Annotation of imach/src/imach.c, revision 1.69
1.69 ! brouard 1: /* $Id: imach.c,v 1.68 2003/02/04 12:40:59 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
1.66 brouard 35: states. This elementary transition (by month, quarter,
36: semester or year) is modelled as a multinomial logistic. The hPx
1.53 brouard 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:
1.66 brouard 86: char version[80]="Imach version 0.91, 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: {
1.66 brouard 859: /* Computes the transition matrix starting at age 'age' over
860: 'nhstepm*hstepm*stepm' months (i.e. until
861: age (in years) age+nhstepm*hstepm*stepm/12) by multiplying
862: nhstepm*hstepm matrices.
1.53 brouard 863: Output is stored in matrix po[i][j][h] for h every 'hstepm' step
1.66 brouard 864: (typically every 2 years instead of every month which is too big
865: for the memory).
1.53 brouard 866: Model is determined by parameters x and covariates have to be
867: included manually here.
868:
869: */
870:
871: int i, j, d, h, k;
872: double **out, cov[NCOVMAX];
873: double **newm;
874:
875: /* Hstepm could be zero and should return the unit matrix */
876: for (i=1;i<=nlstate+ndeath;i++)
877: for (j=1;j<=nlstate+ndeath;j++){
878: oldm[i][j]=(i==j ? 1.0 : 0.0);
879: po[i][j][0]=(i==j ? 1.0 : 0.0);
880: }
881: /* Even if hstepm = 1, at least one multiplication by the unit matrix */
882: for(h=1; h <=nhstepm; h++){
883: for(d=1; d <=hstepm; d++){
884: newm=savm;
885: /* Covariates have to be included here again */
886: cov[1]=1.;
887: cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
888: for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
889: for (k=1; k<=cptcovage;k++)
890: cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
891: for (k=1; k<=cptcovprod;k++)
892: cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
893:
894:
895: /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
896: /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
897: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,
898: pmij(pmmij,cov,ncovmodel,x,nlstate));
899: savm=oldm;
900: oldm=newm;
901: }
902: for(i=1; i<=nlstate+ndeath; i++)
903: for(j=1;j<=nlstate+ndeath;j++) {
904: po[i][j][h]=newm[i][j];
905: /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);
906: */
907: }
908: } /* end h */
909: return po;
910: }
911:
912:
913: /*************** log-likelihood *************/
914: double func( double *x)
915: {
916: int i, ii, j, k, mi, d, kk;
917: double l, ll[NLSTATEMAX], cov[NCOVMAX];
918: double **out;
919: double sw; /* Sum of weights */
920: double lli; /* Individual log likelihood */
1.59 brouard 921: int s1, s2;
1.68 lievre 922: double bbh, survp;
1.53 brouard 923: long ipmx;
924: /*extern weight */
925: /* We are differentiating ll according to initial status */
926: /* for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
927: /*for(i=1;i<imx;i++)
928: printf(" %d\n",s[4][i]);
929: */
930: cov[1]=1.;
931:
932: for(k=1; k<=nlstate; k++) ll[k]=0.;
1.61 brouard 933:
934: if(mle==1){
935: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
936: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
937: for(mi=1; mi<= wav[i]-1; mi++){
938: for (ii=1;ii<=nlstate+ndeath;ii++)
939: for (j=1;j<=nlstate+ndeath;j++){
940: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
941: savm[ii][j]=(ii==j ? 1.0 : 0.0);
942: }
943: for(d=0; d<dh[mi][i]; d++){
944: newm=savm;
945: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
946: for (kk=1; kk<=cptcovage;kk++) {
947: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
948: }
949: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
950: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
951: savm=oldm;
952: oldm=newm;
953: } /* end mult */
1.53 brouard 954:
1.61 brouard 955: /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
956: /* But now since version 0.9 we anticipate for bias and large stepm.
957: * If stepm is larger than one month (smallest stepm) and if the exact delay
958: * (in months) between two waves is not a multiple of stepm, we rounded to
959: * the nearest (and in case of equal distance, to the lowest) interval but now
960: * we keep into memory the bias bh[mi][i] and also the previous matrix product
961: * (i.e to dh[mi][i]-1) saved in 'savm'. The we inter(extra)polate the
962: * probability in order to take into account the bias as a fraction of the way
963: * from savm to out if bh is neagtive or even beyond if bh is positive. bh varies
964: * -stepm/2 to stepm/2 .
965: * For stepm=1 the results are the same as for previous versions of Imach.
966: * For stepm > 1 the results are less biased than in previous versions.
967: */
968: s1=s[mw[mi][i]][i];
969: s2=s[mw[mi+1][i]][i];
1.64 lievre 970: bbh=(double)bh[mi][i]/(double)stepm;
971: /* bias is positive if real duration
972: * is higher than the multiple of stepm and negative otherwise.
973: */
974: /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
975: lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*(savm[s1][s2])):log((1.+bbh)*out[s1][s2])); /* linear interpolation */
976: /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
977: /*if(lli ==000.0)*/
978: /*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); */
979: ipmx +=1;
980: sw += weight[i];
981: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
982: } /* end of wave */
983: } /* end of individual */
984: } else if(mle==2){
985: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
986: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
987: for(mi=1; mi<= wav[i]-1; mi++){
988: for (ii=1;ii<=nlstate+ndeath;ii++)
989: for (j=1;j<=nlstate+ndeath;j++){
990: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
991: savm[ii][j]=(ii==j ? 1.0 : 0.0);
992: }
993: for(d=0; d<=dh[mi][i]; d++){
994: newm=savm;
995: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
996: for (kk=1; kk<=cptcovage;kk++) {
997: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
998: }
999: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1000: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1001: savm=oldm;
1002: oldm=newm;
1003: } /* end mult */
1004:
1005: /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
1006: /* But now since version 0.9 we anticipate for bias and large stepm.
1007: * If stepm is larger than one month (smallest stepm) and if the exact delay
1008: * (in months) between two waves is not a multiple of stepm, we rounded to
1009: * the nearest (and in case of equal distance, to the lowest) interval but now
1010: * we keep into memory the bias bh[mi][i] and also the previous matrix product
1011: * (i.e to dh[mi][i]-1) saved in 'savm'. The we inter(extra)polate the
1012: * probability in order to take into account the bias as a fraction of the way
1013: * from savm to out if bh is neagtive or even beyond if bh is positive. bh varies
1014: * -stepm/2 to stepm/2 .
1015: * For stepm=1 the results are the same as for previous versions of Imach.
1016: * For stepm > 1 the results are less biased than in previous versions.
1017: */
1018: s1=s[mw[mi][i]][i];
1019: s2=s[mw[mi+1][i]][i];
1020: bbh=(double)bh[mi][i]/(double)stepm;
1021: /* bias is positive if real duration
1022: * is higher than the multiple of stepm and negative otherwise.
1023: */
1.63 lievre 1024: lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*(savm[s1][s2])):log((1.+bbh)*out[s1][s2])); /* linear interpolation */
1.64 lievre 1025: /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
1026: /*lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.-+bh)*out[s1][s2])); */ /* exponential interpolation */
1027: /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
1028: /*if(lli ==000.0)*/
1029: /*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); */
1030: ipmx +=1;
1031: sw += weight[i];
1032: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1033: } /* end of wave */
1034: } /* end of individual */
1035: } else if(mle==3){ /* exponential inter-extrapolation */
1036: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1037: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
1038: for(mi=1; mi<= wav[i]-1; mi++){
1039: for (ii=1;ii<=nlstate+ndeath;ii++)
1040: for (j=1;j<=nlstate+ndeath;j++){
1041: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1042: savm[ii][j]=(ii==j ? 1.0 : 0.0);
1043: }
1044: for(d=0; d<dh[mi][i]; d++){
1045: newm=savm;
1046: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
1047: for (kk=1; kk<=cptcovage;kk++) {
1048: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
1049: }
1050: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1051: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1052: savm=oldm;
1053: oldm=newm;
1054: } /* end mult */
1055:
1056: /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
1057: /* But now since version 0.9 we anticipate for bias and large stepm.
1058: * If stepm is larger than one month (smallest stepm) and if the exact delay
1059: * (in months) between two waves is not a multiple of stepm, we rounded to
1060: * the nearest (and in case of equal distance, to the lowest) interval but now
1061: * we keep into memory the bias bh[mi][i] and also the previous matrix product
1062: * (i.e to dh[mi][i]-1) saved in 'savm'. The we inter(extra)polate the
1063: * probability in order to take into account the bias as a fraction of the way
1064: * from savm to out if bh is neagtive or even beyond if bh is positive. bh varies
1065: * -stepm/2 to stepm/2 .
1066: * For stepm=1 the results are the same as for previous versions of Imach.
1067: * For stepm > 1 the results are less biased than in previous versions.
1068: */
1069: s1=s[mw[mi][i]][i];
1070: s2=s[mw[mi+1][i]][i];
1071: bbh=(double)bh[mi][i]/(double)stepm;
1072: /* bias is positive if real duration
1073: * is higher than the multiple of stepm and negative otherwise.
1074: */
1075: /* lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*(savm[s1][s2])):log((1.+bbh)*out[s1][s2])); */ /* linear interpolation */
1076: lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2])); /* exponential inter-extrapolation */
1.61 brouard 1077: /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
1078: /*if(lli ==000.0)*/
1079: /*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); */
1080: ipmx +=1;
1081: sw += weight[i];
1082: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1083: } /* end of wave */
1084: } /* end of individual */
1.64 lievre 1085: }else{ /* ml=4 no inter-extrapolation */
1.61 brouard 1086: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1087: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
1088: for(mi=1; mi<= wav[i]-1; mi++){
1089: for (ii=1;ii<=nlstate+ndeath;ii++)
1090: for (j=1;j<=nlstate+ndeath;j++){
1091: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1092: savm[ii][j]=(ii==j ? 1.0 : 0.0);
1093: }
1094: for(d=0; d<dh[mi][i]; d++){
1095: newm=savm;
1096: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
1097: for (kk=1; kk<=cptcovage;kk++) {
1098: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
1099: }
1100:
1101: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1102: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1103: savm=oldm;
1104: oldm=newm;
1105: } /* end mult */
1106:
1107: lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
1108: ipmx +=1;
1109: sw += weight[i];
1110: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1111: } /* end of wave */
1112: } /* end of individual */
1113: } /* End of if */
1.53 brouard 1114: for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
1115: /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
1116: l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
1117: return -l;
1118: }
1119:
1120:
1121: /*********** Maximum Likelihood Estimation ***************/
1122:
1123: void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
1124: {
1125: int i,j, iter;
1126: double **xi,*delti;
1127: double fret;
1128: xi=matrix(1,npar,1,npar);
1129: for (i=1;i<=npar;i++)
1130: for (j=1;j<=npar;j++)
1131: xi[i][j]=(i==j ? 1.0 : 0.0);
1132: printf("Powell\n"); fprintf(ficlog,"Powell\n");
1133: powell(p,xi,npar,ftol,&iter,&fret,func);
1134:
1135: printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));
1.65 lievre 1136: fprintf(ficlog,"\n#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
1.53 brouard 1137: fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
1138:
1139: }
1140:
1141: /**** Computes Hessian and covariance matrix ***/
1142: void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
1143: {
1144: double **a,**y,*x,pd;
1145: double **hess;
1146: int i, j,jk;
1147: int *indx;
1148:
1149: double hessii(double p[], double delta, int theta, double delti[]);
1150: double hessij(double p[], double delti[], int i, int j);
1151: void lubksb(double **a, int npar, int *indx, double b[]) ;
1152: void ludcmp(double **a, int npar, int *indx, double *d) ;
1153:
1154: hess=matrix(1,npar,1,npar);
1155:
1156: printf("\nCalculation of the hessian matrix. Wait...\n");
1157: fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
1158: for (i=1;i<=npar;i++){
1159: printf("%d",i);fflush(stdout);
1160: fprintf(ficlog,"%d",i);fflush(ficlog);
1161: hess[i][i]=hessii(p,ftolhess,i,delti);
1162: /*printf(" %f ",p[i]);*/
1163: /*printf(" %lf ",hess[i][i]);*/
1164: }
1165:
1166: for (i=1;i<=npar;i++) {
1167: for (j=1;j<=npar;j++) {
1168: if (j>i) {
1169: printf(".%d%d",i,j);fflush(stdout);
1170: fprintf(ficlog,".%d%d",i,j);fflush(ficlog);
1171: hess[i][j]=hessij(p,delti,i,j);
1172: hess[j][i]=hess[i][j];
1173: /*printf(" %lf ",hess[i][j]);*/
1174: }
1175: }
1176: }
1177: printf("\n");
1178: fprintf(ficlog,"\n");
1179:
1180: printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
1181: fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
1182:
1183: a=matrix(1,npar,1,npar);
1184: y=matrix(1,npar,1,npar);
1185: x=vector(1,npar);
1186: indx=ivector(1,npar);
1187: for (i=1;i<=npar;i++)
1188: for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
1189: ludcmp(a,npar,indx,&pd);
1190:
1191: for (j=1;j<=npar;j++) {
1192: for (i=1;i<=npar;i++) x[i]=0;
1193: x[j]=1;
1194: lubksb(a,npar,indx,x);
1195: for (i=1;i<=npar;i++){
1196: matcov[i][j]=x[i];
1197: }
1198: }
1199:
1200: printf("\n#Hessian matrix#\n");
1201: fprintf(ficlog,"\n#Hessian matrix#\n");
1202: for (i=1;i<=npar;i++) {
1203: for (j=1;j<=npar;j++) {
1204: printf("%.3e ",hess[i][j]);
1205: fprintf(ficlog,"%.3e ",hess[i][j]);
1206: }
1207: printf("\n");
1208: fprintf(ficlog,"\n");
1209: }
1210:
1211: /* Recompute Inverse */
1212: for (i=1;i<=npar;i++)
1213: for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];
1214: ludcmp(a,npar,indx,&pd);
1215:
1216: /* printf("\n#Hessian matrix recomputed#\n");
1217:
1218: for (j=1;j<=npar;j++) {
1219: for (i=1;i<=npar;i++) x[i]=0;
1220: x[j]=1;
1221: lubksb(a,npar,indx,x);
1222: for (i=1;i<=npar;i++){
1223: y[i][j]=x[i];
1224: printf("%.3e ",y[i][j]);
1225: fprintf(ficlog,"%.3e ",y[i][j]);
1226: }
1227: printf("\n");
1228: fprintf(ficlog,"\n");
1229: }
1230: */
1231:
1232: free_matrix(a,1,npar,1,npar);
1233: free_matrix(y,1,npar,1,npar);
1234: free_vector(x,1,npar);
1235: free_ivector(indx,1,npar);
1236: free_matrix(hess,1,npar,1,npar);
1237:
1238:
1239: }
1240:
1241: /*************** hessian matrix ****************/
1242: double hessii( double x[], double delta, int theta, double delti[])
1243: {
1244: int i;
1245: int l=1, lmax=20;
1246: double k1,k2;
1247: double p2[NPARMAX+1];
1248: double res;
1249: double delt, delts, nkhi=10.,nkhif=1., khi=1.e-4;
1250: double fx;
1251: int k=0,kmax=10;
1252: double l1;
1253:
1254: fx=func(x);
1255: for (i=1;i<=npar;i++) p2[i]=x[i];
1256: for(l=0 ; l <=lmax; l++){
1257: l1=pow(10,l);
1258: delts=delt;
1259: for(k=1 ; k <kmax; k=k+1){
1260: delt = delta*(l1*k);
1261: p2[theta]=x[theta] +delt;
1262: k1=func(p2)-fx;
1263: p2[theta]=x[theta]-delt;
1264: k2=func(p2)-fx;
1265: /*res= (k1-2.0*fx+k2)/delt/delt; */
1266: res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */
1267:
1268: #ifdef DEBUG
1269: 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);
1270: 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);
1271: #endif
1272: /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
1273: if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
1274: k=kmax;
1275: }
1276: else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
1277: k=kmax; l=lmax*10.;
1278: }
1279: else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){
1280: delts=delt;
1281: }
1282: }
1283: }
1284: delti[theta]=delts;
1285: return res;
1286:
1287: }
1288:
1289: double hessij( double x[], double delti[], int thetai,int thetaj)
1290: {
1291: int i;
1292: int l=1, l1, lmax=20;
1293: double k1,k2,k3,k4,res,fx;
1294: double p2[NPARMAX+1];
1295: int k;
1296:
1297: fx=func(x);
1298: for (k=1; k<=2; k++) {
1299: for (i=1;i<=npar;i++) p2[i]=x[i];
1300: p2[thetai]=x[thetai]+delti[thetai]/k;
1301: p2[thetaj]=x[thetaj]+delti[thetaj]/k;
1302: k1=func(p2)-fx;
1303:
1304: p2[thetai]=x[thetai]+delti[thetai]/k;
1305: p2[thetaj]=x[thetaj]-delti[thetaj]/k;
1306: k2=func(p2)-fx;
1307:
1308: p2[thetai]=x[thetai]-delti[thetai]/k;
1309: p2[thetaj]=x[thetaj]+delti[thetaj]/k;
1310: k3=func(p2)-fx;
1311:
1312: p2[thetai]=x[thetai]-delti[thetai]/k;
1313: p2[thetaj]=x[thetaj]-delti[thetaj]/k;
1314: k4=func(p2)-fx;
1315: res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */
1316: #ifdef DEBUG
1317: 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);
1318: 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);
1319: #endif
1320: }
1321: return res;
1322: }
1323:
1324: /************** Inverse of matrix **************/
1325: void ludcmp(double **a, int n, int *indx, double *d)
1326: {
1327: int i,imax,j,k;
1328: double big,dum,sum,temp;
1329: double *vv;
1330:
1331: vv=vector(1,n);
1332: *d=1.0;
1333: for (i=1;i<=n;i++) {
1334: big=0.0;
1335: for (j=1;j<=n;j++)
1336: if ((temp=fabs(a[i][j])) > big) big=temp;
1337: if (big == 0.0) nrerror("Singular matrix in routine ludcmp");
1338: vv[i]=1.0/big;
1339: }
1340: for (j=1;j<=n;j++) {
1341: for (i=1;i<j;i++) {
1342: sum=a[i][j];
1343: for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];
1344: a[i][j]=sum;
1345: }
1346: big=0.0;
1347: for (i=j;i<=n;i++) {
1348: sum=a[i][j];
1349: for (k=1;k<j;k++)
1350: sum -= a[i][k]*a[k][j];
1351: a[i][j]=sum;
1352: if ( (dum=vv[i]*fabs(sum)) >= big) {
1353: big=dum;
1354: imax=i;
1355: }
1356: }
1357: if (j != imax) {
1358: for (k=1;k<=n;k++) {
1359: dum=a[imax][k];
1360: a[imax][k]=a[j][k];
1361: a[j][k]=dum;
1362: }
1363: *d = -(*d);
1364: vv[imax]=vv[j];
1365: }
1366: indx[j]=imax;
1367: if (a[j][j] == 0.0) a[j][j]=TINY;
1368: if (j != n) {
1369: dum=1.0/(a[j][j]);
1370: for (i=j+1;i<=n;i++) a[i][j] *= dum;
1371: }
1372: }
1373: free_vector(vv,1,n); /* Doesn't work */
1374: ;
1375: }
1376:
1377: void lubksb(double **a, int n, int *indx, double b[])
1378: {
1379: int i,ii=0,ip,j;
1380: double sum;
1381:
1382: for (i=1;i<=n;i++) {
1383: ip=indx[i];
1384: sum=b[ip];
1385: b[ip]=b[i];
1386: if (ii)
1387: for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];
1388: else if (sum) ii=i;
1389: b[i]=sum;
1390: }
1391: for (i=n;i>=1;i--) {
1392: sum=b[i];
1393: for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];
1394: b[i]=sum/a[i][i];
1395: }
1396: }
1397:
1398: /************ Frequencies ********************/
1.59 brouard 1399: 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 1400: { /* Some frequencies */
1401:
1402: int i, m, jk, k1,i1, j1, bool, z1,z2,j;
1403: int first;
1404: double ***freq; /* Frequencies */
1405: double *pp;
1406: double pos, k2, dateintsum=0,k2cpt=0;
1407: FILE *ficresp;
1408: char fileresp[FILENAMELENGTH];
1409:
1410: pp=vector(1,nlstate);
1411: probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
1412: strcpy(fileresp,"p");
1413: strcat(fileresp,fileres);
1414: if((ficresp=fopen(fileresp,"w"))==NULL) {
1415: printf("Problem with prevalence resultfile: %s\n", fileresp);
1416: fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
1417: exit(0);
1418: }
1.69 ! brouard 1419: freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);
1.53 brouard 1420: j1=0;
1421:
1422: j=cptcoveff;
1423: if (cptcovn<1) {j=1;ncodemax[1]=1;}
1424:
1425: first=1;
1426:
1427: for(k1=1; k1<=j;k1++){
1428: for(i1=1; i1<=ncodemax[k1];i1++){
1429: j1++;
1430: /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
1431: scanf("%d", i);*/
1432: for (i=-1; i<=nlstate+ndeath; i++)
1433: for (jk=-1; jk<=nlstate+ndeath; jk++)
1434: for(m=agemin; m <= agemax+3; m++)
1435: freq[i][jk][m]=0;
1436:
1437: dateintsum=0;
1438: k2cpt=0;
1439: for (i=1; i<=imx; i++) {
1440: bool=1;
1441: if (cptcovn>0) {
1442: for (z1=1; z1<=cptcoveff; z1++)
1443: if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])
1444: bool=0;
1445: }
1.58 lievre 1446: if (bool==1){
1.53 brouard 1447: for(m=firstpass; m<=lastpass; m++){
1448: k2=anint[m][i]+(mint[m][i]/12.);
1449: if ((k2>=dateprev1) && (k2<=dateprev2)) {
1450: if(agev[m][i]==0) agev[m][i]=agemax+1;
1451: if(agev[m][i]==1) agev[m][i]=agemax+2;
1452: if (m<lastpass) {
1453: freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
1454: freq[s[m][i]][s[m+1][i]][(int) agemax+3] += weight[i];
1455: }
1456:
1457: if ((agev[m][i]>1) && (agev[m][i]< (agemax+3))) {
1458: dateintsum=dateintsum+k2;
1459: k2cpt++;
1460: }
1461: }
1462: }
1463: }
1464: }
1465:
1466: fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);
1467:
1468: if (cptcovn>0) {
1469: fprintf(ficresp, "\n#********** Variable ");
1470: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
1471: fprintf(ficresp, "**********\n#");
1472: }
1473: for(i=1; i<=nlstate;i++)
1474: fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
1475: fprintf(ficresp, "\n");
1476:
1477: for(i=(int)agemin; i <= (int)agemax+3; i++){
1478: if(i==(int)agemax+3){
1479: fprintf(ficlog,"Total");
1480: }else{
1481: if(first==1){
1482: first=0;
1483: printf("See log file for details...\n");
1484: }
1485: fprintf(ficlog,"Age %d", i);
1486: }
1487: for(jk=1; jk <=nlstate ; jk++){
1488: for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
1489: pp[jk] += freq[jk][m][i];
1490: }
1491: for(jk=1; jk <=nlstate ; jk++){
1492: for(m=-1, pos=0; m <=0 ; m++)
1493: pos += freq[jk][m][i];
1494: if(pp[jk]>=1.e-10){
1495: if(first==1){
1496: printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
1497: }
1498: fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
1499: }else{
1500: if(first==1)
1501: printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
1502: fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
1503: }
1504: }
1505:
1506: for(jk=1; jk <=nlstate ; jk++){
1507: for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
1508: pp[jk] += freq[jk][m][i];
1509: }
1510:
1511: for(jk=1,pos=0; jk <=nlstate ; jk++)
1512: pos += pp[jk];
1513: for(jk=1; jk <=nlstate ; jk++){
1514: if(pos>=1.e-5){
1515: if(first==1)
1516: printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
1517: fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
1518: }else{
1519: if(first==1)
1520: printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
1521: fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
1522: }
1523: if( i <= (int) agemax){
1524: if(pos>=1.e-5){
1525: fprintf(ficresp," %d %.5f %.0f %.0f",i,pp[jk]/pos, pp[jk],pos);
1526: probs[i][jk][j1]= pp[jk]/pos;
1527: /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/
1528: }
1529: else
1530: fprintf(ficresp," %d NaNq %.0f %.0f",i,pp[jk],pos);
1531: }
1532: }
1533:
1.69 ! brouard 1534: for(jk=-1; jk <=nlstate+ndeath; jk++)
! 1535: for(m=-1; m <=nlstate+ndeath; m++)
1.53 brouard 1536: if(freq[jk][m][i] !=0 ) {
1537: if(first==1)
1538: printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
1539: fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
1540: }
1541: if(i <= (int) agemax)
1542: fprintf(ficresp,"\n");
1543: if(first==1)
1544: printf("Others in log...\n");
1545: fprintf(ficlog,"\n");
1546: }
1547: }
1548: }
1549: dateintmean=dateintsum/k2cpt;
1550:
1551: fclose(ficresp);
1.69 ! brouard 1552: free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);
1.53 brouard 1553: free_vector(pp,1,nlstate);
1554:
1555: /* End of Freq */
1556: }
1557:
1558: /************ Prevalence ********************/
1.69 ! brouard 1559: 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 calagedatem)
! 1560: {
! 1561: /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
! 1562: in each health status at the date of interview (if between dateprev1 and dateprev2).
! 1563: We still use firstpass and lastpass as another selection.
! 1564: */
1.53 brouard 1565:
1566: int i, m, jk, k1, i1, j1, bool, z1,z2,j;
1567: double ***freq; /* Frequencies */
1568: double *pp;
1.69 ! brouard 1569: double pos;
! 1570: double y2; /* in fractional years */
1.53 brouard 1571:
1572: pp=vector(1,nlstate);
1573:
1.69 ! brouard 1574: freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);
1.53 brouard 1575: j1=0;
1576:
1577: j=cptcoveff;
1578: if (cptcovn<1) {j=1;ncodemax[1]=1;}
1579:
1580: for(k1=1; k1<=j;k1++){
1581: for(i1=1; i1<=ncodemax[k1];i1++){
1582: j1++;
1583:
1.69 ! brouard 1584: for (i=-1; i<=nlstate+ndeath; i++)
! 1585: for (jk=-1; jk<=nlstate+ndeath; jk++)
1.53 brouard 1586: for(m=agemin; m <= agemax+3; m++)
1587: freq[i][jk][m]=0;
1588:
1.69 ! brouard 1589: for (i=1; i<=imx; i++) { /* Each individual */
1.53 brouard 1590: bool=1;
1591: if (cptcovn>0) {
1592: for (z1=1; z1<=cptcoveff; z1++)
1593: if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])
1594: bool=0;
1595: }
1596: if (bool==1) {
1.69 ! brouard 1597: for(m=firstpass; m<=lastpass; m++){/* Other selection (we can limit to certain interviews*/
! 1598: y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
! 1599: if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
1.53 brouard 1600: if(agev[m][i]==0) agev[m][i]=agemax+1;
1601: if(agev[m][i]==1) agev[m][i]=agemax+2;
1602: if (m<lastpass) {
1.69 ! brouard 1603: if (calagedatem>0) /* We compute prevalence at exact age, agev in fractional years */
! 1604: freq[s[m][i]][s[m+1][i]][(int)(agev[m][i]+1-((int)calagedatem %12)/12.)] += weight[i];
1.53 brouard 1605: else
1606: freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
1607: freq[s[m][i]][s[m+1][i]][(int)(agemax+3)] += weight[i];
1608: }
1609: }
1.69 ! brouard 1610: } /* end selection of waves */
1.53 brouard 1611: }
1612: }
1613: for(i=(int)agemin; i <= (int)agemax+3; i++){
1614: for(jk=1; jk <=nlstate ; jk++){
1615: for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
1616: pp[jk] += freq[jk][m][i];
1617: }
1618: for(jk=1; jk <=nlstate ; jk++){
1619: for(m=-1, pos=0; m <=0 ; m++)
1620: pos += freq[jk][m][i];
1621: }
1622:
1623: for(jk=1; jk <=nlstate ; jk++){
1624: for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
1625: pp[jk] += freq[jk][m][i];
1626: }
1627:
1628: for(jk=1,pos=0; jk <=nlstate ; jk++) pos += pp[jk];
1629:
1630: for(jk=1; jk <=nlstate ; jk++){
1631: if( i <= (int) agemax){
1632: if(pos>=1.e-5){
1633: probs[i][jk][j1]= pp[jk]/pos;
1634: }
1635: }
1636: }/* end jk */
1637: }/* end i */
1638: } /* end i1 */
1639: } /* end k1 */
1640:
1641:
1.69 ! brouard 1642: free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);
1.53 brouard 1643: free_vector(pp,1,nlstate);
1644:
1645: } /* End of Freq */
1646:
1647: /************* Waves Concatenation ***************/
1648:
1.59 brouard 1649: 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 1650: {
1651: /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
1652: Death is a valid wave (if date is known).
1653: mw[mi][i] is the mi (mi=1 to wav[i]) effective wave of individual i
1.59 brouard 1654: dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
1.53 brouard 1655: and mw[mi+1][i]. dh depends on stepm.
1656: */
1657:
1658: int i, mi, m;
1659: /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
1660: double sum=0., jmean=0.;*/
1661: int first;
1662: int j, k=0,jk, ju, jl;
1663: double sum=0.;
1664: first=0;
1665: jmin=1e+5;
1666: jmax=-1;
1667: jmean=0.;
1668: for(i=1; i<=imx; i++){
1669: mi=0;
1670: m=firstpass;
1671: while(s[m][i] <= nlstate){
1.69 ! brouard 1672: if(s[m][i]>=1)
1.53 brouard 1673: mw[++mi][i]=m;
1674: if(m >=lastpass)
1675: break;
1676: else
1677: m++;
1678: }/* end while */
1679: if (s[m][i] > nlstate){
1680: mi++; /* Death is another wave */
1681: /* if(mi==0) never been interviewed correctly before death */
1682: /* Only death is a correct wave */
1683: mw[mi][i]=m;
1684: }
1685:
1686: wav[i]=mi;
1687: if(mi==0){
1688: if(first==0){
1689: printf("Warning, no any valid information for:%d line=%d and may be others, see log file\n",num[i],i);
1690: first=1;
1691: }
1692: if(first==1){
1693: fprintf(ficlog,"Warning, no any valid information for:%d line=%d\n",num[i],i);
1694: }
1695: } /* end mi==0 */
1696: }
1697:
1698: for(i=1; i<=imx; i++){
1699: for(mi=1; mi<wav[i];mi++){
1700: if (stepm <=0)
1701: dh[mi][i]=1;
1702: else{
1703: if (s[mw[mi+1][i]][i] > nlstate) {
1704: if (agedc[i] < 2*AGESUP) {
1705: j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);
1706: if(j==0) j=1; /* Survives at least one month after exam */
1707: k=k+1;
1708: if (j >= jmax) jmax=j;
1709: if (j <= jmin) jmin=j;
1710: sum=sum+j;
1711: /*if (j<0) printf("j=%d num=%d \n",j,i); */
1.68 lievre 1712: /* printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
1.53 brouard 1713: }
1714: }
1715: else{
1716: j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
1.68 lievre 1717: /* printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
1.53 brouard 1718: k=k+1;
1719: if (j >= jmax) jmax=j;
1720: else if (j <= jmin)jmin=j;
1721: /* if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
1722: sum=sum+j;
1723: }
1724: jk= j/stepm;
1725: jl= j -jk*stepm;
1726: ju= j -(jk+1)*stepm;
1.64 lievre 1727: if(mle <=1){
1728: if(jl==0){
1729: dh[mi][i]=jk;
1730: bh[mi][i]=0;
1731: }else{ /* We want a negative bias in order to only have interpolation ie
1732: * at the price of an extra matrix product in likelihood */
1733: dh[mi][i]=jk+1;
1734: bh[mi][i]=ju;
1735: }
1736: }else{
1737: if(jl <= -ju){
1738: dh[mi][i]=jk;
1739: bh[mi][i]=jl; /* bias is positive if real duration
1740: * is higher than the multiple of stepm and negative otherwise.
1741: */
1742: }
1743: else{
1744: dh[mi][i]=jk+1;
1745: bh[mi][i]=ju;
1746: }
1747: if(dh[mi][i]==0){
1748: dh[mi][i]=1; /* At least one step */
1749: bh[mi][i]=ju; /* At least one step */
1750: 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);
1751: }
1.59 brouard 1752: }
1.64 lievre 1753: } /* end if mle */
1754: } /* end wave */
1.53 brouard 1755: }
1756: jmean=sum/k;
1757: printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);
1758: fprintf(ficlog,"Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);
1759: }
1760:
1761: /*********** Tricode ****************************/
1762: void tricode(int *Tvar, int **nbcode, int imx)
1763: {
1.58 lievre 1764:
1765: int Ndum[20],ij=1, k, j, i, maxncov=19;
1.53 brouard 1766: int cptcode=0;
1767: cptcoveff=0;
1768:
1.58 lievre 1769: for (k=0; k<maxncov; k++) Ndum[k]=0;
1.53 brouard 1770: for (k=1; k<=7; k++) ncodemax[k]=0;
1771:
1772: for (j=1; j<=(cptcovn+2*cptcovprod); j++) {
1.58 lievre 1773: for (i=1; i<=imx; i++) { /*reads the data file to get the maximum
1774: modality*/
1775: ij=(int)(covar[Tvar[j]][i]); /* ij is the modality of this individual*/
1776: Ndum[ij]++; /*store the modality */
1.53 brouard 1777: /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
1.58 lievre 1778: if (ij > cptcode) cptcode=ij; /* getting the maximum of covariable
1779: Tvar[j]. If V=sex and male is 0 and
1780: female is 1, then cptcode=1.*/
1.53 brouard 1781: }
1782:
1783: for (i=0; i<=cptcode; i++) {
1.58 lievre 1784: 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 1785: }
1.58 lievre 1786:
1.53 brouard 1787: ij=1;
1788: for (i=1; i<=ncodemax[j]; i++) {
1.58 lievre 1789: for (k=0; k<= maxncov; k++) {
1.53 brouard 1790: if (Ndum[k] != 0) {
1791: nbcode[Tvar[j]][ij]=k;
1.58 lievre 1792: /* 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 1793:
1794: ij++;
1795: }
1796: if (ij > ncodemax[j]) break;
1797: }
1798: }
1799: }
1800:
1.58 lievre 1801: for (k=0; k< maxncov; k++) Ndum[k]=0;
1.53 brouard 1802:
1.58 lievre 1803: for (i=1; i<=ncovmodel-2; i++) {
1804: /* 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 1805: ij=Tvar[i];
1.58 lievre 1806: Ndum[ij]++;
1.53 brouard 1807: }
1808:
1809: ij=1;
1.58 lievre 1810: for (i=1; i<= maxncov; i++) {
1.53 brouard 1811: if((Ndum[i]!=0) && (i<=ncovcol)){
1.58 lievre 1812: Tvaraff[ij]=i; /*For printing */
1.53 brouard 1813: ij++;
1814: }
1815: }
1816:
1.58 lievre 1817: cptcoveff=ij-1; /*Number of simple covariates*/
1.53 brouard 1818: }
1819:
1820: /*********** Health Expectancies ****************/
1821:
1822: 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 )
1823:
1824: {
1825: /* Health expectancies */
1826: int i, j, nhstepm, hstepm, h, nstepm, k, cptj;
1827: double age, agelim, hf;
1828: double ***p3mat,***varhe;
1829: double **dnewm,**doldm;
1830: double *xp;
1831: double **gp, **gm;
1832: double ***gradg, ***trgradg;
1833: int theta;
1834:
1835: varhe=ma3x(1,nlstate*2,1,nlstate*2,(int) bage, (int) fage);
1836: xp=vector(1,npar);
1837: dnewm=matrix(1,nlstate*2,1,npar);
1838: doldm=matrix(1,nlstate*2,1,nlstate*2);
1839:
1840: fprintf(ficreseij,"# Health expectancies\n");
1841: fprintf(ficreseij,"# Age");
1842: for(i=1; i<=nlstate;i++)
1843: for(j=1; j<=nlstate;j++)
1844: fprintf(ficreseij," %1d-%1d (SE)",i,j);
1845: fprintf(ficreseij,"\n");
1846:
1847: if(estepm < stepm){
1848: printf ("Problem %d lower than %d\n",estepm, stepm);
1849: }
1850: else hstepm=estepm;
1851: /* We compute the life expectancy from trapezoids spaced every estepm months
1852: * This is mainly to measure the difference between two models: for example
1853: * if stepm=24 months pijx are given only every 2 years and by summing them
1854: * we are calculating an estimate of the Life Expectancy assuming a linear
1.66 brouard 1855: * progression in between and thus overestimating or underestimating according
1.53 brouard 1856: * to the curvature of the survival function. If, for the same date, we
1857: * estimate the model with stepm=1 month, we can keep estepm to 24 months
1858: * to compare the new estimate of Life expectancy with the same linear
1859: * hypothesis. A more precise result, taking into account a more precise
1860: * curvature will be obtained if estepm is as small as stepm. */
1861:
1862: /* For example we decided to compute the life expectancy with the smallest unit */
1863: /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
1864: nhstepm is the number of hstepm from age to agelim
1865: nstepm is the number of stepm from age to agelin.
1866: Look at hpijx to understand the reason of that which relies in memory size
1867: and note for a fixed period like estepm months */
1868: /* We decided (b) to get a life expectancy respecting the most precise curvature of the
1869: survival function given by stepm (the optimization length). Unfortunately it
1870: means that if the survival funtion is printed only each two years of age and if
1871: you sum them up and add 1 year (area under the trapezoids) you won't get the same
1872: results. So we changed our mind and took the option of the best precision.
1873: */
1874: hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
1875:
1876: agelim=AGESUP;
1877: for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
1878: /* nhstepm age range expressed in number of stepm */
1879: nstepm=(int) rint((agelim-age)*YEARM/stepm);
1880: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
1881: /* if (stepm >= YEARM) hstepm=1;*/
1882: nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
1883: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
1884: gradg=ma3x(0,nhstepm,1,npar,1,nlstate*2);
1885: gp=matrix(0,nhstepm,1,nlstate*2);
1886: gm=matrix(0,nhstepm,1,nlstate*2);
1887:
1888: /* Computed by stepm unit matrices, product of hstepm matrices, stored
1889: in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
1890: hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);
1891:
1892:
1893: hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
1894:
1895: /* Computing Variances of health expectancies */
1896:
1897: for(theta=1; theta <=npar; theta++){
1898: for(i=1; i<=npar; i++){
1899: xp[i] = x[i] + (i==theta ?delti[theta]:0);
1900: }
1901: hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
1902:
1903: cptj=0;
1904: for(j=1; j<= nlstate; j++){
1905: for(i=1; i<=nlstate; i++){
1906: cptj=cptj+1;
1907: for(h=0, gp[h][cptj]=0.; h<=nhstepm-1; h++){
1908: gp[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;
1909: }
1910: }
1911: }
1912:
1913:
1914: for(i=1; i<=npar; i++)
1915: xp[i] = x[i] - (i==theta ?delti[theta]:0);
1916: hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
1917:
1918: cptj=0;
1919: for(j=1; j<= nlstate; j++){
1920: for(i=1;i<=nlstate;i++){
1921: cptj=cptj+1;
1922: for(h=0, gm[h][cptj]=0.; h<=nhstepm-1; h++){
1923: gm[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;
1924: }
1925: }
1926: }
1927: for(j=1; j<= nlstate*2; j++)
1928: for(h=0; h<=nhstepm-1; h++){
1929: gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
1930: }
1931: }
1932:
1933: /* End theta */
1934:
1935: trgradg =ma3x(0,nhstepm,1,nlstate*2,1,npar);
1936:
1937: for(h=0; h<=nhstepm-1; h++)
1938: for(j=1; j<=nlstate*2;j++)
1939: for(theta=1; theta <=npar; theta++)
1940: trgradg[h][j][theta]=gradg[h][theta][j];
1941:
1942:
1943: for(i=1;i<=nlstate*2;i++)
1944: for(j=1;j<=nlstate*2;j++)
1945: varhe[i][j][(int)age] =0.;
1946:
1947: printf("%d|",(int)age);fflush(stdout);
1948: fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
1949: for(h=0;h<=nhstepm-1;h++){
1950: for(k=0;k<=nhstepm-1;k++){
1951: matprod2(dnewm,trgradg[h],1,nlstate*2,1,npar,1,npar,matcov);
1952: matprod2(doldm,dnewm,1,nlstate*2,1,npar,1,nlstate*2,gradg[k]);
1953: for(i=1;i<=nlstate*2;i++)
1954: for(j=1;j<=nlstate*2;j++)
1955: varhe[i][j][(int)age] += doldm[i][j]*hf*hf;
1956: }
1957: }
1958: /* Computing expectancies */
1959: for(i=1; i<=nlstate;i++)
1960: for(j=1; j<=nlstate;j++)
1961: for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
1962: eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
1963:
1964: /* 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]);*/
1965:
1966: }
1967:
1968: fprintf(ficreseij,"%3.0f",age );
1969: cptj=0;
1970: for(i=1; i<=nlstate;i++)
1971: for(j=1; j<=nlstate;j++){
1972: cptj++;
1973: fprintf(ficreseij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[cptj][cptj][(int)age]) );
1974: }
1975: fprintf(ficreseij,"\n");
1976:
1977: free_matrix(gm,0,nhstepm,1,nlstate*2);
1978: free_matrix(gp,0,nhstepm,1,nlstate*2);
1979: free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*2);
1980: free_ma3x(trgradg,0,nhstepm,1,nlstate*2,1,npar);
1981: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
1982: }
1983: printf("\n");
1984: fprintf(ficlog,"\n");
1985:
1986: free_vector(xp,1,npar);
1987: free_matrix(dnewm,1,nlstate*2,1,npar);
1988: free_matrix(doldm,1,nlstate*2,1,nlstate*2);
1989: free_ma3x(varhe,1,nlstate*2,1,nlstate*2,(int) bage, (int)fage);
1990: }
1991:
1992: /************ Variance ******************/
1993: 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)
1994: {
1995: /* Variance of health expectancies */
1996: /* double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
1997: /* double **newm;*/
1998: double **dnewm,**doldm;
1999: double **dnewmp,**doldmp;
2000: int i, j, nhstepm, hstepm, h, nstepm ;
2001: int k, cptcode;
2002: double *xp;
2003: double **gp, **gm; /* for var eij */
2004: double ***gradg, ***trgradg; /*for var eij */
2005: double **gradgp, **trgradgp; /* for var p point j */
2006: double *gpp, *gmp; /* for var p point j */
2007: double **varppt; /* for var p point j nlstate to nlstate+ndeath */
2008: double ***p3mat;
2009: double age,agelim, hf;
2010: double ***mobaverage;
2011: int theta;
2012: char digit[4];
1.55 lievre 2013: char digitp[25];
1.53 brouard 2014:
2015: char fileresprobmorprev[FILENAMELENGTH];
2016:
1.55 lievre 2017: if(popbased==1){
1.58 lievre 2018: if(mobilav!=0)
1.55 lievre 2019: strcpy(digitp,"-populbased-mobilav-");
2020: else strcpy(digitp,"-populbased-nomobil-");
2021: }
2022: else
1.53 brouard 2023: strcpy(digitp,"-stablbased-");
1.56 lievre 2024:
1.54 brouard 2025: if (mobilav!=0) {
1.53 brouard 2026: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
1.54 brouard 2027: if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
2028: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
2029: printf(" Error in movingaverage mobilav=%d\n",mobilav);
2030: }
1.53 brouard 2031: }
2032:
2033: strcpy(fileresprobmorprev,"prmorprev");
2034: sprintf(digit,"%-d",ij);
2035: /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
2036: strcat(fileresprobmorprev,digit); /* Tvar to be done */
2037: strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
2038: strcat(fileresprobmorprev,fileres);
2039: if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
2040: printf("Problem with resultfile: %s\n", fileresprobmorprev);
2041: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
2042: }
2043: printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
2044: fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
1.66 brouard 2045: fprintf(ficresprobmorprev,"# probabilities of dying before estepm=%d months for people of exact age and weighted probabilities w1*p1j+w2*p2j+... stand dev in()\n",estepm);
1.53 brouard 2046: fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
2047: for(j=nlstate+1; j<=(nlstate+ndeath);j++){
2048: fprintf(ficresprobmorprev," p.%-d SE",j);
2049: for(i=1; i<=nlstate;i++)
2050: fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
2051: }
2052: fprintf(ficresprobmorprev,"\n");
2053: if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {
2054: printf("Problem with gnuplot file: %s\n", optionfilegnuplot);
2055: fprintf(ficlog,"Problem with gnuplot file: %s\n", optionfilegnuplot);
2056: exit(0);
2057: }
2058: else{
2059: fprintf(ficgp,"\n# Routine varevsij");
2060: }
2061: if((fichtm=fopen(optionfilehtm,"a"))==NULL) {
2062: printf("Problem with html file: %s\n", optionfilehtm);
2063: fprintf(ficlog,"Problem with html file: %s\n", optionfilehtm);
2064: exit(0);
2065: }
2066: else{
1.67 brouard 2067: fprintf(fichtm,"\n<li><h4> Computing probabilities of dying over estepm months as a weighted average (i.e global mortality independent of initial healh state)</h4></li>\n");
2068: fprintf(fichtm,"\n<br>%s <br>\n",digitp);
1.53 brouard 2069: }
2070: varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
2071:
2072: 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");
2073: fprintf(ficresvij,"# Age");
2074: for(i=1; i<=nlstate;i++)
2075: for(j=1; j<=nlstate;j++)
2076: fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);
2077: fprintf(ficresvij,"\n");
2078:
2079: xp=vector(1,npar);
2080: dnewm=matrix(1,nlstate,1,npar);
2081: doldm=matrix(1,nlstate,1,nlstate);
2082: dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
2083: doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
2084:
2085: gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
2086: gpp=vector(nlstate+1,nlstate+ndeath);
2087: gmp=vector(nlstate+1,nlstate+ndeath);
2088: trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
2089:
2090: if(estepm < stepm){
2091: printf ("Problem %d lower than %d\n",estepm, stepm);
2092: }
2093: else hstepm=estepm;
2094: /* For example we decided to compute the life expectancy with the smallest unit */
2095: /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
2096: nhstepm is the number of hstepm from age to agelim
2097: nstepm is the number of stepm from age to agelin.
2098: Look at hpijx to understand the reason of that which relies in memory size
2099: and note for a fixed period like k years */
2100: /* We decided (b) to get a life expectancy respecting the most precise curvature of the
2101: survival function given by stepm (the optimization length). Unfortunately it
1.66 brouard 2102: means that if the survival funtion is printed every two years of age and if
1.53 brouard 2103: you sum them up and add 1 year (area under the trapezoids) you won't get the same
2104: results. So we changed our mind and took the option of the best precision.
2105: */
2106: hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
2107: agelim = AGESUP;
2108: for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
2109: nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
2110: nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
2111: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
2112: gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
2113: gp=matrix(0,nhstepm,1,nlstate);
2114: gm=matrix(0,nhstepm,1,nlstate);
2115:
2116:
2117: for(theta=1; theta <=npar; theta++){
1.66 brouard 2118: for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
1.53 brouard 2119: xp[i] = x[i] + (i==theta ?delti[theta]:0);
2120: }
2121: hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
2122: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
2123:
2124: if (popbased==1) {
1.54 brouard 2125: if(mobilav ==0){
1.53 brouard 2126: for(i=1; i<=nlstate;i++)
2127: prlim[i][i]=probs[(int)age][i][ij];
1.54 brouard 2128: }else{ /* mobilav */
1.53 brouard 2129: for(i=1; i<=nlstate;i++)
2130: prlim[i][i]=mobaverage[(int)age][i][ij];
2131: }
2132: }
2133:
2134: for(j=1; j<= nlstate; j++){
2135: for(h=0; h<=nhstepm; h++){
2136: for(i=1, gp[h][j]=0.;i<=nlstate;i++)
2137: gp[h][j] += prlim[i][i]*p3mat[i][j][h];
2138: }
2139: }
1.66 brouard 2140: /* This for computing probability of death (h=1 means
2141: computed over hstepm matrices product = hstepm*stepm months)
2142: as a weighted average of prlim.
2143: */
1.69 ! brouard 2144: for(j=nlstate+1;j<=nlstate+ndeath;j++){
1.68 lievre 2145: for(i=1,gpp[j]=0.; i<= nlstate; i++)
1.53 brouard 2146: gpp[j] += prlim[i][i]*p3mat[i][j][1];
2147: }
1.66 brouard 2148: /* end probability of death */
1.53 brouard 2149:
1.66 brouard 2150: for(i=1; i<=npar; i++) /* Computes gradient x - delta */
1.53 brouard 2151: xp[i] = x[i] - (i==theta ?delti[theta]:0);
2152: hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
2153: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
2154:
2155: if (popbased==1) {
1.54 brouard 2156: if(mobilav ==0){
1.53 brouard 2157: for(i=1; i<=nlstate;i++)
2158: prlim[i][i]=probs[(int)age][i][ij];
1.54 brouard 2159: }else{ /* mobilav */
1.53 brouard 2160: for(i=1; i<=nlstate;i++)
2161: prlim[i][i]=mobaverage[(int)age][i][ij];
2162: }
2163: }
2164:
2165: for(j=1; j<= nlstate; j++){
2166: for(h=0; h<=nhstepm; h++){
2167: for(i=1, gm[h][j]=0.;i<=nlstate;i++)
2168: gm[h][j] += prlim[i][i]*p3mat[i][j][h];
2169: }
2170: }
1.66 brouard 2171: /* This for computing probability of death (h=1 means
2172: computed over hstepm matrices product = hstepm*stepm months)
2173: as a weighted average of prlim.
2174: */
1.69 ! brouard 2175: for(j=nlstate+1;j<=nlstate+ndeath;j++){
1.68 lievre 2176: for(i=1,gmp[j]=0.; i<= nlstate; i++)
2177: gmp[j] += prlim[i][i]*p3mat[i][j][1];
1.53 brouard 2178: }
1.66 brouard 2179: /* end probability of death */
1.53 brouard 2180:
2181: for(j=1; j<= nlstate; j++) /* vareij */
2182: for(h=0; h<=nhstepm; h++){
2183: gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
2184: }
1.68 lievre 2185:
1.53 brouard 2186: for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
2187: gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
2188: }
2189:
2190: } /* End theta */
2191:
2192: trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
2193:
2194: for(h=0; h<=nhstepm; h++) /* veij */
2195: for(j=1; j<=nlstate;j++)
2196: for(theta=1; theta <=npar; theta++)
2197: trgradg[h][j][theta]=gradg[h][theta][j];
2198:
2199: for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
1.69 ! brouard 2200: for(theta=1; theta <=npar; theta++)
1.53 brouard 2201: trgradgp[j][theta]=gradgp[theta][j];
1.69 ! brouard 2202:
1.53 brouard 2203:
2204: hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
2205: for(i=1;i<=nlstate;i++)
2206: for(j=1;j<=nlstate;j++)
2207: vareij[i][j][(int)age] =0.;
2208:
2209: for(h=0;h<=nhstepm;h++){
2210: for(k=0;k<=nhstepm;k++){
2211: matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
2212: matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
2213: for(i=1;i<=nlstate;i++)
2214: for(j=1;j<=nlstate;j++)
2215: vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
2216: }
2217: }
2218:
2219: /* pptj */
2220: matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
2221: matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
1.68 lievre 2222:
2223: for(j=nlstate+1;j<=nlstate+ndeath;j++)
2224: for(i=nlstate+1;i<=nlstate+ndeath;i++){
1.53 brouard 2225: varppt[j][i]=doldmp[j][i];
2226: /* end ppptj */
1.66 brouard 2227: /* x centered again */
1.53 brouard 2228: hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);
2229: prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);
2230:
2231: if (popbased==1) {
1.54 brouard 2232: if(mobilav ==0){
1.53 brouard 2233: for(i=1; i<=nlstate;i++)
2234: prlim[i][i]=probs[(int)age][i][ij];
1.54 brouard 2235: }else{ /* mobilav */
1.53 brouard 2236: for(i=1; i<=nlstate;i++)
2237: prlim[i][i]=mobaverage[(int)age][i][ij];
2238: }
2239: }
2240:
1.66 brouard 2241: /* This for computing probability of death (h=1 means
2242: computed over hstepm (estepm) matrices product = hstepm*stepm months)
2243: as a weighted average of prlim.
2244: */
1.68 lievre 2245: for(j=nlstate+1;j<=nlstate+ndeath;j++){
2246: for(i=1,gmp[j]=0.;i<= nlstate; i++)
1.53 brouard 2247: gmp[j] += prlim[i][i]*p3mat[i][j][1];
2248: }
1.66 brouard 2249: /* end probability of death */
1.53 brouard 2250:
2251: fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
2252: for(j=nlstate+1; j<=(nlstate+ndeath);j++){
2253: fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
2254: for(i=1; i<=nlstate;i++){
2255: fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
2256: }
2257: }
2258: fprintf(ficresprobmorprev,"\n");
2259:
2260: fprintf(ficresvij,"%.0f ",age );
2261: for(i=1; i<=nlstate;i++)
2262: for(j=1; j<=nlstate;j++){
2263: fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
2264: }
2265: fprintf(ficresvij,"\n");
2266: free_matrix(gp,0,nhstepm,1,nlstate);
2267: free_matrix(gm,0,nhstepm,1,nlstate);
2268: free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
2269: free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
2270: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
2271: } /* End age */
2272: free_vector(gpp,nlstate+1,nlstate+ndeath);
2273: free_vector(gmp,nlstate+1,nlstate+ndeath);
2274: free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
2275: free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
2276: fprintf(ficgp,"\nset noparametric;set nolabel; set ter png small;set size 0.65, 0.65");
2277: /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */
2278: fprintf(ficgp,"\n set log y; set nolog x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
1.67 brouard 2279: /* fprintf(ficgp,"\n plot \"%s\" u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm); */
2280: /* fprintf(ficgp,"\n replot \"%s\" u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm); */
2281: /* fprintf(ficgp,"\n replot \"%s\" u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm); */
2282: fprintf(ficgp,"\n plot \"%s\" u 1:($3) not w l 1 ",fileresprobmorprev);
2283: fprintf(ficgp,"\n replot \"%s\" u 1:(($3+1.96*$4)) t \"95\%% interval\" w l 2 ",fileresprobmorprev);
2284: fprintf(ficgp,"\n replot \"%s\" u 1:(($3-1.96*$4)) not w l 2 ",fileresprobmorprev);
1.53 brouard 2285: fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",fileresprobmorprev,fileresprobmorprev);
1.66 brouard 2286: fprintf(fichtm,"\n<br> Probability is computed over estepm=%d months. <br> <img src=\"varmuptjgr%s%s.png\"> <br>\n", estepm,digitp,digit);
1.53 brouard 2287: /* 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);
2288: */
2289: fprintf(ficgp,"\nset out \"varmuptjgr%s%s.png\";replot;",digitp,digit);
2290:
2291: free_vector(xp,1,npar);
2292: free_matrix(doldm,1,nlstate,1,nlstate);
2293: free_matrix(dnewm,1,nlstate,1,npar);
2294: free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
2295: free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
2296: free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
1.55 lievre 2297: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
1.53 brouard 2298: fclose(ficresprobmorprev);
2299: fclose(ficgp);
2300: fclose(fichtm);
2301: }
2302:
2303: /************ Variance of prevlim ******************/
2304: 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)
2305: {
2306: /* Variance of prevalence limit */
1.59 brouard 2307: /* double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
1.53 brouard 2308: double **newm;
2309: double **dnewm,**doldm;
2310: int i, j, nhstepm, hstepm;
2311: int k, cptcode;
2312: double *xp;
2313: double *gp, *gm;
2314: double **gradg, **trgradg;
2315: double age,agelim;
2316: int theta;
2317:
1.54 brouard 2318: fprintf(ficresvpl,"# Standard deviation of stable prevalences \n");
1.53 brouard 2319: fprintf(ficresvpl,"# Age");
2320: for(i=1; i<=nlstate;i++)
2321: fprintf(ficresvpl," %1d-%1d",i,i);
2322: fprintf(ficresvpl,"\n");
2323:
2324: xp=vector(1,npar);
2325: dnewm=matrix(1,nlstate,1,npar);
2326: doldm=matrix(1,nlstate,1,nlstate);
2327:
2328: hstepm=1*YEARM; /* Every year of age */
2329: hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */
2330: agelim = AGESUP;
2331: for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
2332: nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
2333: if (stepm >= YEARM) hstepm=1;
2334: nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
2335: gradg=matrix(1,npar,1,nlstate);
2336: gp=vector(1,nlstate);
2337: gm=vector(1,nlstate);
2338:
2339: for(theta=1; theta <=npar; theta++){
2340: for(i=1; i<=npar; i++){ /* Computes gradient */
2341: xp[i] = x[i] + (i==theta ?delti[theta]:0);
2342: }
2343: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
2344: for(i=1;i<=nlstate;i++)
2345: gp[i] = prlim[i][i];
2346:
2347: for(i=1; i<=npar; i++) /* Computes gradient */
2348: xp[i] = x[i] - (i==theta ?delti[theta]:0);
2349: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
2350: for(i=1;i<=nlstate;i++)
2351: gm[i] = prlim[i][i];
2352:
2353: for(i=1;i<=nlstate;i++)
2354: gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
2355: } /* End theta */
2356:
2357: trgradg =matrix(1,nlstate,1,npar);
2358:
2359: for(j=1; j<=nlstate;j++)
2360: for(theta=1; theta <=npar; theta++)
2361: trgradg[j][theta]=gradg[theta][j];
2362:
2363: for(i=1;i<=nlstate;i++)
2364: varpl[i][(int)age] =0.;
2365: matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
2366: matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
2367: for(i=1;i<=nlstate;i++)
2368: varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
2369:
2370: fprintf(ficresvpl,"%.0f ",age );
2371: for(i=1; i<=nlstate;i++)
2372: fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
2373: fprintf(ficresvpl,"\n");
2374: free_vector(gp,1,nlstate);
2375: free_vector(gm,1,nlstate);
2376: free_matrix(gradg,1,npar,1,nlstate);
2377: free_matrix(trgradg,1,nlstate,1,npar);
2378: } /* End age */
2379:
2380: free_vector(xp,1,npar);
2381: free_matrix(doldm,1,nlstate,1,npar);
2382: free_matrix(dnewm,1,nlstate,1,nlstate);
2383:
2384: }
2385:
2386: /************ Variance of one-step probabilities ******************/
2387: void varprob(char optionfilefiname[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij, int *Tvar, int **nbcode, int *ncodemax)
2388: {
2389: int i, j=0, i1, k1, l1, t, tj;
2390: int k2, l2, j1, z1;
2391: int k=0,l, cptcode;
2392: int first=1, first1;
2393: double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
2394: double **dnewm,**doldm;
2395: double *xp;
2396: double *gp, *gm;
2397: double **gradg, **trgradg;
2398: double **mu;
2399: double age,agelim, cov[NCOVMAX];
2400: double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
2401: int theta;
2402: char fileresprob[FILENAMELENGTH];
2403: char fileresprobcov[FILENAMELENGTH];
2404: char fileresprobcor[FILENAMELENGTH];
2405:
2406: double ***varpij;
2407:
2408: strcpy(fileresprob,"prob");
2409: strcat(fileresprob,fileres);
2410: if((ficresprob=fopen(fileresprob,"w"))==NULL) {
2411: printf("Problem with resultfile: %s\n", fileresprob);
2412: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
2413: }
2414: strcpy(fileresprobcov,"probcov");
2415: strcat(fileresprobcov,fileres);
2416: if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
2417: printf("Problem with resultfile: %s\n", fileresprobcov);
2418: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
2419: }
2420: strcpy(fileresprobcor,"probcor");
2421: strcat(fileresprobcor,fileres);
2422: if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
2423: printf("Problem with resultfile: %s\n", fileresprobcor);
2424: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
2425: }
2426: printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
2427: fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
2428: printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
2429: fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
2430: printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
2431: fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
2432:
2433: fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
2434: fprintf(ficresprob,"# Age");
2435: fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
2436: fprintf(ficresprobcov,"# Age");
2437: fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
2438: fprintf(ficresprobcov,"# Age");
2439:
2440:
2441: for(i=1; i<=nlstate;i++)
2442: for(j=1; j<=(nlstate+ndeath);j++){
2443: fprintf(ficresprob," p%1d-%1d (SE)",i,j);
2444: fprintf(ficresprobcov," p%1d-%1d ",i,j);
2445: fprintf(ficresprobcor," p%1d-%1d ",i,j);
2446: }
1.69 ! brouard 2447: /* fprintf(ficresprob,"\n");
1.53 brouard 2448: fprintf(ficresprobcov,"\n");
2449: fprintf(ficresprobcor,"\n");
1.69 ! brouard 2450: */
! 2451: xp=vector(1,npar);
1.53 brouard 2452: dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
2453: doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
2454: mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
2455: varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
2456: first=1;
2457: if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {
2458: printf("Problem with gnuplot file: %s\n", optionfilegnuplot);
2459: fprintf(ficlog,"Problem with gnuplot file: %s\n", optionfilegnuplot);
2460: exit(0);
2461: }
2462: else{
2463: fprintf(ficgp,"\n# Routine varprob");
2464: }
2465: if((fichtm=fopen(optionfilehtm,"a"))==NULL) {
2466: printf("Problem with html file: %s\n", optionfilehtm);
2467: fprintf(ficlog,"Problem with html file: %s\n", optionfilehtm);
2468: exit(0);
2469: }
2470: else{
2471: fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
2472: fprintf(fichtm,"\n");
2473:
2474: fprintf(fichtm,"\n<li><h4> Computing matrix of variance-covariance of step probabilities</h4></li>\n");
2475: 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");
2476: 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");
2477:
2478: }
2479:
2480: cov[1]=1;
2481: tj=cptcoveff;
2482: if (cptcovn<1) {tj=1;ncodemax[1]=1;}
2483: j1=0;
2484: for(t=1; t<=tj;t++){
2485: for(i1=1; i1<=ncodemax[t];i1++){
2486: j1++;
2487: if (cptcovn>0) {
2488: fprintf(ficresprob, "\n#********** Variable ");
2489: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
1.69 ! brouard 2490: fprintf(ficresprob, "**********\n#\n");
1.53 brouard 2491: fprintf(ficresprobcov, "\n#********** Variable ");
2492: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
1.69 ! brouard 2493: fprintf(ficresprobcov, "**********\n#\n");
1.53 brouard 2494:
2495: fprintf(ficgp, "\n#********** Variable ");
1.69 ! brouard 2496: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
! 2497: fprintf(ficgp, "**********\n#\n");
1.53 brouard 2498:
2499:
2500: fprintf(fichtm, "\n<hr size=\"2\" color=\"#EC5E5E\">********** Variable ");
2501: for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
2502: fprintf(fichtm, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
2503:
2504: fprintf(ficresprobcor, "\n#********** Variable ");
2505: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
1.69 ! brouard 2506: fprintf(ficresprobcor, "**********\n#");
1.53 brouard 2507: }
2508:
2509: for (age=bage; age<=fage; age ++){
2510: cov[2]=age;
2511: for (k=1; k<=cptcovn;k++) {
2512: cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];
2513: }
2514: for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
2515: for (k=1; k<=cptcovprod;k++)
2516: cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
2517:
2518: gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
2519: trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
2520: gp=vector(1,(nlstate)*(nlstate+ndeath));
2521: gm=vector(1,(nlstate)*(nlstate+ndeath));
2522:
2523: for(theta=1; theta <=npar; theta++){
2524: for(i=1; i<=npar; i++)
2525: xp[i] = x[i] + (i==theta ?delti[theta]:0);
2526:
2527: pmij(pmmij,cov,ncovmodel,xp,nlstate);
2528:
2529: k=0;
2530: for(i=1; i<= (nlstate); i++){
2531: for(j=1; j<=(nlstate+ndeath);j++){
2532: k=k+1;
2533: gp[k]=pmmij[i][j];
2534: }
2535: }
2536:
2537: for(i=1; i<=npar; i++)
2538: xp[i] = x[i] - (i==theta ?delti[theta]:0);
2539:
2540: pmij(pmmij,cov,ncovmodel,xp,nlstate);
2541: k=0;
2542: for(i=1; i<=(nlstate); i++){
2543: for(j=1; j<=(nlstate+ndeath);j++){
2544: k=k+1;
2545: gm[k]=pmmij[i][j];
2546: }
2547: }
2548:
2549: for(i=1; i<= (nlstate)*(nlstate+ndeath); i++)
2550: gradg[theta][i]=(gp[i]-gm[i])/2./delti[theta];
2551: }
2552:
2553: for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
2554: for(theta=1; theta <=npar; theta++)
2555: trgradg[j][theta]=gradg[theta][j];
2556:
2557: matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov);
2558: matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);
1.59 brouard 2559: free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
2560: free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
2561: free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
2562: free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
2563:
1.53 brouard 2564: pmij(pmmij,cov,ncovmodel,x,nlstate);
2565:
2566: k=0;
2567: for(i=1; i<=(nlstate); i++){
2568: for(j=1; j<=(nlstate+ndeath);j++){
2569: k=k+1;
2570: mu[k][(int) age]=pmmij[i][j];
2571: }
2572: }
2573: for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
2574: for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
2575: varpij[i][j][(int)age] = doldm[i][j];
2576:
2577: /*printf("\n%d ",(int)age);
1.59 brouard 2578: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
2579: printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
2580: fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
2581: }*/
1.53 brouard 2582:
2583: fprintf(ficresprob,"\n%d ",(int)age);
2584: fprintf(ficresprobcov,"\n%d ",(int)age);
2585: fprintf(ficresprobcor,"\n%d ",(int)age);
2586:
2587: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)
2588: fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));
2589: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
2590: fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);
2591: fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
2592: }
2593: i=0;
2594: for (k=1; k<=(nlstate);k++){
2595: for (l=1; l<=(nlstate+ndeath);l++){
2596: i=i++;
2597: fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
2598: fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
2599: for (j=1; j<=i;j++){
2600: fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);
2601: fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));
2602: }
2603: }
2604: }/* end of loop for state */
2605: } /* end of loop for age */
2606:
2607: /* Confidence intervalle of pij */
2608: /*
1.59 brouard 2609: fprintf(ficgp,"\nset noparametric;unset label");
2610: fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");
2611: fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
2612: 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);
2613: fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);
2614: fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);
2615: fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);
1.53 brouard 2616: */
2617:
2618: /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
2619: first1=1;
2620: for (k2=1; k2<=(nlstate);k2++){
2621: for (l2=1; l2<=(nlstate+ndeath);l2++){
2622: if(l2==k2) continue;
2623: j=(k2-1)*(nlstate+ndeath)+l2;
2624: for (k1=1; k1<=(nlstate);k1++){
2625: for (l1=1; l1<=(nlstate+ndeath);l1++){
2626: if(l1==k1) continue;
2627: i=(k1-1)*(nlstate+ndeath)+l1;
2628: if(i<=j) continue;
2629: for (age=bage; age<=fage; age ++){
2630: if ((int)age %5==0){
2631: v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;
2632: v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;
2633: cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;
2634: mu1=mu[i][(int) age]/stepm*YEARM ;
2635: mu2=mu[j][(int) age]/stepm*YEARM;
2636: c12=cv12/sqrt(v1*v2);
2637: /* Computing eigen value of matrix of covariance */
2638: lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
2639: lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
2640: /* Eigen vectors */
2641: v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
2642: /*v21=sqrt(1.-v11*v11); *//* error */
2643: v21=(lc1-v1)/cv12*v11;
2644: v12=-v21;
2645: v22=v11;
2646: tnalp=v21/v11;
2647: if(first1==1){
2648: first1=0;
2649: 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);
2650: }
2651: 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);
2652: /*printf(fignu*/
2653: /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */
2654: /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */
2655: if(first==1){
2656: first=0;
2657: fprintf(ficgp,"\nset parametric;unset label");
2658: 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);
2659: fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
2660: 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);
2661: fprintf(fichtm,"\n<br><img src=\"varpijgr%s%d%1d%1d-%1d%1d.png\"> ",optionfilefiname, j1,k1,l1,k2,l2);
2662: fprintf(fichtm,"\n<br> Correlation at age %d (%.3f),",(int) age, c12);
2663: fprintf(ficgp,"\nset out \"varpijgr%s%d%1d%1d-%1d%1d.png\"",optionfilefiname, j1,k1,l1,k2,l2);
2664: fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
2665: fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
2666: 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",\
2667: mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
2668: mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
2669: }else{
2670: first=0;
2671: fprintf(fichtm," %d (%.3f),",(int) age, c12);
2672: fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
2673: fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
2674: 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",\
2675: mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
2676: mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
2677: }/* if first */
2678: } /* age mod 5 */
2679: } /* end loop age */
2680: fprintf(ficgp,"\nset out \"varpijgr%s%d%1d%1d-%1d%1d.png\";replot;",optionfilefiname, j1,k1,l1,k2,l2);
2681: first=1;
2682: } /*l12 */
2683: } /* k12 */
2684: } /*l1 */
2685: }/* k1 */
2686: } /* loop covariates */
2687: }
1.59 brouard 2688: free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
2689: free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
1.53 brouard 2690: free_vector(xp,1,npar);
2691: fclose(ficresprob);
2692: fclose(ficresprobcov);
2693: fclose(ficresprobcor);
2694: fclose(ficgp);
2695: fclose(fichtm);
2696: }
2697:
2698:
2699: /******************* Printing html file ***********/
2700: void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \
2701: int lastpass, int stepm, int weightopt, char model[],\
2702: int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
2703: int popforecast, int estepm ,\
2704: double jprev1, double mprev1,double anprev1, \
2705: double jprev2, double mprev2,double anprev2){
2706: int jj1, k1, i1, cpt;
2707: /*char optionfilehtm[FILENAMELENGTH];*/
2708: if((fichtm=fopen(optionfilehtm,"a"))==NULL) {
2709: printf("Problem with %s \n",optionfilehtm), exit(0);
2710: fprintf(ficlog,"Problem with %s \n",optionfilehtm), exit(0);
2711: }
2712:
2713: fprintf(fichtm,"<ul><li><h4>Result files (first order: no variance)</h4>\n
2714: - 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
2715: - Estimated transition probabilities over %d (stepm) months: <a href=\"pij%s\">pij%s</a><br>\n
2716: - Stable prevalence in each health state: <a href=\"pl%s\">pl%s</a> <br>\n
2717: - Life expectancies by age and initial health status (estepm=%2d months):
2718: <a href=\"e%s\">e%s</a> <br>\n</li>", \
2719: jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,fileres,fileres,stepm,fileres,fileres,fileres,fileres,estepm,fileres,fileres);
2720:
2721: fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
2722:
2723: m=cptcoveff;
2724: if (cptcovn < 1) {m=1;ncodemax[1]=1;}
2725:
2726: jj1=0;
2727: for(k1=1; k1<=m;k1++){
2728: for(i1=1; i1<=ncodemax[k1];i1++){
2729: jj1++;
2730: if (cptcovn > 0) {
2731: fprintf(fichtm,"<hr size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
2732: for (cpt=1; cpt<=cptcoveff;cpt++)
2733: fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
2734: fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
2735: }
2736: /* Pij */
2737: 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>
2738: <img src=\"pe%s%d1.png\">",stepm,strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);
2739: /* Quasi-incidences */
2740: 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>
2741: <img src=\"pe%s%d2.png\">",stepm,strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);
2742: /* Stable prevalence in each health state */
2743: for(cpt=1; cpt<nlstate;cpt++){
2744: fprintf(fichtm,"<br>- Stable prevalence in each health state : p%s%d%d.png<br>
2745: <img src=\"p%s%d%d.png\">",strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);
2746: }
2747: for(cpt=1; cpt<=nlstate;cpt++) {
2748: fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): exp%s%d%d.png <br>
2749: <img src=\"exp%s%d%d.png\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);
2750: }
2751: fprintf(fichtm,"\n<br>- Total life expectancy by age and
2752: health expectancies in states (1) and (2): e%s%d.png<br>
2753: <img src=\"e%s%d.png\">",strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);
2754: } /* end i1 */
2755: }/* End k1 */
2756: fprintf(fichtm,"</ul>");
2757:
2758:
2759: fprintf(fichtm,"\n<br><li><h4> Result files (second order: variances)</h4>\n
2760: - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n
2761: - Variance of one-step probabilities: <a href=\"prob%s\">prob%s</a> <br>\n
2762: - Variance-covariance of one-step probabilities: <a href=\"probcov%s\">probcov%s</a> <br>\n
2763: - Correlation matrix of one-step probabilities: <a href=\"probcor%s\">probcor%s</a> <br>\n
2764: - Variances and covariances of life expectancies by age and initial health status (estepm=%d months): <a href=\"v%s\">v%s</a><br>\n
2765: - Health expectancies with their variances (no covariance): <a href=\"t%s\">t%s</a> <br>\n
2766: - 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);
2767:
2768: if(popforecast==1) fprintf(fichtm,"\n
2769: - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n
2770: - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n
2771: <br>",fileres,fileres,fileres,fileres);
2772: else
2773: 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);
2774: fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
2775:
2776: m=cptcoveff;
2777: if (cptcovn < 1) {m=1;ncodemax[1]=1;}
2778:
2779: jj1=0;
2780: for(k1=1; k1<=m;k1++){
2781: for(i1=1; i1<=ncodemax[k1];i1++){
2782: jj1++;
2783: if (cptcovn > 0) {
2784: fprintf(fichtm,"<hr size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
2785: for (cpt=1; cpt<=cptcoveff;cpt++)
2786: fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
2787: fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
2788: }
2789: for(cpt=1; cpt<=nlstate;cpt++) {
2790: fprintf(fichtm,"<br>- Observed and stationary prevalence (with confident
2791: interval) in state (%d): v%s%d%d.png <br>
2792: <img src=\"v%s%d%d.png\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);
2793: }
2794: } /* end i1 */
2795: }/* End k1 */
2796: fprintf(fichtm,"</ul>");
2797: fclose(fichtm);
2798: }
2799:
2800: /******************* Gnuplot file **************/
2801: void printinggnuplot(char fileres[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
2802:
2803: int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;
2804: int ng;
2805: if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {
2806: printf("Problem with file %s",optionfilegnuplot);
2807: fprintf(ficlog,"Problem with file %s",optionfilegnuplot);
2808: }
2809:
1.54 brouard 2810: /*#ifdef windows */
1.53 brouard 2811: fprintf(ficgp,"cd \"%s\" \n",pathc);
1.54 brouard 2812: /*#endif */
1.53 brouard 2813: m=pow(2,cptcoveff);
2814:
2815: /* 1eme*/
2816: for (cpt=1; cpt<= nlstate ; cpt ++) {
2817: for (k1=1; k1<= m ; k1 ++) {
2818: fprintf(ficgp,"\nset out \"v%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);
2819: 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);
2820:
2821: for (i=1; i<= nlstate ; i ++) {
2822: if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
2823: else fprintf(ficgp," \%%*lf (\%%*lf)");
2824: }
1.69 ! brouard 2825: fprintf(ficgp,"\" t\"Stable prevalence\" w l 0,\"vpl%s\" every :::%d::%d u 1:($2+1.96*$3) \"\%%lf",fileres,k1-1,k1-1);
1.53 brouard 2826: for (i=1; i<= nlstate ; i ++) {
2827: if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
2828: else fprintf(ficgp," \%%*lf (\%%*lf)");
2829: }
1.69 ! brouard 2830: fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"vpl%s\" every :::%d::%d u 1:($2-1.96*$3) \"\%%lf",fileres,k1-1,k1-1);
1.53 brouard 2831: for (i=1; i<= nlstate ; i ++) {
2832: if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
2833: else fprintf(ficgp," \%%*lf (\%%*lf)");
2834: }
2835: fprintf(ficgp,"\" t\"\" w l 1,\"p%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",fileres,k1-1,k1-1,2+4*(cpt-1));
2836: }
2837: }
2838: /*2 eme*/
2839:
2840: for (k1=1; k1<= m ; k1 ++) {
2841: fprintf(ficgp,"\nset out \"e%s%d.png\" \n",strtok(optionfile, "."),k1);
2842: fprintf(ficgp,"set ylabel \"Years\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] ",ageminpar,fage);
2843:
2844: for (i=1; i<= nlstate+1 ; i ++) {
2845: k=2*i;
2846: fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:2 \"\%%lf",fileres,k1-1,k1-1);
2847: for (j=1; j<= nlstate+1 ; j ++) {
2848: if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
2849: else fprintf(ficgp," \%%*lf (\%%*lf)");
2850: }
2851: if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");
2852: else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);
2853: fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",fileres,k1-1,k1-1);
2854: for (j=1; j<= nlstate+1 ; j ++) {
2855: if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
2856: else fprintf(ficgp," \%%*lf (\%%*lf)");
2857: }
2858: fprintf(ficgp,"\" t\"\" w l 0,");
2859: fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",fileres,k1-1,k1-1);
2860: for (j=1; j<= nlstate+1 ; j ++) {
2861: if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
2862: else fprintf(ficgp," \%%*lf (\%%*lf)");
2863: }
2864: if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");
2865: else fprintf(ficgp,"\" t\"\" w l 0,");
2866: }
2867: }
2868:
2869: /*3eme*/
2870:
2871: for (k1=1; k1<= m ; k1 ++) {
2872: for (cpt=1; cpt<= nlstate ; cpt ++) {
2873: k=2+nlstate*(2*cpt-2);
2874: fprintf(ficgp,"\nset out \"exp%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);
2875: fprintf(ficgp,"set ter png small\nset size 0.65,0.65\nplot [%.f:%.f] \"e%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,fileres,k1-1,k1-1,k,cpt);
2876: /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
2877: for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
2878: fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
2879: fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
2880: for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
2881: fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
2882:
2883: */
2884: for (i=1; i< nlstate ; i ++) {
2885: 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);
2886:
2887: }
2888: }
2889: }
2890:
2891: /* CV preval stat */
2892: for (k1=1; k1<= m ; k1 ++) {
2893: for (cpt=1; cpt<nlstate ; cpt ++) {
2894: k=3;
2895: fprintf(ficgp,"\nset out \"p%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);
2896: 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/($%d",ageminpar,agemaxpar,fileres,k1,k+cpt+1,k+1);
2897:
2898: for (i=1; i< nlstate ; i ++)
2899: fprintf(ficgp,"+$%d",k+i+1);
2900: fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);
2901:
2902: l=3+(nlstate+ndeath)*cpt;
2903: fprintf(ficgp,",\"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",fileres,k1,l+cpt+1,l+1);
2904: for (i=1; i< nlstate ; i ++) {
2905: l=3+(nlstate+ndeath)*cpt;
2906: fprintf(ficgp,"+$%d",l+i+1);
2907: }
2908: fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);
2909: }
2910: }
2911:
2912: /* proba elementaires */
2913: for(i=1,jk=1; i <=nlstate; i++){
2914: for(k=1; k <=(nlstate+ndeath); k++){
2915: if (k != i) {
2916: for(j=1; j <=ncovmodel; j++){
2917: fprintf(ficgp,"p%d=%f ",jk,p[jk]);
2918: jk++;
2919: fprintf(ficgp,"\n");
2920: }
2921: }
2922: }
2923: }
2924:
2925: for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/
2926: for(jk=1; jk <=m; jk++) {
2927: fprintf(ficgp,"\nset out \"pe%s%d%d.png\" \n",strtok(optionfile, "."),jk,ng);
2928: if (ng==2)
2929: fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
2930: else
2931: fprintf(ficgp,"\nset title \"Probability\"\n");
2932: fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65\nset log y\nplot [%.f:%.f] ",ageminpar,agemaxpar);
2933: i=1;
2934: for(k2=1; k2<=nlstate; k2++) {
2935: k3=i;
2936: for(k=1; k<=(nlstate+ndeath); k++) {
2937: if (k != k2){
2938: if(ng==2)
2939: fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);
2940: else
2941: fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
2942: ij=1;
2943: for(j=3; j <=ncovmodel; j++) {
2944: if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
2945: fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
2946: ij++;
2947: }
2948: else
2949: fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
2950: }
2951: fprintf(ficgp,")/(1");
2952:
2953: for(k1=1; k1 <=nlstate; k1++){
2954: fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);
2955: ij=1;
2956: for(j=3; j <=ncovmodel; j++){
2957: if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
2958: fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
2959: ij++;
2960: }
2961: else
2962: fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
2963: }
2964: fprintf(ficgp,")");
2965: }
2966: fprintf(ficgp,") t \"p%d%d\" ", k2,k);
2967: if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");
2968: i=i+ncovmodel;
2969: }
2970: } /* end k */
2971: } /* end k2 */
2972: } /* end jk */
2973: } /* end ng */
2974: fclose(ficgp);
2975: } /* end gnuplot */
2976:
2977:
2978: /*************** Moving average **************/
1.54 brouard 2979: int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav){
1.53 brouard 2980:
2981: int i, cpt, cptcod;
1.58 lievre 2982: int modcovmax =1;
1.54 brouard 2983: int mobilavrange, mob;
1.53 brouard 2984: double age;
1.58 lievre 2985:
2986: modcovmax=2*cptcoveff;/* Max number of modalities. We suppose
2987: a covariate has 2 modalities */
2988: if (cptcovn<1) modcovmax=1; /* At least 1 pass */
2989:
1.54 brouard 2990: if(mobilav==1||mobilav ==3 ||mobilav==5 ||mobilav== 7){
2991: if(mobilav==1) mobilavrange=5; /* default */
2992: else mobilavrange=mobilav;
2993: for (age=bage; age<=fage; age++)
2994: for (i=1; i<=nlstate;i++)
1.58 lievre 2995: for (cptcod=1;cptcod<=modcovmax;cptcod++)
1.54 brouard 2996: mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
2997: /* We keep the original values on the extreme ages bage, fage and for
2998: fage+1 and bage-1 we use a 3 terms moving average; for fage+2 bage+2
2999: we use a 5 terms etc. until the borders are no more concerned.
3000: */
3001: for (mob=3;mob <=mobilavrange;mob=mob+2){
3002: for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){
3003: for (i=1; i<=nlstate;i++){
1.58 lievre 3004: for (cptcod=1;cptcod<=modcovmax;cptcod++){
1.54 brouard 3005: mobaverage[(int)age][i][cptcod] =probs[(int)age][i][cptcod];
3006: for (cpt=1;cpt<=(mob-1)/2;cpt++){
3007: mobaverage[(int)age][i][cptcod] +=probs[(int)age-cpt][i][cptcod];
3008: mobaverage[(int)age][i][cptcod] +=probs[(int)age+cpt][i][cptcod];
3009: }
3010: mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/mob;
3011: }
1.53 brouard 3012: }
1.54 brouard 3013: }/* end age */
3014: }/* end mob */
3015: }else return -1;
3016: return 0;
3017: }/* End movingaverage */
1.53 brouard 3018:
3019:
3020: /************** Forecasting ******************/
3021: 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){
1.69 ! brouard 3022: /* proj1, year, month, day of starting projection
! 3023: agemin, agemax range of age
! 3024: dateprev1 dateprev2 range of dates during which prevalence is computed
! 3025:
! 3026: */
! 3027: int yearp, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;
1.53 brouard 3028: int *popage;
1.69 ! brouard 3029: double calagedatem, agelim, kk1, kk2, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
1.53 brouard 3030: double *popeffectif,*popcount;
3031: double ***p3mat;
1.55 lievre 3032: double ***mobaverage;
1.53 brouard 3033: char fileresf[FILENAMELENGTH];
3034:
1.69 ! brouard 3035: agelim=AGESUP;
! 3036: calagedatem=(anproj1+mproj1/12.+jproj1/365.-dateintmean)*YEARM; /* offset
! 3037: from the mean date of interviews between dateprev1 and dateprev2
! 3038: (in fractional years converted to fractional months) */
! 3039: /* Computing age-specific starting prevalence between exact
! 3040: dateprev1 and dateprev2 (in float years) and
! 3041: shifting ages from calagedatem.
! 3042: */
! 3043: prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedatem);
1.53 brouard 3044:
3045: strcpy(fileresf,"f");
3046: strcat(fileresf,fileres);
3047: if((ficresf=fopen(fileresf,"w"))==NULL) {
3048: printf("Problem with forecast resultfile: %s\n", fileresf);
3049: fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);
3050: }
3051: printf("Computing forecasting: result on file '%s' \n", fileresf);
3052: fprintf(ficlog,"Computing forecasting: result on file '%s' \n", fileresf);
3053:
3054: if (cptcoveff==0) ncodemax[cptcoveff]=1;
3055:
1.54 brouard 3056: if (mobilav!=0) {
1.53 brouard 3057: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
1.54 brouard 3058: if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
3059: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
3060: printf(" Error in movingaverage mobilav=%d\n",mobilav);
3061: }
1.53 brouard 3062: }
3063:
3064: stepsize=(int) (stepm+YEARM-1)/YEARM;
3065: if (stepm<=12) stepsize=1;
3066:
3067: agelim=AGESUP;
3068:
3069: hstepm=1;
3070: hstepm=hstepm/stepm;
1.69 ! brouard 3071: yp1=modf(dateintmean,&yp);/* extracts integral of datemean in yp and
! 3072: fractional in yp1 */
1.53 brouard 3073: anprojmean=yp;
3074: yp2=modf((yp1*12),&yp);
3075: mprojmean=yp;
3076: yp1=modf((yp2*30.5),&yp);
3077: jprojmean=yp;
3078: if(jprojmean==0) jprojmean=1;
3079: if(mprojmean==0) jprojmean=1;
3080:
1.69 ! brouard 3081: fprintf(ficresf,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f ",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2);
1.53 brouard 3082:
1.69 ! brouard 3083: for(cptcov=1, k=0;cptcov<=i2;cptcov++){
1.53 brouard 3084: for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
3085: k=k+1;
3086: fprintf(ficresf,"\n#******");
3087: for(j=1;j<=cptcoveff;j++) {
3088: fprintf(ficresf," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
3089: }
3090: fprintf(ficresf,"******\n");
3091: fprintf(ficresf,"# StartingAge FinalAge");
3092: for(j=1; j<=nlstate+ndeath;j++) fprintf(ficresf," P.%d",j);
1.69 ! brouard 3093: for (yearp=0; yearp<=(anproj2-anproj1);yearp++) {
1.53 brouard 3094: fprintf(ficresf,"\n");
3095: fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+cpt);
3096:
1.69 ! brouard 3097: for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){
1.53 brouard 3098: nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);
3099: nhstepm = nhstepm/hstepm;
3100:
3101: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3102: oldm=oldms;savm=savms;
3103: hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
3104:
3105: for (h=0; h<=nhstepm; h++){
1.69 ! brouard 3106: if (h==(int) (calagedatem+YEARM*yearp)) {
! 3107: fprintf(ficresf,"\n");
! 3108: for(j=1;j<=cptcoveff;j++)
! 3109: fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
! 3110: fprintf(ficresf,"%.f %.f ",anproj1+yearp,agedeb+h*hstepm/YEARM*stepm);
1.53 brouard 3111: }
3112: for(j=1; j<=nlstate+ndeath;j++) {
3113: kk1=0.;kk2=0;
3114: for(i=1; i<=nlstate;i++) {
3115: if (mobilav==1)
3116: kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];
3117: else {
3118: kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];
3119: }
3120:
3121: }
1.69 ! brouard 3122: if (h==(int)(calagedatem+12*yearp)){
1.53 brouard 3123: fprintf(ficresf," %.3f", kk1);
3124:
3125: }
3126: }
3127: }
3128: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3129: }
3130: }
3131: }
3132: }
3133:
1.54 brouard 3134: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
1.53 brouard 3135:
3136: fclose(ficresf);
3137: }
3138: /************** Forecasting ******************/
3139: 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){
3140:
3141: int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;
3142: int *popage;
1.69 ! brouard 3143: double calagedatem, agelim, kk1, kk2;
1.53 brouard 3144: double *popeffectif,*popcount;
3145: double ***p3mat,***tabpop,***tabpopprev;
1.55 lievre 3146: double ***mobaverage;
1.53 brouard 3147: char filerespop[FILENAMELENGTH];
3148:
3149: tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
3150: tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
3151: agelim=AGESUP;
1.69 ! brouard 3152: calagedatem=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;
1.53 brouard 3153:
1.69 ! brouard 3154: prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedatem);
1.53 brouard 3155:
3156:
3157: strcpy(filerespop,"pop");
3158: strcat(filerespop,fileres);
3159: if((ficrespop=fopen(filerespop,"w"))==NULL) {
3160: printf("Problem with forecast resultfile: %s\n", filerespop);
3161: fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop);
3162: }
3163: printf("Computing forecasting: result on file '%s' \n", filerespop);
3164: fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop);
3165:
3166: if (cptcoveff==0) ncodemax[cptcoveff]=1;
3167:
1.54 brouard 3168: if (mobilav!=0) {
1.53 brouard 3169: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
1.54 brouard 3170: if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
3171: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
3172: printf(" Error in movingaverage mobilav=%d\n",mobilav);
3173: }
1.53 brouard 3174: }
3175:
3176: stepsize=(int) (stepm+YEARM-1)/YEARM;
3177: if (stepm<=12) stepsize=1;
3178:
3179: agelim=AGESUP;
3180:
3181: hstepm=1;
3182: hstepm=hstepm/stepm;
3183:
3184: if (popforecast==1) {
3185: if((ficpop=fopen(popfile,"r"))==NULL) {
3186: printf("Problem with population file : %s\n",popfile);exit(0);
3187: fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0);
3188: }
3189: popage=ivector(0,AGESUP);
3190: popeffectif=vector(0,AGESUP);
3191: popcount=vector(0,AGESUP);
3192:
3193: i=1;
3194: while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;
3195:
3196: imx=i;
3197: for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];
3198: }
3199:
1.69 ! brouard 3200: for(cptcov=1,k=0;cptcov<=i2;cptcov++){
1.53 brouard 3201: for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
3202: k=k+1;
3203: fprintf(ficrespop,"\n#******");
3204: for(j=1;j<=cptcoveff;j++) {
3205: fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
3206: }
3207: fprintf(ficrespop,"******\n");
3208: fprintf(ficrespop,"# Age");
3209: for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);
3210: if (popforecast==1) fprintf(ficrespop," [Population]");
3211:
3212: for (cpt=0; cpt<=0;cpt++) {
3213: fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);
3214:
1.69 ! brouard 3215: for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){
1.53 brouard 3216: nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);
3217: nhstepm = nhstepm/hstepm;
3218:
3219: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3220: oldm=oldms;savm=savms;
3221: hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
3222:
3223: for (h=0; h<=nhstepm; h++){
1.69 ! brouard 3224: if (h==(int) (calagedatem+YEARM*cpt)) {
1.53 brouard 3225: fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
3226: }
3227: for(j=1; j<=nlstate+ndeath;j++) {
3228: kk1=0.;kk2=0;
3229: for(i=1; i<=nlstate;i++) {
3230: if (mobilav==1)
3231: kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];
3232: else {
3233: kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];
3234: }
3235: }
1.69 ! brouard 3236: if (h==(int)(calagedatem+12*cpt)){
1.53 brouard 3237: tabpop[(int)(agedeb)][j][cptcod]=kk1;
3238: /*fprintf(ficrespop," %.3f", kk1);
3239: if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/
3240: }
3241: }
3242: for(i=1; i<=nlstate;i++){
3243: kk1=0.;
3244: for(j=1; j<=nlstate;j++){
3245: kk1= kk1+tabpop[(int)(agedeb)][j][cptcod];
3246: }
1.69 ! brouard 3247: tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedatem+12*cpt)*hstepm/YEARM*stepm-1)];
1.53 brouard 3248: }
3249:
1.69 ! brouard 3250: if (h==(int)(calagedatem+12*cpt)) for(j=1; j<=nlstate;j++)
1.53 brouard 3251: fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);
3252: }
3253: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3254: }
3255: }
3256:
3257: /******/
3258:
3259: for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) {
3260: fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);
1.69 ! brouard 3261: for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){
1.53 brouard 3262: nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);
3263: nhstepm = nhstepm/hstepm;
3264:
3265: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3266: oldm=oldms;savm=savms;
3267: hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
3268: for (h=0; h<=nhstepm; h++){
1.69 ! brouard 3269: if (h==(int) (calagedatem+YEARM*cpt)) {
1.53 brouard 3270: fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
3271: }
3272: for(j=1; j<=nlstate+ndeath;j++) {
3273: kk1=0.;kk2=0;
3274: for(i=1; i<=nlstate;i++) {
3275: kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];
3276: }
1.69 ! brouard 3277: if (h==(int)(calagedatem+12*cpt)) fprintf(ficresf," %15.2f", kk1);
1.53 brouard 3278: }
3279: }
3280: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3281: }
3282: }
3283: }
3284: }
3285:
1.54 brouard 3286: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
1.53 brouard 3287:
3288: if (popforecast==1) {
3289: free_ivector(popage,0,AGESUP);
3290: free_vector(popeffectif,0,AGESUP);
3291: free_vector(popcount,0,AGESUP);
3292: }
3293: free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
3294: free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
3295: fclose(ficrespop);
3296: }
3297:
3298: /***********************************************/
3299: /**************** Main Program *****************/
3300: /***********************************************/
3301:
3302: int main(int argc, char *argv[])
3303: {
1.61 brouard 3304: int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav);
1.53 brouard 3305: int i,j, k, n=MAXN,iter,m,size,cptcode, cptcod;
3306: double agedeb, agefin,hf;
3307: double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;
3308:
3309: double fret;
3310: double **xi,tmp,delta;
3311:
3312: double dum; /* Dummy variable */
3313: double ***p3mat;
3314: double ***mobaverage;
3315: int *indx;
3316: char line[MAXLINE], linepar[MAXLINE];
3317: char path[80],pathc[80],pathcd[80],pathtot[80],model[80];
3318: int firstobs=1, lastobs=10;
3319: int sdeb, sfin; /* Status at beginning and end */
3320: int c, h , cpt,l;
3321: int ju,jl, mi;
3322: int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;
1.59 brouard 3323: int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,*tab;
1.69 ! brouard 3324: int mobilavproj=0 , prevfcast=0 ; /* moving average of prev, If prevfcast=1 prevalence projection */
1.53 brouard 3325: int mobilav=0,popforecast=0;
3326: int hstepm, nhstepm;
1.69 ! brouard 3327: double jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,jpyram, mpyram,anpyram,jpyram1, mpyram1,anpyram1, calagedatem;
1.53 brouard 3328:
3329: double bage, fage, age, agelim, agebase;
3330: double ftolpl=FTOL;
3331: double **prlim;
3332: double *severity;
3333: double ***param; /* Matrix of parameters */
3334: double *p;
3335: double **matcov; /* Matrix of covariance */
3336: double ***delti3; /* Scale */
3337: double *delti; /* Scale */
3338: double ***eij, ***vareij;
3339: double **varpl; /* Variances of prevalence limits by age */
3340: double *epj, vepp;
3341: double kk1, kk2;
3342: double dateprev1, dateprev2,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2;
3343:
3344: char *alph[]={"a","a","b","c","d","e"}, str[4];
3345:
3346:
3347: char z[1]="c", occ;
3348: #include <sys/time.h>
3349: #include <time.h>
3350: char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];
3351:
3352: /* long total_usecs;
1.59 brouard 3353: struct timeval start_time, end_time;
1.53 brouard 3354:
1.59 brouard 3355: gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */
1.53 brouard 3356: getcwd(pathcd, size);
3357:
3358: printf("\n%s",version);
3359: if(argc <=1){
3360: printf("\nEnter the parameter file name: ");
3361: scanf("%s",pathtot);
3362: }
3363: else{
3364: strcpy(pathtot,argv[1]);
3365: }
3366: /*if(getcwd(pathcd, 80)!= NULL)printf ("Error pathcd\n");*/
3367: /*cygwin_split_path(pathtot,path,optionfile);
3368: printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/
3369: /* cutv(path,optionfile,pathtot,'\\');*/
3370:
3371: split(pathtot,path,optionfile,optionfilext,optionfilefiname);
1.59 brouard 3372: printf("pathtot=%s, path=%s, optionfile=%s optionfilext=%s optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
1.53 brouard 3373: chdir(path);
3374: replace(pathc,path);
3375:
1.59 brouard 3376: /*-------- arguments in the command line --------*/
1.53 brouard 3377:
3378: /* Log file */
3379: strcat(filelog, optionfilefiname);
3380: strcat(filelog,".log"); /* */
3381: if((ficlog=fopen(filelog,"w"))==NULL) {
3382: printf("Problem with logfile %s\n",filelog);
3383: goto end;
3384: }
3385: fprintf(ficlog,"Log filename:%s\n",filelog);
3386: fprintf(ficlog,"\n%s",version);
3387: fprintf(ficlog,"\nEnter the parameter file name: ");
3388: fprintf(ficlog,"pathtot=%s, path=%s, optionfile=%s optionfilext=%s optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
3389: fflush(ficlog);
3390:
3391: /* */
3392: strcpy(fileres,"r");
3393: strcat(fileres, optionfilefiname);
3394: strcat(fileres,".txt"); /* Other files have txt extension */
3395:
3396: /*---------arguments file --------*/
3397:
3398: if((ficpar=fopen(optionfile,"r"))==NULL) {
3399: printf("Problem with optionfile %s\n",optionfile);
3400: fprintf(ficlog,"Problem with optionfile %s\n",optionfile);
3401: goto end;
3402: }
3403:
3404: strcpy(filereso,"o");
3405: strcat(filereso,fileres);
3406: if((ficparo=fopen(filereso,"w"))==NULL) {
3407: printf("Problem with Output resultfile: %s\n", filereso);
3408: fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso);
3409: goto end;
3410: }
3411:
3412: /* Reads comments: lines beginning with '#' */
3413: while((c=getc(ficpar))=='#' && c!= EOF){
3414: ungetc(c,ficpar);
3415: fgets(line, MAXLINE, ficpar);
3416: puts(line);
3417: fputs(line,ficparo);
3418: }
3419: ungetc(c,ficpar);
3420:
3421: 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);
3422: 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);
3423: 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 3424: while((c=getc(ficpar))=='#' && c!= EOF){
1.53 brouard 3425: ungetc(c,ficpar);
3426: fgets(line, MAXLINE, ficpar);
3427: puts(line);
3428: fputs(line,ficparo);
3429: }
3430: ungetc(c,ficpar);
3431:
3432:
3433: covar=matrix(0,NCOVMAX,1,n);
1.58 lievre 3434: cptcovn=0; /*Number of covariates, i.e. number of '+' in model statement*/
1.53 brouard 3435: if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;
3436:
1.58 lievre 3437: ncovmodel=2+cptcovn; /*Number of variables = cptcovn + intercept + age */
1.53 brouard 3438: nvar=ncovmodel-1; /* Suppressing age as a basic covariate */
3439:
3440: /* Read guess parameters */
3441: /* Reads comments: lines beginning with '#' */
3442: while((c=getc(ficpar))=='#' && c!= EOF){
3443: ungetc(c,ficpar);
3444: fgets(line, MAXLINE, ficpar);
3445: puts(line);
3446: fputs(line,ficparo);
3447: }
3448: ungetc(c,ficpar);
3449:
3450: param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
1.59 brouard 3451: for(i=1; i <=nlstate; i++)
1.53 brouard 3452: for(j=1; j <=nlstate+ndeath-1; j++){
3453: fscanf(ficpar,"%1d%1d",&i1,&j1);
3454: fprintf(ficparo,"%1d%1d",i1,j1);
3455: if(mle==1)
3456: printf("%1d%1d",i,j);
3457: fprintf(ficlog,"%1d%1d",i,j);
3458: for(k=1; k<=ncovmodel;k++){
3459: fscanf(ficpar," %lf",¶m[i][j][k]);
3460: if(mle==1){
3461: printf(" %lf",param[i][j][k]);
3462: fprintf(ficlog," %lf",param[i][j][k]);
3463: }
3464: else
3465: fprintf(ficlog," %lf",param[i][j][k]);
3466: fprintf(ficparo," %lf",param[i][j][k]);
3467: }
3468: fscanf(ficpar,"\n");
3469: if(mle==1)
3470: printf("\n");
3471: fprintf(ficlog,"\n");
3472: fprintf(ficparo,"\n");
3473: }
3474:
1.59 brouard 3475: npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/
1.53 brouard 3476:
3477: p=param[1][1];
3478:
3479: /* Reads comments: lines beginning with '#' */
3480: while((c=getc(ficpar))=='#' && c!= EOF){
3481: ungetc(c,ficpar);
3482: fgets(line, MAXLINE, ficpar);
3483: puts(line);
3484: fputs(line,ficparo);
3485: }
3486: ungetc(c,ficpar);
3487:
3488: delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
3489: delti=vector(1,npar); /* Scale of each paramater (output from hesscov) */
3490: for(i=1; i <=nlstate; i++){
3491: for(j=1; j <=nlstate+ndeath-1; j++){
3492: fscanf(ficpar,"%1d%1d",&i1,&j1);
3493: printf("%1d%1d",i,j);
3494: fprintf(ficparo,"%1d%1d",i1,j1);
3495: for(k=1; k<=ncovmodel;k++){
3496: fscanf(ficpar,"%le",&delti3[i][j][k]);
3497: printf(" %le",delti3[i][j][k]);
3498: fprintf(ficparo," %le",delti3[i][j][k]);
3499: }
3500: fscanf(ficpar,"\n");
3501: printf("\n");
3502: fprintf(ficparo,"\n");
3503: }
3504: }
3505: delti=delti3[1][1];
3506:
3507: /* Reads comments: lines beginning with '#' */
3508: while((c=getc(ficpar))=='#' && c!= EOF){
3509: ungetc(c,ficpar);
3510: fgets(line, MAXLINE, ficpar);
3511: puts(line);
3512: fputs(line,ficparo);
3513: }
3514: ungetc(c,ficpar);
3515:
3516: matcov=matrix(1,npar,1,npar);
3517: for(i=1; i <=npar; i++){
3518: fscanf(ficpar,"%s",&str);
3519: if(mle==1)
3520: printf("%s",str);
3521: fprintf(ficlog,"%s",str);
3522: fprintf(ficparo,"%s",str);
3523: for(j=1; j <=i; j++){
3524: fscanf(ficpar," %le",&matcov[i][j]);
3525: if(mle==1){
3526: printf(" %.5le",matcov[i][j]);
3527: fprintf(ficlog," %.5le",matcov[i][j]);
3528: }
3529: else
3530: fprintf(ficlog," %.5le",matcov[i][j]);
3531: fprintf(ficparo," %.5le",matcov[i][j]);
3532: }
3533: fscanf(ficpar,"\n");
3534: if(mle==1)
3535: printf("\n");
3536: fprintf(ficlog,"\n");
3537: fprintf(ficparo,"\n");
3538: }
3539: for(i=1; i <=npar; i++)
3540: for(j=i+1;j<=npar;j++)
3541: matcov[i][j]=matcov[j][i];
3542:
3543: if(mle==1)
3544: printf("\n");
3545: fprintf(ficlog,"\n");
3546:
3547:
1.59 brouard 3548: /*-------- Rewriting paramater file ----------*/
3549: strcpy(rfileres,"r"); /* "Rparameterfile */
3550: strcat(rfileres,optionfilefiname); /* Parameter file first name*/
3551: strcat(rfileres,"."); /* */
3552: strcat(rfileres,optionfilext); /* Other files have txt extension */
3553: if((ficres =fopen(rfileres,"w"))==NULL) {
3554: printf("Problem writing new parameter file: %s\n", fileres);goto end;
3555: fprintf(ficlog,"Problem writing new parameter file: %s\n", fileres);goto end;
3556: }
3557: fprintf(ficres,"#%s\n",version);
1.53 brouard 3558:
1.59 brouard 3559: /*-------- data file ----------*/
3560: if((fic=fopen(datafile,"r"))==NULL) {
3561: printf("Problem with datafile: %s\n", datafile);goto end;
3562: fprintf(ficlog,"Problem with datafile: %s\n", datafile);goto end;
3563: }
3564:
3565: n= lastobs;
3566: severity = vector(1,maxwav);
3567: outcome=imatrix(1,maxwav+1,1,n);
3568: num=ivector(1,n);
3569: moisnais=vector(1,n);
3570: annais=vector(1,n);
3571: moisdc=vector(1,n);
3572: andc=vector(1,n);
3573: agedc=vector(1,n);
3574: cod=ivector(1,n);
3575: weight=vector(1,n);
3576: for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */
3577: mint=matrix(1,maxwav,1,n);
3578: anint=matrix(1,maxwav,1,n);
3579: s=imatrix(1,maxwav+1,1,n);
3580: tab=ivector(1,NCOVMAX);
3581: ncodemax=ivector(1,8);
3582:
3583: i=1;
3584: while (fgets(line, MAXLINE, fic) != NULL) {
3585: if ((i >= firstobs) && (i <=lastobs)) {
1.53 brouard 3586:
1.59 brouard 3587: for (j=maxwav;j>=1;j--){
3588: cutv(stra, strb,line,' '); s[j][i]=atoi(strb);
3589: strcpy(line,stra);
3590: cutv(stra, strb,line,'/'); anint[j][i]=(double)(atoi(strb)); strcpy(line,stra);
3591: cutv(stra, strb,line,' '); mint[j][i]=(double)(atoi(strb)); strcpy(line,stra);
3592: }
1.53 brouard 3593:
1.59 brouard 3594: cutv(stra, strb,line,'/'); andc[i]=(double)(atoi(strb)); strcpy(line,stra);
3595: cutv(stra, strb,line,' '); moisdc[i]=(double)(atoi(strb)); strcpy(line,stra);
1.53 brouard 3596:
1.59 brouard 3597: cutv(stra, strb,line,'/'); annais[i]=(double)(atoi(strb)); strcpy(line,stra);
3598: cutv(stra, strb,line,' '); moisnais[i]=(double)(atoi(strb)); strcpy(line,stra);
1.53 brouard 3599:
1.59 brouard 3600: cutv(stra, strb,line,' '); weight[i]=(double)(atoi(strb)); strcpy(line,stra);
3601: for (j=ncovcol;j>=1;j--){
3602: cutv(stra, strb,line,' '); covar[j][i]=(double)(atoi(strb)); strcpy(line,stra);
3603: }
3604: num[i]=atol(stra);
1.53 brouard 3605:
1.59 brouard 3606: /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){
3607: 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 3608:
1.59 brouard 3609: i=i+1;
3610: }
3611: }
3612: /* printf("ii=%d", ij);
3613: scanf("%d",i);*/
1.53 brouard 3614: imx=i-1; /* Number of individuals */
3615:
3616: /* for (i=1; i<=imx; i++){
3617: if ((s[1][i]==3) && (s[2][i]==2)) s[2][i]=3;
3618: if ((s[2][i]==3) && (s[3][i]==2)) s[3][i]=3;
3619: if ((s[3][i]==3) && (s[4][i]==2)) s[4][i]=3;
3620: }*/
3621: /* for (i=1; i<=imx; i++){
3622: if (s[4][i]==9) s[4][i]=-1;
3623: 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]));}*/
3624:
3625:
3626: /* Calculation of the number of parameter from char model*/
3627: Tvar=ivector(1,15); /* stores the number n of the covariates in Vm+Vn at 1 and m at 2 */
3628: Tprod=ivector(1,15);
3629: Tvaraff=ivector(1,15);
3630: Tvard=imatrix(1,15,1,2);
3631: Tage=ivector(1,15);
3632:
1.58 lievre 3633: if (strlen(model) >1){ /* If there is at least 1 covariate */
1.53 brouard 3634: j=0, j1=0, k1=1, k2=1;
1.58 lievre 3635: j=nbocc(model,'+'); /* j=Number of '+' */
3636: j1=nbocc(model,'*'); /* j1=Number of '*' */
3637: cptcovn=j+1;
3638: cptcovprod=j1; /*Number of products */
1.53 brouard 3639:
3640: strcpy(modelsav,model);
3641: if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){
3642: printf("Error. Non available option model=%s ",model);
3643: fprintf(ficlog,"Error. Non available option model=%s ",model);
3644: goto end;
3645: }
3646:
1.59 brouard 3647: /* This loop fills the array Tvar from the string 'model'.*/
1.58 lievre 3648:
1.53 brouard 3649: for(i=(j+1); i>=1;i--){
3650: cutv(stra,strb,modelsav,'+'); /* keeps in strb after the last + */
1.59 brouard 3651: if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyzes it */
1.53 brouard 3652: /* printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/
3653: /*scanf("%d",i);*/
3654: if (strchr(strb,'*')) { /* Model includes a product */
3655: cutv(strd,strc,strb,'*'); /* strd*strc Vm*Vn (if not *age)*/
3656: if (strcmp(strc,"age")==0) { /* Vn*age */
3657: cptcovprod--;
3658: cutv(strb,stre,strd,'V');
3659: Tvar[i]=atoi(stre); /* computes n in Vn and stores in Tvar*/
3660: cptcovage++;
3661: Tage[cptcovage]=i;
3662: /*printf("stre=%s ", stre);*/
3663: }
3664: else if (strcmp(strd,"age")==0) { /* or age*Vn */
3665: cptcovprod--;
3666: cutv(strb,stre,strc,'V');
3667: Tvar[i]=atoi(stre);
3668: cptcovage++;
3669: Tage[cptcovage]=i;
3670: }
3671: else { /* Age is not in the model */
3672: cutv(strb,stre,strc,'V'); /* strc= Vn, stre is n*/
3673: Tvar[i]=ncovcol+k1;
3674: cutv(strb,strc,strd,'V'); /* strd was Vm, strc is m */
3675: Tprod[k1]=i;
3676: Tvard[k1][1]=atoi(strc); /* m*/
3677: Tvard[k1][2]=atoi(stre); /* n */
3678: Tvar[cptcovn+k2]=Tvard[k1][1];
3679: Tvar[cptcovn+k2+1]=Tvard[k1][2];
3680: for (k=1; k<=lastobs;k++)
3681: covar[ncovcol+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];
3682: k1++;
3683: k2=k2+2;
3684: }
3685: }
3686: else { /* no more sum */
3687: /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/
3688: /* scanf("%d",i);*/
3689: cutv(strd,strc,strb,'V');
3690: Tvar[i]=atoi(strc);
3691: }
3692: strcpy(modelsav,stra);
3693: /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);
3694: scanf("%d",i);*/
3695: } /* end of loop + */
3696: } /* end model */
3697:
1.58 lievre 3698: /*The number n of Vn is stored in Tvar. cptcovage =number of age covariate. Tage gives the position of age. cptcovprod= number of products.
3699: If model=V1+V1*age then Tvar[1]=1 Tvar[2]=1 cptcovage=1 Tage[1]=2 cptcovprod=0*/
3700:
1.53 brouard 3701: /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);
3702: printf("cptcovprod=%d ", cptcovprod);
3703: fprintf(ficlog,"cptcovprod=%d ", cptcovprod);
1.58 lievre 3704:
3705: scanf("%d ",i);
3706: fclose(fic);*/
1.53 brouard 3707:
3708: /* if(mle==1){*/
1.59 brouard 3709: if (weightopt != 1) { /* Maximisation without weights*/
3710: for(i=1;i<=n;i++) weight[i]=1.0;
3711: }
1.53 brouard 3712: /*-calculation of age at interview from date of interview and age at death -*/
1.59 brouard 3713: agev=matrix(1,maxwav,1,imx);
1.53 brouard 3714:
1.59 brouard 3715: for (i=1; i<=imx; i++) {
3716: for(m=2; (m<= maxwav); m++) {
3717: if ((mint[m][i]== 99) && (s[m][i] <= nlstate)){
3718: anint[m][i]=9999;
3719: s[m][i]=-1;
3720: }
3721: if(moisdc[i]==99 && andc[i]==9999 & s[m][i]>nlstate) s[m][i]=-1;
1.53 brouard 3722: }
1.59 brouard 3723: }
1.53 brouard 3724:
1.59 brouard 3725: for (i=1; i<=imx; i++) {
3726: agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);
3727: for(m=1; (m<= maxwav); m++){
1.69 ! brouard 3728: if(s[m][i] >0){
1.59 brouard 3729: if (s[m][i] >= nlstate+1) {
3730: if(agedc[i]>0)
1.69 ! brouard 3731: if(moisdc[i]!=99 && andc[i]!=9999)
! 3732: agev[m][i]=agedc[i];
1.59 brouard 3733: /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/
3734: else {
1.53 brouard 3735: if (andc[i]!=9999){
1.59 brouard 3736: printf("Warning negative age at death: %d line:%d\n",num[i],i);
3737: fprintf(ficlog,"Warning negative age at death: %d line:%d\n",num[i],i);
3738: agev[m][i]=-1;
1.53 brouard 3739: }
3740: }
1.69 ! brouard 3741: }<
! 3742: else if(s[m][i] !=9){ /* Standard case, age in fractional
! 3743: years but with the precision of a
! 3744: month */
1.59 brouard 3745: agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);
3746: if(mint[m][i]==99 || anint[m][i]==9999)
3747: agev[m][i]=1;
3748: else if(agev[m][i] <agemin){
3749: agemin=agev[m][i];
3750: /*printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], agemin);*/
1.53 brouard 3751: }
1.59 brouard 3752: else if(agev[m][i] >agemax){
3753: agemax=agev[m][i];
3754: /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/
1.53 brouard 3755: }
1.59 brouard 3756: /*agev[m][i]=anint[m][i]-annais[i];*/
3757: /* agev[m][i] = age[i]+2*m;*/
1.53 brouard 3758: }
1.59 brouard 3759: else { /* =9 */
1.53 brouard 3760: agev[m][i]=1;
1.59 brouard 3761: s[m][i]=-1;
3762: }
1.53 brouard 3763: }
1.59 brouard 3764: else /*= 0 Unknown */
3765: agev[m][i]=1;
3766: }
1.53 brouard 3767:
1.59 brouard 3768: }
3769: for (i=1; i<=imx; i++) {
3770: for(m=1; (m<= maxwav); m++){
3771: if (s[m][i] > (nlstate+ndeath)) {
3772: 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);
3773: 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);
3774: goto end;
1.53 brouard 3775: }
3776: }
1.59 brouard 3777: }
1.53 brouard 3778:
1.59 brouard 3779: printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);
3780: fprintf(ficlog,"Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);
3781:
3782: free_vector(severity,1,maxwav);
3783: free_imatrix(outcome,1,maxwav+1,1,n);
3784: free_vector(moisnais,1,n);
3785: free_vector(annais,1,n);
3786: /* free_matrix(mint,1,maxwav,1,n);
3787: free_matrix(anint,1,maxwav,1,n);*/
3788: free_vector(moisdc,1,n);
3789: free_vector(andc,1,n);
1.53 brouard 3790:
3791:
1.59 brouard 3792: wav=ivector(1,imx);
3793: dh=imatrix(1,lastpass-firstpass+1,1,imx);
3794: bh=imatrix(1,lastpass-firstpass+1,1,imx);
3795: mw=imatrix(1,lastpass-firstpass+1,1,imx);
1.69 ! brouard 3796:
1.59 brouard 3797: /* Concatenates waves */
3798: concatwav(wav, dh, bh, mw, s, agedc, agev, firstpass, lastpass, imx, nlstate, stepm);
1.53 brouard 3799:
1.59 brouard 3800: /* Routine tricode is to calculate cptcoveff (real number of unique covariates) and to associate covariable number and modality */
1.53 brouard 3801:
1.59 brouard 3802: Tcode=ivector(1,100);
3803: nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);
3804: ncodemax[1]=1;
3805: if (cptcovn > 0) tricode(Tvar,nbcode,imx);
1.53 brouard 3806:
1.59 brouard 3807: codtab=imatrix(1,100,1,10); /* Cross tabulation to get the order of
3808: the estimations*/
3809: h=0;
3810: m=pow(2,cptcoveff);
1.53 brouard 3811:
1.59 brouard 3812: for(k=1;k<=cptcoveff; k++){
3813: for(i=1; i <=(m/pow(2,k));i++){
3814: for(j=1; j <= ncodemax[k]; j++){
3815: for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){
3816: h++;
3817: if (h>m) h=1;codtab[h][k]=j;codtab[h][Tvar[k]]=j;
3818: /* printf("h=%d k=%d j=%d codtab[h][k]=%d tvar[k]=%d \n",h, k,j,codtab[h][k],Tvar[k]);*/
3819: }
3820: }
3821: }
3822: }
3823: /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]);
3824: codtab[1][2]=1;codtab[2][2]=2; */
3825: /* for(i=1; i <=m ;i++){
3826: for(k=1; k <=cptcovn; k++){
3827: printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);
3828: }
3829: printf("\n");
1.53 brouard 3830: }
1.59 brouard 3831: scanf("%d",i);*/
1.53 brouard 3832:
1.59 brouard 3833: /* Calculates basic frequencies. Computes observed prevalence at single age
3834: and prints on file fileres'p'. */
1.53 brouard 3835:
1.60 brouard 3836: pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
3837: oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
3838: newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
3839: savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
3840: oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */
1.53 brouard 3841:
3842:
1.59 brouard 3843: /* For Powell, parameters are in a vector p[] starting at p[1]
3844: so we point p on param[1][1] so that p[1] maps on param[1][1][1] */
3845: p=param[1][1]; /* *(*(*(param +1)+1)+0) */
1.53 brouard 3846:
1.61 brouard 3847: if(mle>=1){ /* Could be 1 or 2 */
1.53 brouard 3848: mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);
1.59 brouard 3849: }
1.53 brouard 3850:
1.59 brouard 3851: /*--------- results files --------------*/
3852: 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 3853:
3854:
1.59 brouard 3855: jk=1;
3856: fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
3857: printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
3858: fprintf(ficlog,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
3859: for(i=1,jk=1; i <=nlstate; i++){
3860: for(k=1; k <=(nlstate+ndeath); k++){
3861: if (k != i)
3862: {
3863: printf("%d%d ",i,k);
3864: fprintf(ficlog,"%d%d ",i,k);
3865: fprintf(ficres,"%1d%1d ",i,k);
3866: for(j=1; j <=ncovmodel; j++){
3867: printf("%f ",p[jk]);
3868: fprintf(ficlog,"%f ",p[jk]);
3869: fprintf(ficres,"%f ",p[jk]);
3870: jk++;
3871: }
3872: printf("\n");
3873: fprintf(ficlog,"\n");
3874: fprintf(ficres,"\n");
3875: }
3876: }
3877: }
3878: if(mle==1){
3879: /* Computing hessian and covariance matrix */
3880: ftolhess=ftol; /* Usually correct */
3881: hesscov(matcov, p, npar, delti, ftolhess, func);
3882: }
3883: fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");
3884: printf("# Scales (for hessian or gradient estimation)\n");
3885: fprintf(ficlog,"# Scales (for hessian or gradient estimation)\n");
3886: for(i=1,jk=1; i <=nlstate; i++){
3887: for(j=1; j <=nlstate+ndeath; j++){
3888: if (j!=i) {
3889: fprintf(ficres,"%1d%1d",i,j);
3890: printf("%1d%1d",i,j);
3891: fprintf(ficlog,"%1d%1d",i,j);
3892: for(k=1; k<=ncovmodel;k++){
3893: printf(" %.5e",delti[jk]);
3894: fprintf(ficlog," %.5e",delti[jk]);
3895: fprintf(ficres," %.5e",delti[jk]);
3896: jk++;
3897: }
3898: printf("\n");
3899: fprintf(ficlog,"\n");
3900: fprintf(ficres,"\n");
3901: }
3902: }
3903: }
1.53 brouard 3904:
1.59 brouard 3905: 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");
3906: if(mle==1)
3907: 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");
3908: 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");
3909: for(i=1,k=1;i<=npar;i++){
3910: /* if (k>nlstate) k=1;
3911: i1=(i-1)/(ncovmodel*nlstate)+1;
3912: fprintf(ficres,"%s%d%d",alph[k],i1,tab[i]);
3913: printf("%s%d%d",alph[k],i1,tab[i]);
3914: */
3915: fprintf(ficres,"%3d",i);
3916: if(mle==1)
3917: printf("%3d",i);
3918: fprintf(ficlog,"%3d",i);
3919: for(j=1; j<=i;j++){
3920: fprintf(ficres," %.5e",matcov[i][j]);
3921: if(mle==1)
3922: printf(" %.5e",matcov[i][j]);
3923: fprintf(ficlog," %.5e",matcov[i][j]);
3924: }
3925: fprintf(ficres,"\n");
3926: if(mle==1)
3927: printf("\n");
3928: fprintf(ficlog,"\n");
3929: k++;
3930: }
1.53 brouard 3931:
1.59 brouard 3932: while((c=getc(ficpar))=='#' && c!= EOF){
3933: ungetc(c,ficpar);
3934: fgets(line, MAXLINE, ficpar);
3935: puts(line);
3936: fputs(line,ficparo);
3937: }
3938: ungetc(c,ficpar);
3939:
3940: estepm=0;
3941: fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm);
3942: if (estepm==0 || estepm < stepm) estepm=stepm;
3943: if (fage <= 2) {
3944: bage = ageminpar;
3945: fage = agemaxpar;
3946: }
1.53 brouard 3947:
1.59 brouard 3948: fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");
3949: fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
3950: fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
1.53 brouard 3951:
1.59 brouard 3952: while((c=getc(ficpar))=='#' && c!= EOF){
3953: ungetc(c,ficpar);
3954: fgets(line, MAXLINE, ficpar);
3955: puts(line);
3956: fputs(line,ficparo);
3957: }
3958: ungetc(c,ficpar);
1.53 brouard 3959:
1.59 brouard 3960: 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);
3961: 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);
3962: 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);
1.69 ! brouard 3963: printf("begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
! 3964: fprintf(ficlog,"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 3965:
1.59 brouard 3966: while((c=getc(ficpar))=='#' && c!= EOF){
3967: ungetc(c,ficpar);
3968: fgets(line, MAXLINE, ficpar);
3969: puts(line);
3970: fputs(line,ficparo);
3971: }
3972: ungetc(c,ficpar);
1.53 brouard 3973:
3974:
1.59 brouard 3975: dateprev1=anprev1+mprev1/12.+jprev1/365.;
3976: dateprev2=anprev2+mprev2/12.+jprev2/365.;
1.53 brouard 3977:
3978: fscanf(ficpar,"pop_based=%d\n",&popbased);
3979: fprintf(ficparo,"pop_based=%d\n",popbased);
3980: fprintf(ficres,"pop_based=%d\n",popbased);
3981:
3982: while((c=getc(ficpar))=='#' && c!= EOF){
3983: ungetc(c,ficpar);
3984: fgets(line, MAXLINE, ficpar);
3985: puts(line);
3986: fputs(line,ficparo);
3987: }
3988: ungetc(c,ficpar);
3989:
1.69 ! brouard 3990: fscanf(ficpar,"prevforecast=%d starting-proj-date=%lf/%lf/%lf final-proj-date=%lf/%lf/%lf mobil_average=%d\n",&prevfcast,&jproj1,&mproj1,&anproj1,&jproj2,&mproj2,&anproj2,&mobilavproj);
! 3991: fprintf(ficparo,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",&prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
! 3992: printf("prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobilaverage=%d\n",&prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
! 3993: fprintf(ficlog,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobilaverage=%d\n",&prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
! 3994: fprintf(ficres,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobilaverage=%d\n",&prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
! 3995: /* day and month of proj2 are not used but only year anproj2.*/
1.53 brouard 3996:
1.59 brouard 3997: while((c=getc(ficpar))=='#' && c!= EOF){
1.53 brouard 3998: ungetc(c,ficpar);
3999: fgets(line, MAXLINE, ficpar);
4000: puts(line);
4001: fputs(line,ficparo);
4002: }
4003: ungetc(c,ficpar);
4004:
4005: fscanf(ficpar,"popforecast=%d popfile=%s popfiledate=%lf/%lf/%lf last-popfiledate=%lf/%lf/%lf\n",&popforecast,popfile,&jpyram,&mpyram,&anpyram,&jpyram1,&mpyram1,&anpyram1);
4006: fprintf(ficparo,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);
4007: fprintf(ficres,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);
4008:
1.59 brouard 4009: freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);
1.58 lievre 4010:
1.59 brouard 4011: /*------------ gnuplot -------------*/
4012: strcpy(optionfilegnuplot,optionfilefiname);
4013: strcat(optionfilegnuplot,".gp");
4014: if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {
4015: printf("Problem with file %s",optionfilegnuplot);
4016: }
4017: else{
4018: fprintf(ficgp,"\n# %s\n", version);
4019: fprintf(ficgp,"# %s\n", optionfilegnuplot);
4020: fprintf(ficgp,"set missing 'NaNq'\n");
4021: }
4022: fclose(ficgp);
4023: printinggnuplot(fileres, ageminpar,agemaxpar,fage, pathc,p);
4024: /*--------- index.htm --------*/
1.53 brouard 4025:
4026: strcpy(optionfilehtm,optionfile);
4027: strcat(optionfilehtm,".htm");
4028: if((fichtm=fopen(optionfilehtm,"w"))==NULL) {
4029: printf("Problem with %s \n",optionfilehtm), exit(0);
4030: }
4031:
4032: fprintf(fichtm,"<body> <font size=\"2\">%s </font> <hr size=\"2\" color=\"#EC5E5E\"> \n
4033: Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n
4034: \n
4035: Total number of observations=%d <br>\n
4036: Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n
4037: <hr size=\"2\" color=\"#EC5E5E\">
4038: <ul><li><h4>Parameter files</h4>\n
4039: - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n
4040: - Log file of the run: <a href=\"%s\">%s</a><br>\n
4041: - 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);
4042: fclose(fichtm);
4043:
1.59 brouard 4044: 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 4045:
1.59 brouard 4046: /*------------ free_vector -------------*/
4047: chdir(path);
1.53 brouard 4048:
1.59 brouard 4049: free_ivector(wav,1,imx);
4050: free_imatrix(dh,1,lastpass-firstpass+1,1,imx);
4051: free_imatrix(bh,1,lastpass-firstpass+1,1,imx);
4052: free_imatrix(mw,1,lastpass-firstpass+1,1,imx);
4053: free_ivector(num,1,n);
4054: free_vector(agedc,1,n);
1.65 lievre 4055: /*free_matrix(covar,0,NCOVMAX,1,n);*/
1.59 brouard 4056: /*free_matrix(covar,1,NCOVMAX,1,n);*/
4057: fclose(ficparo);
4058: fclose(ficres);
1.53 brouard 4059:
4060:
1.54 brouard 4061: /*--------------- Prevalence limit (stable prevalence) --------------*/
1.53 brouard 4062:
4063: strcpy(filerespl,"pl");
4064: strcat(filerespl,fileres);
4065: if((ficrespl=fopen(filerespl,"w"))==NULL) {
1.54 brouard 4066: printf("Problem with stable prevalence resultfile: %s\n", filerespl);goto end;
4067: fprintf(ficlog,"Problem with stable prevalence resultfile: %s\n", filerespl);goto end;
1.53 brouard 4068: }
1.54 brouard 4069: printf("Computing stable prevalence: result on file '%s' \n", filerespl);
4070: fprintf(ficlog,"Computing stable prevalence: result on file '%s' \n", filerespl);
4071: fprintf(ficrespl,"#Stable prevalence \n");
1.53 brouard 4072: fprintf(ficrespl,"#Age ");
4073: for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);
4074: fprintf(ficrespl,"\n");
4075:
4076: prlim=matrix(1,nlstate,1,nlstate);
1.59 brouard 4077:
1.53 brouard 4078: agebase=ageminpar;
4079: agelim=agemaxpar;
4080: ftolpl=1.e-10;
4081: i1=cptcoveff;
4082: if (cptcovn < 1){i1=1;}
4083:
1.59 brouard 4084: for(cptcov=1,k=0;cptcov<=i1;cptcov++){
1.53 brouard 4085: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
1.59 brouard 4086: k=k+1;
4087: /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/
4088: fprintf(ficrespl,"\n#******");
4089: printf("\n#******");
4090: fprintf(ficlog,"\n#******");
4091: for(j=1;j<=cptcoveff;j++) {
4092: fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
4093: printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
4094: fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
4095: }
4096: fprintf(ficrespl,"******\n");
4097: printf("******\n");
4098: fprintf(ficlog,"******\n");
1.53 brouard 4099:
1.59 brouard 4100: for (age=agebase; age<=agelim; age++){
4101: prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
1.69 ! brouard 4102: fprintf(ficrespl,"%.0f ",age );
! 4103: for(j=1;j<=cptcoveff;j++)
! 4104: fprintf(ficrespl,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
1.59 brouard 4105: for(i=1; i<=nlstate;i++)
1.53 brouard 4106: fprintf(ficrespl," %.5f", prlim[i][i]);
1.59 brouard 4107: fprintf(ficrespl,"\n");
1.53 brouard 4108: }
4109: }
1.59 brouard 4110: }
1.53 brouard 4111: fclose(ficrespl);
4112:
4113: /*------------- h Pij x at various ages ------------*/
4114:
4115: strcpy(filerespij,"pij"); strcat(filerespij,fileres);
4116: if((ficrespij=fopen(filerespij,"w"))==NULL) {
4117: printf("Problem with Pij resultfile: %s\n", filerespij);goto end;
4118: fprintf(ficlog,"Problem with Pij resultfile: %s\n", filerespij);goto end;
4119: }
4120: printf("Computing pij: result on file '%s' \n", filerespij);
4121: fprintf(ficlog,"Computing pij: result on file '%s' \n", filerespij);
4122:
4123: stepsize=(int) (stepm+YEARM-1)/YEARM;
4124: /*if (stepm<=24) stepsize=2;*/
4125:
4126: agelim=AGESUP;
4127: hstepm=stepsize*YEARM; /* Every year of age */
4128: hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */
4129:
4130: /* hstepm=1; aff par mois*/
4131:
1.59 brouard 4132: for(cptcov=1,k=0;cptcov<=i1;cptcov++){
1.53 brouard 4133: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
4134: k=k+1;
1.59 brouard 4135: fprintf(ficrespij,"\n#****** ");
4136: for(j=1;j<=cptcoveff;j++)
4137: fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
4138: fprintf(ficrespij,"******\n");
1.53 brouard 4139:
1.59 brouard 4140: for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */
4141: nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
4142: nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
4143:
4144: /* nhstepm=nhstepm*YEARM; aff par mois*/
4145:
4146: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4147: oldm=oldms;savm=savms;
4148: hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
4149: fprintf(ficrespij,"# Age");
4150: for(i=1; i<=nlstate;i++)
4151: for(j=1; j<=nlstate+ndeath;j++)
4152: fprintf(ficrespij," %1d-%1d",i,j);
4153: fprintf(ficrespij,"\n");
4154: for (h=0; h<=nhstepm; h++){
4155: fprintf(ficrespij,"%d %f %f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );
1.53 brouard 4156: for(i=1; i<=nlstate;i++)
4157: for(j=1; j<=nlstate+ndeath;j++)
1.59 brouard 4158: fprintf(ficrespij," %.5f", p3mat[i][j][h]);
1.53 brouard 4159: fprintf(ficrespij,"\n");
4160: }
1.59 brouard 4161: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4162: fprintf(ficrespij,"\n");
4163: }
1.53 brouard 4164: }
4165: }
4166:
4167: varprob(optionfilefiname, matcov, p, delti, nlstate, (int) bage, (int) fage,k,Tvar,nbcode, ncodemax);
4168:
4169: fclose(ficrespij);
4170:
4171:
4172: /*---------- Forecasting ------------------*/
1.69 ! brouard 4173: /*if((stepm == 1) && (strcmp(model,".")==0)){*/
! 4174: if(prevfcast==1){
! 4175: if(stepm ==1){
! 4176: prevforecast(fileres, anproj1,mproj1,jproj1, agemin,agemax, dateprev1, dateprev2,mobilavproj, agedeb, fage, popforecast, popfile, anproj2,p, i1);
! 4177: if (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);
! 4178: }
! 4179: else{
! 4180: erreur=108;
! 4181: 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);
! 4182: 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);
1.68 lievre 4183: }
1.69 ! brouard 4184: }
1.53 brouard 4185:
4186:
4187: /*---------- Health expectancies and variances ------------*/
4188:
4189: strcpy(filerest,"t");
4190: strcat(filerest,fileres);
4191: if((ficrest=fopen(filerest,"w"))==NULL) {
4192: printf("Problem with total LE resultfile: %s\n", filerest);goto end;
4193: fprintf(ficlog,"Problem with total LE resultfile: %s\n", filerest);goto end;
4194: }
4195: printf("Computing Total LEs with variances: file '%s' \n", filerest);
4196: fprintf(ficlog,"Computing Total LEs with variances: file '%s' \n", filerest);
4197:
4198:
4199: strcpy(filerese,"e");
4200: strcat(filerese,fileres);
4201: if((ficreseij=fopen(filerese,"w"))==NULL) {
4202: printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
4203: fprintf(ficlog,"Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
4204: }
4205: printf("Computing Health Expectancies: result on file '%s' \n", filerese);
4206: fprintf(ficlog,"Computing Health Expectancies: result on file '%s' \n", filerese);
1.68 lievre 4207:
1.53 brouard 4208: strcpy(fileresv,"v");
4209: strcat(fileresv,fileres);
4210: if((ficresvij=fopen(fileresv,"w"))==NULL) {
4211: printf("Problem with variance resultfile: %s\n", fileresv);exit(0);
4212: fprintf(ficlog,"Problem with variance resultfile: %s\n", fileresv);exit(0);
4213: }
4214: printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
4215: fprintf(ficlog,"Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
1.58 lievre 4216:
1.69 ! brouard 4217: calagedatem=-1;
1.58 lievre 4218:
1.69 ! brouard 4219: prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedatem);
1.58 lievre 4220:
1.54 brouard 4221: if (mobilav!=0) {
1.53 brouard 4222: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
1.54 brouard 4223: if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
4224: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
4225: printf(" Error in movingaverage mobilav=%d\n",mobilav);
4226: }
1.53 brouard 4227: }
4228:
1.59 brouard 4229: for(cptcov=1,k=0;cptcov<=i1;cptcov++){
1.53 brouard 4230: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
4231: k=k+1;
4232: fprintf(ficrest,"\n#****** ");
4233: for(j=1;j<=cptcoveff;j++)
4234: fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
4235: fprintf(ficrest,"******\n");
4236:
4237: fprintf(ficreseij,"\n#****** ");
4238: for(j=1;j<=cptcoveff;j++)
4239: fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
4240: fprintf(ficreseij,"******\n");
4241:
4242: fprintf(ficresvij,"\n#****** ");
4243: for(j=1;j<=cptcoveff;j++)
4244: fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
4245: fprintf(ficresvij,"******\n");
4246:
4247: eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
4248: oldm=oldms;savm=savms;
4249: evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov);
4250:
4251: vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
4252: oldm=oldms;savm=savms;
4253: varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,0, mobilav);
4254: if(popbased==1){
4255: 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 4256: }
1.53 brouard 4257:
4258:
4259: fprintf(ficrest,"#Total LEs with variances: e.. (std) ");
4260: for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);
4261: fprintf(ficrest,"\n");
4262:
4263: epj=vector(1,nlstate+1);
4264: for(age=bage; age <=fage ;age++){
4265: prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
4266: if (popbased==1) {
1.54 brouard 4267: if(mobilav ==0){
1.53 brouard 4268: for(i=1; i<=nlstate;i++)
4269: prlim[i][i]=probs[(int)age][i][k];
1.54 brouard 4270: }else{ /* mobilav */
1.53 brouard 4271: for(i=1; i<=nlstate;i++)
4272: prlim[i][i]=mobaverage[(int)age][i][k];
4273: }
4274: }
4275:
4276: fprintf(ficrest," %4.0f",age);
4277: for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){
4278: for(i=1, epj[j]=0.;i <=nlstate;i++) {
4279: epj[j] += prlim[i][i]*eij[i][j][(int)age];
4280: /* printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/
4281: }
4282: epj[nlstate+1] +=epj[j];
4283: }
4284:
4285: for(i=1, vepp=0.;i <=nlstate;i++)
4286: for(j=1;j <=nlstate;j++)
4287: vepp += vareij[i][j][(int)age];
4288: fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));
4289: for(j=1;j <=nlstate;j++){
4290: fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));
4291: }
4292: fprintf(ficrest,"\n");
4293: }
1.59 brouard 4294: free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
4295: free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);
4296: free_vector(epj,1,nlstate+1);
1.53 brouard 4297: }
4298: }
1.59 brouard 4299: free_vector(weight,1,n);
4300: free_imatrix(Tvard,1,15,1,2);
4301: free_imatrix(s,1,maxwav+1,1,n);
4302: free_matrix(anint,1,maxwav,1,n);
4303: free_matrix(mint,1,maxwav,1,n);
4304: free_ivector(cod,1,n);
4305: free_ivector(tab,1,NCOVMAX);
1.53 brouard 4306: fclose(ficreseij);
4307: fclose(ficresvij);
4308: fclose(ficrest);
4309: fclose(ficpar);
4310:
1.54 brouard 4311: /*------- Variance of stable prevalence------*/
1.53 brouard 4312:
4313: strcpy(fileresvpl,"vpl");
4314: strcat(fileresvpl,fileres);
4315: if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {
1.54 brouard 4316: printf("Problem with variance of stable prevalence resultfile: %s\n", fileresvpl);
1.53 brouard 4317: exit(0);
4318: }
1.54 brouard 4319: printf("Computing Variance-covariance of stable prevalence: file '%s' \n", fileresvpl);
1.53 brouard 4320:
1.59 brouard 4321: for(cptcov=1,k=0;cptcov<=i1;cptcov++){
1.53 brouard 4322: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
4323: k=k+1;
4324: fprintf(ficresvpl,"\n#****** ");
4325: for(j=1;j<=cptcoveff;j++)
4326: fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
4327: fprintf(ficresvpl,"******\n");
4328:
4329: varpl=matrix(1,nlstate,(int) bage, (int) fage);
4330: oldm=oldms;savm=savms;
1.59 brouard 4331: varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);
4332: free_matrix(varpl,1,nlstate,(int) bage, (int)fage);
1.53 brouard 4333: }
1.59 brouard 4334: }
1.53 brouard 4335:
4336: fclose(ficresvpl);
4337:
4338: /*---------- End : free ----------------*/
4339: free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);
4340: free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);
4341: free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);
4342: free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);
1.65 lievre 4343:
4344: free_matrix(covar,0,NCOVMAX,1,n);
1.53 brouard 4345: free_matrix(matcov,1,npar,1,npar);
4346: free_vector(delti,1,npar);
4347: free_matrix(agev,1,maxwav,1,imx);
4348: free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
1.54 brouard 4349: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
1.59 brouard 4350: free_ivector(ncodemax,1,8);
4351: free_ivector(Tvar,1,15);
4352: free_ivector(Tprod,1,15);
4353: free_ivector(Tvaraff,1,15);
4354: free_ivector(Tage,1,15);
4355: free_ivector(Tcode,1,100);
1.53 brouard 4356:
4357: fprintf(fichtm,"\n</body>");
4358: fclose(fichtm);
4359: fclose(ficgp);
4360:
4361:
4362: if(erreur >0){
4363: printf("End of Imach with error or warning %d\n",erreur);
4364: fprintf(ficlog,"End of Imach with error or warning %d\n",erreur);
4365: }else{
4366: printf("End of Imach\n");
4367: fprintf(ficlog,"End of Imach\n");
4368: }
4369: printf("See log file on %s\n",filelog);
4370: fclose(ficlog);
4371: /* gettimeofday(&end_time, (struct timezone*)0);*/ /* after time */
4372:
4373: /* 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);*/
4374: /*printf("Total time was %d uSec.\n", total_usecs);*/
4375: /*------ End -----------*/
4376:
1.59 brouard 4377: end:
1.53 brouard 4378: #ifdef windows
4379: /* chdir(pathcd);*/
4380: #endif
4381: /*system("wgnuplot graph.plt");*/
4382: /*system("../gp37mgw/wgnuplot graph.plt");*/
4383: /*system("cd ../gp37mgw");*/
4384: /* system("..\\gp37mgw\\wgnuplot graph.plt");*/
1.59 brouard 4385: strcpy(plotcmd,GNUPLOTPROGRAM);
4386: strcat(plotcmd," ");
4387: strcat(plotcmd,optionfilegnuplot);
4388: printf("Starting: %s\n",plotcmd);fflush(stdout);
4389: system(plotcmd);
1.53 brouard 4390:
1.54 brouard 4391: /*#ifdef windows*/
1.53 brouard 4392: while (z[0] != 'q') {
4393: /* chdir(path); */
4394: printf("\nType e to edit output files, g to graph again, c to start again, and q for exiting: ");
4395: scanf("%s",z);
4396: if (z[0] == 'c') system("./imach");
4397: else if (z[0] == 'e') system(optionfilehtm);
4398: else if (z[0] == 'g') system(plotcmd);
4399: else if (z[0] == 'q') exit(0);
4400: }
1.54 brouard 4401: /*#endif */
1.53 brouard 4402: }
4403:
4404:
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