Annotation of imach096d/src/imach.c, revision 1.82
1.82 ! brouard 1: /* $Id: imach.c,v 1.81 2003/06/05 15:41:51 brouard Exp $
! 2: $State$
! 3: $Log$
! 4: */
! 5: /*
1.53 brouard 6: Interpolated Markov Chain
7:
8: Short summary of the programme:
9:
10: This program computes Healthy Life Expectancies from
11: cross-longitudinal data. Cross-longitudinal data consist in: -1- a
12: first survey ("cross") where individuals from different ages are
13: interviewed on their health status or degree of disability (in the
14: case of a health survey which is our main interest) -2- at least a
15: second wave of interviews ("longitudinal") which measure each change
16: (if any) in individual health status. Health expectancies are
17: computed from the time spent in each health state according to a
18: model. More health states you consider, more time is necessary to reach the
19: Maximum Likelihood of the parameters involved in the model. The
20: simplest model is the multinomial logistic model where pij is the
21: probability to be observed in state j at the second wave
22: conditional to be observed in state i at the first wave. Therefore
23: the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where
24: 'age' is age and 'sex' is a covariate. If you want to have a more
25: complex model than "constant and age", you should modify the program
26: where the markup *Covariates have to be included here again* invites
27: you to do it. More covariates you add, slower the
28: convergence.
29:
30: The advantage of this computer programme, compared to a simple
31: multinomial logistic model, is clear when the delay between waves is not
32: identical for each individual. Also, if a individual missed an
33: intermediate interview, the information is lost, but taken into
34: account using an interpolation or extrapolation.
35:
36: hPijx is the probability to be observed in state i at age x+h
37: conditional to the observed state i at age x. The delay 'h' can be
38: split into an exact number (nh*stepm) of unobserved intermediate
1.66 brouard 39: states. This elementary transition (by month, quarter,
40: semester or year) is modelled as a multinomial logistic. The hPx
1.53 brouard 41: matrix is simply the matrix product of nh*stepm elementary matrices
42: and the contribution of each individual to the likelihood is simply
43: hPijx.
44:
45: Also this programme outputs the covariance matrix of the parameters but also
1.54 brouard 46: of the life expectancies. It also computes the stable prevalence.
1.53 brouard 47:
48: Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).
49: Institut national d'études démographiques, Paris.
50: This software have been partly granted by Euro-REVES, a concerted action
51: from the European Union.
52: It is copyrighted identically to a GNU software product, ie programme and
53: software can be distributed freely for non commercial use. Latest version
54: can be accessed at http://euroreves.ined.fr/imach .
1.74 brouard 55:
56: Help to debug: LD_PRELOAD=/usr/local/lib/libnjamd.so ./imach foo.imach
57: or better on gdb : set env LD_PRELOAD=/usr/local/lib/libnjamd.so
58:
1.53 brouard 59: **********************************************************************/
1.74 brouard 60: /*
61: main
62: read parameterfile
63: read datafile
64: concatwav
65: if (mle >= 1)
66: mlikeli
67: print results files
68: if mle==1
69: computes hessian
70: read end of parameter file: agemin, agemax, bage, fage, estepm
71: begin-prev-date,...
72: open gnuplot file
73: open html file
74: stable prevalence
75: for age prevalim()
76: h Pij x
77: variance of p varprob
78: forecasting if prevfcast==1 prevforecast call prevalence()
79: health expectancies
80: Variance-covariance of DFLE
81: prevalence()
82: movingaverage()
83: varevsij()
84: if popbased==1 varevsij(,popbased)
85: total life expectancies
86: Variance of stable prevalence
87: end
88: */
89:
90:
91:
1.53 brouard 92:
93: #include <math.h>
94: #include <stdio.h>
95: #include <stdlib.h>
96: #include <unistd.h>
97:
98: #define MAXLINE 256
99: #define GNUPLOTPROGRAM "gnuplot"
100: /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
101: #define FILENAMELENGTH 80
102: /*#define DEBUG*/
1.55 lievre 103: #define windows
1.53 brouard 104: #define GLOCK_ERROR_NOPATH -1 /* empty path */
105: #define GLOCK_ERROR_GETCWD -2 /* cannot get cwd */
106:
107: #define MAXPARM 30 /* Maximum number of parameters for the optimization */
108: #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */
109:
110: #define NINTERVMAX 8
111: #define NLSTATEMAX 8 /* Maximum number of live states (for func) */
112: #define NDEATHMAX 8 /* Maximum number of dead states (for func) */
113: #define NCOVMAX 8 /* Maximum number of covariates */
114: #define MAXN 20000
115: #define YEARM 12. /* Number of months per year */
116: #define AGESUP 130
117: #define AGEBASE 40
118: #ifdef windows
119: #define DIRSEPARATOR '\\'
120: #define ODIRSEPARATOR '/'
121: #else
122: #define DIRSEPARATOR '/'
123: #define ODIRSEPARATOR '\\'
124: #endif
125:
1.82 ! brouard 126: /* $Id: imach.c,v 1.81 2003/06/05 15:41:51 brouard Exp $ */
1.81 brouard 127: /* $State: Exp $ */
1.80 brouard 128:
1.82 ! brouard 129: char version[]="Imach version 0.95a1, June 2003, INED-EUROREVES ";
! 130: char fullversion[]="$Revision: 1.81 $ $Date: 2003/06/05 15:41:51 $";
1.53 brouard 131: int erreur; /* Error number */
132: int nvar;
133: int cptcovn=0, cptcovage=0, cptcoveff=0,cptcov;
134: int npar=NPARMAX;
135: int nlstate=2; /* Number of live states */
136: int ndeath=1; /* Number of dead states */
137: int ncovmodel, ncovcol; /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
138: int popbased=0;
139:
140: int *wav; /* Number of waves for this individuual 0 is possible */
141: int maxwav; /* Maxim number of waves */
142: int jmin, jmax; /* min, max spacing between 2 waves */
143: int mle, weightopt;
144: int **mw; /* mw[mi][i] is number of the mi wave for this individual */
145: int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
1.59 brouard 146: int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between
147: * wave mi and wave mi+1 is not an exact multiple of stepm. */
1.53 brouard 148: double jmean; /* Mean space between 2 waves */
149: double **oldm, **newm, **savm; /* Working pointers to matrices */
150: double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
151: FILE *fic,*ficpar, *ficparo,*ficres, *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
1.76 brouard 152: FILE *ficlog, *ficrespow;
1.53 brouard 153: FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
154: FILE *ficresprobmorprev;
155: FILE *fichtm; /* Html File */
156: FILE *ficreseij;
157: char filerese[FILENAMELENGTH];
158: FILE *ficresvij;
159: char fileresv[FILENAMELENGTH];
160: FILE *ficresvpl;
161: char fileresvpl[FILENAMELENGTH];
162: char title[MAXLINE];
163: char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH], filerespl[FILENAMELENGTH];
164: char optionfilext[10], optionfilefiname[FILENAMELENGTH], plotcmd[FILENAMELENGTH];
165:
166: char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
167: char filelog[FILENAMELENGTH]; /* Log file */
168: char filerest[FILENAMELENGTH];
169: char fileregp[FILENAMELENGTH];
170: char popfile[FILENAMELENGTH];
171:
172: char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH];
173:
174: #define NR_END 1
175: #define FREE_ARG char*
176: #define FTOL 1.0e-10
177:
178: #define NRANSI
179: #define ITMAX 200
180:
181: #define TOL 2.0e-4
182:
183: #define CGOLD 0.3819660
184: #define ZEPS 1.0e-10
185: #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);
186:
187: #define GOLD 1.618034
188: #define GLIMIT 100.0
189: #define TINY 1.0e-20
190:
191: static double maxarg1,maxarg2;
192: #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
193: #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
194:
195: #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
196: #define rint(a) floor(a+0.5)
197:
198: static double sqrarg;
199: #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
200: #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}
201:
202: int imx;
203: int stepm;
204: /* Stepm, step in month: minimum step interpolation*/
205:
206: int estepm;
207: /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
208:
209: int m,nb;
210: int *num, firstpass=0, lastpass=4,*cod, *ncodemax, *Tage;
211: double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
1.55 lievre 212: double **pmmij, ***probs;
1.53 brouard 213: double dateintmean=0;
214:
215: double *weight;
216: int **s; /* Status */
217: double *agedc, **covar, idx;
218: int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;
219:
220: double ftol=FTOL; /* Tolerance for computing Max Likelihood */
221: double ftolhess; /* Tolerance for computing hessian */
222:
223: /**************** split *************************/
224: static int split( char *path, char *dirc, char *name, char *ext, char *finame )
225: {
1.59 brouard 226: char *ss; /* pointer */
227: int l1, l2; /* length counters */
1.53 brouard 228:
1.59 brouard 229: l1 = strlen(path ); /* length of path */
230: if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
231: ss= strrchr( path, DIRSEPARATOR ); /* find last / */
232: if ( ss == NULL ) { /* no directory, so use current */
233: /*if(strrchr(path, ODIRSEPARATOR )==NULL)
234: printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
1.74 brouard 235: /* get current working directory */
236: /* extern char* getcwd ( char *buf , int len);*/
1.59 brouard 237: if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {
238: return( GLOCK_ERROR_GETCWD );
239: }
240: strcpy( name, path ); /* we've got it */
241: } else { /* strip direcotry from path */
242: ss++; /* after this, the filename */
243: l2 = strlen( ss ); /* length of filename */
244: if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
245: strcpy( name, ss ); /* save file name */
246: strncpy( dirc, path, l1 - l2 ); /* now the directory */
247: dirc[l1-l2] = 0; /* add zero */
248: }
249: l1 = strlen( dirc ); /* length of directory */
1.53 brouard 250: #ifdef windows
1.59 brouard 251: if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; }
1.53 brouard 252: #else
1.59 brouard 253: if ( dirc[l1-1] != '/' ) { dirc[l1] = '/'; dirc[l1+1] = 0; }
1.53 brouard 254: #endif
1.59 brouard 255: ss = strrchr( name, '.' ); /* find last / */
256: ss++;
257: strcpy(ext,ss); /* save extension */
258: l1= strlen( name);
259: l2= strlen(ss)+1;
260: strncpy( finame, name, l1-l2);
261: finame[l1-l2]= 0;
262: return( 0 ); /* we're done */
1.53 brouard 263: }
264:
265:
266: /******************************************/
267:
268: void replace(char *s, char*t)
269: {
270: int i;
271: int lg=20;
272: i=0;
273: lg=strlen(t);
274: for(i=0; i<= lg; i++) {
275: (s[i] = t[i]);
276: if (t[i]== '\\') s[i]='/';
277: }
278: }
279:
280: int nbocc(char *s, char occ)
281: {
282: int i,j=0;
283: int lg=20;
284: i=0;
285: lg=strlen(s);
286: for(i=0; i<= lg; i++) {
287: if (s[i] == occ ) j++;
288: }
289: return j;
290: }
291:
292: void cutv(char *u,char *v, char*t, char occ)
293: {
294: /* cuts string t into u and v where u is ended by char occ excluding it
295: and v is after occ excluding it too : ex cutv(u,v,"abcdef2ghi2j",2)
296: gives u="abcedf" and v="ghi2j" */
297: int i,lg,j,p=0;
298: i=0;
299: for(j=0; j<=strlen(t)-1; j++) {
300: if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;
301: }
302:
303: lg=strlen(t);
304: for(j=0; j<p; j++) {
305: (u[j] = t[j]);
306: }
307: u[p]='\0';
308:
309: for(j=0; j<= lg; j++) {
310: if (j>=(p+1))(v[j-p-1] = t[j]);
311: }
312: }
313:
314: /********************** nrerror ********************/
315:
316: void nrerror(char error_text[])
317: {
318: fprintf(stderr,"ERREUR ...\n");
319: fprintf(stderr,"%s\n",error_text);
1.59 brouard 320: exit(EXIT_FAILURE);
1.53 brouard 321: }
322: /*********************** vector *******************/
323: double *vector(int nl, int nh)
324: {
325: double *v;
326: v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
327: if (!v) nrerror("allocation failure in vector");
328: return v-nl+NR_END;
329: }
330:
331: /************************ free vector ******************/
332: void free_vector(double*v, int nl, int nh)
333: {
334: free((FREE_ARG)(v+nl-NR_END));
335: }
336:
337: /************************ivector *******************************/
1.76 brouard 338: char *cvector(long nl,long nh)
339: {
340: char *v;
341: v=(char *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(char)));
342: if (!v) nrerror("allocation failure in cvector");
343: return v-nl+NR_END;
344: }
345:
346: /******************free ivector **************************/
347: void free_cvector(char *v, long nl, long nh)
348: {
349: free((FREE_ARG)(v+nl-NR_END));
350: }
351:
352: /************************ivector *******************************/
1.53 brouard 353: int *ivector(long nl,long nh)
354: {
355: int *v;
356: v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
357: if (!v) nrerror("allocation failure in ivector");
358: return v-nl+NR_END;
359: }
360:
361: /******************free ivector **************************/
362: void free_ivector(int *v, long nl, long nh)
363: {
364: free((FREE_ARG)(v+nl-NR_END));
365: }
366:
367: /******************* imatrix *******************************/
368: int **imatrix(long nrl, long nrh, long ncl, long nch)
369: /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */
370: {
371: long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;
372: int **m;
373:
374: /* allocate pointers to rows */
375: m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));
376: if (!m) nrerror("allocation failure 1 in matrix()");
377: m += NR_END;
378: m -= nrl;
379:
380:
381: /* allocate rows and set pointers to them */
382: m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));
383: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
384: m[nrl] += NR_END;
385: m[nrl] -= ncl;
386:
387: for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;
388:
389: /* return pointer to array of pointers to rows */
390: return m;
391: }
392:
393: /****************** free_imatrix *************************/
394: void free_imatrix(m,nrl,nrh,ncl,nch)
395: int **m;
396: long nch,ncl,nrh,nrl;
397: /* free an int matrix allocated by imatrix() */
398: {
399: free((FREE_ARG) (m[nrl]+ncl-NR_END));
400: free((FREE_ARG) (m+nrl-NR_END));
401: }
402:
403: /******************* matrix *******************************/
404: double **matrix(long nrl, long nrh, long ncl, long nch)
405: {
406: long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
407: double **m;
408:
409: m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
410: if (!m) nrerror("allocation failure 1 in matrix()");
411: m += NR_END;
412: m -= nrl;
413:
414: m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
415: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
416: m[nrl] += NR_END;
417: m[nrl] -= ncl;
418:
419: for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
420: return m;
1.74 brouard 421: /* print *(*(m+1)+70) ou print m[1][70]; print m+1 or print &(m[1])
422: */
1.53 brouard 423: }
424:
425: /*************************free matrix ************************/
426: void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
427: {
428: free((FREE_ARG)(m[nrl]+ncl-NR_END));
429: free((FREE_ARG)(m+nrl-NR_END));
430: }
431:
432: /******************* ma3x *******************************/
433: double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
434: {
435: long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
436: double ***m;
437:
438: m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
439: if (!m) nrerror("allocation failure 1 in matrix()");
440: m += NR_END;
441: m -= nrl;
442:
443: m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
444: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
445: m[nrl] += NR_END;
446: m[nrl] -= ncl;
447:
448: for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
449:
450: m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
451: if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
452: m[nrl][ncl] += NR_END;
453: m[nrl][ncl] -= nll;
454: for (j=ncl+1; j<=nch; j++)
455: m[nrl][j]=m[nrl][j-1]+nlay;
456:
457: for (i=nrl+1; i<=nrh; i++) {
458: m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
459: for (j=ncl+1; j<=nch; j++)
460: m[i][j]=m[i][j-1]+nlay;
461: }
1.74 brouard 462: return m;
463: /* gdb: p *(m+1) <=> p m[1] and p (m+1) <=> p (m+1) <=> p &(m[1])
464: &(m[i][j][k]) <=> *((*(m+i) + j)+k)
465: */
1.53 brouard 466: }
467:
468: /*************************free ma3x ************************/
469: void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
470: {
471: free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
472: free((FREE_ARG)(m[nrl]+ncl-NR_END));
473: free((FREE_ARG)(m+nrl-NR_END));
474: }
475:
476: /***************** f1dim *************************/
477: extern int ncom;
478: extern double *pcom,*xicom;
479: extern double (*nrfunc)(double []);
480:
481: double f1dim(double x)
482: {
483: int j;
484: double f;
485: double *xt;
486:
487: xt=vector(1,ncom);
488: for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];
489: f=(*nrfunc)(xt);
490: free_vector(xt,1,ncom);
491: return f;
492: }
493:
494: /*****************brent *************************/
495: double brent(double ax, double bx, double cx, double (*f)(double), double tol, double *xmin)
496: {
497: int iter;
498: double a,b,d,etemp;
499: double fu,fv,fw,fx;
500: double ftemp;
501: double p,q,r,tol1,tol2,u,v,w,x,xm;
502: double e=0.0;
503:
504: a=(ax < cx ? ax : cx);
505: b=(ax > cx ? ax : cx);
506: x=w=v=bx;
507: fw=fv=fx=(*f)(x);
508: for (iter=1;iter<=ITMAX;iter++) {
509: xm=0.5*(a+b);
510: tol2=2.0*(tol1=tol*fabs(x)+ZEPS);
511: /* if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
512: printf(".");fflush(stdout);
513: fprintf(ficlog,".");fflush(ficlog);
514: #ifdef DEBUG
515: 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);
516: 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);
517: /* if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
518: #endif
519: if (fabs(x-xm) <= (tol2-0.5*(b-a))){
520: *xmin=x;
521: return fx;
522: }
523: ftemp=fu;
524: if (fabs(e) > tol1) {
525: r=(x-w)*(fx-fv);
526: q=(x-v)*(fx-fw);
527: p=(x-v)*q-(x-w)*r;
528: q=2.0*(q-r);
529: if (q > 0.0) p = -p;
530: q=fabs(q);
531: etemp=e;
532: e=d;
533: if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))
534: d=CGOLD*(e=(x >= xm ? a-x : b-x));
535: else {
536: d=p/q;
537: u=x+d;
538: if (u-a < tol2 || b-u < tol2)
539: d=SIGN(tol1,xm-x);
540: }
541: } else {
542: d=CGOLD*(e=(x >= xm ? a-x : b-x));
543: }
544: u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));
545: fu=(*f)(u);
546: if (fu <= fx) {
547: if (u >= x) a=x; else b=x;
548: SHFT(v,w,x,u)
549: SHFT(fv,fw,fx,fu)
550: } else {
551: if (u < x) a=u; else b=u;
552: if (fu <= fw || w == x) {
553: v=w;
554: w=u;
555: fv=fw;
556: fw=fu;
557: } else if (fu <= fv || v == x || v == w) {
558: v=u;
559: fv=fu;
560: }
561: }
562: }
563: nrerror("Too many iterations in brent");
564: *xmin=x;
565: return fx;
566: }
567:
568: /****************** mnbrak ***********************/
569:
570: void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,
571: double (*func)(double))
572: {
573: double ulim,u,r,q, dum;
574: double fu;
575:
576: *fa=(*func)(*ax);
577: *fb=(*func)(*bx);
578: if (*fb > *fa) {
579: SHFT(dum,*ax,*bx,dum)
580: SHFT(dum,*fb,*fa,dum)
581: }
582: *cx=(*bx)+GOLD*(*bx-*ax);
583: *fc=(*func)(*cx);
584: while (*fb > *fc) {
585: r=(*bx-*ax)*(*fb-*fc);
586: q=(*bx-*cx)*(*fb-*fa);
587: u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/
588: (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r));
589: ulim=(*bx)+GLIMIT*(*cx-*bx);
590: if ((*bx-u)*(u-*cx) > 0.0) {
591: fu=(*func)(u);
592: } else if ((*cx-u)*(u-ulim) > 0.0) {
593: fu=(*func)(u);
594: if (fu < *fc) {
595: SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))
596: SHFT(*fb,*fc,fu,(*func)(u))
597: }
598: } else if ((u-ulim)*(ulim-*cx) >= 0.0) {
599: u=ulim;
600: fu=(*func)(u);
601: } else {
602: u=(*cx)+GOLD*(*cx-*bx);
603: fu=(*func)(u);
604: }
605: SHFT(*ax,*bx,*cx,u)
606: SHFT(*fa,*fb,*fc,fu)
607: }
608: }
609:
610: /*************** linmin ************************/
611:
612: int ncom;
613: double *pcom,*xicom;
614: double (*nrfunc)(double []);
615:
616: void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))
617: {
618: double brent(double ax, double bx, double cx,
619: double (*f)(double), double tol, double *xmin);
620: double f1dim(double x);
621: void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,
622: double *fc, double (*func)(double));
623: int j;
624: double xx,xmin,bx,ax;
625: double fx,fb,fa;
626:
627: ncom=n;
628: pcom=vector(1,n);
629: xicom=vector(1,n);
630: nrfunc=func;
631: for (j=1;j<=n;j++) {
632: pcom[j]=p[j];
633: xicom[j]=xi[j];
634: }
635: ax=0.0;
636: xx=1.0;
637: mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim);
638: *fret=brent(ax,xx,bx,f1dim,TOL,&xmin);
639: #ifdef DEBUG
640: printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
641: fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
642: #endif
643: for (j=1;j<=n;j++) {
644: xi[j] *= xmin;
645: p[j] += xi[j];
646: }
647: free_vector(xicom,1,n);
648: free_vector(pcom,1,n);
649: }
650:
651: /*************** powell ************************/
652: void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,
653: double (*func)(double []))
654: {
655: void linmin(double p[], double xi[], int n, double *fret,
656: double (*func)(double []));
657: int i,ibig,j;
658: double del,t,*pt,*ptt,*xit;
659: double fp,fptt;
660: double *xits;
661: pt=vector(1,n);
662: ptt=vector(1,n);
663: xit=vector(1,n);
664: xits=vector(1,n);
665: *fret=(*func)(p);
666: for (j=1;j<=n;j++) pt[j]=p[j];
667: for (*iter=1;;++(*iter)) {
668: fp=(*fret);
669: ibig=0;
670: del=0.0;
671: printf("\nPowell iter=%d -2*LL=%.12f",*iter,*fret);
672: fprintf(ficlog,"\nPowell iter=%d -2*LL=%.12f",*iter,*fret);
1.76 brouard 673: fprintf(ficrespow,"%d %.12f",*iter,*fret);
674: for (i=1;i<=n;i++) {
1.53 brouard 675: printf(" %d %.12f",i, p[i]);
1.76 brouard 676: fprintf(ficlog," %d %.12lf",i, p[i]);
677: fprintf(ficrespow," %.12lf", p[i]);
678: }
1.53 brouard 679: printf("\n");
680: fprintf(ficlog,"\n");
1.76 brouard 681: fprintf(ficrespow,"\n");
1.53 brouard 682: for (i=1;i<=n;i++) {
683: for (j=1;j<=n;j++) xit[j]=xi[j][i];
684: fptt=(*fret);
685: #ifdef DEBUG
686: printf("fret=%lf \n",*fret);
687: fprintf(ficlog,"fret=%lf \n",*fret);
688: #endif
689: printf("%d",i);fflush(stdout);
690: fprintf(ficlog,"%d",i);fflush(ficlog);
691: linmin(p,xit,n,fret,func);
692: if (fabs(fptt-(*fret)) > del) {
693: del=fabs(fptt-(*fret));
694: ibig=i;
695: }
696: #ifdef DEBUG
697: printf("%d %.12e",i,(*fret));
698: fprintf(ficlog,"%d %.12e",i,(*fret));
699: for (j=1;j<=n;j++) {
700: xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
701: printf(" x(%d)=%.12e",j,xit[j]);
702: fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
703: }
704: for(j=1;j<=n;j++) {
705: printf(" p=%.12e",p[j]);
706: fprintf(ficlog," p=%.12e",p[j]);
707: }
708: printf("\n");
709: fprintf(ficlog,"\n");
710: #endif
711: }
712: if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {
713: #ifdef DEBUG
714: int k[2],l;
715: k[0]=1;
716: k[1]=-1;
717: printf("Max: %.12e",(*func)(p));
718: fprintf(ficlog,"Max: %.12e",(*func)(p));
719: for (j=1;j<=n;j++) {
720: printf(" %.12e",p[j]);
721: fprintf(ficlog," %.12e",p[j]);
722: }
723: printf("\n");
724: fprintf(ficlog,"\n");
725: for(l=0;l<=1;l++) {
726: for (j=1;j<=n;j++) {
727: ptt[j]=p[j]+(p[j]-pt[j])*k[l];
728: printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
729: fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
730: }
731: printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
732: fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
733: }
734: #endif
735:
736:
737: free_vector(xit,1,n);
738: free_vector(xits,1,n);
739: free_vector(ptt,1,n);
740: free_vector(pt,1,n);
741: return;
742: }
743: if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");
744: for (j=1;j<=n;j++) {
745: ptt[j]=2.0*p[j]-pt[j];
746: xit[j]=p[j]-pt[j];
747: pt[j]=p[j];
748: }
749: fptt=(*func)(ptt);
750: if (fptt < fp) {
751: t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt);
752: if (t < 0.0) {
753: linmin(p,xit,n,fret,func);
754: for (j=1;j<=n;j++) {
755: xi[j][ibig]=xi[j][n];
756: xi[j][n]=xit[j];
757: }
758: #ifdef DEBUG
759: printf("Direction changed last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
760: fprintf(ficlog,"Direction changed last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
761: for(j=1;j<=n;j++){
762: printf(" %.12e",xit[j]);
763: fprintf(ficlog," %.12e",xit[j]);
764: }
765: printf("\n");
766: fprintf(ficlog,"\n");
767: #endif
1.54 brouard 768: }
1.53 brouard 769: }
770: }
771: }
772:
1.54 brouard 773: /**** Prevalence limit (stable prevalence) ****************/
1.53 brouard 774:
775: double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)
776: {
777: /* Computes the prevalence limit in each live state at age x by left multiplying the unit
778: matrix by transitions matrix until convergence is reached */
779:
780: int i, ii,j,k;
781: double min, max, maxmin, maxmax,sumnew=0.;
782: double **matprod2();
783: double **out, cov[NCOVMAX], **pmij();
784: double **newm;
785: double agefin, delaymax=50 ; /* Max number of years to converge */
786:
787: for (ii=1;ii<=nlstate+ndeath;ii++)
788: for (j=1;j<=nlstate+ndeath;j++){
789: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
790: }
791:
792: cov[1]=1.;
793:
794: /* Even if hstepm = 1, at least one multiplication by the unit matrix */
795: for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
796: newm=savm;
797: /* Covariates have to be included here again */
798: cov[2]=agefin;
799:
800: for (k=1; k<=cptcovn;k++) {
801: cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
802: /* 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]]);*/
803: }
804: for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
805: for (k=1; k<=cptcovprod;k++)
806: cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
807:
808: /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
809: /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
810: /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
811: out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);
812:
813: savm=oldm;
814: oldm=newm;
815: maxmax=0.;
816: for(j=1;j<=nlstate;j++){
817: min=1.;
818: max=0.;
819: for(i=1; i<=nlstate; i++) {
820: sumnew=0;
821: for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
822: prlim[i][j]= newm[i][j]/(1-sumnew);
823: max=FMAX(max,prlim[i][j]);
824: min=FMIN(min,prlim[i][j]);
825: }
826: maxmin=max-min;
827: maxmax=FMAX(maxmax,maxmin);
828: }
829: if(maxmax < ftolpl){
830: return prlim;
831: }
832: }
833: }
834:
835: /*************** transition probabilities ***************/
836:
837: double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
838: {
839: double s1, s2;
840: /*double t34;*/
841: int i,j,j1, nc, ii, jj;
842:
843: for(i=1; i<= nlstate; i++){
844: for(j=1; j<i;j++){
845: for (nc=1, s2=0.;nc <=ncovmodel; nc++){
846: /*s2 += param[i][j][nc]*cov[nc];*/
847: s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
848: /*printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2);*/
849: }
850: ps[i][j]=s2;
851: /*printf("s1=%.17e, s2=%.17e\n",s1,s2);*/
852: }
853: for(j=i+1; j<=nlstate+ndeath;j++){
854: for (nc=1, s2=0.;nc <=ncovmodel; nc++){
855: s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
856: /*printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2);*/
857: }
858: ps[i][j]=s2;
859: }
860: }
861: /*ps[3][2]=1;*/
862:
863: for(i=1; i<= nlstate; i++){
864: s1=0;
865: for(j=1; j<i; j++)
866: s1+=exp(ps[i][j]);
867: for(j=i+1; j<=nlstate+ndeath; j++)
868: s1+=exp(ps[i][j]);
869: ps[i][i]=1./(s1+1.);
870: for(j=1; j<i; j++)
871: ps[i][j]= exp(ps[i][j])*ps[i][i];
872: for(j=i+1; j<=nlstate+ndeath; j++)
873: ps[i][j]= exp(ps[i][j])*ps[i][i];
874: /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
875: } /* end i */
876:
877: for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
878: for(jj=1; jj<= nlstate+ndeath; jj++){
879: ps[ii][jj]=0;
880: ps[ii][ii]=1;
881: }
882: }
883:
884:
885: /* for(ii=1; ii<= nlstate+ndeath; ii++){
886: for(jj=1; jj<= nlstate+ndeath; jj++){
887: printf("%lf ",ps[ii][jj]);
888: }
889: printf("\n ");
890: }
891: printf("\n ");printf("%lf ",cov[2]);*/
892: /*
893: for(i=1; i<= npar; i++) printf("%f ",x[i]);
894: goto end;*/
895: return ps;
896: }
897:
898: /**************** Product of 2 matrices ******************/
899:
900: double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)
901: {
902: /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
903: b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
904: /* in, b, out are matrice of pointers which should have been initialized
905: before: only the contents of out is modified. The function returns
906: a pointer to pointers identical to out */
907: long i, j, k;
908: for(i=nrl; i<= nrh; i++)
909: for(k=ncolol; k<=ncoloh; k++)
910: for(j=ncl,out[i][k]=0.; j<=nch; j++)
911: out[i][k] +=in[i][j]*b[j][k];
912:
913: return out;
914: }
915:
916:
917: /************* Higher Matrix Product ***************/
918:
919: double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
920: {
1.66 brouard 921: /* Computes the transition matrix starting at age 'age' over
922: 'nhstepm*hstepm*stepm' months (i.e. until
923: age (in years) age+nhstepm*hstepm*stepm/12) by multiplying
924: nhstepm*hstepm matrices.
1.53 brouard 925: Output is stored in matrix po[i][j][h] for h every 'hstepm' step
1.66 brouard 926: (typically every 2 years instead of every month which is too big
927: for the memory).
1.53 brouard 928: Model is determined by parameters x and covariates have to be
929: included manually here.
930:
931: */
932:
933: int i, j, d, h, k;
934: double **out, cov[NCOVMAX];
935: double **newm;
936:
937: /* Hstepm could be zero and should return the unit matrix */
938: for (i=1;i<=nlstate+ndeath;i++)
939: for (j=1;j<=nlstate+ndeath;j++){
940: oldm[i][j]=(i==j ? 1.0 : 0.0);
941: po[i][j][0]=(i==j ? 1.0 : 0.0);
942: }
943: /* Even if hstepm = 1, at least one multiplication by the unit matrix */
944: for(h=1; h <=nhstepm; h++){
945: for(d=1; d <=hstepm; d++){
946: newm=savm;
947: /* Covariates have to be included here again */
948: cov[1]=1.;
949: cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
950: for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
951: for (k=1; k<=cptcovage;k++)
952: cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
953: for (k=1; k<=cptcovprod;k++)
954: cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
955:
956:
957: /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
958: /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
959: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,
960: pmij(pmmij,cov,ncovmodel,x,nlstate));
961: savm=oldm;
962: oldm=newm;
963: }
964: for(i=1; i<=nlstate+ndeath; i++)
965: for(j=1;j<=nlstate+ndeath;j++) {
966: po[i][j][h]=newm[i][j];
967: /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);
968: */
969: }
970: } /* end h */
971: return po;
972: }
973:
974:
975: /*************** log-likelihood *************/
976: double func( double *x)
977: {
978: int i, ii, j, k, mi, d, kk;
979: double l, ll[NLSTATEMAX], cov[NCOVMAX];
980: double **out;
981: double sw; /* Sum of weights */
982: double lli; /* Individual log likelihood */
1.59 brouard 983: int s1, s2;
1.68 lievre 984: double bbh, survp;
1.53 brouard 985: long ipmx;
986: /*extern weight */
987: /* We are differentiating ll according to initial status */
988: /* for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
989: /*for(i=1;i<imx;i++)
990: printf(" %d\n",s[4][i]);
991: */
992: cov[1]=1.;
993:
994: for(k=1; k<=nlstate; k++) ll[k]=0.;
1.61 brouard 995:
996: if(mle==1){
997: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
998: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
999: for(mi=1; mi<= wav[i]-1; mi++){
1000: for (ii=1;ii<=nlstate+ndeath;ii++)
1001: for (j=1;j<=nlstate+ndeath;j++){
1002: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1003: savm[ii][j]=(ii==j ? 1.0 : 0.0);
1004: }
1005: for(d=0; d<dh[mi][i]; d++){
1006: newm=savm;
1007: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
1008: for (kk=1; kk<=cptcovage;kk++) {
1009: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
1010: }
1011: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1012: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1013: savm=oldm;
1014: oldm=newm;
1015: } /* end mult */
1.53 brouard 1016:
1.61 brouard 1017: /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
1018: /* But now since version 0.9 we anticipate for bias and large stepm.
1019: * If stepm is larger than one month (smallest stepm) and if the exact delay
1020: * (in months) between two waves is not a multiple of stepm, we rounded to
1021: * the nearest (and in case of equal distance, to the lowest) interval but now
1022: * we keep into memory the bias bh[mi][i] and also the previous matrix product
1023: * (i.e to dh[mi][i]-1) saved in 'savm'. The we inter(extra)polate the
1024: * probability in order to take into account the bias as a fraction of the way
1025: * from savm to out if bh is neagtive or even beyond if bh is positive. bh varies
1026: * -stepm/2 to stepm/2 .
1027: * For stepm=1 the results are the same as for previous versions of Imach.
1028: * For stepm > 1 the results are less biased than in previous versions.
1029: */
1030: s1=s[mw[mi][i]][i];
1031: s2=s[mw[mi+1][i]][i];
1.64 lievre 1032: bbh=(double)bh[mi][i]/(double)stepm;
1033: /* bias is positive if real duration
1034: * is higher than the multiple of stepm and negative otherwise.
1035: */
1036: /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
1.71 brouard 1037: if( s2 > nlstate){
1038: /* i.e. if s2 is a death state and if the date of death is known then the contribution
1039: to the likelihood is the probability to die between last step unit time and current
1040: step unit time, which is also the differences between probability to die before dh
1041: and probability to die before dh-stepm .
1042: In version up to 0.92 likelihood was computed
1043: as if date of death was unknown. Death was treated as any other
1044: health state: the date of the interview describes the actual state
1045: and not the date of a change in health state. The former idea was
1046: to consider that at each interview the state was recorded
1047: (healthy, disable or death) and IMaCh was corrected; but when we
1048: introduced the exact date of death then we should have modified
1049: the contribution of an exact death to the likelihood. This new
1050: contribution is smaller and very dependent of the step unit
1051: stepm. It is no more the probability to die between last interview
1052: and month of death but the probability to survive from last
1053: interview up to one month before death multiplied by the
1054: probability to die within a month. Thanks to Chris
1055: Jackson for correcting this bug. Former versions increased
1056: mortality artificially. The bad side is that we add another loop
1057: which slows down the processing. The difference can be up to 10%
1058: lower mortality.
1059: */
1060: lli=log(out[s1][s2] - savm[s1][s2]);
1061: }else{
1062: lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
1063: /* 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 */
1064: }
1.64 lievre 1065: /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
1066: /*if(lli ==000.0)*/
1067: /*printf("bbh= %f lli=%f savm=%f out=%f %d\n",bbh,lli,savm[s1][s2], out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]],i); */
1.71 brouard 1068: ipmx +=1;
1.64 lievre 1069: sw += weight[i];
1070: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1071: } /* end of wave */
1072: } /* end of individual */
1073: } else if(mle==2){
1074: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1075: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
1076: for(mi=1; mi<= wav[i]-1; mi++){
1077: for (ii=1;ii<=nlstate+ndeath;ii++)
1078: for (j=1;j<=nlstate+ndeath;j++){
1079: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1080: savm[ii][j]=(ii==j ? 1.0 : 0.0);
1081: }
1082: for(d=0; d<=dh[mi][i]; d++){
1083: newm=savm;
1084: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
1085: for (kk=1; kk<=cptcovage;kk++) {
1086: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
1087: }
1088: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1089: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1090: savm=oldm;
1091: oldm=newm;
1092: } /* end mult */
1093:
1094: /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
1095: /* But now since version 0.9 we anticipate for bias and large stepm.
1096: * If stepm is larger than one month (smallest stepm) and if the exact delay
1097: * (in months) between two waves is not a multiple of stepm, we rounded to
1098: * the nearest (and in case of equal distance, to the lowest) interval but now
1099: * we keep into memory the bias bh[mi][i] and also the previous matrix product
1100: * (i.e to dh[mi][i]-1) saved in 'savm'. The we inter(extra)polate the
1101: * probability in order to take into account the bias as a fraction of the way
1102: * from savm to out if bh is neagtive or even beyond if bh is positive. bh varies
1103: * -stepm/2 to stepm/2 .
1104: * For stepm=1 the results are the same as for previous versions of Imach.
1105: * For stepm > 1 the results are less biased than in previous versions.
1106: */
1107: s1=s[mw[mi][i]][i];
1108: s2=s[mw[mi+1][i]][i];
1109: bbh=(double)bh[mi][i]/(double)stepm;
1110: /* bias is positive if real duration
1111: * is higher than the multiple of stepm and negative otherwise.
1112: */
1.63 lievre 1113: 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 1114: /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
1115: /*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 */
1116: /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
1117: /*if(lli ==000.0)*/
1118: /*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); */
1119: ipmx +=1;
1120: sw += weight[i];
1121: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1122: } /* end of wave */
1123: } /* end of individual */
1124: } else if(mle==3){ /* exponential inter-extrapolation */
1125: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1126: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
1127: for(mi=1; mi<= wav[i]-1; mi++){
1128: for (ii=1;ii<=nlstate+ndeath;ii++)
1129: for (j=1;j<=nlstate+ndeath;j++){
1130: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1131: savm[ii][j]=(ii==j ? 1.0 : 0.0);
1132: }
1133: for(d=0; d<dh[mi][i]; d++){
1134: newm=savm;
1135: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
1136: for (kk=1; kk<=cptcovage;kk++) {
1137: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
1138: }
1139: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1140: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1141: savm=oldm;
1142: oldm=newm;
1143: } /* end mult */
1144:
1145: /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
1146: /* But now since version 0.9 we anticipate for bias and large stepm.
1147: * If stepm is larger than one month (smallest stepm) and if the exact delay
1148: * (in months) between two waves is not a multiple of stepm, we rounded to
1149: * the nearest (and in case of equal distance, to the lowest) interval but now
1150: * we keep into memory the bias bh[mi][i] and also the previous matrix product
1151: * (i.e to dh[mi][i]-1) saved in 'savm'. The we inter(extra)polate the
1152: * probability in order to take into account the bias as a fraction of the way
1153: * from savm to out if bh is neagtive or even beyond if bh is positive. bh varies
1154: * -stepm/2 to stepm/2 .
1155: * For stepm=1 the results are the same as for previous versions of Imach.
1156: * For stepm > 1 the results are less biased than in previous versions.
1157: */
1158: s1=s[mw[mi][i]][i];
1159: s2=s[mw[mi+1][i]][i];
1160: bbh=(double)bh[mi][i]/(double)stepm;
1161: /* bias is positive if real duration
1162: * is higher than the multiple of stepm and negative otherwise.
1163: */
1164: /* 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 */
1165: 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 1166: /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
1167: /*if(lli ==000.0)*/
1168: /*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); */
1169: ipmx +=1;
1170: sw += weight[i];
1171: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1172: } /* end of wave */
1173: } /* end of individual */
1.64 lievre 1174: }else{ /* ml=4 no inter-extrapolation */
1.61 brouard 1175: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1176: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
1177: for(mi=1; mi<= wav[i]-1; mi++){
1178: for (ii=1;ii<=nlstate+ndeath;ii++)
1179: for (j=1;j<=nlstate+ndeath;j++){
1180: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1181: savm[ii][j]=(ii==j ? 1.0 : 0.0);
1182: }
1183: for(d=0; d<dh[mi][i]; d++){
1184: newm=savm;
1185: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
1186: for (kk=1; kk<=cptcovage;kk++) {
1187: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
1188: }
1189:
1190: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1191: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1192: savm=oldm;
1193: oldm=newm;
1194: } /* end mult */
1195:
1196: lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
1197: ipmx +=1;
1198: sw += weight[i];
1199: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1200: } /* end of wave */
1201: } /* end of individual */
1202: } /* End of if */
1.53 brouard 1203: for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
1204: /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
1205: l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
1206: return -l;
1207: }
1208:
1209:
1210: /*********** Maximum Likelihood Estimation ***************/
1211:
1212: void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
1213: {
1214: int i,j, iter;
1.74 brouard 1215: double **xi;
1.53 brouard 1216: double fret;
1.76 brouard 1217: char filerespow[FILENAMELENGTH];
1.53 brouard 1218: xi=matrix(1,npar,1,npar);
1219: for (i=1;i<=npar;i++)
1220: for (j=1;j<=npar;j++)
1221: xi[i][j]=(i==j ? 1.0 : 0.0);
1222: printf("Powell\n"); fprintf(ficlog,"Powell\n");
1.76 brouard 1223: strcpy(filerespow,"pow");
1224: strcat(filerespow,fileres);
1225: if((ficrespow=fopen(filerespow,"w"))==NULL) {
1226: printf("Problem with resultfile: %s\n", filerespow);
1227: fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
1228: }
1229: fprintf(ficrespow,"# Powell\n# iter -2*LL");
1230: for (i=1;i<=nlstate;i++)
1231: for(j=1;j<=nlstate+ndeath;j++)
1232: if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
1233: fprintf(ficrespow,"\n");
1.53 brouard 1234: powell(p,xi,npar,ftol,&iter,&fret,func);
1235:
1.76 brouard 1236: fclose(ficrespow);
1237: printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));
1.65 lievre 1238: fprintf(ficlog,"\n#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
1.53 brouard 1239: fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
1240:
1241: }
1242:
1243: /**** Computes Hessian and covariance matrix ***/
1244: void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
1245: {
1246: double **a,**y,*x,pd;
1247: double **hess;
1248: int i, j,jk;
1249: int *indx;
1250:
1251: double hessii(double p[], double delta, int theta, double delti[]);
1252: double hessij(double p[], double delti[], int i, int j);
1253: void lubksb(double **a, int npar, int *indx, double b[]) ;
1254: void ludcmp(double **a, int npar, int *indx, double *d) ;
1255:
1256: hess=matrix(1,npar,1,npar);
1257:
1258: printf("\nCalculation of the hessian matrix. Wait...\n");
1259: fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
1260: for (i=1;i<=npar;i++){
1261: printf("%d",i);fflush(stdout);
1262: fprintf(ficlog,"%d",i);fflush(ficlog);
1263: hess[i][i]=hessii(p,ftolhess,i,delti);
1264: /*printf(" %f ",p[i]);*/
1265: /*printf(" %lf ",hess[i][i]);*/
1266: }
1267:
1268: for (i=1;i<=npar;i++) {
1269: for (j=1;j<=npar;j++) {
1270: if (j>i) {
1271: printf(".%d%d",i,j);fflush(stdout);
1272: fprintf(ficlog,".%d%d",i,j);fflush(ficlog);
1273: hess[i][j]=hessij(p,delti,i,j);
1274: hess[j][i]=hess[i][j];
1275: /*printf(" %lf ",hess[i][j]);*/
1276: }
1277: }
1278: }
1279: printf("\n");
1280: fprintf(ficlog,"\n");
1281:
1282: printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
1283: fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
1284:
1285: a=matrix(1,npar,1,npar);
1286: y=matrix(1,npar,1,npar);
1287: x=vector(1,npar);
1288: indx=ivector(1,npar);
1289: for (i=1;i<=npar;i++)
1290: for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
1291: ludcmp(a,npar,indx,&pd);
1292:
1293: for (j=1;j<=npar;j++) {
1294: for (i=1;i<=npar;i++) x[i]=0;
1295: x[j]=1;
1296: lubksb(a,npar,indx,x);
1297: for (i=1;i<=npar;i++){
1298: matcov[i][j]=x[i];
1299: }
1300: }
1301:
1302: printf("\n#Hessian matrix#\n");
1303: fprintf(ficlog,"\n#Hessian matrix#\n");
1304: for (i=1;i<=npar;i++) {
1305: for (j=1;j<=npar;j++) {
1306: printf("%.3e ",hess[i][j]);
1307: fprintf(ficlog,"%.3e ",hess[i][j]);
1308: }
1309: printf("\n");
1310: fprintf(ficlog,"\n");
1311: }
1312:
1313: /* Recompute Inverse */
1314: for (i=1;i<=npar;i++)
1315: for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];
1316: ludcmp(a,npar,indx,&pd);
1317:
1318: /* printf("\n#Hessian matrix recomputed#\n");
1319:
1320: for (j=1;j<=npar;j++) {
1321: for (i=1;i<=npar;i++) x[i]=0;
1322: x[j]=1;
1323: lubksb(a,npar,indx,x);
1324: for (i=1;i<=npar;i++){
1325: y[i][j]=x[i];
1326: printf("%.3e ",y[i][j]);
1327: fprintf(ficlog,"%.3e ",y[i][j]);
1328: }
1329: printf("\n");
1330: fprintf(ficlog,"\n");
1331: }
1332: */
1333:
1334: free_matrix(a,1,npar,1,npar);
1335: free_matrix(y,1,npar,1,npar);
1336: free_vector(x,1,npar);
1337: free_ivector(indx,1,npar);
1338: free_matrix(hess,1,npar,1,npar);
1339:
1340:
1341: }
1342:
1343: /*************** hessian matrix ****************/
1344: double hessii( double x[], double delta, int theta, double delti[])
1345: {
1346: int i;
1347: int l=1, lmax=20;
1348: double k1,k2;
1349: double p2[NPARMAX+1];
1350: double res;
1351: double delt, delts, nkhi=10.,nkhif=1., khi=1.e-4;
1352: double fx;
1353: int k=0,kmax=10;
1354: double l1;
1355:
1356: fx=func(x);
1357: for (i=1;i<=npar;i++) p2[i]=x[i];
1358: for(l=0 ; l <=lmax; l++){
1359: l1=pow(10,l);
1360: delts=delt;
1361: for(k=1 ; k <kmax; k=k+1){
1362: delt = delta*(l1*k);
1363: p2[theta]=x[theta] +delt;
1364: k1=func(p2)-fx;
1365: p2[theta]=x[theta]-delt;
1366: k2=func(p2)-fx;
1367: /*res= (k1-2.0*fx+k2)/delt/delt; */
1368: res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */
1369:
1370: #ifdef DEBUG
1371: 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);
1372: 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);
1373: #endif
1374: /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
1375: if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
1376: k=kmax;
1377: }
1378: else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
1379: k=kmax; l=lmax*10.;
1380: }
1381: else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){
1382: delts=delt;
1383: }
1384: }
1385: }
1386: delti[theta]=delts;
1387: return res;
1388:
1389: }
1390:
1391: double hessij( double x[], double delti[], int thetai,int thetaj)
1392: {
1393: int i;
1394: int l=1, l1, lmax=20;
1395: double k1,k2,k3,k4,res,fx;
1396: double p2[NPARMAX+1];
1397: int k;
1398:
1399: fx=func(x);
1400: for (k=1; k<=2; k++) {
1401: for (i=1;i<=npar;i++) p2[i]=x[i];
1402: p2[thetai]=x[thetai]+delti[thetai]/k;
1403: p2[thetaj]=x[thetaj]+delti[thetaj]/k;
1404: k1=func(p2)-fx;
1405:
1406: p2[thetai]=x[thetai]+delti[thetai]/k;
1407: p2[thetaj]=x[thetaj]-delti[thetaj]/k;
1408: k2=func(p2)-fx;
1409:
1410: p2[thetai]=x[thetai]-delti[thetai]/k;
1411: p2[thetaj]=x[thetaj]+delti[thetaj]/k;
1412: k3=func(p2)-fx;
1413:
1414: p2[thetai]=x[thetai]-delti[thetai]/k;
1415: p2[thetaj]=x[thetaj]-delti[thetaj]/k;
1416: k4=func(p2)-fx;
1417: res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */
1418: #ifdef DEBUG
1419: 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);
1420: 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);
1421: #endif
1422: }
1423: return res;
1424: }
1425:
1426: /************** Inverse of matrix **************/
1427: void ludcmp(double **a, int n, int *indx, double *d)
1428: {
1429: int i,imax,j,k;
1430: double big,dum,sum,temp;
1431: double *vv;
1432:
1433: vv=vector(1,n);
1434: *d=1.0;
1435: for (i=1;i<=n;i++) {
1436: big=0.0;
1437: for (j=1;j<=n;j++)
1438: if ((temp=fabs(a[i][j])) > big) big=temp;
1439: if (big == 0.0) nrerror("Singular matrix in routine ludcmp");
1440: vv[i]=1.0/big;
1441: }
1442: for (j=1;j<=n;j++) {
1443: for (i=1;i<j;i++) {
1444: sum=a[i][j];
1445: for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];
1446: a[i][j]=sum;
1447: }
1448: big=0.0;
1449: for (i=j;i<=n;i++) {
1450: sum=a[i][j];
1451: for (k=1;k<j;k++)
1452: sum -= a[i][k]*a[k][j];
1453: a[i][j]=sum;
1454: if ( (dum=vv[i]*fabs(sum)) >= big) {
1455: big=dum;
1456: imax=i;
1457: }
1458: }
1459: if (j != imax) {
1460: for (k=1;k<=n;k++) {
1461: dum=a[imax][k];
1462: a[imax][k]=a[j][k];
1463: a[j][k]=dum;
1464: }
1465: *d = -(*d);
1466: vv[imax]=vv[j];
1467: }
1468: indx[j]=imax;
1469: if (a[j][j] == 0.0) a[j][j]=TINY;
1470: if (j != n) {
1471: dum=1.0/(a[j][j]);
1472: for (i=j+1;i<=n;i++) a[i][j] *= dum;
1473: }
1474: }
1475: free_vector(vv,1,n); /* Doesn't work */
1476: ;
1477: }
1478:
1479: void lubksb(double **a, int n, int *indx, double b[])
1480: {
1481: int i,ii=0,ip,j;
1482: double sum;
1483:
1484: for (i=1;i<=n;i++) {
1485: ip=indx[i];
1486: sum=b[ip];
1487: b[ip]=b[i];
1488: if (ii)
1489: for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];
1490: else if (sum) ii=i;
1491: b[i]=sum;
1492: }
1493: for (i=n;i>=1;i--) {
1494: sum=b[i];
1495: for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];
1496: b[i]=sum/a[i][i];
1497: }
1498: }
1499:
1500: /************ Frequencies ********************/
1.74 brouard 1501: void freqsummary(char fileres[], int iagemin, int iagemax, 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 1502: { /* Some frequencies */
1503:
1504: int i, m, jk, k1,i1, j1, bool, z1,z2,j;
1505: int first;
1506: double ***freq; /* Frequencies */
1.73 lievre 1507: double *pp, **prop;
1508: double pos,posprop, k2, dateintsum=0,k2cpt=0;
1.53 brouard 1509: FILE *ficresp;
1510: char fileresp[FILENAMELENGTH];
1511:
1512: pp=vector(1,nlstate);
1.74 brouard 1513: prop=matrix(1,nlstate,iagemin,iagemax+3);
1.53 brouard 1514: strcpy(fileresp,"p");
1515: strcat(fileresp,fileres);
1516: if((ficresp=fopen(fileresp,"w"))==NULL) {
1517: printf("Problem with prevalence resultfile: %s\n", fileresp);
1518: fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
1519: exit(0);
1520: }
1.74 brouard 1521: freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);
1.53 brouard 1522: j1=0;
1523:
1524: j=cptcoveff;
1525: if (cptcovn<1) {j=1;ncodemax[1]=1;}
1526:
1527: first=1;
1528:
1529: for(k1=1; k1<=j;k1++){
1530: for(i1=1; i1<=ncodemax[k1];i1++){
1531: j1++;
1532: /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
1533: scanf("%d", i);*/
1534: for (i=-1; i<=nlstate+ndeath; i++)
1535: for (jk=-1; jk<=nlstate+ndeath; jk++)
1.74 brouard 1536: for(m=iagemin; m <= iagemax+3; m++)
1.53 brouard 1537: freq[i][jk][m]=0;
1.73 lievre 1538:
1539: for (i=1; i<=nlstate; i++)
1.74 brouard 1540: for(m=iagemin; m <= iagemax+3; m++)
1.73 lievre 1541: prop[i][m]=0;
1.53 brouard 1542:
1543: dateintsum=0;
1544: k2cpt=0;
1545: for (i=1; i<=imx; i++) {
1546: bool=1;
1547: if (cptcovn>0) {
1548: for (z1=1; z1<=cptcoveff; z1++)
1549: if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])
1550: bool=0;
1551: }
1.58 lievre 1552: if (bool==1){
1.53 brouard 1553: for(m=firstpass; m<=lastpass; m++){
1554: k2=anint[m][i]+(mint[m][i]/12.);
1555: if ((k2>=dateprev1) && (k2<=dateprev2)) {
1.74 brouard 1556: if(agev[m][i]==0) agev[m][i]=iagemax+1;
1557: if(agev[m][i]==1) agev[m][i]=iagemax+2;
1.73 lievre 1558: if (s[m][i]>0 && s[m][i]<=nlstate) prop[s[m][i]][(int)agev[m][i]] += weight[i];
1.53 brouard 1559: if (m<lastpass) {
1560: freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
1.74 brouard 1561: freq[s[m][i]][s[m+1][i]][iagemax+3] += weight[i];
1.53 brouard 1562: }
1563:
1.74 brouard 1564: if ((agev[m][i]>1) && (agev[m][i]< (iagemax+3))) {
1.53 brouard 1565: dateintsum=dateintsum+k2;
1566: k2cpt++;
1567: }
1568: }
1569: }
1570: }
1571: }
1572:
1573: fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);
1574:
1575: if (cptcovn>0) {
1576: fprintf(ficresp, "\n#********** Variable ");
1577: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
1578: fprintf(ficresp, "**********\n#");
1579: }
1580: for(i=1; i<=nlstate;i++)
1581: fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
1582: fprintf(ficresp, "\n");
1583:
1.74 brouard 1584: for(i=iagemin; i <= iagemax+3; i++){
1585: if(i==iagemax+3){
1.53 brouard 1586: fprintf(ficlog,"Total");
1587: }else{
1588: if(first==1){
1589: first=0;
1590: printf("See log file for details...\n");
1591: }
1592: fprintf(ficlog,"Age %d", i);
1593: }
1594: for(jk=1; jk <=nlstate ; jk++){
1595: for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
1596: pp[jk] += freq[jk][m][i];
1597: }
1598: for(jk=1; jk <=nlstate ; jk++){
1599: for(m=-1, pos=0; m <=0 ; m++)
1600: pos += freq[jk][m][i];
1601: if(pp[jk]>=1.e-10){
1602: if(first==1){
1603: printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
1604: }
1605: fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
1606: }else{
1607: if(first==1)
1608: printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
1609: fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
1610: }
1611: }
1612:
1613: for(jk=1; jk <=nlstate ; jk++){
1614: for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
1615: pp[jk] += freq[jk][m][i];
1.73 lievre 1616: }
1617: for(jk=1,pos=0,posprop=0; jk <=nlstate ; jk++){
1618: pos += pp[jk];
1619: posprop += prop[jk][i];
1.53 brouard 1620: }
1621: for(jk=1; jk <=nlstate ; jk++){
1622: if(pos>=1.e-5){
1623: if(first==1)
1624: printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
1625: fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
1626: }else{
1627: if(first==1)
1628: printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
1629: fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
1630: }
1.74 brouard 1631: if( i <= iagemax){
1.53 brouard 1632: if(pos>=1.e-5){
1.73 lievre 1633: fprintf(ficresp," %d %.5f %.0f %.0f",i,prop[jk][i]/posprop, prop[jk][i],posprop);
1.53 brouard 1634: probs[i][jk][j1]= pp[jk]/pos;
1635: /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/
1636: }
1637: else
1.73 lievre 1638: fprintf(ficresp," %d NaNq %.0f %.0f",i,prop[jk][i],posprop);
1.53 brouard 1639: }
1640: }
1641:
1.69 brouard 1642: for(jk=-1; jk <=nlstate+ndeath; jk++)
1643: for(m=-1; m <=nlstate+ndeath; m++)
1.53 brouard 1644: if(freq[jk][m][i] !=0 ) {
1645: if(first==1)
1646: printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
1647: fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
1648: }
1.74 brouard 1649: if(i <= iagemax)
1.53 brouard 1650: fprintf(ficresp,"\n");
1651: if(first==1)
1652: printf("Others in log...\n");
1653: fprintf(ficlog,"\n");
1654: }
1655: }
1656: }
1657: dateintmean=dateintsum/k2cpt;
1658:
1659: fclose(ficresp);
1.74 brouard 1660: free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);
1.53 brouard 1661: free_vector(pp,1,nlstate);
1.74 brouard 1662: free_matrix(prop,1,nlstate,iagemin, iagemax+3);
1.53 brouard 1663: /* End of Freq */
1664: }
1665:
1666: /************ Prevalence ********************/
1.74 brouard 1667: void prevalence(double agemin, double agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax,double **mint,double **anint, double dateprev1,double dateprev2, int firstpass, int lastpass)
1.69 brouard 1668: {
1669: /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
1670: in each health status at the date of interview (if between dateprev1 and dateprev2).
1671: We still use firstpass and lastpass as another selection.
1672: */
1.53 brouard 1673:
1674: int i, m, jk, k1, i1, j1, bool, z1,z2,j;
1675: double ***freq; /* Frequencies */
1.73 lievre 1676: double *pp, **prop;
1677: double pos,posprop;
1.69 brouard 1678: double y2; /* in fractional years */
1.74 brouard 1679: int iagemin, iagemax;
1.53 brouard 1680:
1.74 brouard 1681: iagemin= (int) agemin;
1682: iagemax= (int) agemax;
1683: /*pp=vector(1,nlstate);*/
1684: prop=matrix(1,nlstate,iagemin,iagemax+3);
1685: /* freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
1.53 brouard 1686: j1=0;
1687:
1688: j=cptcoveff;
1689: if (cptcovn<1) {j=1;ncodemax[1]=1;}
1690:
1691: for(k1=1; k1<=j;k1++){
1692: for(i1=1; i1<=ncodemax[k1];i1++){
1693: j1++;
1694:
1.73 lievre 1695: for (i=1; i<=nlstate; i++)
1.74 brouard 1696: for(m=iagemin; m <= iagemax+3; m++)
1697: prop[i][m]=0.0;
1.53 brouard 1698:
1.69 brouard 1699: for (i=1; i<=imx; i++) { /* Each individual */
1.53 brouard 1700: bool=1;
1701: if (cptcovn>0) {
1702: for (z1=1; z1<=cptcoveff; z1++)
1703: if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])
1704: bool=0;
1705: }
1706: if (bool==1) {
1.69 brouard 1707: for(m=firstpass; m<=lastpass; m++){/* Other selection (we can limit to certain interviews*/
1708: y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
1709: if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
1.74 brouard 1710: if(agev[m][i]==0) agev[m][i]=iagemax+1;
1711: if(agev[m][i]==1) agev[m][i]=iagemax+2;
1712: if((int)agev[m][i] <iagemin || (int)agev[m][i] >iagemax+3) printf("Error on individual =%d agev[m][i]=%f m=%d\n",i, agev[m][i],m);
1713: if (s[m][i]>0 && s[m][i]<=nlstate) {
1714: /*if(i>4620) printf(" i=%d m=%d s[m][i]=%d (int)agev[m][i]=%d weight[i]=%f prop=%f\n",i,m,s[m][i],(int)agev[m][m],weight[i],prop[s[m][i]][(int)agev[m][i]]);*/
1715: prop[s[m][i]][(int)agev[m][i]] += weight[i];
1716: prop[s[m][i]][iagemax+3] += weight[i];
1717: }
1.53 brouard 1718: }
1.69 brouard 1719: } /* end selection of waves */
1.53 brouard 1720: }
1721: }
1.74 brouard 1722: for(i=iagemin; i <= iagemax+3; i++){
1.53 brouard 1723:
1.74 brouard 1724: for(jk=1,posprop=0; jk <=nlstate ; jk++) {
1725: posprop += prop[jk][i];
1726: }
1727:
1728: for(jk=1; jk <=nlstate ; jk++){
1729: if( i <= iagemax){
1730: if(posprop>=1.e-5){
1731: probs[i][jk][j1]= prop[jk][i]/posprop;
1732: }
1733: }
1734: }/* end jk */
1735: }/* end i */
1.53 brouard 1736: } /* end i1 */
1737: } /* end k1 */
1738:
1.74 brouard 1739: /* free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
1740: /*free_vector(pp,1,nlstate);*/
1741: free_matrix(prop,1,nlstate, iagemin,iagemax+3);
1742: } /* End of prevalence */
1.53 brouard 1743:
1744: /************* Waves Concatenation ***************/
1745:
1.59 brouard 1746: 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 1747: {
1748: /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
1749: Death is a valid wave (if date is known).
1750: mw[mi][i] is the mi (mi=1 to wav[i]) effective wave of individual i
1.59 brouard 1751: dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
1.53 brouard 1752: and mw[mi+1][i]. dh depends on stepm.
1753: */
1754:
1755: int i, mi, m;
1756: /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
1757: double sum=0., jmean=0.;*/
1758: int first;
1759: int j, k=0,jk, ju, jl;
1760: double sum=0.;
1761: first=0;
1762: jmin=1e+5;
1763: jmax=-1;
1764: jmean=0.;
1765: for(i=1; i<=imx; i++){
1766: mi=0;
1767: m=firstpass;
1768: while(s[m][i] <= nlstate){
1.69 brouard 1769: if(s[m][i]>=1)
1.53 brouard 1770: mw[++mi][i]=m;
1771: if(m >=lastpass)
1772: break;
1773: else
1774: m++;
1775: }/* end while */
1776: if (s[m][i] > nlstate){
1777: mi++; /* Death is another wave */
1778: /* if(mi==0) never been interviewed correctly before death */
1779: /* Only death is a correct wave */
1780: mw[mi][i]=m;
1781: }
1782:
1783: wav[i]=mi;
1784: if(mi==0){
1785: if(first==0){
1.77 brouard 1786: printf("Warning! None valid information for:%d line=%d (skipped) and may be others, see log file\n",num[i],i);
1.53 brouard 1787: first=1;
1788: }
1789: if(first==1){
1.77 brouard 1790: fprintf(ficlog,"Warning! None valid information for:%d line=%d (skipped)\n",num[i],i);
1.53 brouard 1791: }
1792: } /* end mi==0 */
1.77 brouard 1793: } /* End individuals */
1.53 brouard 1794:
1795: for(i=1; i<=imx; i++){
1796: for(mi=1; mi<wav[i];mi++){
1797: if (stepm <=0)
1798: dh[mi][i]=1;
1799: else{
1.77 brouard 1800: if (s[mw[mi+1][i]][i] > nlstate) { /* A death */
1.53 brouard 1801: if (agedc[i] < 2*AGESUP) {
1802: j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);
1803: if(j==0) j=1; /* Survives at least one month after exam */
1804: k=k+1;
1805: if (j >= jmax) jmax=j;
1806: if (j <= jmin) jmin=j;
1807: sum=sum+j;
1.77 brouard 1808: /*if (j<0) printf("j=%d num=%d \n",j,i);*/
1.68 lievre 1809: /* printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
1.78 brouard 1810: if(j<0)printf("Error! Negative delay (%d to death) between waves %d and %d of individual %d at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
1.53 brouard 1811: }
1812: }
1813: else{
1814: j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
1.68 lievre 1815: /* printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
1.53 brouard 1816: k=k+1;
1817: if (j >= jmax) jmax=j;
1818: else if (j <= jmin)jmin=j;
1819: /* if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
1.73 lievre 1820: /*printf("%d %lf %d %d %d\n", i,agev[mw[mi][i]][i],j,s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);*/
1.78 brouard 1821: if(j<0)printf("Error! Negative delay (%d) between waves %d and %d of individual %d at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
1.53 brouard 1822: sum=sum+j;
1823: }
1824: jk= j/stepm;
1825: jl= j -jk*stepm;
1826: ju= j -(jk+1)*stepm;
1.64 lievre 1827: if(mle <=1){
1828: if(jl==0){
1829: dh[mi][i]=jk;
1830: bh[mi][i]=0;
1831: }else{ /* We want a negative bias in order to only have interpolation ie
1832: * at the price of an extra matrix product in likelihood */
1833: dh[mi][i]=jk+1;
1834: bh[mi][i]=ju;
1835: }
1836: }else{
1837: if(jl <= -ju){
1838: dh[mi][i]=jk;
1839: bh[mi][i]=jl; /* bias is positive if real duration
1840: * is higher than the multiple of stepm and negative otherwise.
1841: */
1842: }
1843: else{
1844: dh[mi][i]=jk+1;
1845: bh[mi][i]=ju;
1846: }
1847: if(dh[mi][i]==0){
1848: dh[mi][i]=1; /* At least one step */
1849: bh[mi][i]=ju; /* At least one step */
1.71 brouard 1850: /* 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);*/
1.64 lievre 1851: }
1.59 brouard 1852: }
1.64 lievre 1853: } /* end if mle */
1854: } /* end wave */
1.53 brouard 1855: }
1856: jmean=sum/k;
1857: printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);
1858: fprintf(ficlog,"Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);
1859: }
1860:
1861: /*********** Tricode ****************************/
1862: void tricode(int *Tvar, int **nbcode, int imx)
1863: {
1.58 lievre 1864:
1865: int Ndum[20],ij=1, k, j, i, maxncov=19;
1.53 brouard 1866: int cptcode=0;
1867: cptcoveff=0;
1868:
1.58 lievre 1869: for (k=0; k<maxncov; k++) Ndum[k]=0;
1.53 brouard 1870: for (k=1; k<=7; k++) ncodemax[k]=0;
1871:
1872: for (j=1; j<=(cptcovn+2*cptcovprod); j++) {
1.58 lievre 1873: for (i=1; i<=imx; i++) { /*reads the data file to get the maximum
1874: modality*/
1875: ij=(int)(covar[Tvar[j]][i]); /* ij is the modality of this individual*/
1876: Ndum[ij]++; /*store the modality */
1.53 brouard 1877: /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
1.58 lievre 1878: if (ij > cptcode) cptcode=ij; /* getting the maximum of covariable
1879: Tvar[j]. If V=sex and male is 0 and
1880: female is 1, then cptcode=1.*/
1.53 brouard 1881: }
1882:
1883: for (i=0; i<=cptcode; i++) {
1.58 lievre 1884: 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 1885: }
1.58 lievre 1886:
1.53 brouard 1887: ij=1;
1888: for (i=1; i<=ncodemax[j]; i++) {
1.58 lievre 1889: for (k=0; k<= maxncov; k++) {
1.53 brouard 1890: if (Ndum[k] != 0) {
1891: nbcode[Tvar[j]][ij]=k;
1.58 lievre 1892: /* 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 1893:
1894: ij++;
1895: }
1896: if (ij > ncodemax[j]) break;
1897: }
1898: }
1899: }
1900:
1.58 lievre 1901: for (k=0; k< maxncov; k++) Ndum[k]=0;
1.53 brouard 1902:
1.58 lievre 1903: for (i=1; i<=ncovmodel-2; i++) {
1904: /* 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 1905: ij=Tvar[i];
1.58 lievre 1906: Ndum[ij]++;
1.53 brouard 1907: }
1908:
1909: ij=1;
1.58 lievre 1910: for (i=1; i<= maxncov; i++) {
1.53 brouard 1911: if((Ndum[i]!=0) && (i<=ncovcol)){
1.58 lievre 1912: Tvaraff[ij]=i; /*For printing */
1.53 brouard 1913: ij++;
1914: }
1915: }
1916:
1.58 lievre 1917: cptcoveff=ij-1; /*Number of simple covariates*/
1.53 brouard 1918: }
1919:
1920: /*********** Health Expectancies ****************/
1921:
1922: 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 )
1923:
1924: {
1925: /* Health expectancies */
1926: int i, j, nhstepm, hstepm, h, nstepm, k, cptj;
1927: double age, agelim, hf;
1928: double ***p3mat,***varhe;
1929: double **dnewm,**doldm;
1930: double *xp;
1931: double **gp, **gm;
1932: double ***gradg, ***trgradg;
1933: int theta;
1934:
1.74 brouard 1935: varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage);
1.53 brouard 1936: xp=vector(1,npar);
1.74 brouard 1937: dnewm=matrix(1,nlstate*nlstate,1,npar);
1938: doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate);
1.53 brouard 1939:
1940: fprintf(ficreseij,"# Health expectancies\n");
1941: fprintf(ficreseij,"# Age");
1942: for(i=1; i<=nlstate;i++)
1943: for(j=1; j<=nlstate;j++)
1944: fprintf(ficreseij," %1d-%1d (SE)",i,j);
1945: fprintf(ficreseij,"\n");
1946:
1947: if(estepm < stepm){
1948: printf ("Problem %d lower than %d\n",estepm, stepm);
1949: }
1950: else hstepm=estepm;
1951: /* We compute the life expectancy from trapezoids spaced every estepm months
1952: * This is mainly to measure the difference between two models: for example
1953: * if stepm=24 months pijx are given only every 2 years and by summing them
1954: * we are calculating an estimate of the Life Expectancy assuming a linear
1.66 brouard 1955: * progression in between and thus overestimating or underestimating according
1.53 brouard 1956: * to the curvature of the survival function. If, for the same date, we
1957: * estimate the model with stepm=1 month, we can keep estepm to 24 months
1958: * to compare the new estimate of Life expectancy with the same linear
1959: * hypothesis. A more precise result, taking into account a more precise
1960: * curvature will be obtained if estepm is as small as stepm. */
1961:
1962: /* For example we decided to compute the life expectancy with the smallest unit */
1963: /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
1964: nhstepm is the number of hstepm from age to agelim
1965: nstepm is the number of stepm from age to agelin.
1966: Look at hpijx to understand the reason of that which relies in memory size
1967: and note for a fixed period like estepm months */
1968: /* We decided (b) to get a life expectancy respecting the most precise curvature of the
1969: survival function given by stepm (the optimization length). Unfortunately it
1970: means that if the survival funtion is printed only each two years of age and if
1971: you sum them up and add 1 year (area under the trapezoids) you won't get the same
1972: results. So we changed our mind and took the option of the best precision.
1973: */
1974: hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
1975:
1976: agelim=AGESUP;
1977: for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
1978: /* nhstepm age range expressed in number of stepm */
1979: nstepm=(int) rint((agelim-age)*YEARM/stepm);
1980: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
1981: /* if (stepm >= YEARM) hstepm=1;*/
1982: nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
1983: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
1.74 brouard 1984: gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);
1985: gp=matrix(0,nhstepm,1,nlstate*nlstate);
1986: gm=matrix(0,nhstepm,1,nlstate*nlstate);
1.53 brouard 1987:
1988: /* Computed by stepm unit matrices, product of hstepm matrices, stored
1989: in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
1990: hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);
1991:
1992:
1993: hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
1994:
1995: /* Computing Variances of health expectancies */
1996:
1997: for(theta=1; theta <=npar; theta++){
1998: for(i=1; i<=npar; i++){
1999: xp[i] = x[i] + (i==theta ?delti[theta]:0);
2000: }
2001: hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
2002:
2003: cptj=0;
2004: for(j=1; j<= nlstate; j++){
2005: for(i=1; i<=nlstate; i++){
2006: cptj=cptj+1;
2007: for(h=0, gp[h][cptj]=0.; h<=nhstepm-1; h++){
2008: gp[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;
2009: }
2010: }
2011: }
2012:
2013:
2014: for(i=1; i<=npar; i++)
2015: xp[i] = x[i] - (i==theta ?delti[theta]:0);
2016: hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
2017:
2018: cptj=0;
2019: for(j=1; j<= nlstate; j++){
2020: for(i=1;i<=nlstate;i++){
2021: cptj=cptj+1;
2022: for(h=0, gm[h][cptj]=0.; h<=nhstepm-1; h++){
1.77 brouard 2023:
1.53 brouard 2024: gm[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;
2025: }
2026: }
2027: }
1.74 brouard 2028: for(j=1; j<= nlstate*nlstate; j++)
1.53 brouard 2029: for(h=0; h<=nhstepm-1; h++){
2030: gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
2031: }
2032: }
2033:
2034: /* End theta */
2035:
1.74 brouard 2036: trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar);
1.53 brouard 2037:
2038: for(h=0; h<=nhstepm-1; h++)
1.74 brouard 2039: for(j=1; j<=nlstate*nlstate;j++)
1.53 brouard 2040: for(theta=1; theta <=npar; theta++)
2041: trgradg[h][j][theta]=gradg[h][theta][j];
2042:
2043:
1.74 brouard 2044: for(i=1;i<=nlstate*nlstate;i++)
2045: for(j=1;j<=nlstate*nlstate;j++)
1.53 brouard 2046: varhe[i][j][(int)age] =0.;
2047:
2048: printf("%d|",(int)age);fflush(stdout);
2049: fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
2050: for(h=0;h<=nhstepm-1;h++){
2051: for(k=0;k<=nhstepm-1;k++){
1.74 brouard 2052: matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov);
2053: matprod2(doldm,dnewm,1,nlstate*nlstate,1,npar,1,nlstate*nlstate,gradg[k]);
2054: for(i=1;i<=nlstate*nlstate;i++)
2055: for(j=1;j<=nlstate*nlstate;j++)
1.53 brouard 2056: varhe[i][j][(int)age] += doldm[i][j]*hf*hf;
2057: }
2058: }
2059: /* Computing expectancies */
2060: for(i=1; i<=nlstate;i++)
2061: for(j=1; j<=nlstate;j++)
2062: for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
2063: eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
2064:
2065: /* 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]);*/
2066:
2067: }
2068:
2069: fprintf(ficreseij,"%3.0f",age );
2070: cptj=0;
2071: for(i=1; i<=nlstate;i++)
2072: for(j=1; j<=nlstate;j++){
2073: cptj++;
2074: fprintf(ficreseij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[cptj][cptj][(int)age]) );
2075: }
2076: fprintf(ficreseij,"\n");
2077:
1.74 brouard 2078: free_matrix(gm,0,nhstepm,1,nlstate*nlstate);
2079: free_matrix(gp,0,nhstepm,1,nlstate*nlstate);
2080: free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*nlstate);
2081: free_ma3x(trgradg,0,nhstepm,1,nlstate*nlstate,1,npar);
1.53 brouard 2082: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
2083: }
2084: printf("\n");
2085: fprintf(ficlog,"\n");
2086:
2087: free_vector(xp,1,npar);
1.74 brouard 2088: free_matrix(dnewm,1,nlstate*nlstate,1,npar);
2089: free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate);
2090: free_ma3x(varhe,1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int)fage);
1.53 brouard 2091: }
2092:
2093: /************ Variance ******************/
2094: 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)
2095: {
2096: /* Variance of health expectancies */
2097: /* double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
2098: /* double **newm;*/
2099: double **dnewm,**doldm;
2100: double **dnewmp,**doldmp;
2101: int i, j, nhstepm, hstepm, h, nstepm ;
2102: int k, cptcode;
2103: double *xp;
2104: double **gp, **gm; /* for var eij */
2105: double ***gradg, ***trgradg; /*for var eij */
2106: double **gradgp, **trgradgp; /* for var p point j */
2107: double *gpp, *gmp; /* for var p point j */
2108: double **varppt; /* for var p point j nlstate to nlstate+ndeath */
2109: double ***p3mat;
2110: double age,agelim, hf;
2111: double ***mobaverage;
2112: int theta;
2113: char digit[4];
1.55 lievre 2114: char digitp[25];
1.53 brouard 2115:
2116: char fileresprobmorprev[FILENAMELENGTH];
2117:
1.55 lievre 2118: if(popbased==1){
1.58 lievre 2119: if(mobilav!=0)
1.55 lievre 2120: strcpy(digitp,"-populbased-mobilav-");
2121: else strcpy(digitp,"-populbased-nomobil-");
2122: }
2123: else
1.53 brouard 2124: strcpy(digitp,"-stablbased-");
1.56 lievre 2125:
1.54 brouard 2126: if (mobilav!=0) {
1.53 brouard 2127: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
1.54 brouard 2128: if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
2129: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
2130: printf(" Error in movingaverage mobilav=%d\n",mobilav);
2131: }
1.53 brouard 2132: }
2133:
2134: strcpy(fileresprobmorprev,"prmorprev");
2135: sprintf(digit,"%-d",ij);
2136: /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
2137: strcat(fileresprobmorprev,digit); /* Tvar to be done */
2138: strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
2139: strcat(fileresprobmorprev,fileres);
2140: if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
2141: printf("Problem with resultfile: %s\n", fileresprobmorprev);
2142: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
2143: }
2144: printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
2145: fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
1.66 brouard 2146: 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 2147: fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
2148: for(j=nlstate+1; j<=(nlstate+ndeath);j++){
2149: fprintf(ficresprobmorprev," p.%-d SE",j);
2150: for(i=1; i<=nlstate;i++)
2151: fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
2152: }
2153: fprintf(ficresprobmorprev,"\n");
2154: if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {
2155: printf("Problem with gnuplot file: %s\n", optionfilegnuplot);
2156: fprintf(ficlog,"Problem with gnuplot file: %s\n", optionfilegnuplot);
2157: exit(0);
2158: }
2159: else{
2160: fprintf(ficgp,"\n# Routine varevsij");
2161: }
2162: if((fichtm=fopen(optionfilehtm,"a"))==NULL) {
2163: printf("Problem with html file: %s\n", optionfilehtm);
2164: fprintf(ficlog,"Problem with html file: %s\n", optionfilehtm);
2165: exit(0);
2166: }
2167: else{
1.67 brouard 2168: 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");
2169: fprintf(fichtm,"\n<br>%s <br>\n",digitp);
1.53 brouard 2170: }
2171: varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
2172:
2173: 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");
2174: fprintf(ficresvij,"# Age");
2175: for(i=1; i<=nlstate;i++)
2176: for(j=1; j<=nlstate;j++)
2177: fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);
2178: fprintf(ficresvij,"\n");
2179:
2180: xp=vector(1,npar);
2181: dnewm=matrix(1,nlstate,1,npar);
2182: doldm=matrix(1,nlstate,1,nlstate);
2183: dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
2184: doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
2185:
2186: gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
2187: gpp=vector(nlstate+1,nlstate+ndeath);
2188: gmp=vector(nlstate+1,nlstate+ndeath);
2189: trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
2190:
2191: if(estepm < stepm){
2192: printf ("Problem %d lower than %d\n",estepm, stepm);
2193: }
2194: else hstepm=estepm;
2195: /* For example we decided to compute the life expectancy with the smallest unit */
2196: /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
2197: nhstepm is the number of hstepm from age to agelim
2198: nstepm is the number of stepm from age to agelin.
2199: Look at hpijx to understand the reason of that which relies in memory size
2200: and note for a fixed period like k years */
2201: /* We decided (b) to get a life expectancy respecting the most precise curvature of the
2202: survival function given by stepm (the optimization length). Unfortunately it
1.66 brouard 2203: means that if the survival funtion is printed every two years of age and if
1.53 brouard 2204: you sum them up and add 1 year (area under the trapezoids) you won't get the same
2205: results. So we changed our mind and took the option of the best precision.
2206: */
2207: hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
2208: agelim = AGESUP;
2209: for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
2210: nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
2211: nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
2212: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
2213: gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
2214: gp=matrix(0,nhstepm,1,nlstate);
2215: gm=matrix(0,nhstepm,1,nlstate);
2216:
2217:
2218: for(theta=1; theta <=npar; theta++){
1.66 brouard 2219: for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
1.53 brouard 2220: xp[i] = x[i] + (i==theta ?delti[theta]:0);
2221: }
2222: hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
2223: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
2224:
2225: if (popbased==1) {
1.54 brouard 2226: if(mobilav ==0){
1.53 brouard 2227: for(i=1; i<=nlstate;i++)
2228: prlim[i][i]=probs[(int)age][i][ij];
1.54 brouard 2229: }else{ /* mobilav */
1.53 brouard 2230: for(i=1; i<=nlstate;i++)
2231: prlim[i][i]=mobaverage[(int)age][i][ij];
2232: }
2233: }
2234:
2235: for(j=1; j<= nlstate; j++){
2236: for(h=0; h<=nhstepm; h++){
2237: for(i=1, gp[h][j]=0.;i<=nlstate;i++)
2238: gp[h][j] += prlim[i][i]*p3mat[i][j][h];
2239: }
2240: }
1.66 brouard 2241: /* This for computing probability of death (h=1 means
2242: computed over hstepm matrices product = hstepm*stepm months)
2243: as a weighted average of prlim.
2244: */
1.69 brouard 2245: for(j=nlstate+1;j<=nlstate+ndeath;j++){
1.68 lievre 2246: for(i=1,gpp[j]=0.; i<= nlstate; i++)
1.53 brouard 2247: gpp[j] += prlim[i][i]*p3mat[i][j][1];
2248: }
1.66 brouard 2249: /* end probability of death */
1.53 brouard 2250:
1.66 brouard 2251: for(i=1; i<=npar; i++) /* Computes gradient x - delta */
1.53 brouard 2252: xp[i] = x[i] - (i==theta ?delti[theta]:0);
2253: hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
2254: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
2255:
2256: if (popbased==1) {
1.54 brouard 2257: if(mobilav ==0){
1.53 brouard 2258: for(i=1; i<=nlstate;i++)
2259: prlim[i][i]=probs[(int)age][i][ij];
1.54 brouard 2260: }else{ /* mobilav */
1.53 brouard 2261: for(i=1; i<=nlstate;i++)
2262: prlim[i][i]=mobaverage[(int)age][i][ij];
2263: }
2264: }
2265:
2266: for(j=1; j<= nlstate; j++){
2267: for(h=0; h<=nhstepm; h++){
2268: for(i=1, gm[h][j]=0.;i<=nlstate;i++)
2269: gm[h][j] += prlim[i][i]*p3mat[i][j][h];
2270: }
2271: }
1.66 brouard 2272: /* This for computing probability of death (h=1 means
2273: computed over hstepm matrices product = hstepm*stepm months)
2274: as a weighted average of prlim.
2275: */
1.69 brouard 2276: for(j=nlstate+1;j<=nlstate+ndeath;j++){
1.68 lievre 2277: for(i=1,gmp[j]=0.; i<= nlstate; i++)
2278: gmp[j] += prlim[i][i]*p3mat[i][j][1];
1.53 brouard 2279: }
1.66 brouard 2280: /* end probability of death */
1.53 brouard 2281:
2282: for(j=1; j<= nlstate; j++) /* vareij */
2283: for(h=0; h<=nhstepm; h++){
2284: gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
2285: }
1.68 lievre 2286:
1.53 brouard 2287: for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
2288: gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
2289: }
2290:
2291: } /* End theta */
2292:
2293: trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
2294:
2295: for(h=0; h<=nhstepm; h++) /* veij */
2296: for(j=1; j<=nlstate;j++)
2297: for(theta=1; theta <=npar; theta++)
2298: trgradg[h][j][theta]=gradg[h][theta][j];
2299:
2300: for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
1.69 brouard 2301: for(theta=1; theta <=npar; theta++)
1.53 brouard 2302: trgradgp[j][theta]=gradgp[theta][j];
1.69 brouard 2303:
1.53 brouard 2304:
2305: hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
2306: for(i=1;i<=nlstate;i++)
2307: for(j=1;j<=nlstate;j++)
2308: vareij[i][j][(int)age] =0.;
2309:
2310: for(h=0;h<=nhstepm;h++){
2311: for(k=0;k<=nhstepm;k++){
2312: matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
2313: matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
2314: for(i=1;i<=nlstate;i++)
2315: for(j=1;j<=nlstate;j++)
2316: vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
2317: }
2318: }
1.70 brouard 2319:
1.53 brouard 2320: /* pptj */
2321: matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
2322: matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
1.70 brouard 2323: for(j=nlstate+1;j<=nlstate+ndeath;j++)
2324: for(i=nlstate+1;i<=nlstate+ndeath;i++)
1.53 brouard 2325: varppt[j][i]=doldmp[j][i];
2326: /* end ppptj */
1.66 brouard 2327: /* x centered again */
1.53 brouard 2328: hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);
2329: prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);
2330:
2331: if (popbased==1) {
1.54 brouard 2332: if(mobilav ==0){
1.53 brouard 2333: for(i=1; i<=nlstate;i++)
2334: prlim[i][i]=probs[(int)age][i][ij];
1.54 brouard 2335: }else{ /* mobilav */
1.53 brouard 2336: for(i=1; i<=nlstate;i++)
2337: prlim[i][i]=mobaverage[(int)age][i][ij];
2338: }
2339: }
1.70 brouard 2340:
1.66 brouard 2341: /* This for computing probability of death (h=1 means
2342: computed over hstepm (estepm) matrices product = hstepm*stepm months)
2343: as a weighted average of prlim.
2344: */
1.68 lievre 2345: for(j=nlstate+1;j<=nlstate+ndeath;j++){
2346: for(i=1,gmp[j]=0.;i<= nlstate; i++)
1.53 brouard 2347: gmp[j] += prlim[i][i]*p3mat[i][j][1];
2348: }
1.66 brouard 2349: /* end probability of death */
1.53 brouard 2350:
2351: fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
2352: for(j=nlstate+1; j<=(nlstate+ndeath);j++){
2353: fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
2354: for(i=1; i<=nlstate;i++){
2355: fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
2356: }
2357: }
2358: fprintf(ficresprobmorprev,"\n");
2359:
2360: fprintf(ficresvij,"%.0f ",age );
2361: for(i=1; i<=nlstate;i++)
2362: for(j=1; j<=nlstate;j++){
2363: fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
2364: }
2365: fprintf(ficresvij,"\n");
2366: free_matrix(gp,0,nhstepm,1,nlstate);
2367: free_matrix(gm,0,nhstepm,1,nlstate);
2368: free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
2369: free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
2370: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
2371: } /* End age */
2372: free_vector(gpp,nlstate+1,nlstate+ndeath);
2373: free_vector(gmp,nlstate+1,nlstate+ndeath);
2374: free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
2375: free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
2376: fprintf(ficgp,"\nset noparametric;set nolabel; set ter png small;set size 0.65, 0.65");
2377: /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */
2378: fprintf(ficgp,"\n set log y; set nolog x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
1.67 brouard 2379: /* fprintf(ficgp,"\n plot \"%s\" u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm); */
2380: /* fprintf(ficgp,"\n replot \"%s\" u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm); */
2381: /* fprintf(ficgp,"\n replot \"%s\" u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm); */
2382: fprintf(ficgp,"\n plot \"%s\" u 1:($3) not w l 1 ",fileresprobmorprev);
2383: fprintf(ficgp,"\n replot \"%s\" u 1:(($3+1.96*$4)) t \"95\%% interval\" w l 2 ",fileresprobmorprev);
2384: fprintf(ficgp,"\n replot \"%s\" u 1:(($3-1.96*$4)) not w l 2 ",fileresprobmorprev);
1.53 brouard 2385: fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",fileresprobmorprev,fileresprobmorprev);
1.71 brouard 2386: fprintf(fichtm,"\n<br> Probability is computed over estepm=%d months. <br> <img src=\"varmuptjgr%s%s%s.png\"> <br>\n", estepm,digitp,optionfilefiname,digit);
1.53 brouard 2387: /* 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);
2388: */
1.71 brouard 2389: fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.png\";replot;",digitp,optionfilefiname,digit);
1.53 brouard 2390:
2391: free_vector(xp,1,npar);
2392: free_matrix(doldm,1,nlstate,1,nlstate);
2393: free_matrix(dnewm,1,nlstate,1,npar);
2394: free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
2395: free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
2396: free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
1.55 lievre 2397: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
1.53 brouard 2398: fclose(ficresprobmorprev);
2399: fclose(ficgp);
2400: fclose(fichtm);
1.70 brouard 2401: }
1.53 brouard 2402:
2403: /************ Variance of prevlim ******************/
2404: 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)
2405: {
2406: /* Variance of prevalence limit */
1.59 brouard 2407: /* double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
1.53 brouard 2408: double **newm;
2409: double **dnewm,**doldm;
2410: int i, j, nhstepm, hstepm;
2411: int k, cptcode;
2412: double *xp;
2413: double *gp, *gm;
2414: double **gradg, **trgradg;
2415: double age,agelim;
2416: int theta;
2417:
1.54 brouard 2418: fprintf(ficresvpl,"# Standard deviation of stable prevalences \n");
1.53 brouard 2419: fprintf(ficresvpl,"# Age");
2420: for(i=1; i<=nlstate;i++)
2421: fprintf(ficresvpl," %1d-%1d",i,i);
2422: fprintf(ficresvpl,"\n");
2423:
2424: xp=vector(1,npar);
2425: dnewm=matrix(1,nlstate,1,npar);
2426: doldm=matrix(1,nlstate,1,nlstate);
2427:
2428: hstepm=1*YEARM; /* Every year of age */
2429: hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */
2430: agelim = AGESUP;
2431: for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
2432: nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
2433: if (stepm >= YEARM) hstepm=1;
2434: nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
2435: gradg=matrix(1,npar,1,nlstate);
2436: gp=vector(1,nlstate);
2437: gm=vector(1,nlstate);
2438:
2439: for(theta=1; theta <=npar; theta++){
2440: for(i=1; i<=npar; i++){ /* Computes gradient */
2441: xp[i] = x[i] + (i==theta ?delti[theta]:0);
2442: }
2443: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
2444: for(i=1;i<=nlstate;i++)
2445: gp[i] = prlim[i][i];
2446:
2447: for(i=1; i<=npar; i++) /* Computes gradient */
2448: xp[i] = x[i] - (i==theta ?delti[theta]:0);
2449: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
2450: for(i=1;i<=nlstate;i++)
2451: gm[i] = prlim[i][i];
2452:
2453: for(i=1;i<=nlstate;i++)
2454: gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
2455: } /* End theta */
2456:
2457: trgradg =matrix(1,nlstate,1,npar);
2458:
2459: for(j=1; j<=nlstate;j++)
2460: for(theta=1; theta <=npar; theta++)
2461: trgradg[j][theta]=gradg[theta][j];
2462:
2463: for(i=1;i<=nlstate;i++)
2464: varpl[i][(int)age] =0.;
2465: matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
2466: matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
2467: for(i=1;i<=nlstate;i++)
2468: varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
2469:
2470: fprintf(ficresvpl,"%.0f ",age );
2471: for(i=1; i<=nlstate;i++)
2472: fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
2473: fprintf(ficresvpl,"\n");
2474: free_vector(gp,1,nlstate);
2475: free_vector(gm,1,nlstate);
2476: free_matrix(gradg,1,npar,1,nlstate);
2477: free_matrix(trgradg,1,nlstate,1,npar);
2478: } /* End age */
2479:
2480: free_vector(xp,1,npar);
2481: free_matrix(doldm,1,nlstate,1,npar);
2482: free_matrix(dnewm,1,nlstate,1,nlstate);
2483:
2484: }
2485:
2486: /************ Variance of one-step probabilities ******************/
2487: void varprob(char optionfilefiname[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij, int *Tvar, int **nbcode, int *ncodemax)
2488: {
2489: int i, j=0, i1, k1, l1, t, tj;
2490: int k2, l2, j1, z1;
2491: int k=0,l, cptcode;
2492: int first=1, first1;
2493: double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
2494: double **dnewm,**doldm;
2495: double *xp;
2496: double *gp, *gm;
2497: double **gradg, **trgradg;
2498: double **mu;
2499: double age,agelim, cov[NCOVMAX];
2500: double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
2501: int theta;
2502: char fileresprob[FILENAMELENGTH];
2503: char fileresprobcov[FILENAMELENGTH];
2504: char fileresprobcor[FILENAMELENGTH];
2505:
2506: double ***varpij;
2507:
2508: strcpy(fileresprob,"prob");
2509: strcat(fileresprob,fileres);
2510: if((ficresprob=fopen(fileresprob,"w"))==NULL) {
2511: printf("Problem with resultfile: %s\n", fileresprob);
2512: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
2513: }
2514: strcpy(fileresprobcov,"probcov");
2515: strcat(fileresprobcov,fileres);
2516: if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
2517: printf("Problem with resultfile: %s\n", fileresprobcov);
2518: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
2519: }
2520: strcpy(fileresprobcor,"probcor");
2521: strcat(fileresprobcor,fileres);
2522: if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
2523: printf("Problem with resultfile: %s\n", fileresprobcor);
2524: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
2525: }
2526: printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
2527: fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
2528: printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
2529: fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
2530: printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
2531: fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
2532:
2533: fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
2534: fprintf(ficresprob,"# Age");
2535: fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
2536: fprintf(ficresprobcov,"# Age");
2537: fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
2538: fprintf(ficresprobcov,"# Age");
2539:
2540:
2541: for(i=1; i<=nlstate;i++)
2542: for(j=1; j<=(nlstate+ndeath);j++){
2543: fprintf(ficresprob," p%1d-%1d (SE)",i,j);
2544: fprintf(ficresprobcov," p%1d-%1d ",i,j);
2545: fprintf(ficresprobcor," p%1d-%1d ",i,j);
2546: }
1.69 brouard 2547: /* fprintf(ficresprob,"\n");
1.53 brouard 2548: fprintf(ficresprobcov,"\n");
2549: fprintf(ficresprobcor,"\n");
1.69 brouard 2550: */
2551: xp=vector(1,npar);
1.53 brouard 2552: dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
2553: doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
2554: mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
2555: varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
2556: first=1;
2557: if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {
2558: printf("Problem with gnuplot file: %s\n", optionfilegnuplot);
2559: fprintf(ficlog,"Problem with gnuplot file: %s\n", optionfilegnuplot);
2560: exit(0);
2561: }
2562: else{
2563: fprintf(ficgp,"\n# Routine varprob");
2564: }
2565: if((fichtm=fopen(optionfilehtm,"a"))==NULL) {
2566: printf("Problem with html file: %s\n", optionfilehtm);
2567: fprintf(ficlog,"Problem with html file: %s\n", optionfilehtm);
2568: exit(0);
2569: }
2570: else{
2571: fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
2572: fprintf(fichtm,"\n");
2573:
2574: fprintf(fichtm,"\n<li><h4> Computing matrix of variance-covariance of step probabilities</h4></li>\n");
2575: 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");
2576: 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");
2577:
2578: }
2579:
2580: cov[1]=1;
2581: tj=cptcoveff;
2582: if (cptcovn<1) {tj=1;ncodemax[1]=1;}
2583: j1=0;
2584: for(t=1; t<=tj;t++){
2585: for(i1=1; i1<=ncodemax[t];i1++){
2586: j1++;
2587: if (cptcovn>0) {
2588: fprintf(ficresprob, "\n#********** Variable ");
2589: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
1.69 brouard 2590: fprintf(ficresprob, "**********\n#\n");
1.53 brouard 2591: fprintf(ficresprobcov, "\n#********** Variable ");
2592: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
1.69 brouard 2593: fprintf(ficresprobcov, "**********\n#\n");
1.53 brouard 2594:
2595: fprintf(ficgp, "\n#********** Variable ");
1.69 brouard 2596: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
2597: fprintf(ficgp, "**********\n#\n");
1.53 brouard 2598:
2599:
2600: fprintf(fichtm, "\n<hr size=\"2\" color=\"#EC5E5E\">********** Variable ");
2601: for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
2602: fprintf(fichtm, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
2603:
2604: fprintf(ficresprobcor, "\n#********** Variable ");
2605: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
1.69 brouard 2606: fprintf(ficresprobcor, "**********\n#");
1.53 brouard 2607: }
2608:
2609: for (age=bage; age<=fage; age ++){
2610: cov[2]=age;
2611: for (k=1; k<=cptcovn;k++) {
2612: cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];
2613: }
2614: for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
2615: for (k=1; k<=cptcovprod;k++)
2616: cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
2617:
2618: gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
2619: trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
2620: gp=vector(1,(nlstate)*(nlstate+ndeath));
2621: gm=vector(1,(nlstate)*(nlstate+ndeath));
2622:
2623: for(theta=1; theta <=npar; theta++){
2624: for(i=1; i<=npar; i++)
1.74 brouard 2625: xp[i] = x[i] + (i==theta ?delti[theta]:(double)0);
1.53 brouard 2626:
2627: pmij(pmmij,cov,ncovmodel,xp,nlstate);
2628:
2629: k=0;
2630: for(i=1; i<= (nlstate); i++){
2631: for(j=1; j<=(nlstate+ndeath);j++){
2632: k=k+1;
2633: gp[k]=pmmij[i][j];
2634: }
2635: }
2636:
2637: for(i=1; i<=npar; i++)
1.74 brouard 2638: xp[i] = x[i] - (i==theta ?delti[theta]:(double)0);
1.53 brouard 2639:
2640: pmij(pmmij,cov,ncovmodel,xp,nlstate);
2641: k=0;
2642: for(i=1; i<=(nlstate); i++){
2643: for(j=1; j<=(nlstate+ndeath);j++){
2644: k=k+1;
2645: gm[k]=pmmij[i][j];
2646: }
2647: }
2648:
2649: for(i=1; i<= (nlstate)*(nlstate+ndeath); i++)
1.74 brouard 2650: gradg[theta][i]=(gp[i]-gm[i])/(double)2./delti[theta];
1.53 brouard 2651: }
2652:
2653: for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
2654: for(theta=1; theta <=npar; theta++)
2655: trgradg[j][theta]=gradg[theta][j];
2656:
2657: matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov);
2658: matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);
1.59 brouard 2659: free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
2660: free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
2661: free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
2662: free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
2663:
1.53 brouard 2664: pmij(pmmij,cov,ncovmodel,x,nlstate);
2665:
2666: k=0;
2667: for(i=1; i<=(nlstate); i++){
2668: for(j=1; j<=(nlstate+ndeath);j++){
2669: k=k+1;
2670: mu[k][(int) age]=pmmij[i][j];
2671: }
2672: }
2673: for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
2674: for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
2675: varpij[i][j][(int)age] = doldm[i][j];
2676:
2677: /*printf("\n%d ",(int)age);
1.59 brouard 2678: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
2679: printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
2680: fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
2681: }*/
1.53 brouard 2682:
2683: fprintf(ficresprob,"\n%d ",(int)age);
2684: fprintf(ficresprobcov,"\n%d ",(int)age);
2685: fprintf(ficresprobcor,"\n%d ",(int)age);
2686:
2687: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)
2688: fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));
2689: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
2690: fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);
2691: fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
2692: }
2693: i=0;
2694: for (k=1; k<=(nlstate);k++){
2695: for (l=1; l<=(nlstate+ndeath);l++){
2696: i=i++;
2697: fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
2698: fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
2699: for (j=1; j<=i;j++){
2700: fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);
2701: fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));
2702: }
2703: }
2704: }/* end of loop for state */
2705: } /* end of loop for age */
2706:
2707: /* Confidence intervalle of pij */
2708: /*
1.59 brouard 2709: fprintf(ficgp,"\nset noparametric;unset label");
2710: fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");
2711: fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
2712: 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);
2713: fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);
2714: fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);
2715: fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);
1.53 brouard 2716: */
2717:
2718: /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
2719: first1=1;
2720: for (k2=1; k2<=(nlstate);k2++){
2721: for (l2=1; l2<=(nlstate+ndeath);l2++){
2722: if(l2==k2) continue;
2723: j=(k2-1)*(nlstate+ndeath)+l2;
2724: for (k1=1; k1<=(nlstate);k1++){
2725: for (l1=1; l1<=(nlstate+ndeath);l1++){
2726: if(l1==k1) continue;
2727: i=(k1-1)*(nlstate+ndeath)+l1;
2728: if(i<=j) continue;
2729: for (age=bage; age<=fage; age ++){
2730: if ((int)age %5==0){
2731: v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;
2732: v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;
2733: cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;
2734: mu1=mu[i][(int) age]/stepm*YEARM ;
2735: mu2=mu[j][(int) age]/stepm*YEARM;
2736: c12=cv12/sqrt(v1*v2);
2737: /* Computing eigen value of matrix of covariance */
2738: lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
2739: lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
2740: /* Eigen vectors */
2741: v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
2742: /*v21=sqrt(1.-v11*v11); *//* error */
2743: v21=(lc1-v1)/cv12*v11;
2744: v12=-v21;
2745: v22=v11;
2746: tnalp=v21/v11;
2747: if(first1==1){
2748: first1=0;
2749: 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);
2750: }
2751: 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);
2752: /*printf(fignu*/
2753: /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */
2754: /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */
2755: if(first==1){
2756: first=0;
2757: fprintf(ficgp,"\nset parametric;unset label");
2758: 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);
2759: fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
2760: 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);
2761: fprintf(fichtm,"\n<br><img src=\"varpijgr%s%d%1d%1d-%1d%1d.png\"> ",optionfilefiname, j1,k1,l1,k2,l2);
2762: fprintf(fichtm,"\n<br> Correlation at age %d (%.3f),",(int) age, c12);
2763: fprintf(ficgp,"\nset out \"varpijgr%s%d%1d%1d-%1d%1d.png\"",optionfilefiname, j1,k1,l1,k2,l2);
2764: fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
2765: fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
2766: 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",\
2767: mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
2768: mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
2769: }else{
2770: first=0;
2771: fprintf(fichtm," %d (%.3f),",(int) age, c12);
2772: fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
2773: fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
2774: 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",\
2775: mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
2776: mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
2777: }/* if first */
2778: } /* age mod 5 */
2779: } /* end loop age */
2780: fprintf(ficgp,"\nset out \"varpijgr%s%d%1d%1d-%1d%1d.png\";replot;",optionfilefiname, j1,k1,l1,k2,l2);
2781: first=1;
2782: } /*l12 */
2783: } /* k12 */
2784: } /*l1 */
2785: }/* k1 */
2786: } /* loop covariates */
2787: }
1.59 brouard 2788: free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
2789: free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
1.53 brouard 2790: free_vector(xp,1,npar);
2791: fclose(ficresprob);
2792: fclose(ficresprobcov);
2793: fclose(ficresprobcor);
2794: fclose(ficgp);
2795: fclose(fichtm);
2796: }
2797:
2798:
2799: /******************* Printing html file ***********/
2800: void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \
2801: int lastpass, int stepm, int weightopt, char model[],\
2802: int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
2803: int popforecast, int estepm ,\
2804: double jprev1, double mprev1,double anprev1, \
2805: double jprev2, double mprev2,double anprev2){
2806: int jj1, k1, i1, cpt;
2807: /*char optionfilehtm[FILENAMELENGTH];*/
2808: if((fichtm=fopen(optionfilehtm,"a"))==NULL) {
2809: printf("Problem with %s \n",optionfilehtm), exit(0);
2810: fprintf(ficlog,"Problem with %s \n",optionfilehtm), exit(0);
2811: }
2812:
2813: fprintf(fichtm,"<ul><li><h4>Result files (first order: no variance)</h4>\n
2814: - 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
2815: - Estimated transition probabilities over %d (stepm) months: <a href=\"pij%s\">pij%s</a><br>\n
2816: - Stable prevalence in each health state: <a href=\"pl%s\">pl%s</a> <br>\n
2817: - Life expectancies by age and initial health status (estepm=%2d months):
2818: <a href=\"e%s\">e%s</a> <br>\n</li>", \
2819: jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,fileres,fileres,stepm,fileres,fileres,fileres,fileres,estepm,fileres,fileres);
2820:
2821: fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
2822:
2823: m=cptcoveff;
2824: if (cptcovn < 1) {m=1;ncodemax[1]=1;}
2825:
2826: jj1=0;
2827: for(k1=1; k1<=m;k1++){
2828: for(i1=1; i1<=ncodemax[k1];i1++){
2829: jj1++;
2830: if (cptcovn > 0) {
2831: fprintf(fichtm,"<hr size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
2832: for (cpt=1; cpt<=cptcoveff;cpt++)
2833: fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
2834: fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
2835: }
2836: /* Pij */
1.76 brouard 2837: 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>
1.53 brouard 2838: <img src=\"pe%s%d1.png\">",stepm,strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);
2839: /* Quasi-incidences */
2840: 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>
2841: <img src=\"pe%s%d2.png\">",stepm,strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);
2842: /* Stable prevalence in each health state */
2843: for(cpt=1; cpt<nlstate;cpt++){
2844: fprintf(fichtm,"<br>- Stable prevalence in each health state : p%s%d%d.png<br>
2845: <img src=\"p%s%d%d.png\">",strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);
2846: }
2847: for(cpt=1; cpt<=nlstate;cpt++) {
2848: fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): exp%s%d%d.png <br>
2849: <img src=\"exp%s%d%d.png\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);
2850: }
2851: fprintf(fichtm,"\n<br>- Total life expectancy by age and
2852: health expectancies in states (1) and (2): e%s%d.png<br>
2853: <img src=\"e%s%d.png\">",strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);
2854: } /* end i1 */
2855: }/* End k1 */
2856: fprintf(fichtm,"</ul>");
2857:
2858:
2859: fprintf(fichtm,"\n<br><li><h4> Result files (second order: variances)</h4>\n
2860: - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n
2861: - Variance of one-step probabilities: <a href=\"prob%s\">prob%s</a> <br>\n
2862: - Variance-covariance of one-step probabilities: <a href=\"probcov%s\">probcov%s</a> <br>\n
2863: - Correlation matrix of one-step probabilities: <a href=\"probcor%s\">probcor%s</a> <br>\n
2864: - Variances and covariances of life expectancies by age and initial health status (estepm=%d months): <a href=\"v%s\">v%s</a><br>\n
2865: - Health expectancies with their variances (no covariance): <a href=\"t%s\">t%s</a> <br>\n
2866: - 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);
2867:
1.76 brouard 2868: /* if(popforecast==1) fprintf(fichtm,"\n */
2869: /* - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n */
2870: /* - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n */
2871: /* <br>",fileres,fileres,fileres,fileres); */
2872: /* else */
2873: /* 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); */
1.53 brouard 2874: fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
2875:
2876: m=cptcoveff;
2877: if (cptcovn < 1) {m=1;ncodemax[1]=1;}
2878:
2879: jj1=0;
2880: for(k1=1; k1<=m;k1++){
2881: for(i1=1; i1<=ncodemax[k1];i1++){
2882: jj1++;
2883: if (cptcovn > 0) {
2884: fprintf(fichtm,"<hr size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
2885: for (cpt=1; cpt<=cptcoveff;cpt++)
2886: fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
2887: fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
2888: }
2889: for(cpt=1; cpt<=nlstate;cpt++) {
1.76 brouard 2890: fprintf(fichtm,"<br>- Observed and period prevalence (with confident
1.53 brouard 2891: interval) in state (%d): v%s%d%d.png <br>
2892: <img src=\"v%s%d%d.png\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);
2893: }
2894: } /* end i1 */
2895: }/* End k1 */
2896: fprintf(fichtm,"</ul>");
2897: fclose(fichtm);
2898: }
2899:
2900: /******************* Gnuplot file **************/
2901: void printinggnuplot(char fileres[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
2902:
2903: int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;
2904: int ng;
2905: if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {
2906: printf("Problem with file %s",optionfilegnuplot);
2907: fprintf(ficlog,"Problem with file %s",optionfilegnuplot);
2908: }
2909:
1.54 brouard 2910: /*#ifdef windows */
1.53 brouard 2911: fprintf(ficgp,"cd \"%s\" \n",pathc);
1.54 brouard 2912: /*#endif */
1.53 brouard 2913: m=pow(2,cptcoveff);
2914:
2915: /* 1eme*/
2916: for (cpt=1; cpt<= nlstate ; cpt ++) {
2917: for (k1=1; k1<= m ; k1 ++) {
2918: fprintf(ficgp,"\nset out \"v%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);
2919: 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);
2920:
2921: for (i=1; i<= nlstate ; i ++) {
2922: if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
2923: else fprintf(ficgp," \%%*lf (\%%*lf)");
2924: }
1.69 brouard 2925: 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 2926: for (i=1; i<= nlstate ; i ++) {
2927: if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
2928: else fprintf(ficgp," \%%*lf (\%%*lf)");
2929: }
1.69 brouard 2930: fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"vpl%s\" every :::%d::%d u 1:($2-1.96*$3) \"\%%lf",fileres,k1-1,k1-1);
1.53 brouard 2931: for (i=1; i<= nlstate ; i ++) {
2932: if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
2933: else fprintf(ficgp," \%%*lf (\%%*lf)");
2934: }
2935: fprintf(ficgp,"\" t\"\" w l 1,\"p%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",fileres,k1-1,k1-1,2+4*(cpt-1));
2936: }
2937: }
2938: /*2 eme*/
2939:
2940: for (k1=1; k1<= m ; k1 ++) {
2941: fprintf(ficgp,"\nset out \"e%s%d.png\" \n",strtok(optionfile, "."),k1);
2942: fprintf(ficgp,"set ylabel \"Years\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] ",ageminpar,fage);
2943:
2944: for (i=1; i<= nlstate+1 ; i ++) {
2945: k=2*i;
2946: fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:2 \"\%%lf",fileres,k1-1,k1-1);
2947: for (j=1; j<= nlstate+1 ; j ++) {
2948: if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
2949: else fprintf(ficgp," \%%*lf (\%%*lf)");
2950: }
2951: if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");
2952: else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);
2953: fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",fileres,k1-1,k1-1);
2954: for (j=1; j<= nlstate+1 ; j ++) {
2955: if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
2956: else fprintf(ficgp," \%%*lf (\%%*lf)");
2957: }
2958: fprintf(ficgp,"\" t\"\" w l 0,");
2959: fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",fileres,k1-1,k1-1);
2960: for (j=1; j<= nlstate+1 ; j ++) {
2961: if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
2962: else fprintf(ficgp," \%%*lf (\%%*lf)");
2963: }
2964: if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");
2965: else fprintf(ficgp,"\" t\"\" w l 0,");
2966: }
2967: }
2968:
2969: /*3eme*/
2970:
2971: for (k1=1; k1<= m ; k1 ++) {
2972: for (cpt=1; cpt<= nlstate ; cpt ++) {
2973: k=2+nlstate*(2*cpt-2);
2974: fprintf(ficgp,"\nset out \"exp%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);
2975: fprintf(ficgp,"set ter png small\nset size 0.65,0.65\nplot [%.f:%.f] \"e%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,fileres,k1-1,k1-1,k,cpt);
2976: /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
2977: for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
2978: fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
2979: fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
2980: for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
2981: fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
2982:
2983: */
2984: for (i=1; i< nlstate ; i ++) {
2985: 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);
2986:
2987: }
2988: }
2989: }
2990:
1.76 brouard 2991: /* CV preval stable (period) */
1.53 brouard 2992: for (k1=1; k1<= m ; k1 ++) {
1.76 brouard 2993: for (cpt=1; cpt<=nlstate ; cpt ++) {
1.53 brouard 2994: k=3;
2995: fprintf(ficgp,"\nset out \"p%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);
2996: 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/($%d",ageminpar,agemaxpar,fileres,k1,k+cpt+1,k+1);
2997:
1.76 brouard 2998: for (i=1; i<= nlstate ; i ++)
1.53 brouard 2999: fprintf(ficgp,"+$%d",k+i+1);
3000: fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);
3001:
3002: l=3+(nlstate+ndeath)*cpt;
3003: fprintf(ficgp,",\"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",fileres,k1,l+cpt+1,l+1);
3004: for (i=1; i< nlstate ; i ++) {
3005: l=3+(nlstate+ndeath)*cpt;
3006: fprintf(ficgp,"+$%d",l+i+1);
3007: }
3008: fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);
3009: }
3010: }
3011:
3012: /* proba elementaires */
3013: for(i=1,jk=1; i <=nlstate; i++){
3014: for(k=1; k <=(nlstate+ndeath); k++){
3015: if (k != i) {
3016: for(j=1; j <=ncovmodel; j++){
3017: fprintf(ficgp,"p%d=%f ",jk,p[jk]);
3018: jk++;
3019: fprintf(ficgp,"\n");
3020: }
3021: }
3022: }
3023: }
3024:
3025: for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/
3026: for(jk=1; jk <=m; jk++) {
3027: fprintf(ficgp,"\nset out \"pe%s%d%d.png\" \n",strtok(optionfile, "."),jk,ng);
3028: if (ng==2)
3029: fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
3030: else
3031: fprintf(ficgp,"\nset title \"Probability\"\n");
3032: fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65\nset log y\nplot [%.f:%.f] ",ageminpar,agemaxpar);
3033: i=1;
3034: for(k2=1; k2<=nlstate; k2++) {
3035: k3=i;
3036: for(k=1; k<=(nlstate+ndeath); k++) {
3037: if (k != k2){
3038: if(ng==2)
3039: fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);
3040: else
3041: fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
3042: ij=1;
3043: for(j=3; j <=ncovmodel; j++) {
3044: if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
3045: fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
3046: ij++;
3047: }
3048: else
3049: fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
3050: }
3051: fprintf(ficgp,")/(1");
3052:
3053: for(k1=1; k1 <=nlstate; k1++){
3054: fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);
3055: ij=1;
3056: for(j=3; j <=ncovmodel; j++){
3057: if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
3058: fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
3059: ij++;
3060: }
3061: else
3062: fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
3063: }
3064: fprintf(ficgp,")");
3065: }
3066: fprintf(ficgp,") t \"p%d%d\" ", k2,k);
3067: if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");
3068: i=i+ncovmodel;
3069: }
3070: } /* end k */
3071: } /* end k2 */
3072: } /* end jk */
3073: } /* end ng */
3074: fclose(ficgp);
3075: } /* end gnuplot */
3076:
3077:
3078: /*************** Moving average **************/
1.54 brouard 3079: int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav){
1.53 brouard 3080:
3081: int i, cpt, cptcod;
1.58 lievre 3082: int modcovmax =1;
1.54 brouard 3083: int mobilavrange, mob;
1.53 brouard 3084: double age;
1.58 lievre 3085:
3086: modcovmax=2*cptcoveff;/* Max number of modalities. We suppose
3087: a covariate has 2 modalities */
3088: if (cptcovn<1) modcovmax=1; /* At least 1 pass */
3089:
1.54 brouard 3090: if(mobilav==1||mobilav ==3 ||mobilav==5 ||mobilav== 7){
3091: if(mobilav==1) mobilavrange=5; /* default */
3092: else mobilavrange=mobilav;
3093: for (age=bage; age<=fage; age++)
3094: for (i=1; i<=nlstate;i++)
1.58 lievre 3095: for (cptcod=1;cptcod<=modcovmax;cptcod++)
1.54 brouard 3096: mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
3097: /* We keep the original values on the extreme ages bage, fage and for
3098: fage+1 and bage-1 we use a 3 terms moving average; for fage+2 bage+2
3099: we use a 5 terms etc. until the borders are no more concerned.
3100: */
3101: for (mob=3;mob <=mobilavrange;mob=mob+2){
3102: for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){
3103: for (i=1; i<=nlstate;i++){
1.58 lievre 3104: for (cptcod=1;cptcod<=modcovmax;cptcod++){
1.54 brouard 3105: mobaverage[(int)age][i][cptcod] =probs[(int)age][i][cptcod];
3106: for (cpt=1;cpt<=(mob-1)/2;cpt++){
3107: mobaverage[(int)age][i][cptcod] +=probs[(int)age-cpt][i][cptcod];
3108: mobaverage[(int)age][i][cptcod] +=probs[(int)age+cpt][i][cptcod];
3109: }
3110: mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/mob;
3111: }
1.53 brouard 3112: }
1.54 brouard 3113: }/* end age */
3114: }/* end mob */
3115: }else return -1;
3116: return 0;
3117: }/* End movingaverage */
1.53 brouard 3118:
3119:
3120: /************** Forecasting ******************/
1.70 brouard 3121: prevforecast(char fileres[], double anproj1, double mproj1, double jproj1, double ageminpar, double agemax, double dateprev1, double dateprev2, int mobilav, double bage, double fage, int firstpass, int lastpass, double anproj2, double p[], int cptcoveff){
1.69 brouard 3122: /* proj1, year, month, day of starting projection
3123: agemin, agemax range of age
3124: dateprev1 dateprev2 range of dates during which prevalence is computed
1.70 brouard 3125: anproj2 year of en of projection (same day and month as proj1).
1.69 brouard 3126: */
1.73 lievre 3127: int yearp, stepsize, hstepm, nhstepm, j, k, c, cptcod, i, h, i1;
1.53 brouard 3128: int *popage;
1.70 brouard 3129: double agec; /* generic age */
3130: double agelim, ppij, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
1.53 brouard 3131: double *popeffectif,*popcount;
3132: double ***p3mat;
1.55 lievre 3133: double ***mobaverage;
1.53 brouard 3134: char fileresf[FILENAMELENGTH];
3135:
1.69 brouard 3136: agelim=AGESUP;
1.70 brouard 3137: prevalence(ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
1.53 brouard 3138:
3139: strcpy(fileresf,"f");
3140: strcat(fileresf,fileres);
3141: if((ficresf=fopen(fileresf,"w"))==NULL) {
3142: printf("Problem with forecast resultfile: %s\n", fileresf);
3143: fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);
3144: }
3145: printf("Computing forecasting: result on file '%s' \n", fileresf);
3146: fprintf(ficlog,"Computing forecasting: result on file '%s' \n", fileresf);
3147:
3148: if (cptcoveff==0) ncodemax[cptcoveff]=1;
3149:
1.54 brouard 3150: if (mobilav!=0) {
1.53 brouard 3151: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
1.54 brouard 3152: if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
3153: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
3154: printf(" Error in movingaverage mobilav=%d\n",mobilav);
3155: }
1.53 brouard 3156: }
3157:
3158: stepsize=(int) (stepm+YEARM-1)/YEARM;
3159: if (stepm<=12) stepsize=1;
1.74 brouard 3160: if(estepm < stepm){
3161: printf ("Problem %d lower than %d\n",estepm, stepm);
3162: }
3163: else hstepm=estepm;
3164:
1.53 brouard 3165: hstepm=hstepm/stepm;
1.69 brouard 3166: yp1=modf(dateintmean,&yp);/* extracts integral of datemean in yp and
3167: fractional in yp1 */
1.53 brouard 3168: anprojmean=yp;
3169: yp2=modf((yp1*12),&yp);
3170: mprojmean=yp;
3171: yp1=modf((yp2*30.5),&yp);
3172: jprojmean=yp;
3173: if(jprojmean==0) jprojmean=1;
3174: if(mprojmean==0) jprojmean=1;
1.73 lievre 3175:
3176: i1=cptcoveff;
3177: if (cptcovn < 1){i1=1;}
1.53 brouard 3178:
1.70 brouard 3179: fprintf(ficresf,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2);
1.53 brouard 3180:
1.70 brouard 3181: fprintf(ficresf,"#****** Routine prevforecast **\n");
1.73 lievre 3182:
1.75 brouard 3183: /* if (h==(int)(YEARM*yearp)){ */
1.73 lievre 3184: for(cptcov=1, k=0;cptcov<=i1;cptcov++){
1.53 brouard 3185: for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
3186: k=k+1;
3187: fprintf(ficresf,"\n#******");
3188: for(j=1;j<=cptcoveff;j++) {
1.70 brouard 3189: fprintf(ficresf," V%d=%d, hpijx=probability over h years, hp.jx is weighted by observed prev ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
1.53 brouard 3190: }
3191: fprintf(ficresf,"******\n");
1.70 brouard 3192: fprintf(ficresf,"# Covariate valuofcovar yearproj age");
3193: for(j=1; j<=nlstate+ndeath;j++){
3194: for(i=1; i<=nlstate;i++)
3195: fprintf(ficresf," p%d%d",i,j);
3196: fprintf(ficresf," p.%d",j);
3197: }
1.74 brouard 3198: for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) {
1.53 brouard 3199: fprintf(ficresf,"\n");
1.70 brouard 3200: fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+yearp);
1.53 brouard 3201:
1.71 brouard 3202: for (agec=fage; agec>=(ageminpar-1); agec--){
1.70 brouard 3203: nhstepm=(int) rint((agelim-agec)*YEARM/stepm);
1.53 brouard 3204: nhstepm = nhstepm/hstepm;
3205: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3206: oldm=oldms;savm=savms;
1.70 brouard 3207: hpxij(p3mat,nhstepm,agec,hstepm,p,nlstate,stepm,oldm,savm, k);
1.53 brouard 3208:
3209: for (h=0; h<=nhstepm; h++){
1.75 brouard 3210: if (h*hstepm/YEARM*stepm ==yearp) {
1.69 brouard 3211: fprintf(ficresf,"\n");
3212: for(j=1;j<=cptcoveff;j++)
3213: fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
1.70 brouard 3214: fprintf(ficresf,"%.f %.f ",anproj1+yearp,agec+h*hstepm/YEARM*stepm);
1.53 brouard 3215: }
3216: for(j=1; j<=nlstate+ndeath;j++) {
1.70 brouard 3217: ppij=0.;
1.71 brouard 3218: for(i=1; i<=nlstate;i++) {
1.53 brouard 3219: if (mobilav==1)
1.71 brouard 3220: ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][i][cptcod];
1.53 brouard 3221: else {
1.71 brouard 3222: ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][cptcod];
1.53 brouard 3223: }
1.75 brouard 3224: if (h*hstepm/YEARM*stepm== yearp) {
1.70 brouard 3225: fprintf(ficresf," %.3f", p3mat[i][j][h]);
1.75 brouard 3226: }
3227: } /* end i */
3228: if (h*hstepm/YEARM*stepm==yearp) {
1.70 brouard 3229: fprintf(ficresf," %.3f", ppij);
1.53 brouard 3230: }
1.75 brouard 3231: }/* end j */
3232: } /* end h */
1.53 brouard 3233: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
1.75 brouard 3234: } /* end agec */
3235: } /* end yearp */
3236: } /* end cptcod */
3237: } /* end cptcov */
1.53 brouard 3238:
1.54 brouard 3239: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
1.53 brouard 3240:
3241: fclose(ficresf);
3242: }
1.70 brouard 3243:
3244: /************** Forecasting *****not tested NB*************/
1.53 brouard 3245: 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){
3246:
3247: int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;
3248: int *popage;
1.69 brouard 3249: double calagedatem, agelim, kk1, kk2;
1.53 brouard 3250: double *popeffectif,*popcount;
3251: double ***p3mat,***tabpop,***tabpopprev;
1.55 lievre 3252: double ***mobaverage;
1.53 brouard 3253: char filerespop[FILENAMELENGTH];
3254:
3255: tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
3256: tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
3257: agelim=AGESUP;
1.69 brouard 3258: calagedatem=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;
1.53 brouard 3259:
1.70 brouard 3260: prevalence(ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
1.53 brouard 3261:
3262:
3263: strcpy(filerespop,"pop");
3264: strcat(filerespop,fileres);
3265: if((ficrespop=fopen(filerespop,"w"))==NULL) {
3266: printf("Problem with forecast resultfile: %s\n", filerespop);
3267: fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop);
3268: }
3269: printf("Computing forecasting: result on file '%s' \n", filerespop);
3270: fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop);
3271:
3272: if (cptcoveff==0) ncodemax[cptcoveff]=1;
3273:
1.54 brouard 3274: if (mobilav!=0) {
1.53 brouard 3275: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
1.54 brouard 3276: if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
3277: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
3278: printf(" Error in movingaverage mobilav=%d\n",mobilav);
3279: }
1.53 brouard 3280: }
3281:
3282: stepsize=(int) (stepm+YEARM-1)/YEARM;
3283: if (stepm<=12) stepsize=1;
3284:
3285: agelim=AGESUP;
3286:
3287: hstepm=1;
3288: hstepm=hstepm/stepm;
3289:
3290: if (popforecast==1) {
3291: if((ficpop=fopen(popfile,"r"))==NULL) {
3292: printf("Problem with population file : %s\n",popfile);exit(0);
3293: fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0);
3294: }
3295: popage=ivector(0,AGESUP);
3296: popeffectif=vector(0,AGESUP);
3297: popcount=vector(0,AGESUP);
3298:
3299: i=1;
3300: while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;
3301:
3302: imx=i;
3303: for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];
3304: }
3305:
1.69 brouard 3306: for(cptcov=1,k=0;cptcov<=i2;cptcov++){
1.53 brouard 3307: for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
3308: k=k+1;
3309: fprintf(ficrespop,"\n#******");
3310: for(j=1;j<=cptcoveff;j++) {
3311: fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
3312: }
3313: fprintf(ficrespop,"******\n");
3314: fprintf(ficrespop,"# Age");
3315: for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);
3316: if (popforecast==1) fprintf(ficrespop," [Population]");
3317:
3318: for (cpt=0; cpt<=0;cpt++) {
3319: fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);
3320:
1.69 brouard 3321: for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){
1.53 brouard 3322: nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);
3323: nhstepm = nhstepm/hstepm;
3324:
3325: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3326: oldm=oldms;savm=savms;
3327: hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
3328:
3329: for (h=0; h<=nhstepm; h++){
1.69 brouard 3330: if (h==(int) (calagedatem+YEARM*cpt)) {
1.53 brouard 3331: fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
3332: }
3333: for(j=1; j<=nlstate+ndeath;j++) {
3334: kk1=0.;kk2=0;
3335: for(i=1; i<=nlstate;i++) {
3336: if (mobilav==1)
3337: kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];
3338: else {
3339: kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];
3340: }
3341: }
1.69 brouard 3342: if (h==(int)(calagedatem+12*cpt)){
1.53 brouard 3343: tabpop[(int)(agedeb)][j][cptcod]=kk1;
3344: /*fprintf(ficrespop," %.3f", kk1);
3345: if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/
3346: }
3347: }
3348: for(i=1; i<=nlstate;i++){
3349: kk1=0.;
3350: for(j=1; j<=nlstate;j++){
3351: kk1= kk1+tabpop[(int)(agedeb)][j][cptcod];
3352: }
1.69 brouard 3353: tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedatem+12*cpt)*hstepm/YEARM*stepm-1)];
1.53 brouard 3354: }
3355:
1.69 brouard 3356: if (h==(int)(calagedatem+12*cpt)) for(j=1; j<=nlstate;j++)
1.53 brouard 3357: fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);
3358: }
3359: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3360: }
3361: }
3362:
3363: /******/
3364:
3365: for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) {
3366: fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);
1.69 brouard 3367: for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){
1.53 brouard 3368: nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);
3369: nhstepm = nhstepm/hstepm;
3370:
3371: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3372: oldm=oldms;savm=savms;
3373: hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
3374: for (h=0; h<=nhstepm; h++){
1.69 brouard 3375: if (h==(int) (calagedatem+YEARM*cpt)) {
1.53 brouard 3376: fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
3377: }
3378: for(j=1; j<=nlstate+ndeath;j++) {
3379: kk1=0.;kk2=0;
3380: for(i=1; i<=nlstate;i++) {
3381: kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];
3382: }
1.69 brouard 3383: if (h==(int)(calagedatem+12*cpt)) fprintf(ficresf," %15.2f", kk1);
1.53 brouard 3384: }
3385: }
3386: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3387: }
3388: }
3389: }
3390: }
3391:
1.54 brouard 3392: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
1.53 brouard 3393:
3394: if (popforecast==1) {
3395: free_ivector(popage,0,AGESUP);
3396: free_vector(popeffectif,0,AGESUP);
3397: free_vector(popcount,0,AGESUP);
3398: }
3399: free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
3400: free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
3401: fclose(ficrespop);
3402: }
3403:
3404: /***********************************************/
3405: /**************** Main Program *****************/
3406: /***********************************************/
3407:
3408: int main(int argc, char *argv[])
3409: {
1.61 brouard 3410: int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav);
1.74 brouard 3411: int i,j, k, n=MAXN,iter,m,size=100,cptcode, cptcod;
1.53 brouard 3412: double agedeb, agefin,hf;
3413: double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;
3414:
3415: double fret;
3416: double **xi,tmp,delta;
3417:
3418: double dum; /* Dummy variable */
3419: double ***p3mat;
3420: double ***mobaverage;
3421: int *indx;
3422: char line[MAXLINE], linepar[MAXLINE];
3423: char path[80],pathc[80],pathcd[80],pathtot[80],model[80];
3424: int firstobs=1, lastobs=10;
3425: int sdeb, sfin; /* Status at beginning and end */
3426: int c, h , cpt,l;
3427: int ju,jl, mi;
3428: int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;
1.59 brouard 3429: int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,*tab;
1.69 brouard 3430: int mobilavproj=0 , prevfcast=0 ; /* moving average of prev, If prevfcast=1 prevalence projection */
1.53 brouard 3431: int mobilav=0,popforecast=0;
3432: int hstepm, nhstepm;
1.74 brouard 3433: double jprev1=1, mprev1=1,anprev1=2000,jprev2=1, mprev2=1,anprev2=2000;
3434: double jpyram=1, mpyram=1,anpyram=2000,jpyram1=1, mpyram1=1,anpyram1=2000;
1.53 brouard 3435:
3436: double bage, fage, age, agelim, agebase;
3437: double ftolpl=FTOL;
3438: double **prlim;
3439: double *severity;
3440: double ***param; /* Matrix of parameters */
3441: double *p;
3442: double **matcov; /* Matrix of covariance */
3443: double ***delti3; /* Scale */
3444: double *delti; /* Scale */
3445: double ***eij, ***vareij;
3446: double **varpl; /* Variances of prevalence limits by age */
3447: double *epj, vepp;
3448: double kk1, kk2;
1.74 brouard 3449: double dateprev1, dateprev2,jproj1=1,mproj1=1,anproj1=2000,jproj2=1,mproj2=1,anproj2=2000;
1.53 brouard 3450:
3451: char *alph[]={"a","a","b","c","d","e"}, str[4];
3452:
3453:
3454: char z[1]="c", occ;
3455: #include <sys/time.h>
3456: #include <time.h>
3457: char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];
3458:
3459: /* long total_usecs;
1.59 brouard 3460: struct timeval start_time, end_time;
1.53 brouard 3461:
1.59 brouard 3462: gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */
1.53 brouard 3463: getcwd(pathcd, size);
3464:
1.81 brouard 3465: printf("\n%s\n%s",version,fullversion);
1.53 brouard 3466: if(argc <=1){
3467: printf("\nEnter the parameter file name: ");
3468: scanf("%s",pathtot);
3469: }
3470: else{
3471: strcpy(pathtot,argv[1]);
3472: }
3473: /*if(getcwd(pathcd, 80)!= NULL)printf ("Error pathcd\n");*/
3474: /*cygwin_split_path(pathtot,path,optionfile);
3475: printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/
3476: /* cutv(path,optionfile,pathtot,'\\');*/
3477:
3478: split(pathtot,path,optionfile,optionfilext,optionfilefiname);
1.59 brouard 3479: printf("pathtot=%s, path=%s, optionfile=%s optionfilext=%s optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
1.53 brouard 3480: chdir(path);
3481: replace(pathc,path);
3482:
1.59 brouard 3483: /*-------- arguments in the command line --------*/
1.53 brouard 3484:
3485: /* Log file */
3486: strcat(filelog, optionfilefiname);
3487: strcat(filelog,".log"); /* */
3488: if((ficlog=fopen(filelog,"w"))==NULL) {
3489: printf("Problem with logfile %s\n",filelog);
3490: goto end;
3491: }
3492: fprintf(ficlog,"Log filename:%s\n",filelog);
3493: fprintf(ficlog,"\n%s",version);
3494: fprintf(ficlog,"\nEnter the parameter file name: ");
3495: fprintf(ficlog,"pathtot=%s, path=%s, optionfile=%s optionfilext=%s optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
3496: fflush(ficlog);
3497:
3498: /* */
3499: strcpy(fileres,"r");
3500: strcat(fileres, optionfilefiname);
3501: strcat(fileres,".txt"); /* Other files have txt extension */
3502:
3503: /*---------arguments file --------*/
3504:
3505: if((ficpar=fopen(optionfile,"r"))==NULL) {
3506: printf("Problem with optionfile %s\n",optionfile);
3507: fprintf(ficlog,"Problem with optionfile %s\n",optionfile);
3508: goto end;
3509: }
3510:
3511: strcpy(filereso,"o");
3512: strcat(filereso,fileres);
3513: if((ficparo=fopen(filereso,"w"))==NULL) {
3514: printf("Problem with Output resultfile: %s\n", filereso);
3515: fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso);
3516: goto end;
3517: }
3518:
3519: /* Reads comments: lines beginning with '#' */
3520: while((c=getc(ficpar))=='#' && c!= EOF){
3521: ungetc(c,ficpar);
3522: fgets(line, MAXLINE, ficpar);
3523: puts(line);
3524: fputs(line,ficparo);
3525: }
3526: ungetc(c,ficpar);
3527:
3528: 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);
3529: 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);
3530: 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 3531: while((c=getc(ficpar))=='#' && c!= EOF){
1.53 brouard 3532: ungetc(c,ficpar);
3533: fgets(line, MAXLINE, ficpar);
3534: puts(line);
3535: fputs(line,ficparo);
3536: }
3537: ungetc(c,ficpar);
3538:
3539:
3540: covar=matrix(0,NCOVMAX,1,n);
1.58 lievre 3541: cptcovn=0; /*Number of covariates, i.e. number of '+' in model statement*/
1.53 brouard 3542: if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;
3543:
1.58 lievre 3544: ncovmodel=2+cptcovn; /*Number of variables = cptcovn + intercept + age */
1.53 brouard 3545: nvar=ncovmodel-1; /* Suppressing age as a basic covariate */
3546:
3547: /* Read guess parameters */
3548: /* Reads comments: lines beginning with '#' */
3549: while((c=getc(ficpar))=='#' && c!= EOF){
3550: ungetc(c,ficpar);
3551: fgets(line, MAXLINE, ficpar);
3552: puts(line);
3553: fputs(line,ficparo);
3554: }
3555: ungetc(c,ficpar);
3556:
3557: param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
1.59 brouard 3558: for(i=1; i <=nlstate; i++)
1.53 brouard 3559: for(j=1; j <=nlstate+ndeath-1; j++){
3560: fscanf(ficpar,"%1d%1d",&i1,&j1);
3561: fprintf(ficparo,"%1d%1d",i1,j1);
3562: if(mle==1)
3563: printf("%1d%1d",i,j);
3564: fprintf(ficlog,"%1d%1d",i,j);
3565: for(k=1; k<=ncovmodel;k++){
3566: fscanf(ficpar," %lf",¶m[i][j][k]);
3567: if(mle==1){
3568: printf(" %lf",param[i][j][k]);
3569: fprintf(ficlog," %lf",param[i][j][k]);
3570: }
3571: else
3572: fprintf(ficlog," %lf",param[i][j][k]);
3573: fprintf(ficparo," %lf",param[i][j][k]);
3574: }
3575: fscanf(ficpar,"\n");
3576: if(mle==1)
3577: printf("\n");
3578: fprintf(ficlog,"\n");
3579: fprintf(ficparo,"\n");
3580: }
3581:
1.59 brouard 3582: npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/
1.53 brouard 3583:
3584: p=param[1][1];
3585:
3586: /* Reads comments: lines beginning with '#' */
3587: while((c=getc(ficpar))=='#' && c!= EOF){
3588: ungetc(c,ficpar);
3589: fgets(line, MAXLINE, ficpar);
3590: puts(line);
3591: fputs(line,ficparo);
3592: }
3593: ungetc(c,ficpar);
3594:
3595: delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
1.74 brouard 3596: /* delti=vector(1,npar); *//* Scale of each paramater (output from hesscov) */
1.53 brouard 3597: for(i=1; i <=nlstate; i++){
3598: for(j=1; j <=nlstate+ndeath-1; j++){
3599: fscanf(ficpar,"%1d%1d",&i1,&j1);
3600: printf("%1d%1d",i,j);
3601: fprintf(ficparo,"%1d%1d",i1,j1);
3602: for(k=1; k<=ncovmodel;k++){
3603: fscanf(ficpar,"%le",&delti3[i][j][k]);
3604: printf(" %le",delti3[i][j][k]);
3605: fprintf(ficparo," %le",delti3[i][j][k]);
3606: }
3607: fscanf(ficpar,"\n");
3608: printf("\n");
3609: fprintf(ficparo,"\n");
3610: }
3611: }
3612: delti=delti3[1][1];
1.74 brouard 3613:
3614:
3615: /* free_ma3x(delti3,1,nlstate,1,nlstate+ndeath-1,1,ncovmodel); */ /* Hasn't to to freed here otherwise delti is no more allocated */
1.53 brouard 3616:
3617: /* Reads comments: lines beginning with '#' */
3618: while((c=getc(ficpar))=='#' && c!= EOF){
3619: ungetc(c,ficpar);
3620: fgets(line, MAXLINE, ficpar);
3621: puts(line);
3622: fputs(line,ficparo);
3623: }
3624: ungetc(c,ficpar);
3625:
3626: matcov=matrix(1,npar,1,npar);
3627: for(i=1; i <=npar; i++){
3628: fscanf(ficpar,"%s",&str);
3629: if(mle==1)
3630: printf("%s",str);
3631: fprintf(ficlog,"%s",str);
3632: fprintf(ficparo,"%s",str);
3633: for(j=1; j <=i; j++){
3634: fscanf(ficpar," %le",&matcov[i][j]);
3635: if(mle==1){
3636: printf(" %.5le",matcov[i][j]);
3637: fprintf(ficlog," %.5le",matcov[i][j]);
3638: }
3639: else
3640: fprintf(ficlog," %.5le",matcov[i][j]);
3641: fprintf(ficparo," %.5le",matcov[i][j]);
3642: }
3643: fscanf(ficpar,"\n");
3644: if(mle==1)
3645: printf("\n");
3646: fprintf(ficlog,"\n");
3647: fprintf(ficparo,"\n");
3648: }
3649: for(i=1; i <=npar; i++)
3650: for(j=i+1;j<=npar;j++)
3651: matcov[i][j]=matcov[j][i];
3652:
3653: if(mle==1)
3654: printf("\n");
3655: fprintf(ficlog,"\n");
3656:
3657:
1.59 brouard 3658: /*-------- Rewriting paramater file ----------*/
3659: strcpy(rfileres,"r"); /* "Rparameterfile */
3660: strcat(rfileres,optionfilefiname); /* Parameter file first name*/
3661: strcat(rfileres,"."); /* */
3662: strcat(rfileres,optionfilext); /* Other files have txt extension */
3663: if((ficres =fopen(rfileres,"w"))==NULL) {
3664: printf("Problem writing new parameter file: %s\n", fileres);goto end;
3665: fprintf(ficlog,"Problem writing new parameter file: %s\n", fileres);goto end;
3666: }
3667: fprintf(ficres,"#%s\n",version);
1.53 brouard 3668:
1.59 brouard 3669: /*-------- data file ----------*/
3670: if((fic=fopen(datafile,"r"))==NULL) {
3671: printf("Problem with datafile: %s\n", datafile);goto end;
3672: fprintf(ficlog,"Problem with datafile: %s\n", datafile);goto end;
3673: }
3674:
3675: n= lastobs;
3676: severity = vector(1,maxwav);
3677: outcome=imatrix(1,maxwav+1,1,n);
3678: num=ivector(1,n);
3679: moisnais=vector(1,n);
3680: annais=vector(1,n);
3681: moisdc=vector(1,n);
3682: andc=vector(1,n);
3683: agedc=vector(1,n);
3684: cod=ivector(1,n);
3685: weight=vector(1,n);
3686: for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */
3687: mint=matrix(1,maxwav,1,n);
3688: anint=matrix(1,maxwav,1,n);
3689: s=imatrix(1,maxwav+1,1,n);
3690: tab=ivector(1,NCOVMAX);
3691: ncodemax=ivector(1,8);
3692:
3693: i=1;
3694: while (fgets(line, MAXLINE, fic) != NULL) {
3695: if ((i >= firstobs) && (i <=lastobs)) {
1.53 brouard 3696:
1.59 brouard 3697: for (j=maxwav;j>=1;j--){
3698: cutv(stra, strb,line,' '); s[j][i]=atoi(strb);
3699: strcpy(line,stra);
3700: cutv(stra, strb,line,'/'); anint[j][i]=(double)(atoi(strb)); strcpy(line,stra);
3701: cutv(stra, strb,line,' '); mint[j][i]=(double)(atoi(strb)); strcpy(line,stra);
3702: }
1.53 brouard 3703:
1.59 brouard 3704: cutv(stra, strb,line,'/'); andc[i]=(double)(atoi(strb)); strcpy(line,stra);
3705: cutv(stra, strb,line,' '); moisdc[i]=(double)(atoi(strb)); strcpy(line,stra);
1.53 brouard 3706:
1.59 brouard 3707: cutv(stra, strb,line,'/'); annais[i]=(double)(atoi(strb)); strcpy(line,stra);
3708: cutv(stra, strb,line,' '); moisnais[i]=(double)(atoi(strb)); strcpy(line,stra);
1.53 brouard 3709:
1.59 brouard 3710: cutv(stra, strb,line,' '); weight[i]=(double)(atoi(strb)); strcpy(line,stra);
3711: for (j=ncovcol;j>=1;j--){
3712: cutv(stra, strb,line,' '); covar[j][i]=(double)(atoi(strb)); strcpy(line,stra);
3713: }
3714: num[i]=atol(stra);
1.53 brouard 3715:
1.59 brouard 3716: /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){
3717: 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 3718:
1.59 brouard 3719: i=i+1;
3720: }
3721: }
3722: /* printf("ii=%d", ij);
3723: scanf("%d",i);*/
1.53 brouard 3724: imx=i-1; /* Number of individuals */
3725:
3726: /* for (i=1; i<=imx; i++){
3727: if ((s[1][i]==3) && (s[2][i]==2)) s[2][i]=3;
3728: if ((s[2][i]==3) && (s[3][i]==2)) s[3][i]=3;
3729: if ((s[3][i]==3) && (s[4][i]==2)) s[4][i]=3;
3730: }*/
3731: /* for (i=1; i<=imx; i++){
3732: if (s[4][i]==9) s[4][i]=-1;
3733: 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]));}*/
3734:
1.71 brouard 3735: for (i=1; i<=imx; i++)
1.53 brouard 3736:
1.71 brouard 3737: /*if ((s[3][i]==3) || (s[4][i]==3)) weight[i]=0.08;
3738: else weight[i]=1;*/
3739:
1.53 brouard 3740: /* Calculation of the number of parameter from char model*/
3741: Tvar=ivector(1,15); /* stores the number n of the covariates in Vm+Vn at 1 and m at 2 */
3742: Tprod=ivector(1,15);
3743: Tvaraff=ivector(1,15);
3744: Tvard=imatrix(1,15,1,2);
3745: Tage=ivector(1,15);
3746:
1.58 lievre 3747: if (strlen(model) >1){ /* If there is at least 1 covariate */
1.53 brouard 3748: j=0, j1=0, k1=1, k2=1;
1.58 lievre 3749: j=nbocc(model,'+'); /* j=Number of '+' */
3750: j1=nbocc(model,'*'); /* j1=Number of '*' */
3751: cptcovn=j+1;
3752: cptcovprod=j1; /*Number of products */
1.53 brouard 3753:
3754: strcpy(modelsav,model);
3755: if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){
3756: printf("Error. Non available option model=%s ",model);
3757: fprintf(ficlog,"Error. Non available option model=%s ",model);
3758: goto end;
3759: }
3760:
1.59 brouard 3761: /* This loop fills the array Tvar from the string 'model'.*/
1.58 lievre 3762:
1.53 brouard 3763: for(i=(j+1); i>=1;i--){
3764: cutv(stra,strb,modelsav,'+'); /* keeps in strb after the last + */
1.59 brouard 3765: if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyzes it */
1.53 brouard 3766: /* printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/
3767: /*scanf("%d",i);*/
3768: if (strchr(strb,'*')) { /* Model includes a product */
3769: cutv(strd,strc,strb,'*'); /* strd*strc Vm*Vn (if not *age)*/
3770: if (strcmp(strc,"age")==0) { /* Vn*age */
3771: cptcovprod--;
3772: cutv(strb,stre,strd,'V');
3773: Tvar[i]=atoi(stre); /* computes n in Vn and stores in Tvar*/
3774: cptcovage++;
3775: Tage[cptcovage]=i;
3776: /*printf("stre=%s ", stre);*/
3777: }
3778: else if (strcmp(strd,"age")==0) { /* or age*Vn */
3779: cptcovprod--;
3780: cutv(strb,stre,strc,'V');
3781: Tvar[i]=atoi(stre);
3782: cptcovage++;
3783: Tage[cptcovage]=i;
3784: }
3785: else { /* Age is not in the model */
3786: cutv(strb,stre,strc,'V'); /* strc= Vn, stre is n*/
3787: Tvar[i]=ncovcol+k1;
3788: cutv(strb,strc,strd,'V'); /* strd was Vm, strc is m */
3789: Tprod[k1]=i;
3790: Tvard[k1][1]=atoi(strc); /* m*/
3791: Tvard[k1][2]=atoi(stre); /* n */
3792: Tvar[cptcovn+k2]=Tvard[k1][1];
3793: Tvar[cptcovn+k2+1]=Tvard[k1][2];
3794: for (k=1; k<=lastobs;k++)
3795: covar[ncovcol+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];
3796: k1++;
3797: k2=k2+2;
3798: }
3799: }
3800: else { /* no more sum */
3801: /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/
3802: /* scanf("%d",i);*/
3803: cutv(strd,strc,strb,'V');
3804: Tvar[i]=atoi(strc);
3805: }
3806: strcpy(modelsav,stra);
3807: /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);
3808: scanf("%d",i);*/
3809: } /* end of loop + */
3810: } /* end model */
3811:
1.58 lievre 3812: /*The number n of Vn is stored in Tvar. cptcovage =number of age covariate. Tage gives the position of age. cptcovprod= number of products.
3813: If model=V1+V1*age then Tvar[1]=1 Tvar[2]=1 cptcovage=1 Tage[1]=2 cptcovprod=0*/
3814:
1.53 brouard 3815: /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);
3816: printf("cptcovprod=%d ", cptcovprod);
3817: fprintf(ficlog,"cptcovprod=%d ", cptcovprod);
1.58 lievre 3818:
3819: scanf("%d ",i);
3820: fclose(fic);*/
1.53 brouard 3821:
3822: /* if(mle==1){*/
1.59 brouard 3823: if (weightopt != 1) { /* Maximisation without weights*/
3824: for(i=1;i<=n;i++) weight[i]=1.0;
3825: }
1.53 brouard 3826: /*-calculation of age at interview from date of interview and age at death -*/
1.59 brouard 3827: agev=matrix(1,maxwav,1,imx);
1.53 brouard 3828:
1.59 brouard 3829: for (i=1; i<=imx; i++) {
3830: for(m=2; (m<= maxwav); m++) {
1.76 brouard 3831: if (((int)mint[m][i]== 99) && (s[m][i] <= nlstate)){
1.59 brouard 3832: anint[m][i]=9999;
3833: s[m][i]=-1;
3834: }
1.76 brouard 3835: if((int)moisdc[i]==99 && (int)andc[i]==9999 && s[m][i]>nlstate){
1.77 brouard 3836: printf("Error! Date of death (month %2d and year %4d) of individual %d on line %d was unknown, you must set an arbitrary year of death or he/she is skipped and results are biased\n",(int)moisdc[i],(int)andc[i],num[i],i);
3837: fprintf(ficlog,"Error! Date of death (month %2d and year %4d) of individual %d on line %d was unknown, you must set an arbitrary year of death or he/she is skipped and results are biased\n",(int)moisdc[i],(int)andc[i],num[i],i);
1.76 brouard 3838: s[m][i]=-1;
3839: }
3840: if((int)moisdc[i]==99 && (int)andc[i]!=9999 && s[m][i]>nlstate){
1.77 brouard 3841: printf("Error! Month of death of individual %d on line %d was unknown %2d, you should set it otherwise the information on the death is skipped and results are biased.\n",num[i],i,(int)moisdc[i]);
3842: fprintf(ficlog,"Error! Month of death of individual %d on line %d was unknown %f, you should set it otherwise the information on the death is skipped and results are biased.\n",num[i],i,moisdc[i]);
1.76 brouard 3843: s[m][i]=-1;
3844: }
1.53 brouard 3845: }
1.59 brouard 3846: }
1.53 brouard 3847:
1.59 brouard 3848: for (i=1; i<=imx; i++) {
3849: agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);
1.71 brouard 3850: for(m=firstpass; (m<= lastpass); m++){
1.69 brouard 3851: if(s[m][i] >0){
1.59 brouard 3852: if (s[m][i] >= nlstate+1) {
3853: if(agedc[i]>0)
1.76 brouard 3854: if((int)moisdc[i]!=99 && (int)andc[i]!=9999)
1.69 brouard 3855: agev[m][i]=agedc[i];
1.59 brouard 3856: /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/
3857: else {
1.76 brouard 3858: if ((int)andc[i]!=9999){
1.59 brouard 3859: printf("Warning negative age at death: %d line:%d\n",num[i],i);
3860: fprintf(ficlog,"Warning negative age at death: %d line:%d\n",num[i],i);
3861: agev[m][i]=-1;
1.53 brouard 3862: }
3863: }
1.70 brouard 3864: }
1.69 brouard 3865: else if(s[m][i] !=9){ /* Standard case, age in fractional
3866: years but with the precision of a
3867: month */
1.59 brouard 3868: agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);
1.76 brouard 3869: if((int)mint[m][i]==99 || (int)anint[m][i]==9999)
1.59 brouard 3870: agev[m][i]=1;
3871: else if(agev[m][i] <agemin){
3872: agemin=agev[m][i];
3873: /*printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], agemin);*/
1.53 brouard 3874: }
1.59 brouard 3875: else if(agev[m][i] >agemax){
3876: agemax=agev[m][i];
3877: /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/
1.53 brouard 3878: }
1.59 brouard 3879: /*agev[m][i]=anint[m][i]-annais[i];*/
3880: /* agev[m][i] = age[i]+2*m;*/
1.53 brouard 3881: }
1.59 brouard 3882: else { /* =9 */
1.53 brouard 3883: agev[m][i]=1;
1.59 brouard 3884: s[m][i]=-1;
3885: }
1.53 brouard 3886: }
1.59 brouard 3887: else /*= 0 Unknown */
3888: agev[m][i]=1;
3889: }
1.53 brouard 3890:
1.59 brouard 3891: }
3892: for (i=1; i<=imx; i++) {
1.71 brouard 3893: for(m=firstpass; (m<=lastpass); m++){
1.59 brouard 3894: if (s[m][i] > (nlstate+ndeath)) {
3895: 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);
3896: 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);
3897: goto end;
1.53 brouard 3898: }
3899: }
1.59 brouard 3900: }
1.53 brouard 3901:
1.71 brouard 3902: /*for (i=1; i<=imx; i++){
3903: for (m=firstpass; (m<lastpass); m++){
3904: printf("%d %d %.lf %d %d\n", num[i],(covar[1][i]),agev[m][i],s[m][i],s[m+1][i]);
3905: }
3906:
3907: }*/
3908:
1.59 brouard 3909: printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);
3910: fprintf(ficlog,"Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);
3911:
3912: free_vector(severity,1,maxwav);
3913: free_imatrix(outcome,1,maxwav+1,1,n);
3914: free_vector(moisnais,1,n);
3915: free_vector(annais,1,n);
3916: /* free_matrix(mint,1,maxwav,1,n);
3917: free_matrix(anint,1,maxwav,1,n);*/
3918: free_vector(moisdc,1,n);
3919: free_vector(andc,1,n);
1.53 brouard 3920:
3921:
1.59 brouard 3922: wav=ivector(1,imx);
3923: dh=imatrix(1,lastpass-firstpass+1,1,imx);
3924: bh=imatrix(1,lastpass-firstpass+1,1,imx);
3925: mw=imatrix(1,lastpass-firstpass+1,1,imx);
1.69 brouard 3926:
1.59 brouard 3927: /* Concatenates waves */
3928: concatwav(wav, dh, bh, mw, s, agedc, agev, firstpass, lastpass, imx, nlstate, stepm);
1.53 brouard 3929:
1.59 brouard 3930: /* Routine tricode is to calculate cptcoveff (real number of unique covariates) and to associate covariable number and modality */
1.53 brouard 3931:
1.59 brouard 3932: Tcode=ivector(1,100);
3933: nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);
3934: ncodemax[1]=1;
3935: if (cptcovn > 0) tricode(Tvar,nbcode,imx);
1.53 brouard 3936:
1.59 brouard 3937: codtab=imatrix(1,100,1,10); /* Cross tabulation to get the order of
3938: the estimations*/
3939: h=0;
3940: m=pow(2,cptcoveff);
1.53 brouard 3941:
1.59 brouard 3942: for(k=1;k<=cptcoveff; k++){
3943: for(i=1; i <=(m/pow(2,k));i++){
3944: for(j=1; j <= ncodemax[k]; j++){
3945: for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){
3946: h++;
3947: if (h>m) h=1;codtab[h][k]=j;codtab[h][Tvar[k]]=j;
3948: /* printf("h=%d k=%d j=%d codtab[h][k]=%d tvar[k]=%d \n",h, k,j,codtab[h][k],Tvar[k]);*/
3949: }
3950: }
3951: }
3952: }
3953: /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]);
3954: codtab[1][2]=1;codtab[2][2]=2; */
3955: /* for(i=1; i <=m ;i++){
3956: for(k=1; k <=cptcovn; k++){
3957: printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);
3958: }
3959: printf("\n");
1.53 brouard 3960: }
1.59 brouard 3961: scanf("%d",i);*/
1.53 brouard 3962:
1.59 brouard 3963: /* Calculates basic frequencies. Computes observed prevalence at single age
3964: and prints on file fileres'p'. */
1.53 brouard 3965:
1.60 brouard 3966: pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
3967: oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
3968: newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
3969: savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
3970: oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */
1.53 brouard 3971:
3972:
1.59 brouard 3973: /* For Powell, parameters are in a vector p[] starting at p[1]
3974: so we point p on param[1][1] so that p[1] maps on param[1][1][1] */
3975: p=param[1][1]; /* *(*(*(param +1)+1)+0) */
1.53 brouard 3976:
1.61 brouard 3977: if(mle>=1){ /* Could be 1 or 2 */
1.53 brouard 3978: mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);
1.59 brouard 3979: }
1.53 brouard 3980:
1.59 brouard 3981: /*--------- results files --------------*/
3982: 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 3983:
3984:
1.59 brouard 3985: jk=1;
3986: fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
3987: printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
3988: fprintf(ficlog,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
3989: for(i=1,jk=1; i <=nlstate; i++){
3990: for(k=1; k <=(nlstate+ndeath); k++){
3991: if (k != i)
3992: {
3993: printf("%d%d ",i,k);
3994: fprintf(ficlog,"%d%d ",i,k);
3995: fprintf(ficres,"%1d%1d ",i,k);
3996: for(j=1; j <=ncovmodel; j++){
3997: printf("%f ",p[jk]);
3998: fprintf(ficlog,"%f ",p[jk]);
3999: fprintf(ficres,"%f ",p[jk]);
4000: jk++;
4001: }
4002: printf("\n");
4003: fprintf(ficlog,"\n");
4004: fprintf(ficres,"\n");
4005: }
4006: }
4007: }
4008: if(mle==1){
4009: /* Computing hessian and covariance matrix */
4010: ftolhess=ftol; /* Usually correct */
4011: hesscov(matcov, p, npar, delti, ftolhess, func);
4012: }
4013: fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");
4014: printf("# Scales (for hessian or gradient estimation)\n");
4015: fprintf(ficlog,"# Scales (for hessian or gradient estimation)\n");
4016: for(i=1,jk=1; i <=nlstate; i++){
4017: for(j=1; j <=nlstate+ndeath; j++){
4018: if (j!=i) {
4019: fprintf(ficres,"%1d%1d",i,j);
4020: printf("%1d%1d",i,j);
4021: fprintf(ficlog,"%1d%1d",i,j);
4022: for(k=1; k<=ncovmodel;k++){
4023: printf(" %.5e",delti[jk]);
4024: fprintf(ficlog," %.5e",delti[jk]);
4025: fprintf(ficres," %.5e",delti[jk]);
4026: jk++;
4027: }
4028: printf("\n");
4029: fprintf(ficlog,"\n");
4030: fprintf(ficres,"\n");
4031: }
4032: }
4033: }
1.53 brouard 4034:
1.59 brouard 4035: 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");
4036: if(mle==1)
4037: 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");
4038: 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");
4039: for(i=1,k=1;i<=npar;i++){
4040: /* if (k>nlstate) k=1;
4041: i1=(i-1)/(ncovmodel*nlstate)+1;
4042: fprintf(ficres,"%s%d%d",alph[k],i1,tab[i]);
4043: printf("%s%d%d",alph[k],i1,tab[i]);
4044: */
4045: fprintf(ficres,"%3d",i);
4046: if(mle==1)
4047: printf("%3d",i);
4048: fprintf(ficlog,"%3d",i);
4049: for(j=1; j<=i;j++){
4050: fprintf(ficres," %.5e",matcov[i][j]);
4051: if(mle==1)
4052: printf(" %.5e",matcov[i][j]);
4053: fprintf(ficlog," %.5e",matcov[i][j]);
4054: }
4055: fprintf(ficres,"\n");
4056: if(mle==1)
4057: printf("\n");
4058: fprintf(ficlog,"\n");
4059: k++;
4060: }
1.53 brouard 4061:
1.59 brouard 4062: while((c=getc(ficpar))=='#' && c!= EOF){
4063: ungetc(c,ficpar);
4064: fgets(line, MAXLINE, ficpar);
4065: puts(line);
4066: fputs(line,ficparo);
4067: }
4068: ungetc(c,ficpar);
4069:
4070: estepm=0;
4071: fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm);
4072: if (estepm==0 || estepm < stepm) estepm=stepm;
4073: if (fage <= 2) {
4074: bage = ageminpar;
4075: fage = agemaxpar;
4076: }
1.53 brouard 4077:
1.59 brouard 4078: fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");
4079: fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
4080: fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
1.53 brouard 4081:
1.59 brouard 4082: while((c=getc(ficpar))=='#' && c!= EOF){
4083: ungetc(c,ficpar);
4084: fgets(line, MAXLINE, ficpar);
4085: puts(line);
4086: fputs(line,ficparo);
4087: }
4088: ungetc(c,ficpar);
1.53 brouard 4089:
1.59 brouard 4090: 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);
4091: 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);
4092: 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 4093: printf("begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
4094: 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 4095:
1.59 brouard 4096: while((c=getc(ficpar))=='#' && c!= EOF){
4097: ungetc(c,ficpar);
4098: fgets(line, MAXLINE, ficpar);
4099: puts(line);
4100: fputs(line,ficparo);
4101: }
4102: ungetc(c,ficpar);
1.53 brouard 4103:
4104:
1.70 brouard 4105: dateprev1=anprev1+(mprev1-1)/12.+(jprev1-1)/365.;
4106: dateprev2=anprev2+(mprev2-1)/12.+(jprev2-1)/365.;
1.53 brouard 4107:
4108: fscanf(ficpar,"pop_based=%d\n",&popbased);
4109: fprintf(ficparo,"pop_based=%d\n",popbased);
4110: fprintf(ficres,"pop_based=%d\n",popbased);
4111:
4112: while((c=getc(ficpar))=='#' && c!= EOF){
4113: ungetc(c,ficpar);
4114: fgets(line, MAXLINE, ficpar);
4115: puts(line);
4116: fputs(line,ficparo);
4117: }
4118: ungetc(c,ficpar);
4119:
1.69 brouard 4120: 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);
1.70 brouard 4121: 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);
1.71 brouard 4122: printf("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);
4123: fprintf(ficlog,"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);
4124: fprintf(ficres,"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);
1.69 brouard 4125: /* day and month of proj2 are not used but only year anproj2.*/
1.53 brouard 4126:
1.59 brouard 4127: while((c=getc(ficpar))=='#' && c!= EOF){
1.53 brouard 4128: ungetc(c,ficpar);
4129: fgets(line, MAXLINE, ficpar);
4130: puts(line);
4131: fputs(line,ficparo);
4132: }
4133: ungetc(c,ficpar);
4134:
4135: fscanf(ficpar,"popforecast=%d popfile=%s popfiledate=%lf/%lf/%lf last-popfiledate=%lf/%lf/%lf\n",&popforecast,popfile,&jpyram,&mpyram,&anpyram,&jpyram1,&mpyram1,&anpyram1);
4136: fprintf(ficparo,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);
4137: fprintf(ficres,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);
4138:
1.74 brouard 4139: probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
1.59 brouard 4140: freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);
1.58 lievre 4141:
1.59 brouard 4142: /*------------ gnuplot -------------*/
4143: strcpy(optionfilegnuplot,optionfilefiname);
4144: strcat(optionfilegnuplot,".gp");
4145: if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {
4146: printf("Problem with file %s",optionfilegnuplot);
4147: }
4148: else{
4149: fprintf(ficgp,"\n# %s\n", version);
4150: fprintf(ficgp,"# %s\n", optionfilegnuplot);
4151: fprintf(ficgp,"set missing 'NaNq'\n");
4152: }
4153: fclose(ficgp);
4154: printinggnuplot(fileres, ageminpar,agemaxpar,fage, pathc,p);
4155: /*--------- index.htm --------*/
1.53 brouard 4156:
4157: strcpy(optionfilehtm,optionfile);
4158: strcat(optionfilehtm,".htm");
4159: if((fichtm=fopen(optionfilehtm,"w"))==NULL) {
4160: printf("Problem with %s \n",optionfilehtm), exit(0);
4161: }
4162:
4163: fprintf(fichtm,"<body> <font size=\"2\">%s </font> <hr size=\"2\" color=\"#EC5E5E\"> \n
4164: Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n
4165: \n
4166: Total number of observations=%d <br>\n
1.77 brouard 4167: Youngest age at first (selected) pass %.2f, oldest age %.2f<br>\n
1.53 brouard 4168: Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n
4169: <hr size=\"2\" color=\"#EC5E5E\">
4170: <ul><li><h4>Parameter files</h4>\n
4171: - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n
4172: - Log file of the run: <a href=\"%s\">%s</a><br>\n
1.76 brouard 4173: - Gnuplot file name: <a href=\"%s\">%s</a></ul>\n",version,title,datafile,firstpass,lastpass,stepm, weightopt,model,imx,agemin,agemax,jmin,jmax,jmean,fileres,fileres,filelog,filelog,optionfilegnuplot,optionfilegnuplot);
1.74 brouard 4174: fclose(fichtm);
1.53 brouard 4175:
1.59 brouard 4176: 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 4177:
1.59 brouard 4178: /*------------ free_vector -------------*/
4179: chdir(path);
1.53 brouard 4180:
1.59 brouard 4181: free_ivector(wav,1,imx);
4182: free_imatrix(dh,1,lastpass-firstpass+1,1,imx);
4183: free_imatrix(bh,1,lastpass-firstpass+1,1,imx);
4184: free_imatrix(mw,1,lastpass-firstpass+1,1,imx);
4185: free_ivector(num,1,n);
4186: free_vector(agedc,1,n);
1.65 lievre 4187: /*free_matrix(covar,0,NCOVMAX,1,n);*/
1.59 brouard 4188: /*free_matrix(covar,1,NCOVMAX,1,n);*/
4189: fclose(ficparo);
4190: fclose(ficres);
1.53 brouard 4191:
4192:
1.54 brouard 4193: /*--------------- Prevalence limit (stable prevalence) --------------*/
1.53 brouard 4194:
4195: strcpy(filerespl,"pl");
4196: strcat(filerespl,fileres);
4197: if((ficrespl=fopen(filerespl,"w"))==NULL) {
1.54 brouard 4198: printf("Problem with stable prevalence resultfile: %s\n", filerespl);goto end;
4199: fprintf(ficlog,"Problem with stable prevalence resultfile: %s\n", filerespl);goto end;
1.53 brouard 4200: }
1.54 brouard 4201: printf("Computing stable prevalence: result on file '%s' \n", filerespl);
4202: fprintf(ficlog,"Computing stable prevalence: result on file '%s' \n", filerespl);
4203: fprintf(ficrespl,"#Stable prevalence \n");
1.53 brouard 4204: fprintf(ficrespl,"#Age ");
4205: for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);
4206: fprintf(ficrespl,"\n");
4207:
4208: prlim=matrix(1,nlstate,1,nlstate);
1.59 brouard 4209:
1.53 brouard 4210: agebase=ageminpar;
4211: agelim=agemaxpar;
4212: ftolpl=1.e-10;
4213: i1=cptcoveff;
4214: if (cptcovn < 1){i1=1;}
4215:
1.59 brouard 4216: for(cptcov=1,k=0;cptcov<=i1;cptcov++){
1.53 brouard 4217: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
1.59 brouard 4218: k=k+1;
4219: /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/
4220: fprintf(ficrespl,"\n#******");
4221: printf("\n#******");
4222: fprintf(ficlog,"\n#******");
4223: for(j=1;j<=cptcoveff;j++) {
4224: fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
4225: printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
4226: fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
4227: }
4228: fprintf(ficrespl,"******\n");
4229: printf("******\n");
4230: fprintf(ficlog,"******\n");
1.53 brouard 4231:
1.59 brouard 4232: for (age=agebase; age<=agelim; age++){
4233: prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
1.69 brouard 4234: fprintf(ficrespl,"%.0f ",age );
4235: for(j=1;j<=cptcoveff;j++)
4236: fprintf(ficrespl,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
1.59 brouard 4237: for(i=1; i<=nlstate;i++)
1.53 brouard 4238: fprintf(ficrespl," %.5f", prlim[i][i]);
1.59 brouard 4239: fprintf(ficrespl,"\n");
1.53 brouard 4240: }
4241: }
1.59 brouard 4242: }
1.53 brouard 4243: fclose(ficrespl);
4244:
4245: /*------------- h Pij x at various ages ------------*/
4246:
4247: strcpy(filerespij,"pij"); strcat(filerespij,fileres);
4248: if((ficrespij=fopen(filerespij,"w"))==NULL) {
4249: printf("Problem with Pij resultfile: %s\n", filerespij);goto end;
4250: fprintf(ficlog,"Problem with Pij resultfile: %s\n", filerespij);goto end;
4251: }
4252: printf("Computing pij: result on file '%s' \n", filerespij);
4253: fprintf(ficlog,"Computing pij: result on file '%s' \n", filerespij);
4254:
4255: stepsize=(int) (stepm+YEARM-1)/YEARM;
4256: /*if (stepm<=24) stepsize=2;*/
4257:
4258: agelim=AGESUP;
4259: hstepm=stepsize*YEARM; /* Every year of age */
4260: hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */
4261:
4262: /* hstepm=1; aff par mois*/
4263:
1.70 brouard 4264: fprintf(ficrespij,"#****** h Pij x Probability to be in state j at age x+h being in i at x ");
1.59 brouard 4265: for(cptcov=1,k=0;cptcov<=i1;cptcov++){
1.53 brouard 4266: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
4267: k=k+1;
1.59 brouard 4268: fprintf(ficrespij,"\n#****** ");
4269: for(j=1;j<=cptcoveff;j++)
4270: fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
4271: fprintf(ficrespij,"******\n");
1.53 brouard 4272:
1.59 brouard 4273: for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */
4274: nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
4275: nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
4276:
4277: /* nhstepm=nhstepm*YEARM; aff par mois*/
4278:
4279: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4280: oldm=oldms;savm=savms;
4281: hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
1.70 brouard 4282: fprintf(ficrespij,"# Cov Agex agex+h hpijx with i,j=");
1.59 brouard 4283: for(i=1; i<=nlstate;i++)
4284: for(j=1; j<=nlstate+ndeath;j++)
4285: fprintf(ficrespij," %1d-%1d",i,j);
4286: fprintf(ficrespij,"\n");
4287: for (h=0; h<=nhstepm; h++){
1.70 brouard 4288: fprintf(ficrespij,"%d %3.f %3.f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );
1.53 brouard 4289: for(i=1; i<=nlstate;i++)
4290: for(j=1; j<=nlstate+ndeath;j++)
1.59 brouard 4291: fprintf(ficrespij," %.5f", p3mat[i][j][h]);
1.53 brouard 4292: fprintf(ficrespij,"\n");
4293: }
1.59 brouard 4294: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4295: fprintf(ficrespij,"\n");
4296: }
1.53 brouard 4297: }
4298: }
4299:
1.74 brouard 4300: varprob(optionfilefiname, matcov, p, delti, nlstate, bage, fage,k,Tvar,nbcode, ncodemax);
1.53 brouard 4301:
4302: fclose(ficrespij);
4303:
4304:
4305: /*---------- Forecasting ------------------*/
1.69 brouard 4306: /*if((stepm == 1) && (strcmp(model,".")==0)){*/
4307: if(prevfcast==1){
1.74 brouard 4308: /* if(stepm ==1){*/
1.70 brouard 4309: prevforecast(fileres, anproj1, mproj1, jproj1, agemin, agemax, dateprev1, dateprev2, mobilavproj, bage, fage, firstpass, lastpass, anproj2, p, cptcoveff);
1.74 brouard 4310: /* (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);*/
4311: /* } */
4312: /* else{ */
4313: /* erreur=108; */
4314: /* 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); */
4315: /* 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); */
4316: /* } */
1.69 brouard 4317: }
1.53 brouard 4318:
4319:
4320: /*---------- Health expectancies and variances ------------*/
4321:
4322: strcpy(filerest,"t");
4323: strcat(filerest,fileres);
4324: if((ficrest=fopen(filerest,"w"))==NULL) {
4325: printf("Problem with total LE resultfile: %s\n", filerest);goto end;
4326: fprintf(ficlog,"Problem with total LE resultfile: %s\n", filerest);goto end;
4327: }
4328: printf("Computing Total LEs with variances: file '%s' \n", filerest);
4329: fprintf(ficlog,"Computing Total LEs with variances: file '%s' \n", filerest);
4330:
4331:
4332: strcpy(filerese,"e");
4333: strcat(filerese,fileres);
4334: if((ficreseij=fopen(filerese,"w"))==NULL) {
4335: printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
4336: fprintf(ficlog,"Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
4337: }
4338: printf("Computing Health Expectancies: result on file '%s' \n", filerese);
4339: fprintf(ficlog,"Computing Health Expectancies: result on file '%s' \n", filerese);
1.68 lievre 4340:
1.53 brouard 4341: strcpy(fileresv,"v");
4342: strcat(fileresv,fileres);
4343: if((ficresvij=fopen(fileresv,"w"))==NULL) {
4344: printf("Problem with variance resultfile: %s\n", fileresv);exit(0);
4345: fprintf(ficlog,"Problem with variance resultfile: %s\n", fileresv);exit(0);
4346: }
4347: printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
4348: fprintf(ficlog,"Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
1.58 lievre 4349:
1.74 brouard 4350: /* Computes prevalence between agemin (i.e minimal age computed) and no more ageminpar */
4351: prevalence(agemin, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
4352: /* printf("ageminpar=%f, agemax=%f, s[lastpass][imx]=%d, agev[lastpass][imx]=%f, nlstate=%d, imx=%d, mint[lastpass][imx]=%f, anint[lastpass][imx]=%f,dateprev1=%f, dateprev2=%f, firstpass=%d, lastpass=%d\n",\
4353: ageminpar, agemax, s[lastpass][imx], agev[lastpass][imx], nlstate, imx, mint[lastpass][imx],anint[lastpass][imx], dateprev1, dateprev2, firstpass, lastpass);
4354: */
1.58 lievre 4355:
1.54 brouard 4356: if (mobilav!=0) {
1.53 brouard 4357: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
1.54 brouard 4358: if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
4359: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
4360: printf(" Error in movingaverage mobilav=%d\n",mobilav);
4361: }
1.53 brouard 4362: }
4363:
1.59 brouard 4364: for(cptcov=1,k=0;cptcov<=i1;cptcov++){
1.53 brouard 4365: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
4366: k=k+1;
4367: fprintf(ficrest,"\n#****** ");
4368: for(j=1;j<=cptcoveff;j++)
4369: fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
4370: fprintf(ficrest,"******\n");
4371:
4372: fprintf(ficreseij,"\n#****** ");
4373: for(j=1;j<=cptcoveff;j++)
4374: fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
4375: fprintf(ficreseij,"******\n");
4376:
4377: fprintf(ficresvij,"\n#****** ");
4378: for(j=1;j<=cptcoveff;j++)
4379: fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
4380: fprintf(ficresvij,"******\n");
4381:
4382: eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
4383: oldm=oldms;savm=savms;
4384: evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov);
4385:
4386: vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
4387: oldm=oldms;savm=savms;
4388: varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,0, mobilav);
4389: if(popbased==1){
4390: 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 4391: }
1.53 brouard 4392:
4393:
4394: fprintf(ficrest,"#Total LEs with variances: e.. (std) ");
4395: for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);
4396: fprintf(ficrest,"\n");
4397:
4398: epj=vector(1,nlstate+1);
4399: for(age=bage; age <=fage ;age++){
4400: prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
4401: if (popbased==1) {
1.54 brouard 4402: if(mobilav ==0){
1.53 brouard 4403: for(i=1; i<=nlstate;i++)
4404: prlim[i][i]=probs[(int)age][i][k];
1.54 brouard 4405: }else{ /* mobilav */
1.53 brouard 4406: for(i=1; i<=nlstate;i++)
4407: prlim[i][i]=mobaverage[(int)age][i][k];
4408: }
4409: }
4410:
4411: fprintf(ficrest," %4.0f",age);
4412: for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){
4413: for(i=1, epj[j]=0.;i <=nlstate;i++) {
4414: epj[j] += prlim[i][i]*eij[i][j][(int)age];
4415: /* printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/
4416: }
4417: epj[nlstate+1] +=epj[j];
4418: }
4419:
4420: for(i=1, vepp=0.;i <=nlstate;i++)
4421: for(j=1;j <=nlstate;j++)
4422: vepp += vareij[i][j][(int)age];
4423: fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));
4424: for(j=1;j <=nlstate;j++){
4425: fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));
4426: }
4427: fprintf(ficrest,"\n");
4428: }
1.59 brouard 4429: free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
4430: free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);
4431: free_vector(epj,1,nlstate+1);
1.53 brouard 4432: }
4433: }
1.59 brouard 4434: free_vector(weight,1,n);
4435: free_imatrix(Tvard,1,15,1,2);
4436: free_imatrix(s,1,maxwav+1,1,n);
4437: free_matrix(anint,1,maxwav,1,n);
4438: free_matrix(mint,1,maxwav,1,n);
4439: free_ivector(cod,1,n);
4440: free_ivector(tab,1,NCOVMAX);
1.53 brouard 4441: fclose(ficreseij);
4442: fclose(ficresvij);
4443: fclose(ficrest);
4444: fclose(ficpar);
4445:
1.54 brouard 4446: /*------- Variance of stable prevalence------*/
1.53 brouard 4447:
4448: strcpy(fileresvpl,"vpl");
4449: strcat(fileresvpl,fileres);
4450: if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {
1.54 brouard 4451: printf("Problem with variance of stable prevalence resultfile: %s\n", fileresvpl);
1.53 brouard 4452: exit(0);
4453: }
1.54 brouard 4454: printf("Computing Variance-covariance of stable prevalence: file '%s' \n", fileresvpl);
1.53 brouard 4455:
1.59 brouard 4456: for(cptcov=1,k=0;cptcov<=i1;cptcov++){
1.53 brouard 4457: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
4458: k=k+1;
4459: fprintf(ficresvpl,"\n#****** ");
4460: for(j=1;j<=cptcoveff;j++)
4461: fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
4462: fprintf(ficresvpl,"******\n");
4463:
4464: varpl=matrix(1,nlstate,(int) bage, (int) fage);
4465: oldm=oldms;savm=savms;
1.59 brouard 4466: varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);
4467: free_matrix(varpl,1,nlstate,(int) bage, (int)fage);
1.53 brouard 4468: }
1.59 brouard 4469: }
1.53 brouard 4470:
4471: fclose(ficresvpl);
4472:
4473: /*---------- End : free ----------------*/
4474: free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);
4475: free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);
4476: free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);
4477: free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);
1.65 lievre 4478:
4479: free_matrix(covar,0,NCOVMAX,1,n);
1.53 brouard 4480: free_matrix(matcov,1,npar,1,npar);
1.74 brouard 4481: /*free_vector(delti,1,npar);*/
4482: free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
1.53 brouard 4483: free_matrix(agev,1,maxwav,1,imx);
4484: free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
1.54 brouard 4485: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
1.74 brouard 4486: free_ma3x(probs,1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
4487:
1.59 brouard 4488: free_ivector(ncodemax,1,8);
4489: free_ivector(Tvar,1,15);
4490: free_ivector(Tprod,1,15);
4491: free_ivector(Tvaraff,1,15);
4492: free_ivector(Tage,1,15);
4493: free_ivector(Tcode,1,100);
1.53 brouard 4494:
1.74 brouard 4495: /* fclose(fichtm);*/
4496: /* fclose(ficgp);*/ /* ALready done */
1.53 brouard 4497:
4498:
4499: if(erreur >0){
4500: printf("End of Imach with error or warning %d\n",erreur);
4501: fprintf(ficlog,"End of Imach with error or warning %d\n",erreur);
4502: }else{
4503: printf("End of Imach\n");
4504: fprintf(ficlog,"End of Imach\n");
4505: }
4506: printf("See log file on %s\n",filelog);
4507: fclose(ficlog);
4508: /* gettimeofday(&end_time, (struct timezone*)0);*/ /* after time */
4509:
4510: /* 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);*/
4511: /*printf("Total time was %d uSec.\n", total_usecs);*/
4512: /*------ End -----------*/
4513:
1.59 brouard 4514: end:
1.53 brouard 4515: #ifdef windows
4516: /* chdir(pathcd);*/
4517: #endif
4518: /*system("wgnuplot graph.plt");*/
4519: /*system("../gp37mgw/wgnuplot graph.plt");*/
4520: /*system("cd ../gp37mgw");*/
4521: /* system("..\\gp37mgw\\wgnuplot graph.plt");*/
1.59 brouard 4522: strcpy(plotcmd,GNUPLOTPROGRAM);
4523: strcat(plotcmd," ");
4524: strcat(plotcmd,optionfilegnuplot);
1.75 brouard 4525: printf("Starting graphs with: %s",plotcmd);fflush(stdout);
1.59 brouard 4526: system(plotcmd);
1.75 brouard 4527: printf(" Wait...");
1.53 brouard 4528:
1.54 brouard 4529: /*#ifdef windows*/
1.53 brouard 4530: while (z[0] != 'q') {
4531: /* chdir(path); */
4532: printf("\nType e to edit output files, g to graph again, c to start again, and q for exiting: ");
4533: scanf("%s",z);
4534: if (z[0] == 'c') system("./imach");
4535: else if (z[0] == 'e') system(optionfilehtm);
4536: else if (z[0] == 'g') system(plotcmd);
4537: else if (z[0] == 'q') exit(0);
4538: }
1.54 brouard 4539: /*#endif */
1.53 brouard 4540: }
4541:
4542:
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