Annotation of imach096d/src/imach.c, revision 1.83
1.83 ! lievre 1: /* $Id: imach.c,v 1.82 2003/06/05 15:57:20 brouard Exp $
! 2: $State: Exp $
! 3: $Log: imach.c,v $
! 4: Revision 1.82 2003/06/05 15:57:20 brouard
! 5: Add log in imach.c and fullversion number is now printed.
! 6:
1.82 brouard 7: */
8: /*
1.53 brouard 9: Interpolated Markov Chain
10:
11: Short summary of the programme:
12:
13: This program computes Healthy Life Expectancies from
14: cross-longitudinal data. Cross-longitudinal data consist in: -1- a
15: first survey ("cross") where individuals from different ages are
16: interviewed on their health status or degree of disability (in the
17: case of a health survey which is our main interest) -2- at least a
18: second wave of interviews ("longitudinal") which measure each change
19: (if any) in individual health status. Health expectancies are
20: computed from the time spent in each health state according to a
21: model. More health states you consider, more time is necessary to reach the
22: Maximum Likelihood of the parameters involved in the model. The
23: simplest model is the multinomial logistic model where pij is the
24: probability to be observed in state j at the second wave
25: conditional to be observed in state i at the first wave. Therefore
26: the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where
27: 'age' is age and 'sex' is a covariate. If you want to have a more
28: complex model than "constant and age", you should modify the program
29: where the markup *Covariates have to be included here again* invites
30: you to do it. More covariates you add, slower the
31: convergence.
32:
33: The advantage of this computer programme, compared to a simple
34: multinomial logistic model, is clear when the delay between waves is not
35: identical for each individual. Also, if a individual missed an
36: intermediate interview, the information is lost, but taken into
37: account using an interpolation or extrapolation.
38:
39: hPijx is the probability to be observed in state i at age x+h
40: conditional to the observed state i at age x. The delay 'h' can be
41: split into an exact number (nh*stepm) of unobserved intermediate
1.66 brouard 42: states. This elementary transition (by month, quarter,
43: semester or year) is modelled as a multinomial logistic. The hPx
1.53 brouard 44: matrix is simply the matrix product of nh*stepm elementary matrices
45: and the contribution of each individual to the likelihood is simply
46: hPijx.
47:
48: Also this programme outputs the covariance matrix of the parameters but also
1.54 brouard 49: of the life expectancies. It also computes the stable prevalence.
1.53 brouard 50:
51: Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).
52: Institut national d'études démographiques, Paris.
53: This software have been partly granted by Euro-REVES, a concerted action
54: from the European Union.
55: It is copyrighted identically to a GNU software product, ie programme and
56: software can be distributed freely for non commercial use. Latest version
57: can be accessed at http://euroreves.ined.fr/imach .
1.74 brouard 58:
59: Help to debug: LD_PRELOAD=/usr/local/lib/libnjamd.so ./imach foo.imach
60: or better on gdb : set env LD_PRELOAD=/usr/local/lib/libnjamd.so
61:
1.53 brouard 62: **********************************************************************/
1.74 brouard 63: /*
64: main
65: read parameterfile
66: read datafile
67: concatwav
68: if (mle >= 1)
69: mlikeli
70: print results files
71: if mle==1
72: computes hessian
73: read end of parameter file: agemin, agemax, bage, fage, estepm
74: begin-prev-date,...
75: open gnuplot file
76: open html file
77: stable prevalence
78: for age prevalim()
79: h Pij x
80: variance of p varprob
81: forecasting if prevfcast==1 prevforecast call prevalence()
82: health expectancies
83: Variance-covariance of DFLE
84: prevalence()
85: movingaverage()
86: varevsij()
87: if popbased==1 varevsij(,popbased)
88: total life expectancies
89: Variance of stable prevalence
90: end
91: */
92:
93:
94:
1.53 brouard 95:
96: #include <math.h>
97: #include <stdio.h>
98: #include <stdlib.h>
99: #include <unistd.h>
100:
101: #define MAXLINE 256
102: #define GNUPLOTPROGRAM "gnuplot"
103: /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
104: #define FILENAMELENGTH 80
105: /*#define DEBUG*/
1.55 lievre 106: #define windows
1.53 brouard 107: #define GLOCK_ERROR_NOPATH -1 /* empty path */
108: #define GLOCK_ERROR_GETCWD -2 /* cannot get cwd */
109:
110: #define MAXPARM 30 /* Maximum number of parameters for the optimization */
111: #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */
112:
113: #define NINTERVMAX 8
114: #define NLSTATEMAX 8 /* Maximum number of live states (for func) */
115: #define NDEATHMAX 8 /* Maximum number of dead states (for func) */
116: #define NCOVMAX 8 /* Maximum number of covariates */
117: #define MAXN 20000
118: #define YEARM 12. /* Number of months per year */
119: #define AGESUP 130
120: #define AGEBASE 40
121: #ifdef windows
122: #define DIRSEPARATOR '\\'
123: #define ODIRSEPARATOR '/'
124: #else
125: #define DIRSEPARATOR '/'
126: #define ODIRSEPARATOR '\\'
127: #endif
128:
1.83 ! lievre 129: /* $Id: imach.c,v 1.82 2003/06/05 15:57:20 brouard Exp $ */
1.81 brouard 130: /* $State: Exp $ */
1.80 brouard 131:
1.82 brouard 132: char version[]="Imach version 0.95a1, June 2003, INED-EUROREVES ";
1.83 ! lievre 133: char fullversion[]="$Revision: 1.82 $ $Date: 2003/06/05 15:57:20 $";
1.53 brouard 134: int erreur; /* Error number */
135: int nvar;
136: int cptcovn=0, cptcovage=0, cptcoveff=0,cptcov;
137: int npar=NPARMAX;
138: int nlstate=2; /* Number of live states */
139: int ndeath=1; /* Number of dead states */
140: int ncovmodel, ncovcol; /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
141: int popbased=0;
142:
143: int *wav; /* Number of waves for this individuual 0 is possible */
144: int maxwav; /* Maxim number of waves */
145: int jmin, jmax; /* min, max spacing between 2 waves */
146: int mle, weightopt;
147: int **mw; /* mw[mi][i] is number of the mi wave for this individual */
148: int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
1.59 brouard 149: int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between
150: * wave mi and wave mi+1 is not an exact multiple of stepm. */
1.53 brouard 151: double jmean; /* Mean space between 2 waves */
152: double **oldm, **newm, **savm; /* Working pointers to matrices */
153: double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
154: FILE *fic,*ficpar, *ficparo,*ficres, *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
1.76 brouard 155: FILE *ficlog, *ficrespow;
1.53 brouard 156: FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
157: FILE *ficresprobmorprev;
158: FILE *fichtm; /* Html File */
159: FILE *ficreseij;
160: char filerese[FILENAMELENGTH];
161: FILE *ficresvij;
162: char fileresv[FILENAMELENGTH];
163: FILE *ficresvpl;
164: char fileresvpl[FILENAMELENGTH];
165: char title[MAXLINE];
166: char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH], filerespl[FILENAMELENGTH];
167: char optionfilext[10], optionfilefiname[FILENAMELENGTH], plotcmd[FILENAMELENGTH];
168:
169: char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
170: char filelog[FILENAMELENGTH]; /* Log file */
171: char filerest[FILENAMELENGTH];
172: char fileregp[FILENAMELENGTH];
173: char popfile[FILENAMELENGTH];
174:
175: char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH];
176:
177: #define NR_END 1
178: #define FREE_ARG char*
179: #define FTOL 1.0e-10
180:
181: #define NRANSI
182: #define ITMAX 200
183:
184: #define TOL 2.0e-4
185:
186: #define CGOLD 0.3819660
187: #define ZEPS 1.0e-10
188: #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);
189:
190: #define GOLD 1.618034
191: #define GLIMIT 100.0
192: #define TINY 1.0e-20
193:
194: static double maxarg1,maxarg2;
195: #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
196: #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
197:
198: #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
199: #define rint(a) floor(a+0.5)
200:
201: static double sqrarg;
202: #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
203: #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}
204:
205: int imx;
206: int stepm;
207: /* Stepm, step in month: minimum step interpolation*/
208:
209: int estepm;
210: /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
211:
212: int m,nb;
213: int *num, firstpass=0, lastpass=4,*cod, *ncodemax, *Tage;
214: double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
1.55 lievre 215: double **pmmij, ***probs;
1.53 brouard 216: double dateintmean=0;
217:
218: double *weight;
219: int **s; /* Status */
220: double *agedc, **covar, idx;
221: int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;
222:
223: double ftol=FTOL; /* Tolerance for computing Max Likelihood */
224: double ftolhess; /* Tolerance for computing hessian */
225:
226: /**************** split *************************/
227: static int split( char *path, char *dirc, char *name, char *ext, char *finame )
228: {
1.59 brouard 229: char *ss; /* pointer */
230: int l1, l2; /* length counters */
1.53 brouard 231:
1.59 brouard 232: l1 = strlen(path ); /* length of path */
233: if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
234: ss= strrchr( path, DIRSEPARATOR ); /* find last / */
235: if ( ss == NULL ) { /* no directory, so use current */
236: /*if(strrchr(path, ODIRSEPARATOR )==NULL)
237: printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
1.74 brouard 238: /* get current working directory */
239: /* extern char* getcwd ( char *buf , int len);*/
1.59 brouard 240: if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {
241: return( GLOCK_ERROR_GETCWD );
242: }
243: strcpy( name, path ); /* we've got it */
244: } else { /* strip direcotry from path */
245: ss++; /* after this, the filename */
246: l2 = strlen( ss ); /* length of filename */
247: if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
248: strcpy( name, ss ); /* save file name */
249: strncpy( dirc, path, l1 - l2 ); /* now the directory */
250: dirc[l1-l2] = 0; /* add zero */
251: }
252: l1 = strlen( dirc ); /* length of directory */
1.53 brouard 253: #ifdef windows
1.59 brouard 254: if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; }
1.53 brouard 255: #else
1.59 brouard 256: if ( dirc[l1-1] != '/' ) { dirc[l1] = '/'; dirc[l1+1] = 0; }
1.53 brouard 257: #endif
1.59 brouard 258: ss = strrchr( name, '.' ); /* find last / */
259: ss++;
260: strcpy(ext,ss); /* save extension */
261: l1= strlen( name);
262: l2= strlen(ss)+1;
263: strncpy( finame, name, l1-l2);
264: finame[l1-l2]= 0;
265: return( 0 ); /* we're done */
1.53 brouard 266: }
267:
268:
269: /******************************************/
270:
271: void replace(char *s, char*t)
272: {
273: int i;
274: int lg=20;
275: i=0;
276: lg=strlen(t);
277: for(i=0; i<= lg; i++) {
278: (s[i] = t[i]);
279: if (t[i]== '\\') s[i]='/';
280: }
281: }
282:
283: int nbocc(char *s, char occ)
284: {
285: int i,j=0;
286: int lg=20;
287: i=0;
288: lg=strlen(s);
289: for(i=0; i<= lg; i++) {
290: if (s[i] == occ ) j++;
291: }
292: return j;
293: }
294:
295: void cutv(char *u,char *v, char*t, char occ)
296: {
297: /* cuts string t into u and v where u is ended by char occ excluding it
298: and v is after occ excluding it too : ex cutv(u,v,"abcdef2ghi2j",2)
299: gives u="abcedf" and v="ghi2j" */
300: int i,lg,j,p=0;
301: i=0;
302: for(j=0; j<=strlen(t)-1; j++) {
303: if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;
304: }
305:
306: lg=strlen(t);
307: for(j=0; j<p; j++) {
308: (u[j] = t[j]);
309: }
310: u[p]='\0';
311:
312: for(j=0; j<= lg; j++) {
313: if (j>=(p+1))(v[j-p-1] = t[j]);
314: }
315: }
316:
317: /********************** nrerror ********************/
318:
319: void nrerror(char error_text[])
320: {
321: fprintf(stderr,"ERREUR ...\n");
322: fprintf(stderr,"%s\n",error_text);
1.59 brouard 323: exit(EXIT_FAILURE);
1.53 brouard 324: }
325: /*********************** vector *******************/
326: double *vector(int nl, int nh)
327: {
328: double *v;
329: v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
330: if (!v) nrerror("allocation failure in vector");
331: return v-nl+NR_END;
332: }
333:
334: /************************ free vector ******************/
335: void free_vector(double*v, int nl, int nh)
336: {
337: free((FREE_ARG)(v+nl-NR_END));
338: }
339:
340: /************************ivector *******************************/
1.76 brouard 341: char *cvector(long nl,long nh)
342: {
343: char *v;
344: v=(char *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(char)));
345: if (!v) nrerror("allocation failure in cvector");
346: return v-nl+NR_END;
347: }
348:
349: /******************free ivector **************************/
350: void free_cvector(char *v, long nl, long nh)
351: {
352: free((FREE_ARG)(v+nl-NR_END));
353: }
354:
355: /************************ivector *******************************/
1.53 brouard 356: int *ivector(long nl,long nh)
357: {
358: int *v;
359: v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
360: if (!v) nrerror("allocation failure in ivector");
361: return v-nl+NR_END;
362: }
363:
364: /******************free ivector **************************/
365: void free_ivector(int *v, long nl, long nh)
366: {
367: free((FREE_ARG)(v+nl-NR_END));
368: }
369:
370: /******************* imatrix *******************************/
371: int **imatrix(long nrl, long nrh, long ncl, long nch)
372: /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */
373: {
374: long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;
375: int **m;
376:
377: /* allocate pointers to rows */
378: m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));
379: if (!m) nrerror("allocation failure 1 in matrix()");
380: m += NR_END;
381: m -= nrl;
382:
383:
384: /* allocate rows and set pointers to them */
385: m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));
386: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
387: m[nrl] += NR_END;
388: m[nrl] -= ncl;
389:
390: for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;
391:
392: /* return pointer to array of pointers to rows */
393: return m;
394: }
395:
396: /****************** free_imatrix *************************/
397: void free_imatrix(m,nrl,nrh,ncl,nch)
398: int **m;
399: long nch,ncl,nrh,nrl;
400: /* free an int matrix allocated by imatrix() */
401: {
402: free((FREE_ARG) (m[nrl]+ncl-NR_END));
403: free((FREE_ARG) (m+nrl-NR_END));
404: }
405:
406: /******************* matrix *******************************/
407: double **matrix(long nrl, long nrh, long ncl, long nch)
408: {
409: long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
410: double **m;
411:
412: m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
413: if (!m) nrerror("allocation failure 1 in matrix()");
414: m += NR_END;
415: m -= nrl;
416:
417: m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
418: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
419: m[nrl] += NR_END;
420: m[nrl] -= ncl;
421:
422: for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
423: return m;
1.74 brouard 424: /* print *(*(m+1)+70) ou print m[1][70]; print m+1 or print &(m[1])
425: */
1.53 brouard 426: }
427:
428: /*************************free matrix ************************/
429: void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
430: {
431: free((FREE_ARG)(m[nrl]+ncl-NR_END));
432: free((FREE_ARG)(m+nrl-NR_END));
433: }
434:
435: /******************* ma3x *******************************/
436: double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
437: {
438: long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
439: double ***m;
440:
441: m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
442: if (!m) nrerror("allocation failure 1 in matrix()");
443: m += NR_END;
444: m -= nrl;
445:
446: m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
447: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
448: m[nrl] += NR_END;
449: m[nrl] -= ncl;
450:
451: for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
452:
453: m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
454: if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
455: m[nrl][ncl] += NR_END;
456: m[nrl][ncl] -= nll;
457: for (j=ncl+1; j<=nch; j++)
458: m[nrl][j]=m[nrl][j-1]+nlay;
459:
460: for (i=nrl+1; i<=nrh; i++) {
461: m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
462: for (j=ncl+1; j<=nch; j++)
463: m[i][j]=m[i][j-1]+nlay;
464: }
1.74 brouard 465: return m;
466: /* gdb: p *(m+1) <=> p m[1] and p (m+1) <=> p (m+1) <=> p &(m[1])
467: &(m[i][j][k]) <=> *((*(m+i) + j)+k)
468: */
1.53 brouard 469: }
470:
471: /*************************free ma3x ************************/
472: void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
473: {
474: free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
475: free((FREE_ARG)(m[nrl]+ncl-NR_END));
476: free((FREE_ARG)(m+nrl-NR_END));
477: }
478:
479: /***************** f1dim *************************/
480: extern int ncom;
481: extern double *pcom,*xicom;
482: extern double (*nrfunc)(double []);
483:
484: double f1dim(double x)
485: {
486: int j;
487: double f;
488: double *xt;
489:
490: xt=vector(1,ncom);
491: for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];
492: f=(*nrfunc)(xt);
493: free_vector(xt,1,ncom);
494: return f;
495: }
496:
497: /*****************brent *************************/
498: double brent(double ax, double bx, double cx, double (*f)(double), double tol, double *xmin)
499: {
500: int iter;
501: double a,b,d,etemp;
502: double fu,fv,fw,fx;
503: double ftemp;
504: double p,q,r,tol1,tol2,u,v,w,x,xm;
505: double e=0.0;
506:
507: a=(ax < cx ? ax : cx);
508: b=(ax > cx ? ax : cx);
509: x=w=v=bx;
510: fw=fv=fx=(*f)(x);
511: for (iter=1;iter<=ITMAX;iter++) {
512: xm=0.5*(a+b);
513: tol2=2.0*(tol1=tol*fabs(x)+ZEPS);
514: /* if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
515: printf(".");fflush(stdout);
516: fprintf(ficlog,".");fflush(ficlog);
517: #ifdef DEBUG
518: 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);
519: 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);
520: /* if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
521: #endif
522: if (fabs(x-xm) <= (tol2-0.5*(b-a))){
523: *xmin=x;
524: return fx;
525: }
526: ftemp=fu;
527: if (fabs(e) > tol1) {
528: r=(x-w)*(fx-fv);
529: q=(x-v)*(fx-fw);
530: p=(x-v)*q-(x-w)*r;
531: q=2.0*(q-r);
532: if (q > 0.0) p = -p;
533: q=fabs(q);
534: etemp=e;
535: e=d;
536: if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))
537: d=CGOLD*(e=(x >= xm ? a-x : b-x));
538: else {
539: d=p/q;
540: u=x+d;
541: if (u-a < tol2 || b-u < tol2)
542: d=SIGN(tol1,xm-x);
543: }
544: } else {
545: d=CGOLD*(e=(x >= xm ? a-x : b-x));
546: }
547: u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));
548: fu=(*f)(u);
549: if (fu <= fx) {
550: if (u >= x) a=x; else b=x;
551: SHFT(v,w,x,u)
552: SHFT(fv,fw,fx,fu)
553: } else {
554: if (u < x) a=u; else b=u;
555: if (fu <= fw || w == x) {
556: v=w;
557: w=u;
558: fv=fw;
559: fw=fu;
560: } else if (fu <= fv || v == x || v == w) {
561: v=u;
562: fv=fu;
563: }
564: }
565: }
566: nrerror("Too many iterations in brent");
567: *xmin=x;
568: return fx;
569: }
570:
571: /****************** mnbrak ***********************/
572:
573: void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,
574: double (*func)(double))
575: {
576: double ulim,u,r,q, dum;
577: double fu;
578:
579: *fa=(*func)(*ax);
580: *fb=(*func)(*bx);
581: if (*fb > *fa) {
582: SHFT(dum,*ax,*bx,dum)
583: SHFT(dum,*fb,*fa,dum)
584: }
585: *cx=(*bx)+GOLD*(*bx-*ax);
586: *fc=(*func)(*cx);
587: while (*fb > *fc) {
588: r=(*bx-*ax)*(*fb-*fc);
589: q=(*bx-*cx)*(*fb-*fa);
590: u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/
591: (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r));
592: ulim=(*bx)+GLIMIT*(*cx-*bx);
593: if ((*bx-u)*(u-*cx) > 0.0) {
594: fu=(*func)(u);
595: } else if ((*cx-u)*(u-ulim) > 0.0) {
596: fu=(*func)(u);
597: if (fu < *fc) {
598: SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))
599: SHFT(*fb,*fc,fu,(*func)(u))
600: }
601: } else if ((u-ulim)*(ulim-*cx) >= 0.0) {
602: u=ulim;
603: fu=(*func)(u);
604: } else {
605: u=(*cx)+GOLD*(*cx-*bx);
606: fu=(*func)(u);
607: }
608: SHFT(*ax,*bx,*cx,u)
609: SHFT(*fa,*fb,*fc,fu)
610: }
611: }
612:
613: /*************** linmin ************************/
614:
615: int ncom;
616: double *pcom,*xicom;
617: double (*nrfunc)(double []);
618:
619: void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))
620: {
621: double brent(double ax, double bx, double cx,
622: double (*f)(double), double tol, double *xmin);
623: double f1dim(double x);
624: void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,
625: double *fc, double (*func)(double));
626: int j;
627: double xx,xmin,bx,ax;
628: double fx,fb,fa;
629:
630: ncom=n;
631: pcom=vector(1,n);
632: xicom=vector(1,n);
633: nrfunc=func;
634: for (j=1;j<=n;j++) {
635: pcom[j]=p[j];
636: xicom[j]=xi[j];
637: }
638: ax=0.0;
639: xx=1.0;
640: mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim);
641: *fret=brent(ax,xx,bx,f1dim,TOL,&xmin);
642: #ifdef DEBUG
643: printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
644: fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
645: #endif
646: for (j=1;j<=n;j++) {
647: xi[j] *= xmin;
648: p[j] += xi[j];
649: }
650: free_vector(xicom,1,n);
651: free_vector(pcom,1,n);
652: }
653:
654: /*************** powell ************************/
655: void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,
656: double (*func)(double []))
657: {
658: void linmin(double p[], double xi[], int n, double *fret,
659: double (*func)(double []));
660: int i,ibig,j;
661: double del,t,*pt,*ptt,*xit;
662: double fp,fptt;
663: double *xits;
664: pt=vector(1,n);
665: ptt=vector(1,n);
666: xit=vector(1,n);
667: xits=vector(1,n);
668: *fret=(*func)(p);
669: for (j=1;j<=n;j++) pt[j]=p[j];
670: for (*iter=1;;++(*iter)) {
671: fp=(*fret);
672: ibig=0;
673: del=0.0;
674: printf("\nPowell iter=%d -2*LL=%.12f",*iter,*fret);
675: fprintf(ficlog,"\nPowell iter=%d -2*LL=%.12f",*iter,*fret);
1.76 brouard 676: fprintf(ficrespow,"%d %.12f",*iter,*fret);
677: for (i=1;i<=n;i++) {
1.53 brouard 678: printf(" %d %.12f",i, p[i]);
1.76 brouard 679: fprintf(ficlog," %d %.12lf",i, p[i]);
680: fprintf(ficrespow," %.12lf", p[i]);
681: }
1.53 brouard 682: printf("\n");
683: fprintf(ficlog,"\n");
1.76 brouard 684: fprintf(ficrespow,"\n");
1.53 brouard 685: for (i=1;i<=n;i++) {
686: for (j=1;j<=n;j++) xit[j]=xi[j][i];
687: fptt=(*fret);
688: #ifdef DEBUG
689: printf("fret=%lf \n",*fret);
690: fprintf(ficlog,"fret=%lf \n",*fret);
691: #endif
692: printf("%d",i);fflush(stdout);
693: fprintf(ficlog,"%d",i);fflush(ficlog);
694: linmin(p,xit,n,fret,func);
695: if (fabs(fptt-(*fret)) > del) {
696: del=fabs(fptt-(*fret));
697: ibig=i;
698: }
699: #ifdef DEBUG
700: printf("%d %.12e",i,(*fret));
701: fprintf(ficlog,"%d %.12e",i,(*fret));
702: for (j=1;j<=n;j++) {
703: xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
704: printf(" x(%d)=%.12e",j,xit[j]);
705: fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
706: }
707: for(j=1;j<=n;j++) {
708: printf(" p=%.12e",p[j]);
709: fprintf(ficlog," p=%.12e",p[j]);
710: }
711: printf("\n");
712: fprintf(ficlog,"\n");
713: #endif
714: }
715: if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {
716: #ifdef DEBUG
717: int k[2],l;
718: k[0]=1;
719: k[1]=-1;
720: printf("Max: %.12e",(*func)(p));
721: fprintf(ficlog,"Max: %.12e",(*func)(p));
722: for (j=1;j<=n;j++) {
723: printf(" %.12e",p[j]);
724: fprintf(ficlog," %.12e",p[j]);
725: }
726: printf("\n");
727: fprintf(ficlog,"\n");
728: for(l=0;l<=1;l++) {
729: for (j=1;j<=n;j++) {
730: ptt[j]=p[j]+(p[j]-pt[j])*k[l];
731: printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
732: fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
733: }
734: printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
735: fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
736: }
737: #endif
738:
739:
740: free_vector(xit,1,n);
741: free_vector(xits,1,n);
742: free_vector(ptt,1,n);
743: free_vector(pt,1,n);
744: return;
745: }
746: if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");
747: for (j=1;j<=n;j++) {
748: ptt[j]=2.0*p[j]-pt[j];
749: xit[j]=p[j]-pt[j];
750: pt[j]=p[j];
751: }
752: fptt=(*func)(ptt);
753: if (fptt < fp) {
754: t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt);
755: if (t < 0.0) {
756: linmin(p,xit,n,fret,func);
757: for (j=1;j<=n;j++) {
758: xi[j][ibig]=xi[j][n];
759: xi[j][n]=xit[j];
760: }
761: #ifdef DEBUG
762: printf("Direction changed last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
763: fprintf(ficlog,"Direction changed last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
764: for(j=1;j<=n;j++){
765: printf(" %.12e",xit[j]);
766: fprintf(ficlog," %.12e",xit[j]);
767: }
768: printf("\n");
769: fprintf(ficlog,"\n");
770: #endif
1.54 brouard 771: }
1.53 brouard 772: }
773: }
774: }
775:
1.54 brouard 776: /**** Prevalence limit (stable prevalence) ****************/
1.53 brouard 777:
778: double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)
779: {
780: /* Computes the prevalence limit in each live state at age x by left multiplying the unit
781: matrix by transitions matrix until convergence is reached */
782:
783: int i, ii,j,k;
784: double min, max, maxmin, maxmax,sumnew=0.;
785: double **matprod2();
786: double **out, cov[NCOVMAX], **pmij();
787: double **newm;
788: double agefin, delaymax=50 ; /* Max number of years to converge */
789:
790: for (ii=1;ii<=nlstate+ndeath;ii++)
791: for (j=1;j<=nlstate+ndeath;j++){
792: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
793: }
794:
795: cov[1]=1.;
796:
797: /* Even if hstepm = 1, at least one multiplication by the unit matrix */
798: for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
799: newm=savm;
800: /* Covariates have to be included here again */
801: cov[2]=agefin;
802:
803: for (k=1; k<=cptcovn;k++) {
804: cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
805: /* 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]]);*/
806: }
807: for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
808: for (k=1; k<=cptcovprod;k++)
809: cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
810:
811: /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
812: /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
813: /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
814: out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);
815:
816: savm=oldm;
817: oldm=newm;
818: maxmax=0.;
819: for(j=1;j<=nlstate;j++){
820: min=1.;
821: max=0.;
822: for(i=1; i<=nlstate; i++) {
823: sumnew=0;
824: for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
825: prlim[i][j]= newm[i][j]/(1-sumnew);
826: max=FMAX(max,prlim[i][j]);
827: min=FMIN(min,prlim[i][j]);
828: }
829: maxmin=max-min;
830: maxmax=FMAX(maxmax,maxmin);
831: }
832: if(maxmax < ftolpl){
833: return prlim;
834: }
835: }
836: }
837:
838: /*************** transition probabilities ***************/
839:
840: double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
841: {
842: double s1, s2;
843: /*double t34;*/
844: int i,j,j1, nc, ii, jj;
845:
846: for(i=1; i<= nlstate; i++){
847: for(j=1; j<i;j++){
848: for (nc=1, s2=0.;nc <=ncovmodel; nc++){
849: /*s2 += param[i][j][nc]*cov[nc];*/
850: s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
851: /*printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2);*/
852: }
853: ps[i][j]=s2;
854: /*printf("s1=%.17e, s2=%.17e\n",s1,s2);*/
855: }
856: for(j=i+1; j<=nlstate+ndeath;j++){
857: for (nc=1, s2=0.;nc <=ncovmodel; nc++){
858: s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
859: /*printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2);*/
860: }
861: ps[i][j]=s2;
862: }
863: }
864: /*ps[3][2]=1;*/
865:
866: for(i=1; i<= nlstate; i++){
867: s1=0;
868: for(j=1; j<i; j++)
869: s1+=exp(ps[i][j]);
870: for(j=i+1; j<=nlstate+ndeath; j++)
871: s1+=exp(ps[i][j]);
872: ps[i][i]=1./(s1+1.);
873: for(j=1; j<i; j++)
874: ps[i][j]= exp(ps[i][j])*ps[i][i];
875: for(j=i+1; j<=nlstate+ndeath; j++)
876: ps[i][j]= exp(ps[i][j])*ps[i][i];
877: /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
878: } /* end i */
879:
880: for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
881: for(jj=1; jj<= nlstate+ndeath; jj++){
882: ps[ii][jj]=0;
883: ps[ii][ii]=1;
884: }
885: }
886:
887:
888: /* for(ii=1; ii<= nlstate+ndeath; ii++){
889: for(jj=1; jj<= nlstate+ndeath; jj++){
890: printf("%lf ",ps[ii][jj]);
891: }
892: printf("\n ");
893: }
894: printf("\n ");printf("%lf ",cov[2]);*/
895: /*
896: for(i=1; i<= npar; i++) printf("%f ",x[i]);
897: goto end;*/
898: return ps;
899: }
900:
901: /**************** Product of 2 matrices ******************/
902:
903: double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)
904: {
905: /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
906: b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
907: /* in, b, out are matrice of pointers which should have been initialized
908: before: only the contents of out is modified. The function returns
909: a pointer to pointers identical to out */
910: long i, j, k;
911: for(i=nrl; i<= nrh; i++)
912: for(k=ncolol; k<=ncoloh; k++)
913: for(j=ncl,out[i][k]=0.; j<=nch; j++)
914: out[i][k] +=in[i][j]*b[j][k];
915:
916: return out;
917: }
918:
919:
920: /************* Higher Matrix Product ***************/
921:
922: double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
923: {
1.66 brouard 924: /* Computes the transition matrix starting at age 'age' over
925: 'nhstepm*hstepm*stepm' months (i.e. until
926: age (in years) age+nhstepm*hstepm*stepm/12) by multiplying
927: nhstepm*hstepm matrices.
1.53 brouard 928: Output is stored in matrix po[i][j][h] for h every 'hstepm' step
1.66 brouard 929: (typically every 2 years instead of every month which is too big
930: for the memory).
1.53 brouard 931: Model is determined by parameters x and covariates have to be
932: included manually here.
933:
934: */
935:
936: int i, j, d, h, k;
937: double **out, cov[NCOVMAX];
938: double **newm;
939:
940: /* Hstepm could be zero and should return the unit matrix */
941: for (i=1;i<=nlstate+ndeath;i++)
942: for (j=1;j<=nlstate+ndeath;j++){
943: oldm[i][j]=(i==j ? 1.0 : 0.0);
944: po[i][j][0]=(i==j ? 1.0 : 0.0);
945: }
946: /* Even if hstepm = 1, at least one multiplication by the unit matrix */
947: for(h=1; h <=nhstepm; h++){
948: for(d=1; d <=hstepm; d++){
949: newm=savm;
950: /* Covariates have to be included here again */
951: cov[1]=1.;
952: cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
953: for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
954: for (k=1; k<=cptcovage;k++)
955: cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
956: for (k=1; k<=cptcovprod;k++)
957: cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
958:
959:
960: /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
961: /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
962: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,
963: pmij(pmmij,cov,ncovmodel,x,nlstate));
964: savm=oldm;
965: oldm=newm;
966: }
967: for(i=1; i<=nlstate+ndeath; i++)
968: for(j=1;j<=nlstate+ndeath;j++) {
969: po[i][j][h]=newm[i][j];
970: /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);
971: */
972: }
973: } /* end h */
974: return po;
975: }
976:
977:
978: /*************** log-likelihood *************/
979: double func( double *x)
980: {
981: int i, ii, j, k, mi, d, kk;
982: double l, ll[NLSTATEMAX], cov[NCOVMAX];
983: double **out;
984: double sw; /* Sum of weights */
985: double lli; /* Individual log likelihood */
1.59 brouard 986: int s1, s2;
1.68 lievre 987: double bbh, survp;
1.53 brouard 988: long ipmx;
989: /*extern weight */
990: /* We are differentiating ll according to initial status */
991: /* for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
992: /*for(i=1;i<imx;i++)
993: printf(" %d\n",s[4][i]);
994: */
995: cov[1]=1.;
996:
997: for(k=1; k<=nlstate; k++) ll[k]=0.;
1.61 brouard 998:
999: if(mle==1){
1000: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1001: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
1002: for(mi=1; mi<= wav[i]-1; mi++){
1003: for (ii=1;ii<=nlstate+ndeath;ii++)
1004: for (j=1;j<=nlstate+ndeath;j++){
1005: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1006: savm[ii][j]=(ii==j ? 1.0 : 0.0);
1007: }
1008: for(d=0; d<dh[mi][i]; d++){
1009: newm=savm;
1010: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
1011: for (kk=1; kk<=cptcovage;kk++) {
1012: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
1013: }
1014: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1015: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1016: savm=oldm;
1017: oldm=newm;
1018: } /* end mult */
1.53 brouard 1019:
1.61 brouard 1020: /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
1021: /* But now since version 0.9 we anticipate for bias and large stepm.
1022: * If stepm is larger than one month (smallest stepm) and if the exact delay
1023: * (in months) between two waves is not a multiple of stepm, we rounded to
1024: * the nearest (and in case of equal distance, to the lowest) interval but now
1025: * we keep into memory the bias bh[mi][i] and also the previous matrix product
1026: * (i.e to dh[mi][i]-1) saved in 'savm'. The we inter(extra)polate the
1027: * probability in order to take into account the bias as a fraction of the way
1028: * from savm to out if bh is neagtive or even beyond if bh is positive. bh varies
1029: * -stepm/2 to stepm/2 .
1030: * For stepm=1 the results are the same as for previous versions of Imach.
1031: * For stepm > 1 the results are less biased than in previous versions.
1032: */
1033: s1=s[mw[mi][i]][i];
1034: s2=s[mw[mi+1][i]][i];
1.64 lievre 1035: bbh=(double)bh[mi][i]/(double)stepm;
1036: /* bias is positive if real duration
1037: * is higher than the multiple of stepm and negative otherwise.
1038: */
1039: /* 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 1040: if( s2 > nlstate){
1041: /* i.e. if s2 is a death state and if the date of death is known then the contribution
1042: to the likelihood is the probability to die between last step unit time and current
1043: step unit time, which is also the differences between probability to die before dh
1044: and probability to die before dh-stepm .
1045: In version up to 0.92 likelihood was computed
1046: as if date of death was unknown. Death was treated as any other
1047: health state: the date of the interview describes the actual state
1048: and not the date of a change in health state. The former idea was
1049: to consider that at each interview the state was recorded
1050: (healthy, disable or death) and IMaCh was corrected; but when we
1051: introduced the exact date of death then we should have modified
1052: the contribution of an exact death to the likelihood. This new
1053: contribution is smaller and very dependent of the step unit
1054: stepm. It is no more the probability to die between last interview
1055: and month of death but the probability to survive from last
1056: interview up to one month before death multiplied by the
1057: probability to die within a month. Thanks to Chris
1058: Jackson for correcting this bug. Former versions increased
1059: mortality artificially. The bad side is that we add another loop
1060: which slows down the processing. The difference can be up to 10%
1061: lower mortality.
1062: */
1063: lli=log(out[s1][s2] - savm[s1][s2]);
1064: }else{
1065: lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
1066: /* 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 */
1067: }
1.64 lievre 1068: /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
1069: /*if(lli ==000.0)*/
1070: /*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 1071: ipmx +=1;
1.64 lievre 1072: sw += weight[i];
1073: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1074: } /* end of wave */
1075: } /* end of individual */
1076: } else if(mle==2){
1077: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1078: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
1079: for(mi=1; mi<= wav[i]-1; mi++){
1080: for (ii=1;ii<=nlstate+ndeath;ii++)
1081: for (j=1;j<=nlstate+ndeath;j++){
1082: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1083: savm[ii][j]=(ii==j ? 1.0 : 0.0);
1084: }
1085: for(d=0; d<=dh[mi][i]; d++){
1086: newm=savm;
1087: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
1088: for (kk=1; kk<=cptcovage;kk++) {
1089: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
1090: }
1091: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1092: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1093: savm=oldm;
1094: oldm=newm;
1095: } /* end mult */
1096:
1097: /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
1098: /* But now since version 0.9 we anticipate for bias and large stepm.
1099: * If stepm is larger than one month (smallest stepm) and if the exact delay
1100: * (in months) between two waves is not a multiple of stepm, we rounded to
1101: * the nearest (and in case of equal distance, to the lowest) interval but now
1102: * we keep into memory the bias bh[mi][i] and also the previous matrix product
1103: * (i.e to dh[mi][i]-1) saved in 'savm'. The we inter(extra)polate the
1104: * probability in order to take into account the bias as a fraction of the way
1105: * from savm to out if bh is neagtive or even beyond if bh is positive. bh varies
1106: * -stepm/2 to stepm/2 .
1107: * For stepm=1 the results are the same as for previous versions of Imach.
1108: * For stepm > 1 the results are less biased than in previous versions.
1109: */
1110: s1=s[mw[mi][i]][i];
1111: s2=s[mw[mi+1][i]][i];
1112: bbh=(double)bh[mi][i]/(double)stepm;
1113: /* bias is positive if real duration
1114: * is higher than the multiple of stepm and negative otherwise.
1115: */
1.63 lievre 1116: 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 1117: /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
1118: /*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 */
1119: /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
1120: /*if(lli ==000.0)*/
1121: /*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); */
1122: ipmx +=1;
1123: sw += weight[i];
1124: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1125: } /* end of wave */
1126: } /* end of individual */
1127: } else if(mle==3){ /* exponential inter-extrapolation */
1128: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1129: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
1130: for(mi=1; mi<= wav[i]-1; mi++){
1131: for (ii=1;ii<=nlstate+ndeath;ii++)
1132: for (j=1;j<=nlstate+ndeath;j++){
1133: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1134: savm[ii][j]=(ii==j ? 1.0 : 0.0);
1135: }
1136: for(d=0; d<dh[mi][i]; d++){
1137: newm=savm;
1138: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
1139: for (kk=1; kk<=cptcovage;kk++) {
1140: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
1141: }
1142: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1143: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1144: savm=oldm;
1145: oldm=newm;
1146: } /* end mult */
1147:
1148: /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
1149: /* But now since version 0.9 we anticipate for bias and large stepm.
1150: * If stepm is larger than one month (smallest stepm) and if the exact delay
1151: * (in months) between two waves is not a multiple of stepm, we rounded to
1152: * the nearest (and in case of equal distance, to the lowest) interval but now
1153: * we keep into memory the bias bh[mi][i] and also the previous matrix product
1154: * (i.e to dh[mi][i]-1) saved in 'savm'. The we inter(extra)polate the
1155: * probability in order to take into account the bias as a fraction of the way
1156: * from savm to out if bh is neagtive or even beyond if bh is positive. bh varies
1157: * -stepm/2 to stepm/2 .
1158: * For stepm=1 the results are the same as for previous versions of Imach.
1159: * For stepm > 1 the results are less biased than in previous versions.
1160: */
1161: s1=s[mw[mi][i]][i];
1162: s2=s[mw[mi+1][i]][i];
1163: bbh=(double)bh[mi][i]/(double)stepm;
1164: /* bias is positive if real duration
1165: * is higher than the multiple of stepm and negative otherwise.
1166: */
1167: /* 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 */
1168: 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 1169: /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
1170: /*if(lli ==000.0)*/
1171: /*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); */
1172: ipmx +=1;
1173: sw += weight[i];
1174: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1175: } /* end of wave */
1176: } /* end of individual */
1.64 lievre 1177: }else{ /* ml=4 no inter-extrapolation */
1.61 brouard 1178: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1179: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
1180: for(mi=1; mi<= wav[i]-1; mi++){
1181: for (ii=1;ii<=nlstate+ndeath;ii++)
1182: for (j=1;j<=nlstate+ndeath;j++){
1183: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1184: savm[ii][j]=(ii==j ? 1.0 : 0.0);
1185: }
1186: for(d=0; d<dh[mi][i]; d++){
1187: newm=savm;
1188: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
1189: for (kk=1; kk<=cptcovage;kk++) {
1190: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
1191: }
1192:
1193: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1194: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1195: savm=oldm;
1196: oldm=newm;
1197: } /* end mult */
1198:
1199: lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
1200: ipmx +=1;
1201: sw += weight[i];
1202: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1203: } /* end of wave */
1204: } /* end of individual */
1205: } /* End of if */
1.53 brouard 1206: for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
1207: /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
1208: l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
1209: return -l;
1210: }
1211:
1212:
1213: /*********** Maximum Likelihood Estimation ***************/
1214:
1215: void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
1216: {
1217: int i,j, iter;
1.74 brouard 1218: double **xi;
1.53 brouard 1219: double fret;
1.76 brouard 1220: char filerespow[FILENAMELENGTH];
1.53 brouard 1221: xi=matrix(1,npar,1,npar);
1222: for (i=1;i<=npar;i++)
1223: for (j=1;j<=npar;j++)
1224: xi[i][j]=(i==j ? 1.0 : 0.0);
1225: printf("Powell\n"); fprintf(ficlog,"Powell\n");
1.76 brouard 1226: strcpy(filerespow,"pow");
1227: strcat(filerespow,fileres);
1228: if((ficrespow=fopen(filerespow,"w"))==NULL) {
1229: printf("Problem with resultfile: %s\n", filerespow);
1230: fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
1231: }
1232: fprintf(ficrespow,"# Powell\n# iter -2*LL");
1233: for (i=1;i<=nlstate;i++)
1234: for(j=1;j<=nlstate+ndeath;j++)
1235: if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
1236: fprintf(ficrespow,"\n");
1.53 brouard 1237: powell(p,xi,npar,ftol,&iter,&fret,func);
1238:
1.76 brouard 1239: fclose(ficrespow);
1240: printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));
1.65 lievre 1241: fprintf(ficlog,"\n#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
1.53 brouard 1242: fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
1243:
1244: }
1245:
1246: /**** Computes Hessian and covariance matrix ***/
1247: void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
1248: {
1249: double **a,**y,*x,pd;
1250: double **hess;
1251: int i, j,jk;
1252: int *indx;
1253:
1254: double hessii(double p[], double delta, int theta, double delti[]);
1255: double hessij(double p[], double delti[], int i, int j);
1256: void lubksb(double **a, int npar, int *indx, double b[]) ;
1257: void ludcmp(double **a, int npar, int *indx, double *d) ;
1258:
1259: hess=matrix(1,npar,1,npar);
1260:
1261: printf("\nCalculation of the hessian matrix. Wait...\n");
1262: fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
1263: for (i=1;i<=npar;i++){
1264: printf("%d",i);fflush(stdout);
1265: fprintf(ficlog,"%d",i);fflush(ficlog);
1266: hess[i][i]=hessii(p,ftolhess,i,delti);
1267: /*printf(" %f ",p[i]);*/
1268: /*printf(" %lf ",hess[i][i]);*/
1269: }
1270:
1271: for (i=1;i<=npar;i++) {
1272: for (j=1;j<=npar;j++) {
1273: if (j>i) {
1274: printf(".%d%d",i,j);fflush(stdout);
1275: fprintf(ficlog,".%d%d",i,j);fflush(ficlog);
1276: hess[i][j]=hessij(p,delti,i,j);
1277: hess[j][i]=hess[i][j];
1278: /*printf(" %lf ",hess[i][j]);*/
1279: }
1280: }
1281: }
1282: printf("\n");
1283: fprintf(ficlog,"\n");
1284:
1285: printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
1286: fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
1287:
1288: a=matrix(1,npar,1,npar);
1289: y=matrix(1,npar,1,npar);
1290: x=vector(1,npar);
1291: indx=ivector(1,npar);
1292: for (i=1;i<=npar;i++)
1293: for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
1294: ludcmp(a,npar,indx,&pd);
1295:
1296: for (j=1;j<=npar;j++) {
1297: for (i=1;i<=npar;i++) x[i]=0;
1298: x[j]=1;
1299: lubksb(a,npar,indx,x);
1300: for (i=1;i<=npar;i++){
1301: matcov[i][j]=x[i];
1302: }
1303: }
1304:
1305: printf("\n#Hessian matrix#\n");
1306: fprintf(ficlog,"\n#Hessian matrix#\n");
1307: for (i=1;i<=npar;i++) {
1308: for (j=1;j<=npar;j++) {
1309: printf("%.3e ",hess[i][j]);
1310: fprintf(ficlog,"%.3e ",hess[i][j]);
1311: }
1312: printf("\n");
1313: fprintf(ficlog,"\n");
1314: }
1315:
1316: /* Recompute Inverse */
1317: for (i=1;i<=npar;i++)
1318: for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];
1319: ludcmp(a,npar,indx,&pd);
1320:
1321: /* printf("\n#Hessian matrix recomputed#\n");
1322:
1323: for (j=1;j<=npar;j++) {
1324: for (i=1;i<=npar;i++) x[i]=0;
1325: x[j]=1;
1326: lubksb(a,npar,indx,x);
1327: for (i=1;i<=npar;i++){
1328: y[i][j]=x[i];
1329: printf("%.3e ",y[i][j]);
1330: fprintf(ficlog,"%.3e ",y[i][j]);
1331: }
1332: printf("\n");
1333: fprintf(ficlog,"\n");
1334: }
1335: */
1336:
1337: free_matrix(a,1,npar,1,npar);
1338: free_matrix(y,1,npar,1,npar);
1339: free_vector(x,1,npar);
1340: free_ivector(indx,1,npar);
1341: free_matrix(hess,1,npar,1,npar);
1342:
1343:
1344: }
1345:
1346: /*************** hessian matrix ****************/
1347: double hessii( double x[], double delta, int theta, double delti[])
1348: {
1349: int i;
1350: int l=1, lmax=20;
1351: double k1,k2;
1352: double p2[NPARMAX+1];
1353: double res;
1354: double delt, delts, nkhi=10.,nkhif=1., khi=1.e-4;
1355: double fx;
1356: int k=0,kmax=10;
1357: double l1;
1358:
1359: fx=func(x);
1360: for (i=1;i<=npar;i++) p2[i]=x[i];
1361: for(l=0 ; l <=lmax; l++){
1362: l1=pow(10,l);
1363: delts=delt;
1364: for(k=1 ; k <kmax; k=k+1){
1365: delt = delta*(l1*k);
1366: p2[theta]=x[theta] +delt;
1367: k1=func(p2)-fx;
1368: p2[theta]=x[theta]-delt;
1369: k2=func(p2)-fx;
1370: /*res= (k1-2.0*fx+k2)/delt/delt; */
1371: res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */
1372:
1373: #ifdef DEBUG
1374: 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);
1375: 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);
1376: #endif
1377: /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
1378: if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
1379: k=kmax;
1380: }
1381: else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
1382: k=kmax; l=lmax*10.;
1383: }
1384: else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){
1385: delts=delt;
1386: }
1387: }
1388: }
1389: delti[theta]=delts;
1390: return res;
1391:
1392: }
1393:
1394: double hessij( double x[], double delti[], int thetai,int thetaj)
1395: {
1396: int i;
1397: int l=1, l1, lmax=20;
1398: double k1,k2,k3,k4,res,fx;
1399: double p2[NPARMAX+1];
1400: int k;
1401:
1402: fx=func(x);
1403: for (k=1; k<=2; k++) {
1404: for (i=1;i<=npar;i++) p2[i]=x[i];
1405: p2[thetai]=x[thetai]+delti[thetai]/k;
1406: p2[thetaj]=x[thetaj]+delti[thetaj]/k;
1407: k1=func(p2)-fx;
1408:
1409: p2[thetai]=x[thetai]+delti[thetai]/k;
1410: p2[thetaj]=x[thetaj]-delti[thetaj]/k;
1411: k2=func(p2)-fx;
1412:
1413: p2[thetai]=x[thetai]-delti[thetai]/k;
1414: p2[thetaj]=x[thetaj]+delti[thetaj]/k;
1415: k3=func(p2)-fx;
1416:
1417: p2[thetai]=x[thetai]-delti[thetai]/k;
1418: p2[thetaj]=x[thetaj]-delti[thetaj]/k;
1419: k4=func(p2)-fx;
1420: res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */
1421: #ifdef DEBUG
1422: 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);
1423: 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);
1424: #endif
1425: }
1426: return res;
1427: }
1428:
1429: /************** Inverse of matrix **************/
1430: void ludcmp(double **a, int n, int *indx, double *d)
1431: {
1432: int i,imax,j,k;
1433: double big,dum,sum,temp;
1434: double *vv;
1435:
1436: vv=vector(1,n);
1437: *d=1.0;
1438: for (i=1;i<=n;i++) {
1439: big=0.0;
1440: for (j=1;j<=n;j++)
1441: if ((temp=fabs(a[i][j])) > big) big=temp;
1442: if (big == 0.0) nrerror("Singular matrix in routine ludcmp");
1443: vv[i]=1.0/big;
1444: }
1445: for (j=1;j<=n;j++) {
1446: for (i=1;i<j;i++) {
1447: sum=a[i][j];
1448: for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];
1449: a[i][j]=sum;
1450: }
1451: big=0.0;
1452: for (i=j;i<=n;i++) {
1453: sum=a[i][j];
1454: for (k=1;k<j;k++)
1455: sum -= a[i][k]*a[k][j];
1456: a[i][j]=sum;
1457: if ( (dum=vv[i]*fabs(sum)) >= big) {
1458: big=dum;
1459: imax=i;
1460: }
1461: }
1462: if (j != imax) {
1463: for (k=1;k<=n;k++) {
1464: dum=a[imax][k];
1465: a[imax][k]=a[j][k];
1466: a[j][k]=dum;
1467: }
1468: *d = -(*d);
1469: vv[imax]=vv[j];
1470: }
1471: indx[j]=imax;
1472: if (a[j][j] == 0.0) a[j][j]=TINY;
1473: if (j != n) {
1474: dum=1.0/(a[j][j]);
1475: for (i=j+1;i<=n;i++) a[i][j] *= dum;
1476: }
1477: }
1478: free_vector(vv,1,n); /* Doesn't work */
1479: ;
1480: }
1481:
1482: void lubksb(double **a, int n, int *indx, double b[])
1483: {
1484: int i,ii=0,ip,j;
1485: double sum;
1486:
1487: for (i=1;i<=n;i++) {
1488: ip=indx[i];
1489: sum=b[ip];
1490: b[ip]=b[i];
1491: if (ii)
1492: for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];
1493: else if (sum) ii=i;
1494: b[i]=sum;
1495: }
1496: for (i=n;i>=1;i--) {
1497: sum=b[i];
1498: for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];
1499: b[i]=sum/a[i][i];
1500: }
1501: }
1502:
1503: /************ Frequencies ********************/
1.74 brouard 1504: 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 1505: { /* Some frequencies */
1506:
1507: int i, m, jk, k1,i1, j1, bool, z1,z2,j;
1508: int first;
1509: double ***freq; /* Frequencies */
1.73 lievre 1510: double *pp, **prop;
1511: double pos,posprop, k2, dateintsum=0,k2cpt=0;
1.53 brouard 1512: FILE *ficresp;
1513: char fileresp[FILENAMELENGTH];
1514:
1515: pp=vector(1,nlstate);
1.74 brouard 1516: prop=matrix(1,nlstate,iagemin,iagemax+3);
1.53 brouard 1517: strcpy(fileresp,"p");
1518: strcat(fileresp,fileres);
1519: if((ficresp=fopen(fileresp,"w"))==NULL) {
1520: printf("Problem with prevalence resultfile: %s\n", fileresp);
1521: fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
1522: exit(0);
1523: }
1.74 brouard 1524: freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);
1.53 brouard 1525: j1=0;
1526:
1527: j=cptcoveff;
1528: if (cptcovn<1) {j=1;ncodemax[1]=1;}
1529:
1530: first=1;
1531:
1532: for(k1=1; k1<=j;k1++){
1533: for(i1=1; i1<=ncodemax[k1];i1++){
1534: j1++;
1535: /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
1536: scanf("%d", i);*/
1537: for (i=-1; i<=nlstate+ndeath; i++)
1538: for (jk=-1; jk<=nlstate+ndeath; jk++)
1.74 brouard 1539: for(m=iagemin; m <= iagemax+3; m++)
1.53 brouard 1540: freq[i][jk][m]=0;
1.73 lievre 1541:
1542: for (i=1; i<=nlstate; i++)
1.74 brouard 1543: for(m=iagemin; m <= iagemax+3; m++)
1.73 lievre 1544: prop[i][m]=0;
1.53 brouard 1545:
1546: dateintsum=0;
1547: k2cpt=0;
1548: for (i=1; i<=imx; i++) {
1549: bool=1;
1550: if (cptcovn>0) {
1551: for (z1=1; z1<=cptcoveff; z1++)
1552: if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])
1553: bool=0;
1554: }
1.58 lievre 1555: if (bool==1){
1.53 brouard 1556: for(m=firstpass; m<=lastpass; m++){
1557: k2=anint[m][i]+(mint[m][i]/12.);
1558: if ((k2>=dateprev1) && (k2<=dateprev2)) {
1.74 brouard 1559: if(agev[m][i]==0) agev[m][i]=iagemax+1;
1560: if(agev[m][i]==1) agev[m][i]=iagemax+2;
1.73 lievre 1561: if (s[m][i]>0 && s[m][i]<=nlstate) prop[s[m][i]][(int)agev[m][i]] += weight[i];
1.53 brouard 1562: if (m<lastpass) {
1563: freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
1.74 brouard 1564: freq[s[m][i]][s[m+1][i]][iagemax+3] += weight[i];
1.53 brouard 1565: }
1566:
1.74 brouard 1567: if ((agev[m][i]>1) && (agev[m][i]< (iagemax+3))) {
1.53 brouard 1568: dateintsum=dateintsum+k2;
1569: k2cpt++;
1570: }
1571: }
1572: }
1573: }
1574: }
1575:
1576: fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);
1577:
1578: if (cptcovn>0) {
1579: fprintf(ficresp, "\n#********** Variable ");
1580: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
1581: fprintf(ficresp, "**********\n#");
1582: }
1583: for(i=1; i<=nlstate;i++)
1584: fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
1585: fprintf(ficresp, "\n");
1586:
1.74 brouard 1587: for(i=iagemin; i <= iagemax+3; i++){
1588: if(i==iagemax+3){
1.53 brouard 1589: fprintf(ficlog,"Total");
1590: }else{
1591: if(first==1){
1592: first=0;
1593: printf("See log file for details...\n");
1594: }
1595: fprintf(ficlog,"Age %d", i);
1596: }
1597: for(jk=1; jk <=nlstate ; jk++){
1598: for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
1599: pp[jk] += freq[jk][m][i];
1600: }
1601: for(jk=1; jk <=nlstate ; jk++){
1602: for(m=-1, pos=0; m <=0 ; m++)
1603: pos += freq[jk][m][i];
1604: if(pp[jk]>=1.e-10){
1605: if(first==1){
1606: printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
1607: }
1608: fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
1609: }else{
1610: if(first==1)
1611: printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
1612: fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
1613: }
1614: }
1615:
1616: for(jk=1; jk <=nlstate ; jk++){
1617: for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
1618: pp[jk] += freq[jk][m][i];
1.73 lievre 1619: }
1620: for(jk=1,pos=0,posprop=0; jk <=nlstate ; jk++){
1621: pos += pp[jk];
1622: posprop += prop[jk][i];
1.53 brouard 1623: }
1624: for(jk=1; jk <=nlstate ; jk++){
1625: if(pos>=1.e-5){
1626: if(first==1)
1627: printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
1628: fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
1629: }else{
1630: if(first==1)
1631: printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
1632: fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
1633: }
1.74 brouard 1634: if( i <= iagemax){
1.53 brouard 1635: if(pos>=1.e-5){
1.73 lievre 1636: fprintf(ficresp," %d %.5f %.0f %.0f",i,prop[jk][i]/posprop, prop[jk][i],posprop);
1.53 brouard 1637: probs[i][jk][j1]= pp[jk]/pos;
1638: /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/
1639: }
1640: else
1.73 lievre 1641: fprintf(ficresp," %d NaNq %.0f %.0f",i,prop[jk][i],posprop);
1.53 brouard 1642: }
1643: }
1644:
1.69 brouard 1645: for(jk=-1; jk <=nlstate+ndeath; jk++)
1646: for(m=-1; m <=nlstate+ndeath; m++)
1.53 brouard 1647: if(freq[jk][m][i] !=0 ) {
1648: if(first==1)
1649: printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
1650: fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
1651: }
1.74 brouard 1652: if(i <= iagemax)
1.53 brouard 1653: fprintf(ficresp,"\n");
1654: if(first==1)
1655: printf("Others in log...\n");
1656: fprintf(ficlog,"\n");
1657: }
1658: }
1659: }
1660: dateintmean=dateintsum/k2cpt;
1661:
1662: fclose(ficresp);
1.74 brouard 1663: free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);
1.53 brouard 1664: free_vector(pp,1,nlstate);
1.74 brouard 1665: free_matrix(prop,1,nlstate,iagemin, iagemax+3);
1.53 brouard 1666: /* End of Freq */
1667: }
1668:
1669: /************ Prevalence ********************/
1.74 brouard 1670: 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 1671: {
1672: /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
1673: in each health status at the date of interview (if between dateprev1 and dateprev2).
1674: We still use firstpass and lastpass as another selection.
1675: */
1.53 brouard 1676:
1677: int i, m, jk, k1, i1, j1, bool, z1,z2,j;
1678: double ***freq; /* Frequencies */
1.73 lievre 1679: double *pp, **prop;
1680: double pos,posprop;
1.69 brouard 1681: double y2; /* in fractional years */
1.74 brouard 1682: int iagemin, iagemax;
1.53 brouard 1683:
1.74 brouard 1684: iagemin= (int) agemin;
1685: iagemax= (int) agemax;
1686: /*pp=vector(1,nlstate);*/
1687: prop=matrix(1,nlstate,iagemin,iagemax+3);
1688: /* freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
1.53 brouard 1689: j1=0;
1690:
1691: j=cptcoveff;
1692: if (cptcovn<1) {j=1;ncodemax[1]=1;}
1693:
1694: for(k1=1; k1<=j;k1++){
1695: for(i1=1; i1<=ncodemax[k1];i1++){
1696: j1++;
1697:
1.73 lievre 1698: for (i=1; i<=nlstate; i++)
1.74 brouard 1699: for(m=iagemin; m <= iagemax+3; m++)
1700: prop[i][m]=0.0;
1.53 brouard 1701:
1.69 brouard 1702: for (i=1; i<=imx; i++) { /* Each individual */
1.53 brouard 1703: bool=1;
1704: if (cptcovn>0) {
1705: for (z1=1; z1<=cptcoveff; z1++)
1706: if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])
1707: bool=0;
1708: }
1709: if (bool==1) {
1.69 brouard 1710: for(m=firstpass; m<=lastpass; m++){/* Other selection (we can limit to certain interviews*/
1711: y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
1712: if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
1.74 brouard 1713: if(agev[m][i]==0) agev[m][i]=iagemax+1;
1714: if(agev[m][i]==1) agev[m][i]=iagemax+2;
1715: 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);
1716: if (s[m][i]>0 && s[m][i]<=nlstate) {
1717: /*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]]);*/
1718: prop[s[m][i]][(int)agev[m][i]] += weight[i];
1719: prop[s[m][i]][iagemax+3] += weight[i];
1720: }
1.53 brouard 1721: }
1.69 brouard 1722: } /* end selection of waves */
1.53 brouard 1723: }
1724: }
1.74 brouard 1725: for(i=iagemin; i <= iagemax+3; i++){
1.53 brouard 1726:
1.74 brouard 1727: for(jk=1,posprop=0; jk <=nlstate ; jk++) {
1728: posprop += prop[jk][i];
1729: }
1730:
1731: for(jk=1; jk <=nlstate ; jk++){
1732: if( i <= iagemax){
1733: if(posprop>=1.e-5){
1734: probs[i][jk][j1]= prop[jk][i]/posprop;
1735: }
1736: }
1737: }/* end jk */
1738: }/* end i */
1.53 brouard 1739: } /* end i1 */
1740: } /* end k1 */
1741:
1.74 brouard 1742: /* free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
1743: /*free_vector(pp,1,nlstate);*/
1744: free_matrix(prop,1,nlstate, iagemin,iagemax+3);
1745: } /* End of prevalence */
1.53 brouard 1746:
1747: /************* Waves Concatenation ***************/
1748:
1.59 brouard 1749: 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 1750: {
1751: /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
1752: Death is a valid wave (if date is known).
1753: mw[mi][i] is the mi (mi=1 to wav[i]) effective wave of individual i
1.59 brouard 1754: dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
1.53 brouard 1755: and mw[mi+1][i]. dh depends on stepm.
1756: */
1757:
1758: int i, mi, m;
1759: /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
1760: double sum=0., jmean=0.;*/
1761: int first;
1762: int j, k=0,jk, ju, jl;
1763: double sum=0.;
1764: first=0;
1765: jmin=1e+5;
1766: jmax=-1;
1767: jmean=0.;
1768: for(i=1; i<=imx; i++){
1769: mi=0;
1770: m=firstpass;
1771: while(s[m][i] <= nlstate){
1.69 brouard 1772: if(s[m][i]>=1)
1.53 brouard 1773: mw[++mi][i]=m;
1774: if(m >=lastpass)
1775: break;
1776: else
1777: m++;
1778: }/* end while */
1779: if (s[m][i] > nlstate){
1780: mi++; /* Death is another wave */
1781: /* if(mi==0) never been interviewed correctly before death */
1782: /* Only death is a correct wave */
1783: mw[mi][i]=m;
1784: }
1785:
1786: wav[i]=mi;
1787: if(mi==0){
1788: if(first==0){
1.77 brouard 1789: printf("Warning! None valid information for:%d line=%d (skipped) and may be others, see log file\n",num[i],i);
1.53 brouard 1790: first=1;
1791: }
1792: if(first==1){
1.77 brouard 1793: fprintf(ficlog,"Warning! None valid information for:%d line=%d (skipped)\n",num[i],i);
1.53 brouard 1794: }
1795: } /* end mi==0 */
1.77 brouard 1796: } /* End individuals */
1.53 brouard 1797:
1798: for(i=1; i<=imx; i++){
1799: for(mi=1; mi<wav[i];mi++){
1800: if (stepm <=0)
1801: dh[mi][i]=1;
1802: else{
1.77 brouard 1803: if (s[mw[mi+1][i]][i] > nlstate) { /* A death */
1.53 brouard 1804: if (agedc[i] < 2*AGESUP) {
1805: j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);
1806: if(j==0) j=1; /* Survives at least one month after exam */
1807: k=k+1;
1808: if (j >= jmax) jmax=j;
1809: if (j <= jmin) jmin=j;
1810: sum=sum+j;
1.77 brouard 1811: /*if (j<0) printf("j=%d num=%d \n",j,i);*/
1.68 lievre 1812: /* printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
1.78 brouard 1813: 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 1814: }
1815: }
1816: else{
1817: j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
1.68 lievre 1818: /* printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
1.53 brouard 1819: k=k+1;
1820: if (j >= jmax) jmax=j;
1821: else if (j <= jmin)jmin=j;
1822: /* if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
1.73 lievre 1823: /*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 1824: 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 1825: sum=sum+j;
1826: }
1827: jk= j/stepm;
1828: jl= j -jk*stepm;
1829: ju= j -(jk+1)*stepm;
1.64 lievre 1830: if(mle <=1){
1831: if(jl==0){
1832: dh[mi][i]=jk;
1833: bh[mi][i]=0;
1834: }else{ /* We want a negative bias in order to only have interpolation ie
1835: * at the price of an extra matrix product in likelihood */
1836: dh[mi][i]=jk+1;
1837: bh[mi][i]=ju;
1838: }
1839: }else{
1840: if(jl <= -ju){
1841: dh[mi][i]=jk;
1842: bh[mi][i]=jl; /* bias is positive if real duration
1843: * is higher than the multiple of stepm and negative otherwise.
1844: */
1845: }
1846: else{
1847: dh[mi][i]=jk+1;
1848: bh[mi][i]=ju;
1849: }
1850: if(dh[mi][i]==0){
1851: dh[mi][i]=1; /* At least one step */
1852: bh[mi][i]=ju; /* At least one step */
1.71 brouard 1853: /* 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 1854: }
1.59 brouard 1855: }
1.64 lievre 1856: } /* end if mle */
1857: } /* end wave */
1.53 brouard 1858: }
1859: jmean=sum/k;
1860: printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);
1861: fprintf(ficlog,"Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);
1862: }
1863:
1864: /*********** Tricode ****************************/
1865: void tricode(int *Tvar, int **nbcode, int imx)
1866: {
1.58 lievre 1867:
1868: int Ndum[20],ij=1, k, j, i, maxncov=19;
1.53 brouard 1869: int cptcode=0;
1870: cptcoveff=0;
1871:
1.58 lievre 1872: for (k=0; k<maxncov; k++) Ndum[k]=0;
1.53 brouard 1873: for (k=1; k<=7; k++) ncodemax[k]=0;
1874:
1875: for (j=1; j<=(cptcovn+2*cptcovprod); j++) {
1.58 lievre 1876: for (i=1; i<=imx; i++) { /*reads the data file to get the maximum
1877: modality*/
1878: ij=(int)(covar[Tvar[j]][i]); /* ij is the modality of this individual*/
1879: Ndum[ij]++; /*store the modality */
1.53 brouard 1880: /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
1.58 lievre 1881: if (ij > cptcode) cptcode=ij; /* getting the maximum of covariable
1882: Tvar[j]. If V=sex and male is 0 and
1883: female is 1, then cptcode=1.*/
1.53 brouard 1884: }
1885:
1886: for (i=0; i<=cptcode; i++) {
1.58 lievre 1887: 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 1888: }
1.58 lievre 1889:
1.53 brouard 1890: ij=1;
1891: for (i=1; i<=ncodemax[j]; i++) {
1.58 lievre 1892: for (k=0; k<= maxncov; k++) {
1.53 brouard 1893: if (Ndum[k] != 0) {
1894: nbcode[Tvar[j]][ij]=k;
1.58 lievre 1895: /* 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 1896:
1897: ij++;
1898: }
1899: if (ij > ncodemax[j]) break;
1900: }
1901: }
1902: }
1903:
1.58 lievre 1904: for (k=0; k< maxncov; k++) Ndum[k]=0;
1.53 brouard 1905:
1.58 lievre 1906: for (i=1; i<=ncovmodel-2; i++) {
1907: /* 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 1908: ij=Tvar[i];
1.58 lievre 1909: Ndum[ij]++;
1.53 brouard 1910: }
1911:
1912: ij=1;
1.58 lievre 1913: for (i=1; i<= maxncov; i++) {
1.53 brouard 1914: if((Ndum[i]!=0) && (i<=ncovcol)){
1.58 lievre 1915: Tvaraff[ij]=i; /*For printing */
1.53 brouard 1916: ij++;
1917: }
1918: }
1919:
1.58 lievre 1920: cptcoveff=ij-1; /*Number of simple covariates*/
1.53 brouard 1921: }
1922:
1923: /*********** Health Expectancies ****************/
1924:
1925: 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 )
1926:
1927: {
1928: /* Health expectancies */
1929: int i, j, nhstepm, hstepm, h, nstepm, k, cptj;
1930: double age, agelim, hf;
1931: double ***p3mat,***varhe;
1932: double **dnewm,**doldm;
1933: double *xp;
1934: double **gp, **gm;
1935: double ***gradg, ***trgradg;
1936: int theta;
1937:
1.74 brouard 1938: varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage);
1.53 brouard 1939: xp=vector(1,npar);
1.74 brouard 1940: dnewm=matrix(1,nlstate*nlstate,1,npar);
1941: doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate);
1.53 brouard 1942:
1943: fprintf(ficreseij,"# Health expectancies\n");
1944: fprintf(ficreseij,"# Age");
1945: for(i=1; i<=nlstate;i++)
1946: for(j=1; j<=nlstate;j++)
1947: fprintf(ficreseij," %1d-%1d (SE)",i,j);
1948: fprintf(ficreseij,"\n");
1949:
1950: if(estepm < stepm){
1951: printf ("Problem %d lower than %d\n",estepm, stepm);
1952: }
1953: else hstepm=estepm;
1954: /* We compute the life expectancy from trapezoids spaced every estepm months
1955: * This is mainly to measure the difference between two models: for example
1956: * if stepm=24 months pijx are given only every 2 years and by summing them
1957: * we are calculating an estimate of the Life Expectancy assuming a linear
1.66 brouard 1958: * progression in between and thus overestimating or underestimating according
1.53 brouard 1959: * to the curvature of the survival function. If, for the same date, we
1960: * estimate the model with stepm=1 month, we can keep estepm to 24 months
1961: * to compare the new estimate of Life expectancy with the same linear
1962: * hypothesis. A more precise result, taking into account a more precise
1963: * curvature will be obtained if estepm is as small as stepm. */
1964:
1965: /* For example we decided to compute the life expectancy with the smallest unit */
1966: /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
1967: nhstepm is the number of hstepm from age to agelim
1968: nstepm is the number of stepm from age to agelin.
1969: Look at hpijx to understand the reason of that which relies in memory size
1970: and note for a fixed period like estepm months */
1971: /* We decided (b) to get a life expectancy respecting the most precise curvature of the
1972: survival function given by stepm (the optimization length). Unfortunately it
1973: means that if the survival funtion is printed only each two years of age and if
1974: you sum them up and add 1 year (area under the trapezoids) you won't get the same
1975: results. So we changed our mind and took the option of the best precision.
1976: */
1977: hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
1978:
1979: agelim=AGESUP;
1980: for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
1981: /* nhstepm age range expressed in number of stepm */
1982: nstepm=(int) rint((agelim-age)*YEARM/stepm);
1983: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
1984: /* if (stepm >= YEARM) hstepm=1;*/
1985: nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
1986: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
1.74 brouard 1987: gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);
1988: gp=matrix(0,nhstepm,1,nlstate*nlstate);
1989: gm=matrix(0,nhstepm,1,nlstate*nlstate);
1.53 brouard 1990:
1991: /* Computed by stepm unit matrices, product of hstepm matrices, stored
1992: in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
1993: hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);
1994:
1995:
1996: hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
1997:
1998: /* Computing Variances of health expectancies */
1999:
2000: for(theta=1; theta <=npar; theta++){
2001: for(i=1; i<=npar; i++){
2002: xp[i] = x[i] + (i==theta ?delti[theta]:0);
2003: }
2004: hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
2005:
2006: cptj=0;
2007: for(j=1; j<= nlstate; j++){
2008: for(i=1; i<=nlstate; i++){
2009: cptj=cptj+1;
2010: for(h=0, gp[h][cptj]=0.; h<=nhstepm-1; h++){
2011: gp[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;
2012: }
2013: }
2014: }
2015:
2016:
2017: for(i=1; i<=npar; i++)
2018: xp[i] = x[i] - (i==theta ?delti[theta]:0);
2019: hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
2020:
2021: cptj=0;
2022: for(j=1; j<= nlstate; j++){
2023: for(i=1;i<=nlstate;i++){
2024: cptj=cptj+1;
2025: for(h=0, gm[h][cptj]=0.; h<=nhstepm-1; h++){
1.77 brouard 2026:
1.53 brouard 2027: gm[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;
2028: }
2029: }
2030: }
1.74 brouard 2031: for(j=1; j<= nlstate*nlstate; j++)
1.53 brouard 2032: for(h=0; h<=nhstepm-1; h++){
2033: gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
2034: }
2035: }
2036:
2037: /* End theta */
2038:
1.74 brouard 2039: trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar);
1.53 brouard 2040:
2041: for(h=0; h<=nhstepm-1; h++)
1.74 brouard 2042: for(j=1; j<=nlstate*nlstate;j++)
1.53 brouard 2043: for(theta=1; theta <=npar; theta++)
2044: trgradg[h][j][theta]=gradg[h][theta][j];
2045:
2046:
1.74 brouard 2047: for(i=1;i<=nlstate*nlstate;i++)
2048: for(j=1;j<=nlstate*nlstate;j++)
1.53 brouard 2049: varhe[i][j][(int)age] =0.;
2050:
2051: printf("%d|",(int)age);fflush(stdout);
2052: fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
2053: for(h=0;h<=nhstepm-1;h++){
2054: for(k=0;k<=nhstepm-1;k++){
1.74 brouard 2055: matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov);
2056: matprod2(doldm,dnewm,1,nlstate*nlstate,1,npar,1,nlstate*nlstate,gradg[k]);
2057: for(i=1;i<=nlstate*nlstate;i++)
2058: for(j=1;j<=nlstate*nlstate;j++)
1.53 brouard 2059: varhe[i][j][(int)age] += doldm[i][j]*hf*hf;
2060: }
2061: }
2062: /* Computing expectancies */
2063: for(i=1; i<=nlstate;i++)
2064: for(j=1; j<=nlstate;j++)
2065: for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
2066: eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
2067:
2068: /* 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]);*/
2069:
2070: }
2071:
2072: fprintf(ficreseij,"%3.0f",age );
2073: cptj=0;
2074: for(i=1; i<=nlstate;i++)
2075: for(j=1; j<=nlstate;j++){
2076: cptj++;
2077: fprintf(ficreseij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[cptj][cptj][(int)age]) );
2078: }
2079: fprintf(ficreseij,"\n");
2080:
1.74 brouard 2081: free_matrix(gm,0,nhstepm,1,nlstate*nlstate);
2082: free_matrix(gp,0,nhstepm,1,nlstate*nlstate);
2083: free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*nlstate);
2084: free_ma3x(trgradg,0,nhstepm,1,nlstate*nlstate,1,npar);
1.53 brouard 2085: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
2086: }
2087: printf("\n");
2088: fprintf(ficlog,"\n");
2089:
2090: free_vector(xp,1,npar);
1.74 brouard 2091: free_matrix(dnewm,1,nlstate*nlstate,1,npar);
2092: free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate);
2093: free_ma3x(varhe,1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int)fage);
1.53 brouard 2094: }
2095:
2096: /************ Variance ******************/
2097: 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)
2098: {
2099: /* Variance of health expectancies */
2100: /* double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
2101: /* double **newm;*/
2102: double **dnewm,**doldm;
2103: double **dnewmp,**doldmp;
2104: int i, j, nhstepm, hstepm, h, nstepm ;
2105: int k, cptcode;
2106: double *xp;
2107: double **gp, **gm; /* for var eij */
2108: double ***gradg, ***trgradg; /*for var eij */
2109: double **gradgp, **trgradgp; /* for var p point j */
2110: double *gpp, *gmp; /* for var p point j */
2111: double **varppt; /* for var p point j nlstate to nlstate+ndeath */
2112: double ***p3mat;
2113: double age,agelim, hf;
2114: double ***mobaverage;
2115: int theta;
2116: char digit[4];
1.55 lievre 2117: char digitp[25];
1.53 brouard 2118:
2119: char fileresprobmorprev[FILENAMELENGTH];
2120:
1.55 lievre 2121: if(popbased==1){
1.58 lievre 2122: if(mobilav!=0)
1.55 lievre 2123: strcpy(digitp,"-populbased-mobilav-");
2124: else strcpy(digitp,"-populbased-nomobil-");
2125: }
2126: else
1.53 brouard 2127: strcpy(digitp,"-stablbased-");
1.56 lievre 2128:
1.54 brouard 2129: if (mobilav!=0) {
1.53 brouard 2130: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
1.54 brouard 2131: if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
2132: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
2133: printf(" Error in movingaverage mobilav=%d\n",mobilav);
2134: }
1.53 brouard 2135: }
2136:
2137: strcpy(fileresprobmorprev,"prmorprev");
2138: sprintf(digit,"%-d",ij);
2139: /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
2140: strcat(fileresprobmorprev,digit); /* Tvar to be done */
2141: strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
2142: strcat(fileresprobmorprev,fileres);
2143: if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
2144: printf("Problem with resultfile: %s\n", fileresprobmorprev);
2145: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
2146: }
2147: printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
2148: fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
1.66 brouard 2149: 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 2150: fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
2151: for(j=nlstate+1; j<=(nlstate+ndeath);j++){
2152: fprintf(ficresprobmorprev," p.%-d SE",j);
2153: for(i=1; i<=nlstate;i++)
2154: fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
2155: }
2156: fprintf(ficresprobmorprev,"\n");
2157: if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {
2158: printf("Problem with gnuplot file: %s\n", optionfilegnuplot);
2159: fprintf(ficlog,"Problem with gnuplot file: %s\n", optionfilegnuplot);
2160: exit(0);
2161: }
2162: else{
2163: fprintf(ficgp,"\n# Routine varevsij");
2164: }
2165: if((fichtm=fopen(optionfilehtm,"a"))==NULL) {
2166: printf("Problem with html file: %s\n", optionfilehtm);
2167: fprintf(ficlog,"Problem with html file: %s\n", optionfilehtm);
2168: exit(0);
2169: }
2170: else{
1.67 brouard 2171: 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");
2172: fprintf(fichtm,"\n<br>%s <br>\n",digitp);
1.53 brouard 2173: }
2174: varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
2175:
2176: 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");
2177: fprintf(ficresvij,"# Age");
2178: for(i=1; i<=nlstate;i++)
2179: for(j=1; j<=nlstate;j++)
2180: fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);
2181: fprintf(ficresvij,"\n");
2182:
2183: xp=vector(1,npar);
2184: dnewm=matrix(1,nlstate,1,npar);
2185: doldm=matrix(1,nlstate,1,nlstate);
2186: dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
2187: doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
2188:
2189: gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
2190: gpp=vector(nlstate+1,nlstate+ndeath);
2191: gmp=vector(nlstate+1,nlstate+ndeath);
2192: trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
2193:
2194: if(estepm < stepm){
2195: printf ("Problem %d lower than %d\n",estepm, stepm);
2196: }
2197: else hstepm=estepm;
2198: /* For example we decided to compute the life expectancy with the smallest unit */
2199: /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
2200: nhstepm is the number of hstepm from age to agelim
2201: nstepm is the number of stepm from age to agelin.
2202: Look at hpijx to understand the reason of that which relies in memory size
2203: and note for a fixed period like k years */
2204: /* We decided (b) to get a life expectancy respecting the most precise curvature of the
2205: survival function given by stepm (the optimization length). Unfortunately it
1.66 brouard 2206: means that if the survival funtion is printed every two years of age and if
1.53 brouard 2207: you sum them up and add 1 year (area under the trapezoids) you won't get the same
2208: results. So we changed our mind and took the option of the best precision.
2209: */
2210: hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
2211: agelim = AGESUP;
2212: for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
2213: nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
2214: nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
2215: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
2216: gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
2217: gp=matrix(0,nhstepm,1,nlstate);
2218: gm=matrix(0,nhstepm,1,nlstate);
2219:
2220:
2221: for(theta=1; theta <=npar; theta++){
1.66 brouard 2222: for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
1.53 brouard 2223: xp[i] = x[i] + (i==theta ?delti[theta]:0);
2224: }
2225: hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
2226: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
2227:
2228: if (popbased==1) {
1.54 brouard 2229: if(mobilav ==0){
1.53 brouard 2230: for(i=1; i<=nlstate;i++)
2231: prlim[i][i]=probs[(int)age][i][ij];
1.54 brouard 2232: }else{ /* mobilav */
1.53 brouard 2233: for(i=1; i<=nlstate;i++)
2234: prlim[i][i]=mobaverage[(int)age][i][ij];
2235: }
2236: }
2237:
2238: for(j=1; j<= nlstate; j++){
2239: for(h=0; h<=nhstepm; h++){
2240: for(i=1, gp[h][j]=0.;i<=nlstate;i++)
2241: gp[h][j] += prlim[i][i]*p3mat[i][j][h];
2242: }
2243: }
1.66 brouard 2244: /* This for computing probability of death (h=1 means
2245: computed over hstepm matrices product = hstepm*stepm months)
2246: as a weighted average of prlim.
2247: */
1.69 brouard 2248: for(j=nlstate+1;j<=nlstate+ndeath;j++){
1.68 lievre 2249: for(i=1,gpp[j]=0.; i<= nlstate; i++)
1.53 brouard 2250: gpp[j] += prlim[i][i]*p3mat[i][j][1];
2251: }
1.66 brouard 2252: /* end probability of death */
1.53 brouard 2253:
1.66 brouard 2254: for(i=1; i<=npar; i++) /* Computes gradient x - delta */
1.53 brouard 2255: xp[i] = x[i] - (i==theta ?delti[theta]:0);
2256: hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
2257: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
2258:
2259: if (popbased==1) {
1.54 brouard 2260: if(mobilav ==0){
1.53 brouard 2261: for(i=1; i<=nlstate;i++)
2262: prlim[i][i]=probs[(int)age][i][ij];
1.54 brouard 2263: }else{ /* mobilav */
1.53 brouard 2264: for(i=1; i<=nlstate;i++)
2265: prlim[i][i]=mobaverage[(int)age][i][ij];
2266: }
2267: }
2268:
2269: for(j=1; j<= nlstate; j++){
2270: for(h=0; h<=nhstepm; h++){
2271: for(i=1, gm[h][j]=0.;i<=nlstate;i++)
2272: gm[h][j] += prlim[i][i]*p3mat[i][j][h];
2273: }
2274: }
1.66 brouard 2275: /* This for computing probability of death (h=1 means
2276: computed over hstepm matrices product = hstepm*stepm months)
2277: as a weighted average of prlim.
2278: */
1.69 brouard 2279: for(j=nlstate+1;j<=nlstate+ndeath;j++){
1.68 lievre 2280: for(i=1,gmp[j]=0.; i<= nlstate; i++)
2281: gmp[j] += prlim[i][i]*p3mat[i][j][1];
1.53 brouard 2282: }
1.66 brouard 2283: /* end probability of death */
1.53 brouard 2284:
2285: for(j=1; j<= nlstate; j++) /* vareij */
2286: for(h=0; h<=nhstepm; h++){
2287: gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
2288: }
1.68 lievre 2289:
1.53 brouard 2290: for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
2291: gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
2292: }
2293:
2294: } /* End theta */
2295:
2296: trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
2297:
2298: for(h=0; h<=nhstepm; h++) /* veij */
2299: for(j=1; j<=nlstate;j++)
2300: for(theta=1; theta <=npar; theta++)
2301: trgradg[h][j][theta]=gradg[h][theta][j];
2302:
2303: for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
1.69 brouard 2304: for(theta=1; theta <=npar; theta++)
1.53 brouard 2305: trgradgp[j][theta]=gradgp[theta][j];
1.69 brouard 2306:
1.53 brouard 2307:
2308: hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
2309: for(i=1;i<=nlstate;i++)
2310: for(j=1;j<=nlstate;j++)
2311: vareij[i][j][(int)age] =0.;
2312:
2313: for(h=0;h<=nhstepm;h++){
2314: for(k=0;k<=nhstepm;k++){
2315: matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
2316: matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
2317: for(i=1;i<=nlstate;i++)
2318: for(j=1;j<=nlstate;j++)
2319: vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
2320: }
2321: }
1.70 brouard 2322:
1.53 brouard 2323: /* pptj */
2324: matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
2325: matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
1.70 brouard 2326: for(j=nlstate+1;j<=nlstate+ndeath;j++)
2327: for(i=nlstate+1;i<=nlstate+ndeath;i++)
1.53 brouard 2328: varppt[j][i]=doldmp[j][i];
2329: /* end ppptj */
1.66 brouard 2330: /* x centered again */
1.53 brouard 2331: hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);
2332: prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);
2333:
2334: if (popbased==1) {
1.54 brouard 2335: if(mobilav ==0){
1.53 brouard 2336: for(i=1; i<=nlstate;i++)
2337: prlim[i][i]=probs[(int)age][i][ij];
1.54 brouard 2338: }else{ /* mobilav */
1.53 brouard 2339: for(i=1; i<=nlstate;i++)
2340: prlim[i][i]=mobaverage[(int)age][i][ij];
2341: }
2342: }
1.70 brouard 2343:
1.66 brouard 2344: /* This for computing probability of death (h=1 means
2345: computed over hstepm (estepm) matrices product = hstepm*stepm months)
2346: as a weighted average of prlim.
2347: */
1.68 lievre 2348: for(j=nlstate+1;j<=nlstate+ndeath;j++){
2349: for(i=1,gmp[j]=0.;i<= nlstate; i++)
1.53 brouard 2350: gmp[j] += prlim[i][i]*p3mat[i][j][1];
2351: }
1.66 brouard 2352: /* end probability of death */
1.53 brouard 2353:
2354: fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
2355: for(j=nlstate+1; j<=(nlstate+ndeath);j++){
2356: fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
2357: for(i=1; i<=nlstate;i++){
2358: fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
2359: }
2360: }
2361: fprintf(ficresprobmorprev,"\n");
2362:
2363: fprintf(ficresvij,"%.0f ",age );
2364: for(i=1; i<=nlstate;i++)
2365: for(j=1; j<=nlstate;j++){
2366: fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
2367: }
2368: fprintf(ficresvij,"\n");
2369: free_matrix(gp,0,nhstepm,1,nlstate);
2370: free_matrix(gm,0,nhstepm,1,nlstate);
2371: free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
2372: free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
2373: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
2374: } /* End age */
2375: free_vector(gpp,nlstate+1,nlstate+ndeath);
2376: free_vector(gmp,nlstate+1,nlstate+ndeath);
2377: free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
2378: free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
2379: fprintf(ficgp,"\nset noparametric;set nolabel; set ter png small;set size 0.65, 0.65");
2380: /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */
2381: fprintf(ficgp,"\n set log y; set nolog x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
1.67 brouard 2382: /* fprintf(ficgp,"\n plot \"%s\" u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm); */
2383: /* fprintf(ficgp,"\n replot \"%s\" u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm); */
2384: /* fprintf(ficgp,"\n replot \"%s\" u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm); */
2385: fprintf(ficgp,"\n plot \"%s\" u 1:($3) not w l 1 ",fileresprobmorprev);
2386: fprintf(ficgp,"\n replot \"%s\" u 1:(($3+1.96*$4)) t \"95\%% interval\" w l 2 ",fileresprobmorprev);
2387: fprintf(ficgp,"\n replot \"%s\" u 1:(($3-1.96*$4)) not w l 2 ",fileresprobmorprev);
1.53 brouard 2388: fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",fileresprobmorprev,fileresprobmorprev);
1.71 brouard 2389: 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 2390: /* 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);
2391: */
1.71 brouard 2392: fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.png\";replot;",digitp,optionfilefiname,digit);
1.53 brouard 2393:
2394: free_vector(xp,1,npar);
2395: free_matrix(doldm,1,nlstate,1,nlstate);
2396: free_matrix(dnewm,1,nlstate,1,npar);
2397: free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
2398: free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
2399: free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
1.55 lievre 2400: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
1.53 brouard 2401: fclose(ficresprobmorprev);
2402: fclose(ficgp);
2403: fclose(fichtm);
1.70 brouard 2404: }
1.53 brouard 2405:
2406: /************ Variance of prevlim ******************/
2407: 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)
2408: {
2409: /* Variance of prevalence limit */
1.59 brouard 2410: /* double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
1.53 brouard 2411: double **newm;
2412: double **dnewm,**doldm;
2413: int i, j, nhstepm, hstepm;
2414: int k, cptcode;
2415: double *xp;
2416: double *gp, *gm;
2417: double **gradg, **trgradg;
2418: double age,agelim;
2419: int theta;
2420:
1.54 brouard 2421: fprintf(ficresvpl,"# Standard deviation of stable prevalences \n");
1.53 brouard 2422: fprintf(ficresvpl,"# Age");
2423: for(i=1; i<=nlstate;i++)
2424: fprintf(ficresvpl," %1d-%1d",i,i);
2425: fprintf(ficresvpl,"\n");
2426:
2427: xp=vector(1,npar);
2428: dnewm=matrix(1,nlstate,1,npar);
2429: doldm=matrix(1,nlstate,1,nlstate);
2430:
2431: hstepm=1*YEARM; /* Every year of age */
2432: hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */
2433: agelim = AGESUP;
2434: for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
2435: nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
2436: if (stepm >= YEARM) hstepm=1;
2437: nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
2438: gradg=matrix(1,npar,1,nlstate);
2439: gp=vector(1,nlstate);
2440: gm=vector(1,nlstate);
2441:
2442: for(theta=1; theta <=npar; theta++){
2443: for(i=1; i<=npar; i++){ /* Computes gradient */
2444: xp[i] = x[i] + (i==theta ?delti[theta]:0);
2445: }
2446: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
2447: for(i=1;i<=nlstate;i++)
2448: gp[i] = prlim[i][i];
2449:
2450: for(i=1; i<=npar; i++) /* Computes gradient */
2451: xp[i] = x[i] - (i==theta ?delti[theta]:0);
2452: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
2453: for(i=1;i<=nlstate;i++)
2454: gm[i] = prlim[i][i];
2455:
2456: for(i=1;i<=nlstate;i++)
2457: gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
2458: } /* End theta */
2459:
2460: trgradg =matrix(1,nlstate,1,npar);
2461:
2462: for(j=1; j<=nlstate;j++)
2463: for(theta=1; theta <=npar; theta++)
2464: trgradg[j][theta]=gradg[theta][j];
2465:
2466: for(i=1;i<=nlstate;i++)
2467: varpl[i][(int)age] =0.;
2468: matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
2469: matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
2470: for(i=1;i<=nlstate;i++)
2471: varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
2472:
2473: fprintf(ficresvpl,"%.0f ",age );
2474: for(i=1; i<=nlstate;i++)
2475: fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
2476: fprintf(ficresvpl,"\n");
2477: free_vector(gp,1,nlstate);
2478: free_vector(gm,1,nlstate);
2479: free_matrix(gradg,1,npar,1,nlstate);
2480: free_matrix(trgradg,1,nlstate,1,npar);
2481: } /* End age */
2482:
2483: free_vector(xp,1,npar);
2484: free_matrix(doldm,1,nlstate,1,npar);
2485: free_matrix(dnewm,1,nlstate,1,nlstate);
2486:
2487: }
2488:
2489: /************ Variance of one-step probabilities ******************/
2490: void varprob(char optionfilefiname[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij, int *Tvar, int **nbcode, int *ncodemax)
2491: {
2492: int i, j=0, i1, k1, l1, t, tj;
2493: int k2, l2, j1, z1;
2494: int k=0,l, cptcode;
2495: int first=1, first1;
2496: double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
2497: double **dnewm,**doldm;
2498: double *xp;
2499: double *gp, *gm;
2500: double **gradg, **trgradg;
2501: double **mu;
2502: double age,agelim, cov[NCOVMAX];
2503: double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
2504: int theta;
2505: char fileresprob[FILENAMELENGTH];
2506: char fileresprobcov[FILENAMELENGTH];
2507: char fileresprobcor[FILENAMELENGTH];
2508:
2509: double ***varpij;
2510:
2511: strcpy(fileresprob,"prob");
2512: strcat(fileresprob,fileres);
2513: if((ficresprob=fopen(fileresprob,"w"))==NULL) {
2514: printf("Problem with resultfile: %s\n", fileresprob);
2515: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
2516: }
2517: strcpy(fileresprobcov,"probcov");
2518: strcat(fileresprobcov,fileres);
2519: if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
2520: printf("Problem with resultfile: %s\n", fileresprobcov);
2521: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
2522: }
2523: strcpy(fileresprobcor,"probcor");
2524: strcat(fileresprobcor,fileres);
2525: if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
2526: printf("Problem with resultfile: %s\n", fileresprobcor);
2527: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
2528: }
2529: printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
2530: fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
2531: printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
2532: fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
2533: printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
2534: fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
2535:
2536: fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
2537: fprintf(ficresprob,"# Age");
2538: fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
2539: fprintf(ficresprobcov,"# Age");
2540: fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
2541: fprintf(ficresprobcov,"# Age");
2542:
2543:
2544: for(i=1; i<=nlstate;i++)
2545: for(j=1; j<=(nlstate+ndeath);j++){
2546: fprintf(ficresprob," p%1d-%1d (SE)",i,j);
2547: fprintf(ficresprobcov," p%1d-%1d ",i,j);
2548: fprintf(ficresprobcor," p%1d-%1d ",i,j);
2549: }
1.69 brouard 2550: /* fprintf(ficresprob,"\n");
1.53 brouard 2551: fprintf(ficresprobcov,"\n");
2552: fprintf(ficresprobcor,"\n");
1.69 brouard 2553: */
2554: xp=vector(1,npar);
1.53 brouard 2555: dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
2556: doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
2557: mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
2558: varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
2559: first=1;
2560: if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {
2561: printf("Problem with gnuplot file: %s\n", optionfilegnuplot);
2562: fprintf(ficlog,"Problem with gnuplot file: %s\n", optionfilegnuplot);
2563: exit(0);
2564: }
2565: else{
2566: fprintf(ficgp,"\n# Routine varprob");
2567: }
2568: if((fichtm=fopen(optionfilehtm,"a"))==NULL) {
2569: printf("Problem with html file: %s\n", optionfilehtm);
2570: fprintf(ficlog,"Problem with html file: %s\n", optionfilehtm);
2571: exit(0);
2572: }
2573: else{
2574: fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
2575: fprintf(fichtm,"\n");
2576:
2577: fprintf(fichtm,"\n<li><h4> Computing matrix of variance-covariance of step probabilities</h4></li>\n");
2578: 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");
2579: 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");
2580:
2581: }
2582:
2583: cov[1]=1;
2584: tj=cptcoveff;
2585: if (cptcovn<1) {tj=1;ncodemax[1]=1;}
2586: j1=0;
2587: for(t=1; t<=tj;t++){
2588: for(i1=1; i1<=ncodemax[t];i1++){
2589: j1++;
2590: if (cptcovn>0) {
2591: fprintf(ficresprob, "\n#********** Variable ");
2592: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
1.69 brouard 2593: fprintf(ficresprob, "**********\n#\n");
1.53 brouard 2594: fprintf(ficresprobcov, "\n#********** Variable ");
2595: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
1.69 brouard 2596: fprintf(ficresprobcov, "**********\n#\n");
1.53 brouard 2597:
2598: fprintf(ficgp, "\n#********** Variable ");
1.69 brouard 2599: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
2600: fprintf(ficgp, "**********\n#\n");
1.53 brouard 2601:
2602:
2603: fprintf(fichtm, "\n<hr size=\"2\" color=\"#EC5E5E\">********** Variable ");
2604: for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
2605: fprintf(fichtm, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
2606:
2607: fprintf(ficresprobcor, "\n#********** Variable ");
2608: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
1.69 brouard 2609: fprintf(ficresprobcor, "**********\n#");
1.53 brouard 2610: }
2611:
2612: for (age=bage; age<=fage; age ++){
2613: cov[2]=age;
2614: for (k=1; k<=cptcovn;k++) {
2615: cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];
2616: }
2617: for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
2618: for (k=1; k<=cptcovprod;k++)
2619: cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
2620:
2621: gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
2622: trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
2623: gp=vector(1,(nlstate)*(nlstate+ndeath));
2624: gm=vector(1,(nlstate)*(nlstate+ndeath));
2625:
2626: for(theta=1; theta <=npar; theta++){
2627: for(i=1; i<=npar; i++)
1.74 brouard 2628: xp[i] = x[i] + (i==theta ?delti[theta]:(double)0);
1.53 brouard 2629:
2630: pmij(pmmij,cov,ncovmodel,xp,nlstate);
2631:
2632: k=0;
2633: for(i=1; i<= (nlstate); i++){
2634: for(j=1; j<=(nlstate+ndeath);j++){
2635: k=k+1;
2636: gp[k]=pmmij[i][j];
2637: }
2638: }
2639:
2640: for(i=1; i<=npar; i++)
1.74 brouard 2641: xp[i] = x[i] - (i==theta ?delti[theta]:(double)0);
1.53 brouard 2642:
2643: pmij(pmmij,cov,ncovmodel,xp,nlstate);
2644: k=0;
2645: for(i=1; i<=(nlstate); i++){
2646: for(j=1; j<=(nlstate+ndeath);j++){
2647: k=k+1;
2648: gm[k]=pmmij[i][j];
2649: }
2650: }
2651:
2652: for(i=1; i<= (nlstate)*(nlstate+ndeath); i++)
1.74 brouard 2653: gradg[theta][i]=(gp[i]-gm[i])/(double)2./delti[theta];
1.53 brouard 2654: }
2655:
2656: for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
2657: for(theta=1; theta <=npar; theta++)
2658: trgradg[j][theta]=gradg[theta][j];
2659:
2660: matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov);
2661: matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);
1.59 brouard 2662: free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
2663: free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
2664: free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
2665: free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
2666:
1.53 brouard 2667: pmij(pmmij,cov,ncovmodel,x,nlstate);
2668:
2669: k=0;
2670: for(i=1; i<=(nlstate); i++){
2671: for(j=1; j<=(nlstate+ndeath);j++){
2672: k=k+1;
2673: mu[k][(int) age]=pmmij[i][j];
2674: }
2675: }
2676: for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
2677: for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
2678: varpij[i][j][(int)age] = doldm[i][j];
2679:
2680: /*printf("\n%d ",(int)age);
1.59 brouard 2681: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
2682: printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
2683: fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
2684: }*/
1.53 brouard 2685:
2686: fprintf(ficresprob,"\n%d ",(int)age);
2687: fprintf(ficresprobcov,"\n%d ",(int)age);
2688: fprintf(ficresprobcor,"\n%d ",(int)age);
2689:
2690: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)
2691: fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));
2692: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
2693: fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);
2694: fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
2695: }
2696: i=0;
2697: for (k=1; k<=(nlstate);k++){
2698: for (l=1; l<=(nlstate+ndeath);l++){
2699: i=i++;
2700: fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
2701: fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
2702: for (j=1; j<=i;j++){
2703: fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);
2704: fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));
2705: }
2706: }
2707: }/* end of loop for state */
2708: } /* end of loop for age */
2709:
2710: /* Confidence intervalle of pij */
2711: /*
1.59 brouard 2712: fprintf(ficgp,"\nset noparametric;unset label");
2713: fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");
2714: fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
2715: 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);
2716: fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);
2717: fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);
2718: fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);
1.53 brouard 2719: */
2720:
2721: /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
2722: first1=1;
2723: for (k2=1; k2<=(nlstate);k2++){
2724: for (l2=1; l2<=(nlstate+ndeath);l2++){
2725: if(l2==k2) continue;
2726: j=(k2-1)*(nlstate+ndeath)+l2;
2727: for (k1=1; k1<=(nlstate);k1++){
2728: for (l1=1; l1<=(nlstate+ndeath);l1++){
2729: if(l1==k1) continue;
2730: i=(k1-1)*(nlstate+ndeath)+l1;
2731: if(i<=j) continue;
2732: for (age=bage; age<=fage; age ++){
2733: if ((int)age %5==0){
2734: v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;
2735: v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;
2736: cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;
2737: mu1=mu[i][(int) age]/stepm*YEARM ;
2738: mu2=mu[j][(int) age]/stepm*YEARM;
2739: c12=cv12/sqrt(v1*v2);
2740: /* Computing eigen value of matrix of covariance */
2741: lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
2742: lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
2743: /* Eigen vectors */
2744: v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
2745: /*v21=sqrt(1.-v11*v11); *//* error */
2746: v21=(lc1-v1)/cv12*v11;
2747: v12=-v21;
2748: v22=v11;
2749: tnalp=v21/v11;
2750: if(first1==1){
2751: first1=0;
2752: 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);
2753: }
2754: 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);
2755: /*printf(fignu*/
2756: /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */
2757: /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */
2758: if(first==1){
2759: first=0;
2760: fprintf(ficgp,"\nset parametric;unset label");
2761: 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);
2762: fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
2763: 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);
2764: fprintf(fichtm,"\n<br><img src=\"varpijgr%s%d%1d%1d-%1d%1d.png\"> ",optionfilefiname, j1,k1,l1,k2,l2);
2765: fprintf(fichtm,"\n<br> Correlation at age %d (%.3f),",(int) age, c12);
2766: fprintf(ficgp,"\nset out \"varpijgr%s%d%1d%1d-%1d%1d.png\"",optionfilefiname, j1,k1,l1,k2,l2);
2767: fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
2768: fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
2769: 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",\
2770: mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
2771: mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
2772: }else{
2773: first=0;
2774: fprintf(fichtm," %d (%.3f),",(int) age, c12);
2775: fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
2776: fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
2777: 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",\
2778: mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
2779: mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
2780: }/* if first */
2781: } /* age mod 5 */
2782: } /* end loop age */
2783: fprintf(ficgp,"\nset out \"varpijgr%s%d%1d%1d-%1d%1d.png\";replot;",optionfilefiname, j1,k1,l1,k2,l2);
2784: first=1;
2785: } /*l12 */
2786: } /* k12 */
2787: } /*l1 */
2788: }/* k1 */
2789: } /* loop covariates */
2790: }
1.59 brouard 2791: free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
2792: free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
1.53 brouard 2793: free_vector(xp,1,npar);
2794: fclose(ficresprob);
2795: fclose(ficresprobcov);
2796: fclose(ficresprobcor);
2797: fclose(ficgp);
2798: fclose(fichtm);
2799: }
2800:
2801:
2802: /******************* Printing html file ***********/
2803: void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \
2804: int lastpass, int stepm, int weightopt, char model[],\
2805: int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
2806: int popforecast, int estepm ,\
2807: double jprev1, double mprev1,double anprev1, \
2808: double jprev2, double mprev2,double anprev2){
2809: int jj1, k1, i1, cpt;
2810: /*char optionfilehtm[FILENAMELENGTH];*/
2811: if((fichtm=fopen(optionfilehtm,"a"))==NULL) {
2812: printf("Problem with %s \n",optionfilehtm), exit(0);
2813: fprintf(ficlog,"Problem with %s \n",optionfilehtm), exit(0);
2814: }
2815:
2816: fprintf(fichtm,"<ul><li><h4>Result files (first order: no variance)</h4>\n
2817: - 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
2818: - Estimated transition probabilities over %d (stepm) months: <a href=\"pij%s\">pij%s</a><br>\n
2819: - Stable prevalence in each health state: <a href=\"pl%s\">pl%s</a> <br>\n
2820: - Life expectancies by age and initial health status (estepm=%2d months):
2821: <a href=\"e%s\">e%s</a> <br>\n</li>", \
2822: jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,fileres,fileres,stepm,fileres,fileres,fileres,fileres,estepm,fileres,fileres);
2823:
2824: fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
2825:
2826: m=cptcoveff;
2827: if (cptcovn < 1) {m=1;ncodemax[1]=1;}
2828:
2829: jj1=0;
2830: for(k1=1; k1<=m;k1++){
2831: for(i1=1; i1<=ncodemax[k1];i1++){
2832: jj1++;
2833: if (cptcovn > 0) {
2834: fprintf(fichtm,"<hr size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
2835: for (cpt=1; cpt<=cptcoveff;cpt++)
2836: fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
2837: fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
2838: }
2839: /* Pij */
1.76 brouard 2840: 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 2841: <img src=\"pe%s%d1.png\">",stepm,strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);
2842: /* Quasi-incidences */
2843: 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>
2844: <img src=\"pe%s%d2.png\">",stepm,strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);
2845: /* Stable prevalence in each health state */
2846: for(cpt=1; cpt<nlstate;cpt++){
2847: fprintf(fichtm,"<br>- Stable prevalence in each health state : p%s%d%d.png<br>
2848: <img src=\"p%s%d%d.png\">",strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);
2849: }
2850: for(cpt=1; cpt<=nlstate;cpt++) {
2851: fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): exp%s%d%d.png <br>
2852: <img src=\"exp%s%d%d.png\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);
2853: }
2854: fprintf(fichtm,"\n<br>- Total life expectancy by age and
2855: health expectancies in states (1) and (2): e%s%d.png<br>
2856: <img src=\"e%s%d.png\">",strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);
2857: } /* end i1 */
2858: }/* End k1 */
2859: fprintf(fichtm,"</ul>");
2860:
2861:
2862: fprintf(fichtm,"\n<br><li><h4> Result files (second order: variances)</h4>\n
2863: - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n
2864: - Variance of one-step probabilities: <a href=\"prob%s\">prob%s</a> <br>\n
2865: - Variance-covariance of one-step probabilities: <a href=\"probcov%s\">probcov%s</a> <br>\n
2866: - Correlation matrix of one-step probabilities: <a href=\"probcor%s\">probcor%s</a> <br>\n
2867: - Variances and covariances of life expectancies by age and initial health status (estepm=%d months): <a href=\"v%s\">v%s</a><br>\n
2868: - Health expectancies with their variances (no covariance): <a href=\"t%s\">t%s</a> <br>\n
2869: - 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);
2870:
1.76 brouard 2871: /* if(popforecast==1) fprintf(fichtm,"\n */
2872: /* - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n */
2873: /* - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n */
2874: /* <br>",fileres,fileres,fileres,fileres); */
2875: /* else */
2876: /* 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 2877: fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
2878:
2879: m=cptcoveff;
2880: if (cptcovn < 1) {m=1;ncodemax[1]=1;}
2881:
2882: jj1=0;
2883: for(k1=1; k1<=m;k1++){
2884: for(i1=1; i1<=ncodemax[k1];i1++){
2885: jj1++;
2886: if (cptcovn > 0) {
2887: fprintf(fichtm,"<hr size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
2888: for (cpt=1; cpt<=cptcoveff;cpt++)
2889: fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
2890: fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
2891: }
2892: for(cpt=1; cpt<=nlstate;cpt++) {
1.76 brouard 2893: fprintf(fichtm,"<br>- Observed and period prevalence (with confident
1.53 brouard 2894: interval) in state (%d): v%s%d%d.png <br>
2895: <img src=\"v%s%d%d.png\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);
2896: }
2897: } /* end i1 */
2898: }/* End k1 */
2899: fprintf(fichtm,"</ul>");
2900: fclose(fichtm);
2901: }
2902:
2903: /******************* Gnuplot file **************/
2904: void printinggnuplot(char fileres[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
2905:
2906: int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;
2907: int ng;
2908: if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {
2909: printf("Problem with file %s",optionfilegnuplot);
2910: fprintf(ficlog,"Problem with file %s",optionfilegnuplot);
2911: }
2912:
1.54 brouard 2913: /*#ifdef windows */
1.53 brouard 2914: fprintf(ficgp,"cd \"%s\" \n",pathc);
1.54 brouard 2915: /*#endif */
1.53 brouard 2916: m=pow(2,cptcoveff);
2917:
2918: /* 1eme*/
2919: for (cpt=1; cpt<= nlstate ; cpt ++) {
2920: for (k1=1; k1<= m ; k1 ++) {
2921: fprintf(ficgp,"\nset out \"v%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);
2922: 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);
2923:
2924: for (i=1; i<= nlstate ; i ++) {
2925: if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
2926: else fprintf(ficgp," \%%*lf (\%%*lf)");
2927: }
1.69 brouard 2928: 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 2929: for (i=1; i<= nlstate ; i ++) {
2930: if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
2931: else fprintf(ficgp," \%%*lf (\%%*lf)");
2932: }
1.69 brouard 2933: fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"vpl%s\" every :::%d::%d u 1:($2-1.96*$3) \"\%%lf",fileres,k1-1,k1-1);
1.53 brouard 2934: for (i=1; i<= nlstate ; i ++) {
2935: if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
2936: else fprintf(ficgp," \%%*lf (\%%*lf)");
2937: }
2938: fprintf(ficgp,"\" t\"\" w l 1,\"p%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",fileres,k1-1,k1-1,2+4*(cpt-1));
2939: }
2940: }
2941: /*2 eme*/
2942:
2943: for (k1=1; k1<= m ; k1 ++) {
2944: fprintf(ficgp,"\nset out \"e%s%d.png\" \n",strtok(optionfile, "."),k1);
2945: fprintf(ficgp,"set ylabel \"Years\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] ",ageminpar,fage);
2946:
2947: for (i=1; i<= nlstate+1 ; i ++) {
2948: k=2*i;
2949: fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:2 \"\%%lf",fileres,k1-1,k1-1);
2950: for (j=1; j<= nlstate+1 ; j ++) {
2951: if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
2952: else fprintf(ficgp," \%%*lf (\%%*lf)");
2953: }
2954: if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");
2955: else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);
2956: fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",fileres,k1-1,k1-1);
2957: for (j=1; j<= nlstate+1 ; j ++) {
2958: if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
2959: else fprintf(ficgp," \%%*lf (\%%*lf)");
2960: }
2961: fprintf(ficgp,"\" t\"\" w l 0,");
2962: fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",fileres,k1-1,k1-1);
2963: for (j=1; j<= nlstate+1 ; j ++) {
2964: if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
2965: else fprintf(ficgp," \%%*lf (\%%*lf)");
2966: }
2967: if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");
2968: else fprintf(ficgp,"\" t\"\" w l 0,");
2969: }
2970: }
2971:
2972: /*3eme*/
2973:
2974: for (k1=1; k1<= m ; k1 ++) {
2975: for (cpt=1; cpt<= nlstate ; cpt ++) {
2976: k=2+nlstate*(2*cpt-2);
2977: fprintf(ficgp,"\nset out \"exp%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);
2978: fprintf(ficgp,"set ter png small\nset size 0.65,0.65\nplot [%.f:%.f] \"e%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,fileres,k1-1,k1-1,k,cpt);
2979: /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
2980: for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
2981: fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
2982: fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
2983: for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
2984: fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
2985:
2986: */
2987: for (i=1; i< nlstate ; i ++) {
2988: 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);
2989:
2990: }
2991: }
2992: }
2993:
1.76 brouard 2994: /* CV preval stable (period) */
1.53 brouard 2995: for (k1=1; k1<= m ; k1 ++) {
1.76 brouard 2996: for (cpt=1; cpt<=nlstate ; cpt ++) {
1.53 brouard 2997: k=3;
2998: fprintf(ficgp,"\nset out \"p%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);
2999: 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/($%d",ageminpar,agemaxpar,fileres,k1,k+cpt+1,k+1);
3000:
1.83 ! lievre 3001: for (i=1; i< nlstate ; i ++)
1.53 brouard 3002: fprintf(ficgp,"+$%d",k+i+1);
3003: fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);
3004:
3005: l=3+(nlstate+ndeath)*cpt;
3006: fprintf(ficgp,",\"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",fileres,k1,l+cpt+1,l+1);
3007: for (i=1; i< nlstate ; i ++) {
3008: l=3+(nlstate+ndeath)*cpt;
3009: fprintf(ficgp,"+$%d",l+i+1);
3010: }
3011: fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);
3012: }
3013: }
3014:
3015: /* proba elementaires */
3016: for(i=1,jk=1; i <=nlstate; i++){
3017: for(k=1; k <=(nlstate+ndeath); k++){
3018: if (k != i) {
3019: for(j=1; j <=ncovmodel; j++){
3020: fprintf(ficgp,"p%d=%f ",jk,p[jk]);
3021: jk++;
3022: fprintf(ficgp,"\n");
3023: }
3024: }
3025: }
3026: }
3027:
3028: for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/
3029: for(jk=1; jk <=m; jk++) {
3030: fprintf(ficgp,"\nset out \"pe%s%d%d.png\" \n",strtok(optionfile, "."),jk,ng);
3031: if (ng==2)
3032: fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
3033: else
3034: fprintf(ficgp,"\nset title \"Probability\"\n");
3035: fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65\nset log y\nplot [%.f:%.f] ",ageminpar,agemaxpar);
3036: i=1;
3037: for(k2=1; k2<=nlstate; k2++) {
3038: k3=i;
3039: for(k=1; k<=(nlstate+ndeath); k++) {
3040: if (k != k2){
3041: if(ng==2)
3042: fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);
3043: else
3044: fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
3045: ij=1;
3046: for(j=3; j <=ncovmodel; j++) {
3047: if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
3048: fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
3049: ij++;
3050: }
3051: else
3052: fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
3053: }
3054: fprintf(ficgp,")/(1");
3055:
3056: for(k1=1; k1 <=nlstate; k1++){
3057: fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);
3058: ij=1;
3059: for(j=3; j <=ncovmodel; j++){
3060: if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
3061: fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
3062: ij++;
3063: }
3064: else
3065: fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
3066: }
3067: fprintf(ficgp,")");
3068: }
3069: fprintf(ficgp,") t \"p%d%d\" ", k2,k);
3070: if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");
3071: i=i+ncovmodel;
3072: }
3073: } /* end k */
3074: } /* end k2 */
3075: } /* end jk */
3076: } /* end ng */
3077: fclose(ficgp);
3078: } /* end gnuplot */
3079:
3080:
3081: /*************** Moving average **************/
1.54 brouard 3082: int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav){
1.53 brouard 3083:
3084: int i, cpt, cptcod;
1.58 lievre 3085: int modcovmax =1;
1.54 brouard 3086: int mobilavrange, mob;
1.53 brouard 3087: double age;
1.58 lievre 3088:
3089: modcovmax=2*cptcoveff;/* Max number of modalities. We suppose
3090: a covariate has 2 modalities */
3091: if (cptcovn<1) modcovmax=1; /* At least 1 pass */
3092:
1.54 brouard 3093: if(mobilav==1||mobilav ==3 ||mobilav==5 ||mobilav== 7){
3094: if(mobilav==1) mobilavrange=5; /* default */
3095: else mobilavrange=mobilav;
3096: for (age=bage; age<=fage; age++)
3097: for (i=1; i<=nlstate;i++)
1.58 lievre 3098: for (cptcod=1;cptcod<=modcovmax;cptcod++)
1.54 brouard 3099: mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
3100: /* We keep the original values on the extreme ages bage, fage and for
3101: fage+1 and bage-1 we use a 3 terms moving average; for fage+2 bage+2
3102: we use a 5 terms etc. until the borders are no more concerned.
3103: */
3104: for (mob=3;mob <=mobilavrange;mob=mob+2){
3105: for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){
3106: for (i=1; i<=nlstate;i++){
1.58 lievre 3107: for (cptcod=1;cptcod<=modcovmax;cptcod++){
1.54 brouard 3108: mobaverage[(int)age][i][cptcod] =probs[(int)age][i][cptcod];
3109: for (cpt=1;cpt<=(mob-1)/2;cpt++){
3110: mobaverage[(int)age][i][cptcod] +=probs[(int)age-cpt][i][cptcod];
3111: mobaverage[(int)age][i][cptcod] +=probs[(int)age+cpt][i][cptcod];
3112: }
3113: mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/mob;
3114: }
1.53 brouard 3115: }
1.54 brouard 3116: }/* end age */
3117: }/* end mob */
3118: }else return -1;
3119: return 0;
3120: }/* End movingaverage */
1.53 brouard 3121:
3122:
3123: /************** Forecasting ******************/
1.70 brouard 3124: 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 3125: /* proj1, year, month, day of starting projection
3126: agemin, agemax range of age
3127: dateprev1 dateprev2 range of dates during which prevalence is computed
1.70 brouard 3128: anproj2 year of en of projection (same day and month as proj1).
1.69 brouard 3129: */
1.73 lievre 3130: int yearp, stepsize, hstepm, nhstepm, j, k, c, cptcod, i, h, i1;
1.53 brouard 3131: int *popage;
1.70 brouard 3132: double agec; /* generic age */
3133: double agelim, ppij, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
1.53 brouard 3134: double *popeffectif,*popcount;
3135: double ***p3mat;
1.55 lievre 3136: double ***mobaverage;
1.53 brouard 3137: char fileresf[FILENAMELENGTH];
3138:
1.69 brouard 3139: agelim=AGESUP;
1.70 brouard 3140: prevalence(ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
1.53 brouard 3141:
3142: strcpy(fileresf,"f");
3143: strcat(fileresf,fileres);
3144: if((ficresf=fopen(fileresf,"w"))==NULL) {
3145: printf("Problem with forecast resultfile: %s\n", fileresf);
3146: fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);
3147: }
3148: printf("Computing forecasting: result on file '%s' \n", fileresf);
3149: fprintf(ficlog,"Computing forecasting: result on file '%s' \n", fileresf);
3150:
3151: if (cptcoveff==0) ncodemax[cptcoveff]=1;
3152:
1.54 brouard 3153: if (mobilav!=0) {
1.53 brouard 3154: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
1.54 brouard 3155: if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
3156: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
3157: printf(" Error in movingaverage mobilav=%d\n",mobilav);
3158: }
1.53 brouard 3159: }
3160:
3161: stepsize=(int) (stepm+YEARM-1)/YEARM;
3162: if (stepm<=12) stepsize=1;
1.74 brouard 3163: if(estepm < stepm){
3164: printf ("Problem %d lower than %d\n",estepm, stepm);
3165: }
3166: else hstepm=estepm;
3167:
1.53 brouard 3168: hstepm=hstepm/stepm;
1.69 brouard 3169: yp1=modf(dateintmean,&yp);/* extracts integral of datemean in yp and
3170: fractional in yp1 */
1.53 brouard 3171: anprojmean=yp;
3172: yp2=modf((yp1*12),&yp);
3173: mprojmean=yp;
3174: yp1=modf((yp2*30.5),&yp);
3175: jprojmean=yp;
3176: if(jprojmean==0) jprojmean=1;
3177: if(mprojmean==0) jprojmean=1;
1.73 lievre 3178:
3179: i1=cptcoveff;
3180: if (cptcovn < 1){i1=1;}
1.53 brouard 3181:
1.70 brouard 3182: fprintf(ficresf,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2);
1.53 brouard 3183:
1.70 brouard 3184: fprintf(ficresf,"#****** Routine prevforecast **\n");
1.73 lievre 3185:
1.75 brouard 3186: /* if (h==(int)(YEARM*yearp)){ */
1.73 lievre 3187: for(cptcov=1, k=0;cptcov<=i1;cptcov++){
1.53 brouard 3188: for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
3189: k=k+1;
3190: fprintf(ficresf,"\n#******");
3191: for(j=1;j<=cptcoveff;j++) {
1.70 brouard 3192: 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 3193: }
3194: fprintf(ficresf,"******\n");
1.70 brouard 3195: fprintf(ficresf,"# Covariate valuofcovar yearproj age");
3196: for(j=1; j<=nlstate+ndeath;j++){
3197: for(i=1; i<=nlstate;i++)
3198: fprintf(ficresf," p%d%d",i,j);
3199: fprintf(ficresf," p.%d",j);
3200: }
1.74 brouard 3201: for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) {
1.53 brouard 3202: fprintf(ficresf,"\n");
1.70 brouard 3203: fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+yearp);
1.53 brouard 3204:
1.71 brouard 3205: for (agec=fage; agec>=(ageminpar-1); agec--){
1.70 brouard 3206: nhstepm=(int) rint((agelim-agec)*YEARM/stepm);
1.53 brouard 3207: nhstepm = nhstepm/hstepm;
3208: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3209: oldm=oldms;savm=savms;
1.70 brouard 3210: hpxij(p3mat,nhstepm,agec,hstepm,p,nlstate,stepm,oldm,savm, k);
1.53 brouard 3211:
3212: for (h=0; h<=nhstepm; h++){
1.75 brouard 3213: if (h*hstepm/YEARM*stepm ==yearp) {
1.69 brouard 3214: fprintf(ficresf,"\n");
3215: for(j=1;j<=cptcoveff;j++)
3216: fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
1.70 brouard 3217: fprintf(ficresf,"%.f %.f ",anproj1+yearp,agec+h*hstepm/YEARM*stepm);
1.53 brouard 3218: }
3219: for(j=1; j<=nlstate+ndeath;j++) {
1.70 brouard 3220: ppij=0.;
1.71 brouard 3221: for(i=1; i<=nlstate;i++) {
1.53 brouard 3222: if (mobilav==1)
1.71 brouard 3223: ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][i][cptcod];
1.53 brouard 3224: else {
1.71 brouard 3225: ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][cptcod];
1.53 brouard 3226: }
1.75 brouard 3227: if (h*hstepm/YEARM*stepm== yearp) {
1.70 brouard 3228: fprintf(ficresf," %.3f", p3mat[i][j][h]);
1.75 brouard 3229: }
3230: } /* end i */
3231: if (h*hstepm/YEARM*stepm==yearp) {
1.70 brouard 3232: fprintf(ficresf," %.3f", ppij);
1.53 brouard 3233: }
1.75 brouard 3234: }/* end j */
3235: } /* end h */
1.53 brouard 3236: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
1.75 brouard 3237: } /* end agec */
3238: } /* end yearp */
3239: } /* end cptcod */
3240: } /* end cptcov */
1.53 brouard 3241:
1.54 brouard 3242: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
1.53 brouard 3243:
3244: fclose(ficresf);
3245: }
1.70 brouard 3246:
3247: /************** Forecasting *****not tested NB*************/
1.53 brouard 3248: 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){
3249:
3250: int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;
3251: int *popage;
1.69 brouard 3252: double calagedatem, agelim, kk1, kk2;
1.53 brouard 3253: double *popeffectif,*popcount;
3254: double ***p3mat,***tabpop,***tabpopprev;
1.55 lievre 3255: double ***mobaverage;
1.53 brouard 3256: char filerespop[FILENAMELENGTH];
3257:
3258: tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
3259: tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
3260: agelim=AGESUP;
1.69 brouard 3261: calagedatem=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;
1.53 brouard 3262:
1.70 brouard 3263: prevalence(ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
1.53 brouard 3264:
3265:
3266: strcpy(filerespop,"pop");
3267: strcat(filerespop,fileres);
3268: if((ficrespop=fopen(filerespop,"w"))==NULL) {
3269: printf("Problem with forecast resultfile: %s\n", filerespop);
3270: fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop);
3271: }
3272: printf("Computing forecasting: result on file '%s' \n", filerespop);
3273: fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop);
3274:
3275: if (cptcoveff==0) ncodemax[cptcoveff]=1;
3276:
1.54 brouard 3277: if (mobilav!=0) {
1.53 brouard 3278: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
1.54 brouard 3279: if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
3280: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
3281: printf(" Error in movingaverage mobilav=%d\n",mobilav);
3282: }
1.53 brouard 3283: }
3284:
3285: stepsize=(int) (stepm+YEARM-1)/YEARM;
3286: if (stepm<=12) stepsize=1;
3287:
3288: agelim=AGESUP;
3289:
3290: hstepm=1;
3291: hstepm=hstepm/stepm;
3292:
3293: if (popforecast==1) {
3294: if((ficpop=fopen(popfile,"r"))==NULL) {
3295: printf("Problem with population file : %s\n",popfile);exit(0);
3296: fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0);
3297: }
3298: popage=ivector(0,AGESUP);
3299: popeffectif=vector(0,AGESUP);
3300: popcount=vector(0,AGESUP);
3301:
3302: i=1;
3303: while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;
3304:
3305: imx=i;
3306: for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];
3307: }
3308:
1.69 brouard 3309: for(cptcov=1,k=0;cptcov<=i2;cptcov++){
1.53 brouard 3310: for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
3311: k=k+1;
3312: fprintf(ficrespop,"\n#******");
3313: for(j=1;j<=cptcoveff;j++) {
3314: fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
3315: }
3316: fprintf(ficrespop,"******\n");
3317: fprintf(ficrespop,"# Age");
3318: for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);
3319: if (popforecast==1) fprintf(ficrespop," [Population]");
3320:
3321: for (cpt=0; cpt<=0;cpt++) {
3322: fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);
3323:
1.69 brouard 3324: for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){
1.53 brouard 3325: nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);
3326: nhstepm = nhstepm/hstepm;
3327:
3328: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3329: oldm=oldms;savm=savms;
3330: hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
3331:
3332: for (h=0; h<=nhstepm; h++){
1.69 brouard 3333: if (h==(int) (calagedatem+YEARM*cpt)) {
1.53 brouard 3334: fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
3335: }
3336: for(j=1; j<=nlstate+ndeath;j++) {
3337: kk1=0.;kk2=0;
3338: for(i=1; i<=nlstate;i++) {
3339: if (mobilav==1)
3340: kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];
3341: else {
3342: kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];
3343: }
3344: }
1.69 brouard 3345: if (h==(int)(calagedatem+12*cpt)){
1.53 brouard 3346: tabpop[(int)(agedeb)][j][cptcod]=kk1;
3347: /*fprintf(ficrespop," %.3f", kk1);
3348: if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/
3349: }
3350: }
3351: for(i=1; i<=nlstate;i++){
3352: kk1=0.;
3353: for(j=1; j<=nlstate;j++){
3354: kk1= kk1+tabpop[(int)(agedeb)][j][cptcod];
3355: }
1.69 brouard 3356: tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedatem+12*cpt)*hstepm/YEARM*stepm-1)];
1.53 brouard 3357: }
3358:
1.69 brouard 3359: if (h==(int)(calagedatem+12*cpt)) for(j=1; j<=nlstate;j++)
1.53 brouard 3360: fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);
3361: }
3362: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3363: }
3364: }
3365:
3366: /******/
3367:
3368: for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) {
3369: fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);
1.69 brouard 3370: for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){
1.53 brouard 3371: nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);
3372: nhstepm = nhstepm/hstepm;
3373:
3374: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3375: oldm=oldms;savm=savms;
3376: hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
3377: for (h=0; h<=nhstepm; h++){
1.69 brouard 3378: if (h==(int) (calagedatem+YEARM*cpt)) {
1.53 brouard 3379: fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
3380: }
3381: for(j=1; j<=nlstate+ndeath;j++) {
3382: kk1=0.;kk2=0;
3383: for(i=1; i<=nlstate;i++) {
3384: kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];
3385: }
1.69 brouard 3386: if (h==(int)(calagedatem+12*cpt)) fprintf(ficresf," %15.2f", kk1);
1.53 brouard 3387: }
3388: }
3389: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3390: }
3391: }
3392: }
3393: }
3394:
1.54 brouard 3395: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
1.53 brouard 3396:
3397: if (popforecast==1) {
3398: free_ivector(popage,0,AGESUP);
3399: free_vector(popeffectif,0,AGESUP);
3400: free_vector(popcount,0,AGESUP);
3401: }
3402: free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
3403: free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
3404: fclose(ficrespop);
3405: }
3406:
3407: /***********************************************/
3408: /**************** Main Program *****************/
3409: /***********************************************/
3410:
3411: int main(int argc, char *argv[])
3412: {
1.61 brouard 3413: int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav);
1.74 brouard 3414: int i,j, k, n=MAXN,iter,m,size=100,cptcode, cptcod;
1.53 brouard 3415: double agedeb, agefin,hf;
3416: double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;
3417:
3418: double fret;
3419: double **xi,tmp,delta;
3420:
3421: double dum; /* Dummy variable */
3422: double ***p3mat;
3423: double ***mobaverage;
3424: int *indx;
3425: char line[MAXLINE], linepar[MAXLINE];
3426: char path[80],pathc[80],pathcd[80],pathtot[80],model[80];
3427: int firstobs=1, lastobs=10;
3428: int sdeb, sfin; /* Status at beginning and end */
3429: int c, h , cpt,l;
3430: int ju,jl, mi;
3431: int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;
1.59 brouard 3432: int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,*tab;
1.69 brouard 3433: int mobilavproj=0 , prevfcast=0 ; /* moving average of prev, If prevfcast=1 prevalence projection */
1.53 brouard 3434: int mobilav=0,popforecast=0;
3435: int hstepm, nhstepm;
1.74 brouard 3436: double jprev1=1, mprev1=1,anprev1=2000,jprev2=1, mprev2=1,anprev2=2000;
3437: double jpyram=1, mpyram=1,anpyram=2000,jpyram1=1, mpyram1=1,anpyram1=2000;
1.53 brouard 3438:
3439: double bage, fage, age, agelim, agebase;
3440: double ftolpl=FTOL;
3441: double **prlim;
3442: double *severity;
3443: double ***param; /* Matrix of parameters */
3444: double *p;
3445: double **matcov; /* Matrix of covariance */
3446: double ***delti3; /* Scale */
3447: double *delti; /* Scale */
3448: double ***eij, ***vareij;
3449: double **varpl; /* Variances of prevalence limits by age */
3450: double *epj, vepp;
3451: double kk1, kk2;
1.74 brouard 3452: double dateprev1, dateprev2,jproj1=1,mproj1=1,anproj1=2000,jproj2=1,mproj2=1,anproj2=2000;
1.53 brouard 3453:
3454: char *alph[]={"a","a","b","c","d","e"}, str[4];
3455:
3456:
3457: char z[1]="c", occ;
3458: #include <sys/time.h>
3459: #include <time.h>
3460: char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];
3461:
3462: /* long total_usecs;
1.59 brouard 3463: struct timeval start_time, end_time;
1.53 brouard 3464:
1.59 brouard 3465: gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */
1.53 brouard 3466: getcwd(pathcd, size);
3467:
1.81 brouard 3468: printf("\n%s\n%s",version,fullversion);
1.53 brouard 3469: if(argc <=1){
3470: printf("\nEnter the parameter file name: ");
3471: scanf("%s",pathtot);
3472: }
3473: else{
3474: strcpy(pathtot,argv[1]);
3475: }
3476: /*if(getcwd(pathcd, 80)!= NULL)printf ("Error pathcd\n");*/
3477: /*cygwin_split_path(pathtot,path,optionfile);
3478: printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/
3479: /* cutv(path,optionfile,pathtot,'\\');*/
3480:
3481: split(pathtot,path,optionfile,optionfilext,optionfilefiname);
1.59 brouard 3482: printf("pathtot=%s, path=%s, optionfile=%s optionfilext=%s optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
1.53 brouard 3483: chdir(path);
3484: replace(pathc,path);
3485:
1.59 brouard 3486: /*-------- arguments in the command line --------*/
1.53 brouard 3487:
3488: /* Log file */
3489: strcat(filelog, optionfilefiname);
3490: strcat(filelog,".log"); /* */
3491: if((ficlog=fopen(filelog,"w"))==NULL) {
3492: printf("Problem with logfile %s\n",filelog);
3493: goto end;
3494: }
3495: fprintf(ficlog,"Log filename:%s\n",filelog);
3496: fprintf(ficlog,"\n%s",version);
3497: fprintf(ficlog,"\nEnter the parameter file name: ");
3498: fprintf(ficlog,"pathtot=%s, path=%s, optionfile=%s optionfilext=%s optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
3499: fflush(ficlog);
3500:
3501: /* */
3502: strcpy(fileres,"r");
3503: strcat(fileres, optionfilefiname);
3504: strcat(fileres,".txt"); /* Other files have txt extension */
3505:
3506: /*---------arguments file --------*/
3507:
3508: if((ficpar=fopen(optionfile,"r"))==NULL) {
3509: printf("Problem with optionfile %s\n",optionfile);
3510: fprintf(ficlog,"Problem with optionfile %s\n",optionfile);
3511: goto end;
3512: }
3513:
3514: strcpy(filereso,"o");
3515: strcat(filereso,fileres);
3516: if((ficparo=fopen(filereso,"w"))==NULL) {
3517: printf("Problem with Output resultfile: %s\n", filereso);
3518: fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso);
3519: goto end;
3520: }
3521:
3522: /* Reads comments: lines beginning with '#' */
3523: while((c=getc(ficpar))=='#' && c!= EOF){
3524: ungetc(c,ficpar);
3525: fgets(line, MAXLINE, ficpar);
3526: puts(line);
3527: fputs(line,ficparo);
3528: }
3529: ungetc(c,ficpar);
3530:
3531: 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);
3532: 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);
3533: 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 3534: while((c=getc(ficpar))=='#' && c!= EOF){
1.53 brouard 3535: ungetc(c,ficpar);
3536: fgets(line, MAXLINE, ficpar);
3537: puts(line);
3538: fputs(line,ficparo);
3539: }
3540: ungetc(c,ficpar);
3541:
3542:
3543: covar=matrix(0,NCOVMAX,1,n);
1.58 lievre 3544: cptcovn=0; /*Number of covariates, i.e. number of '+' in model statement*/
1.53 brouard 3545: if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;
3546:
1.58 lievre 3547: ncovmodel=2+cptcovn; /*Number of variables = cptcovn + intercept + age */
1.53 brouard 3548: nvar=ncovmodel-1; /* Suppressing age as a basic covariate */
3549:
3550: /* Read guess parameters */
3551: /* Reads comments: lines beginning with '#' */
3552: while((c=getc(ficpar))=='#' && c!= EOF){
3553: ungetc(c,ficpar);
3554: fgets(line, MAXLINE, ficpar);
3555: puts(line);
3556: fputs(line,ficparo);
3557: }
3558: ungetc(c,ficpar);
3559:
3560: param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
1.59 brouard 3561: for(i=1; i <=nlstate; i++)
1.53 brouard 3562: for(j=1; j <=nlstate+ndeath-1; j++){
3563: fscanf(ficpar,"%1d%1d",&i1,&j1);
3564: fprintf(ficparo,"%1d%1d",i1,j1);
3565: if(mle==1)
3566: printf("%1d%1d",i,j);
3567: fprintf(ficlog,"%1d%1d",i,j);
3568: for(k=1; k<=ncovmodel;k++){
3569: fscanf(ficpar," %lf",¶m[i][j][k]);
3570: if(mle==1){
3571: printf(" %lf",param[i][j][k]);
3572: fprintf(ficlog," %lf",param[i][j][k]);
3573: }
3574: else
3575: fprintf(ficlog," %lf",param[i][j][k]);
3576: fprintf(ficparo," %lf",param[i][j][k]);
3577: }
3578: fscanf(ficpar,"\n");
3579: if(mle==1)
3580: printf("\n");
3581: fprintf(ficlog,"\n");
3582: fprintf(ficparo,"\n");
3583: }
3584:
1.59 brouard 3585: npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/
1.53 brouard 3586:
3587: p=param[1][1];
3588:
3589: /* Reads comments: lines beginning with '#' */
3590: while((c=getc(ficpar))=='#' && c!= EOF){
3591: ungetc(c,ficpar);
3592: fgets(line, MAXLINE, ficpar);
3593: puts(line);
3594: fputs(line,ficparo);
3595: }
3596: ungetc(c,ficpar);
3597:
3598: delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
1.74 brouard 3599: /* delti=vector(1,npar); *//* Scale of each paramater (output from hesscov) */
1.53 brouard 3600: for(i=1; i <=nlstate; i++){
3601: for(j=1; j <=nlstate+ndeath-1; j++){
3602: fscanf(ficpar,"%1d%1d",&i1,&j1);
3603: printf("%1d%1d",i,j);
3604: fprintf(ficparo,"%1d%1d",i1,j1);
3605: for(k=1; k<=ncovmodel;k++){
3606: fscanf(ficpar,"%le",&delti3[i][j][k]);
3607: printf(" %le",delti3[i][j][k]);
3608: fprintf(ficparo," %le",delti3[i][j][k]);
3609: }
3610: fscanf(ficpar,"\n");
3611: printf("\n");
3612: fprintf(ficparo,"\n");
3613: }
3614: }
3615: delti=delti3[1][1];
1.74 brouard 3616:
3617:
3618: /* 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 3619:
3620: /* Reads comments: lines beginning with '#' */
3621: while((c=getc(ficpar))=='#' && c!= EOF){
3622: ungetc(c,ficpar);
3623: fgets(line, MAXLINE, ficpar);
3624: puts(line);
3625: fputs(line,ficparo);
3626: }
3627: ungetc(c,ficpar);
3628:
3629: matcov=matrix(1,npar,1,npar);
3630: for(i=1; i <=npar; i++){
3631: fscanf(ficpar,"%s",&str);
3632: if(mle==1)
3633: printf("%s",str);
3634: fprintf(ficlog,"%s",str);
3635: fprintf(ficparo,"%s",str);
3636: for(j=1; j <=i; j++){
3637: fscanf(ficpar," %le",&matcov[i][j]);
3638: if(mle==1){
3639: printf(" %.5le",matcov[i][j]);
3640: fprintf(ficlog," %.5le",matcov[i][j]);
3641: }
3642: else
3643: fprintf(ficlog," %.5le",matcov[i][j]);
3644: fprintf(ficparo," %.5le",matcov[i][j]);
3645: }
3646: fscanf(ficpar,"\n");
3647: if(mle==1)
3648: printf("\n");
3649: fprintf(ficlog,"\n");
3650: fprintf(ficparo,"\n");
3651: }
3652: for(i=1; i <=npar; i++)
3653: for(j=i+1;j<=npar;j++)
3654: matcov[i][j]=matcov[j][i];
3655:
3656: if(mle==1)
3657: printf("\n");
3658: fprintf(ficlog,"\n");
3659:
3660:
1.59 brouard 3661: /*-------- Rewriting paramater file ----------*/
3662: strcpy(rfileres,"r"); /* "Rparameterfile */
3663: strcat(rfileres,optionfilefiname); /* Parameter file first name*/
3664: strcat(rfileres,"."); /* */
3665: strcat(rfileres,optionfilext); /* Other files have txt extension */
3666: if((ficres =fopen(rfileres,"w"))==NULL) {
3667: printf("Problem writing new parameter file: %s\n", fileres);goto end;
3668: fprintf(ficlog,"Problem writing new parameter file: %s\n", fileres);goto end;
3669: }
3670: fprintf(ficres,"#%s\n",version);
1.53 brouard 3671:
1.59 brouard 3672: /*-------- data file ----------*/
3673: if((fic=fopen(datafile,"r"))==NULL) {
3674: printf("Problem with datafile: %s\n", datafile);goto end;
3675: fprintf(ficlog,"Problem with datafile: %s\n", datafile);goto end;
3676: }
3677:
3678: n= lastobs;
3679: severity = vector(1,maxwav);
3680: outcome=imatrix(1,maxwav+1,1,n);
3681: num=ivector(1,n);
3682: moisnais=vector(1,n);
3683: annais=vector(1,n);
3684: moisdc=vector(1,n);
3685: andc=vector(1,n);
3686: agedc=vector(1,n);
3687: cod=ivector(1,n);
3688: weight=vector(1,n);
3689: for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */
3690: mint=matrix(1,maxwav,1,n);
3691: anint=matrix(1,maxwav,1,n);
3692: s=imatrix(1,maxwav+1,1,n);
3693: tab=ivector(1,NCOVMAX);
3694: ncodemax=ivector(1,8);
3695:
3696: i=1;
3697: while (fgets(line, MAXLINE, fic) != NULL) {
3698: if ((i >= firstobs) && (i <=lastobs)) {
1.53 brouard 3699:
1.59 brouard 3700: for (j=maxwav;j>=1;j--){
3701: cutv(stra, strb,line,' '); s[j][i]=atoi(strb);
3702: strcpy(line,stra);
3703: cutv(stra, strb,line,'/'); anint[j][i]=(double)(atoi(strb)); strcpy(line,stra);
3704: cutv(stra, strb,line,' '); mint[j][i]=(double)(atoi(strb)); strcpy(line,stra);
3705: }
1.53 brouard 3706:
1.59 brouard 3707: cutv(stra, strb,line,'/'); andc[i]=(double)(atoi(strb)); strcpy(line,stra);
3708: cutv(stra, strb,line,' '); moisdc[i]=(double)(atoi(strb)); strcpy(line,stra);
1.53 brouard 3709:
1.59 brouard 3710: cutv(stra, strb,line,'/'); annais[i]=(double)(atoi(strb)); strcpy(line,stra);
3711: cutv(stra, strb,line,' '); moisnais[i]=(double)(atoi(strb)); strcpy(line,stra);
1.53 brouard 3712:
1.59 brouard 3713: cutv(stra, strb,line,' '); weight[i]=(double)(atoi(strb)); strcpy(line,stra);
3714: for (j=ncovcol;j>=1;j--){
3715: cutv(stra, strb,line,' '); covar[j][i]=(double)(atoi(strb)); strcpy(line,stra);
3716: }
3717: num[i]=atol(stra);
1.53 brouard 3718:
1.59 brouard 3719: /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){
3720: 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 3721:
1.59 brouard 3722: i=i+1;
3723: }
3724: }
3725: /* printf("ii=%d", ij);
3726: scanf("%d",i);*/
1.53 brouard 3727: imx=i-1; /* Number of individuals */
3728:
3729: /* for (i=1; i<=imx; i++){
3730: if ((s[1][i]==3) && (s[2][i]==2)) s[2][i]=3;
3731: if ((s[2][i]==3) && (s[3][i]==2)) s[3][i]=3;
3732: if ((s[3][i]==3) && (s[4][i]==2)) s[4][i]=3;
3733: }*/
3734: /* for (i=1; i<=imx; i++){
3735: if (s[4][i]==9) s[4][i]=-1;
3736: 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]));}*/
3737:
1.71 brouard 3738: for (i=1; i<=imx; i++)
1.53 brouard 3739:
1.71 brouard 3740: /*if ((s[3][i]==3) || (s[4][i]==3)) weight[i]=0.08;
3741: else weight[i]=1;*/
3742:
1.53 brouard 3743: /* Calculation of the number of parameter from char model*/
3744: Tvar=ivector(1,15); /* stores the number n of the covariates in Vm+Vn at 1 and m at 2 */
3745: Tprod=ivector(1,15);
3746: Tvaraff=ivector(1,15);
3747: Tvard=imatrix(1,15,1,2);
3748: Tage=ivector(1,15);
3749:
1.58 lievre 3750: if (strlen(model) >1){ /* If there is at least 1 covariate */
1.53 brouard 3751: j=0, j1=0, k1=1, k2=1;
1.58 lievre 3752: j=nbocc(model,'+'); /* j=Number of '+' */
3753: j1=nbocc(model,'*'); /* j1=Number of '*' */
3754: cptcovn=j+1;
3755: cptcovprod=j1; /*Number of products */
1.53 brouard 3756:
3757: strcpy(modelsav,model);
3758: if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){
3759: printf("Error. Non available option model=%s ",model);
3760: fprintf(ficlog,"Error. Non available option model=%s ",model);
3761: goto end;
3762: }
3763:
1.59 brouard 3764: /* This loop fills the array Tvar from the string 'model'.*/
1.58 lievre 3765:
1.53 brouard 3766: for(i=(j+1); i>=1;i--){
3767: cutv(stra,strb,modelsav,'+'); /* keeps in strb after the last + */
1.59 brouard 3768: if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyzes it */
1.53 brouard 3769: /* printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/
3770: /*scanf("%d",i);*/
3771: if (strchr(strb,'*')) { /* Model includes a product */
3772: cutv(strd,strc,strb,'*'); /* strd*strc Vm*Vn (if not *age)*/
3773: if (strcmp(strc,"age")==0) { /* Vn*age */
3774: cptcovprod--;
3775: cutv(strb,stre,strd,'V');
3776: Tvar[i]=atoi(stre); /* computes n in Vn and stores in Tvar*/
3777: cptcovage++;
3778: Tage[cptcovage]=i;
3779: /*printf("stre=%s ", stre);*/
3780: }
3781: else if (strcmp(strd,"age")==0) { /* or age*Vn */
3782: cptcovprod--;
3783: cutv(strb,stre,strc,'V');
3784: Tvar[i]=atoi(stre);
3785: cptcovage++;
3786: Tage[cptcovage]=i;
3787: }
3788: else { /* Age is not in the model */
3789: cutv(strb,stre,strc,'V'); /* strc= Vn, stre is n*/
3790: Tvar[i]=ncovcol+k1;
3791: cutv(strb,strc,strd,'V'); /* strd was Vm, strc is m */
3792: Tprod[k1]=i;
3793: Tvard[k1][1]=atoi(strc); /* m*/
3794: Tvard[k1][2]=atoi(stre); /* n */
3795: Tvar[cptcovn+k2]=Tvard[k1][1];
3796: Tvar[cptcovn+k2+1]=Tvard[k1][2];
3797: for (k=1; k<=lastobs;k++)
3798: covar[ncovcol+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];
3799: k1++;
3800: k2=k2+2;
3801: }
3802: }
3803: else { /* no more sum */
3804: /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/
3805: /* scanf("%d",i);*/
3806: cutv(strd,strc,strb,'V');
3807: Tvar[i]=atoi(strc);
3808: }
3809: strcpy(modelsav,stra);
3810: /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);
3811: scanf("%d",i);*/
3812: } /* end of loop + */
3813: } /* end model */
3814:
1.58 lievre 3815: /*The number n of Vn is stored in Tvar. cptcovage =number of age covariate. Tage gives the position of age. cptcovprod= number of products.
3816: If model=V1+V1*age then Tvar[1]=1 Tvar[2]=1 cptcovage=1 Tage[1]=2 cptcovprod=0*/
3817:
1.53 brouard 3818: /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);
3819: printf("cptcovprod=%d ", cptcovprod);
3820: fprintf(ficlog,"cptcovprod=%d ", cptcovprod);
1.58 lievre 3821:
3822: scanf("%d ",i);
3823: fclose(fic);*/
1.53 brouard 3824:
3825: /* if(mle==1){*/
1.59 brouard 3826: if (weightopt != 1) { /* Maximisation without weights*/
3827: for(i=1;i<=n;i++) weight[i]=1.0;
3828: }
1.53 brouard 3829: /*-calculation of age at interview from date of interview and age at death -*/
1.59 brouard 3830: agev=matrix(1,maxwav,1,imx);
1.53 brouard 3831:
1.59 brouard 3832: for (i=1; i<=imx; i++) {
3833: for(m=2; (m<= maxwav); m++) {
1.76 brouard 3834: if (((int)mint[m][i]== 99) && (s[m][i] <= nlstate)){
1.59 brouard 3835: anint[m][i]=9999;
3836: s[m][i]=-1;
3837: }
1.76 brouard 3838: if((int)moisdc[i]==99 && (int)andc[i]==9999 && s[m][i]>nlstate){
1.77 brouard 3839: 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);
3840: 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 3841: s[m][i]=-1;
3842: }
3843: if((int)moisdc[i]==99 && (int)andc[i]!=9999 && s[m][i]>nlstate){
1.77 brouard 3844: 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]);
3845: 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 3846: s[m][i]=-1;
3847: }
1.53 brouard 3848: }
1.59 brouard 3849: }
1.53 brouard 3850:
1.59 brouard 3851: for (i=1; i<=imx; i++) {
3852: agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);
1.71 brouard 3853: for(m=firstpass; (m<= lastpass); m++){
1.69 brouard 3854: if(s[m][i] >0){
1.59 brouard 3855: if (s[m][i] >= nlstate+1) {
3856: if(agedc[i]>0)
1.76 brouard 3857: if((int)moisdc[i]!=99 && (int)andc[i]!=9999)
1.69 brouard 3858: agev[m][i]=agedc[i];
1.59 brouard 3859: /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/
3860: else {
1.76 brouard 3861: if ((int)andc[i]!=9999){
1.59 brouard 3862: printf("Warning negative age at death: %d line:%d\n",num[i],i);
3863: fprintf(ficlog,"Warning negative age at death: %d line:%d\n",num[i],i);
3864: agev[m][i]=-1;
1.53 brouard 3865: }
3866: }
1.70 brouard 3867: }
1.69 brouard 3868: else if(s[m][i] !=9){ /* Standard case, age in fractional
3869: years but with the precision of a
3870: month */
1.59 brouard 3871: agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);
1.76 brouard 3872: if((int)mint[m][i]==99 || (int)anint[m][i]==9999)
1.59 brouard 3873: agev[m][i]=1;
3874: else if(agev[m][i] <agemin){
3875: agemin=agev[m][i];
3876: /*printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], agemin);*/
1.53 brouard 3877: }
1.59 brouard 3878: else if(agev[m][i] >agemax){
3879: agemax=agev[m][i];
3880: /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/
1.53 brouard 3881: }
1.59 brouard 3882: /*agev[m][i]=anint[m][i]-annais[i];*/
3883: /* agev[m][i] = age[i]+2*m;*/
1.53 brouard 3884: }
1.59 brouard 3885: else { /* =9 */
1.53 brouard 3886: agev[m][i]=1;
1.59 brouard 3887: s[m][i]=-1;
3888: }
1.53 brouard 3889: }
1.59 brouard 3890: else /*= 0 Unknown */
3891: agev[m][i]=1;
3892: }
1.53 brouard 3893:
1.59 brouard 3894: }
3895: for (i=1; i<=imx; i++) {
1.71 brouard 3896: for(m=firstpass; (m<=lastpass); m++){
1.59 brouard 3897: if (s[m][i] > (nlstate+ndeath)) {
3898: 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);
3899: 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);
3900: goto end;
1.53 brouard 3901: }
3902: }
1.59 brouard 3903: }
1.53 brouard 3904:
1.71 brouard 3905: /*for (i=1; i<=imx; i++){
3906: for (m=firstpass; (m<lastpass); m++){
3907: printf("%d %d %.lf %d %d\n", num[i],(covar[1][i]),agev[m][i],s[m][i],s[m+1][i]);
3908: }
3909:
3910: }*/
3911:
1.59 brouard 3912: printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);
3913: fprintf(ficlog,"Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);
3914:
3915: free_vector(severity,1,maxwav);
3916: free_imatrix(outcome,1,maxwav+1,1,n);
3917: free_vector(moisnais,1,n);
3918: free_vector(annais,1,n);
3919: /* free_matrix(mint,1,maxwav,1,n);
3920: free_matrix(anint,1,maxwav,1,n);*/
3921: free_vector(moisdc,1,n);
3922: free_vector(andc,1,n);
1.53 brouard 3923:
3924:
1.59 brouard 3925: wav=ivector(1,imx);
3926: dh=imatrix(1,lastpass-firstpass+1,1,imx);
3927: bh=imatrix(1,lastpass-firstpass+1,1,imx);
3928: mw=imatrix(1,lastpass-firstpass+1,1,imx);
1.69 brouard 3929:
1.59 brouard 3930: /* Concatenates waves */
3931: concatwav(wav, dh, bh, mw, s, agedc, agev, firstpass, lastpass, imx, nlstate, stepm);
1.53 brouard 3932:
1.59 brouard 3933: /* Routine tricode is to calculate cptcoveff (real number of unique covariates) and to associate covariable number and modality */
1.53 brouard 3934:
1.59 brouard 3935: Tcode=ivector(1,100);
3936: nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);
3937: ncodemax[1]=1;
3938: if (cptcovn > 0) tricode(Tvar,nbcode,imx);
1.53 brouard 3939:
1.59 brouard 3940: codtab=imatrix(1,100,1,10); /* Cross tabulation to get the order of
3941: the estimations*/
3942: h=0;
3943: m=pow(2,cptcoveff);
1.53 brouard 3944:
1.59 brouard 3945: for(k=1;k<=cptcoveff; k++){
3946: for(i=1; i <=(m/pow(2,k));i++){
3947: for(j=1; j <= ncodemax[k]; j++){
3948: for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){
3949: h++;
3950: if (h>m) h=1;codtab[h][k]=j;codtab[h][Tvar[k]]=j;
3951: /* printf("h=%d k=%d j=%d codtab[h][k]=%d tvar[k]=%d \n",h, k,j,codtab[h][k],Tvar[k]);*/
3952: }
3953: }
3954: }
3955: }
3956: /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]);
3957: codtab[1][2]=1;codtab[2][2]=2; */
3958: /* for(i=1; i <=m ;i++){
3959: for(k=1; k <=cptcovn; k++){
3960: printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);
3961: }
3962: printf("\n");
1.53 brouard 3963: }
1.59 brouard 3964: scanf("%d",i);*/
1.53 brouard 3965:
1.59 brouard 3966: /* Calculates basic frequencies. Computes observed prevalence at single age
3967: and prints on file fileres'p'. */
1.53 brouard 3968:
1.60 brouard 3969: pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
3970: oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
3971: newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
3972: savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
3973: oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */
1.53 brouard 3974:
3975:
1.59 brouard 3976: /* For Powell, parameters are in a vector p[] starting at p[1]
3977: so we point p on param[1][1] so that p[1] maps on param[1][1][1] */
3978: p=param[1][1]; /* *(*(*(param +1)+1)+0) */
1.53 brouard 3979:
1.61 brouard 3980: if(mle>=1){ /* Could be 1 or 2 */
1.53 brouard 3981: mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);
1.59 brouard 3982: }
1.53 brouard 3983:
1.59 brouard 3984: /*--------- results files --------------*/
3985: 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 3986:
3987:
1.59 brouard 3988: jk=1;
3989: fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
3990: printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
3991: fprintf(ficlog,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
3992: for(i=1,jk=1; i <=nlstate; i++){
3993: for(k=1; k <=(nlstate+ndeath); k++){
3994: if (k != i)
3995: {
3996: printf("%d%d ",i,k);
3997: fprintf(ficlog,"%d%d ",i,k);
3998: fprintf(ficres,"%1d%1d ",i,k);
3999: for(j=1; j <=ncovmodel; j++){
4000: printf("%f ",p[jk]);
4001: fprintf(ficlog,"%f ",p[jk]);
4002: fprintf(ficres,"%f ",p[jk]);
4003: jk++;
4004: }
4005: printf("\n");
4006: fprintf(ficlog,"\n");
4007: fprintf(ficres,"\n");
4008: }
4009: }
4010: }
4011: if(mle==1){
4012: /* Computing hessian and covariance matrix */
4013: ftolhess=ftol; /* Usually correct */
4014: hesscov(matcov, p, npar, delti, ftolhess, func);
4015: }
4016: fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");
4017: printf("# Scales (for hessian or gradient estimation)\n");
4018: fprintf(ficlog,"# Scales (for hessian or gradient estimation)\n");
4019: for(i=1,jk=1; i <=nlstate; i++){
4020: for(j=1; j <=nlstate+ndeath; j++){
4021: if (j!=i) {
4022: fprintf(ficres,"%1d%1d",i,j);
4023: printf("%1d%1d",i,j);
4024: fprintf(ficlog,"%1d%1d",i,j);
4025: for(k=1; k<=ncovmodel;k++){
4026: printf(" %.5e",delti[jk]);
4027: fprintf(ficlog," %.5e",delti[jk]);
4028: fprintf(ficres," %.5e",delti[jk]);
4029: jk++;
4030: }
4031: printf("\n");
4032: fprintf(ficlog,"\n");
4033: fprintf(ficres,"\n");
4034: }
4035: }
4036: }
1.53 brouard 4037:
1.59 brouard 4038: 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");
4039: if(mle==1)
4040: 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");
4041: 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");
4042: for(i=1,k=1;i<=npar;i++){
4043: /* if (k>nlstate) k=1;
4044: i1=(i-1)/(ncovmodel*nlstate)+1;
4045: fprintf(ficres,"%s%d%d",alph[k],i1,tab[i]);
4046: printf("%s%d%d",alph[k],i1,tab[i]);
4047: */
4048: fprintf(ficres,"%3d",i);
4049: if(mle==1)
4050: printf("%3d",i);
4051: fprintf(ficlog,"%3d",i);
4052: for(j=1; j<=i;j++){
4053: fprintf(ficres," %.5e",matcov[i][j]);
4054: if(mle==1)
4055: printf(" %.5e",matcov[i][j]);
4056: fprintf(ficlog," %.5e",matcov[i][j]);
4057: }
4058: fprintf(ficres,"\n");
4059: if(mle==1)
4060: printf("\n");
4061: fprintf(ficlog,"\n");
4062: k++;
4063: }
1.53 brouard 4064:
1.59 brouard 4065: while((c=getc(ficpar))=='#' && c!= EOF){
4066: ungetc(c,ficpar);
4067: fgets(line, MAXLINE, ficpar);
4068: puts(line);
4069: fputs(line,ficparo);
4070: }
4071: ungetc(c,ficpar);
4072:
4073: estepm=0;
4074: fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm);
4075: if (estepm==0 || estepm < stepm) estepm=stepm;
4076: if (fage <= 2) {
4077: bage = ageminpar;
4078: fage = agemaxpar;
4079: }
1.53 brouard 4080:
1.59 brouard 4081: fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");
4082: fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
4083: fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
1.53 brouard 4084:
1.59 brouard 4085: while((c=getc(ficpar))=='#' && c!= EOF){
4086: ungetc(c,ficpar);
4087: fgets(line, MAXLINE, ficpar);
4088: puts(line);
4089: fputs(line,ficparo);
4090: }
4091: ungetc(c,ficpar);
1.53 brouard 4092:
1.59 brouard 4093: 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);
4094: 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);
4095: 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 4096: printf("begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
4097: 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 4098:
1.59 brouard 4099: while((c=getc(ficpar))=='#' && c!= EOF){
4100: ungetc(c,ficpar);
4101: fgets(line, MAXLINE, ficpar);
4102: puts(line);
4103: fputs(line,ficparo);
4104: }
4105: ungetc(c,ficpar);
1.53 brouard 4106:
4107:
1.70 brouard 4108: dateprev1=anprev1+(mprev1-1)/12.+(jprev1-1)/365.;
4109: dateprev2=anprev2+(mprev2-1)/12.+(jprev2-1)/365.;
1.53 brouard 4110:
4111: fscanf(ficpar,"pop_based=%d\n",&popbased);
4112: fprintf(ficparo,"pop_based=%d\n",popbased);
4113: fprintf(ficres,"pop_based=%d\n",popbased);
4114:
4115: while((c=getc(ficpar))=='#' && c!= EOF){
4116: ungetc(c,ficpar);
4117: fgets(line, MAXLINE, ficpar);
4118: puts(line);
4119: fputs(line,ficparo);
4120: }
4121: ungetc(c,ficpar);
4122:
1.69 brouard 4123: 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 4124: 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 4125: 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);
4126: 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);
4127: 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 4128: /* day and month of proj2 are not used but only year anproj2.*/
1.53 brouard 4129:
1.59 brouard 4130: while((c=getc(ficpar))=='#' && c!= EOF){
1.53 brouard 4131: ungetc(c,ficpar);
4132: fgets(line, MAXLINE, ficpar);
4133: puts(line);
4134: fputs(line,ficparo);
4135: }
4136: ungetc(c,ficpar);
4137:
4138: fscanf(ficpar,"popforecast=%d popfile=%s popfiledate=%lf/%lf/%lf last-popfiledate=%lf/%lf/%lf\n",&popforecast,popfile,&jpyram,&mpyram,&anpyram,&jpyram1,&mpyram1,&anpyram1);
4139: fprintf(ficparo,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);
4140: fprintf(ficres,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);
4141:
1.74 brouard 4142: probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
1.59 brouard 4143: freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);
1.58 lievre 4144:
1.59 brouard 4145: /*------------ gnuplot -------------*/
4146: strcpy(optionfilegnuplot,optionfilefiname);
4147: strcat(optionfilegnuplot,".gp");
4148: if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {
4149: printf("Problem with file %s",optionfilegnuplot);
4150: }
4151: else{
4152: fprintf(ficgp,"\n# %s\n", version);
4153: fprintf(ficgp,"# %s\n", optionfilegnuplot);
4154: fprintf(ficgp,"set missing 'NaNq'\n");
4155: }
4156: fclose(ficgp);
4157: printinggnuplot(fileres, ageminpar,agemaxpar,fage, pathc,p);
4158: /*--------- index.htm --------*/
1.53 brouard 4159:
4160: strcpy(optionfilehtm,optionfile);
4161: strcat(optionfilehtm,".htm");
4162: if((fichtm=fopen(optionfilehtm,"w"))==NULL) {
4163: printf("Problem with %s \n",optionfilehtm), exit(0);
4164: }
4165:
4166: fprintf(fichtm,"<body> <font size=\"2\">%s </font> <hr size=\"2\" color=\"#EC5E5E\"> \n
4167: Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n
4168: \n
4169: Total number of observations=%d <br>\n
1.77 brouard 4170: Youngest age at first (selected) pass %.2f, oldest age %.2f<br>\n
1.53 brouard 4171: Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n
4172: <hr size=\"2\" color=\"#EC5E5E\">
4173: <ul><li><h4>Parameter files</h4>\n
4174: - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n
4175: - Log file of the run: <a href=\"%s\">%s</a><br>\n
1.76 brouard 4176: - 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 4177: fclose(fichtm);
1.53 brouard 4178:
1.59 brouard 4179: 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 4180:
1.59 brouard 4181: /*------------ free_vector -------------*/
4182: chdir(path);
1.53 brouard 4183:
1.59 brouard 4184: free_ivector(wav,1,imx);
4185: free_imatrix(dh,1,lastpass-firstpass+1,1,imx);
4186: free_imatrix(bh,1,lastpass-firstpass+1,1,imx);
4187: free_imatrix(mw,1,lastpass-firstpass+1,1,imx);
4188: free_ivector(num,1,n);
4189: free_vector(agedc,1,n);
1.65 lievre 4190: /*free_matrix(covar,0,NCOVMAX,1,n);*/
1.59 brouard 4191: /*free_matrix(covar,1,NCOVMAX,1,n);*/
4192: fclose(ficparo);
4193: fclose(ficres);
1.53 brouard 4194:
4195:
1.54 brouard 4196: /*--------------- Prevalence limit (stable prevalence) --------------*/
1.53 brouard 4197:
4198: strcpy(filerespl,"pl");
4199: strcat(filerespl,fileres);
4200: if((ficrespl=fopen(filerespl,"w"))==NULL) {
1.54 brouard 4201: printf("Problem with stable prevalence resultfile: %s\n", filerespl);goto end;
4202: fprintf(ficlog,"Problem with stable prevalence resultfile: %s\n", filerespl);goto end;
1.53 brouard 4203: }
1.54 brouard 4204: printf("Computing stable prevalence: result on file '%s' \n", filerespl);
4205: fprintf(ficlog,"Computing stable prevalence: result on file '%s' \n", filerespl);
4206: fprintf(ficrespl,"#Stable prevalence \n");
1.53 brouard 4207: fprintf(ficrespl,"#Age ");
4208: for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);
4209: fprintf(ficrespl,"\n");
4210:
4211: prlim=matrix(1,nlstate,1,nlstate);
1.59 brouard 4212:
1.53 brouard 4213: agebase=ageminpar;
4214: agelim=agemaxpar;
4215: ftolpl=1.e-10;
4216: i1=cptcoveff;
4217: if (cptcovn < 1){i1=1;}
4218:
1.59 brouard 4219: for(cptcov=1,k=0;cptcov<=i1;cptcov++){
1.53 brouard 4220: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
1.59 brouard 4221: k=k+1;
4222: /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/
4223: fprintf(ficrespl,"\n#******");
4224: printf("\n#******");
4225: fprintf(ficlog,"\n#******");
4226: for(j=1;j<=cptcoveff;j++) {
4227: fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
4228: printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
4229: fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
4230: }
4231: fprintf(ficrespl,"******\n");
4232: printf("******\n");
4233: fprintf(ficlog,"******\n");
1.53 brouard 4234:
1.59 brouard 4235: for (age=agebase; age<=agelim; age++){
4236: prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
1.69 brouard 4237: fprintf(ficrespl,"%.0f ",age );
4238: for(j=1;j<=cptcoveff;j++)
4239: fprintf(ficrespl,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
1.59 brouard 4240: for(i=1; i<=nlstate;i++)
1.53 brouard 4241: fprintf(ficrespl," %.5f", prlim[i][i]);
1.59 brouard 4242: fprintf(ficrespl,"\n");
1.53 brouard 4243: }
4244: }
1.59 brouard 4245: }
1.53 brouard 4246: fclose(ficrespl);
4247:
4248: /*------------- h Pij x at various ages ------------*/
4249:
4250: strcpy(filerespij,"pij"); strcat(filerespij,fileres);
4251: if((ficrespij=fopen(filerespij,"w"))==NULL) {
4252: printf("Problem with Pij resultfile: %s\n", filerespij);goto end;
4253: fprintf(ficlog,"Problem with Pij resultfile: %s\n", filerespij);goto end;
4254: }
4255: printf("Computing pij: result on file '%s' \n", filerespij);
4256: fprintf(ficlog,"Computing pij: result on file '%s' \n", filerespij);
4257:
4258: stepsize=(int) (stepm+YEARM-1)/YEARM;
4259: /*if (stepm<=24) stepsize=2;*/
4260:
4261: agelim=AGESUP;
4262: hstepm=stepsize*YEARM; /* Every year of age */
4263: hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */
4264:
4265: /* hstepm=1; aff par mois*/
4266:
1.70 brouard 4267: fprintf(ficrespij,"#****** h Pij x Probability to be in state j at age x+h being in i at x ");
1.59 brouard 4268: for(cptcov=1,k=0;cptcov<=i1;cptcov++){
1.53 brouard 4269: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
4270: k=k+1;
1.59 brouard 4271: fprintf(ficrespij,"\n#****** ");
4272: for(j=1;j<=cptcoveff;j++)
4273: fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
4274: fprintf(ficrespij,"******\n");
1.53 brouard 4275:
1.59 brouard 4276: for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */
4277: nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
4278: nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
4279:
4280: /* nhstepm=nhstepm*YEARM; aff par mois*/
4281:
4282: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4283: oldm=oldms;savm=savms;
4284: hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
1.70 brouard 4285: fprintf(ficrespij,"# Cov Agex agex+h hpijx with i,j=");
1.59 brouard 4286: for(i=1; i<=nlstate;i++)
4287: for(j=1; j<=nlstate+ndeath;j++)
4288: fprintf(ficrespij," %1d-%1d",i,j);
4289: fprintf(ficrespij,"\n");
4290: for (h=0; h<=nhstepm; h++){
1.70 brouard 4291: fprintf(ficrespij,"%d %3.f %3.f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );
1.53 brouard 4292: for(i=1; i<=nlstate;i++)
4293: for(j=1; j<=nlstate+ndeath;j++)
1.59 brouard 4294: fprintf(ficrespij," %.5f", p3mat[i][j][h]);
1.53 brouard 4295: fprintf(ficrespij,"\n");
4296: }
1.59 brouard 4297: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4298: fprintf(ficrespij,"\n");
4299: }
1.53 brouard 4300: }
4301: }
4302:
1.74 brouard 4303: varprob(optionfilefiname, matcov, p, delti, nlstate, bage, fage,k,Tvar,nbcode, ncodemax);
1.53 brouard 4304:
4305: fclose(ficrespij);
4306:
4307:
4308: /*---------- Forecasting ------------------*/
1.69 brouard 4309: /*if((stepm == 1) && (strcmp(model,".")==0)){*/
4310: if(prevfcast==1){
1.74 brouard 4311: /* if(stepm ==1){*/
1.70 brouard 4312: prevforecast(fileres, anproj1, mproj1, jproj1, agemin, agemax, dateprev1, dateprev2, mobilavproj, bage, fage, firstpass, lastpass, anproj2, p, cptcoveff);
1.74 brouard 4313: /* (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);*/
4314: /* } */
4315: /* else{ */
4316: /* erreur=108; */
4317: /* 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); */
4318: /* 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); */
4319: /* } */
1.69 brouard 4320: }
1.53 brouard 4321:
4322:
4323: /*---------- Health expectancies and variances ------------*/
4324:
4325: strcpy(filerest,"t");
4326: strcat(filerest,fileres);
4327: if((ficrest=fopen(filerest,"w"))==NULL) {
4328: printf("Problem with total LE resultfile: %s\n", filerest);goto end;
4329: fprintf(ficlog,"Problem with total LE resultfile: %s\n", filerest);goto end;
4330: }
4331: printf("Computing Total LEs with variances: file '%s' \n", filerest);
4332: fprintf(ficlog,"Computing Total LEs with variances: file '%s' \n", filerest);
4333:
4334:
4335: strcpy(filerese,"e");
4336: strcat(filerese,fileres);
4337: if((ficreseij=fopen(filerese,"w"))==NULL) {
4338: printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
4339: fprintf(ficlog,"Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
4340: }
4341: printf("Computing Health Expectancies: result on file '%s' \n", filerese);
4342: fprintf(ficlog,"Computing Health Expectancies: result on file '%s' \n", filerese);
1.68 lievre 4343:
1.53 brouard 4344: strcpy(fileresv,"v");
4345: strcat(fileresv,fileres);
4346: if((ficresvij=fopen(fileresv,"w"))==NULL) {
4347: printf("Problem with variance resultfile: %s\n", fileresv);exit(0);
4348: fprintf(ficlog,"Problem with variance resultfile: %s\n", fileresv);exit(0);
4349: }
4350: printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
4351: fprintf(ficlog,"Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
1.58 lievre 4352:
1.74 brouard 4353: /* Computes prevalence between agemin (i.e minimal age computed) and no more ageminpar */
4354: prevalence(agemin, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
4355: /* 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",\
4356: ageminpar, agemax, s[lastpass][imx], agev[lastpass][imx], nlstate, imx, mint[lastpass][imx],anint[lastpass][imx], dateprev1, dateprev2, firstpass, lastpass);
4357: */
1.58 lievre 4358:
1.54 brouard 4359: if (mobilav!=0) {
1.53 brouard 4360: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
1.54 brouard 4361: if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
4362: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
4363: printf(" Error in movingaverage mobilav=%d\n",mobilav);
4364: }
1.53 brouard 4365: }
4366:
1.59 brouard 4367: for(cptcov=1,k=0;cptcov<=i1;cptcov++){
1.53 brouard 4368: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
4369: k=k+1;
4370: fprintf(ficrest,"\n#****** ");
4371: for(j=1;j<=cptcoveff;j++)
4372: fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
4373: fprintf(ficrest,"******\n");
4374:
4375: fprintf(ficreseij,"\n#****** ");
4376: for(j=1;j<=cptcoveff;j++)
4377: fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
4378: fprintf(ficreseij,"******\n");
4379:
4380: fprintf(ficresvij,"\n#****** ");
4381: for(j=1;j<=cptcoveff;j++)
4382: fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
4383: fprintf(ficresvij,"******\n");
4384:
4385: eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
4386: oldm=oldms;savm=savms;
4387: evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov);
4388:
4389: vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
4390: oldm=oldms;savm=savms;
4391: varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,0, mobilav);
4392: if(popbased==1){
4393: 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 4394: }
1.53 brouard 4395:
4396:
4397: fprintf(ficrest,"#Total LEs with variances: e.. (std) ");
4398: for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);
4399: fprintf(ficrest,"\n");
4400:
4401: epj=vector(1,nlstate+1);
4402: for(age=bage; age <=fage ;age++){
4403: prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
4404: if (popbased==1) {
1.54 brouard 4405: if(mobilav ==0){
1.53 brouard 4406: for(i=1; i<=nlstate;i++)
4407: prlim[i][i]=probs[(int)age][i][k];
1.54 brouard 4408: }else{ /* mobilav */
1.53 brouard 4409: for(i=1; i<=nlstate;i++)
4410: prlim[i][i]=mobaverage[(int)age][i][k];
4411: }
4412: }
4413:
4414: fprintf(ficrest," %4.0f",age);
4415: for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){
4416: for(i=1, epj[j]=0.;i <=nlstate;i++) {
4417: epj[j] += prlim[i][i]*eij[i][j][(int)age];
4418: /* printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/
4419: }
4420: epj[nlstate+1] +=epj[j];
4421: }
4422:
4423: for(i=1, vepp=0.;i <=nlstate;i++)
4424: for(j=1;j <=nlstate;j++)
4425: vepp += vareij[i][j][(int)age];
4426: fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));
4427: for(j=1;j <=nlstate;j++){
4428: fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));
4429: }
4430: fprintf(ficrest,"\n");
4431: }
1.59 brouard 4432: free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
4433: free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);
4434: free_vector(epj,1,nlstate+1);
1.53 brouard 4435: }
4436: }
1.59 brouard 4437: free_vector(weight,1,n);
4438: free_imatrix(Tvard,1,15,1,2);
4439: free_imatrix(s,1,maxwav+1,1,n);
4440: free_matrix(anint,1,maxwav,1,n);
4441: free_matrix(mint,1,maxwav,1,n);
4442: free_ivector(cod,1,n);
4443: free_ivector(tab,1,NCOVMAX);
1.53 brouard 4444: fclose(ficreseij);
4445: fclose(ficresvij);
4446: fclose(ficrest);
4447: fclose(ficpar);
4448:
1.54 brouard 4449: /*------- Variance of stable prevalence------*/
1.53 brouard 4450:
4451: strcpy(fileresvpl,"vpl");
4452: strcat(fileresvpl,fileres);
4453: if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {
1.54 brouard 4454: printf("Problem with variance of stable prevalence resultfile: %s\n", fileresvpl);
1.53 brouard 4455: exit(0);
4456: }
1.54 brouard 4457: printf("Computing Variance-covariance of stable prevalence: file '%s' \n", fileresvpl);
1.53 brouard 4458:
1.59 brouard 4459: for(cptcov=1,k=0;cptcov<=i1;cptcov++){
1.53 brouard 4460: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
4461: k=k+1;
4462: fprintf(ficresvpl,"\n#****** ");
4463: for(j=1;j<=cptcoveff;j++)
4464: fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
4465: fprintf(ficresvpl,"******\n");
4466:
4467: varpl=matrix(1,nlstate,(int) bage, (int) fage);
4468: oldm=oldms;savm=savms;
1.59 brouard 4469: varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);
4470: free_matrix(varpl,1,nlstate,(int) bage, (int)fage);
1.53 brouard 4471: }
1.59 brouard 4472: }
1.53 brouard 4473:
4474: fclose(ficresvpl);
4475:
4476: /*---------- End : free ----------------*/
4477: free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);
4478: free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);
4479: free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);
4480: free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);
1.65 lievre 4481:
4482: free_matrix(covar,0,NCOVMAX,1,n);
1.53 brouard 4483: free_matrix(matcov,1,npar,1,npar);
1.74 brouard 4484: /*free_vector(delti,1,npar);*/
4485: free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
1.53 brouard 4486: free_matrix(agev,1,maxwav,1,imx);
4487: free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
1.54 brouard 4488: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
1.74 brouard 4489: free_ma3x(probs,1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
4490:
1.59 brouard 4491: free_ivector(ncodemax,1,8);
4492: free_ivector(Tvar,1,15);
4493: free_ivector(Tprod,1,15);
4494: free_ivector(Tvaraff,1,15);
4495: free_ivector(Tage,1,15);
4496: free_ivector(Tcode,1,100);
1.53 brouard 4497:
1.74 brouard 4498: /* fclose(fichtm);*/
4499: /* fclose(ficgp);*/ /* ALready done */
1.53 brouard 4500:
4501:
4502: if(erreur >0){
4503: printf("End of Imach with error or warning %d\n",erreur);
4504: fprintf(ficlog,"End of Imach with error or warning %d\n",erreur);
4505: }else{
4506: printf("End of Imach\n");
4507: fprintf(ficlog,"End of Imach\n");
4508: }
4509: printf("See log file on %s\n",filelog);
4510: fclose(ficlog);
4511: /* gettimeofday(&end_time, (struct timezone*)0);*/ /* after time */
4512:
4513: /* 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);*/
4514: /*printf("Total time was %d uSec.\n", total_usecs);*/
4515: /*------ End -----------*/
4516:
1.59 brouard 4517: end:
1.53 brouard 4518: #ifdef windows
4519: /* chdir(pathcd);*/
4520: #endif
4521: /*system("wgnuplot graph.plt");*/
4522: /*system("../gp37mgw/wgnuplot graph.plt");*/
4523: /*system("cd ../gp37mgw");*/
4524: /* system("..\\gp37mgw\\wgnuplot graph.plt");*/
1.59 brouard 4525: strcpy(plotcmd,GNUPLOTPROGRAM);
4526: strcat(plotcmd," ");
4527: strcat(plotcmd,optionfilegnuplot);
1.75 brouard 4528: printf("Starting graphs with: %s",plotcmd);fflush(stdout);
1.59 brouard 4529: system(plotcmd);
1.75 brouard 4530: printf(" Wait...");
1.53 brouard 4531:
1.54 brouard 4532: /*#ifdef windows*/
1.53 brouard 4533: while (z[0] != 'q') {
4534: /* chdir(path); */
4535: printf("\nType e to edit output files, g to graph again, c to start again, and q for exiting: ");
4536: scanf("%s",z);
4537: if (z[0] == 'c') system("./imach");
4538: else if (z[0] == 'e') system(optionfilehtm);
4539: else if (z[0] == 'g') system(plotcmd);
4540: else if (z[0] == 'q') exit(0);
4541: }
1.54 brouard 4542: /*#endif */
1.53 brouard 4543: }
4544:
4545:
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