Annotation of imach/src/imach.c, revision 1.79
1.79 ! brouard 1: /* $Id: imach.c,v 1.78 2003/05/27 17:26:53 brouard Exp $
1.53 brouard 2: Interpolated Markov Chain
3:
4: Short summary of the programme:
5:
6: This program computes Healthy Life Expectancies from
7: cross-longitudinal data. Cross-longitudinal data consist in: -1- a
8: first survey ("cross") where individuals from different ages are
9: interviewed on their health status or degree of disability (in the
10: case of a health survey which is our main interest) -2- at least a
11: second wave of interviews ("longitudinal") which measure each change
12: (if any) in individual health status. Health expectancies are
13: computed from the time spent in each health state according to a
14: model. More health states you consider, more time is necessary to reach the
15: Maximum Likelihood of the parameters involved in the model. The
16: simplest model is the multinomial logistic model where pij is the
17: probability to be observed in state j at the second wave
18: conditional to be observed in state i at the first wave. Therefore
19: the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where
20: 'age' is age and 'sex' is a covariate. If you want to have a more
21: complex model than "constant and age", you should modify the program
22: where the markup *Covariates have to be included here again* invites
23: you to do it. More covariates you add, slower the
24: convergence.
25:
26: The advantage of this computer programme, compared to a simple
27: multinomial logistic model, is clear when the delay between waves is not
28: identical for each individual. Also, if a individual missed an
29: intermediate interview, the information is lost, but taken into
30: account using an interpolation or extrapolation.
31:
32: hPijx is the probability to be observed in state i at age x+h
33: conditional to the observed state i at age x. The delay 'h' can be
34: split into an exact number (nh*stepm) of unobserved intermediate
1.66 brouard 35: states. This elementary transition (by month, quarter,
36: semester or year) is modelled as a multinomial logistic. The hPx
1.53 brouard 37: matrix is simply the matrix product of nh*stepm elementary matrices
38: and the contribution of each individual to the likelihood is simply
39: hPijx.
40:
41: Also this programme outputs the covariance matrix of the parameters but also
1.54 brouard 42: of the life expectancies. It also computes the stable prevalence.
1.53 brouard 43:
44: Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).
45: Institut national d'études démographiques, Paris.
46: This software have been partly granted by Euro-REVES, a concerted action
47: from the European Union.
48: It is copyrighted identically to a GNU software product, ie programme and
49: software can be distributed freely for non commercial use. Latest version
50: can be accessed at http://euroreves.ined.fr/imach .
1.74 brouard 51:
52: Help to debug: LD_PRELOAD=/usr/local/lib/libnjamd.so ./imach foo.imach
53: or better on gdb : set env LD_PRELOAD=/usr/local/lib/libnjamd.so
54:
1.53 brouard 55: **********************************************************************/
1.74 brouard 56: /*
57: main
58: read parameterfile
59: read datafile
60: concatwav
61: if (mle >= 1)
62: mlikeli
63: print results files
64: if mle==1
65: computes hessian
66: read end of parameter file: agemin, agemax, bage, fage, estepm
67: begin-prev-date,...
68: open gnuplot file
69: open html file
70: stable prevalence
71: for age prevalim()
72: h Pij x
73: variance of p varprob
74: forecasting if prevfcast==1 prevforecast call prevalence()
75: health expectancies
76: Variance-covariance of DFLE
77: prevalence()
78: movingaverage()
79: varevsij()
80: if popbased==1 varevsij(,popbased)
81: total life expectancies
82: Variance of stable prevalence
83: end
84: */
85:
86:
87:
1.53 brouard 88:
89: #include <math.h>
90: #include <stdio.h>
91: #include <stdlib.h>
92: #include <unistd.h>
93:
94: #define MAXLINE 256
95: #define GNUPLOTPROGRAM "gnuplot"
96: /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
97: #define FILENAMELENGTH 80
98: /*#define DEBUG*/
1.55 lievre 99: #define windows
1.53 brouard 100: #define GLOCK_ERROR_NOPATH -1 /* empty path */
101: #define GLOCK_ERROR_GETCWD -2 /* cannot get cwd */
102:
103: #define MAXPARM 30 /* Maximum number of parameters for the optimization */
104: #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */
105:
106: #define NINTERVMAX 8
107: #define NLSTATEMAX 8 /* Maximum number of live states (for func) */
108: #define NDEATHMAX 8 /* Maximum number of dead states (for func) */
109: #define NCOVMAX 8 /* Maximum number of covariates */
110: #define MAXN 20000
111: #define YEARM 12. /* Number of months per year */
112: #define AGESUP 130
113: #define AGEBASE 40
114: #ifdef windows
115: #define DIRSEPARATOR '\\'
116: #define ODIRSEPARATOR '/'
117: #else
118: #define DIRSEPARATOR '/'
119: #define ODIRSEPARATOR '\\'
120: #endif
121:
1.79 ! brouard 122: /* $Id$ */
! 123: /* $Log$ */
! 124: char version[80]="Imach version 0.95a1, June 2003, INED-EUROREVES ";
1.53 brouard 125: int erreur; /* Error number */
126: int nvar;
127: int cptcovn=0, cptcovage=0, cptcoveff=0,cptcov;
128: int npar=NPARMAX;
129: int nlstate=2; /* Number of live states */
130: int ndeath=1; /* Number of dead states */
131: int ncovmodel, ncovcol; /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
132: int popbased=0;
133:
134: int *wav; /* Number of waves for this individuual 0 is possible */
135: int maxwav; /* Maxim number of waves */
136: int jmin, jmax; /* min, max spacing between 2 waves */
137: int mle, weightopt;
138: int **mw; /* mw[mi][i] is number of the mi wave for this individual */
139: int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
1.59 brouard 140: int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between
141: * wave mi and wave mi+1 is not an exact multiple of stepm. */
1.53 brouard 142: double jmean; /* Mean space between 2 waves */
143: double **oldm, **newm, **savm; /* Working pointers to matrices */
144: double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
145: FILE *fic,*ficpar, *ficparo,*ficres, *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
1.76 brouard 146: FILE *ficlog, *ficrespow;
1.53 brouard 147: FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
148: FILE *ficresprobmorprev;
149: FILE *fichtm; /* Html File */
150: FILE *ficreseij;
151: char filerese[FILENAMELENGTH];
152: FILE *ficresvij;
153: char fileresv[FILENAMELENGTH];
154: FILE *ficresvpl;
155: char fileresvpl[FILENAMELENGTH];
156: char title[MAXLINE];
157: char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH], filerespl[FILENAMELENGTH];
158: char optionfilext[10], optionfilefiname[FILENAMELENGTH], plotcmd[FILENAMELENGTH];
159:
160: char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
161: char filelog[FILENAMELENGTH]; /* Log file */
162: char filerest[FILENAMELENGTH];
163: char fileregp[FILENAMELENGTH];
164: char popfile[FILENAMELENGTH];
165:
166: char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH];
167:
168: #define NR_END 1
169: #define FREE_ARG char*
170: #define FTOL 1.0e-10
171:
172: #define NRANSI
173: #define ITMAX 200
174:
175: #define TOL 2.0e-4
176:
177: #define CGOLD 0.3819660
178: #define ZEPS 1.0e-10
179: #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);
180:
181: #define GOLD 1.618034
182: #define GLIMIT 100.0
183: #define TINY 1.0e-20
184:
185: static double maxarg1,maxarg2;
186: #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
187: #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
188:
189: #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
190: #define rint(a) floor(a+0.5)
191:
192: static double sqrarg;
193: #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
194: #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}
195:
196: int imx;
197: int stepm;
198: /* Stepm, step in month: minimum step interpolation*/
199:
200: int estepm;
201: /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
202:
203: int m,nb;
204: int *num, firstpass=0, lastpass=4,*cod, *ncodemax, *Tage;
205: double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
1.55 lievre 206: double **pmmij, ***probs;
1.53 brouard 207: double dateintmean=0;
208:
209: double *weight;
210: int **s; /* Status */
211: double *agedc, **covar, idx;
212: int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;
213:
214: double ftol=FTOL; /* Tolerance for computing Max Likelihood */
215: double ftolhess; /* Tolerance for computing hessian */
216:
217: /**************** split *************************/
218: static int split( char *path, char *dirc, char *name, char *ext, char *finame )
219: {
1.59 brouard 220: char *ss; /* pointer */
221: int l1, l2; /* length counters */
1.53 brouard 222:
1.59 brouard 223: l1 = strlen(path ); /* length of path */
224: if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
225: ss= strrchr( path, DIRSEPARATOR ); /* find last / */
226: if ( ss == NULL ) { /* no directory, so use current */
227: /*if(strrchr(path, ODIRSEPARATOR )==NULL)
228: printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
1.74 brouard 229: /* get current working directory */
230: /* extern char* getcwd ( char *buf , int len);*/
1.59 brouard 231: if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {
232: return( GLOCK_ERROR_GETCWD );
233: }
234: strcpy( name, path ); /* we've got it */
235: } else { /* strip direcotry from path */
236: ss++; /* after this, the filename */
237: l2 = strlen( ss ); /* length of filename */
238: if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
239: strcpy( name, ss ); /* save file name */
240: strncpy( dirc, path, l1 - l2 ); /* now the directory */
241: dirc[l1-l2] = 0; /* add zero */
242: }
243: l1 = strlen( dirc ); /* length of directory */
1.53 brouard 244: #ifdef windows
1.59 brouard 245: if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; }
1.53 brouard 246: #else
1.59 brouard 247: if ( dirc[l1-1] != '/' ) { dirc[l1] = '/'; dirc[l1+1] = 0; }
1.53 brouard 248: #endif
1.59 brouard 249: ss = strrchr( name, '.' ); /* find last / */
250: ss++;
251: strcpy(ext,ss); /* save extension */
252: l1= strlen( name);
253: l2= strlen(ss)+1;
254: strncpy( finame, name, l1-l2);
255: finame[l1-l2]= 0;
256: return( 0 ); /* we're done */
1.53 brouard 257: }
258:
259:
260: /******************************************/
261:
262: void replace(char *s, char*t)
263: {
264: int i;
265: int lg=20;
266: i=0;
267: lg=strlen(t);
268: for(i=0; i<= lg; i++) {
269: (s[i] = t[i]);
270: if (t[i]== '\\') s[i]='/';
271: }
272: }
273:
274: int nbocc(char *s, char occ)
275: {
276: int i,j=0;
277: int lg=20;
278: i=0;
279: lg=strlen(s);
280: for(i=0; i<= lg; i++) {
281: if (s[i] == occ ) j++;
282: }
283: return j;
284: }
285:
286: void cutv(char *u,char *v, char*t, char occ)
287: {
288: /* cuts string t into u and v where u is ended by char occ excluding it
289: and v is after occ excluding it too : ex cutv(u,v,"abcdef2ghi2j",2)
290: gives u="abcedf" and v="ghi2j" */
291: int i,lg,j,p=0;
292: i=0;
293: for(j=0; j<=strlen(t)-1; j++) {
294: if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;
295: }
296:
297: lg=strlen(t);
298: for(j=0; j<p; j++) {
299: (u[j] = t[j]);
300: }
301: u[p]='\0';
302:
303: for(j=0; j<= lg; j++) {
304: if (j>=(p+1))(v[j-p-1] = t[j]);
305: }
306: }
307:
308: /********************** nrerror ********************/
309:
310: void nrerror(char error_text[])
311: {
312: fprintf(stderr,"ERREUR ...\n");
313: fprintf(stderr,"%s\n",error_text);
1.59 brouard 314: exit(EXIT_FAILURE);
1.53 brouard 315: }
316: /*********************** vector *******************/
317: double *vector(int nl, int nh)
318: {
319: double *v;
320: v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
321: if (!v) nrerror("allocation failure in vector");
322: return v-nl+NR_END;
323: }
324:
325: /************************ free vector ******************/
326: void free_vector(double*v, int nl, int nh)
327: {
328: free((FREE_ARG)(v+nl-NR_END));
329: }
330:
331: /************************ivector *******************************/
1.76 brouard 332: char *cvector(long nl,long nh)
333: {
334: char *v;
335: v=(char *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(char)));
336: if (!v) nrerror("allocation failure in cvector");
337: return v-nl+NR_END;
338: }
339:
340: /******************free ivector **************************/
341: void free_cvector(char *v, long nl, long nh)
342: {
343: free((FREE_ARG)(v+nl-NR_END));
344: }
345:
346: /************************ivector *******************************/
1.53 brouard 347: int *ivector(long nl,long nh)
348: {
349: int *v;
350: v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
351: if (!v) nrerror("allocation failure in ivector");
352: return v-nl+NR_END;
353: }
354:
355: /******************free ivector **************************/
356: void free_ivector(int *v, long nl, long nh)
357: {
358: free((FREE_ARG)(v+nl-NR_END));
359: }
360:
361: /******************* imatrix *******************************/
362: int **imatrix(long nrl, long nrh, long ncl, long nch)
363: /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */
364: {
365: long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;
366: int **m;
367:
368: /* allocate pointers to rows */
369: m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));
370: if (!m) nrerror("allocation failure 1 in matrix()");
371: m += NR_END;
372: m -= nrl;
373:
374:
375: /* allocate rows and set pointers to them */
376: m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));
377: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
378: m[nrl] += NR_END;
379: m[nrl] -= ncl;
380:
381: for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;
382:
383: /* return pointer to array of pointers to rows */
384: return m;
385: }
386:
387: /****************** free_imatrix *************************/
388: void free_imatrix(m,nrl,nrh,ncl,nch)
389: int **m;
390: long nch,ncl,nrh,nrl;
391: /* free an int matrix allocated by imatrix() */
392: {
393: free((FREE_ARG) (m[nrl]+ncl-NR_END));
394: free((FREE_ARG) (m+nrl-NR_END));
395: }
396:
397: /******************* matrix *******************************/
398: double **matrix(long nrl, long nrh, long ncl, long nch)
399: {
400: long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
401: double **m;
402:
403: m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
404: if (!m) nrerror("allocation failure 1 in matrix()");
405: m += NR_END;
406: m -= nrl;
407:
408: m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
409: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
410: m[nrl] += NR_END;
411: m[nrl] -= ncl;
412:
413: for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
414: return m;
1.74 brouard 415: /* print *(*(m+1)+70) ou print m[1][70]; print m+1 or print &(m[1])
416: */
1.53 brouard 417: }
418:
419: /*************************free matrix ************************/
420: void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
421: {
422: free((FREE_ARG)(m[nrl]+ncl-NR_END));
423: free((FREE_ARG)(m+nrl-NR_END));
424: }
425:
426: /******************* ma3x *******************************/
427: double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
428: {
429: long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
430: double ***m;
431:
432: m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
433: if (!m) nrerror("allocation failure 1 in matrix()");
434: m += NR_END;
435: m -= nrl;
436:
437: m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
438: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
439: m[nrl] += NR_END;
440: m[nrl] -= ncl;
441:
442: for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
443:
444: m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
445: if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
446: m[nrl][ncl] += NR_END;
447: m[nrl][ncl] -= nll;
448: for (j=ncl+1; j<=nch; j++)
449: m[nrl][j]=m[nrl][j-1]+nlay;
450:
451: for (i=nrl+1; i<=nrh; i++) {
452: m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
453: for (j=ncl+1; j<=nch; j++)
454: m[i][j]=m[i][j-1]+nlay;
455: }
1.74 brouard 456: return m;
457: /* gdb: p *(m+1) <=> p m[1] and p (m+1) <=> p (m+1) <=> p &(m[1])
458: &(m[i][j][k]) <=> *((*(m+i) + j)+k)
459: */
1.53 brouard 460: }
461:
462: /*************************free ma3x ************************/
463: void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
464: {
465: free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
466: free((FREE_ARG)(m[nrl]+ncl-NR_END));
467: free((FREE_ARG)(m+nrl-NR_END));
468: }
469:
470: /***************** f1dim *************************/
471: extern int ncom;
472: extern double *pcom,*xicom;
473: extern double (*nrfunc)(double []);
474:
475: double f1dim(double x)
476: {
477: int j;
478: double f;
479: double *xt;
480:
481: xt=vector(1,ncom);
482: for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];
483: f=(*nrfunc)(xt);
484: free_vector(xt,1,ncom);
485: return f;
486: }
487:
488: /*****************brent *************************/
489: double brent(double ax, double bx, double cx, double (*f)(double), double tol, double *xmin)
490: {
491: int iter;
492: double a,b,d,etemp;
493: double fu,fv,fw,fx;
494: double ftemp;
495: double p,q,r,tol1,tol2,u,v,w,x,xm;
496: double e=0.0;
497:
498: a=(ax < cx ? ax : cx);
499: b=(ax > cx ? ax : cx);
500: x=w=v=bx;
501: fw=fv=fx=(*f)(x);
502: for (iter=1;iter<=ITMAX;iter++) {
503: xm=0.5*(a+b);
504: tol2=2.0*(tol1=tol*fabs(x)+ZEPS);
505: /* if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
506: printf(".");fflush(stdout);
507: fprintf(ficlog,".");fflush(ficlog);
508: #ifdef DEBUG
509: 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);
510: 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);
511: /* if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
512: #endif
513: if (fabs(x-xm) <= (tol2-0.5*(b-a))){
514: *xmin=x;
515: return fx;
516: }
517: ftemp=fu;
518: if (fabs(e) > tol1) {
519: r=(x-w)*(fx-fv);
520: q=(x-v)*(fx-fw);
521: p=(x-v)*q-(x-w)*r;
522: q=2.0*(q-r);
523: if (q > 0.0) p = -p;
524: q=fabs(q);
525: etemp=e;
526: e=d;
527: if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))
528: d=CGOLD*(e=(x >= xm ? a-x : b-x));
529: else {
530: d=p/q;
531: u=x+d;
532: if (u-a < tol2 || b-u < tol2)
533: d=SIGN(tol1,xm-x);
534: }
535: } else {
536: d=CGOLD*(e=(x >= xm ? a-x : b-x));
537: }
538: u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));
539: fu=(*f)(u);
540: if (fu <= fx) {
541: if (u >= x) a=x; else b=x;
542: SHFT(v,w,x,u)
543: SHFT(fv,fw,fx,fu)
544: } else {
545: if (u < x) a=u; else b=u;
546: if (fu <= fw || w == x) {
547: v=w;
548: w=u;
549: fv=fw;
550: fw=fu;
551: } else if (fu <= fv || v == x || v == w) {
552: v=u;
553: fv=fu;
554: }
555: }
556: }
557: nrerror("Too many iterations in brent");
558: *xmin=x;
559: return fx;
560: }
561:
562: /****************** mnbrak ***********************/
563:
564: void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,
565: double (*func)(double))
566: {
567: double ulim,u,r,q, dum;
568: double fu;
569:
570: *fa=(*func)(*ax);
571: *fb=(*func)(*bx);
572: if (*fb > *fa) {
573: SHFT(dum,*ax,*bx,dum)
574: SHFT(dum,*fb,*fa,dum)
575: }
576: *cx=(*bx)+GOLD*(*bx-*ax);
577: *fc=(*func)(*cx);
578: while (*fb > *fc) {
579: r=(*bx-*ax)*(*fb-*fc);
580: q=(*bx-*cx)*(*fb-*fa);
581: u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/
582: (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r));
583: ulim=(*bx)+GLIMIT*(*cx-*bx);
584: if ((*bx-u)*(u-*cx) > 0.0) {
585: fu=(*func)(u);
586: } else if ((*cx-u)*(u-ulim) > 0.0) {
587: fu=(*func)(u);
588: if (fu < *fc) {
589: SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))
590: SHFT(*fb,*fc,fu,(*func)(u))
591: }
592: } else if ((u-ulim)*(ulim-*cx) >= 0.0) {
593: u=ulim;
594: fu=(*func)(u);
595: } else {
596: u=(*cx)+GOLD*(*cx-*bx);
597: fu=(*func)(u);
598: }
599: SHFT(*ax,*bx,*cx,u)
600: SHFT(*fa,*fb,*fc,fu)
601: }
602: }
603:
604: /*************** linmin ************************/
605:
606: int ncom;
607: double *pcom,*xicom;
608: double (*nrfunc)(double []);
609:
610: void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))
611: {
612: double brent(double ax, double bx, double cx,
613: double (*f)(double), double tol, double *xmin);
614: double f1dim(double x);
615: void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,
616: double *fc, double (*func)(double));
617: int j;
618: double xx,xmin,bx,ax;
619: double fx,fb,fa;
620:
621: ncom=n;
622: pcom=vector(1,n);
623: xicom=vector(1,n);
624: nrfunc=func;
625: for (j=1;j<=n;j++) {
626: pcom[j]=p[j];
627: xicom[j]=xi[j];
628: }
629: ax=0.0;
630: xx=1.0;
631: mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim);
632: *fret=brent(ax,xx,bx,f1dim,TOL,&xmin);
633: #ifdef DEBUG
634: printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
635: fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
636: #endif
637: for (j=1;j<=n;j++) {
638: xi[j] *= xmin;
639: p[j] += xi[j];
640: }
641: free_vector(xicom,1,n);
642: free_vector(pcom,1,n);
643: }
644:
645: /*************** powell ************************/
646: void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,
647: double (*func)(double []))
648: {
649: void linmin(double p[], double xi[], int n, double *fret,
650: double (*func)(double []));
651: int i,ibig,j;
652: double del,t,*pt,*ptt,*xit;
653: double fp,fptt;
654: double *xits;
655: pt=vector(1,n);
656: ptt=vector(1,n);
657: xit=vector(1,n);
658: xits=vector(1,n);
659: *fret=(*func)(p);
660: for (j=1;j<=n;j++) pt[j]=p[j];
661: for (*iter=1;;++(*iter)) {
662: fp=(*fret);
663: ibig=0;
664: del=0.0;
665: printf("\nPowell iter=%d -2*LL=%.12f",*iter,*fret);
666: fprintf(ficlog,"\nPowell iter=%d -2*LL=%.12f",*iter,*fret);
1.76 brouard 667: fprintf(ficrespow,"%d %.12f",*iter,*fret);
668: for (i=1;i<=n;i++) {
1.53 brouard 669: printf(" %d %.12f",i, p[i]);
1.76 brouard 670: fprintf(ficlog," %d %.12lf",i, p[i]);
671: fprintf(ficrespow," %.12lf", p[i]);
672: }
1.53 brouard 673: printf("\n");
674: fprintf(ficlog,"\n");
1.76 brouard 675: fprintf(ficrespow,"\n");
1.53 brouard 676: for (i=1;i<=n;i++) {
677: for (j=1;j<=n;j++) xit[j]=xi[j][i];
678: fptt=(*fret);
679: #ifdef DEBUG
680: printf("fret=%lf \n",*fret);
681: fprintf(ficlog,"fret=%lf \n",*fret);
682: #endif
683: printf("%d",i);fflush(stdout);
684: fprintf(ficlog,"%d",i);fflush(ficlog);
685: linmin(p,xit,n,fret,func);
686: if (fabs(fptt-(*fret)) > del) {
687: del=fabs(fptt-(*fret));
688: ibig=i;
689: }
690: #ifdef DEBUG
691: printf("%d %.12e",i,(*fret));
692: fprintf(ficlog,"%d %.12e",i,(*fret));
693: for (j=1;j<=n;j++) {
694: xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
695: printf(" x(%d)=%.12e",j,xit[j]);
696: fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
697: }
698: for(j=1;j<=n;j++) {
699: printf(" p=%.12e",p[j]);
700: fprintf(ficlog," p=%.12e",p[j]);
701: }
702: printf("\n");
703: fprintf(ficlog,"\n");
704: #endif
705: }
706: if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {
707: #ifdef DEBUG
708: int k[2],l;
709: k[0]=1;
710: k[1]=-1;
711: printf("Max: %.12e",(*func)(p));
712: fprintf(ficlog,"Max: %.12e",(*func)(p));
713: for (j=1;j<=n;j++) {
714: printf(" %.12e",p[j]);
715: fprintf(ficlog," %.12e",p[j]);
716: }
717: printf("\n");
718: fprintf(ficlog,"\n");
719: for(l=0;l<=1;l++) {
720: for (j=1;j<=n;j++) {
721: ptt[j]=p[j]+(p[j]-pt[j])*k[l];
722: printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
723: fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
724: }
725: printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
726: fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
727: }
728: #endif
729:
730:
731: free_vector(xit,1,n);
732: free_vector(xits,1,n);
733: free_vector(ptt,1,n);
734: free_vector(pt,1,n);
735: return;
736: }
737: if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");
738: for (j=1;j<=n;j++) {
739: ptt[j]=2.0*p[j]-pt[j];
740: xit[j]=p[j]-pt[j];
741: pt[j]=p[j];
742: }
743: fptt=(*func)(ptt);
744: if (fptt < fp) {
745: t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt);
746: if (t < 0.0) {
747: linmin(p,xit,n,fret,func);
748: for (j=1;j<=n;j++) {
749: xi[j][ibig]=xi[j][n];
750: xi[j][n]=xit[j];
751: }
752: #ifdef DEBUG
753: printf("Direction changed last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
754: fprintf(ficlog,"Direction changed last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
755: for(j=1;j<=n;j++){
756: printf(" %.12e",xit[j]);
757: fprintf(ficlog," %.12e",xit[j]);
758: }
759: printf("\n");
760: fprintf(ficlog,"\n");
761: #endif
1.54 brouard 762: }
1.53 brouard 763: }
764: }
765: }
766:
1.54 brouard 767: /**** Prevalence limit (stable prevalence) ****************/
1.53 brouard 768:
769: double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)
770: {
771: /* Computes the prevalence limit in each live state at age x by left multiplying the unit
772: matrix by transitions matrix until convergence is reached */
773:
774: int i, ii,j,k;
775: double min, max, maxmin, maxmax,sumnew=0.;
776: double **matprod2();
777: double **out, cov[NCOVMAX], **pmij();
778: double **newm;
779: double agefin, delaymax=50 ; /* Max number of years to converge */
780:
781: for (ii=1;ii<=nlstate+ndeath;ii++)
782: for (j=1;j<=nlstate+ndeath;j++){
783: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
784: }
785:
786: cov[1]=1.;
787:
788: /* Even if hstepm = 1, at least one multiplication by the unit matrix */
789: for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
790: newm=savm;
791: /* Covariates have to be included here again */
792: cov[2]=agefin;
793:
794: for (k=1; k<=cptcovn;k++) {
795: cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
796: /* 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]]);*/
797: }
798: for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
799: for (k=1; k<=cptcovprod;k++)
800: cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
801:
802: /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
803: /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
804: /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
805: out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);
806:
807: savm=oldm;
808: oldm=newm;
809: maxmax=0.;
810: for(j=1;j<=nlstate;j++){
811: min=1.;
812: max=0.;
813: for(i=1; i<=nlstate; i++) {
814: sumnew=0;
815: for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
816: prlim[i][j]= newm[i][j]/(1-sumnew);
817: max=FMAX(max,prlim[i][j]);
818: min=FMIN(min,prlim[i][j]);
819: }
820: maxmin=max-min;
821: maxmax=FMAX(maxmax,maxmin);
822: }
823: if(maxmax < ftolpl){
824: return prlim;
825: }
826: }
827: }
828:
829: /*************** transition probabilities ***************/
830:
831: double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
832: {
833: double s1, s2;
834: /*double t34;*/
835: int i,j,j1, nc, ii, jj;
836:
837: for(i=1; i<= nlstate; i++){
838: for(j=1; j<i;j++){
839: for (nc=1, s2=0.;nc <=ncovmodel; nc++){
840: /*s2 += param[i][j][nc]*cov[nc];*/
841: s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
842: /*printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2);*/
843: }
844: ps[i][j]=s2;
845: /*printf("s1=%.17e, s2=%.17e\n",s1,s2);*/
846: }
847: for(j=i+1; j<=nlstate+ndeath;j++){
848: for (nc=1, s2=0.;nc <=ncovmodel; nc++){
849: s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
850: /*printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2);*/
851: }
852: ps[i][j]=s2;
853: }
854: }
855: /*ps[3][2]=1;*/
856:
857: for(i=1; i<= nlstate; i++){
858: s1=0;
859: for(j=1; j<i; j++)
860: s1+=exp(ps[i][j]);
861: for(j=i+1; j<=nlstate+ndeath; j++)
862: s1+=exp(ps[i][j]);
863: ps[i][i]=1./(s1+1.);
864: for(j=1; j<i; j++)
865: ps[i][j]= exp(ps[i][j])*ps[i][i];
866: for(j=i+1; j<=nlstate+ndeath; j++)
867: ps[i][j]= exp(ps[i][j])*ps[i][i];
868: /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
869: } /* end i */
870:
871: for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
872: for(jj=1; jj<= nlstate+ndeath; jj++){
873: ps[ii][jj]=0;
874: ps[ii][ii]=1;
875: }
876: }
877:
878:
879: /* for(ii=1; ii<= nlstate+ndeath; ii++){
880: for(jj=1; jj<= nlstate+ndeath; jj++){
881: printf("%lf ",ps[ii][jj]);
882: }
883: printf("\n ");
884: }
885: printf("\n ");printf("%lf ",cov[2]);*/
886: /*
887: for(i=1; i<= npar; i++) printf("%f ",x[i]);
888: goto end;*/
889: return ps;
890: }
891:
892: /**************** Product of 2 matrices ******************/
893:
894: double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)
895: {
896: /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
897: b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
898: /* in, b, out are matrice of pointers which should have been initialized
899: before: only the contents of out is modified. The function returns
900: a pointer to pointers identical to out */
901: long i, j, k;
902: for(i=nrl; i<= nrh; i++)
903: for(k=ncolol; k<=ncoloh; k++)
904: for(j=ncl,out[i][k]=0.; j<=nch; j++)
905: out[i][k] +=in[i][j]*b[j][k];
906:
907: return out;
908: }
909:
910:
911: /************* Higher Matrix Product ***************/
912:
913: double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
914: {
1.66 brouard 915: /* Computes the transition matrix starting at age 'age' over
916: 'nhstepm*hstepm*stepm' months (i.e. until
917: age (in years) age+nhstepm*hstepm*stepm/12) by multiplying
918: nhstepm*hstepm matrices.
1.53 brouard 919: Output is stored in matrix po[i][j][h] for h every 'hstepm' step
1.66 brouard 920: (typically every 2 years instead of every month which is too big
921: for the memory).
1.53 brouard 922: Model is determined by parameters x and covariates have to be
923: included manually here.
924:
925: */
926:
927: int i, j, d, h, k;
928: double **out, cov[NCOVMAX];
929: double **newm;
930:
931: /* Hstepm could be zero and should return the unit matrix */
932: for (i=1;i<=nlstate+ndeath;i++)
933: for (j=1;j<=nlstate+ndeath;j++){
934: oldm[i][j]=(i==j ? 1.0 : 0.0);
935: po[i][j][0]=(i==j ? 1.0 : 0.0);
936: }
937: /* Even if hstepm = 1, at least one multiplication by the unit matrix */
938: for(h=1; h <=nhstepm; h++){
939: for(d=1; d <=hstepm; d++){
940: newm=savm;
941: /* Covariates have to be included here again */
942: cov[1]=1.;
943: cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
944: for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
945: for (k=1; k<=cptcovage;k++)
946: cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
947: for (k=1; k<=cptcovprod;k++)
948: cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
949:
950:
951: /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
952: /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
953: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,
954: pmij(pmmij,cov,ncovmodel,x,nlstate));
955: savm=oldm;
956: oldm=newm;
957: }
958: for(i=1; i<=nlstate+ndeath; i++)
959: for(j=1;j<=nlstate+ndeath;j++) {
960: po[i][j][h]=newm[i][j];
961: /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);
962: */
963: }
964: } /* end h */
965: return po;
966: }
967:
968:
969: /*************** log-likelihood *************/
970: double func( double *x)
971: {
972: int i, ii, j, k, mi, d, kk;
973: double l, ll[NLSTATEMAX], cov[NCOVMAX];
974: double **out;
975: double sw; /* Sum of weights */
976: double lli; /* Individual log likelihood */
1.59 brouard 977: int s1, s2;
1.68 lievre 978: double bbh, survp;
1.53 brouard 979: long ipmx;
980: /*extern weight */
981: /* We are differentiating ll according to initial status */
982: /* for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
983: /*for(i=1;i<imx;i++)
984: printf(" %d\n",s[4][i]);
985: */
986: cov[1]=1.;
987:
988: for(k=1; k<=nlstate; k++) ll[k]=0.;
1.61 brouard 989:
990: if(mle==1){
991: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
992: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
993: for(mi=1; mi<= wav[i]-1; mi++){
994: for (ii=1;ii<=nlstate+ndeath;ii++)
995: for (j=1;j<=nlstate+ndeath;j++){
996: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
997: savm[ii][j]=(ii==j ? 1.0 : 0.0);
998: }
999: for(d=0; d<dh[mi][i]; d++){
1000: newm=savm;
1001: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
1002: for (kk=1; kk<=cptcovage;kk++) {
1003: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
1004: }
1005: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1006: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1007: savm=oldm;
1008: oldm=newm;
1009: } /* end mult */
1.53 brouard 1010:
1.61 brouard 1011: /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
1012: /* But now since version 0.9 we anticipate for bias and large stepm.
1013: * If stepm is larger than one month (smallest stepm) and if the exact delay
1014: * (in months) between two waves is not a multiple of stepm, we rounded to
1015: * the nearest (and in case of equal distance, to the lowest) interval but now
1016: * we keep into memory the bias bh[mi][i] and also the previous matrix product
1017: * (i.e to dh[mi][i]-1) saved in 'savm'. The we inter(extra)polate the
1018: * probability in order to take into account the bias as a fraction of the way
1019: * from savm to out if bh is neagtive or even beyond if bh is positive. bh varies
1020: * -stepm/2 to stepm/2 .
1021: * For stepm=1 the results are the same as for previous versions of Imach.
1022: * For stepm > 1 the results are less biased than in previous versions.
1023: */
1024: s1=s[mw[mi][i]][i];
1025: s2=s[mw[mi+1][i]][i];
1.64 lievre 1026: bbh=(double)bh[mi][i]/(double)stepm;
1027: /* bias is positive if real duration
1028: * is higher than the multiple of stepm and negative otherwise.
1029: */
1030: /* 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 1031: if( s2 > nlstate){
1032: /* i.e. if s2 is a death state and if the date of death is known then the contribution
1033: to the likelihood is the probability to die between last step unit time and current
1034: step unit time, which is also the differences between probability to die before dh
1035: and probability to die before dh-stepm .
1036: In version up to 0.92 likelihood was computed
1037: as if date of death was unknown. Death was treated as any other
1038: health state: the date of the interview describes the actual state
1039: and not the date of a change in health state. The former idea was
1040: to consider that at each interview the state was recorded
1041: (healthy, disable or death) and IMaCh was corrected; but when we
1042: introduced the exact date of death then we should have modified
1043: the contribution of an exact death to the likelihood. This new
1044: contribution is smaller and very dependent of the step unit
1045: stepm. It is no more the probability to die between last interview
1046: and month of death but the probability to survive from last
1047: interview up to one month before death multiplied by the
1048: probability to die within a month. Thanks to Chris
1049: Jackson for correcting this bug. Former versions increased
1050: mortality artificially. The bad side is that we add another loop
1051: which slows down the processing. The difference can be up to 10%
1052: lower mortality.
1053: */
1054: lli=log(out[s1][s2] - savm[s1][s2]);
1055: }else{
1056: lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
1057: /* 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 */
1058: }
1.64 lievre 1059: /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
1060: /*if(lli ==000.0)*/
1061: /*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 1062: ipmx +=1;
1.64 lievre 1063: sw += weight[i];
1064: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1065: } /* end of wave */
1066: } /* end of individual */
1067: } else if(mle==2){
1068: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1069: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
1070: for(mi=1; mi<= wav[i]-1; mi++){
1071: for (ii=1;ii<=nlstate+ndeath;ii++)
1072: for (j=1;j<=nlstate+ndeath;j++){
1073: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1074: savm[ii][j]=(ii==j ? 1.0 : 0.0);
1075: }
1076: for(d=0; d<=dh[mi][i]; d++){
1077: newm=savm;
1078: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
1079: for (kk=1; kk<=cptcovage;kk++) {
1080: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
1081: }
1082: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1083: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1084: savm=oldm;
1085: oldm=newm;
1086: } /* end mult */
1087:
1088: /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
1089: /* But now since version 0.9 we anticipate for bias and large stepm.
1090: * If stepm is larger than one month (smallest stepm) and if the exact delay
1091: * (in months) between two waves is not a multiple of stepm, we rounded to
1092: * the nearest (and in case of equal distance, to the lowest) interval but now
1093: * we keep into memory the bias bh[mi][i] and also the previous matrix product
1094: * (i.e to dh[mi][i]-1) saved in 'savm'. The we inter(extra)polate the
1095: * probability in order to take into account the bias as a fraction of the way
1096: * from savm to out if bh is neagtive or even beyond if bh is positive. bh varies
1097: * -stepm/2 to stepm/2 .
1098: * For stepm=1 the results are the same as for previous versions of Imach.
1099: * For stepm > 1 the results are less biased than in previous versions.
1100: */
1101: s1=s[mw[mi][i]][i];
1102: s2=s[mw[mi+1][i]][i];
1103: bbh=(double)bh[mi][i]/(double)stepm;
1104: /* bias is positive if real duration
1105: * is higher than the multiple of stepm and negative otherwise.
1106: */
1.63 lievre 1107: 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 1108: /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
1109: /*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 */
1110: /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
1111: /*if(lli ==000.0)*/
1112: /*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); */
1113: ipmx +=1;
1114: sw += weight[i];
1115: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1116: } /* end of wave */
1117: } /* end of individual */
1118: } else if(mle==3){ /* exponential inter-extrapolation */
1119: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1120: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
1121: for(mi=1; mi<= wav[i]-1; mi++){
1122: for (ii=1;ii<=nlstate+ndeath;ii++)
1123: for (j=1;j<=nlstate+ndeath;j++){
1124: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1125: savm[ii][j]=(ii==j ? 1.0 : 0.0);
1126: }
1127: for(d=0; d<dh[mi][i]; d++){
1128: newm=savm;
1129: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
1130: for (kk=1; kk<=cptcovage;kk++) {
1131: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
1132: }
1133: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1134: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1135: savm=oldm;
1136: oldm=newm;
1137: } /* end mult */
1138:
1139: /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
1140: /* But now since version 0.9 we anticipate for bias and large stepm.
1141: * If stepm is larger than one month (smallest stepm) and if the exact delay
1142: * (in months) between two waves is not a multiple of stepm, we rounded to
1143: * the nearest (and in case of equal distance, to the lowest) interval but now
1144: * we keep into memory the bias bh[mi][i] and also the previous matrix product
1145: * (i.e to dh[mi][i]-1) saved in 'savm'. The we inter(extra)polate the
1146: * probability in order to take into account the bias as a fraction of the way
1147: * from savm to out if bh is neagtive or even beyond if bh is positive. bh varies
1148: * -stepm/2 to stepm/2 .
1149: * For stepm=1 the results are the same as for previous versions of Imach.
1150: * For stepm > 1 the results are less biased than in previous versions.
1151: */
1152: s1=s[mw[mi][i]][i];
1153: s2=s[mw[mi+1][i]][i];
1154: bbh=(double)bh[mi][i]/(double)stepm;
1155: /* bias is positive if real duration
1156: * is higher than the multiple of stepm and negative otherwise.
1157: */
1158: /* 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 */
1159: 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 1160: /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
1161: /*if(lli ==000.0)*/
1162: /*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); */
1163: ipmx +=1;
1164: sw += weight[i];
1165: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1166: } /* end of wave */
1167: } /* end of individual */
1.64 lievre 1168: }else{ /* ml=4 no inter-extrapolation */
1.61 brouard 1169: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1170: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
1171: for(mi=1; mi<= wav[i]-1; mi++){
1172: for (ii=1;ii<=nlstate+ndeath;ii++)
1173: for (j=1;j<=nlstate+ndeath;j++){
1174: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1175: savm[ii][j]=(ii==j ? 1.0 : 0.0);
1176: }
1177: for(d=0; d<dh[mi][i]; d++){
1178: newm=savm;
1179: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
1180: for (kk=1; kk<=cptcovage;kk++) {
1181: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
1182: }
1183:
1184: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1185: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1186: savm=oldm;
1187: oldm=newm;
1188: } /* end mult */
1189:
1190: lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
1191: ipmx +=1;
1192: sw += weight[i];
1193: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1194: } /* end of wave */
1195: } /* end of individual */
1196: } /* End of if */
1.53 brouard 1197: for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
1198: /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
1199: l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
1200: return -l;
1201: }
1202:
1203:
1204: /*********** Maximum Likelihood Estimation ***************/
1205:
1206: void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
1207: {
1208: int i,j, iter;
1.74 brouard 1209: double **xi;
1.53 brouard 1210: double fret;
1.76 brouard 1211: char filerespow[FILENAMELENGTH];
1.53 brouard 1212: xi=matrix(1,npar,1,npar);
1213: for (i=1;i<=npar;i++)
1214: for (j=1;j<=npar;j++)
1215: xi[i][j]=(i==j ? 1.0 : 0.0);
1216: printf("Powell\n"); fprintf(ficlog,"Powell\n");
1.76 brouard 1217: strcpy(filerespow,"pow");
1218: strcat(filerespow,fileres);
1219: if((ficrespow=fopen(filerespow,"w"))==NULL) {
1220: printf("Problem with resultfile: %s\n", filerespow);
1221: fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
1222: }
1223: fprintf(ficrespow,"# Powell\n# iter -2*LL");
1224: for (i=1;i<=nlstate;i++)
1225: for(j=1;j<=nlstate+ndeath;j++)
1226: if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
1227: fprintf(ficrespow,"\n");
1.53 brouard 1228: powell(p,xi,npar,ftol,&iter,&fret,func);
1229:
1.76 brouard 1230: fclose(ficrespow);
1231: printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));
1.65 lievre 1232: fprintf(ficlog,"\n#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
1.53 brouard 1233: fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
1234:
1235: }
1236:
1237: /**** Computes Hessian and covariance matrix ***/
1238: void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
1239: {
1240: double **a,**y,*x,pd;
1241: double **hess;
1242: int i, j,jk;
1243: int *indx;
1244:
1245: double hessii(double p[], double delta, int theta, double delti[]);
1246: double hessij(double p[], double delti[], int i, int j);
1247: void lubksb(double **a, int npar, int *indx, double b[]) ;
1248: void ludcmp(double **a, int npar, int *indx, double *d) ;
1249:
1250: hess=matrix(1,npar,1,npar);
1251:
1252: printf("\nCalculation of the hessian matrix. Wait...\n");
1253: fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
1254: for (i=1;i<=npar;i++){
1255: printf("%d",i);fflush(stdout);
1256: fprintf(ficlog,"%d",i);fflush(ficlog);
1257: hess[i][i]=hessii(p,ftolhess,i,delti);
1258: /*printf(" %f ",p[i]);*/
1259: /*printf(" %lf ",hess[i][i]);*/
1260: }
1261:
1262: for (i=1;i<=npar;i++) {
1263: for (j=1;j<=npar;j++) {
1264: if (j>i) {
1265: printf(".%d%d",i,j);fflush(stdout);
1266: fprintf(ficlog,".%d%d",i,j);fflush(ficlog);
1267: hess[i][j]=hessij(p,delti,i,j);
1268: hess[j][i]=hess[i][j];
1269: /*printf(" %lf ",hess[i][j]);*/
1270: }
1271: }
1272: }
1273: printf("\n");
1274: fprintf(ficlog,"\n");
1275:
1276: printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
1277: fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
1278:
1279: a=matrix(1,npar,1,npar);
1280: y=matrix(1,npar,1,npar);
1281: x=vector(1,npar);
1282: indx=ivector(1,npar);
1283: for (i=1;i<=npar;i++)
1284: for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
1285: ludcmp(a,npar,indx,&pd);
1286:
1287: for (j=1;j<=npar;j++) {
1288: for (i=1;i<=npar;i++) x[i]=0;
1289: x[j]=1;
1290: lubksb(a,npar,indx,x);
1291: for (i=1;i<=npar;i++){
1292: matcov[i][j]=x[i];
1293: }
1294: }
1295:
1296: printf("\n#Hessian matrix#\n");
1297: fprintf(ficlog,"\n#Hessian matrix#\n");
1298: for (i=1;i<=npar;i++) {
1299: for (j=1;j<=npar;j++) {
1300: printf("%.3e ",hess[i][j]);
1301: fprintf(ficlog,"%.3e ",hess[i][j]);
1302: }
1303: printf("\n");
1304: fprintf(ficlog,"\n");
1305: }
1306:
1307: /* Recompute Inverse */
1308: for (i=1;i<=npar;i++)
1309: for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];
1310: ludcmp(a,npar,indx,&pd);
1311:
1312: /* printf("\n#Hessian matrix recomputed#\n");
1313:
1314: for (j=1;j<=npar;j++) {
1315: for (i=1;i<=npar;i++) x[i]=0;
1316: x[j]=1;
1317: lubksb(a,npar,indx,x);
1318: for (i=1;i<=npar;i++){
1319: y[i][j]=x[i];
1320: printf("%.3e ",y[i][j]);
1321: fprintf(ficlog,"%.3e ",y[i][j]);
1322: }
1323: printf("\n");
1324: fprintf(ficlog,"\n");
1325: }
1326: */
1327:
1328: free_matrix(a,1,npar,1,npar);
1329: free_matrix(y,1,npar,1,npar);
1330: free_vector(x,1,npar);
1331: free_ivector(indx,1,npar);
1332: free_matrix(hess,1,npar,1,npar);
1333:
1334:
1335: }
1336:
1337: /*************** hessian matrix ****************/
1338: double hessii( double x[], double delta, int theta, double delti[])
1339: {
1340: int i;
1341: int l=1, lmax=20;
1342: double k1,k2;
1343: double p2[NPARMAX+1];
1344: double res;
1345: double delt, delts, nkhi=10.,nkhif=1., khi=1.e-4;
1346: double fx;
1347: int k=0,kmax=10;
1348: double l1;
1349:
1350: fx=func(x);
1351: for (i=1;i<=npar;i++) p2[i]=x[i];
1352: for(l=0 ; l <=lmax; l++){
1353: l1=pow(10,l);
1354: delts=delt;
1355: for(k=1 ; k <kmax; k=k+1){
1356: delt = delta*(l1*k);
1357: p2[theta]=x[theta] +delt;
1358: k1=func(p2)-fx;
1359: p2[theta]=x[theta]-delt;
1360: k2=func(p2)-fx;
1361: /*res= (k1-2.0*fx+k2)/delt/delt; */
1362: res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */
1363:
1364: #ifdef DEBUG
1365: 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);
1366: 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);
1367: #endif
1368: /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
1369: if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
1370: k=kmax;
1371: }
1372: else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
1373: k=kmax; l=lmax*10.;
1374: }
1375: else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){
1376: delts=delt;
1377: }
1378: }
1379: }
1380: delti[theta]=delts;
1381: return res;
1382:
1383: }
1384:
1385: double hessij( double x[], double delti[], int thetai,int thetaj)
1386: {
1387: int i;
1388: int l=1, l1, lmax=20;
1389: double k1,k2,k3,k4,res,fx;
1390: double p2[NPARMAX+1];
1391: int k;
1392:
1393: fx=func(x);
1394: for (k=1; k<=2; k++) {
1395: for (i=1;i<=npar;i++) p2[i]=x[i];
1396: p2[thetai]=x[thetai]+delti[thetai]/k;
1397: p2[thetaj]=x[thetaj]+delti[thetaj]/k;
1398: k1=func(p2)-fx;
1399:
1400: p2[thetai]=x[thetai]+delti[thetai]/k;
1401: p2[thetaj]=x[thetaj]-delti[thetaj]/k;
1402: k2=func(p2)-fx;
1403:
1404: p2[thetai]=x[thetai]-delti[thetai]/k;
1405: p2[thetaj]=x[thetaj]+delti[thetaj]/k;
1406: k3=func(p2)-fx;
1407:
1408: p2[thetai]=x[thetai]-delti[thetai]/k;
1409: p2[thetaj]=x[thetaj]-delti[thetaj]/k;
1410: k4=func(p2)-fx;
1411: res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */
1412: #ifdef DEBUG
1413: 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);
1414: 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);
1415: #endif
1416: }
1417: return res;
1418: }
1419:
1420: /************** Inverse of matrix **************/
1421: void ludcmp(double **a, int n, int *indx, double *d)
1422: {
1423: int i,imax,j,k;
1424: double big,dum,sum,temp;
1425: double *vv;
1426:
1427: vv=vector(1,n);
1428: *d=1.0;
1429: for (i=1;i<=n;i++) {
1430: big=0.0;
1431: for (j=1;j<=n;j++)
1432: if ((temp=fabs(a[i][j])) > big) big=temp;
1433: if (big == 0.0) nrerror("Singular matrix in routine ludcmp");
1434: vv[i]=1.0/big;
1435: }
1436: for (j=1;j<=n;j++) {
1437: for (i=1;i<j;i++) {
1438: sum=a[i][j];
1439: for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];
1440: a[i][j]=sum;
1441: }
1442: big=0.0;
1443: for (i=j;i<=n;i++) {
1444: sum=a[i][j];
1445: for (k=1;k<j;k++)
1446: sum -= a[i][k]*a[k][j];
1447: a[i][j]=sum;
1448: if ( (dum=vv[i]*fabs(sum)) >= big) {
1449: big=dum;
1450: imax=i;
1451: }
1452: }
1453: if (j != imax) {
1454: for (k=1;k<=n;k++) {
1455: dum=a[imax][k];
1456: a[imax][k]=a[j][k];
1457: a[j][k]=dum;
1458: }
1459: *d = -(*d);
1460: vv[imax]=vv[j];
1461: }
1462: indx[j]=imax;
1463: if (a[j][j] == 0.0) a[j][j]=TINY;
1464: if (j != n) {
1465: dum=1.0/(a[j][j]);
1466: for (i=j+1;i<=n;i++) a[i][j] *= dum;
1467: }
1468: }
1469: free_vector(vv,1,n); /* Doesn't work */
1470: ;
1471: }
1472:
1473: void lubksb(double **a, int n, int *indx, double b[])
1474: {
1475: int i,ii=0,ip,j;
1476: double sum;
1477:
1478: for (i=1;i<=n;i++) {
1479: ip=indx[i];
1480: sum=b[ip];
1481: b[ip]=b[i];
1482: if (ii)
1483: for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];
1484: else if (sum) ii=i;
1485: b[i]=sum;
1486: }
1487: for (i=n;i>=1;i--) {
1488: sum=b[i];
1489: for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];
1490: b[i]=sum/a[i][i];
1491: }
1492: }
1493:
1494: /************ Frequencies ********************/
1.74 brouard 1495: 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 1496: { /* Some frequencies */
1497:
1498: int i, m, jk, k1,i1, j1, bool, z1,z2,j;
1499: int first;
1500: double ***freq; /* Frequencies */
1.73 lievre 1501: double *pp, **prop;
1502: double pos,posprop, k2, dateintsum=0,k2cpt=0;
1.53 brouard 1503: FILE *ficresp;
1504: char fileresp[FILENAMELENGTH];
1505:
1506: pp=vector(1,nlstate);
1.74 brouard 1507: prop=matrix(1,nlstate,iagemin,iagemax+3);
1.53 brouard 1508: strcpy(fileresp,"p");
1509: strcat(fileresp,fileres);
1510: if((ficresp=fopen(fileresp,"w"))==NULL) {
1511: printf("Problem with prevalence resultfile: %s\n", fileresp);
1512: fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
1513: exit(0);
1514: }
1.74 brouard 1515: freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);
1.53 brouard 1516: j1=0;
1517:
1518: j=cptcoveff;
1519: if (cptcovn<1) {j=1;ncodemax[1]=1;}
1520:
1521: first=1;
1522:
1523: for(k1=1; k1<=j;k1++){
1524: for(i1=1; i1<=ncodemax[k1];i1++){
1525: j1++;
1526: /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
1527: scanf("%d", i);*/
1528: for (i=-1; i<=nlstate+ndeath; i++)
1529: for (jk=-1; jk<=nlstate+ndeath; jk++)
1.74 brouard 1530: for(m=iagemin; m <= iagemax+3; m++)
1.53 brouard 1531: freq[i][jk][m]=0;
1.73 lievre 1532:
1533: for (i=1; i<=nlstate; i++)
1.74 brouard 1534: for(m=iagemin; m <= iagemax+3; m++)
1.73 lievre 1535: prop[i][m]=0;
1.53 brouard 1536:
1537: dateintsum=0;
1538: k2cpt=0;
1539: for (i=1; i<=imx; i++) {
1540: bool=1;
1541: if (cptcovn>0) {
1542: for (z1=1; z1<=cptcoveff; z1++)
1543: if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])
1544: bool=0;
1545: }
1.58 lievre 1546: if (bool==1){
1.53 brouard 1547: for(m=firstpass; m<=lastpass; m++){
1548: k2=anint[m][i]+(mint[m][i]/12.);
1549: if ((k2>=dateprev1) && (k2<=dateprev2)) {
1.74 brouard 1550: if(agev[m][i]==0) agev[m][i]=iagemax+1;
1551: if(agev[m][i]==1) agev[m][i]=iagemax+2;
1.73 lievre 1552: if (s[m][i]>0 && s[m][i]<=nlstate) prop[s[m][i]][(int)agev[m][i]] += weight[i];
1.53 brouard 1553: if (m<lastpass) {
1554: freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
1.74 brouard 1555: freq[s[m][i]][s[m+1][i]][iagemax+3] += weight[i];
1.53 brouard 1556: }
1557:
1.74 brouard 1558: if ((agev[m][i]>1) && (agev[m][i]< (iagemax+3))) {
1.53 brouard 1559: dateintsum=dateintsum+k2;
1560: k2cpt++;
1561: }
1562: }
1563: }
1564: }
1565: }
1566:
1567: fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);
1568:
1569: if (cptcovn>0) {
1570: fprintf(ficresp, "\n#********** Variable ");
1571: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
1572: fprintf(ficresp, "**********\n#");
1573: }
1574: for(i=1; i<=nlstate;i++)
1575: fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
1576: fprintf(ficresp, "\n");
1577:
1.74 brouard 1578: for(i=iagemin; i <= iagemax+3; i++){
1579: if(i==iagemax+3){
1.53 brouard 1580: fprintf(ficlog,"Total");
1581: }else{
1582: if(first==1){
1583: first=0;
1584: printf("See log file for details...\n");
1585: }
1586: fprintf(ficlog,"Age %d", i);
1587: }
1588: for(jk=1; jk <=nlstate ; jk++){
1589: for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
1590: pp[jk] += freq[jk][m][i];
1591: }
1592: for(jk=1; jk <=nlstate ; jk++){
1593: for(m=-1, pos=0; m <=0 ; m++)
1594: pos += freq[jk][m][i];
1595: if(pp[jk]>=1.e-10){
1596: if(first==1){
1597: printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
1598: }
1599: fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
1600: }else{
1601: if(first==1)
1602: printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
1603: fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
1604: }
1605: }
1606:
1607: for(jk=1; jk <=nlstate ; jk++){
1608: for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
1609: pp[jk] += freq[jk][m][i];
1.73 lievre 1610: }
1611: for(jk=1,pos=0,posprop=0; jk <=nlstate ; jk++){
1612: pos += pp[jk];
1613: posprop += prop[jk][i];
1.53 brouard 1614: }
1615: for(jk=1; jk <=nlstate ; jk++){
1616: if(pos>=1.e-5){
1617: if(first==1)
1618: printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
1619: fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
1620: }else{
1621: if(first==1)
1622: printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
1623: fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
1624: }
1.74 brouard 1625: if( i <= iagemax){
1.53 brouard 1626: if(pos>=1.e-5){
1.73 lievre 1627: fprintf(ficresp," %d %.5f %.0f %.0f",i,prop[jk][i]/posprop, prop[jk][i],posprop);
1.53 brouard 1628: probs[i][jk][j1]= pp[jk]/pos;
1629: /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/
1630: }
1631: else
1.73 lievre 1632: fprintf(ficresp," %d NaNq %.0f %.0f",i,prop[jk][i],posprop);
1.53 brouard 1633: }
1634: }
1635:
1.69 brouard 1636: for(jk=-1; jk <=nlstate+ndeath; jk++)
1637: for(m=-1; m <=nlstate+ndeath; m++)
1.53 brouard 1638: if(freq[jk][m][i] !=0 ) {
1639: if(first==1)
1640: printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
1641: fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
1642: }
1.74 brouard 1643: if(i <= iagemax)
1.53 brouard 1644: fprintf(ficresp,"\n");
1645: if(first==1)
1646: printf("Others in log...\n");
1647: fprintf(ficlog,"\n");
1648: }
1649: }
1650: }
1651: dateintmean=dateintsum/k2cpt;
1652:
1653: fclose(ficresp);
1.74 brouard 1654: free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);
1.53 brouard 1655: free_vector(pp,1,nlstate);
1.74 brouard 1656: free_matrix(prop,1,nlstate,iagemin, iagemax+3);
1.53 brouard 1657: /* End of Freq */
1658: }
1659:
1660: /************ Prevalence ********************/
1.74 brouard 1661: 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 1662: {
1663: /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
1664: in each health status at the date of interview (if between dateprev1 and dateprev2).
1665: We still use firstpass and lastpass as another selection.
1666: */
1.53 brouard 1667:
1668: int i, m, jk, k1, i1, j1, bool, z1,z2,j;
1669: double ***freq; /* Frequencies */
1.73 lievre 1670: double *pp, **prop;
1671: double pos,posprop;
1.69 brouard 1672: double y2; /* in fractional years */
1.74 brouard 1673: int iagemin, iagemax;
1.53 brouard 1674:
1.74 brouard 1675: iagemin= (int) agemin;
1676: iagemax= (int) agemax;
1677: /*pp=vector(1,nlstate);*/
1678: prop=matrix(1,nlstate,iagemin,iagemax+3);
1679: /* freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
1.53 brouard 1680: j1=0;
1681:
1682: j=cptcoveff;
1683: if (cptcovn<1) {j=1;ncodemax[1]=1;}
1684:
1685: for(k1=1; k1<=j;k1++){
1686: for(i1=1; i1<=ncodemax[k1];i1++){
1687: j1++;
1688:
1.73 lievre 1689: for (i=1; i<=nlstate; i++)
1.74 brouard 1690: for(m=iagemin; m <= iagemax+3; m++)
1691: prop[i][m]=0.0;
1.53 brouard 1692:
1.69 brouard 1693: for (i=1; i<=imx; i++) { /* Each individual */
1.53 brouard 1694: bool=1;
1695: if (cptcovn>0) {
1696: for (z1=1; z1<=cptcoveff; z1++)
1697: if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])
1698: bool=0;
1699: }
1700: if (bool==1) {
1.69 brouard 1701: for(m=firstpass; m<=lastpass; m++){/* Other selection (we can limit to certain interviews*/
1702: y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
1703: if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
1.74 brouard 1704: if(agev[m][i]==0) agev[m][i]=iagemax+1;
1705: if(agev[m][i]==1) agev[m][i]=iagemax+2;
1706: 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);
1707: if (s[m][i]>0 && s[m][i]<=nlstate) {
1708: /*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]]);*/
1709: prop[s[m][i]][(int)agev[m][i]] += weight[i];
1710: prop[s[m][i]][iagemax+3] += weight[i];
1711: }
1.53 brouard 1712: }
1.69 brouard 1713: } /* end selection of waves */
1.53 brouard 1714: }
1715: }
1.74 brouard 1716: for(i=iagemin; i <= iagemax+3; i++){
1.53 brouard 1717:
1.74 brouard 1718: for(jk=1,posprop=0; jk <=nlstate ; jk++) {
1719: posprop += prop[jk][i];
1720: }
1721:
1722: for(jk=1; jk <=nlstate ; jk++){
1723: if( i <= iagemax){
1724: if(posprop>=1.e-5){
1725: probs[i][jk][j1]= prop[jk][i]/posprop;
1726: }
1727: }
1728: }/* end jk */
1729: }/* end i */
1.53 brouard 1730: } /* end i1 */
1731: } /* end k1 */
1732:
1.74 brouard 1733: /* free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
1734: /*free_vector(pp,1,nlstate);*/
1735: free_matrix(prop,1,nlstate, iagemin,iagemax+3);
1736: } /* End of prevalence */
1.53 brouard 1737:
1738: /************* Waves Concatenation ***************/
1739:
1.59 brouard 1740: 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 1741: {
1742: /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
1743: Death is a valid wave (if date is known).
1744: mw[mi][i] is the mi (mi=1 to wav[i]) effective wave of individual i
1.59 brouard 1745: dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
1.53 brouard 1746: and mw[mi+1][i]. dh depends on stepm.
1747: */
1748:
1749: int i, mi, m;
1750: /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
1751: double sum=0., jmean=0.;*/
1752: int first;
1753: int j, k=0,jk, ju, jl;
1754: double sum=0.;
1755: first=0;
1756: jmin=1e+5;
1757: jmax=-1;
1758: jmean=0.;
1759: for(i=1; i<=imx; i++){
1760: mi=0;
1761: m=firstpass;
1762: while(s[m][i] <= nlstate){
1.69 brouard 1763: if(s[m][i]>=1)
1.53 brouard 1764: mw[++mi][i]=m;
1765: if(m >=lastpass)
1766: break;
1767: else
1768: m++;
1769: }/* end while */
1770: if (s[m][i] > nlstate){
1771: mi++; /* Death is another wave */
1772: /* if(mi==0) never been interviewed correctly before death */
1773: /* Only death is a correct wave */
1774: mw[mi][i]=m;
1775: }
1776:
1777: wav[i]=mi;
1778: if(mi==0){
1779: if(first==0){
1.77 brouard 1780: printf("Warning! None valid information for:%d line=%d (skipped) and may be others, see log file\n",num[i],i);
1.53 brouard 1781: first=1;
1782: }
1783: if(first==1){
1.77 brouard 1784: fprintf(ficlog,"Warning! None valid information for:%d line=%d (skipped)\n",num[i],i);
1.53 brouard 1785: }
1786: } /* end mi==0 */
1.77 brouard 1787: } /* End individuals */
1.53 brouard 1788:
1789: for(i=1; i<=imx; i++){
1790: for(mi=1; mi<wav[i];mi++){
1791: if (stepm <=0)
1792: dh[mi][i]=1;
1793: else{
1.77 brouard 1794: if (s[mw[mi+1][i]][i] > nlstate) { /* A death */
1.53 brouard 1795: if (agedc[i] < 2*AGESUP) {
1796: j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);
1797: if(j==0) j=1; /* Survives at least one month after exam */
1798: k=k+1;
1799: if (j >= jmax) jmax=j;
1800: if (j <= jmin) jmin=j;
1801: sum=sum+j;
1.77 brouard 1802: /*if (j<0) printf("j=%d num=%d \n",j,i);*/
1.68 lievre 1803: /* printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
1.78 brouard 1804: 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 1805: }
1806: }
1807: else{
1808: j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
1.68 lievre 1809: /* printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
1.53 brouard 1810: k=k+1;
1811: if (j >= jmax) jmax=j;
1812: else if (j <= jmin)jmin=j;
1813: /* if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
1.73 lievre 1814: /*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 1815: 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 1816: sum=sum+j;
1817: }
1818: jk= j/stepm;
1819: jl= j -jk*stepm;
1820: ju= j -(jk+1)*stepm;
1.64 lievre 1821: if(mle <=1){
1822: if(jl==0){
1823: dh[mi][i]=jk;
1824: bh[mi][i]=0;
1825: }else{ /* We want a negative bias in order to only have interpolation ie
1826: * at the price of an extra matrix product in likelihood */
1827: dh[mi][i]=jk+1;
1828: bh[mi][i]=ju;
1829: }
1830: }else{
1831: if(jl <= -ju){
1832: dh[mi][i]=jk;
1833: bh[mi][i]=jl; /* bias is positive if real duration
1834: * is higher than the multiple of stepm and negative otherwise.
1835: */
1836: }
1837: else{
1838: dh[mi][i]=jk+1;
1839: bh[mi][i]=ju;
1840: }
1841: if(dh[mi][i]==0){
1842: dh[mi][i]=1; /* At least one step */
1843: bh[mi][i]=ju; /* At least one step */
1.71 brouard 1844: /* 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 1845: }
1.59 brouard 1846: }
1.64 lievre 1847: } /* end if mle */
1848: } /* end wave */
1.53 brouard 1849: }
1850: jmean=sum/k;
1851: printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);
1852: fprintf(ficlog,"Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);
1853: }
1854:
1855: /*********** Tricode ****************************/
1856: void tricode(int *Tvar, int **nbcode, int imx)
1857: {
1.58 lievre 1858:
1859: int Ndum[20],ij=1, k, j, i, maxncov=19;
1.53 brouard 1860: int cptcode=0;
1861: cptcoveff=0;
1862:
1.58 lievre 1863: for (k=0; k<maxncov; k++) Ndum[k]=0;
1.53 brouard 1864: for (k=1; k<=7; k++) ncodemax[k]=0;
1865:
1866: for (j=1; j<=(cptcovn+2*cptcovprod); j++) {
1.58 lievre 1867: for (i=1; i<=imx; i++) { /*reads the data file to get the maximum
1868: modality*/
1869: ij=(int)(covar[Tvar[j]][i]); /* ij is the modality of this individual*/
1870: Ndum[ij]++; /*store the modality */
1.53 brouard 1871: /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
1.58 lievre 1872: if (ij > cptcode) cptcode=ij; /* getting the maximum of covariable
1873: Tvar[j]. If V=sex and male is 0 and
1874: female is 1, then cptcode=1.*/
1.53 brouard 1875: }
1876:
1877: for (i=0; i<=cptcode; i++) {
1.58 lievre 1878: 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 1879: }
1.58 lievre 1880:
1.53 brouard 1881: ij=1;
1882: for (i=1; i<=ncodemax[j]; i++) {
1.58 lievre 1883: for (k=0; k<= maxncov; k++) {
1.53 brouard 1884: if (Ndum[k] != 0) {
1885: nbcode[Tvar[j]][ij]=k;
1.58 lievre 1886: /* 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 1887:
1888: ij++;
1889: }
1890: if (ij > ncodemax[j]) break;
1891: }
1892: }
1893: }
1894:
1.58 lievre 1895: for (k=0; k< maxncov; k++) Ndum[k]=0;
1.53 brouard 1896:
1.58 lievre 1897: for (i=1; i<=ncovmodel-2; i++) {
1898: /* 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 1899: ij=Tvar[i];
1.58 lievre 1900: Ndum[ij]++;
1.53 brouard 1901: }
1902:
1903: ij=1;
1.58 lievre 1904: for (i=1; i<= maxncov; i++) {
1.53 brouard 1905: if((Ndum[i]!=0) && (i<=ncovcol)){
1.58 lievre 1906: Tvaraff[ij]=i; /*For printing */
1.53 brouard 1907: ij++;
1908: }
1909: }
1910:
1.58 lievre 1911: cptcoveff=ij-1; /*Number of simple covariates*/
1.53 brouard 1912: }
1913:
1914: /*********** Health Expectancies ****************/
1915:
1916: 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 )
1917:
1918: {
1919: /* Health expectancies */
1920: int i, j, nhstepm, hstepm, h, nstepm, k, cptj;
1921: double age, agelim, hf;
1922: double ***p3mat,***varhe;
1923: double **dnewm,**doldm;
1924: double *xp;
1925: double **gp, **gm;
1926: double ***gradg, ***trgradg;
1927: int theta;
1928:
1.74 brouard 1929: varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage);
1.53 brouard 1930: xp=vector(1,npar);
1.74 brouard 1931: dnewm=matrix(1,nlstate*nlstate,1,npar);
1932: doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate);
1.53 brouard 1933:
1934: fprintf(ficreseij,"# Health expectancies\n");
1935: fprintf(ficreseij,"# Age");
1936: for(i=1; i<=nlstate;i++)
1937: for(j=1; j<=nlstate;j++)
1938: fprintf(ficreseij," %1d-%1d (SE)",i,j);
1939: fprintf(ficreseij,"\n");
1940:
1941: if(estepm < stepm){
1942: printf ("Problem %d lower than %d\n",estepm, stepm);
1943: }
1944: else hstepm=estepm;
1945: /* We compute the life expectancy from trapezoids spaced every estepm months
1946: * This is mainly to measure the difference between two models: for example
1947: * if stepm=24 months pijx are given only every 2 years and by summing them
1948: * we are calculating an estimate of the Life Expectancy assuming a linear
1.66 brouard 1949: * progression in between and thus overestimating or underestimating according
1.53 brouard 1950: * to the curvature of the survival function. If, for the same date, we
1951: * estimate the model with stepm=1 month, we can keep estepm to 24 months
1952: * to compare the new estimate of Life expectancy with the same linear
1953: * hypothesis. A more precise result, taking into account a more precise
1954: * curvature will be obtained if estepm is as small as stepm. */
1955:
1956: /* For example we decided to compute the life expectancy with the smallest unit */
1957: /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
1958: nhstepm is the number of hstepm from age to agelim
1959: nstepm is the number of stepm from age to agelin.
1960: Look at hpijx to understand the reason of that which relies in memory size
1961: and note for a fixed period like estepm months */
1962: /* We decided (b) to get a life expectancy respecting the most precise curvature of the
1963: survival function given by stepm (the optimization length). Unfortunately it
1964: means that if the survival funtion is printed only each two years of age and if
1965: you sum them up and add 1 year (area under the trapezoids) you won't get the same
1966: results. So we changed our mind and took the option of the best precision.
1967: */
1968: hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
1969:
1970: agelim=AGESUP;
1971: for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
1972: /* nhstepm age range expressed in number of stepm */
1973: nstepm=(int) rint((agelim-age)*YEARM/stepm);
1974: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
1975: /* if (stepm >= YEARM) hstepm=1;*/
1976: nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
1977: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
1.74 brouard 1978: gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);
1979: gp=matrix(0,nhstepm,1,nlstate*nlstate);
1980: gm=matrix(0,nhstepm,1,nlstate*nlstate);
1.53 brouard 1981:
1982: /* Computed by stepm unit matrices, product of hstepm matrices, stored
1983: in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
1984: hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);
1985:
1986:
1987: hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
1988:
1989: /* Computing Variances of health expectancies */
1990:
1991: for(theta=1; theta <=npar; theta++){
1992: for(i=1; i<=npar; i++){
1993: xp[i] = x[i] + (i==theta ?delti[theta]:0);
1994: }
1995: hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
1996:
1997: cptj=0;
1998: for(j=1; j<= nlstate; j++){
1999: for(i=1; i<=nlstate; i++){
2000: cptj=cptj+1;
2001: for(h=0, gp[h][cptj]=0.; h<=nhstepm-1; h++){
2002: gp[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;
2003: }
2004: }
2005: }
2006:
2007:
2008: for(i=1; i<=npar; i++)
2009: xp[i] = x[i] - (i==theta ?delti[theta]:0);
2010: hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
2011:
2012: cptj=0;
2013: for(j=1; j<= nlstate; j++){
2014: for(i=1;i<=nlstate;i++){
2015: cptj=cptj+1;
2016: for(h=0, gm[h][cptj]=0.; h<=nhstepm-1; h++){
1.77 brouard 2017:
1.53 brouard 2018: gm[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;
2019: }
2020: }
2021: }
1.74 brouard 2022: for(j=1; j<= nlstate*nlstate; j++)
1.53 brouard 2023: for(h=0; h<=nhstepm-1; h++){
2024: gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
2025: }
2026: }
2027:
2028: /* End theta */
2029:
1.74 brouard 2030: trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar);
1.53 brouard 2031:
2032: for(h=0; h<=nhstepm-1; h++)
1.74 brouard 2033: for(j=1; j<=nlstate*nlstate;j++)
1.53 brouard 2034: for(theta=1; theta <=npar; theta++)
2035: trgradg[h][j][theta]=gradg[h][theta][j];
2036:
2037:
1.74 brouard 2038: for(i=1;i<=nlstate*nlstate;i++)
2039: for(j=1;j<=nlstate*nlstate;j++)
1.53 brouard 2040: varhe[i][j][(int)age] =0.;
2041:
2042: printf("%d|",(int)age);fflush(stdout);
2043: fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
2044: for(h=0;h<=nhstepm-1;h++){
2045: for(k=0;k<=nhstepm-1;k++){
1.74 brouard 2046: matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov);
2047: matprod2(doldm,dnewm,1,nlstate*nlstate,1,npar,1,nlstate*nlstate,gradg[k]);
2048: for(i=1;i<=nlstate*nlstate;i++)
2049: for(j=1;j<=nlstate*nlstate;j++)
1.53 brouard 2050: varhe[i][j][(int)age] += doldm[i][j]*hf*hf;
2051: }
2052: }
2053: /* Computing expectancies */
2054: for(i=1; i<=nlstate;i++)
2055: for(j=1; j<=nlstate;j++)
2056: for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
2057: eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
2058:
2059: /* 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]);*/
2060:
2061: }
2062:
2063: fprintf(ficreseij,"%3.0f",age );
2064: cptj=0;
2065: for(i=1; i<=nlstate;i++)
2066: for(j=1; j<=nlstate;j++){
2067: cptj++;
2068: fprintf(ficreseij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[cptj][cptj][(int)age]) );
2069: }
2070: fprintf(ficreseij,"\n");
2071:
1.74 brouard 2072: free_matrix(gm,0,nhstepm,1,nlstate*nlstate);
2073: free_matrix(gp,0,nhstepm,1,nlstate*nlstate);
2074: free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*nlstate);
2075: free_ma3x(trgradg,0,nhstepm,1,nlstate*nlstate,1,npar);
1.53 brouard 2076: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
2077: }
2078: printf("\n");
2079: fprintf(ficlog,"\n");
2080:
2081: free_vector(xp,1,npar);
1.74 brouard 2082: free_matrix(dnewm,1,nlstate*nlstate,1,npar);
2083: free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate);
2084: free_ma3x(varhe,1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int)fage);
1.53 brouard 2085: }
2086:
2087: /************ Variance ******************/
2088: 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)
2089: {
2090: /* Variance of health expectancies */
2091: /* double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
2092: /* double **newm;*/
2093: double **dnewm,**doldm;
2094: double **dnewmp,**doldmp;
2095: int i, j, nhstepm, hstepm, h, nstepm ;
2096: int k, cptcode;
2097: double *xp;
2098: double **gp, **gm; /* for var eij */
2099: double ***gradg, ***trgradg; /*for var eij */
2100: double **gradgp, **trgradgp; /* for var p point j */
2101: double *gpp, *gmp; /* for var p point j */
2102: double **varppt; /* for var p point j nlstate to nlstate+ndeath */
2103: double ***p3mat;
2104: double age,agelim, hf;
2105: double ***mobaverage;
2106: int theta;
2107: char digit[4];
1.55 lievre 2108: char digitp[25];
1.53 brouard 2109:
2110: char fileresprobmorprev[FILENAMELENGTH];
2111:
1.55 lievre 2112: if(popbased==1){
1.58 lievre 2113: if(mobilav!=0)
1.55 lievre 2114: strcpy(digitp,"-populbased-mobilav-");
2115: else strcpy(digitp,"-populbased-nomobil-");
2116: }
2117: else
1.53 brouard 2118: strcpy(digitp,"-stablbased-");
1.56 lievre 2119:
1.54 brouard 2120: if (mobilav!=0) {
1.53 brouard 2121: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
1.54 brouard 2122: if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
2123: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
2124: printf(" Error in movingaverage mobilav=%d\n",mobilav);
2125: }
1.53 brouard 2126: }
2127:
2128: strcpy(fileresprobmorprev,"prmorprev");
2129: sprintf(digit,"%-d",ij);
2130: /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
2131: strcat(fileresprobmorprev,digit); /* Tvar to be done */
2132: strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
2133: strcat(fileresprobmorprev,fileres);
2134: if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
2135: printf("Problem with resultfile: %s\n", fileresprobmorprev);
2136: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
2137: }
2138: printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
2139: fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
1.66 brouard 2140: 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 2141: fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
2142: for(j=nlstate+1; j<=(nlstate+ndeath);j++){
2143: fprintf(ficresprobmorprev," p.%-d SE",j);
2144: for(i=1; i<=nlstate;i++)
2145: fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
2146: }
2147: fprintf(ficresprobmorprev,"\n");
2148: if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {
2149: printf("Problem with gnuplot file: %s\n", optionfilegnuplot);
2150: fprintf(ficlog,"Problem with gnuplot file: %s\n", optionfilegnuplot);
2151: exit(0);
2152: }
2153: else{
2154: fprintf(ficgp,"\n# Routine varevsij");
2155: }
2156: if((fichtm=fopen(optionfilehtm,"a"))==NULL) {
2157: printf("Problem with html file: %s\n", optionfilehtm);
2158: fprintf(ficlog,"Problem with html file: %s\n", optionfilehtm);
2159: exit(0);
2160: }
2161: else{
1.67 brouard 2162: 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");
2163: fprintf(fichtm,"\n<br>%s <br>\n",digitp);
1.53 brouard 2164: }
2165: varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
2166:
2167: 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");
2168: fprintf(ficresvij,"# Age");
2169: for(i=1; i<=nlstate;i++)
2170: for(j=1; j<=nlstate;j++)
2171: fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);
2172: fprintf(ficresvij,"\n");
2173:
2174: xp=vector(1,npar);
2175: dnewm=matrix(1,nlstate,1,npar);
2176: doldm=matrix(1,nlstate,1,nlstate);
2177: dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
2178: doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
2179:
2180: gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
2181: gpp=vector(nlstate+1,nlstate+ndeath);
2182: gmp=vector(nlstate+1,nlstate+ndeath);
2183: trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
2184:
2185: if(estepm < stepm){
2186: printf ("Problem %d lower than %d\n",estepm, stepm);
2187: }
2188: else hstepm=estepm;
2189: /* For example we decided to compute the life expectancy with the smallest unit */
2190: /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
2191: nhstepm is the number of hstepm from age to agelim
2192: nstepm is the number of stepm from age to agelin.
2193: Look at hpijx to understand the reason of that which relies in memory size
2194: and note for a fixed period like k years */
2195: /* We decided (b) to get a life expectancy respecting the most precise curvature of the
2196: survival function given by stepm (the optimization length). Unfortunately it
1.66 brouard 2197: means that if the survival funtion is printed every two years of age and if
1.53 brouard 2198: you sum them up and add 1 year (area under the trapezoids) you won't get the same
2199: results. So we changed our mind and took the option of the best precision.
2200: */
2201: hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
2202: agelim = AGESUP;
2203: for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
2204: nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
2205: nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
2206: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
2207: gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
2208: gp=matrix(0,nhstepm,1,nlstate);
2209: gm=matrix(0,nhstepm,1,nlstate);
2210:
2211:
2212: for(theta=1; theta <=npar; theta++){
1.66 brouard 2213: for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
1.53 brouard 2214: xp[i] = x[i] + (i==theta ?delti[theta]:0);
2215: }
2216: hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
2217: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
2218:
2219: if (popbased==1) {
1.54 brouard 2220: if(mobilav ==0){
1.53 brouard 2221: for(i=1; i<=nlstate;i++)
2222: prlim[i][i]=probs[(int)age][i][ij];
1.54 brouard 2223: }else{ /* mobilav */
1.53 brouard 2224: for(i=1; i<=nlstate;i++)
2225: prlim[i][i]=mobaverage[(int)age][i][ij];
2226: }
2227: }
2228:
2229: for(j=1; j<= nlstate; j++){
2230: for(h=0; h<=nhstepm; h++){
2231: for(i=1, gp[h][j]=0.;i<=nlstate;i++)
2232: gp[h][j] += prlim[i][i]*p3mat[i][j][h];
2233: }
2234: }
1.66 brouard 2235: /* This for computing probability of death (h=1 means
2236: computed over hstepm matrices product = hstepm*stepm months)
2237: as a weighted average of prlim.
2238: */
1.69 brouard 2239: for(j=nlstate+1;j<=nlstate+ndeath;j++){
1.68 lievre 2240: for(i=1,gpp[j]=0.; i<= nlstate; i++)
1.53 brouard 2241: gpp[j] += prlim[i][i]*p3mat[i][j][1];
2242: }
1.66 brouard 2243: /* end probability of death */
1.53 brouard 2244:
1.66 brouard 2245: for(i=1; i<=npar; i++) /* Computes gradient x - delta */
1.53 brouard 2246: xp[i] = x[i] - (i==theta ?delti[theta]:0);
2247: hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
2248: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
2249:
2250: if (popbased==1) {
1.54 brouard 2251: if(mobilav ==0){
1.53 brouard 2252: for(i=1; i<=nlstate;i++)
2253: prlim[i][i]=probs[(int)age][i][ij];
1.54 brouard 2254: }else{ /* mobilav */
1.53 brouard 2255: for(i=1; i<=nlstate;i++)
2256: prlim[i][i]=mobaverage[(int)age][i][ij];
2257: }
2258: }
2259:
2260: for(j=1; j<= nlstate; j++){
2261: for(h=0; h<=nhstepm; h++){
2262: for(i=1, gm[h][j]=0.;i<=nlstate;i++)
2263: gm[h][j] += prlim[i][i]*p3mat[i][j][h];
2264: }
2265: }
1.66 brouard 2266: /* This for computing probability of death (h=1 means
2267: computed over hstepm matrices product = hstepm*stepm months)
2268: as a weighted average of prlim.
2269: */
1.69 brouard 2270: for(j=nlstate+1;j<=nlstate+ndeath;j++){
1.68 lievre 2271: for(i=1,gmp[j]=0.; i<= nlstate; i++)
2272: gmp[j] += prlim[i][i]*p3mat[i][j][1];
1.53 brouard 2273: }
1.66 brouard 2274: /* end probability of death */
1.53 brouard 2275:
2276: for(j=1; j<= nlstate; j++) /* vareij */
2277: for(h=0; h<=nhstepm; h++){
2278: gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
2279: }
1.68 lievre 2280:
1.53 brouard 2281: for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
2282: gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
2283: }
2284:
2285: } /* End theta */
2286:
2287: trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
2288:
2289: for(h=0; h<=nhstepm; h++) /* veij */
2290: for(j=1; j<=nlstate;j++)
2291: for(theta=1; theta <=npar; theta++)
2292: trgradg[h][j][theta]=gradg[h][theta][j];
2293:
2294: for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
1.69 brouard 2295: for(theta=1; theta <=npar; theta++)
1.53 brouard 2296: trgradgp[j][theta]=gradgp[theta][j];
1.69 brouard 2297:
1.53 brouard 2298:
2299: hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
2300: for(i=1;i<=nlstate;i++)
2301: for(j=1;j<=nlstate;j++)
2302: vareij[i][j][(int)age] =0.;
2303:
2304: for(h=0;h<=nhstepm;h++){
2305: for(k=0;k<=nhstepm;k++){
2306: matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
2307: matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
2308: for(i=1;i<=nlstate;i++)
2309: for(j=1;j<=nlstate;j++)
2310: vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
2311: }
2312: }
1.70 brouard 2313:
1.53 brouard 2314: /* pptj */
2315: matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
2316: matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
1.70 brouard 2317: for(j=nlstate+1;j<=nlstate+ndeath;j++)
2318: for(i=nlstate+1;i<=nlstate+ndeath;i++)
1.53 brouard 2319: varppt[j][i]=doldmp[j][i];
2320: /* end ppptj */
1.66 brouard 2321: /* x centered again */
1.53 brouard 2322: hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);
2323: prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);
2324:
2325: if (popbased==1) {
1.54 brouard 2326: if(mobilav ==0){
1.53 brouard 2327: for(i=1; i<=nlstate;i++)
2328: prlim[i][i]=probs[(int)age][i][ij];
1.54 brouard 2329: }else{ /* mobilav */
1.53 brouard 2330: for(i=1; i<=nlstate;i++)
2331: prlim[i][i]=mobaverage[(int)age][i][ij];
2332: }
2333: }
1.70 brouard 2334:
1.66 brouard 2335: /* This for computing probability of death (h=1 means
2336: computed over hstepm (estepm) matrices product = hstepm*stepm months)
2337: as a weighted average of prlim.
2338: */
1.68 lievre 2339: for(j=nlstate+1;j<=nlstate+ndeath;j++){
2340: for(i=1,gmp[j]=0.;i<= nlstate; i++)
1.53 brouard 2341: gmp[j] += prlim[i][i]*p3mat[i][j][1];
2342: }
1.66 brouard 2343: /* end probability of death */
1.53 brouard 2344:
2345: fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
2346: for(j=nlstate+1; j<=(nlstate+ndeath);j++){
2347: fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
2348: for(i=1; i<=nlstate;i++){
2349: fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
2350: }
2351: }
2352: fprintf(ficresprobmorprev,"\n");
2353:
2354: fprintf(ficresvij,"%.0f ",age );
2355: for(i=1; i<=nlstate;i++)
2356: for(j=1; j<=nlstate;j++){
2357: fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
2358: }
2359: fprintf(ficresvij,"\n");
2360: free_matrix(gp,0,nhstepm,1,nlstate);
2361: free_matrix(gm,0,nhstepm,1,nlstate);
2362: free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
2363: free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
2364: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
2365: } /* End age */
2366: free_vector(gpp,nlstate+1,nlstate+ndeath);
2367: free_vector(gmp,nlstate+1,nlstate+ndeath);
2368: free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
2369: free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
2370: fprintf(ficgp,"\nset noparametric;set nolabel; set ter png small;set size 0.65, 0.65");
2371: /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */
2372: fprintf(ficgp,"\n set log y; set nolog x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
1.67 brouard 2373: /* fprintf(ficgp,"\n plot \"%s\" u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm); */
2374: /* fprintf(ficgp,"\n replot \"%s\" u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm); */
2375: /* fprintf(ficgp,"\n replot \"%s\" u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm); */
2376: fprintf(ficgp,"\n plot \"%s\" u 1:($3) not w l 1 ",fileresprobmorprev);
2377: fprintf(ficgp,"\n replot \"%s\" u 1:(($3+1.96*$4)) t \"95\%% interval\" w l 2 ",fileresprobmorprev);
2378: fprintf(ficgp,"\n replot \"%s\" u 1:(($3-1.96*$4)) not w l 2 ",fileresprobmorprev);
1.53 brouard 2379: fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",fileresprobmorprev,fileresprobmorprev);
1.71 brouard 2380: 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 2381: /* 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);
2382: */
1.71 brouard 2383: fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.png\";replot;",digitp,optionfilefiname,digit);
1.53 brouard 2384:
2385: free_vector(xp,1,npar);
2386: free_matrix(doldm,1,nlstate,1,nlstate);
2387: free_matrix(dnewm,1,nlstate,1,npar);
2388: free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
2389: free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
2390: free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
1.55 lievre 2391: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
1.53 brouard 2392: fclose(ficresprobmorprev);
2393: fclose(ficgp);
2394: fclose(fichtm);
1.70 brouard 2395: }
1.53 brouard 2396:
2397: /************ Variance of prevlim ******************/
2398: 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)
2399: {
2400: /* Variance of prevalence limit */
1.59 brouard 2401: /* double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
1.53 brouard 2402: double **newm;
2403: double **dnewm,**doldm;
2404: int i, j, nhstepm, hstepm;
2405: int k, cptcode;
2406: double *xp;
2407: double *gp, *gm;
2408: double **gradg, **trgradg;
2409: double age,agelim;
2410: int theta;
2411:
1.54 brouard 2412: fprintf(ficresvpl,"# Standard deviation of stable prevalences \n");
1.53 brouard 2413: fprintf(ficresvpl,"# Age");
2414: for(i=1; i<=nlstate;i++)
2415: fprintf(ficresvpl," %1d-%1d",i,i);
2416: fprintf(ficresvpl,"\n");
2417:
2418: xp=vector(1,npar);
2419: dnewm=matrix(1,nlstate,1,npar);
2420: doldm=matrix(1,nlstate,1,nlstate);
2421:
2422: hstepm=1*YEARM; /* Every year of age */
2423: hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */
2424: agelim = AGESUP;
2425: for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
2426: nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
2427: if (stepm >= YEARM) hstepm=1;
2428: nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
2429: gradg=matrix(1,npar,1,nlstate);
2430: gp=vector(1,nlstate);
2431: gm=vector(1,nlstate);
2432:
2433: for(theta=1; theta <=npar; theta++){
2434: for(i=1; i<=npar; i++){ /* Computes gradient */
2435: xp[i] = x[i] + (i==theta ?delti[theta]:0);
2436: }
2437: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
2438: for(i=1;i<=nlstate;i++)
2439: gp[i] = prlim[i][i];
2440:
2441: for(i=1; i<=npar; i++) /* Computes gradient */
2442: xp[i] = x[i] - (i==theta ?delti[theta]:0);
2443: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
2444: for(i=1;i<=nlstate;i++)
2445: gm[i] = prlim[i][i];
2446:
2447: for(i=1;i<=nlstate;i++)
2448: gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
2449: } /* End theta */
2450:
2451: trgradg =matrix(1,nlstate,1,npar);
2452:
2453: for(j=1; j<=nlstate;j++)
2454: for(theta=1; theta <=npar; theta++)
2455: trgradg[j][theta]=gradg[theta][j];
2456:
2457: for(i=1;i<=nlstate;i++)
2458: varpl[i][(int)age] =0.;
2459: matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
2460: matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
2461: for(i=1;i<=nlstate;i++)
2462: varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
2463:
2464: fprintf(ficresvpl,"%.0f ",age );
2465: for(i=1; i<=nlstate;i++)
2466: fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
2467: fprintf(ficresvpl,"\n");
2468: free_vector(gp,1,nlstate);
2469: free_vector(gm,1,nlstate);
2470: free_matrix(gradg,1,npar,1,nlstate);
2471: free_matrix(trgradg,1,nlstate,1,npar);
2472: } /* End age */
2473:
2474: free_vector(xp,1,npar);
2475: free_matrix(doldm,1,nlstate,1,npar);
2476: free_matrix(dnewm,1,nlstate,1,nlstate);
2477:
2478: }
2479:
2480: /************ Variance of one-step probabilities ******************/
2481: void varprob(char optionfilefiname[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij, int *Tvar, int **nbcode, int *ncodemax)
2482: {
2483: int i, j=0, i1, k1, l1, t, tj;
2484: int k2, l2, j1, z1;
2485: int k=0,l, cptcode;
2486: int first=1, first1;
2487: double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
2488: double **dnewm,**doldm;
2489: double *xp;
2490: double *gp, *gm;
2491: double **gradg, **trgradg;
2492: double **mu;
2493: double age,agelim, cov[NCOVMAX];
2494: double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
2495: int theta;
2496: char fileresprob[FILENAMELENGTH];
2497: char fileresprobcov[FILENAMELENGTH];
2498: char fileresprobcor[FILENAMELENGTH];
2499:
2500: double ***varpij;
2501:
2502: strcpy(fileresprob,"prob");
2503: strcat(fileresprob,fileres);
2504: if((ficresprob=fopen(fileresprob,"w"))==NULL) {
2505: printf("Problem with resultfile: %s\n", fileresprob);
2506: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
2507: }
2508: strcpy(fileresprobcov,"probcov");
2509: strcat(fileresprobcov,fileres);
2510: if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
2511: printf("Problem with resultfile: %s\n", fileresprobcov);
2512: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
2513: }
2514: strcpy(fileresprobcor,"probcor");
2515: strcat(fileresprobcor,fileres);
2516: if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
2517: printf("Problem with resultfile: %s\n", fileresprobcor);
2518: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
2519: }
2520: printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
2521: fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
2522: printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
2523: fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
2524: printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
2525: fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
2526:
2527: fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
2528: fprintf(ficresprob,"# Age");
2529: fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
2530: fprintf(ficresprobcov,"# Age");
2531: fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
2532: fprintf(ficresprobcov,"# Age");
2533:
2534:
2535: for(i=1; i<=nlstate;i++)
2536: for(j=1; j<=(nlstate+ndeath);j++){
2537: fprintf(ficresprob," p%1d-%1d (SE)",i,j);
2538: fprintf(ficresprobcov," p%1d-%1d ",i,j);
2539: fprintf(ficresprobcor," p%1d-%1d ",i,j);
2540: }
1.69 brouard 2541: /* fprintf(ficresprob,"\n");
1.53 brouard 2542: fprintf(ficresprobcov,"\n");
2543: fprintf(ficresprobcor,"\n");
1.69 brouard 2544: */
2545: xp=vector(1,npar);
1.53 brouard 2546: dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
2547: doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
2548: mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
2549: varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
2550: first=1;
2551: if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {
2552: printf("Problem with gnuplot file: %s\n", optionfilegnuplot);
2553: fprintf(ficlog,"Problem with gnuplot file: %s\n", optionfilegnuplot);
2554: exit(0);
2555: }
2556: else{
2557: fprintf(ficgp,"\n# Routine varprob");
2558: }
2559: if((fichtm=fopen(optionfilehtm,"a"))==NULL) {
2560: printf("Problem with html file: %s\n", optionfilehtm);
2561: fprintf(ficlog,"Problem with html file: %s\n", optionfilehtm);
2562: exit(0);
2563: }
2564: else{
2565: fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
2566: fprintf(fichtm,"\n");
2567:
2568: fprintf(fichtm,"\n<li><h4> Computing matrix of variance-covariance of step probabilities</h4></li>\n");
2569: 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");
2570: 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");
2571:
2572: }
2573:
2574: cov[1]=1;
2575: tj=cptcoveff;
2576: if (cptcovn<1) {tj=1;ncodemax[1]=1;}
2577: j1=0;
2578: for(t=1; t<=tj;t++){
2579: for(i1=1; i1<=ncodemax[t];i1++){
2580: j1++;
2581: if (cptcovn>0) {
2582: fprintf(ficresprob, "\n#********** Variable ");
2583: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
1.69 brouard 2584: fprintf(ficresprob, "**********\n#\n");
1.53 brouard 2585: fprintf(ficresprobcov, "\n#********** Variable ");
2586: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
1.69 brouard 2587: fprintf(ficresprobcov, "**********\n#\n");
1.53 brouard 2588:
2589: fprintf(ficgp, "\n#********** Variable ");
1.69 brouard 2590: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
2591: fprintf(ficgp, "**********\n#\n");
1.53 brouard 2592:
2593:
2594: fprintf(fichtm, "\n<hr size=\"2\" color=\"#EC5E5E\">********** Variable ");
2595: for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
2596: fprintf(fichtm, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
2597:
2598: fprintf(ficresprobcor, "\n#********** Variable ");
2599: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
1.69 brouard 2600: fprintf(ficresprobcor, "**********\n#");
1.53 brouard 2601: }
2602:
2603: for (age=bage; age<=fage; age ++){
2604: cov[2]=age;
2605: for (k=1; k<=cptcovn;k++) {
2606: cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];
2607: }
2608: for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
2609: for (k=1; k<=cptcovprod;k++)
2610: cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
2611:
2612: gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
2613: trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
2614: gp=vector(1,(nlstate)*(nlstate+ndeath));
2615: gm=vector(1,(nlstate)*(nlstate+ndeath));
2616:
2617: for(theta=1; theta <=npar; theta++){
2618: for(i=1; i<=npar; i++)
1.74 brouard 2619: xp[i] = x[i] + (i==theta ?delti[theta]:(double)0);
1.53 brouard 2620:
2621: pmij(pmmij,cov,ncovmodel,xp,nlstate);
2622:
2623: k=0;
2624: for(i=1; i<= (nlstate); i++){
2625: for(j=1; j<=(nlstate+ndeath);j++){
2626: k=k+1;
2627: gp[k]=pmmij[i][j];
2628: }
2629: }
2630:
2631: for(i=1; i<=npar; i++)
1.74 brouard 2632: xp[i] = x[i] - (i==theta ?delti[theta]:(double)0);
1.53 brouard 2633:
2634: pmij(pmmij,cov,ncovmodel,xp,nlstate);
2635: k=0;
2636: for(i=1; i<=(nlstate); i++){
2637: for(j=1; j<=(nlstate+ndeath);j++){
2638: k=k+1;
2639: gm[k]=pmmij[i][j];
2640: }
2641: }
2642:
2643: for(i=1; i<= (nlstate)*(nlstate+ndeath); i++)
1.74 brouard 2644: gradg[theta][i]=(gp[i]-gm[i])/(double)2./delti[theta];
1.53 brouard 2645: }
2646:
2647: for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
2648: for(theta=1; theta <=npar; theta++)
2649: trgradg[j][theta]=gradg[theta][j];
2650:
2651: matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov);
2652: matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);
1.59 brouard 2653: free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
2654: free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
2655: free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
2656: free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
2657:
1.53 brouard 2658: pmij(pmmij,cov,ncovmodel,x,nlstate);
2659:
2660: k=0;
2661: for(i=1; i<=(nlstate); i++){
2662: for(j=1; j<=(nlstate+ndeath);j++){
2663: k=k+1;
2664: mu[k][(int) age]=pmmij[i][j];
2665: }
2666: }
2667: for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
2668: for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
2669: varpij[i][j][(int)age] = doldm[i][j];
2670:
2671: /*printf("\n%d ",(int)age);
1.59 brouard 2672: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
2673: printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
2674: fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
2675: }*/
1.53 brouard 2676:
2677: fprintf(ficresprob,"\n%d ",(int)age);
2678: fprintf(ficresprobcov,"\n%d ",(int)age);
2679: fprintf(ficresprobcor,"\n%d ",(int)age);
2680:
2681: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)
2682: fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));
2683: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
2684: fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);
2685: fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
2686: }
2687: i=0;
2688: for (k=1; k<=(nlstate);k++){
2689: for (l=1; l<=(nlstate+ndeath);l++){
2690: i=i++;
2691: fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
2692: fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
2693: for (j=1; j<=i;j++){
2694: fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);
2695: fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));
2696: }
2697: }
2698: }/* end of loop for state */
2699: } /* end of loop for age */
2700:
2701: /* Confidence intervalle of pij */
2702: /*
1.59 brouard 2703: fprintf(ficgp,"\nset noparametric;unset label");
2704: fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");
2705: fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
2706: 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);
2707: fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);
2708: fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);
2709: fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);
1.53 brouard 2710: */
2711:
2712: /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
2713: first1=1;
2714: for (k2=1; k2<=(nlstate);k2++){
2715: for (l2=1; l2<=(nlstate+ndeath);l2++){
2716: if(l2==k2) continue;
2717: j=(k2-1)*(nlstate+ndeath)+l2;
2718: for (k1=1; k1<=(nlstate);k1++){
2719: for (l1=1; l1<=(nlstate+ndeath);l1++){
2720: if(l1==k1) continue;
2721: i=(k1-1)*(nlstate+ndeath)+l1;
2722: if(i<=j) continue;
2723: for (age=bage; age<=fage; age ++){
2724: if ((int)age %5==0){
2725: v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;
2726: v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;
2727: cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;
2728: mu1=mu[i][(int) age]/stepm*YEARM ;
2729: mu2=mu[j][(int) age]/stepm*YEARM;
2730: c12=cv12/sqrt(v1*v2);
2731: /* Computing eigen value of matrix of covariance */
2732: lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
2733: lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
2734: /* Eigen vectors */
2735: v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
2736: /*v21=sqrt(1.-v11*v11); *//* error */
2737: v21=(lc1-v1)/cv12*v11;
2738: v12=-v21;
2739: v22=v11;
2740: tnalp=v21/v11;
2741: if(first1==1){
2742: first1=0;
2743: 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);
2744: }
2745: 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);
2746: /*printf(fignu*/
2747: /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */
2748: /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */
2749: if(first==1){
2750: first=0;
2751: fprintf(ficgp,"\nset parametric;unset label");
2752: 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);
2753: fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
2754: 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);
2755: fprintf(fichtm,"\n<br><img src=\"varpijgr%s%d%1d%1d-%1d%1d.png\"> ",optionfilefiname, j1,k1,l1,k2,l2);
2756: fprintf(fichtm,"\n<br> Correlation at age %d (%.3f),",(int) age, c12);
2757: fprintf(ficgp,"\nset out \"varpijgr%s%d%1d%1d-%1d%1d.png\"",optionfilefiname, j1,k1,l1,k2,l2);
2758: fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
2759: fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
2760: 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",\
2761: mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
2762: mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
2763: }else{
2764: first=0;
2765: fprintf(fichtm," %d (%.3f),",(int) age, c12);
2766: fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
2767: fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
2768: 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",\
2769: mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
2770: mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
2771: }/* if first */
2772: } /* age mod 5 */
2773: } /* end loop age */
2774: fprintf(ficgp,"\nset out \"varpijgr%s%d%1d%1d-%1d%1d.png\";replot;",optionfilefiname, j1,k1,l1,k2,l2);
2775: first=1;
2776: } /*l12 */
2777: } /* k12 */
2778: } /*l1 */
2779: }/* k1 */
2780: } /* loop covariates */
2781: }
1.59 brouard 2782: free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
2783: free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
1.53 brouard 2784: free_vector(xp,1,npar);
2785: fclose(ficresprob);
2786: fclose(ficresprobcov);
2787: fclose(ficresprobcor);
2788: fclose(ficgp);
2789: fclose(fichtm);
2790: }
2791:
2792:
2793: /******************* Printing html file ***********/
2794: void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \
2795: int lastpass, int stepm, int weightopt, char model[],\
2796: int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
2797: int popforecast, int estepm ,\
2798: double jprev1, double mprev1,double anprev1, \
2799: double jprev2, double mprev2,double anprev2){
2800: int jj1, k1, i1, cpt;
2801: /*char optionfilehtm[FILENAMELENGTH];*/
2802: if((fichtm=fopen(optionfilehtm,"a"))==NULL) {
2803: printf("Problem with %s \n",optionfilehtm), exit(0);
2804: fprintf(ficlog,"Problem with %s \n",optionfilehtm), exit(0);
2805: }
2806:
2807: fprintf(fichtm,"<ul><li><h4>Result files (first order: no variance)</h4>\n
2808: - 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
2809: - Estimated transition probabilities over %d (stepm) months: <a href=\"pij%s\">pij%s</a><br>\n
2810: - Stable prevalence in each health state: <a href=\"pl%s\">pl%s</a> <br>\n
2811: - Life expectancies by age and initial health status (estepm=%2d months):
2812: <a href=\"e%s\">e%s</a> <br>\n</li>", \
2813: jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,fileres,fileres,stepm,fileres,fileres,fileres,fileres,estepm,fileres,fileres);
2814:
2815: fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
2816:
2817: m=cptcoveff;
2818: if (cptcovn < 1) {m=1;ncodemax[1]=1;}
2819:
2820: jj1=0;
2821: for(k1=1; k1<=m;k1++){
2822: for(i1=1; i1<=ncodemax[k1];i1++){
2823: jj1++;
2824: if (cptcovn > 0) {
2825: fprintf(fichtm,"<hr size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
2826: for (cpt=1; cpt<=cptcoveff;cpt++)
2827: fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
2828: fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
2829: }
2830: /* Pij */
1.76 brouard 2831: 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 2832: <img src=\"pe%s%d1.png\">",stepm,strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);
2833: /* Quasi-incidences */
2834: 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>
2835: <img src=\"pe%s%d2.png\">",stepm,strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);
2836: /* Stable prevalence in each health state */
2837: for(cpt=1; cpt<nlstate;cpt++){
2838: fprintf(fichtm,"<br>- Stable prevalence in each health state : p%s%d%d.png<br>
2839: <img src=\"p%s%d%d.png\">",strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);
2840: }
2841: for(cpt=1; cpt<=nlstate;cpt++) {
2842: fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): exp%s%d%d.png <br>
2843: <img src=\"exp%s%d%d.png\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);
2844: }
2845: fprintf(fichtm,"\n<br>- Total life expectancy by age and
2846: health expectancies in states (1) and (2): e%s%d.png<br>
2847: <img src=\"e%s%d.png\">",strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);
2848: } /* end i1 */
2849: }/* End k1 */
2850: fprintf(fichtm,"</ul>");
2851:
2852:
2853: fprintf(fichtm,"\n<br><li><h4> Result files (second order: variances)</h4>\n
2854: - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n
2855: - Variance of one-step probabilities: <a href=\"prob%s\">prob%s</a> <br>\n
2856: - Variance-covariance of one-step probabilities: <a href=\"probcov%s\">probcov%s</a> <br>\n
2857: - Correlation matrix of one-step probabilities: <a href=\"probcor%s\">probcor%s</a> <br>\n
2858: - Variances and covariances of life expectancies by age and initial health status (estepm=%d months): <a href=\"v%s\">v%s</a><br>\n
2859: - Health expectancies with their variances (no covariance): <a href=\"t%s\">t%s</a> <br>\n
2860: - 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);
2861:
1.76 brouard 2862: /* if(popforecast==1) fprintf(fichtm,"\n */
2863: /* - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n */
2864: /* - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n */
2865: /* <br>",fileres,fileres,fileres,fileres); */
2866: /* else */
2867: /* 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 2868: fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
2869:
2870: m=cptcoveff;
2871: if (cptcovn < 1) {m=1;ncodemax[1]=1;}
2872:
2873: jj1=0;
2874: for(k1=1; k1<=m;k1++){
2875: for(i1=1; i1<=ncodemax[k1];i1++){
2876: jj1++;
2877: if (cptcovn > 0) {
2878: fprintf(fichtm,"<hr size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
2879: for (cpt=1; cpt<=cptcoveff;cpt++)
2880: fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
2881: fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
2882: }
2883: for(cpt=1; cpt<=nlstate;cpt++) {
1.76 brouard 2884: fprintf(fichtm,"<br>- Observed and period prevalence (with confident
1.53 brouard 2885: interval) in state (%d): v%s%d%d.png <br>
2886: <img src=\"v%s%d%d.png\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);
2887: }
2888: } /* end i1 */
2889: }/* End k1 */
2890: fprintf(fichtm,"</ul>");
2891: fclose(fichtm);
2892: }
2893:
2894: /******************* Gnuplot file **************/
2895: void printinggnuplot(char fileres[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
2896:
2897: int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;
2898: int ng;
2899: if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {
2900: printf("Problem with file %s",optionfilegnuplot);
2901: fprintf(ficlog,"Problem with file %s",optionfilegnuplot);
2902: }
2903:
1.54 brouard 2904: /*#ifdef windows */
1.53 brouard 2905: fprintf(ficgp,"cd \"%s\" \n",pathc);
1.54 brouard 2906: /*#endif */
1.53 brouard 2907: m=pow(2,cptcoveff);
2908:
2909: /* 1eme*/
2910: for (cpt=1; cpt<= nlstate ; cpt ++) {
2911: for (k1=1; k1<= m ; k1 ++) {
2912: fprintf(ficgp,"\nset out \"v%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);
2913: 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);
2914:
2915: for (i=1; i<= nlstate ; i ++) {
2916: if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
2917: else fprintf(ficgp," \%%*lf (\%%*lf)");
2918: }
1.69 brouard 2919: 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 2920: for (i=1; i<= nlstate ; i ++) {
2921: if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
2922: else fprintf(ficgp," \%%*lf (\%%*lf)");
2923: }
1.69 brouard 2924: fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"vpl%s\" every :::%d::%d u 1:($2-1.96*$3) \"\%%lf",fileres,k1-1,k1-1);
1.53 brouard 2925: for (i=1; i<= nlstate ; i ++) {
2926: if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
2927: else fprintf(ficgp," \%%*lf (\%%*lf)");
2928: }
2929: fprintf(ficgp,"\" t\"\" w l 1,\"p%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",fileres,k1-1,k1-1,2+4*(cpt-1));
2930: }
2931: }
2932: /*2 eme*/
2933:
2934: for (k1=1; k1<= m ; k1 ++) {
2935: fprintf(ficgp,"\nset out \"e%s%d.png\" \n",strtok(optionfile, "."),k1);
2936: fprintf(ficgp,"set ylabel \"Years\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] ",ageminpar,fage);
2937:
2938: for (i=1; i<= nlstate+1 ; i ++) {
2939: k=2*i;
2940: fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:2 \"\%%lf",fileres,k1-1,k1-1);
2941: for (j=1; j<= nlstate+1 ; j ++) {
2942: if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
2943: else fprintf(ficgp," \%%*lf (\%%*lf)");
2944: }
2945: if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");
2946: else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);
2947: fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",fileres,k1-1,k1-1);
2948: for (j=1; j<= nlstate+1 ; j ++) {
2949: if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
2950: else fprintf(ficgp," \%%*lf (\%%*lf)");
2951: }
2952: fprintf(ficgp,"\" t\"\" w l 0,");
2953: fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",fileres,k1-1,k1-1);
2954: for (j=1; j<= nlstate+1 ; j ++) {
2955: if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
2956: else fprintf(ficgp," \%%*lf (\%%*lf)");
2957: }
2958: if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");
2959: else fprintf(ficgp,"\" t\"\" w l 0,");
2960: }
2961: }
2962:
2963: /*3eme*/
2964:
2965: for (k1=1; k1<= m ; k1 ++) {
2966: for (cpt=1; cpt<= nlstate ; cpt ++) {
2967: k=2+nlstate*(2*cpt-2);
2968: fprintf(ficgp,"\nset out \"exp%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);
2969: fprintf(ficgp,"set ter png small\nset size 0.65,0.65\nplot [%.f:%.f] \"e%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,fileres,k1-1,k1-1,k,cpt);
2970: /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
2971: for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
2972: fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
2973: fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
2974: for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
2975: fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
2976:
2977: */
2978: for (i=1; i< nlstate ; i ++) {
2979: 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);
2980:
2981: }
2982: }
2983: }
2984:
1.76 brouard 2985: /* CV preval stable (period) */
1.53 brouard 2986: for (k1=1; k1<= m ; k1 ++) {
1.76 brouard 2987: for (cpt=1; cpt<=nlstate ; cpt ++) {
1.53 brouard 2988: k=3;
2989: fprintf(ficgp,"\nset out \"p%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);
2990: 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/($%d",ageminpar,agemaxpar,fileres,k1,k+cpt+1,k+1);
2991:
1.76 brouard 2992: for (i=1; i<= nlstate ; i ++)
1.53 brouard 2993: fprintf(ficgp,"+$%d",k+i+1);
2994: fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);
2995:
2996: l=3+(nlstate+ndeath)*cpt;
2997: fprintf(ficgp,",\"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",fileres,k1,l+cpt+1,l+1);
2998: for (i=1; i< nlstate ; i ++) {
2999: l=3+(nlstate+ndeath)*cpt;
3000: fprintf(ficgp,"+$%d",l+i+1);
3001: }
3002: fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);
3003: }
3004: }
3005:
3006: /* proba elementaires */
3007: for(i=1,jk=1; i <=nlstate; i++){
3008: for(k=1; k <=(nlstate+ndeath); k++){
3009: if (k != i) {
3010: for(j=1; j <=ncovmodel; j++){
3011: fprintf(ficgp,"p%d=%f ",jk,p[jk]);
3012: jk++;
3013: fprintf(ficgp,"\n");
3014: }
3015: }
3016: }
3017: }
3018:
3019: for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/
3020: for(jk=1; jk <=m; jk++) {
3021: fprintf(ficgp,"\nset out \"pe%s%d%d.png\" \n",strtok(optionfile, "."),jk,ng);
3022: if (ng==2)
3023: fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
3024: else
3025: fprintf(ficgp,"\nset title \"Probability\"\n");
3026: fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65\nset log y\nplot [%.f:%.f] ",ageminpar,agemaxpar);
3027: i=1;
3028: for(k2=1; k2<=nlstate; k2++) {
3029: k3=i;
3030: for(k=1; k<=(nlstate+ndeath); k++) {
3031: if (k != k2){
3032: if(ng==2)
3033: fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);
3034: else
3035: fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
3036: ij=1;
3037: for(j=3; j <=ncovmodel; j++) {
3038: if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
3039: fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
3040: ij++;
3041: }
3042: else
3043: fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
3044: }
3045: fprintf(ficgp,")/(1");
3046:
3047: for(k1=1; k1 <=nlstate; k1++){
3048: fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);
3049: ij=1;
3050: for(j=3; j <=ncovmodel; j++){
3051: if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
3052: fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
3053: ij++;
3054: }
3055: else
3056: fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
3057: }
3058: fprintf(ficgp,")");
3059: }
3060: fprintf(ficgp,") t \"p%d%d\" ", k2,k);
3061: if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");
3062: i=i+ncovmodel;
3063: }
3064: } /* end k */
3065: } /* end k2 */
3066: } /* end jk */
3067: } /* end ng */
3068: fclose(ficgp);
3069: } /* end gnuplot */
3070:
3071:
3072: /*************** Moving average **************/
1.54 brouard 3073: int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav){
1.53 brouard 3074:
3075: int i, cpt, cptcod;
1.58 lievre 3076: int modcovmax =1;
1.54 brouard 3077: int mobilavrange, mob;
1.53 brouard 3078: double age;
1.58 lievre 3079:
3080: modcovmax=2*cptcoveff;/* Max number of modalities. We suppose
3081: a covariate has 2 modalities */
3082: if (cptcovn<1) modcovmax=1; /* At least 1 pass */
3083:
1.54 brouard 3084: if(mobilav==1||mobilav ==3 ||mobilav==5 ||mobilav== 7){
3085: if(mobilav==1) mobilavrange=5; /* default */
3086: else mobilavrange=mobilav;
3087: for (age=bage; age<=fage; age++)
3088: for (i=1; i<=nlstate;i++)
1.58 lievre 3089: for (cptcod=1;cptcod<=modcovmax;cptcod++)
1.54 brouard 3090: mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
3091: /* We keep the original values on the extreme ages bage, fage and for
3092: fage+1 and bage-1 we use a 3 terms moving average; for fage+2 bage+2
3093: we use a 5 terms etc. until the borders are no more concerned.
3094: */
3095: for (mob=3;mob <=mobilavrange;mob=mob+2){
3096: for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; 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: for (cpt=1;cpt<=(mob-1)/2;cpt++){
3101: mobaverage[(int)age][i][cptcod] +=probs[(int)age-cpt][i][cptcod];
3102: mobaverage[(int)age][i][cptcod] +=probs[(int)age+cpt][i][cptcod];
3103: }
3104: mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/mob;
3105: }
1.53 brouard 3106: }
1.54 brouard 3107: }/* end age */
3108: }/* end mob */
3109: }else return -1;
3110: return 0;
3111: }/* End movingaverage */
1.53 brouard 3112:
3113:
3114: /************** Forecasting ******************/
1.70 brouard 3115: 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 3116: /* proj1, year, month, day of starting projection
3117: agemin, agemax range of age
3118: dateprev1 dateprev2 range of dates during which prevalence is computed
1.70 brouard 3119: anproj2 year of en of projection (same day and month as proj1).
1.69 brouard 3120: */
1.73 lievre 3121: int yearp, stepsize, hstepm, nhstepm, j, k, c, cptcod, i, h, i1;
1.53 brouard 3122: int *popage;
1.70 brouard 3123: double agec; /* generic age */
3124: double agelim, ppij, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
1.53 brouard 3125: double *popeffectif,*popcount;
3126: double ***p3mat;
1.55 lievre 3127: double ***mobaverage;
1.53 brouard 3128: char fileresf[FILENAMELENGTH];
3129:
1.69 brouard 3130: agelim=AGESUP;
1.70 brouard 3131: prevalence(ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
1.53 brouard 3132:
3133: strcpy(fileresf,"f");
3134: strcat(fileresf,fileres);
3135: if((ficresf=fopen(fileresf,"w"))==NULL) {
3136: printf("Problem with forecast resultfile: %s\n", fileresf);
3137: fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);
3138: }
3139: printf("Computing forecasting: result on file '%s' \n", fileresf);
3140: fprintf(ficlog,"Computing forecasting: result on file '%s' \n", fileresf);
3141:
3142: if (cptcoveff==0) ncodemax[cptcoveff]=1;
3143:
1.54 brouard 3144: if (mobilav!=0) {
1.53 brouard 3145: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
1.54 brouard 3146: if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
3147: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
3148: printf(" Error in movingaverage mobilav=%d\n",mobilav);
3149: }
1.53 brouard 3150: }
3151:
3152: stepsize=(int) (stepm+YEARM-1)/YEARM;
3153: if (stepm<=12) stepsize=1;
1.74 brouard 3154: if(estepm < stepm){
3155: printf ("Problem %d lower than %d\n",estepm, stepm);
3156: }
3157: else hstepm=estepm;
3158:
1.53 brouard 3159: hstepm=hstepm/stepm;
1.69 brouard 3160: yp1=modf(dateintmean,&yp);/* extracts integral of datemean in yp and
3161: fractional in yp1 */
1.53 brouard 3162: anprojmean=yp;
3163: yp2=modf((yp1*12),&yp);
3164: mprojmean=yp;
3165: yp1=modf((yp2*30.5),&yp);
3166: jprojmean=yp;
3167: if(jprojmean==0) jprojmean=1;
3168: if(mprojmean==0) jprojmean=1;
1.73 lievre 3169:
3170: i1=cptcoveff;
3171: if (cptcovn < 1){i1=1;}
1.53 brouard 3172:
1.70 brouard 3173: fprintf(ficresf,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2);
1.53 brouard 3174:
1.70 brouard 3175: fprintf(ficresf,"#****** Routine prevforecast **\n");
1.73 lievre 3176:
1.75 brouard 3177: /* if (h==(int)(YEARM*yearp)){ */
1.73 lievre 3178: for(cptcov=1, k=0;cptcov<=i1;cptcov++){
1.53 brouard 3179: for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
3180: k=k+1;
3181: fprintf(ficresf,"\n#******");
3182: for(j=1;j<=cptcoveff;j++) {
1.70 brouard 3183: 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 3184: }
3185: fprintf(ficresf,"******\n");
1.70 brouard 3186: fprintf(ficresf,"# Covariate valuofcovar yearproj age");
3187: for(j=1; j<=nlstate+ndeath;j++){
3188: for(i=1; i<=nlstate;i++)
3189: fprintf(ficresf," p%d%d",i,j);
3190: fprintf(ficresf," p.%d",j);
3191: }
1.74 brouard 3192: for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) {
1.53 brouard 3193: fprintf(ficresf,"\n");
1.70 brouard 3194: fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+yearp);
1.53 brouard 3195:
1.71 brouard 3196: for (agec=fage; agec>=(ageminpar-1); agec--){
1.70 brouard 3197: nhstepm=(int) rint((agelim-agec)*YEARM/stepm);
1.53 brouard 3198: nhstepm = nhstepm/hstepm;
3199: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3200: oldm=oldms;savm=savms;
1.70 brouard 3201: hpxij(p3mat,nhstepm,agec,hstepm,p,nlstate,stepm,oldm,savm, k);
1.53 brouard 3202:
3203: for (h=0; h<=nhstepm; h++){
1.75 brouard 3204: if (h*hstepm/YEARM*stepm ==yearp) {
1.69 brouard 3205: fprintf(ficresf,"\n");
3206: for(j=1;j<=cptcoveff;j++)
3207: fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
1.70 brouard 3208: fprintf(ficresf,"%.f %.f ",anproj1+yearp,agec+h*hstepm/YEARM*stepm);
1.53 brouard 3209: }
3210: for(j=1; j<=nlstate+ndeath;j++) {
1.70 brouard 3211: ppij=0.;
1.71 brouard 3212: for(i=1; i<=nlstate;i++) {
1.53 brouard 3213: if (mobilav==1)
1.71 brouard 3214: ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][i][cptcod];
1.53 brouard 3215: else {
1.71 brouard 3216: ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][cptcod];
1.53 brouard 3217: }
1.75 brouard 3218: if (h*hstepm/YEARM*stepm== yearp) {
1.70 brouard 3219: fprintf(ficresf," %.3f", p3mat[i][j][h]);
1.75 brouard 3220: }
3221: } /* end i */
3222: if (h*hstepm/YEARM*stepm==yearp) {
1.70 brouard 3223: fprintf(ficresf," %.3f", ppij);
1.53 brouard 3224: }
1.75 brouard 3225: }/* end j */
3226: } /* end h */
1.53 brouard 3227: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
1.75 brouard 3228: } /* end agec */
3229: } /* end yearp */
3230: } /* end cptcod */
3231: } /* end cptcov */
1.53 brouard 3232:
1.54 brouard 3233: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
1.53 brouard 3234:
3235: fclose(ficresf);
3236: }
1.70 brouard 3237:
3238: /************** Forecasting *****not tested NB*************/
1.53 brouard 3239: 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){
3240:
3241: int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;
3242: int *popage;
1.69 brouard 3243: double calagedatem, agelim, kk1, kk2;
1.53 brouard 3244: double *popeffectif,*popcount;
3245: double ***p3mat,***tabpop,***tabpopprev;
1.55 lievre 3246: double ***mobaverage;
1.53 brouard 3247: char filerespop[FILENAMELENGTH];
3248:
3249: tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
3250: tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
3251: agelim=AGESUP;
1.69 brouard 3252: calagedatem=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;
1.53 brouard 3253:
1.70 brouard 3254: prevalence(ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
1.53 brouard 3255:
3256:
3257: strcpy(filerespop,"pop");
3258: strcat(filerespop,fileres);
3259: if((ficrespop=fopen(filerespop,"w"))==NULL) {
3260: printf("Problem with forecast resultfile: %s\n", filerespop);
3261: fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop);
3262: }
3263: printf("Computing forecasting: result on file '%s' \n", filerespop);
3264: fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop);
3265:
3266: if (cptcoveff==0) ncodemax[cptcoveff]=1;
3267:
1.54 brouard 3268: if (mobilav!=0) {
1.53 brouard 3269: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
1.54 brouard 3270: if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
3271: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
3272: printf(" Error in movingaverage mobilav=%d\n",mobilav);
3273: }
1.53 brouard 3274: }
3275:
3276: stepsize=(int) (stepm+YEARM-1)/YEARM;
3277: if (stepm<=12) stepsize=1;
3278:
3279: agelim=AGESUP;
3280:
3281: hstepm=1;
3282: hstepm=hstepm/stepm;
3283:
3284: if (popforecast==1) {
3285: if((ficpop=fopen(popfile,"r"))==NULL) {
3286: printf("Problem with population file : %s\n",popfile);exit(0);
3287: fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0);
3288: }
3289: popage=ivector(0,AGESUP);
3290: popeffectif=vector(0,AGESUP);
3291: popcount=vector(0,AGESUP);
3292:
3293: i=1;
3294: while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;
3295:
3296: imx=i;
3297: for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];
3298: }
3299:
1.69 brouard 3300: for(cptcov=1,k=0;cptcov<=i2;cptcov++){
1.53 brouard 3301: for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
3302: k=k+1;
3303: fprintf(ficrespop,"\n#******");
3304: for(j=1;j<=cptcoveff;j++) {
3305: fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
3306: }
3307: fprintf(ficrespop,"******\n");
3308: fprintf(ficrespop,"# Age");
3309: for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);
3310: if (popforecast==1) fprintf(ficrespop," [Population]");
3311:
3312: for (cpt=0; cpt<=0;cpt++) {
3313: fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);
3314:
1.69 brouard 3315: for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){
1.53 brouard 3316: nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);
3317: nhstepm = nhstepm/hstepm;
3318:
3319: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3320: oldm=oldms;savm=savms;
3321: hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
3322:
3323: for (h=0; h<=nhstepm; h++){
1.69 brouard 3324: if (h==(int) (calagedatem+YEARM*cpt)) {
1.53 brouard 3325: fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
3326: }
3327: for(j=1; j<=nlstate+ndeath;j++) {
3328: kk1=0.;kk2=0;
3329: for(i=1; i<=nlstate;i++) {
3330: if (mobilav==1)
3331: kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];
3332: else {
3333: kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];
3334: }
3335: }
1.69 brouard 3336: if (h==(int)(calagedatem+12*cpt)){
1.53 brouard 3337: tabpop[(int)(agedeb)][j][cptcod]=kk1;
3338: /*fprintf(ficrespop," %.3f", kk1);
3339: if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/
3340: }
3341: }
3342: for(i=1; i<=nlstate;i++){
3343: kk1=0.;
3344: for(j=1; j<=nlstate;j++){
3345: kk1= kk1+tabpop[(int)(agedeb)][j][cptcod];
3346: }
1.69 brouard 3347: tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedatem+12*cpt)*hstepm/YEARM*stepm-1)];
1.53 brouard 3348: }
3349:
1.69 brouard 3350: if (h==(int)(calagedatem+12*cpt)) for(j=1; j<=nlstate;j++)
1.53 brouard 3351: fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);
3352: }
3353: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3354: }
3355: }
3356:
3357: /******/
3358:
3359: for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) {
3360: fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);
1.69 brouard 3361: for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){
1.53 brouard 3362: nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);
3363: nhstepm = nhstepm/hstepm;
3364:
3365: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3366: oldm=oldms;savm=savms;
3367: hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
3368: for (h=0; h<=nhstepm; h++){
1.69 brouard 3369: if (h==(int) (calagedatem+YEARM*cpt)) {
1.53 brouard 3370: fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
3371: }
3372: for(j=1; j<=nlstate+ndeath;j++) {
3373: kk1=0.;kk2=0;
3374: for(i=1; i<=nlstate;i++) {
3375: kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];
3376: }
1.69 brouard 3377: if (h==(int)(calagedatem+12*cpt)) fprintf(ficresf," %15.2f", kk1);
1.53 brouard 3378: }
3379: }
3380: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3381: }
3382: }
3383: }
3384: }
3385:
1.54 brouard 3386: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
1.53 brouard 3387:
3388: if (popforecast==1) {
3389: free_ivector(popage,0,AGESUP);
3390: free_vector(popeffectif,0,AGESUP);
3391: free_vector(popcount,0,AGESUP);
3392: }
3393: free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
3394: free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
3395: fclose(ficrespop);
3396: }
3397:
3398: /***********************************************/
3399: /**************** Main Program *****************/
3400: /***********************************************/
3401:
3402: int main(int argc, char *argv[])
3403: {
1.61 brouard 3404: int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav);
1.74 brouard 3405: int i,j, k, n=MAXN,iter,m,size=100,cptcode, cptcod;
1.53 brouard 3406: double agedeb, agefin,hf;
3407: double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;
3408:
3409: double fret;
3410: double **xi,tmp,delta;
3411:
3412: double dum; /* Dummy variable */
3413: double ***p3mat;
3414: double ***mobaverage;
3415: int *indx;
3416: char line[MAXLINE], linepar[MAXLINE];
3417: char path[80],pathc[80],pathcd[80],pathtot[80],model[80];
3418: int firstobs=1, lastobs=10;
3419: int sdeb, sfin; /* Status at beginning and end */
3420: int c, h , cpt,l;
3421: int ju,jl, mi;
3422: int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;
1.59 brouard 3423: int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,*tab;
1.69 brouard 3424: int mobilavproj=0 , prevfcast=0 ; /* moving average of prev, If prevfcast=1 prevalence projection */
1.53 brouard 3425: int mobilav=0,popforecast=0;
3426: int hstepm, nhstepm;
1.74 brouard 3427: double jprev1=1, mprev1=1,anprev1=2000,jprev2=1, mprev2=1,anprev2=2000;
3428: double jpyram=1, mpyram=1,anpyram=2000,jpyram1=1, mpyram1=1,anpyram1=2000;
1.53 brouard 3429:
3430: double bage, fage, age, agelim, agebase;
3431: double ftolpl=FTOL;
3432: double **prlim;
3433: double *severity;
3434: double ***param; /* Matrix of parameters */
3435: double *p;
3436: double **matcov; /* Matrix of covariance */
3437: double ***delti3; /* Scale */
3438: double *delti; /* Scale */
3439: double ***eij, ***vareij;
3440: double **varpl; /* Variances of prevalence limits by age */
3441: double *epj, vepp;
3442: double kk1, kk2;
1.74 brouard 3443: double dateprev1, dateprev2,jproj1=1,mproj1=1,anproj1=2000,jproj2=1,mproj2=1,anproj2=2000;
1.53 brouard 3444:
3445: char *alph[]={"a","a","b","c","d","e"}, str[4];
3446:
3447:
3448: char z[1]="c", occ;
3449: #include <sys/time.h>
3450: #include <time.h>
3451: char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];
3452:
3453: /* long total_usecs;
1.59 brouard 3454: struct timeval start_time, end_time;
1.53 brouard 3455:
1.59 brouard 3456: gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */
1.53 brouard 3457: getcwd(pathcd, size);
3458:
3459: printf("\n%s",version);
3460: if(argc <=1){
3461: printf("\nEnter the parameter file name: ");
3462: scanf("%s",pathtot);
3463: }
3464: else{
3465: strcpy(pathtot,argv[1]);
3466: }
3467: /*if(getcwd(pathcd, 80)!= NULL)printf ("Error pathcd\n");*/
3468: /*cygwin_split_path(pathtot,path,optionfile);
3469: printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/
3470: /* cutv(path,optionfile,pathtot,'\\');*/
3471:
3472: split(pathtot,path,optionfile,optionfilext,optionfilefiname);
1.59 brouard 3473: printf("pathtot=%s, path=%s, optionfile=%s optionfilext=%s optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
1.53 brouard 3474: chdir(path);
3475: replace(pathc,path);
3476:
1.59 brouard 3477: /*-------- arguments in the command line --------*/
1.53 brouard 3478:
3479: /* Log file */
3480: strcat(filelog, optionfilefiname);
3481: strcat(filelog,".log"); /* */
3482: if((ficlog=fopen(filelog,"w"))==NULL) {
3483: printf("Problem with logfile %s\n",filelog);
3484: goto end;
3485: }
3486: fprintf(ficlog,"Log filename:%s\n",filelog);
3487: fprintf(ficlog,"\n%s",version);
3488: fprintf(ficlog,"\nEnter the parameter file name: ");
3489: fprintf(ficlog,"pathtot=%s, path=%s, optionfile=%s optionfilext=%s optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
3490: fflush(ficlog);
3491:
3492: /* */
3493: strcpy(fileres,"r");
3494: strcat(fileres, optionfilefiname);
3495: strcat(fileres,".txt"); /* Other files have txt extension */
3496:
3497: /*---------arguments file --------*/
3498:
3499: if((ficpar=fopen(optionfile,"r"))==NULL) {
3500: printf("Problem with optionfile %s\n",optionfile);
3501: fprintf(ficlog,"Problem with optionfile %s\n",optionfile);
3502: goto end;
3503: }
3504:
3505: strcpy(filereso,"o");
3506: strcat(filereso,fileres);
3507: if((ficparo=fopen(filereso,"w"))==NULL) {
3508: printf("Problem with Output resultfile: %s\n", filereso);
3509: fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso);
3510: goto end;
3511: }
3512:
3513: /* Reads comments: lines beginning with '#' */
3514: while((c=getc(ficpar))=='#' && c!= EOF){
3515: ungetc(c,ficpar);
3516: fgets(line, MAXLINE, ficpar);
3517: puts(line);
3518: fputs(line,ficparo);
3519: }
3520: ungetc(c,ficpar);
3521:
3522: 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);
3523: 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);
3524: 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 3525: while((c=getc(ficpar))=='#' && c!= EOF){
1.53 brouard 3526: ungetc(c,ficpar);
3527: fgets(line, MAXLINE, ficpar);
3528: puts(line);
3529: fputs(line,ficparo);
3530: }
3531: ungetc(c,ficpar);
3532:
3533:
3534: covar=matrix(0,NCOVMAX,1,n);
1.58 lievre 3535: cptcovn=0; /*Number of covariates, i.e. number of '+' in model statement*/
1.53 brouard 3536: if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;
3537:
1.58 lievre 3538: ncovmodel=2+cptcovn; /*Number of variables = cptcovn + intercept + age */
1.53 brouard 3539: nvar=ncovmodel-1; /* Suppressing age as a basic covariate */
3540:
3541: /* Read guess parameters */
3542: /* Reads comments: lines beginning with '#' */
3543: while((c=getc(ficpar))=='#' && c!= EOF){
3544: ungetc(c,ficpar);
3545: fgets(line, MAXLINE, ficpar);
3546: puts(line);
3547: fputs(line,ficparo);
3548: }
3549: ungetc(c,ficpar);
3550:
3551: param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
1.59 brouard 3552: for(i=1; i <=nlstate; i++)
1.53 brouard 3553: for(j=1; j <=nlstate+ndeath-1; j++){
3554: fscanf(ficpar,"%1d%1d",&i1,&j1);
3555: fprintf(ficparo,"%1d%1d",i1,j1);
3556: if(mle==1)
3557: printf("%1d%1d",i,j);
3558: fprintf(ficlog,"%1d%1d",i,j);
3559: for(k=1; k<=ncovmodel;k++){
3560: fscanf(ficpar," %lf",¶m[i][j][k]);
3561: if(mle==1){
3562: printf(" %lf",param[i][j][k]);
3563: fprintf(ficlog," %lf",param[i][j][k]);
3564: }
3565: else
3566: fprintf(ficlog," %lf",param[i][j][k]);
3567: fprintf(ficparo," %lf",param[i][j][k]);
3568: }
3569: fscanf(ficpar,"\n");
3570: if(mle==1)
3571: printf("\n");
3572: fprintf(ficlog,"\n");
3573: fprintf(ficparo,"\n");
3574: }
3575:
1.59 brouard 3576: npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/
1.53 brouard 3577:
3578: p=param[1][1];
3579:
3580: /* Reads comments: lines beginning with '#' */
3581: while((c=getc(ficpar))=='#' && c!= EOF){
3582: ungetc(c,ficpar);
3583: fgets(line, MAXLINE, ficpar);
3584: puts(line);
3585: fputs(line,ficparo);
3586: }
3587: ungetc(c,ficpar);
3588:
3589: delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
1.74 brouard 3590: /* delti=vector(1,npar); *//* Scale of each paramater (output from hesscov) */
1.53 brouard 3591: for(i=1; i <=nlstate; i++){
3592: for(j=1; j <=nlstate+ndeath-1; j++){
3593: fscanf(ficpar,"%1d%1d",&i1,&j1);
3594: printf("%1d%1d",i,j);
3595: fprintf(ficparo,"%1d%1d",i1,j1);
3596: for(k=1; k<=ncovmodel;k++){
3597: fscanf(ficpar,"%le",&delti3[i][j][k]);
3598: printf(" %le",delti3[i][j][k]);
3599: fprintf(ficparo," %le",delti3[i][j][k]);
3600: }
3601: fscanf(ficpar,"\n");
3602: printf("\n");
3603: fprintf(ficparo,"\n");
3604: }
3605: }
3606: delti=delti3[1][1];
1.74 brouard 3607:
3608:
3609: /* 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 3610:
3611: /* Reads comments: lines beginning with '#' */
3612: while((c=getc(ficpar))=='#' && c!= EOF){
3613: ungetc(c,ficpar);
3614: fgets(line, MAXLINE, ficpar);
3615: puts(line);
3616: fputs(line,ficparo);
3617: }
3618: ungetc(c,ficpar);
3619:
3620: matcov=matrix(1,npar,1,npar);
3621: for(i=1; i <=npar; i++){
3622: fscanf(ficpar,"%s",&str);
3623: if(mle==1)
3624: printf("%s",str);
3625: fprintf(ficlog,"%s",str);
3626: fprintf(ficparo,"%s",str);
3627: for(j=1; j <=i; j++){
3628: fscanf(ficpar," %le",&matcov[i][j]);
3629: if(mle==1){
3630: printf(" %.5le",matcov[i][j]);
3631: fprintf(ficlog," %.5le",matcov[i][j]);
3632: }
3633: else
3634: fprintf(ficlog," %.5le",matcov[i][j]);
3635: fprintf(ficparo," %.5le",matcov[i][j]);
3636: }
3637: fscanf(ficpar,"\n");
3638: if(mle==1)
3639: printf("\n");
3640: fprintf(ficlog,"\n");
3641: fprintf(ficparo,"\n");
3642: }
3643: for(i=1; i <=npar; i++)
3644: for(j=i+1;j<=npar;j++)
3645: matcov[i][j]=matcov[j][i];
3646:
3647: if(mle==1)
3648: printf("\n");
3649: fprintf(ficlog,"\n");
3650:
3651:
1.59 brouard 3652: /*-------- Rewriting paramater file ----------*/
3653: strcpy(rfileres,"r"); /* "Rparameterfile */
3654: strcat(rfileres,optionfilefiname); /* Parameter file first name*/
3655: strcat(rfileres,"."); /* */
3656: strcat(rfileres,optionfilext); /* Other files have txt extension */
3657: if((ficres =fopen(rfileres,"w"))==NULL) {
3658: printf("Problem writing new parameter file: %s\n", fileres);goto end;
3659: fprintf(ficlog,"Problem writing new parameter file: %s\n", fileres);goto end;
3660: }
3661: fprintf(ficres,"#%s\n",version);
1.53 brouard 3662:
1.59 brouard 3663: /*-------- data file ----------*/
3664: if((fic=fopen(datafile,"r"))==NULL) {
3665: printf("Problem with datafile: %s\n", datafile);goto end;
3666: fprintf(ficlog,"Problem with datafile: %s\n", datafile);goto end;
3667: }
3668:
3669: n= lastobs;
3670: severity = vector(1,maxwav);
3671: outcome=imatrix(1,maxwav+1,1,n);
3672: num=ivector(1,n);
3673: moisnais=vector(1,n);
3674: annais=vector(1,n);
3675: moisdc=vector(1,n);
3676: andc=vector(1,n);
3677: agedc=vector(1,n);
3678: cod=ivector(1,n);
3679: weight=vector(1,n);
3680: for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */
3681: mint=matrix(1,maxwav,1,n);
3682: anint=matrix(1,maxwav,1,n);
3683: s=imatrix(1,maxwav+1,1,n);
3684: tab=ivector(1,NCOVMAX);
3685: ncodemax=ivector(1,8);
3686:
3687: i=1;
3688: while (fgets(line, MAXLINE, fic) != NULL) {
3689: if ((i >= firstobs) && (i <=lastobs)) {
1.53 brouard 3690:
1.59 brouard 3691: for (j=maxwav;j>=1;j--){
3692: cutv(stra, strb,line,' '); s[j][i]=atoi(strb);
3693: strcpy(line,stra);
3694: cutv(stra, strb,line,'/'); anint[j][i]=(double)(atoi(strb)); strcpy(line,stra);
3695: cutv(stra, strb,line,' '); mint[j][i]=(double)(atoi(strb)); strcpy(line,stra);
3696: }
1.53 brouard 3697:
1.59 brouard 3698: cutv(stra, strb,line,'/'); andc[i]=(double)(atoi(strb)); strcpy(line,stra);
3699: cutv(stra, strb,line,' '); moisdc[i]=(double)(atoi(strb)); strcpy(line,stra);
1.53 brouard 3700:
1.59 brouard 3701: cutv(stra, strb,line,'/'); annais[i]=(double)(atoi(strb)); strcpy(line,stra);
3702: cutv(stra, strb,line,' '); moisnais[i]=(double)(atoi(strb)); strcpy(line,stra);
1.53 brouard 3703:
1.59 brouard 3704: cutv(stra, strb,line,' '); weight[i]=(double)(atoi(strb)); strcpy(line,stra);
3705: for (j=ncovcol;j>=1;j--){
3706: cutv(stra, strb,line,' '); covar[j][i]=(double)(atoi(strb)); strcpy(line,stra);
3707: }
3708: num[i]=atol(stra);
1.53 brouard 3709:
1.59 brouard 3710: /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){
3711: 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 3712:
1.59 brouard 3713: i=i+1;
3714: }
3715: }
3716: /* printf("ii=%d", ij);
3717: scanf("%d",i);*/
1.53 brouard 3718: imx=i-1; /* Number of individuals */
3719:
3720: /* for (i=1; i<=imx; i++){
3721: if ((s[1][i]==3) && (s[2][i]==2)) s[2][i]=3;
3722: if ((s[2][i]==3) && (s[3][i]==2)) s[3][i]=3;
3723: if ((s[3][i]==3) && (s[4][i]==2)) s[4][i]=3;
3724: }*/
3725: /* for (i=1; i<=imx; i++){
3726: if (s[4][i]==9) s[4][i]=-1;
3727: 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]));}*/
3728:
1.71 brouard 3729: for (i=1; i<=imx; i++)
1.53 brouard 3730:
1.71 brouard 3731: /*if ((s[3][i]==3) || (s[4][i]==3)) weight[i]=0.08;
3732: else weight[i]=1;*/
3733:
1.53 brouard 3734: /* Calculation of the number of parameter from char model*/
3735: Tvar=ivector(1,15); /* stores the number n of the covariates in Vm+Vn at 1 and m at 2 */
3736: Tprod=ivector(1,15);
3737: Tvaraff=ivector(1,15);
3738: Tvard=imatrix(1,15,1,2);
3739: Tage=ivector(1,15);
3740:
1.58 lievre 3741: if (strlen(model) >1){ /* If there is at least 1 covariate */
1.53 brouard 3742: j=0, j1=0, k1=1, k2=1;
1.58 lievre 3743: j=nbocc(model,'+'); /* j=Number of '+' */
3744: j1=nbocc(model,'*'); /* j1=Number of '*' */
3745: cptcovn=j+1;
3746: cptcovprod=j1; /*Number of products */
1.53 brouard 3747:
3748: strcpy(modelsav,model);
3749: if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){
3750: printf("Error. Non available option model=%s ",model);
3751: fprintf(ficlog,"Error. Non available option model=%s ",model);
3752: goto end;
3753: }
3754:
1.59 brouard 3755: /* This loop fills the array Tvar from the string 'model'.*/
1.58 lievre 3756:
1.53 brouard 3757: for(i=(j+1); i>=1;i--){
3758: cutv(stra,strb,modelsav,'+'); /* keeps in strb after the last + */
1.59 brouard 3759: if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyzes it */
1.53 brouard 3760: /* printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/
3761: /*scanf("%d",i);*/
3762: if (strchr(strb,'*')) { /* Model includes a product */
3763: cutv(strd,strc,strb,'*'); /* strd*strc Vm*Vn (if not *age)*/
3764: if (strcmp(strc,"age")==0) { /* Vn*age */
3765: cptcovprod--;
3766: cutv(strb,stre,strd,'V');
3767: Tvar[i]=atoi(stre); /* computes n in Vn and stores in Tvar*/
3768: cptcovage++;
3769: Tage[cptcovage]=i;
3770: /*printf("stre=%s ", stre);*/
3771: }
3772: else if (strcmp(strd,"age")==0) { /* or age*Vn */
3773: cptcovprod--;
3774: cutv(strb,stre,strc,'V');
3775: Tvar[i]=atoi(stre);
3776: cptcovage++;
3777: Tage[cptcovage]=i;
3778: }
3779: else { /* Age is not in the model */
3780: cutv(strb,stre,strc,'V'); /* strc= Vn, stre is n*/
3781: Tvar[i]=ncovcol+k1;
3782: cutv(strb,strc,strd,'V'); /* strd was Vm, strc is m */
3783: Tprod[k1]=i;
3784: Tvard[k1][1]=atoi(strc); /* m*/
3785: Tvard[k1][2]=atoi(stre); /* n */
3786: Tvar[cptcovn+k2]=Tvard[k1][1];
3787: Tvar[cptcovn+k2+1]=Tvard[k1][2];
3788: for (k=1; k<=lastobs;k++)
3789: covar[ncovcol+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];
3790: k1++;
3791: k2=k2+2;
3792: }
3793: }
3794: else { /* no more sum */
3795: /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/
3796: /* scanf("%d",i);*/
3797: cutv(strd,strc,strb,'V');
3798: Tvar[i]=atoi(strc);
3799: }
3800: strcpy(modelsav,stra);
3801: /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);
3802: scanf("%d",i);*/
3803: } /* end of loop + */
3804: } /* end model */
3805:
1.58 lievre 3806: /*The number n of Vn is stored in Tvar. cptcovage =number of age covariate. Tage gives the position of age. cptcovprod= number of products.
3807: If model=V1+V1*age then Tvar[1]=1 Tvar[2]=1 cptcovage=1 Tage[1]=2 cptcovprod=0*/
3808:
1.53 brouard 3809: /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);
3810: printf("cptcovprod=%d ", cptcovprod);
3811: fprintf(ficlog,"cptcovprod=%d ", cptcovprod);
1.58 lievre 3812:
3813: scanf("%d ",i);
3814: fclose(fic);*/
1.53 brouard 3815:
3816: /* if(mle==1){*/
1.59 brouard 3817: if (weightopt != 1) { /* Maximisation without weights*/
3818: for(i=1;i<=n;i++) weight[i]=1.0;
3819: }
1.53 brouard 3820: /*-calculation of age at interview from date of interview and age at death -*/
1.59 brouard 3821: agev=matrix(1,maxwav,1,imx);
1.53 brouard 3822:
1.59 brouard 3823: for (i=1; i<=imx; i++) {
3824: for(m=2; (m<= maxwav); m++) {
1.76 brouard 3825: if (((int)mint[m][i]== 99) && (s[m][i] <= nlstate)){
1.59 brouard 3826: anint[m][i]=9999;
3827: s[m][i]=-1;
3828: }
1.76 brouard 3829: if((int)moisdc[i]==99 && (int)andc[i]==9999 && s[m][i]>nlstate){
1.77 brouard 3830: 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);
3831: 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 3832: s[m][i]=-1;
3833: }
3834: if((int)moisdc[i]==99 && (int)andc[i]!=9999 && s[m][i]>nlstate){
1.77 brouard 3835: 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]);
3836: 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 3837: s[m][i]=-1;
3838: }
1.53 brouard 3839: }
1.59 brouard 3840: }
1.53 brouard 3841:
1.59 brouard 3842: for (i=1; i<=imx; i++) {
3843: agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);
1.71 brouard 3844: for(m=firstpass; (m<= lastpass); m++){
1.69 brouard 3845: if(s[m][i] >0){
1.59 brouard 3846: if (s[m][i] >= nlstate+1) {
3847: if(agedc[i]>0)
1.76 brouard 3848: if((int)moisdc[i]!=99 && (int)andc[i]!=9999)
1.69 brouard 3849: agev[m][i]=agedc[i];
1.59 brouard 3850: /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/
3851: else {
1.76 brouard 3852: if ((int)andc[i]!=9999){
1.59 brouard 3853: printf("Warning negative age at death: %d line:%d\n",num[i],i);
3854: fprintf(ficlog,"Warning negative age at death: %d line:%d\n",num[i],i);
3855: agev[m][i]=-1;
1.53 brouard 3856: }
3857: }
1.70 brouard 3858: }
1.69 brouard 3859: else if(s[m][i] !=9){ /* Standard case, age in fractional
3860: years but with the precision of a
3861: month */
1.59 brouard 3862: agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);
1.76 brouard 3863: if((int)mint[m][i]==99 || (int)anint[m][i]==9999)
1.59 brouard 3864: agev[m][i]=1;
3865: else if(agev[m][i] <agemin){
3866: agemin=agev[m][i];
3867: /*printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], agemin);*/
1.53 brouard 3868: }
1.59 brouard 3869: else if(agev[m][i] >agemax){
3870: agemax=agev[m][i];
3871: /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/
1.53 brouard 3872: }
1.59 brouard 3873: /*agev[m][i]=anint[m][i]-annais[i];*/
3874: /* agev[m][i] = age[i]+2*m;*/
1.53 brouard 3875: }
1.59 brouard 3876: else { /* =9 */
1.53 brouard 3877: agev[m][i]=1;
1.59 brouard 3878: s[m][i]=-1;
3879: }
1.53 brouard 3880: }
1.59 brouard 3881: else /*= 0 Unknown */
3882: agev[m][i]=1;
3883: }
1.53 brouard 3884:
1.59 brouard 3885: }
3886: for (i=1; i<=imx; i++) {
1.71 brouard 3887: for(m=firstpass; (m<=lastpass); m++){
1.59 brouard 3888: if (s[m][i] > (nlstate+ndeath)) {
3889: 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);
3890: 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);
3891: goto end;
1.53 brouard 3892: }
3893: }
1.59 brouard 3894: }
1.53 brouard 3895:
1.71 brouard 3896: /*for (i=1; i<=imx; i++){
3897: for (m=firstpass; (m<lastpass); m++){
3898: printf("%d %d %.lf %d %d\n", num[i],(covar[1][i]),agev[m][i],s[m][i],s[m+1][i]);
3899: }
3900:
3901: }*/
3902:
1.59 brouard 3903: printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);
3904: fprintf(ficlog,"Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);
3905:
3906: free_vector(severity,1,maxwav);
3907: free_imatrix(outcome,1,maxwav+1,1,n);
3908: free_vector(moisnais,1,n);
3909: free_vector(annais,1,n);
3910: /* free_matrix(mint,1,maxwav,1,n);
3911: free_matrix(anint,1,maxwav,1,n);*/
3912: free_vector(moisdc,1,n);
3913: free_vector(andc,1,n);
1.53 brouard 3914:
3915:
1.59 brouard 3916: wav=ivector(1,imx);
3917: dh=imatrix(1,lastpass-firstpass+1,1,imx);
3918: bh=imatrix(1,lastpass-firstpass+1,1,imx);
3919: mw=imatrix(1,lastpass-firstpass+1,1,imx);
1.69 brouard 3920:
1.59 brouard 3921: /* Concatenates waves */
3922: concatwav(wav, dh, bh, mw, s, agedc, agev, firstpass, lastpass, imx, nlstate, stepm);
1.53 brouard 3923:
1.59 brouard 3924: /* Routine tricode is to calculate cptcoveff (real number of unique covariates) and to associate covariable number and modality */
1.53 brouard 3925:
1.59 brouard 3926: Tcode=ivector(1,100);
3927: nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);
3928: ncodemax[1]=1;
3929: if (cptcovn > 0) tricode(Tvar,nbcode,imx);
1.53 brouard 3930:
1.59 brouard 3931: codtab=imatrix(1,100,1,10); /* Cross tabulation to get the order of
3932: the estimations*/
3933: h=0;
3934: m=pow(2,cptcoveff);
1.53 brouard 3935:
1.59 brouard 3936: for(k=1;k<=cptcoveff; k++){
3937: for(i=1; i <=(m/pow(2,k));i++){
3938: for(j=1; j <= ncodemax[k]; j++){
3939: for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){
3940: h++;
3941: if (h>m) h=1;codtab[h][k]=j;codtab[h][Tvar[k]]=j;
3942: /* printf("h=%d k=%d j=%d codtab[h][k]=%d tvar[k]=%d \n",h, k,j,codtab[h][k],Tvar[k]);*/
3943: }
3944: }
3945: }
3946: }
3947: /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]);
3948: codtab[1][2]=1;codtab[2][2]=2; */
3949: /* for(i=1; i <=m ;i++){
3950: for(k=1; k <=cptcovn; k++){
3951: printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);
3952: }
3953: printf("\n");
1.53 brouard 3954: }
1.59 brouard 3955: scanf("%d",i);*/
1.53 brouard 3956:
1.59 brouard 3957: /* Calculates basic frequencies. Computes observed prevalence at single age
3958: and prints on file fileres'p'. */
1.53 brouard 3959:
1.60 brouard 3960: pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
3961: oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
3962: newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
3963: savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
3964: oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */
1.53 brouard 3965:
3966:
1.59 brouard 3967: /* For Powell, parameters are in a vector p[] starting at p[1]
3968: so we point p on param[1][1] so that p[1] maps on param[1][1][1] */
3969: p=param[1][1]; /* *(*(*(param +1)+1)+0) */
1.53 brouard 3970:
1.61 brouard 3971: if(mle>=1){ /* Could be 1 or 2 */
1.53 brouard 3972: mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);
1.59 brouard 3973: }
1.53 brouard 3974:
1.59 brouard 3975: /*--------- results files --------------*/
3976: 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 3977:
3978:
1.59 brouard 3979: jk=1;
3980: fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
3981: printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
3982: fprintf(ficlog,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
3983: for(i=1,jk=1; i <=nlstate; i++){
3984: for(k=1; k <=(nlstate+ndeath); k++){
3985: if (k != i)
3986: {
3987: printf("%d%d ",i,k);
3988: fprintf(ficlog,"%d%d ",i,k);
3989: fprintf(ficres,"%1d%1d ",i,k);
3990: for(j=1; j <=ncovmodel; j++){
3991: printf("%f ",p[jk]);
3992: fprintf(ficlog,"%f ",p[jk]);
3993: fprintf(ficres,"%f ",p[jk]);
3994: jk++;
3995: }
3996: printf("\n");
3997: fprintf(ficlog,"\n");
3998: fprintf(ficres,"\n");
3999: }
4000: }
4001: }
4002: if(mle==1){
4003: /* Computing hessian and covariance matrix */
4004: ftolhess=ftol; /* Usually correct */
4005: hesscov(matcov, p, npar, delti, ftolhess, func);
4006: }
4007: fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");
4008: printf("# Scales (for hessian or gradient estimation)\n");
4009: fprintf(ficlog,"# Scales (for hessian or gradient estimation)\n");
4010: for(i=1,jk=1; i <=nlstate; i++){
4011: for(j=1; j <=nlstate+ndeath; j++){
4012: if (j!=i) {
4013: fprintf(ficres,"%1d%1d",i,j);
4014: printf("%1d%1d",i,j);
4015: fprintf(ficlog,"%1d%1d",i,j);
4016: for(k=1; k<=ncovmodel;k++){
4017: printf(" %.5e",delti[jk]);
4018: fprintf(ficlog," %.5e",delti[jk]);
4019: fprintf(ficres," %.5e",delti[jk]);
4020: jk++;
4021: }
4022: printf("\n");
4023: fprintf(ficlog,"\n");
4024: fprintf(ficres,"\n");
4025: }
4026: }
4027: }
1.53 brouard 4028:
1.59 brouard 4029: 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");
4030: if(mle==1)
4031: 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");
4032: 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");
4033: for(i=1,k=1;i<=npar;i++){
4034: /* if (k>nlstate) k=1;
4035: i1=(i-1)/(ncovmodel*nlstate)+1;
4036: fprintf(ficres,"%s%d%d",alph[k],i1,tab[i]);
4037: printf("%s%d%d",alph[k],i1,tab[i]);
4038: */
4039: fprintf(ficres,"%3d",i);
4040: if(mle==1)
4041: printf("%3d",i);
4042: fprintf(ficlog,"%3d",i);
4043: for(j=1; j<=i;j++){
4044: fprintf(ficres," %.5e",matcov[i][j]);
4045: if(mle==1)
4046: printf(" %.5e",matcov[i][j]);
4047: fprintf(ficlog," %.5e",matcov[i][j]);
4048: }
4049: fprintf(ficres,"\n");
4050: if(mle==1)
4051: printf("\n");
4052: fprintf(ficlog,"\n");
4053: k++;
4054: }
1.53 brouard 4055:
1.59 brouard 4056: while((c=getc(ficpar))=='#' && c!= EOF){
4057: ungetc(c,ficpar);
4058: fgets(line, MAXLINE, ficpar);
4059: puts(line);
4060: fputs(line,ficparo);
4061: }
4062: ungetc(c,ficpar);
4063:
4064: estepm=0;
4065: fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm);
4066: if (estepm==0 || estepm < stepm) estepm=stepm;
4067: if (fage <= 2) {
4068: bage = ageminpar;
4069: fage = agemaxpar;
4070: }
1.53 brouard 4071:
1.59 brouard 4072: fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");
4073: fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
4074: fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
1.53 brouard 4075:
1.59 brouard 4076: while((c=getc(ficpar))=='#' && c!= EOF){
4077: ungetc(c,ficpar);
4078: fgets(line, MAXLINE, ficpar);
4079: puts(line);
4080: fputs(line,ficparo);
4081: }
4082: ungetc(c,ficpar);
1.53 brouard 4083:
1.59 brouard 4084: 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);
4085: 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);
4086: 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 4087: printf("begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
4088: 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 4089:
1.59 brouard 4090: while((c=getc(ficpar))=='#' && c!= EOF){
4091: ungetc(c,ficpar);
4092: fgets(line, MAXLINE, ficpar);
4093: puts(line);
4094: fputs(line,ficparo);
4095: }
4096: ungetc(c,ficpar);
1.53 brouard 4097:
4098:
1.70 brouard 4099: dateprev1=anprev1+(mprev1-1)/12.+(jprev1-1)/365.;
4100: dateprev2=anprev2+(mprev2-1)/12.+(jprev2-1)/365.;
1.53 brouard 4101:
4102: fscanf(ficpar,"pop_based=%d\n",&popbased);
4103: fprintf(ficparo,"pop_based=%d\n",popbased);
4104: fprintf(ficres,"pop_based=%d\n",popbased);
4105:
4106: while((c=getc(ficpar))=='#' && c!= EOF){
4107: ungetc(c,ficpar);
4108: fgets(line, MAXLINE, ficpar);
4109: puts(line);
4110: fputs(line,ficparo);
4111: }
4112: ungetc(c,ficpar);
4113:
1.69 brouard 4114: 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 4115: 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 4116: 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);
4117: 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);
4118: 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 4119: /* day and month of proj2 are not used but only year anproj2.*/
1.53 brouard 4120:
1.59 brouard 4121: while((c=getc(ficpar))=='#' && c!= EOF){
1.53 brouard 4122: ungetc(c,ficpar);
4123: fgets(line, MAXLINE, ficpar);
4124: puts(line);
4125: fputs(line,ficparo);
4126: }
4127: ungetc(c,ficpar);
4128:
4129: fscanf(ficpar,"popforecast=%d popfile=%s popfiledate=%lf/%lf/%lf last-popfiledate=%lf/%lf/%lf\n",&popforecast,popfile,&jpyram,&mpyram,&anpyram,&jpyram1,&mpyram1,&anpyram1);
4130: fprintf(ficparo,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);
4131: fprintf(ficres,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);
4132:
1.74 brouard 4133: probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
1.59 brouard 4134: freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);
1.58 lievre 4135:
1.59 brouard 4136: /*------------ gnuplot -------------*/
4137: strcpy(optionfilegnuplot,optionfilefiname);
4138: strcat(optionfilegnuplot,".gp");
4139: if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {
4140: printf("Problem with file %s",optionfilegnuplot);
4141: }
4142: else{
4143: fprintf(ficgp,"\n# %s\n", version);
4144: fprintf(ficgp,"# %s\n", optionfilegnuplot);
4145: fprintf(ficgp,"set missing 'NaNq'\n");
4146: }
4147: fclose(ficgp);
4148: printinggnuplot(fileres, ageminpar,agemaxpar,fage, pathc,p);
4149: /*--------- index.htm --------*/
1.53 brouard 4150:
4151: strcpy(optionfilehtm,optionfile);
4152: strcat(optionfilehtm,".htm");
4153: if((fichtm=fopen(optionfilehtm,"w"))==NULL) {
4154: printf("Problem with %s \n",optionfilehtm), exit(0);
4155: }
4156:
4157: fprintf(fichtm,"<body> <font size=\"2\">%s </font> <hr size=\"2\" color=\"#EC5E5E\"> \n
4158: Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n
4159: \n
4160: Total number of observations=%d <br>\n
1.77 brouard 4161: Youngest age at first (selected) pass %.2f, oldest age %.2f<br>\n
1.53 brouard 4162: Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n
4163: <hr size=\"2\" color=\"#EC5E5E\">
4164: <ul><li><h4>Parameter files</h4>\n
4165: - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n
4166: - Log file of the run: <a href=\"%s\">%s</a><br>\n
1.76 brouard 4167: - 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 4168: fclose(fichtm);
1.53 brouard 4169:
1.59 brouard 4170: 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 4171:
1.59 brouard 4172: /*------------ free_vector -------------*/
4173: chdir(path);
1.53 brouard 4174:
1.59 brouard 4175: free_ivector(wav,1,imx);
4176: free_imatrix(dh,1,lastpass-firstpass+1,1,imx);
4177: free_imatrix(bh,1,lastpass-firstpass+1,1,imx);
4178: free_imatrix(mw,1,lastpass-firstpass+1,1,imx);
4179: free_ivector(num,1,n);
4180: free_vector(agedc,1,n);
1.65 lievre 4181: /*free_matrix(covar,0,NCOVMAX,1,n);*/
1.59 brouard 4182: /*free_matrix(covar,1,NCOVMAX,1,n);*/
4183: fclose(ficparo);
4184: fclose(ficres);
1.53 brouard 4185:
4186:
1.54 brouard 4187: /*--------------- Prevalence limit (stable prevalence) --------------*/
1.53 brouard 4188:
4189: strcpy(filerespl,"pl");
4190: strcat(filerespl,fileres);
4191: if((ficrespl=fopen(filerespl,"w"))==NULL) {
1.54 brouard 4192: printf("Problem with stable prevalence resultfile: %s\n", filerespl);goto end;
4193: fprintf(ficlog,"Problem with stable prevalence resultfile: %s\n", filerespl);goto end;
1.53 brouard 4194: }
1.54 brouard 4195: printf("Computing stable prevalence: result on file '%s' \n", filerespl);
4196: fprintf(ficlog,"Computing stable prevalence: result on file '%s' \n", filerespl);
4197: fprintf(ficrespl,"#Stable prevalence \n");
1.53 brouard 4198: fprintf(ficrespl,"#Age ");
4199: for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);
4200: fprintf(ficrespl,"\n");
4201:
4202: prlim=matrix(1,nlstate,1,nlstate);
1.59 brouard 4203:
1.53 brouard 4204: agebase=ageminpar;
4205: agelim=agemaxpar;
4206: ftolpl=1.e-10;
4207: i1=cptcoveff;
4208: if (cptcovn < 1){i1=1;}
4209:
1.59 brouard 4210: for(cptcov=1,k=0;cptcov<=i1;cptcov++){
1.53 brouard 4211: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
1.59 brouard 4212: k=k+1;
4213: /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/
4214: fprintf(ficrespl,"\n#******");
4215: printf("\n#******");
4216: fprintf(ficlog,"\n#******");
4217: for(j=1;j<=cptcoveff;j++) {
4218: fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
4219: printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
4220: fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
4221: }
4222: fprintf(ficrespl,"******\n");
4223: printf("******\n");
4224: fprintf(ficlog,"******\n");
1.53 brouard 4225:
1.59 brouard 4226: for (age=agebase; age<=agelim; age++){
4227: prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
1.69 brouard 4228: fprintf(ficrespl,"%.0f ",age );
4229: for(j=1;j<=cptcoveff;j++)
4230: fprintf(ficrespl,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
1.59 brouard 4231: for(i=1; i<=nlstate;i++)
1.53 brouard 4232: fprintf(ficrespl," %.5f", prlim[i][i]);
1.59 brouard 4233: fprintf(ficrespl,"\n");
1.53 brouard 4234: }
4235: }
1.59 brouard 4236: }
1.53 brouard 4237: fclose(ficrespl);
4238:
4239: /*------------- h Pij x at various ages ------------*/
4240:
4241: strcpy(filerespij,"pij"); strcat(filerespij,fileres);
4242: if((ficrespij=fopen(filerespij,"w"))==NULL) {
4243: printf("Problem with Pij resultfile: %s\n", filerespij);goto end;
4244: fprintf(ficlog,"Problem with Pij resultfile: %s\n", filerespij);goto end;
4245: }
4246: printf("Computing pij: result on file '%s' \n", filerespij);
4247: fprintf(ficlog,"Computing pij: result on file '%s' \n", filerespij);
4248:
4249: stepsize=(int) (stepm+YEARM-1)/YEARM;
4250: /*if (stepm<=24) stepsize=2;*/
4251:
4252: agelim=AGESUP;
4253: hstepm=stepsize*YEARM; /* Every year of age */
4254: hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */
4255:
4256: /* hstepm=1; aff par mois*/
4257:
1.70 brouard 4258: fprintf(ficrespij,"#****** h Pij x Probability to be in state j at age x+h being in i at x ");
1.59 brouard 4259: for(cptcov=1,k=0;cptcov<=i1;cptcov++){
1.53 brouard 4260: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
4261: k=k+1;
1.59 brouard 4262: fprintf(ficrespij,"\n#****** ");
4263: for(j=1;j<=cptcoveff;j++)
4264: fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
4265: fprintf(ficrespij,"******\n");
1.53 brouard 4266:
1.59 brouard 4267: for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */
4268: nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
4269: nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
4270:
4271: /* nhstepm=nhstepm*YEARM; aff par mois*/
4272:
4273: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4274: oldm=oldms;savm=savms;
4275: hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
1.70 brouard 4276: fprintf(ficrespij,"# Cov Agex agex+h hpijx with i,j=");
1.59 brouard 4277: for(i=1; i<=nlstate;i++)
4278: for(j=1; j<=nlstate+ndeath;j++)
4279: fprintf(ficrespij," %1d-%1d",i,j);
4280: fprintf(ficrespij,"\n");
4281: for (h=0; h<=nhstepm; h++){
1.70 brouard 4282: fprintf(ficrespij,"%d %3.f %3.f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );
1.53 brouard 4283: for(i=1; i<=nlstate;i++)
4284: for(j=1; j<=nlstate+ndeath;j++)
1.59 brouard 4285: fprintf(ficrespij," %.5f", p3mat[i][j][h]);
1.53 brouard 4286: fprintf(ficrespij,"\n");
4287: }
1.59 brouard 4288: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4289: fprintf(ficrespij,"\n");
4290: }
1.53 brouard 4291: }
4292: }
4293:
1.74 brouard 4294: varprob(optionfilefiname, matcov, p, delti, nlstate, bage, fage,k,Tvar,nbcode, ncodemax);
1.53 brouard 4295:
4296: fclose(ficrespij);
4297:
4298:
4299: /*---------- Forecasting ------------------*/
1.69 brouard 4300: /*if((stepm == 1) && (strcmp(model,".")==0)){*/
4301: if(prevfcast==1){
1.74 brouard 4302: /* if(stepm ==1){*/
1.70 brouard 4303: prevforecast(fileres, anproj1, mproj1, jproj1, agemin, agemax, dateprev1, dateprev2, mobilavproj, bage, fage, firstpass, lastpass, anproj2, p, cptcoveff);
1.74 brouard 4304: /* (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);*/
4305: /* } */
4306: /* else{ */
4307: /* erreur=108; */
4308: /* 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); */
4309: /* 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); */
4310: /* } */
1.69 brouard 4311: }
1.53 brouard 4312:
4313:
4314: /*---------- Health expectancies and variances ------------*/
4315:
4316: strcpy(filerest,"t");
4317: strcat(filerest,fileres);
4318: if((ficrest=fopen(filerest,"w"))==NULL) {
4319: printf("Problem with total LE resultfile: %s\n", filerest);goto end;
4320: fprintf(ficlog,"Problem with total LE resultfile: %s\n", filerest);goto end;
4321: }
4322: printf("Computing Total LEs with variances: file '%s' \n", filerest);
4323: fprintf(ficlog,"Computing Total LEs with variances: file '%s' \n", filerest);
4324:
4325:
4326: strcpy(filerese,"e");
4327: strcat(filerese,fileres);
4328: if((ficreseij=fopen(filerese,"w"))==NULL) {
4329: printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
4330: fprintf(ficlog,"Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
4331: }
4332: printf("Computing Health Expectancies: result on file '%s' \n", filerese);
4333: fprintf(ficlog,"Computing Health Expectancies: result on file '%s' \n", filerese);
1.68 lievre 4334:
1.53 brouard 4335: strcpy(fileresv,"v");
4336: strcat(fileresv,fileres);
4337: if((ficresvij=fopen(fileresv,"w"))==NULL) {
4338: printf("Problem with variance resultfile: %s\n", fileresv);exit(0);
4339: fprintf(ficlog,"Problem with variance resultfile: %s\n", fileresv);exit(0);
4340: }
4341: printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
4342: fprintf(ficlog,"Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
1.58 lievre 4343:
1.74 brouard 4344: /* Computes prevalence between agemin (i.e minimal age computed) and no more ageminpar */
4345: prevalence(agemin, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
4346: /* 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",\
4347: ageminpar, agemax, s[lastpass][imx], agev[lastpass][imx], nlstate, imx, mint[lastpass][imx],anint[lastpass][imx], dateprev1, dateprev2, firstpass, lastpass);
4348: */
1.58 lievre 4349:
1.54 brouard 4350: if (mobilav!=0) {
1.53 brouard 4351: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
1.54 brouard 4352: if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
4353: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
4354: printf(" Error in movingaverage mobilav=%d\n",mobilav);
4355: }
1.53 brouard 4356: }
4357:
1.59 brouard 4358: for(cptcov=1,k=0;cptcov<=i1;cptcov++){
1.53 brouard 4359: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
4360: k=k+1;
4361: fprintf(ficrest,"\n#****** ");
4362: for(j=1;j<=cptcoveff;j++)
4363: fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
4364: fprintf(ficrest,"******\n");
4365:
4366: fprintf(ficreseij,"\n#****** ");
4367: for(j=1;j<=cptcoveff;j++)
4368: fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
4369: fprintf(ficreseij,"******\n");
4370:
4371: fprintf(ficresvij,"\n#****** ");
4372: for(j=1;j<=cptcoveff;j++)
4373: fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
4374: fprintf(ficresvij,"******\n");
4375:
4376: eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
4377: oldm=oldms;savm=savms;
4378: evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov);
4379:
4380: vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
4381: oldm=oldms;savm=savms;
4382: varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,0, mobilav);
4383: if(popbased==1){
4384: 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 4385: }
1.53 brouard 4386:
4387:
4388: fprintf(ficrest,"#Total LEs with variances: e.. (std) ");
4389: for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);
4390: fprintf(ficrest,"\n");
4391:
4392: epj=vector(1,nlstate+1);
4393: for(age=bage; age <=fage ;age++){
4394: prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
4395: if (popbased==1) {
1.54 brouard 4396: if(mobilav ==0){
1.53 brouard 4397: for(i=1; i<=nlstate;i++)
4398: prlim[i][i]=probs[(int)age][i][k];
1.54 brouard 4399: }else{ /* mobilav */
1.53 brouard 4400: for(i=1; i<=nlstate;i++)
4401: prlim[i][i]=mobaverage[(int)age][i][k];
4402: }
4403: }
4404:
4405: fprintf(ficrest," %4.0f",age);
4406: for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){
4407: for(i=1, epj[j]=0.;i <=nlstate;i++) {
4408: epj[j] += prlim[i][i]*eij[i][j][(int)age];
4409: /* printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/
4410: }
4411: epj[nlstate+1] +=epj[j];
4412: }
4413:
4414: for(i=1, vepp=0.;i <=nlstate;i++)
4415: for(j=1;j <=nlstate;j++)
4416: vepp += vareij[i][j][(int)age];
4417: fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));
4418: for(j=1;j <=nlstate;j++){
4419: fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));
4420: }
4421: fprintf(ficrest,"\n");
4422: }
1.59 brouard 4423: free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
4424: free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);
4425: free_vector(epj,1,nlstate+1);
1.53 brouard 4426: }
4427: }
1.59 brouard 4428: free_vector(weight,1,n);
4429: free_imatrix(Tvard,1,15,1,2);
4430: free_imatrix(s,1,maxwav+1,1,n);
4431: free_matrix(anint,1,maxwav,1,n);
4432: free_matrix(mint,1,maxwav,1,n);
4433: free_ivector(cod,1,n);
4434: free_ivector(tab,1,NCOVMAX);
1.53 brouard 4435: fclose(ficreseij);
4436: fclose(ficresvij);
4437: fclose(ficrest);
4438: fclose(ficpar);
4439:
1.54 brouard 4440: /*------- Variance of stable prevalence------*/
1.53 brouard 4441:
4442: strcpy(fileresvpl,"vpl");
4443: strcat(fileresvpl,fileres);
4444: if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {
1.54 brouard 4445: printf("Problem with variance of stable prevalence resultfile: %s\n", fileresvpl);
1.53 brouard 4446: exit(0);
4447: }
1.54 brouard 4448: printf("Computing Variance-covariance of stable prevalence: file '%s' \n", fileresvpl);
1.53 brouard 4449:
1.59 brouard 4450: for(cptcov=1,k=0;cptcov<=i1;cptcov++){
1.53 brouard 4451: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
4452: k=k+1;
4453: fprintf(ficresvpl,"\n#****** ");
4454: for(j=1;j<=cptcoveff;j++)
4455: fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
4456: fprintf(ficresvpl,"******\n");
4457:
4458: varpl=matrix(1,nlstate,(int) bage, (int) fage);
4459: oldm=oldms;savm=savms;
1.59 brouard 4460: varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);
4461: free_matrix(varpl,1,nlstate,(int) bage, (int)fage);
1.53 brouard 4462: }
1.59 brouard 4463: }
1.53 brouard 4464:
4465: fclose(ficresvpl);
4466:
4467: /*---------- End : free ----------------*/
4468: free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);
4469: free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);
4470: free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);
4471: free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);
1.65 lievre 4472:
4473: free_matrix(covar,0,NCOVMAX,1,n);
1.53 brouard 4474: free_matrix(matcov,1,npar,1,npar);
1.74 brouard 4475: /*free_vector(delti,1,npar);*/
4476: free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
1.53 brouard 4477: free_matrix(agev,1,maxwav,1,imx);
4478: free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
1.54 brouard 4479: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
1.74 brouard 4480: free_ma3x(probs,1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
4481:
1.59 brouard 4482: free_ivector(ncodemax,1,8);
4483: free_ivector(Tvar,1,15);
4484: free_ivector(Tprod,1,15);
4485: free_ivector(Tvaraff,1,15);
4486: free_ivector(Tage,1,15);
4487: free_ivector(Tcode,1,100);
1.53 brouard 4488:
1.74 brouard 4489: /* fclose(fichtm);*/
4490: /* fclose(ficgp);*/ /* ALready done */
1.53 brouard 4491:
4492:
4493: if(erreur >0){
4494: printf("End of Imach with error or warning %d\n",erreur);
4495: fprintf(ficlog,"End of Imach with error or warning %d\n",erreur);
4496: }else{
4497: printf("End of Imach\n");
4498: fprintf(ficlog,"End of Imach\n");
4499: }
4500: printf("See log file on %s\n",filelog);
4501: fclose(ficlog);
4502: /* gettimeofday(&end_time, (struct timezone*)0);*/ /* after time */
4503:
4504: /* 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);*/
4505: /*printf("Total time was %d uSec.\n", total_usecs);*/
4506: /*------ End -----------*/
4507:
1.59 brouard 4508: end:
1.53 brouard 4509: #ifdef windows
4510: /* chdir(pathcd);*/
4511: #endif
4512: /*system("wgnuplot graph.plt");*/
4513: /*system("../gp37mgw/wgnuplot graph.plt");*/
4514: /*system("cd ../gp37mgw");*/
4515: /* system("..\\gp37mgw\\wgnuplot graph.plt");*/
1.59 brouard 4516: strcpy(plotcmd,GNUPLOTPROGRAM);
4517: strcat(plotcmd," ");
4518: strcat(plotcmd,optionfilegnuplot);
1.75 brouard 4519: printf("Starting graphs with: %s",plotcmd);fflush(stdout);
1.59 brouard 4520: system(plotcmd);
1.75 brouard 4521: printf(" Wait...");
1.53 brouard 4522:
1.54 brouard 4523: /*#ifdef windows*/
1.53 brouard 4524: while (z[0] != 'q') {
4525: /* chdir(path); */
4526: printf("\nType e to edit output files, g to graph again, c to start again, and q for exiting: ");
4527: scanf("%s",z);
4528: if (z[0] == 'c') system("./imach");
4529: else if (z[0] == 'e') system(optionfilehtm);
4530: else if (z[0] == 'g') system(plotcmd);
4531: else if (z[0] == 'q') exit(0);
4532: }
1.54 brouard 4533: /*#endif */
1.53 brouard 4534: }
4535:
4536:
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