Annotation of imach/src/imach.c, revision 1.84
1.84 ! brouard 1: /* $Id: imach.c,v 1.83 2003/06/10 13:39:11 lievre Exp $
1.83 lievre 2: $State: Exp $
3: $Log: imach.c,v $
1.84 ! brouard 4: Revision 1.83 2003/06/10 13:39:11 lievre
! 5: *** empty log message ***
! 6:
1.83 lievre 7: Revision 1.82 2003/06/05 15:57:20 brouard
8: Add log in imach.c and fullversion number is now printed.
9:
1.82 brouard 10: */
11: /*
1.53 brouard 12: Interpolated Markov Chain
13:
14: Short summary of the programme:
15:
16: This program computes Healthy Life Expectancies from
17: cross-longitudinal data. Cross-longitudinal data consist in: -1- a
18: first survey ("cross") where individuals from different ages are
19: interviewed on their health status or degree of disability (in the
20: case of a health survey which is our main interest) -2- at least a
21: second wave of interviews ("longitudinal") which measure each change
22: (if any) in individual health status. Health expectancies are
23: computed from the time spent in each health state according to a
24: model. More health states you consider, more time is necessary to reach the
25: Maximum Likelihood of the parameters involved in the model. The
26: simplest model is the multinomial logistic model where pij is the
27: probability to be observed in state j at the second wave
28: conditional to be observed in state i at the first wave. Therefore
29: the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where
30: 'age' is age and 'sex' is a covariate. If you want to have a more
31: complex model than "constant and age", you should modify the program
32: where the markup *Covariates have to be included here again* invites
33: you to do it. More covariates you add, slower the
34: convergence.
35:
36: The advantage of this computer programme, compared to a simple
37: multinomial logistic model, is clear when the delay between waves is not
38: identical for each individual. Also, if a individual missed an
39: intermediate interview, the information is lost, but taken into
40: account using an interpolation or extrapolation.
41:
42: hPijx is the probability to be observed in state i at age x+h
43: conditional to the observed state i at age x. The delay 'h' can be
44: split into an exact number (nh*stepm) of unobserved intermediate
1.66 brouard 45: states. This elementary transition (by month, quarter,
46: semester or year) is modelled as a multinomial logistic. The hPx
1.53 brouard 47: matrix is simply the matrix product of nh*stepm elementary matrices
48: and the contribution of each individual to the likelihood is simply
49: hPijx.
50:
51: Also this programme outputs the covariance matrix of the parameters but also
1.54 brouard 52: of the life expectancies. It also computes the stable prevalence.
1.53 brouard 53:
54: Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).
55: Institut national d'études démographiques, Paris.
56: This software have been partly granted by Euro-REVES, a concerted action
57: from the European Union.
58: It is copyrighted identically to a GNU software product, ie programme and
59: software can be distributed freely for non commercial use. Latest version
60: can be accessed at http://euroreves.ined.fr/imach .
1.74 brouard 61:
62: Help to debug: LD_PRELOAD=/usr/local/lib/libnjamd.so ./imach foo.imach
63: or better on gdb : set env LD_PRELOAD=/usr/local/lib/libnjamd.so
64:
1.53 brouard 65: **********************************************************************/
1.74 brouard 66: /*
67: main
68: read parameterfile
69: read datafile
70: concatwav
1.84 ! brouard 71: freqsummary
1.74 brouard 72: if (mle >= 1)
73: mlikeli
74: print results files
75: if mle==1
76: computes hessian
77: read end of parameter file: agemin, agemax, bage, fage, estepm
78: begin-prev-date,...
79: open gnuplot file
80: open html file
81: stable prevalence
82: for age prevalim()
83: h Pij x
84: variance of p varprob
85: forecasting if prevfcast==1 prevforecast call prevalence()
86: health expectancies
87: Variance-covariance of DFLE
88: prevalence()
89: movingaverage()
90: varevsij()
91: if popbased==1 varevsij(,popbased)
92: total life expectancies
93: Variance of stable prevalence
94: end
95: */
96:
97:
98:
1.53 brouard 99:
100: #include <math.h>
101: #include <stdio.h>
102: #include <stdlib.h>
103: #include <unistd.h>
104:
105: #define MAXLINE 256
106: #define GNUPLOTPROGRAM "gnuplot"
107: /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
108: #define FILENAMELENGTH 80
109: /*#define DEBUG*/
1.55 lievre 110: #define windows
1.53 brouard 111: #define GLOCK_ERROR_NOPATH -1 /* empty path */
112: #define GLOCK_ERROR_GETCWD -2 /* cannot get cwd */
113:
114: #define MAXPARM 30 /* Maximum number of parameters for the optimization */
115: #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */
116:
117: #define NINTERVMAX 8
118: #define NLSTATEMAX 8 /* Maximum number of live states (for func) */
119: #define NDEATHMAX 8 /* Maximum number of dead states (for func) */
120: #define NCOVMAX 8 /* Maximum number of covariates */
121: #define MAXN 20000
122: #define YEARM 12. /* Number of months per year */
123: #define AGESUP 130
124: #define AGEBASE 40
125: #ifdef windows
126: #define DIRSEPARATOR '\\'
127: #define ODIRSEPARATOR '/'
128: #else
129: #define DIRSEPARATOR '/'
130: #define ODIRSEPARATOR '\\'
131: #endif
132:
1.84 ! brouard 133: /* $Id: imach.c,v 1.83 2003/06/10 13:39:11 lievre Exp $ */
1.81 brouard 134: /* $State: Exp $ */
1.80 brouard 135:
1.84 ! brouard 136: char version[]="Imach version 0.95a2, June 2003, INED-EUROREVES ";
! 137: char fullversion[]="$Revision: 1.83 $ $Date: 2003/06/10 13:39:11 $";
1.53 brouard 138: int erreur; /* Error number */
139: int nvar;
140: int cptcovn=0, cptcovage=0, cptcoveff=0,cptcov;
141: int npar=NPARMAX;
142: int nlstate=2; /* Number of live states */
143: int ndeath=1; /* Number of dead states */
144: int ncovmodel, ncovcol; /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
145: int popbased=0;
146:
147: int *wav; /* Number of waves for this individuual 0 is possible */
148: int maxwav; /* Maxim number of waves */
149: int jmin, jmax; /* min, max spacing between 2 waves */
150: int mle, weightopt;
151: int **mw; /* mw[mi][i] is number of the mi wave for this individual */
152: int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
1.59 brouard 153: int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between
154: * wave mi and wave mi+1 is not an exact multiple of stepm. */
1.53 brouard 155: double jmean; /* Mean space between 2 waves */
156: double **oldm, **newm, **savm; /* Working pointers to matrices */
157: double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
158: FILE *fic,*ficpar, *ficparo,*ficres, *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
1.76 brouard 159: FILE *ficlog, *ficrespow;
1.53 brouard 160: FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
161: FILE *ficresprobmorprev;
162: FILE *fichtm; /* Html File */
163: FILE *ficreseij;
164: char filerese[FILENAMELENGTH];
165: FILE *ficresvij;
166: char fileresv[FILENAMELENGTH];
167: FILE *ficresvpl;
168: char fileresvpl[FILENAMELENGTH];
169: char title[MAXLINE];
170: char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH], filerespl[FILENAMELENGTH];
171: char optionfilext[10], optionfilefiname[FILENAMELENGTH], plotcmd[FILENAMELENGTH];
172:
173: char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
174: char filelog[FILENAMELENGTH]; /* Log file */
175: char filerest[FILENAMELENGTH];
176: char fileregp[FILENAMELENGTH];
177: char popfile[FILENAMELENGTH];
178:
179: char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH];
180:
181: #define NR_END 1
182: #define FREE_ARG char*
183: #define FTOL 1.0e-10
184:
185: #define NRANSI
186: #define ITMAX 200
187:
188: #define TOL 2.0e-4
189:
190: #define CGOLD 0.3819660
191: #define ZEPS 1.0e-10
192: #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);
193:
194: #define GOLD 1.618034
195: #define GLIMIT 100.0
196: #define TINY 1.0e-20
197:
198: static double maxarg1,maxarg2;
199: #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
200: #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
201:
202: #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
203: #define rint(a) floor(a+0.5)
204:
205: static double sqrarg;
206: #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
207: #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}
208:
209: int imx;
210: int stepm;
211: /* Stepm, step in month: minimum step interpolation*/
212:
213: int estepm;
214: /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
215:
216: int m,nb;
217: int *num, firstpass=0, lastpass=4,*cod, *ncodemax, *Tage;
218: double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
1.55 lievre 219: double **pmmij, ***probs;
1.53 brouard 220: double dateintmean=0;
221:
222: double *weight;
223: int **s; /* Status */
224: double *agedc, **covar, idx;
225: int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;
226:
227: double ftol=FTOL; /* Tolerance for computing Max Likelihood */
228: double ftolhess; /* Tolerance for computing hessian */
229:
230: /**************** split *************************/
231: static int split( char *path, char *dirc, char *name, char *ext, char *finame )
232: {
1.59 brouard 233: char *ss; /* pointer */
234: int l1, l2; /* length counters */
1.53 brouard 235:
1.59 brouard 236: l1 = strlen(path ); /* length of path */
237: if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
238: ss= strrchr( path, DIRSEPARATOR ); /* find last / */
239: if ( ss == NULL ) { /* no directory, so use current */
240: /*if(strrchr(path, ODIRSEPARATOR )==NULL)
241: printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
1.74 brouard 242: /* get current working directory */
243: /* extern char* getcwd ( char *buf , int len);*/
1.59 brouard 244: if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {
245: return( GLOCK_ERROR_GETCWD );
246: }
247: strcpy( name, path ); /* we've got it */
248: } else { /* strip direcotry from path */
249: ss++; /* after this, the filename */
250: l2 = strlen( ss ); /* length of filename */
251: if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
252: strcpy( name, ss ); /* save file name */
253: strncpy( dirc, path, l1 - l2 ); /* now the directory */
254: dirc[l1-l2] = 0; /* add zero */
255: }
256: l1 = strlen( dirc ); /* length of directory */
1.53 brouard 257: #ifdef windows
1.59 brouard 258: if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; }
1.53 brouard 259: #else
1.59 brouard 260: if ( dirc[l1-1] != '/' ) { dirc[l1] = '/'; dirc[l1+1] = 0; }
1.53 brouard 261: #endif
1.59 brouard 262: ss = strrchr( name, '.' ); /* find last / */
263: ss++;
264: strcpy(ext,ss); /* save extension */
265: l1= strlen( name);
266: l2= strlen(ss)+1;
267: strncpy( finame, name, l1-l2);
268: finame[l1-l2]= 0;
269: return( 0 ); /* we're done */
1.53 brouard 270: }
271:
272:
273: /******************************************/
274:
275: void replace(char *s, char*t)
276: {
277: int i;
278: int lg=20;
279: i=0;
280: lg=strlen(t);
281: for(i=0; i<= lg; i++) {
282: (s[i] = t[i]);
283: if (t[i]== '\\') s[i]='/';
284: }
285: }
286:
287: int nbocc(char *s, char occ)
288: {
289: int i,j=0;
290: int lg=20;
291: i=0;
292: lg=strlen(s);
293: for(i=0; i<= lg; i++) {
294: if (s[i] == occ ) j++;
295: }
296: return j;
297: }
298:
299: void cutv(char *u,char *v, char*t, char occ)
300: {
301: /* cuts string t into u and v where u is ended by char occ excluding it
302: and v is after occ excluding it too : ex cutv(u,v,"abcdef2ghi2j",2)
303: gives u="abcedf" and v="ghi2j" */
304: int i,lg,j,p=0;
305: i=0;
306: for(j=0; j<=strlen(t)-1; j++) {
307: if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;
308: }
309:
310: lg=strlen(t);
311: for(j=0; j<p; j++) {
312: (u[j] = t[j]);
313: }
314: u[p]='\0';
315:
316: for(j=0; j<= lg; j++) {
317: if (j>=(p+1))(v[j-p-1] = t[j]);
318: }
319: }
320:
321: /********************** nrerror ********************/
322:
323: void nrerror(char error_text[])
324: {
325: fprintf(stderr,"ERREUR ...\n");
326: fprintf(stderr,"%s\n",error_text);
1.59 brouard 327: exit(EXIT_FAILURE);
1.53 brouard 328: }
329: /*********************** vector *******************/
330: double *vector(int nl, int nh)
331: {
332: double *v;
333: v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
334: if (!v) nrerror("allocation failure in vector");
335: return v-nl+NR_END;
336: }
337:
338: /************************ free vector ******************/
339: void free_vector(double*v, int nl, int nh)
340: {
341: free((FREE_ARG)(v+nl-NR_END));
342: }
343:
344: /************************ivector *******************************/
1.76 brouard 345: char *cvector(long nl,long nh)
346: {
347: char *v;
348: v=(char *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(char)));
349: if (!v) nrerror("allocation failure in cvector");
350: return v-nl+NR_END;
351: }
352:
353: /******************free ivector **************************/
354: void free_cvector(char *v, long nl, long nh)
355: {
356: free((FREE_ARG)(v+nl-NR_END));
357: }
358:
359: /************************ivector *******************************/
1.53 brouard 360: int *ivector(long nl,long nh)
361: {
362: int *v;
363: v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
364: if (!v) nrerror("allocation failure in ivector");
365: return v-nl+NR_END;
366: }
367:
368: /******************free ivector **************************/
369: void free_ivector(int *v, long nl, long nh)
370: {
371: free((FREE_ARG)(v+nl-NR_END));
372: }
373:
374: /******************* imatrix *******************************/
375: int **imatrix(long nrl, long nrh, long ncl, long nch)
376: /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */
377: {
378: long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;
379: int **m;
380:
381: /* allocate pointers to rows */
382: m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));
383: if (!m) nrerror("allocation failure 1 in matrix()");
384: m += NR_END;
385: m -= nrl;
386:
387:
388: /* allocate rows and set pointers to them */
389: m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));
390: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
391: m[nrl] += NR_END;
392: m[nrl] -= ncl;
393:
394: for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;
395:
396: /* return pointer to array of pointers to rows */
397: return m;
398: }
399:
400: /****************** free_imatrix *************************/
401: void free_imatrix(m,nrl,nrh,ncl,nch)
402: int **m;
403: long nch,ncl,nrh,nrl;
404: /* free an int matrix allocated by imatrix() */
405: {
406: free((FREE_ARG) (m[nrl]+ncl-NR_END));
407: free((FREE_ARG) (m+nrl-NR_END));
408: }
409:
410: /******************* matrix *******************************/
411: double **matrix(long nrl, long nrh, long ncl, long nch)
412: {
413: long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
414: double **m;
415:
416: m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
417: if (!m) nrerror("allocation failure 1 in matrix()");
418: m += NR_END;
419: m -= nrl;
420:
421: m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
422: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
423: m[nrl] += NR_END;
424: m[nrl] -= ncl;
425:
426: for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
427: return m;
1.74 brouard 428: /* print *(*(m+1)+70) ou print m[1][70]; print m+1 or print &(m[1])
429: */
1.53 brouard 430: }
431:
432: /*************************free matrix ************************/
433: void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
434: {
435: free((FREE_ARG)(m[nrl]+ncl-NR_END));
436: free((FREE_ARG)(m+nrl-NR_END));
437: }
438:
439: /******************* ma3x *******************************/
440: double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
441: {
442: long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
443: double ***m;
444:
445: m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
446: if (!m) nrerror("allocation failure 1 in matrix()");
447: m += NR_END;
448: m -= nrl;
449:
450: m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
451: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
452: m[nrl] += NR_END;
453: m[nrl] -= ncl;
454:
455: for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
456:
457: m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
458: if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
459: m[nrl][ncl] += NR_END;
460: m[nrl][ncl] -= nll;
461: for (j=ncl+1; j<=nch; j++)
462: m[nrl][j]=m[nrl][j-1]+nlay;
463:
464: for (i=nrl+1; i<=nrh; i++) {
465: m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
466: for (j=ncl+1; j<=nch; j++)
467: m[i][j]=m[i][j-1]+nlay;
468: }
1.74 brouard 469: return m;
470: /* gdb: p *(m+1) <=> p m[1] and p (m+1) <=> p (m+1) <=> p &(m[1])
471: &(m[i][j][k]) <=> *((*(m+i) + j)+k)
472: */
1.53 brouard 473: }
474:
475: /*************************free ma3x ************************/
476: void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
477: {
478: free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
479: free((FREE_ARG)(m[nrl]+ncl-NR_END));
480: free((FREE_ARG)(m+nrl-NR_END));
481: }
482:
483: /***************** f1dim *************************/
484: extern int ncom;
485: extern double *pcom,*xicom;
486: extern double (*nrfunc)(double []);
487:
488: double f1dim(double x)
489: {
490: int j;
491: double f;
492: double *xt;
493:
494: xt=vector(1,ncom);
495: for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];
496: f=(*nrfunc)(xt);
497: free_vector(xt,1,ncom);
498: return f;
499: }
500:
501: /*****************brent *************************/
502: double brent(double ax, double bx, double cx, double (*f)(double), double tol, double *xmin)
503: {
504: int iter;
505: double a,b,d,etemp;
506: double fu,fv,fw,fx;
507: double ftemp;
508: double p,q,r,tol1,tol2,u,v,w,x,xm;
509: double e=0.0;
510:
511: a=(ax < cx ? ax : cx);
512: b=(ax > cx ? ax : cx);
513: x=w=v=bx;
514: fw=fv=fx=(*f)(x);
515: for (iter=1;iter<=ITMAX;iter++) {
516: xm=0.5*(a+b);
517: tol2=2.0*(tol1=tol*fabs(x)+ZEPS);
518: /* if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
519: printf(".");fflush(stdout);
520: fprintf(ficlog,".");fflush(ficlog);
521: #ifdef DEBUG
522: 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);
523: 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);
524: /* if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
525: #endif
526: if (fabs(x-xm) <= (tol2-0.5*(b-a))){
527: *xmin=x;
528: return fx;
529: }
530: ftemp=fu;
531: if (fabs(e) > tol1) {
532: r=(x-w)*(fx-fv);
533: q=(x-v)*(fx-fw);
534: p=(x-v)*q-(x-w)*r;
535: q=2.0*(q-r);
536: if (q > 0.0) p = -p;
537: q=fabs(q);
538: etemp=e;
539: e=d;
540: if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))
541: d=CGOLD*(e=(x >= xm ? a-x : b-x));
542: else {
543: d=p/q;
544: u=x+d;
545: if (u-a < tol2 || b-u < tol2)
546: d=SIGN(tol1,xm-x);
547: }
548: } else {
549: d=CGOLD*(e=(x >= xm ? a-x : b-x));
550: }
551: u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));
552: fu=(*f)(u);
553: if (fu <= fx) {
554: if (u >= x) a=x; else b=x;
555: SHFT(v,w,x,u)
556: SHFT(fv,fw,fx,fu)
557: } else {
558: if (u < x) a=u; else b=u;
559: if (fu <= fw || w == x) {
560: v=w;
561: w=u;
562: fv=fw;
563: fw=fu;
564: } else if (fu <= fv || v == x || v == w) {
565: v=u;
566: fv=fu;
567: }
568: }
569: }
570: nrerror("Too many iterations in brent");
571: *xmin=x;
572: return fx;
573: }
574:
575: /****************** mnbrak ***********************/
576:
577: void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,
578: double (*func)(double))
579: {
580: double ulim,u,r,q, dum;
581: double fu;
582:
583: *fa=(*func)(*ax);
584: *fb=(*func)(*bx);
585: if (*fb > *fa) {
586: SHFT(dum,*ax,*bx,dum)
587: SHFT(dum,*fb,*fa,dum)
588: }
589: *cx=(*bx)+GOLD*(*bx-*ax);
590: *fc=(*func)(*cx);
591: while (*fb > *fc) {
592: r=(*bx-*ax)*(*fb-*fc);
593: q=(*bx-*cx)*(*fb-*fa);
594: u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/
595: (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r));
596: ulim=(*bx)+GLIMIT*(*cx-*bx);
597: if ((*bx-u)*(u-*cx) > 0.0) {
598: fu=(*func)(u);
599: } else if ((*cx-u)*(u-ulim) > 0.0) {
600: fu=(*func)(u);
601: if (fu < *fc) {
602: SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))
603: SHFT(*fb,*fc,fu,(*func)(u))
604: }
605: } else if ((u-ulim)*(ulim-*cx) >= 0.0) {
606: u=ulim;
607: fu=(*func)(u);
608: } else {
609: u=(*cx)+GOLD*(*cx-*bx);
610: fu=(*func)(u);
611: }
612: SHFT(*ax,*bx,*cx,u)
613: SHFT(*fa,*fb,*fc,fu)
614: }
615: }
616:
617: /*************** linmin ************************/
618:
619: int ncom;
620: double *pcom,*xicom;
621: double (*nrfunc)(double []);
622:
623: void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))
624: {
625: double brent(double ax, double bx, double cx,
626: double (*f)(double), double tol, double *xmin);
627: double f1dim(double x);
628: void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,
629: double *fc, double (*func)(double));
630: int j;
631: double xx,xmin,bx,ax;
632: double fx,fb,fa;
633:
634: ncom=n;
635: pcom=vector(1,n);
636: xicom=vector(1,n);
637: nrfunc=func;
638: for (j=1;j<=n;j++) {
639: pcom[j]=p[j];
640: xicom[j]=xi[j];
641: }
642: ax=0.0;
643: xx=1.0;
644: mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim);
645: *fret=brent(ax,xx,bx,f1dim,TOL,&xmin);
646: #ifdef DEBUG
647: printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
648: fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
649: #endif
650: for (j=1;j<=n;j++) {
651: xi[j] *= xmin;
652: p[j] += xi[j];
653: }
654: free_vector(xicom,1,n);
655: free_vector(pcom,1,n);
656: }
657:
658: /*************** powell ************************/
659: void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,
660: double (*func)(double []))
661: {
662: void linmin(double p[], double xi[], int n, double *fret,
663: double (*func)(double []));
664: int i,ibig,j;
665: double del,t,*pt,*ptt,*xit;
666: double fp,fptt;
667: double *xits;
668: pt=vector(1,n);
669: ptt=vector(1,n);
670: xit=vector(1,n);
671: xits=vector(1,n);
672: *fret=(*func)(p);
673: for (j=1;j<=n;j++) pt[j]=p[j];
674: for (*iter=1;;++(*iter)) {
675: fp=(*fret);
676: ibig=0;
677: del=0.0;
678: printf("\nPowell iter=%d -2*LL=%.12f",*iter,*fret);
679: fprintf(ficlog,"\nPowell iter=%d -2*LL=%.12f",*iter,*fret);
1.76 brouard 680: fprintf(ficrespow,"%d %.12f",*iter,*fret);
681: for (i=1;i<=n;i++) {
1.53 brouard 682: printf(" %d %.12f",i, p[i]);
1.76 brouard 683: fprintf(ficlog," %d %.12lf",i, p[i]);
684: fprintf(ficrespow," %.12lf", p[i]);
685: }
1.53 brouard 686: printf("\n");
687: fprintf(ficlog,"\n");
1.76 brouard 688: fprintf(ficrespow,"\n");
1.53 brouard 689: for (i=1;i<=n;i++) {
690: for (j=1;j<=n;j++) xit[j]=xi[j][i];
691: fptt=(*fret);
692: #ifdef DEBUG
693: printf("fret=%lf \n",*fret);
694: fprintf(ficlog,"fret=%lf \n",*fret);
695: #endif
696: printf("%d",i);fflush(stdout);
697: fprintf(ficlog,"%d",i);fflush(ficlog);
698: linmin(p,xit,n,fret,func);
699: if (fabs(fptt-(*fret)) > del) {
700: del=fabs(fptt-(*fret));
701: ibig=i;
702: }
703: #ifdef DEBUG
704: printf("%d %.12e",i,(*fret));
705: fprintf(ficlog,"%d %.12e",i,(*fret));
706: for (j=1;j<=n;j++) {
707: xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
708: printf(" x(%d)=%.12e",j,xit[j]);
709: fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
710: }
711: for(j=1;j<=n;j++) {
712: printf(" p=%.12e",p[j]);
713: fprintf(ficlog," p=%.12e",p[j]);
714: }
715: printf("\n");
716: fprintf(ficlog,"\n");
717: #endif
718: }
719: if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {
720: #ifdef DEBUG
721: int k[2],l;
722: k[0]=1;
723: k[1]=-1;
724: printf("Max: %.12e",(*func)(p));
725: fprintf(ficlog,"Max: %.12e",(*func)(p));
726: for (j=1;j<=n;j++) {
727: printf(" %.12e",p[j]);
728: fprintf(ficlog," %.12e",p[j]);
729: }
730: printf("\n");
731: fprintf(ficlog,"\n");
732: for(l=0;l<=1;l++) {
733: for (j=1;j<=n;j++) {
734: ptt[j]=p[j]+(p[j]-pt[j])*k[l];
735: printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
736: fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
737: }
738: printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
739: fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
740: }
741: #endif
742:
743:
744: free_vector(xit,1,n);
745: free_vector(xits,1,n);
746: free_vector(ptt,1,n);
747: free_vector(pt,1,n);
748: return;
749: }
750: if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");
751: for (j=1;j<=n;j++) {
752: ptt[j]=2.0*p[j]-pt[j];
753: xit[j]=p[j]-pt[j];
754: pt[j]=p[j];
755: }
756: fptt=(*func)(ptt);
757: if (fptt < fp) {
758: t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt);
759: if (t < 0.0) {
760: linmin(p,xit,n,fret,func);
761: for (j=1;j<=n;j++) {
762: xi[j][ibig]=xi[j][n];
763: xi[j][n]=xit[j];
764: }
765: #ifdef DEBUG
766: printf("Direction changed last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
767: fprintf(ficlog,"Direction changed last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
768: for(j=1;j<=n;j++){
769: printf(" %.12e",xit[j]);
770: fprintf(ficlog," %.12e",xit[j]);
771: }
772: printf("\n");
773: fprintf(ficlog,"\n");
774: #endif
1.54 brouard 775: }
1.53 brouard 776: }
777: }
778: }
779:
1.54 brouard 780: /**** Prevalence limit (stable prevalence) ****************/
1.53 brouard 781:
782: double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)
783: {
784: /* Computes the prevalence limit in each live state at age x by left multiplying the unit
785: matrix by transitions matrix until convergence is reached */
786:
787: int i, ii,j,k;
788: double min, max, maxmin, maxmax,sumnew=0.;
789: double **matprod2();
790: double **out, cov[NCOVMAX], **pmij();
791: double **newm;
792: double agefin, delaymax=50 ; /* Max number of years to converge */
793:
794: for (ii=1;ii<=nlstate+ndeath;ii++)
795: for (j=1;j<=nlstate+ndeath;j++){
796: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
797: }
798:
799: cov[1]=1.;
800:
801: /* Even if hstepm = 1, at least one multiplication by the unit matrix */
802: for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
803: newm=savm;
804: /* Covariates have to be included here again */
805: cov[2]=agefin;
806:
807: for (k=1; k<=cptcovn;k++) {
808: cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
809: /* 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]]);*/
810: }
811: for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
812: for (k=1; k<=cptcovprod;k++)
813: cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
814:
815: /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
816: /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
817: /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
818: out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);
819:
820: savm=oldm;
821: oldm=newm;
822: maxmax=0.;
823: for(j=1;j<=nlstate;j++){
824: min=1.;
825: max=0.;
826: for(i=1; i<=nlstate; i++) {
827: sumnew=0;
828: for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
829: prlim[i][j]= newm[i][j]/(1-sumnew);
830: max=FMAX(max,prlim[i][j]);
831: min=FMIN(min,prlim[i][j]);
832: }
833: maxmin=max-min;
834: maxmax=FMAX(maxmax,maxmin);
835: }
836: if(maxmax < ftolpl){
837: return prlim;
838: }
839: }
840: }
841:
842: /*************** transition probabilities ***************/
843:
844: double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
845: {
846: double s1, s2;
847: /*double t34;*/
848: int i,j,j1, nc, ii, jj;
849:
850: for(i=1; i<= nlstate; i++){
851: for(j=1; j<i;j++){
852: for (nc=1, s2=0.;nc <=ncovmodel; nc++){
853: /*s2 += param[i][j][nc]*cov[nc];*/
854: s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
855: /*printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2);*/
856: }
857: ps[i][j]=s2;
858: /*printf("s1=%.17e, s2=%.17e\n",s1,s2);*/
859: }
860: for(j=i+1; j<=nlstate+ndeath;j++){
861: for (nc=1, s2=0.;nc <=ncovmodel; nc++){
862: s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
863: /*printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2);*/
864: }
865: ps[i][j]=s2;
866: }
867: }
868: /*ps[3][2]=1;*/
869:
870: for(i=1; i<= nlstate; i++){
871: s1=0;
872: for(j=1; j<i; j++)
873: s1+=exp(ps[i][j]);
874: for(j=i+1; j<=nlstate+ndeath; j++)
875: s1+=exp(ps[i][j]);
876: ps[i][i]=1./(s1+1.);
877: for(j=1; j<i; j++)
878: ps[i][j]= exp(ps[i][j])*ps[i][i];
879: for(j=i+1; j<=nlstate+ndeath; j++)
880: ps[i][j]= exp(ps[i][j])*ps[i][i];
881: /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
882: } /* end i */
883:
884: for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
885: for(jj=1; jj<= nlstate+ndeath; jj++){
886: ps[ii][jj]=0;
887: ps[ii][ii]=1;
888: }
889: }
890:
891:
892: /* for(ii=1; ii<= nlstate+ndeath; ii++){
893: for(jj=1; jj<= nlstate+ndeath; jj++){
894: printf("%lf ",ps[ii][jj]);
895: }
896: printf("\n ");
897: }
898: printf("\n ");printf("%lf ",cov[2]);*/
899: /*
900: for(i=1; i<= npar; i++) printf("%f ",x[i]);
901: goto end;*/
902: return ps;
903: }
904:
905: /**************** Product of 2 matrices ******************/
906:
907: double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)
908: {
909: /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
910: b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
911: /* in, b, out are matrice of pointers which should have been initialized
912: before: only the contents of out is modified. The function returns
913: a pointer to pointers identical to out */
914: long i, j, k;
915: for(i=nrl; i<= nrh; i++)
916: for(k=ncolol; k<=ncoloh; k++)
917: for(j=ncl,out[i][k]=0.; j<=nch; j++)
918: out[i][k] +=in[i][j]*b[j][k];
919:
920: return out;
921: }
922:
923:
924: /************* Higher Matrix Product ***************/
925:
926: double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
927: {
1.66 brouard 928: /* Computes the transition matrix starting at age 'age' over
929: 'nhstepm*hstepm*stepm' months (i.e. until
930: age (in years) age+nhstepm*hstepm*stepm/12) by multiplying
931: nhstepm*hstepm matrices.
1.53 brouard 932: Output is stored in matrix po[i][j][h] for h every 'hstepm' step
1.66 brouard 933: (typically every 2 years instead of every month which is too big
934: for the memory).
1.53 brouard 935: Model is determined by parameters x and covariates have to be
936: included manually here.
937:
938: */
939:
940: int i, j, d, h, k;
941: double **out, cov[NCOVMAX];
942: double **newm;
943:
944: /* Hstepm could be zero and should return the unit matrix */
945: for (i=1;i<=nlstate+ndeath;i++)
946: for (j=1;j<=nlstate+ndeath;j++){
947: oldm[i][j]=(i==j ? 1.0 : 0.0);
948: po[i][j][0]=(i==j ? 1.0 : 0.0);
949: }
950: /* Even if hstepm = 1, at least one multiplication by the unit matrix */
951: for(h=1; h <=nhstepm; h++){
952: for(d=1; d <=hstepm; d++){
953: newm=savm;
954: /* Covariates have to be included here again */
955: cov[1]=1.;
956: cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
957: for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
958: for (k=1; k<=cptcovage;k++)
959: cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
960: for (k=1; k<=cptcovprod;k++)
961: cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
962:
963:
964: /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
965: /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
966: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,
967: pmij(pmmij,cov,ncovmodel,x,nlstate));
968: savm=oldm;
969: oldm=newm;
970: }
971: for(i=1; i<=nlstate+ndeath; i++)
972: for(j=1;j<=nlstate+ndeath;j++) {
973: po[i][j][h]=newm[i][j];
974: /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);
975: */
976: }
977: } /* end h */
978: return po;
979: }
980:
981:
982: /*************** log-likelihood *************/
983: double func( double *x)
984: {
985: int i, ii, j, k, mi, d, kk;
986: double l, ll[NLSTATEMAX], cov[NCOVMAX];
987: double **out;
988: double sw; /* Sum of weights */
989: double lli; /* Individual log likelihood */
1.59 brouard 990: int s1, s2;
1.68 lievre 991: double bbh, survp;
1.53 brouard 992: long ipmx;
993: /*extern weight */
994: /* We are differentiating ll according to initial status */
995: /* for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
996: /*for(i=1;i<imx;i++)
997: printf(" %d\n",s[4][i]);
998: */
999: cov[1]=1.;
1000:
1001: for(k=1; k<=nlstate; k++) ll[k]=0.;
1.61 brouard 1002:
1003: if(mle==1){
1004: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1005: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
1006: for(mi=1; mi<= wav[i]-1; mi++){
1007: for (ii=1;ii<=nlstate+ndeath;ii++)
1008: for (j=1;j<=nlstate+ndeath;j++){
1009: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1010: savm[ii][j]=(ii==j ? 1.0 : 0.0);
1011: }
1012: for(d=0; d<dh[mi][i]; d++){
1013: newm=savm;
1014: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
1015: for (kk=1; kk<=cptcovage;kk++) {
1016: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
1017: }
1018: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1019: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1020: savm=oldm;
1021: oldm=newm;
1022: } /* end mult */
1.53 brouard 1023:
1.61 brouard 1024: /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
1025: /* But now since version 0.9 we anticipate for bias and large stepm.
1026: * If stepm is larger than one month (smallest stepm) and if the exact delay
1027: * (in months) between two waves is not a multiple of stepm, we rounded to
1028: * the nearest (and in case of equal distance, to the lowest) interval but now
1029: * we keep into memory the bias bh[mi][i] and also the previous matrix product
1030: * (i.e to dh[mi][i]-1) saved in 'savm'. The we inter(extra)polate the
1031: * probability in order to take into account the bias as a fraction of the way
1032: * from savm to out if bh is neagtive or even beyond if bh is positive. bh varies
1033: * -stepm/2 to stepm/2 .
1034: * For stepm=1 the results are the same as for previous versions of Imach.
1035: * For stepm > 1 the results are less biased than in previous versions.
1036: */
1037: s1=s[mw[mi][i]][i];
1038: s2=s[mw[mi+1][i]][i];
1.64 lievre 1039: bbh=(double)bh[mi][i]/(double)stepm;
1040: /* bias is positive if real duration
1041: * is higher than the multiple of stepm and negative otherwise.
1042: */
1043: /* 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 1044: if( s2 > nlstate){
1045: /* i.e. if s2 is a death state and if the date of death is known then the contribution
1046: to the likelihood is the probability to die between last step unit time and current
1047: step unit time, which is also the differences between probability to die before dh
1048: and probability to die before dh-stepm .
1049: In version up to 0.92 likelihood was computed
1050: as if date of death was unknown. Death was treated as any other
1051: health state: the date of the interview describes the actual state
1052: and not the date of a change in health state. The former idea was
1053: to consider that at each interview the state was recorded
1054: (healthy, disable or death) and IMaCh was corrected; but when we
1055: introduced the exact date of death then we should have modified
1056: the contribution of an exact death to the likelihood. This new
1057: contribution is smaller and very dependent of the step unit
1058: stepm. It is no more the probability to die between last interview
1059: and month of death but the probability to survive from last
1060: interview up to one month before death multiplied by the
1061: probability to die within a month. Thanks to Chris
1062: Jackson for correcting this bug. Former versions increased
1063: mortality artificially. The bad side is that we add another loop
1064: which slows down the processing. The difference can be up to 10%
1065: lower mortality.
1066: */
1067: lli=log(out[s1][s2] - savm[s1][s2]);
1068: }else{
1069: lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
1070: /* 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 */
1071: }
1.64 lievre 1072: /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
1073: /*if(lli ==000.0)*/
1074: /*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 1075: ipmx +=1;
1.64 lievre 1076: sw += weight[i];
1077: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1078: } /* end of wave */
1079: } /* end of individual */
1080: } else if(mle==2){
1081: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1082: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
1083: for(mi=1; mi<= wav[i]-1; mi++){
1084: for (ii=1;ii<=nlstate+ndeath;ii++)
1085: for (j=1;j<=nlstate+ndeath;j++){
1086: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1087: savm[ii][j]=(ii==j ? 1.0 : 0.0);
1088: }
1089: for(d=0; d<=dh[mi][i]; d++){
1090: newm=savm;
1091: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
1092: for (kk=1; kk<=cptcovage;kk++) {
1093: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
1094: }
1095: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1096: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1097: savm=oldm;
1098: oldm=newm;
1099: } /* end mult */
1100:
1101: /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
1102: /* But now since version 0.9 we anticipate for bias and large stepm.
1103: * If stepm is larger than one month (smallest stepm) and if the exact delay
1104: * (in months) between two waves is not a multiple of stepm, we rounded to
1105: * the nearest (and in case of equal distance, to the lowest) interval but now
1106: * we keep into memory the bias bh[mi][i] and also the previous matrix product
1107: * (i.e to dh[mi][i]-1) saved in 'savm'. The we inter(extra)polate the
1108: * probability in order to take into account the bias as a fraction of the way
1109: * from savm to out if bh is neagtive or even beyond if bh is positive. bh varies
1110: * -stepm/2 to stepm/2 .
1111: * For stepm=1 the results are the same as for previous versions of Imach.
1112: * For stepm > 1 the results are less biased than in previous versions.
1113: */
1114: s1=s[mw[mi][i]][i];
1115: s2=s[mw[mi+1][i]][i];
1116: bbh=(double)bh[mi][i]/(double)stepm;
1117: /* bias is positive if real duration
1118: * is higher than the multiple of stepm and negative otherwise.
1119: */
1.63 lievre 1120: 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 1121: /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
1122: /*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 */
1123: /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
1124: /*if(lli ==000.0)*/
1125: /*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); */
1126: ipmx +=1;
1127: sw += weight[i];
1128: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1129: } /* end of wave */
1130: } /* end of individual */
1131: } else if(mle==3){ /* exponential inter-extrapolation */
1132: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1133: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
1134: for(mi=1; mi<= wav[i]-1; mi++){
1135: for (ii=1;ii<=nlstate+ndeath;ii++)
1136: for (j=1;j<=nlstate+ndeath;j++){
1137: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1138: savm[ii][j]=(ii==j ? 1.0 : 0.0);
1139: }
1140: for(d=0; d<dh[mi][i]; d++){
1141: newm=savm;
1142: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
1143: for (kk=1; kk<=cptcovage;kk++) {
1144: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
1145: }
1146: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1147: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1148: savm=oldm;
1149: oldm=newm;
1150: } /* end mult */
1151:
1152: /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
1153: /* But now since version 0.9 we anticipate for bias and large stepm.
1154: * If stepm is larger than one month (smallest stepm) and if the exact delay
1155: * (in months) between two waves is not a multiple of stepm, we rounded to
1156: * the nearest (and in case of equal distance, to the lowest) interval but now
1157: * we keep into memory the bias bh[mi][i] and also the previous matrix product
1158: * (i.e to dh[mi][i]-1) saved in 'savm'. The we inter(extra)polate the
1159: * probability in order to take into account the bias as a fraction of the way
1160: * from savm to out if bh is neagtive or even beyond if bh is positive. bh varies
1161: * -stepm/2 to stepm/2 .
1162: * For stepm=1 the results are the same as for previous versions of Imach.
1163: * For stepm > 1 the results are less biased than in previous versions.
1164: */
1165: s1=s[mw[mi][i]][i];
1166: s2=s[mw[mi+1][i]][i];
1167: bbh=(double)bh[mi][i]/(double)stepm;
1168: /* bias is positive if real duration
1169: * is higher than the multiple of stepm and negative otherwise.
1170: */
1171: /* 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 */
1172: 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 1173: /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
1174: /*if(lli ==000.0)*/
1175: /*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); */
1176: ipmx +=1;
1177: sw += weight[i];
1178: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1179: } /* end of wave */
1180: } /* end of individual */
1.84 ! brouard 1181: }else if (mle==4){ /* ml=4 no inter-extrapolation */
1.61 brouard 1182: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1183: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
1184: for(mi=1; mi<= wav[i]-1; mi++){
1185: for (ii=1;ii<=nlstate+ndeath;ii++)
1186: for (j=1;j<=nlstate+ndeath;j++){
1187: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1188: savm[ii][j]=(ii==j ? 1.0 : 0.0);
1189: }
1190: for(d=0; d<dh[mi][i]; d++){
1191: newm=savm;
1192: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
1193: for (kk=1; kk<=cptcovage;kk++) {
1194: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
1195: }
1196:
1197: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1198: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1199: savm=oldm;
1200: oldm=newm;
1201: } /* end mult */
1202:
1.84 ! brouard 1203: s1=s[mw[mi][i]][i];
! 1204: s2=s[mw[mi+1][i]][i];
! 1205: if( s2 > nlstate){
! 1206: lli=log(out[s1][s2] - savm[s1][s2]);
! 1207: }else{
! 1208: lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
! 1209: }
! 1210: ipmx +=1;
! 1211: sw += weight[i];
! 1212: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
! 1213: /*printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]);*/
! 1214: } /* end of wave */
! 1215: } /* end of individual */
! 1216: }else{ /* ml=5 no inter-extrapolation no jackson =0.8a */
! 1217: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
! 1218: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
! 1219: for(mi=1; mi<= wav[i]-1; mi++){
! 1220: for (ii=1;ii<=nlstate+ndeath;ii++)
! 1221: for (j=1;j<=nlstate+ndeath;j++){
! 1222: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
! 1223: savm[ii][j]=(ii==j ? 1.0 : 0.0);
! 1224: }
! 1225: for(d=0; d<dh[mi][i]; d++){
! 1226: newm=savm;
! 1227: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
! 1228: for (kk=1; kk<=cptcovage;kk++) {
! 1229: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
! 1230: }
! 1231:
! 1232: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
! 1233: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
! 1234: savm=oldm;
! 1235: oldm=newm;
! 1236: } /* end mult */
! 1237:
! 1238: s1=s[mw[mi][i]][i];
! 1239: s2=s[mw[mi+1][i]][i];
1.61 brouard 1240: lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
1241: ipmx +=1;
1242: sw += weight[i];
1243: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1.84 ! brouard 1244: /*printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]);*/
1.61 brouard 1245: } /* end of wave */
1246: } /* end of individual */
1247: } /* End of if */
1.53 brouard 1248: for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
1249: /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
1250: l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
1.84 ! brouard 1251: /*exit(0); */
1.53 brouard 1252: return -l;
1253: }
1254:
1255:
1256: /*********** Maximum Likelihood Estimation ***************/
1257:
1258: void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
1259: {
1260: int i,j, iter;
1.74 brouard 1261: double **xi;
1.53 brouard 1262: double fret;
1.76 brouard 1263: char filerespow[FILENAMELENGTH];
1.53 brouard 1264: xi=matrix(1,npar,1,npar);
1265: for (i=1;i<=npar;i++)
1266: for (j=1;j<=npar;j++)
1267: xi[i][j]=(i==j ? 1.0 : 0.0);
1268: printf("Powell\n"); fprintf(ficlog,"Powell\n");
1.76 brouard 1269: strcpy(filerespow,"pow");
1270: strcat(filerespow,fileres);
1271: if((ficrespow=fopen(filerespow,"w"))==NULL) {
1272: printf("Problem with resultfile: %s\n", filerespow);
1273: fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
1274: }
1275: fprintf(ficrespow,"# Powell\n# iter -2*LL");
1276: for (i=1;i<=nlstate;i++)
1277: for(j=1;j<=nlstate+ndeath;j++)
1278: if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
1279: fprintf(ficrespow,"\n");
1.53 brouard 1280: powell(p,xi,npar,ftol,&iter,&fret,func);
1281:
1.76 brouard 1282: fclose(ficrespow);
1283: printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));
1.65 lievre 1284: fprintf(ficlog,"\n#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
1.53 brouard 1285: fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
1286:
1287: }
1288:
1289: /**** Computes Hessian and covariance matrix ***/
1290: void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
1291: {
1292: double **a,**y,*x,pd;
1293: double **hess;
1294: int i, j,jk;
1295: int *indx;
1296:
1297: double hessii(double p[], double delta, int theta, double delti[]);
1298: double hessij(double p[], double delti[], int i, int j);
1299: void lubksb(double **a, int npar, int *indx, double b[]) ;
1300: void ludcmp(double **a, int npar, int *indx, double *d) ;
1301:
1302: hess=matrix(1,npar,1,npar);
1303:
1304: printf("\nCalculation of the hessian matrix. Wait...\n");
1305: fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
1306: for (i=1;i<=npar;i++){
1307: printf("%d",i);fflush(stdout);
1308: fprintf(ficlog,"%d",i);fflush(ficlog);
1309: hess[i][i]=hessii(p,ftolhess,i,delti);
1310: /*printf(" %f ",p[i]);*/
1311: /*printf(" %lf ",hess[i][i]);*/
1312: }
1313:
1314: for (i=1;i<=npar;i++) {
1315: for (j=1;j<=npar;j++) {
1316: if (j>i) {
1317: printf(".%d%d",i,j);fflush(stdout);
1318: fprintf(ficlog,".%d%d",i,j);fflush(ficlog);
1319: hess[i][j]=hessij(p,delti,i,j);
1320: hess[j][i]=hess[i][j];
1321: /*printf(" %lf ",hess[i][j]);*/
1322: }
1323: }
1324: }
1325: printf("\n");
1326: fprintf(ficlog,"\n");
1327:
1328: printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
1329: fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
1330:
1331: a=matrix(1,npar,1,npar);
1332: y=matrix(1,npar,1,npar);
1333: x=vector(1,npar);
1334: indx=ivector(1,npar);
1335: for (i=1;i<=npar;i++)
1336: for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
1337: ludcmp(a,npar,indx,&pd);
1338:
1339: for (j=1;j<=npar;j++) {
1340: for (i=1;i<=npar;i++) x[i]=0;
1341: x[j]=1;
1342: lubksb(a,npar,indx,x);
1343: for (i=1;i<=npar;i++){
1344: matcov[i][j]=x[i];
1345: }
1346: }
1347:
1348: printf("\n#Hessian matrix#\n");
1349: fprintf(ficlog,"\n#Hessian matrix#\n");
1350: for (i=1;i<=npar;i++) {
1351: for (j=1;j<=npar;j++) {
1352: printf("%.3e ",hess[i][j]);
1353: fprintf(ficlog,"%.3e ",hess[i][j]);
1354: }
1355: printf("\n");
1356: fprintf(ficlog,"\n");
1357: }
1358:
1359: /* Recompute Inverse */
1360: for (i=1;i<=npar;i++)
1361: for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];
1362: ludcmp(a,npar,indx,&pd);
1363:
1364: /* printf("\n#Hessian matrix recomputed#\n");
1365:
1366: for (j=1;j<=npar;j++) {
1367: for (i=1;i<=npar;i++) x[i]=0;
1368: x[j]=1;
1369: lubksb(a,npar,indx,x);
1370: for (i=1;i<=npar;i++){
1371: y[i][j]=x[i];
1372: printf("%.3e ",y[i][j]);
1373: fprintf(ficlog,"%.3e ",y[i][j]);
1374: }
1375: printf("\n");
1376: fprintf(ficlog,"\n");
1377: }
1378: */
1379:
1380: free_matrix(a,1,npar,1,npar);
1381: free_matrix(y,1,npar,1,npar);
1382: free_vector(x,1,npar);
1383: free_ivector(indx,1,npar);
1384: free_matrix(hess,1,npar,1,npar);
1385:
1386:
1387: }
1388:
1389: /*************** hessian matrix ****************/
1390: double hessii( double x[], double delta, int theta, double delti[])
1391: {
1392: int i;
1393: int l=1, lmax=20;
1394: double k1,k2;
1395: double p2[NPARMAX+1];
1396: double res;
1397: double delt, delts, nkhi=10.,nkhif=1., khi=1.e-4;
1398: double fx;
1399: int k=0,kmax=10;
1400: double l1;
1401:
1402: fx=func(x);
1403: for (i=1;i<=npar;i++) p2[i]=x[i];
1404: for(l=0 ; l <=lmax; l++){
1405: l1=pow(10,l);
1406: delts=delt;
1407: for(k=1 ; k <kmax; k=k+1){
1408: delt = delta*(l1*k);
1409: p2[theta]=x[theta] +delt;
1410: k1=func(p2)-fx;
1411: p2[theta]=x[theta]-delt;
1412: k2=func(p2)-fx;
1413: /*res= (k1-2.0*fx+k2)/delt/delt; */
1414: res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */
1415:
1416: #ifdef DEBUG
1417: 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);
1418: 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);
1419: #endif
1420: /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
1421: if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
1422: k=kmax;
1423: }
1424: else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
1425: k=kmax; l=lmax*10.;
1426: }
1427: else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){
1428: delts=delt;
1429: }
1430: }
1431: }
1432: delti[theta]=delts;
1433: return res;
1434:
1435: }
1436:
1437: double hessij( double x[], double delti[], int thetai,int thetaj)
1438: {
1439: int i;
1440: int l=1, l1, lmax=20;
1441: double k1,k2,k3,k4,res,fx;
1442: double p2[NPARMAX+1];
1443: int k;
1444:
1445: fx=func(x);
1446: for (k=1; k<=2; k++) {
1447: for (i=1;i<=npar;i++) p2[i]=x[i];
1448: p2[thetai]=x[thetai]+delti[thetai]/k;
1449: p2[thetaj]=x[thetaj]+delti[thetaj]/k;
1450: k1=func(p2)-fx;
1451:
1452: p2[thetai]=x[thetai]+delti[thetai]/k;
1453: p2[thetaj]=x[thetaj]-delti[thetaj]/k;
1454: k2=func(p2)-fx;
1455:
1456: p2[thetai]=x[thetai]-delti[thetai]/k;
1457: p2[thetaj]=x[thetaj]+delti[thetaj]/k;
1458: k3=func(p2)-fx;
1459:
1460: p2[thetai]=x[thetai]-delti[thetai]/k;
1461: p2[thetaj]=x[thetaj]-delti[thetaj]/k;
1462: k4=func(p2)-fx;
1463: res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */
1464: #ifdef DEBUG
1465: 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);
1466: 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);
1467: #endif
1468: }
1469: return res;
1470: }
1471:
1472: /************** Inverse of matrix **************/
1473: void ludcmp(double **a, int n, int *indx, double *d)
1474: {
1475: int i,imax,j,k;
1476: double big,dum,sum,temp;
1477: double *vv;
1478:
1479: vv=vector(1,n);
1480: *d=1.0;
1481: for (i=1;i<=n;i++) {
1482: big=0.0;
1483: for (j=1;j<=n;j++)
1484: if ((temp=fabs(a[i][j])) > big) big=temp;
1485: if (big == 0.0) nrerror("Singular matrix in routine ludcmp");
1486: vv[i]=1.0/big;
1487: }
1488: for (j=1;j<=n;j++) {
1489: for (i=1;i<j;i++) {
1490: sum=a[i][j];
1491: for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];
1492: a[i][j]=sum;
1493: }
1494: big=0.0;
1495: for (i=j;i<=n;i++) {
1496: sum=a[i][j];
1497: for (k=1;k<j;k++)
1498: sum -= a[i][k]*a[k][j];
1499: a[i][j]=sum;
1500: if ( (dum=vv[i]*fabs(sum)) >= big) {
1501: big=dum;
1502: imax=i;
1503: }
1504: }
1505: if (j != imax) {
1506: for (k=1;k<=n;k++) {
1507: dum=a[imax][k];
1508: a[imax][k]=a[j][k];
1509: a[j][k]=dum;
1510: }
1511: *d = -(*d);
1512: vv[imax]=vv[j];
1513: }
1514: indx[j]=imax;
1515: if (a[j][j] == 0.0) a[j][j]=TINY;
1516: if (j != n) {
1517: dum=1.0/(a[j][j]);
1518: for (i=j+1;i<=n;i++) a[i][j] *= dum;
1519: }
1520: }
1521: free_vector(vv,1,n); /* Doesn't work */
1522: ;
1523: }
1524:
1525: void lubksb(double **a, int n, int *indx, double b[])
1526: {
1527: int i,ii=0,ip,j;
1528: double sum;
1529:
1530: for (i=1;i<=n;i++) {
1531: ip=indx[i];
1532: sum=b[ip];
1533: b[ip]=b[i];
1534: if (ii)
1535: for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];
1536: else if (sum) ii=i;
1537: b[i]=sum;
1538: }
1539: for (i=n;i>=1;i--) {
1540: sum=b[i];
1541: for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];
1542: b[i]=sum/a[i][i];
1543: }
1544: }
1545:
1546: /************ Frequencies ********************/
1.84 ! brouard 1547: 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)
1.53 brouard 1548: { /* Some frequencies */
1549:
1550: int i, m, jk, k1,i1, j1, bool, z1,z2,j;
1551: int first;
1552: double ***freq; /* Frequencies */
1.73 lievre 1553: double *pp, **prop;
1554: double pos,posprop, k2, dateintsum=0,k2cpt=0;
1.53 brouard 1555: FILE *ficresp;
1556: char fileresp[FILENAMELENGTH];
1557:
1558: pp=vector(1,nlstate);
1.74 brouard 1559: prop=matrix(1,nlstate,iagemin,iagemax+3);
1.53 brouard 1560: strcpy(fileresp,"p");
1561: strcat(fileresp,fileres);
1562: if((ficresp=fopen(fileresp,"w"))==NULL) {
1563: printf("Problem with prevalence resultfile: %s\n", fileresp);
1564: fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
1565: exit(0);
1566: }
1.74 brouard 1567: freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);
1.53 brouard 1568: j1=0;
1569:
1570: j=cptcoveff;
1571: if (cptcovn<1) {j=1;ncodemax[1]=1;}
1572:
1573: first=1;
1574:
1575: for(k1=1; k1<=j;k1++){
1576: for(i1=1; i1<=ncodemax[k1];i1++){
1577: j1++;
1578: /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
1579: scanf("%d", i);*/
1580: for (i=-1; i<=nlstate+ndeath; i++)
1581: for (jk=-1; jk<=nlstate+ndeath; jk++)
1.74 brouard 1582: for(m=iagemin; m <= iagemax+3; m++)
1.53 brouard 1583: freq[i][jk][m]=0;
1.73 lievre 1584:
1585: for (i=1; i<=nlstate; i++)
1.74 brouard 1586: for(m=iagemin; m <= iagemax+3; m++)
1.73 lievre 1587: prop[i][m]=0;
1.53 brouard 1588:
1589: dateintsum=0;
1590: k2cpt=0;
1591: for (i=1; i<=imx; i++) {
1592: bool=1;
1593: if (cptcovn>0) {
1594: for (z1=1; z1<=cptcoveff; z1++)
1595: if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])
1596: bool=0;
1597: }
1.58 lievre 1598: if (bool==1){
1.53 brouard 1599: for(m=firstpass; m<=lastpass; m++){
1600: k2=anint[m][i]+(mint[m][i]/12.);
1.84 ! brouard 1601: /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/
1.74 brouard 1602: if(agev[m][i]==0) agev[m][i]=iagemax+1;
1603: if(agev[m][i]==1) agev[m][i]=iagemax+2;
1.73 lievre 1604: if (s[m][i]>0 && s[m][i]<=nlstate) prop[s[m][i]][(int)agev[m][i]] += weight[i];
1.53 brouard 1605: if (m<lastpass) {
1606: freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
1.74 brouard 1607: freq[s[m][i]][s[m+1][i]][iagemax+3] += weight[i];
1.53 brouard 1608: }
1609:
1.74 brouard 1610: if ((agev[m][i]>1) && (agev[m][i]< (iagemax+3))) {
1.53 brouard 1611: dateintsum=dateintsum+k2;
1612: k2cpt++;
1613: }
1.84 ! brouard 1614: /*}*/
1.53 brouard 1615: }
1616: }
1617: }
1618:
1.84 ! brouard 1619: /* fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
1.53 brouard 1620:
1621: if (cptcovn>0) {
1622: fprintf(ficresp, "\n#********** Variable ");
1623: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
1624: fprintf(ficresp, "**********\n#");
1625: }
1626: for(i=1; i<=nlstate;i++)
1627: fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
1628: fprintf(ficresp, "\n");
1629:
1.74 brouard 1630: for(i=iagemin; i <= iagemax+3; i++){
1631: if(i==iagemax+3){
1.53 brouard 1632: fprintf(ficlog,"Total");
1633: }else{
1634: if(first==1){
1635: first=0;
1636: printf("See log file for details...\n");
1637: }
1638: fprintf(ficlog,"Age %d", i);
1639: }
1640: for(jk=1; jk <=nlstate ; jk++){
1641: for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
1642: pp[jk] += freq[jk][m][i];
1643: }
1644: for(jk=1; jk <=nlstate ; jk++){
1645: for(m=-1, pos=0; m <=0 ; m++)
1646: pos += freq[jk][m][i];
1647: if(pp[jk]>=1.e-10){
1648: if(first==1){
1649: printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
1650: }
1651: fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
1652: }else{
1653: if(first==1)
1654: printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
1655: fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
1656: }
1657: }
1658:
1659: for(jk=1; jk <=nlstate ; jk++){
1660: for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
1661: pp[jk] += freq[jk][m][i];
1.73 lievre 1662: }
1663: for(jk=1,pos=0,posprop=0; jk <=nlstate ; jk++){
1664: pos += pp[jk];
1665: posprop += prop[jk][i];
1.53 brouard 1666: }
1667: for(jk=1; jk <=nlstate ; jk++){
1668: if(pos>=1.e-5){
1669: if(first==1)
1670: printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
1671: fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
1672: }else{
1673: if(first==1)
1674: printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
1675: fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
1676: }
1.74 brouard 1677: if( i <= iagemax){
1.53 brouard 1678: if(pos>=1.e-5){
1.73 lievre 1679: fprintf(ficresp," %d %.5f %.0f %.0f",i,prop[jk][i]/posprop, prop[jk][i],posprop);
1.84 ! brouard 1680: /*probs[i][jk][j1]= pp[jk]/pos;*/
1.53 brouard 1681: /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/
1682: }
1683: else
1.73 lievre 1684: fprintf(ficresp," %d NaNq %.0f %.0f",i,prop[jk][i],posprop);
1.53 brouard 1685: }
1686: }
1687:
1.69 brouard 1688: for(jk=-1; jk <=nlstate+ndeath; jk++)
1689: for(m=-1; m <=nlstate+ndeath; m++)
1.53 brouard 1690: if(freq[jk][m][i] !=0 ) {
1691: if(first==1)
1692: printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
1693: fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
1694: }
1.74 brouard 1695: if(i <= iagemax)
1.53 brouard 1696: fprintf(ficresp,"\n");
1697: if(first==1)
1698: printf("Others in log...\n");
1699: fprintf(ficlog,"\n");
1700: }
1701: }
1702: }
1703: dateintmean=dateintsum/k2cpt;
1704:
1705: fclose(ficresp);
1.74 brouard 1706: free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);
1.53 brouard 1707: free_vector(pp,1,nlstate);
1.74 brouard 1708: free_matrix(prop,1,nlstate,iagemin, iagemax+3);
1.53 brouard 1709: /* End of Freq */
1710: }
1711:
1712: /************ Prevalence ********************/
1.84 ! brouard 1713: void prevalence(double ***probs, 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 1714: {
1715: /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
1716: in each health status at the date of interview (if between dateprev1 and dateprev2).
1717: We still use firstpass and lastpass as another selection.
1718: */
1.53 brouard 1719:
1720: int i, m, jk, k1, i1, j1, bool, z1,z2,j;
1721: double ***freq; /* Frequencies */
1.73 lievre 1722: double *pp, **prop;
1723: double pos,posprop;
1.69 brouard 1724: double y2; /* in fractional years */
1.74 brouard 1725: int iagemin, iagemax;
1.53 brouard 1726:
1.74 brouard 1727: iagemin= (int) agemin;
1728: iagemax= (int) agemax;
1729: /*pp=vector(1,nlstate);*/
1730: prop=matrix(1,nlstate,iagemin,iagemax+3);
1731: /* freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
1.53 brouard 1732: j1=0;
1733:
1734: j=cptcoveff;
1735: if (cptcovn<1) {j=1;ncodemax[1]=1;}
1736:
1737: for(k1=1; k1<=j;k1++){
1738: for(i1=1; i1<=ncodemax[k1];i1++){
1739: j1++;
1740:
1.73 lievre 1741: for (i=1; i<=nlstate; i++)
1.74 brouard 1742: for(m=iagemin; m <= iagemax+3; m++)
1743: prop[i][m]=0.0;
1.53 brouard 1744:
1.69 brouard 1745: for (i=1; i<=imx; i++) { /* Each individual */
1.53 brouard 1746: bool=1;
1747: if (cptcovn>0) {
1748: for (z1=1; z1<=cptcoveff; z1++)
1749: if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])
1750: bool=0;
1751: }
1752: if (bool==1) {
1.69 brouard 1753: for(m=firstpass; m<=lastpass; m++){/* Other selection (we can limit to certain interviews*/
1754: y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
1755: if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
1.74 brouard 1756: if(agev[m][i]==0) agev[m][i]=iagemax+1;
1757: if(agev[m][i]==1) agev[m][i]=iagemax+2;
1758: 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);
1759: if (s[m][i]>0 && s[m][i]<=nlstate) {
1760: /*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]]);*/
1761: prop[s[m][i]][(int)agev[m][i]] += weight[i];
1762: prop[s[m][i]][iagemax+3] += weight[i];
1763: }
1.53 brouard 1764: }
1.69 brouard 1765: } /* end selection of waves */
1.53 brouard 1766: }
1767: }
1.74 brouard 1768: for(i=iagemin; i <= iagemax+3; i++){
1.53 brouard 1769:
1.74 brouard 1770: for(jk=1,posprop=0; jk <=nlstate ; jk++) {
1771: posprop += prop[jk][i];
1772: }
1773:
1774: for(jk=1; jk <=nlstate ; jk++){
1775: if( i <= iagemax){
1776: if(posprop>=1.e-5){
1777: probs[i][jk][j1]= prop[jk][i]/posprop;
1778: }
1779: }
1780: }/* end jk */
1781: }/* end i */
1.53 brouard 1782: } /* end i1 */
1783: } /* end k1 */
1784:
1.74 brouard 1785: /* free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
1786: /*free_vector(pp,1,nlstate);*/
1787: free_matrix(prop,1,nlstate, iagemin,iagemax+3);
1788: } /* End of prevalence */
1.53 brouard 1789:
1790: /************* Waves Concatenation ***************/
1791:
1.59 brouard 1792: 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 1793: {
1794: /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
1795: Death is a valid wave (if date is known).
1796: mw[mi][i] is the mi (mi=1 to wav[i]) effective wave of individual i
1.59 brouard 1797: dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
1.53 brouard 1798: and mw[mi+1][i]. dh depends on stepm.
1799: */
1800:
1801: int i, mi, m;
1802: /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
1803: double sum=0., jmean=0.;*/
1804: int first;
1805: int j, k=0,jk, ju, jl;
1806: double sum=0.;
1807: first=0;
1808: jmin=1e+5;
1809: jmax=-1;
1810: jmean=0.;
1811: for(i=1; i<=imx; i++){
1812: mi=0;
1813: m=firstpass;
1814: while(s[m][i] <= nlstate){
1.69 brouard 1815: if(s[m][i]>=1)
1.53 brouard 1816: mw[++mi][i]=m;
1817: if(m >=lastpass)
1818: break;
1819: else
1820: m++;
1821: }/* end while */
1822: if (s[m][i] > nlstate){
1823: mi++; /* Death is another wave */
1824: /* if(mi==0) never been interviewed correctly before death */
1825: /* Only death is a correct wave */
1826: mw[mi][i]=m;
1827: }
1828:
1829: wav[i]=mi;
1830: if(mi==0){
1831: if(first==0){
1.77 brouard 1832: printf("Warning! None valid information for:%d line=%d (skipped) and may be others, see log file\n",num[i],i);
1.53 brouard 1833: first=1;
1834: }
1835: if(first==1){
1.77 brouard 1836: fprintf(ficlog,"Warning! None valid information for:%d line=%d (skipped)\n",num[i],i);
1.53 brouard 1837: }
1838: } /* end mi==0 */
1.77 brouard 1839: } /* End individuals */
1.53 brouard 1840:
1841: for(i=1; i<=imx; i++){
1842: for(mi=1; mi<wav[i];mi++){
1843: if (stepm <=0)
1844: dh[mi][i]=1;
1845: else{
1.77 brouard 1846: if (s[mw[mi+1][i]][i] > nlstate) { /* A death */
1.53 brouard 1847: if (agedc[i] < 2*AGESUP) {
1848: j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);
1849: if(j==0) j=1; /* Survives at least one month after exam */
1850: k=k+1;
1851: if (j >= jmax) jmax=j;
1852: if (j <= jmin) jmin=j;
1853: sum=sum+j;
1.77 brouard 1854: /*if (j<0) printf("j=%d num=%d \n",j,i);*/
1.68 lievre 1855: /* printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
1.78 brouard 1856: 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 1857: }
1858: }
1859: else{
1860: j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
1.68 lievre 1861: /* printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
1.53 brouard 1862: k=k+1;
1863: if (j >= jmax) jmax=j;
1864: else if (j <= jmin)jmin=j;
1865: /* if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
1.73 lievre 1866: /*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 1867: 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 1868: sum=sum+j;
1869: }
1870: jk= j/stepm;
1871: jl= j -jk*stepm;
1872: ju= j -(jk+1)*stepm;
1.64 lievre 1873: if(mle <=1){
1874: if(jl==0){
1875: dh[mi][i]=jk;
1876: bh[mi][i]=0;
1877: }else{ /* We want a negative bias in order to only have interpolation ie
1878: * at the price of an extra matrix product in likelihood */
1879: dh[mi][i]=jk+1;
1880: bh[mi][i]=ju;
1881: }
1882: }else{
1883: if(jl <= -ju){
1884: dh[mi][i]=jk;
1885: bh[mi][i]=jl; /* bias is positive if real duration
1886: * is higher than the multiple of stepm and negative otherwise.
1887: */
1888: }
1889: else{
1890: dh[mi][i]=jk+1;
1891: bh[mi][i]=ju;
1892: }
1893: if(dh[mi][i]==0){
1894: dh[mi][i]=1; /* At least one step */
1895: bh[mi][i]=ju; /* At least one step */
1.71 brouard 1896: /* 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 1897: }
1.59 brouard 1898: }
1.64 lievre 1899: } /* end if mle */
1900: } /* end wave */
1.53 brouard 1901: }
1902: jmean=sum/k;
1903: printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);
1904: fprintf(ficlog,"Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);
1905: }
1906:
1907: /*********** Tricode ****************************/
1908: void tricode(int *Tvar, int **nbcode, int imx)
1909: {
1.58 lievre 1910:
1911: int Ndum[20],ij=1, k, j, i, maxncov=19;
1.53 brouard 1912: int cptcode=0;
1913: cptcoveff=0;
1914:
1.58 lievre 1915: for (k=0; k<maxncov; k++) Ndum[k]=0;
1.53 brouard 1916: for (k=1; k<=7; k++) ncodemax[k]=0;
1917:
1918: for (j=1; j<=(cptcovn+2*cptcovprod); j++) {
1.58 lievre 1919: for (i=1; i<=imx; i++) { /*reads the data file to get the maximum
1920: modality*/
1921: ij=(int)(covar[Tvar[j]][i]); /* ij is the modality of this individual*/
1922: Ndum[ij]++; /*store the modality */
1.53 brouard 1923: /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
1.58 lievre 1924: if (ij > cptcode) cptcode=ij; /* getting the maximum of covariable
1925: Tvar[j]. If V=sex and male is 0 and
1926: female is 1, then cptcode=1.*/
1.53 brouard 1927: }
1928:
1929: for (i=0; i<=cptcode; i++) {
1.58 lievre 1930: 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 1931: }
1.58 lievre 1932:
1.53 brouard 1933: ij=1;
1934: for (i=1; i<=ncodemax[j]; i++) {
1.58 lievre 1935: for (k=0; k<= maxncov; k++) {
1.53 brouard 1936: if (Ndum[k] != 0) {
1937: nbcode[Tvar[j]][ij]=k;
1.58 lievre 1938: /* 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 1939:
1940: ij++;
1941: }
1942: if (ij > ncodemax[j]) break;
1943: }
1944: }
1945: }
1946:
1.58 lievre 1947: for (k=0; k< maxncov; k++) Ndum[k]=0;
1.53 brouard 1948:
1.58 lievre 1949: for (i=1; i<=ncovmodel-2; i++) {
1950: /* 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 1951: ij=Tvar[i];
1.58 lievre 1952: Ndum[ij]++;
1.53 brouard 1953: }
1954:
1955: ij=1;
1.58 lievre 1956: for (i=1; i<= maxncov; i++) {
1.53 brouard 1957: if((Ndum[i]!=0) && (i<=ncovcol)){
1.58 lievre 1958: Tvaraff[ij]=i; /*For printing */
1.53 brouard 1959: ij++;
1960: }
1961: }
1962:
1.58 lievre 1963: cptcoveff=ij-1; /*Number of simple covariates*/
1.53 brouard 1964: }
1965:
1966: /*********** Health Expectancies ****************/
1967:
1968: 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 )
1969:
1970: {
1971: /* Health expectancies */
1972: int i, j, nhstepm, hstepm, h, nstepm, k, cptj;
1973: double age, agelim, hf;
1974: double ***p3mat,***varhe;
1975: double **dnewm,**doldm;
1976: double *xp;
1977: double **gp, **gm;
1978: double ***gradg, ***trgradg;
1979: int theta;
1980:
1.74 brouard 1981: varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage);
1.53 brouard 1982: xp=vector(1,npar);
1.74 brouard 1983: dnewm=matrix(1,nlstate*nlstate,1,npar);
1984: doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate);
1.53 brouard 1985:
1986: fprintf(ficreseij,"# Health expectancies\n");
1987: fprintf(ficreseij,"# Age");
1988: for(i=1; i<=nlstate;i++)
1989: for(j=1; j<=nlstate;j++)
1990: fprintf(ficreseij," %1d-%1d (SE)",i,j);
1991: fprintf(ficreseij,"\n");
1992:
1993: if(estepm < stepm){
1994: printf ("Problem %d lower than %d\n",estepm, stepm);
1995: }
1996: else hstepm=estepm;
1997: /* We compute the life expectancy from trapezoids spaced every estepm months
1998: * This is mainly to measure the difference between two models: for example
1999: * if stepm=24 months pijx are given only every 2 years and by summing them
2000: * we are calculating an estimate of the Life Expectancy assuming a linear
1.66 brouard 2001: * progression in between and thus overestimating or underestimating according
1.53 brouard 2002: * to the curvature of the survival function. If, for the same date, we
2003: * estimate the model with stepm=1 month, we can keep estepm to 24 months
2004: * to compare the new estimate of Life expectancy with the same linear
2005: * hypothesis. A more precise result, taking into account a more precise
2006: * curvature will be obtained if estepm is as small as stepm. */
2007:
2008: /* For example we decided to compute the life expectancy with the smallest unit */
2009: /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
2010: nhstepm is the number of hstepm from age to agelim
2011: nstepm is the number of stepm from age to agelin.
2012: Look at hpijx to understand the reason of that which relies in memory size
2013: and note for a fixed period like estepm months */
2014: /* We decided (b) to get a life expectancy respecting the most precise curvature of the
2015: survival function given by stepm (the optimization length). Unfortunately it
2016: means that if the survival funtion is printed only each two years of age and if
2017: you sum them up and add 1 year (area under the trapezoids) you won't get the same
2018: results. So we changed our mind and took the option of the best precision.
2019: */
2020: hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
2021:
2022: agelim=AGESUP;
2023: for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
2024: /* nhstepm age range expressed in number of stepm */
2025: nstepm=(int) rint((agelim-age)*YEARM/stepm);
2026: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
2027: /* if (stepm >= YEARM) hstepm=1;*/
2028: nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
2029: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
1.74 brouard 2030: gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);
2031: gp=matrix(0,nhstepm,1,nlstate*nlstate);
2032: gm=matrix(0,nhstepm,1,nlstate*nlstate);
1.53 brouard 2033:
2034: /* Computed by stepm unit matrices, product of hstepm matrices, stored
2035: in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
2036: hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);
2037:
2038:
2039: hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
2040:
2041: /* Computing Variances of health expectancies */
2042:
2043: for(theta=1; theta <=npar; theta++){
2044: for(i=1; i<=npar; i++){
2045: xp[i] = x[i] + (i==theta ?delti[theta]:0);
2046: }
2047: hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
2048:
2049: cptj=0;
2050: for(j=1; j<= nlstate; j++){
2051: for(i=1; i<=nlstate; i++){
2052: cptj=cptj+1;
2053: for(h=0, gp[h][cptj]=0.; h<=nhstepm-1; h++){
2054: gp[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;
2055: }
2056: }
2057: }
2058:
2059:
2060: for(i=1; i<=npar; i++)
2061: xp[i] = x[i] - (i==theta ?delti[theta]:0);
2062: hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
2063:
2064: cptj=0;
2065: for(j=1; j<= nlstate; j++){
2066: for(i=1;i<=nlstate;i++){
2067: cptj=cptj+1;
2068: for(h=0, gm[h][cptj]=0.; h<=nhstepm-1; h++){
1.77 brouard 2069:
1.53 brouard 2070: gm[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;
2071: }
2072: }
2073: }
1.74 brouard 2074: for(j=1; j<= nlstate*nlstate; j++)
1.53 brouard 2075: for(h=0; h<=nhstepm-1; h++){
2076: gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
2077: }
2078: }
2079:
2080: /* End theta */
2081:
1.74 brouard 2082: trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar);
1.53 brouard 2083:
2084: for(h=0; h<=nhstepm-1; h++)
1.74 brouard 2085: for(j=1; j<=nlstate*nlstate;j++)
1.53 brouard 2086: for(theta=1; theta <=npar; theta++)
2087: trgradg[h][j][theta]=gradg[h][theta][j];
2088:
2089:
1.74 brouard 2090: for(i=1;i<=nlstate*nlstate;i++)
2091: for(j=1;j<=nlstate*nlstate;j++)
1.53 brouard 2092: varhe[i][j][(int)age] =0.;
2093:
2094: printf("%d|",(int)age);fflush(stdout);
2095: fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
2096: for(h=0;h<=nhstepm-1;h++){
2097: for(k=0;k<=nhstepm-1;k++){
1.74 brouard 2098: matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov);
2099: matprod2(doldm,dnewm,1,nlstate*nlstate,1,npar,1,nlstate*nlstate,gradg[k]);
2100: for(i=1;i<=nlstate*nlstate;i++)
2101: for(j=1;j<=nlstate*nlstate;j++)
1.53 brouard 2102: varhe[i][j][(int)age] += doldm[i][j]*hf*hf;
2103: }
2104: }
2105: /* Computing expectancies */
2106: for(i=1; i<=nlstate;i++)
2107: for(j=1; j<=nlstate;j++)
2108: for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
2109: eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
2110:
2111: /* 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]);*/
2112:
2113: }
2114:
2115: fprintf(ficreseij,"%3.0f",age );
2116: cptj=0;
2117: for(i=1; i<=nlstate;i++)
2118: for(j=1; j<=nlstate;j++){
2119: cptj++;
2120: fprintf(ficreseij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[cptj][cptj][(int)age]) );
2121: }
2122: fprintf(ficreseij,"\n");
2123:
1.74 brouard 2124: free_matrix(gm,0,nhstepm,1,nlstate*nlstate);
2125: free_matrix(gp,0,nhstepm,1,nlstate*nlstate);
2126: free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*nlstate);
2127: free_ma3x(trgradg,0,nhstepm,1,nlstate*nlstate,1,npar);
1.53 brouard 2128: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
2129: }
2130: printf("\n");
2131: fprintf(ficlog,"\n");
2132:
2133: free_vector(xp,1,npar);
1.74 brouard 2134: free_matrix(dnewm,1,nlstate*nlstate,1,npar);
2135: free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate);
2136: free_ma3x(varhe,1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int)fage);
1.53 brouard 2137: }
2138:
2139: /************ Variance ******************/
2140: 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)
2141: {
2142: /* Variance of health expectancies */
2143: /* double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
2144: /* double **newm;*/
2145: double **dnewm,**doldm;
2146: double **dnewmp,**doldmp;
2147: int i, j, nhstepm, hstepm, h, nstepm ;
2148: int k, cptcode;
2149: double *xp;
2150: double **gp, **gm; /* for var eij */
2151: double ***gradg, ***trgradg; /*for var eij */
2152: double **gradgp, **trgradgp; /* for var p point j */
2153: double *gpp, *gmp; /* for var p point j */
2154: double **varppt; /* for var p point j nlstate to nlstate+ndeath */
2155: double ***p3mat;
2156: double age,agelim, hf;
2157: double ***mobaverage;
2158: int theta;
2159: char digit[4];
1.55 lievre 2160: char digitp[25];
1.53 brouard 2161:
2162: char fileresprobmorprev[FILENAMELENGTH];
2163:
1.55 lievre 2164: if(popbased==1){
1.58 lievre 2165: if(mobilav!=0)
1.55 lievre 2166: strcpy(digitp,"-populbased-mobilav-");
2167: else strcpy(digitp,"-populbased-nomobil-");
2168: }
2169: else
1.53 brouard 2170: strcpy(digitp,"-stablbased-");
1.56 lievre 2171:
1.54 brouard 2172: if (mobilav!=0) {
1.53 brouard 2173: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
1.54 brouard 2174: if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
2175: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
2176: printf(" Error in movingaverage mobilav=%d\n",mobilav);
2177: }
1.53 brouard 2178: }
2179:
2180: strcpy(fileresprobmorprev,"prmorprev");
2181: sprintf(digit,"%-d",ij);
2182: /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
2183: strcat(fileresprobmorprev,digit); /* Tvar to be done */
2184: strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
2185: strcat(fileresprobmorprev,fileres);
2186: if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
2187: printf("Problem with resultfile: %s\n", fileresprobmorprev);
2188: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
2189: }
2190: printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
2191: fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
1.66 brouard 2192: 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 2193: fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
2194: for(j=nlstate+1; j<=(nlstate+ndeath);j++){
2195: fprintf(ficresprobmorprev," p.%-d SE",j);
2196: for(i=1; i<=nlstate;i++)
2197: fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
2198: }
2199: fprintf(ficresprobmorprev,"\n");
2200: if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {
2201: printf("Problem with gnuplot file: %s\n", optionfilegnuplot);
2202: fprintf(ficlog,"Problem with gnuplot file: %s\n", optionfilegnuplot);
2203: exit(0);
2204: }
2205: else{
2206: fprintf(ficgp,"\n# Routine varevsij");
2207: }
2208: if((fichtm=fopen(optionfilehtm,"a"))==NULL) {
2209: printf("Problem with html file: %s\n", optionfilehtm);
2210: fprintf(ficlog,"Problem with html file: %s\n", optionfilehtm);
2211: exit(0);
2212: }
2213: else{
1.67 brouard 2214: 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");
2215: fprintf(fichtm,"\n<br>%s <br>\n",digitp);
1.53 brouard 2216: }
2217: varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
2218:
2219: 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");
2220: fprintf(ficresvij,"# Age");
2221: for(i=1; i<=nlstate;i++)
2222: for(j=1; j<=nlstate;j++)
2223: fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);
2224: fprintf(ficresvij,"\n");
2225:
2226: xp=vector(1,npar);
2227: dnewm=matrix(1,nlstate,1,npar);
2228: doldm=matrix(1,nlstate,1,nlstate);
2229: dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
2230: doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
2231:
2232: gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
2233: gpp=vector(nlstate+1,nlstate+ndeath);
2234: gmp=vector(nlstate+1,nlstate+ndeath);
2235: trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
2236:
2237: if(estepm < stepm){
2238: printf ("Problem %d lower than %d\n",estepm, stepm);
2239: }
2240: else hstepm=estepm;
2241: /* For example we decided to compute the life expectancy with the smallest unit */
2242: /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
2243: nhstepm is the number of hstepm from age to agelim
2244: nstepm is the number of stepm from age to agelin.
2245: Look at hpijx to understand the reason of that which relies in memory size
2246: and note for a fixed period like k years */
2247: /* We decided (b) to get a life expectancy respecting the most precise curvature of the
2248: survival function given by stepm (the optimization length). Unfortunately it
1.66 brouard 2249: means that if the survival funtion is printed every two years of age and if
1.53 brouard 2250: you sum them up and add 1 year (area under the trapezoids) you won't get the same
2251: results. So we changed our mind and took the option of the best precision.
2252: */
2253: hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
2254: agelim = AGESUP;
2255: for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
2256: nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
2257: nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
2258: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
2259: gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
2260: gp=matrix(0,nhstepm,1,nlstate);
2261: gm=matrix(0,nhstepm,1,nlstate);
2262:
2263:
2264: for(theta=1; theta <=npar; theta++){
1.66 brouard 2265: for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
1.53 brouard 2266: xp[i] = x[i] + (i==theta ?delti[theta]:0);
2267: }
2268: hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
2269: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
2270:
2271: if (popbased==1) {
1.54 brouard 2272: if(mobilav ==0){
1.53 brouard 2273: for(i=1; i<=nlstate;i++)
2274: prlim[i][i]=probs[(int)age][i][ij];
1.54 brouard 2275: }else{ /* mobilav */
1.53 brouard 2276: for(i=1; i<=nlstate;i++)
2277: prlim[i][i]=mobaverage[(int)age][i][ij];
2278: }
2279: }
2280:
2281: for(j=1; j<= nlstate; j++){
2282: for(h=0; h<=nhstepm; h++){
2283: for(i=1, gp[h][j]=0.;i<=nlstate;i++)
2284: gp[h][j] += prlim[i][i]*p3mat[i][j][h];
2285: }
2286: }
1.66 brouard 2287: /* This for computing probability of death (h=1 means
2288: computed over hstepm matrices product = hstepm*stepm months)
2289: as a weighted average of prlim.
2290: */
1.69 brouard 2291: for(j=nlstate+1;j<=nlstate+ndeath;j++){
1.68 lievre 2292: for(i=1,gpp[j]=0.; i<= nlstate; i++)
1.53 brouard 2293: gpp[j] += prlim[i][i]*p3mat[i][j][1];
2294: }
1.66 brouard 2295: /* end probability of death */
1.53 brouard 2296:
1.66 brouard 2297: for(i=1; i<=npar; i++) /* Computes gradient x - delta */
1.53 brouard 2298: xp[i] = x[i] - (i==theta ?delti[theta]:0);
2299: hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
2300: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
2301:
2302: if (popbased==1) {
1.54 brouard 2303: if(mobilav ==0){
1.53 brouard 2304: for(i=1; i<=nlstate;i++)
2305: prlim[i][i]=probs[(int)age][i][ij];
1.54 brouard 2306: }else{ /* mobilav */
1.53 brouard 2307: for(i=1; i<=nlstate;i++)
2308: prlim[i][i]=mobaverage[(int)age][i][ij];
2309: }
2310: }
2311:
2312: for(j=1; j<= nlstate; j++){
2313: for(h=0; h<=nhstepm; h++){
2314: for(i=1, gm[h][j]=0.;i<=nlstate;i++)
2315: gm[h][j] += prlim[i][i]*p3mat[i][j][h];
2316: }
2317: }
1.66 brouard 2318: /* This for computing probability of death (h=1 means
2319: computed over hstepm matrices product = hstepm*stepm months)
2320: as a weighted average of prlim.
2321: */
1.69 brouard 2322: for(j=nlstate+1;j<=nlstate+ndeath;j++){
1.68 lievre 2323: for(i=1,gmp[j]=0.; i<= nlstate; i++)
2324: gmp[j] += prlim[i][i]*p3mat[i][j][1];
1.53 brouard 2325: }
1.66 brouard 2326: /* end probability of death */
1.53 brouard 2327:
2328: for(j=1; j<= nlstate; j++) /* vareij */
2329: for(h=0; h<=nhstepm; h++){
2330: gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
2331: }
1.68 lievre 2332:
1.53 brouard 2333: for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
2334: gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
2335: }
2336:
2337: } /* End theta */
2338:
2339: trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
2340:
2341: for(h=0; h<=nhstepm; h++) /* veij */
2342: for(j=1; j<=nlstate;j++)
2343: for(theta=1; theta <=npar; theta++)
2344: trgradg[h][j][theta]=gradg[h][theta][j];
2345:
2346: for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
1.69 brouard 2347: for(theta=1; theta <=npar; theta++)
1.53 brouard 2348: trgradgp[j][theta]=gradgp[theta][j];
1.69 brouard 2349:
1.53 brouard 2350:
2351: hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
2352: for(i=1;i<=nlstate;i++)
2353: for(j=1;j<=nlstate;j++)
2354: vareij[i][j][(int)age] =0.;
2355:
2356: for(h=0;h<=nhstepm;h++){
2357: for(k=0;k<=nhstepm;k++){
2358: matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
2359: matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
2360: for(i=1;i<=nlstate;i++)
2361: for(j=1;j<=nlstate;j++)
2362: vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
2363: }
2364: }
1.70 brouard 2365:
1.53 brouard 2366: /* pptj */
2367: matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
2368: matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
1.70 brouard 2369: for(j=nlstate+1;j<=nlstate+ndeath;j++)
2370: for(i=nlstate+1;i<=nlstate+ndeath;i++)
1.53 brouard 2371: varppt[j][i]=doldmp[j][i];
2372: /* end ppptj */
1.66 brouard 2373: /* x centered again */
1.53 brouard 2374: hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);
2375: prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);
2376:
2377: if (popbased==1) {
1.54 brouard 2378: if(mobilav ==0){
1.53 brouard 2379: for(i=1; i<=nlstate;i++)
2380: prlim[i][i]=probs[(int)age][i][ij];
1.54 brouard 2381: }else{ /* mobilav */
1.53 brouard 2382: for(i=1; i<=nlstate;i++)
2383: prlim[i][i]=mobaverage[(int)age][i][ij];
2384: }
2385: }
1.70 brouard 2386:
1.66 brouard 2387: /* This for computing probability of death (h=1 means
2388: computed over hstepm (estepm) matrices product = hstepm*stepm months)
2389: as a weighted average of prlim.
2390: */
1.68 lievre 2391: for(j=nlstate+1;j<=nlstate+ndeath;j++){
2392: for(i=1,gmp[j]=0.;i<= nlstate; i++)
1.53 brouard 2393: gmp[j] += prlim[i][i]*p3mat[i][j][1];
2394: }
1.66 brouard 2395: /* end probability of death */
1.53 brouard 2396:
2397: fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
2398: for(j=nlstate+1; j<=(nlstate+ndeath);j++){
2399: fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
2400: for(i=1; i<=nlstate;i++){
2401: fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
2402: }
2403: }
2404: fprintf(ficresprobmorprev,"\n");
2405:
2406: fprintf(ficresvij,"%.0f ",age );
2407: for(i=1; i<=nlstate;i++)
2408: for(j=1; j<=nlstate;j++){
2409: fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
2410: }
2411: fprintf(ficresvij,"\n");
2412: free_matrix(gp,0,nhstepm,1,nlstate);
2413: free_matrix(gm,0,nhstepm,1,nlstate);
2414: free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
2415: free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
2416: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
2417: } /* End age */
2418: free_vector(gpp,nlstate+1,nlstate+ndeath);
2419: free_vector(gmp,nlstate+1,nlstate+ndeath);
2420: free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
2421: free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
2422: fprintf(ficgp,"\nset noparametric;set nolabel; set ter png small;set size 0.65, 0.65");
2423: /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */
2424: fprintf(ficgp,"\n set log y; set nolog x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
1.67 brouard 2425: /* fprintf(ficgp,"\n plot \"%s\" u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm); */
2426: /* fprintf(ficgp,"\n replot \"%s\" u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm); */
2427: /* fprintf(ficgp,"\n replot \"%s\" u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm); */
2428: fprintf(ficgp,"\n plot \"%s\" u 1:($3) not w l 1 ",fileresprobmorprev);
2429: fprintf(ficgp,"\n replot \"%s\" u 1:(($3+1.96*$4)) t \"95\%% interval\" w l 2 ",fileresprobmorprev);
2430: fprintf(ficgp,"\n replot \"%s\" u 1:(($3-1.96*$4)) not w l 2 ",fileresprobmorprev);
1.53 brouard 2431: fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",fileresprobmorprev,fileresprobmorprev);
1.71 brouard 2432: 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 2433: /* 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);
2434: */
1.71 brouard 2435: fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.png\";replot;",digitp,optionfilefiname,digit);
1.53 brouard 2436:
2437: free_vector(xp,1,npar);
2438: free_matrix(doldm,1,nlstate,1,nlstate);
2439: free_matrix(dnewm,1,nlstate,1,npar);
2440: free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
2441: free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
2442: free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
1.55 lievre 2443: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
1.53 brouard 2444: fclose(ficresprobmorprev);
2445: fclose(ficgp);
2446: fclose(fichtm);
1.84 ! brouard 2447: } /* end varevsij */
1.53 brouard 2448:
2449: /************ Variance of prevlim ******************/
2450: 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)
2451: {
2452: /* Variance of prevalence limit */
1.59 brouard 2453: /* double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
1.53 brouard 2454: double **newm;
2455: double **dnewm,**doldm;
2456: int i, j, nhstepm, hstepm;
2457: int k, cptcode;
2458: double *xp;
2459: double *gp, *gm;
2460: double **gradg, **trgradg;
2461: double age,agelim;
2462: int theta;
2463:
1.54 brouard 2464: fprintf(ficresvpl,"# Standard deviation of stable prevalences \n");
1.53 brouard 2465: fprintf(ficresvpl,"# Age");
2466: for(i=1; i<=nlstate;i++)
2467: fprintf(ficresvpl," %1d-%1d",i,i);
2468: fprintf(ficresvpl,"\n");
2469:
2470: xp=vector(1,npar);
2471: dnewm=matrix(1,nlstate,1,npar);
2472: doldm=matrix(1,nlstate,1,nlstate);
2473:
2474: hstepm=1*YEARM; /* Every year of age */
2475: hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */
2476: agelim = AGESUP;
2477: for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
2478: nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
2479: if (stepm >= YEARM) hstepm=1;
2480: nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
2481: gradg=matrix(1,npar,1,nlstate);
2482: gp=vector(1,nlstate);
2483: gm=vector(1,nlstate);
2484:
2485: for(theta=1; theta <=npar; theta++){
2486: for(i=1; i<=npar; i++){ /* Computes gradient */
2487: xp[i] = x[i] + (i==theta ?delti[theta]:0);
2488: }
2489: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
2490: for(i=1;i<=nlstate;i++)
2491: gp[i] = prlim[i][i];
2492:
2493: for(i=1; i<=npar; i++) /* Computes gradient */
2494: xp[i] = x[i] - (i==theta ?delti[theta]:0);
2495: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
2496: for(i=1;i<=nlstate;i++)
2497: gm[i] = prlim[i][i];
2498:
2499: for(i=1;i<=nlstate;i++)
2500: gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
2501: } /* End theta */
2502:
2503: trgradg =matrix(1,nlstate,1,npar);
2504:
2505: for(j=1; j<=nlstate;j++)
2506: for(theta=1; theta <=npar; theta++)
2507: trgradg[j][theta]=gradg[theta][j];
2508:
2509: for(i=1;i<=nlstate;i++)
2510: varpl[i][(int)age] =0.;
2511: matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
2512: matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
2513: for(i=1;i<=nlstate;i++)
2514: varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
2515:
2516: fprintf(ficresvpl,"%.0f ",age );
2517: for(i=1; i<=nlstate;i++)
2518: fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
2519: fprintf(ficresvpl,"\n");
2520: free_vector(gp,1,nlstate);
2521: free_vector(gm,1,nlstate);
2522: free_matrix(gradg,1,npar,1,nlstate);
2523: free_matrix(trgradg,1,nlstate,1,npar);
2524: } /* End age */
2525:
2526: free_vector(xp,1,npar);
2527: free_matrix(doldm,1,nlstate,1,npar);
2528: free_matrix(dnewm,1,nlstate,1,nlstate);
2529:
2530: }
2531:
2532: /************ Variance of one-step probabilities ******************/
2533: void varprob(char optionfilefiname[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij, int *Tvar, int **nbcode, int *ncodemax)
2534: {
2535: int i, j=0, i1, k1, l1, t, tj;
2536: int k2, l2, j1, z1;
2537: int k=0,l, cptcode;
2538: int first=1, first1;
2539: double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
2540: double **dnewm,**doldm;
2541: double *xp;
2542: double *gp, *gm;
2543: double **gradg, **trgradg;
2544: double **mu;
2545: double age,agelim, cov[NCOVMAX];
2546: double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
2547: int theta;
2548: char fileresprob[FILENAMELENGTH];
2549: char fileresprobcov[FILENAMELENGTH];
2550: char fileresprobcor[FILENAMELENGTH];
2551:
2552: double ***varpij;
2553:
2554: strcpy(fileresprob,"prob");
2555: strcat(fileresprob,fileres);
2556: if((ficresprob=fopen(fileresprob,"w"))==NULL) {
2557: printf("Problem with resultfile: %s\n", fileresprob);
2558: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
2559: }
2560: strcpy(fileresprobcov,"probcov");
2561: strcat(fileresprobcov,fileres);
2562: if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
2563: printf("Problem with resultfile: %s\n", fileresprobcov);
2564: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
2565: }
2566: strcpy(fileresprobcor,"probcor");
2567: strcat(fileresprobcor,fileres);
2568: if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
2569: printf("Problem with resultfile: %s\n", fileresprobcor);
2570: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
2571: }
2572: printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
2573: fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
2574: printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
2575: fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
2576: printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
2577: fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
2578:
2579: fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
2580: fprintf(ficresprob,"# Age");
2581: fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
2582: fprintf(ficresprobcov,"# Age");
2583: fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
2584: fprintf(ficresprobcov,"# Age");
2585:
2586:
2587: for(i=1; i<=nlstate;i++)
2588: for(j=1; j<=(nlstate+ndeath);j++){
2589: fprintf(ficresprob," p%1d-%1d (SE)",i,j);
2590: fprintf(ficresprobcov," p%1d-%1d ",i,j);
2591: fprintf(ficresprobcor," p%1d-%1d ",i,j);
2592: }
1.69 brouard 2593: /* fprintf(ficresprob,"\n");
1.53 brouard 2594: fprintf(ficresprobcov,"\n");
2595: fprintf(ficresprobcor,"\n");
1.69 brouard 2596: */
2597: xp=vector(1,npar);
1.53 brouard 2598: dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
2599: doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
2600: mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
2601: varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
2602: first=1;
2603: if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {
2604: printf("Problem with gnuplot file: %s\n", optionfilegnuplot);
2605: fprintf(ficlog,"Problem with gnuplot file: %s\n", optionfilegnuplot);
2606: exit(0);
2607: }
2608: else{
2609: fprintf(ficgp,"\n# Routine varprob");
2610: }
2611: if((fichtm=fopen(optionfilehtm,"a"))==NULL) {
2612: printf("Problem with html file: %s\n", optionfilehtm);
2613: fprintf(ficlog,"Problem with html file: %s\n", optionfilehtm);
2614: exit(0);
2615: }
2616: else{
2617: fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
2618: fprintf(fichtm,"\n");
2619:
2620: fprintf(fichtm,"\n<li><h4> Computing matrix of variance-covariance of step probabilities</h4></li>\n");
2621: 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");
2622: 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");
2623:
2624: }
2625:
2626: cov[1]=1;
2627: tj=cptcoveff;
2628: if (cptcovn<1) {tj=1;ncodemax[1]=1;}
2629: j1=0;
2630: for(t=1; t<=tj;t++){
2631: for(i1=1; i1<=ncodemax[t];i1++){
2632: j1++;
2633: if (cptcovn>0) {
2634: fprintf(ficresprob, "\n#********** Variable ");
2635: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
1.69 brouard 2636: fprintf(ficresprob, "**********\n#\n");
1.53 brouard 2637: fprintf(ficresprobcov, "\n#********** Variable ");
2638: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
1.69 brouard 2639: fprintf(ficresprobcov, "**********\n#\n");
1.53 brouard 2640:
2641: fprintf(ficgp, "\n#********** Variable ");
1.69 brouard 2642: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
2643: fprintf(ficgp, "**********\n#\n");
1.53 brouard 2644:
2645:
2646: fprintf(fichtm, "\n<hr size=\"2\" color=\"#EC5E5E\">********** Variable ");
2647: for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
2648: fprintf(fichtm, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
2649:
2650: fprintf(ficresprobcor, "\n#********** Variable ");
2651: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
1.69 brouard 2652: fprintf(ficresprobcor, "**********\n#");
1.53 brouard 2653: }
2654:
2655: for (age=bage; age<=fage; age ++){
2656: cov[2]=age;
2657: for (k=1; k<=cptcovn;k++) {
2658: cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];
2659: }
2660: for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
2661: for (k=1; k<=cptcovprod;k++)
2662: cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
2663:
2664: gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
2665: trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
2666: gp=vector(1,(nlstate)*(nlstate+ndeath));
2667: gm=vector(1,(nlstate)*(nlstate+ndeath));
2668:
2669: for(theta=1; theta <=npar; theta++){
2670: for(i=1; i<=npar; i++)
1.74 brouard 2671: xp[i] = x[i] + (i==theta ?delti[theta]:(double)0);
1.53 brouard 2672:
2673: pmij(pmmij,cov,ncovmodel,xp,nlstate);
2674:
2675: k=0;
2676: for(i=1; i<= (nlstate); i++){
2677: for(j=1; j<=(nlstate+ndeath);j++){
2678: k=k+1;
2679: gp[k]=pmmij[i][j];
2680: }
2681: }
2682:
2683: for(i=1; i<=npar; i++)
1.74 brouard 2684: xp[i] = x[i] - (i==theta ?delti[theta]:(double)0);
1.53 brouard 2685:
2686: pmij(pmmij,cov,ncovmodel,xp,nlstate);
2687: k=0;
2688: for(i=1; i<=(nlstate); i++){
2689: for(j=1; j<=(nlstate+ndeath);j++){
2690: k=k+1;
2691: gm[k]=pmmij[i][j];
2692: }
2693: }
2694:
2695: for(i=1; i<= (nlstate)*(nlstate+ndeath); i++)
1.74 brouard 2696: gradg[theta][i]=(gp[i]-gm[i])/(double)2./delti[theta];
1.53 brouard 2697: }
2698:
2699: for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
2700: for(theta=1; theta <=npar; theta++)
2701: trgradg[j][theta]=gradg[theta][j];
2702:
2703: matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov);
2704: matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);
1.59 brouard 2705: free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
2706: free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
2707: free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
2708: free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
2709:
1.53 brouard 2710: pmij(pmmij,cov,ncovmodel,x,nlstate);
2711:
2712: k=0;
2713: for(i=1; i<=(nlstate); i++){
2714: for(j=1; j<=(nlstate+ndeath);j++){
2715: k=k+1;
2716: mu[k][(int) age]=pmmij[i][j];
2717: }
2718: }
2719: for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
2720: for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
2721: varpij[i][j][(int)age] = doldm[i][j];
2722:
2723: /*printf("\n%d ",(int)age);
1.59 brouard 2724: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
2725: printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
2726: fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
2727: }*/
1.53 brouard 2728:
2729: fprintf(ficresprob,"\n%d ",(int)age);
2730: fprintf(ficresprobcov,"\n%d ",(int)age);
2731: fprintf(ficresprobcor,"\n%d ",(int)age);
2732:
2733: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)
2734: fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));
2735: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
2736: fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);
2737: fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
2738: }
2739: i=0;
2740: for (k=1; k<=(nlstate);k++){
2741: for (l=1; l<=(nlstate+ndeath);l++){
2742: i=i++;
2743: fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
2744: fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
2745: for (j=1; j<=i;j++){
2746: fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);
2747: fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));
2748: }
2749: }
2750: }/* end of loop for state */
2751: } /* end of loop for age */
2752:
2753: /* Confidence intervalle of pij */
2754: /*
1.59 brouard 2755: fprintf(ficgp,"\nset noparametric;unset label");
2756: fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");
2757: fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
2758: 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);
2759: fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);
2760: fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);
2761: fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);
1.53 brouard 2762: */
2763:
2764: /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
2765: first1=1;
2766: for (k2=1; k2<=(nlstate);k2++){
2767: for (l2=1; l2<=(nlstate+ndeath);l2++){
2768: if(l2==k2) continue;
2769: j=(k2-1)*(nlstate+ndeath)+l2;
2770: for (k1=1; k1<=(nlstate);k1++){
2771: for (l1=1; l1<=(nlstate+ndeath);l1++){
2772: if(l1==k1) continue;
2773: i=(k1-1)*(nlstate+ndeath)+l1;
2774: if(i<=j) continue;
2775: for (age=bage; age<=fage; age ++){
2776: if ((int)age %5==0){
2777: v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;
2778: v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;
2779: cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;
2780: mu1=mu[i][(int) age]/stepm*YEARM ;
2781: mu2=mu[j][(int) age]/stepm*YEARM;
2782: c12=cv12/sqrt(v1*v2);
2783: /* Computing eigen value of matrix of covariance */
2784: lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
2785: lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
2786: /* Eigen vectors */
2787: v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
2788: /*v21=sqrt(1.-v11*v11); *//* error */
2789: v21=(lc1-v1)/cv12*v11;
2790: v12=-v21;
2791: v22=v11;
2792: tnalp=v21/v11;
2793: if(first1==1){
2794: first1=0;
2795: 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);
2796: }
2797: 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);
2798: /*printf(fignu*/
2799: /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */
2800: /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */
2801: if(first==1){
2802: first=0;
2803: fprintf(ficgp,"\nset parametric;unset label");
2804: 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);
2805: fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
2806: 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);
2807: fprintf(fichtm,"\n<br><img src=\"varpijgr%s%d%1d%1d-%1d%1d.png\"> ",optionfilefiname, j1,k1,l1,k2,l2);
2808: fprintf(fichtm,"\n<br> Correlation at age %d (%.3f),",(int) age, c12);
2809: fprintf(ficgp,"\nset out \"varpijgr%s%d%1d%1d-%1d%1d.png\"",optionfilefiname, j1,k1,l1,k2,l2);
2810: fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
2811: fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
2812: 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",\
2813: mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
2814: mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
2815: }else{
2816: first=0;
2817: fprintf(fichtm," %d (%.3f),",(int) age, c12);
2818: fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
2819: fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
2820: 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",\
2821: mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
2822: mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
2823: }/* if first */
2824: } /* age mod 5 */
2825: } /* end loop age */
2826: fprintf(ficgp,"\nset out \"varpijgr%s%d%1d%1d-%1d%1d.png\";replot;",optionfilefiname, j1,k1,l1,k2,l2);
2827: first=1;
2828: } /*l12 */
2829: } /* k12 */
2830: } /*l1 */
2831: }/* k1 */
2832: } /* loop covariates */
2833: }
1.59 brouard 2834: free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
2835: free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
1.53 brouard 2836: free_vector(xp,1,npar);
2837: fclose(ficresprob);
2838: fclose(ficresprobcov);
2839: fclose(ficresprobcor);
2840: fclose(ficgp);
2841: fclose(fichtm);
2842: }
2843:
2844:
2845: /******************* Printing html file ***********/
2846: void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \
2847: int lastpass, int stepm, int weightopt, char model[],\
2848: int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
2849: int popforecast, int estepm ,\
2850: double jprev1, double mprev1,double anprev1, \
2851: double jprev2, double mprev2,double anprev2){
2852: int jj1, k1, i1, cpt;
2853: /*char optionfilehtm[FILENAMELENGTH];*/
2854: if((fichtm=fopen(optionfilehtm,"a"))==NULL) {
2855: printf("Problem with %s \n",optionfilehtm), exit(0);
2856: fprintf(ficlog,"Problem with %s \n",optionfilehtm), exit(0);
2857: }
2858:
2859: fprintf(fichtm,"<ul><li><h4>Result files (first order: no variance)</h4>\n
2860: - 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
2861: - Estimated transition probabilities over %d (stepm) months: <a href=\"pij%s\">pij%s</a><br>\n
2862: - Stable prevalence in each health state: <a href=\"pl%s\">pl%s</a> <br>\n
2863: - Life expectancies by age and initial health status (estepm=%2d months):
2864: <a href=\"e%s\">e%s</a> <br>\n</li>", \
2865: jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,fileres,fileres,stepm,fileres,fileres,fileres,fileres,estepm,fileres,fileres);
2866:
2867: fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
2868:
2869: m=cptcoveff;
2870: if (cptcovn < 1) {m=1;ncodemax[1]=1;}
2871:
2872: jj1=0;
2873: for(k1=1; k1<=m;k1++){
2874: for(i1=1; i1<=ncodemax[k1];i1++){
2875: jj1++;
2876: if (cptcovn > 0) {
2877: fprintf(fichtm,"<hr size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
2878: for (cpt=1; cpt<=cptcoveff;cpt++)
2879: fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
2880: fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
2881: }
2882: /* Pij */
1.76 brouard 2883: 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 2884: <img src=\"pe%s%d1.png\">",stepm,strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);
2885: /* Quasi-incidences */
2886: 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>
2887: <img src=\"pe%s%d2.png\">",stepm,strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);
2888: /* Stable prevalence in each health state */
2889: for(cpt=1; cpt<nlstate;cpt++){
2890: fprintf(fichtm,"<br>- Stable prevalence in each health state : p%s%d%d.png<br>
2891: <img src=\"p%s%d%d.png\">",strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);
2892: }
2893: for(cpt=1; cpt<=nlstate;cpt++) {
2894: fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): exp%s%d%d.png <br>
2895: <img src=\"exp%s%d%d.png\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);
2896: }
2897: fprintf(fichtm,"\n<br>- Total life expectancy by age and
2898: health expectancies in states (1) and (2): e%s%d.png<br>
2899: <img src=\"e%s%d.png\">",strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);
2900: } /* end i1 */
2901: }/* End k1 */
2902: fprintf(fichtm,"</ul>");
2903:
2904:
2905: fprintf(fichtm,"\n<br><li><h4> Result files (second order: variances)</h4>\n
2906: - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n
2907: - Variance of one-step probabilities: <a href=\"prob%s\">prob%s</a> <br>\n
2908: - Variance-covariance of one-step probabilities: <a href=\"probcov%s\">probcov%s</a> <br>\n
2909: - Correlation matrix of one-step probabilities: <a href=\"probcor%s\">probcor%s</a> <br>\n
2910: - Variances and covariances of life expectancies by age and initial health status (estepm=%d months): <a href=\"v%s\">v%s</a><br>\n
2911: - Health expectancies with their variances (no covariance): <a href=\"t%s\">t%s</a> <br>\n
2912: - 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);
2913:
1.76 brouard 2914: /* if(popforecast==1) fprintf(fichtm,"\n */
2915: /* - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n */
2916: /* - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n */
2917: /* <br>",fileres,fileres,fileres,fileres); */
2918: /* else */
2919: /* 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 2920: fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
2921:
2922: m=cptcoveff;
2923: if (cptcovn < 1) {m=1;ncodemax[1]=1;}
2924:
2925: jj1=0;
2926: for(k1=1; k1<=m;k1++){
2927: for(i1=1; i1<=ncodemax[k1];i1++){
2928: jj1++;
2929: if (cptcovn > 0) {
2930: fprintf(fichtm,"<hr size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
2931: for (cpt=1; cpt<=cptcoveff;cpt++)
2932: fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
2933: fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
2934: }
2935: for(cpt=1; cpt<=nlstate;cpt++) {
1.76 brouard 2936: fprintf(fichtm,"<br>- Observed and period prevalence (with confident
1.53 brouard 2937: interval) in state (%d): v%s%d%d.png <br>
2938: <img src=\"v%s%d%d.png\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);
2939: }
2940: } /* end i1 */
2941: }/* End k1 */
2942: fprintf(fichtm,"</ul>");
2943: fclose(fichtm);
2944: }
2945:
2946: /******************* Gnuplot file **************/
2947: void printinggnuplot(char fileres[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
2948:
2949: int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;
2950: int ng;
2951: if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {
2952: printf("Problem with file %s",optionfilegnuplot);
2953: fprintf(ficlog,"Problem with file %s",optionfilegnuplot);
2954: }
2955:
1.54 brouard 2956: /*#ifdef windows */
1.53 brouard 2957: fprintf(ficgp,"cd \"%s\" \n",pathc);
1.54 brouard 2958: /*#endif */
1.53 brouard 2959: m=pow(2,cptcoveff);
2960:
2961: /* 1eme*/
2962: for (cpt=1; cpt<= nlstate ; cpt ++) {
2963: for (k1=1; k1<= m ; k1 ++) {
2964: fprintf(ficgp,"\nset out \"v%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);
2965: 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);
2966:
2967: for (i=1; i<= nlstate ; i ++) {
2968: if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
2969: else fprintf(ficgp," \%%*lf (\%%*lf)");
2970: }
1.69 brouard 2971: 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 2972: for (i=1; i<= nlstate ; i ++) {
2973: if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
2974: else fprintf(ficgp," \%%*lf (\%%*lf)");
2975: }
1.69 brouard 2976: fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"vpl%s\" every :::%d::%d u 1:($2-1.96*$3) \"\%%lf",fileres,k1-1,k1-1);
1.53 brouard 2977: for (i=1; i<= nlstate ; i ++) {
2978: if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
2979: else fprintf(ficgp," \%%*lf (\%%*lf)");
2980: }
2981: fprintf(ficgp,"\" t\"\" w l 1,\"p%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",fileres,k1-1,k1-1,2+4*(cpt-1));
2982: }
2983: }
2984: /*2 eme*/
2985:
2986: for (k1=1; k1<= m ; k1 ++) {
2987: fprintf(ficgp,"\nset out \"e%s%d.png\" \n",strtok(optionfile, "."),k1);
2988: fprintf(ficgp,"set ylabel \"Years\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] ",ageminpar,fage);
2989:
2990: for (i=1; i<= nlstate+1 ; i ++) {
2991: k=2*i;
2992: fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:2 \"\%%lf",fileres,k1-1,k1-1);
2993: for (j=1; j<= nlstate+1 ; j ++) {
2994: if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
2995: else fprintf(ficgp," \%%*lf (\%%*lf)");
2996: }
2997: if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");
2998: else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);
2999: fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",fileres,k1-1,k1-1);
3000: for (j=1; j<= nlstate+1 ; j ++) {
3001: if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
3002: else fprintf(ficgp," \%%*lf (\%%*lf)");
3003: }
3004: fprintf(ficgp,"\" t\"\" w l 0,");
3005: fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",fileres,k1-1,k1-1);
3006: for (j=1; j<= nlstate+1 ; j ++) {
3007: if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
3008: else fprintf(ficgp," \%%*lf (\%%*lf)");
3009: }
3010: if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");
3011: else fprintf(ficgp,"\" t\"\" w l 0,");
3012: }
3013: }
3014:
3015: /*3eme*/
3016:
3017: for (k1=1; k1<= m ; k1 ++) {
3018: for (cpt=1; cpt<= nlstate ; cpt ++) {
3019: k=2+nlstate*(2*cpt-2);
3020: fprintf(ficgp,"\nset out \"exp%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);
3021: fprintf(ficgp,"set ter png small\nset size 0.65,0.65\nplot [%.f:%.f] \"e%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,fileres,k1-1,k1-1,k,cpt);
3022: /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
3023: for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
3024: fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
3025: fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
3026: for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
3027: fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
3028:
3029: */
3030: for (i=1; i< nlstate ; i ++) {
3031: 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);
3032:
3033: }
3034: }
3035: }
3036:
1.76 brouard 3037: /* CV preval stable (period) */
1.53 brouard 3038: for (k1=1; k1<= m ; k1 ++) {
1.76 brouard 3039: for (cpt=1; cpt<=nlstate ; cpt ++) {
1.53 brouard 3040: k=3;
3041: fprintf(ficgp,"\nset out \"p%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);
3042: 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/($%d",ageminpar,agemaxpar,fileres,k1,k+cpt+1,k+1);
3043:
1.83 lievre 3044: for (i=1; i< nlstate ; i ++)
1.53 brouard 3045: fprintf(ficgp,"+$%d",k+i+1);
3046: fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);
3047:
3048: l=3+(nlstate+ndeath)*cpt;
3049: fprintf(ficgp,",\"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",fileres,k1,l+cpt+1,l+1);
3050: for (i=1; i< nlstate ; i ++) {
3051: l=3+(nlstate+ndeath)*cpt;
3052: fprintf(ficgp,"+$%d",l+i+1);
3053: }
3054: fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);
3055: }
3056: }
3057:
3058: /* proba elementaires */
3059: for(i=1,jk=1; i <=nlstate; i++){
3060: for(k=1; k <=(nlstate+ndeath); k++){
3061: if (k != i) {
3062: for(j=1; j <=ncovmodel; j++){
3063: fprintf(ficgp,"p%d=%f ",jk,p[jk]);
3064: jk++;
3065: fprintf(ficgp,"\n");
3066: }
3067: }
3068: }
3069: }
3070:
3071: for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/
3072: for(jk=1; jk <=m; jk++) {
3073: fprintf(ficgp,"\nset out \"pe%s%d%d.png\" \n",strtok(optionfile, "."),jk,ng);
3074: if (ng==2)
3075: fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
3076: else
3077: fprintf(ficgp,"\nset title \"Probability\"\n");
3078: fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65\nset log y\nplot [%.f:%.f] ",ageminpar,agemaxpar);
3079: i=1;
3080: for(k2=1; k2<=nlstate; k2++) {
3081: k3=i;
3082: for(k=1; k<=(nlstate+ndeath); k++) {
3083: if (k != k2){
3084: if(ng==2)
3085: fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);
3086: else
3087: fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
3088: ij=1;
3089: for(j=3; j <=ncovmodel; j++) {
3090: if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
3091: fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
3092: ij++;
3093: }
3094: else
3095: fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
3096: }
3097: fprintf(ficgp,")/(1");
3098:
3099: for(k1=1; k1 <=nlstate; k1++){
3100: fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);
3101: ij=1;
3102: for(j=3; j <=ncovmodel; j++){
3103: if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
3104: fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
3105: ij++;
3106: }
3107: else
3108: fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
3109: }
3110: fprintf(ficgp,")");
3111: }
3112: fprintf(ficgp,") t \"p%d%d\" ", k2,k);
3113: if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");
3114: i=i+ncovmodel;
3115: }
3116: } /* end k */
3117: } /* end k2 */
3118: } /* end jk */
3119: } /* end ng */
3120: fclose(ficgp);
3121: } /* end gnuplot */
3122:
3123:
3124: /*************** Moving average **************/
1.54 brouard 3125: int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav){
1.53 brouard 3126:
3127: int i, cpt, cptcod;
1.58 lievre 3128: int modcovmax =1;
1.54 brouard 3129: int mobilavrange, mob;
1.53 brouard 3130: double age;
1.58 lievre 3131:
3132: modcovmax=2*cptcoveff;/* Max number of modalities. We suppose
3133: a covariate has 2 modalities */
3134: if (cptcovn<1) modcovmax=1; /* At least 1 pass */
3135:
1.54 brouard 3136: if(mobilav==1||mobilav ==3 ||mobilav==5 ||mobilav== 7){
3137: if(mobilav==1) mobilavrange=5; /* default */
3138: else mobilavrange=mobilav;
3139: for (age=bage; age<=fage; age++)
3140: for (i=1; i<=nlstate;i++)
1.58 lievre 3141: for (cptcod=1;cptcod<=modcovmax;cptcod++)
1.54 brouard 3142: mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
3143: /* We keep the original values on the extreme ages bage, fage and for
3144: fage+1 and bage-1 we use a 3 terms moving average; for fage+2 bage+2
3145: we use a 5 terms etc. until the borders are no more concerned.
3146: */
3147: for (mob=3;mob <=mobilavrange;mob=mob+2){
3148: for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){
3149: for (i=1; i<=nlstate;i++){
1.58 lievre 3150: for (cptcod=1;cptcod<=modcovmax;cptcod++){
1.54 brouard 3151: mobaverage[(int)age][i][cptcod] =probs[(int)age][i][cptcod];
3152: for (cpt=1;cpt<=(mob-1)/2;cpt++){
3153: mobaverage[(int)age][i][cptcod] +=probs[(int)age-cpt][i][cptcod];
3154: mobaverage[(int)age][i][cptcod] +=probs[(int)age+cpt][i][cptcod];
3155: }
3156: mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/mob;
3157: }
1.53 brouard 3158: }
1.54 brouard 3159: }/* end age */
3160: }/* end mob */
3161: }else return -1;
3162: return 0;
3163: }/* End movingaverage */
1.53 brouard 3164:
3165:
3166: /************** Forecasting ******************/
1.70 brouard 3167: 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 3168: /* proj1, year, month, day of starting projection
3169: agemin, agemax range of age
3170: dateprev1 dateprev2 range of dates during which prevalence is computed
1.70 brouard 3171: anproj2 year of en of projection (same day and month as proj1).
1.69 brouard 3172: */
1.73 lievre 3173: int yearp, stepsize, hstepm, nhstepm, j, k, c, cptcod, i, h, i1;
1.53 brouard 3174: int *popage;
1.70 brouard 3175: double agec; /* generic age */
3176: double agelim, ppij, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
1.53 brouard 3177: double *popeffectif,*popcount;
3178: double ***p3mat;
1.55 lievre 3179: double ***mobaverage;
1.53 brouard 3180: char fileresf[FILENAMELENGTH];
3181:
1.69 brouard 3182: agelim=AGESUP;
1.84 ! brouard 3183: prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
1.53 brouard 3184:
3185: strcpy(fileresf,"f");
3186: strcat(fileresf,fileres);
3187: if((ficresf=fopen(fileresf,"w"))==NULL) {
3188: printf("Problem with forecast resultfile: %s\n", fileresf);
3189: fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);
3190: }
3191: printf("Computing forecasting: result on file '%s' \n", fileresf);
3192: fprintf(ficlog,"Computing forecasting: result on file '%s' \n", fileresf);
3193:
3194: if (cptcoveff==0) ncodemax[cptcoveff]=1;
3195:
1.54 brouard 3196: if (mobilav!=0) {
1.53 brouard 3197: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
1.54 brouard 3198: if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
3199: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
3200: printf(" Error in movingaverage mobilav=%d\n",mobilav);
3201: }
1.53 brouard 3202: }
3203:
3204: stepsize=(int) (stepm+YEARM-1)/YEARM;
3205: if (stepm<=12) stepsize=1;
1.74 brouard 3206: if(estepm < stepm){
3207: printf ("Problem %d lower than %d\n",estepm, stepm);
3208: }
3209: else hstepm=estepm;
3210:
1.53 brouard 3211: hstepm=hstepm/stepm;
1.69 brouard 3212: yp1=modf(dateintmean,&yp);/* extracts integral of datemean in yp and
3213: fractional in yp1 */
1.53 brouard 3214: anprojmean=yp;
3215: yp2=modf((yp1*12),&yp);
3216: mprojmean=yp;
3217: yp1=modf((yp2*30.5),&yp);
3218: jprojmean=yp;
3219: if(jprojmean==0) jprojmean=1;
3220: if(mprojmean==0) jprojmean=1;
1.73 lievre 3221:
3222: i1=cptcoveff;
3223: if (cptcovn < 1){i1=1;}
1.53 brouard 3224:
1.70 brouard 3225: fprintf(ficresf,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2);
1.53 brouard 3226:
1.70 brouard 3227: fprintf(ficresf,"#****** Routine prevforecast **\n");
1.73 lievre 3228:
1.75 brouard 3229: /* if (h==(int)(YEARM*yearp)){ */
1.73 lievre 3230: for(cptcov=1, k=0;cptcov<=i1;cptcov++){
1.53 brouard 3231: for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
3232: k=k+1;
3233: fprintf(ficresf,"\n#******");
3234: for(j=1;j<=cptcoveff;j++) {
1.70 brouard 3235: 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 3236: }
3237: fprintf(ficresf,"******\n");
1.70 brouard 3238: fprintf(ficresf,"# Covariate valuofcovar yearproj age");
3239: for(j=1; j<=nlstate+ndeath;j++){
3240: for(i=1; i<=nlstate;i++)
3241: fprintf(ficresf," p%d%d",i,j);
3242: fprintf(ficresf," p.%d",j);
3243: }
1.74 brouard 3244: for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) {
1.53 brouard 3245: fprintf(ficresf,"\n");
1.70 brouard 3246: fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+yearp);
1.53 brouard 3247:
1.71 brouard 3248: for (agec=fage; agec>=(ageminpar-1); agec--){
1.70 brouard 3249: nhstepm=(int) rint((agelim-agec)*YEARM/stepm);
1.53 brouard 3250: nhstepm = nhstepm/hstepm;
3251: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3252: oldm=oldms;savm=savms;
1.70 brouard 3253: hpxij(p3mat,nhstepm,agec,hstepm,p,nlstate,stepm,oldm,savm, k);
1.53 brouard 3254:
3255: for (h=0; h<=nhstepm; h++){
1.75 brouard 3256: if (h*hstepm/YEARM*stepm ==yearp) {
1.69 brouard 3257: fprintf(ficresf,"\n");
3258: for(j=1;j<=cptcoveff;j++)
3259: fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
1.70 brouard 3260: fprintf(ficresf,"%.f %.f ",anproj1+yearp,agec+h*hstepm/YEARM*stepm);
1.53 brouard 3261: }
3262: for(j=1; j<=nlstate+ndeath;j++) {
1.70 brouard 3263: ppij=0.;
1.71 brouard 3264: for(i=1; i<=nlstate;i++) {
1.53 brouard 3265: if (mobilav==1)
1.71 brouard 3266: ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][i][cptcod];
1.53 brouard 3267: else {
1.71 brouard 3268: ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][cptcod];
1.53 brouard 3269: }
1.75 brouard 3270: if (h*hstepm/YEARM*stepm== yearp) {
1.70 brouard 3271: fprintf(ficresf," %.3f", p3mat[i][j][h]);
1.75 brouard 3272: }
3273: } /* end i */
3274: if (h*hstepm/YEARM*stepm==yearp) {
1.70 brouard 3275: fprintf(ficresf," %.3f", ppij);
1.53 brouard 3276: }
1.75 brouard 3277: }/* end j */
3278: } /* end h */
1.53 brouard 3279: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
1.75 brouard 3280: } /* end agec */
3281: } /* end yearp */
3282: } /* end cptcod */
3283: } /* end cptcov */
1.53 brouard 3284:
1.54 brouard 3285: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
1.53 brouard 3286:
3287: fclose(ficresf);
3288: }
1.70 brouard 3289:
3290: /************** Forecasting *****not tested NB*************/
1.53 brouard 3291: 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){
3292:
3293: int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;
3294: int *popage;
1.69 brouard 3295: double calagedatem, agelim, kk1, kk2;
1.53 brouard 3296: double *popeffectif,*popcount;
3297: double ***p3mat,***tabpop,***tabpopprev;
1.55 lievre 3298: double ***mobaverage;
1.53 brouard 3299: char filerespop[FILENAMELENGTH];
3300:
3301: tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
3302: tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
3303: agelim=AGESUP;
1.69 brouard 3304: calagedatem=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;
1.53 brouard 3305:
1.84 ! brouard 3306: prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
1.53 brouard 3307:
3308:
3309: strcpy(filerespop,"pop");
3310: strcat(filerespop,fileres);
3311: if((ficrespop=fopen(filerespop,"w"))==NULL) {
3312: printf("Problem with forecast resultfile: %s\n", filerespop);
3313: fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop);
3314: }
3315: printf("Computing forecasting: result on file '%s' \n", filerespop);
3316: fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop);
3317:
3318: if (cptcoveff==0) ncodemax[cptcoveff]=1;
3319:
1.54 brouard 3320: if (mobilav!=0) {
1.53 brouard 3321: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
1.54 brouard 3322: if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
3323: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
3324: printf(" Error in movingaverage mobilav=%d\n",mobilav);
3325: }
1.53 brouard 3326: }
3327:
3328: stepsize=(int) (stepm+YEARM-1)/YEARM;
3329: if (stepm<=12) stepsize=1;
3330:
3331: agelim=AGESUP;
3332:
3333: hstepm=1;
3334: hstepm=hstepm/stepm;
3335:
3336: if (popforecast==1) {
3337: if((ficpop=fopen(popfile,"r"))==NULL) {
3338: printf("Problem with population file : %s\n",popfile);exit(0);
3339: fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0);
3340: }
3341: popage=ivector(0,AGESUP);
3342: popeffectif=vector(0,AGESUP);
3343: popcount=vector(0,AGESUP);
3344:
3345: i=1;
3346: while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;
3347:
3348: imx=i;
3349: for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];
3350: }
3351:
1.69 brouard 3352: for(cptcov=1,k=0;cptcov<=i2;cptcov++){
1.53 brouard 3353: for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
3354: k=k+1;
3355: fprintf(ficrespop,"\n#******");
3356: for(j=1;j<=cptcoveff;j++) {
3357: fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
3358: }
3359: fprintf(ficrespop,"******\n");
3360: fprintf(ficrespop,"# Age");
3361: for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);
3362: if (popforecast==1) fprintf(ficrespop," [Population]");
3363:
3364: for (cpt=0; cpt<=0;cpt++) {
3365: fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);
3366:
1.69 brouard 3367: for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){
1.53 brouard 3368: nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);
3369: nhstepm = nhstepm/hstepm;
3370:
3371: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3372: oldm=oldms;savm=savms;
3373: hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
3374:
3375: for (h=0; h<=nhstepm; h++){
1.69 brouard 3376: if (h==(int) (calagedatem+YEARM*cpt)) {
1.53 brouard 3377: fprintf(ficrespop,"\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: if (mobilav==1)
3383: kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];
3384: else {
3385: kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];
3386: }
3387: }
1.69 brouard 3388: if (h==(int)(calagedatem+12*cpt)){
1.53 brouard 3389: tabpop[(int)(agedeb)][j][cptcod]=kk1;
3390: /*fprintf(ficrespop," %.3f", kk1);
3391: if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/
3392: }
3393: }
3394: for(i=1; i<=nlstate;i++){
3395: kk1=0.;
3396: for(j=1; j<=nlstate;j++){
3397: kk1= kk1+tabpop[(int)(agedeb)][j][cptcod];
3398: }
1.69 brouard 3399: tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedatem+12*cpt)*hstepm/YEARM*stepm-1)];
1.53 brouard 3400: }
3401:
1.69 brouard 3402: if (h==(int)(calagedatem+12*cpt)) for(j=1; j<=nlstate;j++)
1.53 brouard 3403: fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);
3404: }
3405: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3406: }
3407: }
3408:
3409: /******/
3410:
3411: for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) {
3412: fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);
1.69 brouard 3413: for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){
1.53 brouard 3414: nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);
3415: nhstepm = nhstepm/hstepm;
3416:
3417: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3418: oldm=oldms;savm=savms;
3419: hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
3420: for (h=0; h<=nhstepm; h++){
1.69 brouard 3421: if (h==(int) (calagedatem+YEARM*cpt)) {
1.53 brouard 3422: fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
3423: }
3424: for(j=1; j<=nlstate+ndeath;j++) {
3425: kk1=0.;kk2=0;
3426: for(i=1; i<=nlstate;i++) {
3427: kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];
3428: }
1.69 brouard 3429: if (h==(int)(calagedatem+12*cpt)) fprintf(ficresf," %15.2f", kk1);
1.53 brouard 3430: }
3431: }
3432: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3433: }
3434: }
3435: }
3436: }
3437:
1.54 brouard 3438: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
1.53 brouard 3439:
3440: if (popforecast==1) {
3441: free_ivector(popage,0,AGESUP);
3442: free_vector(popeffectif,0,AGESUP);
3443: free_vector(popcount,0,AGESUP);
3444: }
3445: free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
3446: free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
3447: fclose(ficrespop);
1.84 ! brouard 3448: } /* End of popforecast */
1.53 brouard 3449:
3450: /***********************************************/
3451: /**************** Main Program *****************/
3452: /***********************************************/
3453:
3454: int main(int argc, char *argv[])
3455: {
1.61 brouard 3456: int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav);
1.74 brouard 3457: int i,j, k, n=MAXN,iter,m,size=100,cptcode, cptcod;
1.53 brouard 3458: double agedeb, agefin,hf;
3459: double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;
3460:
3461: double fret;
3462: double **xi,tmp,delta;
3463:
3464: double dum; /* Dummy variable */
3465: double ***p3mat;
3466: double ***mobaverage;
3467: int *indx;
3468: char line[MAXLINE], linepar[MAXLINE];
3469: char path[80],pathc[80],pathcd[80],pathtot[80],model[80];
3470: int firstobs=1, lastobs=10;
3471: int sdeb, sfin; /* Status at beginning and end */
3472: int c, h , cpt,l;
3473: int ju,jl, mi;
3474: int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;
1.59 brouard 3475: int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,*tab;
1.69 brouard 3476: int mobilavproj=0 , prevfcast=0 ; /* moving average of prev, If prevfcast=1 prevalence projection */
1.53 brouard 3477: int mobilav=0,popforecast=0;
3478: int hstepm, nhstepm;
1.74 brouard 3479: double jprev1=1, mprev1=1,anprev1=2000,jprev2=1, mprev2=1,anprev2=2000;
3480: double jpyram=1, mpyram=1,anpyram=2000,jpyram1=1, mpyram1=1,anpyram1=2000;
1.53 brouard 3481:
3482: double bage, fage, age, agelim, agebase;
3483: double ftolpl=FTOL;
3484: double **prlim;
3485: double *severity;
3486: double ***param; /* Matrix of parameters */
3487: double *p;
3488: double **matcov; /* Matrix of covariance */
3489: double ***delti3; /* Scale */
3490: double *delti; /* Scale */
3491: double ***eij, ***vareij;
3492: double **varpl; /* Variances of prevalence limits by age */
3493: double *epj, vepp;
3494: double kk1, kk2;
1.74 brouard 3495: double dateprev1, dateprev2,jproj1=1,mproj1=1,anproj1=2000,jproj2=1,mproj2=1,anproj2=2000;
1.53 brouard 3496:
3497: char *alph[]={"a","a","b","c","d","e"}, str[4];
3498:
3499:
3500: char z[1]="c", occ;
3501: #include <sys/time.h>
3502: #include <time.h>
3503: char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];
3504:
3505: /* long total_usecs;
1.59 brouard 3506: struct timeval start_time, end_time;
1.53 brouard 3507:
1.59 brouard 3508: gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */
1.53 brouard 3509: getcwd(pathcd, size);
3510:
1.81 brouard 3511: printf("\n%s\n%s",version,fullversion);
1.53 brouard 3512: if(argc <=1){
3513: printf("\nEnter the parameter file name: ");
3514: scanf("%s",pathtot);
3515: }
3516: else{
3517: strcpy(pathtot,argv[1]);
3518: }
3519: /*if(getcwd(pathcd, 80)!= NULL)printf ("Error pathcd\n");*/
3520: /*cygwin_split_path(pathtot,path,optionfile);
3521: printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/
3522: /* cutv(path,optionfile,pathtot,'\\');*/
3523:
3524: split(pathtot,path,optionfile,optionfilext,optionfilefiname);
1.59 brouard 3525: printf("pathtot=%s, path=%s, optionfile=%s optionfilext=%s optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
1.53 brouard 3526: chdir(path);
3527: replace(pathc,path);
3528:
1.59 brouard 3529: /*-------- arguments in the command line --------*/
1.53 brouard 3530:
3531: /* Log file */
3532: strcat(filelog, optionfilefiname);
3533: strcat(filelog,".log"); /* */
3534: if((ficlog=fopen(filelog,"w"))==NULL) {
3535: printf("Problem with logfile %s\n",filelog);
3536: goto end;
3537: }
3538: fprintf(ficlog,"Log filename:%s\n",filelog);
3539: fprintf(ficlog,"\n%s",version);
3540: fprintf(ficlog,"\nEnter the parameter file name: ");
3541: fprintf(ficlog,"pathtot=%s, path=%s, optionfile=%s optionfilext=%s optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
3542: fflush(ficlog);
3543:
3544: /* */
3545: strcpy(fileres,"r");
3546: strcat(fileres, optionfilefiname);
3547: strcat(fileres,".txt"); /* Other files have txt extension */
3548:
3549: /*---------arguments file --------*/
3550:
3551: if((ficpar=fopen(optionfile,"r"))==NULL) {
3552: printf("Problem with optionfile %s\n",optionfile);
3553: fprintf(ficlog,"Problem with optionfile %s\n",optionfile);
3554: goto end;
3555: }
3556:
3557: strcpy(filereso,"o");
3558: strcat(filereso,fileres);
3559: if((ficparo=fopen(filereso,"w"))==NULL) {
3560: printf("Problem with Output resultfile: %s\n", filereso);
3561: fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso);
3562: goto end;
3563: }
3564:
3565: /* Reads comments: lines beginning with '#' */
3566: while((c=getc(ficpar))=='#' && c!= EOF){
3567: ungetc(c,ficpar);
3568: fgets(line, MAXLINE, ficpar);
3569: puts(line);
3570: fputs(line,ficparo);
3571: }
3572: ungetc(c,ficpar);
3573:
3574: 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);
3575: 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);
3576: 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 3577: while((c=getc(ficpar))=='#' && c!= EOF){
1.53 brouard 3578: ungetc(c,ficpar);
3579: fgets(line, MAXLINE, ficpar);
3580: puts(line);
3581: fputs(line,ficparo);
3582: }
3583: ungetc(c,ficpar);
3584:
3585:
3586: covar=matrix(0,NCOVMAX,1,n);
1.58 lievre 3587: cptcovn=0; /*Number of covariates, i.e. number of '+' in model statement*/
1.53 brouard 3588: if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;
3589:
1.58 lievre 3590: ncovmodel=2+cptcovn; /*Number of variables = cptcovn + intercept + age */
1.53 brouard 3591: nvar=ncovmodel-1; /* Suppressing age as a basic covariate */
3592:
3593: /* Read guess parameters */
3594: /* Reads comments: lines beginning with '#' */
3595: while((c=getc(ficpar))=='#' && c!= EOF){
3596: ungetc(c,ficpar);
3597: fgets(line, MAXLINE, ficpar);
3598: puts(line);
3599: fputs(line,ficparo);
3600: }
3601: ungetc(c,ficpar);
3602:
3603: param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
1.59 brouard 3604: for(i=1; i <=nlstate; i++)
1.53 brouard 3605: for(j=1; j <=nlstate+ndeath-1; j++){
3606: fscanf(ficpar,"%1d%1d",&i1,&j1);
3607: fprintf(ficparo,"%1d%1d",i1,j1);
3608: if(mle==1)
3609: printf("%1d%1d",i,j);
3610: fprintf(ficlog,"%1d%1d",i,j);
3611: for(k=1; k<=ncovmodel;k++){
3612: fscanf(ficpar," %lf",¶m[i][j][k]);
3613: if(mle==1){
3614: printf(" %lf",param[i][j][k]);
3615: fprintf(ficlog," %lf",param[i][j][k]);
3616: }
3617: else
3618: fprintf(ficlog," %lf",param[i][j][k]);
3619: fprintf(ficparo," %lf",param[i][j][k]);
3620: }
3621: fscanf(ficpar,"\n");
3622: if(mle==1)
3623: printf("\n");
3624: fprintf(ficlog,"\n");
3625: fprintf(ficparo,"\n");
3626: }
3627:
1.59 brouard 3628: npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/
1.53 brouard 3629:
3630: p=param[1][1];
3631:
3632: /* Reads comments: lines beginning with '#' */
3633: while((c=getc(ficpar))=='#' && c!= EOF){
3634: ungetc(c,ficpar);
3635: fgets(line, MAXLINE, ficpar);
3636: puts(line);
3637: fputs(line,ficparo);
3638: }
3639: ungetc(c,ficpar);
3640:
3641: delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
1.74 brouard 3642: /* delti=vector(1,npar); *//* Scale of each paramater (output from hesscov) */
1.53 brouard 3643: for(i=1; i <=nlstate; i++){
3644: for(j=1; j <=nlstate+ndeath-1; j++){
3645: fscanf(ficpar,"%1d%1d",&i1,&j1);
3646: printf("%1d%1d",i,j);
3647: fprintf(ficparo,"%1d%1d",i1,j1);
3648: for(k=1; k<=ncovmodel;k++){
3649: fscanf(ficpar,"%le",&delti3[i][j][k]);
3650: printf(" %le",delti3[i][j][k]);
3651: fprintf(ficparo," %le",delti3[i][j][k]);
3652: }
3653: fscanf(ficpar,"\n");
3654: printf("\n");
3655: fprintf(ficparo,"\n");
3656: }
3657: }
3658: delti=delti3[1][1];
1.74 brouard 3659:
3660:
3661: /* 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 3662:
3663: /* Reads comments: lines beginning with '#' */
3664: while((c=getc(ficpar))=='#' && c!= EOF){
3665: ungetc(c,ficpar);
3666: fgets(line, MAXLINE, ficpar);
3667: puts(line);
3668: fputs(line,ficparo);
3669: }
3670: ungetc(c,ficpar);
3671:
3672: matcov=matrix(1,npar,1,npar);
3673: for(i=1; i <=npar; i++){
3674: fscanf(ficpar,"%s",&str);
3675: if(mle==1)
3676: printf("%s",str);
3677: fprintf(ficlog,"%s",str);
3678: fprintf(ficparo,"%s",str);
3679: for(j=1; j <=i; j++){
3680: fscanf(ficpar," %le",&matcov[i][j]);
3681: if(mle==1){
3682: printf(" %.5le",matcov[i][j]);
3683: fprintf(ficlog," %.5le",matcov[i][j]);
3684: }
3685: else
3686: fprintf(ficlog," %.5le",matcov[i][j]);
3687: fprintf(ficparo," %.5le",matcov[i][j]);
3688: }
3689: fscanf(ficpar,"\n");
3690: if(mle==1)
3691: printf("\n");
3692: fprintf(ficlog,"\n");
3693: fprintf(ficparo,"\n");
3694: }
3695: for(i=1; i <=npar; i++)
3696: for(j=i+1;j<=npar;j++)
3697: matcov[i][j]=matcov[j][i];
3698:
3699: if(mle==1)
3700: printf("\n");
3701: fprintf(ficlog,"\n");
3702:
3703:
1.59 brouard 3704: /*-------- Rewriting paramater file ----------*/
3705: strcpy(rfileres,"r"); /* "Rparameterfile */
3706: strcat(rfileres,optionfilefiname); /* Parameter file first name*/
3707: strcat(rfileres,"."); /* */
3708: strcat(rfileres,optionfilext); /* Other files have txt extension */
3709: if((ficres =fopen(rfileres,"w"))==NULL) {
3710: printf("Problem writing new parameter file: %s\n", fileres);goto end;
3711: fprintf(ficlog,"Problem writing new parameter file: %s\n", fileres);goto end;
3712: }
3713: fprintf(ficres,"#%s\n",version);
1.53 brouard 3714:
1.59 brouard 3715: /*-------- data file ----------*/
3716: if((fic=fopen(datafile,"r"))==NULL) {
3717: printf("Problem with datafile: %s\n", datafile);goto end;
3718: fprintf(ficlog,"Problem with datafile: %s\n", datafile);goto end;
3719: }
3720:
3721: n= lastobs;
3722: severity = vector(1,maxwav);
3723: outcome=imatrix(1,maxwav+1,1,n);
3724: num=ivector(1,n);
3725: moisnais=vector(1,n);
3726: annais=vector(1,n);
3727: moisdc=vector(1,n);
3728: andc=vector(1,n);
3729: agedc=vector(1,n);
3730: cod=ivector(1,n);
3731: weight=vector(1,n);
3732: for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */
3733: mint=matrix(1,maxwav,1,n);
3734: anint=matrix(1,maxwav,1,n);
3735: s=imatrix(1,maxwav+1,1,n);
3736: tab=ivector(1,NCOVMAX);
3737: ncodemax=ivector(1,8);
3738:
3739: i=1;
3740: while (fgets(line, MAXLINE, fic) != NULL) {
3741: if ((i >= firstobs) && (i <=lastobs)) {
1.53 brouard 3742:
1.59 brouard 3743: for (j=maxwav;j>=1;j--){
3744: cutv(stra, strb,line,' '); s[j][i]=atoi(strb);
3745: strcpy(line,stra);
3746: cutv(stra, strb,line,'/'); anint[j][i]=(double)(atoi(strb)); strcpy(line,stra);
3747: cutv(stra, strb,line,' '); mint[j][i]=(double)(atoi(strb)); strcpy(line,stra);
3748: }
1.53 brouard 3749:
1.59 brouard 3750: cutv(stra, strb,line,'/'); andc[i]=(double)(atoi(strb)); strcpy(line,stra);
3751: cutv(stra, strb,line,' '); moisdc[i]=(double)(atoi(strb)); strcpy(line,stra);
1.53 brouard 3752:
1.59 brouard 3753: cutv(stra, strb,line,'/'); annais[i]=(double)(atoi(strb)); strcpy(line,stra);
3754: cutv(stra, strb,line,' '); moisnais[i]=(double)(atoi(strb)); strcpy(line,stra);
1.53 brouard 3755:
1.59 brouard 3756: cutv(stra, strb,line,' '); weight[i]=(double)(atoi(strb)); strcpy(line,stra);
3757: for (j=ncovcol;j>=1;j--){
3758: cutv(stra, strb,line,' '); covar[j][i]=(double)(atoi(strb)); strcpy(line,stra);
3759: }
3760: num[i]=atol(stra);
1.53 brouard 3761:
1.59 brouard 3762: /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){
3763: 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 3764:
1.59 brouard 3765: i=i+1;
3766: }
3767: }
3768: /* printf("ii=%d", ij);
3769: scanf("%d",i);*/
1.53 brouard 3770: imx=i-1; /* Number of individuals */
3771:
3772: /* for (i=1; i<=imx; i++){
3773: if ((s[1][i]==3) && (s[2][i]==2)) s[2][i]=3;
3774: if ((s[2][i]==3) && (s[3][i]==2)) s[3][i]=3;
3775: if ((s[3][i]==3) && (s[4][i]==2)) s[4][i]=3;
3776: }*/
3777: /* for (i=1; i<=imx; i++){
3778: if (s[4][i]==9) s[4][i]=-1;
3779: 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]));}*/
3780:
1.71 brouard 3781: for (i=1; i<=imx; i++)
1.53 brouard 3782:
1.71 brouard 3783: /*if ((s[3][i]==3) || (s[4][i]==3)) weight[i]=0.08;
3784: else weight[i]=1;*/
3785:
1.53 brouard 3786: /* Calculation of the number of parameter from char model*/
3787: Tvar=ivector(1,15); /* stores the number n of the covariates in Vm+Vn at 1 and m at 2 */
3788: Tprod=ivector(1,15);
3789: Tvaraff=ivector(1,15);
3790: Tvard=imatrix(1,15,1,2);
3791: Tage=ivector(1,15);
3792:
1.58 lievre 3793: if (strlen(model) >1){ /* If there is at least 1 covariate */
1.53 brouard 3794: j=0, j1=0, k1=1, k2=1;
1.58 lievre 3795: j=nbocc(model,'+'); /* j=Number of '+' */
3796: j1=nbocc(model,'*'); /* j1=Number of '*' */
3797: cptcovn=j+1;
3798: cptcovprod=j1; /*Number of products */
1.53 brouard 3799:
3800: strcpy(modelsav,model);
3801: if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){
3802: printf("Error. Non available option model=%s ",model);
3803: fprintf(ficlog,"Error. Non available option model=%s ",model);
3804: goto end;
3805: }
3806:
1.59 brouard 3807: /* This loop fills the array Tvar from the string 'model'.*/
1.58 lievre 3808:
1.53 brouard 3809: for(i=(j+1); i>=1;i--){
3810: cutv(stra,strb,modelsav,'+'); /* keeps in strb after the last + */
1.59 brouard 3811: if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyzes it */
1.53 brouard 3812: /* printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/
3813: /*scanf("%d",i);*/
3814: if (strchr(strb,'*')) { /* Model includes a product */
3815: cutv(strd,strc,strb,'*'); /* strd*strc Vm*Vn (if not *age)*/
3816: if (strcmp(strc,"age")==0) { /* Vn*age */
3817: cptcovprod--;
3818: cutv(strb,stre,strd,'V');
3819: Tvar[i]=atoi(stre); /* computes n in Vn and stores in Tvar*/
3820: cptcovage++;
3821: Tage[cptcovage]=i;
3822: /*printf("stre=%s ", stre);*/
3823: }
3824: else if (strcmp(strd,"age")==0) { /* or age*Vn */
3825: cptcovprod--;
3826: cutv(strb,stre,strc,'V');
3827: Tvar[i]=atoi(stre);
3828: cptcovage++;
3829: Tage[cptcovage]=i;
3830: }
3831: else { /* Age is not in the model */
3832: cutv(strb,stre,strc,'V'); /* strc= Vn, stre is n*/
3833: Tvar[i]=ncovcol+k1;
3834: cutv(strb,strc,strd,'V'); /* strd was Vm, strc is m */
3835: Tprod[k1]=i;
3836: Tvard[k1][1]=atoi(strc); /* m*/
3837: Tvard[k1][2]=atoi(stre); /* n */
3838: Tvar[cptcovn+k2]=Tvard[k1][1];
3839: Tvar[cptcovn+k2+1]=Tvard[k1][2];
3840: for (k=1; k<=lastobs;k++)
3841: covar[ncovcol+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];
3842: k1++;
3843: k2=k2+2;
3844: }
3845: }
3846: else { /* no more sum */
3847: /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/
3848: /* scanf("%d",i);*/
3849: cutv(strd,strc,strb,'V');
3850: Tvar[i]=atoi(strc);
3851: }
3852: strcpy(modelsav,stra);
3853: /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);
3854: scanf("%d",i);*/
3855: } /* end of loop + */
3856: } /* end model */
3857:
1.58 lievre 3858: /*The number n of Vn is stored in Tvar. cptcovage =number of age covariate. Tage gives the position of age. cptcovprod= number of products.
3859: If model=V1+V1*age then Tvar[1]=1 Tvar[2]=1 cptcovage=1 Tage[1]=2 cptcovprod=0*/
3860:
1.53 brouard 3861: /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);
3862: printf("cptcovprod=%d ", cptcovprod);
3863: fprintf(ficlog,"cptcovprod=%d ", cptcovprod);
1.58 lievre 3864:
3865: scanf("%d ",i);
3866: fclose(fic);*/
1.53 brouard 3867:
3868: /* if(mle==1){*/
1.59 brouard 3869: if (weightopt != 1) { /* Maximisation without weights*/
3870: for(i=1;i<=n;i++) weight[i]=1.0;
3871: }
1.53 brouard 3872: /*-calculation of age at interview from date of interview and age at death -*/
1.59 brouard 3873: agev=matrix(1,maxwav,1,imx);
1.53 brouard 3874:
1.59 brouard 3875: for (i=1; i<=imx; i++) {
3876: for(m=2; (m<= maxwav); m++) {
1.76 brouard 3877: if (((int)mint[m][i]== 99) && (s[m][i] <= nlstate)){
1.59 brouard 3878: anint[m][i]=9999;
3879: s[m][i]=-1;
3880: }
1.76 brouard 3881: if((int)moisdc[i]==99 && (int)andc[i]==9999 && s[m][i]>nlstate){
1.77 brouard 3882: 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);
3883: 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 3884: s[m][i]=-1;
3885: }
3886: if((int)moisdc[i]==99 && (int)andc[i]!=9999 && s[m][i]>nlstate){
1.77 brouard 3887: 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]);
3888: 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]);
1.84 ! brouard 3889: s[m][i]=-1; /* We prefer to skip it (and to skip it in version 0.8a1 too */
1.76 brouard 3890: }
1.53 brouard 3891: }
1.59 brouard 3892: }
1.53 brouard 3893:
1.59 brouard 3894: for (i=1; i<=imx; i++) {
3895: agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);
1.71 brouard 3896: for(m=firstpass; (m<= lastpass); m++){
1.69 brouard 3897: if(s[m][i] >0){
1.59 brouard 3898: if (s[m][i] >= nlstate+1) {
3899: if(agedc[i]>0)
1.76 brouard 3900: if((int)moisdc[i]!=99 && (int)andc[i]!=9999)
1.69 brouard 3901: agev[m][i]=agedc[i];
1.59 brouard 3902: /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/
3903: else {
1.76 brouard 3904: if ((int)andc[i]!=9999){
1.59 brouard 3905: printf("Warning negative age at death: %d line:%d\n",num[i],i);
3906: fprintf(ficlog,"Warning negative age at death: %d line:%d\n",num[i],i);
3907: agev[m][i]=-1;
1.53 brouard 3908: }
3909: }
1.70 brouard 3910: }
1.69 brouard 3911: else if(s[m][i] !=9){ /* Standard case, age in fractional
3912: years but with the precision of a
3913: month */
1.59 brouard 3914: agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);
1.76 brouard 3915: if((int)mint[m][i]==99 || (int)anint[m][i]==9999)
1.59 brouard 3916: agev[m][i]=1;
3917: else if(agev[m][i] <agemin){
3918: agemin=agev[m][i];
3919: /*printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], agemin);*/
1.53 brouard 3920: }
1.59 brouard 3921: else if(agev[m][i] >agemax){
3922: agemax=agev[m][i];
3923: /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/
1.53 brouard 3924: }
1.59 brouard 3925: /*agev[m][i]=anint[m][i]-annais[i];*/
3926: /* agev[m][i] = age[i]+2*m;*/
1.53 brouard 3927: }
1.59 brouard 3928: else { /* =9 */
1.53 brouard 3929: agev[m][i]=1;
1.59 brouard 3930: s[m][i]=-1;
3931: }
1.53 brouard 3932: }
1.59 brouard 3933: else /*= 0 Unknown */
3934: agev[m][i]=1;
3935: }
1.53 brouard 3936:
1.59 brouard 3937: }
3938: for (i=1; i<=imx; i++) {
1.71 brouard 3939: for(m=firstpass; (m<=lastpass); m++){
1.59 brouard 3940: if (s[m][i] > (nlstate+ndeath)) {
3941: 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);
3942: 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);
3943: goto end;
1.53 brouard 3944: }
3945: }
1.59 brouard 3946: }
1.53 brouard 3947:
1.71 brouard 3948: /*for (i=1; i<=imx; i++){
3949: for (m=firstpass; (m<lastpass); m++){
3950: printf("%d %d %.lf %d %d\n", num[i],(covar[1][i]),agev[m][i],s[m][i],s[m+1][i]);
3951: }
3952:
3953: }*/
3954:
1.59 brouard 3955: printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);
3956: fprintf(ficlog,"Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);
3957:
3958: free_vector(severity,1,maxwav);
3959: free_imatrix(outcome,1,maxwav+1,1,n);
3960: free_vector(moisnais,1,n);
3961: free_vector(annais,1,n);
3962: /* free_matrix(mint,1,maxwav,1,n);
3963: free_matrix(anint,1,maxwav,1,n);*/
3964: free_vector(moisdc,1,n);
3965: free_vector(andc,1,n);
1.53 brouard 3966:
3967:
1.59 brouard 3968: wav=ivector(1,imx);
3969: dh=imatrix(1,lastpass-firstpass+1,1,imx);
3970: bh=imatrix(1,lastpass-firstpass+1,1,imx);
3971: mw=imatrix(1,lastpass-firstpass+1,1,imx);
1.69 brouard 3972:
1.59 brouard 3973: /* Concatenates waves */
3974: concatwav(wav, dh, bh, mw, s, agedc, agev, firstpass, lastpass, imx, nlstate, stepm);
1.53 brouard 3975:
1.59 brouard 3976: /* Routine tricode is to calculate cptcoveff (real number of unique covariates) and to associate covariable number and modality */
1.53 brouard 3977:
1.59 brouard 3978: Tcode=ivector(1,100);
3979: nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);
3980: ncodemax[1]=1;
3981: if (cptcovn > 0) tricode(Tvar,nbcode,imx);
1.53 brouard 3982:
1.59 brouard 3983: codtab=imatrix(1,100,1,10); /* Cross tabulation to get the order of
3984: the estimations*/
3985: h=0;
3986: m=pow(2,cptcoveff);
1.53 brouard 3987:
1.59 brouard 3988: for(k=1;k<=cptcoveff; k++){
3989: for(i=1; i <=(m/pow(2,k));i++){
3990: for(j=1; j <= ncodemax[k]; j++){
3991: for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){
3992: h++;
3993: if (h>m) h=1;codtab[h][k]=j;codtab[h][Tvar[k]]=j;
3994: /* printf("h=%d k=%d j=%d codtab[h][k]=%d tvar[k]=%d \n",h, k,j,codtab[h][k],Tvar[k]);*/
3995: }
3996: }
3997: }
3998: }
3999: /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]);
4000: codtab[1][2]=1;codtab[2][2]=2; */
4001: /* for(i=1; i <=m ;i++){
4002: for(k=1; k <=cptcovn; k++){
4003: printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);
4004: }
4005: printf("\n");
1.53 brouard 4006: }
1.59 brouard 4007: scanf("%d",i);*/
1.53 brouard 4008:
1.59 brouard 4009: /* Calculates basic frequencies. Computes observed prevalence at single age
4010: and prints on file fileres'p'. */
1.84 ! brouard 4011: freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint);
1.53 brouard 4012:
1.60 brouard 4013: pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
4014: oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
4015: newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
4016: savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
4017: oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */
1.53 brouard 4018:
4019:
1.59 brouard 4020: /* For Powell, parameters are in a vector p[] starting at p[1]
4021: so we point p on param[1][1] so that p[1] maps on param[1][1][1] */
4022: p=param[1][1]; /* *(*(*(param +1)+1)+0) */
1.53 brouard 4023:
1.61 brouard 4024: if(mle>=1){ /* Could be 1 or 2 */
1.53 brouard 4025: mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);
1.59 brouard 4026: }
1.53 brouard 4027:
1.59 brouard 4028: /*--------- results files --------------*/
4029: 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 4030:
4031:
1.59 brouard 4032: jk=1;
4033: fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
4034: printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
4035: fprintf(ficlog,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
4036: for(i=1,jk=1; i <=nlstate; i++){
4037: for(k=1; k <=(nlstate+ndeath); k++){
4038: if (k != i)
4039: {
4040: printf("%d%d ",i,k);
4041: fprintf(ficlog,"%d%d ",i,k);
4042: fprintf(ficres,"%1d%1d ",i,k);
4043: for(j=1; j <=ncovmodel; j++){
4044: printf("%f ",p[jk]);
4045: fprintf(ficlog,"%f ",p[jk]);
4046: fprintf(ficres,"%f ",p[jk]);
4047: jk++;
4048: }
4049: printf("\n");
4050: fprintf(ficlog,"\n");
4051: fprintf(ficres,"\n");
4052: }
4053: }
4054: }
1.84 ! brouard 4055: if(mle!=0){
1.59 brouard 4056: /* Computing hessian and covariance matrix */
4057: ftolhess=ftol; /* Usually correct */
4058: hesscov(matcov, p, npar, delti, ftolhess, func);
4059: }
4060: fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");
4061: printf("# Scales (for hessian or gradient estimation)\n");
4062: fprintf(ficlog,"# Scales (for hessian or gradient estimation)\n");
4063: for(i=1,jk=1; i <=nlstate; i++){
4064: for(j=1; j <=nlstate+ndeath; j++){
4065: if (j!=i) {
4066: fprintf(ficres,"%1d%1d",i,j);
4067: printf("%1d%1d",i,j);
4068: fprintf(ficlog,"%1d%1d",i,j);
4069: for(k=1; k<=ncovmodel;k++){
4070: printf(" %.5e",delti[jk]);
4071: fprintf(ficlog," %.5e",delti[jk]);
4072: fprintf(ficres," %.5e",delti[jk]);
4073: jk++;
4074: }
4075: printf("\n");
4076: fprintf(ficlog,"\n");
4077: fprintf(ficres,"\n");
4078: }
4079: }
4080: }
1.53 brouard 4081:
1.59 brouard 4082: 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");
4083: if(mle==1)
4084: 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");
4085: 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");
4086: for(i=1,k=1;i<=npar;i++){
4087: /* if (k>nlstate) k=1;
4088: i1=(i-1)/(ncovmodel*nlstate)+1;
4089: fprintf(ficres,"%s%d%d",alph[k],i1,tab[i]);
4090: printf("%s%d%d",alph[k],i1,tab[i]);
4091: */
4092: fprintf(ficres,"%3d",i);
4093: if(mle==1)
4094: printf("%3d",i);
4095: fprintf(ficlog,"%3d",i);
4096: for(j=1; j<=i;j++){
4097: fprintf(ficres," %.5e",matcov[i][j]);
4098: if(mle==1)
4099: printf(" %.5e",matcov[i][j]);
4100: fprintf(ficlog," %.5e",matcov[i][j]);
4101: }
4102: fprintf(ficres,"\n");
4103: if(mle==1)
4104: printf("\n");
4105: fprintf(ficlog,"\n");
4106: k++;
4107: }
1.53 brouard 4108:
1.59 brouard 4109: while((c=getc(ficpar))=='#' && c!= EOF){
4110: ungetc(c,ficpar);
4111: fgets(line, MAXLINE, ficpar);
4112: puts(line);
4113: fputs(line,ficparo);
4114: }
4115: ungetc(c,ficpar);
4116:
4117: estepm=0;
4118: fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm);
4119: if (estepm==0 || estepm < stepm) estepm=stepm;
4120: if (fage <= 2) {
4121: bage = ageminpar;
4122: fage = agemaxpar;
4123: }
1.53 brouard 4124:
1.59 brouard 4125: fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");
4126: fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
4127: fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
1.53 brouard 4128:
1.59 brouard 4129: while((c=getc(ficpar))=='#' && c!= EOF){
4130: ungetc(c,ficpar);
4131: fgets(line, MAXLINE, ficpar);
4132: puts(line);
4133: fputs(line,ficparo);
4134: }
4135: ungetc(c,ficpar);
1.53 brouard 4136:
1.59 brouard 4137: 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);
4138: 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);
4139: 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 4140: printf("begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
4141: 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 4142:
1.59 brouard 4143: while((c=getc(ficpar))=='#' && c!= EOF){
4144: ungetc(c,ficpar);
4145: fgets(line, MAXLINE, ficpar);
4146: puts(line);
4147: fputs(line,ficparo);
4148: }
4149: ungetc(c,ficpar);
1.53 brouard 4150:
4151:
1.70 brouard 4152: dateprev1=anprev1+(mprev1-1)/12.+(jprev1-1)/365.;
4153: dateprev2=anprev2+(mprev2-1)/12.+(jprev2-1)/365.;
1.53 brouard 4154:
4155: fscanf(ficpar,"pop_based=%d\n",&popbased);
4156: fprintf(ficparo,"pop_based=%d\n",popbased);
4157: fprintf(ficres,"pop_based=%d\n",popbased);
4158:
4159: while((c=getc(ficpar))=='#' && c!= EOF){
4160: ungetc(c,ficpar);
4161: fgets(line, MAXLINE, ficpar);
4162: puts(line);
4163: fputs(line,ficparo);
4164: }
4165: ungetc(c,ficpar);
4166:
1.69 brouard 4167: 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 4168: 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 4169: 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);
4170: 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);
4171: 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 4172: /* day and month of proj2 are not used but only year anproj2.*/
1.53 brouard 4173:
1.59 brouard 4174: while((c=getc(ficpar))=='#' && c!= EOF){
1.53 brouard 4175: ungetc(c,ficpar);
4176: fgets(line, MAXLINE, ficpar);
4177: puts(line);
4178: fputs(line,ficparo);
4179: }
4180: ungetc(c,ficpar);
4181:
4182: fscanf(ficpar,"popforecast=%d popfile=%s popfiledate=%lf/%lf/%lf last-popfiledate=%lf/%lf/%lf\n",&popforecast,popfile,&jpyram,&mpyram,&anpyram,&jpyram1,&mpyram1,&anpyram1);
4183: fprintf(ficparo,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);
4184: fprintf(ficres,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);
4185:
1.84 ! brouard 4186: freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint);
! 4187: /*,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
1.58 lievre 4188:
1.59 brouard 4189: /*------------ gnuplot -------------*/
4190: strcpy(optionfilegnuplot,optionfilefiname);
4191: strcat(optionfilegnuplot,".gp");
4192: if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {
4193: printf("Problem with file %s",optionfilegnuplot);
4194: }
4195: else{
4196: fprintf(ficgp,"\n# %s\n", version);
4197: fprintf(ficgp,"# %s\n", optionfilegnuplot);
4198: fprintf(ficgp,"set missing 'NaNq'\n");
4199: }
4200: fclose(ficgp);
4201: printinggnuplot(fileres, ageminpar,agemaxpar,fage, pathc,p);
4202: /*--------- index.htm --------*/
1.53 brouard 4203:
4204: strcpy(optionfilehtm,optionfile);
4205: strcat(optionfilehtm,".htm");
4206: if((fichtm=fopen(optionfilehtm,"w"))==NULL) {
4207: printf("Problem with %s \n",optionfilehtm), exit(0);
4208: }
4209:
4210: fprintf(fichtm,"<body> <font size=\"2\">%s </font> <hr size=\"2\" color=\"#EC5E5E\"> \n
4211: Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n
4212: \n
4213: Total number of observations=%d <br>\n
1.77 brouard 4214: Youngest age at first (selected) pass %.2f, oldest age %.2f<br>\n
1.53 brouard 4215: Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n
4216: <hr size=\"2\" color=\"#EC5E5E\">
4217: <ul><li><h4>Parameter files</h4>\n
4218: - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n
4219: - Log file of the run: <a href=\"%s\">%s</a><br>\n
1.76 brouard 4220: - 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 4221: fclose(fichtm);
1.53 brouard 4222:
1.59 brouard 4223: 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 4224:
1.59 brouard 4225: /*------------ free_vector -------------*/
4226: chdir(path);
1.53 brouard 4227:
1.59 brouard 4228: free_ivector(wav,1,imx);
4229: free_imatrix(dh,1,lastpass-firstpass+1,1,imx);
4230: free_imatrix(bh,1,lastpass-firstpass+1,1,imx);
4231: free_imatrix(mw,1,lastpass-firstpass+1,1,imx);
4232: free_ivector(num,1,n);
4233: free_vector(agedc,1,n);
1.65 lievre 4234: /*free_matrix(covar,0,NCOVMAX,1,n);*/
1.59 brouard 4235: /*free_matrix(covar,1,NCOVMAX,1,n);*/
4236: fclose(ficparo);
4237: fclose(ficres);
1.53 brouard 4238:
4239:
1.54 brouard 4240: /*--------------- Prevalence limit (stable prevalence) --------------*/
1.53 brouard 4241:
4242: strcpy(filerespl,"pl");
4243: strcat(filerespl,fileres);
4244: if((ficrespl=fopen(filerespl,"w"))==NULL) {
1.54 brouard 4245: printf("Problem with stable prevalence resultfile: %s\n", filerespl);goto end;
4246: fprintf(ficlog,"Problem with stable prevalence resultfile: %s\n", filerespl);goto end;
1.53 brouard 4247: }
1.54 brouard 4248: printf("Computing stable prevalence: result on file '%s' \n", filerespl);
4249: fprintf(ficlog,"Computing stable prevalence: result on file '%s' \n", filerespl);
4250: fprintf(ficrespl,"#Stable prevalence \n");
1.53 brouard 4251: fprintf(ficrespl,"#Age ");
4252: for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);
4253: fprintf(ficrespl,"\n");
4254:
4255: prlim=matrix(1,nlstate,1,nlstate);
1.59 brouard 4256:
1.53 brouard 4257: agebase=ageminpar;
4258: agelim=agemaxpar;
4259: ftolpl=1.e-10;
4260: i1=cptcoveff;
4261: if (cptcovn < 1){i1=1;}
4262:
1.59 brouard 4263: for(cptcov=1,k=0;cptcov<=i1;cptcov++){
1.53 brouard 4264: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
1.59 brouard 4265: k=k+1;
4266: /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/
4267: fprintf(ficrespl,"\n#******");
4268: printf("\n#******");
4269: fprintf(ficlog,"\n#******");
4270: for(j=1;j<=cptcoveff;j++) {
4271: fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
4272: printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
4273: fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
4274: }
4275: fprintf(ficrespl,"******\n");
4276: printf("******\n");
4277: fprintf(ficlog,"******\n");
1.53 brouard 4278:
1.59 brouard 4279: for (age=agebase; age<=agelim; age++){
4280: prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
1.69 brouard 4281: fprintf(ficrespl,"%.0f ",age );
4282: for(j=1;j<=cptcoveff;j++)
4283: fprintf(ficrespl,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
1.59 brouard 4284: for(i=1; i<=nlstate;i++)
1.53 brouard 4285: fprintf(ficrespl," %.5f", prlim[i][i]);
1.59 brouard 4286: fprintf(ficrespl,"\n");
1.53 brouard 4287: }
4288: }
1.59 brouard 4289: }
1.53 brouard 4290: fclose(ficrespl);
4291:
4292: /*------------- h Pij x at various ages ------------*/
4293:
4294: strcpy(filerespij,"pij"); strcat(filerespij,fileres);
4295: if((ficrespij=fopen(filerespij,"w"))==NULL) {
4296: printf("Problem with Pij resultfile: %s\n", filerespij);goto end;
4297: fprintf(ficlog,"Problem with Pij resultfile: %s\n", filerespij);goto end;
4298: }
4299: printf("Computing pij: result on file '%s' \n", filerespij);
4300: fprintf(ficlog,"Computing pij: result on file '%s' \n", filerespij);
4301:
4302: stepsize=(int) (stepm+YEARM-1)/YEARM;
4303: /*if (stepm<=24) stepsize=2;*/
4304:
4305: agelim=AGESUP;
4306: hstepm=stepsize*YEARM; /* Every year of age */
4307: hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */
4308:
4309: /* hstepm=1; aff par mois*/
4310:
1.70 brouard 4311: fprintf(ficrespij,"#****** h Pij x Probability to be in state j at age x+h being in i at x ");
1.59 brouard 4312: for(cptcov=1,k=0;cptcov<=i1;cptcov++){
1.53 brouard 4313: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
4314: k=k+1;
1.59 brouard 4315: fprintf(ficrespij,"\n#****** ");
4316: for(j=1;j<=cptcoveff;j++)
4317: fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
4318: fprintf(ficrespij,"******\n");
1.53 brouard 4319:
1.59 brouard 4320: for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */
4321: nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
4322: nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
4323:
4324: /* nhstepm=nhstepm*YEARM; aff par mois*/
4325:
4326: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4327: oldm=oldms;savm=savms;
4328: hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
1.70 brouard 4329: fprintf(ficrespij,"# Cov Agex agex+h hpijx with i,j=");
1.59 brouard 4330: for(i=1; i<=nlstate;i++)
4331: for(j=1; j<=nlstate+ndeath;j++)
4332: fprintf(ficrespij," %1d-%1d",i,j);
4333: fprintf(ficrespij,"\n");
4334: for (h=0; h<=nhstepm; h++){
1.70 brouard 4335: fprintf(ficrespij,"%d %3.f %3.f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );
1.53 brouard 4336: for(i=1; i<=nlstate;i++)
4337: for(j=1; j<=nlstate+ndeath;j++)
1.59 brouard 4338: fprintf(ficrespij," %.5f", p3mat[i][j][h]);
1.53 brouard 4339: fprintf(ficrespij,"\n");
4340: }
1.59 brouard 4341: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4342: fprintf(ficrespij,"\n");
4343: }
1.53 brouard 4344: }
4345: }
4346:
1.74 brouard 4347: varprob(optionfilefiname, matcov, p, delti, nlstate, bage, fage,k,Tvar,nbcode, ncodemax);
1.53 brouard 4348:
4349: fclose(ficrespij);
4350:
1.84 ! brouard 4351: probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
1.53 brouard 4352:
4353: /*---------- Forecasting ------------------*/
1.69 brouard 4354: /*if((stepm == 1) && (strcmp(model,".")==0)){*/
4355: if(prevfcast==1){
1.74 brouard 4356: /* if(stepm ==1){*/
1.70 brouard 4357: prevforecast(fileres, anproj1, mproj1, jproj1, agemin, agemax, dateprev1, dateprev2, mobilavproj, bage, fage, firstpass, lastpass, anproj2, p, cptcoveff);
1.74 brouard 4358: /* (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);*/
4359: /* } */
4360: /* else{ */
4361: /* erreur=108; */
4362: /* 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); */
4363: /* 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); */
4364: /* } */
1.69 brouard 4365: }
1.53 brouard 4366:
4367:
4368: /*---------- Health expectancies and variances ------------*/
4369:
4370: strcpy(filerest,"t");
4371: strcat(filerest,fileres);
4372: if((ficrest=fopen(filerest,"w"))==NULL) {
4373: printf("Problem with total LE resultfile: %s\n", filerest);goto end;
4374: fprintf(ficlog,"Problem with total LE resultfile: %s\n", filerest);goto end;
4375: }
4376: printf("Computing Total LEs with variances: file '%s' \n", filerest);
4377: fprintf(ficlog,"Computing Total LEs with variances: file '%s' \n", filerest);
4378:
4379:
4380: strcpy(filerese,"e");
4381: strcat(filerese,fileres);
4382: if((ficreseij=fopen(filerese,"w"))==NULL) {
4383: printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
4384: fprintf(ficlog,"Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
4385: }
4386: printf("Computing Health Expectancies: result on file '%s' \n", filerese);
4387: fprintf(ficlog,"Computing Health Expectancies: result on file '%s' \n", filerese);
1.68 lievre 4388:
1.53 brouard 4389: strcpy(fileresv,"v");
4390: strcat(fileresv,fileres);
4391: if((ficresvij=fopen(fileresv,"w"))==NULL) {
4392: printf("Problem with variance resultfile: %s\n", fileresv);exit(0);
4393: fprintf(ficlog,"Problem with variance resultfile: %s\n", fileresv);exit(0);
4394: }
4395: printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
4396: fprintf(ficlog,"Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
1.58 lievre 4397:
1.74 brouard 4398: /* Computes prevalence between agemin (i.e minimal age computed) and no more ageminpar */
1.84 ! brouard 4399: prevalence(probs, agemin, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
1.74 brouard 4400: /* 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",\
4401: ageminpar, agemax, s[lastpass][imx], agev[lastpass][imx], nlstate, imx, mint[lastpass][imx],anint[lastpass][imx], dateprev1, dateprev2, firstpass, lastpass);
4402: */
1.58 lievre 4403:
1.54 brouard 4404: if (mobilav!=0) {
1.53 brouard 4405: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
1.54 brouard 4406: if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
4407: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
4408: printf(" Error in movingaverage mobilav=%d\n",mobilav);
4409: }
1.53 brouard 4410: }
4411:
1.59 brouard 4412: for(cptcov=1,k=0;cptcov<=i1;cptcov++){
1.53 brouard 4413: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
4414: k=k+1;
4415: fprintf(ficrest,"\n#****** ");
4416: for(j=1;j<=cptcoveff;j++)
4417: fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
4418: fprintf(ficrest,"******\n");
4419:
4420: fprintf(ficreseij,"\n#****** ");
4421: for(j=1;j<=cptcoveff;j++)
4422: fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
4423: fprintf(ficreseij,"******\n");
4424:
4425: fprintf(ficresvij,"\n#****** ");
4426: for(j=1;j<=cptcoveff;j++)
4427: fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
4428: fprintf(ficresvij,"******\n");
4429:
4430: eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
4431: oldm=oldms;savm=savms;
4432: evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov);
4433:
4434: vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
4435: oldm=oldms;savm=savms;
4436: varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,0, mobilav);
4437: if(popbased==1){
4438: 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 4439: }
1.53 brouard 4440:
4441:
4442: fprintf(ficrest,"#Total LEs with variances: e.. (std) ");
4443: for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);
4444: fprintf(ficrest,"\n");
4445:
4446: epj=vector(1,nlstate+1);
4447: for(age=bage; age <=fage ;age++){
4448: prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
4449: if (popbased==1) {
1.54 brouard 4450: if(mobilav ==0){
1.53 brouard 4451: for(i=1; i<=nlstate;i++)
4452: prlim[i][i]=probs[(int)age][i][k];
1.54 brouard 4453: }else{ /* mobilav */
1.53 brouard 4454: for(i=1; i<=nlstate;i++)
4455: prlim[i][i]=mobaverage[(int)age][i][k];
4456: }
4457: }
4458:
4459: fprintf(ficrest," %4.0f",age);
4460: for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){
4461: for(i=1, epj[j]=0.;i <=nlstate;i++) {
4462: epj[j] += prlim[i][i]*eij[i][j][(int)age];
4463: /* printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/
4464: }
4465: epj[nlstate+1] +=epj[j];
4466: }
4467:
4468: for(i=1, vepp=0.;i <=nlstate;i++)
4469: for(j=1;j <=nlstate;j++)
4470: vepp += vareij[i][j][(int)age];
4471: fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));
4472: for(j=1;j <=nlstate;j++){
4473: fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));
4474: }
4475: fprintf(ficrest,"\n");
4476: }
1.59 brouard 4477: free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
4478: free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);
4479: free_vector(epj,1,nlstate+1);
1.53 brouard 4480: }
4481: }
1.59 brouard 4482: free_vector(weight,1,n);
4483: free_imatrix(Tvard,1,15,1,2);
4484: free_imatrix(s,1,maxwav+1,1,n);
4485: free_matrix(anint,1,maxwav,1,n);
4486: free_matrix(mint,1,maxwav,1,n);
4487: free_ivector(cod,1,n);
4488: free_ivector(tab,1,NCOVMAX);
1.53 brouard 4489: fclose(ficreseij);
4490: fclose(ficresvij);
4491: fclose(ficrest);
4492: fclose(ficpar);
4493:
1.54 brouard 4494: /*------- Variance of stable prevalence------*/
1.53 brouard 4495:
4496: strcpy(fileresvpl,"vpl");
4497: strcat(fileresvpl,fileres);
4498: if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {
1.54 brouard 4499: printf("Problem with variance of stable prevalence resultfile: %s\n", fileresvpl);
1.53 brouard 4500: exit(0);
4501: }
1.54 brouard 4502: printf("Computing Variance-covariance of stable prevalence: file '%s' \n", fileresvpl);
1.53 brouard 4503:
1.59 brouard 4504: for(cptcov=1,k=0;cptcov<=i1;cptcov++){
1.53 brouard 4505: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
4506: k=k+1;
4507: fprintf(ficresvpl,"\n#****** ");
4508: for(j=1;j<=cptcoveff;j++)
4509: fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
4510: fprintf(ficresvpl,"******\n");
4511:
4512: varpl=matrix(1,nlstate,(int) bage, (int) fage);
4513: oldm=oldms;savm=savms;
1.59 brouard 4514: varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);
4515: free_matrix(varpl,1,nlstate,(int) bage, (int)fage);
1.53 brouard 4516: }
1.59 brouard 4517: }
1.53 brouard 4518:
4519: fclose(ficresvpl);
4520:
4521: /*---------- End : free ----------------*/
4522: free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);
4523: free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);
4524: free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);
4525: free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);
1.65 lievre 4526:
4527: free_matrix(covar,0,NCOVMAX,1,n);
1.53 brouard 4528: free_matrix(matcov,1,npar,1,npar);
1.74 brouard 4529: /*free_vector(delti,1,npar);*/
4530: free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
1.53 brouard 4531: free_matrix(agev,1,maxwav,1,imx);
4532: free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
1.54 brouard 4533: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
1.74 brouard 4534: free_ma3x(probs,1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
4535:
1.59 brouard 4536: free_ivector(ncodemax,1,8);
4537: free_ivector(Tvar,1,15);
4538: free_ivector(Tprod,1,15);
4539: free_ivector(Tvaraff,1,15);
4540: free_ivector(Tage,1,15);
4541: free_ivector(Tcode,1,100);
1.53 brouard 4542:
1.74 brouard 4543: /* fclose(fichtm);*/
4544: /* fclose(ficgp);*/ /* ALready done */
1.53 brouard 4545:
4546:
4547: if(erreur >0){
4548: printf("End of Imach with error or warning %d\n",erreur);
4549: fprintf(ficlog,"End of Imach with error or warning %d\n",erreur);
4550: }else{
4551: printf("End of Imach\n");
4552: fprintf(ficlog,"End of Imach\n");
4553: }
4554: printf("See log file on %s\n",filelog);
4555: fclose(ficlog);
4556: /* gettimeofday(&end_time, (struct timezone*)0);*/ /* after time */
4557:
4558: /* 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);*/
4559: /*printf("Total time was %d uSec.\n", total_usecs);*/
4560: /*------ End -----------*/
4561:
1.59 brouard 4562: end:
1.53 brouard 4563: #ifdef windows
4564: /* chdir(pathcd);*/
4565: #endif
4566: /*system("wgnuplot graph.plt");*/
4567: /*system("../gp37mgw/wgnuplot graph.plt");*/
4568: /*system("cd ../gp37mgw");*/
4569: /* system("..\\gp37mgw\\wgnuplot graph.plt");*/
1.59 brouard 4570: strcpy(plotcmd,GNUPLOTPROGRAM);
4571: strcat(plotcmd," ");
4572: strcat(plotcmd,optionfilegnuplot);
1.75 brouard 4573: printf("Starting graphs with: %s",plotcmd);fflush(stdout);
1.59 brouard 4574: system(plotcmd);
1.75 brouard 4575: printf(" Wait...");
1.53 brouard 4576:
1.54 brouard 4577: /*#ifdef windows*/
1.53 brouard 4578: while (z[0] != 'q') {
4579: /* chdir(path); */
4580: printf("\nType e to edit output files, g to graph again, c to start again, and q for exiting: ");
4581: scanf("%s",z);
4582: if (z[0] == 'c') system("./imach");
4583: else if (z[0] == 'e') system(optionfilehtm);
4584: else if (z[0] == 'g') system(plotcmd);
4585: else if (z[0] == 'q') exit(0);
4586: }
1.54 brouard 4587: /*#endif */
1.53 brouard 4588: }
4589:
4590:
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