Annotation of imach096d/src/imach.c, revision 1.85
1.85 ! brouard 1: /* $Id: imach.c,v 1.84 2003/06/13 21:44:43 brouard Exp $
1.83 lievre 2: $State: Exp $
3: $Log: imach.c,v $
1.85 ! brouard 4: Revision 1.84 2003/06/13 21:44:43 brouard
! 5: * imach.c (Repository): Replace "freqsummary" at a correct
! 6: place. It differs from routine "prevalence" which may be called
! 7: many times. Probs is memory consuming and must be used with
! 8: parcimony.
! 9: Version 0.95a2 (should output exactly the same maximization than 0.8a2)
! 10:
1.84 brouard 11: Revision 1.83 2003/06/10 13:39:11 lievre
12: *** empty log message ***
13:
1.83 lievre 14: Revision 1.82 2003/06/05 15:57:20 brouard
15: Add log in imach.c and fullversion number is now printed.
16:
1.82 brouard 17: */
18: /*
1.53 brouard 19: Interpolated Markov Chain
20:
21: Short summary of the programme:
22:
23: This program computes Healthy Life Expectancies from
24: cross-longitudinal data. Cross-longitudinal data consist in: -1- a
25: first survey ("cross") where individuals from different ages are
26: interviewed on their health status or degree of disability (in the
27: case of a health survey which is our main interest) -2- at least a
28: second wave of interviews ("longitudinal") which measure each change
29: (if any) in individual health status. Health expectancies are
30: computed from the time spent in each health state according to a
31: model. More health states you consider, more time is necessary to reach the
32: Maximum Likelihood of the parameters involved in the model. The
33: simplest model is the multinomial logistic model where pij is the
34: probability to be observed in state j at the second wave
35: conditional to be observed in state i at the first wave. Therefore
36: the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where
37: 'age' is age and 'sex' is a covariate. If you want to have a more
38: complex model than "constant and age", you should modify the program
39: where the markup *Covariates have to be included here again* invites
40: you to do it. More covariates you add, slower the
41: convergence.
42:
43: The advantage of this computer programme, compared to a simple
44: multinomial logistic model, is clear when the delay between waves is not
45: identical for each individual. Also, if a individual missed an
46: intermediate interview, the information is lost, but taken into
47: account using an interpolation or extrapolation.
48:
49: hPijx is the probability to be observed in state i at age x+h
50: conditional to the observed state i at age x. The delay 'h' can be
51: split into an exact number (nh*stepm) of unobserved intermediate
1.66 brouard 52: states. This elementary transition (by month, quarter,
53: semester or year) is modelled as a multinomial logistic. The hPx
1.53 brouard 54: matrix is simply the matrix product of nh*stepm elementary matrices
55: and the contribution of each individual to the likelihood is simply
56: hPijx.
57:
58: Also this programme outputs the covariance matrix of the parameters but also
1.54 brouard 59: of the life expectancies. It also computes the stable prevalence.
1.53 brouard 60:
61: Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).
62: Institut national d'études démographiques, Paris.
63: This software have been partly granted by Euro-REVES, a concerted action
64: from the European Union.
65: It is copyrighted identically to a GNU software product, ie programme and
66: software can be distributed freely for non commercial use. Latest version
67: can be accessed at http://euroreves.ined.fr/imach .
1.74 brouard 68:
69: Help to debug: LD_PRELOAD=/usr/local/lib/libnjamd.so ./imach foo.imach
70: or better on gdb : set env LD_PRELOAD=/usr/local/lib/libnjamd.so
71:
1.53 brouard 72: **********************************************************************/
1.74 brouard 73: /*
74: main
75: read parameterfile
76: read datafile
77: concatwav
1.84 brouard 78: freqsummary
1.74 brouard 79: if (mle >= 1)
80: mlikeli
81: print results files
82: if mle==1
83: computes hessian
84: read end of parameter file: agemin, agemax, bage, fage, estepm
85: begin-prev-date,...
86: open gnuplot file
87: open html file
88: stable prevalence
89: for age prevalim()
90: h Pij x
91: variance of p varprob
92: forecasting if prevfcast==1 prevforecast call prevalence()
93: health expectancies
94: Variance-covariance of DFLE
95: prevalence()
96: movingaverage()
97: varevsij()
98: if popbased==1 varevsij(,popbased)
99: total life expectancies
100: Variance of stable prevalence
101: end
102: */
103:
104:
105:
1.53 brouard 106:
107: #include <math.h>
108: #include <stdio.h>
109: #include <stdlib.h>
110: #include <unistd.h>
111:
112: #define MAXLINE 256
113: #define GNUPLOTPROGRAM "gnuplot"
114: /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
1.85 ! brouard 115: #define FILENAMELENGTH 132
1.53 brouard 116: /*#define DEBUG*/
1.85 ! brouard 117: /*#define windows*/
1.53 brouard 118: #define GLOCK_ERROR_NOPATH -1 /* empty path */
119: #define GLOCK_ERROR_GETCWD -2 /* cannot get cwd */
120:
121: #define MAXPARM 30 /* Maximum number of parameters for the optimization */
122: #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */
123:
124: #define NINTERVMAX 8
125: #define NLSTATEMAX 8 /* Maximum number of live states (for func) */
126: #define NDEATHMAX 8 /* Maximum number of dead states (for func) */
127: #define NCOVMAX 8 /* Maximum number of covariates */
128: #define MAXN 20000
129: #define YEARM 12. /* Number of months per year */
130: #define AGESUP 130
131: #define AGEBASE 40
1.85 ! brouard 132: #ifdef unix
! 133: #define DIRSEPARATOR '/'
! 134: #define ODIRSEPARATOR '\\'
! 135: #else
1.53 brouard 136: #define DIRSEPARATOR '\\'
137: #define ODIRSEPARATOR '/'
138: #endif
139:
1.85 ! brouard 140: /* $Id: imach.c,v 1.84 2003/06/13 21:44:43 brouard Exp $ */
1.81 brouard 141: /* $State: Exp $ */
1.80 brouard 142:
1.84 brouard 143: char version[]="Imach version 0.95a2, June 2003, INED-EUROREVES ";
1.85 ! brouard 144: char fullversion[]="$Revision: 1.84 $ $Date: 2003/06/13 21:44:43 $";
1.53 brouard 145: int erreur; /* Error number */
146: int nvar;
147: int cptcovn=0, cptcovage=0, cptcoveff=0,cptcov;
148: int npar=NPARMAX;
149: int nlstate=2; /* Number of live states */
150: int ndeath=1; /* Number of dead states */
151: int ncovmodel, ncovcol; /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
152: int popbased=0;
153:
154: int *wav; /* Number of waves for this individuual 0 is possible */
155: int maxwav; /* Maxim number of waves */
156: int jmin, jmax; /* min, max spacing between 2 waves */
157: int mle, weightopt;
158: int **mw; /* mw[mi][i] is number of the mi wave for this individual */
159: int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
1.59 brouard 160: int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between
161: * wave mi and wave mi+1 is not an exact multiple of stepm. */
1.53 brouard 162: double jmean; /* Mean space between 2 waves */
163: double **oldm, **newm, **savm; /* Working pointers to matrices */
164: double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
165: FILE *fic,*ficpar, *ficparo,*ficres, *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
1.76 brouard 166: FILE *ficlog, *ficrespow;
1.85 ! brouard 167: int globpr; /* Global variable for printing or not */
! 168: double fretone; /* Only one call to likelihood */
! 169: long ipmx; /* Number of contributions */
! 170: double sw; /* Sum of weights */
! 171: char fileresilk[FILENAMELENGTH]; /* File of individual contributions to the likelihood */
! 172: FILE *ficresilk;
1.53 brouard 173: FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
174: FILE *ficresprobmorprev;
175: FILE *fichtm; /* Html File */
176: FILE *ficreseij;
177: char filerese[FILENAMELENGTH];
178: FILE *ficresvij;
179: char fileresv[FILENAMELENGTH];
180: FILE *ficresvpl;
181: char fileresvpl[FILENAMELENGTH];
182: char title[MAXLINE];
183: char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH], filerespl[FILENAMELENGTH];
184: char optionfilext[10], optionfilefiname[FILENAMELENGTH], plotcmd[FILENAMELENGTH];
185:
186: char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
187: char filelog[FILENAMELENGTH]; /* Log file */
188: char filerest[FILENAMELENGTH];
189: char fileregp[FILENAMELENGTH];
190: char popfile[FILENAMELENGTH];
191:
192: char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH];
193:
194: #define NR_END 1
195: #define FREE_ARG char*
196: #define FTOL 1.0e-10
197:
198: #define NRANSI
199: #define ITMAX 200
200:
201: #define TOL 2.0e-4
202:
203: #define CGOLD 0.3819660
204: #define ZEPS 1.0e-10
205: #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);
206:
207: #define GOLD 1.618034
208: #define GLIMIT 100.0
209: #define TINY 1.0e-20
210:
211: static double maxarg1,maxarg2;
212: #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
213: #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
214:
215: #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
216: #define rint(a) floor(a+0.5)
217:
218: static double sqrarg;
219: #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
220: #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}
221:
222: int imx;
223: int stepm;
224: /* Stepm, step in month: minimum step interpolation*/
225:
226: int estepm;
227: /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
228:
229: int m,nb;
1.85 ! brouard 230: long *num;
! 231: int firstpass=0, lastpass=4,*cod, *ncodemax, *Tage;
1.53 brouard 232: double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
1.55 lievre 233: double **pmmij, ***probs;
1.53 brouard 234: double dateintmean=0;
235:
236: double *weight;
237: int **s; /* Status */
238: double *agedc, **covar, idx;
239: int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;
240:
241: double ftol=FTOL; /* Tolerance for computing Max Likelihood */
242: double ftolhess; /* Tolerance for computing hessian */
243:
244: /**************** split *************************/
245: static int split( char *path, char *dirc, char *name, char *ext, char *finame )
246: {
1.59 brouard 247: char *ss; /* pointer */
248: int l1, l2; /* length counters */
1.53 brouard 249:
1.59 brouard 250: l1 = strlen(path ); /* length of path */
251: if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
252: ss= strrchr( path, DIRSEPARATOR ); /* find last / */
253: if ( ss == NULL ) { /* no directory, so use current */
254: /*if(strrchr(path, ODIRSEPARATOR )==NULL)
255: printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
1.74 brouard 256: /* get current working directory */
257: /* extern char* getcwd ( char *buf , int len);*/
1.59 brouard 258: if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {
259: return( GLOCK_ERROR_GETCWD );
260: }
261: strcpy( name, path ); /* we've got it */
262: } else { /* strip direcotry from path */
263: ss++; /* after this, the filename */
264: l2 = strlen( ss ); /* length of filename */
265: if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
266: strcpy( name, ss ); /* save file name */
267: strncpy( dirc, path, l1 - l2 ); /* now the directory */
268: dirc[l1-l2] = 0; /* add zero */
269: }
270: l1 = strlen( dirc ); /* length of directory */
1.85 ! brouard 271: /*#ifdef windows
1.59 brouard 272: if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; }
1.53 brouard 273: #else
1.59 brouard 274: if ( dirc[l1-1] != '/' ) { dirc[l1] = '/'; dirc[l1+1] = 0; }
1.53 brouard 275: #endif
1.85 ! brouard 276: */
1.59 brouard 277: ss = strrchr( name, '.' ); /* find last / */
278: ss++;
279: strcpy(ext,ss); /* save extension */
280: l1= strlen( name);
281: l2= strlen(ss)+1;
282: strncpy( finame, name, l1-l2);
283: finame[l1-l2]= 0;
284: return( 0 ); /* we're done */
1.53 brouard 285: }
286:
287:
288: /******************************************/
289:
290: void replace(char *s, char*t)
291: {
292: int i;
293: int lg=20;
294: i=0;
295: lg=strlen(t);
296: for(i=0; i<= lg; i++) {
297: (s[i] = t[i]);
298: if (t[i]== '\\') s[i]='/';
299: }
300: }
301:
302: int nbocc(char *s, char occ)
303: {
304: int i,j=0;
305: int lg=20;
306: i=0;
307: lg=strlen(s);
308: for(i=0; i<= lg; i++) {
309: if (s[i] == occ ) j++;
310: }
311: return j;
312: }
313:
314: void cutv(char *u,char *v, char*t, char occ)
315: {
316: /* cuts string t into u and v where u is ended by char occ excluding it
317: and v is after occ excluding it too : ex cutv(u,v,"abcdef2ghi2j",2)
318: gives u="abcedf" and v="ghi2j" */
319: int i,lg,j,p=0;
320: i=0;
321: for(j=0; j<=strlen(t)-1; j++) {
322: if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;
323: }
324:
325: lg=strlen(t);
326: for(j=0; j<p; j++) {
327: (u[j] = t[j]);
328: }
329: u[p]='\0';
330:
331: for(j=0; j<= lg; j++) {
332: if (j>=(p+1))(v[j-p-1] = t[j]);
333: }
334: }
335:
336: /********************** nrerror ********************/
337:
338: void nrerror(char error_text[])
339: {
340: fprintf(stderr,"ERREUR ...\n");
341: fprintf(stderr,"%s\n",error_text);
1.59 brouard 342: exit(EXIT_FAILURE);
1.53 brouard 343: }
344: /*********************** vector *******************/
345: double *vector(int nl, int nh)
346: {
347: double *v;
348: v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
349: if (!v) nrerror("allocation failure in vector");
350: return v-nl+NR_END;
351: }
352:
353: /************************ free vector ******************/
354: void free_vector(double*v, int nl, int nh)
355: {
356: free((FREE_ARG)(v+nl-NR_END));
357: }
358:
359: /************************ivector *******************************/
1.85 ! brouard 360: int *ivector(long nl,long nh)
1.76 brouard 361: {
1.85 ! brouard 362: int *v;
! 363: v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
! 364: if (!v) nrerror("allocation failure in ivector");
1.76 brouard 365: return v-nl+NR_END;
366: }
367:
368: /******************free ivector **************************/
1.85 ! brouard 369: void free_ivector(int *v, long nl, long nh)
1.76 brouard 370: {
371: free((FREE_ARG)(v+nl-NR_END));
372: }
373:
1.85 ! brouard 374: /************************lvector *******************************/
! 375: long *lvector(long nl,long nh)
1.53 brouard 376: {
1.85 ! brouard 377: long *v;
! 378: v=(long *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(long)));
1.53 brouard 379: if (!v) nrerror("allocation failure in ivector");
380: return v-nl+NR_END;
381: }
382:
1.85 ! brouard 383: /******************free lvector **************************/
! 384: void free_lvector(long *v, long nl, long nh)
1.53 brouard 385: {
386: free((FREE_ARG)(v+nl-NR_END));
387: }
388:
389: /******************* imatrix *******************************/
390: int **imatrix(long nrl, long nrh, long ncl, long nch)
391: /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */
392: {
393: long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;
394: int **m;
395:
396: /* allocate pointers to rows */
397: m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));
398: if (!m) nrerror("allocation failure 1 in matrix()");
399: m += NR_END;
400: m -= nrl;
401:
402:
403: /* allocate rows and set pointers to them */
404: m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));
405: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
406: m[nrl] += NR_END;
407: m[nrl] -= ncl;
408:
409: for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;
410:
411: /* return pointer to array of pointers to rows */
412: return m;
413: }
414:
415: /****************** free_imatrix *************************/
416: void free_imatrix(m,nrl,nrh,ncl,nch)
417: int **m;
418: long nch,ncl,nrh,nrl;
419: /* free an int matrix allocated by imatrix() */
420: {
421: free((FREE_ARG) (m[nrl]+ncl-NR_END));
422: free((FREE_ARG) (m+nrl-NR_END));
423: }
424:
425: /******************* matrix *******************************/
426: double **matrix(long nrl, long nrh, long ncl, long nch)
427: {
428: long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
429: double **m;
430:
431: m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
432: if (!m) nrerror("allocation failure 1 in matrix()");
433: m += NR_END;
434: m -= nrl;
435:
436: m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
437: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
438: m[nrl] += NR_END;
439: m[nrl] -= ncl;
440:
441: for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
442: return m;
1.85 ! brouard 443: /* print *(*(m+1)+70) or print m[1][70]; print m+1 or print &(m[1])
1.74 brouard 444: */
1.53 brouard 445: }
446:
447: /*************************free matrix ************************/
448: void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
449: {
450: free((FREE_ARG)(m[nrl]+ncl-NR_END));
451: free((FREE_ARG)(m+nrl-NR_END));
452: }
453:
454: /******************* ma3x *******************************/
455: double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
456: {
457: long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
458: double ***m;
459:
460: m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
461: if (!m) nrerror("allocation failure 1 in matrix()");
462: m += NR_END;
463: m -= nrl;
464:
465: m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
466: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
467: m[nrl] += NR_END;
468: m[nrl] -= ncl;
469:
470: for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
471:
472: m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
473: if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
474: m[nrl][ncl] += NR_END;
475: m[nrl][ncl] -= nll;
476: for (j=ncl+1; j<=nch; j++)
477: m[nrl][j]=m[nrl][j-1]+nlay;
478:
479: for (i=nrl+1; i<=nrh; i++) {
480: m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
481: for (j=ncl+1; j<=nch; j++)
482: m[i][j]=m[i][j-1]+nlay;
483: }
1.74 brouard 484: return m;
485: /* gdb: p *(m+1) <=> p m[1] and p (m+1) <=> p (m+1) <=> p &(m[1])
486: &(m[i][j][k]) <=> *((*(m+i) + j)+k)
487: */
1.53 brouard 488: }
489:
490: /*************************free ma3x ************************/
491: void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
492: {
493: free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
494: free((FREE_ARG)(m[nrl]+ncl-NR_END));
495: free((FREE_ARG)(m+nrl-NR_END));
496: }
497:
498: /***************** f1dim *************************/
499: extern int ncom;
500: extern double *pcom,*xicom;
501: extern double (*nrfunc)(double []);
502:
503: double f1dim(double x)
504: {
505: int j;
506: double f;
507: double *xt;
508:
509: xt=vector(1,ncom);
510: for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];
511: f=(*nrfunc)(xt);
512: free_vector(xt,1,ncom);
513: return f;
514: }
515:
516: /*****************brent *************************/
517: double brent(double ax, double bx, double cx, double (*f)(double), double tol, double *xmin)
518: {
519: int iter;
520: double a,b,d,etemp;
521: double fu,fv,fw,fx;
522: double ftemp;
523: double p,q,r,tol1,tol2,u,v,w,x,xm;
524: double e=0.0;
525:
526: a=(ax < cx ? ax : cx);
527: b=(ax > cx ? ax : cx);
528: x=w=v=bx;
529: fw=fv=fx=(*f)(x);
530: for (iter=1;iter<=ITMAX;iter++) {
531: xm=0.5*(a+b);
532: tol2=2.0*(tol1=tol*fabs(x)+ZEPS);
533: /* if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
534: printf(".");fflush(stdout);
535: fprintf(ficlog,".");fflush(ficlog);
536: #ifdef DEBUG
537: 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);
538: 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);
539: /* if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
540: #endif
541: if (fabs(x-xm) <= (tol2-0.5*(b-a))){
542: *xmin=x;
543: return fx;
544: }
545: ftemp=fu;
546: if (fabs(e) > tol1) {
547: r=(x-w)*(fx-fv);
548: q=(x-v)*(fx-fw);
549: p=(x-v)*q-(x-w)*r;
550: q=2.0*(q-r);
551: if (q > 0.0) p = -p;
552: q=fabs(q);
553: etemp=e;
554: e=d;
555: if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))
556: d=CGOLD*(e=(x >= xm ? a-x : b-x));
557: else {
558: d=p/q;
559: u=x+d;
560: if (u-a < tol2 || b-u < tol2)
561: d=SIGN(tol1,xm-x);
562: }
563: } else {
564: d=CGOLD*(e=(x >= xm ? a-x : b-x));
565: }
566: u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));
567: fu=(*f)(u);
568: if (fu <= fx) {
569: if (u >= x) a=x; else b=x;
570: SHFT(v,w,x,u)
571: SHFT(fv,fw,fx,fu)
572: } else {
573: if (u < x) a=u; else b=u;
574: if (fu <= fw || w == x) {
575: v=w;
576: w=u;
577: fv=fw;
578: fw=fu;
579: } else if (fu <= fv || v == x || v == w) {
580: v=u;
581: fv=fu;
582: }
583: }
584: }
585: nrerror("Too many iterations in brent");
586: *xmin=x;
587: return fx;
588: }
589:
590: /****************** mnbrak ***********************/
591:
592: void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,
593: double (*func)(double))
594: {
595: double ulim,u,r,q, dum;
596: double fu;
597:
598: *fa=(*func)(*ax);
599: *fb=(*func)(*bx);
600: if (*fb > *fa) {
601: SHFT(dum,*ax,*bx,dum)
602: SHFT(dum,*fb,*fa,dum)
603: }
604: *cx=(*bx)+GOLD*(*bx-*ax);
605: *fc=(*func)(*cx);
606: while (*fb > *fc) {
607: r=(*bx-*ax)*(*fb-*fc);
608: q=(*bx-*cx)*(*fb-*fa);
609: u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/
610: (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r));
611: ulim=(*bx)+GLIMIT*(*cx-*bx);
612: if ((*bx-u)*(u-*cx) > 0.0) {
613: fu=(*func)(u);
614: } else if ((*cx-u)*(u-ulim) > 0.0) {
615: fu=(*func)(u);
616: if (fu < *fc) {
617: SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))
618: SHFT(*fb,*fc,fu,(*func)(u))
619: }
620: } else if ((u-ulim)*(ulim-*cx) >= 0.0) {
621: u=ulim;
622: fu=(*func)(u);
623: } else {
624: u=(*cx)+GOLD*(*cx-*bx);
625: fu=(*func)(u);
626: }
627: SHFT(*ax,*bx,*cx,u)
628: SHFT(*fa,*fb,*fc,fu)
629: }
630: }
631:
632: /*************** linmin ************************/
633:
634: int ncom;
635: double *pcom,*xicom;
636: double (*nrfunc)(double []);
637:
638: void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))
639: {
640: double brent(double ax, double bx, double cx,
641: double (*f)(double), double tol, double *xmin);
642: double f1dim(double x);
643: void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,
644: double *fc, double (*func)(double));
645: int j;
646: double xx,xmin,bx,ax;
647: double fx,fb,fa;
648:
649: ncom=n;
650: pcom=vector(1,n);
651: xicom=vector(1,n);
652: nrfunc=func;
653: for (j=1;j<=n;j++) {
654: pcom[j]=p[j];
655: xicom[j]=xi[j];
656: }
657: ax=0.0;
658: xx=1.0;
659: mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim);
660: *fret=brent(ax,xx,bx,f1dim,TOL,&xmin);
661: #ifdef DEBUG
662: printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
663: fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
664: #endif
665: for (j=1;j<=n;j++) {
666: xi[j] *= xmin;
667: p[j] += xi[j];
668: }
669: free_vector(xicom,1,n);
670: free_vector(pcom,1,n);
671: }
672:
673: /*************** powell ************************/
674: void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,
675: double (*func)(double []))
676: {
677: void linmin(double p[], double xi[], int n, double *fret,
678: double (*func)(double []));
679: int i,ibig,j;
680: double del,t,*pt,*ptt,*xit;
681: double fp,fptt;
682: double *xits;
683: pt=vector(1,n);
684: ptt=vector(1,n);
685: xit=vector(1,n);
686: xits=vector(1,n);
687: *fret=(*func)(p);
688: for (j=1;j<=n;j++) pt[j]=p[j];
689: for (*iter=1;;++(*iter)) {
690: fp=(*fret);
691: ibig=0;
692: del=0.0;
693: printf("\nPowell iter=%d -2*LL=%.12f",*iter,*fret);
694: fprintf(ficlog,"\nPowell iter=%d -2*LL=%.12f",*iter,*fret);
1.76 brouard 695: fprintf(ficrespow,"%d %.12f",*iter,*fret);
696: for (i=1;i<=n;i++) {
1.53 brouard 697: printf(" %d %.12f",i, p[i]);
1.76 brouard 698: fprintf(ficlog," %d %.12lf",i, p[i]);
699: fprintf(ficrespow," %.12lf", p[i]);
700: }
1.53 brouard 701: printf("\n");
702: fprintf(ficlog,"\n");
1.76 brouard 703: fprintf(ficrespow,"\n");
1.53 brouard 704: for (i=1;i<=n;i++) {
705: for (j=1;j<=n;j++) xit[j]=xi[j][i];
706: fptt=(*fret);
707: #ifdef DEBUG
708: printf("fret=%lf \n",*fret);
709: fprintf(ficlog,"fret=%lf \n",*fret);
710: #endif
711: printf("%d",i);fflush(stdout);
712: fprintf(ficlog,"%d",i);fflush(ficlog);
713: linmin(p,xit,n,fret,func);
714: if (fabs(fptt-(*fret)) > del) {
715: del=fabs(fptt-(*fret));
716: ibig=i;
717: }
718: #ifdef DEBUG
719: printf("%d %.12e",i,(*fret));
720: fprintf(ficlog,"%d %.12e",i,(*fret));
721: for (j=1;j<=n;j++) {
722: xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
723: printf(" x(%d)=%.12e",j,xit[j]);
724: fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
725: }
726: for(j=1;j<=n;j++) {
727: printf(" p=%.12e",p[j]);
728: fprintf(ficlog," p=%.12e",p[j]);
729: }
730: printf("\n");
731: fprintf(ficlog,"\n");
732: #endif
733: }
734: if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {
735: #ifdef DEBUG
736: int k[2],l;
737: k[0]=1;
738: k[1]=-1;
739: printf("Max: %.12e",(*func)(p));
740: fprintf(ficlog,"Max: %.12e",(*func)(p));
741: for (j=1;j<=n;j++) {
742: printf(" %.12e",p[j]);
743: fprintf(ficlog," %.12e",p[j]);
744: }
745: printf("\n");
746: fprintf(ficlog,"\n");
747: for(l=0;l<=1;l++) {
748: for (j=1;j<=n;j++) {
749: ptt[j]=p[j]+(p[j]-pt[j])*k[l];
750: printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
751: fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
752: }
753: printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
754: fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
755: }
756: #endif
757:
758:
759: free_vector(xit,1,n);
760: free_vector(xits,1,n);
761: free_vector(ptt,1,n);
762: free_vector(pt,1,n);
763: return;
764: }
765: if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");
766: for (j=1;j<=n;j++) {
767: ptt[j]=2.0*p[j]-pt[j];
768: xit[j]=p[j]-pt[j];
769: pt[j]=p[j];
770: }
771: fptt=(*func)(ptt);
772: if (fptt < fp) {
773: t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt);
774: if (t < 0.0) {
775: linmin(p,xit,n,fret,func);
776: for (j=1;j<=n;j++) {
777: xi[j][ibig]=xi[j][n];
778: xi[j][n]=xit[j];
779: }
780: #ifdef DEBUG
781: printf("Direction changed last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
782: fprintf(ficlog,"Direction changed last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
783: for(j=1;j<=n;j++){
784: printf(" %.12e",xit[j]);
785: fprintf(ficlog," %.12e",xit[j]);
786: }
787: printf("\n");
788: fprintf(ficlog,"\n");
789: #endif
1.54 brouard 790: }
1.53 brouard 791: }
792: }
793: }
794:
1.54 brouard 795: /**** Prevalence limit (stable prevalence) ****************/
1.53 brouard 796:
797: double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)
798: {
799: /* Computes the prevalence limit in each live state at age x by left multiplying the unit
800: matrix by transitions matrix until convergence is reached */
801:
802: int i, ii,j,k;
803: double min, max, maxmin, maxmax,sumnew=0.;
804: double **matprod2();
805: double **out, cov[NCOVMAX], **pmij();
806: double **newm;
807: double agefin, delaymax=50 ; /* Max number of years to converge */
808:
809: for (ii=1;ii<=nlstate+ndeath;ii++)
810: for (j=1;j<=nlstate+ndeath;j++){
811: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
812: }
813:
814: cov[1]=1.;
815:
816: /* Even if hstepm = 1, at least one multiplication by the unit matrix */
817: for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
818: newm=savm;
819: /* Covariates have to be included here again */
820: cov[2]=agefin;
821:
822: for (k=1; k<=cptcovn;k++) {
823: cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
824: /* 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]]);*/
825: }
826: for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
827: for (k=1; k<=cptcovprod;k++)
828: cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
829:
830: /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
831: /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
832: /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
833: out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);
834:
835: savm=oldm;
836: oldm=newm;
837: maxmax=0.;
838: for(j=1;j<=nlstate;j++){
839: min=1.;
840: max=0.;
841: for(i=1; i<=nlstate; i++) {
842: sumnew=0;
843: for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
844: prlim[i][j]= newm[i][j]/(1-sumnew);
845: max=FMAX(max,prlim[i][j]);
846: min=FMIN(min,prlim[i][j]);
847: }
848: maxmin=max-min;
849: maxmax=FMAX(maxmax,maxmin);
850: }
851: if(maxmax < ftolpl){
852: return prlim;
853: }
854: }
855: }
856:
857: /*************** transition probabilities ***************/
858:
859: double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
860: {
861: double s1, s2;
862: /*double t34;*/
863: int i,j,j1, nc, ii, jj;
864:
865: for(i=1; i<= nlstate; i++){
866: for(j=1; j<i;j++){
867: for (nc=1, s2=0.;nc <=ncovmodel; nc++){
868: /*s2 += param[i][j][nc]*cov[nc];*/
869: s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
870: /*printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2);*/
871: }
872: ps[i][j]=s2;
873: /*printf("s1=%.17e, s2=%.17e\n",s1,s2);*/
874: }
875: for(j=i+1; j<=nlstate+ndeath;j++){
876: for (nc=1, s2=0.;nc <=ncovmodel; nc++){
877: s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
878: /*printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2);*/
879: }
880: ps[i][j]=s2;
881: }
882: }
883: /*ps[3][2]=1;*/
884:
885: for(i=1; i<= nlstate; i++){
886: s1=0;
887: for(j=1; j<i; j++)
888: s1+=exp(ps[i][j]);
889: for(j=i+1; j<=nlstate+ndeath; j++)
890: s1+=exp(ps[i][j]);
891: ps[i][i]=1./(s1+1.);
892: for(j=1; j<i; j++)
893: ps[i][j]= exp(ps[i][j])*ps[i][i];
894: for(j=i+1; j<=nlstate+ndeath; j++)
895: ps[i][j]= exp(ps[i][j])*ps[i][i];
896: /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
897: } /* end i */
898:
899: for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
900: for(jj=1; jj<= nlstate+ndeath; jj++){
901: ps[ii][jj]=0;
902: ps[ii][ii]=1;
903: }
904: }
905:
906:
907: /* for(ii=1; ii<= nlstate+ndeath; ii++){
908: for(jj=1; jj<= nlstate+ndeath; jj++){
909: printf("%lf ",ps[ii][jj]);
910: }
911: printf("\n ");
912: }
913: printf("\n ");printf("%lf ",cov[2]);*/
914: /*
915: for(i=1; i<= npar; i++) printf("%f ",x[i]);
916: goto end;*/
917: return ps;
918: }
919:
920: /**************** Product of 2 matrices ******************/
921:
922: double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)
923: {
924: /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
925: b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
926: /* in, b, out are matrice of pointers which should have been initialized
927: before: only the contents of out is modified. The function returns
928: a pointer to pointers identical to out */
929: long i, j, k;
930: for(i=nrl; i<= nrh; i++)
931: for(k=ncolol; k<=ncoloh; k++)
932: for(j=ncl,out[i][k]=0.; j<=nch; j++)
933: out[i][k] +=in[i][j]*b[j][k];
934:
935: return out;
936: }
937:
938:
939: /************* Higher Matrix Product ***************/
940:
941: double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
942: {
1.66 brouard 943: /* Computes the transition matrix starting at age 'age' over
944: 'nhstepm*hstepm*stepm' months (i.e. until
945: age (in years) age+nhstepm*hstepm*stepm/12) by multiplying
946: nhstepm*hstepm matrices.
1.53 brouard 947: Output is stored in matrix po[i][j][h] for h every 'hstepm' step
1.66 brouard 948: (typically every 2 years instead of every month which is too big
949: for the memory).
1.53 brouard 950: Model is determined by parameters x and covariates have to be
951: included manually here.
952:
953: */
954:
955: int i, j, d, h, k;
956: double **out, cov[NCOVMAX];
957: double **newm;
958:
959: /* Hstepm could be zero and should return the unit matrix */
960: for (i=1;i<=nlstate+ndeath;i++)
961: for (j=1;j<=nlstate+ndeath;j++){
962: oldm[i][j]=(i==j ? 1.0 : 0.0);
963: po[i][j][0]=(i==j ? 1.0 : 0.0);
964: }
965: /* Even if hstepm = 1, at least one multiplication by the unit matrix */
966: for(h=1; h <=nhstepm; h++){
967: for(d=1; d <=hstepm; d++){
968: newm=savm;
969: /* Covariates have to be included here again */
970: cov[1]=1.;
971: cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
972: for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
973: for (k=1; k<=cptcovage;k++)
974: cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
975: for (k=1; k<=cptcovprod;k++)
976: cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
977:
978:
979: /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
980: /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
981: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,
982: pmij(pmmij,cov,ncovmodel,x,nlstate));
983: savm=oldm;
984: oldm=newm;
985: }
986: for(i=1; i<=nlstate+ndeath; i++)
987: for(j=1;j<=nlstate+ndeath;j++) {
988: po[i][j][h]=newm[i][j];
989: /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);
990: */
991: }
992: } /* end h */
993: return po;
994: }
995:
996:
997: /*************** log-likelihood *************/
998: double func( double *x)
999: {
1000: int i, ii, j, k, mi, d, kk;
1001: double l, ll[NLSTATEMAX], cov[NCOVMAX];
1002: double **out;
1003: double sw; /* Sum of weights */
1004: double lli; /* Individual log likelihood */
1.59 brouard 1005: int s1, s2;
1.68 lievre 1006: double bbh, survp;
1.53 brouard 1007: long ipmx;
1008: /*extern weight */
1009: /* We are differentiating ll according to initial status */
1010: /* for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
1011: /*for(i=1;i<imx;i++)
1012: printf(" %d\n",s[4][i]);
1013: */
1014: cov[1]=1.;
1015:
1016: for(k=1; k<=nlstate; k++) ll[k]=0.;
1.61 brouard 1017:
1018: if(mle==1){
1019: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1020: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
1021: for(mi=1; mi<= wav[i]-1; mi++){
1022: for (ii=1;ii<=nlstate+ndeath;ii++)
1023: for (j=1;j<=nlstate+ndeath;j++){
1024: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1025: savm[ii][j]=(ii==j ? 1.0 : 0.0);
1026: }
1027: for(d=0; d<dh[mi][i]; d++){
1028: newm=savm;
1029: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
1030: for (kk=1; kk<=cptcovage;kk++) {
1031: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
1032: }
1033: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1034: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1035: savm=oldm;
1036: oldm=newm;
1037: } /* end mult */
1.53 brouard 1038:
1.61 brouard 1039: /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
1040: /* But now since version 0.9 we anticipate for bias and large stepm.
1041: * If stepm is larger than one month (smallest stepm) and if the exact delay
1042: * (in months) between two waves is not a multiple of stepm, we rounded to
1043: * the nearest (and in case of equal distance, to the lowest) interval but now
1044: * we keep into memory the bias bh[mi][i] and also the previous matrix product
1045: * (i.e to dh[mi][i]-1) saved in 'savm'. The we inter(extra)polate the
1046: * probability in order to take into account the bias as a fraction of the way
1047: * from savm to out if bh is neagtive or even beyond if bh is positive. bh varies
1048: * -stepm/2 to stepm/2 .
1049: * For stepm=1 the results are the same as for previous versions of Imach.
1050: * For stepm > 1 the results are less biased than in previous versions.
1051: */
1052: s1=s[mw[mi][i]][i];
1053: s2=s[mw[mi+1][i]][i];
1.64 lievre 1054: bbh=(double)bh[mi][i]/(double)stepm;
1055: /* bias is positive if real duration
1056: * is higher than the multiple of stepm and negative otherwise.
1057: */
1058: /* 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 1059: if( s2 > nlstate){
1060: /* i.e. if s2 is a death state and if the date of death is known then the contribution
1061: to the likelihood is the probability to die between last step unit time and current
1062: step unit time, which is also the differences between probability to die before dh
1063: and probability to die before dh-stepm .
1064: In version up to 0.92 likelihood was computed
1065: as if date of death was unknown. Death was treated as any other
1066: health state: the date of the interview describes the actual state
1067: and not the date of a change in health state. The former idea was
1068: to consider that at each interview the state was recorded
1069: (healthy, disable or death) and IMaCh was corrected; but when we
1070: introduced the exact date of death then we should have modified
1071: the contribution of an exact death to the likelihood. This new
1072: contribution is smaller and very dependent of the step unit
1073: stepm. It is no more the probability to die between last interview
1074: and month of death but the probability to survive from last
1075: interview up to one month before death multiplied by the
1076: probability to die within a month. Thanks to Chris
1077: Jackson for correcting this bug. Former versions increased
1078: mortality artificially. The bad side is that we add another loop
1079: which slows down the processing. The difference can be up to 10%
1080: lower mortality.
1081: */
1082: lli=log(out[s1][s2] - savm[s1][s2]);
1083: }else{
1084: lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
1085: /* 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 */
1086: }
1.64 lievre 1087: /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
1088: /*if(lli ==000.0)*/
1089: /*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 1090: ipmx +=1;
1.64 lievre 1091: sw += weight[i];
1092: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1093: } /* end of wave */
1094: } /* end of individual */
1095: } else if(mle==2){
1096: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1097: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
1098: for(mi=1; mi<= wav[i]-1; mi++){
1099: for (ii=1;ii<=nlstate+ndeath;ii++)
1100: for (j=1;j<=nlstate+ndeath;j++){
1101: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1102: savm[ii][j]=(ii==j ? 1.0 : 0.0);
1103: }
1104: for(d=0; d<=dh[mi][i]; d++){
1105: newm=savm;
1106: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
1107: for (kk=1; kk<=cptcovage;kk++) {
1108: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
1109: }
1110: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1111: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1112: savm=oldm;
1113: oldm=newm;
1114: } /* end mult */
1115:
1116: /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
1117: /* But now since version 0.9 we anticipate for bias and large stepm.
1118: * If stepm is larger than one month (smallest stepm) and if the exact delay
1119: * (in months) between two waves is not a multiple of stepm, we rounded to
1120: * the nearest (and in case of equal distance, to the lowest) interval but now
1121: * we keep into memory the bias bh[mi][i] and also the previous matrix product
1122: * (i.e to dh[mi][i]-1) saved in 'savm'. The we inter(extra)polate the
1123: * probability in order to take into account the bias as a fraction of the way
1124: * from savm to out if bh is neagtive or even beyond if bh is positive. bh varies
1125: * -stepm/2 to stepm/2 .
1126: * For stepm=1 the results are the same as for previous versions of Imach.
1127: * For stepm > 1 the results are less biased than in previous versions.
1128: */
1129: s1=s[mw[mi][i]][i];
1130: s2=s[mw[mi+1][i]][i];
1131: bbh=(double)bh[mi][i]/(double)stepm;
1132: /* bias is positive if real duration
1133: * is higher than the multiple of stepm and negative otherwise.
1134: */
1.63 lievre 1135: 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 1136: /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
1137: /*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 */
1138: /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
1139: /*if(lli ==000.0)*/
1140: /*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); */
1141: ipmx +=1;
1142: sw += weight[i];
1143: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1144: } /* end of wave */
1145: } /* end of individual */
1146: } else if(mle==3){ /* exponential inter-extrapolation */
1147: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1148: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
1149: for(mi=1; mi<= wav[i]-1; mi++){
1150: for (ii=1;ii<=nlstate+ndeath;ii++)
1151: for (j=1;j<=nlstate+ndeath;j++){
1152: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1153: savm[ii][j]=(ii==j ? 1.0 : 0.0);
1154: }
1155: for(d=0; d<dh[mi][i]; d++){
1156: newm=savm;
1157: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
1158: for (kk=1; kk<=cptcovage;kk++) {
1159: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
1160: }
1161: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1162: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1163: savm=oldm;
1164: oldm=newm;
1165: } /* end mult */
1166:
1167: /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
1168: /* But now since version 0.9 we anticipate for bias and large stepm.
1169: * If stepm is larger than one month (smallest stepm) and if the exact delay
1170: * (in months) between two waves is not a multiple of stepm, we rounded to
1171: * the nearest (and in case of equal distance, to the lowest) interval but now
1172: * we keep into memory the bias bh[mi][i] and also the previous matrix product
1173: * (i.e to dh[mi][i]-1) saved in 'savm'. The we inter(extra)polate the
1174: * probability in order to take into account the bias as a fraction of the way
1175: * from savm to out if bh is neagtive or even beyond if bh is positive. bh varies
1176: * -stepm/2 to stepm/2 .
1177: * For stepm=1 the results are the same as for previous versions of Imach.
1178: * For stepm > 1 the results are less biased than in previous versions.
1179: */
1180: s1=s[mw[mi][i]][i];
1181: s2=s[mw[mi+1][i]][i];
1182: bbh=(double)bh[mi][i]/(double)stepm;
1183: /* bias is positive if real duration
1184: * is higher than the multiple of stepm and negative otherwise.
1185: */
1186: /* 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 */
1187: 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 1188: /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
1189: /*if(lli ==000.0)*/
1190: /*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); */
1191: ipmx +=1;
1192: sw += weight[i];
1193: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1194: } /* end of wave */
1195: } /* end of individual */
1.84 brouard 1196: }else if (mle==4){ /* ml=4 no inter-extrapolation */
1.61 brouard 1197: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1198: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
1199: for(mi=1; mi<= wav[i]-1; mi++){
1200: for (ii=1;ii<=nlstate+ndeath;ii++)
1201: for (j=1;j<=nlstate+ndeath;j++){
1202: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1203: savm[ii][j]=(ii==j ? 1.0 : 0.0);
1204: }
1205: for(d=0; d<dh[mi][i]; d++){
1206: newm=savm;
1207: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
1208: for (kk=1; kk<=cptcovage;kk++) {
1209: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
1210: }
1211:
1212: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1213: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1214: savm=oldm;
1215: oldm=newm;
1216: } /* end mult */
1217:
1.84 brouard 1218: s1=s[mw[mi][i]][i];
1219: s2=s[mw[mi+1][i]][i];
1220: if( s2 > nlstate){
1221: lli=log(out[s1][s2] - savm[s1][s2]);
1222: }else{
1223: lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
1224: }
1225: ipmx +=1;
1226: sw += weight[i];
1227: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1.85 ! brouard 1228: /* 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]); */
1.84 brouard 1229: } /* end of wave */
1230: } /* end of individual */
1231: }else{ /* ml=5 no inter-extrapolation no jackson =0.8a */
1232: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1233: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
1234: for(mi=1; mi<= wav[i]-1; mi++){
1235: for (ii=1;ii<=nlstate+ndeath;ii++)
1236: for (j=1;j<=nlstate+ndeath;j++){
1237: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1238: savm[ii][j]=(ii==j ? 1.0 : 0.0);
1239: }
1240: for(d=0; d<dh[mi][i]; d++){
1241: newm=savm;
1242: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
1243: for (kk=1; kk<=cptcovage;kk++) {
1244: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
1245: }
1246:
1247: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1248: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1249: savm=oldm;
1250: oldm=newm;
1251: } /* end mult */
1252:
1253: s1=s[mw[mi][i]][i];
1254: s2=s[mw[mi+1][i]][i];
1.61 brouard 1255: lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
1256: ipmx +=1;
1257: sw += weight[i];
1258: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1.84 brouard 1259: /*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 1260: } /* end of wave */
1261: } /* end of individual */
1262: } /* End of if */
1.53 brouard 1263: for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
1264: /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
1265: l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
1.85 ! brouard 1266: return -l;
! 1267: }
! 1268:
! 1269: /*************** log-likelihood *************/
! 1270: double funcone( double *x)
! 1271: {
! 1272: int i, ii, j, k, mi, d, kk;
! 1273: double l, ll[NLSTATEMAX], cov[NCOVMAX];
! 1274: double **out;
! 1275: double lli; /* Individual log likelihood */
! 1276: int s1, s2;
! 1277: double bbh, survp;
! 1278: /*extern weight */
! 1279: /* We are differentiating ll according to initial status */
! 1280: /* for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
! 1281: /*for(i=1;i<imx;i++)
! 1282: printf(" %d\n",s[4][i]);
! 1283: */
! 1284: cov[1]=1.;
! 1285:
! 1286: for(k=1; k<=nlstate; k++) ll[k]=0.;
! 1287:
! 1288: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
! 1289: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
! 1290: for(mi=1; mi<= wav[i]-1; mi++){
! 1291: for (ii=1;ii<=nlstate+ndeath;ii++)
! 1292: for (j=1;j<=nlstate+ndeath;j++){
! 1293: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
! 1294: savm[ii][j]=(ii==j ? 1.0 : 0.0);
! 1295: }
! 1296: for(d=0; d<dh[mi][i]; d++){
! 1297: newm=savm;
! 1298: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
! 1299: for (kk=1; kk<=cptcovage;kk++) {
! 1300: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
! 1301: }
! 1302: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
! 1303: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
! 1304: savm=oldm;
! 1305: oldm=newm;
! 1306: } /* end mult */
! 1307:
! 1308: s1=s[mw[mi][i]][i];
! 1309: s2=s[mw[mi+1][i]][i];
! 1310: bbh=(double)bh[mi][i]/(double)stepm;
! 1311: /* bias is positive if real duration
! 1312: * is higher than the multiple of stepm and negative otherwise.
! 1313: */
! 1314: if( s2 > nlstate && (mle <5) ){ /* Jackson */
! 1315: lli=log(out[s1][s2] - savm[s1][s2]);
! 1316: } else if (mle==1){
! 1317: lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
! 1318: } else if(mle==2){
! 1319: 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 */
! 1320: } else if(mle==3){ /* exponential inter-extrapolation */
! 1321: lli= (savm[s1][s2]>(double)1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2])); /* exponential inter-extrapolation */
! 1322: } else if (mle==4){ /* mle=4 no inter-extrapolation */
! 1323: lli=log(out[s1][s2]); /* Original formula */
! 1324: } else{ /* ml>=5 no inter-extrapolation no jackson =0.8a */
! 1325: lli=log(out[s1][s2]); /* Original formula */
! 1326: } /* End of if */
! 1327: ipmx +=1;
! 1328: sw += weight[i];
! 1329: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
! 1330: /* 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]); */
! 1331: if(globpr){
! 1332: fprintf(ficresilk,"%6d %1d %1d %1d %1d %3d %10.6f %6.4f %10.6f %10.6f %10.6f ", \
! 1333: i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],2*weight[i]*lli,out[s1][s2],savm[s1][s2]);
! 1334: for(k=1,l=0.; k<=nlstate; k++)
! 1335: fprintf(ficresilk," %10.6f",ll[k]);
! 1336: fprintf(ficresilk,"\n");
! 1337: }
! 1338: } /* end of wave */
! 1339: } /* end of individual */
! 1340: for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
! 1341: /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
! 1342: l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
1.53 brouard 1343: return -l;
1344: }
1345:
1346:
1.85 ! brouard 1347: void likelione(FILE *ficres,double p[], int npar, int nlstate, int *globpr, long *ipmx, double *sw, double *fretone, double (*funcone)(double []))
! 1348: {
! 1349: /* This routine should help understanding what is done with the selection of individuals/waves and
! 1350: to check the exact contribution to the likelihood.
! 1351: Plotting could be done.
! 1352: */
! 1353: int k;
! 1354: if(globpr !=0){ /* Just counts and sums no printings */
! 1355: strcpy(fileresilk,"ilk");
! 1356: strcat(fileresilk,fileres);
! 1357: if((ficresilk=fopen(fileresilk,"w"))==NULL) {
! 1358: printf("Problem with resultfile: %s\n", fileresilk);
! 1359: fprintf(ficlog,"Problem with resultfile: %s\n", fileresilk);
! 1360: }
! 1361: fprintf(ficresilk, "# individual(line's record) s1 s2 wave# effective_wave# number_of_product_matrix pij weight 2ln(pij)*weight 0pij_x 0pij_(x-stepm) cumulating_loglikeli_by_health_state");
! 1362: fprintf(ficresilk, "# i s1 s2 mi mw dh likeli weight out sav ");
! 1363: /* i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],2*weight[i]*lli,out[s1][s2],savm[s1][s2]); */
! 1364: for(k=1; k<=nlstate; k++)
! 1365: fprintf(ficresilk," ll[%d]",k);
! 1366: fprintf(ficresilk,"\n");
! 1367: }
! 1368:
! 1369: *fretone=(*funcone)(p);
! 1370: if(globpr !=0)
! 1371: fclose(ficresilk);
! 1372: return;
! 1373: }
! 1374:
1.53 brouard 1375: /*********** Maximum Likelihood Estimation ***************/
1376:
1377: void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
1378: {
1379: int i,j, iter;
1.74 brouard 1380: double **xi;
1.53 brouard 1381: double fret;
1.85 ! brouard 1382: double fretone; /* Only one call to likelihood */
1.76 brouard 1383: char filerespow[FILENAMELENGTH];
1.53 brouard 1384: xi=matrix(1,npar,1,npar);
1385: for (i=1;i<=npar;i++)
1386: for (j=1;j<=npar;j++)
1387: xi[i][j]=(i==j ? 1.0 : 0.0);
1388: printf("Powell\n"); fprintf(ficlog,"Powell\n");
1.76 brouard 1389: strcpy(filerespow,"pow");
1390: strcat(filerespow,fileres);
1391: if((ficrespow=fopen(filerespow,"w"))==NULL) {
1392: printf("Problem with resultfile: %s\n", filerespow);
1393: fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
1394: }
1395: fprintf(ficrespow,"# Powell\n# iter -2*LL");
1396: for (i=1;i<=nlstate;i++)
1397: for(j=1;j<=nlstate+ndeath;j++)
1398: if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
1399: fprintf(ficrespow,"\n");
1.85 ! brouard 1400:
1.53 brouard 1401: powell(p,xi,npar,ftol,&iter,&fret,func);
1402:
1.76 brouard 1403: fclose(ficrespow);
1404: printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));
1.65 lievre 1405: fprintf(ficlog,"\n#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
1.53 brouard 1406: fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
1407:
1408: }
1409:
1410: /**** Computes Hessian and covariance matrix ***/
1411: void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
1412: {
1413: double **a,**y,*x,pd;
1414: double **hess;
1415: int i, j,jk;
1416: int *indx;
1417:
1418: double hessii(double p[], double delta, int theta, double delti[]);
1419: double hessij(double p[], double delti[], int i, int j);
1420: void lubksb(double **a, int npar, int *indx, double b[]) ;
1421: void ludcmp(double **a, int npar, int *indx, double *d) ;
1422:
1423: hess=matrix(1,npar,1,npar);
1424:
1425: printf("\nCalculation of the hessian matrix. Wait...\n");
1426: fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
1427: for (i=1;i<=npar;i++){
1428: printf("%d",i);fflush(stdout);
1429: fprintf(ficlog,"%d",i);fflush(ficlog);
1430: hess[i][i]=hessii(p,ftolhess,i,delti);
1431: /*printf(" %f ",p[i]);*/
1432: /*printf(" %lf ",hess[i][i]);*/
1433: }
1434:
1435: for (i=1;i<=npar;i++) {
1436: for (j=1;j<=npar;j++) {
1437: if (j>i) {
1438: printf(".%d%d",i,j);fflush(stdout);
1439: fprintf(ficlog,".%d%d",i,j);fflush(ficlog);
1440: hess[i][j]=hessij(p,delti,i,j);
1441: hess[j][i]=hess[i][j];
1442: /*printf(" %lf ",hess[i][j]);*/
1443: }
1444: }
1445: }
1446: printf("\n");
1447: fprintf(ficlog,"\n");
1448:
1449: printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
1450: fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
1451:
1452: a=matrix(1,npar,1,npar);
1453: y=matrix(1,npar,1,npar);
1454: x=vector(1,npar);
1455: indx=ivector(1,npar);
1456: for (i=1;i<=npar;i++)
1457: for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
1458: ludcmp(a,npar,indx,&pd);
1459:
1460: for (j=1;j<=npar;j++) {
1461: for (i=1;i<=npar;i++) x[i]=0;
1462: x[j]=1;
1463: lubksb(a,npar,indx,x);
1464: for (i=1;i<=npar;i++){
1465: matcov[i][j]=x[i];
1466: }
1467: }
1468:
1469: printf("\n#Hessian matrix#\n");
1470: fprintf(ficlog,"\n#Hessian matrix#\n");
1471: for (i=1;i<=npar;i++) {
1472: for (j=1;j<=npar;j++) {
1473: printf("%.3e ",hess[i][j]);
1474: fprintf(ficlog,"%.3e ",hess[i][j]);
1475: }
1476: printf("\n");
1477: fprintf(ficlog,"\n");
1478: }
1479:
1480: /* Recompute Inverse */
1481: for (i=1;i<=npar;i++)
1482: for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];
1483: ludcmp(a,npar,indx,&pd);
1484:
1485: /* printf("\n#Hessian matrix recomputed#\n");
1486:
1487: for (j=1;j<=npar;j++) {
1488: for (i=1;i<=npar;i++) x[i]=0;
1489: x[j]=1;
1490: lubksb(a,npar,indx,x);
1491: for (i=1;i<=npar;i++){
1492: y[i][j]=x[i];
1493: printf("%.3e ",y[i][j]);
1494: fprintf(ficlog,"%.3e ",y[i][j]);
1495: }
1496: printf("\n");
1497: fprintf(ficlog,"\n");
1498: }
1499: */
1500:
1501: free_matrix(a,1,npar,1,npar);
1502: free_matrix(y,1,npar,1,npar);
1503: free_vector(x,1,npar);
1504: free_ivector(indx,1,npar);
1505: free_matrix(hess,1,npar,1,npar);
1506:
1507:
1508: }
1509:
1510: /*************** hessian matrix ****************/
1511: double hessii( double x[], double delta, int theta, double delti[])
1512: {
1513: int i;
1514: int l=1, lmax=20;
1515: double k1,k2;
1516: double p2[NPARMAX+1];
1517: double res;
1518: double delt, delts, nkhi=10.,nkhif=1., khi=1.e-4;
1519: double fx;
1520: int k=0,kmax=10;
1521: double l1;
1522:
1523: fx=func(x);
1524: for (i=1;i<=npar;i++) p2[i]=x[i];
1525: for(l=0 ; l <=lmax; l++){
1526: l1=pow(10,l);
1527: delts=delt;
1528: for(k=1 ; k <kmax; k=k+1){
1529: delt = delta*(l1*k);
1530: p2[theta]=x[theta] +delt;
1531: k1=func(p2)-fx;
1532: p2[theta]=x[theta]-delt;
1533: k2=func(p2)-fx;
1534: /*res= (k1-2.0*fx+k2)/delt/delt; */
1535: res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */
1536:
1537: #ifdef DEBUG
1538: 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);
1539: 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);
1540: #endif
1541: /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
1542: if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
1543: k=kmax;
1544: }
1545: else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
1546: k=kmax; l=lmax*10.;
1547: }
1548: else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){
1549: delts=delt;
1550: }
1551: }
1552: }
1553: delti[theta]=delts;
1554: return res;
1555:
1556: }
1557:
1558: double hessij( double x[], double delti[], int thetai,int thetaj)
1559: {
1560: int i;
1561: int l=1, l1, lmax=20;
1562: double k1,k2,k3,k4,res,fx;
1563: double p2[NPARMAX+1];
1564: int k;
1565:
1566: fx=func(x);
1567: for (k=1; k<=2; k++) {
1568: for (i=1;i<=npar;i++) p2[i]=x[i];
1569: p2[thetai]=x[thetai]+delti[thetai]/k;
1570: p2[thetaj]=x[thetaj]+delti[thetaj]/k;
1571: k1=func(p2)-fx;
1572:
1573: p2[thetai]=x[thetai]+delti[thetai]/k;
1574: p2[thetaj]=x[thetaj]-delti[thetaj]/k;
1575: k2=func(p2)-fx;
1576:
1577: p2[thetai]=x[thetai]-delti[thetai]/k;
1578: p2[thetaj]=x[thetaj]+delti[thetaj]/k;
1579: k3=func(p2)-fx;
1580:
1581: p2[thetai]=x[thetai]-delti[thetai]/k;
1582: p2[thetaj]=x[thetaj]-delti[thetaj]/k;
1583: k4=func(p2)-fx;
1584: res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */
1585: #ifdef DEBUG
1586: 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);
1587: 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);
1588: #endif
1589: }
1590: return res;
1591: }
1592:
1593: /************** Inverse of matrix **************/
1594: void ludcmp(double **a, int n, int *indx, double *d)
1595: {
1596: int i,imax,j,k;
1597: double big,dum,sum,temp;
1598: double *vv;
1599:
1600: vv=vector(1,n);
1601: *d=1.0;
1602: for (i=1;i<=n;i++) {
1603: big=0.0;
1604: for (j=1;j<=n;j++)
1605: if ((temp=fabs(a[i][j])) > big) big=temp;
1606: if (big == 0.0) nrerror("Singular matrix in routine ludcmp");
1607: vv[i]=1.0/big;
1608: }
1609: for (j=1;j<=n;j++) {
1610: for (i=1;i<j;i++) {
1611: sum=a[i][j];
1612: for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];
1613: a[i][j]=sum;
1614: }
1615: big=0.0;
1616: for (i=j;i<=n;i++) {
1617: sum=a[i][j];
1618: for (k=1;k<j;k++)
1619: sum -= a[i][k]*a[k][j];
1620: a[i][j]=sum;
1621: if ( (dum=vv[i]*fabs(sum)) >= big) {
1622: big=dum;
1623: imax=i;
1624: }
1625: }
1626: if (j != imax) {
1627: for (k=1;k<=n;k++) {
1628: dum=a[imax][k];
1629: a[imax][k]=a[j][k];
1630: a[j][k]=dum;
1631: }
1632: *d = -(*d);
1633: vv[imax]=vv[j];
1634: }
1635: indx[j]=imax;
1636: if (a[j][j] == 0.0) a[j][j]=TINY;
1637: if (j != n) {
1638: dum=1.0/(a[j][j]);
1639: for (i=j+1;i<=n;i++) a[i][j] *= dum;
1640: }
1641: }
1642: free_vector(vv,1,n); /* Doesn't work */
1643: ;
1644: }
1645:
1646: void lubksb(double **a, int n, int *indx, double b[])
1647: {
1648: int i,ii=0,ip,j;
1649: double sum;
1650:
1651: for (i=1;i<=n;i++) {
1652: ip=indx[i];
1653: sum=b[ip];
1654: b[ip]=b[i];
1655: if (ii)
1656: for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];
1657: else if (sum) ii=i;
1658: b[i]=sum;
1659: }
1660: for (i=n;i>=1;i--) {
1661: sum=b[i];
1662: for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];
1663: b[i]=sum/a[i][i];
1664: }
1665: }
1666:
1667: /************ Frequencies ********************/
1.84 brouard 1668: 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 1669: { /* Some frequencies */
1670:
1671: int i, m, jk, k1,i1, j1, bool, z1,z2,j;
1672: int first;
1673: double ***freq; /* Frequencies */
1.73 lievre 1674: double *pp, **prop;
1675: double pos,posprop, k2, dateintsum=0,k2cpt=0;
1.53 brouard 1676: FILE *ficresp;
1677: char fileresp[FILENAMELENGTH];
1678:
1679: pp=vector(1,nlstate);
1.74 brouard 1680: prop=matrix(1,nlstate,iagemin,iagemax+3);
1.53 brouard 1681: strcpy(fileresp,"p");
1682: strcat(fileresp,fileres);
1683: if((ficresp=fopen(fileresp,"w"))==NULL) {
1684: printf("Problem with prevalence resultfile: %s\n", fileresp);
1685: fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
1686: exit(0);
1687: }
1.74 brouard 1688: freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);
1.53 brouard 1689: j1=0;
1690:
1691: j=cptcoveff;
1692: if (cptcovn<1) {j=1;ncodemax[1]=1;}
1693:
1694: first=1;
1695:
1696: for(k1=1; k1<=j;k1++){
1697: for(i1=1; i1<=ncodemax[k1];i1++){
1698: j1++;
1699: /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
1700: scanf("%d", i);*/
1701: for (i=-1; i<=nlstate+ndeath; i++)
1702: for (jk=-1; jk<=nlstate+ndeath; jk++)
1.74 brouard 1703: for(m=iagemin; m <= iagemax+3; m++)
1.53 brouard 1704: freq[i][jk][m]=0;
1.73 lievre 1705:
1706: for (i=1; i<=nlstate; i++)
1.74 brouard 1707: for(m=iagemin; m <= iagemax+3; m++)
1.73 lievre 1708: prop[i][m]=0;
1.53 brouard 1709:
1710: dateintsum=0;
1711: k2cpt=0;
1712: for (i=1; i<=imx; i++) {
1713: bool=1;
1714: if (cptcovn>0) {
1715: for (z1=1; z1<=cptcoveff; z1++)
1716: if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])
1717: bool=0;
1718: }
1.58 lievre 1719: if (bool==1){
1.53 brouard 1720: for(m=firstpass; m<=lastpass; m++){
1721: k2=anint[m][i]+(mint[m][i]/12.);
1.84 brouard 1722: /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/
1.74 brouard 1723: if(agev[m][i]==0) agev[m][i]=iagemax+1;
1724: if(agev[m][i]==1) agev[m][i]=iagemax+2;
1.73 lievre 1725: if (s[m][i]>0 && s[m][i]<=nlstate) prop[s[m][i]][(int)agev[m][i]] += weight[i];
1.53 brouard 1726: if (m<lastpass) {
1727: freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
1.74 brouard 1728: freq[s[m][i]][s[m+1][i]][iagemax+3] += weight[i];
1.53 brouard 1729: }
1730:
1.74 brouard 1731: if ((agev[m][i]>1) && (agev[m][i]< (iagemax+3))) {
1.53 brouard 1732: dateintsum=dateintsum+k2;
1733: k2cpt++;
1734: }
1.84 brouard 1735: /*}*/
1.53 brouard 1736: }
1737: }
1738: }
1739:
1.84 brouard 1740: /* fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
1.53 brouard 1741:
1742: if (cptcovn>0) {
1743: fprintf(ficresp, "\n#********** Variable ");
1744: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
1745: fprintf(ficresp, "**********\n#");
1746: }
1747: for(i=1; i<=nlstate;i++)
1748: fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
1749: fprintf(ficresp, "\n");
1750:
1.74 brouard 1751: for(i=iagemin; i <= iagemax+3; i++){
1752: if(i==iagemax+3){
1.53 brouard 1753: fprintf(ficlog,"Total");
1754: }else{
1755: if(first==1){
1756: first=0;
1757: printf("See log file for details...\n");
1758: }
1759: fprintf(ficlog,"Age %d", i);
1760: }
1761: for(jk=1; jk <=nlstate ; jk++){
1762: for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
1763: pp[jk] += freq[jk][m][i];
1764: }
1765: for(jk=1; jk <=nlstate ; jk++){
1766: for(m=-1, pos=0; m <=0 ; m++)
1767: pos += freq[jk][m][i];
1768: if(pp[jk]>=1.e-10){
1769: if(first==1){
1770: printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
1771: }
1772: fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
1773: }else{
1774: if(first==1)
1775: printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
1776: fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
1777: }
1778: }
1779:
1780: for(jk=1; jk <=nlstate ; jk++){
1781: for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
1782: pp[jk] += freq[jk][m][i];
1.73 lievre 1783: }
1784: for(jk=1,pos=0,posprop=0; jk <=nlstate ; jk++){
1785: pos += pp[jk];
1786: posprop += prop[jk][i];
1.53 brouard 1787: }
1788: for(jk=1; jk <=nlstate ; jk++){
1789: if(pos>=1.e-5){
1790: if(first==1)
1791: printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
1792: fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
1793: }else{
1794: if(first==1)
1795: printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
1796: fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
1797: }
1.74 brouard 1798: if( i <= iagemax){
1.53 brouard 1799: if(pos>=1.e-5){
1.73 lievre 1800: fprintf(ficresp," %d %.5f %.0f %.0f",i,prop[jk][i]/posprop, prop[jk][i],posprop);
1.84 brouard 1801: /*probs[i][jk][j1]= pp[jk]/pos;*/
1.53 brouard 1802: /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/
1803: }
1804: else
1.73 lievre 1805: fprintf(ficresp," %d NaNq %.0f %.0f",i,prop[jk][i],posprop);
1.53 brouard 1806: }
1807: }
1808:
1.69 brouard 1809: for(jk=-1; jk <=nlstate+ndeath; jk++)
1810: for(m=-1; m <=nlstate+ndeath; m++)
1.53 brouard 1811: if(freq[jk][m][i] !=0 ) {
1812: if(first==1)
1813: printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
1814: fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
1815: }
1.74 brouard 1816: if(i <= iagemax)
1.53 brouard 1817: fprintf(ficresp,"\n");
1818: if(first==1)
1819: printf("Others in log...\n");
1820: fprintf(ficlog,"\n");
1821: }
1822: }
1823: }
1824: dateintmean=dateintsum/k2cpt;
1825:
1826: fclose(ficresp);
1.74 brouard 1827: free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);
1.53 brouard 1828: free_vector(pp,1,nlstate);
1.74 brouard 1829: free_matrix(prop,1,nlstate,iagemin, iagemax+3);
1.53 brouard 1830: /* End of Freq */
1831: }
1832:
1833: /************ Prevalence ********************/
1.84 brouard 1834: 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 1835: {
1836: /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
1837: in each health status at the date of interview (if between dateprev1 and dateprev2).
1838: We still use firstpass and lastpass as another selection.
1839: */
1.53 brouard 1840:
1841: int i, m, jk, k1, i1, j1, bool, z1,z2,j;
1842: double ***freq; /* Frequencies */
1.73 lievre 1843: double *pp, **prop;
1844: double pos,posprop;
1.69 brouard 1845: double y2; /* in fractional years */
1.74 brouard 1846: int iagemin, iagemax;
1.53 brouard 1847:
1.74 brouard 1848: iagemin= (int) agemin;
1849: iagemax= (int) agemax;
1850: /*pp=vector(1,nlstate);*/
1851: prop=matrix(1,nlstate,iagemin,iagemax+3);
1852: /* freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
1.53 brouard 1853: j1=0;
1854:
1855: j=cptcoveff;
1856: if (cptcovn<1) {j=1;ncodemax[1]=1;}
1857:
1858: for(k1=1; k1<=j;k1++){
1859: for(i1=1; i1<=ncodemax[k1];i1++){
1860: j1++;
1861:
1.73 lievre 1862: for (i=1; i<=nlstate; i++)
1.74 brouard 1863: for(m=iagemin; m <= iagemax+3; m++)
1864: prop[i][m]=0.0;
1.53 brouard 1865:
1.69 brouard 1866: for (i=1; i<=imx; i++) { /* Each individual */
1.53 brouard 1867: bool=1;
1868: if (cptcovn>0) {
1869: for (z1=1; z1<=cptcoveff; z1++)
1870: if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])
1871: bool=0;
1872: }
1873: if (bool==1) {
1.69 brouard 1874: for(m=firstpass; m<=lastpass; m++){/* Other selection (we can limit to certain interviews*/
1875: y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
1876: if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
1.74 brouard 1877: if(agev[m][i]==0) agev[m][i]=iagemax+1;
1878: if(agev[m][i]==1) agev[m][i]=iagemax+2;
1879: 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);
1880: if (s[m][i]>0 && s[m][i]<=nlstate) {
1881: /*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]]);*/
1882: prop[s[m][i]][(int)agev[m][i]] += weight[i];
1883: prop[s[m][i]][iagemax+3] += weight[i];
1884: }
1.53 brouard 1885: }
1.69 brouard 1886: } /* end selection of waves */
1.53 brouard 1887: }
1888: }
1.74 brouard 1889: for(i=iagemin; i <= iagemax+3; i++){
1.53 brouard 1890:
1.74 brouard 1891: for(jk=1,posprop=0; jk <=nlstate ; jk++) {
1892: posprop += prop[jk][i];
1893: }
1894:
1895: for(jk=1; jk <=nlstate ; jk++){
1896: if( i <= iagemax){
1897: if(posprop>=1.e-5){
1898: probs[i][jk][j1]= prop[jk][i]/posprop;
1899: }
1900: }
1901: }/* end jk */
1902: }/* end i */
1.53 brouard 1903: } /* end i1 */
1904: } /* end k1 */
1905:
1.74 brouard 1906: /* free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
1907: /*free_vector(pp,1,nlstate);*/
1908: free_matrix(prop,1,nlstate, iagemin,iagemax+3);
1909: } /* End of prevalence */
1.53 brouard 1910:
1911: /************* Waves Concatenation ***************/
1912:
1.59 brouard 1913: 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 1914: {
1915: /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
1916: Death is a valid wave (if date is known).
1917: mw[mi][i] is the mi (mi=1 to wav[i]) effective wave of individual i
1.59 brouard 1918: dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
1.53 brouard 1919: and mw[mi+1][i]. dh depends on stepm.
1920: */
1921:
1922: int i, mi, m;
1923: /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
1924: double sum=0., jmean=0.;*/
1925: int first;
1926: int j, k=0,jk, ju, jl;
1927: double sum=0.;
1928: first=0;
1929: jmin=1e+5;
1930: jmax=-1;
1931: jmean=0.;
1932: for(i=1; i<=imx; i++){
1933: mi=0;
1934: m=firstpass;
1935: while(s[m][i] <= nlstate){
1.69 brouard 1936: if(s[m][i]>=1)
1.53 brouard 1937: mw[++mi][i]=m;
1938: if(m >=lastpass)
1939: break;
1940: else
1941: m++;
1942: }/* end while */
1943: if (s[m][i] > nlstate){
1944: mi++; /* Death is another wave */
1945: /* if(mi==0) never been interviewed correctly before death */
1946: /* Only death is a correct wave */
1947: mw[mi][i]=m;
1948: }
1949:
1950: wav[i]=mi;
1951: if(mi==0){
1952: if(first==0){
1.85 ! brouard 1953: printf("Warning! None valid information for:%ld line=%d (skipped) and may be others, see log file\n",num[i],i);
1.53 brouard 1954: first=1;
1955: }
1956: if(first==1){
1.85 ! brouard 1957: fprintf(ficlog,"Warning! None valid information for:%ld line=%d (skipped)\n",num[i],i);
1.53 brouard 1958: }
1959: } /* end mi==0 */
1.77 brouard 1960: } /* End individuals */
1.53 brouard 1961:
1962: for(i=1; i<=imx; i++){
1963: for(mi=1; mi<wav[i];mi++){
1964: if (stepm <=0)
1965: dh[mi][i]=1;
1966: else{
1.77 brouard 1967: if (s[mw[mi+1][i]][i] > nlstate) { /* A death */
1.53 brouard 1968: if (agedc[i] < 2*AGESUP) {
1.85 ! brouard 1969: j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);
! 1970: if(j==0) j=1; /* Survives at least one month after exam */
! 1971: else if(j<0){
! 1972: printf("Error! Negative delay (%d to death) between waves %d and %d of individual %ld 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]);
! 1973: j=1; /* Careful Patch */
! 1974: printf(" We assumed that the date of interview was correct (and not the date of death) and postponed the death %d month(s) (one stepm) after the interview.\n You MUST fixe the contradiction between dates.\n",stepm);
! 1975: printf("Error! Negative delay (%d to death) between waves %d and %d of individual %ld 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]);
! 1976: fprintf(ficlog," We assumed that the date of interview was correct (and not the date of death) and postponed the death %d month(s) (one stepm) after the interview.\n You MUST fix the contradiction between dates.\n",stepm);
! 1977: }
! 1978: k=k+1;
! 1979: if (j >= jmax) jmax=j;
! 1980: if (j <= jmin) jmin=j;
! 1981: sum=sum+j;
! 1982: /*if (j<0) printf("j=%d num=%d \n",j,i);*/
! 1983: /* printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
1.53 brouard 1984: }
1985: }
1986: else{
1987: j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
1.68 lievre 1988: /* printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
1.53 brouard 1989: k=k+1;
1990: if (j >= jmax) jmax=j;
1991: else if (j <= jmin)jmin=j;
1992: /* if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
1.73 lievre 1993: /*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]);*/
1.85 ! brouard 1994: if(j<0){
! 1995: printf("Error! Negative delay (%d) between waves %d and %d of individual %ld 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]);
! 1996: fprintf(ficlog,"Error! Negative delay (%d) between waves %d and %d of individual %ld 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]);
! 1997: }
1.53 brouard 1998: sum=sum+j;
1999: }
2000: jk= j/stepm;
2001: jl= j -jk*stepm;
2002: ju= j -(jk+1)*stepm;
1.85 ! brouard 2003: if(mle <=1){ /* only if we use a the linear-interpoloation pseudo-likelihood */
1.64 lievre 2004: if(jl==0){
2005: dh[mi][i]=jk;
2006: bh[mi][i]=0;
2007: }else{ /* We want a negative bias in order to only have interpolation ie
2008: * at the price of an extra matrix product in likelihood */
2009: dh[mi][i]=jk+1;
2010: bh[mi][i]=ju;
2011: }
2012: }else{
2013: if(jl <= -ju){
2014: dh[mi][i]=jk;
2015: bh[mi][i]=jl; /* bias is positive if real duration
2016: * is higher than the multiple of stepm and negative otherwise.
2017: */
2018: }
2019: else{
2020: dh[mi][i]=jk+1;
2021: bh[mi][i]=ju;
2022: }
2023: if(dh[mi][i]==0){
2024: dh[mi][i]=1; /* At least one step */
2025: bh[mi][i]=ju; /* At least one step */
1.71 brouard 2026: /* 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 2027: }
1.85 ! brouard 2028: } /* end if mle */
! 2029: }
1.64 lievre 2030: } /* end wave */
1.53 brouard 2031: }
2032: jmean=sum/k;
2033: printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);
2034: fprintf(ficlog,"Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);
2035: }
2036:
2037: /*********** Tricode ****************************/
2038: void tricode(int *Tvar, int **nbcode, int imx)
2039: {
1.58 lievre 2040:
2041: int Ndum[20],ij=1, k, j, i, maxncov=19;
1.53 brouard 2042: int cptcode=0;
2043: cptcoveff=0;
2044:
1.58 lievre 2045: for (k=0; k<maxncov; k++) Ndum[k]=0;
1.53 brouard 2046: for (k=1; k<=7; k++) ncodemax[k]=0;
2047:
2048: for (j=1; j<=(cptcovn+2*cptcovprod); j++) {
1.58 lievre 2049: for (i=1; i<=imx; i++) { /*reads the data file to get the maximum
2050: modality*/
2051: ij=(int)(covar[Tvar[j]][i]); /* ij is the modality of this individual*/
2052: Ndum[ij]++; /*store the modality */
1.53 brouard 2053: /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
1.58 lievre 2054: if (ij > cptcode) cptcode=ij; /* getting the maximum of covariable
2055: Tvar[j]. If V=sex and male is 0 and
2056: female is 1, then cptcode=1.*/
1.53 brouard 2057: }
2058:
2059: for (i=0; i<=cptcode; i++) {
1.58 lievre 2060: 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 2061: }
1.58 lievre 2062:
1.53 brouard 2063: ij=1;
2064: for (i=1; i<=ncodemax[j]; i++) {
1.58 lievre 2065: for (k=0; k<= maxncov; k++) {
1.53 brouard 2066: if (Ndum[k] != 0) {
2067: nbcode[Tvar[j]][ij]=k;
1.58 lievre 2068: /* 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 2069:
2070: ij++;
2071: }
2072: if (ij > ncodemax[j]) break;
2073: }
2074: }
2075: }
2076:
1.58 lievre 2077: for (k=0; k< maxncov; k++) Ndum[k]=0;
1.53 brouard 2078:
1.58 lievre 2079: for (i=1; i<=ncovmodel-2; i++) {
2080: /* 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 2081: ij=Tvar[i];
1.58 lievre 2082: Ndum[ij]++;
1.53 brouard 2083: }
2084:
2085: ij=1;
1.58 lievre 2086: for (i=1; i<= maxncov; i++) {
1.53 brouard 2087: if((Ndum[i]!=0) && (i<=ncovcol)){
1.58 lievre 2088: Tvaraff[ij]=i; /*For printing */
1.53 brouard 2089: ij++;
2090: }
2091: }
2092:
1.58 lievre 2093: cptcoveff=ij-1; /*Number of simple covariates*/
1.53 brouard 2094: }
2095:
2096: /*********** Health Expectancies ****************/
2097:
2098: 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 )
2099:
2100: {
2101: /* Health expectancies */
2102: int i, j, nhstepm, hstepm, h, nstepm, k, cptj;
2103: double age, agelim, hf;
2104: double ***p3mat,***varhe;
2105: double **dnewm,**doldm;
2106: double *xp;
2107: double **gp, **gm;
2108: double ***gradg, ***trgradg;
2109: int theta;
2110:
1.74 brouard 2111: varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage);
1.53 brouard 2112: xp=vector(1,npar);
1.74 brouard 2113: dnewm=matrix(1,nlstate*nlstate,1,npar);
2114: doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate);
1.53 brouard 2115:
2116: fprintf(ficreseij,"# Health expectancies\n");
2117: fprintf(ficreseij,"# Age");
2118: for(i=1; i<=nlstate;i++)
2119: for(j=1; j<=nlstate;j++)
2120: fprintf(ficreseij," %1d-%1d (SE)",i,j);
2121: fprintf(ficreseij,"\n");
2122:
2123: if(estepm < stepm){
2124: printf ("Problem %d lower than %d\n",estepm, stepm);
2125: }
2126: else hstepm=estepm;
2127: /* We compute the life expectancy from trapezoids spaced every estepm months
2128: * This is mainly to measure the difference between two models: for example
2129: * if stepm=24 months pijx are given only every 2 years and by summing them
2130: * we are calculating an estimate of the Life Expectancy assuming a linear
1.66 brouard 2131: * progression in between and thus overestimating or underestimating according
1.53 brouard 2132: * to the curvature of the survival function. If, for the same date, we
2133: * estimate the model with stepm=1 month, we can keep estepm to 24 months
2134: * to compare the new estimate of Life expectancy with the same linear
2135: * hypothesis. A more precise result, taking into account a more precise
2136: * curvature will be obtained if estepm is as small as stepm. */
2137:
2138: /* For example we decided to compute the life expectancy with the smallest unit */
2139: /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
2140: nhstepm is the number of hstepm from age to agelim
2141: nstepm is the number of stepm from age to agelin.
2142: Look at hpijx to understand the reason of that which relies in memory size
2143: and note for a fixed period like estepm months */
2144: /* We decided (b) to get a life expectancy respecting the most precise curvature of the
2145: survival function given by stepm (the optimization length). Unfortunately it
2146: means that if the survival funtion is printed only each two years of age and if
2147: you sum them up and add 1 year (area under the trapezoids) you won't get the same
2148: results. So we changed our mind and took the option of the best precision.
2149: */
2150: hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
2151:
2152: agelim=AGESUP;
2153: for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
2154: /* nhstepm age range expressed in number of stepm */
2155: nstepm=(int) rint((agelim-age)*YEARM/stepm);
2156: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
2157: /* if (stepm >= YEARM) hstepm=1;*/
2158: nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
2159: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
1.74 brouard 2160: gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);
2161: gp=matrix(0,nhstepm,1,nlstate*nlstate);
2162: gm=matrix(0,nhstepm,1,nlstate*nlstate);
1.53 brouard 2163:
2164: /* Computed by stepm unit matrices, product of hstepm matrices, stored
2165: in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
2166: hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);
2167:
2168:
2169: hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
2170:
2171: /* Computing Variances of health expectancies */
2172:
2173: for(theta=1; theta <=npar; theta++){
2174: for(i=1; i<=npar; i++){
2175: xp[i] = x[i] + (i==theta ?delti[theta]:0);
2176: }
2177: hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
2178:
2179: cptj=0;
2180: for(j=1; j<= nlstate; j++){
2181: for(i=1; i<=nlstate; i++){
2182: cptj=cptj+1;
2183: for(h=0, gp[h][cptj]=0.; h<=nhstepm-1; h++){
2184: gp[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;
2185: }
2186: }
2187: }
2188:
2189:
2190: for(i=1; i<=npar; i++)
2191: xp[i] = x[i] - (i==theta ?delti[theta]:0);
2192: hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
2193:
2194: cptj=0;
2195: for(j=1; j<= nlstate; j++){
2196: for(i=1;i<=nlstate;i++){
2197: cptj=cptj+1;
2198: for(h=0, gm[h][cptj]=0.; h<=nhstepm-1; h++){
1.77 brouard 2199:
1.53 brouard 2200: gm[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;
2201: }
2202: }
2203: }
1.74 brouard 2204: for(j=1; j<= nlstate*nlstate; j++)
1.53 brouard 2205: for(h=0; h<=nhstepm-1; h++){
2206: gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
2207: }
2208: }
2209:
2210: /* End theta */
2211:
1.74 brouard 2212: trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar);
1.53 brouard 2213:
2214: for(h=0; h<=nhstepm-1; h++)
1.74 brouard 2215: for(j=1; j<=nlstate*nlstate;j++)
1.53 brouard 2216: for(theta=1; theta <=npar; theta++)
2217: trgradg[h][j][theta]=gradg[h][theta][j];
2218:
2219:
1.74 brouard 2220: for(i=1;i<=nlstate*nlstate;i++)
2221: for(j=1;j<=nlstate*nlstate;j++)
1.53 brouard 2222: varhe[i][j][(int)age] =0.;
2223:
2224: printf("%d|",(int)age);fflush(stdout);
2225: fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
2226: for(h=0;h<=nhstepm-1;h++){
2227: for(k=0;k<=nhstepm-1;k++){
1.74 brouard 2228: matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov);
2229: matprod2(doldm,dnewm,1,nlstate*nlstate,1,npar,1,nlstate*nlstate,gradg[k]);
2230: for(i=1;i<=nlstate*nlstate;i++)
2231: for(j=1;j<=nlstate*nlstate;j++)
1.53 brouard 2232: varhe[i][j][(int)age] += doldm[i][j]*hf*hf;
2233: }
2234: }
2235: /* Computing expectancies */
2236: for(i=1; i<=nlstate;i++)
2237: for(j=1; j<=nlstate;j++)
2238: for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
2239: eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
2240:
2241: /* 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]);*/
2242:
2243: }
2244:
2245: fprintf(ficreseij,"%3.0f",age );
2246: cptj=0;
2247: for(i=1; i<=nlstate;i++)
2248: for(j=1; j<=nlstate;j++){
2249: cptj++;
2250: fprintf(ficreseij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[cptj][cptj][(int)age]) );
2251: }
2252: fprintf(ficreseij,"\n");
2253:
1.74 brouard 2254: free_matrix(gm,0,nhstepm,1,nlstate*nlstate);
2255: free_matrix(gp,0,nhstepm,1,nlstate*nlstate);
2256: free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*nlstate);
2257: free_ma3x(trgradg,0,nhstepm,1,nlstate*nlstate,1,npar);
1.53 brouard 2258: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
2259: }
2260: printf("\n");
2261: fprintf(ficlog,"\n");
2262:
2263: free_vector(xp,1,npar);
1.74 brouard 2264: free_matrix(dnewm,1,nlstate*nlstate,1,npar);
2265: free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate);
2266: free_ma3x(varhe,1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int)fage);
1.53 brouard 2267: }
2268:
2269: /************ Variance ******************/
2270: 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)
2271: {
2272: /* Variance of health expectancies */
2273: /* double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
2274: /* double **newm;*/
2275: double **dnewm,**doldm;
2276: double **dnewmp,**doldmp;
2277: int i, j, nhstepm, hstepm, h, nstepm ;
2278: int k, cptcode;
2279: double *xp;
2280: double **gp, **gm; /* for var eij */
2281: double ***gradg, ***trgradg; /*for var eij */
2282: double **gradgp, **trgradgp; /* for var p point j */
2283: double *gpp, *gmp; /* for var p point j */
2284: double **varppt; /* for var p point j nlstate to nlstate+ndeath */
2285: double ***p3mat;
2286: double age,agelim, hf;
2287: double ***mobaverage;
2288: int theta;
2289: char digit[4];
1.55 lievre 2290: char digitp[25];
1.53 brouard 2291:
2292: char fileresprobmorprev[FILENAMELENGTH];
2293:
1.55 lievre 2294: if(popbased==1){
1.58 lievre 2295: if(mobilav!=0)
1.55 lievre 2296: strcpy(digitp,"-populbased-mobilav-");
2297: else strcpy(digitp,"-populbased-nomobil-");
2298: }
2299: else
1.53 brouard 2300: strcpy(digitp,"-stablbased-");
1.56 lievre 2301:
1.54 brouard 2302: if (mobilav!=0) {
1.53 brouard 2303: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
1.54 brouard 2304: if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
2305: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
2306: printf(" Error in movingaverage mobilav=%d\n",mobilav);
2307: }
1.53 brouard 2308: }
2309:
2310: strcpy(fileresprobmorprev,"prmorprev");
2311: sprintf(digit,"%-d",ij);
2312: /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
2313: strcat(fileresprobmorprev,digit); /* Tvar to be done */
2314: strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
2315: strcat(fileresprobmorprev,fileres);
2316: if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
2317: printf("Problem with resultfile: %s\n", fileresprobmorprev);
2318: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
2319: }
2320: printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
2321: fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
1.66 brouard 2322: 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 2323: fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
2324: for(j=nlstate+1; j<=(nlstate+ndeath);j++){
2325: fprintf(ficresprobmorprev," p.%-d SE",j);
2326: for(i=1; i<=nlstate;i++)
2327: fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
2328: }
2329: fprintf(ficresprobmorprev,"\n");
2330: if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {
2331: printf("Problem with gnuplot file: %s\n", optionfilegnuplot);
2332: fprintf(ficlog,"Problem with gnuplot file: %s\n", optionfilegnuplot);
2333: exit(0);
2334: }
2335: else{
2336: fprintf(ficgp,"\n# Routine varevsij");
2337: }
2338: if((fichtm=fopen(optionfilehtm,"a"))==NULL) {
2339: printf("Problem with html file: %s\n", optionfilehtm);
2340: fprintf(ficlog,"Problem with html file: %s\n", optionfilehtm);
2341: exit(0);
2342: }
2343: else{
1.67 brouard 2344: 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");
2345: fprintf(fichtm,"\n<br>%s <br>\n",digitp);
1.53 brouard 2346: }
2347: varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
2348:
2349: 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");
2350: fprintf(ficresvij,"# Age");
2351: for(i=1; i<=nlstate;i++)
2352: for(j=1; j<=nlstate;j++)
2353: fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);
2354: fprintf(ficresvij,"\n");
2355:
2356: xp=vector(1,npar);
2357: dnewm=matrix(1,nlstate,1,npar);
2358: doldm=matrix(1,nlstate,1,nlstate);
2359: dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
2360: doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
2361:
2362: gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
2363: gpp=vector(nlstate+1,nlstate+ndeath);
2364: gmp=vector(nlstate+1,nlstate+ndeath);
2365: trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
2366:
2367: if(estepm < stepm){
2368: printf ("Problem %d lower than %d\n",estepm, stepm);
2369: }
2370: else hstepm=estepm;
2371: /* For example we decided to compute the life expectancy with the smallest unit */
2372: /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
2373: nhstepm is the number of hstepm from age to agelim
2374: nstepm is the number of stepm from age to agelin.
2375: Look at hpijx to understand the reason of that which relies in memory size
2376: and note for a fixed period like k years */
2377: /* We decided (b) to get a life expectancy respecting the most precise curvature of the
2378: survival function given by stepm (the optimization length). Unfortunately it
1.66 brouard 2379: means that if the survival funtion is printed every two years of age and if
1.53 brouard 2380: you sum them up and add 1 year (area under the trapezoids) you won't get the same
2381: results. So we changed our mind and took the option of the best precision.
2382: */
2383: hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
2384: agelim = AGESUP;
2385: for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
2386: nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
2387: nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
2388: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
2389: gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
2390: gp=matrix(0,nhstepm,1,nlstate);
2391: gm=matrix(0,nhstepm,1,nlstate);
2392:
2393:
2394: for(theta=1; theta <=npar; theta++){
1.66 brouard 2395: for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
1.53 brouard 2396: xp[i] = x[i] + (i==theta ?delti[theta]:0);
2397: }
2398: hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
2399: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
2400:
2401: if (popbased==1) {
1.54 brouard 2402: if(mobilav ==0){
1.53 brouard 2403: for(i=1; i<=nlstate;i++)
2404: prlim[i][i]=probs[(int)age][i][ij];
1.54 brouard 2405: }else{ /* mobilav */
1.53 brouard 2406: for(i=1; i<=nlstate;i++)
2407: prlim[i][i]=mobaverage[(int)age][i][ij];
2408: }
2409: }
2410:
2411: for(j=1; j<= nlstate; j++){
2412: for(h=0; h<=nhstepm; h++){
2413: for(i=1, gp[h][j]=0.;i<=nlstate;i++)
2414: gp[h][j] += prlim[i][i]*p3mat[i][j][h];
2415: }
2416: }
1.66 brouard 2417: /* This for computing probability of death (h=1 means
2418: computed over hstepm matrices product = hstepm*stepm months)
2419: as a weighted average of prlim.
2420: */
1.69 brouard 2421: for(j=nlstate+1;j<=nlstate+ndeath;j++){
1.68 lievre 2422: for(i=1,gpp[j]=0.; i<= nlstate; i++)
1.53 brouard 2423: gpp[j] += prlim[i][i]*p3mat[i][j][1];
2424: }
1.66 brouard 2425: /* end probability of death */
1.53 brouard 2426:
1.66 brouard 2427: for(i=1; i<=npar; i++) /* Computes gradient x - delta */
1.53 brouard 2428: xp[i] = x[i] - (i==theta ?delti[theta]:0);
2429: hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
2430: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
2431:
2432: if (popbased==1) {
1.54 brouard 2433: if(mobilav ==0){
1.53 brouard 2434: for(i=1; i<=nlstate;i++)
2435: prlim[i][i]=probs[(int)age][i][ij];
1.54 brouard 2436: }else{ /* mobilav */
1.53 brouard 2437: for(i=1; i<=nlstate;i++)
2438: prlim[i][i]=mobaverage[(int)age][i][ij];
2439: }
2440: }
2441:
2442: for(j=1; j<= nlstate; j++){
2443: for(h=0; h<=nhstepm; h++){
2444: for(i=1, gm[h][j]=0.;i<=nlstate;i++)
2445: gm[h][j] += prlim[i][i]*p3mat[i][j][h];
2446: }
2447: }
1.66 brouard 2448: /* This for computing probability of death (h=1 means
2449: computed over hstepm matrices product = hstepm*stepm months)
2450: as a weighted average of prlim.
2451: */
1.69 brouard 2452: for(j=nlstate+1;j<=nlstate+ndeath;j++){
1.68 lievre 2453: for(i=1,gmp[j]=0.; i<= nlstate; i++)
2454: gmp[j] += prlim[i][i]*p3mat[i][j][1];
1.53 brouard 2455: }
1.66 brouard 2456: /* end probability of death */
1.53 brouard 2457:
2458: for(j=1; j<= nlstate; j++) /* vareij */
2459: for(h=0; h<=nhstepm; h++){
2460: gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
2461: }
1.68 lievre 2462:
1.53 brouard 2463: for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
2464: gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
2465: }
2466:
2467: } /* End theta */
2468:
2469: trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
2470:
2471: for(h=0; h<=nhstepm; h++) /* veij */
2472: for(j=1; j<=nlstate;j++)
2473: for(theta=1; theta <=npar; theta++)
2474: trgradg[h][j][theta]=gradg[h][theta][j];
2475:
2476: for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
1.69 brouard 2477: for(theta=1; theta <=npar; theta++)
1.53 brouard 2478: trgradgp[j][theta]=gradgp[theta][j];
1.69 brouard 2479:
1.53 brouard 2480:
2481: hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
2482: for(i=1;i<=nlstate;i++)
2483: for(j=1;j<=nlstate;j++)
2484: vareij[i][j][(int)age] =0.;
2485:
2486: for(h=0;h<=nhstepm;h++){
2487: for(k=0;k<=nhstepm;k++){
2488: matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
2489: matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
2490: for(i=1;i<=nlstate;i++)
2491: for(j=1;j<=nlstate;j++)
2492: vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
2493: }
2494: }
1.70 brouard 2495:
1.53 brouard 2496: /* pptj */
2497: matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
2498: matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
1.70 brouard 2499: for(j=nlstate+1;j<=nlstate+ndeath;j++)
2500: for(i=nlstate+1;i<=nlstate+ndeath;i++)
1.53 brouard 2501: varppt[j][i]=doldmp[j][i];
2502: /* end ppptj */
1.66 brouard 2503: /* x centered again */
1.53 brouard 2504: hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);
2505: prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);
2506:
2507: if (popbased==1) {
1.54 brouard 2508: if(mobilav ==0){
1.53 brouard 2509: for(i=1; i<=nlstate;i++)
2510: prlim[i][i]=probs[(int)age][i][ij];
1.54 brouard 2511: }else{ /* mobilav */
1.53 brouard 2512: for(i=1; i<=nlstate;i++)
2513: prlim[i][i]=mobaverage[(int)age][i][ij];
2514: }
2515: }
1.70 brouard 2516:
1.66 brouard 2517: /* This for computing probability of death (h=1 means
2518: computed over hstepm (estepm) matrices product = hstepm*stepm months)
2519: as a weighted average of prlim.
2520: */
1.68 lievre 2521: for(j=nlstate+1;j<=nlstate+ndeath;j++){
2522: for(i=1,gmp[j]=0.;i<= nlstate; i++)
1.53 brouard 2523: gmp[j] += prlim[i][i]*p3mat[i][j][1];
2524: }
1.66 brouard 2525: /* end probability of death */
1.53 brouard 2526:
2527: fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
2528: for(j=nlstate+1; j<=(nlstate+ndeath);j++){
2529: fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
2530: for(i=1; i<=nlstate;i++){
2531: fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
2532: }
2533: }
2534: fprintf(ficresprobmorprev,"\n");
2535:
2536: fprintf(ficresvij,"%.0f ",age );
2537: for(i=1; i<=nlstate;i++)
2538: for(j=1; j<=nlstate;j++){
2539: fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
2540: }
2541: fprintf(ficresvij,"\n");
2542: free_matrix(gp,0,nhstepm,1,nlstate);
2543: free_matrix(gm,0,nhstepm,1,nlstate);
2544: free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
2545: free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
2546: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
2547: } /* End age */
2548: free_vector(gpp,nlstate+1,nlstate+ndeath);
2549: free_vector(gmp,nlstate+1,nlstate+ndeath);
2550: free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
2551: free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
2552: fprintf(ficgp,"\nset noparametric;set nolabel; set ter png small;set size 0.65, 0.65");
2553: /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */
2554: fprintf(ficgp,"\n set log y; set nolog x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
1.67 brouard 2555: /* fprintf(ficgp,"\n plot \"%s\" u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm); */
2556: /* fprintf(ficgp,"\n replot \"%s\" u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm); */
2557: /* fprintf(ficgp,"\n replot \"%s\" u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm); */
2558: fprintf(ficgp,"\n plot \"%s\" u 1:($3) not w l 1 ",fileresprobmorprev);
2559: fprintf(ficgp,"\n replot \"%s\" u 1:(($3+1.96*$4)) t \"95\%% interval\" w l 2 ",fileresprobmorprev);
2560: fprintf(ficgp,"\n replot \"%s\" u 1:(($3-1.96*$4)) not w l 2 ",fileresprobmorprev);
1.53 brouard 2561: fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",fileresprobmorprev,fileresprobmorprev);
1.71 brouard 2562: 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 2563: /* 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);
2564: */
1.71 brouard 2565: fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.png\";replot;",digitp,optionfilefiname,digit);
1.53 brouard 2566:
2567: free_vector(xp,1,npar);
2568: free_matrix(doldm,1,nlstate,1,nlstate);
2569: free_matrix(dnewm,1,nlstate,1,npar);
2570: free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
2571: free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
2572: free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
1.55 lievre 2573: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
1.53 brouard 2574: fclose(ficresprobmorprev);
2575: fclose(ficgp);
2576: fclose(fichtm);
1.84 brouard 2577: } /* end varevsij */
1.53 brouard 2578:
2579: /************ Variance of prevlim ******************/
2580: 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)
2581: {
2582: /* Variance of prevalence limit */
1.59 brouard 2583: /* double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
1.53 brouard 2584: double **newm;
2585: double **dnewm,**doldm;
2586: int i, j, nhstepm, hstepm;
2587: int k, cptcode;
2588: double *xp;
2589: double *gp, *gm;
2590: double **gradg, **trgradg;
2591: double age,agelim;
2592: int theta;
2593:
1.54 brouard 2594: fprintf(ficresvpl,"# Standard deviation of stable prevalences \n");
1.53 brouard 2595: fprintf(ficresvpl,"# Age");
2596: for(i=1; i<=nlstate;i++)
2597: fprintf(ficresvpl," %1d-%1d",i,i);
2598: fprintf(ficresvpl,"\n");
2599:
2600: xp=vector(1,npar);
2601: dnewm=matrix(1,nlstate,1,npar);
2602: doldm=matrix(1,nlstate,1,nlstate);
2603:
2604: hstepm=1*YEARM; /* Every year of age */
2605: hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */
2606: agelim = AGESUP;
2607: for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
2608: nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
2609: if (stepm >= YEARM) hstepm=1;
2610: nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
2611: gradg=matrix(1,npar,1,nlstate);
2612: gp=vector(1,nlstate);
2613: gm=vector(1,nlstate);
2614:
2615: for(theta=1; theta <=npar; theta++){
2616: for(i=1; i<=npar; i++){ /* Computes gradient */
2617: xp[i] = x[i] + (i==theta ?delti[theta]:0);
2618: }
2619: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
2620: for(i=1;i<=nlstate;i++)
2621: gp[i] = prlim[i][i];
2622:
2623: for(i=1; i<=npar; i++) /* Computes gradient */
2624: xp[i] = x[i] - (i==theta ?delti[theta]:0);
2625: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
2626: for(i=1;i<=nlstate;i++)
2627: gm[i] = prlim[i][i];
2628:
2629: for(i=1;i<=nlstate;i++)
2630: gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
2631: } /* End theta */
2632:
2633: trgradg =matrix(1,nlstate,1,npar);
2634:
2635: for(j=1; j<=nlstate;j++)
2636: for(theta=1; theta <=npar; theta++)
2637: trgradg[j][theta]=gradg[theta][j];
2638:
2639: for(i=1;i<=nlstate;i++)
2640: varpl[i][(int)age] =0.;
2641: matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
2642: matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
2643: for(i=1;i<=nlstate;i++)
2644: varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
2645:
2646: fprintf(ficresvpl,"%.0f ",age );
2647: for(i=1; i<=nlstate;i++)
2648: fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
2649: fprintf(ficresvpl,"\n");
2650: free_vector(gp,1,nlstate);
2651: free_vector(gm,1,nlstate);
2652: free_matrix(gradg,1,npar,1,nlstate);
2653: free_matrix(trgradg,1,nlstate,1,npar);
2654: } /* End age */
2655:
2656: free_vector(xp,1,npar);
2657: free_matrix(doldm,1,nlstate,1,npar);
2658: free_matrix(dnewm,1,nlstate,1,nlstate);
2659:
2660: }
2661:
2662: /************ Variance of one-step probabilities ******************/
2663: void varprob(char optionfilefiname[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij, int *Tvar, int **nbcode, int *ncodemax)
2664: {
2665: int i, j=0, i1, k1, l1, t, tj;
2666: int k2, l2, j1, z1;
2667: int k=0,l, cptcode;
2668: int first=1, first1;
2669: double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
2670: double **dnewm,**doldm;
2671: double *xp;
2672: double *gp, *gm;
2673: double **gradg, **trgradg;
2674: double **mu;
2675: double age,agelim, cov[NCOVMAX];
2676: double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
2677: int theta;
2678: char fileresprob[FILENAMELENGTH];
2679: char fileresprobcov[FILENAMELENGTH];
2680: char fileresprobcor[FILENAMELENGTH];
2681:
2682: double ***varpij;
2683:
2684: strcpy(fileresprob,"prob");
2685: strcat(fileresprob,fileres);
2686: if((ficresprob=fopen(fileresprob,"w"))==NULL) {
2687: printf("Problem with resultfile: %s\n", fileresprob);
2688: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
2689: }
2690: strcpy(fileresprobcov,"probcov");
2691: strcat(fileresprobcov,fileres);
2692: if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
2693: printf("Problem with resultfile: %s\n", fileresprobcov);
2694: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
2695: }
2696: strcpy(fileresprobcor,"probcor");
2697: strcat(fileresprobcor,fileres);
2698: if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
2699: printf("Problem with resultfile: %s\n", fileresprobcor);
2700: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
2701: }
2702: printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
2703: fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
2704: printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
2705: fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
2706: printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
2707: fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
2708:
2709: fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
2710: fprintf(ficresprob,"# Age");
2711: fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
2712: fprintf(ficresprobcov,"# Age");
2713: fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
2714: fprintf(ficresprobcov,"# Age");
2715:
2716:
2717: for(i=1; i<=nlstate;i++)
2718: for(j=1; j<=(nlstate+ndeath);j++){
2719: fprintf(ficresprob," p%1d-%1d (SE)",i,j);
2720: fprintf(ficresprobcov," p%1d-%1d ",i,j);
2721: fprintf(ficresprobcor," p%1d-%1d ",i,j);
2722: }
1.69 brouard 2723: /* fprintf(ficresprob,"\n");
1.53 brouard 2724: fprintf(ficresprobcov,"\n");
2725: fprintf(ficresprobcor,"\n");
1.69 brouard 2726: */
2727: xp=vector(1,npar);
1.53 brouard 2728: dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
2729: doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
2730: mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
2731: varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
2732: first=1;
2733: if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {
2734: printf("Problem with gnuplot file: %s\n", optionfilegnuplot);
2735: fprintf(ficlog,"Problem with gnuplot file: %s\n", optionfilegnuplot);
2736: exit(0);
2737: }
2738: else{
2739: fprintf(ficgp,"\n# Routine varprob");
2740: }
2741: if((fichtm=fopen(optionfilehtm,"a"))==NULL) {
2742: printf("Problem with html file: %s\n", optionfilehtm);
2743: fprintf(ficlog,"Problem with html file: %s\n", optionfilehtm);
2744: exit(0);
2745: }
2746: else{
2747: fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
2748: fprintf(fichtm,"\n");
2749:
2750: fprintf(fichtm,"\n<li><h4> Computing matrix of variance-covariance of step probabilities</h4></li>\n");
2751: 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");
2752: 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");
2753:
2754: }
2755:
2756: cov[1]=1;
2757: tj=cptcoveff;
2758: if (cptcovn<1) {tj=1;ncodemax[1]=1;}
2759: j1=0;
2760: for(t=1; t<=tj;t++){
2761: for(i1=1; i1<=ncodemax[t];i1++){
2762: j1++;
2763: if (cptcovn>0) {
2764: fprintf(ficresprob, "\n#********** Variable ");
2765: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
1.69 brouard 2766: fprintf(ficresprob, "**********\n#\n");
1.53 brouard 2767: fprintf(ficresprobcov, "\n#********** Variable ");
2768: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
1.69 brouard 2769: fprintf(ficresprobcov, "**********\n#\n");
1.53 brouard 2770:
2771: fprintf(ficgp, "\n#********** Variable ");
1.69 brouard 2772: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
2773: fprintf(ficgp, "**********\n#\n");
1.53 brouard 2774:
2775:
2776: fprintf(fichtm, "\n<hr size=\"2\" color=\"#EC5E5E\">********** Variable ");
2777: for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
2778: fprintf(fichtm, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
2779:
2780: fprintf(ficresprobcor, "\n#********** Variable ");
2781: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
1.69 brouard 2782: fprintf(ficresprobcor, "**********\n#");
1.53 brouard 2783: }
2784:
2785: for (age=bage; age<=fage; age ++){
2786: cov[2]=age;
2787: for (k=1; k<=cptcovn;k++) {
2788: cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];
2789: }
2790: for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
2791: for (k=1; k<=cptcovprod;k++)
2792: cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
2793:
2794: gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
2795: trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
2796: gp=vector(1,(nlstate)*(nlstate+ndeath));
2797: gm=vector(1,(nlstate)*(nlstate+ndeath));
2798:
2799: for(theta=1; theta <=npar; theta++){
2800: for(i=1; i<=npar; i++)
1.74 brouard 2801: xp[i] = x[i] + (i==theta ?delti[theta]:(double)0);
1.53 brouard 2802:
2803: pmij(pmmij,cov,ncovmodel,xp,nlstate);
2804:
2805: k=0;
2806: for(i=1; i<= (nlstate); i++){
2807: for(j=1; j<=(nlstate+ndeath);j++){
2808: k=k+1;
2809: gp[k]=pmmij[i][j];
2810: }
2811: }
2812:
2813: for(i=1; i<=npar; i++)
1.74 brouard 2814: xp[i] = x[i] - (i==theta ?delti[theta]:(double)0);
1.53 brouard 2815:
2816: pmij(pmmij,cov,ncovmodel,xp,nlstate);
2817: k=0;
2818: for(i=1; i<=(nlstate); i++){
2819: for(j=1; j<=(nlstate+ndeath);j++){
2820: k=k+1;
2821: gm[k]=pmmij[i][j];
2822: }
2823: }
2824:
2825: for(i=1; i<= (nlstate)*(nlstate+ndeath); i++)
1.74 brouard 2826: gradg[theta][i]=(gp[i]-gm[i])/(double)2./delti[theta];
1.53 brouard 2827: }
2828:
2829: for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
2830: for(theta=1; theta <=npar; theta++)
2831: trgradg[j][theta]=gradg[theta][j];
2832:
2833: matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov);
2834: matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);
1.59 brouard 2835: free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
2836: free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
2837: free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
2838: free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
2839:
1.53 brouard 2840: pmij(pmmij,cov,ncovmodel,x,nlstate);
2841:
2842: k=0;
2843: for(i=1; i<=(nlstate); i++){
2844: for(j=1; j<=(nlstate+ndeath);j++){
2845: k=k+1;
2846: mu[k][(int) age]=pmmij[i][j];
2847: }
2848: }
2849: for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
2850: for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
2851: varpij[i][j][(int)age] = doldm[i][j];
2852:
2853: /*printf("\n%d ",(int)age);
1.59 brouard 2854: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
2855: printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
2856: fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
2857: }*/
1.53 brouard 2858:
2859: fprintf(ficresprob,"\n%d ",(int)age);
2860: fprintf(ficresprobcov,"\n%d ",(int)age);
2861: fprintf(ficresprobcor,"\n%d ",(int)age);
2862:
2863: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)
2864: fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));
2865: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
2866: fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);
2867: fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
2868: }
2869: i=0;
2870: for (k=1; k<=(nlstate);k++){
2871: for (l=1; l<=(nlstate+ndeath);l++){
2872: i=i++;
2873: fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
2874: fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
2875: for (j=1; j<=i;j++){
2876: fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);
2877: fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));
2878: }
2879: }
2880: }/* end of loop for state */
2881: } /* end of loop for age */
2882:
2883: /* Confidence intervalle of pij */
2884: /*
1.59 brouard 2885: fprintf(ficgp,"\nset noparametric;unset label");
2886: fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");
2887: fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
2888: 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);
2889: fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);
2890: fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);
2891: fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);
1.53 brouard 2892: */
2893:
2894: /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
2895: first1=1;
2896: for (k2=1; k2<=(nlstate);k2++){
2897: for (l2=1; l2<=(nlstate+ndeath);l2++){
2898: if(l2==k2) continue;
2899: j=(k2-1)*(nlstate+ndeath)+l2;
2900: for (k1=1; k1<=(nlstate);k1++){
2901: for (l1=1; l1<=(nlstate+ndeath);l1++){
2902: if(l1==k1) continue;
2903: i=(k1-1)*(nlstate+ndeath)+l1;
2904: if(i<=j) continue;
2905: for (age=bage; age<=fage; age ++){
2906: if ((int)age %5==0){
2907: v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;
2908: v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;
2909: cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;
2910: mu1=mu[i][(int) age]/stepm*YEARM ;
2911: mu2=mu[j][(int) age]/stepm*YEARM;
2912: c12=cv12/sqrt(v1*v2);
2913: /* Computing eigen value of matrix of covariance */
2914: lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
2915: lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
2916: /* Eigen vectors */
2917: v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
2918: /*v21=sqrt(1.-v11*v11); *//* error */
2919: v21=(lc1-v1)/cv12*v11;
2920: v12=-v21;
2921: v22=v11;
2922: tnalp=v21/v11;
2923: if(first1==1){
2924: first1=0;
2925: 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);
2926: }
2927: 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);
2928: /*printf(fignu*/
2929: /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */
2930: /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */
2931: if(first==1){
2932: first=0;
2933: fprintf(ficgp,"\nset parametric;unset label");
2934: 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);
2935: fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
2936: 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);
2937: fprintf(fichtm,"\n<br><img src=\"varpijgr%s%d%1d%1d-%1d%1d.png\"> ",optionfilefiname, j1,k1,l1,k2,l2);
2938: fprintf(fichtm,"\n<br> Correlation at age %d (%.3f),",(int) age, c12);
2939: fprintf(ficgp,"\nset out \"varpijgr%s%d%1d%1d-%1d%1d.png\"",optionfilefiname, j1,k1,l1,k2,l2);
2940: fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
2941: fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
2942: 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",\
2943: mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
2944: mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
2945: }else{
2946: first=0;
2947: fprintf(fichtm," %d (%.3f),",(int) age, c12);
2948: fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
2949: fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
2950: 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",\
2951: mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
2952: mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
2953: }/* if first */
2954: } /* age mod 5 */
2955: } /* end loop age */
2956: fprintf(ficgp,"\nset out \"varpijgr%s%d%1d%1d-%1d%1d.png\";replot;",optionfilefiname, j1,k1,l1,k2,l2);
2957: first=1;
2958: } /*l12 */
2959: } /* k12 */
2960: } /*l1 */
2961: }/* k1 */
2962: } /* loop covariates */
2963: }
1.59 brouard 2964: free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
2965: free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
1.53 brouard 2966: free_vector(xp,1,npar);
2967: fclose(ficresprob);
2968: fclose(ficresprobcov);
2969: fclose(ficresprobcor);
2970: fclose(ficgp);
2971: fclose(fichtm);
2972: }
2973:
2974:
2975: /******************* Printing html file ***********/
2976: void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \
2977: int lastpass, int stepm, int weightopt, char model[],\
2978: int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
2979: int popforecast, int estepm ,\
2980: double jprev1, double mprev1,double anprev1, \
2981: double jprev2, double mprev2,double anprev2){
2982: int jj1, k1, i1, cpt;
2983: /*char optionfilehtm[FILENAMELENGTH];*/
2984: if((fichtm=fopen(optionfilehtm,"a"))==NULL) {
2985: printf("Problem with %s \n",optionfilehtm), exit(0);
2986: fprintf(ficlog,"Problem with %s \n",optionfilehtm), exit(0);
2987: }
2988:
1.85 ! brouard 2989: fprintf(fichtm,"<ul><li><h4>Result files (first order: no variance)</h4>\n \
! 2990: - 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 \
! 2991: - Estimated transition probabilities over %d (stepm) months: <a href=\"pij%s\">pij%s</a><br>\n \
! 2992: - Stable prevalence in each health state: <a href=\"pl%s\">pl%s</a> <br>\n \
! 2993: - Life expectancies by age and initial health status (estepm=%2d months): \
1.53 brouard 2994: <a href=\"e%s\">e%s</a> <br>\n</li>", \
2995: jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,fileres,fileres,stepm,fileres,fileres,fileres,fileres,estepm,fileres,fileres);
2996:
2997: fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
2998:
2999: m=cptcoveff;
3000: if (cptcovn < 1) {m=1;ncodemax[1]=1;}
3001:
3002: jj1=0;
3003: for(k1=1; k1<=m;k1++){
3004: for(i1=1; i1<=ncodemax[k1];i1++){
3005: jj1++;
3006: if (cptcovn > 0) {
3007: fprintf(fichtm,"<hr size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
3008: for (cpt=1; cpt<=cptcoveff;cpt++)
3009: fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
3010: fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
3011: }
3012: /* Pij */
1.85 ! brouard 3013: 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 3014: <img src=\"pe%s%d1.png\">",stepm,strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);
3015: /* Quasi-incidences */
1.85 ! brouard 3016: fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months\
! 3017: before but expressed in per year i.e. quasi incidences if stepm is small and probabilities too: pe%s%d2.png<br> \
1.53 brouard 3018: <img src=\"pe%s%d2.png\">",stepm,strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);
3019: /* Stable prevalence in each health state */
3020: for(cpt=1; cpt<nlstate;cpt++){
1.85 ! brouard 3021: fprintf(fichtm,"<br>- Stable prevalence in each health state : p%s%d%d.png<br> \
1.53 brouard 3022: <img src=\"p%s%d%d.png\">",strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);
3023: }
3024: for(cpt=1; cpt<=nlstate;cpt++) {
1.85 ! brouard 3025: fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): exp%s%d%d.png <br> \
1.53 brouard 3026: <img src=\"exp%s%d%d.png\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);
3027: }
1.85 ! brouard 3028: fprintf(fichtm,"\n<br>- Total life expectancy by age and \
! 3029: health expectancies in states (1) and (2): e%s%d.png<br>\
1.53 brouard 3030: <img src=\"e%s%d.png\">",strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);
3031: } /* end i1 */
3032: }/* End k1 */
3033: fprintf(fichtm,"</ul>");
3034:
3035:
1.85 ! brouard 3036: fprintf(fichtm,"\n<br><li><h4> Result files (second order: variances)</h4>\n\
! 3037: - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n\
! 3038: - Variance of one-step probabilities: <a href=\"prob%s\">prob%s</a> <br>\n\
! 3039: - Variance-covariance of one-step probabilities: <a href=\"probcov%s\">probcov%s</a> <br>\n\
! 3040: - Correlation matrix of one-step probabilities: <a href=\"probcor%s\">probcor%s</a> <br>\n\
! 3041: - Variances and covariances of life expectancies by age and initial health status (estepm=%d months): <a href=\"v%s\">v%s</a><br>\n\
! 3042: - Health expectancies with their variances (no covariance): <a href=\"t%s\">t%s</a> <br>\n\
1.53 brouard 3043: - 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);
3044:
1.76 brouard 3045: /* if(popforecast==1) fprintf(fichtm,"\n */
3046: /* - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n */
3047: /* - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n */
3048: /* <br>",fileres,fileres,fileres,fileres); */
3049: /* else */
3050: /* 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 3051: fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
3052:
3053: m=cptcoveff;
3054: if (cptcovn < 1) {m=1;ncodemax[1]=1;}
3055:
3056: jj1=0;
3057: for(k1=1; k1<=m;k1++){
3058: for(i1=1; i1<=ncodemax[k1];i1++){
3059: jj1++;
3060: if (cptcovn > 0) {
3061: fprintf(fichtm,"<hr size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
3062: for (cpt=1; cpt<=cptcoveff;cpt++)
3063: fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
3064: fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
3065: }
3066: for(cpt=1; cpt<=nlstate;cpt++) {
1.85 ! brouard 3067: fprintf(fichtm,"<br>- Observed and period prevalence (with confident\
! 3068: interval) in state (%d): v%s%d%d.png <br>\
1.53 brouard 3069: <img src=\"v%s%d%d.png\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);
3070: }
3071: } /* end i1 */
3072: }/* End k1 */
3073: fprintf(fichtm,"</ul>");
3074: fclose(fichtm);
3075: }
3076:
3077: /******************* Gnuplot file **************/
3078: void printinggnuplot(char fileres[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
3079:
3080: int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;
3081: int ng;
3082: if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {
3083: printf("Problem with file %s",optionfilegnuplot);
3084: fprintf(ficlog,"Problem with file %s",optionfilegnuplot);
3085: }
3086:
1.54 brouard 3087: /*#ifdef windows */
1.53 brouard 3088: fprintf(ficgp,"cd \"%s\" \n",pathc);
1.54 brouard 3089: /*#endif */
1.53 brouard 3090: m=pow(2,cptcoveff);
3091:
3092: /* 1eme*/
3093: for (cpt=1; cpt<= nlstate ; cpt ++) {
3094: for (k1=1; k1<= m ; k1 ++) {
3095: fprintf(ficgp,"\nset out \"v%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);
3096: 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);
3097:
3098: for (i=1; i<= nlstate ; i ++) {
3099: if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
3100: else fprintf(ficgp," \%%*lf (\%%*lf)");
3101: }
1.69 brouard 3102: 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 3103: for (i=1; i<= nlstate ; i ++) {
3104: if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
3105: else fprintf(ficgp," \%%*lf (\%%*lf)");
3106: }
1.69 brouard 3107: fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"vpl%s\" every :::%d::%d u 1:($2-1.96*$3) \"\%%lf",fileres,k1-1,k1-1);
1.53 brouard 3108: for (i=1; i<= nlstate ; i ++) {
3109: if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
3110: else fprintf(ficgp," \%%*lf (\%%*lf)");
3111: }
3112: fprintf(ficgp,"\" t\"\" w l 1,\"p%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",fileres,k1-1,k1-1,2+4*(cpt-1));
3113: }
3114: }
3115: /*2 eme*/
3116:
3117: for (k1=1; k1<= m ; k1 ++) {
3118: fprintf(ficgp,"\nset out \"e%s%d.png\" \n",strtok(optionfile, "."),k1);
3119: fprintf(ficgp,"set ylabel \"Years\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] ",ageminpar,fage);
3120:
3121: for (i=1; i<= nlstate+1 ; i ++) {
3122: k=2*i;
3123: fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:2 \"\%%lf",fileres,k1-1,k1-1);
3124: for (j=1; j<= nlstate+1 ; j ++) {
3125: if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
3126: else fprintf(ficgp," \%%*lf (\%%*lf)");
3127: }
3128: if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");
3129: else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);
3130: fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",fileres,k1-1,k1-1);
3131: for (j=1; j<= nlstate+1 ; j ++) {
3132: if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
3133: else fprintf(ficgp," \%%*lf (\%%*lf)");
3134: }
3135: fprintf(ficgp,"\" t\"\" w l 0,");
3136: fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",fileres,k1-1,k1-1);
3137: for (j=1; j<= nlstate+1 ; j ++) {
3138: if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
3139: else fprintf(ficgp," \%%*lf (\%%*lf)");
3140: }
3141: if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");
3142: else fprintf(ficgp,"\" t\"\" w l 0,");
3143: }
3144: }
3145:
3146: /*3eme*/
3147:
3148: for (k1=1; k1<= m ; k1 ++) {
3149: for (cpt=1; cpt<= nlstate ; cpt ++) {
3150: k=2+nlstate*(2*cpt-2);
3151: fprintf(ficgp,"\nset out \"exp%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);
3152: fprintf(ficgp,"set ter png small\nset size 0.65,0.65\nplot [%.f:%.f] \"e%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,fileres,k1-1,k1-1,k,cpt);
3153: /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
3154: for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
3155: fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
3156: fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
3157: for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
3158: fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
3159:
3160: */
3161: for (i=1; i< nlstate ; i ++) {
3162: 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);
3163:
3164: }
3165: }
3166: }
3167:
1.76 brouard 3168: /* CV preval stable (period) */
1.53 brouard 3169: for (k1=1; k1<= m ; k1 ++) {
1.76 brouard 3170: for (cpt=1; cpt<=nlstate ; cpt ++) {
1.53 brouard 3171: k=3;
3172: fprintf(ficgp,"\nset out \"p%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);
3173: 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/($%d",ageminpar,agemaxpar,fileres,k1,k+cpt+1,k+1);
3174:
1.83 lievre 3175: for (i=1; i< nlstate ; i ++)
1.53 brouard 3176: fprintf(ficgp,"+$%d",k+i+1);
3177: fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);
3178:
3179: l=3+(nlstate+ndeath)*cpt;
3180: fprintf(ficgp,",\"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",fileres,k1,l+cpt+1,l+1);
3181: for (i=1; i< nlstate ; i ++) {
3182: l=3+(nlstate+ndeath)*cpt;
3183: fprintf(ficgp,"+$%d",l+i+1);
3184: }
3185: fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);
3186: }
3187: }
3188:
3189: /* proba elementaires */
3190: for(i=1,jk=1; i <=nlstate; i++){
3191: for(k=1; k <=(nlstate+ndeath); k++){
3192: if (k != i) {
3193: for(j=1; j <=ncovmodel; j++){
3194: fprintf(ficgp,"p%d=%f ",jk,p[jk]);
3195: jk++;
3196: fprintf(ficgp,"\n");
3197: }
3198: }
3199: }
3200: }
3201:
3202: for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/
3203: for(jk=1; jk <=m; jk++) {
3204: fprintf(ficgp,"\nset out \"pe%s%d%d.png\" \n",strtok(optionfile, "."),jk,ng);
3205: if (ng==2)
3206: fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
3207: else
3208: fprintf(ficgp,"\nset title \"Probability\"\n");
3209: fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65\nset log y\nplot [%.f:%.f] ",ageminpar,agemaxpar);
3210: i=1;
3211: for(k2=1; k2<=nlstate; k2++) {
3212: k3=i;
3213: for(k=1; k<=(nlstate+ndeath); k++) {
3214: if (k != k2){
3215: if(ng==2)
3216: fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);
3217: else
3218: fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
3219: ij=1;
3220: for(j=3; j <=ncovmodel; j++) {
3221: if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
3222: fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
3223: ij++;
3224: }
3225: else
3226: fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
3227: }
3228: fprintf(ficgp,")/(1");
3229:
3230: for(k1=1; k1 <=nlstate; k1++){
3231: fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);
3232: ij=1;
3233: for(j=3; j <=ncovmodel; j++){
3234: if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
3235: fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
3236: ij++;
3237: }
3238: else
3239: fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
3240: }
3241: fprintf(ficgp,")");
3242: }
3243: fprintf(ficgp,") t \"p%d%d\" ", k2,k);
3244: if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");
3245: i=i+ncovmodel;
3246: }
3247: } /* end k */
3248: } /* end k2 */
3249: } /* end jk */
3250: } /* end ng */
3251: fclose(ficgp);
3252: } /* end gnuplot */
3253:
3254:
3255: /*************** Moving average **************/
1.54 brouard 3256: int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav){
1.53 brouard 3257:
3258: int i, cpt, cptcod;
1.58 lievre 3259: int modcovmax =1;
1.54 brouard 3260: int mobilavrange, mob;
1.53 brouard 3261: double age;
1.58 lievre 3262:
3263: modcovmax=2*cptcoveff;/* Max number of modalities. We suppose
3264: a covariate has 2 modalities */
3265: if (cptcovn<1) modcovmax=1; /* At least 1 pass */
3266:
1.54 brouard 3267: if(mobilav==1||mobilav ==3 ||mobilav==5 ||mobilav== 7){
3268: if(mobilav==1) mobilavrange=5; /* default */
3269: else mobilavrange=mobilav;
3270: for (age=bage; age<=fage; age++)
3271: for (i=1; i<=nlstate;i++)
1.58 lievre 3272: for (cptcod=1;cptcod<=modcovmax;cptcod++)
1.54 brouard 3273: mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
3274: /* We keep the original values on the extreme ages bage, fage and for
3275: fage+1 and bage-1 we use a 3 terms moving average; for fage+2 bage+2
3276: we use a 5 terms etc. until the borders are no more concerned.
3277: */
3278: for (mob=3;mob <=mobilavrange;mob=mob+2){
3279: for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){
3280: for (i=1; i<=nlstate;i++){
1.58 lievre 3281: for (cptcod=1;cptcod<=modcovmax;cptcod++){
1.54 brouard 3282: mobaverage[(int)age][i][cptcod] =probs[(int)age][i][cptcod];
3283: for (cpt=1;cpt<=(mob-1)/2;cpt++){
3284: mobaverage[(int)age][i][cptcod] +=probs[(int)age-cpt][i][cptcod];
3285: mobaverage[(int)age][i][cptcod] +=probs[(int)age+cpt][i][cptcod];
3286: }
3287: mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/mob;
3288: }
1.53 brouard 3289: }
1.54 brouard 3290: }/* end age */
3291: }/* end mob */
3292: }else return -1;
3293: return 0;
3294: }/* End movingaverage */
1.53 brouard 3295:
3296:
3297: /************** Forecasting ******************/
1.70 brouard 3298: 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 3299: /* proj1, year, month, day of starting projection
3300: agemin, agemax range of age
3301: dateprev1 dateprev2 range of dates during which prevalence is computed
1.70 brouard 3302: anproj2 year of en of projection (same day and month as proj1).
1.69 brouard 3303: */
1.73 lievre 3304: int yearp, stepsize, hstepm, nhstepm, j, k, c, cptcod, i, h, i1;
1.53 brouard 3305: int *popage;
1.70 brouard 3306: double agec; /* generic age */
3307: double agelim, ppij, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
1.53 brouard 3308: double *popeffectif,*popcount;
3309: double ***p3mat;
1.55 lievre 3310: double ***mobaverage;
1.53 brouard 3311: char fileresf[FILENAMELENGTH];
3312:
1.69 brouard 3313: agelim=AGESUP;
1.84 brouard 3314: prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
1.53 brouard 3315:
3316: strcpy(fileresf,"f");
3317: strcat(fileresf,fileres);
3318: if((ficresf=fopen(fileresf,"w"))==NULL) {
3319: printf("Problem with forecast resultfile: %s\n", fileresf);
3320: fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);
3321: }
3322: printf("Computing forecasting: result on file '%s' \n", fileresf);
3323: fprintf(ficlog,"Computing forecasting: result on file '%s' \n", fileresf);
3324:
3325: if (cptcoveff==0) ncodemax[cptcoveff]=1;
3326:
1.54 brouard 3327: if (mobilav!=0) {
1.53 brouard 3328: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
1.54 brouard 3329: if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
3330: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
3331: printf(" Error in movingaverage mobilav=%d\n",mobilav);
3332: }
1.53 brouard 3333: }
3334:
3335: stepsize=(int) (stepm+YEARM-1)/YEARM;
3336: if (stepm<=12) stepsize=1;
1.74 brouard 3337: if(estepm < stepm){
3338: printf ("Problem %d lower than %d\n",estepm, stepm);
3339: }
3340: else hstepm=estepm;
3341:
1.53 brouard 3342: hstepm=hstepm/stepm;
1.69 brouard 3343: yp1=modf(dateintmean,&yp);/* extracts integral of datemean in yp and
3344: fractional in yp1 */
1.53 brouard 3345: anprojmean=yp;
3346: yp2=modf((yp1*12),&yp);
3347: mprojmean=yp;
3348: yp1=modf((yp2*30.5),&yp);
3349: jprojmean=yp;
3350: if(jprojmean==0) jprojmean=1;
3351: if(mprojmean==0) jprojmean=1;
1.73 lievre 3352:
3353: i1=cptcoveff;
3354: if (cptcovn < 1){i1=1;}
1.53 brouard 3355:
1.70 brouard 3356: fprintf(ficresf,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2);
1.53 brouard 3357:
1.70 brouard 3358: fprintf(ficresf,"#****** Routine prevforecast **\n");
1.73 lievre 3359:
1.75 brouard 3360: /* if (h==(int)(YEARM*yearp)){ */
1.73 lievre 3361: for(cptcov=1, k=0;cptcov<=i1;cptcov++){
1.53 brouard 3362: for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
3363: k=k+1;
3364: fprintf(ficresf,"\n#******");
3365: for(j=1;j<=cptcoveff;j++) {
1.70 brouard 3366: 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 3367: }
3368: fprintf(ficresf,"******\n");
1.70 brouard 3369: fprintf(ficresf,"# Covariate valuofcovar yearproj age");
3370: for(j=1; j<=nlstate+ndeath;j++){
3371: for(i=1; i<=nlstate;i++)
3372: fprintf(ficresf," p%d%d",i,j);
3373: fprintf(ficresf," p.%d",j);
3374: }
1.74 brouard 3375: for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) {
1.53 brouard 3376: fprintf(ficresf,"\n");
1.70 brouard 3377: fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+yearp);
1.53 brouard 3378:
1.71 brouard 3379: for (agec=fage; agec>=(ageminpar-1); agec--){
1.70 brouard 3380: nhstepm=(int) rint((agelim-agec)*YEARM/stepm);
1.53 brouard 3381: nhstepm = nhstepm/hstepm;
3382: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3383: oldm=oldms;savm=savms;
1.70 brouard 3384: hpxij(p3mat,nhstepm,agec,hstepm,p,nlstate,stepm,oldm,savm, k);
1.53 brouard 3385:
3386: for (h=0; h<=nhstepm; h++){
1.75 brouard 3387: if (h*hstepm/YEARM*stepm ==yearp) {
1.69 brouard 3388: fprintf(ficresf,"\n");
3389: for(j=1;j<=cptcoveff;j++)
3390: fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
1.70 brouard 3391: fprintf(ficresf,"%.f %.f ",anproj1+yearp,agec+h*hstepm/YEARM*stepm);
1.53 brouard 3392: }
3393: for(j=1; j<=nlstate+ndeath;j++) {
1.70 brouard 3394: ppij=0.;
1.71 brouard 3395: for(i=1; i<=nlstate;i++) {
1.53 brouard 3396: if (mobilav==1)
1.71 brouard 3397: ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][i][cptcod];
1.53 brouard 3398: else {
1.71 brouard 3399: ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][cptcod];
1.53 brouard 3400: }
1.75 brouard 3401: if (h*hstepm/YEARM*stepm== yearp) {
1.70 brouard 3402: fprintf(ficresf," %.3f", p3mat[i][j][h]);
1.75 brouard 3403: }
3404: } /* end i */
3405: if (h*hstepm/YEARM*stepm==yearp) {
1.70 brouard 3406: fprintf(ficresf," %.3f", ppij);
1.53 brouard 3407: }
1.75 brouard 3408: }/* end j */
3409: } /* end h */
1.53 brouard 3410: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
1.75 brouard 3411: } /* end agec */
3412: } /* end yearp */
3413: } /* end cptcod */
3414: } /* end cptcov */
1.53 brouard 3415:
1.54 brouard 3416: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
1.53 brouard 3417:
3418: fclose(ficresf);
3419: }
1.70 brouard 3420:
3421: /************** Forecasting *****not tested NB*************/
1.53 brouard 3422: 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){
3423:
3424: int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;
3425: int *popage;
1.69 brouard 3426: double calagedatem, agelim, kk1, kk2;
1.53 brouard 3427: double *popeffectif,*popcount;
3428: double ***p3mat,***tabpop,***tabpopprev;
1.55 lievre 3429: double ***mobaverage;
1.53 brouard 3430: char filerespop[FILENAMELENGTH];
3431:
3432: tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
3433: tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
3434: agelim=AGESUP;
1.69 brouard 3435: calagedatem=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;
1.53 brouard 3436:
1.84 brouard 3437: prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
1.53 brouard 3438:
3439:
3440: strcpy(filerespop,"pop");
3441: strcat(filerespop,fileres);
3442: if((ficrespop=fopen(filerespop,"w"))==NULL) {
3443: printf("Problem with forecast resultfile: %s\n", filerespop);
3444: fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop);
3445: }
3446: printf("Computing forecasting: result on file '%s' \n", filerespop);
3447: fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop);
3448:
3449: if (cptcoveff==0) ncodemax[cptcoveff]=1;
3450:
1.54 brouard 3451: if (mobilav!=0) {
1.53 brouard 3452: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
1.54 brouard 3453: if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
3454: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
3455: printf(" Error in movingaverage mobilav=%d\n",mobilav);
3456: }
1.53 brouard 3457: }
3458:
3459: stepsize=(int) (stepm+YEARM-1)/YEARM;
3460: if (stepm<=12) stepsize=1;
3461:
3462: agelim=AGESUP;
3463:
3464: hstepm=1;
3465: hstepm=hstepm/stepm;
3466:
3467: if (popforecast==1) {
3468: if((ficpop=fopen(popfile,"r"))==NULL) {
3469: printf("Problem with population file : %s\n",popfile);exit(0);
3470: fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0);
3471: }
3472: popage=ivector(0,AGESUP);
3473: popeffectif=vector(0,AGESUP);
3474: popcount=vector(0,AGESUP);
3475:
3476: i=1;
3477: while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;
3478:
3479: imx=i;
3480: for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];
3481: }
3482:
1.69 brouard 3483: for(cptcov=1,k=0;cptcov<=i2;cptcov++){
1.53 brouard 3484: for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
3485: k=k+1;
3486: fprintf(ficrespop,"\n#******");
3487: for(j=1;j<=cptcoveff;j++) {
3488: fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
3489: }
3490: fprintf(ficrespop,"******\n");
3491: fprintf(ficrespop,"# Age");
3492: for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);
3493: if (popforecast==1) fprintf(ficrespop," [Population]");
3494:
3495: for (cpt=0; cpt<=0;cpt++) {
3496: fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);
3497:
1.69 brouard 3498: for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){
1.53 brouard 3499: nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);
3500: nhstepm = nhstepm/hstepm;
3501:
3502: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3503: oldm=oldms;savm=savms;
3504: hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
3505:
3506: for (h=0; h<=nhstepm; h++){
1.69 brouard 3507: if (h==(int) (calagedatem+YEARM*cpt)) {
1.53 brouard 3508: fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
3509: }
3510: for(j=1; j<=nlstate+ndeath;j++) {
3511: kk1=0.;kk2=0;
3512: for(i=1; i<=nlstate;i++) {
3513: if (mobilav==1)
3514: kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];
3515: else {
3516: kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];
3517: }
3518: }
1.69 brouard 3519: if (h==(int)(calagedatem+12*cpt)){
1.53 brouard 3520: tabpop[(int)(agedeb)][j][cptcod]=kk1;
3521: /*fprintf(ficrespop," %.3f", kk1);
3522: if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/
3523: }
3524: }
3525: for(i=1; i<=nlstate;i++){
3526: kk1=0.;
3527: for(j=1; j<=nlstate;j++){
3528: kk1= kk1+tabpop[(int)(agedeb)][j][cptcod];
3529: }
1.69 brouard 3530: tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedatem+12*cpt)*hstepm/YEARM*stepm-1)];
1.53 brouard 3531: }
3532:
1.69 brouard 3533: if (h==(int)(calagedatem+12*cpt)) for(j=1; j<=nlstate;j++)
1.53 brouard 3534: fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);
3535: }
3536: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3537: }
3538: }
3539:
3540: /******/
3541:
3542: for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) {
3543: fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);
1.69 brouard 3544: for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){
1.53 brouard 3545: nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);
3546: nhstepm = nhstepm/hstepm;
3547:
3548: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3549: oldm=oldms;savm=savms;
3550: hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
3551: for (h=0; h<=nhstepm; h++){
1.69 brouard 3552: if (h==(int) (calagedatem+YEARM*cpt)) {
1.53 brouard 3553: fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
3554: }
3555: for(j=1; j<=nlstate+ndeath;j++) {
3556: kk1=0.;kk2=0;
3557: for(i=1; i<=nlstate;i++) {
3558: kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];
3559: }
1.69 brouard 3560: if (h==(int)(calagedatem+12*cpt)) fprintf(ficresf," %15.2f", kk1);
1.53 brouard 3561: }
3562: }
3563: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3564: }
3565: }
3566: }
3567: }
3568:
1.54 brouard 3569: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
1.53 brouard 3570:
3571: if (popforecast==1) {
3572: free_ivector(popage,0,AGESUP);
3573: free_vector(popeffectif,0,AGESUP);
3574: free_vector(popcount,0,AGESUP);
3575: }
3576: free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
3577: free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
3578: fclose(ficrespop);
1.84 brouard 3579: } /* End of popforecast */
1.53 brouard 3580:
3581: /***********************************************/
3582: /**************** Main Program *****************/
3583: /***********************************************/
3584:
3585: int main(int argc, char *argv[])
3586: {
1.61 brouard 3587: int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav);
1.74 brouard 3588: int i,j, k, n=MAXN,iter,m,size=100,cptcode, cptcod;
1.85 ! brouard 3589: int jj;
! 3590: int numlinepar=0; /* Current linenumber of parameter file */
1.53 brouard 3591: double agedeb, agefin,hf;
3592: double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;
3593:
3594: double fret;
3595: double **xi,tmp,delta;
3596:
3597: double dum; /* Dummy variable */
3598: double ***p3mat;
3599: double ***mobaverage;
3600: int *indx;
3601: char line[MAXLINE], linepar[MAXLINE];
1.85 ! brouard 3602: char path[132],pathc[132],pathcd[132],pathtot[132],model[132];
1.53 brouard 3603: int firstobs=1, lastobs=10;
3604: int sdeb, sfin; /* Status at beginning and end */
3605: int c, h , cpt,l;
3606: int ju,jl, mi;
3607: int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;
1.59 brouard 3608: int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,*tab;
1.69 brouard 3609: int mobilavproj=0 , prevfcast=0 ; /* moving average of prev, If prevfcast=1 prevalence projection */
1.53 brouard 3610: int mobilav=0,popforecast=0;
3611: int hstepm, nhstepm;
1.74 brouard 3612: double jprev1=1, mprev1=1,anprev1=2000,jprev2=1, mprev2=1,anprev2=2000;
3613: double jpyram=1, mpyram=1,anpyram=2000,jpyram1=1, mpyram1=1,anpyram1=2000;
1.53 brouard 3614:
3615: double bage, fage, age, agelim, agebase;
3616: double ftolpl=FTOL;
3617: double **prlim;
3618: double *severity;
3619: double ***param; /* Matrix of parameters */
3620: double *p;
3621: double **matcov; /* Matrix of covariance */
3622: double ***delti3; /* Scale */
3623: double *delti; /* Scale */
3624: double ***eij, ***vareij;
3625: double **varpl; /* Variances of prevalence limits by age */
3626: double *epj, vepp;
3627: double kk1, kk2;
1.74 brouard 3628: double dateprev1, dateprev2,jproj1=1,mproj1=1,anproj1=2000,jproj2=1,mproj2=1,anproj2=2000;
1.53 brouard 3629:
3630: char *alph[]={"a","a","b","c","d","e"}, str[4];
3631:
3632:
3633: char z[1]="c", occ;
3634: #include <sys/time.h>
3635: #include <time.h>
3636: char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];
1.85 ! brouard 3637: char *strt, *strtend;
! 3638: char *stratrunc;
! 3639: int lstra;
! 3640:
! 3641: long total_usecs;
! 3642: struct timeval start_time, end_time, curr_time;
! 3643: struct timezone tzp;
! 3644: extern int gettimeofday();
! 3645: struct tm tmg, tm, *gmtime(), *localtime();
! 3646: long time_value;
! 3647: extern long time();
1.53 brouard 3648:
1.85 ! brouard 3649: /* gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */
! 3650: (void) gettimeofday(&start_time,&tzp);
! 3651: tm = *localtime(&start_time.tv_sec);
! 3652: tmg = *gmtime(&start_time.tv_sec);
! 3653: strt=asctime(&tm);
! 3654: /* printf("Localtime (at start)=%s",strt); */
! 3655: /* tp.tv_sec = tp.tv_sec +86400; */
! 3656: /* tm = *localtime(&start_time.tv_sec); */
! 3657: /* tmg.tm_year=tmg.tm_year +dsign*dyear; */
! 3658: /* tmg.tm_mon=tmg.tm_mon +dsign*dmonth; */
! 3659: /* tmg.tm_hour=tmg.tm_hour + 1; */
! 3660: /* tp.tv_sec = mktime(&tmg); */
! 3661: /* strt=asctime(&tmg); */
! 3662: /* printf("Time(after) =%s",strt); */
! 3663: /* (void) time (&time_value);
! 3664: * printf("time=%d,t-=%d\n",time_value,time_value-86400);
! 3665: * tm = *localtime(&time_value);
! 3666: * strt=asctime(&tm);
! 3667: * printf("tim_value=%d,asctime=%s\n",time_value,strt);
! 3668: */
! 3669:
1.53 brouard 3670: getcwd(pathcd, size);
3671:
1.81 brouard 3672: printf("\n%s\n%s",version,fullversion);
1.53 brouard 3673: if(argc <=1){
3674: printf("\nEnter the parameter file name: ");
3675: scanf("%s",pathtot);
3676: }
3677: else{
3678: strcpy(pathtot,argv[1]);
3679: }
1.85 ! brouard 3680: /*if(getcwd(pathcd, 132)!= NULL)printf ("Error pathcd\n");*/
1.53 brouard 3681: /*cygwin_split_path(pathtot,path,optionfile);
3682: printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/
3683: /* cutv(path,optionfile,pathtot,'\\');*/
3684:
3685: split(pathtot,path,optionfile,optionfilext,optionfilefiname);
1.85 ! brouard 3686: printf("pathtot=%s,\npath=%s,\noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
1.53 brouard 3687: chdir(path);
3688: replace(pathc,path);
3689:
1.59 brouard 3690: /*-------- arguments in the command line --------*/
1.53 brouard 3691:
3692: /* Log file */
3693: strcat(filelog, optionfilefiname);
3694: strcat(filelog,".log"); /* */
3695: if((ficlog=fopen(filelog,"w"))==NULL) {
3696: printf("Problem with logfile %s\n",filelog);
3697: goto end;
3698: }
3699: fprintf(ficlog,"Log filename:%s\n",filelog);
1.85 ! brouard 3700: fprintf(ficlog,"\n%s\n%s",version,fullversion);
1.53 brouard 3701: fprintf(ficlog,"\nEnter the parameter file name: ");
3702: fprintf(ficlog,"pathtot=%s, path=%s, optionfile=%s optionfilext=%s optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
1.85 ! brouard 3703: printf("Localtime (at start)=%s",strt);
! 3704: fprintf(ficlog,"Localtime (at start)=%s",strt);
1.53 brouard 3705: fflush(ficlog);
3706:
3707: /* */
3708: strcpy(fileres,"r");
3709: strcat(fileres, optionfilefiname);
3710: strcat(fileres,".txt"); /* Other files have txt extension */
3711:
3712: /*---------arguments file --------*/
3713:
3714: if((ficpar=fopen(optionfile,"r"))==NULL) {
3715: printf("Problem with optionfile %s\n",optionfile);
3716: fprintf(ficlog,"Problem with optionfile %s\n",optionfile);
1.85 ! brouard 3717: fflush(ficlog);
1.53 brouard 3718: goto end;
3719: }
3720:
3721: strcpy(filereso,"o");
3722: strcat(filereso,fileres);
3723: if((ficparo=fopen(filereso,"w"))==NULL) {
3724: printf("Problem with Output resultfile: %s\n", filereso);
3725: fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso);
1.85 ! brouard 3726: fflush(ficlog);
1.53 brouard 3727: goto end;
3728: }
3729:
3730: /* Reads comments: lines beginning with '#' */
1.85 ! brouard 3731: numlinepar=0;
1.53 brouard 3732: while((c=getc(ficpar))=='#' && c!= EOF){
3733: ungetc(c,ficpar);
3734: fgets(line, MAXLINE, ficpar);
1.85 ! brouard 3735: numlinepar++;
1.53 brouard 3736: puts(line);
3737: fputs(line,ficparo);
1.85 ! brouard 3738: fputs(line,ficlog);
1.53 brouard 3739: }
3740: ungetc(c,ficpar);
3741:
3742: 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);
1.85 ! brouard 3743: numlinepar++;
1.53 brouard 3744: 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);
3745: 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);
1.85 ! brouard 3746: fprintf(ficlog,"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);
! 3747: fflush(ficlog);
1.59 brouard 3748: while((c=getc(ficpar))=='#' && c!= EOF){
1.53 brouard 3749: ungetc(c,ficpar);
3750: fgets(line, MAXLINE, ficpar);
1.85 ! brouard 3751: numlinepar++;
1.53 brouard 3752: puts(line);
3753: fputs(line,ficparo);
1.85 ! brouard 3754: fputs(line,ficlog);
1.53 brouard 3755: }
3756: ungetc(c,ficpar);
1.85 ! brouard 3757:
1.53 brouard 3758:
3759: covar=matrix(0,NCOVMAX,1,n);
1.58 lievre 3760: cptcovn=0; /*Number of covariates, i.e. number of '+' in model statement*/
1.53 brouard 3761: if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;
3762:
1.58 lievre 3763: ncovmodel=2+cptcovn; /*Number of variables = cptcovn + intercept + age */
1.53 brouard 3764: nvar=ncovmodel-1; /* Suppressing age as a basic covariate */
3765:
3766: /* Read guess parameters */
3767: /* Reads comments: lines beginning with '#' */
3768: while((c=getc(ficpar))=='#' && c!= EOF){
3769: ungetc(c,ficpar);
3770: fgets(line, MAXLINE, ficpar);
1.85 ! brouard 3771: numlinepar++;
1.53 brouard 3772: puts(line);
3773: fputs(line,ficparo);
1.85 ! brouard 3774: fputs(line,ficlog);
1.53 brouard 3775: }
3776: ungetc(c,ficpar);
1.85 ! brouard 3777:
1.53 brouard 3778: param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
1.85 ! brouard 3779: for(i=1; i <=nlstate; i++){
! 3780: j=0;
! 3781: for(jj=1; jj <=nlstate+ndeath; jj++){
! 3782: if(jj==i) continue;
! 3783: j++;
1.53 brouard 3784: fscanf(ficpar,"%1d%1d",&i1,&j1);
1.85 ! brouard 3785: if ((i1 != i) && (j1 != j)){
! 3786: printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n",numlinepar, i,j, i1, j1);
! 3787: exit(1);
! 3788: }
1.53 brouard 3789: fprintf(ficparo,"%1d%1d",i1,j1);
3790: if(mle==1)
3791: printf("%1d%1d",i,j);
3792: fprintf(ficlog,"%1d%1d",i,j);
3793: for(k=1; k<=ncovmodel;k++){
3794: fscanf(ficpar," %lf",¶m[i][j][k]);
3795: if(mle==1){
3796: printf(" %lf",param[i][j][k]);
3797: fprintf(ficlog," %lf",param[i][j][k]);
3798: }
3799: else
3800: fprintf(ficlog," %lf",param[i][j][k]);
3801: fprintf(ficparo," %lf",param[i][j][k]);
3802: }
3803: fscanf(ficpar,"\n");
1.85 ! brouard 3804: numlinepar++;
1.53 brouard 3805: if(mle==1)
3806: printf("\n");
3807: fprintf(ficlog,"\n");
3808: fprintf(ficparo,"\n");
3809: }
1.85 ! brouard 3810: }
! 3811: fflush(ficlog);
! 3812:
1.59 brouard 3813: npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/
1.53 brouard 3814:
3815: p=param[1][1];
3816:
3817: /* Reads comments: lines beginning with '#' */
3818: while((c=getc(ficpar))=='#' && c!= EOF){
3819: ungetc(c,ficpar);
3820: fgets(line, MAXLINE, ficpar);
1.85 ! brouard 3821: numlinepar++;
1.53 brouard 3822: puts(line);
3823: fputs(line,ficparo);
1.85 ! brouard 3824: fputs(line,ficlog);
1.53 brouard 3825: }
3826: ungetc(c,ficpar);
3827:
3828: delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
1.74 brouard 3829: /* delti=vector(1,npar); *//* Scale of each paramater (output from hesscov) */
1.53 brouard 3830: for(i=1; i <=nlstate; i++){
3831: for(j=1; j <=nlstate+ndeath-1; j++){
3832: fscanf(ficpar,"%1d%1d",&i1,&j1);
1.85 ! brouard 3833: if ((i1-i)*(j1-j)!=0){
! 3834: printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n",numlinepar, i,j, i1, j1);
! 3835: exit(1);
! 3836: }
1.53 brouard 3837: printf("%1d%1d",i,j);
3838: fprintf(ficparo,"%1d%1d",i1,j1);
1.85 ! brouard 3839: fprintf(ficlog,"%1d%1d",i1,j1);
1.53 brouard 3840: for(k=1; k<=ncovmodel;k++){
3841: fscanf(ficpar,"%le",&delti3[i][j][k]);
3842: printf(" %le",delti3[i][j][k]);
3843: fprintf(ficparo," %le",delti3[i][j][k]);
1.85 ! brouard 3844: fprintf(ficlog," %le",delti3[i][j][k]);
1.53 brouard 3845: }
3846: fscanf(ficpar,"\n");
1.85 ! brouard 3847: numlinepar++;
1.53 brouard 3848: printf("\n");
3849: fprintf(ficparo,"\n");
1.85 ! brouard 3850: fprintf(ficlog,"\n");
1.53 brouard 3851: }
3852: }
1.85 ! brouard 3853: fflush(ficlog);
! 3854:
1.53 brouard 3855: delti=delti3[1][1];
1.74 brouard 3856:
3857:
3858: /* 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 3859:
3860: /* Reads comments: lines beginning with '#' */
3861: while((c=getc(ficpar))=='#' && c!= EOF){
3862: ungetc(c,ficpar);
3863: fgets(line, MAXLINE, ficpar);
1.85 ! brouard 3864: numlinepar++;
1.53 brouard 3865: puts(line);
3866: fputs(line,ficparo);
1.85 ! brouard 3867: fputs(line,ficlog);
1.53 brouard 3868: }
3869: ungetc(c,ficpar);
3870:
3871: matcov=matrix(1,npar,1,npar);
3872: for(i=1; i <=npar; i++){
3873: fscanf(ficpar,"%s",&str);
3874: if(mle==1)
3875: printf("%s",str);
3876: fprintf(ficlog,"%s",str);
3877: fprintf(ficparo,"%s",str);
3878: for(j=1; j <=i; j++){
3879: fscanf(ficpar," %le",&matcov[i][j]);
3880: if(mle==1){
3881: printf(" %.5le",matcov[i][j]);
3882: }
1.85 ! brouard 3883: fprintf(ficlog," %.5le",matcov[i][j]);
1.53 brouard 3884: fprintf(ficparo," %.5le",matcov[i][j]);
3885: }
3886: fscanf(ficpar,"\n");
1.85 ! brouard 3887: numlinepar++;
1.53 brouard 3888: if(mle==1)
3889: printf("\n");
3890: fprintf(ficlog,"\n");
3891: fprintf(ficparo,"\n");
3892: }
3893: for(i=1; i <=npar; i++)
3894: for(j=i+1;j<=npar;j++)
3895: matcov[i][j]=matcov[j][i];
3896:
3897: if(mle==1)
3898: printf("\n");
3899: fprintf(ficlog,"\n");
3900:
1.85 ! brouard 3901: fflush(ficlog);
1.53 brouard 3902:
1.59 brouard 3903: /*-------- Rewriting paramater file ----------*/
3904: strcpy(rfileres,"r"); /* "Rparameterfile */
3905: strcat(rfileres,optionfilefiname); /* Parameter file first name*/
3906: strcat(rfileres,"."); /* */
3907: strcat(rfileres,optionfilext); /* Other files have txt extension */
3908: if((ficres =fopen(rfileres,"w"))==NULL) {
3909: printf("Problem writing new parameter file: %s\n", fileres);goto end;
3910: fprintf(ficlog,"Problem writing new parameter file: %s\n", fileres);goto end;
3911: }
3912: fprintf(ficres,"#%s\n",version);
1.53 brouard 3913:
1.59 brouard 3914: /*-------- data file ----------*/
3915: if((fic=fopen(datafile,"r"))==NULL) {
3916: printf("Problem with datafile: %s\n", datafile);goto end;
3917: fprintf(ficlog,"Problem with datafile: %s\n", datafile);goto end;
3918: }
3919:
3920: n= lastobs;
3921: severity = vector(1,maxwav);
3922: outcome=imatrix(1,maxwav+1,1,n);
1.85 ! brouard 3923: num=lvector(1,n);
1.59 brouard 3924: moisnais=vector(1,n);
3925: annais=vector(1,n);
3926: moisdc=vector(1,n);
3927: andc=vector(1,n);
3928: agedc=vector(1,n);
3929: cod=ivector(1,n);
3930: weight=vector(1,n);
3931: for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */
3932: mint=matrix(1,maxwav,1,n);
3933: anint=matrix(1,maxwav,1,n);
3934: s=imatrix(1,maxwav+1,1,n);
3935: tab=ivector(1,NCOVMAX);
3936: ncodemax=ivector(1,8);
3937:
3938: i=1;
3939: while (fgets(line, MAXLINE, fic) != NULL) {
3940: if ((i >= firstobs) && (i <=lastobs)) {
1.53 brouard 3941:
1.59 brouard 3942: for (j=maxwav;j>=1;j--){
3943: cutv(stra, strb,line,' '); s[j][i]=atoi(strb);
3944: strcpy(line,stra);
3945: cutv(stra, strb,line,'/'); anint[j][i]=(double)(atoi(strb)); strcpy(line,stra);
3946: cutv(stra, strb,line,' '); mint[j][i]=(double)(atoi(strb)); strcpy(line,stra);
3947: }
1.53 brouard 3948:
1.59 brouard 3949: cutv(stra, strb,line,'/'); andc[i]=(double)(atoi(strb)); strcpy(line,stra);
3950: cutv(stra, strb,line,' '); moisdc[i]=(double)(atoi(strb)); strcpy(line,stra);
1.53 brouard 3951:
1.59 brouard 3952: cutv(stra, strb,line,'/'); annais[i]=(double)(atoi(strb)); strcpy(line,stra);
3953: cutv(stra, strb,line,' '); moisnais[i]=(double)(atoi(strb)); strcpy(line,stra);
1.53 brouard 3954:
1.59 brouard 3955: cutv(stra, strb,line,' '); weight[i]=(double)(atoi(strb)); strcpy(line,stra);
3956: for (j=ncovcol;j>=1;j--){
3957: cutv(stra, strb,line,' '); covar[j][i]=(double)(atoi(strb)); strcpy(line,stra);
3958: }
1.85 ! brouard 3959: lstra=strlen(stra);
! 3960: if(lstra > 9){ /* More than 2**32 or max of what printf can write with %ld */
! 3961: stratrunc = &(stra[lstra-9]);
! 3962: num[i]=atol(stratrunc);
! 3963: }
! 3964: else
! 3965: num[i]=atol(stra);
1.53 brouard 3966:
1.59 brouard 3967: /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){
1.85 ! brouard 3968: printf("%ld %.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 3969:
1.59 brouard 3970: i=i+1;
3971: }
3972: }
3973: /* printf("ii=%d", ij);
3974: scanf("%d",i);*/
1.53 brouard 3975: imx=i-1; /* Number of individuals */
3976:
3977: /* for (i=1; i<=imx; i++){
3978: if ((s[1][i]==3) && (s[2][i]==2)) s[2][i]=3;
3979: if ((s[2][i]==3) && (s[3][i]==2)) s[3][i]=3;
3980: if ((s[3][i]==3) && (s[4][i]==2)) s[4][i]=3;
3981: }*/
3982: /* for (i=1; i<=imx; i++){
3983: if (s[4][i]==9) s[4][i]=-1;
1.85 ! brouard 3984: printf("%ld %.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]));}*/
1.53 brouard 3985:
1.71 brouard 3986: for (i=1; i<=imx; i++)
1.53 brouard 3987:
1.71 brouard 3988: /*if ((s[3][i]==3) || (s[4][i]==3)) weight[i]=0.08;
3989: else weight[i]=1;*/
3990:
1.53 brouard 3991: /* Calculation of the number of parameter from char model*/
3992: Tvar=ivector(1,15); /* stores the number n of the covariates in Vm+Vn at 1 and m at 2 */
3993: Tprod=ivector(1,15);
3994: Tvaraff=ivector(1,15);
3995: Tvard=imatrix(1,15,1,2);
3996: Tage=ivector(1,15);
3997:
1.58 lievre 3998: if (strlen(model) >1){ /* If there is at least 1 covariate */
1.53 brouard 3999: j=0, j1=0, k1=1, k2=1;
1.58 lievre 4000: j=nbocc(model,'+'); /* j=Number of '+' */
4001: j1=nbocc(model,'*'); /* j1=Number of '*' */
4002: cptcovn=j+1;
4003: cptcovprod=j1; /*Number of products */
1.53 brouard 4004:
4005: strcpy(modelsav,model);
4006: if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){
4007: printf("Error. Non available option model=%s ",model);
4008: fprintf(ficlog,"Error. Non available option model=%s ",model);
4009: goto end;
4010: }
4011:
1.59 brouard 4012: /* This loop fills the array Tvar from the string 'model'.*/
1.58 lievre 4013:
1.53 brouard 4014: for(i=(j+1); i>=1;i--){
4015: cutv(stra,strb,modelsav,'+'); /* keeps in strb after the last + */
1.59 brouard 4016: if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyzes it */
1.53 brouard 4017: /* printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/
4018: /*scanf("%d",i);*/
4019: if (strchr(strb,'*')) { /* Model includes a product */
4020: cutv(strd,strc,strb,'*'); /* strd*strc Vm*Vn (if not *age)*/
4021: if (strcmp(strc,"age")==0) { /* Vn*age */
4022: cptcovprod--;
4023: cutv(strb,stre,strd,'V');
4024: Tvar[i]=atoi(stre); /* computes n in Vn and stores in Tvar*/
4025: cptcovage++;
4026: Tage[cptcovage]=i;
4027: /*printf("stre=%s ", stre);*/
4028: }
4029: else if (strcmp(strd,"age")==0) { /* or age*Vn */
4030: cptcovprod--;
4031: cutv(strb,stre,strc,'V');
4032: Tvar[i]=atoi(stre);
4033: cptcovage++;
4034: Tage[cptcovage]=i;
4035: }
4036: else { /* Age is not in the model */
4037: cutv(strb,stre,strc,'V'); /* strc= Vn, stre is n*/
4038: Tvar[i]=ncovcol+k1;
4039: cutv(strb,strc,strd,'V'); /* strd was Vm, strc is m */
4040: Tprod[k1]=i;
4041: Tvard[k1][1]=atoi(strc); /* m*/
4042: Tvard[k1][2]=atoi(stre); /* n */
4043: Tvar[cptcovn+k2]=Tvard[k1][1];
4044: Tvar[cptcovn+k2+1]=Tvard[k1][2];
4045: for (k=1; k<=lastobs;k++)
4046: covar[ncovcol+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];
4047: k1++;
4048: k2=k2+2;
4049: }
4050: }
4051: else { /* no more sum */
4052: /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/
4053: /* scanf("%d",i);*/
4054: cutv(strd,strc,strb,'V');
4055: Tvar[i]=atoi(strc);
4056: }
4057: strcpy(modelsav,stra);
4058: /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);
4059: scanf("%d",i);*/
4060: } /* end of loop + */
4061: } /* end model */
4062:
1.58 lievre 4063: /*The number n of Vn is stored in Tvar. cptcovage =number of age covariate. Tage gives the position of age. cptcovprod= number of products.
4064: If model=V1+V1*age then Tvar[1]=1 Tvar[2]=1 cptcovage=1 Tage[1]=2 cptcovprod=0*/
4065:
1.53 brouard 4066: /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);
4067: printf("cptcovprod=%d ", cptcovprod);
4068: fprintf(ficlog,"cptcovprod=%d ", cptcovprod);
1.58 lievre 4069:
4070: scanf("%d ",i);
4071: fclose(fic);*/
1.53 brouard 4072:
4073: /* if(mle==1){*/
1.59 brouard 4074: if (weightopt != 1) { /* Maximisation without weights*/
4075: for(i=1;i<=n;i++) weight[i]=1.0;
4076: }
1.53 brouard 4077: /*-calculation of age at interview from date of interview and age at death -*/
1.59 brouard 4078: agev=matrix(1,maxwav,1,imx);
1.53 brouard 4079:
1.59 brouard 4080: for (i=1; i<=imx; i++) {
4081: for(m=2; (m<= maxwav); m++) {
1.76 brouard 4082: if (((int)mint[m][i]== 99) && (s[m][i] <= nlstate)){
1.59 brouard 4083: anint[m][i]=9999;
4084: s[m][i]=-1;
4085: }
1.76 brouard 4086: if((int)moisdc[i]==99 && (int)andc[i]==9999 && s[m][i]>nlstate){
1.85 ! brouard 4087: printf("Error! Date of death (month %2d and year %4d) of individual %ld 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);
! 4088: fprintf(ficlog,"Error! Date of death (month %2d and year %4d) of individual %ld 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 4089: s[m][i]=-1;
4090: }
4091: if((int)moisdc[i]==99 && (int)andc[i]!=9999 && s[m][i]>nlstate){
1.85 ! brouard 4092: printf("Error! Month of death of individual %ld 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]);
! 4093: fprintf(ficlog,"Error! Month of death of individual %ld 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 4094: s[m][i]=-1; /* We prefer to skip it (and to skip it in version 0.8a1 too */
1.76 brouard 4095: }
1.53 brouard 4096: }
1.59 brouard 4097: }
1.53 brouard 4098:
1.59 brouard 4099: for (i=1; i<=imx; i++) {
4100: agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);
1.71 brouard 4101: for(m=firstpass; (m<= lastpass); m++){
1.69 brouard 4102: if(s[m][i] >0){
1.59 brouard 4103: if (s[m][i] >= nlstate+1) {
4104: if(agedc[i]>0)
1.76 brouard 4105: if((int)moisdc[i]!=99 && (int)andc[i]!=9999)
1.69 brouard 4106: agev[m][i]=agedc[i];
1.59 brouard 4107: /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/
4108: else {
1.76 brouard 4109: if ((int)andc[i]!=9999){
1.85 ! brouard 4110: printf("Warning negative age at death: %ld line:%d\n",num[i],i);
! 4111: fprintf(ficlog,"Warning negative age at death: %ld line:%d\n",num[i],i);
1.59 brouard 4112: agev[m][i]=-1;
1.53 brouard 4113: }
4114: }
1.70 brouard 4115: }
1.69 brouard 4116: else if(s[m][i] !=9){ /* Standard case, age in fractional
4117: years but with the precision of a
4118: month */
1.59 brouard 4119: agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);
1.76 brouard 4120: if((int)mint[m][i]==99 || (int)anint[m][i]==9999)
1.59 brouard 4121: agev[m][i]=1;
4122: else if(agev[m][i] <agemin){
4123: agemin=agev[m][i];
4124: /*printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], agemin);*/
1.53 brouard 4125: }
1.59 brouard 4126: else if(agev[m][i] >agemax){
4127: agemax=agev[m][i];
4128: /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/
1.53 brouard 4129: }
1.59 brouard 4130: /*agev[m][i]=anint[m][i]-annais[i];*/
4131: /* agev[m][i] = age[i]+2*m;*/
1.53 brouard 4132: }
1.59 brouard 4133: else { /* =9 */
1.53 brouard 4134: agev[m][i]=1;
1.59 brouard 4135: s[m][i]=-1;
4136: }
1.53 brouard 4137: }
1.59 brouard 4138: else /*= 0 Unknown */
4139: agev[m][i]=1;
4140: }
1.53 brouard 4141:
1.59 brouard 4142: }
4143: for (i=1; i<=imx; i++) {
1.71 brouard 4144: for(m=firstpass; (m<=lastpass); m++){
1.59 brouard 4145: if (s[m][i] > (nlstate+ndeath)) {
4146: 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);
4147: 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);
4148: goto end;
1.53 brouard 4149: }
4150: }
1.59 brouard 4151: }
1.53 brouard 4152:
1.71 brouard 4153: /*for (i=1; i<=imx; i++){
4154: for (m=firstpass; (m<lastpass); m++){
1.85 ! brouard 4155: printf("%ld %d %.lf %d %d\n", num[i],(covar[1][i]),agev[m][i],s[m][i],s[m+1][i]);
1.71 brouard 4156: }
4157:
4158: }*/
4159:
1.59 brouard 4160: printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);
4161: fprintf(ficlog,"Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);
4162:
4163: free_vector(severity,1,maxwav);
4164: free_imatrix(outcome,1,maxwav+1,1,n);
4165: free_vector(moisnais,1,n);
4166: free_vector(annais,1,n);
4167: /* free_matrix(mint,1,maxwav,1,n);
4168: free_matrix(anint,1,maxwav,1,n);*/
4169: free_vector(moisdc,1,n);
4170: free_vector(andc,1,n);
1.53 brouard 4171:
4172:
1.59 brouard 4173: wav=ivector(1,imx);
4174: dh=imatrix(1,lastpass-firstpass+1,1,imx);
4175: bh=imatrix(1,lastpass-firstpass+1,1,imx);
4176: mw=imatrix(1,lastpass-firstpass+1,1,imx);
1.69 brouard 4177:
1.59 brouard 4178: /* Concatenates waves */
4179: concatwav(wav, dh, bh, mw, s, agedc, agev, firstpass, lastpass, imx, nlstate, stepm);
1.53 brouard 4180:
1.59 brouard 4181: /* Routine tricode is to calculate cptcoveff (real number of unique covariates) and to associate covariable number and modality */
1.53 brouard 4182:
1.59 brouard 4183: Tcode=ivector(1,100);
4184: nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);
4185: ncodemax[1]=1;
4186: if (cptcovn > 0) tricode(Tvar,nbcode,imx);
1.53 brouard 4187:
1.59 brouard 4188: codtab=imatrix(1,100,1,10); /* Cross tabulation to get the order of
4189: the estimations*/
4190: h=0;
4191: m=pow(2,cptcoveff);
1.53 brouard 4192:
1.59 brouard 4193: for(k=1;k<=cptcoveff; k++){
4194: for(i=1; i <=(m/pow(2,k));i++){
4195: for(j=1; j <= ncodemax[k]; j++){
4196: for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){
4197: h++;
4198: if (h>m) h=1;codtab[h][k]=j;codtab[h][Tvar[k]]=j;
4199: /* printf("h=%d k=%d j=%d codtab[h][k]=%d tvar[k]=%d \n",h, k,j,codtab[h][k],Tvar[k]);*/
4200: }
4201: }
4202: }
4203: }
4204: /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]);
4205: codtab[1][2]=1;codtab[2][2]=2; */
4206: /* for(i=1; i <=m ;i++){
4207: for(k=1; k <=cptcovn; k++){
4208: printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);
4209: }
4210: printf("\n");
1.53 brouard 4211: }
1.59 brouard 4212: scanf("%d",i);*/
1.53 brouard 4213:
1.59 brouard 4214: /* Calculates basic frequencies. Computes observed prevalence at single age
4215: and prints on file fileres'p'. */
1.84 brouard 4216: freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint);
1.53 brouard 4217:
1.60 brouard 4218: pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
4219: oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
4220: newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
4221: savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
4222: oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */
1.53 brouard 4223:
4224:
1.59 brouard 4225: /* For Powell, parameters are in a vector p[] starting at p[1]
4226: so we point p on param[1][1] so that p[1] maps on param[1][1][1] */
4227: p=param[1][1]; /* *(*(*(param +1)+1)+0) */
1.53 brouard 4228:
1.85 ! brouard 4229: globpr=0; /* To get ipmx number of contributions and sum of weights*/
! 4230: likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
! 4231: printf("First Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
! 4232: for (k=1; k<=npar;k++)
! 4233: printf(" %d %8.5f",k,p[k]);
! 4234: printf("\n");
! 4235: globpr=1; /* to print the contributions */
! 4236: likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
! 4237: printf("Second Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
! 4238: for (k=1; k<=npar;k++)
! 4239: printf(" %d %8.5f",k,p[k]);
! 4240: printf("\n");
1.61 brouard 4241: if(mle>=1){ /* Could be 1 or 2 */
1.53 brouard 4242: mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);
1.59 brouard 4243: }
1.53 brouard 4244:
1.59 brouard 4245: /*--------- results files --------------*/
4246: 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 4247:
4248:
1.59 brouard 4249: jk=1;
4250: fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
4251: printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
4252: fprintf(ficlog,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
4253: for(i=1,jk=1; i <=nlstate; i++){
4254: for(k=1; k <=(nlstate+ndeath); k++){
4255: if (k != i)
4256: {
4257: printf("%d%d ",i,k);
4258: fprintf(ficlog,"%d%d ",i,k);
4259: fprintf(ficres,"%1d%1d ",i,k);
4260: for(j=1; j <=ncovmodel; j++){
4261: printf("%f ",p[jk]);
4262: fprintf(ficlog,"%f ",p[jk]);
4263: fprintf(ficres,"%f ",p[jk]);
4264: jk++;
4265: }
4266: printf("\n");
4267: fprintf(ficlog,"\n");
4268: fprintf(ficres,"\n");
4269: }
4270: }
4271: }
1.84 brouard 4272: if(mle!=0){
1.59 brouard 4273: /* Computing hessian and covariance matrix */
4274: ftolhess=ftol; /* Usually correct */
4275: hesscov(matcov, p, npar, delti, ftolhess, func);
4276: }
4277: fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");
4278: printf("# Scales (for hessian or gradient estimation)\n");
4279: fprintf(ficlog,"# Scales (for hessian or gradient estimation)\n");
4280: for(i=1,jk=1; i <=nlstate; i++){
4281: for(j=1; j <=nlstate+ndeath; j++){
4282: if (j!=i) {
4283: fprintf(ficres,"%1d%1d",i,j);
4284: printf("%1d%1d",i,j);
4285: fprintf(ficlog,"%1d%1d",i,j);
4286: for(k=1; k<=ncovmodel;k++){
4287: printf(" %.5e",delti[jk]);
4288: fprintf(ficlog," %.5e",delti[jk]);
4289: fprintf(ficres," %.5e",delti[jk]);
4290: jk++;
4291: }
4292: printf("\n");
4293: fprintf(ficlog,"\n");
4294: fprintf(ficres,"\n");
4295: }
4296: }
4297: }
1.53 brouard 4298:
1.59 brouard 4299: 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");
4300: if(mle==1)
4301: 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");
4302: 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");
4303: for(i=1,k=1;i<=npar;i++){
4304: /* if (k>nlstate) k=1;
4305: i1=(i-1)/(ncovmodel*nlstate)+1;
4306: fprintf(ficres,"%s%d%d",alph[k],i1,tab[i]);
4307: printf("%s%d%d",alph[k],i1,tab[i]);
4308: */
4309: fprintf(ficres,"%3d",i);
4310: if(mle==1)
4311: printf("%3d",i);
4312: fprintf(ficlog,"%3d",i);
4313: for(j=1; j<=i;j++){
4314: fprintf(ficres," %.5e",matcov[i][j]);
4315: if(mle==1)
4316: printf(" %.5e",matcov[i][j]);
4317: fprintf(ficlog," %.5e",matcov[i][j]);
4318: }
4319: fprintf(ficres,"\n");
4320: if(mle==1)
4321: printf("\n");
4322: fprintf(ficlog,"\n");
4323: k++;
4324: }
1.53 brouard 4325:
1.59 brouard 4326: while((c=getc(ficpar))=='#' && c!= EOF){
4327: ungetc(c,ficpar);
4328: fgets(line, MAXLINE, ficpar);
4329: puts(line);
4330: fputs(line,ficparo);
4331: }
4332: ungetc(c,ficpar);
4333:
4334: estepm=0;
4335: fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm);
4336: if (estepm==0 || estepm < stepm) estepm=stepm;
4337: if (fage <= 2) {
4338: bage = ageminpar;
4339: fage = agemaxpar;
4340: }
1.53 brouard 4341:
1.59 brouard 4342: fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");
4343: fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
4344: fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
1.53 brouard 4345:
1.59 brouard 4346: while((c=getc(ficpar))=='#' && c!= EOF){
4347: ungetc(c,ficpar);
4348: fgets(line, MAXLINE, ficpar);
4349: puts(line);
4350: fputs(line,ficparo);
4351: }
4352: ungetc(c,ficpar);
1.53 brouard 4353:
1.59 brouard 4354: 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);
4355: 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);
4356: 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 4357: printf("begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
4358: 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 4359:
1.59 brouard 4360: while((c=getc(ficpar))=='#' && c!= EOF){
4361: ungetc(c,ficpar);
4362: fgets(line, MAXLINE, ficpar);
4363: puts(line);
4364: fputs(line,ficparo);
4365: }
4366: ungetc(c,ficpar);
1.53 brouard 4367:
4368:
1.70 brouard 4369: dateprev1=anprev1+(mprev1-1)/12.+(jprev1-1)/365.;
4370: dateprev2=anprev2+(mprev2-1)/12.+(jprev2-1)/365.;
1.53 brouard 4371:
4372: fscanf(ficpar,"pop_based=%d\n",&popbased);
4373: fprintf(ficparo,"pop_based=%d\n",popbased);
4374: fprintf(ficres,"pop_based=%d\n",popbased);
4375:
4376: while((c=getc(ficpar))=='#' && c!= EOF){
4377: ungetc(c,ficpar);
4378: fgets(line, MAXLINE, ficpar);
4379: puts(line);
4380: fputs(line,ficparo);
4381: }
4382: ungetc(c,ficpar);
4383:
1.69 brouard 4384: 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 4385: 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 4386: 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);
4387: 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);
4388: 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 4389: /* day and month of proj2 are not used but only year anproj2.*/
1.53 brouard 4390:
1.59 brouard 4391: while((c=getc(ficpar))=='#' && c!= EOF){
1.53 brouard 4392: ungetc(c,ficpar);
4393: fgets(line, MAXLINE, ficpar);
4394: puts(line);
4395: fputs(line,ficparo);
4396: }
4397: ungetc(c,ficpar);
4398:
4399: fscanf(ficpar,"popforecast=%d popfile=%s popfiledate=%lf/%lf/%lf last-popfiledate=%lf/%lf/%lf\n",&popforecast,popfile,&jpyram,&mpyram,&anpyram,&jpyram1,&mpyram1,&anpyram1);
4400: fprintf(ficparo,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);
4401: fprintf(ficres,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);
4402:
1.84 brouard 4403: freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint);
4404: /*,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
1.58 lievre 4405:
1.59 brouard 4406: /*------------ gnuplot -------------*/
4407: strcpy(optionfilegnuplot,optionfilefiname);
4408: strcat(optionfilegnuplot,".gp");
4409: if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {
4410: printf("Problem with file %s",optionfilegnuplot);
4411: }
4412: else{
4413: fprintf(ficgp,"\n# %s\n", version);
4414: fprintf(ficgp,"# %s\n", optionfilegnuplot);
4415: fprintf(ficgp,"set missing 'NaNq'\n");
4416: }
4417: fclose(ficgp);
4418: printinggnuplot(fileres, ageminpar,agemaxpar,fage, pathc,p);
4419: /*--------- index.htm --------*/
1.53 brouard 4420:
4421: strcpy(optionfilehtm,optionfile);
4422: strcat(optionfilehtm,".htm");
4423: if((fichtm=fopen(optionfilehtm,"w"))==NULL) {
4424: printf("Problem with %s \n",optionfilehtm), exit(0);
4425: }
4426:
1.85 ! brouard 4427: fprintf(fichtm,"<body> <font size=\"2\">%s </font> <hr size=\"2\" color=\"#EC5E5E\"> \n\
! 4428: Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n\
! 4429: \n\
! 4430: Total number of observations=%d <br>\n\
! 4431: Youngest age at first (selected) pass %.2f, oldest age %.2f<br>\n\
! 4432: Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n\
! 4433: <hr size=\"2\" color=\"#EC5E5E\">\
! 4434: <ul><li><h4>Parameter files</h4>\n\
! 4435: - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n\
! 4436: - Log file of the run: <a href=\"%s\">%s</a><br>\n\
! 4437: - Gnuplot file name: <a href=\"%s\">%s</a></ul>\n",\
! 4438: version,title,datafile,firstpass,lastpass,stepm, weightopt,\
! 4439: model,imx,agemin,agemax,jmin,jmax,jmean,fileres,fileres,\
! 4440: filelog,filelog,optionfilegnuplot,optionfilegnuplot);
! 4441: fclose(fichtm);
1.53 brouard 4442:
1.85 ! brouard 4443: printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,\
! 4444: model,imx,jmin,jmax,jmean,rfileres,popforecast,estepm,\
! 4445: jprev1,mprev1,anprev1,jprev2,mprev2,anprev2);
1.53 brouard 4446:
1.59 brouard 4447: /*------------ free_vector -------------*/
4448: chdir(path);
1.53 brouard 4449:
1.59 brouard 4450: free_ivector(wav,1,imx);
4451: free_imatrix(dh,1,lastpass-firstpass+1,1,imx);
4452: free_imatrix(bh,1,lastpass-firstpass+1,1,imx);
4453: free_imatrix(mw,1,lastpass-firstpass+1,1,imx);
1.85 ! brouard 4454: free_lvector(num,1,n);
1.59 brouard 4455: free_vector(agedc,1,n);
1.65 lievre 4456: /*free_matrix(covar,0,NCOVMAX,1,n);*/
1.59 brouard 4457: /*free_matrix(covar,1,NCOVMAX,1,n);*/
4458: fclose(ficparo);
4459: fclose(ficres);
1.53 brouard 4460:
4461:
1.54 brouard 4462: /*--------------- Prevalence limit (stable prevalence) --------------*/
1.53 brouard 4463:
4464: strcpy(filerespl,"pl");
4465: strcat(filerespl,fileres);
4466: if((ficrespl=fopen(filerespl,"w"))==NULL) {
1.54 brouard 4467: printf("Problem with stable prevalence resultfile: %s\n", filerespl);goto end;
4468: fprintf(ficlog,"Problem with stable prevalence resultfile: %s\n", filerespl);goto end;
1.53 brouard 4469: }
1.54 brouard 4470: printf("Computing stable prevalence: result on file '%s' \n", filerespl);
4471: fprintf(ficlog,"Computing stable prevalence: result on file '%s' \n", filerespl);
4472: fprintf(ficrespl,"#Stable prevalence \n");
1.53 brouard 4473: fprintf(ficrespl,"#Age ");
4474: for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);
4475: fprintf(ficrespl,"\n");
4476:
4477: prlim=matrix(1,nlstate,1,nlstate);
1.59 brouard 4478:
1.53 brouard 4479: agebase=ageminpar;
4480: agelim=agemaxpar;
4481: ftolpl=1.e-10;
4482: i1=cptcoveff;
4483: if (cptcovn < 1){i1=1;}
4484:
1.59 brouard 4485: for(cptcov=1,k=0;cptcov<=i1;cptcov++){
1.53 brouard 4486: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
1.59 brouard 4487: k=k+1;
4488: /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/
4489: fprintf(ficrespl,"\n#******");
4490: printf("\n#******");
4491: fprintf(ficlog,"\n#******");
4492: for(j=1;j<=cptcoveff;j++) {
4493: fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
4494: printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
4495: fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
4496: }
4497: fprintf(ficrespl,"******\n");
4498: printf("******\n");
4499: fprintf(ficlog,"******\n");
1.53 brouard 4500:
1.59 brouard 4501: for (age=agebase; age<=agelim; age++){
4502: prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
1.69 brouard 4503: fprintf(ficrespl,"%.0f ",age );
4504: for(j=1;j<=cptcoveff;j++)
4505: fprintf(ficrespl,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
1.59 brouard 4506: for(i=1; i<=nlstate;i++)
1.53 brouard 4507: fprintf(ficrespl," %.5f", prlim[i][i]);
1.59 brouard 4508: fprintf(ficrespl,"\n");
1.53 brouard 4509: }
4510: }
1.59 brouard 4511: }
1.53 brouard 4512: fclose(ficrespl);
4513:
4514: /*------------- h Pij x at various ages ------------*/
4515:
4516: strcpy(filerespij,"pij"); strcat(filerespij,fileres);
4517: if((ficrespij=fopen(filerespij,"w"))==NULL) {
4518: printf("Problem with Pij resultfile: %s\n", filerespij);goto end;
4519: fprintf(ficlog,"Problem with Pij resultfile: %s\n", filerespij);goto end;
4520: }
4521: printf("Computing pij: result on file '%s' \n", filerespij);
4522: fprintf(ficlog,"Computing pij: result on file '%s' \n", filerespij);
4523:
4524: stepsize=(int) (stepm+YEARM-1)/YEARM;
4525: /*if (stepm<=24) stepsize=2;*/
4526:
4527: agelim=AGESUP;
4528: hstepm=stepsize*YEARM; /* Every year of age */
4529: hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */
4530:
4531: /* hstepm=1; aff par mois*/
4532:
1.70 brouard 4533: fprintf(ficrespij,"#****** h Pij x Probability to be in state j at age x+h being in i at x ");
1.59 brouard 4534: for(cptcov=1,k=0;cptcov<=i1;cptcov++){
1.53 brouard 4535: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
4536: k=k+1;
1.59 brouard 4537: fprintf(ficrespij,"\n#****** ");
4538: for(j=1;j<=cptcoveff;j++)
4539: fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
4540: fprintf(ficrespij,"******\n");
1.53 brouard 4541:
1.59 brouard 4542: for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */
4543: nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
4544: nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
4545:
4546: /* nhstepm=nhstepm*YEARM; aff par mois*/
4547:
4548: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4549: oldm=oldms;savm=savms;
4550: hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
1.70 brouard 4551: fprintf(ficrespij,"# Cov Agex agex+h hpijx with i,j=");
1.59 brouard 4552: for(i=1; i<=nlstate;i++)
4553: for(j=1; j<=nlstate+ndeath;j++)
4554: fprintf(ficrespij," %1d-%1d",i,j);
4555: fprintf(ficrespij,"\n");
4556: for (h=0; h<=nhstepm; h++){
1.70 brouard 4557: fprintf(ficrespij,"%d %3.f %3.f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );
1.53 brouard 4558: for(i=1; i<=nlstate;i++)
4559: for(j=1; j<=nlstate+ndeath;j++)
1.59 brouard 4560: fprintf(ficrespij," %.5f", p3mat[i][j][h]);
1.53 brouard 4561: fprintf(ficrespij,"\n");
4562: }
1.59 brouard 4563: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4564: fprintf(ficrespij,"\n");
4565: }
1.53 brouard 4566: }
4567: }
4568:
1.74 brouard 4569: varprob(optionfilefiname, matcov, p, delti, nlstate, bage, fage,k,Tvar,nbcode, ncodemax);
1.53 brouard 4570:
4571: fclose(ficrespij);
4572:
1.84 brouard 4573: probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
1.53 brouard 4574:
4575: /*---------- Forecasting ------------------*/
1.69 brouard 4576: /*if((stepm == 1) && (strcmp(model,".")==0)){*/
4577: if(prevfcast==1){
1.74 brouard 4578: /* if(stepm ==1){*/
1.70 brouard 4579: prevforecast(fileres, anproj1, mproj1, jproj1, agemin, agemax, dateprev1, dateprev2, mobilavproj, bage, fage, firstpass, lastpass, anproj2, p, cptcoveff);
1.74 brouard 4580: /* (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);*/
4581: /* } */
4582: /* else{ */
4583: /* erreur=108; */
4584: /* 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); */
4585: /* 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); */
4586: /* } */
1.69 brouard 4587: }
1.53 brouard 4588:
4589:
4590: /*---------- Health expectancies and variances ------------*/
4591:
4592: strcpy(filerest,"t");
4593: strcat(filerest,fileres);
4594: if((ficrest=fopen(filerest,"w"))==NULL) {
4595: printf("Problem with total LE resultfile: %s\n", filerest);goto end;
4596: fprintf(ficlog,"Problem with total LE resultfile: %s\n", filerest);goto end;
4597: }
4598: printf("Computing Total LEs with variances: file '%s' \n", filerest);
4599: fprintf(ficlog,"Computing Total LEs with variances: file '%s' \n", filerest);
4600:
4601:
4602: strcpy(filerese,"e");
4603: strcat(filerese,fileres);
4604: if((ficreseij=fopen(filerese,"w"))==NULL) {
4605: printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
4606: fprintf(ficlog,"Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
4607: }
4608: printf("Computing Health Expectancies: result on file '%s' \n", filerese);
4609: fprintf(ficlog,"Computing Health Expectancies: result on file '%s' \n", filerese);
1.68 lievre 4610:
1.53 brouard 4611: strcpy(fileresv,"v");
4612: strcat(fileresv,fileres);
4613: if((ficresvij=fopen(fileresv,"w"))==NULL) {
4614: printf("Problem with variance resultfile: %s\n", fileresv);exit(0);
4615: fprintf(ficlog,"Problem with variance resultfile: %s\n", fileresv);exit(0);
4616: }
4617: printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
4618: fprintf(ficlog,"Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
1.58 lievre 4619:
1.74 brouard 4620: /* Computes prevalence between agemin (i.e minimal age computed) and no more ageminpar */
1.84 brouard 4621: prevalence(probs, agemin, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
1.74 brouard 4622: /* 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",\
4623: ageminpar, agemax, s[lastpass][imx], agev[lastpass][imx], nlstate, imx, mint[lastpass][imx],anint[lastpass][imx], dateprev1, dateprev2, firstpass, lastpass);
4624: */
1.58 lievre 4625:
1.54 brouard 4626: if (mobilav!=0) {
1.53 brouard 4627: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
1.54 brouard 4628: if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
4629: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
4630: printf(" Error in movingaverage mobilav=%d\n",mobilav);
4631: }
1.53 brouard 4632: }
4633:
1.59 brouard 4634: for(cptcov=1,k=0;cptcov<=i1;cptcov++){
1.53 brouard 4635: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
4636: k=k+1;
4637: fprintf(ficrest,"\n#****** ");
4638: for(j=1;j<=cptcoveff;j++)
4639: fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
4640: fprintf(ficrest,"******\n");
4641:
4642: fprintf(ficreseij,"\n#****** ");
4643: for(j=1;j<=cptcoveff;j++)
4644: fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
4645: fprintf(ficreseij,"******\n");
4646:
4647: fprintf(ficresvij,"\n#****** ");
4648: for(j=1;j<=cptcoveff;j++)
4649: fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
4650: fprintf(ficresvij,"******\n");
4651:
4652: eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
4653: oldm=oldms;savm=savms;
4654: evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov);
4655:
4656: vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
4657: oldm=oldms;savm=savms;
4658: varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,0, mobilav);
4659: if(popbased==1){
4660: 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 4661: }
1.53 brouard 4662:
4663:
4664: fprintf(ficrest,"#Total LEs with variances: e.. (std) ");
4665: for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);
4666: fprintf(ficrest,"\n");
4667:
4668: epj=vector(1,nlstate+1);
4669: for(age=bage; age <=fage ;age++){
4670: prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
4671: if (popbased==1) {
1.54 brouard 4672: if(mobilav ==0){
1.53 brouard 4673: for(i=1; i<=nlstate;i++)
4674: prlim[i][i]=probs[(int)age][i][k];
1.54 brouard 4675: }else{ /* mobilav */
1.53 brouard 4676: for(i=1; i<=nlstate;i++)
4677: prlim[i][i]=mobaverage[(int)age][i][k];
4678: }
4679: }
4680:
4681: fprintf(ficrest," %4.0f",age);
4682: for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){
4683: for(i=1, epj[j]=0.;i <=nlstate;i++) {
4684: epj[j] += prlim[i][i]*eij[i][j][(int)age];
4685: /* printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/
4686: }
4687: epj[nlstate+1] +=epj[j];
4688: }
4689:
4690: for(i=1, vepp=0.;i <=nlstate;i++)
4691: for(j=1;j <=nlstate;j++)
4692: vepp += vareij[i][j][(int)age];
4693: fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));
4694: for(j=1;j <=nlstate;j++){
4695: fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));
4696: }
4697: fprintf(ficrest,"\n");
4698: }
1.59 brouard 4699: free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
4700: free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);
4701: free_vector(epj,1,nlstate+1);
1.53 brouard 4702: }
4703: }
1.59 brouard 4704: free_vector(weight,1,n);
4705: free_imatrix(Tvard,1,15,1,2);
4706: free_imatrix(s,1,maxwav+1,1,n);
4707: free_matrix(anint,1,maxwav,1,n);
4708: free_matrix(mint,1,maxwav,1,n);
4709: free_ivector(cod,1,n);
4710: free_ivector(tab,1,NCOVMAX);
1.53 brouard 4711: fclose(ficreseij);
4712: fclose(ficresvij);
4713: fclose(ficrest);
4714: fclose(ficpar);
4715:
1.54 brouard 4716: /*------- Variance of stable prevalence------*/
1.53 brouard 4717:
4718: strcpy(fileresvpl,"vpl");
4719: strcat(fileresvpl,fileres);
4720: if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {
1.54 brouard 4721: printf("Problem with variance of stable prevalence resultfile: %s\n", fileresvpl);
1.53 brouard 4722: exit(0);
4723: }
1.54 brouard 4724: printf("Computing Variance-covariance of stable prevalence: file '%s' \n", fileresvpl);
1.53 brouard 4725:
1.59 brouard 4726: for(cptcov=1,k=0;cptcov<=i1;cptcov++){
1.53 brouard 4727: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
4728: k=k+1;
4729: fprintf(ficresvpl,"\n#****** ");
4730: for(j=1;j<=cptcoveff;j++)
4731: fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
4732: fprintf(ficresvpl,"******\n");
4733:
4734: varpl=matrix(1,nlstate,(int) bage, (int) fage);
4735: oldm=oldms;savm=savms;
1.59 brouard 4736: varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);
4737: free_matrix(varpl,1,nlstate,(int) bage, (int)fage);
1.53 brouard 4738: }
1.59 brouard 4739: }
1.53 brouard 4740:
4741: fclose(ficresvpl);
4742:
4743: /*---------- End : free ----------------*/
4744: free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);
4745: free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);
4746: free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);
4747: free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);
1.65 lievre 4748:
4749: free_matrix(covar,0,NCOVMAX,1,n);
1.53 brouard 4750: free_matrix(matcov,1,npar,1,npar);
1.74 brouard 4751: /*free_vector(delti,1,npar);*/
4752: free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
1.53 brouard 4753: free_matrix(agev,1,maxwav,1,imx);
4754: free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
1.54 brouard 4755: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
1.74 brouard 4756: free_ma3x(probs,1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
4757:
1.59 brouard 4758: free_ivector(ncodemax,1,8);
4759: free_ivector(Tvar,1,15);
4760: free_ivector(Tprod,1,15);
4761: free_ivector(Tvaraff,1,15);
4762: free_ivector(Tage,1,15);
4763: free_ivector(Tcode,1,100);
1.53 brouard 4764:
1.74 brouard 4765: /* fclose(fichtm);*/
4766: /* fclose(ficgp);*/ /* ALready done */
1.53 brouard 4767:
4768:
4769: if(erreur >0){
4770: printf("End of Imach with error or warning %d\n",erreur);
4771: fprintf(ficlog,"End of Imach with error or warning %d\n",erreur);
4772: }else{
4773: printf("End of Imach\n");
4774: fprintf(ficlog,"End of Imach\n");
4775: }
4776: printf("See log file on %s\n",filelog);
4777: fclose(ficlog);
4778: /* gettimeofday(&end_time, (struct timezone*)0);*/ /* after time */
1.85 ! brouard 4779: (void) gettimeofday(&end_time,&tzp);
! 4780: tm = *localtime(&end_time.tv_sec);
! 4781: tmg = *gmtime(&end_time.tv_sec);
! 4782: strtend=asctime(&tm);
! 4783: printf("Localtime at start %s and at end=%s",strt, strtend);
! 4784: fprintf(ficlog,"Localtime at start %s and at end=%s",strt, strtend);
! 4785: /* printf("Total time used %d Sec\n", asc_time(end_time.tv_sec -start_time.tv_sec);*/
! 4786:
! 4787: 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);
! 4788: fprintf(ficlog,"Total time was %d Sec. %d uSec.\n", end_time.tv_sec -start_time.tv_sec, end_time.tv_usec -start_time.tv_usec);
! 4789: /* printf("Total time was %d uSec.\n", total_usecs);*/
1.53 brouard 4790: /*------ End -----------*/
4791:
1.59 brouard 4792: end:
1.53 brouard 4793: #ifdef windows
4794: /* chdir(pathcd);*/
4795: #endif
4796: /*system("wgnuplot graph.plt");*/
4797: /*system("../gp37mgw/wgnuplot graph.plt");*/
4798: /*system("cd ../gp37mgw");*/
4799: /* system("..\\gp37mgw\\wgnuplot graph.plt");*/
1.59 brouard 4800: strcpy(plotcmd,GNUPLOTPROGRAM);
4801: strcat(plotcmd," ");
4802: strcat(plotcmd,optionfilegnuplot);
1.75 brouard 4803: printf("Starting graphs with: %s",plotcmd);fflush(stdout);
1.59 brouard 4804: system(plotcmd);
1.75 brouard 4805: printf(" Wait...");
1.53 brouard 4806:
1.54 brouard 4807: /*#ifdef windows*/
1.53 brouard 4808: while (z[0] != 'q') {
4809: /* chdir(path); */
4810: printf("\nType e to edit output files, g to graph again, c to start again, and q for exiting: ");
4811: scanf("%s",z);
4812: if (z[0] == 'c') system("./imach");
4813: else if (z[0] == 'e') system(optionfilehtm);
4814: else if (z[0] == 'g') system(plotcmd);
4815: else if (z[0] == 'q') exit(0);
4816: }
1.54 brouard 4817: /*#endif */
1.53 brouard 4818: }
4819:
4820:
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