Annotation of imach096d/src/imach.c, revision 1.59
1.59 ! brouard 1: /* $Id: imach.c,v 1.58 2002/07/26 12:29:55 lievre 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:
1.59 ! brouard 86: char version[80]="Imach version 0.9, November 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 */
1.59 ! brouard 102: int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between
! 103: * wave mi and wave mi+1 is not an exact multiple of stepm. */
1.53 brouard 104: double jmean; /* Mean space between 2 waves */
105: double **oldm, **newm, **savm; /* Working pointers to matrices */
106: double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
107: FILE *fic,*ficpar, *ficparo,*ficres, *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
108: FILE *ficlog;
109: FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
110: FILE *ficresprobmorprev;
111: FILE *fichtm; /* Html File */
112: FILE *ficreseij;
113: char filerese[FILENAMELENGTH];
114: FILE *ficresvij;
115: char fileresv[FILENAMELENGTH];
116: FILE *ficresvpl;
117: char fileresvpl[FILENAMELENGTH];
118: char title[MAXLINE];
119: char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH], filerespl[FILENAMELENGTH];
120: char optionfilext[10], optionfilefiname[FILENAMELENGTH], plotcmd[FILENAMELENGTH];
121:
122: char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
123: char filelog[FILENAMELENGTH]; /* Log file */
124: char filerest[FILENAMELENGTH];
125: char fileregp[FILENAMELENGTH];
126: char popfile[FILENAMELENGTH];
127:
128: char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH];
129:
130: #define NR_END 1
131: #define FREE_ARG char*
132: #define FTOL 1.0e-10
133:
134: #define NRANSI
135: #define ITMAX 200
136:
137: #define TOL 2.0e-4
138:
139: #define CGOLD 0.3819660
140: #define ZEPS 1.0e-10
141: #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);
142:
143: #define GOLD 1.618034
144: #define GLIMIT 100.0
145: #define TINY 1.0e-20
146:
147: static double maxarg1,maxarg2;
148: #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
149: #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
150:
151: #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
152: #define rint(a) floor(a+0.5)
153:
154: static double sqrarg;
155: #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
156: #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}
157:
158: int imx;
159: int stepm;
160: /* Stepm, step in month: minimum step interpolation*/
161:
162: int estepm;
163: /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
164:
165: int m,nb;
166: int *num, firstpass=0, lastpass=4,*cod, *ncodemax, *Tage;
167: double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
1.55 lievre 168: double **pmmij, ***probs;
1.53 brouard 169: double dateintmean=0;
170:
171: double *weight;
172: int **s; /* Status */
173: double *agedc, **covar, idx;
174: int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;
175:
176: double ftol=FTOL; /* Tolerance for computing Max Likelihood */
177: double ftolhess; /* Tolerance for computing hessian */
178:
179: /**************** split *************************/
180: static int split( char *path, char *dirc, char *name, char *ext, char *finame )
181: {
1.59 ! brouard 182: char *ss; /* pointer */
! 183: int l1, l2; /* length counters */
1.53 brouard 184:
1.59 ! brouard 185: l1 = strlen(path ); /* length of path */
! 186: if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
! 187: ss= strrchr( path, DIRSEPARATOR ); /* find last / */
! 188: if ( ss == NULL ) { /* no directory, so use current */
! 189: /*if(strrchr(path, ODIRSEPARATOR )==NULL)
! 190: printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
1.53 brouard 191: #if defined(__bsd__) /* get current working directory */
1.59 ! brouard 192: extern char *getwd( );
1.53 brouard 193:
1.59 ! brouard 194: if ( getwd( dirc ) == NULL ) {
1.53 brouard 195: #else
1.59 ! brouard 196: extern char *getcwd( );
1.53 brouard 197:
1.59 ! brouard 198: if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {
1.53 brouard 199: #endif
1.59 ! brouard 200: return( GLOCK_ERROR_GETCWD );
! 201: }
! 202: strcpy( name, path ); /* we've got it */
! 203: } else { /* strip direcotry from path */
! 204: ss++; /* after this, the filename */
! 205: l2 = strlen( ss ); /* length of filename */
! 206: if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
! 207: strcpy( name, ss ); /* save file name */
! 208: strncpy( dirc, path, l1 - l2 ); /* now the directory */
! 209: dirc[l1-l2] = 0; /* add zero */
! 210: }
! 211: l1 = strlen( dirc ); /* length of directory */
1.53 brouard 212: #ifdef windows
1.59 ! brouard 213: if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; }
1.53 brouard 214: #else
1.59 ! brouard 215: if ( dirc[l1-1] != '/' ) { dirc[l1] = '/'; dirc[l1+1] = 0; }
1.53 brouard 216: #endif
1.59 ! brouard 217: ss = strrchr( name, '.' ); /* find last / */
! 218: ss++;
! 219: strcpy(ext,ss); /* save extension */
! 220: l1= strlen( name);
! 221: l2= strlen(ss)+1;
! 222: strncpy( finame, name, l1-l2);
! 223: finame[l1-l2]= 0;
! 224: return( 0 ); /* we're done */
1.53 brouard 225: }
226:
227:
228: /******************************************/
229:
230: void replace(char *s, char*t)
231: {
232: int i;
233: int lg=20;
234: i=0;
235: lg=strlen(t);
236: for(i=0; i<= lg; i++) {
237: (s[i] = t[i]);
238: if (t[i]== '\\') s[i]='/';
239: }
240: }
241:
242: int nbocc(char *s, char occ)
243: {
244: int i,j=0;
245: int lg=20;
246: i=0;
247: lg=strlen(s);
248: for(i=0; i<= lg; i++) {
249: if (s[i] == occ ) j++;
250: }
251: return j;
252: }
253:
254: void cutv(char *u,char *v, char*t, char occ)
255: {
256: /* cuts string t into u and v where u is ended by char occ excluding it
257: and v is after occ excluding it too : ex cutv(u,v,"abcdef2ghi2j",2)
258: gives u="abcedf" and v="ghi2j" */
259: int i,lg,j,p=0;
260: i=0;
261: for(j=0; j<=strlen(t)-1; j++) {
262: if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;
263: }
264:
265: lg=strlen(t);
266: for(j=0; j<p; j++) {
267: (u[j] = t[j]);
268: }
269: u[p]='\0';
270:
271: for(j=0; j<= lg; j++) {
272: if (j>=(p+1))(v[j-p-1] = t[j]);
273: }
274: }
275:
276: /********************** nrerror ********************/
277:
278: void nrerror(char error_text[])
279: {
280: fprintf(stderr,"ERREUR ...\n");
281: fprintf(stderr,"%s\n",error_text);
1.59 ! brouard 282: exit(EXIT_FAILURE);
1.53 brouard 283: }
284: /*********************** vector *******************/
285: double *vector(int nl, int nh)
286: {
287: double *v;
288: v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
289: if (!v) nrerror("allocation failure in vector");
290: return v-nl+NR_END;
291: }
292:
293: /************************ free vector ******************/
294: void free_vector(double*v, int nl, int nh)
295: {
296: free((FREE_ARG)(v+nl-NR_END));
297: }
298:
299: /************************ivector *******************************/
300: int *ivector(long nl,long nh)
301: {
302: int *v;
303: v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
304: if (!v) nrerror("allocation failure in ivector");
305: return v-nl+NR_END;
306: }
307:
308: /******************free ivector **************************/
309: void free_ivector(int *v, long nl, long nh)
310: {
311: free((FREE_ARG)(v+nl-NR_END));
312: }
313:
314: /******************* imatrix *******************************/
315: int **imatrix(long nrl, long nrh, long ncl, long nch)
316: /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */
317: {
318: long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;
319: int **m;
320:
321: /* allocate pointers to rows */
322: m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));
323: if (!m) nrerror("allocation failure 1 in matrix()");
324: m += NR_END;
325: m -= nrl;
326:
327:
328: /* allocate rows and set pointers to them */
329: m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));
330: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
331: m[nrl] += NR_END;
332: m[nrl] -= ncl;
333:
334: for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;
335:
336: /* return pointer to array of pointers to rows */
337: return m;
338: }
339:
340: /****************** free_imatrix *************************/
341: void free_imatrix(m,nrl,nrh,ncl,nch)
342: int **m;
343: long nch,ncl,nrh,nrl;
344: /* free an int matrix allocated by imatrix() */
345: {
346: free((FREE_ARG) (m[nrl]+ncl-NR_END));
347: free((FREE_ARG) (m+nrl-NR_END));
348: }
349:
350: /******************* matrix *******************************/
351: double **matrix(long nrl, long nrh, long ncl, long nch)
352: {
353: long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
354: double **m;
355:
356: m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
357: if (!m) nrerror("allocation failure 1 in matrix()");
358: m += NR_END;
359: m -= nrl;
360:
361: m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
362: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
363: m[nrl] += NR_END;
364: m[nrl] -= ncl;
365:
366: for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
367: return m;
368: }
369:
370: /*************************free matrix ************************/
371: void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
372: {
373: free((FREE_ARG)(m[nrl]+ncl-NR_END));
374: free((FREE_ARG)(m+nrl-NR_END));
375: }
376:
377: /******************* ma3x *******************************/
378: double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
379: {
380: long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
381: double ***m;
382:
383: m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
384: if (!m) nrerror("allocation failure 1 in matrix()");
385: m += NR_END;
386: m -= nrl;
387:
388: m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
389: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
390: m[nrl] += NR_END;
391: m[nrl] -= ncl;
392:
393: for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
394:
395: m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
396: if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
397: m[nrl][ncl] += NR_END;
398: m[nrl][ncl] -= nll;
399: for (j=ncl+1; j<=nch; j++)
400: m[nrl][j]=m[nrl][j-1]+nlay;
401:
402: for (i=nrl+1; i<=nrh; i++) {
403: m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
404: for (j=ncl+1; j<=nch; j++)
405: m[i][j]=m[i][j-1]+nlay;
406: }
407: return m;
408: }
409:
410: /*************************free ma3x ************************/
411: void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
412: {
413: free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
414: free((FREE_ARG)(m[nrl]+ncl-NR_END));
415: free((FREE_ARG)(m+nrl-NR_END));
416: }
417:
418: /***************** f1dim *************************/
419: extern int ncom;
420: extern double *pcom,*xicom;
421: extern double (*nrfunc)(double []);
422:
423: double f1dim(double x)
424: {
425: int j;
426: double f;
427: double *xt;
428:
429: xt=vector(1,ncom);
430: for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];
431: f=(*nrfunc)(xt);
432: free_vector(xt,1,ncom);
433: return f;
434: }
435:
436: /*****************brent *************************/
437: double brent(double ax, double bx, double cx, double (*f)(double), double tol, double *xmin)
438: {
439: int iter;
440: double a,b,d,etemp;
441: double fu,fv,fw,fx;
442: double ftemp;
443: double p,q,r,tol1,tol2,u,v,w,x,xm;
444: double e=0.0;
445:
446: a=(ax < cx ? ax : cx);
447: b=(ax > cx ? ax : cx);
448: x=w=v=bx;
449: fw=fv=fx=(*f)(x);
450: for (iter=1;iter<=ITMAX;iter++) {
451: xm=0.5*(a+b);
452: tol2=2.0*(tol1=tol*fabs(x)+ZEPS);
453: /* if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
454: printf(".");fflush(stdout);
455: fprintf(ficlog,".");fflush(ficlog);
456: #ifdef DEBUG
457: 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);
458: 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);
459: /* if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
460: #endif
461: if (fabs(x-xm) <= (tol2-0.5*(b-a))){
462: *xmin=x;
463: return fx;
464: }
465: ftemp=fu;
466: if (fabs(e) > tol1) {
467: r=(x-w)*(fx-fv);
468: q=(x-v)*(fx-fw);
469: p=(x-v)*q-(x-w)*r;
470: q=2.0*(q-r);
471: if (q > 0.0) p = -p;
472: q=fabs(q);
473: etemp=e;
474: e=d;
475: if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))
476: d=CGOLD*(e=(x >= xm ? a-x : b-x));
477: else {
478: d=p/q;
479: u=x+d;
480: if (u-a < tol2 || b-u < tol2)
481: d=SIGN(tol1,xm-x);
482: }
483: } else {
484: d=CGOLD*(e=(x >= xm ? a-x : b-x));
485: }
486: u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));
487: fu=(*f)(u);
488: if (fu <= fx) {
489: if (u >= x) a=x; else b=x;
490: SHFT(v,w,x,u)
491: SHFT(fv,fw,fx,fu)
492: } else {
493: if (u < x) a=u; else b=u;
494: if (fu <= fw || w == x) {
495: v=w;
496: w=u;
497: fv=fw;
498: fw=fu;
499: } else if (fu <= fv || v == x || v == w) {
500: v=u;
501: fv=fu;
502: }
503: }
504: }
505: nrerror("Too many iterations in brent");
506: *xmin=x;
507: return fx;
508: }
509:
510: /****************** mnbrak ***********************/
511:
512: void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,
513: double (*func)(double))
514: {
515: double ulim,u,r,q, dum;
516: double fu;
517:
518: *fa=(*func)(*ax);
519: *fb=(*func)(*bx);
520: if (*fb > *fa) {
521: SHFT(dum,*ax,*bx,dum)
522: SHFT(dum,*fb,*fa,dum)
523: }
524: *cx=(*bx)+GOLD*(*bx-*ax);
525: *fc=(*func)(*cx);
526: while (*fb > *fc) {
527: r=(*bx-*ax)*(*fb-*fc);
528: q=(*bx-*cx)*(*fb-*fa);
529: u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/
530: (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r));
531: ulim=(*bx)+GLIMIT*(*cx-*bx);
532: if ((*bx-u)*(u-*cx) > 0.0) {
533: fu=(*func)(u);
534: } else if ((*cx-u)*(u-ulim) > 0.0) {
535: fu=(*func)(u);
536: if (fu < *fc) {
537: SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))
538: SHFT(*fb,*fc,fu,(*func)(u))
539: }
540: } else if ((u-ulim)*(ulim-*cx) >= 0.0) {
541: u=ulim;
542: fu=(*func)(u);
543: } else {
544: u=(*cx)+GOLD*(*cx-*bx);
545: fu=(*func)(u);
546: }
547: SHFT(*ax,*bx,*cx,u)
548: SHFT(*fa,*fb,*fc,fu)
549: }
550: }
551:
552: /*************** linmin ************************/
553:
554: int ncom;
555: double *pcom,*xicom;
556: double (*nrfunc)(double []);
557:
558: void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))
559: {
560: double brent(double ax, double bx, double cx,
561: double (*f)(double), double tol, double *xmin);
562: double f1dim(double x);
563: void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,
564: double *fc, double (*func)(double));
565: int j;
566: double xx,xmin,bx,ax;
567: double fx,fb,fa;
568:
569: ncom=n;
570: pcom=vector(1,n);
571: xicom=vector(1,n);
572: nrfunc=func;
573: for (j=1;j<=n;j++) {
574: pcom[j]=p[j];
575: xicom[j]=xi[j];
576: }
577: ax=0.0;
578: xx=1.0;
579: mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim);
580: *fret=brent(ax,xx,bx,f1dim,TOL,&xmin);
581: #ifdef DEBUG
582: printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
583: fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
584: #endif
585: for (j=1;j<=n;j++) {
586: xi[j] *= xmin;
587: p[j] += xi[j];
588: }
589: free_vector(xicom,1,n);
590: free_vector(pcom,1,n);
591: }
592:
593: /*************** powell ************************/
594: void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,
595: double (*func)(double []))
596: {
597: void linmin(double p[], double xi[], int n, double *fret,
598: double (*func)(double []));
599: int i,ibig,j;
600: double del,t,*pt,*ptt,*xit;
601: double fp,fptt;
602: double *xits;
603: pt=vector(1,n);
604: ptt=vector(1,n);
605: xit=vector(1,n);
606: xits=vector(1,n);
607: *fret=(*func)(p);
608: for (j=1;j<=n;j++) pt[j]=p[j];
609: for (*iter=1;;++(*iter)) {
610: fp=(*fret);
611: ibig=0;
612: del=0.0;
613: printf("\nPowell iter=%d -2*LL=%.12f",*iter,*fret);
614: fprintf(ficlog,"\nPowell iter=%d -2*LL=%.12f",*iter,*fret);
615: for (i=1;i<=n;i++)
616: printf(" %d %.12f",i, p[i]);
617: fprintf(ficlog," %d %.12f",i, p[i]);
618: printf("\n");
619: fprintf(ficlog,"\n");
620: for (i=1;i<=n;i++) {
621: for (j=1;j<=n;j++) xit[j]=xi[j][i];
622: fptt=(*fret);
623: #ifdef DEBUG
624: printf("fret=%lf \n",*fret);
625: fprintf(ficlog,"fret=%lf \n",*fret);
626: #endif
627: printf("%d",i);fflush(stdout);
628: fprintf(ficlog,"%d",i);fflush(ficlog);
629: linmin(p,xit,n,fret,func);
630: if (fabs(fptt-(*fret)) > del) {
631: del=fabs(fptt-(*fret));
632: ibig=i;
633: }
634: #ifdef DEBUG
635: printf("%d %.12e",i,(*fret));
636: fprintf(ficlog,"%d %.12e",i,(*fret));
637: for (j=1;j<=n;j++) {
638: xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
639: printf(" x(%d)=%.12e",j,xit[j]);
640: fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
641: }
642: for(j=1;j<=n;j++) {
643: printf(" p=%.12e",p[j]);
644: fprintf(ficlog," p=%.12e",p[j]);
645: }
646: printf("\n");
647: fprintf(ficlog,"\n");
648: #endif
649: }
650: if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {
651: #ifdef DEBUG
652: int k[2],l;
653: k[0]=1;
654: k[1]=-1;
655: printf("Max: %.12e",(*func)(p));
656: fprintf(ficlog,"Max: %.12e",(*func)(p));
657: for (j=1;j<=n;j++) {
658: printf(" %.12e",p[j]);
659: fprintf(ficlog," %.12e",p[j]);
660: }
661: printf("\n");
662: fprintf(ficlog,"\n");
663: for(l=0;l<=1;l++) {
664: for (j=1;j<=n;j++) {
665: ptt[j]=p[j]+(p[j]-pt[j])*k[l];
666: printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
667: fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
668: }
669: printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
670: fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
671: }
672: #endif
673:
674:
675: free_vector(xit,1,n);
676: free_vector(xits,1,n);
677: free_vector(ptt,1,n);
678: free_vector(pt,1,n);
679: return;
680: }
681: if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");
682: for (j=1;j<=n;j++) {
683: ptt[j]=2.0*p[j]-pt[j];
684: xit[j]=p[j]-pt[j];
685: pt[j]=p[j];
686: }
687: fptt=(*func)(ptt);
688: if (fptt < fp) {
689: t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt);
690: if (t < 0.0) {
691: linmin(p,xit,n,fret,func);
692: for (j=1;j<=n;j++) {
693: xi[j][ibig]=xi[j][n];
694: xi[j][n]=xit[j];
695: }
696: #ifdef DEBUG
697: printf("Direction changed last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
698: fprintf(ficlog,"Direction changed last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
699: for(j=1;j<=n;j++){
700: printf(" %.12e",xit[j]);
701: fprintf(ficlog," %.12e",xit[j]);
702: }
703: printf("\n");
704: fprintf(ficlog,"\n");
705: #endif
1.54 brouard 706: }
1.53 brouard 707: }
708: }
709: }
710:
1.54 brouard 711: /**** Prevalence limit (stable prevalence) ****************/
1.53 brouard 712:
713: double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)
714: {
715: /* Computes the prevalence limit in each live state at age x by left multiplying the unit
716: matrix by transitions matrix until convergence is reached */
717:
718: int i, ii,j,k;
719: double min, max, maxmin, maxmax,sumnew=0.;
720: double **matprod2();
721: double **out, cov[NCOVMAX], **pmij();
722: double **newm;
723: double agefin, delaymax=50 ; /* Max number of years to converge */
724:
725: for (ii=1;ii<=nlstate+ndeath;ii++)
726: for (j=1;j<=nlstate+ndeath;j++){
727: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
728: }
729:
730: cov[1]=1.;
731:
732: /* Even if hstepm = 1, at least one multiplication by the unit matrix */
733: for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
734: newm=savm;
735: /* Covariates have to be included here again */
736: cov[2]=agefin;
737:
738: for (k=1; k<=cptcovn;k++) {
739: cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
740: /* 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]]);*/
741: }
742: for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
743: for (k=1; k<=cptcovprod;k++)
744: cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
745:
746: /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
747: /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
748: /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
749: out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);
750:
751: savm=oldm;
752: oldm=newm;
753: maxmax=0.;
754: for(j=1;j<=nlstate;j++){
755: min=1.;
756: max=0.;
757: for(i=1; i<=nlstate; i++) {
758: sumnew=0;
759: for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
760: prlim[i][j]= newm[i][j]/(1-sumnew);
761: max=FMAX(max,prlim[i][j]);
762: min=FMIN(min,prlim[i][j]);
763: }
764: maxmin=max-min;
765: maxmax=FMAX(maxmax,maxmin);
766: }
767: if(maxmax < ftolpl){
768: return prlim;
769: }
770: }
771: }
772:
773: /*************** transition probabilities ***************/
774:
775: double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
776: {
777: double s1, s2;
778: /*double t34;*/
779: int i,j,j1, nc, ii, jj;
780:
781: for(i=1; i<= nlstate; i++){
782: for(j=1; j<i;j++){
783: for (nc=1, s2=0.;nc <=ncovmodel; nc++){
784: /*s2 += param[i][j][nc]*cov[nc];*/
785: s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
786: /*printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2);*/
787: }
788: ps[i][j]=s2;
789: /*printf("s1=%.17e, s2=%.17e\n",s1,s2);*/
790: }
791: for(j=i+1; j<=nlstate+ndeath;j++){
792: for (nc=1, s2=0.;nc <=ncovmodel; nc++){
793: s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
794: /*printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2);*/
795: }
796: ps[i][j]=s2;
797: }
798: }
799: /*ps[3][2]=1;*/
800:
801: for(i=1; i<= nlstate; i++){
802: s1=0;
803: for(j=1; j<i; j++)
804: s1+=exp(ps[i][j]);
805: for(j=i+1; j<=nlstate+ndeath; j++)
806: s1+=exp(ps[i][j]);
807: ps[i][i]=1./(s1+1.);
808: for(j=1; j<i; j++)
809: ps[i][j]= exp(ps[i][j])*ps[i][i];
810: for(j=i+1; j<=nlstate+ndeath; j++)
811: ps[i][j]= exp(ps[i][j])*ps[i][i];
812: /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
813: } /* end i */
814:
815: for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
816: for(jj=1; jj<= nlstate+ndeath; jj++){
817: ps[ii][jj]=0;
818: ps[ii][ii]=1;
819: }
820: }
821:
822:
823: /* for(ii=1; ii<= nlstate+ndeath; ii++){
824: for(jj=1; jj<= nlstate+ndeath; jj++){
825: printf("%lf ",ps[ii][jj]);
826: }
827: printf("\n ");
828: }
829: printf("\n ");printf("%lf ",cov[2]);*/
830: /*
831: for(i=1; i<= npar; i++) printf("%f ",x[i]);
832: goto end;*/
833: return ps;
834: }
835:
836: /**************** Product of 2 matrices ******************/
837:
838: double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)
839: {
840: /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
841: b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
842: /* in, b, out are matrice of pointers which should have been initialized
843: before: only the contents of out is modified. The function returns
844: a pointer to pointers identical to out */
845: long i, j, k;
846: for(i=nrl; i<= nrh; i++)
847: for(k=ncolol; k<=ncoloh; k++)
848: for(j=ncl,out[i][k]=0.; j<=nch; j++)
849: out[i][k] +=in[i][j]*b[j][k];
850:
851: return out;
852: }
853:
854:
855: /************* Higher Matrix Product ***************/
856:
857: double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
858: {
859: /* Computes the transition matrix starting at age 'age' over 'nhstepm*hstepm*stepm' month
860: duration (i.e. until
861: age (in years) age+nhstepm*stepm/12) by multiplying nhstepm*hstepm matrices.
862: Output is stored in matrix po[i][j][h] for h every 'hstepm' step
863: (typically every 2 years instead of every month which is too big).
864: Model is determined by parameters x and covariates have to be
865: included manually here.
866:
867: */
868:
869: int i, j, d, h, k;
870: double **out, cov[NCOVMAX];
871: double **newm;
872:
873: /* Hstepm could be zero and should return the unit matrix */
874: for (i=1;i<=nlstate+ndeath;i++)
875: for (j=1;j<=nlstate+ndeath;j++){
876: oldm[i][j]=(i==j ? 1.0 : 0.0);
877: po[i][j][0]=(i==j ? 1.0 : 0.0);
878: }
879: /* Even if hstepm = 1, at least one multiplication by the unit matrix */
880: for(h=1; h <=nhstepm; h++){
881: for(d=1; d <=hstepm; d++){
882: newm=savm;
883: /* Covariates have to be included here again */
884: cov[1]=1.;
885: cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
886: for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
887: for (k=1; k<=cptcovage;k++)
888: cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
889: for (k=1; k<=cptcovprod;k++)
890: cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
891:
892:
893: /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
894: /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
895: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,
896: pmij(pmmij,cov,ncovmodel,x,nlstate));
897: savm=oldm;
898: oldm=newm;
899: }
900: for(i=1; i<=nlstate+ndeath; i++)
901: for(j=1;j<=nlstate+ndeath;j++) {
902: po[i][j][h]=newm[i][j];
903: /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);
904: */
905: }
906: } /* end h */
907: return po;
908: }
909:
910:
911: /*************** log-likelihood *************/
912: double func( double *x)
913: {
914: int i, ii, j, k, mi, d, kk;
915: double l, ll[NLSTATEMAX], cov[NCOVMAX];
916: double **out;
917: double sw; /* Sum of weights */
918: double lli; /* Individual log likelihood */
1.59 ! brouard 919: int s1, s2;
! 920: double bbh;
1.53 brouard 921: long ipmx;
922: /*extern weight */
923: /* We are differentiating ll according to initial status */
924: /* for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
925: /*for(i=1;i<imx;i++)
926: printf(" %d\n",s[4][i]);
927: */
928: cov[1]=1.;
929:
930: for(k=1; k<=nlstate; k++) ll[k]=0.;
931: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
932: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
933: for(mi=1; mi<= wav[i]-1; mi++){
934: for (ii=1;ii<=nlstate+ndeath;ii++)
1.59 ! brouard 935: for (j=1;j<=nlstate+ndeath;j++){
! 936: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
! 937: savm[ii][j]=(ii==j ? 1.0 : 0.0);
! 938: }
1.53 brouard 939: for(d=0; d<dh[mi][i]; d++){
940: newm=savm;
941: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
942: for (kk=1; kk<=cptcovage;kk++) {
943: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
944: }
945:
946: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
947: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
948: savm=oldm;
949: oldm=newm;
950:
951:
952: } /* end mult */
953:
1.59 ! brouard 954: /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
! 955: /* But now since version 0.9 we anticipate for bias and large stepm.
! 956: * If stepm is larger than one month (smallest stepm) and if the exact delay
! 957: * (in months) between two waves is not a multiple of stepm, we rounded to
! 958: * the nearest (and in case of equal distance, to the lowest) interval but now
! 959: * we keep into memory the bias bh[mi][i] and also the previous matrix product
! 960: * (i.e to dh[mi][i]-1) saved in 'savm'. The we inter(extra)polate the
! 961: * probability in order to take into account the bias as a fraction of the way
! 962: * from savm to out if bh is neagtive or even beyond if bh is positive. bh varies
! 963: * -stepm/2 to stepm/2 .
! 964: * For stepm=1 the results are the same as for previous versions of Imach.
! 965: * For stepm > 1 the results are less biased than in previous versions.
! 966: */
! 967: s1=s[mw[mi][i]][i];
! 968: s2=s[mw[mi+1][i]][i];
! 969: bbh=(double)bh[mi][i]/(double)stepm;
! 970: lli= (savm[s1][s2]>(double)1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.-bbh)*out[s1][s2]));
! 971: /*lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.-bbh)*out[s1][s2]));*/
! 972: /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
! 973: /*if(lli ==000.0)*/
! 974: /*printf("bbh= %f lli=%f savm=%f out=%f %d\n",bbh,lli,savm[s1][s2], out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]],i); */
1.53 brouard 975: ipmx +=1;
976: sw += weight[i];
977: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
978: } /* end of wave */
979: } /* end of individual */
980:
981: for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
982: /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
983: l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
984: return -l;
985: }
986:
987:
988: /*********** Maximum Likelihood Estimation ***************/
989:
990: void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
991: {
992: int i,j, iter;
993: double **xi,*delti;
994: double fret;
995: xi=matrix(1,npar,1,npar);
996: for (i=1;i<=npar;i++)
997: for (j=1;j<=npar;j++)
998: xi[i][j]=(i==j ? 1.0 : 0.0);
999: printf("Powell\n"); fprintf(ficlog,"Powell\n");
1000: powell(p,xi,npar,ftol,&iter,&fret,func);
1001:
1002: printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));
1003: fprintf(ficlog,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
1004: fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
1005:
1006: }
1007:
1008: /**** Computes Hessian and covariance matrix ***/
1009: void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
1010: {
1011: double **a,**y,*x,pd;
1012: double **hess;
1013: int i, j,jk;
1014: int *indx;
1015:
1016: double hessii(double p[], double delta, int theta, double delti[]);
1017: double hessij(double p[], double delti[], int i, int j);
1018: void lubksb(double **a, int npar, int *indx, double b[]) ;
1019: void ludcmp(double **a, int npar, int *indx, double *d) ;
1020:
1021: hess=matrix(1,npar,1,npar);
1022:
1023: printf("\nCalculation of the hessian matrix. Wait...\n");
1024: fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
1025: for (i=1;i<=npar;i++){
1026: printf("%d",i);fflush(stdout);
1027: fprintf(ficlog,"%d",i);fflush(ficlog);
1028: hess[i][i]=hessii(p,ftolhess,i,delti);
1029: /*printf(" %f ",p[i]);*/
1030: /*printf(" %lf ",hess[i][i]);*/
1031: }
1032:
1033: for (i=1;i<=npar;i++) {
1034: for (j=1;j<=npar;j++) {
1035: if (j>i) {
1036: printf(".%d%d",i,j);fflush(stdout);
1037: fprintf(ficlog,".%d%d",i,j);fflush(ficlog);
1038: hess[i][j]=hessij(p,delti,i,j);
1039: hess[j][i]=hess[i][j];
1040: /*printf(" %lf ",hess[i][j]);*/
1041: }
1042: }
1043: }
1044: printf("\n");
1045: fprintf(ficlog,"\n");
1046:
1047: printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
1048: fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
1049:
1050: a=matrix(1,npar,1,npar);
1051: y=matrix(1,npar,1,npar);
1052: x=vector(1,npar);
1053: indx=ivector(1,npar);
1054: for (i=1;i<=npar;i++)
1055: for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
1056: ludcmp(a,npar,indx,&pd);
1057:
1058: for (j=1;j<=npar;j++) {
1059: for (i=1;i<=npar;i++) x[i]=0;
1060: x[j]=1;
1061: lubksb(a,npar,indx,x);
1062: for (i=1;i<=npar;i++){
1063: matcov[i][j]=x[i];
1064: }
1065: }
1066:
1067: printf("\n#Hessian matrix#\n");
1068: fprintf(ficlog,"\n#Hessian matrix#\n");
1069: for (i=1;i<=npar;i++) {
1070: for (j=1;j<=npar;j++) {
1071: printf("%.3e ",hess[i][j]);
1072: fprintf(ficlog,"%.3e ",hess[i][j]);
1073: }
1074: printf("\n");
1075: fprintf(ficlog,"\n");
1076: }
1077:
1078: /* Recompute Inverse */
1079: for (i=1;i<=npar;i++)
1080: for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];
1081: ludcmp(a,npar,indx,&pd);
1082:
1083: /* printf("\n#Hessian matrix recomputed#\n");
1084:
1085: for (j=1;j<=npar;j++) {
1086: for (i=1;i<=npar;i++) x[i]=0;
1087: x[j]=1;
1088: lubksb(a,npar,indx,x);
1089: for (i=1;i<=npar;i++){
1090: y[i][j]=x[i];
1091: printf("%.3e ",y[i][j]);
1092: fprintf(ficlog,"%.3e ",y[i][j]);
1093: }
1094: printf("\n");
1095: fprintf(ficlog,"\n");
1096: }
1097: */
1098:
1099: free_matrix(a,1,npar,1,npar);
1100: free_matrix(y,1,npar,1,npar);
1101: free_vector(x,1,npar);
1102: free_ivector(indx,1,npar);
1103: free_matrix(hess,1,npar,1,npar);
1104:
1105:
1106: }
1107:
1108: /*************** hessian matrix ****************/
1109: double hessii( double x[], double delta, int theta, double delti[])
1110: {
1111: int i;
1112: int l=1, lmax=20;
1113: double k1,k2;
1114: double p2[NPARMAX+1];
1115: double res;
1116: double delt, delts, nkhi=10.,nkhif=1., khi=1.e-4;
1117: double fx;
1118: int k=0,kmax=10;
1119: double l1;
1120:
1121: fx=func(x);
1122: for (i=1;i<=npar;i++) p2[i]=x[i];
1123: for(l=0 ; l <=lmax; l++){
1124: l1=pow(10,l);
1125: delts=delt;
1126: for(k=1 ; k <kmax; k=k+1){
1127: delt = delta*(l1*k);
1128: p2[theta]=x[theta] +delt;
1129: k1=func(p2)-fx;
1130: p2[theta]=x[theta]-delt;
1131: k2=func(p2)-fx;
1132: /*res= (k1-2.0*fx+k2)/delt/delt; */
1133: res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */
1134:
1135: #ifdef DEBUG
1136: 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);
1137: 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);
1138: #endif
1139: /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
1140: if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
1141: k=kmax;
1142: }
1143: else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
1144: k=kmax; l=lmax*10.;
1145: }
1146: else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){
1147: delts=delt;
1148: }
1149: }
1150: }
1151: delti[theta]=delts;
1152: return res;
1153:
1154: }
1155:
1156: double hessij( double x[], double delti[], int thetai,int thetaj)
1157: {
1158: int i;
1159: int l=1, l1, lmax=20;
1160: double k1,k2,k3,k4,res,fx;
1161: double p2[NPARMAX+1];
1162: int k;
1163:
1164: fx=func(x);
1165: for (k=1; k<=2; k++) {
1166: for (i=1;i<=npar;i++) p2[i]=x[i];
1167: p2[thetai]=x[thetai]+delti[thetai]/k;
1168: p2[thetaj]=x[thetaj]+delti[thetaj]/k;
1169: k1=func(p2)-fx;
1170:
1171: p2[thetai]=x[thetai]+delti[thetai]/k;
1172: p2[thetaj]=x[thetaj]-delti[thetaj]/k;
1173: k2=func(p2)-fx;
1174:
1175: p2[thetai]=x[thetai]-delti[thetai]/k;
1176: p2[thetaj]=x[thetaj]+delti[thetaj]/k;
1177: k3=func(p2)-fx;
1178:
1179: p2[thetai]=x[thetai]-delti[thetai]/k;
1180: p2[thetaj]=x[thetaj]-delti[thetaj]/k;
1181: k4=func(p2)-fx;
1182: res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */
1183: #ifdef DEBUG
1184: 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);
1185: 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);
1186: #endif
1187: }
1188: return res;
1189: }
1190:
1191: /************** Inverse of matrix **************/
1192: void ludcmp(double **a, int n, int *indx, double *d)
1193: {
1194: int i,imax,j,k;
1195: double big,dum,sum,temp;
1196: double *vv;
1197:
1198: vv=vector(1,n);
1199: *d=1.0;
1200: for (i=1;i<=n;i++) {
1201: big=0.0;
1202: for (j=1;j<=n;j++)
1203: if ((temp=fabs(a[i][j])) > big) big=temp;
1204: if (big == 0.0) nrerror("Singular matrix in routine ludcmp");
1205: vv[i]=1.0/big;
1206: }
1207: for (j=1;j<=n;j++) {
1208: for (i=1;i<j;i++) {
1209: sum=a[i][j];
1210: for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];
1211: a[i][j]=sum;
1212: }
1213: big=0.0;
1214: for (i=j;i<=n;i++) {
1215: sum=a[i][j];
1216: for (k=1;k<j;k++)
1217: sum -= a[i][k]*a[k][j];
1218: a[i][j]=sum;
1219: if ( (dum=vv[i]*fabs(sum)) >= big) {
1220: big=dum;
1221: imax=i;
1222: }
1223: }
1224: if (j != imax) {
1225: for (k=1;k<=n;k++) {
1226: dum=a[imax][k];
1227: a[imax][k]=a[j][k];
1228: a[j][k]=dum;
1229: }
1230: *d = -(*d);
1231: vv[imax]=vv[j];
1232: }
1233: indx[j]=imax;
1234: if (a[j][j] == 0.0) a[j][j]=TINY;
1235: if (j != n) {
1236: dum=1.0/(a[j][j]);
1237: for (i=j+1;i<=n;i++) a[i][j] *= dum;
1238: }
1239: }
1240: free_vector(vv,1,n); /* Doesn't work */
1241: ;
1242: }
1243:
1244: void lubksb(double **a, int n, int *indx, double b[])
1245: {
1246: int i,ii=0,ip,j;
1247: double sum;
1248:
1249: for (i=1;i<=n;i++) {
1250: ip=indx[i];
1251: sum=b[ip];
1252: b[ip]=b[i];
1253: if (ii)
1254: for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];
1255: else if (sum) ii=i;
1256: b[i]=sum;
1257: }
1258: for (i=n;i>=1;i--) {
1259: sum=b[i];
1260: for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];
1261: b[i]=sum/a[i][i];
1262: }
1263: }
1264:
1265: /************ Frequencies ********************/
1.59 ! brouard 1266: void freqsummary(char fileres[], int agemin, int agemax, int **s, double **agev, int nlstate, int imx, int *Tvaraff, int **nbcode, int *ncodemax,double **mint,double **anint, double dateprev1,double dateprev2,double jprev1, double mprev1,double anprev1,double jprev2, double mprev2,double anprev2)
1.53 brouard 1267: { /* Some frequencies */
1268:
1269: int i, m, jk, k1,i1, j1, bool, z1,z2,j;
1270: int first;
1271: double ***freq; /* Frequencies */
1272: double *pp;
1273: double pos, k2, dateintsum=0,k2cpt=0;
1274: FILE *ficresp;
1275: char fileresp[FILENAMELENGTH];
1276:
1277: pp=vector(1,nlstate);
1278: probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
1279: strcpy(fileresp,"p");
1280: strcat(fileresp,fileres);
1281: if((ficresp=fopen(fileresp,"w"))==NULL) {
1282: printf("Problem with prevalence resultfile: %s\n", fileresp);
1283: fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
1284: exit(0);
1285: }
1286: freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);
1287: j1=0;
1288:
1289: j=cptcoveff;
1290: if (cptcovn<1) {j=1;ncodemax[1]=1;}
1291:
1292: first=1;
1293:
1294: for(k1=1; k1<=j;k1++){
1295: for(i1=1; i1<=ncodemax[k1];i1++){
1296: j1++;
1297: /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
1298: scanf("%d", i);*/
1299: for (i=-1; i<=nlstate+ndeath; i++)
1300: for (jk=-1; jk<=nlstate+ndeath; jk++)
1301: for(m=agemin; m <= agemax+3; m++)
1302: freq[i][jk][m]=0;
1303:
1304: dateintsum=0;
1305: k2cpt=0;
1306: for (i=1; i<=imx; i++) {
1307: bool=1;
1308: if (cptcovn>0) {
1309: for (z1=1; z1<=cptcoveff; z1++)
1310: if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])
1311: bool=0;
1312: }
1.58 lievre 1313: if (bool==1){
1.53 brouard 1314: for(m=firstpass; m<=lastpass; m++){
1315: k2=anint[m][i]+(mint[m][i]/12.);
1316: if ((k2>=dateprev1) && (k2<=dateprev2)) {
1317: if(agev[m][i]==0) agev[m][i]=agemax+1;
1318: if(agev[m][i]==1) agev[m][i]=agemax+2;
1319: if (m<lastpass) {
1320: freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
1321: freq[s[m][i]][s[m+1][i]][(int) agemax+3] += weight[i];
1322: }
1323:
1324: if ((agev[m][i]>1) && (agev[m][i]< (agemax+3))) {
1325: dateintsum=dateintsum+k2;
1326: k2cpt++;
1327: }
1328: }
1329: }
1330: }
1331: }
1332:
1333: fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);
1334:
1335: if (cptcovn>0) {
1336: fprintf(ficresp, "\n#********** Variable ");
1337: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
1338: fprintf(ficresp, "**********\n#");
1339: }
1340: for(i=1; i<=nlstate;i++)
1341: fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
1342: fprintf(ficresp, "\n");
1343:
1344: for(i=(int)agemin; i <= (int)agemax+3; i++){
1345: if(i==(int)agemax+3){
1346: fprintf(ficlog,"Total");
1347: }else{
1348: if(first==1){
1349: first=0;
1350: printf("See log file for details...\n");
1351: }
1352: fprintf(ficlog,"Age %d", i);
1353: }
1354: for(jk=1; jk <=nlstate ; jk++){
1355: for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
1356: pp[jk] += freq[jk][m][i];
1357: }
1358: for(jk=1; jk <=nlstate ; jk++){
1359: for(m=-1, pos=0; m <=0 ; m++)
1360: pos += freq[jk][m][i];
1361: if(pp[jk]>=1.e-10){
1362: if(first==1){
1363: printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
1364: }
1365: fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
1366: }else{
1367: if(first==1)
1368: printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
1369: fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
1370: }
1371: }
1372:
1373: for(jk=1; jk <=nlstate ; jk++){
1374: for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
1375: pp[jk] += freq[jk][m][i];
1376: }
1377:
1378: for(jk=1,pos=0; jk <=nlstate ; jk++)
1379: pos += pp[jk];
1380: for(jk=1; jk <=nlstate ; jk++){
1381: if(pos>=1.e-5){
1382: if(first==1)
1383: printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
1384: fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
1385: }else{
1386: if(first==1)
1387: printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
1388: fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
1389: }
1390: if( i <= (int) agemax){
1391: if(pos>=1.e-5){
1392: fprintf(ficresp," %d %.5f %.0f %.0f",i,pp[jk]/pos, pp[jk],pos);
1393: probs[i][jk][j1]= pp[jk]/pos;
1394: /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/
1395: }
1396: else
1397: fprintf(ficresp," %d NaNq %.0f %.0f",i,pp[jk],pos);
1398: }
1399: }
1400:
1401: for(jk=-1; jk <=nlstate+ndeath; jk++)
1402: for(m=-1; m <=nlstate+ndeath; m++)
1403: if(freq[jk][m][i] !=0 ) {
1404: if(first==1)
1405: printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
1406: fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
1407: }
1408: if(i <= (int) agemax)
1409: fprintf(ficresp,"\n");
1410: if(first==1)
1411: printf("Others in log...\n");
1412: fprintf(ficlog,"\n");
1413: }
1414: }
1415: }
1416: dateintmean=dateintsum/k2cpt;
1417:
1418: fclose(ficresp);
1419: free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);
1420: free_vector(pp,1,nlstate);
1421:
1422: /* End of Freq */
1423: }
1424:
1425: /************ Prevalence ********************/
1426: 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)
1427: { /* Some frequencies */
1428:
1429: int i, m, jk, k1, i1, j1, bool, z1,z2,j;
1430: double ***freq; /* Frequencies */
1431: double *pp;
1432: double pos, k2;
1433:
1434: pp=vector(1,nlstate);
1435:
1436: freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);
1437: j1=0;
1438:
1439: j=cptcoveff;
1440: if (cptcovn<1) {j=1;ncodemax[1]=1;}
1441:
1442: for(k1=1; k1<=j;k1++){
1443: for(i1=1; i1<=ncodemax[k1];i1++){
1444: j1++;
1445:
1446: for (i=-1; i<=nlstate+ndeath; i++)
1447: for (jk=-1; jk<=nlstate+ndeath; jk++)
1448: for(m=agemin; m <= agemax+3; m++)
1449: freq[i][jk][m]=0;
1450:
1451: for (i=1; i<=imx; i++) {
1452: bool=1;
1453: if (cptcovn>0) {
1454: for (z1=1; z1<=cptcoveff; z1++)
1455: if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])
1456: bool=0;
1457: }
1458: if (bool==1) {
1459: for(m=firstpass; m<=lastpass; m++){
1460: k2=anint[m][i]+(mint[m][i]/12.);
1461: if ((k2>=dateprev1) && (k2<=dateprev2)) {
1462: if(agev[m][i]==0) agev[m][i]=agemax+1;
1463: if(agev[m][i]==1) agev[m][i]=agemax+2;
1464: if (m<lastpass) {
1465: if (calagedate>0)
1466: freq[s[m][i]][s[m+1][i]][(int)(agev[m][i]+1-((int)calagedate %12)/12.)] += weight[i];
1467: else
1468: freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
1469: freq[s[m][i]][s[m+1][i]][(int)(agemax+3)] += weight[i];
1470: }
1471: }
1472: }
1473: }
1474: }
1475: for(i=(int)agemin; i <= (int)agemax+3; i++){
1476: for(jk=1; jk <=nlstate ; jk++){
1477: for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
1478: pp[jk] += freq[jk][m][i];
1479: }
1480: for(jk=1; jk <=nlstate ; jk++){
1481: for(m=-1, pos=0; m <=0 ; m++)
1482: pos += freq[jk][m][i];
1483: }
1484:
1485: for(jk=1; jk <=nlstate ; jk++){
1486: for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
1487: pp[jk] += freq[jk][m][i];
1488: }
1489:
1490: for(jk=1,pos=0; jk <=nlstate ; jk++) pos += pp[jk];
1491:
1492: for(jk=1; jk <=nlstate ; jk++){
1493: if( i <= (int) agemax){
1494: if(pos>=1.e-5){
1495: probs[i][jk][j1]= pp[jk]/pos;
1496: }
1497: }
1498: }/* end jk */
1499: }/* end i */
1500: } /* end i1 */
1501: } /* end k1 */
1502:
1503:
1504: free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);
1505: free_vector(pp,1,nlstate);
1506:
1507: } /* End of Freq */
1508:
1509: /************* Waves Concatenation ***************/
1510:
1.59 ! brouard 1511: void concatwav(int wav[], int **dh, int **bh, int **mw, int **s, double *agedc, double **agev, int firstpass, int lastpass, int imx, int nlstate, int stepm)
1.53 brouard 1512: {
1513: /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
1514: Death is a valid wave (if date is known).
1515: mw[mi][i] is the mi (mi=1 to wav[i]) effective wave of individual i
1.59 ! brouard 1516: dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
1.53 brouard 1517: and mw[mi+1][i]. dh depends on stepm.
1518: */
1519:
1520: int i, mi, m;
1521: /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
1522: double sum=0., jmean=0.;*/
1523: int first;
1524: int j, k=0,jk, ju, jl;
1525: double sum=0.;
1526: first=0;
1527: jmin=1e+5;
1528: jmax=-1;
1529: jmean=0.;
1530: for(i=1; i<=imx; i++){
1531: mi=0;
1532: m=firstpass;
1533: while(s[m][i] <= nlstate){
1534: if(s[m][i]>=1)
1535: mw[++mi][i]=m;
1536: if(m >=lastpass)
1537: break;
1538: else
1539: m++;
1540: }/* end while */
1541: if (s[m][i] > nlstate){
1542: mi++; /* Death is another wave */
1543: /* if(mi==0) never been interviewed correctly before death */
1544: /* Only death is a correct wave */
1545: mw[mi][i]=m;
1546: }
1547:
1548: wav[i]=mi;
1549: if(mi==0){
1550: if(first==0){
1551: printf("Warning, no any valid information for:%d line=%d and may be others, see log file\n",num[i],i);
1552: first=1;
1553: }
1554: if(first==1){
1555: fprintf(ficlog,"Warning, no any valid information for:%d line=%d\n",num[i],i);
1556: }
1557: } /* end mi==0 */
1558: }
1559:
1560: for(i=1; i<=imx; i++){
1561: for(mi=1; mi<wav[i];mi++){
1562: if (stepm <=0)
1563: dh[mi][i]=1;
1564: else{
1565: if (s[mw[mi+1][i]][i] > nlstate) {
1566: if (agedc[i] < 2*AGESUP) {
1567: j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);
1568: if(j==0) j=1; /* Survives at least one month after exam */
1569: k=k+1;
1570: if (j >= jmax) jmax=j;
1571: if (j <= jmin) jmin=j;
1572: sum=sum+j;
1573: /*if (j<0) printf("j=%d num=%d \n",j,i); */
1574: }
1575: }
1576: else{
1577: j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
1578: k=k+1;
1579: if (j >= jmax) jmax=j;
1580: else if (j <= jmin)jmin=j;
1581: /* if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
1582: sum=sum+j;
1583: }
1584: jk= j/stepm;
1585: jl= j -jk*stepm;
1586: ju= j -(jk+1)*stepm;
1.59 ! brouard 1587: if(jl <= -ju){
1.53 brouard 1588: dh[mi][i]=jk;
1.59 ! brouard 1589: bh[mi][i]=jl;
! 1590: }
! 1591: else{
1.53 brouard 1592: dh[mi][i]=jk+1;
1.59 ! brouard 1593: bh[mi][i]=ju;
! 1594: }
! 1595: if(dh[mi][i]==0){
1.53 brouard 1596: dh[mi][i]=1; /* At least one step */
1.59 ! brouard 1597: bh[mi][i]=ju; /* At least one step */
! 1598: printf(" bh=%d ju=%d jl=%d dh=%d jk=%d stepm=%d %d\n",bh[mi][i],ju,jl,dh[mi][i],jk,stepm,i);
! 1599: }
! 1600: if(i==298 || i==287 || i==763 ||i==1061)printf(" bh=%d ju=%d jl=%d dh=%d jk=%d stepm=%d",bh[mi][i],ju,jl,dh[mi][i],jk,stepm);
1.53 brouard 1601: }
1602: }
1603: }
1604: jmean=sum/k;
1605: printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);
1606: fprintf(ficlog,"Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);
1607: }
1608:
1609: /*********** Tricode ****************************/
1610: void tricode(int *Tvar, int **nbcode, int imx)
1611: {
1.58 lievre 1612:
1613: int Ndum[20],ij=1, k, j, i, maxncov=19;
1.53 brouard 1614: int cptcode=0;
1615: cptcoveff=0;
1616:
1.58 lievre 1617: for (k=0; k<maxncov; k++) Ndum[k]=0;
1.53 brouard 1618: for (k=1; k<=7; k++) ncodemax[k]=0;
1619:
1620: for (j=1; j<=(cptcovn+2*cptcovprod); j++) {
1.58 lievre 1621: for (i=1; i<=imx; i++) { /*reads the data file to get the maximum
1622: modality*/
1623: ij=(int)(covar[Tvar[j]][i]); /* ij is the modality of this individual*/
1624: Ndum[ij]++; /*store the modality */
1.53 brouard 1625: /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
1.58 lievre 1626: if (ij > cptcode) cptcode=ij; /* getting the maximum of covariable
1627: Tvar[j]. If V=sex and male is 0 and
1628: female is 1, then cptcode=1.*/
1.53 brouard 1629: }
1630:
1631: for (i=0; i<=cptcode; i++) {
1.58 lievre 1632: if(Ndum[i]!=0) ncodemax[j]++; /* Nomber of modalities of the j th covariates. In fact ncodemax[j]=2 (dichotom. variables) but it can be more */
1.53 brouard 1633: }
1.58 lievre 1634:
1.53 brouard 1635: ij=1;
1636: for (i=1; i<=ncodemax[j]; i++) {
1.58 lievre 1637: for (k=0; k<= maxncov; k++) {
1.53 brouard 1638: if (Ndum[k] != 0) {
1639: nbcode[Tvar[j]][ij]=k;
1.58 lievre 1640: /* store the modality in an array. k is a modality. If we have model=V1+V1*sex then: nbcode[1][1]=0 ; nbcode[1][2]=1; nbcode[2][1]=0 ; nbcode[2][2]=1; */
1.53 brouard 1641:
1642: ij++;
1643: }
1644: if (ij > ncodemax[j]) break;
1645: }
1646: }
1647: }
1648:
1.58 lievre 1649: for (k=0; k< maxncov; k++) Ndum[k]=0;
1.53 brouard 1650:
1.58 lievre 1651: for (i=1; i<=ncovmodel-2; i++) {
1652: /* Listing of all covariables in staement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/
1.53 brouard 1653: ij=Tvar[i];
1.58 lievre 1654: Ndum[ij]++;
1.53 brouard 1655: }
1656:
1657: ij=1;
1.58 lievre 1658: for (i=1; i<= maxncov; i++) {
1.53 brouard 1659: if((Ndum[i]!=0) && (i<=ncovcol)){
1.58 lievre 1660: Tvaraff[ij]=i; /*For printing */
1.53 brouard 1661: ij++;
1662: }
1663: }
1664:
1.58 lievre 1665: cptcoveff=ij-1; /*Number of simple covariates*/
1.53 brouard 1666: }
1667:
1668: /*********** Health Expectancies ****************/
1669:
1670: 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 )
1671:
1672: {
1673: /* Health expectancies */
1674: int i, j, nhstepm, hstepm, h, nstepm, k, cptj;
1675: double age, agelim, hf;
1676: double ***p3mat,***varhe;
1677: double **dnewm,**doldm;
1678: double *xp;
1679: double **gp, **gm;
1680: double ***gradg, ***trgradg;
1681: int theta;
1682:
1683: varhe=ma3x(1,nlstate*2,1,nlstate*2,(int) bage, (int) fage);
1684: xp=vector(1,npar);
1685: dnewm=matrix(1,nlstate*2,1,npar);
1686: doldm=matrix(1,nlstate*2,1,nlstate*2);
1687:
1688: fprintf(ficreseij,"# Health expectancies\n");
1689: fprintf(ficreseij,"# Age");
1690: for(i=1; i<=nlstate;i++)
1691: for(j=1; j<=nlstate;j++)
1692: fprintf(ficreseij," %1d-%1d (SE)",i,j);
1693: fprintf(ficreseij,"\n");
1694:
1695: if(estepm < stepm){
1696: printf ("Problem %d lower than %d\n",estepm, stepm);
1697: }
1698: else hstepm=estepm;
1699: /* We compute the life expectancy from trapezoids spaced every estepm months
1700: * This is mainly to measure the difference between two models: for example
1701: * if stepm=24 months pijx are given only every 2 years and by summing them
1702: * we are calculating an estimate of the Life Expectancy assuming a linear
1703: * progression inbetween and thus overestimating or underestimating according
1704: * to the curvature of the survival function. If, for the same date, we
1705: * estimate the model with stepm=1 month, we can keep estepm to 24 months
1706: * to compare the new estimate of Life expectancy with the same linear
1707: * hypothesis. A more precise result, taking into account a more precise
1708: * curvature will be obtained if estepm is as small as stepm. */
1709:
1710: /* For example we decided to compute the life expectancy with the smallest unit */
1711: /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
1712: nhstepm is the number of hstepm from age to agelim
1713: nstepm is the number of stepm from age to agelin.
1714: Look at hpijx to understand the reason of that which relies in memory size
1715: and note for a fixed period like estepm months */
1716: /* We decided (b) to get a life expectancy respecting the most precise curvature of the
1717: survival function given by stepm (the optimization length). Unfortunately it
1718: means that if the survival funtion is printed only each two years of age and if
1719: you sum them up and add 1 year (area under the trapezoids) you won't get the same
1720: results. So we changed our mind and took the option of the best precision.
1721: */
1722: hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
1723:
1724: agelim=AGESUP;
1725: for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
1726: /* nhstepm age range expressed in number of stepm */
1727: nstepm=(int) rint((agelim-age)*YEARM/stepm);
1728: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
1729: /* if (stepm >= YEARM) hstepm=1;*/
1730: nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
1731: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
1732: gradg=ma3x(0,nhstepm,1,npar,1,nlstate*2);
1733: gp=matrix(0,nhstepm,1,nlstate*2);
1734: gm=matrix(0,nhstepm,1,nlstate*2);
1735:
1736: /* Computed by stepm unit matrices, product of hstepm matrices, stored
1737: in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
1738: hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);
1739:
1740:
1741: hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
1742:
1743: /* Computing Variances of health expectancies */
1744:
1745: for(theta=1; theta <=npar; theta++){
1746: for(i=1; i<=npar; i++){
1747: xp[i] = x[i] + (i==theta ?delti[theta]:0);
1748: }
1749: hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
1750:
1751: cptj=0;
1752: for(j=1; j<= nlstate; j++){
1753: for(i=1; i<=nlstate; i++){
1754: cptj=cptj+1;
1755: for(h=0, gp[h][cptj]=0.; h<=nhstepm-1; h++){
1756: gp[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;
1757: }
1758: }
1759: }
1760:
1761:
1762: for(i=1; i<=npar; i++)
1763: xp[i] = x[i] - (i==theta ?delti[theta]:0);
1764: hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
1765:
1766: cptj=0;
1767: for(j=1; j<= nlstate; j++){
1768: for(i=1;i<=nlstate;i++){
1769: cptj=cptj+1;
1770: for(h=0, gm[h][cptj]=0.; h<=nhstepm-1; h++){
1771: gm[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;
1772: }
1773: }
1774: }
1775: for(j=1; j<= nlstate*2; j++)
1776: for(h=0; h<=nhstepm-1; h++){
1777: gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
1778: }
1779: }
1780:
1781: /* End theta */
1782:
1783: trgradg =ma3x(0,nhstepm,1,nlstate*2,1,npar);
1784:
1785: for(h=0; h<=nhstepm-1; h++)
1786: for(j=1; j<=nlstate*2;j++)
1787: for(theta=1; theta <=npar; theta++)
1788: trgradg[h][j][theta]=gradg[h][theta][j];
1789:
1790:
1791: for(i=1;i<=nlstate*2;i++)
1792: for(j=1;j<=nlstate*2;j++)
1793: varhe[i][j][(int)age] =0.;
1794:
1795: printf("%d|",(int)age);fflush(stdout);
1796: fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
1797: for(h=0;h<=nhstepm-1;h++){
1798: for(k=0;k<=nhstepm-1;k++){
1799: matprod2(dnewm,trgradg[h],1,nlstate*2,1,npar,1,npar,matcov);
1800: matprod2(doldm,dnewm,1,nlstate*2,1,npar,1,nlstate*2,gradg[k]);
1801: for(i=1;i<=nlstate*2;i++)
1802: for(j=1;j<=nlstate*2;j++)
1803: varhe[i][j][(int)age] += doldm[i][j]*hf*hf;
1804: }
1805: }
1806: /* Computing expectancies */
1807: for(i=1; i<=nlstate;i++)
1808: for(j=1; j<=nlstate;j++)
1809: for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
1810: eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
1811:
1812: /* 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]);*/
1813:
1814: }
1815:
1816: fprintf(ficreseij,"%3.0f",age );
1817: cptj=0;
1818: for(i=1; i<=nlstate;i++)
1819: for(j=1; j<=nlstate;j++){
1820: cptj++;
1821: fprintf(ficreseij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[cptj][cptj][(int)age]) );
1822: }
1823: fprintf(ficreseij,"\n");
1824:
1825: free_matrix(gm,0,nhstepm,1,nlstate*2);
1826: free_matrix(gp,0,nhstepm,1,nlstate*2);
1827: free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*2);
1828: free_ma3x(trgradg,0,nhstepm,1,nlstate*2,1,npar);
1829: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
1830: }
1831: printf("\n");
1832: fprintf(ficlog,"\n");
1833:
1834: free_vector(xp,1,npar);
1835: free_matrix(dnewm,1,nlstate*2,1,npar);
1836: free_matrix(doldm,1,nlstate*2,1,nlstate*2);
1837: free_ma3x(varhe,1,nlstate*2,1,nlstate*2,(int) bage, (int)fage);
1838: }
1839:
1840: /************ Variance ******************/
1841: 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)
1842: {
1843: /* Variance of health expectancies */
1844: /* double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
1845: /* double **newm;*/
1846: double **dnewm,**doldm;
1847: double **dnewmp,**doldmp;
1848: int i, j, nhstepm, hstepm, h, nstepm ;
1849: int k, cptcode;
1850: double *xp;
1851: double **gp, **gm; /* for var eij */
1852: double ***gradg, ***trgradg; /*for var eij */
1853: double **gradgp, **trgradgp; /* for var p point j */
1854: double *gpp, *gmp; /* for var p point j */
1855: double **varppt; /* for var p point j nlstate to nlstate+ndeath */
1856: double ***p3mat;
1857: double age,agelim, hf;
1858: double ***mobaverage;
1859: int theta;
1860: char digit[4];
1.55 lievre 1861: char digitp[25];
1.53 brouard 1862:
1863: char fileresprobmorprev[FILENAMELENGTH];
1864:
1.55 lievre 1865: if(popbased==1){
1.58 lievre 1866: if(mobilav!=0)
1.55 lievre 1867: strcpy(digitp,"-populbased-mobilav-");
1868: else strcpy(digitp,"-populbased-nomobil-");
1869: }
1870: else
1.53 brouard 1871: strcpy(digitp,"-stablbased-");
1.56 lievre 1872:
1.54 brouard 1873: if (mobilav!=0) {
1.53 brouard 1874: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
1.54 brouard 1875: if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
1876: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
1877: printf(" Error in movingaverage mobilav=%d\n",mobilav);
1878: }
1.53 brouard 1879: }
1880:
1881: strcpy(fileresprobmorprev,"prmorprev");
1882: sprintf(digit,"%-d",ij);
1883: /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
1884: strcat(fileresprobmorprev,digit); /* Tvar to be done */
1885: strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
1886: strcat(fileresprobmorprev,fileres);
1887: if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
1888: printf("Problem with resultfile: %s\n", fileresprobmorprev);
1889: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
1890: }
1891: printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
1892: fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
1893: fprintf(ficresprobmorprev,"# probabilities of dying during a year and weighted mean w1*p1j+w2*p2j+... stand dev in()\n");
1894: fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
1895: for(j=nlstate+1; j<=(nlstate+ndeath);j++){
1896: fprintf(ficresprobmorprev," p.%-d SE",j);
1897: for(i=1; i<=nlstate;i++)
1898: fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
1899: }
1900: fprintf(ficresprobmorprev,"\n");
1901: if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {
1902: printf("Problem with gnuplot file: %s\n", optionfilegnuplot);
1903: fprintf(ficlog,"Problem with gnuplot file: %s\n", optionfilegnuplot);
1904: exit(0);
1905: }
1906: else{
1907: fprintf(ficgp,"\n# Routine varevsij");
1908: }
1909: if((fichtm=fopen(optionfilehtm,"a"))==NULL) {
1910: printf("Problem with html file: %s\n", optionfilehtm);
1911: fprintf(ficlog,"Problem with html file: %s\n", optionfilehtm);
1912: exit(0);
1913: }
1914: else{
1915: 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");
1916: fprintf(fichtm,"\n<br>%s (à revoir) <br>\n",digitp);
1917: }
1918: varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
1919:
1920: 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");
1921: fprintf(ficresvij,"# Age");
1922: for(i=1; i<=nlstate;i++)
1923: for(j=1; j<=nlstate;j++)
1924: fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);
1925: fprintf(ficresvij,"\n");
1926:
1927: xp=vector(1,npar);
1928: dnewm=matrix(1,nlstate,1,npar);
1929: doldm=matrix(1,nlstate,1,nlstate);
1930: dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
1931: doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
1932:
1933: gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
1934: gpp=vector(nlstate+1,nlstate+ndeath);
1935: gmp=vector(nlstate+1,nlstate+ndeath);
1936: trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
1937:
1938: if(estepm < stepm){
1939: printf ("Problem %d lower than %d\n",estepm, stepm);
1940: }
1941: else hstepm=estepm;
1942: /* For example we decided to compute the life expectancy with the smallest unit */
1943: /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
1944: nhstepm is the number of hstepm from age to agelim
1945: nstepm is the number of stepm from age to agelin.
1946: Look at hpijx to understand the reason of that which relies in memory size
1947: and note for a fixed period like k years */
1948: /* We decided (b) to get a life expectancy respecting the most precise curvature of the
1949: survival function given by stepm (the optimization length). Unfortunately it
1950: means that if the survival funtion is printed only each two years of age and if
1951: you sum them up and add 1 year (area under the trapezoids) you won't get the same
1952: results. So we changed our mind and took the option of the best precision.
1953: */
1954: hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
1955: agelim = AGESUP;
1956: for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
1957: nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
1958: nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
1959: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
1960: gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
1961: gp=matrix(0,nhstepm,1,nlstate);
1962: gm=matrix(0,nhstepm,1,nlstate);
1963:
1964:
1965: for(theta=1; theta <=npar; theta++){
1966: for(i=1; i<=npar; i++){ /* Computes gradient */
1967: xp[i] = x[i] + (i==theta ?delti[theta]:0);
1968: }
1969: hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
1970: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
1971:
1972: if (popbased==1) {
1.54 brouard 1973: if(mobilav ==0){
1.53 brouard 1974: for(i=1; i<=nlstate;i++)
1975: prlim[i][i]=probs[(int)age][i][ij];
1.54 brouard 1976: }else{ /* mobilav */
1.53 brouard 1977: for(i=1; i<=nlstate;i++)
1978: prlim[i][i]=mobaverage[(int)age][i][ij];
1979: }
1980: }
1981:
1982: for(j=1; j<= nlstate; j++){
1983: for(h=0; h<=nhstepm; h++){
1984: for(i=1, gp[h][j]=0.;i<=nlstate;i++)
1985: gp[h][j] += prlim[i][i]*p3mat[i][j][h];
1986: }
1987: }
1988: /* This for computing forces of mortality (h=1)as a weighted average */
1989: for(j=nlstate+1,gpp[j]=0.;j<=nlstate+ndeath;j++){
1990: for(i=1; i<= nlstate; i++)
1991: gpp[j] += prlim[i][i]*p3mat[i][j][1];
1992: }
1993: /* end force of mortality */
1994:
1995: for(i=1; i<=npar; i++) /* Computes gradient */
1996: xp[i] = x[i] - (i==theta ?delti[theta]:0);
1997: hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
1998: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
1999:
2000: if (popbased==1) {
1.54 brouard 2001: if(mobilav ==0){
1.53 brouard 2002: for(i=1; i<=nlstate;i++)
2003: prlim[i][i]=probs[(int)age][i][ij];
1.54 brouard 2004: }else{ /* mobilav */
1.53 brouard 2005: for(i=1; i<=nlstate;i++)
2006: prlim[i][i]=mobaverage[(int)age][i][ij];
2007: }
2008: }
2009:
2010: for(j=1; j<= nlstate; j++){
2011: for(h=0; h<=nhstepm; h++){
2012: for(i=1, gm[h][j]=0.;i<=nlstate;i++)
2013: gm[h][j] += prlim[i][i]*p3mat[i][j][h];
2014: }
2015: }
2016: /* This for computing force of mortality (h=1)as a weighted average */
2017: for(j=nlstate+1,gmp[j]=0.;j<=nlstate+ndeath;j++){
2018: for(i=1; i<= nlstate; i++)
2019: gmp[j] += prlim[i][i]*p3mat[i][j][1];
2020: }
2021: /* end force of mortality */
2022:
2023: for(j=1; j<= nlstate; j++) /* vareij */
2024: for(h=0; h<=nhstepm; h++){
2025: gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
2026: }
2027: for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
2028: gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
2029: }
2030:
2031: } /* End theta */
2032:
2033: trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
2034:
2035: for(h=0; h<=nhstepm; h++) /* veij */
2036: for(j=1; j<=nlstate;j++)
2037: for(theta=1; theta <=npar; theta++)
2038: trgradg[h][j][theta]=gradg[h][theta][j];
2039:
2040: for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
2041: for(theta=1; theta <=npar; theta++)
2042: trgradgp[j][theta]=gradgp[theta][j];
2043:
2044: hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
2045: for(i=1;i<=nlstate;i++)
2046: for(j=1;j<=nlstate;j++)
2047: vareij[i][j][(int)age] =0.;
2048:
2049: for(h=0;h<=nhstepm;h++){
2050: for(k=0;k<=nhstepm;k++){
2051: matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
2052: matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
2053: for(i=1;i<=nlstate;i++)
2054: for(j=1;j<=nlstate;j++)
2055: vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
2056: }
2057: }
2058:
2059: /* pptj */
2060: matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
2061: matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
2062: for(j=nlstate+1;j<=nlstate+ndeath;j++)
2063: for(i=nlstate+1;i<=nlstate+ndeath;i++)
2064: varppt[j][i]=doldmp[j][i];
2065: /* end ppptj */
2066: hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);
2067: prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);
2068:
2069: if (popbased==1) {
1.54 brouard 2070: if(mobilav ==0){
1.53 brouard 2071: for(i=1; i<=nlstate;i++)
2072: prlim[i][i]=probs[(int)age][i][ij];
1.54 brouard 2073: }else{ /* mobilav */
1.53 brouard 2074: for(i=1; i<=nlstate;i++)
2075: prlim[i][i]=mobaverage[(int)age][i][ij];
2076: }
2077: }
2078:
2079: /* This for computing force of mortality (h=1)as a weighted average */
2080: for(j=nlstate+1,gmp[j]=0.;j<=nlstate+ndeath;j++){
2081: for(i=1; i<= nlstate; i++)
2082: gmp[j] += prlim[i][i]*p3mat[i][j][1];
2083: }
2084: /* end force of mortality */
2085:
2086: fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
2087: for(j=nlstate+1; j<=(nlstate+ndeath);j++){
2088: fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
2089: for(i=1; i<=nlstate;i++){
2090: fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
2091: }
2092: }
2093: fprintf(ficresprobmorprev,"\n");
2094:
2095: fprintf(ficresvij,"%.0f ",age );
2096: for(i=1; i<=nlstate;i++)
2097: for(j=1; j<=nlstate;j++){
2098: fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
2099: }
2100: fprintf(ficresvij,"\n");
2101: free_matrix(gp,0,nhstepm,1,nlstate);
2102: free_matrix(gm,0,nhstepm,1,nlstate);
2103: free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
2104: free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
2105: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
2106: } /* End age */
2107: free_vector(gpp,nlstate+1,nlstate+ndeath);
2108: free_vector(gmp,nlstate+1,nlstate+ndeath);
2109: free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
2110: free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
2111: fprintf(ficgp,"\nset noparametric;set nolabel; set ter png small;set size 0.65, 0.65");
2112: /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */
2113: fprintf(ficgp,"\n set log y; set nolog x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
2114: fprintf(ficgp,"\n plot \"%s\" u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm);
2115: fprintf(ficgp,"\n replot \"%s\" u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm);
2116: fprintf(ficgp,"\n replot \"%s\" u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm);
2117: fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",fileresprobmorprev,fileresprobmorprev);
2118: fprintf(fichtm,"\n<br> Probability is computed over estepm=%d months. <br> <img src=\"varmuptjgr%s%s.png\"> <br>\n", stepm,digitp,digit);
2119: /* 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);
2120: */
2121: fprintf(ficgp,"\nset out \"varmuptjgr%s%s.png\";replot;",digitp,digit);
2122:
2123: free_vector(xp,1,npar);
2124: free_matrix(doldm,1,nlstate,1,nlstate);
2125: free_matrix(dnewm,1,nlstate,1,npar);
2126: free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
2127: free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
2128: free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
1.55 lievre 2129: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
1.53 brouard 2130: fclose(ficresprobmorprev);
2131: fclose(ficgp);
2132: fclose(fichtm);
2133: }
2134:
2135: /************ Variance of prevlim ******************/
2136: 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)
2137: {
2138: /* Variance of prevalence limit */
1.59 ! brouard 2139: /* double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
1.53 brouard 2140: double **newm;
2141: double **dnewm,**doldm;
2142: int i, j, nhstepm, hstepm;
2143: int k, cptcode;
2144: double *xp;
2145: double *gp, *gm;
2146: double **gradg, **trgradg;
2147: double age,agelim;
2148: int theta;
2149:
1.54 brouard 2150: fprintf(ficresvpl,"# Standard deviation of stable prevalences \n");
1.53 brouard 2151: fprintf(ficresvpl,"# Age");
2152: for(i=1; i<=nlstate;i++)
2153: fprintf(ficresvpl," %1d-%1d",i,i);
2154: fprintf(ficresvpl,"\n");
2155:
2156: xp=vector(1,npar);
2157: dnewm=matrix(1,nlstate,1,npar);
2158: doldm=matrix(1,nlstate,1,nlstate);
2159:
2160: hstepm=1*YEARM; /* Every year of age */
2161: hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */
2162: agelim = AGESUP;
2163: for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
2164: nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
2165: if (stepm >= YEARM) hstepm=1;
2166: nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
2167: gradg=matrix(1,npar,1,nlstate);
2168: gp=vector(1,nlstate);
2169: gm=vector(1,nlstate);
2170:
2171: for(theta=1; theta <=npar; theta++){
2172: for(i=1; i<=npar; i++){ /* Computes gradient */
2173: xp[i] = x[i] + (i==theta ?delti[theta]:0);
2174: }
2175: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
2176: for(i=1;i<=nlstate;i++)
2177: gp[i] = prlim[i][i];
2178:
2179: for(i=1; i<=npar; i++) /* Computes gradient */
2180: xp[i] = x[i] - (i==theta ?delti[theta]:0);
2181: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
2182: for(i=1;i<=nlstate;i++)
2183: gm[i] = prlim[i][i];
2184:
2185: for(i=1;i<=nlstate;i++)
2186: gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
2187: } /* End theta */
2188:
2189: trgradg =matrix(1,nlstate,1,npar);
2190:
2191: for(j=1; j<=nlstate;j++)
2192: for(theta=1; theta <=npar; theta++)
2193: trgradg[j][theta]=gradg[theta][j];
2194:
2195: for(i=1;i<=nlstate;i++)
2196: varpl[i][(int)age] =0.;
2197: matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
2198: matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
2199: for(i=1;i<=nlstate;i++)
2200: varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
2201:
2202: fprintf(ficresvpl,"%.0f ",age );
2203: for(i=1; i<=nlstate;i++)
2204: fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
2205: fprintf(ficresvpl,"\n");
2206: free_vector(gp,1,nlstate);
2207: free_vector(gm,1,nlstate);
2208: free_matrix(gradg,1,npar,1,nlstate);
2209: free_matrix(trgradg,1,nlstate,1,npar);
2210: } /* End age */
2211:
2212: free_vector(xp,1,npar);
2213: free_matrix(doldm,1,nlstate,1,npar);
2214: free_matrix(dnewm,1,nlstate,1,nlstate);
2215:
2216: }
2217:
2218: /************ Variance of one-step probabilities ******************/
2219: void varprob(char optionfilefiname[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij, int *Tvar, int **nbcode, int *ncodemax)
2220: {
2221: int i, j=0, i1, k1, l1, t, tj;
2222: int k2, l2, j1, z1;
2223: int k=0,l, cptcode;
2224: int first=1, first1;
2225: double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
2226: double **dnewm,**doldm;
2227: double *xp;
2228: double *gp, *gm;
2229: double **gradg, **trgradg;
2230: double **mu;
2231: double age,agelim, cov[NCOVMAX];
2232: double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
2233: int theta;
2234: char fileresprob[FILENAMELENGTH];
2235: char fileresprobcov[FILENAMELENGTH];
2236: char fileresprobcor[FILENAMELENGTH];
2237:
2238: double ***varpij;
2239:
2240: strcpy(fileresprob,"prob");
2241: strcat(fileresprob,fileres);
2242: if((ficresprob=fopen(fileresprob,"w"))==NULL) {
2243: printf("Problem with resultfile: %s\n", fileresprob);
2244: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
2245: }
2246: strcpy(fileresprobcov,"probcov");
2247: strcat(fileresprobcov,fileres);
2248: if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
2249: printf("Problem with resultfile: %s\n", fileresprobcov);
2250: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
2251: }
2252: strcpy(fileresprobcor,"probcor");
2253: strcat(fileresprobcor,fileres);
2254: if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
2255: printf("Problem with resultfile: %s\n", fileresprobcor);
2256: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
2257: }
2258: printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
2259: fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
2260: printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
2261: fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
2262: printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
2263: fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
2264:
2265: fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
2266: fprintf(ficresprob,"# Age");
2267: fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
2268: fprintf(ficresprobcov,"# Age");
2269: fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
2270: fprintf(ficresprobcov,"# Age");
2271:
2272:
2273: for(i=1; i<=nlstate;i++)
2274: for(j=1; j<=(nlstate+ndeath);j++){
2275: fprintf(ficresprob," p%1d-%1d (SE)",i,j);
2276: fprintf(ficresprobcov," p%1d-%1d ",i,j);
2277: fprintf(ficresprobcor," p%1d-%1d ",i,j);
2278: }
2279: fprintf(ficresprob,"\n");
2280: fprintf(ficresprobcov,"\n");
2281: fprintf(ficresprobcor,"\n");
2282: xp=vector(1,npar);
2283: dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
2284: doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
2285: mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
2286: varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
2287: first=1;
2288: if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {
2289: printf("Problem with gnuplot file: %s\n", optionfilegnuplot);
2290: fprintf(ficlog,"Problem with gnuplot file: %s\n", optionfilegnuplot);
2291: exit(0);
2292: }
2293: else{
2294: fprintf(ficgp,"\n# Routine varprob");
2295: }
2296: if((fichtm=fopen(optionfilehtm,"a"))==NULL) {
2297: printf("Problem with html file: %s\n", optionfilehtm);
2298: fprintf(ficlog,"Problem with html file: %s\n", optionfilehtm);
2299: exit(0);
2300: }
2301: else{
2302: fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
2303: fprintf(fichtm,"\n");
2304:
2305: fprintf(fichtm,"\n<li><h4> Computing matrix of variance-covariance of step probabilities</h4></li>\n");
2306: 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");
2307: 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");
2308:
2309: }
2310:
2311: cov[1]=1;
2312: tj=cptcoveff;
2313: if (cptcovn<1) {tj=1;ncodemax[1]=1;}
2314: j1=0;
2315: for(t=1; t<=tj;t++){
2316: for(i1=1; i1<=ncodemax[t];i1++){
2317: j1++;
2318: if (cptcovn>0) {
2319: fprintf(ficresprob, "\n#********** Variable ");
2320: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
2321: fprintf(ficresprob, "**********\n#");
2322: fprintf(ficresprobcov, "\n#********** Variable ");
2323: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
2324: fprintf(ficresprobcov, "**********\n#");
2325:
2326: fprintf(ficgp, "\n#********** Variable ");
2327: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, "# V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
2328: fprintf(ficgp, "**********\n#");
2329:
2330:
2331: fprintf(fichtm, "\n<hr size=\"2\" color=\"#EC5E5E\">********** Variable ");
2332: for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
2333: fprintf(fichtm, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
2334:
2335: fprintf(ficresprobcor, "\n#********** Variable ");
2336: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
2337: fprintf(ficgp, "**********\n#");
2338: }
2339:
2340: for (age=bage; age<=fage; age ++){
2341: cov[2]=age;
2342: for (k=1; k<=cptcovn;k++) {
2343: cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];
2344: }
2345: for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
2346: for (k=1; k<=cptcovprod;k++)
2347: cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
2348:
2349: gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
2350: trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
2351: gp=vector(1,(nlstate)*(nlstate+ndeath));
2352: gm=vector(1,(nlstate)*(nlstate+ndeath));
2353:
2354: for(theta=1; theta <=npar; theta++){
2355: for(i=1; i<=npar; i++)
2356: xp[i] = x[i] + (i==theta ?delti[theta]:0);
2357:
2358: pmij(pmmij,cov,ncovmodel,xp,nlstate);
2359:
2360: k=0;
2361: for(i=1; i<= (nlstate); i++){
2362: for(j=1; j<=(nlstate+ndeath);j++){
2363: k=k+1;
2364: gp[k]=pmmij[i][j];
2365: }
2366: }
2367:
2368: for(i=1; i<=npar; i++)
2369: xp[i] = x[i] - (i==theta ?delti[theta]:0);
2370:
2371: pmij(pmmij,cov,ncovmodel,xp,nlstate);
2372: k=0;
2373: for(i=1; i<=(nlstate); i++){
2374: for(j=1; j<=(nlstate+ndeath);j++){
2375: k=k+1;
2376: gm[k]=pmmij[i][j];
2377: }
2378: }
2379:
2380: for(i=1; i<= (nlstate)*(nlstate+ndeath); i++)
2381: gradg[theta][i]=(gp[i]-gm[i])/2./delti[theta];
2382: }
2383:
2384: for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
2385: for(theta=1; theta <=npar; theta++)
2386: trgradg[j][theta]=gradg[theta][j];
2387:
2388: matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov);
2389: matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);
1.59 ! brouard 2390: free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
! 2391: free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
! 2392: free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
! 2393: free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
! 2394:
1.53 brouard 2395: pmij(pmmij,cov,ncovmodel,x,nlstate);
2396:
2397: k=0;
2398: for(i=1; i<=(nlstate); i++){
2399: for(j=1; j<=(nlstate+ndeath);j++){
2400: k=k+1;
2401: mu[k][(int) age]=pmmij[i][j];
2402: }
2403: }
2404: for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
2405: for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
2406: varpij[i][j][(int)age] = doldm[i][j];
2407:
2408: /*printf("\n%d ",(int)age);
1.59 ! brouard 2409: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
! 2410: printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
! 2411: fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
! 2412: }*/
1.53 brouard 2413:
2414: fprintf(ficresprob,"\n%d ",(int)age);
2415: fprintf(ficresprobcov,"\n%d ",(int)age);
2416: fprintf(ficresprobcor,"\n%d ",(int)age);
2417:
2418: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)
2419: fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));
2420: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
2421: fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);
2422: fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
2423: }
2424: i=0;
2425: for (k=1; k<=(nlstate);k++){
2426: for (l=1; l<=(nlstate+ndeath);l++){
2427: i=i++;
2428: fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
2429: fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
2430: for (j=1; j<=i;j++){
2431: fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);
2432: fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));
2433: }
2434: }
2435: }/* end of loop for state */
2436: } /* end of loop for age */
2437:
2438: /* Confidence intervalle of pij */
2439: /*
1.59 ! brouard 2440: fprintf(ficgp,"\nset noparametric;unset label");
! 2441: fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");
! 2442: fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
! 2443: 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);
! 2444: fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);
! 2445: fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);
! 2446: fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);
1.53 brouard 2447: */
2448:
2449: /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
2450: first1=1;
2451: for (k2=1; k2<=(nlstate);k2++){
2452: for (l2=1; l2<=(nlstate+ndeath);l2++){
2453: if(l2==k2) continue;
2454: j=(k2-1)*(nlstate+ndeath)+l2;
2455: for (k1=1; k1<=(nlstate);k1++){
2456: for (l1=1; l1<=(nlstate+ndeath);l1++){
2457: if(l1==k1) continue;
2458: i=(k1-1)*(nlstate+ndeath)+l1;
2459: if(i<=j) continue;
2460: for (age=bage; age<=fage; age ++){
2461: if ((int)age %5==0){
2462: v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;
2463: v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;
2464: cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;
2465: mu1=mu[i][(int) age]/stepm*YEARM ;
2466: mu2=mu[j][(int) age]/stepm*YEARM;
2467: c12=cv12/sqrt(v1*v2);
2468: /* Computing eigen value of matrix of covariance */
2469: lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
2470: lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
2471: /* Eigen vectors */
2472: v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
2473: /*v21=sqrt(1.-v11*v11); *//* error */
2474: v21=(lc1-v1)/cv12*v11;
2475: v12=-v21;
2476: v22=v11;
2477: tnalp=v21/v11;
2478: if(first1==1){
2479: first1=0;
2480: 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);
2481: }
2482: 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);
2483: /*printf(fignu*/
2484: /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */
2485: /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */
2486: if(first==1){
2487: first=0;
2488: fprintf(ficgp,"\nset parametric;unset label");
2489: 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);
2490: fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
2491: 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);
2492: fprintf(fichtm,"\n<br><img src=\"varpijgr%s%d%1d%1d-%1d%1d.png\"> ",optionfilefiname, j1,k1,l1,k2,l2);
2493: fprintf(fichtm,"\n<br> Correlation at age %d (%.3f),",(int) age, c12);
2494: fprintf(ficgp,"\nset out \"varpijgr%s%d%1d%1d-%1d%1d.png\"",optionfilefiname, j1,k1,l1,k2,l2);
2495: fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
2496: fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
2497: 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",\
2498: mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
2499: mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
2500: }else{
2501: first=0;
2502: fprintf(fichtm," %d (%.3f),",(int) age, c12);
2503: fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
2504: fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
2505: 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",\
2506: mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
2507: mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
2508: }/* if first */
2509: } /* age mod 5 */
2510: } /* end loop age */
2511: fprintf(ficgp,"\nset out \"varpijgr%s%d%1d%1d-%1d%1d.png\";replot;",optionfilefiname, j1,k1,l1,k2,l2);
2512: first=1;
2513: } /*l12 */
2514: } /* k12 */
2515: } /*l1 */
2516: }/* k1 */
2517: } /* loop covariates */
2518: }
1.59 ! brouard 2519: free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
! 2520: free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
1.53 brouard 2521: free_vector(xp,1,npar);
2522: fclose(ficresprob);
2523: fclose(ficresprobcov);
2524: fclose(ficresprobcor);
2525: fclose(ficgp);
2526: fclose(fichtm);
2527: }
2528:
2529:
2530: /******************* Printing html file ***********/
2531: void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \
2532: int lastpass, int stepm, int weightopt, char model[],\
2533: int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
2534: int popforecast, int estepm ,\
2535: double jprev1, double mprev1,double anprev1, \
2536: double jprev2, double mprev2,double anprev2){
2537: int jj1, k1, i1, cpt;
2538: /*char optionfilehtm[FILENAMELENGTH];*/
2539: if((fichtm=fopen(optionfilehtm,"a"))==NULL) {
2540: printf("Problem with %s \n",optionfilehtm), exit(0);
2541: fprintf(ficlog,"Problem with %s \n",optionfilehtm), exit(0);
2542: }
2543:
2544: fprintf(fichtm,"<ul><li><h4>Result files (first order: no variance)</h4>\n
2545: - 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
2546: - Estimated transition probabilities over %d (stepm) months: <a href=\"pij%s\">pij%s</a><br>\n
2547: - Stable prevalence in each health state: <a href=\"pl%s\">pl%s</a> <br>\n
2548: - Life expectancies by age and initial health status (estepm=%2d months):
2549: <a href=\"e%s\">e%s</a> <br>\n</li>", \
2550: jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,fileres,fileres,stepm,fileres,fileres,fileres,fileres,estepm,fileres,fileres);
2551:
2552: fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
2553:
2554: m=cptcoveff;
2555: if (cptcovn < 1) {m=1;ncodemax[1]=1;}
2556:
2557: jj1=0;
2558: for(k1=1; k1<=m;k1++){
2559: for(i1=1; i1<=ncodemax[k1];i1++){
2560: jj1++;
2561: if (cptcovn > 0) {
2562: fprintf(fichtm,"<hr size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
2563: for (cpt=1; cpt<=cptcoveff;cpt++)
2564: fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
2565: fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
2566: }
2567: /* Pij */
2568: 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>
2569: <img src=\"pe%s%d1.png\">",stepm,strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);
2570: /* Quasi-incidences */
2571: 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>
2572: <img src=\"pe%s%d2.png\">",stepm,strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);
2573: /* Stable prevalence in each health state */
2574: for(cpt=1; cpt<nlstate;cpt++){
2575: fprintf(fichtm,"<br>- Stable prevalence in each health state : p%s%d%d.png<br>
2576: <img src=\"p%s%d%d.png\">",strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);
2577: }
2578: for(cpt=1; cpt<=nlstate;cpt++) {
2579: fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): exp%s%d%d.png <br>
2580: <img src=\"exp%s%d%d.png\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);
2581: }
2582: fprintf(fichtm,"\n<br>- Total life expectancy by age and
2583: health expectancies in states (1) and (2): e%s%d.png<br>
2584: <img src=\"e%s%d.png\">",strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);
2585: } /* end i1 */
2586: }/* End k1 */
2587: fprintf(fichtm,"</ul>");
2588:
2589:
2590: fprintf(fichtm,"\n<br><li><h4> Result files (second order: variances)</h4>\n
2591: - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n
2592: - Variance of one-step probabilities: <a href=\"prob%s\">prob%s</a> <br>\n
2593: - Variance-covariance of one-step probabilities: <a href=\"probcov%s\">probcov%s</a> <br>\n
2594: - Correlation matrix of one-step probabilities: <a href=\"probcor%s\">probcor%s</a> <br>\n
2595: - Variances and covariances of life expectancies by age and initial health status (estepm=%d months): <a href=\"v%s\">v%s</a><br>\n
2596: - Health expectancies with their variances (no covariance): <a href=\"t%s\">t%s</a> <br>\n
2597: - 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);
2598:
2599: if(popforecast==1) fprintf(fichtm,"\n
2600: - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n
2601: - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n
2602: <br>",fileres,fileres,fileres,fileres);
2603: else
2604: 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);
2605: fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
2606:
2607: m=cptcoveff;
2608: if (cptcovn < 1) {m=1;ncodemax[1]=1;}
2609:
2610: jj1=0;
2611: for(k1=1; k1<=m;k1++){
2612: for(i1=1; i1<=ncodemax[k1];i1++){
2613: jj1++;
2614: if (cptcovn > 0) {
2615: fprintf(fichtm,"<hr size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
2616: for (cpt=1; cpt<=cptcoveff;cpt++)
2617: fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
2618: fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
2619: }
2620: for(cpt=1; cpt<=nlstate;cpt++) {
2621: fprintf(fichtm,"<br>- Observed and stationary prevalence (with confident
2622: interval) in state (%d): v%s%d%d.png <br>
2623: <img src=\"v%s%d%d.png\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);
2624: }
2625: } /* end i1 */
2626: }/* End k1 */
2627: fprintf(fichtm,"</ul>");
2628: fclose(fichtm);
2629: }
2630:
2631: /******************* Gnuplot file **************/
2632: void printinggnuplot(char fileres[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
2633:
2634: int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;
2635: int ng;
2636: if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {
2637: printf("Problem with file %s",optionfilegnuplot);
2638: fprintf(ficlog,"Problem with file %s",optionfilegnuplot);
2639: }
2640:
1.54 brouard 2641: /*#ifdef windows */
1.53 brouard 2642: fprintf(ficgp,"cd \"%s\" \n",pathc);
1.54 brouard 2643: /*#endif */
1.53 brouard 2644: m=pow(2,cptcoveff);
2645:
2646: /* 1eme*/
2647: for (cpt=1; cpt<= nlstate ; cpt ++) {
2648: for (k1=1; k1<= m ; k1 ++) {
2649: fprintf(ficgp,"\nset out \"v%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);
2650: 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);
2651:
2652: for (i=1; i<= nlstate ; i ++) {
2653: if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
2654: else fprintf(ficgp," \%%*lf (\%%*lf)");
2655: }
1.54 brouard 2656: 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 2657: for (i=1; i<= nlstate ; i ++) {
2658: if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
2659: else fprintf(ficgp," \%%*lf (\%%*lf)");
2660: }
2661: fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"vpl%s\" every :::%d::%d u 1:($2-2*$3) \"\%%lf",fileres,k1-1,k1-1);
2662: for (i=1; i<= nlstate ; i ++) {
2663: if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
2664: else fprintf(ficgp," \%%*lf (\%%*lf)");
2665: }
2666: fprintf(ficgp,"\" t\"\" w l 1,\"p%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",fileres,k1-1,k1-1,2+4*(cpt-1));
2667: }
2668: }
2669: /*2 eme*/
2670:
2671: for (k1=1; k1<= m ; k1 ++) {
2672: fprintf(ficgp,"\nset out \"e%s%d.png\" \n",strtok(optionfile, "."),k1);
2673: fprintf(ficgp,"set ylabel \"Years\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] ",ageminpar,fage);
2674:
2675: for (i=1; i<= nlstate+1 ; i ++) {
2676: k=2*i;
2677: fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:2 \"\%%lf",fileres,k1-1,k1-1);
2678: for (j=1; j<= nlstate+1 ; j ++) {
2679: if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
2680: else fprintf(ficgp," \%%*lf (\%%*lf)");
2681: }
2682: if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");
2683: else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);
2684: fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",fileres,k1-1,k1-1);
2685: for (j=1; j<= nlstate+1 ; j ++) {
2686: if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
2687: else fprintf(ficgp," \%%*lf (\%%*lf)");
2688: }
2689: fprintf(ficgp,"\" t\"\" w l 0,");
2690: fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",fileres,k1-1,k1-1);
2691: for (j=1; j<= nlstate+1 ; j ++) {
2692: if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
2693: else fprintf(ficgp," \%%*lf (\%%*lf)");
2694: }
2695: if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");
2696: else fprintf(ficgp,"\" t\"\" w l 0,");
2697: }
2698: }
2699:
2700: /*3eme*/
2701:
2702: for (k1=1; k1<= m ; k1 ++) {
2703: for (cpt=1; cpt<= nlstate ; cpt ++) {
2704: k=2+nlstate*(2*cpt-2);
2705: fprintf(ficgp,"\nset out \"exp%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);
2706: fprintf(ficgp,"set ter png small\nset size 0.65,0.65\nplot [%.f:%.f] \"e%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,fileres,k1-1,k1-1,k,cpt);
2707: /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
2708: for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
2709: fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
2710: fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
2711: for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
2712: fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
2713:
2714: */
2715: for (i=1; i< nlstate ; i ++) {
2716: 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);
2717:
2718: }
2719: }
2720: }
2721:
2722: /* CV preval stat */
2723: for (k1=1; k1<= m ; k1 ++) {
2724: for (cpt=1; cpt<nlstate ; cpt ++) {
2725: k=3;
2726: fprintf(ficgp,"\nset out \"p%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);
2727: 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/($%d",ageminpar,agemaxpar,fileres,k1,k+cpt+1,k+1);
2728:
2729: for (i=1; i< nlstate ; i ++)
2730: fprintf(ficgp,"+$%d",k+i+1);
2731: fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);
2732:
2733: l=3+(nlstate+ndeath)*cpt;
2734: fprintf(ficgp,",\"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",fileres,k1,l+cpt+1,l+1);
2735: for (i=1; i< nlstate ; i ++) {
2736: l=3+(nlstate+ndeath)*cpt;
2737: fprintf(ficgp,"+$%d",l+i+1);
2738: }
2739: fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);
2740: }
2741: }
2742:
2743: /* proba elementaires */
2744: for(i=1,jk=1; i <=nlstate; i++){
2745: for(k=1; k <=(nlstate+ndeath); k++){
2746: if (k != i) {
2747: for(j=1; j <=ncovmodel; j++){
2748: fprintf(ficgp,"p%d=%f ",jk,p[jk]);
2749: jk++;
2750: fprintf(ficgp,"\n");
2751: }
2752: }
2753: }
2754: }
2755:
2756: for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/
2757: for(jk=1; jk <=m; jk++) {
2758: fprintf(ficgp,"\nset out \"pe%s%d%d.png\" \n",strtok(optionfile, "."),jk,ng);
2759: if (ng==2)
2760: fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
2761: else
2762: fprintf(ficgp,"\nset title \"Probability\"\n");
2763: fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65\nset log y\nplot [%.f:%.f] ",ageminpar,agemaxpar);
2764: i=1;
2765: for(k2=1; k2<=nlstate; k2++) {
2766: k3=i;
2767: for(k=1; k<=(nlstate+ndeath); k++) {
2768: if (k != k2){
2769: if(ng==2)
2770: fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);
2771: else
2772: fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
2773: ij=1;
2774: for(j=3; j <=ncovmodel; j++) {
2775: if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
2776: fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
2777: ij++;
2778: }
2779: else
2780: fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
2781: }
2782: fprintf(ficgp,")/(1");
2783:
2784: for(k1=1; k1 <=nlstate; k1++){
2785: fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);
2786: ij=1;
2787: for(j=3; j <=ncovmodel; j++){
2788: if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
2789: fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
2790: ij++;
2791: }
2792: else
2793: fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
2794: }
2795: fprintf(ficgp,")");
2796: }
2797: fprintf(ficgp,") t \"p%d%d\" ", k2,k);
2798: if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");
2799: i=i+ncovmodel;
2800: }
2801: } /* end k */
2802: } /* end k2 */
2803: } /* end jk */
2804: } /* end ng */
2805: fclose(ficgp);
2806: } /* end gnuplot */
2807:
2808:
2809: /*************** Moving average **************/
1.54 brouard 2810: int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav){
1.53 brouard 2811:
2812: int i, cpt, cptcod;
1.58 lievre 2813: int modcovmax =1;
1.54 brouard 2814: int mobilavrange, mob;
1.53 brouard 2815: double age;
1.58 lievre 2816:
2817: modcovmax=2*cptcoveff;/* Max number of modalities. We suppose
2818: a covariate has 2 modalities */
2819: if (cptcovn<1) modcovmax=1; /* At least 1 pass */
2820:
1.54 brouard 2821: if(mobilav==1||mobilav ==3 ||mobilav==5 ||mobilav== 7){
2822: if(mobilav==1) mobilavrange=5; /* default */
2823: else mobilavrange=mobilav;
2824: for (age=bage; age<=fage; age++)
2825: for (i=1; i<=nlstate;i++)
1.58 lievre 2826: for (cptcod=1;cptcod<=modcovmax;cptcod++)
1.54 brouard 2827: mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
2828: /* We keep the original values on the extreme ages bage, fage and for
2829: fage+1 and bage-1 we use a 3 terms moving average; for fage+2 bage+2
2830: we use a 5 terms etc. until the borders are no more concerned.
2831: */
2832: for (mob=3;mob <=mobilavrange;mob=mob+2){
2833: for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){
2834: for (i=1; i<=nlstate;i++){
1.58 lievre 2835: for (cptcod=1;cptcod<=modcovmax;cptcod++){
1.54 brouard 2836: mobaverage[(int)age][i][cptcod] =probs[(int)age][i][cptcod];
2837: for (cpt=1;cpt<=(mob-1)/2;cpt++){
2838: mobaverage[(int)age][i][cptcod] +=probs[(int)age-cpt][i][cptcod];
2839: mobaverage[(int)age][i][cptcod] +=probs[(int)age+cpt][i][cptcod];
2840: }
2841: mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/mob;
2842: }
1.53 brouard 2843: }
1.54 brouard 2844: }/* end age */
2845: }/* end mob */
2846: }else return -1;
2847: return 0;
2848: }/* End movingaverage */
1.53 brouard 2849:
2850:
2851: /************** Forecasting ******************/
2852: 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){
2853:
2854: int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;
2855: int *popage;
2856: double calagedate, agelim, kk1, kk2, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
2857: double *popeffectif,*popcount;
2858: double ***p3mat;
1.55 lievre 2859: double ***mobaverage;
1.53 brouard 2860: char fileresf[FILENAMELENGTH];
2861:
2862: agelim=AGESUP;
1.58 lievre 2863: calagedate=(anproj1+mproj1/12.+jproj1/365.-dateintmean)*YEARM;
1.53 brouard 2864:
2865: prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);
2866:
2867:
2868: strcpy(fileresf,"f");
2869: strcat(fileresf,fileres);
2870: if((ficresf=fopen(fileresf,"w"))==NULL) {
2871: printf("Problem with forecast resultfile: %s\n", fileresf);
2872: fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);
2873: }
2874: printf("Computing forecasting: result on file '%s' \n", fileresf);
2875: fprintf(ficlog,"Computing forecasting: result on file '%s' \n", fileresf);
2876:
2877: if (cptcoveff==0) ncodemax[cptcoveff]=1;
2878:
1.54 brouard 2879: if (mobilav!=0) {
1.53 brouard 2880: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
1.54 brouard 2881: if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
2882: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
2883: printf(" Error in movingaverage mobilav=%d\n",mobilav);
2884: }
1.53 brouard 2885: }
2886:
2887: stepsize=(int) (stepm+YEARM-1)/YEARM;
2888: if (stepm<=12) stepsize=1;
2889:
2890: agelim=AGESUP;
2891:
2892: hstepm=1;
2893: hstepm=hstepm/stepm;
2894: yp1=modf(dateintmean,&yp);
2895: anprojmean=yp;
2896: yp2=modf((yp1*12),&yp);
2897: mprojmean=yp;
2898: yp1=modf((yp2*30.5),&yp);
2899: jprojmean=yp;
2900: if(jprojmean==0) jprojmean=1;
2901: if(mprojmean==0) jprojmean=1;
2902:
2903: fprintf(ficresf,"# Estimated date of observed prevalence: %.lf/%.lf/%.lf ",jprojmean,mprojmean,anprojmean);
2904:
2905: for(cptcov=1;cptcov<=i2;cptcov++){
2906: for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
2907: k=k+1;
2908: fprintf(ficresf,"\n#******");
2909: for(j=1;j<=cptcoveff;j++) {
2910: fprintf(ficresf," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
2911: }
2912: fprintf(ficresf,"******\n");
2913: fprintf(ficresf,"# StartingAge FinalAge");
2914: for(j=1; j<=nlstate+ndeath;j++) fprintf(ficresf," P.%d",j);
2915:
2916:
2917: for (cpt=0; cpt<=(anproj2-anproj1);cpt++) {
2918: fprintf(ficresf,"\n");
2919: fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+cpt);
2920:
2921: for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){
2922: nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);
2923: nhstepm = nhstepm/hstepm;
2924:
2925: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
2926: oldm=oldms;savm=savms;
2927: hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
2928:
2929: for (h=0; h<=nhstepm; h++){
2930: if (h==(int) (calagedate+YEARM*cpt)) {
2931: fprintf(ficresf,"\n %.f %.f ",anproj1+cpt,agedeb+h*hstepm/YEARM*stepm);
2932: }
2933: for(j=1; j<=nlstate+ndeath;j++) {
2934: kk1=0.;kk2=0;
2935: for(i=1; i<=nlstate;i++) {
2936: if (mobilav==1)
2937: kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];
2938: else {
2939: kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];
2940: }
2941:
2942: }
2943: if (h==(int)(calagedate+12*cpt)){
2944: fprintf(ficresf," %.3f", kk1);
2945:
2946: }
2947: }
2948: }
2949: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
2950: }
2951: }
2952: }
2953: }
2954:
1.54 brouard 2955: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
1.53 brouard 2956:
2957: fclose(ficresf);
2958: }
2959: /************** Forecasting ******************/
2960: 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){
2961:
2962: int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;
2963: int *popage;
1.59 ! brouard 2964: double calagedate, agelim, kk1, kk2;
1.53 brouard 2965: double *popeffectif,*popcount;
2966: double ***p3mat,***tabpop,***tabpopprev;
1.55 lievre 2967: double ***mobaverage;
1.53 brouard 2968: char filerespop[FILENAMELENGTH];
2969:
2970: tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
2971: tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
2972: agelim=AGESUP;
2973: calagedate=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;
2974:
2975: prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);
2976:
2977:
2978: strcpy(filerespop,"pop");
2979: strcat(filerespop,fileres);
2980: if((ficrespop=fopen(filerespop,"w"))==NULL) {
2981: printf("Problem with forecast resultfile: %s\n", filerespop);
2982: fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop);
2983: }
2984: printf("Computing forecasting: result on file '%s' \n", filerespop);
2985: fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop);
2986:
2987: if (cptcoveff==0) ncodemax[cptcoveff]=1;
2988:
1.54 brouard 2989: if (mobilav!=0) {
1.53 brouard 2990: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
1.54 brouard 2991: if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
2992: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
2993: printf(" Error in movingaverage mobilav=%d\n",mobilav);
2994: }
1.53 brouard 2995: }
2996:
2997: stepsize=(int) (stepm+YEARM-1)/YEARM;
2998: if (stepm<=12) stepsize=1;
2999:
3000: agelim=AGESUP;
3001:
3002: hstepm=1;
3003: hstepm=hstepm/stepm;
3004:
3005: if (popforecast==1) {
3006: if((ficpop=fopen(popfile,"r"))==NULL) {
3007: printf("Problem with population file : %s\n",popfile);exit(0);
3008: fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0);
3009: }
3010: popage=ivector(0,AGESUP);
3011: popeffectif=vector(0,AGESUP);
3012: popcount=vector(0,AGESUP);
3013:
3014: i=1;
3015: while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;
3016:
3017: imx=i;
3018: for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];
3019: }
3020:
3021: for(cptcov=1;cptcov<=i2;cptcov++){
3022: for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
3023: k=k+1;
3024: fprintf(ficrespop,"\n#******");
3025: for(j=1;j<=cptcoveff;j++) {
3026: fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
3027: }
3028: fprintf(ficrespop,"******\n");
3029: fprintf(ficrespop,"# Age");
3030: for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);
3031: if (popforecast==1) fprintf(ficrespop," [Population]");
3032:
3033: for (cpt=0; cpt<=0;cpt++) {
3034: fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);
3035:
3036: for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){
3037: nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);
3038: nhstepm = nhstepm/hstepm;
3039:
3040: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3041: oldm=oldms;savm=savms;
3042: hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
3043:
3044: for (h=0; h<=nhstepm; h++){
3045: if (h==(int) (calagedate+YEARM*cpt)) {
3046: fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
3047: }
3048: for(j=1; j<=nlstate+ndeath;j++) {
3049: kk1=0.;kk2=0;
3050: for(i=1; i<=nlstate;i++) {
3051: if (mobilav==1)
3052: kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];
3053: else {
3054: kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];
3055: }
3056: }
3057: if (h==(int)(calagedate+12*cpt)){
3058: tabpop[(int)(agedeb)][j][cptcod]=kk1;
3059: /*fprintf(ficrespop," %.3f", kk1);
3060: if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/
3061: }
3062: }
3063: for(i=1; i<=nlstate;i++){
3064: kk1=0.;
3065: for(j=1; j<=nlstate;j++){
3066: kk1= kk1+tabpop[(int)(agedeb)][j][cptcod];
3067: }
3068: tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedate+12*cpt)*hstepm/YEARM*stepm-1)];
3069: }
3070:
3071: if (h==(int)(calagedate+12*cpt)) for(j=1; j<=nlstate;j++)
3072: fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);
3073: }
3074: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3075: }
3076: }
3077:
3078: /******/
3079:
3080: for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) {
3081: fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);
3082: for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){
3083: nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);
3084: nhstepm = nhstepm/hstepm;
3085:
3086: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3087: oldm=oldms;savm=savms;
3088: hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
3089: for (h=0; h<=nhstepm; h++){
3090: if (h==(int) (calagedate+YEARM*cpt)) {
3091: fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
3092: }
3093: for(j=1; j<=nlstate+ndeath;j++) {
3094: kk1=0.;kk2=0;
3095: for(i=1; i<=nlstate;i++) {
3096: kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];
3097: }
3098: if (h==(int)(calagedate+12*cpt)) fprintf(ficresf," %15.2f", kk1);
3099: }
3100: }
3101: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3102: }
3103: }
3104: }
3105: }
3106:
1.54 brouard 3107: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
1.53 brouard 3108:
3109: if (popforecast==1) {
3110: free_ivector(popage,0,AGESUP);
3111: free_vector(popeffectif,0,AGESUP);
3112: free_vector(popcount,0,AGESUP);
3113: }
3114: free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
3115: free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
3116: fclose(ficrespop);
3117: }
3118:
3119: /***********************************************/
3120: /**************** Main Program *****************/
3121: /***********************************************/
3122:
3123: int main(int argc, char *argv[])
3124: {
3125:
3126: int i,j, k, n=MAXN,iter,m,size,cptcode, cptcod;
3127: double agedeb, agefin,hf;
3128: double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;
3129:
3130: double fret;
3131: double **xi,tmp,delta;
3132:
3133: double dum; /* Dummy variable */
3134: double ***p3mat;
3135: double ***mobaverage;
3136: int *indx;
3137: char line[MAXLINE], linepar[MAXLINE];
3138: char path[80],pathc[80],pathcd[80],pathtot[80],model[80];
3139: int firstobs=1, lastobs=10;
3140: int sdeb, sfin; /* Status at beginning and end */
3141: int c, h , cpt,l;
3142: int ju,jl, mi;
3143: int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;
1.59 ! brouard 3144: int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,*tab;
1.53 brouard 3145: int mobilav=0,popforecast=0;
3146: int hstepm, nhstepm;
3147: double jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,jpyram, mpyram,anpyram,jpyram1, mpyram1,anpyram1, calagedate;
3148:
3149: double bage, fage, age, agelim, agebase;
3150: double ftolpl=FTOL;
3151: double **prlim;
3152: double *severity;
3153: double ***param; /* Matrix of parameters */
3154: double *p;
3155: double **matcov; /* Matrix of covariance */
3156: double ***delti3; /* Scale */
3157: double *delti; /* Scale */
3158: double ***eij, ***vareij;
3159: double **varpl; /* Variances of prevalence limits by age */
3160: double *epj, vepp;
3161: double kk1, kk2;
3162: double dateprev1, dateprev2,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2;
1.59 ! brouard 3163: /*int *movingaverage; */
1.53 brouard 3164:
3165: char *alph[]={"a","a","b","c","d","e"}, str[4];
3166:
3167:
3168: char z[1]="c", occ;
3169: #include <sys/time.h>
3170: #include <time.h>
3171: char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];
3172:
3173: /* long total_usecs;
1.59 ! brouard 3174: struct timeval start_time, end_time;
1.53 brouard 3175:
1.59 ! brouard 3176: gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */
1.53 brouard 3177: getcwd(pathcd, size);
3178:
3179: printf("\n%s",version);
3180: if(argc <=1){
3181: printf("\nEnter the parameter file name: ");
3182: scanf("%s",pathtot);
3183: }
3184: else{
3185: strcpy(pathtot,argv[1]);
3186: }
3187: /*if(getcwd(pathcd, 80)!= NULL)printf ("Error pathcd\n");*/
3188: /*cygwin_split_path(pathtot,path,optionfile);
3189: printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/
3190: /* cutv(path,optionfile,pathtot,'\\');*/
3191:
3192: split(pathtot,path,optionfile,optionfilext,optionfilefiname);
1.59 ! brouard 3193: printf("pathtot=%s, path=%s, optionfile=%s optionfilext=%s optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
1.53 brouard 3194: chdir(path);
3195: replace(pathc,path);
3196:
1.59 ! brouard 3197: /*-------- arguments in the command line --------*/
1.53 brouard 3198:
3199: /* Log file */
3200: strcat(filelog, optionfilefiname);
3201: strcat(filelog,".log"); /* */
3202: if((ficlog=fopen(filelog,"w"))==NULL) {
3203: printf("Problem with logfile %s\n",filelog);
3204: goto end;
3205: }
3206: fprintf(ficlog,"Log filename:%s\n",filelog);
3207: fprintf(ficlog,"\n%s",version);
3208: fprintf(ficlog,"\nEnter the parameter file name: ");
3209: fprintf(ficlog,"pathtot=%s, path=%s, optionfile=%s optionfilext=%s optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
3210: fflush(ficlog);
3211:
3212: /* */
3213: strcpy(fileres,"r");
3214: strcat(fileres, optionfilefiname);
3215: strcat(fileres,".txt"); /* Other files have txt extension */
3216:
3217: /*---------arguments file --------*/
3218:
3219: if((ficpar=fopen(optionfile,"r"))==NULL) {
3220: printf("Problem with optionfile %s\n",optionfile);
3221: fprintf(ficlog,"Problem with optionfile %s\n",optionfile);
3222: goto end;
3223: }
3224:
3225: strcpy(filereso,"o");
3226: strcat(filereso,fileres);
3227: if((ficparo=fopen(filereso,"w"))==NULL) {
3228: printf("Problem with Output resultfile: %s\n", filereso);
3229: fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso);
3230: goto end;
3231: }
3232:
3233: /* Reads comments: lines beginning with '#' */
3234: while((c=getc(ficpar))=='#' && c!= EOF){
3235: ungetc(c,ficpar);
3236: fgets(line, MAXLINE, ficpar);
3237: puts(line);
3238: fputs(line,ficparo);
3239: }
3240: ungetc(c,ficpar);
3241:
3242: 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);
3243: 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);
3244: 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);
1.59 ! brouard 3245: while((c=getc(ficpar))=='#' && c!= EOF){
1.53 brouard 3246: ungetc(c,ficpar);
3247: fgets(line, MAXLINE, ficpar);
3248: puts(line);
3249: fputs(line,ficparo);
3250: }
3251: ungetc(c,ficpar);
3252:
3253:
3254: covar=matrix(0,NCOVMAX,1,n);
1.58 lievre 3255: cptcovn=0; /*Number of covariates, i.e. number of '+' in model statement*/
1.53 brouard 3256: if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;
3257:
1.58 lievre 3258: ncovmodel=2+cptcovn; /*Number of variables = cptcovn + intercept + age */
1.53 brouard 3259: nvar=ncovmodel-1; /* Suppressing age as a basic covariate */
3260:
3261: /* Read guess parameters */
3262: /* Reads comments: lines beginning with '#' */
3263: while((c=getc(ficpar))=='#' && c!= EOF){
3264: ungetc(c,ficpar);
3265: fgets(line, MAXLINE, ficpar);
3266: puts(line);
3267: fputs(line,ficparo);
3268: }
3269: ungetc(c,ficpar);
3270:
3271: param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
1.59 ! brouard 3272: for(i=1; i <=nlstate; i++)
1.53 brouard 3273: for(j=1; j <=nlstate+ndeath-1; j++){
3274: fscanf(ficpar,"%1d%1d",&i1,&j1);
3275: fprintf(ficparo,"%1d%1d",i1,j1);
3276: if(mle==1)
3277: printf("%1d%1d",i,j);
3278: fprintf(ficlog,"%1d%1d",i,j);
3279: for(k=1; k<=ncovmodel;k++){
3280: fscanf(ficpar," %lf",¶m[i][j][k]);
3281: if(mle==1){
3282: printf(" %lf",param[i][j][k]);
3283: fprintf(ficlog," %lf",param[i][j][k]);
3284: }
3285: else
3286: fprintf(ficlog," %lf",param[i][j][k]);
3287: fprintf(ficparo," %lf",param[i][j][k]);
3288: }
3289: fscanf(ficpar,"\n");
3290: if(mle==1)
3291: printf("\n");
3292: fprintf(ficlog,"\n");
3293: fprintf(ficparo,"\n");
3294: }
3295:
1.59 ! brouard 3296: npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/
1.53 brouard 3297:
3298: p=param[1][1];
3299:
3300: /* Reads comments: lines beginning with '#' */
3301: while((c=getc(ficpar))=='#' && c!= EOF){
3302: ungetc(c,ficpar);
3303: fgets(line, MAXLINE, ficpar);
3304: puts(line);
3305: fputs(line,ficparo);
3306: }
3307: ungetc(c,ficpar);
3308:
3309: delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
3310: delti=vector(1,npar); /* Scale of each paramater (output from hesscov) */
3311: for(i=1; i <=nlstate; i++){
3312: for(j=1; j <=nlstate+ndeath-1; j++){
3313: fscanf(ficpar,"%1d%1d",&i1,&j1);
3314: printf("%1d%1d",i,j);
3315: fprintf(ficparo,"%1d%1d",i1,j1);
3316: for(k=1; k<=ncovmodel;k++){
3317: fscanf(ficpar,"%le",&delti3[i][j][k]);
3318: printf(" %le",delti3[i][j][k]);
3319: fprintf(ficparo," %le",delti3[i][j][k]);
3320: }
3321: fscanf(ficpar,"\n");
3322: printf("\n");
3323: fprintf(ficparo,"\n");
3324: }
3325: }
3326: delti=delti3[1][1];
3327:
3328: /* Reads comments: lines beginning with '#' */
3329: while((c=getc(ficpar))=='#' && c!= EOF){
3330: ungetc(c,ficpar);
3331: fgets(line, MAXLINE, ficpar);
3332: puts(line);
3333: fputs(line,ficparo);
3334: }
3335: ungetc(c,ficpar);
3336:
3337: matcov=matrix(1,npar,1,npar);
3338: for(i=1; i <=npar; i++){
3339: fscanf(ficpar,"%s",&str);
3340: if(mle==1)
3341: printf("%s",str);
3342: fprintf(ficlog,"%s",str);
3343: fprintf(ficparo,"%s",str);
3344: for(j=1; j <=i; j++){
3345: fscanf(ficpar," %le",&matcov[i][j]);
3346: if(mle==1){
3347: printf(" %.5le",matcov[i][j]);
3348: fprintf(ficlog," %.5le",matcov[i][j]);
3349: }
3350: else
3351: fprintf(ficlog," %.5le",matcov[i][j]);
3352: fprintf(ficparo," %.5le",matcov[i][j]);
3353: }
3354: fscanf(ficpar,"\n");
3355: if(mle==1)
3356: printf("\n");
3357: fprintf(ficlog,"\n");
3358: fprintf(ficparo,"\n");
3359: }
3360: for(i=1; i <=npar; i++)
3361: for(j=i+1;j<=npar;j++)
3362: matcov[i][j]=matcov[j][i];
3363:
3364: if(mle==1)
3365: printf("\n");
3366: fprintf(ficlog,"\n");
3367:
3368:
1.59 ! brouard 3369: /*-------- Rewriting paramater file ----------*/
! 3370: strcpy(rfileres,"r"); /* "Rparameterfile */
! 3371: strcat(rfileres,optionfilefiname); /* Parameter file first name*/
! 3372: strcat(rfileres,"."); /* */
! 3373: strcat(rfileres,optionfilext); /* Other files have txt extension */
! 3374: if((ficres =fopen(rfileres,"w"))==NULL) {
! 3375: printf("Problem writing new parameter file: %s\n", fileres);goto end;
! 3376: fprintf(ficlog,"Problem writing new parameter file: %s\n", fileres);goto end;
! 3377: }
! 3378: fprintf(ficres,"#%s\n",version);
1.53 brouard 3379:
1.59 ! brouard 3380: /*-------- data file ----------*/
! 3381: if((fic=fopen(datafile,"r"))==NULL) {
! 3382: printf("Problem with datafile: %s\n", datafile);goto end;
! 3383: fprintf(ficlog,"Problem with datafile: %s\n", datafile);goto end;
! 3384: }
! 3385:
! 3386: n= lastobs;
! 3387: severity = vector(1,maxwav);
! 3388: outcome=imatrix(1,maxwav+1,1,n);
! 3389: num=ivector(1,n);
! 3390: moisnais=vector(1,n);
! 3391: annais=vector(1,n);
! 3392: moisdc=vector(1,n);
! 3393: andc=vector(1,n);
! 3394: agedc=vector(1,n);
! 3395: cod=ivector(1,n);
! 3396: weight=vector(1,n);
! 3397: for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */
! 3398: mint=matrix(1,maxwav,1,n);
! 3399: anint=matrix(1,maxwav,1,n);
! 3400: s=imatrix(1,maxwav+1,1,n);
! 3401: tab=ivector(1,NCOVMAX);
! 3402: ncodemax=ivector(1,8);
! 3403:
! 3404: i=1;
! 3405: while (fgets(line, MAXLINE, fic) != NULL) {
! 3406: if ((i >= firstobs) && (i <=lastobs)) {
1.53 brouard 3407:
1.59 ! brouard 3408: for (j=maxwav;j>=1;j--){
! 3409: cutv(stra, strb,line,' '); s[j][i]=atoi(strb);
! 3410: strcpy(line,stra);
! 3411: cutv(stra, strb,line,'/'); anint[j][i]=(double)(atoi(strb)); strcpy(line,stra);
! 3412: cutv(stra, strb,line,' '); mint[j][i]=(double)(atoi(strb)); strcpy(line,stra);
! 3413: }
1.53 brouard 3414:
1.59 ! brouard 3415: cutv(stra, strb,line,'/'); andc[i]=(double)(atoi(strb)); strcpy(line,stra);
! 3416: cutv(stra, strb,line,' '); moisdc[i]=(double)(atoi(strb)); strcpy(line,stra);
1.53 brouard 3417:
1.59 ! brouard 3418: cutv(stra, strb,line,'/'); annais[i]=(double)(atoi(strb)); strcpy(line,stra);
! 3419: cutv(stra, strb,line,' '); moisnais[i]=(double)(atoi(strb)); strcpy(line,stra);
1.53 brouard 3420:
1.59 ! brouard 3421: cutv(stra, strb,line,' '); weight[i]=(double)(atoi(strb)); strcpy(line,stra);
! 3422: for (j=ncovcol;j>=1;j--){
! 3423: cutv(stra, strb,line,' '); covar[j][i]=(double)(atoi(strb)); strcpy(line,stra);
! 3424: }
! 3425: num[i]=atol(stra);
1.53 brouard 3426:
1.59 ! brouard 3427: /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){
! 3428: 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;}*/
1.53 brouard 3429:
1.59 ! brouard 3430: i=i+1;
! 3431: }
! 3432: }
! 3433: /* printf("ii=%d", ij);
! 3434: scanf("%d",i);*/
1.53 brouard 3435: imx=i-1; /* Number of individuals */
3436:
3437: /* for (i=1; i<=imx; i++){
3438: if ((s[1][i]==3) && (s[2][i]==2)) s[2][i]=3;
3439: if ((s[2][i]==3) && (s[3][i]==2)) s[3][i]=3;
3440: if ((s[3][i]==3) && (s[4][i]==2)) s[4][i]=3;
3441: }*/
3442: /* for (i=1; i<=imx; i++){
3443: if (s[4][i]==9) s[4][i]=-1;
3444: 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]));}*/
3445:
3446:
3447: /* Calculation of the number of parameter from char model*/
3448: Tvar=ivector(1,15); /* stores the number n of the covariates in Vm+Vn at 1 and m at 2 */
3449: Tprod=ivector(1,15);
3450: Tvaraff=ivector(1,15);
3451: Tvard=imatrix(1,15,1,2);
3452: Tage=ivector(1,15);
3453:
1.58 lievre 3454: if (strlen(model) >1){ /* If there is at least 1 covariate */
1.53 brouard 3455: j=0, j1=0, k1=1, k2=1;
1.58 lievre 3456: j=nbocc(model,'+'); /* j=Number of '+' */
3457: j1=nbocc(model,'*'); /* j1=Number of '*' */
3458: cptcovn=j+1;
3459: cptcovprod=j1; /*Number of products */
1.53 brouard 3460:
3461: strcpy(modelsav,model);
3462: if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){
3463: printf("Error. Non available option model=%s ",model);
3464: fprintf(ficlog,"Error. Non available option model=%s ",model);
3465: goto end;
3466: }
3467:
1.59 ! brouard 3468: /* This loop fills the array Tvar from the string 'model'.*/
1.58 lievre 3469:
1.53 brouard 3470: for(i=(j+1); i>=1;i--){
3471: cutv(stra,strb,modelsav,'+'); /* keeps in strb after the last + */
1.59 ! brouard 3472: if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyzes it */
1.53 brouard 3473: /* printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/
3474: /*scanf("%d",i);*/
3475: if (strchr(strb,'*')) { /* Model includes a product */
3476: cutv(strd,strc,strb,'*'); /* strd*strc Vm*Vn (if not *age)*/
3477: if (strcmp(strc,"age")==0) { /* Vn*age */
3478: cptcovprod--;
3479: cutv(strb,stre,strd,'V');
3480: Tvar[i]=atoi(stre); /* computes n in Vn and stores in Tvar*/
3481: cptcovage++;
3482: Tage[cptcovage]=i;
3483: /*printf("stre=%s ", stre);*/
3484: }
3485: else if (strcmp(strd,"age")==0) { /* or age*Vn */
3486: cptcovprod--;
3487: cutv(strb,stre,strc,'V');
3488: Tvar[i]=atoi(stre);
3489: cptcovage++;
3490: Tage[cptcovage]=i;
3491: }
3492: else { /* Age is not in the model */
3493: cutv(strb,stre,strc,'V'); /* strc= Vn, stre is n*/
3494: Tvar[i]=ncovcol+k1;
3495: cutv(strb,strc,strd,'V'); /* strd was Vm, strc is m */
3496: Tprod[k1]=i;
3497: Tvard[k1][1]=atoi(strc); /* m*/
3498: Tvard[k1][2]=atoi(stre); /* n */
3499: Tvar[cptcovn+k2]=Tvard[k1][1];
3500: Tvar[cptcovn+k2+1]=Tvard[k1][2];
3501: for (k=1; k<=lastobs;k++)
3502: covar[ncovcol+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];
3503: k1++;
3504: k2=k2+2;
3505: }
3506: }
3507: else { /* no more sum */
3508: /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/
3509: /* scanf("%d",i);*/
3510: cutv(strd,strc,strb,'V');
3511: Tvar[i]=atoi(strc);
3512: }
3513: strcpy(modelsav,stra);
3514: /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);
3515: scanf("%d",i);*/
3516: } /* end of loop + */
3517: } /* end model */
3518:
1.58 lievre 3519: /*The number n of Vn is stored in Tvar. cptcovage =number of age covariate. Tage gives the position of age. cptcovprod= number of products.
3520: If model=V1+V1*age then Tvar[1]=1 Tvar[2]=1 cptcovage=1 Tage[1]=2 cptcovprod=0*/
3521:
1.53 brouard 3522: /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);
3523: printf("cptcovprod=%d ", cptcovprod);
3524: fprintf(ficlog,"cptcovprod=%d ", cptcovprod);
1.58 lievre 3525:
3526: scanf("%d ",i);
3527: fclose(fic);*/
1.53 brouard 3528:
3529: /* if(mle==1){*/
1.59 ! brouard 3530: if (weightopt != 1) { /* Maximisation without weights*/
! 3531: for(i=1;i<=n;i++) weight[i]=1.0;
! 3532: }
1.53 brouard 3533: /*-calculation of age at interview from date of interview and age at death -*/
1.59 ! brouard 3534: agev=matrix(1,maxwav,1,imx);
1.53 brouard 3535:
1.59 ! brouard 3536: for (i=1; i<=imx; i++) {
! 3537: for(m=2; (m<= maxwav); m++) {
! 3538: if ((mint[m][i]== 99) && (s[m][i] <= nlstate)){
! 3539: anint[m][i]=9999;
! 3540: s[m][i]=-1;
! 3541: }
! 3542: if(moisdc[i]==99 && andc[i]==9999 & s[m][i]>nlstate) s[m][i]=-1;
1.53 brouard 3543: }
1.59 ! brouard 3544: }
1.53 brouard 3545:
1.59 ! brouard 3546: for (i=1; i<=imx; i++) {
! 3547: agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);
! 3548: for(m=1; (m<= maxwav); m++){
! 3549: if(s[m][i] >0){
! 3550: if (s[m][i] >= nlstate+1) {
! 3551: if(agedc[i]>0)
! 3552: if(moisdc[i]!=99 && andc[i]!=9999)
! 3553: agev[m][i]=agedc[i];
! 3554: /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/
! 3555: else {
1.53 brouard 3556: if (andc[i]!=9999){
1.59 ! brouard 3557: printf("Warning negative age at death: %d line:%d\n",num[i],i);
! 3558: fprintf(ficlog,"Warning negative age at death: %d line:%d\n",num[i],i);
! 3559: agev[m][i]=-1;
1.53 brouard 3560: }
3561: }
1.59 ! brouard 3562: }
! 3563: else if(s[m][i] !=9){ /* Should no more exist */
! 3564: agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);
! 3565: if(mint[m][i]==99 || anint[m][i]==9999)
! 3566: agev[m][i]=1;
! 3567: else if(agev[m][i] <agemin){
! 3568: agemin=agev[m][i];
! 3569: /*printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], agemin);*/
1.53 brouard 3570: }
1.59 ! brouard 3571: else if(agev[m][i] >agemax){
! 3572: agemax=agev[m][i];
! 3573: /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/
1.53 brouard 3574: }
1.59 ! brouard 3575: /*agev[m][i]=anint[m][i]-annais[i];*/
! 3576: /* agev[m][i] = age[i]+2*m;*/
1.53 brouard 3577: }
1.59 ! brouard 3578: else { /* =9 */
1.53 brouard 3579: agev[m][i]=1;
1.59 ! brouard 3580: s[m][i]=-1;
! 3581: }
1.53 brouard 3582: }
1.59 ! brouard 3583: else /*= 0 Unknown */
! 3584: agev[m][i]=1;
! 3585: }
1.53 brouard 3586:
1.59 ! brouard 3587: }
! 3588: for (i=1; i<=imx; i++) {
! 3589: for(m=1; (m<= maxwav); m++){
! 3590: if (s[m][i] > (nlstate+ndeath)) {
! 3591: 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);
! 3592: 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);
! 3593: goto end;
1.53 brouard 3594: }
3595: }
1.59 ! brouard 3596: }
1.53 brouard 3597:
1.59 ! brouard 3598: printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);
! 3599: fprintf(ficlog,"Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);
! 3600:
! 3601: free_vector(severity,1,maxwav);
! 3602: free_imatrix(outcome,1,maxwav+1,1,n);
! 3603: free_vector(moisnais,1,n);
! 3604: free_vector(annais,1,n);
! 3605: /* free_matrix(mint,1,maxwav,1,n);
! 3606: free_matrix(anint,1,maxwav,1,n);*/
! 3607: free_vector(moisdc,1,n);
! 3608: free_vector(andc,1,n);
1.53 brouard 3609:
3610:
1.59 ! brouard 3611: wav=ivector(1,imx);
! 3612: dh=imatrix(1,lastpass-firstpass+1,1,imx);
! 3613: bh=imatrix(1,lastpass-firstpass+1,1,imx);
! 3614: mw=imatrix(1,lastpass-firstpass+1,1,imx);
1.53 brouard 3615:
1.59 ! brouard 3616: /* Concatenates waves */
! 3617: concatwav(wav, dh, bh, mw, s, agedc, agev, firstpass, lastpass, imx, nlstate, stepm);
1.53 brouard 3618:
1.59 ! brouard 3619: /* Routine tricode is to calculate cptcoveff (real number of unique covariates) and to associate covariable number and modality */
1.53 brouard 3620:
1.59 ! brouard 3621: Tcode=ivector(1,100);
! 3622: nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);
! 3623: ncodemax[1]=1;
! 3624: if (cptcovn > 0) tricode(Tvar,nbcode,imx);
1.53 brouard 3625:
1.59 ! brouard 3626: codtab=imatrix(1,100,1,10); /* Cross tabulation to get the order of
! 3627: the estimations*/
! 3628: h=0;
! 3629: m=pow(2,cptcoveff);
1.53 brouard 3630:
1.59 ! brouard 3631: for(k=1;k<=cptcoveff; k++){
! 3632: for(i=1; i <=(m/pow(2,k));i++){
! 3633: for(j=1; j <= ncodemax[k]; j++){
! 3634: for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){
! 3635: h++;
! 3636: if (h>m) h=1;codtab[h][k]=j;codtab[h][Tvar[k]]=j;
! 3637: /* printf("h=%d k=%d j=%d codtab[h][k]=%d tvar[k]=%d \n",h, k,j,codtab[h][k],Tvar[k]);*/
! 3638: }
! 3639: }
! 3640: }
! 3641: }
! 3642: /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]);
! 3643: codtab[1][2]=1;codtab[2][2]=2; */
! 3644: /* for(i=1; i <=m ;i++){
! 3645: for(k=1; k <=cptcovn; k++){
! 3646: printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);
! 3647: }
! 3648: printf("\n");
1.53 brouard 3649: }
1.59 ! brouard 3650: scanf("%d",i);*/
1.53 brouard 3651:
1.59 ! brouard 3652: /* Calculates basic frequencies. Computes observed prevalence at single age
! 3653: and prints on file fileres'p'. */
1.53 brouard 3654:
3655:
3656:
1.59 ! brouard 3657: /* For Powell, parameters are in a vector p[] starting at p[1]
! 3658: so we point p on param[1][1] so that p[1] maps on param[1][1][1] */
! 3659: p=param[1][1]; /* *(*(*(param +1)+1)+0) */
1.53 brouard 3660:
1.59 ! brouard 3661: if(mle==1){
1.53 brouard 3662: mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);
1.59 ! brouard 3663: }
1.53 brouard 3664:
1.59 ! brouard 3665: /*--------- results files --------------*/
! 3666: 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);
1.53 brouard 3667:
3668:
1.59 ! brouard 3669: jk=1;
! 3670: fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
! 3671: printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
! 3672: fprintf(ficlog,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
! 3673: for(i=1,jk=1; i <=nlstate; i++){
! 3674: for(k=1; k <=(nlstate+ndeath); k++){
! 3675: if (k != i)
! 3676: {
! 3677: printf("%d%d ",i,k);
! 3678: fprintf(ficlog,"%d%d ",i,k);
! 3679: fprintf(ficres,"%1d%1d ",i,k);
! 3680: for(j=1; j <=ncovmodel; j++){
! 3681: printf("%f ",p[jk]);
! 3682: fprintf(ficlog,"%f ",p[jk]);
! 3683: fprintf(ficres,"%f ",p[jk]);
! 3684: jk++;
! 3685: }
! 3686: printf("\n");
! 3687: fprintf(ficlog,"\n");
! 3688: fprintf(ficres,"\n");
! 3689: }
! 3690: }
! 3691: }
! 3692: if(mle==1){
! 3693: /* Computing hessian and covariance matrix */
! 3694: ftolhess=ftol; /* Usually correct */
! 3695: hesscov(matcov, p, npar, delti, ftolhess, func);
! 3696: }
! 3697: fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");
! 3698: printf("# Scales (for hessian or gradient estimation)\n");
! 3699: fprintf(ficlog,"# Scales (for hessian or gradient estimation)\n");
! 3700: for(i=1,jk=1; i <=nlstate; i++){
! 3701: for(j=1; j <=nlstate+ndeath; j++){
! 3702: if (j!=i) {
! 3703: fprintf(ficres,"%1d%1d",i,j);
! 3704: printf("%1d%1d",i,j);
! 3705: fprintf(ficlog,"%1d%1d",i,j);
! 3706: for(k=1; k<=ncovmodel;k++){
! 3707: printf(" %.5e",delti[jk]);
! 3708: fprintf(ficlog," %.5e",delti[jk]);
! 3709: fprintf(ficres," %.5e",delti[jk]);
! 3710: jk++;
! 3711: }
! 3712: printf("\n");
! 3713: fprintf(ficlog,"\n");
! 3714: fprintf(ficres,"\n");
! 3715: }
! 3716: }
! 3717: }
1.53 brouard 3718:
1.59 ! brouard 3719: 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");
! 3720: if(mle==1)
! 3721: 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");
! 3722: 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");
! 3723: for(i=1,k=1;i<=npar;i++){
! 3724: /* if (k>nlstate) k=1;
! 3725: i1=(i-1)/(ncovmodel*nlstate)+1;
! 3726: fprintf(ficres,"%s%d%d",alph[k],i1,tab[i]);
! 3727: printf("%s%d%d",alph[k],i1,tab[i]);
! 3728: */
! 3729: fprintf(ficres,"%3d",i);
! 3730: if(mle==1)
! 3731: printf("%3d",i);
! 3732: fprintf(ficlog,"%3d",i);
! 3733: for(j=1; j<=i;j++){
! 3734: fprintf(ficres," %.5e",matcov[i][j]);
! 3735: if(mle==1)
! 3736: printf(" %.5e",matcov[i][j]);
! 3737: fprintf(ficlog," %.5e",matcov[i][j]);
! 3738: }
! 3739: fprintf(ficres,"\n");
! 3740: if(mle==1)
! 3741: printf("\n");
! 3742: fprintf(ficlog,"\n");
! 3743: k++;
! 3744: }
1.53 brouard 3745:
1.59 ! brouard 3746: while((c=getc(ficpar))=='#' && c!= EOF){
! 3747: ungetc(c,ficpar);
! 3748: fgets(line, MAXLINE, ficpar);
! 3749: puts(line);
! 3750: fputs(line,ficparo);
! 3751: }
! 3752: ungetc(c,ficpar);
! 3753:
! 3754: estepm=0;
! 3755: fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm);
! 3756: if (estepm==0 || estepm < stepm) estepm=stepm;
! 3757: if (fage <= 2) {
! 3758: bage = ageminpar;
! 3759: fage = agemaxpar;
! 3760: }
1.53 brouard 3761:
1.59 ! brouard 3762: fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");
! 3763: fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
! 3764: fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
1.53 brouard 3765:
1.59 ! brouard 3766: while((c=getc(ficpar))=='#' && c!= EOF){
! 3767: ungetc(c,ficpar);
! 3768: fgets(line, MAXLINE, ficpar);
! 3769: puts(line);
! 3770: fputs(line,ficparo);
! 3771: }
! 3772: ungetc(c,ficpar);
1.53 brouard 3773:
1.59 ! brouard 3774: 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);
! 3775: 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);
! 3776: 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);
1.53 brouard 3777:
1.59 ! brouard 3778: while((c=getc(ficpar))=='#' && c!= EOF){
! 3779: ungetc(c,ficpar);
! 3780: fgets(line, MAXLINE, ficpar);
! 3781: puts(line);
! 3782: fputs(line,ficparo);
! 3783: }
! 3784: ungetc(c,ficpar);
1.53 brouard 3785:
3786:
1.59 ! brouard 3787: dateprev1=anprev1+mprev1/12.+jprev1/365.;
! 3788: dateprev2=anprev2+mprev2/12.+jprev2/365.;
1.53 brouard 3789:
3790: fscanf(ficpar,"pop_based=%d\n",&popbased);
3791: fprintf(ficparo,"pop_based=%d\n",popbased);
3792: fprintf(ficres,"pop_based=%d\n",popbased);
3793:
3794: while((c=getc(ficpar))=='#' && c!= EOF){
3795: ungetc(c,ficpar);
3796: fgets(line, MAXLINE, ficpar);
3797: puts(line);
3798: fputs(line,ficparo);
3799: }
3800: ungetc(c,ficpar);
3801:
3802: fscanf(ficpar,"starting-proj-date=%lf/%lf/%lf final-proj-date=%lf/%lf/%lf\n",&jproj1,&mproj1,&anproj1,&jproj2,&mproj2,&anproj2);
1.59 ! brouard 3803: fprintf(ficparo,"starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf\n",jproj1,mproj1,anproj1,jproj2,mproj2,anproj2);
! 3804: fprintf(ficres,"starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf\n",jproj1,mproj1,anproj1,jproj2,mproj2,anproj2);
1.53 brouard 3805:
3806:
1.59 ! brouard 3807: while((c=getc(ficpar))=='#' && c!= EOF){
1.53 brouard 3808: ungetc(c,ficpar);
3809: fgets(line, MAXLINE, ficpar);
3810: puts(line);
3811: fputs(line,ficparo);
3812: }
3813: ungetc(c,ficpar);
3814:
3815: fscanf(ficpar,"popforecast=%d popfile=%s popfiledate=%lf/%lf/%lf last-popfiledate=%lf/%lf/%lf\n",&popforecast,popfile,&jpyram,&mpyram,&anpyram,&jpyram1,&mpyram1,&anpyram1);
3816: fprintf(ficparo,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);
3817: fprintf(ficres,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);
3818:
1.59 ! brouard 3819: freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);
1.58 lievre 3820:
1.59 ! brouard 3821: /*------------ gnuplot -------------*/
! 3822: strcpy(optionfilegnuplot,optionfilefiname);
! 3823: strcat(optionfilegnuplot,".gp");
! 3824: if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {
! 3825: printf("Problem with file %s",optionfilegnuplot);
! 3826: }
! 3827: else{
! 3828: fprintf(ficgp,"\n# %s\n", version);
! 3829: fprintf(ficgp,"# %s\n", optionfilegnuplot);
! 3830: fprintf(ficgp,"set missing 'NaNq'\n");
! 3831: }
! 3832: fclose(ficgp);
! 3833: printinggnuplot(fileres, ageminpar,agemaxpar,fage, pathc,p);
! 3834: /*--------- index.htm --------*/
1.53 brouard 3835:
3836: strcpy(optionfilehtm,optionfile);
3837: strcat(optionfilehtm,".htm");
3838: if((fichtm=fopen(optionfilehtm,"w"))==NULL) {
3839: printf("Problem with %s \n",optionfilehtm), exit(0);
3840: }
3841:
3842: fprintf(fichtm,"<body> <font size=\"2\">%s </font> <hr size=\"2\" color=\"#EC5E5E\"> \n
3843: Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n
3844: \n
3845: Total number of observations=%d <br>\n
3846: Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n
3847: <hr size=\"2\" color=\"#EC5E5E\">
3848: <ul><li><h4>Parameter files</h4>\n
3849: - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n
3850: - Log file of the run: <a href=\"%s\">%s</a><br>\n
3851: - 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);
3852: fclose(fichtm);
3853:
1.59 ! brouard 3854: printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,model,imx,jmin,jmax,jmean,rfileres,popforecast,estepm,jprev1,mprev1,anprev1,jprev2,mprev2,anprev2);
1.53 brouard 3855:
1.59 ! brouard 3856: /*------------ free_vector -------------*/
! 3857: chdir(path);
1.53 brouard 3858:
1.59 ! brouard 3859: free_ivector(wav,1,imx);
! 3860: free_imatrix(dh,1,lastpass-firstpass+1,1,imx);
! 3861: free_imatrix(bh,1,lastpass-firstpass+1,1,imx);
! 3862: free_imatrix(mw,1,lastpass-firstpass+1,1,imx);
! 3863: free_ivector(num,1,n);
! 3864: free_vector(agedc,1,n);
! 3865: free_matrix(covar,0,NCOVMAX,1,n);
! 3866: /*free_matrix(covar,1,NCOVMAX,1,n);*/
! 3867: fclose(ficparo);
! 3868: fclose(ficres);
1.53 brouard 3869:
3870:
1.54 brouard 3871: /*--------------- Prevalence limit (stable prevalence) --------------*/
1.53 brouard 3872:
3873: strcpy(filerespl,"pl");
3874: strcat(filerespl,fileres);
3875: if((ficrespl=fopen(filerespl,"w"))==NULL) {
1.54 brouard 3876: printf("Problem with stable prevalence resultfile: %s\n", filerespl);goto end;
3877: fprintf(ficlog,"Problem with stable prevalence resultfile: %s\n", filerespl);goto end;
1.53 brouard 3878: }
1.54 brouard 3879: printf("Computing stable prevalence: result on file '%s' \n", filerespl);
3880: fprintf(ficlog,"Computing stable prevalence: result on file '%s' \n", filerespl);
3881: fprintf(ficrespl,"#Stable prevalence \n");
1.53 brouard 3882: fprintf(ficrespl,"#Age ");
3883: for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);
3884: fprintf(ficrespl,"\n");
3885:
3886: prlim=matrix(1,nlstate,1,nlstate);
3887: pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
3888: oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
3889: newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
3890: savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
3891: oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */
1.59 ! brouard 3892:
1.53 brouard 3893: agebase=ageminpar;
3894: agelim=agemaxpar;
3895: ftolpl=1.e-10;
3896: i1=cptcoveff;
3897: if (cptcovn < 1){i1=1;}
3898:
1.59 ! brouard 3899: for(cptcov=1,k=0;cptcov<=i1;cptcov++){
1.53 brouard 3900: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
1.59 ! brouard 3901: k=k+1;
! 3902: /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/
! 3903: fprintf(ficrespl,"\n#******");
! 3904: printf("\n#******");
! 3905: fprintf(ficlog,"\n#******");
! 3906: for(j=1;j<=cptcoveff;j++) {
! 3907: fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
! 3908: printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
! 3909: fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
! 3910: }
! 3911: fprintf(ficrespl,"******\n");
! 3912: printf("******\n");
! 3913: fprintf(ficlog,"******\n");
1.53 brouard 3914:
1.59 ! brouard 3915: for (age=agebase; age<=agelim; age++){
! 3916: prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
! 3917: fprintf(ficrespl,"%.0f",age );
! 3918: for(i=1; i<=nlstate;i++)
1.53 brouard 3919: fprintf(ficrespl," %.5f", prlim[i][i]);
1.59 ! brouard 3920: fprintf(ficrespl,"\n");
1.53 brouard 3921: }
3922: }
1.59 ! brouard 3923: }
1.53 brouard 3924: fclose(ficrespl);
3925:
3926: /*------------- h Pij x at various ages ------------*/
3927:
3928: strcpy(filerespij,"pij"); strcat(filerespij,fileres);
3929: if((ficrespij=fopen(filerespij,"w"))==NULL) {
3930: printf("Problem with Pij resultfile: %s\n", filerespij);goto end;
3931: fprintf(ficlog,"Problem with Pij resultfile: %s\n", filerespij);goto end;
3932: }
3933: printf("Computing pij: result on file '%s' \n", filerespij);
3934: fprintf(ficlog,"Computing pij: result on file '%s' \n", filerespij);
3935:
3936: stepsize=(int) (stepm+YEARM-1)/YEARM;
3937: /*if (stepm<=24) stepsize=2;*/
3938:
3939: agelim=AGESUP;
3940: hstepm=stepsize*YEARM; /* Every year of age */
3941: hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */
3942:
3943: /* hstepm=1; aff par mois*/
3944:
1.59 ! brouard 3945: for(cptcov=1,k=0;cptcov<=i1;cptcov++){
1.53 brouard 3946: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
3947: k=k+1;
1.59 ! brouard 3948: fprintf(ficrespij,"\n#****** ");
! 3949: for(j=1;j<=cptcoveff;j++)
! 3950: fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
! 3951: fprintf(ficrespij,"******\n");
1.53 brouard 3952:
1.59 ! brouard 3953: for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */
! 3954: nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
! 3955: nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
! 3956:
! 3957: /* nhstepm=nhstepm*YEARM; aff par mois*/
! 3958:
! 3959: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
! 3960: oldm=oldms;savm=savms;
! 3961: hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
! 3962: fprintf(ficrespij,"# Age");
! 3963: for(i=1; i<=nlstate;i++)
! 3964: for(j=1; j<=nlstate+ndeath;j++)
! 3965: fprintf(ficrespij," %1d-%1d",i,j);
! 3966: fprintf(ficrespij,"\n");
! 3967: for (h=0; h<=nhstepm; h++){
! 3968: fprintf(ficrespij,"%d %f %f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );
1.53 brouard 3969: for(i=1; i<=nlstate;i++)
3970: for(j=1; j<=nlstate+ndeath;j++)
1.59 ! brouard 3971: fprintf(ficrespij," %.5f", p3mat[i][j][h]);
1.53 brouard 3972: fprintf(ficrespij,"\n");
3973: }
1.59 ! brouard 3974: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
! 3975: fprintf(ficrespij,"\n");
! 3976: }
1.53 brouard 3977: }
3978: }
3979:
3980: varprob(optionfilefiname, matcov, p, delti, nlstate, (int) bage, (int) fage,k,Tvar,nbcode, ncodemax);
3981:
3982: fclose(ficrespij);
3983:
3984:
3985: /*---------- Forecasting ------------------*/
3986: if((stepm == 1) && (strcmp(model,".")==0)){
3987: prevforecast(fileres, anproj1,mproj1,jproj1, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anproj2,p, i1);
3988: if (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);
3989: }
3990: else{
3991: erreur=108;
3992: 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);
3993: 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);
3994: }
3995:
3996:
3997: /*---------- Health expectancies and variances ------------*/
3998:
3999: strcpy(filerest,"t");
4000: strcat(filerest,fileres);
4001: if((ficrest=fopen(filerest,"w"))==NULL) {
4002: printf("Problem with total LE resultfile: %s\n", filerest);goto end;
4003: fprintf(ficlog,"Problem with total LE resultfile: %s\n", filerest);goto end;
4004: }
4005: printf("Computing Total LEs with variances: file '%s' \n", filerest);
4006: fprintf(ficlog,"Computing Total LEs with variances: file '%s' \n", filerest);
4007:
4008:
4009: strcpy(filerese,"e");
4010: strcat(filerese,fileres);
4011: if((ficreseij=fopen(filerese,"w"))==NULL) {
4012: printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
4013: fprintf(ficlog,"Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
4014: }
4015: printf("Computing Health Expectancies: result on file '%s' \n", filerese);
4016: fprintf(ficlog,"Computing Health Expectancies: result on file '%s' \n", filerese);
4017:
4018: strcpy(fileresv,"v");
4019: strcat(fileresv,fileres);
4020: if((ficresvij=fopen(fileresv,"w"))==NULL) {
4021: printf("Problem with variance resultfile: %s\n", fileresv);exit(0);
4022: fprintf(ficlog,"Problem with variance resultfile: %s\n", fileresv);exit(0);
4023: }
4024: printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
4025: fprintf(ficlog,"Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
1.58 lievre 4026:
1.53 brouard 4027: calagedate=-1;
1.58 lievre 4028:
1.53 brouard 4029: prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);
1.58 lievre 4030:
1.54 brouard 4031: if (mobilav!=0) {
1.53 brouard 4032: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
1.54 brouard 4033: if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
4034: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
4035: printf(" Error in movingaverage mobilav=%d\n",mobilav);
4036: }
1.53 brouard 4037: }
4038:
1.59 ! brouard 4039: for(cptcov=1,k=0;cptcov<=i1;cptcov++){
1.53 brouard 4040: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
4041: k=k+1;
4042: fprintf(ficrest,"\n#****** ");
4043: for(j=1;j<=cptcoveff;j++)
4044: fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
4045: fprintf(ficrest,"******\n");
4046:
4047: fprintf(ficreseij,"\n#****** ");
4048: for(j=1;j<=cptcoveff;j++)
4049: fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
4050: fprintf(ficreseij,"******\n");
4051:
4052: fprintf(ficresvij,"\n#****** ");
4053: for(j=1;j<=cptcoveff;j++)
4054: fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
4055: fprintf(ficresvij,"******\n");
4056:
4057: eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
4058: oldm=oldms;savm=savms;
4059: evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov);
4060:
4061: vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
4062: oldm=oldms;savm=savms;
4063: varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,0, mobilav);
4064: if(popbased==1){
4065: varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,popbased,mobilav);
1.59 ! brouard 4066: }
1.53 brouard 4067:
4068:
4069: fprintf(ficrest,"#Total LEs with variances: e.. (std) ");
4070: for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);
4071: fprintf(ficrest,"\n");
4072:
4073: epj=vector(1,nlstate+1);
4074: for(age=bage; age <=fage ;age++){
4075: prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
4076: if (popbased==1) {
1.54 brouard 4077: if(mobilav ==0){
1.53 brouard 4078: for(i=1; i<=nlstate;i++)
4079: prlim[i][i]=probs[(int)age][i][k];
1.54 brouard 4080: }else{ /* mobilav */
1.53 brouard 4081: for(i=1; i<=nlstate;i++)
4082: prlim[i][i]=mobaverage[(int)age][i][k];
4083: }
4084: }
4085:
4086: fprintf(ficrest," %4.0f",age);
4087: for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){
4088: for(i=1, epj[j]=0.;i <=nlstate;i++) {
4089: epj[j] += prlim[i][i]*eij[i][j][(int)age];
4090: /* printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/
4091: }
4092: epj[nlstate+1] +=epj[j];
4093: }
4094:
4095: for(i=1, vepp=0.;i <=nlstate;i++)
4096: for(j=1;j <=nlstate;j++)
4097: vepp += vareij[i][j][(int)age];
4098: fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));
4099: for(j=1;j <=nlstate;j++){
4100: fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));
4101: }
4102: fprintf(ficrest,"\n");
4103: }
1.59 ! brouard 4104: free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
! 4105: free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);
! 4106: free_vector(epj,1,nlstate+1);
1.53 brouard 4107: }
4108: }
1.59 ! brouard 4109: free_vector(weight,1,n);
! 4110: free_imatrix(Tvard,1,15,1,2);
! 4111: free_imatrix(s,1,maxwav+1,1,n);
! 4112: free_matrix(anint,1,maxwav,1,n);
! 4113: free_matrix(mint,1,maxwav,1,n);
! 4114: free_ivector(cod,1,n);
! 4115: free_ivector(tab,1,NCOVMAX);
1.53 brouard 4116: fclose(ficreseij);
4117: fclose(ficresvij);
4118: fclose(ficrest);
4119: fclose(ficpar);
4120:
1.54 brouard 4121: /*------- Variance of stable prevalence------*/
1.53 brouard 4122:
4123: strcpy(fileresvpl,"vpl");
4124: strcat(fileresvpl,fileres);
4125: if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {
1.54 brouard 4126: printf("Problem with variance of stable prevalence resultfile: %s\n", fileresvpl);
1.53 brouard 4127: exit(0);
4128: }
1.54 brouard 4129: printf("Computing Variance-covariance of stable prevalence: file '%s' \n", fileresvpl);
1.53 brouard 4130:
1.59 ! brouard 4131: for(cptcov=1,k=0;cptcov<=i1;cptcov++){
1.53 brouard 4132: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
4133: k=k+1;
4134: fprintf(ficresvpl,"\n#****** ");
4135: for(j=1;j<=cptcoveff;j++)
4136: fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
4137: fprintf(ficresvpl,"******\n");
4138:
4139: varpl=matrix(1,nlstate,(int) bage, (int) fage);
4140: oldm=oldms;savm=savms;
1.59 ! brouard 4141: varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);
! 4142: free_matrix(varpl,1,nlstate,(int) bage, (int)fage);
1.53 brouard 4143: }
1.59 ! brouard 4144: }
1.53 brouard 4145:
4146: fclose(ficresvpl);
4147:
4148: /*---------- End : free ----------------*/
4149: free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);
4150: free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);
4151: free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);
4152: free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);
4153:
4154: free_matrix(matcov,1,npar,1,npar);
4155: free_vector(delti,1,npar);
4156: free_matrix(agev,1,maxwav,1,imx);
4157: free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
1.54 brouard 4158: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
1.59 ! brouard 4159: free_ivector(ncodemax,1,8);
! 4160: free_ivector(Tvar,1,15);
! 4161: free_ivector(Tprod,1,15);
! 4162: free_ivector(Tvaraff,1,15);
! 4163: free_ivector(Tage,1,15);
! 4164: free_ivector(Tcode,1,100);
1.53 brouard 4165:
4166: fprintf(fichtm,"\n</body>");
4167: fclose(fichtm);
4168: fclose(ficgp);
4169:
4170:
4171: if(erreur >0){
4172: printf("End of Imach with error or warning %d\n",erreur);
4173: fprintf(ficlog,"End of Imach with error or warning %d\n",erreur);
4174: }else{
4175: printf("End of Imach\n");
4176: fprintf(ficlog,"End of Imach\n");
4177: }
4178: printf("See log file on %s\n",filelog);
4179: fclose(ficlog);
4180: /* gettimeofday(&end_time, (struct timezone*)0);*/ /* after time */
4181:
4182: /* 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);*/
4183: /*printf("Total time was %d uSec.\n", total_usecs);*/
4184: /*------ End -----------*/
4185:
1.59 ! brouard 4186: end:
1.53 brouard 4187: #ifdef windows
4188: /* chdir(pathcd);*/
4189: #endif
4190: /*system("wgnuplot graph.plt");*/
4191: /*system("../gp37mgw/wgnuplot graph.plt");*/
4192: /*system("cd ../gp37mgw");*/
4193: /* system("..\\gp37mgw\\wgnuplot graph.plt");*/
1.59 ! brouard 4194: strcpy(plotcmd,GNUPLOTPROGRAM);
! 4195: strcat(plotcmd," ");
! 4196: strcat(plotcmd,optionfilegnuplot);
! 4197: printf("Starting: %s\n",plotcmd);fflush(stdout);
! 4198: system(plotcmd);
1.53 brouard 4199:
1.54 brouard 4200: /*#ifdef windows*/
1.53 brouard 4201: while (z[0] != 'q') {
4202: /* chdir(path); */
4203: printf("\nType e to edit output files, g to graph again, c to start again, and q for exiting: ");
4204: scanf("%s",z);
4205: if (z[0] == 'c') system("./imach");
4206: else if (z[0] == 'e') system(optionfilehtm);
4207: else if (z[0] == 'g') system(plotcmd);
4208: else if (z[0] == 'q') exit(0);
4209: }
1.54 brouard 4210: /*#endif */
1.53 brouard 4211: }
4212:
4213:
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