 2 years/6 months = 4 */
2878: yp1=modf(dateintmean,&yp);
2879: anprojmean=yp;
2880: yp2=modf((yp1*12),&yp);
2881: mprojmean=yp;
2882: yp1=modf((yp2*30.5),&yp);
2883: jprojmean=yp;
2884: if(jprojmean==0) jprojmean=1;
2885: if(mprojmean==0) jprojmean=1;
2886:
2887: fprintf(ficresf,"# Estimated date of observed prevalence: %.lf/%.lf/%.lf ",jprojmean,mprojmean,anprojmean);
2888:
2889: if (popforecast==1) {
2890: if((ficpop=fopen(popfile,"r"))==NULL) {
2891: printf("Problem with population file : %s\n",popfile);goto end;
2892: }
2893: popage=ivector(0,AGESUP);
2894: popeffectif=vector(0,AGESUP);
2895: popcount=vector(0,AGESUP);
2896:
2897: i=1;
2898: while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF)
2899: {
2900: i=i+1;
2901: }
2902: imx=i;
2903:
2904: for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];
2905: }
2906:
2907: for(cptcov=1;cptcov<=i1;cptcov++){
2908: for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
2909: k=k+1;
2910: fprintf(ficresf,"\n#******");
2911: for(j=1;j<=cptcoveff;j++) {
2912: fprintf(ficresf," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
2913: }
2914: fprintf(ficresf,"******\n");
2915: fprintf(ficresf,"# StartingAge FinalAge");
2916: for(j=1; j<=nlstate+ndeath;j++) fprintf(ficresf," P.%d",j);
2917: if (popforecast==1) fprintf(ficresf," [Population]");
2918:
2919: for (cpt=0; cpt<4;cpt++) {
2920: fprintf(ficresf,"\n");
2921: fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+cpt);
2922:
2923: for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(bage-((int)calagedate %12)/12.); agedeb--){ /* If stepm=6 months */
2924: nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);
2925: nhstepm = nhstepm/hstepm;
2926: /*printf("agedeb=%.lf stepm=%d hstepm=%d nhstepm=%d \n",agedeb,stepm,hstepm,nhstepm);*/
2927:
2928: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
2929: oldm=oldms;savm=savms;
2930: hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
2931:
2932: for (h=0; h<=nhstepm; h++){
2933: if (h==(int) (calagedate+YEARM*cpt)) {
2934: fprintf(ficresf,"\n %.f ",agedeb+h*hstepm/YEARM*stepm);
2935: }
2936: for(j=1; j<=nlstate+ndeath;j++) {
2937: kk1=0.;kk2=0;
2938: for(i=1; i<=nlstate;i++) {
2939: if (mobilav==1)
2940: kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];
2941: else {
2942: kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];
2943: /* fprintf(ficresf," p3=%.3f p=%.3f ", p3mat[i][j][h], probs[(int)(agedeb)+1][i][cptcod]);*/
2944: }
2945:
2946: if (popforecast==1) kk2=kk1*popeffectif[(int)agedeb];
2947: }
2948:
2949: if (h==(int)(calagedate+12*cpt)){
2950: fprintf(ficresf," %.3f", kk1);
2951:
2952: if (popforecast==1) fprintf(ficresf," [%.f]", kk2);
2953: }
2954: }
2955: }
2956: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
2957: }
2958: }
2959: }
2960: }
2961: if (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
2962: if (popforecast==1) {
2963: free_ivector(popage,0,AGESUP);
2964: free_vector(popeffectif,0,AGESUP);
2965: free_vector(popcount,0,AGESUP);
2966: }
2967: free_imatrix(s,1,maxwav+1,1,n);
2968: free_vector(weight,1,n);
2969: fclose(ficresf);
2970: }/* End forecasting */
2971: else{
2972: erreur=108;
2973: printf("Error %d!! You can only forecast the prevalences if the optimization\n has been performed with stepm = 1 (month) instead of %d\n", erreur, stepm);
2974: }
2975:
2976: /*---------- Health expectancies and variances ------------*/
2977:
2978: strcpy(filerest,"t");
2979: strcat(filerest,fileres);
2980: if((ficrest=fopen(filerest,"w"))==NULL) {
2981: printf("Problem with total LE resultfile: %s\n", filerest);goto end;
2982: }
2983: printf("Computing Total LEs with variances: file '%s' \n", filerest);
2984:
2985:
2986: strcpy(filerese,"e");
2987: strcat(filerese,fileres);
2988: if((ficreseij=fopen(filerese,"w"))==NULL) {
2989: printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
2990: }
2991: printf("Computing Health Expectancies: result on file '%s' \n", filerese);
2992:
2993: strcpy(fileresv,"v");
2994: strcat(fileresv,fileres);
2995: if((ficresvij=fopen(fileresv,"w"))==NULL) {
2996: printf("Problem with variance resultfile: %s\n", fileresv);exit(0);
2997: }
2998: printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
2999:
3000: k=0;
3001: for(cptcov=1;cptcov<=i1;cptcov++){
3002: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
3003: k=k+1;
3004: fprintf(ficrest,"\n#****** ");
3005: for(j=1;j<=cptcoveff;j++)
3006: fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
3007: fprintf(ficrest,"******\n");
3008:
3009: fprintf(ficreseij,"\n#****** ");
3010: for(j=1;j<=cptcoveff;j++)
3011: fprintf(ficreseij,"V%d=%d ",j,nbcode[j][codtab[k][j]]);
3012: fprintf(ficreseij,"******\n");
3013:
3014: fprintf(ficresvij,"\n#****** ");
3015: for(j=1;j<=cptcoveff;j++)
3016: fprintf(ficresvij,"V%d=%d ",j,nbcode[j][codtab[k][j]]);
3017: fprintf(ficresvij,"******\n");
3018:
3019: eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
3020: oldm=oldms;savm=savms;
3021: evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k);
3022: vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
3023: oldm=oldms;savm=savms;
3024: varevsij(fileres, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);
3025:
3026: fprintf(ficrest,"#Total LEs with variances: e.. (std) ");
3027: for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);
3028: fprintf(ficrest,"\n");
3029:
3030: hf=1;
3031: if (stepm >= YEARM) hf=stepm/YEARM;
3032: epj=vector(1,nlstate+1);
3033: for(age=bage; age <=fage ;age++){
3034: prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
3035: if (popbased==1) {
3036: for(i=1; i<=nlstate;i++)
3037: prlim[i][i]=probs[(int)age][i][k];
3038: }
3039:
3040: fprintf(ficrest," %.0f",age);
3041: for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){
3042: for(i=1, epj[j]=0.;i <=nlstate;i++) {
3043: epj[j] += prlim[i][i]*hf*eij[i][j][(int)age];
3044: }
3045: epj[nlstate+1] +=epj[j];
3046: }
3047: for(i=1, vepp=0.;i <=nlstate;i++)
3048: for(j=1;j <=nlstate;j++)
3049: vepp += vareij[i][j][(int)age];
3050: fprintf(ficrest," %.2f (%.2f)", epj[nlstate+1],hf*sqrt(vepp));
3051: for(j=1;j <=nlstate;j++){
3052: fprintf(ficrest," %.2f (%.2f)", epj[j],hf*sqrt(vareij[j][j][(int)age]));
3053: }
3054: fprintf(ficrest,"\n");
3055: }
3056: }
3057: }
3058:
3059:
3060:
3061:
3062: fclose(ficreseij);
3063: fclose(ficresvij);
3064: fclose(ficrest);
3065: fclose(ficpar);
3066: free_vector(epj,1,nlstate+1);
3067: /* scanf("%d ",i); */
3068:
3069: /*------- Variance limit prevalence------*/
3070:
3071: strcpy(fileresvpl,"vpl");
3072: strcat(fileresvpl,fileres);
3073: if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {
3074: printf("Problem with variance prev lim resultfile: %s\n", fileresvpl);
3075: exit(0);
3076: }
3077: printf("Computing Variance-covariance of Prevalence limit: file '%s' \n", fileresvpl);
3078:
3079: k=0;
3080: for(cptcov=1;cptcov<=i1;cptcov++){
3081: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
3082: k=k+1;
3083: fprintf(ficresvpl,"\n#****** ");
3084: for(j=1;j<=cptcoveff;j++)
3085: fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
3086: fprintf(ficresvpl,"******\n");
3087:
3088: varpl=matrix(1,nlstate,(int) bage, (int) fage);
3089: oldm=oldms;savm=savms;
3090: varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);
3091: }
3092: }
3093:
3094: fclose(ficresvpl);
3095:
3096: /*---------- End : free ----------------*/
3097: free_matrix(varpl,1,nlstate,(int) bage, (int)fage);
3098:
3099: free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);
3100: free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
3101:
3102:
3103: free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);
3104: free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);
3105: free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);
3106: free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);
3107:
3108: free_matrix(matcov,1,npar,1,npar);
3109: free_vector(delti,1,npar);
3110:
3111: free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
3112:
3113: if(erreur >0)
3114: printf("End of Imach with error %d\n",erreur);
3115: else printf("End of Imach\n");
3116: /* gettimeofday(&end_time, (struct timezone*)0);*/ /* after time */
3117:
3118: /* 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);*/
3119: /*printf("Total time was %d uSec.\n", total_usecs);*/
3120: /*------ End -----------*/
3121:
3122:
3123: end:
3124: #ifdef windows
3125: chdir(pathcd);
3126: #endif
3127:
3128: system("..\\gp37mgw\\wgnuplot graph.plt");
3129:
3130: #ifdef windows
3131: while (z[0] != 'q') {
3132: chdir(pathcd);
3133: printf("\nType e to edit output files, c to start again, and q for exiting: ");
3134: scanf("%s",z);
3135: if (z[0] == 'c') system("./imach");
3136: else if (z[0] == 'e') {
3137: chdir(path);
3138: system(optionfilehtm);
3139: }
3140: else if (z[0] == 'q') exit(0);
3141: }
3142: #endif
3143: }
3144:
3145:
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