Annotation of imach/src/imach.c, revision 1.80
1.80 ! brouard 1: /* $Id: imach.c,v 1.79 2003/06/05 15:17:23 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:
1.80 ! brouard 122: /* $Id: imach.c,v 1.79 2003/06/05 15:17:23 brouard Exp $ */
! 123: /* $Log: imach.c,v $
! 124: /* Revision 1.79 2003/06/05 15:17:23 brouard
! 125: /* *** empty log message ***
! 126: /* */
! 127: /* $Revision$ */
! 128: /* $Date$ */
! 129: /* $State$ */
! 130:
1.79 brouard 131: char version[80]="Imach version 0.95a1, June 2003, INED-EUROREVES ";
1.53 brouard 132: int erreur; /* Error number */
133: int nvar;
134: int cptcovn=0, cptcovage=0, cptcoveff=0,cptcov;
135: int npar=NPARMAX;
136: int nlstate=2; /* Number of live states */
137: int ndeath=1; /* Number of dead states */
138: int ncovmodel, ncovcol; /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
139: int popbased=0;
140:
141: int *wav; /* Number of waves for this individuual 0 is possible */
142: int maxwav; /* Maxim number of waves */
143: int jmin, jmax; /* min, max spacing between 2 waves */
144: int mle, weightopt;
145: int **mw; /* mw[mi][i] is number of the mi wave for this individual */
146: int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
1.59 brouard 147: int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between
148: * wave mi and wave mi+1 is not an exact multiple of stepm. */
1.53 brouard 149: double jmean; /* Mean space between 2 waves */
150: double **oldm, **newm, **savm; /* Working pointers to matrices */
151: double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
152: FILE *fic,*ficpar, *ficparo,*ficres, *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
1.76 brouard 153: FILE *ficlog, *ficrespow;
1.53 brouard 154: FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
155: FILE *ficresprobmorprev;
156: FILE *fichtm; /* Html File */
157: FILE *ficreseij;
158: char filerese[FILENAMELENGTH];
159: FILE *ficresvij;
160: char fileresv[FILENAMELENGTH];
161: FILE *ficresvpl;
162: char fileresvpl[FILENAMELENGTH];
163: char title[MAXLINE];
164: char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH], filerespl[FILENAMELENGTH];
165: char optionfilext[10], optionfilefiname[FILENAMELENGTH], plotcmd[FILENAMELENGTH];
166:
167: char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
168: char filelog[FILENAMELENGTH]; /* Log file */
169: char filerest[FILENAMELENGTH];
170: char fileregp[FILENAMELENGTH];
171: char popfile[FILENAMELENGTH];
172:
173: char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH];
174:
175: #define NR_END 1
176: #define FREE_ARG char*
177: #define FTOL 1.0e-10
178:
179: #define NRANSI
180: #define ITMAX 200
181:
182: #define TOL 2.0e-4
183:
184: #define CGOLD 0.3819660
185: #define ZEPS 1.0e-10
186: #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);
187:
188: #define GOLD 1.618034
189: #define GLIMIT 100.0
190: #define TINY 1.0e-20
191:
192: static double maxarg1,maxarg2;
193: #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
194: #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
195:
196: #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
197: #define rint(a) floor(a+0.5)
198:
199: static double sqrarg;
200: #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
201: #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}
202:
203: int imx;
204: int stepm;
205: /* Stepm, step in month: minimum step interpolation*/
206:
207: int estepm;
208: /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
209:
210: int m,nb;
211: int *num, firstpass=0, lastpass=4,*cod, *ncodemax, *Tage;
212: double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
1.55 lievre 213: double **pmmij, ***probs;
1.53 brouard 214: double dateintmean=0;
215:
216: double *weight;
217: int **s; /* Status */
218: double *agedc, **covar, idx;
219: int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;
220:
221: double ftol=FTOL; /* Tolerance for computing Max Likelihood */
222: double ftolhess; /* Tolerance for computing hessian */
223:
224: /**************** split *************************/
225: static int split( char *path, char *dirc, char *name, char *ext, char *finame )
226: {
1.59 brouard 227: char *ss; /* pointer */
228: int l1, l2; /* length counters */
1.53 brouard 229:
1.59 brouard 230: l1 = strlen(path ); /* length of path */
231: if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
232: ss= strrchr( path, DIRSEPARATOR ); /* find last / */
233: if ( ss == NULL ) { /* no directory, so use current */
234: /*if(strrchr(path, ODIRSEPARATOR )==NULL)
235: printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
1.74 brouard 236: /* get current working directory */
237: /* extern char* getcwd ( char *buf , int len);*/
1.59 brouard 238: if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {
239: return( GLOCK_ERROR_GETCWD );
240: }
241: strcpy( name, path ); /* we've got it */
242: } else { /* strip direcotry from path */
243: ss++; /* after this, the filename */
244: l2 = strlen( ss ); /* length of filename */
245: if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
246: strcpy( name, ss ); /* save file name */
247: strncpy( dirc, path, l1 - l2 ); /* now the directory */
248: dirc[l1-l2] = 0; /* add zero */
249: }
250: l1 = strlen( dirc ); /* length of directory */
1.53 brouard 251: #ifdef windows
1.59 brouard 252: if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; }
1.53 brouard 253: #else
1.59 brouard 254: if ( dirc[l1-1] != '/' ) { dirc[l1] = '/'; dirc[l1+1] = 0; }
1.53 brouard 255: #endif
1.59 brouard 256: ss = strrchr( name, '.' ); /* find last / */
257: ss++;
258: strcpy(ext,ss); /* save extension */
259: l1= strlen( name);
260: l2= strlen(ss)+1;
261: strncpy( finame, name, l1-l2);
262: finame[l1-l2]= 0;
263: return( 0 ); /* we're done */
1.53 brouard 264: }
265:
266:
267: /******************************************/
268:
269: void replace(char *s, char*t)
270: {
271: int i;
272: int lg=20;
273: i=0;
274: lg=strlen(t);
275: for(i=0; i<= lg; i++) {
276: (s[i] = t[i]);
277: if (t[i]== '\\') s[i]='/';
278: }
279: }
280:
281: int nbocc(char *s, char occ)
282: {
283: int i,j=0;
284: int lg=20;
285: i=0;
286: lg=strlen(s);
287: for(i=0; i<= lg; i++) {
288: if (s[i] == occ ) j++;
289: }
290: return j;
291: }
292:
293: void cutv(char *u,char *v, char*t, char occ)
294: {
295: /* cuts string t into u and v where u is ended by char occ excluding it
296: and v is after occ excluding it too : ex cutv(u,v,"abcdef2ghi2j",2)
297: gives u="abcedf" and v="ghi2j" */
298: int i,lg,j,p=0;
299: i=0;
300: for(j=0; j<=strlen(t)-1; j++) {
301: if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;
302: }
303:
304: lg=strlen(t);
305: for(j=0; j<p; j++) {
306: (u[j] = t[j]);
307: }
308: u[p]='\0';
309:
310: for(j=0; j<= lg; j++) {
311: if (j>=(p+1))(v[j-p-1] = t[j]);
312: }
313: }
314:
315: /********************** nrerror ********************/
316:
317: void nrerror(char error_text[])
318: {
319: fprintf(stderr,"ERREUR ...\n");
320: fprintf(stderr,"%s\n",error_text);
1.59 brouard 321: exit(EXIT_FAILURE);
1.53 brouard 322: }
323: /*********************** vector *******************/
324: double *vector(int nl, int nh)
325: {
326: double *v;
327: v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
328: if (!v) nrerror("allocation failure in vector");
329: return v-nl+NR_END;
330: }
331:
332: /************************ free vector ******************/
333: void free_vector(double*v, int nl, int nh)
334: {
335: free((FREE_ARG)(v+nl-NR_END));
336: }
337:
338: /************************ivector *******************************/
1.76 brouard 339: char *cvector(long nl,long nh)
340: {
341: char *v;
342: v=(char *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(char)));
343: if (!v) nrerror("allocation failure in cvector");
344: return v-nl+NR_END;
345: }
346:
347: /******************free ivector **************************/
348: void free_cvector(char *v, long nl, long nh)
349: {
350: free((FREE_ARG)(v+nl-NR_END));
351: }
352:
353: /************************ivector *******************************/
1.53 brouard 354: int *ivector(long nl,long nh)
355: {
356: int *v;
357: v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
358: if (!v) nrerror("allocation failure in ivector");
359: return v-nl+NR_END;
360: }
361:
362: /******************free ivector **************************/
363: void free_ivector(int *v, long nl, long nh)
364: {
365: free((FREE_ARG)(v+nl-NR_END));
366: }
367:
368: /******************* imatrix *******************************/
369: int **imatrix(long nrl, long nrh, long ncl, long nch)
370: /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */
371: {
372: long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;
373: int **m;
374:
375: /* allocate pointers to rows */
376: m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));
377: if (!m) nrerror("allocation failure 1 in matrix()");
378: m += NR_END;
379: m -= nrl;
380:
381:
382: /* allocate rows and set pointers to them */
383: m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));
384: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
385: m[nrl] += NR_END;
386: m[nrl] -= ncl;
387:
388: for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;
389:
390: /* return pointer to array of pointers to rows */
391: return m;
392: }
393:
394: /****************** free_imatrix *************************/
395: void free_imatrix(m,nrl,nrh,ncl,nch)
396: int **m;
397: long nch,ncl,nrh,nrl;
398: /* free an int matrix allocated by imatrix() */
399: {
400: free((FREE_ARG) (m[nrl]+ncl-NR_END));
401: free((FREE_ARG) (m+nrl-NR_END));
402: }
403:
404: /******************* matrix *******************************/
405: double **matrix(long nrl, long nrh, long ncl, long nch)
406: {
407: long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
408: double **m;
409:
410: m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
411: if (!m) nrerror("allocation failure 1 in matrix()");
412: m += NR_END;
413: m -= nrl;
414:
415: m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
416: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
417: m[nrl] += NR_END;
418: m[nrl] -= ncl;
419:
420: for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
421: return m;
1.74 brouard 422: /* print *(*(m+1)+70) ou print m[1][70]; print m+1 or print &(m[1])
423: */
1.53 brouard 424: }
425:
426: /*************************free matrix ************************/
427: void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
428: {
429: free((FREE_ARG)(m[nrl]+ncl-NR_END));
430: free((FREE_ARG)(m+nrl-NR_END));
431: }
432:
433: /******************* ma3x *******************************/
434: double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
435: {
436: long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
437: double ***m;
438:
439: m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
440: if (!m) nrerror("allocation failure 1 in matrix()");
441: m += NR_END;
442: m -= nrl;
443:
444: m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
445: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
446: m[nrl] += NR_END;
447: m[nrl] -= ncl;
448:
449: for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
450:
451: m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
452: if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
453: m[nrl][ncl] += NR_END;
454: m[nrl][ncl] -= nll;
455: for (j=ncl+1; j<=nch; j++)
456: m[nrl][j]=m[nrl][j-1]+nlay;
457:
458: for (i=nrl+1; i<=nrh; i++) {
459: m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
460: for (j=ncl+1; j<=nch; j++)
461: m[i][j]=m[i][j-1]+nlay;
462: }
1.74 brouard 463: return m;
464: /* gdb: p *(m+1) <=> p m[1] and p (m+1) <=> p (m+1) <=> p &(m[1])
465: &(m[i][j][k]) <=> *((*(m+i) + j)+k)
466: */
1.53 brouard 467: }
468:
469: /*************************free ma3x ************************/
470: void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
471: {
472: free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
473: free((FREE_ARG)(m[nrl]+ncl-NR_END));
474: free((FREE_ARG)(m+nrl-NR_END));
475: }
476:
477: /***************** f1dim *************************/
478: extern int ncom;
479: extern double *pcom,*xicom;
480: extern double (*nrfunc)(double []);
481:
482: double f1dim(double x)
483: {
484: int j;
485: double f;
486: double *xt;
487:
488: xt=vector(1,ncom);
489: for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];
490: f=(*nrfunc)(xt);
491: free_vector(xt,1,ncom);
492: return f;
493: }
494:
495: /*****************brent *************************/
496: double brent(double ax, double bx, double cx, double (*f)(double), double tol, double *xmin)
497: {
498: int iter;
499: double a,b,d,etemp;
500: double fu,fv,fw,fx;
501: double ftemp;
502: double p,q,r,tol1,tol2,u,v,w,x,xm;
503: double e=0.0;
504:
505: a=(ax < cx ? ax : cx);
506: b=(ax > cx ? ax : cx);
507: x=w=v=bx;
508: fw=fv=fx=(*f)(x);
509: for (iter=1;iter<=ITMAX;iter++) {
510: xm=0.5*(a+b);
511: tol2=2.0*(tol1=tol*fabs(x)+ZEPS);
512: /* if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
513: printf(".");fflush(stdout);
514: fprintf(ficlog,".");fflush(ficlog);
515: #ifdef DEBUG
516: 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);
517: 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);
518: /* if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
519: #endif
520: if (fabs(x-xm) <= (tol2-0.5*(b-a))){
521: *xmin=x;
522: return fx;
523: }
524: ftemp=fu;
525: if (fabs(e) > tol1) {
526: r=(x-w)*(fx-fv);
527: q=(x-v)*(fx-fw);
528: p=(x-v)*q-(x-w)*r;
529: q=2.0*(q-r);
530: if (q > 0.0) p = -p;
531: q=fabs(q);
532: etemp=e;
533: e=d;
534: if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))
535: d=CGOLD*(e=(x >= xm ? a-x : b-x));
536: else {
537: d=p/q;
538: u=x+d;
539: if (u-a < tol2 || b-u < tol2)
540: d=SIGN(tol1,xm-x);
541: }
542: } else {
543: d=CGOLD*(e=(x >= xm ? a-x : b-x));
544: }
545: u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));
546: fu=(*f)(u);
547: if (fu <= fx) {
548: if (u >= x) a=x; else b=x;
549: SHFT(v,w,x,u)
550: SHFT(fv,fw,fx,fu)
551: } else {
552: if (u < x) a=u; else b=u;
553: if (fu <= fw || w == x) {
554: v=w;
555: w=u;
556: fv=fw;
557: fw=fu;
558: } else if (fu <= fv || v == x || v == w) {
559: v=u;
560: fv=fu;
561: }
562: }
563: }
564: nrerror("Too many iterations in brent");
565: *xmin=x;
566: return fx;
567: }
568:
569: /****************** mnbrak ***********************/
570:
571: void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,
572: double (*func)(double))
573: {
574: double ulim,u,r,q, dum;
575: double fu;
576:
577: *fa=(*func)(*ax);
578: *fb=(*func)(*bx);
579: if (*fb > *fa) {
580: SHFT(dum,*ax,*bx,dum)
581: SHFT(dum,*fb,*fa,dum)
582: }
583: *cx=(*bx)+GOLD*(*bx-*ax);
584: *fc=(*func)(*cx);
585: while (*fb > *fc) {
586: r=(*bx-*ax)*(*fb-*fc);
587: q=(*bx-*cx)*(*fb-*fa);
588: u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/
589: (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r));
590: ulim=(*bx)+GLIMIT*(*cx-*bx);
591: if ((*bx-u)*(u-*cx) > 0.0) {
592: fu=(*func)(u);
593: } else if ((*cx-u)*(u-ulim) > 0.0) {
594: fu=(*func)(u);
595: if (fu < *fc) {
596: SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))
597: SHFT(*fb,*fc,fu,(*func)(u))
598: }
599: } else if ((u-ulim)*(ulim-*cx) >= 0.0) {
600: u=ulim;
601: fu=(*func)(u);
602: } else {
603: u=(*cx)+GOLD*(*cx-*bx);
604: fu=(*func)(u);
605: }
606: SHFT(*ax,*bx,*cx,u)
607: SHFT(*fa,*fb,*fc,fu)
608: }
609: }
610:
611: /*************** linmin ************************/
612:
613: int ncom;
614: double *pcom,*xicom;
615: double (*nrfunc)(double []);
616:
617: void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))
618: {
619: double brent(double ax, double bx, double cx,
620: double (*f)(double), double tol, double *xmin);
621: double f1dim(double x);
622: void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,
623: double *fc, double (*func)(double));
624: int j;
625: double xx,xmin,bx,ax;
626: double fx,fb,fa;
627:
628: ncom=n;
629: pcom=vector(1,n);
630: xicom=vector(1,n);
631: nrfunc=func;
632: for (j=1;j<=n;j++) {
633: pcom[j]=p[j];
634: xicom[j]=xi[j];
635: }
636: ax=0.0;
637: xx=1.0;
638: mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim);
639: *fret=brent(ax,xx,bx,f1dim,TOL,&xmin);
640: #ifdef DEBUG
641: printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
642: fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
643: #endif
644: for (j=1;j<=n;j++) {
645: xi[j] *= xmin;
646: p[j] += xi[j];
647: }
648: free_vector(xicom,1,n);
649: free_vector(pcom,1,n);
650: }
651:
652: /*************** powell ************************/
653: void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,
654: double (*func)(double []))
655: {
656: void linmin(double p[], double xi[], int n, double *fret,
657: double (*func)(double []));
658: int i,ibig,j;
659: double del,t,*pt,*ptt,*xit;
660: double fp,fptt;
661: double *xits;
662: pt=vector(1,n);
663: ptt=vector(1,n);
664: xit=vector(1,n);
665: xits=vector(1,n);
666: *fret=(*func)(p);
667: for (j=1;j<=n;j++) pt[j]=p[j];
668: for (*iter=1;;++(*iter)) {
669: fp=(*fret);
670: ibig=0;
671: del=0.0;
672: printf("\nPowell iter=%d -2*LL=%.12f",*iter,*fret);
673: fprintf(ficlog,"\nPowell iter=%d -2*LL=%.12f",*iter,*fret);
1.76 brouard 674: fprintf(ficrespow,"%d %.12f",*iter,*fret);
675: for (i=1;i<=n;i++) {
1.53 brouard 676: printf(" %d %.12f",i, p[i]);
1.76 brouard 677: fprintf(ficlog," %d %.12lf",i, p[i]);
678: fprintf(ficrespow," %.12lf", p[i]);
679: }
1.53 brouard 680: printf("\n");
681: fprintf(ficlog,"\n");
1.76 brouard 682: fprintf(ficrespow,"\n");
1.53 brouard 683: for (i=1;i<=n;i++) {
684: for (j=1;j<=n;j++) xit[j]=xi[j][i];
685: fptt=(*fret);
686: #ifdef DEBUG
687: printf("fret=%lf \n",*fret);
688: fprintf(ficlog,"fret=%lf \n",*fret);
689: #endif
690: printf("%d",i);fflush(stdout);
691: fprintf(ficlog,"%d",i);fflush(ficlog);
692: linmin(p,xit,n,fret,func);
693: if (fabs(fptt-(*fret)) > del) {
694: del=fabs(fptt-(*fret));
695: ibig=i;
696: }
697: #ifdef DEBUG
698: printf("%d %.12e",i,(*fret));
699: fprintf(ficlog,"%d %.12e",i,(*fret));
700: for (j=1;j<=n;j++) {
701: xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
702: printf(" x(%d)=%.12e",j,xit[j]);
703: fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
704: }
705: for(j=1;j<=n;j++) {
706: printf(" p=%.12e",p[j]);
707: fprintf(ficlog," p=%.12e",p[j]);
708: }
709: printf("\n");
710: fprintf(ficlog,"\n");
711: #endif
712: }
713: if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {
714: #ifdef DEBUG
715: int k[2],l;
716: k[0]=1;
717: k[1]=-1;
718: printf("Max: %.12e",(*func)(p));
719: fprintf(ficlog,"Max: %.12e",(*func)(p));
720: for (j=1;j<=n;j++) {
721: printf(" %.12e",p[j]);
722: fprintf(ficlog," %.12e",p[j]);
723: }
724: printf("\n");
725: fprintf(ficlog,"\n");
726: for(l=0;l<=1;l++) {
727: for (j=1;j<=n;j++) {
728: ptt[j]=p[j]+(p[j]-pt[j])*k[l];
729: printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
730: fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
731: }
732: printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
733: fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
734: }
735: #endif
736:
737:
738: free_vector(xit,1,n);
739: free_vector(xits,1,n);
740: free_vector(ptt,1,n);
741: free_vector(pt,1,n);
742: return;
743: }
744: if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");
745: for (j=1;j<=n;j++) {
746: ptt[j]=2.0*p[j]-pt[j];
747: xit[j]=p[j]-pt[j];
748: pt[j]=p[j];
749: }
750: fptt=(*func)(ptt);
751: if (fptt < fp) {
752: t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt);
753: if (t < 0.0) {
754: linmin(p,xit,n,fret,func);
755: for (j=1;j<=n;j++) {
756: xi[j][ibig]=xi[j][n];
757: xi[j][n]=xit[j];
758: }
759: #ifdef DEBUG
760: printf("Direction changed last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
761: fprintf(ficlog,"Direction changed last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
762: for(j=1;j<=n;j++){
763: printf(" %.12e",xit[j]);
764: fprintf(ficlog," %.12e",xit[j]);
765: }
766: printf("\n");
767: fprintf(ficlog,"\n");
768: #endif
1.54 brouard 769: }
1.53 brouard 770: }
771: }
772: }
773:
1.54 brouard 774: /**** Prevalence limit (stable prevalence) ****************/
1.53 brouard 775:
776: double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)
777: {
778: /* Computes the prevalence limit in each live state at age x by left multiplying the unit
779: matrix by transitions matrix until convergence is reached */
780:
781: int i, ii,j,k;
782: double min, max, maxmin, maxmax,sumnew=0.;
783: double **matprod2();
784: double **out, cov[NCOVMAX], **pmij();
785: double **newm;
786: double agefin, delaymax=50 ; /* Max number of years to converge */
787:
788: for (ii=1;ii<=nlstate+ndeath;ii++)
789: for (j=1;j<=nlstate+ndeath;j++){
790: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
791: }
792:
793: cov[1]=1.;
794:
795: /* Even if hstepm = 1, at least one multiplication by the unit matrix */
796: for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
797: newm=savm;
798: /* Covariates have to be included here again */
799: cov[2]=agefin;
800:
801: for (k=1; k<=cptcovn;k++) {
802: cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
803: /* 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]]);*/
804: }
805: for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
806: for (k=1; k<=cptcovprod;k++)
807: cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
808:
809: /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
810: /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
811: /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
812: out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);
813:
814: savm=oldm;
815: oldm=newm;
816: maxmax=0.;
817: for(j=1;j<=nlstate;j++){
818: min=1.;
819: max=0.;
820: for(i=1; i<=nlstate; i++) {
821: sumnew=0;
822: for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
823: prlim[i][j]= newm[i][j]/(1-sumnew);
824: max=FMAX(max,prlim[i][j]);
825: min=FMIN(min,prlim[i][j]);
826: }
827: maxmin=max-min;
828: maxmax=FMAX(maxmax,maxmin);
829: }
830: if(maxmax < ftolpl){
831: return prlim;
832: }
833: }
834: }
835:
836: /*************** transition probabilities ***************/
837:
838: double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
839: {
840: double s1, s2;
841: /*double t34;*/
842: int i,j,j1, nc, ii, jj;
843:
844: for(i=1; i<= nlstate; i++){
845: for(j=1; j<i;j++){
846: for (nc=1, s2=0.;nc <=ncovmodel; nc++){
847: /*s2 += param[i][j][nc]*cov[nc];*/
848: s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
849: /*printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2);*/
850: }
851: ps[i][j]=s2;
852: /*printf("s1=%.17e, s2=%.17e\n",s1,s2);*/
853: }
854: for(j=i+1; j<=nlstate+ndeath;j++){
855: for (nc=1, s2=0.;nc <=ncovmodel; nc++){
856: s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
857: /*printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2);*/
858: }
859: ps[i][j]=s2;
860: }
861: }
862: /*ps[3][2]=1;*/
863:
864: for(i=1; i<= nlstate; i++){
865: s1=0;
866: for(j=1; j<i; j++)
867: s1+=exp(ps[i][j]);
868: for(j=i+1; j<=nlstate+ndeath; j++)
869: s1+=exp(ps[i][j]);
870: ps[i][i]=1./(s1+1.);
871: for(j=1; j<i; j++)
872: ps[i][j]= exp(ps[i][j])*ps[i][i];
873: for(j=i+1; j<=nlstate+ndeath; j++)
874: ps[i][j]= exp(ps[i][j])*ps[i][i];
875: /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
876: } /* end i */
877:
878: for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
879: for(jj=1; jj<= nlstate+ndeath; jj++){
880: ps[ii][jj]=0;
881: ps[ii][ii]=1;
882: }
883: }
884:
885:
886: /* for(ii=1; ii<= nlstate+ndeath; ii++){
887: for(jj=1; jj<= nlstate+ndeath; jj++){
888: printf("%lf ",ps[ii][jj]);
889: }
890: printf("\n ");
891: }
892: printf("\n ");printf("%lf ",cov[2]);*/
893: /*
894: for(i=1; i<= npar; i++) printf("%f ",x[i]);
895: goto end;*/
896: return ps;
897: }
898:
899: /**************** Product of 2 matrices ******************/
900:
901: double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)
902: {
903: /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
904: b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
905: /* in, b, out are matrice of pointers which should have been initialized
906: before: only the contents of out is modified. The function returns
907: a pointer to pointers identical to out */
908: long i, j, k;
909: for(i=nrl; i<= nrh; i++)
910: for(k=ncolol; k<=ncoloh; k++)
911: for(j=ncl,out[i][k]=0.; j<=nch; j++)
912: out[i][k] +=in[i][j]*b[j][k];
913:
914: return out;
915: }
916:
917:
918: /************* Higher Matrix Product ***************/
919:
920: double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
921: {
1.66 brouard 922: /* Computes the transition matrix starting at age 'age' over
923: 'nhstepm*hstepm*stepm' months (i.e. until
924: age (in years) age+nhstepm*hstepm*stepm/12) by multiplying
925: nhstepm*hstepm matrices.
1.53 brouard 926: Output is stored in matrix po[i][j][h] for h every 'hstepm' step
1.66 brouard 927: (typically every 2 years instead of every month which is too big
928: for the memory).
1.53 brouard 929: Model is determined by parameters x and covariates have to be
930: included manually here.
931:
932: */
933:
934: int i, j, d, h, k;
935: double **out, cov[NCOVMAX];
936: double **newm;
937:
938: /* Hstepm could be zero and should return the unit matrix */
939: for (i=1;i<=nlstate+ndeath;i++)
940: for (j=1;j<=nlstate+ndeath;j++){
941: oldm[i][j]=(i==j ? 1.0 : 0.0);
942: po[i][j][0]=(i==j ? 1.0 : 0.0);
943: }
944: /* Even if hstepm = 1, at least one multiplication by the unit matrix */
945: for(h=1; h <=nhstepm; h++){
946: for(d=1; d <=hstepm; d++){
947: newm=savm;
948: /* Covariates have to be included here again */
949: cov[1]=1.;
950: cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
951: for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
952: for (k=1; k<=cptcovage;k++)
953: cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
954: for (k=1; k<=cptcovprod;k++)
955: cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
956:
957:
958: /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
959: /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
960: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,
961: pmij(pmmij,cov,ncovmodel,x,nlstate));
962: savm=oldm;
963: oldm=newm;
964: }
965: for(i=1; i<=nlstate+ndeath; i++)
966: for(j=1;j<=nlstate+ndeath;j++) {
967: po[i][j][h]=newm[i][j];
968: /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);
969: */
970: }
971: } /* end h */
972: return po;
973: }
974:
975:
976: /*************** log-likelihood *************/
977: double func( double *x)
978: {
979: int i, ii, j, k, mi, d, kk;
980: double l, ll[NLSTATEMAX], cov[NCOVMAX];
981: double **out;
982: double sw; /* Sum of weights */
983: double lli; /* Individual log likelihood */
1.59 brouard 984: int s1, s2;
1.68 lievre 985: double bbh, survp;
1.53 brouard 986: long ipmx;
987: /*extern weight */
988: /* We are differentiating ll according to initial status */
989: /* for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
990: /*for(i=1;i<imx;i++)
991: printf(" %d\n",s[4][i]);
992: */
993: cov[1]=1.;
994:
995: for(k=1; k<=nlstate; k++) ll[k]=0.;
1.61 brouard 996:
997: if(mle==1){
998: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
999: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
1000: for(mi=1; mi<= wav[i]-1; mi++){
1001: for (ii=1;ii<=nlstate+ndeath;ii++)
1002: for (j=1;j<=nlstate+ndeath;j++){
1003: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1004: savm[ii][j]=(ii==j ? 1.0 : 0.0);
1005: }
1006: for(d=0; d<dh[mi][i]; d++){
1007: newm=savm;
1008: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
1009: for (kk=1; kk<=cptcovage;kk++) {
1010: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
1011: }
1012: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1013: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1014: savm=oldm;
1015: oldm=newm;
1016: } /* end mult */
1.53 brouard 1017:
1.61 brouard 1018: /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
1019: /* But now since version 0.9 we anticipate for bias and large stepm.
1020: * If stepm is larger than one month (smallest stepm) and if the exact delay
1021: * (in months) between two waves is not a multiple of stepm, we rounded to
1022: * the nearest (and in case of equal distance, to the lowest) interval but now
1023: * we keep into memory the bias bh[mi][i] and also the previous matrix product
1024: * (i.e to dh[mi][i]-1) saved in 'savm'. The we inter(extra)polate the
1025: * probability in order to take into account the bias as a fraction of the way
1026: * from savm to out if bh is neagtive or even beyond if bh is positive. bh varies
1027: * -stepm/2 to stepm/2 .
1028: * For stepm=1 the results are the same as for previous versions of Imach.
1029: * For stepm > 1 the results are less biased than in previous versions.
1030: */
1031: s1=s[mw[mi][i]][i];
1032: s2=s[mw[mi+1][i]][i];
1.64 lievre 1033: bbh=(double)bh[mi][i]/(double)stepm;
1034: /* bias is positive if real duration
1035: * is higher than the multiple of stepm and negative otherwise.
1036: */
1037: /* 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 1038: if( s2 > nlstate){
1039: /* i.e. if s2 is a death state and if the date of death is known then the contribution
1040: to the likelihood is the probability to die between last step unit time and current
1041: step unit time, which is also the differences between probability to die before dh
1042: and probability to die before dh-stepm .
1043: In version up to 0.92 likelihood was computed
1044: as if date of death was unknown. Death was treated as any other
1045: health state: the date of the interview describes the actual state
1046: and not the date of a change in health state. The former idea was
1047: to consider that at each interview the state was recorded
1048: (healthy, disable or death) and IMaCh was corrected; but when we
1049: introduced the exact date of death then we should have modified
1050: the contribution of an exact death to the likelihood. This new
1051: contribution is smaller and very dependent of the step unit
1052: stepm. It is no more the probability to die between last interview
1053: and month of death but the probability to survive from last
1054: interview up to one month before death multiplied by the
1055: probability to die within a month. Thanks to Chris
1056: Jackson for correcting this bug. Former versions increased
1057: mortality artificially. The bad side is that we add another loop
1058: which slows down the processing. The difference can be up to 10%
1059: lower mortality.
1060: */
1061: lli=log(out[s1][s2] - savm[s1][s2]);
1062: }else{
1063: lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
1064: /* 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 */
1065: }
1.64 lievre 1066: /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
1067: /*if(lli ==000.0)*/
1068: /*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 1069: ipmx +=1;
1.64 lievre 1070: sw += weight[i];
1071: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1072: } /* end of wave */
1073: } /* end of individual */
1074: } else if(mle==2){
1075: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1076: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
1077: for(mi=1; mi<= wav[i]-1; mi++){
1078: for (ii=1;ii<=nlstate+ndeath;ii++)
1079: for (j=1;j<=nlstate+ndeath;j++){
1080: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1081: savm[ii][j]=(ii==j ? 1.0 : 0.0);
1082: }
1083: for(d=0; d<=dh[mi][i]; d++){
1084: newm=savm;
1085: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
1086: for (kk=1; kk<=cptcovage;kk++) {
1087: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
1088: }
1089: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1090: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1091: savm=oldm;
1092: oldm=newm;
1093: } /* end mult */
1094:
1095: /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
1096: /* But now since version 0.9 we anticipate for bias and large stepm.
1097: * If stepm is larger than one month (smallest stepm) and if the exact delay
1098: * (in months) between two waves is not a multiple of stepm, we rounded to
1099: * the nearest (and in case of equal distance, to the lowest) interval but now
1100: * we keep into memory the bias bh[mi][i] and also the previous matrix product
1101: * (i.e to dh[mi][i]-1) saved in 'savm'. The we inter(extra)polate the
1102: * probability in order to take into account the bias as a fraction of the way
1103: * from savm to out if bh is neagtive or even beyond if bh is positive. bh varies
1104: * -stepm/2 to stepm/2 .
1105: * For stepm=1 the results are the same as for previous versions of Imach.
1106: * For stepm > 1 the results are less biased than in previous versions.
1107: */
1108: s1=s[mw[mi][i]][i];
1109: s2=s[mw[mi+1][i]][i];
1110: bbh=(double)bh[mi][i]/(double)stepm;
1111: /* bias is positive if real duration
1112: * is higher than the multiple of stepm and negative otherwise.
1113: */
1.63 lievre 1114: 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 1115: /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
1116: /*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 */
1117: /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
1118: /*if(lli ==000.0)*/
1119: /*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); */
1120: ipmx +=1;
1121: sw += weight[i];
1122: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1123: } /* end of wave */
1124: } /* end of individual */
1125: } else if(mle==3){ /* exponential inter-extrapolation */
1126: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1127: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
1128: for(mi=1; mi<= wav[i]-1; mi++){
1129: for (ii=1;ii<=nlstate+ndeath;ii++)
1130: for (j=1;j<=nlstate+ndeath;j++){
1131: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1132: savm[ii][j]=(ii==j ? 1.0 : 0.0);
1133: }
1134: for(d=0; d<dh[mi][i]; d++){
1135: newm=savm;
1136: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
1137: for (kk=1; kk<=cptcovage;kk++) {
1138: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
1139: }
1140: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1141: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1142: savm=oldm;
1143: oldm=newm;
1144: } /* end mult */
1145:
1146: /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
1147: /* But now since version 0.9 we anticipate for bias and large stepm.
1148: * If stepm is larger than one month (smallest stepm) and if the exact delay
1149: * (in months) between two waves is not a multiple of stepm, we rounded to
1150: * the nearest (and in case of equal distance, to the lowest) interval but now
1151: * we keep into memory the bias bh[mi][i] and also the previous matrix product
1152: * (i.e to dh[mi][i]-1) saved in 'savm'. The we inter(extra)polate the
1153: * probability in order to take into account the bias as a fraction of the way
1154: * from savm to out if bh is neagtive or even beyond if bh is positive. bh varies
1155: * -stepm/2 to stepm/2 .
1156: * For stepm=1 the results are the same as for previous versions of Imach.
1157: * For stepm > 1 the results are less biased than in previous versions.
1158: */
1159: s1=s[mw[mi][i]][i];
1160: s2=s[mw[mi+1][i]][i];
1161: bbh=(double)bh[mi][i]/(double)stepm;
1162: /* bias is positive if real duration
1163: * is higher than the multiple of stepm and negative otherwise.
1164: */
1165: /* 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 */
1166: 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 1167: /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
1168: /*if(lli ==000.0)*/
1169: /*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); */
1170: ipmx +=1;
1171: sw += weight[i];
1172: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1173: } /* end of wave */
1174: } /* end of individual */
1.64 lievre 1175: }else{ /* ml=4 no inter-extrapolation */
1.61 brouard 1176: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1177: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
1178: for(mi=1; mi<= wav[i]-1; mi++){
1179: for (ii=1;ii<=nlstate+ndeath;ii++)
1180: for (j=1;j<=nlstate+ndeath;j++){
1181: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1182: savm[ii][j]=(ii==j ? 1.0 : 0.0);
1183: }
1184: for(d=0; d<dh[mi][i]; d++){
1185: newm=savm;
1186: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
1187: for (kk=1; kk<=cptcovage;kk++) {
1188: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
1189: }
1190:
1191: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1192: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1193: savm=oldm;
1194: oldm=newm;
1195: } /* end mult */
1196:
1197: lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
1198: ipmx +=1;
1199: sw += weight[i];
1200: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1201: } /* end of wave */
1202: } /* end of individual */
1203: } /* End of if */
1.53 brouard 1204: for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
1205: /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
1206: l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
1207: return -l;
1208: }
1209:
1210:
1211: /*********** Maximum Likelihood Estimation ***************/
1212:
1213: void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
1214: {
1215: int i,j, iter;
1.74 brouard 1216: double **xi;
1.53 brouard 1217: double fret;
1.76 brouard 1218: char filerespow[FILENAMELENGTH];
1.53 brouard 1219: xi=matrix(1,npar,1,npar);
1220: for (i=1;i<=npar;i++)
1221: for (j=1;j<=npar;j++)
1222: xi[i][j]=(i==j ? 1.0 : 0.0);
1223: printf("Powell\n"); fprintf(ficlog,"Powell\n");
1.76 brouard 1224: strcpy(filerespow,"pow");
1225: strcat(filerespow,fileres);
1226: if((ficrespow=fopen(filerespow,"w"))==NULL) {
1227: printf("Problem with resultfile: %s\n", filerespow);
1228: fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
1229: }
1230: fprintf(ficrespow,"# Powell\n# iter -2*LL");
1231: for (i=1;i<=nlstate;i++)
1232: for(j=1;j<=nlstate+ndeath;j++)
1233: if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
1234: fprintf(ficrespow,"\n");
1.53 brouard 1235: powell(p,xi,npar,ftol,&iter,&fret,func);
1236:
1.76 brouard 1237: fclose(ficrespow);
1238: printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));
1.65 lievre 1239: fprintf(ficlog,"\n#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
1.53 brouard 1240: fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
1241:
1242: }
1243:
1244: /**** Computes Hessian and covariance matrix ***/
1245: void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
1246: {
1247: double **a,**y,*x,pd;
1248: double **hess;
1249: int i, j,jk;
1250: int *indx;
1251:
1252: double hessii(double p[], double delta, int theta, double delti[]);
1253: double hessij(double p[], double delti[], int i, int j);
1254: void lubksb(double **a, int npar, int *indx, double b[]) ;
1255: void ludcmp(double **a, int npar, int *indx, double *d) ;
1256:
1257: hess=matrix(1,npar,1,npar);
1258:
1259: printf("\nCalculation of the hessian matrix. Wait...\n");
1260: fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
1261: for (i=1;i<=npar;i++){
1262: printf("%d",i);fflush(stdout);
1263: fprintf(ficlog,"%d",i);fflush(ficlog);
1264: hess[i][i]=hessii(p,ftolhess,i,delti);
1265: /*printf(" %f ",p[i]);*/
1266: /*printf(" %lf ",hess[i][i]);*/
1267: }
1268:
1269: for (i=1;i<=npar;i++) {
1270: for (j=1;j<=npar;j++) {
1271: if (j>i) {
1272: printf(".%d%d",i,j);fflush(stdout);
1273: fprintf(ficlog,".%d%d",i,j);fflush(ficlog);
1274: hess[i][j]=hessij(p,delti,i,j);
1275: hess[j][i]=hess[i][j];
1276: /*printf(" %lf ",hess[i][j]);*/
1277: }
1278: }
1279: }
1280: printf("\n");
1281: fprintf(ficlog,"\n");
1282:
1283: printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
1284: fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
1285:
1286: a=matrix(1,npar,1,npar);
1287: y=matrix(1,npar,1,npar);
1288: x=vector(1,npar);
1289: indx=ivector(1,npar);
1290: for (i=1;i<=npar;i++)
1291: for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
1292: ludcmp(a,npar,indx,&pd);
1293:
1294: for (j=1;j<=npar;j++) {
1295: for (i=1;i<=npar;i++) x[i]=0;
1296: x[j]=1;
1297: lubksb(a,npar,indx,x);
1298: for (i=1;i<=npar;i++){
1299: matcov[i][j]=x[i];
1300: }
1301: }
1302:
1303: printf("\n#Hessian matrix#\n");
1304: fprintf(ficlog,"\n#Hessian matrix#\n");
1305: for (i=1;i<=npar;i++) {
1306: for (j=1;j<=npar;j++) {
1307: printf("%.3e ",hess[i][j]);
1308: fprintf(ficlog,"%.3e ",hess[i][j]);
1309: }
1310: printf("\n");
1311: fprintf(ficlog,"\n");
1312: }
1313:
1314: /* Recompute Inverse */
1315: for (i=1;i<=npar;i++)
1316: for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];
1317: ludcmp(a,npar,indx,&pd);
1318:
1319: /* printf("\n#Hessian matrix recomputed#\n");
1320:
1321: for (j=1;j<=npar;j++) {
1322: for (i=1;i<=npar;i++) x[i]=0;
1323: x[j]=1;
1324: lubksb(a,npar,indx,x);
1325: for (i=1;i<=npar;i++){
1326: y[i][j]=x[i];
1327: printf("%.3e ",y[i][j]);
1328: fprintf(ficlog,"%.3e ",y[i][j]);
1329: }
1330: printf("\n");
1331: fprintf(ficlog,"\n");
1332: }
1333: */
1334:
1335: free_matrix(a,1,npar,1,npar);
1336: free_matrix(y,1,npar,1,npar);
1337: free_vector(x,1,npar);
1338: free_ivector(indx,1,npar);
1339: free_matrix(hess,1,npar,1,npar);
1340:
1341:
1342: }
1343:
1344: /*************** hessian matrix ****************/
1345: double hessii( double x[], double delta, int theta, double delti[])
1346: {
1347: int i;
1348: int l=1, lmax=20;
1349: double k1,k2;
1350: double p2[NPARMAX+1];
1351: double res;
1352: double delt, delts, nkhi=10.,nkhif=1., khi=1.e-4;
1353: double fx;
1354: int k=0,kmax=10;
1355: double l1;
1356:
1357: fx=func(x);
1358: for (i=1;i<=npar;i++) p2[i]=x[i];
1359: for(l=0 ; l <=lmax; l++){
1360: l1=pow(10,l);
1361: delts=delt;
1362: for(k=1 ; k <kmax; k=k+1){
1363: delt = delta*(l1*k);
1364: p2[theta]=x[theta] +delt;
1365: k1=func(p2)-fx;
1366: p2[theta]=x[theta]-delt;
1367: k2=func(p2)-fx;
1368: /*res= (k1-2.0*fx+k2)/delt/delt; */
1369: res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */
1370:
1371: #ifdef DEBUG
1372: 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);
1373: 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);
1374: #endif
1375: /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
1376: if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
1377: k=kmax;
1378: }
1379: else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
1380: k=kmax; l=lmax*10.;
1381: }
1382: else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){
1383: delts=delt;
1384: }
1385: }
1386: }
1387: delti[theta]=delts;
1388: return res;
1389:
1390: }
1391:
1392: double hessij( double x[], double delti[], int thetai,int thetaj)
1393: {
1394: int i;
1395: int l=1, l1, lmax=20;
1396: double k1,k2,k3,k4,res,fx;
1397: double p2[NPARMAX+1];
1398: int k;
1399:
1400: fx=func(x);
1401: for (k=1; k<=2; k++) {
1402: for (i=1;i<=npar;i++) p2[i]=x[i];
1403: p2[thetai]=x[thetai]+delti[thetai]/k;
1404: p2[thetaj]=x[thetaj]+delti[thetaj]/k;
1405: k1=func(p2)-fx;
1406:
1407: p2[thetai]=x[thetai]+delti[thetai]/k;
1408: p2[thetaj]=x[thetaj]-delti[thetaj]/k;
1409: k2=func(p2)-fx;
1410:
1411: p2[thetai]=x[thetai]-delti[thetai]/k;
1412: p2[thetaj]=x[thetaj]+delti[thetaj]/k;
1413: k3=func(p2)-fx;
1414:
1415: p2[thetai]=x[thetai]-delti[thetai]/k;
1416: p2[thetaj]=x[thetaj]-delti[thetaj]/k;
1417: k4=func(p2)-fx;
1418: res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */
1419: #ifdef DEBUG
1420: 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);
1421: 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);
1422: #endif
1423: }
1424: return res;
1425: }
1426:
1427: /************** Inverse of matrix **************/
1428: void ludcmp(double **a, int n, int *indx, double *d)
1429: {
1430: int i,imax,j,k;
1431: double big,dum,sum,temp;
1432: double *vv;
1433:
1434: vv=vector(1,n);
1435: *d=1.0;
1436: for (i=1;i<=n;i++) {
1437: big=0.0;
1438: for (j=1;j<=n;j++)
1439: if ((temp=fabs(a[i][j])) > big) big=temp;
1440: if (big == 0.0) nrerror("Singular matrix in routine ludcmp");
1441: vv[i]=1.0/big;
1442: }
1443: for (j=1;j<=n;j++) {
1444: for (i=1;i<j;i++) {
1445: sum=a[i][j];
1446: for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];
1447: a[i][j]=sum;
1448: }
1449: big=0.0;
1450: for (i=j;i<=n;i++) {
1451: sum=a[i][j];
1452: for (k=1;k<j;k++)
1453: sum -= a[i][k]*a[k][j];
1454: a[i][j]=sum;
1455: if ( (dum=vv[i]*fabs(sum)) >= big) {
1456: big=dum;
1457: imax=i;
1458: }
1459: }
1460: if (j != imax) {
1461: for (k=1;k<=n;k++) {
1462: dum=a[imax][k];
1463: a[imax][k]=a[j][k];
1464: a[j][k]=dum;
1465: }
1466: *d = -(*d);
1467: vv[imax]=vv[j];
1468: }
1469: indx[j]=imax;
1470: if (a[j][j] == 0.0) a[j][j]=TINY;
1471: if (j != n) {
1472: dum=1.0/(a[j][j]);
1473: for (i=j+1;i<=n;i++) a[i][j] *= dum;
1474: }
1475: }
1476: free_vector(vv,1,n); /* Doesn't work */
1477: ;
1478: }
1479:
1480: void lubksb(double **a, int n, int *indx, double b[])
1481: {
1482: int i,ii=0,ip,j;
1483: double sum;
1484:
1485: for (i=1;i<=n;i++) {
1486: ip=indx[i];
1487: sum=b[ip];
1488: b[ip]=b[i];
1489: if (ii)
1490: for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];
1491: else if (sum) ii=i;
1492: b[i]=sum;
1493: }
1494: for (i=n;i>=1;i--) {
1495: sum=b[i];
1496: for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];
1497: b[i]=sum/a[i][i];
1498: }
1499: }
1500:
1501: /************ Frequencies ********************/
1.74 brouard 1502: 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 1503: { /* Some frequencies */
1504:
1505: int i, m, jk, k1,i1, j1, bool, z1,z2,j;
1506: int first;
1507: double ***freq; /* Frequencies */
1.73 lievre 1508: double *pp, **prop;
1509: double pos,posprop, k2, dateintsum=0,k2cpt=0;
1.53 brouard 1510: FILE *ficresp;
1511: char fileresp[FILENAMELENGTH];
1512:
1513: pp=vector(1,nlstate);
1.74 brouard 1514: prop=matrix(1,nlstate,iagemin,iagemax+3);
1.53 brouard 1515: strcpy(fileresp,"p");
1516: strcat(fileresp,fileres);
1517: if((ficresp=fopen(fileresp,"w"))==NULL) {
1518: printf("Problem with prevalence resultfile: %s\n", fileresp);
1519: fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
1520: exit(0);
1521: }
1.74 brouard 1522: freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);
1.53 brouard 1523: j1=0;
1524:
1525: j=cptcoveff;
1526: if (cptcovn<1) {j=1;ncodemax[1]=1;}
1527:
1528: first=1;
1529:
1530: for(k1=1; k1<=j;k1++){
1531: for(i1=1; i1<=ncodemax[k1];i1++){
1532: j1++;
1533: /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
1534: scanf("%d", i);*/
1535: for (i=-1; i<=nlstate+ndeath; i++)
1536: for (jk=-1; jk<=nlstate+ndeath; jk++)
1.74 brouard 1537: for(m=iagemin; m <= iagemax+3; m++)
1.53 brouard 1538: freq[i][jk][m]=0;
1.73 lievre 1539:
1540: for (i=1; i<=nlstate; i++)
1.74 brouard 1541: for(m=iagemin; m <= iagemax+3; m++)
1.73 lievre 1542: prop[i][m]=0;
1.53 brouard 1543:
1544: dateintsum=0;
1545: k2cpt=0;
1546: for (i=1; i<=imx; i++) {
1547: bool=1;
1548: if (cptcovn>0) {
1549: for (z1=1; z1<=cptcoveff; z1++)
1550: if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])
1551: bool=0;
1552: }
1.58 lievre 1553: if (bool==1){
1.53 brouard 1554: for(m=firstpass; m<=lastpass; m++){
1555: k2=anint[m][i]+(mint[m][i]/12.);
1556: if ((k2>=dateprev1) && (k2<=dateprev2)) {
1.74 brouard 1557: if(agev[m][i]==0) agev[m][i]=iagemax+1;
1558: if(agev[m][i]==1) agev[m][i]=iagemax+2;
1.73 lievre 1559: if (s[m][i]>0 && s[m][i]<=nlstate) prop[s[m][i]][(int)agev[m][i]] += weight[i];
1.53 brouard 1560: if (m<lastpass) {
1561: freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
1.74 brouard 1562: freq[s[m][i]][s[m+1][i]][iagemax+3] += weight[i];
1.53 brouard 1563: }
1564:
1.74 brouard 1565: if ((agev[m][i]>1) && (agev[m][i]< (iagemax+3))) {
1.53 brouard 1566: dateintsum=dateintsum+k2;
1567: k2cpt++;
1568: }
1569: }
1570: }
1571: }
1572: }
1573:
1574: fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);
1575:
1576: if (cptcovn>0) {
1577: fprintf(ficresp, "\n#********** Variable ");
1578: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
1579: fprintf(ficresp, "**********\n#");
1580: }
1581: for(i=1; i<=nlstate;i++)
1582: fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
1583: fprintf(ficresp, "\n");
1584:
1.74 brouard 1585: for(i=iagemin; i <= iagemax+3; i++){
1586: if(i==iagemax+3){
1.53 brouard 1587: fprintf(ficlog,"Total");
1588: }else{
1589: if(first==1){
1590: first=0;
1591: printf("See log file for details...\n");
1592: }
1593: fprintf(ficlog,"Age %d", i);
1594: }
1595: for(jk=1; jk <=nlstate ; jk++){
1596: for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
1597: pp[jk] += freq[jk][m][i];
1598: }
1599: for(jk=1; jk <=nlstate ; jk++){
1600: for(m=-1, pos=0; m <=0 ; m++)
1601: pos += freq[jk][m][i];
1602: if(pp[jk]>=1.e-10){
1603: if(first==1){
1604: printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
1605: }
1606: fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
1607: }else{
1608: if(first==1)
1609: printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
1610: fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
1611: }
1612: }
1613:
1614: for(jk=1; jk <=nlstate ; jk++){
1615: for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
1616: pp[jk] += freq[jk][m][i];
1.73 lievre 1617: }
1618: for(jk=1,pos=0,posprop=0; jk <=nlstate ; jk++){
1619: pos += pp[jk];
1620: posprop += prop[jk][i];
1.53 brouard 1621: }
1622: for(jk=1; jk <=nlstate ; jk++){
1623: if(pos>=1.e-5){
1624: if(first==1)
1625: printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
1626: fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
1627: }else{
1628: if(first==1)
1629: printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
1630: fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
1631: }
1.74 brouard 1632: if( i <= iagemax){
1.53 brouard 1633: if(pos>=1.e-5){
1.73 lievre 1634: fprintf(ficresp," %d %.5f %.0f %.0f",i,prop[jk][i]/posprop, prop[jk][i],posprop);
1.53 brouard 1635: probs[i][jk][j1]= pp[jk]/pos;
1636: /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/
1637: }
1638: else
1.73 lievre 1639: fprintf(ficresp," %d NaNq %.0f %.0f",i,prop[jk][i],posprop);
1.53 brouard 1640: }
1641: }
1642:
1.69 brouard 1643: for(jk=-1; jk <=nlstate+ndeath; jk++)
1644: for(m=-1; m <=nlstate+ndeath; m++)
1.53 brouard 1645: if(freq[jk][m][i] !=0 ) {
1646: if(first==1)
1647: printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
1648: fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
1649: }
1.74 brouard 1650: if(i <= iagemax)
1.53 brouard 1651: fprintf(ficresp,"\n");
1652: if(first==1)
1653: printf("Others in log...\n");
1654: fprintf(ficlog,"\n");
1655: }
1656: }
1657: }
1658: dateintmean=dateintsum/k2cpt;
1659:
1660: fclose(ficresp);
1.74 brouard 1661: free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);
1.53 brouard 1662: free_vector(pp,1,nlstate);
1.74 brouard 1663: free_matrix(prop,1,nlstate,iagemin, iagemax+3);
1.53 brouard 1664: /* End of Freq */
1665: }
1666:
1667: /************ Prevalence ********************/
1.74 brouard 1668: 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 1669: {
1670: /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
1671: in each health status at the date of interview (if between dateprev1 and dateprev2).
1672: We still use firstpass and lastpass as another selection.
1673: */
1.53 brouard 1674:
1675: int i, m, jk, k1, i1, j1, bool, z1,z2,j;
1676: double ***freq; /* Frequencies */
1.73 lievre 1677: double *pp, **prop;
1678: double pos,posprop;
1.69 brouard 1679: double y2; /* in fractional years */
1.74 brouard 1680: int iagemin, iagemax;
1.53 brouard 1681:
1.74 brouard 1682: iagemin= (int) agemin;
1683: iagemax= (int) agemax;
1684: /*pp=vector(1,nlstate);*/
1685: prop=matrix(1,nlstate,iagemin,iagemax+3);
1686: /* freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
1.53 brouard 1687: j1=0;
1688:
1689: j=cptcoveff;
1690: if (cptcovn<1) {j=1;ncodemax[1]=1;}
1691:
1692: for(k1=1; k1<=j;k1++){
1693: for(i1=1; i1<=ncodemax[k1];i1++){
1694: j1++;
1695:
1.73 lievre 1696: for (i=1; i<=nlstate; i++)
1.74 brouard 1697: for(m=iagemin; m <= iagemax+3; m++)
1698: prop[i][m]=0.0;
1.53 brouard 1699:
1.69 brouard 1700: for (i=1; i<=imx; i++) { /* Each individual */
1.53 brouard 1701: bool=1;
1702: if (cptcovn>0) {
1703: for (z1=1; z1<=cptcoveff; z1++)
1704: if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])
1705: bool=0;
1706: }
1707: if (bool==1) {
1.69 brouard 1708: for(m=firstpass; m<=lastpass; m++){/* Other selection (we can limit to certain interviews*/
1709: y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
1710: if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
1.74 brouard 1711: if(agev[m][i]==0) agev[m][i]=iagemax+1;
1712: if(agev[m][i]==1) agev[m][i]=iagemax+2;
1713: 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);
1714: if (s[m][i]>0 && s[m][i]<=nlstate) {
1715: /*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]]);*/
1716: prop[s[m][i]][(int)agev[m][i]] += weight[i];
1717: prop[s[m][i]][iagemax+3] += weight[i];
1718: }
1.53 brouard 1719: }
1.69 brouard 1720: } /* end selection of waves */
1.53 brouard 1721: }
1722: }
1.74 brouard 1723: for(i=iagemin; i <= iagemax+3; i++){
1.53 brouard 1724:
1.74 brouard 1725: for(jk=1,posprop=0; jk <=nlstate ; jk++) {
1726: posprop += prop[jk][i];
1727: }
1728:
1729: for(jk=1; jk <=nlstate ; jk++){
1730: if( i <= iagemax){
1731: if(posprop>=1.e-5){
1732: probs[i][jk][j1]= prop[jk][i]/posprop;
1733: }
1734: }
1735: }/* end jk */
1736: }/* end i */
1.53 brouard 1737: } /* end i1 */
1738: } /* end k1 */
1739:
1.74 brouard 1740: /* free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
1741: /*free_vector(pp,1,nlstate);*/
1742: free_matrix(prop,1,nlstate, iagemin,iagemax+3);
1743: } /* End of prevalence */
1.53 brouard 1744:
1745: /************* Waves Concatenation ***************/
1746:
1.59 brouard 1747: 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 1748: {
1749: /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
1750: Death is a valid wave (if date is known).
1751: mw[mi][i] is the mi (mi=1 to wav[i]) effective wave of individual i
1.59 brouard 1752: dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
1.53 brouard 1753: and mw[mi+1][i]. dh depends on stepm.
1754: */
1755:
1756: int i, mi, m;
1757: /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
1758: double sum=0., jmean=0.;*/
1759: int first;
1760: int j, k=0,jk, ju, jl;
1761: double sum=0.;
1762: first=0;
1763: jmin=1e+5;
1764: jmax=-1;
1765: jmean=0.;
1766: for(i=1; i<=imx; i++){
1767: mi=0;
1768: m=firstpass;
1769: while(s[m][i] <= nlstate){
1.69 brouard 1770: if(s[m][i]>=1)
1.53 brouard 1771: mw[++mi][i]=m;
1772: if(m >=lastpass)
1773: break;
1774: else
1775: m++;
1776: }/* end while */
1777: if (s[m][i] > nlstate){
1778: mi++; /* Death is another wave */
1779: /* if(mi==0) never been interviewed correctly before death */
1780: /* Only death is a correct wave */
1781: mw[mi][i]=m;
1782: }
1783:
1784: wav[i]=mi;
1785: if(mi==0){
1786: if(first==0){
1.77 brouard 1787: printf("Warning! None valid information for:%d line=%d (skipped) and may be others, see log file\n",num[i],i);
1.53 brouard 1788: first=1;
1789: }
1790: if(first==1){
1.77 brouard 1791: fprintf(ficlog,"Warning! None valid information for:%d line=%d (skipped)\n",num[i],i);
1.53 brouard 1792: }
1793: } /* end mi==0 */
1.77 brouard 1794: } /* End individuals */
1.53 brouard 1795:
1796: for(i=1; i<=imx; i++){
1797: for(mi=1; mi<wav[i];mi++){
1798: if (stepm <=0)
1799: dh[mi][i]=1;
1800: else{
1.77 brouard 1801: if (s[mw[mi+1][i]][i] > nlstate) { /* A death */
1.53 brouard 1802: if (agedc[i] < 2*AGESUP) {
1803: j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);
1804: if(j==0) j=1; /* Survives at least one month after exam */
1805: k=k+1;
1806: if (j >= jmax) jmax=j;
1807: if (j <= jmin) jmin=j;
1808: sum=sum+j;
1.77 brouard 1809: /*if (j<0) printf("j=%d num=%d \n",j,i);*/
1.68 lievre 1810: /* printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
1.78 brouard 1811: 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 1812: }
1813: }
1814: else{
1815: j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
1.68 lievre 1816: /* printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
1.53 brouard 1817: k=k+1;
1818: if (j >= jmax) jmax=j;
1819: else if (j <= jmin)jmin=j;
1820: /* if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
1.73 lievre 1821: /*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 1822: 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 1823: sum=sum+j;
1824: }
1825: jk= j/stepm;
1826: jl= j -jk*stepm;
1827: ju= j -(jk+1)*stepm;
1.64 lievre 1828: if(mle <=1){
1829: if(jl==0){
1830: dh[mi][i]=jk;
1831: bh[mi][i]=0;
1832: }else{ /* We want a negative bias in order to only have interpolation ie
1833: * at the price of an extra matrix product in likelihood */
1834: dh[mi][i]=jk+1;
1835: bh[mi][i]=ju;
1836: }
1837: }else{
1838: if(jl <= -ju){
1839: dh[mi][i]=jk;
1840: bh[mi][i]=jl; /* bias is positive if real duration
1841: * is higher than the multiple of stepm and negative otherwise.
1842: */
1843: }
1844: else{
1845: dh[mi][i]=jk+1;
1846: bh[mi][i]=ju;
1847: }
1848: if(dh[mi][i]==0){
1849: dh[mi][i]=1; /* At least one step */
1850: bh[mi][i]=ju; /* At least one step */
1.71 brouard 1851: /* 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 1852: }
1.59 brouard 1853: }
1.64 lievre 1854: } /* end if mle */
1855: } /* end wave */
1.53 brouard 1856: }
1857: jmean=sum/k;
1858: printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);
1859: fprintf(ficlog,"Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);
1860: }
1861:
1862: /*********** Tricode ****************************/
1863: void tricode(int *Tvar, int **nbcode, int imx)
1864: {
1.58 lievre 1865:
1866: int Ndum[20],ij=1, k, j, i, maxncov=19;
1.53 brouard 1867: int cptcode=0;
1868: cptcoveff=0;
1869:
1.58 lievre 1870: for (k=0; k<maxncov; k++) Ndum[k]=0;
1.53 brouard 1871: for (k=1; k<=7; k++) ncodemax[k]=0;
1872:
1873: for (j=1; j<=(cptcovn+2*cptcovprod); j++) {
1.58 lievre 1874: for (i=1; i<=imx; i++) { /*reads the data file to get the maximum
1875: modality*/
1876: ij=(int)(covar[Tvar[j]][i]); /* ij is the modality of this individual*/
1877: Ndum[ij]++; /*store the modality */
1.53 brouard 1878: /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
1.58 lievre 1879: if (ij > cptcode) cptcode=ij; /* getting the maximum of covariable
1880: Tvar[j]. If V=sex and male is 0 and
1881: female is 1, then cptcode=1.*/
1.53 brouard 1882: }
1883:
1884: for (i=0; i<=cptcode; i++) {
1.58 lievre 1885: 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 1886: }
1.58 lievre 1887:
1.53 brouard 1888: ij=1;
1889: for (i=1; i<=ncodemax[j]; i++) {
1.58 lievre 1890: for (k=0; k<= maxncov; k++) {
1.53 brouard 1891: if (Ndum[k] != 0) {
1892: nbcode[Tvar[j]][ij]=k;
1.58 lievre 1893: /* 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 1894:
1895: ij++;
1896: }
1897: if (ij > ncodemax[j]) break;
1898: }
1899: }
1900: }
1901:
1.58 lievre 1902: for (k=0; k< maxncov; k++) Ndum[k]=0;
1.53 brouard 1903:
1.58 lievre 1904: for (i=1; i<=ncovmodel-2; i++) {
1905: /* 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 1906: ij=Tvar[i];
1.58 lievre 1907: Ndum[ij]++;
1.53 brouard 1908: }
1909:
1910: ij=1;
1.58 lievre 1911: for (i=1; i<= maxncov; i++) {
1.53 brouard 1912: if((Ndum[i]!=0) && (i<=ncovcol)){
1.58 lievre 1913: Tvaraff[ij]=i; /*For printing */
1.53 brouard 1914: ij++;
1915: }
1916: }
1917:
1.58 lievre 1918: cptcoveff=ij-1; /*Number of simple covariates*/
1.53 brouard 1919: }
1920:
1921: /*********** Health Expectancies ****************/
1922:
1923: 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 )
1924:
1925: {
1926: /* Health expectancies */
1927: int i, j, nhstepm, hstepm, h, nstepm, k, cptj;
1928: double age, agelim, hf;
1929: double ***p3mat,***varhe;
1930: double **dnewm,**doldm;
1931: double *xp;
1932: double **gp, **gm;
1933: double ***gradg, ***trgradg;
1934: int theta;
1935:
1.74 brouard 1936: varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage);
1.53 brouard 1937: xp=vector(1,npar);
1.74 brouard 1938: dnewm=matrix(1,nlstate*nlstate,1,npar);
1939: doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate);
1.53 brouard 1940:
1941: fprintf(ficreseij,"# Health expectancies\n");
1942: fprintf(ficreseij,"# Age");
1943: for(i=1; i<=nlstate;i++)
1944: for(j=1; j<=nlstate;j++)
1945: fprintf(ficreseij," %1d-%1d (SE)",i,j);
1946: fprintf(ficreseij,"\n");
1947:
1948: if(estepm < stepm){
1949: printf ("Problem %d lower than %d\n",estepm, stepm);
1950: }
1951: else hstepm=estepm;
1952: /* We compute the life expectancy from trapezoids spaced every estepm months
1953: * This is mainly to measure the difference between two models: for example
1954: * if stepm=24 months pijx are given only every 2 years and by summing them
1955: * we are calculating an estimate of the Life Expectancy assuming a linear
1.66 brouard 1956: * progression in between and thus overestimating or underestimating according
1.53 brouard 1957: * to the curvature of the survival function. If, for the same date, we
1958: * estimate the model with stepm=1 month, we can keep estepm to 24 months
1959: * to compare the new estimate of Life expectancy with the same linear
1960: * hypothesis. A more precise result, taking into account a more precise
1961: * curvature will be obtained if estepm is as small as stepm. */
1962:
1963: /* For example we decided to compute the life expectancy with the smallest unit */
1964: /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
1965: nhstepm is the number of hstepm from age to agelim
1966: nstepm is the number of stepm from age to agelin.
1967: Look at hpijx to understand the reason of that which relies in memory size
1968: and note for a fixed period like estepm months */
1969: /* We decided (b) to get a life expectancy respecting the most precise curvature of the
1970: survival function given by stepm (the optimization length). Unfortunately it
1971: means that if the survival funtion is printed only each two years of age and if
1972: you sum them up and add 1 year (area under the trapezoids) you won't get the same
1973: results. So we changed our mind and took the option of the best precision.
1974: */
1975: hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
1976:
1977: agelim=AGESUP;
1978: for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
1979: /* nhstepm age range expressed in number of stepm */
1980: nstepm=(int) rint((agelim-age)*YEARM/stepm);
1981: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
1982: /* if (stepm >= YEARM) hstepm=1;*/
1983: nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
1984: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
1.74 brouard 1985: gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);
1986: gp=matrix(0,nhstepm,1,nlstate*nlstate);
1987: gm=matrix(0,nhstepm,1,nlstate*nlstate);
1.53 brouard 1988:
1989: /* Computed by stepm unit matrices, product of hstepm matrices, stored
1990: in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
1991: hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);
1992:
1993:
1994: hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
1995:
1996: /* Computing Variances of health expectancies */
1997:
1998: for(theta=1; theta <=npar; theta++){
1999: for(i=1; i<=npar; i++){
2000: xp[i] = x[i] + (i==theta ?delti[theta]:0);
2001: }
2002: hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
2003:
2004: cptj=0;
2005: for(j=1; j<= nlstate; j++){
2006: for(i=1; i<=nlstate; i++){
2007: cptj=cptj+1;
2008: for(h=0, gp[h][cptj]=0.; h<=nhstepm-1; h++){
2009: gp[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;
2010: }
2011: }
2012: }
2013:
2014:
2015: for(i=1; i<=npar; i++)
2016: xp[i] = x[i] - (i==theta ?delti[theta]:0);
2017: hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
2018:
2019: cptj=0;
2020: for(j=1; j<= nlstate; j++){
2021: for(i=1;i<=nlstate;i++){
2022: cptj=cptj+1;
2023: for(h=0, gm[h][cptj]=0.; h<=nhstepm-1; h++){
1.77 brouard 2024:
1.53 brouard 2025: gm[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;
2026: }
2027: }
2028: }
1.74 brouard 2029: for(j=1; j<= nlstate*nlstate; j++)
1.53 brouard 2030: for(h=0; h<=nhstepm-1; h++){
2031: gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
2032: }
2033: }
2034:
2035: /* End theta */
2036:
1.74 brouard 2037: trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar);
1.53 brouard 2038:
2039: for(h=0; h<=nhstepm-1; h++)
1.74 brouard 2040: for(j=1; j<=nlstate*nlstate;j++)
1.53 brouard 2041: for(theta=1; theta <=npar; theta++)
2042: trgradg[h][j][theta]=gradg[h][theta][j];
2043:
2044:
1.74 brouard 2045: for(i=1;i<=nlstate*nlstate;i++)
2046: for(j=1;j<=nlstate*nlstate;j++)
1.53 brouard 2047: varhe[i][j][(int)age] =0.;
2048:
2049: printf("%d|",(int)age);fflush(stdout);
2050: fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
2051: for(h=0;h<=nhstepm-1;h++){
2052: for(k=0;k<=nhstepm-1;k++){
1.74 brouard 2053: matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov);
2054: matprod2(doldm,dnewm,1,nlstate*nlstate,1,npar,1,nlstate*nlstate,gradg[k]);
2055: for(i=1;i<=nlstate*nlstate;i++)
2056: for(j=1;j<=nlstate*nlstate;j++)
1.53 brouard 2057: varhe[i][j][(int)age] += doldm[i][j]*hf*hf;
2058: }
2059: }
2060: /* Computing expectancies */
2061: for(i=1; i<=nlstate;i++)
2062: for(j=1; j<=nlstate;j++)
2063: for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
2064: eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
2065:
2066: /* 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]);*/
2067:
2068: }
2069:
2070: fprintf(ficreseij,"%3.0f",age );
2071: cptj=0;
2072: for(i=1; i<=nlstate;i++)
2073: for(j=1; j<=nlstate;j++){
2074: cptj++;
2075: fprintf(ficreseij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[cptj][cptj][(int)age]) );
2076: }
2077: fprintf(ficreseij,"\n");
2078:
1.74 brouard 2079: free_matrix(gm,0,nhstepm,1,nlstate*nlstate);
2080: free_matrix(gp,0,nhstepm,1,nlstate*nlstate);
2081: free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*nlstate);
2082: free_ma3x(trgradg,0,nhstepm,1,nlstate*nlstate,1,npar);
1.53 brouard 2083: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
2084: }
2085: printf("\n");
2086: fprintf(ficlog,"\n");
2087:
2088: free_vector(xp,1,npar);
1.74 brouard 2089: free_matrix(dnewm,1,nlstate*nlstate,1,npar);
2090: free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate);
2091: free_ma3x(varhe,1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int)fage);
1.53 brouard 2092: }
2093:
2094: /************ Variance ******************/
2095: 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)
2096: {
2097: /* Variance of health expectancies */
2098: /* double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
2099: /* double **newm;*/
2100: double **dnewm,**doldm;
2101: double **dnewmp,**doldmp;
2102: int i, j, nhstepm, hstepm, h, nstepm ;
2103: int k, cptcode;
2104: double *xp;
2105: double **gp, **gm; /* for var eij */
2106: double ***gradg, ***trgradg; /*for var eij */
2107: double **gradgp, **trgradgp; /* for var p point j */
2108: double *gpp, *gmp; /* for var p point j */
2109: double **varppt; /* for var p point j nlstate to nlstate+ndeath */
2110: double ***p3mat;
2111: double age,agelim, hf;
2112: double ***mobaverage;
2113: int theta;
2114: char digit[4];
1.55 lievre 2115: char digitp[25];
1.53 brouard 2116:
2117: char fileresprobmorprev[FILENAMELENGTH];
2118:
1.55 lievre 2119: if(popbased==1){
1.58 lievre 2120: if(mobilav!=0)
1.55 lievre 2121: strcpy(digitp,"-populbased-mobilav-");
2122: else strcpy(digitp,"-populbased-nomobil-");
2123: }
2124: else
1.53 brouard 2125: strcpy(digitp,"-stablbased-");
1.56 lievre 2126:
1.54 brouard 2127: if (mobilav!=0) {
1.53 brouard 2128: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
1.54 brouard 2129: if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
2130: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
2131: printf(" Error in movingaverage mobilav=%d\n",mobilav);
2132: }
1.53 brouard 2133: }
2134:
2135: strcpy(fileresprobmorprev,"prmorprev");
2136: sprintf(digit,"%-d",ij);
2137: /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
2138: strcat(fileresprobmorprev,digit); /* Tvar to be done */
2139: strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
2140: strcat(fileresprobmorprev,fileres);
2141: if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
2142: printf("Problem with resultfile: %s\n", fileresprobmorprev);
2143: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
2144: }
2145: printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
2146: fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
1.66 brouard 2147: 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 2148: fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
2149: for(j=nlstate+1; j<=(nlstate+ndeath);j++){
2150: fprintf(ficresprobmorprev," p.%-d SE",j);
2151: for(i=1; i<=nlstate;i++)
2152: fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
2153: }
2154: fprintf(ficresprobmorprev,"\n");
2155: if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {
2156: printf("Problem with gnuplot file: %s\n", optionfilegnuplot);
2157: fprintf(ficlog,"Problem with gnuplot file: %s\n", optionfilegnuplot);
2158: exit(0);
2159: }
2160: else{
2161: fprintf(ficgp,"\n# Routine varevsij");
2162: }
2163: if((fichtm=fopen(optionfilehtm,"a"))==NULL) {
2164: printf("Problem with html file: %s\n", optionfilehtm);
2165: fprintf(ficlog,"Problem with html file: %s\n", optionfilehtm);
2166: exit(0);
2167: }
2168: else{
1.67 brouard 2169: 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");
2170: fprintf(fichtm,"\n<br>%s <br>\n",digitp);
1.53 brouard 2171: }
2172: varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
2173:
2174: 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");
2175: fprintf(ficresvij,"# Age");
2176: for(i=1; i<=nlstate;i++)
2177: for(j=1; j<=nlstate;j++)
2178: fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);
2179: fprintf(ficresvij,"\n");
2180:
2181: xp=vector(1,npar);
2182: dnewm=matrix(1,nlstate,1,npar);
2183: doldm=matrix(1,nlstate,1,nlstate);
2184: dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
2185: doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
2186:
2187: gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
2188: gpp=vector(nlstate+1,nlstate+ndeath);
2189: gmp=vector(nlstate+1,nlstate+ndeath);
2190: trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
2191:
2192: if(estepm < stepm){
2193: printf ("Problem %d lower than %d\n",estepm, stepm);
2194: }
2195: else hstepm=estepm;
2196: /* For example we decided to compute the life expectancy with the smallest unit */
2197: /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
2198: nhstepm is the number of hstepm from age to agelim
2199: nstepm is the number of stepm from age to agelin.
2200: Look at hpijx to understand the reason of that which relies in memory size
2201: and note for a fixed period like k years */
2202: /* We decided (b) to get a life expectancy respecting the most precise curvature of the
2203: survival function given by stepm (the optimization length). Unfortunately it
1.66 brouard 2204: means that if the survival funtion is printed every two years of age and if
1.53 brouard 2205: you sum them up and add 1 year (area under the trapezoids) you won't get the same
2206: results. So we changed our mind and took the option of the best precision.
2207: */
2208: hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
2209: agelim = AGESUP;
2210: for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
2211: nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
2212: nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
2213: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
2214: gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
2215: gp=matrix(0,nhstepm,1,nlstate);
2216: gm=matrix(0,nhstepm,1,nlstate);
2217:
2218:
2219: for(theta=1; theta <=npar; theta++){
1.66 brouard 2220: for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
1.53 brouard 2221: xp[i] = x[i] + (i==theta ?delti[theta]:0);
2222: }
2223: hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
2224: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
2225:
2226: if (popbased==1) {
1.54 brouard 2227: if(mobilav ==0){
1.53 brouard 2228: for(i=1; i<=nlstate;i++)
2229: prlim[i][i]=probs[(int)age][i][ij];
1.54 brouard 2230: }else{ /* mobilav */
1.53 brouard 2231: for(i=1; i<=nlstate;i++)
2232: prlim[i][i]=mobaverage[(int)age][i][ij];
2233: }
2234: }
2235:
2236: for(j=1; j<= nlstate; j++){
2237: for(h=0; h<=nhstepm; h++){
2238: for(i=1, gp[h][j]=0.;i<=nlstate;i++)
2239: gp[h][j] += prlim[i][i]*p3mat[i][j][h];
2240: }
2241: }
1.66 brouard 2242: /* This for computing probability of death (h=1 means
2243: computed over hstepm matrices product = hstepm*stepm months)
2244: as a weighted average of prlim.
2245: */
1.69 brouard 2246: for(j=nlstate+1;j<=nlstate+ndeath;j++){
1.68 lievre 2247: for(i=1,gpp[j]=0.; i<= nlstate; i++)
1.53 brouard 2248: gpp[j] += prlim[i][i]*p3mat[i][j][1];
2249: }
1.66 brouard 2250: /* end probability of death */
1.53 brouard 2251:
1.66 brouard 2252: for(i=1; i<=npar; i++) /* Computes gradient x - delta */
1.53 brouard 2253: xp[i] = x[i] - (i==theta ?delti[theta]:0);
2254: hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
2255: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
2256:
2257: if (popbased==1) {
1.54 brouard 2258: if(mobilav ==0){
1.53 brouard 2259: for(i=1; i<=nlstate;i++)
2260: prlim[i][i]=probs[(int)age][i][ij];
1.54 brouard 2261: }else{ /* mobilav */
1.53 brouard 2262: for(i=1; i<=nlstate;i++)
2263: prlim[i][i]=mobaverage[(int)age][i][ij];
2264: }
2265: }
2266:
2267: for(j=1; j<= nlstate; j++){
2268: for(h=0; h<=nhstepm; h++){
2269: for(i=1, gm[h][j]=0.;i<=nlstate;i++)
2270: gm[h][j] += prlim[i][i]*p3mat[i][j][h];
2271: }
2272: }
1.66 brouard 2273: /* This for computing probability of death (h=1 means
2274: computed over hstepm matrices product = hstepm*stepm months)
2275: as a weighted average of prlim.
2276: */
1.69 brouard 2277: for(j=nlstate+1;j<=nlstate+ndeath;j++){
1.68 lievre 2278: for(i=1,gmp[j]=0.; i<= nlstate; i++)
2279: gmp[j] += prlim[i][i]*p3mat[i][j][1];
1.53 brouard 2280: }
1.66 brouard 2281: /* end probability of death */
1.53 brouard 2282:
2283: for(j=1; j<= nlstate; j++) /* vareij */
2284: for(h=0; h<=nhstepm; h++){
2285: gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
2286: }
1.68 lievre 2287:
1.53 brouard 2288: for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
2289: gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
2290: }
2291:
2292: } /* End theta */
2293:
2294: trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
2295:
2296: for(h=0; h<=nhstepm; h++) /* veij */
2297: for(j=1; j<=nlstate;j++)
2298: for(theta=1; theta <=npar; theta++)
2299: trgradg[h][j][theta]=gradg[h][theta][j];
2300:
2301: for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
1.69 brouard 2302: for(theta=1; theta <=npar; theta++)
1.53 brouard 2303: trgradgp[j][theta]=gradgp[theta][j];
1.69 brouard 2304:
1.53 brouard 2305:
2306: hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
2307: for(i=1;i<=nlstate;i++)
2308: for(j=1;j<=nlstate;j++)
2309: vareij[i][j][(int)age] =0.;
2310:
2311: for(h=0;h<=nhstepm;h++){
2312: for(k=0;k<=nhstepm;k++){
2313: matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
2314: matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
2315: for(i=1;i<=nlstate;i++)
2316: for(j=1;j<=nlstate;j++)
2317: vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
2318: }
2319: }
1.70 brouard 2320:
1.53 brouard 2321: /* pptj */
2322: matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
2323: matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
1.70 brouard 2324: for(j=nlstate+1;j<=nlstate+ndeath;j++)
2325: for(i=nlstate+1;i<=nlstate+ndeath;i++)
1.53 brouard 2326: varppt[j][i]=doldmp[j][i];
2327: /* end ppptj */
1.66 brouard 2328: /* x centered again */
1.53 brouard 2329: hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);
2330: prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);
2331:
2332: if (popbased==1) {
1.54 brouard 2333: if(mobilav ==0){
1.53 brouard 2334: for(i=1; i<=nlstate;i++)
2335: prlim[i][i]=probs[(int)age][i][ij];
1.54 brouard 2336: }else{ /* mobilav */
1.53 brouard 2337: for(i=1; i<=nlstate;i++)
2338: prlim[i][i]=mobaverage[(int)age][i][ij];
2339: }
2340: }
1.70 brouard 2341:
1.66 brouard 2342: /* This for computing probability of death (h=1 means
2343: computed over hstepm (estepm) matrices product = hstepm*stepm months)
2344: as a weighted average of prlim.
2345: */
1.68 lievre 2346: for(j=nlstate+1;j<=nlstate+ndeath;j++){
2347: for(i=1,gmp[j]=0.;i<= nlstate; i++)
1.53 brouard 2348: gmp[j] += prlim[i][i]*p3mat[i][j][1];
2349: }
1.66 brouard 2350: /* end probability of death */
1.53 brouard 2351:
2352: fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
2353: for(j=nlstate+1; j<=(nlstate+ndeath);j++){
2354: fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
2355: for(i=1; i<=nlstate;i++){
2356: fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
2357: }
2358: }
2359: fprintf(ficresprobmorprev,"\n");
2360:
2361: fprintf(ficresvij,"%.0f ",age );
2362: for(i=1; i<=nlstate;i++)
2363: for(j=1; j<=nlstate;j++){
2364: fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
2365: }
2366: fprintf(ficresvij,"\n");
2367: free_matrix(gp,0,nhstepm,1,nlstate);
2368: free_matrix(gm,0,nhstepm,1,nlstate);
2369: free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
2370: free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
2371: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
2372: } /* End age */
2373: free_vector(gpp,nlstate+1,nlstate+ndeath);
2374: free_vector(gmp,nlstate+1,nlstate+ndeath);
2375: free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
2376: free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
2377: fprintf(ficgp,"\nset noparametric;set nolabel; set ter png small;set size 0.65, 0.65");
2378: /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */
2379: fprintf(ficgp,"\n set log y; set nolog x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
1.67 brouard 2380: /* fprintf(ficgp,"\n plot \"%s\" u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm); */
2381: /* fprintf(ficgp,"\n replot \"%s\" u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm); */
2382: /* fprintf(ficgp,"\n replot \"%s\" u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm); */
2383: fprintf(ficgp,"\n plot \"%s\" u 1:($3) not w l 1 ",fileresprobmorprev);
2384: fprintf(ficgp,"\n replot \"%s\" u 1:(($3+1.96*$4)) t \"95\%% interval\" w l 2 ",fileresprobmorprev);
2385: fprintf(ficgp,"\n replot \"%s\" u 1:(($3-1.96*$4)) not w l 2 ",fileresprobmorprev);
1.53 brouard 2386: fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",fileresprobmorprev,fileresprobmorprev);
1.71 brouard 2387: 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 2388: /* 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);
2389: */
1.71 brouard 2390: fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.png\";replot;",digitp,optionfilefiname,digit);
1.53 brouard 2391:
2392: free_vector(xp,1,npar);
2393: free_matrix(doldm,1,nlstate,1,nlstate);
2394: free_matrix(dnewm,1,nlstate,1,npar);
2395: free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
2396: free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
2397: free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
1.55 lievre 2398: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
1.53 brouard 2399: fclose(ficresprobmorprev);
2400: fclose(ficgp);
2401: fclose(fichtm);
1.70 brouard 2402: }
1.53 brouard 2403:
2404: /************ Variance of prevlim ******************/
2405: 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)
2406: {
2407: /* Variance of prevalence limit */
1.59 brouard 2408: /* double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
1.53 brouard 2409: double **newm;
2410: double **dnewm,**doldm;
2411: int i, j, nhstepm, hstepm;
2412: int k, cptcode;
2413: double *xp;
2414: double *gp, *gm;
2415: double **gradg, **trgradg;
2416: double age,agelim;
2417: int theta;
2418:
1.54 brouard 2419: fprintf(ficresvpl,"# Standard deviation of stable prevalences \n");
1.53 brouard 2420: fprintf(ficresvpl,"# Age");
2421: for(i=1; i<=nlstate;i++)
2422: fprintf(ficresvpl," %1d-%1d",i,i);
2423: fprintf(ficresvpl,"\n");
2424:
2425: xp=vector(1,npar);
2426: dnewm=matrix(1,nlstate,1,npar);
2427: doldm=matrix(1,nlstate,1,nlstate);
2428:
2429: hstepm=1*YEARM; /* Every year of age */
2430: hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */
2431: agelim = AGESUP;
2432: for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
2433: nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
2434: if (stepm >= YEARM) hstepm=1;
2435: nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
2436: gradg=matrix(1,npar,1,nlstate);
2437: gp=vector(1,nlstate);
2438: gm=vector(1,nlstate);
2439:
2440: for(theta=1; theta <=npar; theta++){
2441: for(i=1; i<=npar; i++){ /* Computes gradient */
2442: xp[i] = x[i] + (i==theta ?delti[theta]:0);
2443: }
2444: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
2445: for(i=1;i<=nlstate;i++)
2446: gp[i] = prlim[i][i];
2447:
2448: for(i=1; i<=npar; i++) /* Computes gradient */
2449: xp[i] = x[i] - (i==theta ?delti[theta]:0);
2450: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
2451: for(i=1;i<=nlstate;i++)
2452: gm[i] = prlim[i][i];
2453:
2454: for(i=1;i<=nlstate;i++)
2455: gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
2456: } /* End theta */
2457:
2458: trgradg =matrix(1,nlstate,1,npar);
2459:
2460: for(j=1; j<=nlstate;j++)
2461: for(theta=1; theta <=npar; theta++)
2462: trgradg[j][theta]=gradg[theta][j];
2463:
2464: for(i=1;i<=nlstate;i++)
2465: varpl[i][(int)age] =0.;
2466: matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
2467: matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
2468: for(i=1;i<=nlstate;i++)
2469: varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
2470:
2471: fprintf(ficresvpl,"%.0f ",age );
2472: for(i=1; i<=nlstate;i++)
2473: fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
2474: fprintf(ficresvpl,"\n");
2475: free_vector(gp,1,nlstate);
2476: free_vector(gm,1,nlstate);
2477: free_matrix(gradg,1,npar,1,nlstate);
2478: free_matrix(trgradg,1,nlstate,1,npar);
2479: } /* End age */
2480:
2481: free_vector(xp,1,npar);
2482: free_matrix(doldm,1,nlstate,1,npar);
2483: free_matrix(dnewm,1,nlstate,1,nlstate);
2484:
2485: }
2486:
2487: /************ Variance of one-step probabilities ******************/
2488: void varprob(char optionfilefiname[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij, int *Tvar, int **nbcode, int *ncodemax)
2489: {
2490: int i, j=0, i1, k1, l1, t, tj;
2491: int k2, l2, j1, z1;
2492: int k=0,l, cptcode;
2493: int first=1, first1;
2494: double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
2495: double **dnewm,**doldm;
2496: double *xp;
2497: double *gp, *gm;
2498: double **gradg, **trgradg;
2499: double **mu;
2500: double age,agelim, cov[NCOVMAX];
2501: double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
2502: int theta;
2503: char fileresprob[FILENAMELENGTH];
2504: char fileresprobcov[FILENAMELENGTH];
2505: char fileresprobcor[FILENAMELENGTH];
2506:
2507: double ***varpij;
2508:
2509: strcpy(fileresprob,"prob");
2510: strcat(fileresprob,fileres);
2511: if((ficresprob=fopen(fileresprob,"w"))==NULL) {
2512: printf("Problem with resultfile: %s\n", fileresprob);
2513: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
2514: }
2515: strcpy(fileresprobcov,"probcov");
2516: strcat(fileresprobcov,fileres);
2517: if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
2518: printf("Problem with resultfile: %s\n", fileresprobcov);
2519: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
2520: }
2521: strcpy(fileresprobcor,"probcor");
2522: strcat(fileresprobcor,fileres);
2523: if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
2524: printf("Problem with resultfile: %s\n", fileresprobcor);
2525: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
2526: }
2527: printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
2528: fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
2529: printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
2530: fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
2531: printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
2532: fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
2533:
2534: fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
2535: fprintf(ficresprob,"# Age");
2536: fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
2537: fprintf(ficresprobcov,"# Age");
2538: fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
2539: fprintf(ficresprobcov,"# Age");
2540:
2541:
2542: for(i=1; i<=nlstate;i++)
2543: for(j=1; j<=(nlstate+ndeath);j++){
2544: fprintf(ficresprob," p%1d-%1d (SE)",i,j);
2545: fprintf(ficresprobcov," p%1d-%1d ",i,j);
2546: fprintf(ficresprobcor," p%1d-%1d ",i,j);
2547: }
1.69 brouard 2548: /* fprintf(ficresprob,"\n");
1.53 brouard 2549: fprintf(ficresprobcov,"\n");
2550: fprintf(ficresprobcor,"\n");
1.69 brouard 2551: */
2552: xp=vector(1,npar);
1.53 brouard 2553: dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
2554: doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
2555: mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
2556: varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
2557: first=1;
2558: if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {
2559: printf("Problem with gnuplot file: %s\n", optionfilegnuplot);
2560: fprintf(ficlog,"Problem with gnuplot file: %s\n", optionfilegnuplot);
2561: exit(0);
2562: }
2563: else{
2564: fprintf(ficgp,"\n# Routine varprob");
2565: }
2566: if((fichtm=fopen(optionfilehtm,"a"))==NULL) {
2567: printf("Problem with html file: %s\n", optionfilehtm);
2568: fprintf(ficlog,"Problem with html file: %s\n", optionfilehtm);
2569: exit(0);
2570: }
2571: else{
2572: fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
2573: fprintf(fichtm,"\n");
2574:
2575: fprintf(fichtm,"\n<li><h4> Computing matrix of variance-covariance of step probabilities</h4></li>\n");
2576: 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");
2577: 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");
2578:
2579: }
2580:
2581: cov[1]=1;
2582: tj=cptcoveff;
2583: if (cptcovn<1) {tj=1;ncodemax[1]=1;}
2584: j1=0;
2585: for(t=1; t<=tj;t++){
2586: for(i1=1; i1<=ncodemax[t];i1++){
2587: j1++;
2588: if (cptcovn>0) {
2589: fprintf(ficresprob, "\n#********** Variable ");
2590: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
1.69 brouard 2591: fprintf(ficresprob, "**********\n#\n");
1.53 brouard 2592: fprintf(ficresprobcov, "\n#********** Variable ");
2593: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
1.69 brouard 2594: fprintf(ficresprobcov, "**********\n#\n");
1.53 brouard 2595:
2596: fprintf(ficgp, "\n#********** Variable ");
1.69 brouard 2597: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
2598: fprintf(ficgp, "**********\n#\n");
1.53 brouard 2599:
2600:
2601: fprintf(fichtm, "\n<hr size=\"2\" color=\"#EC5E5E\">********** Variable ");
2602: for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
2603: fprintf(fichtm, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
2604:
2605: fprintf(ficresprobcor, "\n#********** Variable ");
2606: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
1.69 brouard 2607: fprintf(ficresprobcor, "**********\n#");
1.53 brouard 2608: }
2609:
2610: for (age=bage; age<=fage; age ++){
2611: cov[2]=age;
2612: for (k=1; k<=cptcovn;k++) {
2613: cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];
2614: }
2615: for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
2616: for (k=1; k<=cptcovprod;k++)
2617: cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
2618:
2619: gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
2620: trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
2621: gp=vector(1,(nlstate)*(nlstate+ndeath));
2622: gm=vector(1,(nlstate)*(nlstate+ndeath));
2623:
2624: for(theta=1; theta <=npar; theta++){
2625: for(i=1; i<=npar; i++)
1.74 brouard 2626: xp[i] = x[i] + (i==theta ?delti[theta]:(double)0);
1.53 brouard 2627:
2628: pmij(pmmij,cov,ncovmodel,xp,nlstate);
2629:
2630: k=0;
2631: for(i=1; i<= (nlstate); i++){
2632: for(j=1; j<=(nlstate+ndeath);j++){
2633: k=k+1;
2634: gp[k]=pmmij[i][j];
2635: }
2636: }
2637:
2638: for(i=1; i<=npar; i++)
1.74 brouard 2639: xp[i] = x[i] - (i==theta ?delti[theta]:(double)0);
1.53 brouard 2640:
2641: pmij(pmmij,cov,ncovmodel,xp,nlstate);
2642: k=0;
2643: for(i=1; i<=(nlstate); i++){
2644: for(j=1; j<=(nlstate+ndeath);j++){
2645: k=k+1;
2646: gm[k]=pmmij[i][j];
2647: }
2648: }
2649:
2650: for(i=1; i<= (nlstate)*(nlstate+ndeath); i++)
1.74 brouard 2651: gradg[theta][i]=(gp[i]-gm[i])/(double)2./delti[theta];
1.53 brouard 2652: }
2653:
2654: for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
2655: for(theta=1; theta <=npar; theta++)
2656: trgradg[j][theta]=gradg[theta][j];
2657:
2658: matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov);
2659: matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);
1.59 brouard 2660: free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
2661: free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
2662: free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
2663: free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
2664:
1.53 brouard 2665: pmij(pmmij,cov,ncovmodel,x,nlstate);
2666:
2667: k=0;
2668: for(i=1; i<=(nlstate); i++){
2669: for(j=1; j<=(nlstate+ndeath);j++){
2670: k=k+1;
2671: mu[k][(int) age]=pmmij[i][j];
2672: }
2673: }
2674: for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
2675: for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
2676: varpij[i][j][(int)age] = doldm[i][j];
2677:
2678: /*printf("\n%d ",(int)age);
1.59 brouard 2679: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
2680: printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
2681: fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
2682: }*/
1.53 brouard 2683:
2684: fprintf(ficresprob,"\n%d ",(int)age);
2685: fprintf(ficresprobcov,"\n%d ",(int)age);
2686: fprintf(ficresprobcor,"\n%d ",(int)age);
2687:
2688: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)
2689: fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));
2690: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
2691: fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);
2692: fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
2693: }
2694: i=0;
2695: for (k=1; k<=(nlstate);k++){
2696: for (l=1; l<=(nlstate+ndeath);l++){
2697: i=i++;
2698: fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
2699: fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
2700: for (j=1; j<=i;j++){
2701: fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);
2702: fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));
2703: }
2704: }
2705: }/* end of loop for state */
2706: } /* end of loop for age */
2707:
2708: /* Confidence intervalle of pij */
2709: /*
1.59 brouard 2710: fprintf(ficgp,"\nset noparametric;unset label");
2711: fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");
2712: fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
2713: 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);
2714: fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);
2715: fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);
2716: fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);
1.53 brouard 2717: */
2718:
2719: /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
2720: first1=1;
2721: for (k2=1; k2<=(nlstate);k2++){
2722: for (l2=1; l2<=(nlstate+ndeath);l2++){
2723: if(l2==k2) continue;
2724: j=(k2-1)*(nlstate+ndeath)+l2;
2725: for (k1=1; k1<=(nlstate);k1++){
2726: for (l1=1; l1<=(nlstate+ndeath);l1++){
2727: if(l1==k1) continue;
2728: i=(k1-1)*(nlstate+ndeath)+l1;
2729: if(i<=j) continue;
2730: for (age=bage; age<=fage; age ++){
2731: if ((int)age %5==0){
2732: v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;
2733: v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;
2734: cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;
2735: mu1=mu[i][(int) age]/stepm*YEARM ;
2736: mu2=mu[j][(int) age]/stepm*YEARM;
2737: c12=cv12/sqrt(v1*v2);
2738: /* Computing eigen value of matrix of covariance */
2739: lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
2740: lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
2741: /* Eigen vectors */
2742: v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
2743: /*v21=sqrt(1.-v11*v11); *//* error */
2744: v21=(lc1-v1)/cv12*v11;
2745: v12=-v21;
2746: v22=v11;
2747: tnalp=v21/v11;
2748: if(first1==1){
2749: first1=0;
2750: 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);
2751: }
2752: 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);
2753: /*printf(fignu*/
2754: /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */
2755: /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */
2756: if(first==1){
2757: first=0;
2758: fprintf(ficgp,"\nset parametric;unset label");
2759: 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);
2760: fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
2761: 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);
2762: fprintf(fichtm,"\n<br><img src=\"varpijgr%s%d%1d%1d-%1d%1d.png\"> ",optionfilefiname, j1,k1,l1,k2,l2);
2763: fprintf(fichtm,"\n<br> Correlation at age %d (%.3f),",(int) age, c12);
2764: fprintf(ficgp,"\nset out \"varpijgr%s%d%1d%1d-%1d%1d.png\"",optionfilefiname, j1,k1,l1,k2,l2);
2765: fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
2766: fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
2767: 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",\
2768: mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
2769: mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
2770: }else{
2771: first=0;
2772: fprintf(fichtm," %d (%.3f),",(int) age, c12);
2773: fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
2774: fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
2775: 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",\
2776: mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
2777: mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
2778: }/* if first */
2779: } /* age mod 5 */
2780: } /* end loop age */
2781: fprintf(ficgp,"\nset out \"varpijgr%s%d%1d%1d-%1d%1d.png\";replot;",optionfilefiname, j1,k1,l1,k2,l2);
2782: first=1;
2783: } /*l12 */
2784: } /* k12 */
2785: } /*l1 */
2786: }/* k1 */
2787: } /* loop covariates */
2788: }
1.59 brouard 2789: free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
2790: free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
1.53 brouard 2791: free_vector(xp,1,npar);
2792: fclose(ficresprob);
2793: fclose(ficresprobcov);
2794: fclose(ficresprobcor);
2795: fclose(ficgp);
2796: fclose(fichtm);
2797: }
2798:
2799:
2800: /******************* Printing html file ***********/
2801: void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \
2802: int lastpass, int stepm, int weightopt, char model[],\
2803: int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
2804: int popforecast, int estepm ,\
2805: double jprev1, double mprev1,double anprev1, \
2806: double jprev2, double mprev2,double anprev2){
2807: int jj1, k1, i1, cpt;
2808: /*char optionfilehtm[FILENAMELENGTH];*/
2809: if((fichtm=fopen(optionfilehtm,"a"))==NULL) {
2810: printf("Problem with %s \n",optionfilehtm), exit(0);
2811: fprintf(ficlog,"Problem with %s \n",optionfilehtm), exit(0);
2812: }
2813:
2814: fprintf(fichtm,"<ul><li><h4>Result files (first order: no variance)</h4>\n
2815: - 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
2816: - Estimated transition probabilities over %d (stepm) months: <a href=\"pij%s\">pij%s</a><br>\n
2817: - Stable prevalence in each health state: <a href=\"pl%s\">pl%s</a> <br>\n
2818: - Life expectancies by age and initial health status (estepm=%2d months):
2819: <a href=\"e%s\">e%s</a> <br>\n</li>", \
2820: jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,fileres,fileres,stepm,fileres,fileres,fileres,fileres,estepm,fileres,fileres);
2821:
2822: fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
2823:
2824: m=cptcoveff;
2825: if (cptcovn < 1) {m=1;ncodemax[1]=1;}
2826:
2827: jj1=0;
2828: for(k1=1; k1<=m;k1++){
2829: for(i1=1; i1<=ncodemax[k1];i1++){
2830: jj1++;
2831: if (cptcovn > 0) {
2832: fprintf(fichtm,"<hr size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
2833: for (cpt=1; cpt<=cptcoveff;cpt++)
2834: fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
2835: fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
2836: }
2837: /* Pij */
1.76 brouard 2838: 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 2839: <img src=\"pe%s%d1.png\">",stepm,strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);
2840: /* Quasi-incidences */
2841: 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>
2842: <img src=\"pe%s%d2.png\">",stepm,strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);
2843: /* Stable prevalence in each health state */
2844: for(cpt=1; cpt<nlstate;cpt++){
2845: fprintf(fichtm,"<br>- Stable prevalence in each health state : p%s%d%d.png<br>
2846: <img src=\"p%s%d%d.png\">",strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);
2847: }
2848: for(cpt=1; cpt<=nlstate;cpt++) {
2849: fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): exp%s%d%d.png <br>
2850: <img src=\"exp%s%d%d.png\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);
2851: }
2852: fprintf(fichtm,"\n<br>- Total life expectancy by age and
2853: health expectancies in states (1) and (2): e%s%d.png<br>
2854: <img src=\"e%s%d.png\">",strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);
2855: } /* end i1 */
2856: }/* End k1 */
2857: fprintf(fichtm,"</ul>");
2858:
2859:
2860: fprintf(fichtm,"\n<br><li><h4> Result files (second order: variances)</h4>\n
2861: - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n
2862: - Variance of one-step probabilities: <a href=\"prob%s\">prob%s</a> <br>\n
2863: - Variance-covariance of one-step probabilities: <a href=\"probcov%s\">probcov%s</a> <br>\n
2864: - Correlation matrix of one-step probabilities: <a href=\"probcor%s\">probcor%s</a> <br>\n
2865: - Variances and covariances of life expectancies by age and initial health status (estepm=%d months): <a href=\"v%s\">v%s</a><br>\n
2866: - Health expectancies with their variances (no covariance): <a href=\"t%s\">t%s</a> <br>\n
2867: - 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);
2868:
1.76 brouard 2869: /* if(popforecast==1) fprintf(fichtm,"\n */
2870: /* - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n */
2871: /* - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n */
2872: /* <br>",fileres,fileres,fileres,fileres); */
2873: /* else */
2874: /* 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 2875: fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
2876:
2877: m=cptcoveff;
2878: if (cptcovn < 1) {m=1;ncodemax[1]=1;}
2879:
2880: jj1=0;
2881: for(k1=1; k1<=m;k1++){
2882: for(i1=1; i1<=ncodemax[k1];i1++){
2883: jj1++;
2884: if (cptcovn > 0) {
2885: fprintf(fichtm,"<hr size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
2886: for (cpt=1; cpt<=cptcoveff;cpt++)
2887: fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
2888: fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
2889: }
2890: for(cpt=1; cpt<=nlstate;cpt++) {
1.76 brouard 2891: fprintf(fichtm,"<br>- Observed and period prevalence (with confident
1.53 brouard 2892: interval) in state (%d): v%s%d%d.png <br>
2893: <img src=\"v%s%d%d.png\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);
2894: }
2895: } /* end i1 */
2896: }/* End k1 */
2897: fprintf(fichtm,"</ul>");
2898: fclose(fichtm);
2899: }
2900:
2901: /******************* Gnuplot file **************/
2902: void printinggnuplot(char fileres[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
2903:
2904: int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;
2905: int ng;
2906: if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {
2907: printf("Problem with file %s",optionfilegnuplot);
2908: fprintf(ficlog,"Problem with file %s",optionfilegnuplot);
2909: }
2910:
1.54 brouard 2911: /*#ifdef windows */
1.53 brouard 2912: fprintf(ficgp,"cd \"%s\" \n",pathc);
1.54 brouard 2913: /*#endif */
1.53 brouard 2914: m=pow(2,cptcoveff);
2915:
2916: /* 1eme*/
2917: for (cpt=1; cpt<= nlstate ; cpt ++) {
2918: for (k1=1; k1<= m ; k1 ++) {
2919: fprintf(ficgp,"\nset out \"v%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);
2920: 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);
2921:
2922: for (i=1; i<= nlstate ; i ++) {
2923: if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
2924: else fprintf(ficgp," \%%*lf (\%%*lf)");
2925: }
1.69 brouard 2926: 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 2927: for (i=1; i<= nlstate ; i ++) {
2928: if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
2929: else fprintf(ficgp," \%%*lf (\%%*lf)");
2930: }
1.69 brouard 2931: fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"vpl%s\" every :::%d::%d u 1:($2-1.96*$3) \"\%%lf",fileres,k1-1,k1-1);
1.53 brouard 2932: for (i=1; i<= nlstate ; i ++) {
2933: if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
2934: else fprintf(ficgp," \%%*lf (\%%*lf)");
2935: }
2936: fprintf(ficgp,"\" t\"\" w l 1,\"p%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",fileres,k1-1,k1-1,2+4*(cpt-1));
2937: }
2938: }
2939: /*2 eme*/
2940:
2941: for (k1=1; k1<= m ; k1 ++) {
2942: fprintf(ficgp,"\nset out \"e%s%d.png\" \n",strtok(optionfile, "."),k1);
2943: fprintf(ficgp,"set ylabel \"Years\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] ",ageminpar,fage);
2944:
2945: for (i=1; i<= nlstate+1 ; i ++) {
2946: k=2*i;
2947: fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:2 \"\%%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: if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");
2953: else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);
2954: fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",fileres,k1-1,k1-1);
2955: for (j=1; j<= nlstate+1 ; j ++) {
2956: if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
2957: else fprintf(ficgp," \%%*lf (\%%*lf)");
2958: }
2959: fprintf(ficgp,"\" t\"\" w l 0,");
2960: fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",fileres,k1-1,k1-1);
2961: for (j=1; j<= nlstate+1 ; j ++) {
2962: if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
2963: else fprintf(ficgp," \%%*lf (\%%*lf)");
2964: }
2965: if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");
2966: else fprintf(ficgp,"\" t\"\" w l 0,");
2967: }
2968: }
2969:
2970: /*3eme*/
2971:
2972: for (k1=1; k1<= m ; k1 ++) {
2973: for (cpt=1; cpt<= nlstate ; cpt ++) {
2974: k=2+nlstate*(2*cpt-2);
2975: fprintf(ficgp,"\nset out \"exp%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);
2976: fprintf(ficgp,"set ter png small\nset size 0.65,0.65\nplot [%.f:%.f] \"e%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,fileres,k1-1,k1-1,k,cpt);
2977: /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
2978: for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
2979: fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
2980: fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
2981: for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
2982: fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
2983:
2984: */
2985: for (i=1; i< nlstate ; i ++) {
2986: 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);
2987:
2988: }
2989: }
2990: }
2991:
1.76 brouard 2992: /* CV preval stable (period) */
1.53 brouard 2993: for (k1=1; k1<= m ; k1 ++) {
1.76 brouard 2994: for (cpt=1; cpt<=nlstate ; cpt ++) {
1.53 brouard 2995: k=3;
2996: fprintf(ficgp,"\nset out \"p%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);
2997: 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/($%d",ageminpar,agemaxpar,fileres,k1,k+cpt+1,k+1);
2998:
1.76 brouard 2999: for (i=1; i<= nlstate ; i ++)
1.53 brouard 3000: fprintf(ficgp,"+$%d",k+i+1);
3001: fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);
3002:
3003: l=3+(nlstate+ndeath)*cpt;
3004: fprintf(ficgp,",\"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",fileres,k1,l+cpt+1,l+1);
3005: for (i=1; i< nlstate ; i ++) {
3006: l=3+(nlstate+ndeath)*cpt;
3007: fprintf(ficgp,"+$%d",l+i+1);
3008: }
3009: fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);
3010: }
3011: }
3012:
3013: /* proba elementaires */
3014: for(i=1,jk=1; i <=nlstate; i++){
3015: for(k=1; k <=(nlstate+ndeath); k++){
3016: if (k != i) {
3017: for(j=1; j <=ncovmodel; j++){
3018: fprintf(ficgp,"p%d=%f ",jk,p[jk]);
3019: jk++;
3020: fprintf(ficgp,"\n");
3021: }
3022: }
3023: }
3024: }
3025:
3026: for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/
3027: for(jk=1; jk <=m; jk++) {
3028: fprintf(ficgp,"\nset out \"pe%s%d%d.png\" \n",strtok(optionfile, "."),jk,ng);
3029: if (ng==2)
3030: fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
3031: else
3032: fprintf(ficgp,"\nset title \"Probability\"\n");
3033: fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65\nset log y\nplot [%.f:%.f] ",ageminpar,agemaxpar);
3034: i=1;
3035: for(k2=1; k2<=nlstate; k2++) {
3036: k3=i;
3037: for(k=1; k<=(nlstate+ndeath); k++) {
3038: if (k != k2){
3039: if(ng==2)
3040: fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);
3041: else
3042: fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
3043: ij=1;
3044: for(j=3; j <=ncovmodel; j++) {
3045: if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
3046: fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
3047: ij++;
3048: }
3049: else
3050: fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
3051: }
3052: fprintf(ficgp,")/(1");
3053:
3054: for(k1=1; k1 <=nlstate; k1++){
3055: fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);
3056: ij=1;
3057: for(j=3; j <=ncovmodel; j++){
3058: if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
3059: fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
3060: ij++;
3061: }
3062: else
3063: fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
3064: }
3065: fprintf(ficgp,")");
3066: }
3067: fprintf(ficgp,") t \"p%d%d\" ", k2,k);
3068: if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");
3069: i=i+ncovmodel;
3070: }
3071: } /* end k */
3072: } /* end k2 */
3073: } /* end jk */
3074: } /* end ng */
3075: fclose(ficgp);
3076: } /* end gnuplot */
3077:
3078:
3079: /*************** Moving average **************/
1.54 brouard 3080: int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav){
1.53 brouard 3081:
3082: int i, cpt, cptcod;
1.58 lievre 3083: int modcovmax =1;
1.54 brouard 3084: int mobilavrange, mob;
1.53 brouard 3085: double age;
1.58 lievre 3086:
3087: modcovmax=2*cptcoveff;/* Max number of modalities. We suppose
3088: a covariate has 2 modalities */
3089: if (cptcovn<1) modcovmax=1; /* At least 1 pass */
3090:
1.54 brouard 3091: if(mobilav==1||mobilav ==3 ||mobilav==5 ||mobilav== 7){
3092: if(mobilav==1) mobilavrange=5; /* default */
3093: else mobilavrange=mobilav;
3094: for (age=bage; age<=fage; age++)
3095: for (i=1; i<=nlstate;i++)
1.58 lievre 3096: for (cptcod=1;cptcod<=modcovmax;cptcod++)
1.54 brouard 3097: mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
3098: /* We keep the original values on the extreme ages bage, fage and for
3099: fage+1 and bage-1 we use a 3 terms moving average; for fage+2 bage+2
3100: we use a 5 terms etc. until the borders are no more concerned.
3101: */
3102: for (mob=3;mob <=mobilavrange;mob=mob+2){
3103: for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){
3104: for (i=1; i<=nlstate;i++){
1.58 lievre 3105: for (cptcod=1;cptcod<=modcovmax;cptcod++){
1.54 brouard 3106: mobaverage[(int)age][i][cptcod] =probs[(int)age][i][cptcod];
3107: for (cpt=1;cpt<=(mob-1)/2;cpt++){
3108: mobaverage[(int)age][i][cptcod] +=probs[(int)age-cpt][i][cptcod];
3109: mobaverage[(int)age][i][cptcod] +=probs[(int)age+cpt][i][cptcod];
3110: }
3111: mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/mob;
3112: }
1.53 brouard 3113: }
1.54 brouard 3114: }/* end age */
3115: }/* end mob */
3116: }else return -1;
3117: return 0;
3118: }/* End movingaverage */
1.53 brouard 3119:
3120:
3121: /************** Forecasting ******************/
1.70 brouard 3122: 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 3123: /* proj1, year, month, day of starting projection
3124: agemin, agemax range of age
3125: dateprev1 dateprev2 range of dates during which prevalence is computed
1.70 brouard 3126: anproj2 year of en of projection (same day and month as proj1).
1.69 brouard 3127: */
1.73 lievre 3128: int yearp, stepsize, hstepm, nhstepm, j, k, c, cptcod, i, h, i1;
1.53 brouard 3129: int *popage;
1.70 brouard 3130: double agec; /* generic age */
3131: double agelim, ppij, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
1.53 brouard 3132: double *popeffectif,*popcount;
3133: double ***p3mat;
1.55 lievre 3134: double ***mobaverage;
1.53 brouard 3135: char fileresf[FILENAMELENGTH];
3136:
1.69 brouard 3137: agelim=AGESUP;
1.70 brouard 3138: prevalence(ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
1.53 brouard 3139:
3140: strcpy(fileresf,"f");
3141: strcat(fileresf,fileres);
3142: if((ficresf=fopen(fileresf,"w"))==NULL) {
3143: printf("Problem with forecast resultfile: %s\n", fileresf);
3144: fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);
3145: }
3146: printf("Computing forecasting: result on file '%s' \n", fileresf);
3147: fprintf(ficlog,"Computing forecasting: result on file '%s' \n", fileresf);
3148:
3149: if (cptcoveff==0) ncodemax[cptcoveff]=1;
3150:
1.54 brouard 3151: if (mobilav!=0) {
1.53 brouard 3152: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
1.54 brouard 3153: if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
3154: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
3155: printf(" Error in movingaverage mobilav=%d\n",mobilav);
3156: }
1.53 brouard 3157: }
3158:
3159: stepsize=(int) (stepm+YEARM-1)/YEARM;
3160: if (stepm<=12) stepsize=1;
1.74 brouard 3161: if(estepm < stepm){
3162: printf ("Problem %d lower than %d\n",estepm, stepm);
3163: }
3164: else hstepm=estepm;
3165:
1.53 brouard 3166: hstepm=hstepm/stepm;
1.69 brouard 3167: yp1=modf(dateintmean,&yp);/* extracts integral of datemean in yp and
3168: fractional in yp1 */
1.53 brouard 3169: anprojmean=yp;
3170: yp2=modf((yp1*12),&yp);
3171: mprojmean=yp;
3172: yp1=modf((yp2*30.5),&yp);
3173: jprojmean=yp;
3174: if(jprojmean==0) jprojmean=1;
3175: if(mprojmean==0) jprojmean=1;
1.73 lievre 3176:
3177: i1=cptcoveff;
3178: if (cptcovn < 1){i1=1;}
1.53 brouard 3179:
1.70 brouard 3180: fprintf(ficresf,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2);
1.53 brouard 3181:
1.70 brouard 3182: fprintf(ficresf,"#****** Routine prevforecast **\n");
1.73 lievre 3183:
1.75 brouard 3184: /* if (h==(int)(YEARM*yearp)){ */
1.73 lievre 3185: for(cptcov=1, k=0;cptcov<=i1;cptcov++){
1.53 brouard 3186: for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
3187: k=k+1;
3188: fprintf(ficresf,"\n#******");
3189: for(j=1;j<=cptcoveff;j++) {
1.70 brouard 3190: 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 3191: }
3192: fprintf(ficresf,"******\n");
1.70 brouard 3193: fprintf(ficresf,"# Covariate valuofcovar yearproj age");
3194: for(j=1; j<=nlstate+ndeath;j++){
3195: for(i=1; i<=nlstate;i++)
3196: fprintf(ficresf," p%d%d",i,j);
3197: fprintf(ficresf," p.%d",j);
3198: }
1.74 brouard 3199: for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) {
1.53 brouard 3200: fprintf(ficresf,"\n");
1.70 brouard 3201: fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+yearp);
1.53 brouard 3202:
1.71 brouard 3203: for (agec=fage; agec>=(ageminpar-1); agec--){
1.70 brouard 3204: nhstepm=(int) rint((agelim-agec)*YEARM/stepm);
1.53 brouard 3205: nhstepm = nhstepm/hstepm;
3206: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3207: oldm=oldms;savm=savms;
1.70 brouard 3208: hpxij(p3mat,nhstepm,agec,hstepm,p,nlstate,stepm,oldm,savm, k);
1.53 brouard 3209:
3210: for (h=0; h<=nhstepm; h++){
1.75 brouard 3211: if (h*hstepm/YEARM*stepm ==yearp) {
1.69 brouard 3212: fprintf(ficresf,"\n");
3213: for(j=1;j<=cptcoveff;j++)
3214: fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
1.70 brouard 3215: fprintf(ficresf,"%.f %.f ",anproj1+yearp,agec+h*hstepm/YEARM*stepm);
1.53 brouard 3216: }
3217: for(j=1; j<=nlstate+ndeath;j++) {
1.70 brouard 3218: ppij=0.;
1.71 brouard 3219: for(i=1; i<=nlstate;i++) {
1.53 brouard 3220: if (mobilav==1)
1.71 brouard 3221: ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][i][cptcod];
1.53 brouard 3222: else {
1.71 brouard 3223: ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][cptcod];
1.53 brouard 3224: }
1.75 brouard 3225: if (h*hstepm/YEARM*stepm== yearp) {
1.70 brouard 3226: fprintf(ficresf," %.3f", p3mat[i][j][h]);
1.75 brouard 3227: }
3228: } /* end i */
3229: if (h*hstepm/YEARM*stepm==yearp) {
1.70 brouard 3230: fprintf(ficresf," %.3f", ppij);
1.53 brouard 3231: }
1.75 brouard 3232: }/* end j */
3233: } /* end h */
1.53 brouard 3234: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
1.75 brouard 3235: } /* end agec */
3236: } /* end yearp */
3237: } /* end cptcod */
3238: } /* end cptcov */
1.53 brouard 3239:
1.54 brouard 3240: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
1.53 brouard 3241:
3242: fclose(ficresf);
3243: }
1.70 brouard 3244:
3245: /************** Forecasting *****not tested NB*************/
1.53 brouard 3246: 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){
3247:
3248: int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;
3249: int *popage;
1.69 brouard 3250: double calagedatem, agelim, kk1, kk2;
1.53 brouard 3251: double *popeffectif,*popcount;
3252: double ***p3mat,***tabpop,***tabpopprev;
1.55 lievre 3253: double ***mobaverage;
1.53 brouard 3254: char filerespop[FILENAMELENGTH];
3255:
3256: tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
3257: tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
3258: agelim=AGESUP;
1.69 brouard 3259: calagedatem=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;
1.53 brouard 3260:
1.70 brouard 3261: prevalence(ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
1.53 brouard 3262:
3263:
3264: strcpy(filerespop,"pop");
3265: strcat(filerespop,fileres);
3266: if((ficrespop=fopen(filerespop,"w"))==NULL) {
3267: printf("Problem with forecast resultfile: %s\n", filerespop);
3268: fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop);
3269: }
3270: printf("Computing forecasting: result on file '%s' \n", filerespop);
3271: fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop);
3272:
3273: if (cptcoveff==0) ncodemax[cptcoveff]=1;
3274:
1.54 brouard 3275: if (mobilav!=0) {
1.53 brouard 3276: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
1.54 brouard 3277: if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
3278: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
3279: printf(" Error in movingaverage mobilav=%d\n",mobilav);
3280: }
1.53 brouard 3281: }
3282:
3283: stepsize=(int) (stepm+YEARM-1)/YEARM;
3284: if (stepm<=12) stepsize=1;
3285:
3286: agelim=AGESUP;
3287:
3288: hstepm=1;
3289: hstepm=hstepm/stepm;
3290:
3291: if (popforecast==1) {
3292: if((ficpop=fopen(popfile,"r"))==NULL) {
3293: printf("Problem with population file : %s\n",popfile);exit(0);
3294: fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0);
3295: }
3296: popage=ivector(0,AGESUP);
3297: popeffectif=vector(0,AGESUP);
3298: popcount=vector(0,AGESUP);
3299:
3300: i=1;
3301: while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;
3302:
3303: imx=i;
3304: for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];
3305: }
3306:
1.69 brouard 3307: for(cptcov=1,k=0;cptcov<=i2;cptcov++){
1.53 brouard 3308: for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
3309: k=k+1;
3310: fprintf(ficrespop,"\n#******");
3311: for(j=1;j<=cptcoveff;j++) {
3312: fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
3313: }
3314: fprintf(ficrespop,"******\n");
3315: fprintf(ficrespop,"# Age");
3316: for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);
3317: if (popforecast==1) fprintf(ficrespop," [Population]");
3318:
3319: for (cpt=0; cpt<=0;cpt++) {
3320: fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);
3321:
1.69 brouard 3322: for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){
1.53 brouard 3323: nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);
3324: nhstepm = nhstepm/hstepm;
3325:
3326: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3327: oldm=oldms;savm=savms;
3328: hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
3329:
3330: for (h=0; h<=nhstepm; h++){
1.69 brouard 3331: if (h==(int) (calagedatem+YEARM*cpt)) {
1.53 brouard 3332: fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
3333: }
3334: for(j=1; j<=nlstate+ndeath;j++) {
3335: kk1=0.;kk2=0;
3336: for(i=1; i<=nlstate;i++) {
3337: if (mobilav==1)
3338: kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];
3339: else {
3340: kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];
3341: }
3342: }
1.69 brouard 3343: if (h==(int)(calagedatem+12*cpt)){
1.53 brouard 3344: tabpop[(int)(agedeb)][j][cptcod]=kk1;
3345: /*fprintf(ficrespop," %.3f", kk1);
3346: if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/
3347: }
3348: }
3349: for(i=1; i<=nlstate;i++){
3350: kk1=0.;
3351: for(j=1; j<=nlstate;j++){
3352: kk1= kk1+tabpop[(int)(agedeb)][j][cptcod];
3353: }
1.69 brouard 3354: tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedatem+12*cpt)*hstepm/YEARM*stepm-1)];
1.53 brouard 3355: }
3356:
1.69 brouard 3357: if (h==(int)(calagedatem+12*cpt)) for(j=1; j<=nlstate;j++)
1.53 brouard 3358: fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);
3359: }
3360: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3361: }
3362: }
3363:
3364: /******/
3365:
3366: for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) {
3367: fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);
1.69 brouard 3368: for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){
1.53 brouard 3369: nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);
3370: nhstepm = nhstepm/hstepm;
3371:
3372: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3373: oldm=oldms;savm=savms;
3374: hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
3375: for (h=0; h<=nhstepm; h++){
1.69 brouard 3376: if (h==(int) (calagedatem+YEARM*cpt)) {
1.53 brouard 3377: fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
3378: }
3379: for(j=1; j<=nlstate+ndeath;j++) {
3380: kk1=0.;kk2=0;
3381: for(i=1; i<=nlstate;i++) {
3382: kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];
3383: }
1.69 brouard 3384: if (h==(int)(calagedatem+12*cpt)) fprintf(ficresf," %15.2f", kk1);
1.53 brouard 3385: }
3386: }
3387: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3388: }
3389: }
3390: }
3391: }
3392:
1.54 brouard 3393: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
1.53 brouard 3394:
3395: if (popforecast==1) {
3396: free_ivector(popage,0,AGESUP);
3397: free_vector(popeffectif,0,AGESUP);
3398: free_vector(popcount,0,AGESUP);
3399: }
3400: free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
3401: free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
3402: fclose(ficrespop);
3403: }
3404:
3405: /***********************************************/
3406: /**************** Main Program *****************/
3407: /***********************************************/
3408:
3409: int main(int argc, char *argv[])
3410: {
1.61 brouard 3411: int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav);
1.74 brouard 3412: int i,j, k, n=MAXN,iter,m,size=100,cptcode, cptcod;
1.53 brouard 3413: double agedeb, agefin,hf;
3414: double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;
3415:
3416: double fret;
3417: double **xi,tmp,delta;
3418:
3419: double dum; /* Dummy variable */
3420: double ***p3mat;
3421: double ***mobaverage;
3422: int *indx;
3423: char line[MAXLINE], linepar[MAXLINE];
3424: char path[80],pathc[80],pathcd[80],pathtot[80],model[80];
3425: int firstobs=1, lastobs=10;
3426: int sdeb, sfin; /* Status at beginning and end */
3427: int c, h , cpt,l;
3428: int ju,jl, mi;
3429: int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;
1.59 brouard 3430: int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,*tab;
1.69 brouard 3431: int mobilavproj=0 , prevfcast=0 ; /* moving average of prev, If prevfcast=1 prevalence projection */
1.53 brouard 3432: int mobilav=0,popforecast=0;
3433: int hstepm, nhstepm;
1.74 brouard 3434: double jprev1=1, mprev1=1,anprev1=2000,jprev2=1, mprev2=1,anprev2=2000;
3435: double jpyram=1, mpyram=1,anpyram=2000,jpyram1=1, mpyram1=1,anpyram1=2000;
1.53 brouard 3436:
3437: double bage, fage, age, agelim, agebase;
3438: double ftolpl=FTOL;
3439: double **prlim;
3440: double *severity;
3441: double ***param; /* Matrix of parameters */
3442: double *p;
3443: double **matcov; /* Matrix of covariance */
3444: double ***delti3; /* Scale */
3445: double *delti; /* Scale */
3446: double ***eij, ***vareij;
3447: double **varpl; /* Variances of prevalence limits by age */
3448: double *epj, vepp;
3449: double kk1, kk2;
1.74 brouard 3450: double dateprev1, dateprev2,jproj1=1,mproj1=1,anproj1=2000,jproj2=1,mproj2=1,anproj2=2000;
1.53 brouard 3451:
3452: char *alph[]={"a","a","b","c","d","e"}, str[4];
3453:
3454:
3455: char z[1]="c", occ;
3456: #include <sys/time.h>
3457: #include <time.h>
3458: char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];
3459:
3460: /* long total_usecs;
1.59 brouard 3461: struct timeval start_time, end_time;
1.53 brouard 3462:
1.59 brouard 3463: gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */
1.53 brouard 3464: getcwd(pathcd, size);
3465:
3466: printf("\n%s",version);
3467: if(argc <=1){
3468: printf("\nEnter the parameter file name: ");
3469: scanf("%s",pathtot);
3470: }
3471: else{
3472: strcpy(pathtot,argv[1]);
3473: }
3474: /*if(getcwd(pathcd, 80)!= NULL)printf ("Error pathcd\n");*/
3475: /*cygwin_split_path(pathtot,path,optionfile);
3476: printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/
3477: /* cutv(path,optionfile,pathtot,'\\');*/
3478:
3479: split(pathtot,path,optionfile,optionfilext,optionfilefiname);
1.59 brouard 3480: printf("pathtot=%s, path=%s, optionfile=%s optionfilext=%s optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
1.53 brouard 3481: chdir(path);
3482: replace(pathc,path);
3483:
1.59 brouard 3484: /*-------- arguments in the command line --------*/
1.53 brouard 3485:
3486: /* Log file */
3487: strcat(filelog, optionfilefiname);
3488: strcat(filelog,".log"); /* */
3489: if((ficlog=fopen(filelog,"w"))==NULL) {
3490: printf("Problem with logfile %s\n",filelog);
3491: goto end;
3492: }
3493: fprintf(ficlog,"Log filename:%s\n",filelog);
3494: fprintf(ficlog,"\n%s",version);
3495: fprintf(ficlog,"\nEnter the parameter file name: ");
3496: fprintf(ficlog,"pathtot=%s, path=%s, optionfile=%s optionfilext=%s optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
3497: fflush(ficlog);
3498:
3499: /* */
3500: strcpy(fileres,"r");
3501: strcat(fileres, optionfilefiname);
3502: strcat(fileres,".txt"); /* Other files have txt extension */
3503:
3504: /*---------arguments file --------*/
3505:
3506: if((ficpar=fopen(optionfile,"r"))==NULL) {
3507: printf("Problem with optionfile %s\n",optionfile);
3508: fprintf(ficlog,"Problem with optionfile %s\n",optionfile);
3509: goto end;
3510: }
3511:
3512: strcpy(filereso,"o");
3513: strcat(filereso,fileres);
3514: if((ficparo=fopen(filereso,"w"))==NULL) {
3515: printf("Problem with Output resultfile: %s\n", filereso);
3516: fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso);
3517: goto end;
3518: }
3519:
3520: /* Reads comments: lines beginning with '#' */
3521: while((c=getc(ficpar))=='#' && c!= EOF){
3522: ungetc(c,ficpar);
3523: fgets(line, MAXLINE, ficpar);
3524: puts(line);
3525: fputs(line,ficparo);
3526: }
3527: ungetc(c,ficpar);
3528:
3529: 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);
3530: 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);
3531: 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 3532: while((c=getc(ficpar))=='#' && c!= EOF){
1.53 brouard 3533: ungetc(c,ficpar);
3534: fgets(line, MAXLINE, ficpar);
3535: puts(line);
3536: fputs(line,ficparo);
3537: }
3538: ungetc(c,ficpar);
3539:
3540:
3541: covar=matrix(0,NCOVMAX,1,n);
1.58 lievre 3542: cptcovn=0; /*Number of covariates, i.e. number of '+' in model statement*/
1.53 brouard 3543: if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;
3544:
1.58 lievre 3545: ncovmodel=2+cptcovn; /*Number of variables = cptcovn + intercept + age */
1.53 brouard 3546: nvar=ncovmodel-1; /* Suppressing age as a basic covariate */
3547:
3548: /* Read guess parameters */
3549: /* Reads comments: lines beginning with '#' */
3550: while((c=getc(ficpar))=='#' && c!= EOF){
3551: ungetc(c,ficpar);
3552: fgets(line, MAXLINE, ficpar);
3553: puts(line);
3554: fputs(line,ficparo);
3555: }
3556: ungetc(c,ficpar);
3557:
3558: param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
1.59 brouard 3559: for(i=1; i <=nlstate; i++)
1.53 brouard 3560: for(j=1; j <=nlstate+ndeath-1; j++){
3561: fscanf(ficpar,"%1d%1d",&i1,&j1);
3562: fprintf(ficparo,"%1d%1d",i1,j1);
3563: if(mle==1)
3564: printf("%1d%1d",i,j);
3565: fprintf(ficlog,"%1d%1d",i,j);
3566: for(k=1; k<=ncovmodel;k++){
3567: fscanf(ficpar," %lf",¶m[i][j][k]);
3568: if(mle==1){
3569: printf(" %lf",param[i][j][k]);
3570: fprintf(ficlog," %lf",param[i][j][k]);
3571: }
3572: else
3573: fprintf(ficlog," %lf",param[i][j][k]);
3574: fprintf(ficparo," %lf",param[i][j][k]);
3575: }
3576: fscanf(ficpar,"\n");
3577: if(mle==1)
3578: printf("\n");
3579: fprintf(ficlog,"\n");
3580: fprintf(ficparo,"\n");
3581: }
3582:
1.59 brouard 3583: npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/
1.53 brouard 3584:
3585: p=param[1][1];
3586:
3587: /* Reads comments: lines beginning with '#' */
3588: while((c=getc(ficpar))=='#' && c!= EOF){
3589: ungetc(c,ficpar);
3590: fgets(line, MAXLINE, ficpar);
3591: puts(line);
3592: fputs(line,ficparo);
3593: }
3594: ungetc(c,ficpar);
3595:
3596: delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
1.74 brouard 3597: /* delti=vector(1,npar); *//* Scale of each paramater (output from hesscov) */
1.53 brouard 3598: for(i=1; i <=nlstate; i++){
3599: for(j=1; j <=nlstate+ndeath-1; j++){
3600: fscanf(ficpar,"%1d%1d",&i1,&j1);
3601: printf("%1d%1d",i,j);
3602: fprintf(ficparo,"%1d%1d",i1,j1);
3603: for(k=1; k<=ncovmodel;k++){
3604: fscanf(ficpar,"%le",&delti3[i][j][k]);
3605: printf(" %le",delti3[i][j][k]);
3606: fprintf(ficparo," %le",delti3[i][j][k]);
3607: }
3608: fscanf(ficpar,"\n");
3609: printf("\n");
3610: fprintf(ficparo,"\n");
3611: }
3612: }
3613: delti=delti3[1][1];
1.74 brouard 3614:
3615:
3616: /* 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 3617:
3618: /* Reads comments: lines beginning with '#' */
3619: while((c=getc(ficpar))=='#' && c!= EOF){
3620: ungetc(c,ficpar);
3621: fgets(line, MAXLINE, ficpar);
3622: puts(line);
3623: fputs(line,ficparo);
3624: }
3625: ungetc(c,ficpar);
3626:
3627: matcov=matrix(1,npar,1,npar);
3628: for(i=1; i <=npar; i++){
3629: fscanf(ficpar,"%s",&str);
3630: if(mle==1)
3631: printf("%s",str);
3632: fprintf(ficlog,"%s",str);
3633: fprintf(ficparo,"%s",str);
3634: for(j=1; j <=i; j++){
3635: fscanf(ficpar," %le",&matcov[i][j]);
3636: if(mle==1){
3637: printf(" %.5le",matcov[i][j]);
3638: fprintf(ficlog," %.5le",matcov[i][j]);
3639: }
3640: else
3641: fprintf(ficlog," %.5le",matcov[i][j]);
3642: fprintf(ficparo," %.5le",matcov[i][j]);
3643: }
3644: fscanf(ficpar,"\n");
3645: if(mle==1)
3646: printf("\n");
3647: fprintf(ficlog,"\n");
3648: fprintf(ficparo,"\n");
3649: }
3650: for(i=1; i <=npar; i++)
3651: for(j=i+1;j<=npar;j++)
3652: matcov[i][j]=matcov[j][i];
3653:
3654: if(mle==1)
3655: printf("\n");
3656: fprintf(ficlog,"\n");
3657:
3658:
1.59 brouard 3659: /*-------- Rewriting paramater file ----------*/
3660: strcpy(rfileres,"r"); /* "Rparameterfile */
3661: strcat(rfileres,optionfilefiname); /* Parameter file first name*/
3662: strcat(rfileres,"."); /* */
3663: strcat(rfileres,optionfilext); /* Other files have txt extension */
3664: if((ficres =fopen(rfileres,"w"))==NULL) {
3665: printf("Problem writing new parameter file: %s\n", fileres);goto end;
3666: fprintf(ficlog,"Problem writing new parameter file: %s\n", fileres);goto end;
3667: }
3668: fprintf(ficres,"#%s\n",version);
1.53 brouard 3669:
1.59 brouard 3670: /*-------- data file ----------*/
3671: if((fic=fopen(datafile,"r"))==NULL) {
3672: printf("Problem with datafile: %s\n", datafile);goto end;
3673: fprintf(ficlog,"Problem with datafile: %s\n", datafile);goto end;
3674: }
3675:
3676: n= lastobs;
3677: severity = vector(1,maxwav);
3678: outcome=imatrix(1,maxwav+1,1,n);
3679: num=ivector(1,n);
3680: moisnais=vector(1,n);
3681: annais=vector(1,n);
3682: moisdc=vector(1,n);
3683: andc=vector(1,n);
3684: agedc=vector(1,n);
3685: cod=ivector(1,n);
3686: weight=vector(1,n);
3687: for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */
3688: mint=matrix(1,maxwav,1,n);
3689: anint=matrix(1,maxwav,1,n);
3690: s=imatrix(1,maxwav+1,1,n);
3691: tab=ivector(1,NCOVMAX);
3692: ncodemax=ivector(1,8);
3693:
3694: i=1;
3695: while (fgets(line, MAXLINE, fic) != NULL) {
3696: if ((i >= firstobs) && (i <=lastobs)) {
1.53 brouard 3697:
1.59 brouard 3698: for (j=maxwav;j>=1;j--){
3699: cutv(stra, strb,line,' '); s[j][i]=atoi(strb);
3700: strcpy(line,stra);
3701: cutv(stra, strb,line,'/'); anint[j][i]=(double)(atoi(strb)); strcpy(line,stra);
3702: cutv(stra, strb,line,' '); mint[j][i]=(double)(atoi(strb)); strcpy(line,stra);
3703: }
1.53 brouard 3704:
1.59 brouard 3705: cutv(stra, strb,line,'/'); andc[i]=(double)(atoi(strb)); strcpy(line,stra);
3706: cutv(stra, strb,line,' '); moisdc[i]=(double)(atoi(strb)); strcpy(line,stra);
1.53 brouard 3707:
1.59 brouard 3708: cutv(stra, strb,line,'/'); annais[i]=(double)(atoi(strb)); strcpy(line,stra);
3709: cutv(stra, strb,line,' '); moisnais[i]=(double)(atoi(strb)); strcpy(line,stra);
1.53 brouard 3710:
1.59 brouard 3711: cutv(stra, strb,line,' '); weight[i]=(double)(atoi(strb)); strcpy(line,stra);
3712: for (j=ncovcol;j>=1;j--){
3713: cutv(stra, strb,line,' '); covar[j][i]=(double)(atoi(strb)); strcpy(line,stra);
3714: }
3715: num[i]=atol(stra);
1.53 brouard 3716:
1.59 brouard 3717: /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){
3718: 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 3719:
1.59 brouard 3720: i=i+1;
3721: }
3722: }
3723: /* printf("ii=%d", ij);
3724: scanf("%d",i);*/
1.53 brouard 3725: imx=i-1; /* Number of individuals */
3726:
3727: /* for (i=1; i<=imx; i++){
3728: if ((s[1][i]==3) && (s[2][i]==2)) s[2][i]=3;
3729: if ((s[2][i]==3) && (s[3][i]==2)) s[3][i]=3;
3730: if ((s[3][i]==3) && (s[4][i]==2)) s[4][i]=3;
3731: }*/
3732: /* for (i=1; i<=imx; i++){
3733: if (s[4][i]==9) s[4][i]=-1;
3734: 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]));}*/
3735:
1.71 brouard 3736: for (i=1; i<=imx; i++)
1.53 brouard 3737:
1.71 brouard 3738: /*if ((s[3][i]==3) || (s[4][i]==3)) weight[i]=0.08;
3739: else weight[i]=1;*/
3740:
1.53 brouard 3741: /* Calculation of the number of parameter from char model*/
3742: Tvar=ivector(1,15); /* stores the number n of the covariates in Vm+Vn at 1 and m at 2 */
3743: Tprod=ivector(1,15);
3744: Tvaraff=ivector(1,15);
3745: Tvard=imatrix(1,15,1,2);
3746: Tage=ivector(1,15);
3747:
1.58 lievre 3748: if (strlen(model) >1){ /* If there is at least 1 covariate */
1.53 brouard 3749: j=0, j1=0, k1=1, k2=1;
1.58 lievre 3750: j=nbocc(model,'+'); /* j=Number of '+' */
3751: j1=nbocc(model,'*'); /* j1=Number of '*' */
3752: cptcovn=j+1;
3753: cptcovprod=j1; /*Number of products */
1.53 brouard 3754:
3755: strcpy(modelsav,model);
3756: if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){
3757: printf("Error. Non available option model=%s ",model);
3758: fprintf(ficlog,"Error. Non available option model=%s ",model);
3759: goto end;
3760: }
3761:
1.59 brouard 3762: /* This loop fills the array Tvar from the string 'model'.*/
1.58 lievre 3763:
1.53 brouard 3764: for(i=(j+1); i>=1;i--){
3765: cutv(stra,strb,modelsav,'+'); /* keeps in strb after the last + */
1.59 brouard 3766: if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyzes it */
1.53 brouard 3767: /* printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/
3768: /*scanf("%d",i);*/
3769: if (strchr(strb,'*')) { /* Model includes a product */
3770: cutv(strd,strc,strb,'*'); /* strd*strc Vm*Vn (if not *age)*/
3771: if (strcmp(strc,"age")==0) { /* Vn*age */
3772: cptcovprod--;
3773: cutv(strb,stre,strd,'V');
3774: Tvar[i]=atoi(stre); /* computes n in Vn and stores in Tvar*/
3775: cptcovage++;
3776: Tage[cptcovage]=i;
3777: /*printf("stre=%s ", stre);*/
3778: }
3779: else if (strcmp(strd,"age")==0) { /* or age*Vn */
3780: cptcovprod--;
3781: cutv(strb,stre,strc,'V');
3782: Tvar[i]=atoi(stre);
3783: cptcovage++;
3784: Tage[cptcovage]=i;
3785: }
3786: else { /* Age is not in the model */
3787: cutv(strb,stre,strc,'V'); /* strc= Vn, stre is n*/
3788: Tvar[i]=ncovcol+k1;
3789: cutv(strb,strc,strd,'V'); /* strd was Vm, strc is m */
3790: Tprod[k1]=i;
3791: Tvard[k1][1]=atoi(strc); /* m*/
3792: Tvard[k1][2]=atoi(stre); /* n */
3793: Tvar[cptcovn+k2]=Tvard[k1][1];
3794: Tvar[cptcovn+k2+1]=Tvard[k1][2];
3795: for (k=1; k<=lastobs;k++)
3796: covar[ncovcol+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];
3797: k1++;
3798: k2=k2+2;
3799: }
3800: }
3801: else { /* no more sum */
3802: /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/
3803: /* scanf("%d",i);*/
3804: cutv(strd,strc,strb,'V');
3805: Tvar[i]=atoi(strc);
3806: }
3807: strcpy(modelsav,stra);
3808: /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);
3809: scanf("%d",i);*/
3810: } /* end of loop + */
3811: } /* end model */
3812:
1.58 lievre 3813: /*The number n of Vn is stored in Tvar. cptcovage =number of age covariate. Tage gives the position of age. cptcovprod= number of products.
3814: If model=V1+V1*age then Tvar[1]=1 Tvar[2]=1 cptcovage=1 Tage[1]=2 cptcovprod=0*/
3815:
1.53 brouard 3816: /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);
3817: printf("cptcovprod=%d ", cptcovprod);
3818: fprintf(ficlog,"cptcovprod=%d ", cptcovprod);
1.58 lievre 3819:
3820: scanf("%d ",i);
3821: fclose(fic);*/
1.53 brouard 3822:
3823: /* if(mle==1){*/
1.59 brouard 3824: if (weightopt != 1) { /* Maximisation without weights*/
3825: for(i=1;i<=n;i++) weight[i]=1.0;
3826: }
1.53 brouard 3827: /*-calculation of age at interview from date of interview and age at death -*/
1.59 brouard 3828: agev=matrix(1,maxwav,1,imx);
1.53 brouard 3829:
1.59 brouard 3830: for (i=1; i<=imx; i++) {
3831: for(m=2; (m<= maxwav); m++) {
1.76 brouard 3832: if (((int)mint[m][i]== 99) && (s[m][i] <= nlstate)){
1.59 brouard 3833: anint[m][i]=9999;
3834: s[m][i]=-1;
3835: }
1.76 brouard 3836: if((int)moisdc[i]==99 && (int)andc[i]==9999 && s[m][i]>nlstate){
1.77 brouard 3837: 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);
3838: 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 3839: s[m][i]=-1;
3840: }
3841: if((int)moisdc[i]==99 && (int)andc[i]!=9999 && s[m][i]>nlstate){
1.77 brouard 3842: 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]);
3843: 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 3844: s[m][i]=-1;
3845: }
1.53 brouard 3846: }
1.59 brouard 3847: }
1.53 brouard 3848:
1.59 brouard 3849: for (i=1; i<=imx; i++) {
3850: agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);
1.71 brouard 3851: for(m=firstpass; (m<= lastpass); m++){
1.69 brouard 3852: if(s[m][i] >0){
1.59 brouard 3853: if (s[m][i] >= nlstate+1) {
3854: if(agedc[i]>0)
1.76 brouard 3855: if((int)moisdc[i]!=99 && (int)andc[i]!=9999)
1.69 brouard 3856: agev[m][i]=agedc[i];
1.59 brouard 3857: /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/
3858: else {
1.76 brouard 3859: if ((int)andc[i]!=9999){
1.59 brouard 3860: printf("Warning negative age at death: %d line:%d\n",num[i],i);
3861: fprintf(ficlog,"Warning negative age at death: %d line:%d\n",num[i],i);
3862: agev[m][i]=-1;
1.53 brouard 3863: }
3864: }
1.70 brouard 3865: }
1.69 brouard 3866: else if(s[m][i] !=9){ /* Standard case, age in fractional
3867: years but with the precision of a
3868: month */
1.59 brouard 3869: agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);
1.76 brouard 3870: if((int)mint[m][i]==99 || (int)anint[m][i]==9999)
1.59 brouard 3871: agev[m][i]=1;
3872: else if(agev[m][i] <agemin){
3873: agemin=agev[m][i];
3874: /*printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], agemin);*/
1.53 brouard 3875: }
1.59 brouard 3876: else if(agev[m][i] >agemax){
3877: agemax=agev[m][i];
3878: /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/
1.53 brouard 3879: }
1.59 brouard 3880: /*agev[m][i]=anint[m][i]-annais[i];*/
3881: /* agev[m][i] = age[i]+2*m;*/
1.53 brouard 3882: }
1.59 brouard 3883: else { /* =9 */
1.53 brouard 3884: agev[m][i]=1;
1.59 brouard 3885: s[m][i]=-1;
3886: }
1.53 brouard 3887: }
1.59 brouard 3888: else /*= 0 Unknown */
3889: agev[m][i]=1;
3890: }
1.53 brouard 3891:
1.59 brouard 3892: }
3893: for (i=1; i<=imx; i++) {
1.71 brouard 3894: for(m=firstpass; (m<=lastpass); m++){
1.59 brouard 3895: if (s[m][i] > (nlstate+ndeath)) {
3896: 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);
3897: 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);
3898: goto end;
1.53 brouard 3899: }
3900: }
1.59 brouard 3901: }
1.53 brouard 3902:
1.71 brouard 3903: /*for (i=1; i<=imx; i++){
3904: for (m=firstpass; (m<lastpass); m++){
3905: printf("%d %d %.lf %d %d\n", num[i],(covar[1][i]),agev[m][i],s[m][i],s[m+1][i]);
3906: }
3907:
3908: }*/
3909:
1.59 brouard 3910: printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);
3911: fprintf(ficlog,"Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);
3912:
3913: free_vector(severity,1,maxwav);
3914: free_imatrix(outcome,1,maxwav+1,1,n);
3915: free_vector(moisnais,1,n);
3916: free_vector(annais,1,n);
3917: /* free_matrix(mint,1,maxwav,1,n);
3918: free_matrix(anint,1,maxwav,1,n);*/
3919: free_vector(moisdc,1,n);
3920: free_vector(andc,1,n);
1.53 brouard 3921:
3922:
1.59 brouard 3923: wav=ivector(1,imx);
3924: dh=imatrix(1,lastpass-firstpass+1,1,imx);
3925: bh=imatrix(1,lastpass-firstpass+1,1,imx);
3926: mw=imatrix(1,lastpass-firstpass+1,1,imx);
1.69 brouard 3927:
1.59 brouard 3928: /* Concatenates waves */
3929: concatwav(wav, dh, bh, mw, s, agedc, agev, firstpass, lastpass, imx, nlstate, stepm);
1.53 brouard 3930:
1.59 brouard 3931: /* Routine tricode is to calculate cptcoveff (real number of unique covariates) and to associate covariable number and modality */
1.53 brouard 3932:
1.59 brouard 3933: Tcode=ivector(1,100);
3934: nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);
3935: ncodemax[1]=1;
3936: if (cptcovn > 0) tricode(Tvar,nbcode,imx);
1.53 brouard 3937:
1.59 brouard 3938: codtab=imatrix(1,100,1,10); /* Cross tabulation to get the order of
3939: the estimations*/
3940: h=0;
3941: m=pow(2,cptcoveff);
1.53 brouard 3942:
1.59 brouard 3943: for(k=1;k<=cptcoveff; k++){
3944: for(i=1; i <=(m/pow(2,k));i++){
3945: for(j=1; j <= ncodemax[k]; j++){
3946: for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){
3947: h++;
3948: if (h>m) h=1;codtab[h][k]=j;codtab[h][Tvar[k]]=j;
3949: /* printf("h=%d k=%d j=%d codtab[h][k]=%d tvar[k]=%d \n",h, k,j,codtab[h][k],Tvar[k]);*/
3950: }
3951: }
3952: }
3953: }
3954: /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]);
3955: codtab[1][2]=1;codtab[2][2]=2; */
3956: /* for(i=1; i <=m ;i++){
3957: for(k=1; k <=cptcovn; k++){
3958: printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);
3959: }
3960: printf("\n");
1.53 brouard 3961: }
1.59 brouard 3962: scanf("%d",i);*/
1.53 brouard 3963:
1.59 brouard 3964: /* Calculates basic frequencies. Computes observed prevalence at single age
3965: and prints on file fileres'p'. */
1.53 brouard 3966:
1.60 brouard 3967: pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
3968: oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
3969: newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
3970: savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
3971: oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */
1.53 brouard 3972:
3973:
1.59 brouard 3974: /* For Powell, parameters are in a vector p[] starting at p[1]
3975: so we point p on param[1][1] so that p[1] maps on param[1][1][1] */
3976: p=param[1][1]; /* *(*(*(param +1)+1)+0) */
1.53 brouard 3977:
1.61 brouard 3978: if(mle>=1){ /* Could be 1 or 2 */
1.53 brouard 3979: mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);
1.59 brouard 3980: }
1.53 brouard 3981:
1.59 brouard 3982: /*--------- results files --------------*/
3983: 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 3984:
3985:
1.59 brouard 3986: jk=1;
3987: fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
3988: printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
3989: fprintf(ficlog,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
3990: for(i=1,jk=1; i <=nlstate; i++){
3991: for(k=1; k <=(nlstate+ndeath); k++){
3992: if (k != i)
3993: {
3994: printf("%d%d ",i,k);
3995: fprintf(ficlog,"%d%d ",i,k);
3996: fprintf(ficres,"%1d%1d ",i,k);
3997: for(j=1; j <=ncovmodel; j++){
3998: printf("%f ",p[jk]);
3999: fprintf(ficlog,"%f ",p[jk]);
4000: fprintf(ficres,"%f ",p[jk]);
4001: jk++;
4002: }
4003: printf("\n");
4004: fprintf(ficlog,"\n");
4005: fprintf(ficres,"\n");
4006: }
4007: }
4008: }
4009: if(mle==1){
4010: /* Computing hessian and covariance matrix */
4011: ftolhess=ftol; /* Usually correct */
4012: hesscov(matcov, p, npar, delti, ftolhess, func);
4013: }
4014: fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");
4015: printf("# Scales (for hessian or gradient estimation)\n");
4016: fprintf(ficlog,"# Scales (for hessian or gradient estimation)\n");
4017: for(i=1,jk=1; i <=nlstate; i++){
4018: for(j=1; j <=nlstate+ndeath; j++){
4019: if (j!=i) {
4020: fprintf(ficres,"%1d%1d",i,j);
4021: printf("%1d%1d",i,j);
4022: fprintf(ficlog,"%1d%1d",i,j);
4023: for(k=1; k<=ncovmodel;k++){
4024: printf(" %.5e",delti[jk]);
4025: fprintf(ficlog," %.5e",delti[jk]);
4026: fprintf(ficres," %.5e",delti[jk]);
4027: jk++;
4028: }
4029: printf("\n");
4030: fprintf(ficlog,"\n");
4031: fprintf(ficres,"\n");
4032: }
4033: }
4034: }
1.53 brouard 4035:
1.59 brouard 4036: 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");
4037: if(mle==1)
4038: 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");
4039: 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");
4040: for(i=1,k=1;i<=npar;i++){
4041: /* if (k>nlstate) k=1;
4042: i1=(i-1)/(ncovmodel*nlstate)+1;
4043: fprintf(ficres,"%s%d%d",alph[k],i1,tab[i]);
4044: printf("%s%d%d",alph[k],i1,tab[i]);
4045: */
4046: fprintf(ficres,"%3d",i);
4047: if(mle==1)
4048: printf("%3d",i);
4049: fprintf(ficlog,"%3d",i);
4050: for(j=1; j<=i;j++){
4051: fprintf(ficres," %.5e",matcov[i][j]);
4052: if(mle==1)
4053: printf(" %.5e",matcov[i][j]);
4054: fprintf(ficlog," %.5e",matcov[i][j]);
4055: }
4056: fprintf(ficres,"\n");
4057: if(mle==1)
4058: printf("\n");
4059: fprintf(ficlog,"\n");
4060: k++;
4061: }
1.53 brouard 4062:
1.59 brouard 4063: while((c=getc(ficpar))=='#' && c!= EOF){
4064: ungetc(c,ficpar);
4065: fgets(line, MAXLINE, ficpar);
4066: puts(line);
4067: fputs(line,ficparo);
4068: }
4069: ungetc(c,ficpar);
4070:
4071: estepm=0;
4072: fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm);
4073: if (estepm==0 || estepm < stepm) estepm=stepm;
4074: if (fage <= 2) {
4075: bage = ageminpar;
4076: fage = agemaxpar;
4077: }
1.53 brouard 4078:
1.59 brouard 4079: fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");
4080: fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
4081: fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
1.53 brouard 4082:
1.59 brouard 4083: while((c=getc(ficpar))=='#' && c!= EOF){
4084: ungetc(c,ficpar);
4085: fgets(line, MAXLINE, ficpar);
4086: puts(line);
4087: fputs(line,ficparo);
4088: }
4089: ungetc(c,ficpar);
1.53 brouard 4090:
1.59 brouard 4091: 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);
4092: 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);
4093: 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 4094: printf("begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
4095: fprintf(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 4096:
1.59 brouard 4097: while((c=getc(ficpar))=='#' && c!= EOF){
4098: ungetc(c,ficpar);
4099: fgets(line, MAXLINE, ficpar);
4100: puts(line);
4101: fputs(line,ficparo);
4102: }
4103: ungetc(c,ficpar);
1.53 brouard 4104:
4105:
1.70 brouard 4106: dateprev1=anprev1+(mprev1-1)/12.+(jprev1-1)/365.;
4107: dateprev2=anprev2+(mprev2-1)/12.+(jprev2-1)/365.;
1.53 brouard 4108:
4109: fscanf(ficpar,"pop_based=%d\n",&popbased);
4110: fprintf(ficparo,"pop_based=%d\n",popbased);
4111: fprintf(ficres,"pop_based=%d\n",popbased);
4112:
4113: while((c=getc(ficpar))=='#' && c!= EOF){
4114: ungetc(c,ficpar);
4115: fgets(line, MAXLINE, ficpar);
4116: puts(line);
4117: fputs(line,ficparo);
4118: }
4119: ungetc(c,ficpar);
4120:
1.69 brouard 4121: 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 4122: 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 4123: 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);
4124: 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);
4125: 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 4126: /* day and month of proj2 are not used but only year anproj2.*/
1.53 brouard 4127:
1.59 brouard 4128: while((c=getc(ficpar))=='#' && c!= EOF){
1.53 brouard 4129: ungetc(c,ficpar);
4130: fgets(line, MAXLINE, ficpar);
4131: puts(line);
4132: fputs(line,ficparo);
4133: }
4134: ungetc(c,ficpar);
4135:
4136: fscanf(ficpar,"popforecast=%d popfile=%s popfiledate=%lf/%lf/%lf last-popfiledate=%lf/%lf/%lf\n",&popforecast,popfile,&jpyram,&mpyram,&anpyram,&jpyram1,&mpyram1,&anpyram1);
4137: fprintf(ficparo,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);
4138: fprintf(ficres,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);
4139:
1.74 brouard 4140: probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
1.59 brouard 4141: freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);
1.58 lievre 4142:
1.59 brouard 4143: /*------------ gnuplot -------------*/
4144: strcpy(optionfilegnuplot,optionfilefiname);
4145: strcat(optionfilegnuplot,".gp");
4146: if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {
4147: printf("Problem with file %s",optionfilegnuplot);
4148: }
4149: else{
4150: fprintf(ficgp,"\n# %s\n", version);
4151: fprintf(ficgp,"# %s\n", optionfilegnuplot);
4152: fprintf(ficgp,"set missing 'NaNq'\n");
4153: }
4154: fclose(ficgp);
4155: printinggnuplot(fileres, ageminpar,agemaxpar,fage, pathc,p);
4156: /*--------- index.htm --------*/
1.53 brouard 4157:
4158: strcpy(optionfilehtm,optionfile);
4159: strcat(optionfilehtm,".htm");
4160: if((fichtm=fopen(optionfilehtm,"w"))==NULL) {
4161: printf("Problem with %s \n",optionfilehtm), exit(0);
4162: }
4163:
4164: fprintf(fichtm,"<body> <font size=\"2\">%s </font> <hr size=\"2\" color=\"#EC5E5E\"> \n
4165: Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n
4166: \n
4167: Total number of observations=%d <br>\n
1.77 brouard 4168: Youngest age at first (selected) pass %.2f, oldest age %.2f<br>\n
1.53 brouard 4169: Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n
4170: <hr size=\"2\" color=\"#EC5E5E\">
4171: <ul><li><h4>Parameter files</h4>\n
4172: - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n
4173: - Log file of the run: <a href=\"%s\">%s</a><br>\n
1.76 brouard 4174: - 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 4175: fclose(fichtm);
1.53 brouard 4176:
1.59 brouard 4177: 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 4178:
1.59 brouard 4179: /*------------ free_vector -------------*/
4180: chdir(path);
1.53 brouard 4181:
1.59 brouard 4182: free_ivector(wav,1,imx);
4183: free_imatrix(dh,1,lastpass-firstpass+1,1,imx);
4184: free_imatrix(bh,1,lastpass-firstpass+1,1,imx);
4185: free_imatrix(mw,1,lastpass-firstpass+1,1,imx);
4186: free_ivector(num,1,n);
4187: free_vector(agedc,1,n);
1.65 lievre 4188: /*free_matrix(covar,0,NCOVMAX,1,n);*/
1.59 brouard 4189: /*free_matrix(covar,1,NCOVMAX,1,n);*/
4190: fclose(ficparo);
4191: fclose(ficres);
1.53 brouard 4192:
4193:
1.54 brouard 4194: /*--------------- Prevalence limit (stable prevalence) --------------*/
1.53 brouard 4195:
4196: strcpy(filerespl,"pl");
4197: strcat(filerespl,fileres);
4198: if((ficrespl=fopen(filerespl,"w"))==NULL) {
1.54 brouard 4199: printf("Problem with stable prevalence resultfile: %s\n", filerespl);goto end;
4200: fprintf(ficlog,"Problem with stable prevalence resultfile: %s\n", filerespl);goto end;
1.53 brouard 4201: }
1.54 brouard 4202: printf("Computing stable prevalence: result on file '%s' \n", filerespl);
4203: fprintf(ficlog,"Computing stable prevalence: result on file '%s' \n", filerespl);
4204: fprintf(ficrespl,"#Stable prevalence \n");
1.53 brouard 4205: fprintf(ficrespl,"#Age ");
4206: for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);
4207: fprintf(ficrespl,"\n");
4208:
4209: prlim=matrix(1,nlstate,1,nlstate);
1.59 brouard 4210:
1.53 brouard 4211: agebase=ageminpar;
4212: agelim=agemaxpar;
4213: ftolpl=1.e-10;
4214: i1=cptcoveff;
4215: if (cptcovn < 1){i1=1;}
4216:
1.59 brouard 4217: for(cptcov=1,k=0;cptcov<=i1;cptcov++){
1.53 brouard 4218: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
1.59 brouard 4219: k=k+1;
4220: /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/
4221: fprintf(ficrespl,"\n#******");
4222: printf("\n#******");
4223: fprintf(ficlog,"\n#******");
4224: for(j=1;j<=cptcoveff;j++) {
4225: fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
4226: printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
4227: fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
4228: }
4229: fprintf(ficrespl,"******\n");
4230: printf("******\n");
4231: fprintf(ficlog,"******\n");
1.53 brouard 4232:
1.59 brouard 4233: for (age=agebase; age<=agelim; age++){
4234: prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
1.69 brouard 4235: fprintf(ficrespl,"%.0f ",age );
4236: for(j=1;j<=cptcoveff;j++)
4237: fprintf(ficrespl,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
1.59 brouard 4238: for(i=1; i<=nlstate;i++)
1.53 brouard 4239: fprintf(ficrespl," %.5f", prlim[i][i]);
1.59 brouard 4240: fprintf(ficrespl,"\n");
1.53 brouard 4241: }
4242: }
1.59 brouard 4243: }
1.53 brouard 4244: fclose(ficrespl);
4245:
4246: /*------------- h Pij x at various ages ------------*/
4247:
4248: strcpy(filerespij,"pij"); strcat(filerespij,fileres);
4249: if((ficrespij=fopen(filerespij,"w"))==NULL) {
4250: printf("Problem with Pij resultfile: %s\n", filerespij);goto end;
4251: fprintf(ficlog,"Problem with Pij resultfile: %s\n", filerespij);goto end;
4252: }
4253: printf("Computing pij: result on file '%s' \n", filerespij);
4254: fprintf(ficlog,"Computing pij: result on file '%s' \n", filerespij);
4255:
4256: stepsize=(int) (stepm+YEARM-1)/YEARM;
4257: /*if (stepm<=24) stepsize=2;*/
4258:
4259: agelim=AGESUP;
4260: hstepm=stepsize*YEARM; /* Every year of age */
4261: hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */
4262:
4263: /* hstepm=1; aff par mois*/
4264:
1.70 brouard 4265: fprintf(ficrespij,"#****** h Pij x Probability to be in state j at age x+h being in i at x ");
1.59 brouard 4266: for(cptcov=1,k=0;cptcov<=i1;cptcov++){
1.53 brouard 4267: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
4268: k=k+1;
1.59 brouard 4269: fprintf(ficrespij,"\n#****** ");
4270: for(j=1;j<=cptcoveff;j++)
4271: fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
4272: fprintf(ficrespij,"******\n");
1.53 brouard 4273:
1.59 brouard 4274: for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */
4275: nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
4276: nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
4277:
4278: /* nhstepm=nhstepm*YEARM; aff par mois*/
4279:
4280: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4281: oldm=oldms;savm=savms;
4282: hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
1.70 brouard 4283: fprintf(ficrespij,"# Cov Agex agex+h hpijx with i,j=");
1.59 brouard 4284: for(i=1; i<=nlstate;i++)
4285: for(j=1; j<=nlstate+ndeath;j++)
4286: fprintf(ficrespij," %1d-%1d",i,j);
4287: fprintf(ficrespij,"\n");
4288: for (h=0; h<=nhstepm; h++){
1.70 brouard 4289: fprintf(ficrespij,"%d %3.f %3.f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );
1.53 brouard 4290: for(i=1; i<=nlstate;i++)
4291: for(j=1; j<=nlstate+ndeath;j++)
1.59 brouard 4292: fprintf(ficrespij," %.5f", p3mat[i][j][h]);
1.53 brouard 4293: fprintf(ficrespij,"\n");
4294: }
1.59 brouard 4295: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4296: fprintf(ficrespij,"\n");
4297: }
1.53 brouard 4298: }
4299: }
4300:
1.74 brouard 4301: varprob(optionfilefiname, matcov, p, delti, nlstate, bage, fage,k,Tvar,nbcode, ncodemax);
1.53 brouard 4302:
4303: fclose(ficrespij);
4304:
4305:
4306: /*---------- Forecasting ------------------*/
1.69 brouard 4307: /*if((stepm == 1) && (strcmp(model,".")==0)){*/
4308: if(prevfcast==1){
1.74 brouard 4309: /* if(stepm ==1){*/
1.70 brouard 4310: prevforecast(fileres, anproj1, mproj1, jproj1, agemin, agemax, dateprev1, dateprev2, mobilavproj, bage, fage, firstpass, lastpass, anproj2, p, cptcoveff);
1.74 brouard 4311: /* (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);*/
4312: /* } */
4313: /* else{ */
4314: /* erreur=108; */
4315: /* 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); */
4316: /* 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); */
4317: /* } */
1.69 brouard 4318: }
1.53 brouard 4319:
4320:
4321: /*---------- Health expectancies and variances ------------*/
4322:
4323: strcpy(filerest,"t");
4324: strcat(filerest,fileres);
4325: if((ficrest=fopen(filerest,"w"))==NULL) {
4326: printf("Problem with total LE resultfile: %s\n", filerest);goto end;
4327: fprintf(ficlog,"Problem with total LE resultfile: %s\n", filerest);goto end;
4328: }
4329: printf("Computing Total LEs with variances: file '%s' \n", filerest);
4330: fprintf(ficlog,"Computing Total LEs with variances: file '%s' \n", filerest);
4331:
4332:
4333: strcpy(filerese,"e");
4334: strcat(filerese,fileres);
4335: if((ficreseij=fopen(filerese,"w"))==NULL) {
4336: printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
4337: fprintf(ficlog,"Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
4338: }
4339: printf("Computing Health Expectancies: result on file '%s' \n", filerese);
4340: fprintf(ficlog,"Computing Health Expectancies: result on file '%s' \n", filerese);
1.68 lievre 4341:
1.53 brouard 4342: strcpy(fileresv,"v");
4343: strcat(fileresv,fileres);
4344: if((ficresvij=fopen(fileresv,"w"))==NULL) {
4345: printf("Problem with variance resultfile: %s\n", fileresv);exit(0);
4346: fprintf(ficlog,"Problem with variance resultfile: %s\n", fileresv);exit(0);
4347: }
4348: printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
4349: fprintf(ficlog,"Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
1.58 lievre 4350:
1.74 brouard 4351: /* Computes prevalence between agemin (i.e minimal age computed) and no more ageminpar */
4352: prevalence(agemin, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
4353: /* 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",\
4354: ageminpar, agemax, s[lastpass][imx], agev[lastpass][imx], nlstate, imx, mint[lastpass][imx],anint[lastpass][imx], dateprev1, dateprev2, firstpass, lastpass);
4355: */
1.58 lievre 4356:
1.54 brouard 4357: if (mobilav!=0) {
1.53 brouard 4358: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
1.54 brouard 4359: if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
4360: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
4361: printf(" Error in movingaverage mobilav=%d\n",mobilav);
4362: }
1.53 brouard 4363: }
4364:
1.59 brouard 4365: for(cptcov=1,k=0;cptcov<=i1;cptcov++){
1.53 brouard 4366: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
4367: k=k+1;
4368: fprintf(ficrest,"\n#****** ");
4369: for(j=1;j<=cptcoveff;j++)
4370: fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
4371: fprintf(ficrest,"******\n");
4372:
4373: fprintf(ficreseij,"\n#****** ");
4374: for(j=1;j<=cptcoveff;j++)
4375: fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
4376: fprintf(ficreseij,"******\n");
4377:
4378: fprintf(ficresvij,"\n#****** ");
4379: for(j=1;j<=cptcoveff;j++)
4380: fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
4381: fprintf(ficresvij,"******\n");
4382:
4383: eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
4384: oldm=oldms;savm=savms;
4385: evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov);
4386:
4387: vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
4388: oldm=oldms;savm=savms;
4389: varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,0, mobilav);
4390: if(popbased==1){
4391: 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 4392: }
1.53 brouard 4393:
4394:
4395: fprintf(ficrest,"#Total LEs with variances: e.. (std) ");
4396: for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);
4397: fprintf(ficrest,"\n");
4398:
4399: epj=vector(1,nlstate+1);
4400: for(age=bage; age <=fage ;age++){
4401: prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
4402: if (popbased==1) {
1.54 brouard 4403: if(mobilav ==0){
1.53 brouard 4404: for(i=1; i<=nlstate;i++)
4405: prlim[i][i]=probs[(int)age][i][k];
1.54 brouard 4406: }else{ /* mobilav */
1.53 brouard 4407: for(i=1; i<=nlstate;i++)
4408: prlim[i][i]=mobaverage[(int)age][i][k];
4409: }
4410: }
4411:
4412: fprintf(ficrest," %4.0f",age);
4413: for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){
4414: for(i=1, epj[j]=0.;i <=nlstate;i++) {
4415: epj[j] += prlim[i][i]*eij[i][j][(int)age];
4416: /* printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/
4417: }
4418: epj[nlstate+1] +=epj[j];
4419: }
4420:
4421: for(i=1, vepp=0.;i <=nlstate;i++)
4422: for(j=1;j <=nlstate;j++)
4423: vepp += vareij[i][j][(int)age];
4424: fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));
4425: for(j=1;j <=nlstate;j++){
4426: fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));
4427: }
4428: fprintf(ficrest,"\n");
4429: }
1.59 brouard 4430: free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
4431: free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);
4432: free_vector(epj,1,nlstate+1);
1.53 brouard 4433: }
4434: }
1.59 brouard 4435: free_vector(weight,1,n);
4436: free_imatrix(Tvard,1,15,1,2);
4437: free_imatrix(s,1,maxwav+1,1,n);
4438: free_matrix(anint,1,maxwav,1,n);
4439: free_matrix(mint,1,maxwav,1,n);
4440: free_ivector(cod,1,n);
4441: free_ivector(tab,1,NCOVMAX);
1.53 brouard 4442: fclose(ficreseij);
4443: fclose(ficresvij);
4444: fclose(ficrest);
4445: fclose(ficpar);
4446:
1.54 brouard 4447: /*------- Variance of stable prevalence------*/
1.53 brouard 4448:
4449: strcpy(fileresvpl,"vpl");
4450: strcat(fileresvpl,fileres);
4451: if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {
1.54 brouard 4452: printf("Problem with variance of stable prevalence resultfile: %s\n", fileresvpl);
1.53 brouard 4453: exit(0);
4454: }
1.54 brouard 4455: printf("Computing Variance-covariance of stable prevalence: file '%s' \n", fileresvpl);
1.53 brouard 4456:
1.59 brouard 4457: for(cptcov=1,k=0;cptcov<=i1;cptcov++){
1.53 brouard 4458: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
4459: k=k+1;
4460: fprintf(ficresvpl,"\n#****** ");
4461: for(j=1;j<=cptcoveff;j++)
4462: fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
4463: fprintf(ficresvpl,"******\n");
4464:
4465: varpl=matrix(1,nlstate,(int) bage, (int) fage);
4466: oldm=oldms;savm=savms;
1.59 brouard 4467: varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);
4468: free_matrix(varpl,1,nlstate,(int) bage, (int)fage);
1.53 brouard 4469: }
1.59 brouard 4470: }
1.53 brouard 4471:
4472: fclose(ficresvpl);
4473:
4474: /*---------- End : free ----------------*/
4475: free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);
4476: free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);
4477: free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);
4478: free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);
1.65 lievre 4479:
4480: free_matrix(covar,0,NCOVMAX,1,n);
1.53 brouard 4481: free_matrix(matcov,1,npar,1,npar);
1.74 brouard 4482: /*free_vector(delti,1,npar);*/
4483: free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
1.53 brouard 4484: free_matrix(agev,1,maxwav,1,imx);
4485: free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
1.54 brouard 4486: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
1.74 brouard 4487: free_ma3x(probs,1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
4488:
1.59 brouard 4489: free_ivector(ncodemax,1,8);
4490: free_ivector(Tvar,1,15);
4491: free_ivector(Tprod,1,15);
4492: free_ivector(Tvaraff,1,15);
4493: free_ivector(Tage,1,15);
4494: free_ivector(Tcode,1,100);
1.53 brouard 4495:
1.74 brouard 4496: /* fclose(fichtm);*/
4497: /* fclose(ficgp);*/ /* ALready done */
1.53 brouard 4498:
4499:
4500: if(erreur >0){
4501: printf("End of Imach with error or warning %d\n",erreur);
4502: fprintf(ficlog,"End of Imach with error or warning %d\n",erreur);
4503: }else{
4504: printf("End of Imach\n");
4505: fprintf(ficlog,"End of Imach\n");
4506: }
4507: printf("See log file on %s\n",filelog);
4508: fclose(ficlog);
4509: /* gettimeofday(&end_time, (struct timezone*)0);*/ /* after time */
4510:
4511: /* 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);*/
4512: /*printf("Total time was %d uSec.\n", total_usecs);*/
4513: /*------ End -----------*/
4514:
1.59 brouard 4515: end:
1.53 brouard 4516: #ifdef windows
4517: /* chdir(pathcd);*/
4518: #endif
4519: /*system("wgnuplot graph.plt");*/
4520: /*system("../gp37mgw/wgnuplot graph.plt");*/
4521: /*system("cd ../gp37mgw");*/
4522: /* system("..\\gp37mgw\\wgnuplot graph.plt");*/
1.59 brouard 4523: strcpy(plotcmd,GNUPLOTPROGRAM);
4524: strcat(plotcmd," ");
4525: strcat(plotcmd,optionfilegnuplot);
1.75 brouard 4526: printf("Starting graphs with: %s",plotcmd);fflush(stdout);
1.59 brouard 4527: system(plotcmd);
1.75 brouard 4528: printf(" Wait...");
1.53 brouard 4529:
1.54 brouard 4530: /*#ifdef windows*/
1.53 brouard 4531: while (z[0] != 'q') {
4532: /* chdir(path); */
4533: printf("\nType e to edit output files, g to graph again, c to start again, and q for exiting: ");
4534: scanf("%s",z);
4535: if (z[0] == 'c') system("./imach");
4536: else if (z[0] == 'e') system(optionfilehtm);
4537: else if (z[0] == 'g') system(plotcmd);
4538: else if (z[0] == 'q') exit(0);
4539: }
1.54 brouard 4540: /*#endif */
1.53 brouard 4541: }
4542:
4543:
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