1: /* $Id: imach.c,v 1.58 2002/07/26 12:29:55 lievre Exp $
2: Interpolated Markov Chain
3:
4: Short summary of the programme:
5:
6: This program computes Healthy Life Expectancies from
7: cross-longitudinal data. Cross-longitudinal data consist in: -1- a
8: first survey ("cross") where individuals from different ages are
9: interviewed on their health status or degree of disability (in the
10: case of a health survey which is our main interest) -2- at least a
11: second wave of interviews ("longitudinal") which measure each change
12: (if any) in individual health status. Health expectancies are
13: computed from the time spent in each health state according to a
14: model. More health states you consider, more time is necessary to reach the
15: Maximum Likelihood of the parameters involved in the model. The
16: simplest model is the multinomial logistic model where pij is the
17: probability to be observed in state j at the second wave
18: conditional to be observed in state i at the first wave. Therefore
19: the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where
20: 'age' is age and 'sex' is a covariate. If you want to have a more
21: complex model than "constant and age", you should modify the program
22: where the markup *Covariates have to be included here again* invites
23: you to do it. More covariates you add, slower the
24: convergence.
25:
26: The advantage of this computer programme, compared to a simple
27: multinomial logistic model, is clear when the delay between waves is not
28: identical for each individual. Also, if a individual missed an
29: intermediate interview, the information is lost, but taken into
30: account using an interpolation or extrapolation.
31:
32: hPijx is the probability to be observed in state i at age x+h
33: conditional to the observed state i at age x. The delay 'h' can be
34: split into an exact number (nh*stepm) of unobserved intermediate
35: states. This elementary transition (by month or quarter trimester,
36: semester or year) is model as a multinomial logistic. The hPx
37: matrix is simply the matrix product of nh*stepm elementary matrices
38: and the contribution of each individual to the likelihood is simply
39: hPijx.
40:
41: Also this programme outputs the covariance matrix of the parameters but also
42: of the life expectancies. It also computes the stable prevalence.
43:
44: Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).
45: Institut national d'études démographiques, Paris.
46: This software have been partly granted by Euro-REVES, a concerted action
47: from the European Union.
48: It is copyrighted identically to a GNU software product, ie programme and
49: software can be distributed freely for non commercial use. Latest version
50: can be accessed at http://euroreves.ined.fr/imach .
51: **********************************************************************/
52:
53: #include <math.h>
54: #include <stdio.h>
55: #include <stdlib.h>
56: #include <unistd.h>
57:
58: #define MAXLINE 256
59: #define GNUPLOTPROGRAM "gnuplot"
60: /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
61: #define FILENAMELENGTH 80
62: /*#define DEBUG*/
63: #define windows
64: #define GLOCK_ERROR_NOPATH -1 /* empty path */
65: #define GLOCK_ERROR_GETCWD -2 /* cannot get cwd */
66:
67: #define MAXPARM 30 /* Maximum number of parameters for the optimization */
68: #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */
69:
70: #define NINTERVMAX 8
71: #define NLSTATEMAX 8 /* Maximum number of live states (for func) */
72: #define NDEATHMAX 8 /* Maximum number of dead states (for func) */
73: #define NCOVMAX 8 /* Maximum number of covariates */
74: #define MAXN 20000
75: #define YEARM 12. /* Number of months per year */
76: #define AGESUP 130
77: #define AGEBASE 40
78: #ifdef windows
79: #define DIRSEPARATOR '\\'
80: #define ODIRSEPARATOR '/'
81: #else
82: #define DIRSEPARATOR '/'
83: #define ODIRSEPARATOR '\\'
84: #endif
85:
86: char version[80]="Imach version 0.8k, July 2002, INED-EUROREVES ";
87: int erreur; /* Error number */
88: int nvar;
89: int cptcovn=0, cptcovage=0, cptcoveff=0,cptcov;
90: int npar=NPARMAX;
91: int nlstate=2; /* Number of live states */
92: int ndeath=1; /* Number of dead states */
93: int ncovmodel, ncovcol; /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
94: int popbased=0;
95:
96: int *wav; /* Number of waves for this individuual 0 is possible */
97: int maxwav; /* Maxim number of waves */
98: int jmin, jmax; /* min, max spacing between 2 waves */
99: int mle, weightopt;
100: int **mw; /* mw[mi][i] is number of the mi wave for this individual */
101: int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
102: double jmean; /* Mean space between 2 waves */
103: double **oldm, **newm, **savm; /* Working pointers to matrices */
104: double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
105: FILE *fic,*ficpar, *ficparo,*ficres, *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
106: FILE *ficlog;
107: FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
108: FILE *ficresprobmorprev;
109: FILE *fichtm; /* Html File */
110: FILE *ficreseij;
111: char filerese[FILENAMELENGTH];
112: FILE *ficresvij;
113: char fileresv[FILENAMELENGTH];
114: FILE *ficresvpl;
115: char fileresvpl[FILENAMELENGTH];
116: char title[MAXLINE];
117: char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH], filerespl[FILENAMELENGTH];
118: char optionfilext[10], optionfilefiname[FILENAMELENGTH], plotcmd[FILENAMELENGTH];
119:
120: char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
121: char filelog[FILENAMELENGTH]; /* Log file */
122: char filerest[FILENAMELENGTH];
123: char fileregp[FILENAMELENGTH];
124: char popfile[FILENAMELENGTH];
125:
126: char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH];
127:
128: #define NR_END 1
129: #define FREE_ARG char*
130: #define FTOL 1.0e-10
131:
132: #define NRANSI
133: #define ITMAX 200
134:
135: #define TOL 2.0e-4
136:
137: #define CGOLD 0.3819660
138: #define ZEPS 1.0e-10
139: #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);
140:
141: #define GOLD 1.618034
142: #define GLIMIT 100.0
143: #define TINY 1.0e-20
144:
145: static double maxarg1,maxarg2;
146: #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
147: #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
148:
149: #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
150: #define rint(a) floor(a+0.5)
151:
152: static double sqrarg;
153: #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
154: #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}
155:
156: int imx;
157: int stepm;
158: /* Stepm, step in month: minimum step interpolation*/
159:
160: int estepm;
161: /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
162:
163: int m,nb;
164: int *num, firstpass=0, lastpass=4,*cod, *ncodemax, *Tage;
165: double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
166: double **pmmij, ***probs;
167: double dateintmean=0;
168:
169: double *weight;
170: int **s; /* Status */
171: double *agedc, **covar, idx;
172: int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;
173:
174: double ftol=FTOL; /* Tolerance for computing Max Likelihood */
175: double ftolhess; /* Tolerance for computing hessian */
176:
177: /**************** split *************************/
178: static int split( char *path, char *dirc, char *name, char *ext, char *finame )
179: {
180: char *s; /* pointer */
181: int l1, l2; /* length counters */
182:
183: l1 = strlen( path ); /* length of path */
184: if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
185: s= strrchr( path, DIRSEPARATOR ); /* find last / */
186: if ( s == NULL ) { /* no directory, so use current */
187: /*if(strrchr(path, ODIRSEPARATOR )==NULL)
188: printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
189: #if defined(__bsd__) /* get current working directory */
190: extern char *getwd( );
191:
192: if ( getwd( dirc ) == NULL ) {
193: #else
194: extern char *getcwd( );
195:
196: if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {
197: #endif
198: return( GLOCK_ERROR_GETCWD );
199: }
200: strcpy( name, path ); /* we've got it */
201: } else { /* strip direcotry from path */
202: s++; /* after this, the filename */
203: l2 = strlen( s ); /* length of filename */
204: if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
205: strcpy( name, s ); /* save file name */
206: strncpy( dirc, path, l1 - l2 ); /* now the directory */
207: dirc[l1-l2] = 0; /* add zero */
208: }
209: l1 = strlen( dirc ); /* length of directory */
210: #ifdef windows
211: if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; }
212: #else
213: if ( dirc[l1-1] != '/' ) { dirc[l1] = '/'; dirc[l1+1] = 0; }
214: #endif
215: s = strrchr( name, '.' ); /* find last / */
216: s++;
217: strcpy(ext,s); /* save extension */
218: l1= strlen( name);
219: l2= strlen( s)+1;
220: strncpy( finame, name, l1-l2);
221: finame[l1-l2]= 0;
222: return( 0 ); /* we're done */
223: }
224:
225:
226: /******************************************/
227:
228: void replace(char *s, char*t)
229: {
230: int i;
231: int lg=20;
232: i=0;
233: lg=strlen(t);
234: for(i=0; i<= lg; i++) {
235: (s[i] = t[i]);
236: if (t[i]== '\\') s[i]='/';
237: }
238: }
239:
240: int nbocc(char *s, char occ)
241: {
242: int i,j=0;
243: int lg=20;
244: i=0;
245: lg=strlen(s);
246: for(i=0; i<= lg; i++) {
247: if (s[i] == occ ) j++;
248: }
249: return j;
250: }
251:
252: void cutv(char *u,char *v, char*t, char occ)
253: {
254: /* cuts string t into u and v where u is ended by char occ excluding it
255: and v is after occ excluding it too : ex cutv(u,v,"abcdef2ghi2j",2)
256: gives u="abcedf" and v="ghi2j" */
257: int i,lg,j,p=0;
258: i=0;
259: for(j=0; j<=strlen(t)-1; j++) {
260: if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;
261: }
262:
263: lg=strlen(t);
264: for(j=0; j<p; j++) {
265: (u[j] = t[j]);
266: }
267: u[p]='\0';
268:
269: for(j=0; j<= lg; j++) {
270: if (j>=(p+1))(v[j-p-1] = t[j]);
271: }
272: }
273:
274: /********************** nrerror ********************/
275:
276: void nrerror(char error_text[])
277: {
278: fprintf(stderr,"ERREUR ...\n");
279: fprintf(stderr,"%s\n",error_text);
280: exit(1);
281: }
282: /*********************** vector *******************/
283: double *vector(int nl, int nh)
284: {
285: double *v;
286: v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
287: if (!v) nrerror("allocation failure in vector");
288: return v-nl+NR_END;
289: }
290:
291: /************************ free vector ******************/
292: void free_vector(double*v, int nl, int nh)
293: {
294: free((FREE_ARG)(v+nl-NR_END));
295: }
296:
297: /************************ivector *******************************/
298: int *ivector(long nl,long nh)
299: {
300: int *v;
301: v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
302: if (!v) nrerror("allocation failure in ivector");
303: return v-nl+NR_END;
304: }
305:
306: /******************free ivector **************************/
307: void free_ivector(int *v, long nl, long nh)
308: {
309: free((FREE_ARG)(v+nl-NR_END));
310: }
311:
312: /******************* imatrix *******************************/
313: int **imatrix(long nrl, long nrh, long ncl, long nch)
314: /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */
315: {
316: long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;
317: int **m;
318:
319: /* allocate pointers to rows */
320: m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));
321: if (!m) nrerror("allocation failure 1 in matrix()");
322: m += NR_END;
323: m -= nrl;
324:
325:
326: /* allocate rows and set pointers to them */
327: m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));
328: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
329: m[nrl] += NR_END;
330: m[nrl] -= ncl;
331:
332: for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;
333:
334: /* return pointer to array of pointers to rows */
335: return m;
336: }
337:
338: /****************** free_imatrix *************************/
339: void free_imatrix(m,nrl,nrh,ncl,nch)
340: int **m;
341: long nch,ncl,nrh,nrl;
342: /* free an int matrix allocated by imatrix() */
343: {
344: free((FREE_ARG) (m[nrl]+ncl-NR_END));
345: free((FREE_ARG) (m+nrl-NR_END));
346: }
347:
348: /******************* matrix *******************************/
349: double **matrix(long nrl, long nrh, long ncl, long nch)
350: {
351: long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
352: double **m;
353:
354: m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
355: if (!m) nrerror("allocation failure 1 in matrix()");
356: m += NR_END;
357: m -= nrl;
358:
359: m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
360: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
361: m[nrl] += NR_END;
362: m[nrl] -= ncl;
363:
364: for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
365: return m;
366: }
367:
368: /*************************free matrix ************************/
369: void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
370: {
371: free((FREE_ARG)(m[nrl]+ncl-NR_END));
372: free((FREE_ARG)(m+nrl-NR_END));
373: }
374:
375: /******************* ma3x *******************************/
376: double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
377: {
378: long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
379: double ***m;
380:
381: m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
382: if (!m) nrerror("allocation failure 1 in matrix()");
383: m += NR_END;
384: m -= nrl;
385:
386: m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
387: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
388: m[nrl] += NR_END;
389: m[nrl] -= ncl;
390:
391: for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
392:
393: m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
394: if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
395: m[nrl][ncl] += NR_END;
396: m[nrl][ncl] -= nll;
397: for (j=ncl+1; j<=nch; j++)
398: m[nrl][j]=m[nrl][j-1]+nlay;
399:
400: for (i=nrl+1; i<=nrh; i++) {
401: m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
402: for (j=ncl+1; j<=nch; j++)
403: m[i][j]=m[i][j-1]+nlay;
404: }
405: return m;
406: }
407:
408: /*************************free ma3x ************************/
409: void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
410: {
411: free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
412: free((FREE_ARG)(m[nrl]+ncl-NR_END));
413: free((FREE_ARG)(m+nrl-NR_END));
414: }
415:
416: /***************** f1dim *************************/
417: extern int ncom;
418: extern double *pcom,*xicom;
419: extern double (*nrfunc)(double []);
420:
421: double f1dim(double x)
422: {
423: int j;
424: double f;
425: double *xt;
426:
427: xt=vector(1,ncom);
428: for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];
429: f=(*nrfunc)(xt);
430: free_vector(xt,1,ncom);
431: return f;
432: }
433:
434: /*****************brent *************************/
435: double brent(double ax, double bx, double cx, double (*f)(double), double tol, double *xmin)
436: {
437: int iter;
438: double a,b,d,etemp;
439: double fu,fv,fw,fx;
440: double ftemp;
441: double p,q,r,tol1,tol2,u,v,w,x,xm;
442: double e=0.0;
443:
444: a=(ax < cx ? ax : cx);
445: b=(ax > cx ? ax : cx);
446: x=w=v=bx;
447: fw=fv=fx=(*f)(x);
448: for (iter=1;iter<=ITMAX;iter++) {
449: xm=0.5*(a+b);
450: tol2=2.0*(tol1=tol*fabs(x)+ZEPS);
451: /* if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
452: printf(".");fflush(stdout);
453: fprintf(ficlog,".");fflush(ficlog);
454: #ifdef DEBUG
455: 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);
456: fprintf(ficlog,"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);
457: /* if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
458: #endif
459: if (fabs(x-xm) <= (tol2-0.5*(b-a))){
460: *xmin=x;
461: return fx;
462: }
463: ftemp=fu;
464: if (fabs(e) > tol1) {
465: r=(x-w)*(fx-fv);
466: q=(x-v)*(fx-fw);
467: p=(x-v)*q-(x-w)*r;
468: q=2.0*(q-r);
469: if (q > 0.0) p = -p;
470: q=fabs(q);
471: etemp=e;
472: e=d;
473: if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))
474: d=CGOLD*(e=(x >= xm ? a-x : b-x));
475: else {
476: d=p/q;
477: u=x+d;
478: if (u-a < tol2 || b-u < tol2)
479: d=SIGN(tol1,xm-x);
480: }
481: } else {
482: d=CGOLD*(e=(x >= xm ? a-x : b-x));
483: }
484: u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));
485: fu=(*f)(u);
486: if (fu <= fx) {
487: if (u >= x) a=x; else b=x;
488: SHFT(v,w,x,u)
489: SHFT(fv,fw,fx,fu)
490: } else {
491: if (u < x) a=u; else b=u;
492: if (fu <= fw || w == x) {
493: v=w;
494: w=u;
495: fv=fw;
496: fw=fu;
497: } else if (fu <= fv || v == x || v == w) {
498: v=u;
499: fv=fu;
500: }
501: }
502: }
503: nrerror("Too many iterations in brent");
504: *xmin=x;
505: return fx;
506: }
507:
508: /****************** mnbrak ***********************/
509:
510: void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,
511: double (*func)(double))
512: {
513: double ulim,u,r,q, dum;
514: double fu;
515:
516: *fa=(*func)(*ax);
517: *fb=(*func)(*bx);
518: if (*fb > *fa) {
519: SHFT(dum,*ax,*bx,dum)
520: SHFT(dum,*fb,*fa,dum)
521: }
522: *cx=(*bx)+GOLD*(*bx-*ax);
523: *fc=(*func)(*cx);
524: while (*fb > *fc) {
525: r=(*bx-*ax)*(*fb-*fc);
526: q=(*bx-*cx)*(*fb-*fa);
527: u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/
528: (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r));
529: ulim=(*bx)+GLIMIT*(*cx-*bx);
530: if ((*bx-u)*(u-*cx) > 0.0) {
531: fu=(*func)(u);
532: } else if ((*cx-u)*(u-ulim) > 0.0) {
533: fu=(*func)(u);
534: if (fu < *fc) {
535: SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))
536: SHFT(*fb,*fc,fu,(*func)(u))
537: }
538: } else if ((u-ulim)*(ulim-*cx) >= 0.0) {
539: u=ulim;
540: fu=(*func)(u);
541: } else {
542: u=(*cx)+GOLD*(*cx-*bx);
543: fu=(*func)(u);
544: }
545: SHFT(*ax,*bx,*cx,u)
546: SHFT(*fa,*fb,*fc,fu)
547: }
548: }
549:
550: /*************** linmin ************************/
551:
552: int ncom;
553: double *pcom,*xicom;
554: double (*nrfunc)(double []);
555:
556: void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))
557: {
558: double brent(double ax, double bx, double cx,
559: double (*f)(double), double tol, double *xmin);
560: double f1dim(double x);
561: void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,
562: double *fc, double (*func)(double));
563: int j;
564: double xx,xmin,bx,ax;
565: double fx,fb,fa;
566:
567: ncom=n;
568: pcom=vector(1,n);
569: xicom=vector(1,n);
570: nrfunc=func;
571: for (j=1;j<=n;j++) {
572: pcom[j]=p[j];
573: xicom[j]=xi[j];
574: }
575: ax=0.0;
576: xx=1.0;
577: mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim);
578: *fret=brent(ax,xx,bx,f1dim,TOL,&xmin);
579: #ifdef DEBUG
580: printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
581: fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
582: #endif
583: for (j=1;j<=n;j++) {
584: xi[j] *= xmin;
585: p[j] += xi[j];
586: }
587: free_vector(xicom,1,n);
588: free_vector(pcom,1,n);
589: }
590:
591: /*************** powell ************************/
592: void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,
593: double (*func)(double []))
594: {
595: void linmin(double p[], double xi[], int n, double *fret,
596: double (*func)(double []));
597: int i,ibig,j;
598: double del,t,*pt,*ptt,*xit;
599: double fp,fptt;
600: double *xits;
601: pt=vector(1,n);
602: ptt=vector(1,n);
603: xit=vector(1,n);
604: xits=vector(1,n);
605: *fret=(*func)(p);
606: for (j=1;j<=n;j++) pt[j]=p[j];
607: for (*iter=1;;++(*iter)) {
608: fp=(*fret);
609: ibig=0;
610: del=0.0;
611: printf("\nPowell iter=%d -2*LL=%.12f",*iter,*fret);
612: fprintf(ficlog,"\nPowell iter=%d -2*LL=%.12f",*iter,*fret);
613: for (i=1;i<=n;i++)
614: printf(" %d %.12f",i, p[i]);
615: fprintf(ficlog," %d %.12f",i, p[i]);
616: printf("\n");
617: fprintf(ficlog,"\n");
618: for (i=1;i<=n;i++) {
619: for (j=1;j<=n;j++) xit[j]=xi[j][i];
620: fptt=(*fret);
621: #ifdef DEBUG
622: printf("fret=%lf \n",*fret);
623: fprintf(ficlog,"fret=%lf \n",*fret);
624: #endif
625: printf("%d",i);fflush(stdout);
626: fprintf(ficlog,"%d",i);fflush(ficlog);
627: linmin(p,xit,n,fret,func);
628: if (fabs(fptt-(*fret)) > del) {
629: del=fabs(fptt-(*fret));
630: ibig=i;
631: }
632: #ifdef DEBUG
633: printf("%d %.12e",i,(*fret));
634: fprintf(ficlog,"%d %.12e",i,(*fret));
635: for (j=1;j<=n;j++) {
636: xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
637: printf(" x(%d)=%.12e",j,xit[j]);
638: fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
639: }
640: for(j=1;j<=n;j++) {
641: printf(" p=%.12e",p[j]);
642: fprintf(ficlog," p=%.12e",p[j]);
643: }
644: printf("\n");
645: fprintf(ficlog,"\n");
646: #endif
647: }
648: if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {
649: #ifdef DEBUG
650: int k[2],l;
651: k[0]=1;
652: k[1]=-1;
653: printf("Max: %.12e",(*func)(p));
654: fprintf(ficlog,"Max: %.12e",(*func)(p));
655: for (j=1;j<=n;j++) {
656: printf(" %.12e",p[j]);
657: fprintf(ficlog," %.12e",p[j]);
658: }
659: printf("\n");
660: fprintf(ficlog,"\n");
661: for(l=0;l<=1;l++) {
662: for (j=1;j<=n;j++) {
663: ptt[j]=p[j]+(p[j]-pt[j])*k[l];
664: printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
665: fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
666: }
667: printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
668: fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
669: }
670: #endif
671:
672:
673: free_vector(xit,1,n);
674: free_vector(xits,1,n);
675: free_vector(ptt,1,n);
676: free_vector(pt,1,n);
677: return;
678: }
679: if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");
680: for (j=1;j<=n;j++) {
681: ptt[j]=2.0*p[j]-pt[j];
682: xit[j]=p[j]-pt[j];
683: pt[j]=p[j];
684: }
685: fptt=(*func)(ptt);
686: if (fptt < fp) {
687: t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt);
688: if (t < 0.0) {
689: linmin(p,xit,n,fret,func);
690: for (j=1;j<=n;j++) {
691: xi[j][ibig]=xi[j][n];
692: xi[j][n]=xit[j];
693: }
694: #ifdef DEBUG
695: printf("Direction changed last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
696: fprintf(ficlog,"Direction changed last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
697: for(j=1;j<=n;j++){
698: printf(" %.12e",xit[j]);
699: fprintf(ficlog," %.12e",xit[j]);
700: }
701: printf("\n");
702: fprintf(ficlog,"\n");
703: #endif
704: }
705: }
706: }
707: }
708:
709: /**** Prevalence limit (stable prevalence) ****************/
710:
711: double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)
712: {
713: /* Computes the prevalence limit in each live state at age x by left multiplying the unit
714: matrix by transitions matrix until convergence is reached */
715:
716: int i, ii,j,k;
717: double min, max, maxmin, maxmax,sumnew=0.;
718: double **matprod2();
719: double **out, cov[NCOVMAX], **pmij();
720: double **newm;
721: double agefin, delaymax=50 ; /* Max number of years to converge */
722:
723: for (ii=1;ii<=nlstate+ndeath;ii++)
724: for (j=1;j<=nlstate+ndeath;j++){
725: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
726: }
727:
728: cov[1]=1.;
729:
730: /* Even if hstepm = 1, at least one multiplication by the unit matrix */
731: for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
732: newm=savm;
733: /* Covariates have to be included here again */
734: cov[2]=agefin;
735:
736: for (k=1; k<=cptcovn;k++) {
737: cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
738: /* printf("ij=%d k=%d Tvar[k]=%d nbcode=%d cov=%lf codtab[ij][Tvar[k]]=%d \n",ij,k, Tvar[k],nbcode[Tvar[k]][codtab[ij][Tvar[k]]],cov[2+k], codtab[ij][Tvar[k]]);*/
739: }
740: for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
741: for (k=1; k<=cptcovprod;k++)
742: cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
743:
744: /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
745: /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
746: /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
747: out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);
748:
749: savm=oldm;
750: oldm=newm;
751: maxmax=0.;
752: for(j=1;j<=nlstate;j++){
753: min=1.;
754: max=0.;
755: for(i=1; i<=nlstate; i++) {
756: sumnew=0;
757: for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
758: prlim[i][j]= newm[i][j]/(1-sumnew);
759: max=FMAX(max,prlim[i][j]);
760: min=FMIN(min,prlim[i][j]);
761: }
762: maxmin=max-min;
763: maxmax=FMAX(maxmax,maxmin);
764: }
765: if(maxmax < ftolpl){
766: return prlim;
767: }
768: }
769: }
770:
771: /*************** transition probabilities ***************/
772:
773: double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
774: {
775: double s1, s2;
776: /*double t34;*/
777: int i,j,j1, nc, ii, jj;
778:
779: for(i=1; i<= nlstate; i++){
780: for(j=1; j<i;j++){
781: for (nc=1, s2=0.;nc <=ncovmodel; nc++){
782: /*s2 += param[i][j][nc]*cov[nc];*/
783: s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
784: /*printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2);*/
785: }
786: ps[i][j]=s2;
787: /*printf("s1=%.17e, s2=%.17e\n",s1,s2);*/
788: }
789: for(j=i+1; j<=nlstate+ndeath;j++){
790: for (nc=1, s2=0.;nc <=ncovmodel; nc++){
791: s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
792: /*printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2);*/
793: }
794: ps[i][j]=s2;
795: }
796: }
797: /*ps[3][2]=1;*/
798:
799: for(i=1; i<= nlstate; i++){
800: s1=0;
801: for(j=1; j<i; j++)
802: s1+=exp(ps[i][j]);
803: for(j=i+1; j<=nlstate+ndeath; j++)
804: s1+=exp(ps[i][j]);
805: ps[i][i]=1./(s1+1.);
806: for(j=1; j<i; j++)
807: ps[i][j]= exp(ps[i][j])*ps[i][i];
808: for(j=i+1; j<=nlstate+ndeath; j++)
809: ps[i][j]= exp(ps[i][j])*ps[i][i];
810: /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
811: } /* end i */
812:
813: for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
814: for(jj=1; jj<= nlstate+ndeath; jj++){
815: ps[ii][jj]=0;
816: ps[ii][ii]=1;
817: }
818: }
819:
820:
821: /* for(ii=1; ii<= nlstate+ndeath; ii++){
822: for(jj=1; jj<= nlstate+ndeath; jj++){
823: printf("%lf ",ps[ii][jj]);
824: }
825: printf("\n ");
826: }
827: printf("\n ");printf("%lf ",cov[2]);*/
828: /*
829: for(i=1; i<= npar; i++) printf("%f ",x[i]);
830: goto end;*/
831: return ps;
832: }
833:
834: /**************** Product of 2 matrices ******************/
835:
836: double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)
837: {
838: /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
839: b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
840: /* in, b, out are matrice of pointers which should have been initialized
841: before: only the contents of out is modified. The function returns
842: a pointer to pointers identical to out */
843: long i, j, k;
844: for(i=nrl; i<= nrh; i++)
845: for(k=ncolol; k<=ncoloh; k++)
846: for(j=ncl,out[i][k]=0.; j<=nch; j++)
847: out[i][k] +=in[i][j]*b[j][k];
848:
849: return out;
850: }
851:
852:
853: /************* Higher Matrix Product ***************/
854:
855: double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
856: {
857: /* Computes the transition matrix starting at age 'age' over 'nhstepm*hstepm*stepm' month
858: duration (i.e. until
859: age (in years) age+nhstepm*stepm/12) by multiplying nhstepm*hstepm matrices.
860: Output is stored in matrix po[i][j][h] for h every 'hstepm' step
861: (typically every 2 years instead of every month which is too big).
862: Model is determined by parameters x and covariates have to be
863: included manually here.
864:
865: */
866:
867: int i, j, d, h, k;
868: double **out, cov[NCOVMAX];
869: double **newm;
870:
871: /* Hstepm could be zero and should return the unit matrix */
872: for (i=1;i<=nlstate+ndeath;i++)
873: for (j=1;j<=nlstate+ndeath;j++){
874: oldm[i][j]=(i==j ? 1.0 : 0.0);
875: po[i][j][0]=(i==j ? 1.0 : 0.0);
876: }
877: /* Even if hstepm = 1, at least one multiplication by the unit matrix */
878: for(h=1; h <=nhstepm; h++){
879: for(d=1; d <=hstepm; d++){
880: newm=savm;
881: /* Covariates have to be included here again */
882: cov[1]=1.;
883: cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
884: for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
885: for (k=1; k<=cptcovage;k++)
886: cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
887: for (k=1; k<=cptcovprod;k++)
888: cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
889:
890:
891: /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
892: /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
893: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,
894: pmij(pmmij,cov,ncovmodel,x,nlstate));
895: savm=oldm;
896: oldm=newm;
897: }
898: for(i=1; i<=nlstate+ndeath; i++)
899: for(j=1;j<=nlstate+ndeath;j++) {
900: po[i][j][h]=newm[i][j];
901: /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);
902: */
903: }
904: } /* end h */
905: return po;
906: }
907:
908:
909: /*************** log-likelihood *************/
910: double func( double *x)
911: {
912: int i, ii, j, k, mi, d, kk;
913: double l, ll[NLSTATEMAX], cov[NCOVMAX];
914: double **out;
915: double sw; /* Sum of weights */
916: double lli; /* Individual log likelihood */
917: long ipmx;
918: /*extern weight */
919: /* We are differentiating ll according to initial status */
920: /* for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
921: /*for(i=1;i<imx;i++)
922: printf(" %d\n",s[4][i]);
923: */
924: cov[1]=1.;
925:
926: for(k=1; k<=nlstate; k++) ll[k]=0.;
927: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
928: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
929: for(mi=1; mi<= wav[i]-1; mi++){
930: for (ii=1;ii<=nlstate+ndeath;ii++)
931: for (j=1;j<=nlstate+ndeath;j++) oldm[ii][j]=(ii==j ? 1.0 : 0.0);
932: for(d=0; d<dh[mi][i]; d++){
933: newm=savm;
934: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
935: for (kk=1; kk<=cptcovage;kk++) {
936: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
937: }
938:
939: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
940: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
941: savm=oldm;
942: oldm=newm;
943:
944:
945: } /* end mult */
946:
947: lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);
948: /* printf(" %f ",out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/
949: ipmx +=1;
950: sw += weight[i];
951: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
952: } /* end of wave */
953: } /* end of individual */
954:
955: for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
956: /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
957: l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
958: return -l;
959: }
960:
961:
962: /*********** Maximum Likelihood Estimation ***************/
963:
964: void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
965: {
966: int i,j, iter;
967: double **xi,*delti;
968: double fret;
969: xi=matrix(1,npar,1,npar);
970: for (i=1;i<=npar;i++)
971: for (j=1;j<=npar;j++)
972: xi[i][j]=(i==j ? 1.0 : 0.0);
973: printf("Powell\n"); fprintf(ficlog,"Powell\n");
974: powell(p,xi,npar,ftol,&iter,&fret,func);
975:
976: printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));
977: fprintf(ficlog,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
978: fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
979:
980: }
981:
982: /**** Computes Hessian and covariance matrix ***/
983: void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
984: {
985: double **a,**y,*x,pd;
986: double **hess;
987: int i, j,jk;
988: int *indx;
989:
990: double hessii(double p[], double delta, int theta, double delti[]);
991: double hessij(double p[], double delti[], int i, int j);
992: void lubksb(double **a, int npar, int *indx, double b[]) ;
993: void ludcmp(double **a, int npar, int *indx, double *d) ;
994:
995: hess=matrix(1,npar,1,npar);
996:
997: printf("\nCalculation of the hessian matrix. Wait...\n");
998: fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
999: for (i=1;i<=npar;i++){
1000: printf("%d",i);fflush(stdout);
1001: fprintf(ficlog,"%d",i);fflush(ficlog);
1002: hess[i][i]=hessii(p,ftolhess,i,delti);
1003: /*printf(" %f ",p[i]);*/
1004: /*printf(" %lf ",hess[i][i]);*/
1005: }
1006:
1007: for (i=1;i<=npar;i++) {
1008: for (j=1;j<=npar;j++) {
1009: if (j>i) {
1010: printf(".%d%d",i,j);fflush(stdout);
1011: fprintf(ficlog,".%d%d",i,j);fflush(ficlog);
1012: hess[i][j]=hessij(p,delti,i,j);
1013: hess[j][i]=hess[i][j];
1014: /*printf(" %lf ",hess[i][j]);*/
1015: }
1016: }
1017: }
1018: printf("\n");
1019: fprintf(ficlog,"\n");
1020:
1021: printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
1022: fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
1023:
1024: a=matrix(1,npar,1,npar);
1025: y=matrix(1,npar,1,npar);
1026: x=vector(1,npar);
1027: indx=ivector(1,npar);
1028: for (i=1;i<=npar;i++)
1029: for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
1030: ludcmp(a,npar,indx,&pd);
1031:
1032: for (j=1;j<=npar;j++) {
1033: for (i=1;i<=npar;i++) x[i]=0;
1034: x[j]=1;
1035: lubksb(a,npar,indx,x);
1036: for (i=1;i<=npar;i++){
1037: matcov[i][j]=x[i];
1038: }
1039: }
1040:
1041: printf("\n#Hessian matrix#\n");
1042: fprintf(ficlog,"\n#Hessian matrix#\n");
1043: for (i=1;i<=npar;i++) {
1044: for (j=1;j<=npar;j++) {
1045: printf("%.3e ",hess[i][j]);
1046: fprintf(ficlog,"%.3e ",hess[i][j]);
1047: }
1048: printf("\n");
1049: fprintf(ficlog,"\n");
1050: }
1051:
1052: /* Recompute Inverse */
1053: for (i=1;i<=npar;i++)
1054: for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];
1055: ludcmp(a,npar,indx,&pd);
1056:
1057: /* printf("\n#Hessian matrix recomputed#\n");
1058:
1059: for (j=1;j<=npar;j++) {
1060: for (i=1;i<=npar;i++) x[i]=0;
1061: x[j]=1;
1062: lubksb(a,npar,indx,x);
1063: for (i=1;i<=npar;i++){
1064: y[i][j]=x[i];
1065: printf("%.3e ",y[i][j]);
1066: fprintf(ficlog,"%.3e ",y[i][j]);
1067: }
1068: printf("\n");
1069: fprintf(ficlog,"\n");
1070: }
1071: */
1072:
1073: free_matrix(a,1,npar,1,npar);
1074: free_matrix(y,1,npar,1,npar);
1075: free_vector(x,1,npar);
1076: free_ivector(indx,1,npar);
1077: free_matrix(hess,1,npar,1,npar);
1078:
1079:
1080: }
1081:
1082: /*************** hessian matrix ****************/
1083: double hessii( double x[], double delta, int theta, double delti[])
1084: {
1085: int i;
1086: int l=1, lmax=20;
1087: double k1,k2;
1088: double p2[NPARMAX+1];
1089: double res;
1090: double delt, delts, nkhi=10.,nkhif=1., khi=1.e-4;
1091: double fx;
1092: int k=0,kmax=10;
1093: double l1;
1094:
1095: fx=func(x);
1096: for (i=1;i<=npar;i++) p2[i]=x[i];
1097: for(l=0 ; l <=lmax; l++){
1098: l1=pow(10,l);
1099: delts=delt;
1100: for(k=1 ; k <kmax; k=k+1){
1101: delt = delta*(l1*k);
1102: p2[theta]=x[theta] +delt;
1103: k1=func(p2)-fx;
1104: p2[theta]=x[theta]-delt;
1105: k2=func(p2)-fx;
1106: /*res= (k1-2.0*fx+k2)/delt/delt; */
1107: res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */
1108:
1109: #ifdef DEBUG
1110: 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);
1111: fprintf(ficlog,"%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);
1112: #endif
1113: /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
1114: if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
1115: k=kmax;
1116: }
1117: else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
1118: k=kmax; l=lmax*10.;
1119: }
1120: else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){
1121: delts=delt;
1122: }
1123: }
1124: }
1125: delti[theta]=delts;
1126: return res;
1127:
1128: }
1129:
1130: double hessij( double x[], double delti[], int thetai,int thetaj)
1131: {
1132: int i;
1133: int l=1, l1, lmax=20;
1134: double k1,k2,k3,k4,res,fx;
1135: double p2[NPARMAX+1];
1136: int k;
1137:
1138: fx=func(x);
1139: for (k=1; k<=2; k++) {
1140: for (i=1;i<=npar;i++) p2[i]=x[i];
1141: p2[thetai]=x[thetai]+delti[thetai]/k;
1142: p2[thetaj]=x[thetaj]+delti[thetaj]/k;
1143: k1=func(p2)-fx;
1144:
1145: p2[thetai]=x[thetai]+delti[thetai]/k;
1146: p2[thetaj]=x[thetaj]-delti[thetaj]/k;
1147: k2=func(p2)-fx;
1148:
1149: p2[thetai]=x[thetai]-delti[thetai]/k;
1150: p2[thetaj]=x[thetaj]+delti[thetaj]/k;
1151: k3=func(p2)-fx;
1152:
1153: p2[thetai]=x[thetai]-delti[thetai]/k;
1154: p2[thetaj]=x[thetaj]-delti[thetaj]/k;
1155: k4=func(p2)-fx;
1156: res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */
1157: #ifdef DEBUG
1158: 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);
1159: fprintf(ficlog,"%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);
1160: #endif
1161: }
1162: return res;
1163: }
1164:
1165: /************** Inverse of matrix **************/
1166: void ludcmp(double **a, int n, int *indx, double *d)
1167: {
1168: int i,imax,j,k;
1169: double big,dum,sum,temp;
1170: double *vv;
1171:
1172: vv=vector(1,n);
1173: *d=1.0;
1174: for (i=1;i<=n;i++) {
1175: big=0.0;
1176: for (j=1;j<=n;j++)
1177: if ((temp=fabs(a[i][j])) > big) big=temp;
1178: if (big == 0.0) nrerror("Singular matrix in routine ludcmp");
1179: vv[i]=1.0/big;
1180: }
1181: for (j=1;j<=n;j++) {
1182: for (i=1;i<j;i++) {
1183: sum=a[i][j];
1184: for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];
1185: a[i][j]=sum;
1186: }
1187: big=0.0;
1188: for (i=j;i<=n;i++) {
1189: sum=a[i][j];
1190: for (k=1;k<j;k++)
1191: sum -= a[i][k]*a[k][j];
1192: a[i][j]=sum;
1193: if ( (dum=vv[i]*fabs(sum)) >= big) {
1194: big=dum;
1195: imax=i;
1196: }
1197: }
1198: if (j != imax) {
1199: for (k=1;k<=n;k++) {
1200: dum=a[imax][k];
1201: a[imax][k]=a[j][k];
1202: a[j][k]=dum;
1203: }
1204: *d = -(*d);
1205: vv[imax]=vv[j];
1206: }
1207: indx[j]=imax;
1208: if (a[j][j] == 0.0) a[j][j]=TINY;
1209: if (j != n) {
1210: dum=1.0/(a[j][j]);
1211: for (i=j+1;i<=n;i++) a[i][j] *= dum;
1212: }
1213: }
1214: free_vector(vv,1,n); /* Doesn't work */
1215: ;
1216: }
1217:
1218: void lubksb(double **a, int n, int *indx, double b[])
1219: {
1220: int i,ii=0,ip,j;
1221: double sum;
1222:
1223: for (i=1;i<=n;i++) {
1224: ip=indx[i];
1225: sum=b[ip];
1226: b[ip]=b[i];
1227: if (ii)
1228: for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];
1229: else if (sum) ii=i;
1230: b[i]=sum;
1231: }
1232: for (i=n;i>=1;i--) {
1233: sum=b[i];
1234: for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];
1235: b[i]=sum/a[i][i];
1236: }
1237: }
1238:
1239: /************ Frequencies ********************/
1240: 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,double jprev1, double mprev1,double anprev1,double jprev2, double mprev2,double anprev2)
1241: { /* Some frequencies */
1242:
1243: int i, m, jk, k1,i1, j1, bool, z1,z2,j;
1244: int first;
1245: double ***freq; /* Frequencies */
1246: double *pp;
1247: double pos, k2, dateintsum=0,k2cpt=0;
1248: FILE *ficresp;
1249: char fileresp[FILENAMELENGTH];
1250:
1251: pp=vector(1,nlstate);
1252: probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
1253: strcpy(fileresp,"p");
1254: strcat(fileresp,fileres);
1255: if((ficresp=fopen(fileresp,"w"))==NULL) {
1256: printf("Problem with prevalence resultfile: %s\n", fileresp);
1257: fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
1258: exit(0);
1259: }
1260: freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);
1261: j1=0;
1262:
1263: j=cptcoveff;
1264: if (cptcovn<1) {j=1;ncodemax[1]=1;}
1265:
1266: first=1;
1267:
1268: for(k1=1; k1<=j;k1++){
1269: for(i1=1; i1<=ncodemax[k1];i1++){
1270: j1++;
1271: /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
1272: scanf("%d", i);*/
1273: for (i=-1; i<=nlstate+ndeath; i++)
1274: for (jk=-1; jk<=nlstate+ndeath; jk++)
1275: for(m=agemin; m <= agemax+3; m++)
1276: freq[i][jk][m]=0;
1277:
1278: dateintsum=0;
1279: k2cpt=0;
1280: for (i=1; i<=imx; i++) {
1281: bool=1;
1282: if (cptcovn>0) {
1283: for (z1=1; z1<=cptcoveff; z1++)
1284: if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])
1285: bool=0;
1286: }
1287: if (bool==1){
1288: for(m=firstpass; m<=lastpass; m++){
1289: k2=anint[m][i]+(mint[m][i]/12.);
1290: if ((k2>=dateprev1) && (k2<=dateprev2)) {
1291: if(agev[m][i]==0) agev[m][i]=agemax+1;
1292: if(agev[m][i]==1) agev[m][i]=agemax+2;
1293: if (m<lastpass) {
1294: freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
1295: freq[s[m][i]][s[m+1][i]][(int) agemax+3] += weight[i];
1296: }
1297:
1298: if ((agev[m][i]>1) && (agev[m][i]< (agemax+3))) {
1299: dateintsum=dateintsum+k2;
1300: k2cpt++;
1301: }
1302: }
1303: }
1304: }
1305: }
1306:
1307: fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);
1308:
1309: if (cptcovn>0) {
1310: fprintf(ficresp, "\n#********** Variable ");
1311: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
1312: fprintf(ficresp, "**********\n#");
1313: }
1314: for(i=1; i<=nlstate;i++)
1315: fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
1316: fprintf(ficresp, "\n");
1317:
1318: for(i=(int)agemin; i <= (int)agemax+3; i++){
1319: if(i==(int)agemax+3){
1320: fprintf(ficlog,"Total");
1321: }else{
1322: if(first==1){
1323: first=0;
1324: printf("See log file for details...\n");
1325: }
1326: fprintf(ficlog,"Age %d", i);
1327: }
1328: for(jk=1; jk <=nlstate ; jk++){
1329: for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
1330: pp[jk] += freq[jk][m][i];
1331: }
1332: for(jk=1; jk <=nlstate ; jk++){
1333: for(m=-1, pos=0; m <=0 ; m++)
1334: pos += freq[jk][m][i];
1335: if(pp[jk]>=1.e-10){
1336: if(first==1){
1337: printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
1338: }
1339: fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
1340: }else{
1341: if(first==1)
1342: printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
1343: fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
1344: }
1345: }
1346:
1347: for(jk=1; jk <=nlstate ; jk++){
1348: for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
1349: pp[jk] += freq[jk][m][i];
1350: }
1351:
1352: for(jk=1,pos=0; jk <=nlstate ; jk++)
1353: pos += pp[jk];
1354: for(jk=1; jk <=nlstate ; jk++){
1355: if(pos>=1.e-5){
1356: if(first==1)
1357: printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
1358: fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
1359: }else{
1360: if(first==1)
1361: printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
1362: fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
1363: }
1364: if( i <= (int) agemax){
1365: if(pos>=1.e-5){
1366: fprintf(ficresp," %d %.5f %.0f %.0f",i,pp[jk]/pos, pp[jk],pos);
1367: probs[i][jk][j1]= pp[jk]/pos;
1368: /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/
1369: }
1370: else
1371: fprintf(ficresp," %d NaNq %.0f %.0f",i,pp[jk],pos);
1372: }
1373: }
1374:
1375: for(jk=-1; jk <=nlstate+ndeath; jk++)
1376: for(m=-1; m <=nlstate+ndeath; m++)
1377: if(freq[jk][m][i] !=0 ) {
1378: if(first==1)
1379: printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
1380: fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
1381: }
1382: if(i <= (int) agemax)
1383: fprintf(ficresp,"\n");
1384: if(first==1)
1385: printf("Others in log...\n");
1386: fprintf(ficlog,"\n");
1387: }
1388: }
1389: }
1390: dateintmean=dateintsum/k2cpt;
1391:
1392: fclose(ficresp);
1393: free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);
1394: free_vector(pp,1,nlstate);
1395:
1396: /* End of Freq */
1397: }
1398:
1399: /************ Prevalence ********************/
1400: void prevalence(int agemin, float 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)
1401: { /* Some frequencies */
1402:
1403: int i, m, jk, k1, i1, j1, bool, z1,z2,j;
1404: double ***freq; /* Frequencies */
1405: double *pp;
1406: double pos, k2;
1407:
1408: pp=vector(1,nlstate);
1409:
1410: freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);
1411: j1=0;
1412:
1413: j=cptcoveff;
1414: if (cptcovn<1) {j=1;ncodemax[1]=1;}
1415:
1416: for(k1=1; k1<=j;k1++){
1417: for(i1=1; i1<=ncodemax[k1];i1++){
1418: j1++;
1419:
1420: for (i=-1; i<=nlstate+ndeath; i++)
1421: for (jk=-1; jk<=nlstate+ndeath; jk++)
1422: for(m=agemin; m <= agemax+3; m++)
1423: freq[i][jk][m]=0;
1424:
1425: for (i=1; i<=imx; i++) {
1426: bool=1;
1427: if (cptcovn>0) {
1428: for (z1=1; z1<=cptcoveff; z1++)
1429: if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])
1430: bool=0;
1431: }
1432: if (bool==1) {
1433: for(m=firstpass; m<=lastpass; m++){
1434: k2=anint[m][i]+(mint[m][i]/12.);
1435: if ((k2>=dateprev1) && (k2<=dateprev2)) {
1436: if(agev[m][i]==0) agev[m][i]=agemax+1;
1437: if(agev[m][i]==1) agev[m][i]=agemax+2;
1438: if (m<lastpass) {
1439: if (calagedate>0)
1440: freq[s[m][i]][s[m+1][i]][(int)(agev[m][i]+1-((int)calagedate %12)/12.)] += weight[i];
1441: else
1442: freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
1443: freq[s[m][i]][s[m+1][i]][(int)(agemax+3)] += weight[i];
1444: }
1445: }
1446: }
1447: }
1448: }
1449: for(i=(int)agemin; i <= (int)agemax+3; i++){
1450: for(jk=1; jk <=nlstate ; jk++){
1451: for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
1452: pp[jk] += freq[jk][m][i];
1453: }
1454: for(jk=1; jk <=nlstate ; jk++){
1455: for(m=-1, pos=0; m <=0 ; m++)
1456: pos += freq[jk][m][i];
1457: }
1458:
1459: for(jk=1; jk <=nlstate ; jk++){
1460: for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
1461: pp[jk] += freq[jk][m][i];
1462: }
1463:
1464: for(jk=1,pos=0; jk <=nlstate ; jk++) pos += pp[jk];
1465:
1466: for(jk=1; jk <=nlstate ; jk++){
1467: if( i <= (int) agemax){
1468: if(pos>=1.e-5){
1469: probs[i][jk][j1]= pp[jk]/pos;
1470: }
1471: }
1472: }/* end jk */
1473: }/* end i */
1474: } /* end i1 */
1475: } /* end k1 */
1476:
1477:
1478: free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);
1479: free_vector(pp,1,nlstate);
1480:
1481: } /* End of Freq */
1482:
1483: /************* Waves Concatenation ***************/
1484:
1485: void concatwav(int wav[], int **dh, int **mw, int **s, double *agedc, double **agev, int firstpass, int lastpass, int imx, int nlstate, int stepm)
1486: {
1487: /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
1488: Death is a valid wave (if date is known).
1489: mw[mi][i] is the mi (mi=1 to wav[i]) effective wave of individual i
1490: dh[m][i] of dh[mw[mi][i][i] is the delay between two effective waves m=mw[mi][i]
1491: and mw[mi+1][i]. dh depends on stepm.
1492: */
1493:
1494: int i, mi, m;
1495: /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
1496: double sum=0., jmean=0.;*/
1497: int first;
1498: int j, k=0,jk, ju, jl;
1499: double sum=0.;
1500: first=0;
1501: jmin=1e+5;
1502: jmax=-1;
1503: jmean=0.;
1504: for(i=1; i<=imx; i++){
1505: mi=0;
1506: m=firstpass;
1507: while(s[m][i] <= nlstate){
1508: if(s[m][i]>=1)
1509: mw[++mi][i]=m;
1510: if(m >=lastpass)
1511: break;
1512: else
1513: m++;
1514: }/* end while */
1515: if (s[m][i] > nlstate){
1516: mi++; /* Death is another wave */
1517: /* if(mi==0) never been interviewed correctly before death */
1518: /* Only death is a correct wave */
1519: mw[mi][i]=m;
1520: }
1521:
1522: wav[i]=mi;
1523: if(mi==0){
1524: if(first==0){
1525: printf("Warning, no any valid information for:%d line=%d and may be others, see log file\n",num[i],i);
1526: first=1;
1527: }
1528: if(first==1){
1529: fprintf(ficlog,"Warning, no any valid information for:%d line=%d\n",num[i],i);
1530: }
1531: } /* end mi==0 */
1532: }
1533:
1534: for(i=1; i<=imx; i++){
1535: for(mi=1; mi<wav[i];mi++){
1536: if (stepm <=0)
1537: dh[mi][i]=1;
1538: else{
1539: if (s[mw[mi+1][i]][i] > nlstate) {
1540: if (agedc[i] < 2*AGESUP) {
1541: j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);
1542: if(j==0) j=1; /* Survives at least one month after exam */
1543: k=k+1;
1544: if (j >= jmax) jmax=j;
1545: if (j <= jmin) jmin=j;
1546: sum=sum+j;
1547: /*if (j<0) printf("j=%d num=%d \n",j,i); */
1548: }
1549: }
1550: else{
1551: j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
1552: k=k+1;
1553: if (j >= jmax) jmax=j;
1554: else if (j <= jmin)jmin=j;
1555: /* if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
1556: sum=sum+j;
1557: }
1558: jk= j/stepm;
1559: jl= j -jk*stepm;
1560: ju= j -(jk+1)*stepm;
1561: if(jl <= -ju)
1562: dh[mi][i]=jk;
1563: else
1564: dh[mi][i]=jk+1;
1565: if(dh[mi][i]==0)
1566: dh[mi][i]=1; /* At least one step */
1567: }
1568: }
1569: }
1570: jmean=sum/k;
1571: printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);
1572: fprintf(ficlog,"Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);
1573: }
1574:
1575: /*********** Tricode ****************************/
1576: void tricode(int *Tvar, int **nbcode, int imx)
1577: {
1578:
1579: int Ndum[20],ij=1, k, j, i, maxncov=19;
1580: int cptcode=0;
1581: cptcoveff=0;
1582:
1583: for (k=0; k<maxncov; k++) Ndum[k]=0;
1584: for (k=1; k<=7; k++) ncodemax[k]=0;
1585:
1586: for (j=1; j<=(cptcovn+2*cptcovprod); j++) {
1587: for (i=1; i<=imx; i++) { /*reads the data file to get the maximum
1588: modality*/
1589: ij=(int)(covar[Tvar[j]][i]); /* ij is the modality of this individual*/
1590: Ndum[ij]++; /*store the modality */
1591: /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
1592: if (ij > cptcode) cptcode=ij; /* getting the maximum of covariable
1593: Tvar[j]. If V=sex and male is 0 and
1594: female is 1, then cptcode=1.*/
1595: }
1596:
1597: for (i=0; i<=cptcode; i++) {
1598: if(Ndum[i]!=0) ncodemax[j]++; /* Nomber of modalities of the j th covariates. In fact ncodemax[j]=2 (dichotom. variables) but it can be more */
1599: }
1600:
1601: ij=1;
1602: for (i=1; i<=ncodemax[j]; i++) {
1603: for (k=0; k<= maxncov; k++) {
1604: if (Ndum[k] != 0) {
1605: nbcode[Tvar[j]][ij]=k;
1606: /* store the modality in an array. k is a modality. If we have model=V1+V1*sex then: nbcode[1][1]=0 ; nbcode[1][2]=1; nbcode[2][1]=0 ; nbcode[2][2]=1; */
1607:
1608: ij++;
1609: }
1610: if (ij > ncodemax[j]) break;
1611: }
1612: }
1613: }
1614:
1615: for (k=0; k< maxncov; k++) Ndum[k]=0;
1616:
1617: for (i=1; i<=ncovmodel-2; i++) {
1618: /* Listing of all covariables in staement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/
1619: ij=Tvar[i];
1620: Ndum[ij]++;
1621: }
1622:
1623: ij=1;
1624: for (i=1; i<= maxncov; i++) {
1625: if((Ndum[i]!=0) && (i<=ncovcol)){
1626: Tvaraff[ij]=i; /*For printing */
1627: ij++;
1628: }
1629: }
1630:
1631: cptcoveff=ij-1; /*Number of simple covariates*/
1632: }
1633:
1634: /*********** Health Expectancies ****************/
1635:
1636: void evsij(char fileres[], double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int ij, int estepm,double delti[],double **matcov )
1637:
1638: {
1639: /* Health expectancies */
1640: int i, j, nhstepm, hstepm, h, nstepm, k, cptj;
1641: double age, agelim, hf;
1642: double ***p3mat,***varhe;
1643: double **dnewm,**doldm;
1644: double *xp;
1645: double **gp, **gm;
1646: double ***gradg, ***trgradg;
1647: int theta;
1648:
1649: varhe=ma3x(1,nlstate*2,1,nlstate*2,(int) bage, (int) fage);
1650: xp=vector(1,npar);
1651: dnewm=matrix(1,nlstate*2,1,npar);
1652: doldm=matrix(1,nlstate*2,1,nlstate*2);
1653:
1654: fprintf(ficreseij,"# Health expectancies\n");
1655: fprintf(ficreseij,"# Age");
1656: for(i=1; i<=nlstate;i++)
1657: for(j=1; j<=nlstate;j++)
1658: fprintf(ficreseij," %1d-%1d (SE)",i,j);
1659: fprintf(ficreseij,"\n");
1660:
1661: if(estepm < stepm){
1662: printf ("Problem %d lower than %d\n",estepm, stepm);
1663: }
1664: else hstepm=estepm;
1665: /* We compute the life expectancy from trapezoids spaced every estepm months
1666: * This is mainly to measure the difference between two models: for example
1667: * if stepm=24 months pijx are given only every 2 years and by summing them
1668: * we are calculating an estimate of the Life Expectancy assuming a linear
1669: * progression inbetween and thus overestimating or underestimating according
1670: * to the curvature of the survival function. If, for the same date, we
1671: * estimate the model with stepm=1 month, we can keep estepm to 24 months
1672: * to compare the new estimate of Life expectancy with the same linear
1673: * hypothesis. A more precise result, taking into account a more precise
1674: * curvature will be obtained if estepm is as small as stepm. */
1675:
1676: /* For example we decided to compute the life expectancy with the smallest unit */
1677: /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
1678: nhstepm is the number of hstepm from age to agelim
1679: nstepm is the number of stepm from age to agelin.
1680: Look at hpijx to understand the reason of that which relies in memory size
1681: and note for a fixed period like estepm months */
1682: /* We decided (b) to get a life expectancy respecting the most precise curvature of the
1683: survival function given by stepm (the optimization length). Unfortunately it
1684: means that if the survival funtion is printed only each two years of age and if
1685: you sum them up and add 1 year (area under the trapezoids) you won't get the same
1686: results. So we changed our mind and took the option of the best precision.
1687: */
1688: hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
1689:
1690: agelim=AGESUP;
1691: for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
1692: /* nhstepm age range expressed in number of stepm */
1693: nstepm=(int) rint((agelim-age)*YEARM/stepm);
1694: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
1695: /* if (stepm >= YEARM) hstepm=1;*/
1696: nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
1697: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
1698: gradg=ma3x(0,nhstepm,1,npar,1,nlstate*2);
1699: gp=matrix(0,nhstepm,1,nlstate*2);
1700: gm=matrix(0,nhstepm,1,nlstate*2);
1701:
1702: /* Computed by stepm unit matrices, product of hstepm matrices, stored
1703: in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
1704: hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);
1705:
1706:
1707: hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
1708:
1709: /* Computing Variances of health expectancies */
1710:
1711: for(theta=1; theta <=npar; theta++){
1712: for(i=1; i<=npar; i++){
1713: xp[i] = x[i] + (i==theta ?delti[theta]:0);
1714: }
1715: hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
1716:
1717: cptj=0;
1718: for(j=1; j<= nlstate; j++){
1719: for(i=1; i<=nlstate; i++){
1720: cptj=cptj+1;
1721: for(h=0, gp[h][cptj]=0.; h<=nhstepm-1; h++){
1722: gp[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;
1723: }
1724: }
1725: }
1726:
1727:
1728: for(i=1; i<=npar; i++)
1729: xp[i] = x[i] - (i==theta ?delti[theta]:0);
1730: hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
1731:
1732: cptj=0;
1733: for(j=1; j<= nlstate; j++){
1734: for(i=1;i<=nlstate;i++){
1735: cptj=cptj+1;
1736: for(h=0, gm[h][cptj]=0.; h<=nhstepm-1; h++){
1737: gm[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;
1738: }
1739: }
1740: }
1741: for(j=1; j<= nlstate*2; j++)
1742: for(h=0; h<=nhstepm-1; h++){
1743: gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
1744: }
1745: }
1746:
1747: /* End theta */
1748:
1749: trgradg =ma3x(0,nhstepm,1,nlstate*2,1,npar);
1750:
1751: for(h=0; h<=nhstepm-1; h++)
1752: for(j=1; j<=nlstate*2;j++)
1753: for(theta=1; theta <=npar; theta++)
1754: trgradg[h][j][theta]=gradg[h][theta][j];
1755:
1756:
1757: for(i=1;i<=nlstate*2;i++)
1758: for(j=1;j<=nlstate*2;j++)
1759: varhe[i][j][(int)age] =0.;
1760:
1761: printf("%d|",(int)age);fflush(stdout);
1762: fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
1763: for(h=0;h<=nhstepm-1;h++){
1764: for(k=0;k<=nhstepm-1;k++){
1765: matprod2(dnewm,trgradg[h],1,nlstate*2,1,npar,1,npar,matcov);
1766: matprod2(doldm,dnewm,1,nlstate*2,1,npar,1,nlstate*2,gradg[k]);
1767: for(i=1;i<=nlstate*2;i++)
1768: for(j=1;j<=nlstate*2;j++)
1769: varhe[i][j][(int)age] += doldm[i][j]*hf*hf;
1770: }
1771: }
1772: /* Computing expectancies */
1773: for(i=1; i<=nlstate;i++)
1774: for(j=1; j<=nlstate;j++)
1775: for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
1776: eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
1777:
1778: /* if((int)age==70)printf("i=%2d,j=%2d,h=%2d,age=%3d,%9.4f,%9.4f,%9.4f\n",i,j,h,(int)age,p3mat[i][j][h],hf,eij[i][j][(int)age]);*/
1779:
1780: }
1781:
1782: fprintf(ficreseij,"%3.0f",age );
1783: cptj=0;
1784: for(i=1; i<=nlstate;i++)
1785: for(j=1; j<=nlstate;j++){
1786: cptj++;
1787: fprintf(ficreseij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[cptj][cptj][(int)age]) );
1788: }
1789: fprintf(ficreseij,"\n");
1790:
1791: free_matrix(gm,0,nhstepm,1,nlstate*2);
1792: free_matrix(gp,0,nhstepm,1,nlstate*2);
1793: free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*2);
1794: free_ma3x(trgradg,0,nhstepm,1,nlstate*2,1,npar);
1795: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
1796: }
1797: printf("\n");
1798: fprintf(ficlog,"\n");
1799:
1800: free_vector(xp,1,npar);
1801: free_matrix(dnewm,1,nlstate*2,1,npar);
1802: free_matrix(doldm,1,nlstate*2,1,nlstate*2);
1803: free_ma3x(varhe,1,nlstate*2,1,nlstate*2,(int) bage, (int)fage);
1804: }
1805:
1806: /************ Variance ******************/
1807: void varevsij(char optionfilefiname[], 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, int estepm, int cptcov, int cptcod, int popbased, int mobilav)
1808: {
1809: /* Variance of health expectancies */
1810: /* double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
1811: /* double **newm;*/
1812: double **dnewm,**doldm;
1813: double **dnewmp,**doldmp;
1814: int i, j, nhstepm, hstepm, h, nstepm ;
1815: int k, cptcode;
1816: double *xp;
1817: double **gp, **gm; /* for var eij */
1818: double ***gradg, ***trgradg; /*for var eij */
1819: double **gradgp, **trgradgp; /* for var p point j */
1820: double *gpp, *gmp; /* for var p point j */
1821: double **varppt; /* for var p point j nlstate to nlstate+ndeath */
1822: double ***p3mat;
1823: double age,agelim, hf;
1824: double ***mobaverage;
1825: int theta;
1826: char digit[4];
1827: char digitp[25];
1828:
1829: char fileresprobmorprev[FILENAMELENGTH];
1830:
1831: if(popbased==1){
1832: if(mobilav!=0)
1833: strcpy(digitp,"-populbased-mobilav-");
1834: else strcpy(digitp,"-populbased-nomobil-");
1835: }
1836: else
1837: strcpy(digitp,"-stablbased-");
1838:
1839: if (mobilav!=0) {
1840: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
1841: if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
1842: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
1843: printf(" Error in movingaverage mobilav=%d\n",mobilav);
1844: }
1845: }
1846:
1847: strcpy(fileresprobmorprev,"prmorprev");
1848: sprintf(digit,"%-d",ij);
1849: /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
1850: strcat(fileresprobmorprev,digit); /* Tvar to be done */
1851: strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
1852: strcat(fileresprobmorprev,fileres);
1853: if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
1854: printf("Problem with resultfile: %s\n", fileresprobmorprev);
1855: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
1856: }
1857: printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
1858: fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
1859: fprintf(ficresprobmorprev,"# probabilities of dying during a year and weighted mean w1*p1j+w2*p2j+... stand dev in()\n");
1860: fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
1861: for(j=nlstate+1; j<=(nlstate+ndeath);j++){
1862: fprintf(ficresprobmorprev," p.%-d SE",j);
1863: for(i=1; i<=nlstate;i++)
1864: fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
1865: }
1866: fprintf(ficresprobmorprev,"\n");
1867: if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {
1868: printf("Problem with gnuplot file: %s\n", optionfilegnuplot);
1869: fprintf(ficlog,"Problem with gnuplot file: %s\n", optionfilegnuplot);
1870: exit(0);
1871: }
1872: else{
1873: fprintf(ficgp,"\n# Routine varevsij");
1874: }
1875: if((fichtm=fopen(optionfilehtm,"a"))==NULL) {
1876: printf("Problem with html file: %s\n", optionfilehtm);
1877: fprintf(ficlog,"Problem with html file: %s\n", optionfilehtm);
1878: exit(0);
1879: }
1880: else{
1881: fprintf(fichtm,"\n<li><h4> Computing probabilities of dying as a weighted average (i.e global mortality independent of initial healh state)</h4></li>\n");
1882: fprintf(fichtm,"\n<br>%s (à revoir) <br>\n",digitp);
1883: }
1884: varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
1885:
1886: fprintf(ficresvij,"# Variance and covariance of health expectancies e.j \n# (weighted average of eij where weights are the stable prevalence in health states i\n");
1887: fprintf(ficresvij,"# Age");
1888: for(i=1; i<=nlstate;i++)
1889: for(j=1; j<=nlstate;j++)
1890: fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);
1891: fprintf(ficresvij,"\n");
1892:
1893: xp=vector(1,npar);
1894: dnewm=matrix(1,nlstate,1,npar);
1895: doldm=matrix(1,nlstate,1,nlstate);
1896: dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
1897: doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
1898:
1899: gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
1900: gpp=vector(nlstate+1,nlstate+ndeath);
1901: gmp=vector(nlstate+1,nlstate+ndeath);
1902: trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
1903:
1904: if(estepm < stepm){
1905: printf ("Problem %d lower than %d\n",estepm, stepm);
1906: }
1907: else hstepm=estepm;
1908: /* For example we decided to compute the life expectancy with the smallest unit */
1909: /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
1910: nhstepm is the number of hstepm from age to agelim
1911: nstepm is the number of stepm from age to agelin.
1912: Look at hpijx to understand the reason of that which relies in memory size
1913: and note for a fixed period like k years */
1914: /* We decided (b) to get a life expectancy respecting the most precise curvature of the
1915: survival function given by stepm (the optimization length). Unfortunately it
1916: means that if the survival funtion is printed only each two years of age and if
1917: you sum them up and add 1 year (area under the trapezoids) you won't get the same
1918: results. So we changed our mind and took the option of the best precision.
1919: */
1920: hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
1921: agelim = AGESUP;
1922: for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
1923: nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
1924: nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
1925: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
1926: gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
1927: gp=matrix(0,nhstepm,1,nlstate);
1928: gm=matrix(0,nhstepm,1,nlstate);
1929:
1930:
1931: for(theta=1; theta <=npar; theta++){
1932: for(i=1; i<=npar; i++){ /* Computes gradient */
1933: xp[i] = x[i] + (i==theta ?delti[theta]:0);
1934: }
1935: hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
1936: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
1937:
1938: if (popbased==1) {
1939: if(mobilav ==0){
1940: for(i=1; i<=nlstate;i++)
1941: prlim[i][i]=probs[(int)age][i][ij];
1942: }else{ /* mobilav */
1943: for(i=1; i<=nlstate;i++)
1944: prlim[i][i]=mobaverage[(int)age][i][ij];
1945: }
1946: }
1947:
1948: for(j=1; j<= nlstate; j++){
1949: for(h=0; h<=nhstepm; h++){
1950: for(i=1, gp[h][j]=0.;i<=nlstate;i++)
1951: gp[h][j] += prlim[i][i]*p3mat[i][j][h];
1952: }
1953: }
1954: /* This for computing forces of mortality (h=1)as a weighted average */
1955: for(j=nlstate+1,gpp[j]=0.;j<=nlstate+ndeath;j++){
1956: for(i=1; i<= nlstate; i++)
1957: gpp[j] += prlim[i][i]*p3mat[i][j][1];
1958: }
1959: /* end force of mortality */
1960:
1961: for(i=1; i<=npar; i++) /* Computes gradient */
1962: xp[i] = x[i] - (i==theta ?delti[theta]:0);
1963: hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
1964: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
1965:
1966: if (popbased==1) {
1967: if(mobilav ==0){
1968: for(i=1; i<=nlstate;i++)
1969: prlim[i][i]=probs[(int)age][i][ij];
1970: }else{ /* mobilav */
1971: for(i=1; i<=nlstate;i++)
1972: prlim[i][i]=mobaverage[(int)age][i][ij];
1973: }
1974: }
1975:
1976: for(j=1; j<= nlstate; j++){
1977: for(h=0; h<=nhstepm; h++){
1978: for(i=1, gm[h][j]=0.;i<=nlstate;i++)
1979: gm[h][j] += prlim[i][i]*p3mat[i][j][h];
1980: }
1981: }
1982: /* This for computing force of mortality (h=1)as a weighted average */
1983: for(j=nlstate+1,gmp[j]=0.;j<=nlstate+ndeath;j++){
1984: for(i=1; i<= nlstate; i++)
1985: gmp[j] += prlim[i][i]*p3mat[i][j][1];
1986: }
1987: /* end force of mortality */
1988:
1989: for(j=1; j<= nlstate; j++) /* vareij */
1990: for(h=0; h<=nhstepm; h++){
1991: gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
1992: }
1993: for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
1994: gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
1995: }
1996:
1997: } /* End theta */
1998:
1999: trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
2000:
2001: for(h=0; h<=nhstepm; h++) /* veij */
2002: for(j=1; j<=nlstate;j++)
2003: for(theta=1; theta <=npar; theta++)
2004: trgradg[h][j][theta]=gradg[h][theta][j];
2005:
2006: for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
2007: for(theta=1; theta <=npar; theta++)
2008: trgradgp[j][theta]=gradgp[theta][j];
2009:
2010: hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
2011: for(i=1;i<=nlstate;i++)
2012: for(j=1;j<=nlstate;j++)
2013: vareij[i][j][(int)age] =0.;
2014:
2015: for(h=0;h<=nhstepm;h++){
2016: for(k=0;k<=nhstepm;k++){
2017: matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
2018: matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
2019: for(i=1;i<=nlstate;i++)
2020: for(j=1;j<=nlstate;j++)
2021: vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
2022: }
2023: }
2024:
2025: /* pptj */
2026: matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
2027: matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
2028: for(j=nlstate+1;j<=nlstate+ndeath;j++)
2029: for(i=nlstate+1;i<=nlstate+ndeath;i++)
2030: varppt[j][i]=doldmp[j][i];
2031: /* end ppptj */
2032: hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);
2033: prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);
2034:
2035: if (popbased==1) {
2036: if(mobilav ==0){
2037: for(i=1; i<=nlstate;i++)
2038: prlim[i][i]=probs[(int)age][i][ij];
2039: }else{ /* mobilav */
2040: for(i=1; i<=nlstate;i++)
2041: prlim[i][i]=mobaverage[(int)age][i][ij];
2042: }
2043: }
2044:
2045: /* This for computing force of mortality (h=1)as a weighted average */
2046: for(j=nlstate+1,gmp[j]=0.;j<=nlstate+ndeath;j++){
2047: for(i=1; i<= nlstate; i++)
2048: gmp[j] += prlim[i][i]*p3mat[i][j][1];
2049: }
2050: /* end force of mortality */
2051:
2052: fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
2053: for(j=nlstate+1; j<=(nlstate+ndeath);j++){
2054: fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
2055: for(i=1; i<=nlstate;i++){
2056: fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
2057: }
2058: }
2059: fprintf(ficresprobmorprev,"\n");
2060:
2061: fprintf(ficresvij,"%.0f ",age );
2062: for(i=1; i<=nlstate;i++)
2063: for(j=1; j<=nlstate;j++){
2064: fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
2065: }
2066: fprintf(ficresvij,"\n");
2067: free_matrix(gp,0,nhstepm,1,nlstate);
2068: free_matrix(gm,0,nhstepm,1,nlstate);
2069: free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
2070: free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
2071: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
2072: } /* End age */
2073: free_vector(gpp,nlstate+1,nlstate+ndeath);
2074: free_vector(gmp,nlstate+1,nlstate+ndeath);
2075: free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
2076: free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
2077: fprintf(ficgp,"\nset noparametric;set nolabel; set ter png small;set size 0.65, 0.65");
2078: /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */
2079: fprintf(ficgp,"\n set log y; set nolog x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
2080: fprintf(ficgp,"\n plot \"%s\" u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm);
2081: fprintf(ficgp,"\n replot \"%s\" u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm);
2082: fprintf(ficgp,"\n replot \"%s\" u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm);
2083: fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",fileresprobmorprev,fileresprobmorprev);
2084: fprintf(fichtm,"\n<br> Probability is computed over estepm=%d months. <br> <img src=\"varmuptjgr%s%s.png\"> <br>\n", stepm,digitp,digit);
2085: /* fprintf(fichtm,"\n<br> Probability is computed over estepm=%d months and then divided by estepm and multiplied by %.0f in order to have the probability to die over a year <br> <img src=\"varmuptjgr%s%s.png\"> <br>\n", stepm,YEARM,digitp,digit);
2086: */
2087: fprintf(ficgp,"\nset out \"varmuptjgr%s%s.png\";replot;",digitp,digit);
2088:
2089: free_vector(xp,1,npar);
2090: free_matrix(doldm,1,nlstate,1,nlstate);
2091: free_matrix(dnewm,1,nlstate,1,npar);
2092: free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
2093: free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
2094: free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
2095: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
2096: fclose(ficresprobmorprev);
2097: fclose(ficgp);
2098: fclose(fichtm);
2099: }
2100:
2101: /************ Variance of prevlim ******************/
2102: 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)
2103: {
2104: /* Variance of prevalence limit */
2105: /* double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
2106: double **newm;
2107: double **dnewm,**doldm;
2108: int i, j, nhstepm, hstepm;
2109: int k, cptcode;
2110: double *xp;
2111: double *gp, *gm;
2112: double **gradg, **trgradg;
2113: double age,agelim;
2114: int theta;
2115:
2116: fprintf(ficresvpl,"# Standard deviation of stable prevalences \n");
2117: fprintf(ficresvpl,"# Age");
2118: for(i=1; i<=nlstate;i++)
2119: fprintf(ficresvpl," %1d-%1d",i,i);
2120: fprintf(ficresvpl,"\n");
2121:
2122: xp=vector(1,npar);
2123: dnewm=matrix(1,nlstate,1,npar);
2124: doldm=matrix(1,nlstate,1,nlstate);
2125:
2126: hstepm=1*YEARM; /* Every year of age */
2127: hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */
2128: agelim = AGESUP;
2129: for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
2130: nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
2131: if (stepm >= YEARM) hstepm=1;
2132: nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
2133: gradg=matrix(1,npar,1,nlstate);
2134: gp=vector(1,nlstate);
2135: gm=vector(1,nlstate);
2136:
2137: for(theta=1; theta <=npar; theta++){
2138: for(i=1; i<=npar; i++){ /* Computes gradient */
2139: xp[i] = x[i] + (i==theta ?delti[theta]:0);
2140: }
2141: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
2142: for(i=1;i<=nlstate;i++)
2143: gp[i] = prlim[i][i];
2144:
2145: for(i=1; i<=npar; i++) /* Computes gradient */
2146: xp[i] = x[i] - (i==theta ?delti[theta]:0);
2147: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
2148: for(i=1;i<=nlstate;i++)
2149: gm[i] = prlim[i][i];
2150:
2151: for(i=1;i<=nlstate;i++)
2152: gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
2153: } /* End theta */
2154:
2155: trgradg =matrix(1,nlstate,1,npar);
2156:
2157: for(j=1; j<=nlstate;j++)
2158: for(theta=1; theta <=npar; theta++)
2159: trgradg[j][theta]=gradg[theta][j];
2160:
2161: for(i=1;i<=nlstate;i++)
2162: varpl[i][(int)age] =0.;
2163: matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
2164: matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
2165: for(i=1;i<=nlstate;i++)
2166: varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
2167:
2168: fprintf(ficresvpl,"%.0f ",age );
2169: for(i=1; i<=nlstate;i++)
2170: fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
2171: fprintf(ficresvpl,"\n");
2172: free_vector(gp,1,nlstate);
2173: free_vector(gm,1,nlstate);
2174: free_matrix(gradg,1,npar,1,nlstate);
2175: free_matrix(trgradg,1,nlstate,1,npar);
2176: } /* End age */
2177:
2178: free_vector(xp,1,npar);
2179: free_matrix(doldm,1,nlstate,1,npar);
2180: free_matrix(dnewm,1,nlstate,1,nlstate);
2181:
2182: }
2183:
2184: /************ Variance of one-step probabilities ******************/
2185: void varprob(char optionfilefiname[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij, int *Tvar, int **nbcode, int *ncodemax)
2186: {
2187: int i, j=0, i1, k1, l1, t, tj;
2188: int k2, l2, j1, z1;
2189: int k=0,l, cptcode;
2190: int first=1, first1;
2191: double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
2192: double **dnewm,**doldm;
2193: double *xp;
2194: double *gp, *gm;
2195: double **gradg, **trgradg;
2196: double **mu;
2197: double age,agelim, cov[NCOVMAX];
2198: double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
2199: int theta;
2200: char fileresprob[FILENAMELENGTH];
2201: char fileresprobcov[FILENAMELENGTH];
2202: char fileresprobcor[FILENAMELENGTH];
2203:
2204: double ***varpij;
2205:
2206: strcpy(fileresprob,"prob");
2207: strcat(fileresprob,fileres);
2208: if((ficresprob=fopen(fileresprob,"w"))==NULL) {
2209: printf("Problem with resultfile: %s\n", fileresprob);
2210: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
2211: }
2212: strcpy(fileresprobcov,"probcov");
2213: strcat(fileresprobcov,fileres);
2214: if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
2215: printf("Problem with resultfile: %s\n", fileresprobcov);
2216: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
2217: }
2218: strcpy(fileresprobcor,"probcor");
2219: strcat(fileresprobcor,fileres);
2220: if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
2221: printf("Problem with resultfile: %s\n", fileresprobcor);
2222: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
2223: }
2224: printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
2225: fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
2226: printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
2227: fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
2228: printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
2229: fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
2230:
2231: fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
2232: fprintf(ficresprob,"# Age");
2233: fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
2234: fprintf(ficresprobcov,"# Age");
2235: fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
2236: fprintf(ficresprobcov,"# Age");
2237:
2238:
2239: for(i=1; i<=nlstate;i++)
2240: for(j=1; j<=(nlstate+ndeath);j++){
2241: fprintf(ficresprob," p%1d-%1d (SE)",i,j);
2242: fprintf(ficresprobcov," p%1d-%1d ",i,j);
2243: fprintf(ficresprobcor," p%1d-%1d ",i,j);
2244: }
2245: fprintf(ficresprob,"\n");
2246: fprintf(ficresprobcov,"\n");
2247: fprintf(ficresprobcor,"\n");
2248: xp=vector(1,npar);
2249: dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
2250: doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
2251: mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
2252: varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
2253: first=1;
2254: if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {
2255: printf("Problem with gnuplot file: %s\n", optionfilegnuplot);
2256: fprintf(ficlog,"Problem with gnuplot file: %s\n", optionfilegnuplot);
2257: exit(0);
2258: }
2259: else{
2260: fprintf(ficgp,"\n# Routine varprob");
2261: }
2262: if((fichtm=fopen(optionfilehtm,"a"))==NULL) {
2263: printf("Problem with html file: %s\n", optionfilehtm);
2264: fprintf(ficlog,"Problem with html file: %s\n", optionfilehtm);
2265: exit(0);
2266: }
2267: else{
2268: fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
2269: fprintf(fichtm,"\n");
2270:
2271: fprintf(fichtm,"\n<li><h4> Computing matrix of variance-covariance of step probabilities</h4></li>\n");
2272: fprintf(fichtm,"\nWe have drawn ellipsoids of confidence around the p<inf>ij</inf>, p<inf>kl</inf> to understand the covariance between two incidences. They are expressed in year<sup>-1</sup> in order to be less dependent of stepm.<br>\n");
2273: fprintf(fichtm,"\n<br> We have drawn x'cov<sup>-1</sup>x = 4 where x is the column vector (pij,pkl). It means that if pij and pkl where uncorrelated the (2X2) matrix would have been (1/(var pij), 0 , 0, 1/(var pkl)), and the confidence interval would be 2 standard deviations wide on each axis. <br> When both incidences are correlated we diagonalised the inverse of the covariance matrix and made the appropriate rotation.<br> \n");
2274:
2275: }
2276:
2277:
2278: cov[1]=1;
2279: tj=cptcoveff;
2280: if (cptcovn<1) {tj=1;ncodemax[1]=1;}
2281: j1=0;
2282: for(t=1; t<=tj;t++){
2283: for(i1=1; i1<=ncodemax[t];i1++){
2284: j1++;
2285:
2286: if (cptcovn>0) {
2287: fprintf(ficresprob, "\n#********** Variable ");
2288: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
2289: fprintf(ficresprob, "**********\n#");
2290: fprintf(ficresprobcov, "\n#********** Variable ");
2291: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
2292: fprintf(ficresprobcov, "**********\n#");
2293:
2294: fprintf(ficgp, "\n#********** Variable ");
2295: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, "# V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
2296: fprintf(ficgp, "**********\n#");
2297:
2298:
2299: fprintf(fichtm, "\n<hr size=\"2\" color=\"#EC5E5E\">********** Variable ");
2300: for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
2301: fprintf(fichtm, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
2302:
2303: fprintf(ficresprobcor, "\n#********** Variable ");
2304: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
2305: fprintf(ficgp, "**********\n#");
2306: }
2307:
2308: for (age=bage; age<=fage; age ++){
2309: cov[2]=age;
2310: for (k=1; k<=cptcovn;k++) {
2311: cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];
2312: }
2313: for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
2314: for (k=1; k<=cptcovprod;k++)
2315: cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
2316:
2317: gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
2318: trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
2319: gp=vector(1,(nlstate)*(nlstate+ndeath));
2320: gm=vector(1,(nlstate)*(nlstate+ndeath));
2321:
2322: for(theta=1; theta <=npar; theta++){
2323: for(i=1; i<=npar; i++)
2324: xp[i] = x[i] + (i==theta ?delti[theta]:0);
2325:
2326: pmij(pmmij,cov,ncovmodel,xp,nlstate);
2327:
2328: k=0;
2329: for(i=1; i<= (nlstate); i++){
2330: for(j=1; j<=(nlstate+ndeath);j++){
2331: k=k+1;
2332: gp[k]=pmmij[i][j];
2333: }
2334: }
2335:
2336: for(i=1; i<=npar; i++)
2337: xp[i] = x[i] - (i==theta ?delti[theta]:0);
2338:
2339: pmij(pmmij,cov,ncovmodel,xp,nlstate);
2340: k=0;
2341: for(i=1; i<=(nlstate); i++){
2342: for(j=1; j<=(nlstate+ndeath);j++){
2343: k=k+1;
2344: gm[k]=pmmij[i][j];
2345: }
2346: }
2347:
2348: for(i=1; i<= (nlstate)*(nlstate+ndeath); i++)
2349: gradg[theta][i]=(gp[i]-gm[i])/2./delti[theta];
2350: }
2351:
2352: for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
2353: for(theta=1; theta <=npar; theta++)
2354: trgradg[j][theta]=gradg[theta][j];
2355:
2356: matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov);
2357: matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);
2358:
2359: pmij(pmmij,cov,ncovmodel,x,nlstate);
2360:
2361: k=0;
2362: for(i=1; i<=(nlstate); i++){
2363: for(j=1; j<=(nlstate+ndeath);j++){
2364: k=k+1;
2365: mu[k][(int) age]=pmmij[i][j];
2366: }
2367: }
2368: for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
2369: for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
2370: varpij[i][j][(int)age] = doldm[i][j];
2371:
2372: /*printf("\n%d ",(int)age);
2373: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
2374: printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
2375: fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
2376: }*/
2377:
2378: fprintf(ficresprob,"\n%d ",(int)age);
2379: fprintf(ficresprobcov,"\n%d ",(int)age);
2380: fprintf(ficresprobcor,"\n%d ",(int)age);
2381:
2382: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)
2383: fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));
2384: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
2385: fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);
2386: fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
2387: }
2388: i=0;
2389: for (k=1; k<=(nlstate);k++){
2390: for (l=1; l<=(nlstate+ndeath);l++){
2391: i=i++;
2392: fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
2393: fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
2394: for (j=1; j<=i;j++){
2395: fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);
2396: fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));
2397: }
2398: }
2399: }/* end of loop for state */
2400: } /* end of loop for age */
2401:
2402: /* Confidence intervalle of pij */
2403: /*
2404: fprintf(ficgp,"\nset noparametric;unset label");
2405: fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");
2406: fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
2407: fprintf(fichtm,"\n<br>Probability with confidence intervals expressed in year<sup>-1</sup> :<a href=\"pijgr%s.png\">pijgr%s.png</A>, ",optionfilefiname,optionfilefiname);
2408: fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);
2409: fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);
2410: fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);
2411: */
2412:
2413: /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
2414: first1=1;
2415: for (k2=1; k2<=(nlstate);k2++){
2416: for (l2=1; l2<=(nlstate+ndeath);l2++){
2417: if(l2==k2) continue;
2418: j=(k2-1)*(nlstate+ndeath)+l2;
2419: for (k1=1; k1<=(nlstate);k1++){
2420: for (l1=1; l1<=(nlstate+ndeath);l1++){
2421: if(l1==k1) continue;
2422: i=(k1-1)*(nlstate+ndeath)+l1;
2423: if(i<=j) continue;
2424: for (age=bage; age<=fage; age ++){
2425: if ((int)age %5==0){
2426: v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;
2427: v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;
2428: cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;
2429: mu1=mu[i][(int) age]/stepm*YEARM ;
2430: mu2=mu[j][(int) age]/stepm*YEARM;
2431: c12=cv12/sqrt(v1*v2);
2432: /* Computing eigen value of matrix of covariance */
2433: lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
2434: lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
2435: /* Eigen vectors */
2436: v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
2437: /*v21=sqrt(1.-v11*v11); *//* error */
2438: v21=(lc1-v1)/cv12*v11;
2439: v12=-v21;
2440: v22=v11;
2441: tnalp=v21/v11;
2442: if(first1==1){
2443: first1=0;
2444: printf("%d %d%d-%d%d mu %.4e %.4e Var %.4e %.4e cor %.3f cov %.4e Eig %.3e %.3e 1stv %.3f %.3f tang %.3f\nOthers in log...\n",(int) age,k1,l1,k2,l2,mu1,mu2,v1,v2,c12,cv12,lc1,lc2,v11,v21,tnalp);
2445: }
2446: fprintf(ficlog,"%d %d%d-%d%d mu %.4e %.4e Var %.4e %.4e cor %.3f cov %.4e Eig %.3e %.3e 1stv %.3f %.3f tan %.3f\n",(int) age,k1,l1,k2,l2,mu1,mu2,v1,v2,c12,cv12,lc1,lc2,v11,v21,tnalp);
2447: /*printf(fignu*/
2448: /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */
2449: /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */
2450: if(first==1){
2451: first=0;
2452: fprintf(ficgp,"\nset parametric;unset label");
2453: fprintf(ficgp,"\nset log y;set log x; set xlabel \"p%1d%1d (year-1)\";set ylabel \"p%1d%1d (year-1)\"",k1,l1,k2,l2);
2454: fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
2455: fprintf(fichtm,"\n<br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup> :<a href=\"varpijgr%s%d%1d%1d-%1d%1d.png\">varpijgr%s%d%1d%1d-%1d%1d.png</A>, ",k1,l1,k2,l2,optionfilefiname, j1,k1,l1,k2,l2,optionfilefiname, j1,k1,l1,k2,l2);
2456: fprintf(fichtm,"\n<br><img src=\"varpijgr%s%d%1d%1d-%1d%1d.png\"> ",optionfilefiname, j1,k1,l1,k2,l2);
2457: fprintf(fichtm,"\n<br> Correlation at age %d (%.3f),",(int) age, c12);
2458: fprintf(ficgp,"\nset out \"varpijgr%s%d%1d%1d-%1d%1d.png\"",optionfilefiname, j1,k1,l1,k2,l2);
2459: fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
2460: fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
2461: fprintf(ficgp,"\nplot [-pi:pi] %11.3e+ %.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)), %11.3e +%.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)) not",\
2462: mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
2463: mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
2464: }else{
2465: first=0;
2466: fprintf(fichtm," %d (%.3f),",(int) age, c12);
2467: fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
2468: fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
2469: fprintf(ficgp,"\nreplot %11.3e+ %.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)), %11.3e +%.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)) not",\
2470: mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
2471: mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
2472: }/* if first */
2473: } /* age mod 5 */
2474: } /* end loop age */
2475: fprintf(ficgp,"\nset out \"varpijgr%s%d%1d%1d-%1d%1d.png\";replot;",optionfilefiname, j1,k1,l1,k2,l2);
2476: first=1;
2477: } /*l12 */
2478: } /* k12 */
2479: } /*l1 */
2480: }/* k1 */
2481: } /* loop covariates */
2482: free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
2483: free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
2484: free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
2485: free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
2486: free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
2487: free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
2488: }
2489: free_vector(xp,1,npar);
2490: fclose(ficresprob);
2491: fclose(ficresprobcov);
2492: fclose(ficresprobcor);
2493: fclose(ficgp);
2494: fclose(fichtm);
2495: }
2496:
2497:
2498: /******************* Printing html file ***********/
2499: void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \
2500: int lastpass, int stepm, int weightopt, char model[],\
2501: int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
2502: int popforecast, int estepm ,\
2503: double jprev1, double mprev1,double anprev1, \
2504: double jprev2, double mprev2,double anprev2){
2505: int jj1, k1, i1, cpt;
2506: /*char optionfilehtm[FILENAMELENGTH];*/
2507: if((fichtm=fopen(optionfilehtm,"a"))==NULL) {
2508: printf("Problem with %s \n",optionfilehtm), exit(0);
2509: fprintf(ficlog,"Problem with %s \n",optionfilehtm), exit(0);
2510: }
2511:
2512: fprintf(fichtm,"<ul><li><h4>Result files (first order: no variance)</h4>\n
2513: - Observed prevalence in each state (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"p%s\">p%s</a> <br>\n
2514: - Estimated transition probabilities over %d (stepm) months: <a href=\"pij%s\">pij%s</a><br>\n
2515: - Stable prevalence in each health state: <a href=\"pl%s\">pl%s</a> <br>\n
2516: - Life expectancies by age and initial health status (estepm=%2d months):
2517: <a href=\"e%s\">e%s</a> <br>\n</li>", \
2518: jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,fileres,fileres,stepm,fileres,fileres,fileres,fileres,estepm,fileres,fileres);
2519:
2520: fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
2521:
2522: m=cptcoveff;
2523: if (cptcovn < 1) {m=1;ncodemax[1]=1;}
2524:
2525: jj1=0;
2526: for(k1=1; k1<=m;k1++){
2527: for(i1=1; i1<=ncodemax[k1];i1++){
2528: jj1++;
2529: if (cptcovn > 0) {
2530: fprintf(fichtm,"<hr size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
2531: for (cpt=1; cpt<=cptcoveff;cpt++)
2532: fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
2533: fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
2534: }
2535: /* Pij */
2536: fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months before: pe%s%d1.png<br>
2537: <img src=\"pe%s%d1.png\">",stepm,strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);
2538: /* Quasi-incidences */
2539: fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months before but expressed in per year i.e. quasi incidences if stepm is small and probabilities too: pe%s%d2.png<br>
2540: <img src=\"pe%s%d2.png\">",stepm,strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);
2541: /* Stable prevalence in each health state */
2542: for(cpt=1; cpt<nlstate;cpt++){
2543: fprintf(fichtm,"<br>- Stable prevalence in each health state : p%s%d%d.png<br>
2544: <img src=\"p%s%d%d.png\">",strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);
2545: }
2546: for(cpt=1; cpt<=nlstate;cpt++) {
2547: fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): exp%s%d%d.png <br>
2548: <img src=\"exp%s%d%d.png\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);
2549: }
2550: fprintf(fichtm,"\n<br>- Total life expectancy by age and
2551: health expectancies in states (1) and (2): e%s%d.png<br>
2552: <img src=\"e%s%d.png\">",strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);
2553: } /* end i1 */
2554: }/* End k1 */
2555: fprintf(fichtm,"</ul>");
2556:
2557:
2558: fprintf(fichtm,"\n<br><li><h4> Result files (second order: variances)</h4>\n
2559: - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n
2560: - Variance of one-step probabilities: <a href=\"prob%s\">prob%s</a> <br>\n
2561: - Variance-covariance of one-step probabilities: <a href=\"probcov%s\">probcov%s</a> <br>\n
2562: - Correlation matrix of one-step probabilities: <a href=\"probcor%s\">probcor%s</a> <br>\n
2563: - Variances and covariances of life expectancies by age and initial health status (estepm=%d months): <a href=\"v%s\">v%s</a><br>\n
2564: - Health expectancies with their variances (no covariance): <a href=\"t%s\">t%s</a> <br>\n
2565: - Standard deviation of stable prevalences: <a href=\"vpl%s\">vpl%s</a> <br>\n",rfileres,rfileres,fileres,fileres,fileres,fileres,fileres,fileres, estepm, fileres,fileres,fileres,fileres,fileres,fileres);
2566:
2567: if(popforecast==1) fprintf(fichtm,"\n
2568: - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n
2569: - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n
2570: <br>",fileres,fileres,fileres,fileres);
2571: else
2572: fprintf(fichtm,"\n No population forecast: popforecast = %d (instead of 1) or stepm = %d (instead of 1) or model=%s (instead of .)<br><br></li>\n",popforecast, stepm, model);
2573: fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
2574:
2575: m=cptcoveff;
2576: if (cptcovn < 1) {m=1;ncodemax[1]=1;}
2577:
2578: jj1=0;
2579: for(k1=1; k1<=m;k1++){
2580: for(i1=1; i1<=ncodemax[k1];i1++){
2581: jj1++;
2582: if (cptcovn > 0) {
2583: fprintf(fichtm,"<hr size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
2584: for (cpt=1; cpt<=cptcoveff;cpt++)
2585: fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
2586: fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
2587: }
2588: for(cpt=1; cpt<=nlstate;cpt++) {
2589: fprintf(fichtm,"<br>- Observed and stationary prevalence (with confident
2590: interval) in state (%d): v%s%d%d.png <br>
2591: <img src=\"v%s%d%d.png\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);
2592: }
2593: } /* end i1 */
2594: }/* End k1 */
2595: fprintf(fichtm,"</ul>");
2596: fclose(fichtm);
2597: }
2598:
2599: /******************* Gnuplot file **************/
2600: void printinggnuplot(char fileres[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
2601:
2602: int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;
2603: int ng;
2604: if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {
2605: printf("Problem with file %s",optionfilegnuplot);
2606: fprintf(ficlog,"Problem with file %s",optionfilegnuplot);
2607: }
2608:
2609: /*#ifdef windows */
2610: fprintf(ficgp,"cd \"%s\" \n",pathc);
2611: /*#endif */
2612: m=pow(2,cptcoveff);
2613:
2614: /* 1eme*/
2615: for (cpt=1; cpt<= nlstate ; cpt ++) {
2616: for (k1=1; k1<= m ; k1 ++) {
2617: fprintf(ficgp,"\nset out \"v%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);
2618: fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] \"vpl%s\" every :::%d::%d u 1:2 \"\%%lf",ageminpar,fage,fileres,k1-1,k1-1);
2619:
2620: for (i=1; i<= nlstate ; i ++) {
2621: if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
2622: else fprintf(ficgp," \%%*lf (\%%*lf)");
2623: }
2624: fprintf(ficgp,"\" t\"Stable prevalence\" w l 0,\"vpl%s\" every :::%d::%d u 1:($2+2*$3) \"\%%lf",fileres,k1-1,k1-1);
2625: for (i=1; i<= nlstate ; i ++) {
2626: if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
2627: else fprintf(ficgp," \%%*lf (\%%*lf)");
2628: }
2629: fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"vpl%s\" every :::%d::%d u 1:($2-2*$3) \"\%%lf",fileres,k1-1,k1-1);
2630: for (i=1; i<= nlstate ; i ++) {
2631: if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
2632: else fprintf(ficgp," \%%*lf (\%%*lf)");
2633: }
2634: fprintf(ficgp,"\" t\"\" w l 1,\"p%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",fileres,k1-1,k1-1,2+4*(cpt-1));
2635: }
2636: }
2637: /*2 eme*/
2638:
2639: for (k1=1; k1<= m ; k1 ++) {
2640: fprintf(ficgp,"\nset out \"e%s%d.png\" \n",strtok(optionfile, "."),k1);
2641: fprintf(ficgp,"set ylabel \"Years\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] ",ageminpar,fage);
2642:
2643: for (i=1; i<= nlstate+1 ; i ++) {
2644: k=2*i;
2645: fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:2 \"\%%lf",fileres,k1-1,k1-1);
2646: for (j=1; j<= nlstate+1 ; j ++) {
2647: if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
2648: else fprintf(ficgp," \%%*lf (\%%*lf)");
2649: }
2650: if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");
2651: else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);
2652: fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",fileres,k1-1,k1-1);
2653: for (j=1; j<= nlstate+1 ; j ++) {
2654: if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
2655: else fprintf(ficgp," \%%*lf (\%%*lf)");
2656: }
2657: fprintf(ficgp,"\" t\"\" w l 0,");
2658: fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",fileres,k1-1,k1-1);
2659: for (j=1; j<= nlstate+1 ; j ++) {
2660: if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
2661: else fprintf(ficgp," \%%*lf (\%%*lf)");
2662: }
2663: if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");
2664: else fprintf(ficgp,"\" t\"\" w l 0,");
2665: }
2666: }
2667:
2668: /*3eme*/
2669:
2670: for (k1=1; k1<= m ; k1 ++) {
2671: for (cpt=1; cpt<= nlstate ; cpt ++) {
2672: k=2+nlstate*(2*cpt-2);
2673: fprintf(ficgp,"\nset out \"exp%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);
2674: fprintf(ficgp,"set ter png small\nset size 0.65,0.65\nplot [%.f:%.f] \"e%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,fileres,k1-1,k1-1,k,cpt);
2675: /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
2676: for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
2677: fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
2678: fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
2679: for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
2680: fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
2681:
2682: */
2683: for (i=1; i< nlstate ; i ++) {
2684: fprintf(ficgp," ,\"e%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",fileres,k1-1,k1-1,k+2*i,cpt,i+1);
2685:
2686: }
2687: }
2688: }
2689:
2690: /* CV preval stat */
2691: for (k1=1; k1<= m ; k1 ++) {
2692: for (cpt=1; cpt<nlstate ; cpt ++) {
2693: k=3;
2694: fprintf(ficgp,"\nset out \"p%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);
2695: fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] \"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",ageminpar,agemaxpar,fileres,k1,k+cpt+1,k+1);
2696:
2697: for (i=1; i< nlstate ; i ++)
2698: fprintf(ficgp,"+$%d",k+i+1);
2699: fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);
2700:
2701: l=3+(nlstate+ndeath)*cpt;
2702: fprintf(ficgp,",\"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",fileres,k1,l+cpt+1,l+1);
2703: for (i=1; i< nlstate ; i ++) {
2704: l=3+(nlstate+ndeath)*cpt;
2705: fprintf(ficgp,"+$%d",l+i+1);
2706: }
2707: fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);
2708: }
2709: }
2710:
2711: /* proba elementaires */
2712: for(i=1,jk=1; i <=nlstate; i++){
2713: for(k=1; k <=(nlstate+ndeath); k++){
2714: if (k != i) {
2715: for(j=1; j <=ncovmodel; j++){
2716: fprintf(ficgp,"p%d=%f ",jk,p[jk]);
2717: jk++;
2718: fprintf(ficgp,"\n");
2719: }
2720: }
2721: }
2722: }
2723:
2724: for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/
2725: for(jk=1; jk <=m; jk++) {
2726: fprintf(ficgp,"\nset out \"pe%s%d%d.png\" \n",strtok(optionfile, "."),jk,ng);
2727: if (ng==2)
2728: fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
2729: else
2730: fprintf(ficgp,"\nset title \"Probability\"\n");
2731: fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65\nset log y\nplot [%.f:%.f] ",ageminpar,agemaxpar);
2732: i=1;
2733: for(k2=1; k2<=nlstate; k2++) {
2734: k3=i;
2735: for(k=1; k<=(nlstate+ndeath); k++) {
2736: if (k != k2){
2737: if(ng==2)
2738: fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);
2739: else
2740: fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
2741: ij=1;
2742: for(j=3; j <=ncovmodel; j++) {
2743: if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
2744: fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
2745: ij++;
2746: }
2747: else
2748: fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
2749: }
2750: fprintf(ficgp,")/(1");
2751:
2752: for(k1=1; k1 <=nlstate; k1++){
2753: fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);
2754: ij=1;
2755: for(j=3; j <=ncovmodel; j++){
2756: if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
2757: fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
2758: ij++;
2759: }
2760: else
2761: fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
2762: }
2763: fprintf(ficgp,")");
2764: }
2765: fprintf(ficgp,") t \"p%d%d\" ", k2,k);
2766: if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");
2767: i=i+ncovmodel;
2768: }
2769: } /* end k */
2770: } /* end k2 */
2771: } /* end jk */
2772: } /* end ng */
2773: fclose(ficgp);
2774: } /* end gnuplot */
2775:
2776:
2777: /*************** Moving average **************/
2778: int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav){
2779:
2780: int i, cpt, cptcod;
2781: int modcovmax =1;
2782: int mobilavrange, mob;
2783: double age;
2784:
2785: modcovmax=2*cptcoveff;/* Max number of modalities. We suppose
2786: a covariate has 2 modalities */
2787: if (cptcovn<1) modcovmax=1; /* At least 1 pass */
2788:
2789: if(mobilav==1||mobilav ==3 ||mobilav==5 ||mobilav== 7){
2790: if(mobilav==1) mobilavrange=5; /* default */
2791: else mobilavrange=mobilav;
2792: for (age=bage; age<=fage; age++)
2793: for (i=1; i<=nlstate;i++)
2794: for (cptcod=1;cptcod<=modcovmax;cptcod++)
2795: mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
2796: /* We keep the original values on the extreme ages bage, fage and for
2797: fage+1 and bage-1 we use a 3 terms moving average; for fage+2 bage+2
2798: we use a 5 terms etc. until the borders are no more concerned.
2799: */
2800: for (mob=3;mob <=mobilavrange;mob=mob+2){
2801: for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){
2802: for (i=1; i<=nlstate;i++){
2803: for (cptcod=1;cptcod<=modcovmax;cptcod++){
2804: mobaverage[(int)age][i][cptcod] =probs[(int)age][i][cptcod];
2805: for (cpt=1;cpt<=(mob-1)/2;cpt++){
2806: mobaverage[(int)age][i][cptcod] +=probs[(int)age-cpt][i][cptcod];
2807: mobaverage[(int)age][i][cptcod] +=probs[(int)age+cpt][i][cptcod];
2808: }
2809: mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/mob;
2810: }
2811: }
2812: }/* end age */
2813: }/* end mob */
2814: }else return -1;
2815: return 0;
2816: }/* End movingaverage */
2817:
2818:
2819: /************** Forecasting ******************/
2820: prevforecast(char fileres[], double anproj1,double mproj1,double jproj1,double ageminpar, double agemax,double dateprev1, double dateprev2, int mobilav, double agedeb, double fage, int popforecast, char popfile[], double anproj2,double p[], int i2){
2821:
2822: int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;
2823: int *popage;
2824: double calagedate, agelim, kk1, kk2, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
2825: double *popeffectif,*popcount;
2826: double ***p3mat;
2827: double ***mobaverage;
2828: char fileresf[FILENAMELENGTH];
2829:
2830: agelim=AGESUP;
2831: calagedate=(anproj1+mproj1/12.+jproj1/365.-dateintmean)*YEARM;
2832:
2833: prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);
2834:
2835:
2836: strcpy(fileresf,"f");
2837: strcat(fileresf,fileres);
2838: if((ficresf=fopen(fileresf,"w"))==NULL) {
2839: printf("Problem with forecast resultfile: %s\n", fileresf);
2840: fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);
2841: }
2842: printf("Computing forecasting: result on file '%s' \n", fileresf);
2843: fprintf(ficlog,"Computing forecasting: result on file '%s' \n", fileresf);
2844:
2845: if (cptcoveff==0) ncodemax[cptcoveff]=1;
2846:
2847: if (mobilav!=0) {
2848: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
2849: if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
2850: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
2851: printf(" Error in movingaverage mobilav=%d\n",mobilav);
2852: }
2853: }
2854:
2855: stepsize=(int) (stepm+YEARM-1)/YEARM;
2856: if (stepm<=12) stepsize=1;
2857:
2858: agelim=AGESUP;
2859:
2860: hstepm=1;
2861: hstepm=hstepm/stepm;
2862: yp1=modf(dateintmean,&yp);
2863: anprojmean=yp;
2864: yp2=modf((yp1*12),&yp);
2865: mprojmean=yp;
2866: yp1=modf((yp2*30.5),&yp);
2867: jprojmean=yp;
2868: if(jprojmean==0) jprojmean=1;
2869: if(mprojmean==0) jprojmean=1;
2870:
2871: fprintf(ficresf,"# Estimated date of observed prevalence: %.lf/%.lf/%.lf ",jprojmean,mprojmean,anprojmean);
2872:
2873: for(cptcov=1;cptcov<=i2;cptcov++){
2874: for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
2875: k=k+1;
2876: fprintf(ficresf,"\n#******");
2877: for(j=1;j<=cptcoveff;j++) {
2878: fprintf(ficresf," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
2879: }
2880: fprintf(ficresf,"******\n");
2881: fprintf(ficresf,"# StartingAge FinalAge");
2882: for(j=1; j<=nlstate+ndeath;j++) fprintf(ficresf," P.%d",j);
2883:
2884:
2885: for (cpt=0; cpt<=(anproj2-anproj1);cpt++) {
2886: fprintf(ficresf,"\n");
2887: fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+cpt);
2888:
2889: for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){
2890: nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);
2891: nhstepm = nhstepm/hstepm;
2892:
2893: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
2894: oldm=oldms;savm=savms;
2895: hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
2896:
2897: for (h=0; h<=nhstepm; h++){
2898: if (h==(int) (calagedate+YEARM*cpt)) {
2899: fprintf(ficresf,"\n %.f %.f ",anproj1+cpt,agedeb+h*hstepm/YEARM*stepm);
2900: }
2901: for(j=1; j<=nlstate+ndeath;j++) {
2902: kk1=0.;kk2=0;
2903: for(i=1; i<=nlstate;i++) {
2904: if (mobilav==1)
2905: kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];
2906: else {
2907: kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];
2908: }
2909:
2910: }
2911: if (h==(int)(calagedate+12*cpt)){
2912: fprintf(ficresf," %.3f", kk1);
2913:
2914: }
2915: }
2916: }
2917: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
2918: }
2919: }
2920: }
2921: }
2922:
2923: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
2924:
2925: fclose(ficresf);
2926: }
2927: /************** Forecasting ******************/
2928: populforecast(char fileres[], double anpyram,double mpyram,double jpyram,double ageminpar, double agemax,double dateprev1, double dateprev2, int mobilav, double agedeb, double fage, int popforecast, char popfile[], double anpyram1,double p[], int i2){
2929:
2930: int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;
2931: int *popage;
2932: double calagedate, agelim, kk1, kk2, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
2933: double *popeffectif,*popcount;
2934: double ***p3mat,***tabpop,***tabpopprev;
2935: double ***mobaverage;
2936: char filerespop[FILENAMELENGTH];
2937:
2938: tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
2939: tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
2940: agelim=AGESUP;
2941: calagedate=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;
2942:
2943: prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);
2944:
2945:
2946: strcpy(filerespop,"pop");
2947: strcat(filerespop,fileres);
2948: if((ficrespop=fopen(filerespop,"w"))==NULL) {
2949: printf("Problem with forecast resultfile: %s\n", filerespop);
2950: fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop);
2951: }
2952: printf("Computing forecasting: result on file '%s' \n", filerespop);
2953: fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop);
2954:
2955: if (cptcoveff==0) ncodemax[cptcoveff]=1;
2956:
2957: if (mobilav!=0) {
2958: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
2959: if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
2960: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
2961: printf(" Error in movingaverage mobilav=%d\n",mobilav);
2962: }
2963: }
2964:
2965: stepsize=(int) (stepm+YEARM-1)/YEARM;
2966: if (stepm<=12) stepsize=1;
2967:
2968: agelim=AGESUP;
2969:
2970: hstepm=1;
2971: hstepm=hstepm/stepm;
2972:
2973: if (popforecast==1) {
2974: if((ficpop=fopen(popfile,"r"))==NULL) {
2975: printf("Problem with population file : %s\n",popfile);exit(0);
2976: fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0);
2977: }
2978: popage=ivector(0,AGESUP);
2979: popeffectif=vector(0,AGESUP);
2980: popcount=vector(0,AGESUP);
2981:
2982: i=1;
2983: while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;
2984:
2985: imx=i;
2986: for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];
2987: }
2988:
2989: for(cptcov=1;cptcov<=i2;cptcov++){
2990: for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
2991: k=k+1;
2992: fprintf(ficrespop,"\n#******");
2993: for(j=1;j<=cptcoveff;j++) {
2994: fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
2995: }
2996: fprintf(ficrespop,"******\n");
2997: fprintf(ficrespop,"# Age");
2998: for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);
2999: if (popforecast==1) fprintf(ficrespop," [Population]");
3000:
3001: for (cpt=0; cpt<=0;cpt++) {
3002: fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);
3003:
3004: for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){
3005: nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);
3006: nhstepm = nhstepm/hstepm;
3007:
3008: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3009: oldm=oldms;savm=savms;
3010: hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
3011:
3012: for (h=0; h<=nhstepm; h++){
3013: if (h==(int) (calagedate+YEARM*cpt)) {
3014: fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
3015: }
3016: for(j=1; j<=nlstate+ndeath;j++) {
3017: kk1=0.;kk2=0;
3018: for(i=1; i<=nlstate;i++) {
3019: if (mobilav==1)
3020: kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];
3021: else {
3022: kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];
3023: }
3024: }
3025: if (h==(int)(calagedate+12*cpt)){
3026: tabpop[(int)(agedeb)][j][cptcod]=kk1;
3027: /*fprintf(ficrespop," %.3f", kk1);
3028: if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/
3029: }
3030: }
3031: for(i=1; i<=nlstate;i++){
3032: kk1=0.;
3033: for(j=1; j<=nlstate;j++){
3034: kk1= kk1+tabpop[(int)(agedeb)][j][cptcod];
3035: }
3036: tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedate+12*cpt)*hstepm/YEARM*stepm-1)];
3037: }
3038:
3039: if (h==(int)(calagedate+12*cpt)) for(j=1; j<=nlstate;j++)
3040: fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);
3041: }
3042: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3043: }
3044: }
3045:
3046: /******/
3047:
3048: for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) {
3049: fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);
3050: for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){
3051: nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);
3052: nhstepm = nhstepm/hstepm;
3053:
3054: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3055: oldm=oldms;savm=savms;
3056: hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
3057: for (h=0; h<=nhstepm; h++){
3058: if (h==(int) (calagedate+YEARM*cpt)) {
3059: fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
3060: }
3061: for(j=1; j<=nlstate+ndeath;j++) {
3062: kk1=0.;kk2=0;
3063: for(i=1; i<=nlstate;i++) {
3064: kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];
3065: }
3066: if (h==(int)(calagedate+12*cpt)) fprintf(ficresf," %15.2f", kk1);
3067: }
3068: }
3069: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3070: }
3071: }
3072: }
3073: }
3074:
3075: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
3076:
3077: if (popforecast==1) {
3078: free_ivector(popage,0,AGESUP);
3079: free_vector(popeffectif,0,AGESUP);
3080: free_vector(popcount,0,AGESUP);
3081: }
3082: free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
3083: free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
3084: fclose(ficrespop);
3085: }
3086:
3087: /***********************************************/
3088: /**************** Main Program *****************/
3089: /***********************************************/
3090:
3091: int main(int argc, char *argv[])
3092: {
3093:
3094: int i,j, k, n=MAXN,iter,m,size,cptcode, cptcod;
3095: double agedeb, agefin,hf;
3096: double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;
3097:
3098: double fret;
3099: double **xi,tmp,delta;
3100:
3101: double dum; /* Dummy variable */
3102: double ***p3mat;
3103: double ***mobaverage;
3104: int *indx;
3105: char line[MAXLINE], linepar[MAXLINE];
3106: char path[80],pathc[80],pathcd[80],pathtot[80],model[80];
3107: int firstobs=1, lastobs=10;
3108: int sdeb, sfin; /* Status at beginning and end */
3109: int c, h , cpt,l;
3110: int ju,jl, mi;
3111: int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;
3112: int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,**adl,*tab;
3113: int mobilav=0,popforecast=0;
3114: int hstepm, nhstepm;
3115: double jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,jpyram, mpyram,anpyram,jpyram1, mpyram1,anpyram1, calagedate;
3116:
3117: double bage, fage, age, agelim, agebase;
3118: double ftolpl=FTOL;
3119: double **prlim;
3120: double *severity;
3121: double ***param; /* Matrix of parameters */
3122: double *p;
3123: double **matcov; /* Matrix of covariance */
3124: double ***delti3; /* Scale */
3125: double *delti; /* Scale */
3126: double ***eij, ***vareij;
3127: double **varpl; /* Variances of prevalence limits by age */
3128: double *epj, vepp;
3129: double kk1, kk2;
3130: double dateprev1, dateprev2,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2;
3131:
3132:
3133: char *alph[]={"a","a","b","c","d","e"}, str[4];
3134:
3135:
3136: char z[1]="c", occ;
3137: #include <sys/time.h>
3138: #include <time.h>
3139: char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];
3140:
3141: /* long total_usecs;
3142: struct timeval start_time, end_time;
3143:
3144: gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */
3145: getcwd(pathcd, size);
3146:
3147: printf("\n%s",version);
3148: if(argc <=1){
3149: printf("\nEnter the parameter file name: ");
3150: scanf("%s",pathtot);
3151: }
3152: else{
3153: strcpy(pathtot,argv[1]);
3154: }
3155: /*if(getcwd(pathcd, 80)!= NULL)printf ("Error pathcd\n");*/
3156: /*cygwin_split_path(pathtot,path,optionfile);
3157: printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/
3158: /* cutv(path,optionfile,pathtot,'\\');*/
3159:
3160: split(pathtot,path,optionfile,optionfilext,optionfilefiname);
3161: printf("pathtot=%s, path=%s, optionfile=%s optionfilext=%s optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
3162: chdir(path);
3163: replace(pathc,path);
3164:
3165: /*-------- arguments in the command line --------*/
3166:
3167: /* Log file */
3168: strcat(filelog, optionfilefiname);
3169: strcat(filelog,".log"); /* */
3170: if((ficlog=fopen(filelog,"w"))==NULL) {
3171: printf("Problem with logfile %s\n",filelog);
3172: goto end;
3173: }
3174: fprintf(ficlog,"Log filename:%s\n",filelog);
3175: fprintf(ficlog,"\n%s",version);
3176: fprintf(ficlog,"\nEnter the parameter file name: ");
3177: fprintf(ficlog,"pathtot=%s, path=%s, optionfile=%s optionfilext=%s optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
3178: fflush(ficlog);
3179:
3180: /* */
3181: strcpy(fileres,"r");
3182: strcat(fileres, optionfilefiname);
3183: strcat(fileres,".txt"); /* Other files have txt extension */
3184:
3185: /*---------arguments file --------*/
3186:
3187: if((ficpar=fopen(optionfile,"r"))==NULL) {
3188: printf("Problem with optionfile %s\n",optionfile);
3189: fprintf(ficlog,"Problem with optionfile %s\n",optionfile);
3190: goto end;
3191: }
3192:
3193: strcpy(filereso,"o");
3194: strcat(filereso,fileres);
3195: if((ficparo=fopen(filereso,"w"))==NULL) {
3196: printf("Problem with Output resultfile: %s\n", filereso);
3197: fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso);
3198: goto end;
3199: }
3200:
3201: /* Reads comments: lines beginning with '#' */
3202: while((c=getc(ficpar))=='#' && c!= EOF){
3203: ungetc(c,ficpar);
3204: fgets(line, MAXLINE, ficpar);
3205: puts(line);
3206: fputs(line,ficparo);
3207: }
3208: ungetc(c,ficpar);
3209:
3210: fscanf(ficpar,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%lf stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d model=%s\n",title, datafile, &lastobs, &firstpass,&lastpass,&ftol, &stepm, &ncovcol, &nlstate,&ndeath, &maxwav, &mle, &weightopt,model);
3211: printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate,ndeath, maxwav, mle, weightopt,model);
3212: fprintf(ficparo,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol,nlstate,ndeath,maxwav, mle, weightopt,model);
3213: while((c=getc(ficpar))=='#' && c!= EOF){
3214: ungetc(c,ficpar);
3215: fgets(line, MAXLINE, ficpar);
3216: puts(line);
3217: fputs(line,ficparo);
3218: }
3219: ungetc(c,ficpar);
3220:
3221:
3222: covar=matrix(0,NCOVMAX,1,n);
3223: cptcovn=0; /*Number of covariates, i.e. number of '+' in model statement*/
3224: if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;
3225:
3226: ncovmodel=2+cptcovn; /*Number of variables = cptcovn + intercept + age */
3227: nvar=ncovmodel-1; /* Suppressing age as a basic covariate */
3228:
3229: /* Read guess parameters */
3230: /* Reads comments: lines beginning with '#' */
3231: while((c=getc(ficpar))=='#' && c!= EOF){
3232: ungetc(c,ficpar);
3233: fgets(line, MAXLINE, ficpar);
3234: puts(line);
3235: fputs(line,ficparo);
3236: }
3237: ungetc(c,ficpar);
3238:
3239: param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
3240: for(i=1; i <=nlstate; i++)
3241: for(j=1; j <=nlstate+ndeath-1; j++){
3242: fscanf(ficpar,"%1d%1d",&i1,&j1);
3243: fprintf(ficparo,"%1d%1d",i1,j1);
3244: if(mle==1)
3245: printf("%1d%1d",i,j);
3246: fprintf(ficlog,"%1d%1d",i,j);
3247: for(k=1; k<=ncovmodel;k++){
3248: fscanf(ficpar," %lf",¶m[i][j][k]);
3249: if(mle==1){
3250: printf(" %lf",param[i][j][k]);
3251: fprintf(ficlog," %lf",param[i][j][k]);
3252: }
3253: else
3254: fprintf(ficlog," %lf",param[i][j][k]);
3255: fprintf(ficparo," %lf",param[i][j][k]);
3256: }
3257: fscanf(ficpar,"\n");
3258: if(mle==1)
3259: printf("\n");
3260: fprintf(ficlog,"\n");
3261: fprintf(ficparo,"\n");
3262: }
3263:
3264: npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/
3265:
3266: p=param[1][1];
3267:
3268: /* Reads comments: lines beginning with '#' */
3269: while((c=getc(ficpar))=='#' && c!= EOF){
3270: ungetc(c,ficpar);
3271: fgets(line, MAXLINE, ficpar);
3272: puts(line);
3273: fputs(line,ficparo);
3274: }
3275: ungetc(c,ficpar);
3276:
3277: delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
3278: delti=vector(1,npar); /* Scale of each paramater (output from hesscov) */
3279: for(i=1; i <=nlstate; i++){
3280: for(j=1; j <=nlstate+ndeath-1; j++){
3281: fscanf(ficpar,"%1d%1d",&i1,&j1);
3282: printf("%1d%1d",i,j);
3283: fprintf(ficparo,"%1d%1d",i1,j1);
3284: for(k=1; k<=ncovmodel;k++){
3285: fscanf(ficpar,"%le",&delti3[i][j][k]);
3286: printf(" %le",delti3[i][j][k]);
3287: fprintf(ficparo," %le",delti3[i][j][k]);
3288: }
3289: fscanf(ficpar,"\n");
3290: printf("\n");
3291: fprintf(ficparo,"\n");
3292: }
3293: }
3294: delti=delti3[1][1];
3295:
3296: /* Reads comments: lines beginning with '#' */
3297: while((c=getc(ficpar))=='#' && c!= EOF){
3298: ungetc(c,ficpar);
3299: fgets(line, MAXLINE, ficpar);
3300: puts(line);
3301: fputs(line,ficparo);
3302: }
3303: ungetc(c,ficpar);
3304:
3305: matcov=matrix(1,npar,1,npar);
3306: for(i=1; i <=npar; i++){
3307: fscanf(ficpar,"%s",&str);
3308: if(mle==1)
3309: printf("%s",str);
3310: fprintf(ficlog,"%s",str);
3311: fprintf(ficparo,"%s",str);
3312: for(j=1; j <=i; j++){
3313: fscanf(ficpar," %le",&matcov[i][j]);
3314: if(mle==1){
3315: printf(" %.5le",matcov[i][j]);
3316: fprintf(ficlog," %.5le",matcov[i][j]);
3317: }
3318: else
3319: fprintf(ficlog," %.5le",matcov[i][j]);
3320: fprintf(ficparo," %.5le",matcov[i][j]);
3321: }
3322: fscanf(ficpar,"\n");
3323: if(mle==1)
3324: printf("\n");
3325: fprintf(ficlog,"\n");
3326: fprintf(ficparo,"\n");
3327: }
3328: for(i=1; i <=npar; i++)
3329: for(j=i+1;j<=npar;j++)
3330: matcov[i][j]=matcov[j][i];
3331:
3332: if(mle==1)
3333: printf("\n");
3334: fprintf(ficlog,"\n");
3335:
3336:
3337: /*-------- Rewriting paramater file ----------*/
3338: strcpy(rfileres,"r"); /* "Rparameterfile */
3339: strcat(rfileres,optionfilefiname); /* Parameter file first name*/
3340: strcat(rfileres,"."); /* */
3341: strcat(rfileres,optionfilext); /* Other files have txt extension */
3342: if((ficres =fopen(rfileres,"w"))==NULL) {
3343: printf("Problem writing new parameter file: %s\n", fileres);goto end;
3344: fprintf(ficlog,"Problem writing new parameter file: %s\n", fileres);goto end;
3345: }
3346: fprintf(ficres,"#%s\n",version);
3347:
3348: /*-------- data file ----------*/
3349: if((fic=fopen(datafile,"r"))==NULL) {
3350: printf("Problem with datafile: %s\n", datafile);goto end;
3351: fprintf(ficlog,"Problem with datafile: %s\n", datafile);goto end;
3352: }
3353:
3354: n= lastobs;
3355: severity = vector(1,maxwav);
3356: outcome=imatrix(1,maxwav+1,1,n);
3357: num=ivector(1,n);
3358: moisnais=vector(1,n);
3359: annais=vector(1,n);
3360: moisdc=vector(1,n);
3361: andc=vector(1,n);
3362: agedc=vector(1,n);
3363: cod=ivector(1,n);
3364: weight=vector(1,n);
3365: for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */
3366: mint=matrix(1,maxwav,1,n);
3367: anint=matrix(1,maxwav,1,n);
3368: s=imatrix(1,maxwav+1,1,n);
3369: adl=imatrix(1,maxwav+1,1,n);
3370: tab=ivector(1,NCOVMAX);
3371: ncodemax=ivector(1,8);
3372:
3373: i=1;
3374: while (fgets(line, MAXLINE, fic) != NULL) {
3375: if ((i >= firstobs) && (i <=lastobs)) {
3376:
3377: for (j=maxwav;j>=1;j--){
3378: cutv(stra, strb,line,' '); s[j][i]=atoi(strb);
3379: strcpy(line,stra);
3380: cutv(stra, strb,line,'/'); anint[j][i]=(double)(atoi(strb)); strcpy(line,stra);
3381: cutv(stra, strb,line,' '); mint[j][i]=(double)(atoi(strb)); strcpy(line,stra);
3382: }
3383:
3384: cutv(stra, strb,line,'/'); andc[i]=(double)(atoi(strb)); strcpy(line,stra);
3385: cutv(stra, strb,line,' '); moisdc[i]=(double)(atoi(strb)); strcpy(line,stra);
3386:
3387: cutv(stra, strb,line,'/'); annais[i]=(double)(atoi(strb)); strcpy(line,stra);
3388: cutv(stra, strb,line,' '); moisnais[i]=(double)(atoi(strb)); strcpy(line,stra);
3389:
3390: cutv(stra, strb,line,' '); weight[i]=(double)(atoi(strb)); strcpy(line,stra);
3391: for (j=ncovcol;j>=1;j--){
3392: cutv(stra, strb,line,' '); covar[j][i]=(double)(atoi(strb)); strcpy(line,stra);
3393: }
3394: num[i]=atol(stra);
3395:
3396: /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){
3397: 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;}*/
3398:
3399: i=i+1;
3400: }
3401: }
3402: /* printf("ii=%d", ij);
3403: scanf("%d",i);*/
3404: imx=i-1; /* Number of individuals */
3405:
3406: /* for (i=1; i<=imx; i++){
3407: if ((s[1][i]==3) && (s[2][i]==2)) s[2][i]=3;
3408: if ((s[2][i]==3) && (s[3][i]==2)) s[3][i]=3;
3409: if ((s[3][i]==3) && (s[4][i]==2)) s[4][i]=3;
3410: }*/
3411: /* for (i=1; i<=imx; i++){
3412: if (s[4][i]==9) s[4][i]=-1;
3413: 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]));}*/
3414:
3415:
3416: /* Calculation of the number of parameter from char model*/
3417: Tvar=ivector(1,15); /* stores the number n of the covariates in Vm+Vn at 1 and m at 2 */
3418: Tprod=ivector(1,15);
3419: Tvaraff=ivector(1,15);
3420: Tvard=imatrix(1,15,1,2);
3421: Tage=ivector(1,15);
3422:
3423: if (strlen(model) >1){ /* If there is at least 1 covariate */
3424: j=0, j1=0, k1=1, k2=1;
3425: j=nbocc(model,'+'); /* j=Number of '+' */
3426: j1=nbocc(model,'*'); /* j1=Number of '*' */
3427: cptcovn=j+1;
3428: cptcovprod=j1; /*Number of products */
3429:
3430: strcpy(modelsav,model);
3431: if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){
3432: printf("Error. Non available option model=%s ",model);
3433: fprintf(ficlog,"Error. Non available option model=%s ",model);
3434: goto end;
3435: }
3436:
3437: /* This loop fill the array Tvar from the string 'model'.*/
3438:
3439: for(i=(j+1); i>=1;i--){
3440: cutv(stra,strb,modelsav,'+'); /* keeps in strb after the last + */
3441: if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyze it */
3442: /* printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/
3443: /*scanf("%d",i);*/
3444: if (strchr(strb,'*')) { /* Model includes a product */
3445: cutv(strd,strc,strb,'*'); /* strd*strc Vm*Vn (if not *age)*/
3446: if (strcmp(strc,"age")==0) { /* Vn*age */
3447: cptcovprod--;
3448: cutv(strb,stre,strd,'V');
3449: Tvar[i]=atoi(stre); /* computes n in Vn and stores in Tvar*/
3450: cptcovage++;
3451: Tage[cptcovage]=i;
3452: /*printf("stre=%s ", stre);*/
3453: }
3454: else if (strcmp(strd,"age")==0) { /* or age*Vn */
3455: cptcovprod--;
3456: cutv(strb,stre,strc,'V');
3457: Tvar[i]=atoi(stre);
3458: cptcovage++;
3459: Tage[cptcovage]=i;
3460: }
3461: else { /* Age is not in the model */
3462: cutv(strb,stre,strc,'V'); /* strc= Vn, stre is n*/
3463: Tvar[i]=ncovcol+k1;
3464: cutv(strb,strc,strd,'V'); /* strd was Vm, strc is m */
3465: Tprod[k1]=i;
3466: Tvard[k1][1]=atoi(strc); /* m*/
3467: Tvard[k1][2]=atoi(stre); /* n */
3468: Tvar[cptcovn+k2]=Tvard[k1][1];
3469: Tvar[cptcovn+k2+1]=Tvard[k1][2];
3470: for (k=1; k<=lastobs;k++)
3471: covar[ncovcol+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];
3472: k1++;
3473: k2=k2+2;
3474: }
3475: }
3476: else { /* no more sum */
3477: /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/
3478: /* scanf("%d",i);*/
3479: cutv(strd,strc,strb,'V');
3480: Tvar[i]=atoi(strc);
3481: }
3482: strcpy(modelsav,stra);
3483: /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);
3484: scanf("%d",i);*/
3485: } /* end of loop + */
3486: } /* end model */
3487:
3488: /*The number n of Vn is stored in Tvar. cptcovage =number of age covariate. Tage gives the position of age. cptcovprod= number of products.
3489: If model=V1+V1*age then Tvar[1]=1 Tvar[2]=1 cptcovage=1 Tage[1]=2 cptcovprod=0*/
3490:
3491: /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);
3492: printf("cptcovprod=%d ", cptcovprod);
3493: fprintf(ficlog,"cptcovprod=%d ", cptcovprod);
3494:
3495: scanf("%d ",i);
3496: fclose(fic);*/
3497:
3498: /* if(mle==1){*/
3499: if (weightopt != 1) { /* Maximisation without weights*/
3500: for(i=1;i<=n;i++) weight[i]=1.0;
3501: }
3502: /*-calculation of age at interview from date of interview and age at death -*/
3503: agev=matrix(1,maxwav,1,imx);
3504:
3505: for (i=1; i<=imx; i++) {
3506: for(m=2; (m<= maxwav); m++) {
3507: if ((mint[m][i]== 99) && (s[m][i] <= nlstate)){
3508: anint[m][i]=9999;
3509: s[m][i]=-1;
3510: }
3511: if(moisdc[i]==99 && andc[i]==9999 & s[m][i]>nlstate) s[m][i]=-1;
3512: }
3513: }
3514:
3515: for (i=1; i<=imx; i++) {
3516: agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);
3517: for(m=1; (m<= maxwav); m++){
3518: if(s[m][i] >0){
3519: if (s[m][i] >= nlstate+1) {
3520: if(agedc[i]>0)
3521: if(moisdc[i]!=99 && andc[i]!=9999)
3522: agev[m][i]=agedc[i];
3523: /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/
3524: else {
3525: if (andc[i]!=9999){
3526: printf("Warning negative age at death: %d line:%d\n",num[i],i);
3527: fprintf(ficlog,"Warning negative age at death: %d line:%d\n",num[i],i);
3528: agev[m][i]=-1;
3529: }
3530: }
3531: }
3532: else if(s[m][i] !=9){ /* Should no more exist */
3533: agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);
3534: if(mint[m][i]==99 || anint[m][i]==9999)
3535: agev[m][i]=1;
3536: else if(agev[m][i] <agemin){
3537: agemin=agev[m][i];
3538: /*printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], agemin);*/
3539: }
3540: else if(agev[m][i] >agemax){
3541: agemax=agev[m][i];
3542: /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/
3543: }
3544: /*agev[m][i]=anint[m][i]-annais[i];*/
3545: /* agev[m][i] = age[i]+2*m;*/
3546: }
3547: else { /* =9 */
3548: agev[m][i]=1;
3549: s[m][i]=-1;
3550: }
3551: }
3552: else /*= 0 Unknown */
3553: agev[m][i]=1;
3554: }
3555:
3556: }
3557: for (i=1; i<=imx; i++) {
3558: for(m=1; (m<= maxwav); m++){
3559: if (s[m][i] > (nlstate+ndeath)) {
3560: printf("Error: on wave %d of individual %d status %d > (nlstate+ndeath)=(%d+%d)=%d\n",m,i,s[m][i],nlstate, ndeath, nlstate+ndeath);
3561: fprintf(ficlog,"Error: on wave %d of individual %d status %d > (nlstate+ndeath)=(%d+%d)=%d\n",m,i,s[m][i],nlstate, ndeath, nlstate+ndeath);
3562: goto end;
3563: }
3564: }
3565: }
3566:
3567: printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);
3568: fprintf(ficlog,"Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);
3569:
3570: free_vector(severity,1,maxwav);
3571: free_imatrix(outcome,1,maxwav+1,1,n);
3572: free_vector(moisnais,1,n);
3573: free_vector(annais,1,n);
3574: /* free_matrix(mint,1,maxwav,1,n);
3575: free_matrix(anint,1,maxwav,1,n);*/
3576: free_vector(moisdc,1,n);
3577: free_vector(andc,1,n);
3578:
3579:
3580: wav=ivector(1,imx);
3581: dh=imatrix(1,lastpass-firstpass+1,1,imx);
3582: mw=imatrix(1,lastpass-firstpass+1,1,imx);
3583:
3584: /* Concatenates waves */
3585: concatwav(wav, dh, mw, s, agedc, agev, firstpass, lastpass, imx, nlstate, stepm);
3586:
3587: /* Routine tricode is to calculate cptcoveff (real number of unique covariates) and to associate covariable number and modality */
3588:
3589: Tcode=ivector(1,100);
3590: nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);
3591: ncodemax[1]=1;
3592: if (cptcovn > 0) tricode(Tvar,nbcode,imx);
3593:
3594: codtab=imatrix(1,100,1,10); /* Cross tabulation to get the order of
3595: the estimations*/
3596: h=0;
3597: m=pow(2,cptcoveff);
3598:
3599: for(k=1;k<=cptcoveff; k++){
3600: for(i=1; i <=(m/pow(2,k));i++){
3601: for(j=1; j <= ncodemax[k]; j++){
3602: for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){
3603: h++;
3604: if (h>m) h=1;codtab[h][k]=j;codtab[h][Tvar[k]]=j;
3605: /* printf("h=%d k=%d j=%d codtab[h][k]=%d tvar[k]=%d \n",h, k,j,codtab[h][k],Tvar[k]);*/
3606: }
3607: }
3608: }
3609: }
3610: /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]);
3611: codtab[1][2]=1;codtab[2][2]=2; */
3612: /* for(i=1; i <=m ;i++){
3613: for(k=1; k <=cptcovn; k++){
3614: printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);
3615: }
3616: printf("\n");
3617: }
3618: scanf("%d",i);*/
3619:
3620: /* Calculates basic frequencies. Computes observed prevalence at single age
3621: and prints on file fileres'p'. */
3622:
3623:
3624:
3625: pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
3626: oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
3627: newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
3628: savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
3629: oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */
3630:
3631: /* For Powell, parameters are in a vector p[] starting at p[1]
3632: so we point p on param[1][1] so that p[1] maps on param[1][1][1] */
3633: p=param[1][1]; /* *(*(*(param +1)+1)+0) */
3634:
3635: if(mle==1){
3636: mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);
3637: }
3638:
3639: /*--------- results files --------------*/
3640: fprintf(ficres,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle= 0 weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate, ndeath, maxwav, weightopt,model);
3641:
3642:
3643: jk=1;
3644: fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
3645: printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
3646: fprintf(ficlog,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
3647: for(i=1,jk=1; i <=nlstate; i++){
3648: for(k=1; k <=(nlstate+ndeath); k++){
3649: if (k != i)
3650: {
3651: printf("%d%d ",i,k);
3652: fprintf(ficlog,"%d%d ",i,k);
3653: fprintf(ficres,"%1d%1d ",i,k);
3654: for(j=1; j <=ncovmodel; j++){
3655: printf("%f ",p[jk]);
3656: fprintf(ficlog,"%f ",p[jk]);
3657: fprintf(ficres,"%f ",p[jk]);
3658: jk++;
3659: }
3660: printf("\n");
3661: fprintf(ficlog,"\n");
3662: fprintf(ficres,"\n");
3663: }
3664: }
3665: }
3666: if(mle==1){
3667: /* Computing hessian and covariance matrix */
3668: ftolhess=ftol; /* Usually correct */
3669: hesscov(matcov, p, npar, delti, ftolhess, func);
3670: }
3671: fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");
3672: printf("# Scales (for hessian or gradient estimation)\n");
3673: fprintf(ficlog,"# Scales (for hessian or gradient estimation)\n");
3674: for(i=1,jk=1; i <=nlstate; i++){
3675: for(j=1; j <=nlstate+ndeath; j++){
3676: if (j!=i) {
3677: fprintf(ficres,"%1d%1d",i,j);
3678: printf("%1d%1d",i,j);
3679: fprintf(ficlog,"%1d%1d",i,j);
3680: for(k=1; k<=ncovmodel;k++){
3681: printf(" %.5e",delti[jk]);
3682: fprintf(ficlog," %.5e",delti[jk]);
3683: fprintf(ficres," %.5e",delti[jk]);
3684: jk++;
3685: }
3686: printf("\n");
3687: fprintf(ficlog,"\n");
3688: fprintf(ficres,"\n");
3689: }
3690: }
3691: }
3692:
3693: k=1;
3694: fprintf(ficres,"# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n# ...\n# 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n");
3695: if(mle==1)
3696: printf("# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n# ...\n# 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n");
3697: fprintf(ficlog,"# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n# ...\n# 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n");
3698: for(i=1;i<=npar;i++){
3699: /* if (k>nlstate) k=1;
3700: i1=(i-1)/(ncovmodel*nlstate)+1;
3701: fprintf(ficres,"%s%d%d",alph[k],i1,tab[i]);
3702: printf("%s%d%d",alph[k],i1,tab[i]);*/
3703: fprintf(ficres,"%3d",i);
3704: if(mle==1)
3705: printf("%3d",i);
3706: fprintf(ficlog,"%3d",i);
3707: for(j=1; j<=i;j++){
3708: fprintf(ficres," %.5e",matcov[i][j]);
3709: if(mle==1)
3710: printf(" %.5e",matcov[i][j]);
3711: fprintf(ficlog," %.5e",matcov[i][j]);
3712: }
3713: fprintf(ficres,"\n");
3714: if(mle==1)
3715: printf("\n");
3716: fprintf(ficlog,"\n");
3717: k++;
3718: }
3719:
3720: while((c=getc(ficpar))=='#' && c!= EOF){
3721: ungetc(c,ficpar);
3722: fgets(line, MAXLINE, ficpar);
3723: puts(line);
3724: fputs(line,ficparo);
3725: }
3726: ungetc(c,ficpar);
3727: estepm=0;
3728: fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm);
3729: if (estepm==0 || estepm < stepm) estepm=stepm;
3730: if (fage <= 2) {
3731: bage = ageminpar;
3732: fage = agemaxpar;
3733: }
3734:
3735: fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");
3736: fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
3737: fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
3738:
3739: while((c=getc(ficpar))=='#' && c!= EOF){
3740: ungetc(c,ficpar);
3741: fgets(line, MAXLINE, ficpar);
3742: puts(line);
3743: fputs(line,ficparo);
3744: }
3745: ungetc(c,ficpar);
3746:
3747: fscanf(ficpar,"begin-prev-date=%lf/%lf/%lf end-prev-date=%lf/%lf/%lf mov_average=%d\n",&jprev1, &mprev1,&anprev1,&jprev2, &mprev2,&anprev2,&mobilav);
3748: fprintf(ficparo,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
3749: fprintf(ficres,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
3750:
3751: while((c=getc(ficpar))=='#' && c!= EOF){
3752: ungetc(c,ficpar);
3753: fgets(line, MAXLINE, ficpar);
3754: puts(line);
3755: fputs(line,ficparo);
3756: }
3757: ungetc(c,ficpar);
3758:
3759:
3760: dateprev1=anprev1+mprev1/12.+jprev1/365.;
3761: dateprev2=anprev2+mprev2/12.+jprev2/365.;
3762:
3763: fscanf(ficpar,"pop_based=%d\n",&popbased);
3764: fprintf(ficparo,"pop_based=%d\n",popbased);
3765: fprintf(ficres,"pop_based=%d\n",popbased);
3766:
3767: while((c=getc(ficpar))=='#' && c!= EOF){
3768: ungetc(c,ficpar);
3769: fgets(line, MAXLINE, ficpar);
3770: puts(line);
3771: fputs(line,ficparo);
3772: }
3773: ungetc(c,ficpar);
3774:
3775: fscanf(ficpar,"starting-proj-date=%lf/%lf/%lf final-proj-date=%lf/%lf/%lf\n",&jproj1,&mproj1,&anproj1,&jproj2,&mproj2,&anproj2);
3776: fprintf(ficparo,"starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf\n",jproj1,mproj1,anproj1,jproj2,mproj2,anproj2);
3777: fprintf(ficres,"starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf\n",jproj1,mproj1,anproj1,jproj2,mproj2,anproj2);
3778:
3779:
3780: while((c=getc(ficpar))=='#' && c!= EOF){
3781: ungetc(c,ficpar);
3782: fgets(line, MAXLINE, ficpar);
3783: puts(line);
3784: fputs(line,ficparo);
3785: }
3786: ungetc(c,ficpar);
3787:
3788: fscanf(ficpar,"popforecast=%d popfile=%s popfiledate=%lf/%lf/%lf last-popfiledate=%lf/%lf/%lf\n",&popforecast,popfile,&jpyram,&mpyram,&anpyram,&jpyram1,&mpyram1,&anpyram1);
3789: fprintf(ficparo,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);
3790: fprintf(ficres,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);
3791:
3792: freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);
3793:
3794: /*------------ gnuplot -------------*/
3795: strcpy(optionfilegnuplot,optionfilefiname);
3796: strcat(optionfilegnuplot,".gp");
3797: if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {
3798: printf("Problem with file %s",optionfilegnuplot);
3799: }
3800: else{
3801: fprintf(ficgp,"\n# %s\n", version);
3802: fprintf(ficgp,"# %s\n", optionfilegnuplot);
3803: fprintf(ficgp,"set missing 'NaNq'\n");
3804: }
3805: fclose(ficgp);
3806: printinggnuplot(fileres, ageminpar,agemaxpar,fage, pathc,p);
3807: /*--------- index.htm --------*/
3808:
3809: strcpy(optionfilehtm,optionfile);
3810: strcat(optionfilehtm,".htm");
3811: if((fichtm=fopen(optionfilehtm,"w"))==NULL) {
3812: printf("Problem with %s \n",optionfilehtm), exit(0);
3813: }
3814:
3815: fprintf(fichtm,"<body> <font size=\"2\">%s </font> <hr size=\"2\" color=\"#EC5E5E\"> \n
3816: Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n
3817: \n
3818: Total number of observations=%d <br>\n
3819: Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n
3820: <hr size=\"2\" color=\"#EC5E5E\">
3821: <ul><li><h4>Parameter files</h4>\n
3822: - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n
3823: - Log file of the run: <a href=\"%s\">%s</a><br>\n
3824: - Gnuplot file name: <a href=\"%s\">%s</a></ul>\n",version,title,datafile,firstpass,lastpass,stepm, weightopt,model,imx,jmin,jmax,jmean,fileres,fileres,filelog,filelog,optionfilegnuplot,optionfilegnuplot);
3825: fclose(fichtm);
3826:
3827: printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,model,imx,jmin,jmax,jmean,rfileres,popforecast,estepm,jprev1,mprev1,anprev1,jprev2,mprev2,anprev2);
3828:
3829: /*------------ free_vector -------------*/
3830: chdir(path);
3831:
3832: free_ivector(wav,1,imx);
3833: free_imatrix(dh,1,lastpass-firstpass+1,1,imx);
3834: free_imatrix(mw,1,lastpass-firstpass+1,1,imx);
3835: free_ivector(num,1,n);
3836: free_vector(agedc,1,n);
3837: /*free_matrix(covar,1,NCOVMAX,1,n);*/
3838: fclose(ficparo);
3839: fclose(ficres);
3840:
3841:
3842: /*--------------- Prevalence limit (stable prevalence) --------------*/
3843:
3844: strcpy(filerespl,"pl");
3845: strcat(filerespl,fileres);
3846: if((ficrespl=fopen(filerespl,"w"))==NULL) {
3847: printf("Problem with stable prevalence resultfile: %s\n", filerespl);goto end;
3848: fprintf(ficlog,"Problem with stable prevalence resultfile: %s\n", filerespl);goto end;
3849: }
3850: printf("Computing stable prevalence: result on file '%s' \n", filerespl);
3851: fprintf(ficlog,"Computing stable prevalence: result on file '%s' \n", filerespl);
3852: fprintf(ficrespl,"#Stable prevalence \n");
3853: fprintf(ficrespl,"#Age ");
3854: for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);
3855: fprintf(ficrespl,"\n");
3856:
3857: prlim=matrix(1,nlstate,1,nlstate);
3858: pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
3859: oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
3860: newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
3861: savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
3862: oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */
3863: k=0;
3864: agebase=ageminpar;
3865: agelim=agemaxpar;
3866: ftolpl=1.e-10;
3867: i1=cptcoveff;
3868: if (cptcovn < 1){i1=1;}
3869:
3870: for(cptcov=1;cptcov<=i1;cptcov++){
3871: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
3872: k=k+1;
3873: /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/
3874: fprintf(ficrespl,"\n#******");
3875: printf("\n#******");
3876: fprintf(ficlog,"\n#******");
3877: for(j=1;j<=cptcoveff;j++) {
3878: fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
3879: printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
3880: fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
3881: }
3882: fprintf(ficrespl,"******\n");
3883: printf("******\n");
3884: fprintf(ficlog,"******\n");
3885:
3886: for (age=agebase; age<=agelim; age++){
3887: prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
3888: fprintf(ficrespl,"%.0f",age );
3889: for(i=1; i<=nlstate;i++)
3890: fprintf(ficrespl," %.5f", prlim[i][i]);
3891: fprintf(ficrespl,"\n");
3892: }
3893: }
3894: }
3895: fclose(ficrespl);
3896:
3897: /*------------- h Pij x at various ages ------------*/
3898:
3899: strcpy(filerespij,"pij"); strcat(filerespij,fileres);
3900: if((ficrespij=fopen(filerespij,"w"))==NULL) {
3901: printf("Problem with Pij resultfile: %s\n", filerespij);goto end;
3902: fprintf(ficlog,"Problem with Pij resultfile: %s\n", filerespij);goto end;
3903: }
3904: printf("Computing pij: result on file '%s' \n", filerespij);
3905: fprintf(ficlog,"Computing pij: result on file '%s' \n", filerespij);
3906:
3907: stepsize=(int) (stepm+YEARM-1)/YEARM;
3908: /*if (stepm<=24) stepsize=2;*/
3909:
3910: agelim=AGESUP;
3911: hstepm=stepsize*YEARM; /* Every year of age */
3912: hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */
3913:
3914: /* hstepm=1; aff par mois*/
3915:
3916: k=0;
3917: for(cptcov=1;cptcov<=i1;cptcov++){
3918: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
3919: k=k+1;
3920: fprintf(ficrespij,"\n#****** ");
3921: for(j=1;j<=cptcoveff;j++)
3922: fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
3923: fprintf(ficrespij,"******\n");
3924:
3925: for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */
3926: nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
3927: nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
3928:
3929: /* nhstepm=nhstepm*YEARM; aff par mois*/
3930:
3931: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3932: oldm=oldms;savm=savms;
3933: hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
3934: fprintf(ficrespij,"# Age");
3935: for(i=1; i<=nlstate;i++)
3936: for(j=1; j<=nlstate+ndeath;j++)
3937: fprintf(ficrespij," %1d-%1d",i,j);
3938: fprintf(ficrespij,"\n");
3939: for (h=0; h<=nhstepm; h++){
3940: fprintf(ficrespij,"%d %f %f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );
3941: for(i=1; i<=nlstate;i++)
3942: for(j=1; j<=nlstate+ndeath;j++)
3943: fprintf(ficrespij," %.5f", p3mat[i][j][h]);
3944: fprintf(ficrespij,"\n");
3945: }
3946: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3947: fprintf(ficrespij,"\n");
3948: }
3949: }
3950: }
3951:
3952: varprob(optionfilefiname, matcov, p, delti, nlstate, (int) bage, (int) fage,k,Tvar,nbcode, ncodemax);
3953:
3954: fclose(ficrespij);
3955:
3956:
3957: /*---------- Forecasting ------------------*/
3958: if((stepm == 1) && (strcmp(model,".")==0)){
3959: prevforecast(fileres, anproj1,mproj1,jproj1, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anproj2,p, i1);
3960: if (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);
3961: }
3962: else{
3963: erreur=108;
3964: printf("Warning %d!! You can only forecast the prevalences if the optimization\n has been performed with stepm = 1 (month) instead of %d or model=. instead of '%s'\n", erreur, stepm, model);
3965: fprintf(ficlog,"Warning %d!! You can only forecast the prevalences if the optimization\n has been performed with stepm = 1 (month) instead of %d or model=. instead of '%s'\n", erreur, stepm, model);
3966: }
3967:
3968:
3969: /*---------- Health expectancies and variances ------------*/
3970:
3971: strcpy(filerest,"t");
3972: strcat(filerest,fileres);
3973: if((ficrest=fopen(filerest,"w"))==NULL) {
3974: printf("Problem with total LE resultfile: %s\n", filerest);goto end;
3975: fprintf(ficlog,"Problem with total LE resultfile: %s\n", filerest);goto end;
3976: }
3977: printf("Computing Total LEs with variances: file '%s' \n", filerest);
3978: fprintf(ficlog,"Computing Total LEs with variances: file '%s' \n", filerest);
3979:
3980:
3981: strcpy(filerese,"e");
3982: strcat(filerese,fileres);
3983: if((ficreseij=fopen(filerese,"w"))==NULL) {
3984: printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
3985: fprintf(ficlog,"Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
3986: }
3987: printf("Computing Health Expectancies: result on file '%s' \n", filerese);
3988: fprintf(ficlog,"Computing Health Expectancies: result on file '%s' \n", filerese);
3989:
3990: strcpy(fileresv,"v");
3991: strcat(fileresv,fileres);
3992: if((ficresvij=fopen(fileresv,"w"))==NULL) {
3993: printf("Problem with variance resultfile: %s\n", fileresv);exit(0);
3994: fprintf(ficlog,"Problem with variance resultfile: %s\n", fileresv);exit(0);
3995: }
3996: printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
3997: fprintf(ficlog,"Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
3998:
3999: calagedate=-1;
4000:
4001: prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);
4002:
4003: if (mobilav!=0) {
4004: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
4005: if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
4006: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
4007: printf(" Error in movingaverage mobilav=%d\n",mobilav);
4008: }
4009: }
4010:
4011: k=0;
4012: for(cptcov=1;cptcov<=i1;cptcov++){
4013: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
4014: k=k+1;
4015: fprintf(ficrest,"\n#****** ");
4016: for(j=1;j<=cptcoveff;j++)
4017: fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
4018: fprintf(ficrest,"******\n");
4019:
4020: fprintf(ficreseij,"\n#****** ");
4021: for(j=1;j<=cptcoveff;j++)
4022: fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
4023: fprintf(ficreseij,"******\n");
4024:
4025: fprintf(ficresvij,"\n#****** ");
4026: for(j=1;j<=cptcoveff;j++)
4027: fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
4028: fprintf(ficresvij,"******\n");
4029:
4030: eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
4031: oldm=oldms;savm=savms;
4032: evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov);
4033:
4034: vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
4035: oldm=oldms;savm=savms;
4036: varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,0, mobilav);
4037: if(popbased==1){
4038: varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,popbased,mobilav);
4039: }
4040:
4041:
4042: fprintf(ficrest,"#Total LEs with variances: e.. (std) ");
4043: for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);
4044: fprintf(ficrest,"\n");
4045:
4046: epj=vector(1,nlstate+1);
4047: for(age=bage; age <=fage ;age++){
4048: prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
4049: if (popbased==1) {
4050: if(mobilav ==0){
4051: for(i=1; i<=nlstate;i++)
4052: prlim[i][i]=probs[(int)age][i][k];
4053: }else{ /* mobilav */
4054: for(i=1; i<=nlstate;i++)
4055: prlim[i][i]=mobaverage[(int)age][i][k];
4056: }
4057: }
4058:
4059: fprintf(ficrest," %4.0f",age);
4060: for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){
4061: for(i=1, epj[j]=0.;i <=nlstate;i++) {
4062: epj[j] += prlim[i][i]*eij[i][j][(int)age];
4063: /* printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/
4064: }
4065: epj[nlstate+1] +=epj[j];
4066: }
4067:
4068: for(i=1, vepp=0.;i <=nlstate;i++)
4069: for(j=1;j <=nlstate;j++)
4070: vepp += vareij[i][j][(int)age];
4071: fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));
4072: for(j=1;j <=nlstate;j++){
4073: fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));
4074: }
4075: fprintf(ficrest,"\n");
4076: }
4077: }
4078: }
4079: free_matrix(mint,1,maxwav,1,n);
4080: free_matrix(anint,1,maxwav,1,n); free_imatrix(s,1,maxwav+1,1,n);
4081: free_vector(weight,1,n);
4082: fclose(ficreseij);
4083: fclose(ficresvij);
4084: fclose(ficrest);
4085: fclose(ficpar);
4086: free_vector(epj,1,nlstate+1);
4087:
4088: /*------- Variance of stable prevalence------*/
4089:
4090: strcpy(fileresvpl,"vpl");
4091: strcat(fileresvpl,fileres);
4092: if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {
4093: printf("Problem with variance of stable prevalence resultfile: %s\n", fileresvpl);
4094: exit(0);
4095: }
4096: printf("Computing Variance-covariance of stable prevalence: file '%s' \n", fileresvpl);
4097:
4098: k=0;
4099: for(cptcov=1;cptcov<=i1;cptcov++){
4100: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
4101: k=k+1;
4102: fprintf(ficresvpl,"\n#****** ");
4103: for(j=1;j<=cptcoveff;j++)
4104: fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
4105: fprintf(ficresvpl,"******\n");
4106:
4107: varpl=matrix(1,nlstate,(int) bage, (int) fage);
4108: oldm=oldms;savm=savms;
4109: varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);
4110: }
4111: }
4112:
4113: fclose(ficresvpl);
4114:
4115: /*---------- End : free ----------------*/
4116: free_matrix(varpl,1,nlstate,(int) bage, (int)fage);
4117:
4118: free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);
4119: free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
4120:
4121:
4122: free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);
4123: free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);
4124: free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);
4125: free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);
4126:
4127: free_matrix(matcov,1,npar,1,npar);
4128: free_vector(delti,1,npar);
4129: free_matrix(agev,1,maxwav,1,imx);
4130: free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
4131: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
4132:
4133: fprintf(fichtm,"\n</body>");
4134: fclose(fichtm);
4135: fclose(ficgp);
4136:
4137:
4138: if(erreur >0){
4139: printf("End of Imach with error or warning %d\n",erreur);
4140: fprintf(ficlog,"End of Imach with error or warning %d\n",erreur);
4141: }else{
4142: printf("End of Imach\n");
4143: fprintf(ficlog,"End of Imach\n");
4144: }
4145: printf("See log file on %s\n",filelog);
4146: fclose(ficlog);
4147: /* gettimeofday(&end_time, (struct timezone*)0);*/ /* after time */
4148:
4149: /* 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);*/
4150: /*printf("Total time was %d uSec.\n", total_usecs);*/
4151: /*------ End -----------*/
4152:
4153:
4154: end:
4155: #ifdef windows
4156: /* chdir(pathcd);*/
4157: #endif
4158: /*system("wgnuplot graph.plt");*/
4159: /*system("../gp37mgw/wgnuplot graph.plt");*/
4160: /*system("cd ../gp37mgw");*/
4161: /* system("..\\gp37mgw\\wgnuplot graph.plt");*/
4162: strcpy(plotcmd,GNUPLOTPROGRAM);
4163: strcat(plotcmd," ");
4164: strcat(plotcmd,optionfilegnuplot);
4165: printf("Starting: %s\n",plotcmd);fflush(stdout);
4166: system(plotcmd);
4167:
4168: /*#ifdef windows*/
4169: while (z[0] != 'q') {
4170: /* chdir(path); */
4171: printf("\nType e to edit output files, g to graph again, c to start again, and q for exiting: ");
4172: scanf("%s",z);
4173: if (z[0] == 'c') system("./imach");
4174: else if (z[0] == 'e') system(optionfilehtm);
4175: else if (z[0] == 'g') system(plotcmd);
4176: else if (z[0] == 'q') exit(0);
4177: }
4178: /*#endif */
4179: }
4180:
4181:
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