Annotation of imach/src/imach.c, revision 1.55
1.55 ! lievre 1: /* $Id: imach.c,v 1.54 2002/07/24 09:07:45 brouard Exp $
1.53 brouard 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
1.54 brouard 42: of the life expectancies. It also computes the stable prevalence.
1.53 brouard 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*/
1.55 ! lievre 63: #define windows
1.53 brouard 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:
1.54 brouard 86: char version[80]="Imach version 0.8k, July 2002, INED-EUROREVES ";
1.53 brouard 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;
1.55 ! lievre 166: double **pmmij, ***probs;
1.53 brouard 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
1.54 brouard 704: }
1.53 brouard 705: }
706: }
707: }
708:
1.54 brouard 709: /**** Prevalence limit (stable prevalence) ****************/
1.53 brouard 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: int Ndum[20],ij=1, k, j, i;
1579: int cptcode=0;
1580: cptcoveff=0;
1581:
1582: for (k=0; k<19; k++) Ndum[k]=0;
1583: for (k=1; k<=7; k++) ncodemax[k]=0;
1584:
1585: for (j=1; j<=(cptcovn+2*cptcovprod); j++) {
1586: for (i=1; i<=imx; i++) {
1587: ij=(int)(covar[Tvar[j]][i]);
1588: Ndum[ij]++;
1589: /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
1590: if (ij > cptcode) cptcode=ij;
1591: }
1592:
1593: for (i=0; i<=cptcode; i++) {
1594: if(Ndum[i]!=0) ncodemax[j]++;
1595: }
1596: ij=1;
1597:
1598:
1599: for (i=1; i<=ncodemax[j]; i++) {
1600: for (k=0; k<=19; k++) {
1601: if (Ndum[k] != 0) {
1602: nbcode[Tvar[j]][ij]=k;
1603:
1604: ij++;
1605: }
1606: if (ij > ncodemax[j]) break;
1607: }
1608: }
1609: }
1610:
1611: for (k=0; k<19; k++) Ndum[k]=0;
1612:
1613: for (i=1; i<=ncovmodel-2; i++) {
1614: ij=Tvar[i];
1615: Ndum[ij]++;
1616: }
1617:
1618: ij=1;
1619: for (i=1; i<=10; i++) {
1620: if((Ndum[i]!=0) && (i<=ncovcol)){
1621: Tvaraff[ij]=i;
1622: ij++;
1623: }
1624: }
1625:
1626: cptcoveff=ij-1;
1627: }
1628:
1629: /*********** Health Expectancies ****************/
1630:
1631: 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 )
1632:
1633: {
1634: /* Health expectancies */
1635: int i, j, nhstepm, hstepm, h, nstepm, k, cptj;
1636: double age, agelim, hf;
1637: double ***p3mat,***varhe;
1638: double **dnewm,**doldm;
1639: double *xp;
1640: double **gp, **gm;
1641: double ***gradg, ***trgradg;
1642: int theta;
1643:
1644: varhe=ma3x(1,nlstate*2,1,nlstate*2,(int) bage, (int) fage);
1645: xp=vector(1,npar);
1646: dnewm=matrix(1,nlstate*2,1,npar);
1647: doldm=matrix(1,nlstate*2,1,nlstate*2);
1648:
1649: fprintf(ficreseij,"# Health expectancies\n");
1650: fprintf(ficreseij,"# Age");
1651: for(i=1; i<=nlstate;i++)
1652: for(j=1; j<=nlstate;j++)
1653: fprintf(ficreseij," %1d-%1d (SE)",i,j);
1654: fprintf(ficreseij,"\n");
1655:
1656: if(estepm < stepm){
1657: printf ("Problem %d lower than %d\n",estepm, stepm);
1658: }
1659: else hstepm=estepm;
1660: /* We compute the life expectancy from trapezoids spaced every estepm months
1661: * This is mainly to measure the difference between two models: for example
1662: * if stepm=24 months pijx are given only every 2 years and by summing them
1663: * we are calculating an estimate of the Life Expectancy assuming a linear
1664: * progression inbetween and thus overestimating or underestimating according
1665: * to the curvature of the survival function. If, for the same date, we
1666: * estimate the model with stepm=1 month, we can keep estepm to 24 months
1667: * to compare the new estimate of Life expectancy with the same linear
1668: * hypothesis. A more precise result, taking into account a more precise
1669: * curvature will be obtained if estepm is as small as stepm. */
1670:
1671: /* For example we decided to compute the life expectancy with the smallest unit */
1672: /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
1673: nhstepm is the number of hstepm from age to agelim
1674: nstepm is the number of stepm from age to agelin.
1675: Look at hpijx to understand the reason of that which relies in memory size
1676: and note for a fixed period like estepm months */
1677: /* We decided (b) to get a life expectancy respecting the most precise curvature of the
1678: survival function given by stepm (the optimization length). Unfortunately it
1679: means that if the survival funtion is printed only each two years of age and if
1680: you sum them up and add 1 year (area under the trapezoids) you won't get the same
1681: results. So we changed our mind and took the option of the best precision.
1682: */
1683: hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
1684:
1685: agelim=AGESUP;
1686: for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
1687: /* nhstepm age range expressed in number of stepm */
1688: nstepm=(int) rint((agelim-age)*YEARM/stepm);
1689: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
1690: /* if (stepm >= YEARM) hstepm=1;*/
1691: nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
1692: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
1693: gradg=ma3x(0,nhstepm,1,npar,1,nlstate*2);
1694: gp=matrix(0,nhstepm,1,nlstate*2);
1695: gm=matrix(0,nhstepm,1,nlstate*2);
1696:
1697: /* Computed by stepm unit matrices, product of hstepm matrices, stored
1698: in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
1699: hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);
1700:
1701:
1702: hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
1703:
1704: /* Computing Variances of health expectancies */
1705:
1706: for(theta=1; theta <=npar; theta++){
1707: for(i=1; i<=npar; i++){
1708: xp[i] = x[i] + (i==theta ?delti[theta]:0);
1709: }
1710: hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
1711:
1712: cptj=0;
1713: for(j=1; j<= nlstate; j++){
1714: for(i=1; i<=nlstate; i++){
1715: cptj=cptj+1;
1716: for(h=0, gp[h][cptj]=0.; h<=nhstepm-1; h++){
1717: gp[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;
1718: }
1719: }
1720: }
1721:
1722:
1723: for(i=1; i<=npar; i++)
1724: xp[i] = x[i] - (i==theta ?delti[theta]:0);
1725: hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
1726:
1727: cptj=0;
1728: for(j=1; j<= nlstate; j++){
1729: for(i=1;i<=nlstate;i++){
1730: cptj=cptj+1;
1731: for(h=0, gm[h][cptj]=0.; h<=nhstepm-1; h++){
1732: gm[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;
1733: }
1734: }
1735: }
1736: for(j=1; j<= nlstate*2; j++)
1737: for(h=0; h<=nhstepm-1; h++){
1738: gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
1739: }
1740: }
1741:
1742: /* End theta */
1743:
1744: trgradg =ma3x(0,nhstepm,1,nlstate*2,1,npar);
1745:
1746: for(h=0; h<=nhstepm-1; h++)
1747: for(j=1; j<=nlstate*2;j++)
1748: for(theta=1; theta <=npar; theta++)
1749: trgradg[h][j][theta]=gradg[h][theta][j];
1750:
1751:
1752: for(i=1;i<=nlstate*2;i++)
1753: for(j=1;j<=nlstate*2;j++)
1754: varhe[i][j][(int)age] =0.;
1755:
1756: printf("%d|",(int)age);fflush(stdout);
1757: fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
1758: for(h=0;h<=nhstepm-1;h++){
1759: for(k=0;k<=nhstepm-1;k++){
1760: matprod2(dnewm,trgradg[h],1,nlstate*2,1,npar,1,npar,matcov);
1761: matprod2(doldm,dnewm,1,nlstate*2,1,npar,1,nlstate*2,gradg[k]);
1762: for(i=1;i<=nlstate*2;i++)
1763: for(j=1;j<=nlstate*2;j++)
1764: varhe[i][j][(int)age] += doldm[i][j]*hf*hf;
1765: }
1766: }
1767: /* Computing expectancies */
1768: for(i=1; i<=nlstate;i++)
1769: for(j=1; j<=nlstate;j++)
1770: for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
1771: eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
1772:
1773: /* 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]);*/
1774:
1775: }
1776:
1777: fprintf(ficreseij,"%3.0f",age );
1778: cptj=0;
1779: for(i=1; i<=nlstate;i++)
1780: for(j=1; j<=nlstate;j++){
1781: cptj++;
1782: fprintf(ficreseij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[cptj][cptj][(int)age]) );
1783: }
1784: fprintf(ficreseij,"\n");
1785:
1786: free_matrix(gm,0,nhstepm,1,nlstate*2);
1787: free_matrix(gp,0,nhstepm,1,nlstate*2);
1788: free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*2);
1789: free_ma3x(trgradg,0,nhstepm,1,nlstate*2,1,npar);
1790: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
1791: }
1792: printf("\n");
1793: fprintf(ficlog,"\n");
1794:
1795: free_vector(xp,1,npar);
1796: free_matrix(dnewm,1,nlstate*2,1,npar);
1797: free_matrix(doldm,1,nlstate*2,1,nlstate*2);
1798: free_ma3x(varhe,1,nlstate*2,1,nlstate*2,(int) bage, (int)fage);
1799: }
1800:
1801: /************ Variance ******************/
1802: 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)
1803: {
1804: /* Variance of health expectancies */
1805: /* double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
1806: /* double **newm;*/
1807: double **dnewm,**doldm;
1808: double **dnewmp,**doldmp;
1809: int i, j, nhstepm, hstepm, h, nstepm ;
1810: int k, cptcode;
1811: double *xp;
1812: double **gp, **gm; /* for var eij */
1813: double ***gradg, ***trgradg; /*for var eij */
1814: double **gradgp, **trgradgp; /* for var p point j */
1815: double *gpp, *gmp; /* for var p point j */
1816: double **varppt; /* for var p point j nlstate to nlstate+ndeath */
1817: double ***p3mat;
1818: double age,agelim, hf;
1819: double ***mobaverage;
1820: int theta;
1821: char digit[4];
1.55 ! lievre 1822: char digitp[25];
1.53 brouard 1823:
1824: char fileresprobmorprev[FILENAMELENGTH];
1825:
1.55 ! lievre 1826: if(popbased==1){
! 1827: if(mobilav==1)
! 1828: strcpy(digitp,"-populbased-mobilav-");
! 1829: else strcpy(digitp,"-populbased-nomobil-");
! 1830: }
! 1831: else
1.53 brouard 1832: strcpy(digitp,"-stablbased-");
1.55 ! lievre 1833: <<<<<<< imach.c
! 1834: if (mobilav!=0) {
! 1835: =======
1.54 brouard 1836: if(mobilav!=0)
1.53 brouard 1837: strcat(digitp,"mobilav-");
1838: else
1839: strcat(digitp,"nomobil-");
1.54 brouard 1840: if (mobilav!=0) {
1.55 ! lievre 1841: >>>>>>> 1.54
1.53 brouard 1842: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
1.54 brouard 1843: if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
1844: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
1845: printf(" Error in movingaverage mobilav=%d\n",mobilav);
1846: }
1.53 brouard 1847: }
1848:
1849: strcpy(fileresprobmorprev,"prmorprev");
1850: sprintf(digit,"%-d",ij);
1851: /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
1852: strcat(fileresprobmorprev,digit); /* Tvar to be done */
1853: strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
1854: strcat(fileresprobmorprev,fileres);
1855: if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
1856: printf("Problem with resultfile: %s\n", fileresprobmorprev);
1857: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
1858: }
1859: printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
1860: fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
1861: fprintf(ficresprobmorprev,"# probabilities of dying during a year and weighted mean w1*p1j+w2*p2j+... stand dev in()\n");
1862: fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
1863: for(j=nlstate+1; j<=(nlstate+ndeath);j++){
1864: fprintf(ficresprobmorprev," p.%-d SE",j);
1865: for(i=1; i<=nlstate;i++)
1866: fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
1867: }
1868: fprintf(ficresprobmorprev,"\n");
1869: if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {
1870: printf("Problem with gnuplot file: %s\n", optionfilegnuplot);
1871: fprintf(ficlog,"Problem with gnuplot file: %s\n", optionfilegnuplot);
1872: exit(0);
1873: }
1874: else{
1875: fprintf(ficgp,"\n# Routine varevsij");
1876: }
1877: if((fichtm=fopen(optionfilehtm,"a"))==NULL) {
1878: printf("Problem with html file: %s\n", optionfilehtm);
1879: fprintf(ficlog,"Problem with html file: %s\n", optionfilehtm);
1880: exit(0);
1881: }
1882: else{
1883: 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");
1884: fprintf(fichtm,"\n<br>%s (à revoir) <br>\n",digitp);
1885: }
1886: varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
1887:
1888: 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");
1889: fprintf(ficresvij,"# Age");
1890: for(i=1; i<=nlstate;i++)
1891: for(j=1; j<=nlstate;j++)
1892: fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);
1893: fprintf(ficresvij,"\n");
1894:
1895: xp=vector(1,npar);
1896: dnewm=matrix(1,nlstate,1,npar);
1897: doldm=matrix(1,nlstate,1,nlstate);
1898: dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
1899: doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
1900:
1901: gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
1902: gpp=vector(nlstate+1,nlstate+ndeath);
1903: gmp=vector(nlstate+1,nlstate+ndeath);
1904: trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
1905:
1906: if(estepm < stepm){
1907: printf ("Problem %d lower than %d\n",estepm, stepm);
1908: }
1909: else hstepm=estepm;
1910: /* For example we decided to compute the life expectancy with the smallest unit */
1911: /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
1912: nhstepm is the number of hstepm from age to agelim
1913: nstepm is the number of stepm from age to agelin.
1914: Look at hpijx to understand the reason of that which relies in memory size
1915: and note for a fixed period like k years */
1916: /* We decided (b) to get a life expectancy respecting the most precise curvature of the
1917: survival function given by stepm (the optimization length). Unfortunately it
1918: means that if the survival funtion is printed only each two years of age and if
1919: you sum them up and add 1 year (area under the trapezoids) you won't get the same
1920: results. So we changed our mind and took the option of the best precision.
1921: */
1922: hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
1923: agelim = AGESUP;
1924: for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
1925: nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
1926: nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
1927: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
1928: gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
1929: gp=matrix(0,nhstepm,1,nlstate);
1930: gm=matrix(0,nhstepm,1,nlstate);
1931:
1932:
1933: for(theta=1; theta <=npar; theta++){
1934: for(i=1; i<=npar; i++){ /* Computes gradient */
1935: xp[i] = x[i] + (i==theta ?delti[theta]:0);
1936: }
1937: hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
1938: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
1939:
1940: if (popbased==1) {
1.54 brouard 1941: if(mobilav ==0){
1.53 brouard 1942: for(i=1; i<=nlstate;i++)
1943: prlim[i][i]=probs[(int)age][i][ij];
1.54 brouard 1944: }else{ /* mobilav */
1.53 brouard 1945: for(i=1; i<=nlstate;i++)
1946: prlim[i][i]=mobaverage[(int)age][i][ij];
1947: }
1948: }
1949:
1950: for(j=1; j<= nlstate; j++){
1951: for(h=0; h<=nhstepm; h++){
1952: for(i=1, gp[h][j]=0.;i<=nlstate;i++)
1953: gp[h][j] += prlim[i][i]*p3mat[i][j][h];
1954: }
1955: }
1956: /* This for computing forces of mortality (h=1)as a weighted average */
1957: for(j=nlstate+1,gpp[j]=0.;j<=nlstate+ndeath;j++){
1958: for(i=1; i<= nlstate; i++)
1959: gpp[j] += prlim[i][i]*p3mat[i][j][1];
1960: }
1961: /* end force of mortality */
1962:
1963: for(i=1; i<=npar; i++) /* Computes gradient */
1964: xp[i] = x[i] - (i==theta ?delti[theta]:0);
1965: hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
1966: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
1967:
1968: if (popbased==1) {
1.54 brouard 1969: if(mobilav ==0){
1.53 brouard 1970: for(i=1; i<=nlstate;i++)
1971: prlim[i][i]=probs[(int)age][i][ij];
1.54 brouard 1972: }else{ /* mobilav */
1.53 brouard 1973: for(i=1; i<=nlstate;i++)
1974: prlim[i][i]=mobaverage[(int)age][i][ij];
1975: }
1976: }
1977:
1978: for(j=1; j<= nlstate; j++){
1979: for(h=0; h<=nhstepm; h++){
1980: for(i=1, gm[h][j]=0.;i<=nlstate;i++)
1981: gm[h][j] += prlim[i][i]*p3mat[i][j][h];
1982: }
1983: }
1984: /* This for computing force of mortality (h=1)as a weighted average */
1985: for(j=nlstate+1,gmp[j]=0.;j<=nlstate+ndeath;j++){
1986: for(i=1; i<= nlstate; i++)
1987: gmp[j] += prlim[i][i]*p3mat[i][j][1];
1988: }
1989: /* end force of mortality */
1990:
1991: for(j=1; j<= nlstate; j++) /* vareij */
1992: for(h=0; h<=nhstepm; h++){
1993: gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
1994: }
1995: for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
1996: gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
1997: }
1998:
1999: } /* End theta */
2000:
2001: trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
2002:
2003: for(h=0; h<=nhstepm; h++) /* veij */
2004: for(j=1; j<=nlstate;j++)
2005: for(theta=1; theta <=npar; theta++)
2006: trgradg[h][j][theta]=gradg[h][theta][j];
2007:
2008: for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
2009: for(theta=1; theta <=npar; theta++)
2010: trgradgp[j][theta]=gradgp[theta][j];
2011:
2012: hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
2013: for(i=1;i<=nlstate;i++)
2014: for(j=1;j<=nlstate;j++)
2015: vareij[i][j][(int)age] =0.;
2016:
2017: for(h=0;h<=nhstepm;h++){
2018: for(k=0;k<=nhstepm;k++){
2019: matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
2020: matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
2021: for(i=1;i<=nlstate;i++)
2022: for(j=1;j<=nlstate;j++)
2023: vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
2024: }
2025: }
2026:
2027: /* pptj */
2028: matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
2029: matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
2030: for(j=nlstate+1;j<=nlstate+ndeath;j++)
2031: for(i=nlstate+1;i<=nlstate+ndeath;i++)
2032: varppt[j][i]=doldmp[j][i];
2033: /* end ppptj */
2034: hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);
2035: prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);
2036:
2037: if (popbased==1) {
1.54 brouard 2038: if(mobilav ==0){
1.53 brouard 2039: for(i=1; i<=nlstate;i++)
2040: prlim[i][i]=probs[(int)age][i][ij];
1.54 brouard 2041: }else{ /* mobilav */
1.53 brouard 2042: for(i=1; i<=nlstate;i++)
2043: prlim[i][i]=mobaverage[(int)age][i][ij];
2044: }
2045: }
2046:
2047: /* This for computing force of mortality (h=1)as a weighted average */
2048: for(j=nlstate+1,gmp[j]=0.;j<=nlstate+ndeath;j++){
2049: for(i=1; i<= nlstate; i++)
2050: gmp[j] += prlim[i][i]*p3mat[i][j][1];
2051: }
2052: /* end force of mortality */
2053:
2054: fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
2055: for(j=nlstate+1; j<=(nlstate+ndeath);j++){
2056: fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
2057: for(i=1; i<=nlstate;i++){
2058: fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
2059: }
2060: }
2061: fprintf(ficresprobmorprev,"\n");
2062:
2063: fprintf(ficresvij,"%.0f ",age );
2064: for(i=1; i<=nlstate;i++)
2065: for(j=1; j<=nlstate;j++){
2066: fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
2067: }
2068: fprintf(ficresvij,"\n");
2069: free_matrix(gp,0,nhstepm,1,nlstate);
2070: free_matrix(gm,0,nhstepm,1,nlstate);
2071: free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
2072: free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
2073: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
2074: } /* End age */
2075: free_vector(gpp,nlstate+1,nlstate+ndeath);
2076: free_vector(gmp,nlstate+1,nlstate+ndeath);
2077: free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
2078: free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
2079: fprintf(ficgp,"\nset noparametric;set nolabel; set ter png small;set size 0.65, 0.65");
2080: /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */
2081: fprintf(ficgp,"\n set log y; set nolog x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
2082: fprintf(ficgp,"\n plot \"%s\" u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm);
2083: fprintf(ficgp,"\n replot \"%s\" u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm);
2084: fprintf(ficgp,"\n replot \"%s\" u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm);
2085: fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",fileresprobmorprev,fileresprobmorprev);
2086: fprintf(fichtm,"\n<br> Probability is computed over estepm=%d months. <br> <img src=\"varmuptjgr%s%s.png\"> <br>\n", stepm,digitp,digit);
2087: /* 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);
2088: */
2089: fprintf(ficgp,"\nset out \"varmuptjgr%s%s.png\";replot;",digitp,digit);
2090:
2091: free_vector(xp,1,npar);
2092: free_matrix(doldm,1,nlstate,1,nlstate);
2093: free_matrix(dnewm,1,nlstate,1,npar);
2094: free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
2095: free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
2096: free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
1.55 ! lievre 2097: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
1.53 brouard 2098: fclose(ficresprobmorprev);
2099: fclose(ficgp);
2100: fclose(fichtm);
2101: }
2102:
2103: /************ Variance of prevlim ******************/
2104: 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)
2105: {
2106: /* Variance of prevalence limit */
2107: /* double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
2108: double **newm;
2109: double **dnewm,**doldm;
2110: int i, j, nhstepm, hstepm;
2111: int k, cptcode;
2112: double *xp;
2113: double *gp, *gm;
2114: double **gradg, **trgradg;
2115: double age,agelim;
2116: int theta;
2117:
1.54 brouard 2118: fprintf(ficresvpl,"# Standard deviation of stable prevalences \n");
1.53 brouard 2119: fprintf(ficresvpl,"# Age");
2120: for(i=1; i<=nlstate;i++)
2121: fprintf(ficresvpl," %1d-%1d",i,i);
2122: fprintf(ficresvpl,"\n");
2123:
2124: xp=vector(1,npar);
2125: dnewm=matrix(1,nlstate,1,npar);
2126: doldm=matrix(1,nlstate,1,nlstate);
2127:
2128: hstepm=1*YEARM; /* Every year of age */
2129: hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */
2130: agelim = AGESUP;
2131: for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
2132: nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
2133: if (stepm >= YEARM) hstepm=1;
2134: nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
2135: gradg=matrix(1,npar,1,nlstate);
2136: gp=vector(1,nlstate);
2137: gm=vector(1,nlstate);
2138:
2139: for(theta=1; theta <=npar; theta++){
2140: for(i=1; i<=npar; i++){ /* Computes gradient */
2141: xp[i] = x[i] + (i==theta ?delti[theta]:0);
2142: }
2143: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
2144: for(i=1;i<=nlstate;i++)
2145: gp[i] = prlim[i][i];
2146:
2147: for(i=1; i<=npar; i++) /* Computes gradient */
2148: xp[i] = x[i] - (i==theta ?delti[theta]:0);
2149: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
2150: for(i=1;i<=nlstate;i++)
2151: gm[i] = prlim[i][i];
2152:
2153: for(i=1;i<=nlstate;i++)
2154: gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
2155: } /* End theta */
2156:
2157: trgradg =matrix(1,nlstate,1,npar);
2158:
2159: for(j=1; j<=nlstate;j++)
2160: for(theta=1; theta <=npar; theta++)
2161: trgradg[j][theta]=gradg[theta][j];
2162:
2163: for(i=1;i<=nlstate;i++)
2164: varpl[i][(int)age] =0.;
2165: matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
2166: matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
2167: for(i=1;i<=nlstate;i++)
2168: varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
2169:
2170: fprintf(ficresvpl,"%.0f ",age );
2171: for(i=1; i<=nlstate;i++)
2172: fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
2173: fprintf(ficresvpl,"\n");
2174: free_vector(gp,1,nlstate);
2175: free_vector(gm,1,nlstate);
2176: free_matrix(gradg,1,npar,1,nlstate);
2177: free_matrix(trgradg,1,nlstate,1,npar);
2178: } /* End age */
2179:
2180: free_vector(xp,1,npar);
2181: free_matrix(doldm,1,nlstate,1,npar);
2182: free_matrix(dnewm,1,nlstate,1,nlstate);
2183:
2184: }
2185:
2186: /************ Variance of one-step probabilities ******************/
2187: void varprob(char optionfilefiname[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij, int *Tvar, int **nbcode, int *ncodemax)
2188: {
2189: int i, j=0, i1, k1, l1, t, tj;
2190: int k2, l2, j1, z1;
2191: int k=0,l, cptcode;
2192: int first=1, first1;
2193: double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
2194: double **dnewm,**doldm;
2195: double *xp;
2196: double *gp, *gm;
2197: double **gradg, **trgradg;
2198: double **mu;
2199: double age,agelim, cov[NCOVMAX];
2200: double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
2201: int theta;
2202: char fileresprob[FILENAMELENGTH];
2203: char fileresprobcov[FILENAMELENGTH];
2204: char fileresprobcor[FILENAMELENGTH];
2205:
2206: double ***varpij;
2207:
2208: strcpy(fileresprob,"prob");
2209: strcat(fileresprob,fileres);
2210: if((ficresprob=fopen(fileresprob,"w"))==NULL) {
2211: printf("Problem with resultfile: %s\n", fileresprob);
2212: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
2213: }
2214: strcpy(fileresprobcov,"probcov");
2215: strcat(fileresprobcov,fileres);
2216: if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
2217: printf("Problem with resultfile: %s\n", fileresprobcov);
2218: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
2219: }
2220: strcpy(fileresprobcor,"probcor");
2221: strcat(fileresprobcor,fileres);
2222: if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
2223: printf("Problem with resultfile: %s\n", fileresprobcor);
2224: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
2225: }
2226: printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
2227: fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
2228: printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
2229: fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
2230: printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
2231: fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
2232:
2233: fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
2234: fprintf(ficresprob,"# Age");
2235: fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
2236: fprintf(ficresprobcov,"# Age");
2237: fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
2238: fprintf(ficresprobcov,"# Age");
2239:
2240:
2241: for(i=1; i<=nlstate;i++)
2242: for(j=1; j<=(nlstate+ndeath);j++){
2243: fprintf(ficresprob," p%1d-%1d (SE)",i,j);
2244: fprintf(ficresprobcov," p%1d-%1d ",i,j);
2245: fprintf(ficresprobcor," p%1d-%1d ",i,j);
2246: }
2247: fprintf(ficresprob,"\n");
2248: fprintf(ficresprobcov,"\n");
2249: fprintf(ficresprobcor,"\n");
2250: xp=vector(1,npar);
2251: dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
2252: doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
2253: mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
2254: varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
2255: first=1;
2256: if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {
2257: printf("Problem with gnuplot file: %s\n", optionfilegnuplot);
2258: fprintf(ficlog,"Problem with gnuplot file: %s\n", optionfilegnuplot);
2259: exit(0);
2260: }
2261: else{
2262: fprintf(ficgp,"\n# Routine varprob");
2263: }
2264: if((fichtm=fopen(optionfilehtm,"a"))==NULL) {
2265: printf("Problem with html file: %s\n", optionfilehtm);
2266: fprintf(ficlog,"Problem with html file: %s\n", optionfilehtm);
2267: exit(0);
2268: }
2269: else{
2270: fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
2271: fprintf(fichtm,"\n");
2272:
2273: fprintf(fichtm,"\n<li><h4> Computing matrix of variance-covariance of step probabilities</h4></li>\n");
2274: 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");
2275: 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");
2276:
2277: }
2278:
2279:
2280: cov[1]=1;
2281: tj=cptcoveff;
2282: if (cptcovn<1) {tj=1;ncodemax[1]=1;}
2283: j1=0;
2284: for(t=1; t<=tj;t++){
2285: for(i1=1; i1<=ncodemax[t];i1++){
2286: j1++;
2287:
2288: if (cptcovn>0) {
2289: fprintf(ficresprob, "\n#********** Variable ");
2290: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
2291: fprintf(ficresprob, "**********\n#");
2292: fprintf(ficresprobcov, "\n#********** Variable ");
2293: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
2294: fprintf(ficresprobcov, "**********\n#");
2295:
2296: fprintf(ficgp, "\n#********** Variable ");
2297: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, "# V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
2298: fprintf(ficgp, "**********\n#");
2299:
2300:
2301: fprintf(fichtm, "\n<hr size=\"2\" color=\"#EC5E5E\">********** Variable ");
2302: for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
2303: fprintf(fichtm, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
2304:
2305: fprintf(ficresprobcor, "\n#********** Variable ");
2306: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
2307: fprintf(ficgp, "**********\n#");
2308: }
2309:
2310: for (age=bage; age<=fage; age ++){
2311: cov[2]=age;
2312: for (k=1; k<=cptcovn;k++) {
2313: cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];
2314: }
2315: for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
2316: for (k=1; k<=cptcovprod;k++)
2317: cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
2318:
2319: gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
2320: trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
2321: gp=vector(1,(nlstate)*(nlstate+ndeath));
2322: gm=vector(1,(nlstate)*(nlstate+ndeath));
2323:
2324: for(theta=1; theta <=npar; theta++){
2325: for(i=1; i<=npar; i++)
2326: xp[i] = x[i] + (i==theta ?delti[theta]:0);
2327:
2328: pmij(pmmij,cov,ncovmodel,xp,nlstate);
2329:
2330: k=0;
2331: for(i=1; i<= (nlstate); i++){
2332: for(j=1; j<=(nlstate+ndeath);j++){
2333: k=k+1;
2334: gp[k]=pmmij[i][j];
2335: }
2336: }
2337:
2338: for(i=1; i<=npar; i++)
2339: xp[i] = x[i] - (i==theta ?delti[theta]:0);
2340:
2341: pmij(pmmij,cov,ncovmodel,xp,nlstate);
2342: k=0;
2343: for(i=1; i<=(nlstate); i++){
2344: for(j=1; j<=(nlstate+ndeath);j++){
2345: k=k+1;
2346: gm[k]=pmmij[i][j];
2347: }
2348: }
2349:
2350: for(i=1; i<= (nlstate)*(nlstate+ndeath); i++)
2351: gradg[theta][i]=(gp[i]-gm[i])/2./delti[theta];
2352: }
2353:
2354: for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
2355: for(theta=1; theta <=npar; theta++)
2356: trgradg[j][theta]=gradg[theta][j];
2357:
2358: matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov);
2359: matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);
2360:
2361: pmij(pmmij,cov,ncovmodel,x,nlstate);
2362:
2363: k=0;
2364: for(i=1; i<=(nlstate); i++){
2365: for(j=1; j<=(nlstate+ndeath);j++){
2366: k=k+1;
2367: mu[k][(int) age]=pmmij[i][j];
2368: }
2369: }
2370: for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
2371: for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
2372: varpij[i][j][(int)age] = doldm[i][j];
2373:
2374: /*printf("\n%d ",(int)age);
2375: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
2376: printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
2377: fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
2378: }*/
2379:
2380: fprintf(ficresprob,"\n%d ",(int)age);
2381: fprintf(ficresprobcov,"\n%d ",(int)age);
2382: fprintf(ficresprobcor,"\n%d ",(int)age);
2383:
2384: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)
2385: fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));
2386: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
2387: fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);
2388: fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
2389: }
2390: i=0;
2391: for (k=1; k<=(nlstate);k++){
2392: for (l=1; l<=(nlstate+ndeath);l++){
2393: i=i++;
2394: fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
2395: fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
2396: for (j=1; j<=i;j++){
2397: fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);
2398: fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));
2399: }
2400: }
2401: }/* end of loop for state */
2402: } /* end of loop for age */
2403:
2404: /* Confidence intervalle of pij */
2405: /*
2406: fprintf(ficgp,"\nset noparametric;unset label");
2407: fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");
2408: fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
2409: 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);
2410: fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);
2411: fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);
2412: fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);
2413: */
2414:
2415: /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
2416: first1=1;
2417: for (k2=1; k2<=(nlstate);k2++){
2418: for (l2=1; l2<=(nlstate+ndeath);l2++){
2419: if(l2==k2) continue;
2420: j=(k2-1)*(nlstate+ndeath)+l2;
2421: for (k1=1; k1<=(nlstate);k1++){
2422: for (l1=1; l1<=(nlstate+ndeath);l1++){
2423: if(l1==k1) continue;
2424: i=(k1-1)*(nlstate+ndeath)+l1;
2425: if(i<=j) continue;
2426: for (age=bage; age<=fage; age ++){
2427: if ((int)age %5==0){
2428: v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;
2429: v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;
2430: cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;
2431: mu1=mu[i][(int) age]/stepm*YEARM ;
2432: mu2=mu[j][(int) age]/stepm*YEARM;
2433: c12=cv12/sqrt(v1*v2);
2434: /* Computing eigen value of matrix of covariance */
2435: lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
2436: lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
2437: /* Eigen vectors */
2438: v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
2439: /*v21=sqrt(1.-v11*v11); *//* error */
2440: v21=(lc1-v1)/cv12*v11;
2441: v12=-v21;
2442: v22=v11;
2443: tnalp=v21/v11;
2444: if(first1==1){
2445: first1=0;
2446: 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);
2447: }
2448: 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);
2449: /*printf(fignu*/
2450: /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */
2451: /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */
2452: if(first==1){
2453: first=0;
2454: fprintf(ficgp,"\nset parametric;unset label");
2455: 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);
2456: fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
2457: 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);
2458: fprintf(fichtm,"\n<br><img src=\"varpijgr%s%d%1d%1d-%1d%1d.png\"> ",optionfilefiname, j1,k1,l1,k2,l2);
2459: fprintf(fichtm,"\n<br> Correlation at age %d (%.3f),",(int) age, c12);
2460: fprintf(ficgp,"\nset out \"varpijgr%s%d%1d%1d-%1d%1d.png\"",optionfilefiname, j1,k1,l1,k2,l2);
2461: fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
2462: fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
2463: 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",\
2464: mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
2465: mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
2466: }else{
2467: first=0;
2468: fprintf(fichtm," %d (%.3f),",(int) age, c12);
2469: fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
2470: fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
2471: 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",\
2472: mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
2473: mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
2474: }/* if first */
2475: } /* age mod 5 */
2476: } /* end loop age */
2477: fprintf(ficgp,"\nset out \"varpijgr%s%d%1d%1d-%1d%1d.png\";replot;",optionfilefiname, j1,k1,l1,k2,l2);
2478: first=1;
2479: } /*l12 */
2480: } /* k12 */
2481: } /*l1 */
2482: }/* k1 */
2483: } /* loop covariates */
2484: free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
2485: free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
2486: free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
2487: free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
2488: free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
2489: free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
2490: }
2491: free_vector(xp,1,npar);
2492: fclose(ficresprob);
2493: fclose(ficresprobcov);
2494: fclose(ficresprobcor);
2495: fclose(ficgp);
2496: fclose(fichtm);
2497: }
2498:
2499:
2500: /******************* Printing html file ***********/
2501: void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \
2502: int lastpass, int stepm, int weightopt, char model[],\
2503: int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
2504: int popforecast, int estepm ,\
2505: double jprev1, double mprev1,double anprev1, \
2506: double jprev2, double mprev2,double anprev2){
2507: int jj1, k1, i1, cpt;
2508: /*char optionfilehtm[FILENAMELENGTH];*/
2509: if((fichtm=fopen(optionfilehtm,"a"))==NULL) {
2510: printf("Problem with %s \n",optionfilehtm), exit(0);
2511: fprintf(ficlog,"Problem with %s \n",optionfilehtm), exit(0);
2512: }
2513:
2514: fprintf(fichtm,"<ul><li><h4>Result files (first order: no variance)</h4>\n
2515: - 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
2516: - Estimated transition probabilities over %d (stepm) months: <a href=\"pij%s\">pij%s</a><br>\n
2517: - Stable prevalence in each health state: <a href=\"pl%s\">pl%s</a> <br>\n
2518: - Life expectancies by age and initial health status (estepm=%2d months):
2519: <a href=\"e%s\">e%s</a> <br>\n</li>", \
2520: jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,fileres,fileres,stepm,fileres,fileres,fileres,fileres,estepm,fileres,fileres);
2521:
2522: fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
2523:
2524: m=cptcoveff;
2525: if (cptcovn < 1) {m=1;ncodemax[1]=1;}
2526:
2527: jj1=0;
2528: for(k1=1; k1<=m;k1++){
2529: for(i1=1; i1<=ncodemax[k1];i1++){
2530: jj1++;
2531: if (cptcovn > 0) {
2532: fprintf(fichtm,"<hr size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
2533: for (cpt=1; cpt<=cptcoveff;cpt++)
2534: fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
2535: fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
2536: }
2537: /* Pij */
2538: 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>
2539: <img src=\"pe%s%d1.png\">",stepm,strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);
2540: /* Quasi-incidences */
2541: 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>
2542: <img src=\"pe%s%d2.png\">",stepm,strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);
2543: /* Stable prevalence in each health state */
2544: for(cpt=1; cpt<nlstate;cpt++){
2545: fprintf(fichtm,"<br>- Stable prevalence in each health state : p%s%d%d.png<br>
2546: <img src=\"p%s%d%d.png\">",strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);
2547: }
2548: for(cpt=1; cpt<=nlstate;cpt++) {
2549: fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): exp%s%d%d.png <br>
2550: <img src=\"exp%s%d%d.png\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);
2551: }
2552: fprintf(fichtm,"\n<br>- Total life expectancy by age and
2553: health expectancies in states (1) and (2): e%s%d.png<br>
2554: <img src=\"e%s%d.png\">",strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);
2555: } /* end i1 */
2556: }/* End k1 */
2557: fprintf(fichtm,"</ul>");
2558:
2559:
2560: fprintf(fichtm,"\n<br><li><h4> Result files (second order: variances)</h4>\n
2561: - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n
2562: - Variance of one-step probabilities: <a href=\"prob%s\">prob%s</a> <br>\n
2563: - Variance-covariance of one-step probabilities: <a href=\"probcov%s\">probcov%s</a> <br>\n
2564: - Correlation matrix of one-step probabilities: <a href=\"probcor%s\">probcor%s</a> <br>\n
2565: - Variances and covariances of life expectancies by age and initial health status (estepm=%d months): <a href=\"v%s\">v%s</a><br>\n
2566: - Health expectancies with their variances (no covariance): <a href=\"t%s\">t%s</a> <br>\n
2567: - 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);
2568:
2569: if(popforecast==1) fprintf(fichtm,"\n
2570: - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n
2571: - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n
2572: <br>",fileres,fileres,fileres,fileres);
2573: else
2574: 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);
2575: fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
2576:
2577: m=cptcoveff;
2578: if (cptcovn < 1) {m=1;ncodemax[1]=1;}
2579:
2580: jj1=0;
2581: for(k1=1; k1<=m;k1++){
2582: for(i1=1; i1<=ncodemax[k1];i1++){
2583: jj1++;
2584: if (cptcovn > 0) {
2585: fprintf(fichtm,"<hr size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
2586: for (cpt=1; cpt<=cptcoveff;cpt++)
2587: fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
2588: fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
2589: }
2590: for(cpt=1; cpt<=nlstate;cpt++) {
2591: fprintf(fichtm,"<br>- Observed and stationary prevalence (with confident
2592: interval) in state (%d): v%s%d%d.png <br>
2593: <img src=\"v%s%d%d.png\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);
2594: }
2595: } /* end i1 */
2596: }/* End k1 */
2597: fprintf(fichtm,"</ul>");
2598: fclose(fichtm);
2599: }
2600:
2601: /******************* Gnuplot file **************/
2602: void printinggnuplot(char fileres[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
2603:
2604: int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;
2605: int ng;
2606: if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {
2607: printf("Problem with file %s",optionfilegnuplot);
2608: fprintf(ficlog,"Problem with file %s",optionfilegnuplot);
2609: }
2610:
1.54 brouard 2611: /*#ifdef windows */
1.53 brouard 2612: fprintf(ficgp,"cd \"%s\" \n",pathc);
1.54 brouard 2613: /*#endif */
1.53 brouard 2614: m=pow(2,cptcoveff);
2615:
2616: /* 1eme*/
2617: for (cpt=1; cpt<= nlstate ; cpt ++) {
2618: for (k1=1; k1<= m ; k1 ++) {
2619: fprintf(ficgp,"\nset out \"v%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);
2620: 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);
2621:
2622: for (i=1; i<= nlstate ; i ++) {
2623: if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
2624: else fprintf(ficgp," \%%*lf (\%%*lf)");
2625: }
1.54 brouard 2626: fprintf(ficgp,"\" t\"Stable prevalence\" w l 0,\"vpl%s\" every :::%d::%d u 1:($2+2*$3) \"\%%lf",fileres,k1-1,k1-1);
1.53 brouard 2627: for (i=1; i<= nlstate ; i ++) {
2628: if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
2629: else fprintf(ficgp," \%%*lf (\%%*lf)");
2630: }
2631: fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"vpl%s\" every :::%d::%d u 1:($2-2*$3) \"\%%lf",fileres,k1-1,k1-1);
2632: for (i=1; i<= nlstate ; i ++) {
2633: if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
2634: else fprintf(ficgp," \%%*lf (\%%*lf)");
2635: }
2636: fprintf(ficgp,"\" t\"\" w l 1,\"p%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",fileres,k1-1,k1-1,2+4*(cpt-1));
2637: }
2638: }
2639: /*2 eme*/
2640:
2641: for (k1=1; k1<= m ; k1 ++) {
2642: fprintf(ficgp,"\nset out \"e%s%d.png\" \n",strtok(optionfile, "."),k1);
2643: fprintf(ficgp,"set ylabel \"Years\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] ",ageminpar,fage);
2644:
2645: for (i=1; i<= nlstate+1 ; i ++) {
2646: k=2*i;
2647: fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:2 \"\%%lf",fileres,k1-1,k1-1);
2648: for (j=1; j<= nlstate+1 ; j ++) {
2649: if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
2650: else fprintf(ficgp," \%%*lf (\%%*lf)");
2651: }
2652: if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");
2653: else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);
2654: fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",fileres,k1-1,k1-1);
2655: for (j=1; j<= nlstate+1 ; j ++) {
2656: if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
2657: else fprintf(ficgp," \%%*lf (\%%*lf)");
2658: }
2659: fprintf(ficgp,"\" t\"\" w l 0,");
2660: fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",fileres,k1-1,k1-1);
2661: for (j=1; j<= nlstate+1 ; j ++) {
2662: if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
2663: else fprintf(ficgp," \%%*lf (\%%*lf)");
2664: }
2665: if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");
2666: else fprintf(ficgp,"\" t\"\" w l 0,");
2667: }
2668: }
2669:
2670: /*3eme*/
2671:
2672: for (k1=1; k1<= m ; k1 ++) {
2673: for (cpt=1; cpt<= nlstate ; cpt ++) {
2674: k=2+nlstate*(2*cpt-2);
2675: fprintf(ficgp,"\nset out \"exp%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);
2676: fprintf(ficgp,"set ter png small\nset size 0.65,0.65\nplot [%.f:%.f] \"e%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,fileres,k1-1,k1-1,k,cpt);
2677: /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
2678: for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
2679: fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
2680: fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
2681: for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
2682: fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
2683:
2684: */
2685: for (i=1; i< nlstate ; i ++) {
2686: 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);
2687:
2688: }
2689: }
2690: }
2691:
2692: /* CV preval stat */
2693: for (k1=1; k1<= m ; k1 ++) {
2694: for (cpt=1; cpt<nlstate ; cpt ++) {
2695: k=3;
2696: fprintf(ficgp,"\nset out \"p%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);
2697: 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/($%d",ageminpar,agemaxpar,fileres,k1,k+cpt+1,k+1);
2698:
2699: for (i=1; i< nlstate ; i ++)
2700: fprintf(ficgp,"+$%d",k+i+1);
2701: fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);
2702:
2703: l=3+(nlstate+ndeath)*cpt;
2704: fprintf(ficgp,",\"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",fileres,k1,l+cpt+1,l+1);
2705: for (i=1; i< nlstate ; i ++) {
2706: l=3+(nlstate+ndeath)*cpt;
2707: fprintf(ficgp,"+$%d",l+i+1);
2708: }
2709: fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);
2710: }
2711: }
2712:
2713: /* proba elementaires */
2714: for(i=1,jk=1; i <=nlstate; i++){
2715: for(k=1; k <=(nlstate+ndeath); k++){
2716: if (k != i) {
2717: for(j=1; j <=ncovmodel; j++){
2718: fprintf(ficgp,"p%d=%f ",jk,p[jk]);
2719: jk++;
2720: fprintf(ficgp,"\n");
2721: }
2722: }
2723: }
2724: }
2725:
2726: for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/
2727: for(jk=1; jk <=m; jk++) {
2728: fprintf(ficgp,"\nset out \"pe%s%d%d.png\" \n",strtok(optionfile, "."),jk,ng);
2729: if (ng==2)
2730: fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
2731: else
2732: fprintf(ficgp,"\nset title \"Probability\"\n");
2733: fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65\nset log y\nplot [%.f:%.f] ",ageminpar,agemaxpar);
2734: i=1;
2735: for(k2=1; k2<=nlstate; k2++) {
2736: k3=i;
2737: for(k=1; k<=(nlstate+ndeath); k++) {
2738: if (k != k2){
2739: if(ng==2)
2740: fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);
2741: else
2742: fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
2743: ij=1;
2744: for(j=3; j <=ncovmodel; j++) {
2745: if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
2746: fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
2747: ij++;
2748: }
2749: else
2750: fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
2751: }
2752: fprintf(ficgp,")/(1");
2753:
2754: for(k1=1; k1 <=nlstate; k1++){
2755: fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);
2756: ij=1;
2757: for(j=3; j <=ncovmodel; j++){
2758: if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
2759: fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
2760: ij++;
2761: }
2762: else
2763: fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
2764: }
2765: fprintf(ficgp,")");
2766: }
2767: fprintf(ficgp,") t \"p%d%d\" ", k2,k);
2768: if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");
2769: i=i+ncovmodel;
2770: }
2771: } /* end k */
2772: } /* end k2 */
2773: } /* end jk */
2774: } /* end ng */
2775: fclose(ficgp);
2776: } /* end gnuplot */
2777:
2778:
2779: /*************** Moving average **************/
1.54 brouard 2780: int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav){
1.53 brouard 2781:
2782: int i, cpt, cptcod;
1.54 brouard 2783: int mobilavrange, mob;
1.53 brouard 2784: double age;
1.54 brouard 2785: if(mobilav==1||mobilav ==3 ||mobilav==5 ||mobilav== 7){
2786: if(mobilav==1) mobilavrange=5; /* default */
2787: else mobilavrange=mobilav;
2788: for (age=bage; age<=fage; age++)
2789: for (i=1; i<=nlstate;i++)
2790: for (cptcod=1;cptcod<=ncodemax[cptcov];cptcod++)
2791: mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
2792: /* We keep the original values on the extreme ages bage, fage and for
2793: fage+1 and bage-1 we use a 3 terms moving average; for fage+2 bage+2
2794: we use a 5 terms etc. until the borders are no more concerned.
2795: */
2796: for (mob=3;mob <=mobilavrange;mob=mob+2){
2797: for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){
2798: for (i=1; i<=nlstate;i++){
2799: for (cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
2800: mobaverage[(int)age][i][cptcod] =probs[(int)age][i][cptcod];
2801: for (cpt=1;cpt<=(mob-1)/2;cpt++){
2802: mobaverage[(int)age][i][cptcod] +=probs[(int)age-cpt][i][cptcod];
2803: mobaverage[(int)age][i][cptcod] +=probs[(int)age+cpt][i][cptcod];
2804: }
2805: mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/mob;
2806: }
1.53 brouard 2807: }
1.54 brouard 2808: }/* end age */
2809: }/* end mob */
2810: }else return -1;
2811: return 0;
2812: }/* End movingaverage */
1.53 brouard 2813:
2814:
2815: /************** Forecasting ******************/
2816: 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){
2817:
2818: int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;
2819: int *popage;
2820: double calagedate, agelim, kk1, kk2, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
2821: double *popeffectif,*popcount;
2822: double ***p3mat;
1.55 ! lievre 2823: double ***mobaverage;
1.53 brouard 2824: char fileresf[FILENAMELENGTH];
2825:
2826: agelim=AGESUP;
2827: calagedate=(anproj1+mproj1/12.+jproj1/365.-dateintmean)*YEARM;
2828:
2829: prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);
2830:
2831:
2832: strcpy(fileresf,"f");
2833: strcat(fileresf,fileres);
2834: if((ficresf=fopen(fileresf,"w"))==NULL) {
2835: printf("Problem with forecast resultfile: %s\n", fileresf);
2836: fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);
2837: }
2838: printf("Computing forecasting: result on file '%s' \n", fileresf);
2839: fprintf(ficlog,"Computing forecasting: result on file '%s' \n", fileresf);
2840:
2841: if (cptcoveff==0) ncodemax[cptcoveff]=1;
2842:
1.54 brouard 2843: if (mobilav!=0) {
1.53 brouard 2844: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
1.54 brouard 2845: if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
2846: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
2847: printf(" Error in movingaverage mobilav=%d\n",mobilav);
2848: }
1.53 brouard 2849: }
2850:
2851: stepsize=(int) (stepm+YEARM-1)/YEARM;
2852: if (stepm<=12) stepsize=1;
2853:
2854: agelim=AGESUP;
2855:
2856: hstepm=1;
2857: hstepm=hstepm/stepm;
2858: yp1=modf(dateintmean,&yp);
2859: anprojmean=yp;
2860: yp2=modf((yp1*12),&yp);
2861: mprojmean=yp;
2862: yp1=modf((yp2*30.5),&yp);
2863: jprojmean=yp;
2864: if(jprojmean==0) jprojmean=1;
2865: if(mprojmean==0) jprojmean=1;
2866:
2867: fprintf(ficresf,"# Estimated date of observed prevalence: %.lf/%.lf/%.lf ",jprojmean,mprojmean,anprojmean);
2868:
2869: for(cptcov=1;cptcov<=i2;cptcov++){
2870: for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
2871: k=k+1;
2872: fprintf(ficresf,"\n#******");
2873: for(j=1;j<=cptcoveff;j++) {
2874: fprintf(ficresf," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
2875: }
2876: fprintf(ficresf,"******\n");
2877: fprintf(ficresf,"# StartingAge FinalAge");
2878: for(j=1; j<=nlstate+ndeath;j++) fprintf(ficresf," P.%d",j);
2879:
2880:
2881: for (cpt=0; cpt<=(anproj2-anproj1);cpt++) {
2882: fprintf(ficresf,"\n");
2883: fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+cpt);
2884:
2885: for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){
2886: nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);
2887: nhstepm = nhstepm/hstepm;
2888:
2889: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
2890: oldm=oldms;savm=savms;
2891: hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
2892:
2893: for (h=0; h<=nhstepm; h++){
2894: if (h==(int) (calagedate+YEARM*cpt)) {
2895: fprintf(ficresf,"\n %.f %.f ",anproj1+cpt,agedeb+h*hstepm/YEARM*stepm);
2896: }
2897: for(j=1; j<=nlstate+ndeath;j++) {
2898: kk1=0.;kk2=0;
2899: for(i=1; i<=nlstate;i++) {
2900: if (mobilav==1)
2901: kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];
2902: else {
2903: kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];
2904: }
2905:
2906: }
2907: if (h==(int)(calagedate+12*cpt)){
2908: fprintf(ficresf," %.3f", kk1);
2909:
2910: }
2911: }
2912: }
2913: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
2914: }
2915: }
2916: }
2917: }
2918:
1.54 brouard 2919: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
1.53 brouard 2920:
2921: fclose(ficresf);
2922: }
2923: /************** Forecasting ******************/
2924: 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){
2925:
2926: int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;
2927: int *popage;
2928: double calagedate, agelim, kk1, kk2, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
2929: double *popeffectif,*popcount;
2930: double ***p3mat,***tabpop,***tabpopprev;
1.55 ! lievre 2931: double ***mobaverage;
1.53 brouard 2932: char filerespop[FILENAMELENGTH];
2933:
2934: tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
2935: tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
2936: agelim=AGESUP;
2937: calagedate=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;
2938:
2939: prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);
2940:
2941:
2942: strcpy(filerespop,"pop");
2943: strcat(filerespop,fileres);
2944: if((ficrespop=fopen(filerespop,"w"))==NULL) {
2945: printf("Problem with forecast resultfile: %s\n", filerespop);
2946: fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop);
2947: }
2948: printf("Computing forecasting: result on file '%s' \n", filerespop);
2949: fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop);
2950:
2951: if (cptcoveff==0) ncodemax[cptcoveff]=1;
2952:
1.54 brouard 2953: if (mobilav!=0) {
1.53 brouard 2954: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
1.54 brouard 2955: if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
2956: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
2957: printf(" Error in movingaverage mobilav=%d\n",mobilav);
2958: }
1.53 brouard 2959: }
2960:
2961: stepsize=(int) (stepm+YEARM-1)/YEARM;
2962: if (stepm<=12) stepsize=1;
2963:
2964: agelim=AGESUP;
2965:
2966: hstepm=1;
2967: hstepm=hstepm/stepm;
2968:
2969: if (popforecast==1) {
2970: if((ficpop=fopen(popfile,"r"))==NULL) {
2971: printf("Problem with population file : %s\n",popfile);exit(0);
2972: fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0);
2973: }
2974: popage=ivector(0,AGESUP);
2975: popeffectif=vector(0,AGESUP);
2976: popcount=vector(0,AGESUP);
2977:
2978: i=1;
2979: while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;
2980:
2981: imx=i;
2982: for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];
2983: }
2984:
2985: for(cptcov=1;cptcov<=i2;cptcov++){
2986: for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
2987: k=k+1;
2988: fprintf(ficrespop,"\n#******");
2989: for(j=1;j<=cptcoveff;j++) {
2990: fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
2991: }
2992: fprintf(ficrespop,"******\n");
2993: fprintf(ficrespop,"# Age");
2994: for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);
2995: if (popforecast==1) fprintf(ficrespop," [Population]");
2996:
2997: for (cpt=0; cpt<=0;cpt++) {
2998: fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);
2999:
3000: for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){
3001: nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);
3002: nhstepm = nhstepm/hstepm;
3003:
3004: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3005: oldm=oldms;savm=savms;
3006: hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
3007:
3008: for (h=0; h<=nhstepm; h++){
3009: if (h==(int) (calagedate+YEARM*cpt)) {
3010: fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
3011: }
3012: for(j=1; j<=nlstate+ndeath;j++) {
3013: kk1=0.;kk2=0;
3014: for(i=1; i<=nlstate;i++) {
3015: if (mobilav==1)
3016: kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];
3017: else {
3018: kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];
3019: }
3020: }
3021: if (h==(int)(calagedate+12*cpt)){
3022: tabpop[(int)(agedeb)][j][cptcod]=kk1;
3023: /*fprintf(ficrespop," %.3f", kk1);
3024: if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/
3025: }
3026: }
3027: for(i=1; i<=nlstate;i++){
3028: kk1=0.;
3029: for(j=1; j<=nlstate;j++){
3030: kk1= kk1+tabpop[(int)(agedeb)][j][cptcod];
3031: }
3032: tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedate+12*cpt)*hstepm/YEARM*stepm-1)];
3033: }
3034:
3035: if (h==(int)(calagedate+12*cpt)) for(j=1; j<=nlstate;j++)
3036: fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);
3037: }
3038: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3039: }
3040: }
3041:
3042: /******/
3043:
3044: for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) {
3045: fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);
3046: for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){
3047: nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);
3048: nhstepm = nhstepm/hstepm;
3049:
3050: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3051: oldm=oldms;savm=savms;
3052: hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
3053: for (h=0; h<=nhstepm; h++){
3054: if (h==(int) (calagedate+YEARM*cpt)) {
3055: fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
3056: }
3057: for(j=1; j<=nlstate+ndeath;j++) {
3058: kk1=0.;kk2=0;
3059: for(i=1; i<=nlstate;i++) {
3060: kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];
3061: }
3062: if (h==(int)(calagedate+12*cpt)) fprintf(ficresf," %15.2f", kk1);
3063: }
3064: }
3065: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3066: }
3067: }
3068: }
3069: }
3070:
1.54 brouard 3071: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
1.53 brouard 3072:
3073: if (popforecast==1) {
3074: free_ivector(popage,0,AGESUP);
3075: free_vector(popeffectif,0,AGESUP);
3076: free_vector(popcount,0,AGESUP);
3077: }
3078: free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
3079: free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
3080: fclose(ficrespop);
3081: }
3082:
3083: /***********************************************/
3084: /**************** Main Program *****************/
3085: /***********************************************/
3086:
3087: int main(int argc, char *argv[])
3088: {
3089:
3090: int i,j, k, n=MAXN,iter,m,size,cptcode, cptcod;
3091: double agedeb, agefin,hf;
3092: double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;
3093:
3094: double fret;
3095: double **xi,tmp,delta;
3096:
3097: double dum; /* Dummy variable */
3098: double ***p3mat;
3099: double ***mobaverage;
3100: int *indx;
3101: char line[MAXLINE], linepar[MAXLINE];
3102: char path[80],pathc[80],pathcd[80],pathtot[80],model[80];
3103: int firstobs=1, lastobs=10;
3104: int sdeb, sfin; /* Status at beginning and end */
3105: int c, h , cpt,l;
3106: int ju,jl, mi;
3107: int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;
3108: int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,**adl,*tab;
3109: int mobilav=0,popforecast=0;
3110: int hstepm, nhstepm;
3111: double jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,jpyram, mpyram,anpyram,jpyram1, mpyram1,anpyram1, calagedate;
3112:
3113: double bage, fage, age, agelim, agebase;
3114: double ftolpl=FTOL;
3115: double **prlim;
3116: double *severity;
3117: double ***param; /* Matrix of parameters */
3118: double *p;
3119: double **matcov; /* Matrix of covariance */
3120: double ***delti3; /* Scale */
3121: double *delti; /* Scale */
3122: double ***eij, ***vareij;
3123: double **varpl; /* Variances of prevalence limits by age */
3124: double *epj, vepp;
3125: double kk1, kk2;
3126: double dateprev1, dateprev2,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2;
3127:
3128:
3129: char *alph[]={"a","a","b","c","d","e"}, str[4];
3130:
3131:
3132: char z[1]="c", occ;
3133: #include <sys/time.h>
3134: #include <time.h>
3135: char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];
3136:
3137: /* long total_usecs;
3138: struct timeval start_time, end_time;
3139:
3140: gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */
3141: getcwd(pathcd, size);
3142:
3143: printf("\n%s",version);
3144: if(argc <=1){
3145: printf("\nEnter the parameter file name: ");
3146: scanf("%s",pathtot);
3147: }
3148: else{
3149: strcpy(pathtot,argv[1]);
3150: }
3151: /*if(getcwd(pathcd, 80)!= NULL)printf ("Error pathcd\n");*/
3152: /*cygwin_split_path(pathtot,path,optionfile);
3153: printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/
3154: /* cutv(path,optionfile,pathtot,'\\');*/
3155:
3156: split(pathtot,path,optionfile,optionfilext,optionfilefiname);
3157: printf("pathtot=%s, path=%s, optionfile=%s optionfilext=%s optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
3158: chdir(path);
3159: replace(pathc,path);
3160:
3161: /*-------- arguments in the command line --------*/
3162:
3163: /* Log file */
3164: strcat(filelog, optionfilefiname);
3165: strcat(filelog,".log"); /* */
3166: if((ficlog=fopen(filelog,"w"))==NULL) {
3167: printf("Problem with logfile %s\n",filelog);
3168: goto end;
3169: }
3170: fprintf(ficlog,"Log filename:%s\n",filelog);
3171: fprintf(ficlog,"\n%s",version);
3172: fprintf(ficlog,"\nEnter the parameter file name: ");
3173: fprintf(ficlog,"pathtot=%s, path=%s, optionfile=%s optionfilext=%s optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
3174: fflush(ficlog);
3175:
3176: /* */
3177: strcpy(fileres,"r");
3178: strcat(fileres, optionfilefiname);
3179: strcat(fileres,".txt"); /* Other files have txt extension */
3180:
3181: /*---------arguments file --------*/
3182:
3183: if((ficpar=fopen(optionfile,"r"))==NULL) {
3184: printf("Problem with optionfile %s\n",optionfile);
3185: fprintf(ficlog,"Problem with optionfile %s\n",optionfile);
3186: goto end;
3187: }
3188:
3189: strcpy(filereso,"o");
3190: strcat(filereso,fileres);
3191: if((ficparo=fopen(filereso,"w"))==NULL) {
3192: printf("Problem with Output resultfile: %s\n", filereso);
3193: fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso);
3194: goto end;
3195: }
3196:
3197: /* Reads comments: lines beginning with '#' */
3198: while((c=getc(ficpar))=='#' && c!= EOF){
3199: ungetc(c,ficpar);
3200: fgets(line, MAXLINE, ficpar);
3201: puts(line);
3202: fputs(line,ficparo);
3203: }
3204: ungetc(c,ficpar);
3205:
3206: 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);
3207: 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);
3208: 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);
3209: while((c=getc(ficpar))=='#' && c!= EOF){
3210: ungetc(c,ficpar);
3211: fgets(line, MAXLINE, ficpar);
3212: puts(line);
3213: fputs(line,ficparo);
3214: }
3215: ungetc(c,ficpar);
3216:
3217:
3218: covar=matrix(0,NCOVMAX,1,n);
3219: cptcovn=0;
3220: if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;
3221:
3222: ncovmodel=2+cptcovn;
3223: nvar=ncovmodel-1; /* Suppressing age as a basic covariate */
3224:
3225: /* Read guess parameters */
3226: /* Reads comments: lines beginning with '#' */
3227: while((c=getc(ficpar))=='#' && c!= EOF){
3228: ungetc(c,ficpar);
3229: fgets(line, MAXLINE, ficpar);
3230: puts(line);
3231: fputs(line,ficparo);
3232: }
3233: ungetc(c,ficpar);
3234:
3235: param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
3236: for(i=1; i <=nlstate; i++)
3237: for(j=1; j <=nlstate+ndeath-1; j++){
3238: fscanf(ficpar,"%1d%1d",&i1,&j1);
3239: fprintf(ficparo,"%1d%1d",i1,j1);
3240: if(mle==1)
3241: printf("%1d%1d",i,j);
3242: fprintf(ficlog,"%1d%1d",i,j);
3243: for(k=1; k<=ncovmodel;k++){
3244: fscanf(ficpar," %lf",¶m[i][j][k]);
3245: if(mle==1){
3246: printf(" %lf",param[i][j][k]);
3247: fprintf(ficlog," %lf",param[i][j][k]);
3248: }
3249: else
3250: fprintf(ficlog," %lf",param[i][j][k]);
3251: fprintf(ficparo," %lf",param[i][j][k]);
3252: }
3253: fscanf(ficpar,"\n");
3254: if(mle==1)
3255: printf("\n");
3256: fprintf(ficlog,"\n");
3257: fprintf(ficparo,"\n");
3258: }
3259:
3260: npar= (nlstate+ndeath-1)*nlstate*ncovmodel;
3261:
3262: p=param[1][1];
3263:
3264: /* Reads comments: lines beginning with '#' */
3265: while((c=getc(ficpar))=='#' && c!= EOF){
3266: ungetc(c,ficpar);
3267: fgets(line, MAXLINE, ficpar);
3268: puts(line);
3269: fputs(line,ficparo);
3270: }
3271: ungetc(c,ficpar);
3272:
3273: delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
3274: delti=vector(1,npar); /* Scale of each paramater (output from hesscov) */
3275: for(i=1; i <=nlstate; i++){
3276: for(j=1; j <=nlstate+ndeath-1; j++){
3277: fscanf(ficpar,"%1d%1d",&i1,&j1);
3278: printf("%1d%1d",i,j);
3279: fprintf(ficparo,"%1d%1d",i1,j1);
3280: for(k=1; k<=ncovmodel;k++){
3281: fscanf(ficpar,"%le",&delti3[i][j][k]);
3282: printf(" %le",delti3[i][j][k]);
3283: fprintf(ficparo," %le",delti3[i][j][k]);
3284: }
3285: fscanf(ficpar,"\n");
3286: printf("\n");
3287: fprintf(ficparo,"\n");
3288: }
3289: }
3290: delti=delti3[1][1];
3291:
3292: /* Reads comments: lines beginning with '#' */
3293: while((c=getc(ficpar))=='#' && c!= EOF){
3294: ungetc(c,ficpar);
3295: fgets(line, MAXLINE, ficpar);
3296: puts(line);
3297: fputs(line,ficparo);
3298: }
3299: ungetc(c,ficpar);
3300:
3301: matcov=matrix(1,npar,1,npar);
3302: for(i=1; i <=npar; i++){
3303: fscanf(ficpar,"%s",&str);
3304: if(mle==1)
3305: printf("%s",str);
3306: fprintf(ficlog,"%s",str);
3307: fprintf(ficparo,"%s",str);
3308: for(j=1; j <=i; j++){
3309: fscanf(ficpar," %le",&matcov[i][j]);
3310: if(mle==1){
3311: printf(" %.5le",matcov[i][j]);
3312: fprintf(ficlog," %.5le",matcov[i][j]);
3313: }
3314: else
3315: fprintf(ficlog," %.5le",matcov[i][j]);
3316: fprintf(ficparo," %.5le",matcov[i][j]);
3317: }
3318: fscanf(ficpar,"\n");
3319: if(mle==1)
3320: printf("\n");
3321: fprintf(ficlog,"\n");
3322: fprintf(ficparo,"\n");
3323: }
3324: for(i=1; i <=npar; i++)
3325: for(j=i+1;j<=npar;j++)
3326: matcov[i][j]=matcov[j][i];
3327:
3328: if(mle==1)
3329: printf("\n");
3330: fprintf(ficlog,"\n");
3331:
3332:
3333: /*-------- Rewriting paramater file ----------*/
3334: strcpy(rfileres,"r"); /* "Rparameterfile */
3335: strcat(rfileres,optionfilefiname); /* Parameter file first name*/
3336: strcat(rfileres,"."); /* */
3337: strcat(rfileres,optionfilext); /* Other files have txt extension */
3338: if((ficres =fopen(rfileres,"w"))==NULL) {
3339: printf("Problem writing new parameter file: %s\n", fileres);goto end;
3340: fprintf(ficlog,"Problem writing new parameter file: %s\n", fileres);goto end;
3341: }
3342: fprintf(ficres,"#%s\n",version);
3343:
3344: /*-------- data file ----------*/
3345: if((fic=fopen(datafile,"r"))==NULL) {
3346: printf("Problem with datafile: %s\n", datafile);goto end;
3347: fprintf(ficlog,"Problem with datafile: %s\n", datafile);goto end;
3348: }
3349:
3350: n= lastobs;
3351: severity = vector(1,maxwav);
3352: outcome=imatrix(1,maxwav+1,1,n);
3353: num=ivector(1,n);
3354: moisnais=vector(1,n);
3355: annais=vector(1,n);
3356: moisdc=vector(1,n);
3357: andc=vector(1,n);
3358: agedc=vector(1,n);
3359: cod=ivector(1,n);
3360: weight=vector(1,n);
3361: for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */
3362: mint=matrix(1,maxwav,1,n);
3363: anint=matrix(1,maxwav,1,n);
3364: s=imatrix(1,maxwav+1,1,n);
3365: adl=imatrix(1,maxwav+1,1,n);
3366: tab=ivector(1,NCOVMAX);
3367: ncodemax=ivector(1,8);
3368:
3369: i=1;
3370: while (fgets(line, MAXLINE, fic) != NULL) {
3371: if ((i >= firstobs) && (i <=lastobs)) {
3372:
3373: for (j=maxwav;j>=1;j--){
3374: cutv(stra, strb,line,' '); s[j][i]=atoi(strb);
3375: strcpy(line,stra);
3376: cutv(stra, strb,line,'/'); anint[j][i]=(double)(atoi(strb)); strcpy(line,stra);
3377: cutv(stra, strb,line,' '); mint[j][i]=(double)(atoi(strb)); strcpy(line,stra);
3378: }
3379:
3380: cutv(stra, strb,line,'/'); andc[i]=(double)(atoi(strb)); strcpy(line,stra);
3381: cutv(stra, strb,line,' '); moisdc[i]=(double)(atoi(strb)); strcpy(line,stra);
3382:
3383: cutv(stra, strb,line,'/'); annais[i]=(double)(atoi(strb)); strcpy(line,stra);
3384: cutv(stra, strb,line,' '); moisnais[i]=(double)(atoi(strb)); strcpy(line,stra);
3385:
3386: cutv(stra, strb,line,' '); weight[i]=(double)(atoi(strb)); strcpy(line,stra);
3387: for (j=ncovcol;j>=1;j--){
3388: cutv(stra, strb,line,' '); covar[j][i]=(double)(atoi(strb)); strcpy(line,stra);
3389: }
3390: num[i]=atol(stra);
3391:
3392: /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){
3393: 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;}*/
3394:
3395: i=i+1;
3396: }
3397: }
3398: /* printf("ii=%d", ij);
3399: scanf("%d",i);*/
3400: imx=i-1; /* Number of individuals */
3401:
3402: /* for (i=1; i<=imx; i++){
3403: if ((s[1][i]==3) && (s[2][i]==2)) s[2][i]=3;
3404: if ((s[2][i]==3) && (s[3][i]==2)) s[3][i]=3;
3405: if ((s[3][i]==3) && (s[4][i]==2)) s[4][i]=3;
3406: }*/
3407: /* for (i=1; i<=imx; i++){
3408: if (s[4][i]==9) s[4][i]=-1;
3409: 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]));}*/
3410:
3411:
3412: /* Calculation of the number of parameter from char model*/
3413: Tvar=ivector(1,15); /* stores the number n of the covariates in Vm+Vn at 1 and m at 2 */
3414: Tprod=ivector(1,15);
3415: Tvaraff=ivector(1,15);
3416: Tvard=imatrix(1,15,1,2);
3417: Tage=ivector(1,15);
3418:
3419: if (strlen(model) >1){
3420: j=0, j1=0, k1=1, k2=1;
3421: j=nbocc(model,'+');
3422: j1=nbocc(model,'*');
3423: cptcovn=j+1;
3424: cptcovprod=j1;
3425:
3426: strcpy(modelsav,model);
3427: if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){
3428: printf("Error. Non available option model=%s ",model);
3429: fprintf(ficlog,"Error. Non available option model=%s ",model);
3430: goto end;
3431: }
3432:
3433: for(i=(j+1); i>=1;i--){
3434: cutv(stra,strb,modelsav,'+'); /* keeps in strb after the last + */
3435: if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyze it */
3436: /* printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/
3437: /*scanf("%d",i);*/
3438: if (strchr(strb,'*')) { /* Model includes a product */
3439: cutv(strd,strc,strb,'*'); /* strd*strc Vm*Vn (if not *age)*/
3440: if (strcmp(strc,"age")==0) { /* Vn*age */
3441: cptcovprod--;
3442: cutv(strb,stre,strd,'V');
3443: Tvar[i]=atoi(stre); /* computes n in Vn and stores in Tvar*/
3444: cptcovage++;
3445: Tage[cptcovage]=i;
3446: /*printf("stre=%s ", stre);*/
3447: }
3448: else if (strcmp(strd,"age")==0) { /* or age*Vn */
3449: cptcovprod--;
3450: cutv(strb,stre,strc,'V');
3451: Tvar[i]=atoi(stre);
3452: cptcovage++;
3453: Tage[cptcovage]=i;
3454: }
3455: else { /* Age is not in the model */
3456: cutv(strb,stre,strc,'V'); /* strc= Vn, stre is n*/
3457: Tvar[i]=ncovcol+k1;
3458: cutv(strb,strc,strd,'V'); /* strd was Vm, strc is m */
3459: Tprod[k1]=i;
3460: Tvard[k1][1]=atoi(strc); /* m*/
3461: Tvard[k1][2]=atoi(stre); /* n */
3462: Tvar[cptcovn+k2]=Tvard[k1][1];
3463: Tvar[cptcovn+k2+1]=Tvard[k1][2];
3464: for (k=1; k<=lastobs;k++)
3465: covar[ncovcol+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];
3466: k1++;
3467: k2=k2+2;
3468: }
3469: }
3470: else { /* no more sum */
3471: /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/
3472: /* scanf("%d",i);*/
3473: cutv(strd,strc,strb,'V');
3474: Tvar[i]=atoi(strc);
3475: }
3476: strcpy(modelsav,stra);
3477: /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);
3478: scanf("%d",i);*/
3479: } /* end of loop + */
3480: } /* end model */
3481:
3482: /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);
3483: printf("cptcovprod=%d ", cptcovprod);
3484: fprintf(ficlog,"cptcovprod=%d ", cptcovprod);
3485: scanf("%d ",i);*/
3486: fclose(fic);
3487:
3488: /* if(mle==1){*/
3489: if (weightopt != 1) { /* Maximisation without weights*/
3490: for(i=1;i<=n;i++) weight[i]=1.0;
3491: }
3492: /*-calculation of age at interview from date of interview and age at death -*/
3493: agev=matrix(1,maxwav,1,imx);
3494:
3495: for (i=1; i<=imx; i++) {
3496: for(m=2; (m<= maxwav); m++) {
3497: if ((mint[m][i]== 99) && (s[m][i] <= nlstate)){
3498: anint[m][i]=9999;
3499: s[m][i]=-1;
3500: }
3501: if(moisdc[i]==99 && andc[i]==9999 & s[m][i]>nlstate) s[m][i]=-1;
3502: }
3503: }
3504:
3505: for (i=1; i<=imx; i++) {
3506: agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);
3507: for(m=1; (m<= maxwav); m++){
3508: if(s[m][i] >0){
3509: if (s[m][i] >= nlstate+1) {
3510: if(agedc[i]>0)
3511: if(moisdc[i]!=99 && andc[i]!=9999)
3512: agev[m][i]=agedc[i];
3513: /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/
3514: else {
3515: if (andc[i]!=9999){
3516: printf("Warning negative age at death: %d line:%d\n",num[i],i);
3517: fprintf(ficlog,"Warning negative age at death: %d line:%d\n",num[i],i);
3518: agev[m][i]=-1;
3519: }
3520: }
3521: }
3522: else if(s[m][i] !=9){ /* Should no more exist */
3523: agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);
3524: if(mint[m][i]==99 || anint[m][i]==9999)
3525: agev[m][i]=1;
3526: else if(agev[m][i] <agemin){
3527: agemin=agev[m][i];
3528: /*printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], agemin);*/
3529: }
3530: else if(agev[m][i] >agemax){
3531: agemax=agev[m][i];
3532: /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/
3533: }
3534: /*agev[m][i]=anint[m][i]-annais[i];*/
3535: /* agev[m][i] = age[i]+2*m;*/
3536: }
3537: else { /* =9 */
3538: agev[m][i]=1;
3539: s[m][i]=-1;
3540: }
3541: }
3542: else /*= 0 Unknown */
3543: agev[m][i]=1;
3544: }
3545:
3546: }
3547: for (i=1; i<=imx; i++) {
3548: for(m=1; (m<= maxwav); m++){
3549: if (s[m][i] > (nlstate+ndeath)) {
3550: 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);
3551: 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);
3552: goto end;
3553: }
3554: }
3555: }
3556:
3557: printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);
3558: fprintf(ficlog,"Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);
3559:
3560: free_vector(severity,1,maxwav);
3561: free_imatrix(outcome,1,maxwav+1,1,n);
3562: free_vector(moisnais,1,n);
3563: free_vector(annais,1,n);
3564: /* free_matrix(mint,1,maxwav,1,n);
3565: free_matrix(anint,1,maxwav,1,n);*/
3566: free_vector(moisdc,1,n);
3567: free_vector(andc,1,n);
3568:
3569:
3570: wav=ivector(1,imx);
3571: dh=imatrix(1,lastpass-firstpass+1,1,imx);
3572: mw=imatrix(1,lastpass-firstpass+1,1,imx);
3573:
3574: /* Concatenates waves */
3575: concatwav(wav, dh, mw, s, agedc, agev, firstpass, lastpass, imx, nlstate, stepm);
3576:
3577:
3578: Tcode=ivector(1,100);
3579: nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);
3580: ncodemax[1]=1;
3581: if (cptcovn > 0) tricode(Tvar,nbcode,imx);
3582:
3583: codtab=imatrix(1,100,1,10);
3584: h=0;
3585: m=pow(2,cptcoveff);
3586:
3587: for(k=1;k<=cptcoveff; k++){
3588: for(i=1; i <=(m/pow(2,k));i++){
3589: for(j=1; j <= ncodemax[k]; j++){
3590: for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){
3591: h++;
3592: if (h>m) h=1;codtab[h][k]=j;codtab[h][Tvar[k]]=j;
3593: /* printf("h=%d k=%d j=%d codtab[h][k]=%d tvar[k]=%d \n",h, k,j,codtab[h][k],Tvar[k]);*/
3594: }
3595: }
3596: }
3597: }
3598: /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]);
3599: codtab[1][2]=1;codtab[2][2]=2; */
3600: /* for(i=1; i <=m ;i++){
3601: for(k=1; k <=cptcovn; k++){
3602: printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);
3603: }
3604: printf("\n");
3605: }
3606: scanf("%d",i);*/
3607:
3608: /* Calculates basic frequencies. Computes observed prevalence at single age
3609: and prints on file fileres'p'. */
3610:
3611:
3612:
3613: pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
3614: oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
3615: newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
3616: savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
3617: oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */
3618:
3619: /* For Powell, parameters are in a vector p[] starting at p[1]
3620: so we point p on param[1][1] so that p[1] maps on param[1][1][1] */
3621: p=param[1][1]; /* *(*(*(param +1)+1)+0) */
3622:
3623: if(mle==1){
3624: mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);
3625: }
3626:
3627: /*--------- results files --------------*/
3628: 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);
3629:
3630:
3631: jk=1;
3632: fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
3633: printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
3634: fprintf(ficlog,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
3635: for(i=1,jk=1; i <=nlstate; i++){
3636: for(k=1; k <=(nlstate+ndeath); k++){
3637: if (k != i)
3638: {
3639: printf("%d%d ",i,k);
3640: fprintf(ficlog,"%d%d ",i,k);
3641: fprintf(ficres,"%1d%1d ",i,k);
3642: for(j=1; j <=ncovmodel; j++){
3643: printf("%f ",p[jk]);
3644: fprintf(ficlog,"%f ",p[jk]);
3645: fprintf(ficres,"%f ",p[jk]);
3646: jk++;
3647: }
3648: printf("\n");
3649: fprintf(ficlog,"\n");
3650: fprintf(ficres,"\n");
3651: }
3652: }
3653: }
3654: if(mle==1){
3655: /* Computing hessian and covariance matrix */
3656: ftolhess=ftol; /* Usually correct */
3657: hesscov(matcov, p, npar, delti, ftolhess, func);
3658: }
3659: fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");
3660: printf("# Scales (for hessian or gradient estimation)\n");
3661: fprintf(ficlog,"# Scales (for hessian or gradient estimation)\n");
3662: for(i=1,jk=1; i <=nlstate; i++){
3663: for(j=1; j <=nlstate+ndeath; j++){
3664: if (j!=i) {
3665: fprintf(ficres,"%1d%1d",i,j);
3666: printf("%1d%1d",i,j);
3667: fprintf(ficlog,"%1d%1d",i,j);
3668: for(k=1; k<=ncovmodel;k++){
3669: printf(" %.5e",delti[jk]);
3670: fprintf(ficlog," %.5e",delti[jk]);
3671: fprintf(ficres," %.5e",delti[jk]);
3672: jk++;
3673: }
3674: printf("\n");
3675: fprintf(ficlog,"\n");
3676: fprintf(ficres,"\n");
3677: }
3678: }
3679: }
3680:
3681: k=1;
3682: 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");
3683: if(mle==1)
3684: 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");
3685: 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");
3686: for(i=1;i<=npar;i++){
3687: /* if (k>nlstate) k=1;
3688: i1=(i-1)/(ncovmodel*nlstate)+1;
3689: fprintf(ficres,"%s%d%d",alph[k],i1,tab[i]);
3690: printf("%s%d%d",alph[k],i1,tab[i]);*/
3691: fprintf(ficres,"%3d",i);
3692: if(mle==1)
3693: printf("%3d",i);
3694: fprintf(ficlog,"%3d",i);
3695: for(j=1; j<=i;j++){
3696: fprintf(ficres," %.5e",matcov[i][j]);
3697: if(mle==1)
3698: printf(" %.5e",matcov[i][j]);
3699: fprintf(ficlog," %.5e",matcov[i][j]);
3700: }
3701: fprintf(ficres,"\n");
3702: if(mle==1)
3703: printf("\n");
3704: fprintf(ficlog,"\n");
3705: k++;
3706: }
3707:
3708: while((c=getc(ficpar))=='#' && c!= EOF){
3709: ungetc(c,ficpar);
3710: fgets(line, MAXLINE, ficpar);
3711: puts(line);
3712: fputs(line,ficparo);
3713: }
3714: ungetc(c,ficpar);
3715: estepm=0;
3716: fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm);
3717: if (estepm==0 || estepm < stepm) estepm=stepm;
3718: if (fage <= 2) {
3719: bage = ageminpar;
3720: fage = agemaxpar;
3721: }
3722:
3723: fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");
3724: fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
3725: fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
3726:
3727: while((c=getc(ficpar))=='#' && c!= EOF){
3728: ungetc(c,ficpar);
3729: fgets(line, MAXLINE, ficpar);
3730: puts(line);
3731: fputs(line,ficparo);
3732: }
3733: ungetc(c,ficpar);
3734:
3735: 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);
3736: 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);
3737: 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);
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:
3748: dateprev1=anprev1+mprev1/12.+jprev1/365.;
3749: dateprev2=anprev2+mprev2/12.+jprev2/365.;
3750:
3751: fscanf(ficpar,"pop_based=%d\n",&popbased);
3752: fprintf(ficparo,"pop_based=%d\n",popbased);
3753: fprintf(ficres,"pop_based=%d\n",popbased);
3754:
3755: while((c=getc(ficpar))=='#' && c!= EOF){
3756: ungetc(c,ficpar);
3757: fgets(line, MAXLINE, ficpar);
3758: puts(line);
3759: fputs(line,ficparo);
3760: }
3761: ungetc(c,ficpar);
3762:
3763: fscanf(ficpar,"starting-proj-date=%lf/%lf/%lf final-proj-date=%lf/%lf/%lf\n",&jproj1,&mproj1,&anproj1,&jproj2,&mproj2,&anproj2);
3764: fprintf(ficparo,"starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf\n",jproj1,mproj1,anproj1,jproj2,mproj2,anproj2);
3765: fprintf(ficres,"starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf\n",jproj1,mproj1,anproj1,jproj2,mproj2,anproj2);
3766:
3767:
3768: while((c=getc(ficpar))=='#' && c!= EOF){
3769: ungetc(c,ficpar);
3770: fgets(line, MAXLINE, ficpar);
3771: puts(line);
3772: fputs(line,ficparo);
3773: }
3774: ungetc(c,ficpar);
3775:
3776: fscanf(ficpar,"popforecast=%d popfile=%s popfiledate=%lf/%lf/%lf last-popfiledate=%lf/%lf/%lf\n",&popforecast,popfile,&jpyram,&mpyram,&anpyram,&jpyram1,&mpyram1,&anpyram1);
3777: fprintf(ficparo,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);
3778: fprintf(ficres,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);
3779:
3780: freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);
3781: /*------------ gnuplot -------------*/
1.54 brouard 3782: strcpy(optionfilegnuplot,optionfilefiname);
3783: strcat(optionfilegnuplot,".gp");
3784: if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {
3785: printf("Problem with file %s",optionfilegnuplot);
3786: }
3787: else{
3788: fprintf(ficgp,"\n# %s\n", version);
3789: fprintf(ficgp,"# %s\n", optionfilegnuplot);
3790: fprintf(ficgp,"set missing 'NaNq'\n");
3791: }
3792: fclose(ficgp);
1.53 brouard 3793: printinggnuplot(fileres, ageminpar,agemaxpar,fage, pathc,p);
3794: /*--------- index.htm --------*/
3795:
3796: strcpy(optionfilehtm,optionfile);
3797: strcat(optionfilehtm,".htm");
3798: if((fichtm=fopen(optionfilehtm,"w"))==NULL) {
3799: printf("Problem with %s \n",optionfilehtm), exit(0);
3800: }
3801:
3802: fprintf(fichtm,"<body> <font size=\"2\">%s </font> <hr size=\"2\" color=\"#EC5E5E\"> \n
3803: Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n
3804: \n
3805: Total number of observations=%d <br>\n
3806: Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n
3807: <hr size=\"2\" color=\"#EC5E5E\">
3808: <ul><li><h4>Parameter files</h4>\n
3809: - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n
3810: - Log file of the run: <a href=\"%s\">%s</a><br>\n
3811: - 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);
3812: fclose(fichtm);
3813:
3814: printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,model,imx,jmin,jmax,jmean,rfileres,popforecast,estepm,jprev1,mprev1,anprev1,jprev2,mprev2,anprev2);
3815:
3816: /*------------ free_vector -------------*/
3817: chdir(path);
3818:
3819: free_ivector(wav,1,imx);
3820: free_imatrix(dh,1,lastpass-firstpass+1,1,imx);
3821: free_imatrix(mw,1,lastpass-firstpass+1,1,imx);
3822: free_ivector(num,1,n);
3823: free_vector(agedc,1,n);
3824: /*free_matrix(covar,1,NCOVMAX,1,n);*/
3825: fclose(ficparo);
3826: fclose(ficres);
3827:
3828:
1.54 brouard 3829: /*--------------- Prevalence limit (stable prevalence) --------------*/
1.53 brouard 3830:
3831: strcpy(filerespl,"pl");
3832: strcat(filerespl,fileres);
3833: if((ficrespl=fopen(filerespl,"w"))==NULL) {
1.54 brouard 3834: printf("Problem with stable prevalence resultfile: %s\n", filerespl);goto end;
3835: fprintf(ficlog,"Problem with stable prevalence resultfile: %s\n", filerespl);goto end;
1.53 brouard 3836: }
1.54 brouard 3837: printf("Computing stable prevalence: result on file '%s' \n", filerespl);
3838: fprintf(ficlog,"Computing stable prevalence: result on file '%s' \n", filerespl);
3839: fprintf(ficrespl,"#Stable prevalence \n");
1.53 brouard 3840: fprintf(ficrespl,"#Age ");
3841: for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);
3842: fprintf(ficrespl,"\n");
3843:
3844: prlim=matrix(1,nlstate,1,nlstate);
3845: pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
3846: oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
3847: newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
3848: savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
3849: oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */
3850: k=0;
3851: agebase=ageminpar;
3852: agelim=agemaxpar;
3853: ftolpl=1.e-10;
3854: i1=cptcoveff;
3855: if (cptcovn < 1){i1=1;}
3856:
3857: for(cptcov=1;cptcov<=i1;cptcov++){
3858: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
3859: k=k+1;
3860: /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/
3861: fprintf(ficrespl,"\n#******");
3862: printf("\n#******");
3863: fprintf(ficlog,"\n#******");
3864: for(j=1;j<=cptcoveff;j++) {
3865: fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
3866: printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
3867: fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
3868: }
3869: fprintf(ficrespl,"******\n");
3870: printf("******\n");
3871: fprintf(ficlog,"******\n");
3872:
3873: for (age=agebase; age<=agelim; age++){
3874: prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
3875: fprintf(ficrespl,"%.0f",age );
3876: for(i=1; i<=nlstate;i++)
3877: fprintf(ficrespl," %.5f", prlim[i][i]);
3878: fprintf(ficrespl,"\n");
3879: }
3880: }
3881: }
3882: fclose(ficrespl);
3883:
3884: /*------------- h Pij x at various ages ------------*/
3885:
3886: strcpy(filerespij,"pij"); strcat(filerespij,fileres);
3887: if((ficrespij=fopen(filerespij,"w"))==NULL) {
3888: printf("Problem with Pij resultfile: %s\n", filerespij);goto end;
3889: fprintf(ficlog,"Problem with Pij resultfile: %s\n", filerespij);goto end;
3890: }
3891: printf("Computing pij: result on file '%s' \n", filerespij);
3892: fprintf(ficlog,"Computing pij: result on file '%s' \n", filerespij);
3893:
3894: stepsize=(int) (stepm+YEARM-1)/YEARM;
3895: /*if (stepm<=24) stepsize=2;*/
3896:
3897: agelim=AGESUP;
3898: hstepm=stepsize*YEARM; /* Every year of age */
3899: hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */
3900:
3901: /* hstepm=1; aff par mois*/
3902:
3903: k=0;
3904: for(cptcov=1;cptcov<=i1;cptcov++){
3905: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
3906: k=k+1;
3907: fprintf(ficrespij,"\n#****** ");
3908: for(j=1;j<=cptcoveff;j++)
3909: fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
3910: fprintf(ficrespij,"******\n");
3911:
3912: for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */
3913: nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
3914: nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
3915:
3916: /* nhstepm=nhstepm*YEARM; aff par mois*/
3917:
3918: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3919: oldm=oldms;savm=savms;
3920: hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
3921: fprintf(ficrespij,"# Age");
3922: for(i=1; i<=nlstate;i++)
3923: for(j=1; j<=nlstate+ndeath;j++)
3924: fprintf(ficrespij," %1d-%1d",i,j);
3925: fprintf(ficrespij,"\n");
3926: for (h=0; h<=nhstepm; h++){
3927: fprintf(ficrespij,"%d %f %f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );
3928: for(i=1; i<=nlstate;i++)
3929: for(j=1; j<=nlstate+ndeath;j++)
3930: fprintf(ficrespij," %.5f", p3mat[i][j][h]);
3931: fprintf(ficrespij,"\n");
3932: }
3933: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3934: fprintf(ficrespij,"\n");
3935: }
3936: }
3937: }
3938:
3939: varprob(optionfilefiname, matcov, p, delti, nlstate, (int) bage, (int) fage,k,Tvar,nbcode, ncodemax);
3940:
3941: fclose(ficrespij);
3942:
3943:
3944: /*---------- Forecasting ------------------*/
3945: if((stepm == 1) && (strcmp(model,".")==0)){
3946: prevforecast(fileres, anproj1,mproj1,jproj1, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anproj2,p, i1);
3947: if (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);
3948: }
3949: else{
3950: erreur=108;
3951: 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);
3952: 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);
3953: }
3954:
3955:
3956: /*---------- Health expectancies and variances ------------*/
3957:
3958: strcpy(filerest,"t");
3959: strcat(filerest,fileres);
3960: if((ficrest=fopen(filerest,"w"))==NULL) {
3961: printf("Problem with total LE resultfile: %s\n", filerest);goto end;
3962: fprintf(ficlog,"Problem with total LE resultfile: %s\n", filerest);goto end;
3963: }
3964: printf("Computing Total LEs with variances: file '%s' \n", filerest);
3965: fprintf(ficlog,"Computing Total LEs with variances: file '%s' \n", filerest);
3966:
3967:
3968: strcpy(filerese,"e");
3969: strcat(filerese,fileres);
3970: if((ficreseij=fopen(filerese,"w"))==NULL) {
3971: printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
3972: fprintf(ficlog,"Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
3973: }
3974: printf("Computing Health Expectancies: result on file '%s' \n", filerese);
3975: fprintf(ficlog,"Computing Health Expectancies: result on file '%s' \n", filerese);
3976:
3977: strcpy(fileresv,"v");
3978: strcat(fileresv,fileres);
3979: if((ficresvij=fopen(fileresv,"w"))==NULL) {
3980: printf("Problem with variance resultfile: %s\n", fileresv);exit(0);
3981: fprintf(ficlog,"Problem with variance resultfile: %s\n", fileresv);exit(0);
3982: }
3983: printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
3984: fprintf(ficlog,"Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
3985: calagedate=-1;
3986: prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);
1.54 brouard 3987: if (mobilav!=0) {
1.53 brouard 3988: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
1.54 brouard 3989: if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
3990: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
3991: printf(" Error in movingaverage mobilav=%d\n",mobilav);
3992: }
1.53 brouard 3993: }
3994:
3995: k=0;
3996: for(cptcov=1;cptcov<=i1;cptcov++){
3997: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
3998: k=k+1;
3999: fprintf(ficrest,"\n#****** ");
4000: for(j=1;j<=cptcoveff;j++)
4001: fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
4002: fprintf(ficrest,"******\n");
4003:
4004: fprintf(ficreseij,"\n#****** ");
4005: for(j=1;j<=cptcoveff;j++)
4006: fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
4007: fprintf(ficreseij,"******\n");
4008:
4009: fprintf(ficresvij,"\n#****** ");
4010: for(j=1;j<=cptcoveff;j++)
4011: fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
4012: fprintf(ficresvij,"******\n");
4013:
4014: eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
4015: oldm=oldms;savm=savms;
4016: evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov);
4017:
4018: vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
4019: oldm=oldms;savm=savms;
4020: varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,0, mobilav);
4021: if(popbased==1){
4022: varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,popbased,mobilav);
4023: }
4024:
4025:
4026: fprintf(ficrest,"#Total LEs with variances: e.. (std) ");
4027: for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);
4028: fprintf(ficrest,"\n");
4029:
4030: epj=vector(1,nlstate+1);
4031: for(age=bage; age <=fage ;age++){
4032: prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
4033: if (popbased==1) {
1.54 brouard 4034: if(mobilav ==0){
1.53 brouard 4035: for(i=1; i<=nlstate;i++)
4036: prlim[i][i]=probs[(int)age][i][k];
1.54 brouard 4037: }else{ /* mobilav */
1.53 brouard 4038: for(i=1; i<=nlstate;i++)
4039: prlim[i][i]=mobaverage[(int)age][i][k];
4040: }
4041: }
4042:
4043: fprintf(ficrest," %4.0f",age);
4044: for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){
4045: for(i=1, epj[j]=0.;i <=nlstate;i++) {
4046: epj[j] += prlim[i][i]*eij[i][j][(int)age];
4047: /* printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/
4048: }
4049: epj[nlstate+1] +=epj[j];
4050: }
4051:
4052: for(i=1, vepp=0.;i <=nlstate;i++)
4053: for(j=1;j <=nlstate;j++)
4054: vepp += vareij[i][j][(int)age];
4055: fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));
4056: for(j=1;j <=nlstate;j++){
4057: fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));
4058: }
4059: fprintf(ficrest,"\n");
4060: }
4061: }
4062: }
4063: free_matrix(mint,1,maxwav,1,n);
4064: free_matrix(anint,1,maxwav,1,n); free_imatrix(s,1,maxwav+1,1,n);
4065: free_vector(weight,1,n);
4066: fclose(ficreseij);
4067: fclose(ficresvij);
4068: fclose(ficrest);
4069: fclose(ficpar);
4070: free_vector(epj,1,nlstate+1);
4071:
1.54 brouard 4072: /*------- Variance of stable prevalence------*/
1.53 brouard 4073:
4074: strcpy(fileresvpl,"vpl");
4075: strcat(fileresvpl,fileres);
4076: if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {
1.54 brouard 4077: printf("Problem with variance of stable prevalence resultfile: %s\n", fileresvpl);
1.53 brouard 4078: exit(0);
4079: }
1.54 brouard 4080: printf("Computing Variance-covariance of stable prevalence: file '%s' \n", fileresvpl);
1.53 brouard 4081:
4082: k=0;
4083: for(cptcov=1;cptcov<=i1;cptcov++){
4084: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
4085: k=k+1;
4086: fprintf(ficresvpl,"\n#****** ");
4087: for(j=1;j<=cptcoveff;j++)
4088: fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
4089: fprintf(ficresvpl,"******\n");
4090:
4091: varpl=matrix(1,nlstate,(int) bage, (int) fage);
4092: oldm=oldms;savm=savms;
4093: varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);
4094: }
4095: }
4096:
4097: fclose(ficresvpl);
4098:
4099: /*---------- End : free ----------------*/
4100: free_matrix(varpl,1,nlstate,(int) bage, (int)fage);
4101:
4102: free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);
4103: free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
4104:
4105:
4106: free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);
4107: free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);
4108: free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);
4109: free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);
4110:
4111: free_matrix(matcov,1,npar,1,npar);
4112: free_vector(delti,1,npar);
4113: free_matrix(agev,1,maxwav,1,imx);
4114: free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
1.54 brouard 4115: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
1.53 brouard 4116:
4117: fprintf(fichtm,"\n</body>");
4118: fclose(fichtm);
4119: fclose(ficgp);
4120:
4121:
4122: if(erreur >0){
4123: printf("End of Imach with error or warning %d\n",erreur);
4124: fprintf(ficlog,"End of Imach with error or warning %d\n",erreur);
4125: }else{
4126: printf("End of Imach\n");
4127: fprintf(ficlog,"End of Imach\n");
4128: }
4129: printf("See log file on %s\n",filelog);
4130: fclose(ficlog);
4131: /* gettimeofday(&end_time, (struct timezone*)0);*/ /* after time */
4132:
4133: /* 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);*/
4134: /*printf("Total time was %d uSec.\n", total_usecs);*/
4135: /*------ End -----------*/
4136:
4137:
4138: end:
4139: #ifdef windows
4140: /* chdir(pathcd);*/
4141: #endif
4142: /*system("wgnuplot graph.plt");*/
4143: /*system("../gp37mgw/wgnuplot graph.plt");*/
4144: /*system("cd ../gp37mgw");*/
4145: /* system("..\\gp37mgw\\wgnuplot graph.plt");*/
4146: strcpy(plotcmd,GNUPLOTPROGRAM);
4147: strcat(plotcmd," ");
4148: strcat(plotcmd,optionfilegnuplot);
1.54 brouard 4149: printf("Starting: %s\n",plotcmd);fflush(stdout);
1.53 brouard 4150: system(plotcmd);
4151:
1.54 brouard 4152: /*#ifdef windows*/
1.53 brouard 4153: while (z[0] != 'q') {
4154: /* chdir(path); */
4155: printf("\nType e to edit output files, g to graph again, c to start again, and q for exiting: ");
4156: scanf("%s",z);
4157: if (z[0] == 'c') system("./imach");
4158: else if (z[0] == 'e') system(optionfilehtm);
4159: else if (z[0] == 'g') system(plotcmd);
4160: else if (z[0] == 'q') exit(0);
4161: }
1.54 brouard 4162: /*#endif */
1.53 brouard 4163: }
4164:
4165:
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