Annotation of imach/src/imach.c, revision 1.90
1.90 ! brouard 1: /* $Id: imach.c,v 1.89 2003/06/24 12:30:52 brouard Exp $
1.83 lievre 2: $State: Exp $
3: $Log: imach.c,v $
1.90 ! brouard 4: Revision 1.89 2003/06/24 12:30:52 brouard
! 5: (Module): Some bugs corrected for windows. Also, when
! 6: mle=-1 a template is output in file "or"mypar.txt with the design
! 7: of the covariance matrix to be input.
! 8:
1.89 brouard 9: Revision 1.88 2003/06/23 17:54:56 brouard
10: * imach.c (Repository): Create a sub-directory where all the secondary files are. Only imach, htm, gp and r(imach) are on the main directory. Correct time and other things.
11:
1.88 brouard 12: Revision 1.87 2003/06/18 12:26:01 brouard
13: Version 0.96
14:
1.87 brouard 15: Revision 1.86 2003/06/17 20:04:08 brouard
16: (Module): Change position of html and gnuplot routines and added
17: routine fileappend.
18:
1.86 brouard 19: Revision 1.85 2003/06/17 13:12:43 brouard
20: * imach.c (Repository): Check when date of death was earlier that
21: current date of interview. It may happen when the death was just
22: prior to the death. In this case, dh was negative and likelihood
23: was wrong (infinity). We still send an "Error" but patch by
24: assuming that the date of death was just one stepm after the
25: interview.
26: (Repository): Because some people have very long ID (first column)
27: we changed int to long in num[] and we added a new lvector for
28: memory allocation. But we also truncated to 8 characters (left
29: truncation)
30: (Repository): No more line truncation errors.
31:
1.85 brouard 32: Revision 1.84 2003/06/13 21:44:43 brouard
33: * imach.c (Repository): Replace "freqsummary" at a correct
34: place. It differs from routine "prevalence" which may be called
35: many times. Probs is memory consuming and must be used with
36: parcimony.
1.86 brouard 37: Version 0.95a3 (should output exactly the same maximization than 0.8a2)
1.85 brouard 38:
1.84 brouard 39: Revision 1.83 2003/06/10 13:39:11 lievre
40: *** empty log message ***
41:
1.83 lievre 42: Revision 1.82 2003/06/05 15:57:20 brouard
43: Add log in imach.c and fullversion number is now printed.
44:
1.82 brouard 45: */
46: /*
1.53 brouard 47: Interpolated Markov Chain
48:
49: Short summary of the programme:
50:
51: This program computes Healthy Life Expectancies from
52: cross-longitudinal data. Cross-longitudinal data consist in: -1- a
53: first survey ("cross") where individuals from different ages are
54: interviewed on their health status or degree of disability (in the
55: case of a health survey which is our main interest) -2- at least a
56: second wave of interviews ("longitudinal") which measure each change
57: (if any) in individual health status. Health expectancies are
58: computed from the time spent in each health state according to a
59: model. More health states you consider, more time is necessary to reach the
60: Maximum Likelihood of the parameters involved in the model. The
61: simplest model is the multinomial logistic model where pij is the
62: probability to be observed in state j at the second wave
63: conditional to be observed in state i at the first wave. Therefore
64: the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where
65: 'age' is age and 'sex' is a covariate. If you want to have a more
66: complex model than "constant and age", you should modify the program
67: where the markup *Covariates have to be included here again* invites
68: you to do it. More covariates you add, slower the
69: convergence.
70:
71: The advantage of this computer programme, compared to a simple
72: multinomial logistic model, is clear when the delay between waves is not
73: identical for each individual. Also, if a individual missed an
74: intermediate interview, the information is lost, but taken into
75: account using an interpolation or extrapolation.
76:
77: hPijx is the probability to be observed in state i at age x+h
78: conditional to the observed state i at age x. The delay 'h' can be
79: split into an exact number (nh*stepm) of unobserved intermediate
1.66 brouard 80: states. This elementary transition (by month, quarter,
81: semester or year) is modelled as a multinomial logistic. The hPx
1.53 brouard 82: matrix is simply the matrix product of nh*stepm elementary matrices
83: and the contribution of each individual to the likelihood is simply
84: hPijx.
85:
86: Also this programme outputs the covariance matrix of the parameters but also
1.54 brouard 87: of the life expectancies. It also computes the stable prevalence.
1.53 brouard 88:
89: Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).
90: Institut national d'études démographiques, Paris.
91: This software have been partly granted by Euro-REVES, a concerted action
92: from the European Union.
93: It is copyrighted identically to a GNU software product, ie programme and
94: software can be distributed freely for non commercial use. Latest version
95: can be accessed at http://euroreves.ined.fr/imach .
1.74 brouard 96:
97: Help to debug: LD_PRELOAD=/usr/local/lib/libnjamd.so ./imach foo.imach
98: or better on gdb : set env LD_PRELOAD=/usr/local/lib/libnjamd.so
99:
1.53 brouard 100: **********************************************************************/
1.74 brouard 101: /*
102: main
103: read parameterfile
104: read datafile
105: concatwav
1.84 brouard 106: freqsummary
1.74 brouard 107: if (mle >= 1)
108: mlikeli
109: print results files
110: if mle==1
111: computes hessian
112: read end of parameter file: agemin, agemax, bage, fage, estepm
113: begin-prev-date,...
114: open gnuplot file
115: open html file
116: stable prevalence
117: for age prevalim()
118: h Pij x
119: variance of p varprob
120: forecasting if prevfcast==1 prevforecast call prevalence()
121: health expectancies
122: Variance-covariance of DFLE
123: prevalence()
124: movingaverage()
125: varevsij()
126: if popbased==1 varevsij(,popbased)
127: total life expectancies
128: Variance of stable prevalence
129: end
130: */
131:
132:
133:
1.53 brouard 134:
135: #include <math.h>
136: #include <stdio.h>
137: #include <stdlib.h>
138: #include <unistd.h>
139:
1.86 brouard 140: #include <sys/time.h>
141: #include <time.h>
142: #include "timeval.h"
143:
1.53 brouard 144: #define MAXLINE 256
145: #define GNUPLOTPROGRAM "gnuplot"
146: /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
1.85 brouard 147: #define FILENAMELENGTH 132
1.53 brouard 148: /*#define DEBUG*/
1.85 brouard 149: /*#define windows*/
1.53 brouard 150: #define GLOCK_ERROR_NOPATH -1 /* empty path */
151: #define GLOCK_ERROR_GETCWD -2 /* cannot get cwd */
152:
153: #define MAXPARM 30 /* Maximum number of parameters for the optimization */
154: #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */
155:
156: #define NINTERVMAX 8
157: #define NLSTATEMAX 8 /* Maximum number of live states (for func) */
158: #define NDEATHMAX 8 /* Maximum number of dead states (for func) */
159: #define NCOVMAX 8 /* Maximum number of covariates */
160: #define MAXN 20000
161: #define YEARM 12. /* Number of months per year */
162: #define AGESUP 130
163: #define AGEBASE 40
1.85 brouard 164: #ifdef unix
165: #define DIRSEPARATOR '/'
166: #define ODIRSEPARATOR '\\'
167: #else
1.53 brouard 168: #define DIRSEPARATOR '\\'
169: #define ODIRSEPARATOR '/'
170: #endif
171:
1.90 ! brouard 172: /* $Id: imach.c,v 1.89 2003/06/24 12:30:52 brouard Exp $ */
1.81 brouard 173: /* $State: Exp $ */
1.80 brouard 174:
1.88 brouard 175: char version[]="Imach version 0.96a, June 2003, INED-EUROREVES ";
1.90 ! brouard 176: char fullversion[]="$Revision: 1.89 $ $Date: 2003/06/24 12:30:52 $";
1.53 brouard 177: int erreur; /* Error number */
178: int nvar;
179: int cptcovn=0, cptcovage=0, cptcoveff=0,cptcov;
180: int npar=NPARMAX;
181: int nlstate=2; /* Number of live states */
182: int ndeath=1; /* Number of dead states */
183: int ncovmodel, ncovcol; /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
184: int popbased=0;
185:
186: int *wav; /* Number of waves for this individuual 0 is possible */
187: int maxwav; /* Maxim number of waves */
188: int jmin, jmax; /* min, max spacing between 2 waves */
1.87 brouard 189: int gipmx, gsw; /* Global variables on the number of contributions
190: to the likelihood and the sum of weights (done by funcone)*/
1.53 brouard 191: int mle, weightopt;
192: int **mw; /* mw[mi][i] is number of the mi wave for this individual */
193: int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
1.59 brouard 194: int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between
195: * wave mi and wave mi+1 is not an exact multiple of stepm. */
1.53 brouard 196: double jmean; /* Mean space between 2 waves */
197: double **oldm, **newm, **savm; /* Working pointers to matrices */
198: double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
199: FILE *fic,*ficpar, *ficparo,*ficres, *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
1.76 brouard 200: FILE *ficlog, *ficrespow;
1.85 brouard 201: int globpr; /* Global variable for printing or not */
202: double fretone; /* Only one call to likelihood */
203: long ipmx; /* Number of contributions */
204: double sw; /* Sum of weights */
205: char fileresilk[FILENAMELENGTH]; /* File of individual contributions to the likelihood */
206: FILE *ficresilk;
1.53 brouard 207: FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
208: FILE *ficresprobmorprev;
209: FILE *fichtm; /* Html File */
210: FILE *ficreseij;
211: char filerese[FILENAMELENGTH];
212: FILE *ficresvij;
213: char fileresv[FILENAMELENGTH];
214: FILE *ficresvpl;
215: char fileresvpl[FILENAMELENGTH];
216: char title[MAXLINE];
217: char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH], filerespl[FILENAMELENGTH];
218: char optionfilext[10], optionfilefiname[FILENAMELENGTH], plotcmd[FILENAMELENGTH];
1.88 brouard 219: char tmpout[FILENAMELENGTH];
220: char command[FILENAMELENGTH];
221: int outcmd=0;
1.53 brouard 222:
223: char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
1.88 brouard 224: char lfileres[FILENAMELENGTH];
1.53 brouard 225: char filelog[FILENAMELENGTH]; /* Log file */
226: char filerest[FILENAMELENGTH];
227: char fileregp[FILENAMELENGTH];
228: char popfile[FILENAMELENGTH];
229:
230: char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH];
231:
232: #define NR_END 1
233: #define FREE_ARG char*
234: #define FTOL 1.0e-10
235:
236: #define NRANSI
237: #define ITMAX 200
238:
239: #define TOL 2.0e-4
240:
241: #define CGOLD 0.3819660
242: #define ZEPS 1.0e-10
243: #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);
244:
245: #define GOLD 1.618034
246: #define GLIMIT 100.0
247: #define TINY 1.0e-20
248:
249: static double maxarg1,maxarg2;
250: #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
251: #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
252:
253: #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
254: #define rint(a) floor(a+0.5)
255:
256: static double sqrarg;
257: #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
258: #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}
259:
260: int imx;
261: int stepm;
262: /* Stepm, step in month: minimum step interpolation*/
263:
264: int estepm;
265: /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
266:
267: int m,nb;
1.85 brouard 268: long *num;
269: int firstpass=0, lastpass=4,*cod, *ncodemax, *Tage;
1.53 brouard 270: double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
1.55 lievre 271: double **pmmij, ***probs;
1.53 brouard 272: double dateintmean=0;
273:
274: double *weight;
275: int **s; /* Status */
276: double *agedc, **covar, idx;
277: int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;
278:
279: double ftol=FTOL; /* Tolerance for computing Max Likelihood */
280: double ftolhess; /* Tolerance for computing hessian */
281:
282: /**************** split *************************/
283: static int split( char *path, char *dirc, char *name, char *ext, char *finame )
284: {
1.59 brouard 285: char *ss; /* pointer */
286: int l1, l2; /* length counters */
1.53 brouard 287:
1.59 brouard 288: l1 = strlen(path ); /* length of path */
289: if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
290: ss= strrchr( path, DIRSEPARATOR ); /* find last / */
291: if ( ss == NULL ) { /* no directory, so use current */
292: /*if(strrchr(path, ODIRSEPARATOR )==NULL)
293: printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
1.74 brouard 294: /* get current working directory */
295: /* extern char* getcwd ( char *buf , int len);*/
1.59 brouard 296: if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {
297: return( GLOCK_ERROR_GETCWD );
298: }
299: strcpy( name, path ); /* we've got it */
300: } else { /* strip direcotry from path */
301: ss++; /* after this, the filename */
302: l2 = strlen( ss ); /* length of filename */
303: if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
304: strcpy( name, ss ); /* save file name */
305: strncpy( dirc, path, l1 - l2 ); /* now the directory */
306: dirc[l1-l2] = 0; /* add zero */
307: }
308: l1 = strlen( dirc ); /* length of directory */
1.85 brouard 309: /*#ifdef windows
1.59 brouard 310: if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; }
1.53 brouard 311: #else
1.59 brouard 312: if ( dirc[l1-1] != '/' ) { dirc[l1] = '/'; dirc[l1+1] = 0; }
1.53 brouard 313: #endif
1.85 brouard 314: */
1.59 brouard 315: ss = strrchr( name, '.' ); /* find last / */
316: ss++;
317: strcpy(ext,ss); /* save extension */
318: l1= strlen( name);
319: l2= strlen(ss)+1;
320: strncpy( finame, name, l1-l2);
321: finame[l1-l2]= 0;
322: return( 0 ); /* we're done */
1.53 brouard 323: }
324:
325:
326: /******************************************/
327:
1.89 brouard 328: void replace_back_to_slash(char *s, char*t)
1.53 brouard 329: {
330: int i;
1.89 brouard 331: int lg=0;
1.53 brouard 332: i=0;
333: lg=strlen(t);
334: for(i=0; i<= lg; i++) {
335: (s[i] = t[i]);
336: if (t[i]== '\\') s[i]='/';
337: }
338: }
339:
340: int nbocc(char *s, char occ)
341: {
342: int i,j=0;
343: int lg=20;
344: i=0;
345: lg=strlen(s);
346: for(i=0; i<= lg; i++) {
347: if (s[i] == occ ) j++;
348: }
349: return j;
350: }
351:
352: void cutv(char *u,char *v, char*t, char occ)
353: {
354: /* cuts string t into u and v where u is ended by char occ excluding it
355: and v is after occ excluding it too : ex cutv(u,v,"abcdef2ghi2j",2)
356: gives u="abcedf" and v="ghi2j" */
357: int i,lg,j,p=0;
358: i=0;
359: for(j=0; j<=strlen(t)-1; j++) {
360: if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;
361: }
362:
363: lg=strlen(t);
364: for(j=0; j<p; j++) {
365: (u[j] = t[j]);
366: }
367: u[p]='\0';
368:
369: for(j=0; j<= lg; j++) {
370: if (j>=(p+1))(v[j-p-1] = t[j]);
371: }
372: }
373:
374: /********************** nrerror ********************/
375:
376: void nrerror(char error_text[])
377: {
378: fprintf(stderr,"ERREUR ...\n");
379: fprintf(stderr,"%s\n",error_text);
1.59 brouard 380: exit(EXIT_FAILURE);
1.53 brouard 381: }
382: /*********************** vector *******************/
383: double *vector(int nl, int nh)
384: {
385: double *v;
386: v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
387: if (!v) nrerror("allocation failure in vector");
388: return v-nl+NR_END;
389: }
390:
391: /************************ free vector ******************/
392: void free_vector(double*v, int nl, int nh)
393: {
394: free((FREE_ARG)(v+nl-NR_END));
395: }
396:
397: /************************ivector *******************************/
1.85 brouard 398: int *ivector(long nl,long nh)
1.76 brouard 399: {
1.85 brouard 400: int *v;
401: v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
402: if (!v) nrerror("allocation failure in ivector");
1.76 brouard 403: return v-nl+NR_END;
404: }
405:
406: /******************free ivector **************************/
1.85 brouard 407: void free_ivector(int *v, long nl, long nh)
1.76 brouard 408: {
409: free((FREE_ARG)(v+nl-NR_END));
410: }
411:
1.85 brouard 412: /************************lvector *******************************/
413: long *lvector(long nl,long nh)
1.53 brouard 414: {
1.85 brouard 415: long *v;
416: v=(long *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(long)));
1.53 brouard 417: if (!v) nrerror("allocation failure in ivector");
418: return v-nl+NR_END;
419: }
420:
1.85 brouard 421: /******************free lvector **************************/
422: void free_lvector(long *v, long nl, long nh)
1.53 brouard 423: {
424: free((FREE_ARG)(v+nl-NR_END));
425: }
426:
427: /******************* imatrix *******************************/
428: int **imatrix(long nrl, long nrh, long ncl, long nch)
429: /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */
430: {
431: long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;
432: int **m;
433:
434: /* allocate pointers to rows */
435: m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));
436: if (!m) nrerror("allocation failure 1 in matrix()");
437: m += NR_END;
438: m -= nrl;
439:
440:
441: /* allocate rows and set pointers to them */
442: m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));
443: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
444: m[nrl] += NR_END;
445: m[nrl] -= ncl;
446:
447: for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;
448:
449: /* return pointer to array of pointers to rows */
450: return m;
451: }
452:
453: /****************** free_imatrix *************************/
454: void free_imatrix(m,nrl,nrh,ncl,nch)
455: int **m;
456: long nch,ncl,nrh,nrl;
457: /* free an int matrix allocated by imatrix() */
458: {
459: free((FREE_ARG) (m[nrl]+ncl-NR_END));
460: free((FREE_ARG) (m+nrl-NR_END));
461: }
462:
463: /******************* matrix *******************************/
464: double **matrix(long nrl, long nrh, long ncl, long nch)
465: {
466: long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
467: double **m;
468:
469: m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
470: if (!m) nrerror("allocation failure 1 in matrix()");
471: m += NR_END;
472: m -= nrl;
473:
474: m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
475: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
476: m[nrl] += NR_END;
477: m[nrl] -= ncl;
478:
479: for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
480: return m;
1.85 brouard 481: /* print *(*(m+1)+70) or print m[1][70]; print m+1 or print &(m[1])
1.74 brouard 482: */
1.53 brouard 483: }
484:
485: /*************************free matrix ************************/
486: void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
487: {
488: free((FREE_ARG)(m[nrl]+ncl-NR_END));
489: free((FREE_ARG)(m+nrl-NR_END));
490: }
491:
492: /******************* ma3x *******************************/
493: double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
494: {
495: long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
496: double ***m;
497:
498: m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
499: if (!m) nrerror("allocation failure 1 in matrix()");
500: m += NR_END;
501: m -= nrl;
502:
503: m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
504: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
505: m[nrl] += NR_END;
506: m[nrl] -= ncl;
507:
508: for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
509:
510: m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
511: if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
512: m[nrl][ncl] += NR_END;
513: m[nrl][ncl] -= nll;
514: for (j=ncl+1; j<=nch; j++)
515: m[nrl][j]=m[nrl][j-1]+nlay;
516:
517: for (i=nrl+1; i<=nrh; i++) {
518: m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
519: for (j=ncl+1; j<=nch; j++)
520: m[i][j]=m[i][j-1]+nlay;
521: }
1.74 brouard 522: return m;
523: /* gdb: p *(m+1) <=> p m[1] and p (m+1) <=> p (m+1) <=> p &(m[1])
524: &(m[i][j][k]) <=> *((*(m+i) + j)+k)
525: */
1.53 brouard 526: }
527:
528: /*************************free ma3x ************************/
529: void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
530: {
531: free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
532: free((FREE_ARG)(m[nrl]+ncl-NR_END));
533: free((FREE_ARG)(m+nrl-NR_END));
534: }
535:
536: /***************** f1dim *************************/
537: extern int ncom;
538: extern double *pcom,*xicom;
539: extern double (*nrfunc)(double []);
540:
541: double f1dim(double x)
542: {
543: int j;
544: double f;
545: double *xt;
546:
547: xt=vector(1,ncom);
548: for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];
549: f=(*nrfunc)(xt);
550: free_vector(xt,1,ncom);
551: return f;
552: }
553:
554: /*****************brent *************************/
555: double brent(double ax, double bx, double cx, double (*f)(double), double tol, double *xmin)
556: {
557: int iter;
558: double a,b,d,etemp;
559: double fu,fv,fw,fx;
560: double ftemp;
561: double p,q,r,tol1,tol2,u,v,w,x,xm;
562: double e=0.0;
563:
564: a=(ax < cx ? ax : cx);
565: b=(ax > cx ? ax : cx);
566: x=w=v=bx;
567: fw=fv=fx=(*f)(x);
568: for (iter=1;iter<=ITMAX;iter++) {
569: xm=0.5*(a+b);
570: tol2=2.0*(tol1=tol*fabs(x)+ZEPS);
571: /* if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
572: printf(".");fflush(stdout);
573: fprintf(ficlog,".");fflush(ficlog);
574: #ifdef DEBUG
575: 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);
576: 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);
577: /* if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
578: #endif
579: if (fabs(x-xm) <= (tol2-0.5*(b-a))){
580: *xmin=x;
581: return fx;
582: }
583: ftemp=fu;
584: if (fabs(e) > tol1) {
585: r=(x-w)*(fx-fv);
586: q=(x-v)*(fx-fw);
587: p=(x-v)*q-(x-w)*r;
588: q=2.0*(q-r);
589: if (q > 0.0) p = -p;
590: q=fabs(q);
591: etemp=e;
592: e=d;
593: if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))
594: d=CGOLD*(e=(x >= xm ? a-x : b-x));
595: else {
596: d=p/q;
597: u=x+d;
598: if (u-a < tol2 || b-u < tol2)
599: d=SIGN(tol1,xm-x);
600: }
601: } else {
602: d=CGOLD*(e=(x >= xm ? a-x : b-x));
603: }
604: u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));
605: fu=(*f)(u);
606: if (fu <= fx) {
607: if (u >= x) a=x; else b=x;
608: SHFT(v,w,x,u)
609: SHFT(fv,fw,fx,fu)
610: } else {
611: if (u < x) a=u; else b=u;
612: if (fu <= fw || w == x) {
613: v=w;
614: w=u;
615: fv=fw;
616: fw=fu;
617: } else if (fu <= fv || v == x || v == w) {
618: v=u;
619: fv=fu;
620: }
621: }
622: }
623: nrerror("Too many iterations in brent");
624: *xmin=x;
625: return fx;
626: }
627:
628: /****************** mnbrak ***********************/
629:
630: void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,
631: double (*func)(double))
632: {
633: double ulim,u,r,q, dum;
634: double fu;
635:
636: *fa=(*func)(*ax);
637: *fb=(*func)(*bx);
638: if (*fb > *fa) {
639: SHFT(dum,*ax,*bx,dum)
640: SHFT(dum,*fb,*fa,dum)
641: }
642: *cx=(*bx)+GOLD*(*bx-*ax);
643: *fc=(*func)(*cx);
644: while (*fb > *fc) {
645: r=(*bx-*ax)*(*fb-*fc);
646: q=(*bx-*cx)*(*fb-*fa);
647: u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/
648: (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r));
649: ulim=(*bx)+GLIMIT*(*cx-*bx);
650: if ((*bx-u)*(u-*cx) > 0.0) {
651: fu=(*func)(u);
652: } else if ((*cx-u)*(u-ulim) > 0.0) {
653: fu=(*func)(u);
654: if (fu < *fc) {
655: SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))
656: SHFT(*fb,*fc,fu,(*func)(u))
657: }
658: } else if ((u-ulim)*(ulim-*cx) >= 0.0) {
659: u=ulim;
660: fu=(*func)(u);
661: } else {
662: u=(*cx)+GOLD*(*cx-*bx);
663: fu=(*func)(u);
664: }
665: SHFT(*ax,*bx,*cx,u)
666: SHFT(*fa,*fb,*fc,fu)
667: }
668: }
669:
670: /*************** linmin ************************/
671:
672: int ncom;
673: double *pcom,*xicom;
674: double (*nrfunc)(double []);
675:
676: void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))
677: {
678: double brent(double ax, double bx, double cx,
679: double (*f)(double), double tol, double *xmin);
680: double f1dim(double x);
681: void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,
682: double *fc, double (*func)(double));
683: int j;
684: double xx,xmin,bx,ax;
685: double fx,fb,fa;
686:
687: ncom=n;
688: pcom=vector(1,n);
689: xicom=vector(1,n);
690: nrfunc=func;
691: for (j=1;j<=n;j++) {
692: pcom[j]=p[j];
693: xicom[j]=xi[j];
694: }
695: ax=0.0;
696: xx=1.0;
697: mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim);
698: *fret=brent(ax,xx,bx,f1dim,TOL,&xmin);
699: #ifdef DEBUG
700: printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
701: fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
702: #endif
703: for (j=1;j<=n;j++) {
704: xi[j] *= xmin;
705: p[j] += xi[j];
706: }
707: free_vector(xicom,1,n);
708: free_vector(pcom,1,n);
709: }
710:
711: /*************** powell ************************/
712: void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,
713: double (*func)(double []))
714: {
715: void linmin(double p[], double xi[], int n, double *fret,
716: double (*func)(double []));
717: int i,ibig,j;
718: double del,t,*pt,*ptt,*xit;
719: double fp,fptt;
720: double *xits;
721: pt=vector(1,n);
722: ptt=vector(1,n);
723: xit=vector(1,n);
724: xits=vector(1,n);
725: *fret=(*func)(p);
726: for (j=1;j<=n;j++) pt[j]=p[j];
727: for (*iter=1;;++(*iter)) {
728: fp=(*fret);
729: ibig=0;
730: del=0.0;
731: printf("\nPowell iter=%d -2*LL=%.12f",*iter,*fret);
732: fprintf(ficlog,"\nPowell iter=%d -2*LL=%.12f",*iter,*fret);
1.76 brouard 733: fprintf(ficrespow,"%d %.12f",*iter,*fret);
734: for (i=1;i<=n;i++) {
1.53 brouard 735: printf(" %d %.12f",i, p[i]);
1.76 brouard 736: fprintf(ficlog," %d %.12lf",i, p[i]);
737: fprintf(ficrespow," %.12lf", p[i]);
738: }
1.53 brouard 739: printf("\n");
740: fprintf(ficlog,"\n");
1.76 brouard 741: fprintf(ficrespow,"\n");
1.53 brouard 742: for (i=1;i<=n;i++) {
743: for (j=1;j<=n;j++) xit[j]=xi[j][i];
744: fptt=(*fret);
745: #ifdef DEBUG
746: printf("fret=%lf \n",*fret);
747: fprintf(ficlog,"fret=%lf \n",*fret);
748: #endif
749: printf("%d",i);fflush(stdout);
750: fprintf(ficlog,"%d",i);fflush(ficlog);
751: linmin(p,xit,n,fret,func);
752: if (fabs(fptt-(*fret)) > del) {
753: del=fabs(fptt-(*fret));
754: ibig=i;
755: }
756: #ifdef DEBUG
757: printf("%d %.12e",i,(*fret));
758: fprintf(ficlog,"%d %.12e",i,(*fret));
759: for (j=1;j<=n;j++) {
760: xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
761: printf(" x(%d)=%.12e",j,xit[j]);
762: fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
763: }
764: for(j=1;j<=n;j++) {
765: printf(" p=%.12e",p[j]);
766: fprintf(ficlog," p=%.12e",p[j]);
767: }
768: printf("\n");
769: fprintf(ficlog,"\n");
770: #endif
771: }
772: if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {
773: #ifdef DEBUG
774: int k[2],l;
775: k[0]=1;
776: k[1]=-1;
777: printf("Max: %.12e",(*func)(p));
778: fprintf(ficlog,"Max: %.12e",(*func)(p));
779: for (j=1;j<=n;j++) {
780: printf(" %.12e",p[j]);
781: fprintf(ficlog," %.12e",p[j]);
782: }
783: printf("\n");
784: fprintf(ficlog,"\n");
785: for(l=0;l<=1;l++) {
786: for (j=1;j<=n;j++) {
787: ptt[j]=p[j]+(p[j]-pt[j])*k[l];
788: printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
789: fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
790: }
791: printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
792: fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
793: }
794: #endif
795:
796:
797: free_vector(xit,1,n);
798: free_vector(xits,1,n);
799: free_vector(ptt,1,n);
800: free_vector(pt,1,n);
801: return;
802: }
803: if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");
804: for (j=1;j<=n;j++) {
805: ptt[j]=2.0*p[j]-pt[j];
806: xit[j]=p[j]-pt[j];
807: pt[j]=p[j];
808: }
809: fptt=(*func)(ptt);
810: if (fptt < fp) {
811: t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt);
812: if (t < 0.0) {
813: linmin(p,xit,n,fret,func);
814: for (j=1;j<=n;j++) {
815: xi[j][ibig]=xi[j][n];
816: xi[j][n]=xit[j];
817: }
818: #ifdef DEBUG
819: printf("Direction changed last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
820: fprintf(ficlog,"Direction changed last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
821: for(j=1;j<=n;j++){
822: printf(" %.12e",xit[j]);
823: fprintf(ficlog," %.12e",xit[j]);
824: }
825: printf("\n");
826: fprintf(ficlog,"\n");
827: #endif
1.54 brouard 828: }
1.53 brouard 829: }
830: }
831: }
832:
1.54 brouard 833: /**** Prevalence limit (stable prevalence) ****************/
1.53 brouard 834:
835: double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)
836: {
837: /* Computes the prevalence limit in each live state at age x by left multiplying the unit
838: matrix by transitions matrix until convergence is reached */
839:
840: int i, ii,j,k;
841: double min, max, maxmin, maxmax,sumnew=0.;
842: double **matprod2();
843: double **out, cov[NCOVMAX], **pmij();
844: double **newm;
845: double agefin, delaymax=50 ; /* Max number of years to converge */
846:
847: for (ii=1;ii<=nlstate+ndeath;ii++)
848: for (j=1;j<=nlstate+ndeath;j++){
849: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
850: }
851:
852: cov[1]=1.;
853:
854: /* Even if hstepm = 1, at least one multiplication by the unit matrix */
855: for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
856: newm=savm;
857: /* Covariates have to be included here again */
858: cov[2]=agefin;
859:
860: for (k=1; k<=cptcovn;k++) {
861: cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
862: /* 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]]);*/
863: }
864: for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
865: for (k=1; k<=cptcovprod;k++)
866: cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
867:
868: /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
869: /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
870: /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
871: out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);
872:
873: savm=oldm;
874: oldm=newm;
875: maxmax=0.;
876: for(j=1;j<=nlstate;j++){
877: min=1.;
878: max=0.;
879: for(i=1; i<=nlstate; i++) {
880: sumnew=0;
881: for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
882: prlim[i][j]= newm[i][j]/(1-sumnew);
883: max=FMAX(max,prlim[i][j]);
884: min=FMIN(min,prlim[i][j]);
885: }
886: maxmin=max-min;
887: maxmax=FMAX(maxmax,maxmin);
888: }
889: if(maxmax < ftolpl){
890: return prlim;
891: }
892: }
893: }
894:
895: /*************** transition probabilities ***************/
896:
897: double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
898: {
899: double s1, s2;
900: /*double t34;*/
901: int i,j,j1, nc, ii, jj;
902:
903: for(i=1; i<= nlstate; i++){
904: for(j=1; j<i;j++){
905: for (nc=1, s2=0.;nc <=ncovmodel; nc++){
906: /*s2 += param[i][j][nc]*cov[nc];*/
907: s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
908: /*printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2);*/
909: }
910: ps[i][j]=s2;
911: /*printf("s1=%.17e, s2=%.17e\n",s1,s2);*/
912: }
913: for(j=i+1; j<=nlstate+ndeath;j++){
914: for (nc=1, s2=0.;nc <=ncovmodel; nc++){
915: s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
916: /*printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2);*/
917: }
918: ps[i][j]=s2;
919: }
920: }
921: /*ps[3][2]=1;*/
922:
923: for(i=1; i<= nlstate; i++){
924: s1=0;
925: for(j=1; j<i; j++)
926: s1+=exp(ps[i][j]);
927: for(j=i+1; j<=nlstate+ndeath; j++)
928: s1+=exp(ps[i][j]);
929: ps[i][i]=1./(s1+1.);
930: for(j=1; j<i; j++)
931: ps[i][j]= exp(ps[i][j])*ps[i][i];
932: for(j=i+1; j<=nlstate+ndeath; j++)
933: ps[i][j]= exp(ps[i][j])*ps[i][i];
934: /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
935: } /* end i */
936:
937: for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
938: for(jj=1; jj<= nlstate+ndeath; jj++){
939: ps[ii][jj]=0;
940: ps[ii][ii]=1;
941: }
942: }
943:
944:
945: /* for(ii=1; ii<= nlstate+ndeath; ii++){
946: for(jj=1; jj<= nlstate+ndeath; jj++){
947: printf("%lf ",ps[ii][jj]);
948: }
949: printf("\n ");
950: }
951: printf("\n ");printf("%lf ",cov[2]);*/
952: /*
953: for(i=1; i<= npar; i++) printf("%f ",x[i]);
954: goto end;*/
955: return ps;
956: }
957:
958: /**************** Product of 2 matrices ******************/
959:
960: double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)
961: {
962: /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
963: b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
964: /* in, b, out are matrice of pointers which should have been initialized
965: before: only the contents of out is modified. The function returns
966: a pointer to pointers identical to out */
967: long i, j, k;
968: for(i=nrl; i<= nrh; i++)
969: for(k=ncolol; k<=ncoloh; k++)
970: for(j=ncl,out[i][k]=0.; j<=nch; j++)
971: out[i][k] +=in[i][j]*b[j][k];
972:
973: return out;
974: }
975:
976:
977: /************* Higher Matrix Product ***************/
978:
979: double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
980: {
1.66 brouard 981: /* Computes the transition matrix starting at age 'age' over
982: 'nhstepm*hstepm*stepm' months (i.e. until
983: age (in years) age+nhstepm*hstepm*stepm/12) by multiplying
984: nhstepm*hstepm matrices.
1.53 brouard 985: Output is stored in matrix po[i][j][h] for h every 'hstepm' step
1.66 brouard 986: (typically every 2 years instead of every month which is too big
987: for the memory).
1.53 brouard 988: Model is determined by parameters x and covariates have to be
989: included manually here.
990:
991: */
992:
993: int i, j, d, h, k;
994: double **out, cov[NCOVMAX];
995: double **newm;
996:
997: /* Hstepm could be zero and should return the unit matrix */
998: for (i=1;i<=nlstate+ndeath;i++)
999: for (j=1;j<=nlstate+ndeath;j++){
1000: oldm[i][j]=(i==j ? 1.0 : 0.0);
1001: po[i][j][0]=(i==j ? 1.0 : 0.0);
1002: }
1003: /* Even if hstepm = 1, at least one multiplication by the unit matrix */
1004: for(h=1; h <=nhstepm; h++){
1005: for(d=1; d <=hstepm; d++){
1006: newm=savm;
1007: /* Covariates have to be included here again */
1008: cov[1]=1.;
1009: cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
1010: for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
1011: for (k=1; k<=cptcovage;k++)
1012: cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
1013: for (k=1; k<=cptcovprod;k++)
1014: cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
1015:
1016:
1017: /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
1018: /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
1019: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,
1020: pmij(pmmij,cov,ncovmodel,x,nlstate));
1021: savm=oldm;
1022: oldm=newm;
1023: }
1024: for(i=1; i<=nlstate+ndeath; i++)
1025: for(j=1;j<=nlstate+ndeath;j++) {
1026: po[i][j][h]=newm[i][j];
1027: /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);
1028: */
1029: }
1030: } /* end h */
1031: return po;
1032: }
1033:
1034:
1035: /*************** log-likelihood *************/
1036: double func( double *x)
1037: {
1038: int i, ii, j, k, mi, d, kk;
1039: double l, ll[NLSTATEMAX], cov[NCOVMAX];
1040: double **out;
1041: double sw; /* Sum of weights */
1042: double lli; /* Individual log likelihood */
1.59 brouard 1043: int s1, s2;
1.68 lievre 1044: double bbh, survp;
1.53 brouard 1045: long ipmx;
1046: /*extern weight */
1047: /* We are differentiating ll according to initial status */
1048: /* for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
1049: /*for(i=1;i<imx;i++)
1050: printf(" %d\n",s[4][i]);
1051: */
1052: cov[1]=1.;
1053:
1054: for(k=1; k<=nlstate; k++) ll[k]=0.;
1.61 brouard 1055:
1056: if(mle==1){
1057: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1058: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
1059: for(mi=1; mi<= wav[i]-1; mi++){
1060: for (ii=1;ii<=nlstate+ndeath;ii++)
1061: for (j=1;j<=nlstate+ndeath;j++){
1062: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1063: savm[ii][j]=(ii==j ? 1.0 : 0.0);
1064: }
1065: for(d=0; d<dh[mi][i]; d++){
1066: newm=savm;
1067: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
1068: for (kk=1; kk<=cptcovage;kk++) {
1069: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
1070: }
1071: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1072: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1073: savm=oldm;
1074: oldm=newm;
1075: } /* end mult */
1.53 brouard 1076:
1.61 brouard 1077: /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
1078: /* But now since version 0.9 we anticipate for bias and large stepm.
1079: * If stepm is larger than one month (smallest stepm) and if the exact delay
1080: * (in months) between two waves is not a multiple of stepm, we rounded to
1081: * the nearest (and in case of equal distance, to the lowest) interval but now
1082: * we keep into memory the bias bh[mi][i] and also the previous matrix product
1083: * (i.e to dh[mi][i]-1) saved in 'savm'. The we inter(extra)polate the
1084: * probability in order to take into account the bias as a fraction of the way
1085: * from savm to out if bh is neagtive or even beyond if bh is positive. bh varies
1086: * -stepm/2 to stepm/2 .
1087: * For stepm=1 the results are the same as for previous versions of Imach.
1088: * For stepm > 1 the results are less biased than in previous versions.
1089: */
1090: s1=s[mw[mi][i]][i];
1091: s2=s[mw[mi+1][i]][i];
1.64 lievre 1092: bbh=(double)bh[mi][i]/(double)stepm;
1093: /* bias is positive if real duration
1094: * is higher than the multiple of stepm and negative otherwise.
1095: */
1096: /* 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 1097: if( s2 > nlstate){
1098: /* i.e. if s2 is a death state and if the date of death is known then the contribution
1099: to the likelihood is the probability to die between last step unit time and current
1100: step unit time, which is also the differences between probability to die before dh
1101: and probability to die before dh-stepm .
1102: In version up to 0.92 likelihood was computed
1103: as if date of death was unknown. Death was treated as any other
1104: health state: the date of the interview describes the actual state
1105: and not the date of a change in health state. The former idea was
1106: to consider that at each interview the state was recorded
1107: (healthy, disable or death) and IMaCh was corrected; but when we
1108: introduced the exact date of death then we should have modified
1109: the contribution of an exact death to the likelihood. This new
1110: contribution is smaller and very dependent of the step unit
1111: stepm. It is no more the probability to die between last interview
1112: and month of death but the probability to survive from last
1113: interview up to one month before death multiplied by the
1114: probability to die within a month. Thanks to Chris
1115: Jackson for correcting this bug. Former versions increased
1116: mortality artificially. The bad side is that we add another loop
1117: which slows down the processing. The difference can be up to 10%
1118: lower mortality.
1119: */
1120: lli=log(out[s1][s2] - savm[s1][s2]);
1121: }else{
1122: lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
1123: /* 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 */
1124: }
1.64 lievre 1125: /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
1126: /*if(lli ==000.0)*/
1127: /*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 1128: ipmx +=1;
1.64 lievre 1129: sw += weight[i];
1130: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1131: } /* end of wave */
1132: } /* end of individual */
1133: } else if(mle==2){
1134: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1135: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
1136: for(mi=1; mi<= wav[i]-1; mi++){
1137: for (ii=1;ii<=nlstate+ndeath;ii++)
1138: for (j=1;j<=nlstate+ndeath;j++){
1139: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1140: savm[ii][j]=(ii==j ? 1.0 : 0.0);
1141: }
1142: for(d=0; d<=dh[mi][i]; d++){
1143: newm=savm;
1144: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
1145: for (kk=1; kk<=cptcovage;kk++) {
1146: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
1147: }
1148: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1149: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1150: savm=oldm;
1151: oldm=newm;
1152: } /* end mult */
1153:
1154: /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
1155: /* But now since version 0.9 we anticipate for bias and large stepm.
1156: * If stepm is larger than one month (smallest stepm) and if the exact delay
1157: * (in months) between two waves is not a multiple of stepm, we rounded to
1158: * the nearest (and in case of equal distance, to the lowest) interval but now
1159: * we keep into memory the bias bh[mi][i] and also the previous matrix product
1160: * (i.e to dh[mi][i]-1) saved in 'savm'. The we inter(extra)polate the
1161: * probability in order to take into account the bias as a fraction of the way
1162: * from savm to out if bh is neagtive or even beyond if bh is positive. bh varies
1163: * -stepm/2 to stepm/2 .
1164: * For stepm=1 the results are the same as for previous versions of Imach.
1165: * For stepm > 1 the results are less biased than in previous versions.
1166: */
1167: s1=s[mw[mi][i]][i];
1168: s2=s[mw[mi+1][i]][i];
1169: bbh=(double)bh[mi][i]/(double)stepm;
1170: /* bias is positive if real duration
1171: * is higher than the multiple of stepm and negative otherwise.
1172: */
1.63 lievre 1173: 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 1174: /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
1175: /*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 */
1176: /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
1177: /*if(lli ==000.0)*/
1178: /*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); */
1179: ipmx +=1;
1180: sw += weight[i];
1181: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1182: } /* end of wave */
1183: } /* end of individual */
1184: } else if(mle==3){ /* exponential inter-extrapolation */
1185: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1186: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
1187: for(mi=1; mi<= wav[i]-1; mi++){
1188: for (ii=1;ii<=nlstate+ndeath;ii++)
1189: for (j=1;j<=nlstate+ndeath;j++){
1190: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1191: savm[ii][j]=(ii==j ? 1.0 : 0.0);
1192: }
1193: for(d=0; d<dh[mi][i]; d++){
1194: newm=savm;
1195: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
1196: for (kk=1; kk<=cptcovage;kk++) {
1197: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
1198: }
1199: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1200: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1201: savm=oldm;
1202: oldm=newm;
1203: } /* end mult */
1204:
1205: /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
1206: /* But now since version 0.9 we anticipate for bias and large stepm.
1207: * If stepm is larger than one month (smallest stepm) and if the exact delay
1208: * (in months) between two waves is not a multiple of stepm, we rounded to
1209: * the nearest (and in case of equal distance, to the lowest) interval but now
1210: * we keep into memory the bias bh[mi][i] and also the previous matrix product
1211: * (i.e to dh[mi][i]-1) saved in 'savm'. The we inter(extra)polate the
1212: * probability in order to take into account the bias as a fraction of the way
1213: * from savm to out if bh is neagtive or even beyond if bh is positive. bh varies
1214: * -stepm/2 to stepm/2 .
1215: * For stepm=1 the results are the same as for previous versions of Imach.
1216: * For stepm > 1 the results are less biased than in previous versions.
1217: */
1218: s1=s[mw[mi][i]][i];
1219: s2=s[mw[mi+1][i]][i];
1220: bbh=(double)bh[mi][i]/(double)stepm;
1221: /* bias is positive if real duration
1222: * is higher than the multiple of stepm and negative otherwise.
1223: */
1224: /* 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 */
1225: 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 1226: /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
1227: /*if(lli ==000.0)*/
1228: /*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); */
1229: ipmx +=1;
1230: sw += weight[i];
1231: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1232: } /* end of wave */
1233: } /* end of individual */
1.84 brouard 1234: }else if (mle==4){ /* ml=4 no inter-extrapolation */
1.61 brouard 1235: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1236: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
1237: for(mi=1; mi<= wav[i]-1; mi++){
1238: for (ii=1;ii<=nlstate+ndeath;ii++)
1239: for (j=1;j<=nlstate+ndeath;j++){
1240: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1241: savm[ii][j]=(ii==j ? 1.0 : 0.0);
1242: }
1243: for(d=0; d<dh[mi][i]; d++){
1244: newm=savm;
1245: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
1246: for (kk=1; kk<=cptcovage;kk++) {
1247: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
1248: }
1249:
1250: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1251: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1252: savm=oldm;
1253: oldm=newm;
1254: } /* end mult */
1255:
1.84 brouard 1256: s1=s[mw[mi][i]][i];
1257: s2=s[mw[mi+1][i]][i];
1258: if( s2 > nlstate){
1259: lli=log(out[s1][s2] - savm[s1][s2]);
1260: }else{
1261: lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
1262: }
1263: ipmx +=1;
1264: sw += weight[i];
1265: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1.85 brouard 1266: /* 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 1267: } /* end of wave */
1268: } /* end of individual */
1269: }else{ /* ml=5 no inter-extrapolation no jackson =0.8a */
1270: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1271: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
1272: for(mi=1; mi<= wav[i]-1; mi++){
1273: for (ii=1;ii<=nlstate+ndeath;ii++)
1274: for (j=1;j<=nlstate+ndeath;j++){
1275: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1276: savm[ii][j]=(ii==j ? 1.0 : 0.0);
1277: }
1278: for(d=0; d<dh[mi][i]; d++){
1279: newm=savm;
1280: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
1281: for (kk=1; kk<=cptcovage;kk++) {
1282: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
1283: }
1284:
1285: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1286: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1287: savm=oldm;
1288: oldm=newm;
1289: } /* end mult */
1290:
1291: s1=s[mw[mi][i]][i];
1292: s2=s[mw[mi+1][i]][i];
1.61 brouard 1293: lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
1294: ipmx +=1;
1295: sw += weight[i];
1296: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1.84 brouard 1297: /*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 1298: } /* end of wave */
1299: } /* end of individual */
1300: } /* End of if */
1.53 brouard 1301: for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
1302: /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
1303: l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
1.85 brouard 1304: return -l;
1305: }
1306:
1307: /*************** log-likelihood *************/
1308: double funcone( double *x)
1309: {
1.87 brouard 1310: /* Same as likeli but slower because of a lot of printf and if */
1.85 brouard 1311: int i, ii, j, k, mi, d, kk;
1312: double l, ll[NLSTATEMAX], cov[NCOVMAX];
1313: double **out;
1314: double lli; /* Individual log likelihood */
1.87 brouard 1315: double llt;
1.85 brouard 1316: int s1, s2;
1317: double bbh, survp;
1318: /*extern weight */
1319: /* We are differentiating ll according to initial status */
1320: /* for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
1321: /*for(i=1;i<imx;i++)
1322: printf(" %d\n",s[4][i]);
1323: */
1324: cov[1]=1.;
1325:
1326: for(k=1; k<=nlstate; k++) ll[k]=0.;
1327:
1328: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1329: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
1330: for(mi=1; mi<= wav[i]-1; mi++){
1331: for (ii=1;ii<=nlstate+ndeath;ii++)
1332: for (j=1;j<=nlstate+ndeath;j++){
1333: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1334: savm[ii][j]=(ii==j ? 1.0 : 0.0);
1335: }
1336: for(d=0; d<dh[mi][i]; d++){
1337: newm=savm;
1338: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
1339: for (kk=1; kk<=cptcovage;kk++) {
1340: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
1341: }
1342: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1343: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1344: savm=oldm;
1345: oldm=newm;
1346: } /* end mult */
1347:
1348: s1=s[mw[mi][i]][i];
1349: s2=s[mw[mi+1][i]][i];
1350: bbh=(double)bh[mi][i]/(double)stepm;
1351: /* bias is positive if real duration
1352: * is higher than the multiple of stepm and negative otherwise.
1353: */
1354: if( s2 > nlstate && (mle <5) ){ /* Jackson */
1355: lli=log(out[s1][s2] - savm[s1][s2]);
1356: } else if (mle==1){
1357: lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
1358: } else if(mle==2){
1359: 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 */
1360: } else if(mle==3){ /* exponential inter-extrapolation */
1361: 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 */
1362: } else if (mle==4){ /* mle=4 no inter-extrapolation */
1363: lli=log(out[s1][s2]); /* Original formula */
1364: } else{ /* ml>=5 no inter-extrapolation no jackson =0.8a */
1365: lli=log(out[s1][s2]); /* Original formula */
1366: } /* End of if */
1367: ipmx +=1;
1368: sw += weight[i];
1369: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1370: /* 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]); */
1371: if(globpr){
1.88 brouard 1372: fprintf(ficresilk,"%9d %6d %1d %1d %1d %1d %3d %10.6f %6.4f\
1.86 brouard 1373: %10.6f %10.6f %10.6f ", \
1374: num[i],i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],
1375: 2*weight[i]*lli,out[s1][s2],savm[s1][s2]);
1.87 brouard 1376: for(k=1,llt=0.,l=0.; k<=nlstate; k++){
1377: llt +=ll[k]*gipmx/gsw;
1378: fprintf(ficresilk," %10.6f",-ll[k]*gipmx/gsw);
1379: }
1380: fprintf(ficresilk," %10.6f\n", -llt);
1.85 brouard 1381: }
1382: } /* end of wave */
1383: } /* end of individual */
1384: for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
1385: /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
1386: l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
1.87 brouard 1387: if(globpr==0){ /* First time we count the contributions and weights */
1388: gipmx=ipmx;
1389: gsw=sw;
1390: }
1.53 brouard 1391: return -l;
1392: }
1393:
1.88 brouard 1394: char *subdirf(char fileres[])
1395: {
1396:
1397: strcpy(tmpout,optionfilefiname);
1398: strcat(tmpout,"/"); /* Add to the right */
1399: strcat(tmpout,fileres);
1400: return tmpout;
1401: }
1402:
1403: char *subdirf2(char fileres[], char *preop)
1404: {
1405:
1406: strcpy(tmpout,optionfilefiname);
1407: strcat(tmpout,"/");
1408: strcat(tmpout,preop);
1409: strcat(tmpout,fileres);
1410: return tmpout;
1411: }
1412: char *subdirf3(char fileres[], char *preop, char *preop2)
1413: {
1414:
1415: strcpy(tmpout,optionfilefiname);
1416: strcat(tmpout,"/");
1417: strcat(tmpout,preop);
1418: strcat(tmpout,preop2);
1419: strcat(tmpout,fileres);
1420: return tmpout;
1421: }
1.53 brouard 1422:
1.87 brouard 1423: void likelione(FILE *ficres,double p[], int npar, int nlstate, int *globpri, long *ipmx, double *sw, double *fretone, double (*funcone)(double []))
1.85 brouard 1424: {
1.87 brouard 1425: /* This routine should help understanding what is done with
1426: the selection of individuals/waves and
1.85 brouard 1427: to check the exact contribution to the likelihood.
1428: Plotting could be done.
1429: */
1430: int k;
1.87 brouard 1431:
1.88 brouard 1432: if(*globpri !=0){ /* Just counts and sums, no printings */
1.85 brouard 1433: strcpy(fileresilk,"ilk");
1434: strcat(fileresilk,fileres);
1435: if((ficresilk=fopen(fileresilk,"w"))==NULL) {
1436: printf("Problem with resultfile: %s\n", fileresilk);
1437: fprintf(ficlog,"Problem with resultfile: %s\n", fileresilk);
1438: }
1.87 brouard 1439: fprintf(ficresilk, "#individual(line's_record) s1 s2 wave# effective_wave# number_of_matrices_product pij weight -2ln(pij)*weight 0pij_x 0pij_(x-stepm) cumulating_loglikeli_by_health_state(reweighted=-2ll*weightXnumber_of_contribs/sum_of_weights) and_total\n");
1.88 brouard 1440: fprintf(ficresilk, "#num_i i s1 s2 mi mw dh likeli weight 2wlli out sav ");
1.85 brouard 1441: /* i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],2*weight[i]*lli,out[s1][s2],savm[s1][s2]); */
1442: for(k=1; k<=nlstate; k++)
1.87 brouard 1443: fprintf(ficresilk," -2*gipw/gsw*weight*ll[%d]++",k);
1444: fprintf(ficresilk," -2*gipw/gsw*weight*ll(total)\n");
1.85 brouard 1445: }
1446:
1447: *fretone=(*funcone)(p);
1.87 brouard 1448: if(*globpri !=0){
1.85 brouard 1449: fclose(ficresilk);
1.88 brouard 1450: fprintf(fichtm,"\n<br>File of contributions to the likelihood: <a href=\"%s\">%s</a><br>\n",subdirf(fileresilk),subdirf(fileresilk));
1.87 brouard 1451: fflush(fichtm);
1452: }
1.85 brouard 1453: return;
1454: }
1455:
1.88 brouard 1456:
1.53 brouard 1457: /*********** Maximum Likelihood Estimation ***************/
1458:
1459: void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
1460: {
1461: int i,j, iter;
1.74 brouard 1462: double **xi;
1.53 brouard 1463: double fret;
1.85 brouard 1464: double fretone; /* Only one call to likelihood */
1.76 brouard 1465: char filerespow[FILENAMELENGTH];
1.53 brouard 1466: xi=matrix(1,npar,1,npar);
1467: for (i=1;i<=npar;i++)
1468: for (j=1;j<=npar;j++)
1469: xi[i][j]=(i==j ? 1.0 : 0.0);
1470: printf("Powell\n"); fprintf(ficlog,"Powell\n");
1.76 brouard 1471: strcpy(filerespow,"pow");
1472: strcat(filerespow,fileres);
1473: if((ficrespow=fopen(filerespow,"w"))==NULL) {
1474: printf("Problem with resultfile: %s\n", filerespow);
1475: fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
1476: }
1477: fprintf(ficrespow,"# Powell\n# iter -2*LL");
1478: for (i=1;i<=nlstate;i++)
1479: for(j=1;j<=nlstate+ndeath;j++)
1480: if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
1481: fprintf(ficrespow,"\n");
1.85 brouard 1482:
1.53 brouard 1483: powell(p,xi,npar,ftol,&iter,&fret,func);
1484:
1.76 brouard 1485: fclose(ficrespow);
1486: printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));
1.65 lievre 1487: fprintf(ficlog,"\n#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
1.53 brouard 1488: fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
1489:
1490: }
1491:
1492: /**** Computes Hessian and covariance matrix ***/
1493: void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
1494: {
1495: double **a,**y,*x,pd;
1496: double **hess;
1497: int i, j,jk;
1498: int *indx;
1499:
1500: double hessii(double p[], double delta, int theta, double delti[]);
1501: double hessij(double p[], double delti[], int i, int j);
1502: void lubksb(double **a, int npar, int *indx, double b[]) ;
1503: void ludcmp(double **a, int npar, int *indx, double *d) ;
1504:
1505: hess=matrix(1,npar,1,npar);
1506:
1507: printf("\nCalculation of the hessian matrix. Wait...\n");
1508: fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
1509: for (i=1;i<=npar;i++){
1510: printf("%d",i);fflush(stdout);
1511: fprintf(ficlog,"%d",i);fflush(ficlog);
1512: hess[i][i]=hessii(p,ftolhess,i,delti);
1513: /*printf(" %f ",p[i]);*/
1514: /*printf(" %lf ",hess[i][i]);*/
1515: }
1516:
1517: for (i=1;i<=npar;i++) {
1518: for (j=1;j<=npar;j++) {
1519: if (j>i) {
1520: printf(".%d%d",i,j);fflush(stdout);
1521: fprintf(ficlog,".%d%d",i,j);fflush(ficlog);
1522: hess[i][j]=hessij(p,delti,i,j);
1523: hess[j][i]=hess[i][j];
1524: /*printf(" %lf ",hess[i][j]);*/
1525: }
1526: }
1527: }
1528: printf("\n");
1529: fprintf(ficlog,"\n");
1530:
1531: printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
1532: fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
1533:
1534: a=matrix(1,npar,1,npar);
1535: y=matrix(1,npar,1,npar);
1536: x=vector(1,npar);
1537: indx=ivector(1,npar);
1538: for (i=1;i<=npar;i++)
1539: for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
1540: ludcmp(a,npar,indx,&pd);
1541:
1542: for (j=1;j<=npar;j++) {
1543: for (i=1;i<=npar;i++) x[i]=0;
1544: x[j]=1;
1545: lubksb(a,npar,indx,x);
1546: for (i=1;i<=npar;i++){
1547: matcov[i][j]=x[i];
1548: }
1549: }
1550:
1551: printf("\n#Hessian matrix#\n");
1552: fprintf(ficlog,"\n#Hessian matrix#\n");
1553: for (i=1;i<=npar;i++) {
1554: for (j=1;j<=npar;j++) {
1555: printf("%.3e ",hess[i][j]);
1556: fprintf(ficlog,"%.3e ",hess[i][j]);
1557: }
1558: printf("\n");
1559: fprintf(ficlog,"\n");
1560: }
1561:
1562: /* Recompute Inverse */
1563: for (i=1;i<=npar;i++)
1564: for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];
1565: ludcmp(a,npar,indx,&pd);
1566:
1567: /* printf("\n#Hessian matrix recomputed#\n");
1568:
1569: for (j=1;j<=npar;j++) {
1570: for (i=1;i<=npar;i++) x[i]=0;
1571: x[j]=1;
1572: lubksb(a,npar,indx,x);
1573: for (i=1;i<=npar;i++){
1574: y[i][j]=x[i];
1575: printf("%.3e ",y[i][j]);
1576: fprintf(ficlog,"%.3e ",y[i][j]);
1577: }
1578: printf("\n");
1579: fprintf(ficlog,"\n");
1580: }
1581: */
1582:
1583: free_matrix(a,1,npar,1,npar);
1584: free_matrix(y,1,npar,1,npar);
1585: free_vector(x,1,npar);
1586: free_ivector(indx,1,npar);
1587: free_matrix(hess,1,npar,1,npar);
1588:
1589:
1590: }
1591:
1592: /*************** hessian matrix ****************/
1593: double hessii( double x[], double delta, int theta, double delti[])
1594: {
1595: int i;
1596: int l=1, lmax=20;
1597: double k1,k2;
1598: double p2[NPARMAX+1];
1599: double res;
1600: double delt, delts, nkhi=10.,nkhif=1., khi=1.e-4;
1601: double fx;
1602: int k=0,kmax=10;
1603: double l1;
1604:
1605: fx=func(x);
1606: for (i=1;i<=npar;i++) p2[i]=x[i];
1607: for(l=0 ; l <=lmax; l++){
1608: l1=pow(10,l);
1609: delts=delt;
1610: for(k=1 ; k <kmax; k=k+1){
1611: delt = delta*(l1*k);
1612: p2[theta]=x[theta] +delt;
1613: k1=func(p2)-fx;
1614: p2[theta]=x[theta]-delt;
1615: k2=func(p2)-fx;
1616: /*res= (k1-2.0*fx+k2)/delt/delt; */
1617: res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */
1618:
1619: #ifdef DEBUG
1620: 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);
1621: 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);
1622: #endif
1623: /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
1624: if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
1625: k=kmax;
1626: }
1627: else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
1628: k=kmax; l=lmax*10.;
1629: }
1630: else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){
1631: delts=delt;
1632: }
1633: }
1634: }
1635: delti[theta]=delts;
1636: return res;
1637:
1638: }
1639:
1640: double hessij( double x[], double delti[], int thetai,int thetaj)
1641: {
1642: int i;
1643: int l=1, l1, lmax=20;
1644: double k1,k2,k3,k4,res,fx;
1645: double p2[NPARMAX+1];
1646: int k;
1647:
1648: fx=func(x);
1649: for (k=1; k<=2; k++) {
1650: for (i=1;i<=npar;i++) p2[i]=x[i];
1651: p2[thetai]=x[thetai]+delti[thetai]/k;
1652: p2[thetaj]=x[thetaj]+delti[thetaj]/k;
1653: k1=func(p2)-fx;
1654:
1655: p2[thetai]=x[thetai]+delti[thetai]/k;
1656: p2[thetaj]=x[thetaj]-delti[thetaj]/k;
1657: k2=func(p2)-fx;
1658:
1659: p2[thetai]=x[thetai]-delti[thetai]/k;
1660: p2[thetaj]=x[thetaj]+delti[thetaj]/k;
1661: k3=func(p2)-fx;
1662:
1663: p2[thetai]=x[thetai]-delti[thetai]/k;
1664: p2[thetaj]=x[thetaj]-delti[thetaj]/k;
1665: k4=func(p2)-fx;
1666: res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */
1667: #ifdef DEBUG
1668: 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);
1669: 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);
1670: #endif
1671: }
1672: return res;
1673: }
1674:
1675: /************** Inverse of matrix **************/
1676: void ludcmp(double **a, int n, int *indx, double *d)
1677: {
1678: int i,imax,j,k;
1679: double big,dum,sum,temp;
1680: double *vv;
1681:
1682: vv=vector(1,n);
1683: *d=1.0;
1684: for (i=1;i<=n;i++) {
1685: big=0.0;
1686: for (j=1;j<=n;j++)
1687: if ((temp=fabs(a[i][j])) > big) big=temp;
1688: if (big == 0.0) nrerror("Singular matrix in routine ludcmp");
1689: vv[i]=1.0/big;
1690: }
1691: for (j=1;j<=n;j++) {
1692: for (i=1;i<j;i++) {
1693: sum=a[i][j];
1694: for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];
1695: a[i][j]=sum;
1696: }
1697: big=0.0;
1698: for (i=j;i<=n;i++) {
1699: sum=a[i][j];
1700: for (k=1;k<j;k++)
1701: sum -= a[i][k]*a[k][j];
1702: a[i][j]=sum;
1703: if ( (dum=vv[i]*fabs(sum)) >= big) {
1704: big=dum;
1705: imax=i;
1706: }
1707: }
1708: if (j != imax) {
1709: for (k=1;k<=n;k++) {
1710: dum=a[imax][k];
1711: a[imax][k]=a[j][k];
1712: a[j][k]=dum;
1713: }
1714: *d = -(*d);
1715: vv[imax]=vv[j];
1716: }
1717: indx[j]=imax;
1718: if (a[j][j] == 0.0) a[j][j]=TINY;
1719: if (j != n) {
1720: dum=1.0/(a[j][j]);
1721: for (i=j+1;i<=n;i++) a[i][j] *= dum;
1722: }
1723: }
1724: free_vector(vv,1,n); /* Doesn't work */
1725: ;
1726: }
1727:
1728: void lubksb(double **a, int n, int *indx, double b[])
1729: {
1730: int i,ii=0,ip,j;
1731: double sum;
1732:
1733: for (i=1;i<=n;i++) {
1734: ip=indx[i];
1735: sum=b[ip];
1736: b[ip]=b[i];
1737: if (ii)
1738: for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];
1739: else if (sum) ii=i;
1740: b[i]=sum;
1741: }
1742: for (i=n;i>=1;i--) {
1743: sum=b[i];
1744: for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];
1745: b[i]=sum/a[i][i];
1746: }
1747: }
1748:
1749: /************ Frequencies ********************/
1.84 brouard 1750: 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 1751: { /* Some frequencies */
1752:
1753: int i, m, jk, k1,i1, j1, bool, z1,z2,j;
1754: int first;
1755: double ***freq; /* Frequencies */
1.73 lievre 1756: double *pp, **prop;
1757: double pos,posprop, k2, dateintsum=0,k2cpt=0;
1.53 brouard 1758: FILE *ficresp;
1759: char fileresp[FILENAMELENGTH];
1760:
1761: pp=vector(1,nlstate);
1.74 brouard 1762: prop=matrix(1,nlstate,iagemin,iagemax+3);
1.53 brouard 1763: strcpy(fileresp,"p");
1764: strcat(fileresp,fileres);
1765: if((ficresp=fopen(fileresp,"w"))==NULL) {
1766: printf("Problem with prevalence resultfile: %s\n", fileresp);
1767: fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
1768: exit(0);
1769: }
1.74 brouard 1770: freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);
1.53 brouard 1771: j1=0;
1772:
1773: j=cptcoveff;
1774: if (cptcovn<1) {j=1;ncodemax[1]=1;}
1775:
1776: first=1;
1777:
1778: for(k1=1; k1<=j;k1++){
1779: for(i1=1; i1<=ncodemax[k1];i1++){
1780: j1++;
1781: /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
1782: scanf("%d", i);*/
1783: for (i=-1; i<=nlstate+ndeath; i++)
1784: for (jk=-1; jk<=nlstate+ndeath; jk++)
1.74 brouard 1785: for(m=iagemin; m <= iagemax+3; m++)
1.53 brouard 1786: freq[i][jk][m]=0;
1.73 lievre 1787:
1788: for (i=1; i<=nlstate; i++)
1.74 brouard 1789: for(m=iagemin; m <= iagemax+3; m++)
1.73 lievre 1790: prop[i][m]=0;
1.53 brouard 1791:
1792: dateintsum=0;
1793: k2cpt=0;
1794: for (i=1; i<=imx; i++) {
1795: bool=1;
1796: if (cptcovn>0) {
1797: for (z1=1; z1<=cptcoveff; z1++)
1798: if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])
1799: bool=0;
1800: }
1.58 lievre 1801: if (bool==1){
1.53 brouard 1802: for(m=firstpass; m<=lastpass; m++){
1803: k2=anint[m][i]+(mint[m][i]/12.);
1.84 brouard 1804: /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/
1.74 brouard 1805: if(agev[m][i]==0) agev[m][i]=iagemax+1;
1806: if(agev[m][i]==1) agev[m][i]=iagemax+2;
1.73 lievre 1807: if (s[m][i]>0 && s[m][i]<=nlstate) prop[s[m][i]][(int)agev[m][i]] += weight[i];
1.53 brouard 1808: if (m<lastpass) {
1809: freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
1.74 brouard 1810: freq[s[m][i]][s[m+1][i]][iagemax+3] += weight[i];
1.53 brouard 1811: }
1812:
1.74 brouard 1813: if ((agev[m][i]>1) && (agev[m][i]< (iagemax+3))) {
1.53 brouard 1814: dateintsum=dateintsum+k2;
1815: k2cpt++;
1816: }
1.84 brouard 1817: /*}*/
1.53 brouard 1818: }
1819: }
1820: }
1821:
1.84 brouard 1822: /* fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
1.53 brouard 1823:
1824: if (cptcovn>0) {
1825: fprintf(ficresp, "\n#********** Variable ");
1826: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
1827: fprintf(ficresp, "**********\n#");
1828: }
1829: for(i=1; i<=nlstate;i++)
1830: fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
1831: fprintf(ficresp, "\n");
1832:
1.74 brouard 1833: for(i=iagemin; i <= iagemax+3; i++){
1834: if(i==iagemax+3){
1.53 brouard 1835: fprintf(ficlog,"Total");
1836: }else{
1837: if(first==1){
1838: first=0;
1839: printf("See log file for details...\n");
1840: }
1841: fprintf(ficlog,"Age %d", i);
1842: }
1843: for(jk=1; jk <=nlstate ; jk++){
1844: for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
1845: pp[jk] += freq[jk][m][i];
1846: }
1847: for(jk=1; jk <=nlstate ; jk++){
1848: for(m=-1, pos=0; m <=0 ; m++)
1849: pos += freq[jk][m][i];
1850: if(pp[jk]>=1.e-10){
1851: if(first==1){
1852: printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
1853: }
1854: fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
1855: }else{
1856: if(first==1)
1857: printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
1858: fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
1859: }
1860: }
1861:
1862: for(jk=1; jk <=nlstate ; jk++){
1863: for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
1864: pp[jk] += freq[jk][m][i];
1.73 lievre 1865: }
1866: for(jk=1,pos=0,posprop=0; jk <=nlstate ; jk++){
1867: pos += pp[jk];
1868: posprop += prop[jk][i];
1.53 brouard 1869: }
1870: for(jk=1; jk <=nlstate ; jk++){
1871: if(pos>=1.e-5){
1872: if(first==1)
1873: printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
1874: fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
1875: }else{
1876: if(first==1)
1877: printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
1878: fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
1879: }
1.74 brouard 1880: if( i <= iagemax){
1.53 brouard 1881: if(pos>=1.e-5){
1.73 lievre 1882: fprintf(ficresp," %d %.5f %.0f %.0f",i,prop[jk][i]/posprop, prop[jk][i],posprop);
1.84 brouard 1883: /*probs[i][jk][j1]= pp[jk]/pos;*/
1.53 brouard 1884: /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/
1885: }
1886: else
1.73 lievre 1887: fprintf(ficresp," %d NaNq %.0f %.0f",i,prop[jk][i],posprop);
1.53 brouard 1888: }
1889: }
1890:
1.69 brouard 1891: for(jk=-1; jk <=nlstate+ndeath; jk++)
1892: for(m=-1; m <=nlstate+ndeath; m++)
1.53 brouard 1893: if(freq[jk][m][i] !=0 ) {
1894: if(first==1)
1895: printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
1896: fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
1897: }
1.74 brouard 1898: if(i <= iagemax)
1.53 brouard 1899: fprintf(ficresp,"\n");
1900: if(first==1)
1901: printf("Others in log...\n");
1902: fprintf(ficlog,"\n");
1903: }
1904: }
1905: }
1906: dateintmean=dateintsum/k2cpt;
1907:
1908: fclose(ficresp);
1.74 brouard 1909: free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);
1.53 brouard 1910: free_vector(pp,1,nlstate);
1.74 brouard 1911: free_matrix(prop,1,nlstate,iagemin, iagemax+3);
1.53 brouard 1912: /* End of Freq */
1913: }
1914:
1915: /************ Prevalence ********************/
1.84 brouard 1916: 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 1917: {
1918: /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
1919: in each health status at the date of interview (if between dateprev1 and dateprev2).
1920: We still use firstpass and lastpass as another selection.
1921: */
1.53 brouard 1922:
1923: int i, m, jk, k1, i1, j1, bool, z1,z2,j;
1924: double ***freq; /* Frequencies */
1.73 lievre 1925: double *pp, **prop;
1926: double pos,posprop;
1.69 brouard 1927: double y2; /* in fractional years */
1.74 brouard 1928: int iagemin, iagemax;
1.53 brouard 1929:
1.74 brouard 1930: iagemin= (int) agemin;
1931: iagemax= (int) agemax;
1932: /*pp=vector(1,nlstate);*/
1933: prop=matrix(1,nlstate,iagemin,iagemax+3);
1934: /* freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
1.53 brouard 1935: j1=0;
1936:
1937: j=cptcoveff;
1938: if (cptcovn<1) {j=1;ncodemax[1]=1;}
1939:
1940: for(k1=1; k1<=j;k1++){
1941: for(i1=1; i1<=ncodemax[k1];i1++){
1942: j1++;
1943:
1.73 lievre 1944: for (i=1; i<=nlstate; i++)
1.74 brouard 1945: for(m=iagemin; m <= iagemax+3; m++)
1946: prop[i][m]=0.0;
1.53 brouard 1947:
1.69 brouard 1948: for (i=1; i<=imx; i++) { /* Each individual */
1.53 brouard 1949: bool=1;
1950: if (cptcovn>0) {
1951: for (z1=1; z1<=cptcoveff; z1++)
1952: if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])
1953: bool=0;
1954: }
1955: if (bool==1) {
1.69 brouard 1956: for(m=firstpass; m<=lastpass; m++){/* Other selection (we can limit to certain interviews*/
1957: y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
1958: if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
1.74 brouard 1959: if(agev[m][i]==0) agev[m][i]=iagemax+1;
1960: if(agev[m][i]==1) agev[m][i]=iagemax+2;
1961: 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);
1962: if (s[m][i]>0 && s[m][i]<=nlstate) {
1963: /*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]]);*/
1964: prop[s[m][i]][(int)agev[m][i]] += weight[i];
1965: prop[s[m][i]][iagemax+3] += weight[i];
1966: }
1.53 brouard 1967: }
1.69 brouard 1968: } /* end selection of waves */
1.53 brouard 1969: }
1970: }
1.74 brouard 1971: for(i=iagemin; i <= iagemax+3; i++){
1.53 brouard 1972:
1.74 brouard 1973: for(jk=1,posprop=0; jk <=nlstate ; jk++) {
1974: posprop += prop[jk][i];
1975: }
1976:
1977: for(jk=1; jk <=nlstate ; jk++){
1978: if( i <= iagemax){
1979: if(posprop>=1.e-5){
1980: probs[i][jk][j1]= prop[jk][i]/posprop;
1981: }
1982: }
1983: }/* end jk */
1984: }/* end i */
1.53 brouard 1985: } /* end i1 */
1986: } /* end k1 */
1987:
1.74 brouard 1988: /* free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
1989: /*free_vector(pp,1,nlstate);*/
1990: free_matrix(prop,1,nlstate, iagemin,iagemax+3);
1991: } /* End of prevalence */
1.53 brouard 1992:
1993: /************* Waves Concatenation ***************/
1994:
1.59 brouard 1995: 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 1996: {
1997: /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
1998: Death is a valid wave (if date is known).
1999: mw[mi][i] is the mi (mi=1 to wav[i]) effective wave of individual i
1.59 brouard 2000: dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
1.53 brouard 2001: and mw[mi+1][i]. dh depends on stepm.
2002: */
2003:
2004: int i, mi, m;
2005: /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
2006: double sum=0., jmean=0.;*/
2007: int first;
2008: int j, k=0,jk, ju, jl;
2009: double sum=0.;
2010: first=0;
2011: jmin=1e+5;
2012: jmax=-1;
2013: jmean=0.;
2014: for(i=1; i<=imx; i++){
2015: mi=0;
2016: m=firstpass;
2017: while(s[m][i] <= nlstate){
1.69 brouard 2018: if(s[m][i]>=1)
1.53 brouard 2019: mw[++mi][i]=m;
2020: if(m >=lastpass)
2021: break;
2022: else
2023: m++;
2024: }/* end while */
2025: if (s[m][i] > nlstate){
2026: mi++; /* Death is another wave */
2027: /* if(mi==0) never been interviewed correctly before death */
2028: /* Only death is a correct wave */
2029: mw[mi][i]=m;
2030: }
2031:
2032: wav[i]=mi;
2033: if(mi==0){
2034: if(first==0){
1.85 brouard 2035: printf("Warning! None valid information for:%ld line=%d (skipped) and may be others, see log file\n",num[i],i);
1.53 brouard 2036: first=1;
2037: }
2038: if(first==1){
1.85 brouard 2039: fprintf(ficlog,"Warning! None valid information for:%ld line=%d (skipped)\n",num[i],i);
1.53 brouard 2040: }
2041: } /* end mi==0 */
1.77 brouard 2042: } /* End individuals */
1.53 brouard 2043:
2044: for(i=1; i<=imx; i++){
2045: for(mi=1; mi<wav[i];mi++){
2046: if (stepm <=0)
2047: dh[mi][i]=1;
2048: else{
1.77 brouard 2049: if (s[mw[mi+1][i]][i] > nlstate) { /* A death */
1.53 brouard 2050: if (agedc[i] < 2*AGESUP) {
1.85 brouard 2051: j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);
2052: if(j==0) j=1; /* Survives at least one month after exam */
2053: else if(j<0){
2054: 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]);
2055: j=1; /* Careful Patch */
1.86 brouard 2056: 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 fix the contradiction between dates.\n",stepm);
1.85 brouard 2057: 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]);
2058: 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);
2059: }
2060: k=k+1;
2061: if (j >= jmax) jmax=j;
2062: if (j <= jmin) jmin=j;
2063: sum=sum+j;
2064: /*if (j<0) printf("j=%d num=%d \n",j,i);*/
2065: /* printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
1.53 brouard 2066: }
2067: }
2068: else{
2069: j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
1.68 lievre 2070: /* printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
1.53 brouard 2071: k=k+1;
2072: if (j >= jmax) jmax=j;
2073: else if (j <= jmin)jmin=j;
2074: /* if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
1.73 lievre 2075: /*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 2076: if(j<0){
2077: 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]);
2078: 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]);
2079: }
1.53 brouard 2080: sum=sum+j;
2081: }
2082: jk= j/stepm;
2083: jl= j -jk*stepm;
2084: ju= j -(jk+1)*stepm;
1.85 brouard 2085: if(mle <=1){ /* only if we use a the linear-interpoloation pseudo-likelihood */
1.64 lievre 2086: if(jl==0){
2087: dh[mi][i]=jk;
2088: bh[mi][i]=0;
2089: }else{ /* We want a negative bias in order to only have interpolation ie
2090: * at the price of an extra matrix product in likelihood */
2091: dh[mi][i]=jk+1;
2092: bh[mi][i]=ju;
2093: }
2094: }else{
2095: if(jl <= -ju){
2096: dh[mi][i]=jk;
2097: bh[mi][i]=jl; /* bias is positive if real duration
2098: * is higher than the multiple of stepm and negative otherwise.
2099: */
2100: }
2101: else{
2102: dh[mi][i]=jk+1;
2103: bh[mi][i]=ju;
2104: }
2105: if(dh[mi][i]==0){
2106: dh[mi][i]=1; /* At least one step */
2107: bh[mi][i]=ju; /* At least one step */
1.71 brouard 2108: /* 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 2109: }
1.85 brouard 2110: } /* end if mle */
2111: }
1.64 lievre 2112: } /* end wave */
1.53 brouard 2113: }
2114: jmean=sum/k;
2115: printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);
2116: fprintf(ficlog,"Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);
2117: }
2118:
2119: /*********** Tricode ****************************/
2120: void tricode(int *Tvar, int **nbcode, int imx)
2121: {
1.58 lievre 2122:
2123: int Ndum[20],ij=1, k, j, i, maxncov=19;
1.53 brouard 2124: int cptcode=0;
2125: cptcoveff=0;
2126:
1.58 lievre 2127: for (k=0; k<maxncov; k++) Ndum[k]=0;
1.53 brouard 2128: for (k=1; k<=7; k++) ncodemax[k]=0;
2129:
2130: for (j=1; j<=(cptcovn+2*cptcovprod); j++) {
1.58 lievre 2131: for (i=1; i<=imx; i++) { /*reads the data file to get the maximum
2132: modality*/
2133: ij=(int)(covar[Tvar[j]][i]); /* ij is the modality of this individual*/
2134: Ndum[ij]++; /*store the modality */
1.53 brouard 2135: /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
1.58 lievre 2136: if (ij > cptcode) cptcode=ij; /* getting the maximum of covariable
2137: Tvar[j]. If V=sex and male is 0 and
2138: female is 1, then cptcode=1.*/
1.53 brouard 2139: }
2140:
2141: for (i=0; i<=cptcode; i++) {
1.58 lievre 2142: 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 2143: }
1.58 lievre 2144:
1.53 brouard 2145: ij=1;
2146: for (i=1; i<=ncodemax[j]; i++) {
1.58 lievre 2147: for (k=0; k<= maxncov; k++) {
1.53 brouard 2148: if (Ndum[k] != 0) {
2149: nbcode[Tvar[j]][ij]=k;
1.58 lievre 2150: /* 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 2151:
2152: ij++;
2153: }
2154: if (ij > ncodemax[j]) break;
2155: }
2156: }
2157: }
2158:
1.58 lievre 2159: for (k=0; k< maxncov; k++) Ndum[k]=0;
1.53 brouard 2160:
1.58 lievre 2161: for (i=1; i<=ncovmodel-2; i++) {
2162: /* 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 2163: ij=Tvar[i];
1.58 lievre 2164: Ndum[ij]++;
1.53 brouard 2165: }
2166:
2167: ij=1;
1.58 lievre 2168: for (i=1; i<= maxncov; i++) {
1.53 brouard 2169: if((Ndum[i]!=0) && (i<=ncovcol)){
1.58 lievre 2170: Tvaraff[ij]=i; /*For printing */
1.53 brouard 2171: ij++;
2172: }
2173: }
2174:
1.58 lievre 2175: cptcoveff=ij-1; /*Number of simple covariates*/
1.53 brouard 2176: }
2177:
2178: /*********** Health Expectancies ****************/
2179:
2180: 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 )
2181:
2182: {
2183: /* Health expectancies */
2184: int i, j, nhstepm, hstepm, h, nstepm, k, cptj;
2185: double age, agelim, hf;
2186: double ***p3mat,***varhe;
2187: double **dnewm,**doldm;
2188: double *xp;
2189: double **gp, **gm;
2190: double ***gradg, ***trgradg;
2191: int theta;
2192:
1.74 brouard 2193: varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage);
1.53 brouard 2194: xp=vector(1,npar);
1.74 brouard 2195: dnewm=matrix(1,nlstate*nlstate,1,npar);
2196: doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate);
1.53 brouard 2197:
2198: fprintf(ficreseij,"# Health expectancies\n");
2199: fprintf(ficreseij,"# Age");
2200: for(i=1; i<=nlstate;i++)
2201: for(j=1; j<=nlstate;j++)
2202: fprintf(ficreseij," %1d-%1d (SE)",i,j);
2203: fprintf(ficreseij,"\n");
2204:
2205: if(estepm < stepm){
2206: printf ("Problem %d lower than %d\n",estepm, stepm);
2207: }
2208: else hstepm=estepm;
2209: /* We compute the life expectancy from trapezoids spaced every estepm months
2210: * This is mainly to measure the difference between two models: for example
2211: * if stepm=24 months pijx are given only every 2 years and by summing them
2212: * we are calculating an estimate of the Life Expectancy assuming a linear
1.66 brouard 2213: * progression in between and thus overestimating or underestimating according
1.53 brouard 2214: * to the curvature of the survival function. If, for the same date, we
2215: * estimate the model with stepm=1 month, we can keep estepm to 24 months
2216: * to compare the new estimate of Life expectancy with the same linear
2217: * hypothesis. A more precise result, taking into account a more precise
2218: * curvature will be obtained if estepm is as small as stepm. */
2219:
2220: /* For example we decided to compute the life expectancy with the smallest unit */
2221: /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
2222: nhstepm is the number of hstepm from age to agelim
2223: nstepm is the number of stepm from age to agelin.
2224: Look at hpijx to understand the reason of that which relies in memory size
2225: and note for a fixed period like estepm months */
2226: /* We decided (b) to get a life expectancy respecting the most precise curvature of the
2227: survival function given by stepm (the optimization length). Unfortunately it
2228: means that if the survival funtion is printed only each two years of age and if
2229: you sum them up and add 1 year (area under the trapezoids) you won't get the same
2230: results. So we changed our mind and took the option of the best precision.
2231: */
2232: hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
2233:
2234: agelim=AGESUP;
2235: for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
2236: /* nhstepm age range expressed in number of stepm */
2237: nstepm=(int) rint((agelim-age)*YEARM/stepm);
2238: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
2239: /* if (stepm >= YEARM) hstepm=1;*/
2240: nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
2241: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
1.74 brouard 2242: gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);
2243: gp=matrix(0,nhstepm,1,nlstate*nlstate);
2244: gm=matrix(0,nhstepm,1,nlstate*nlstate);
1.53 brouard 2245:
2246: /* Computed by stepm unit matrices, product of hstepm matrices, stored
2247: in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
2248: hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);
2249:
2250:
2251: hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
2252:
2253: /* Computing Variances of health expectancies */
2254:
2255: for(theta=1; theta <=npar; theta++){
2256: for(i=1; i<=npar; i++){
2257: xp[i] = x[i] + (i==theta ?delti[theta]:0);
2258: }
2259: hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
2260:
2261: cptj=0;
2262: for(j=1; j<= nlstate; j++){
2263: for(i=1; i<=nlstate; i++){
2264: cptj=cptj+1;
2265: for(h=0, gp[h][cptj]=0.; h<=nhstepm-1; h++){
2266: gp[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;
2267: }
2268: }
2269: }
2270:
2271:
2272: for(i=1; i<=npar; i++)
2273: xp[i] = x[i] - (i==theta ?delti[theta]:0);
2274: hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
2275:
2276: cptj=0;
2277: for(j=1; j<= nlstate; j++){
2278: for(i=1;i<=nlstate;i++){
2279: cptj=cptj+1;
2280: for(h=0, gm[h][cptj]=0.; h<=nhstepm-1; h++){
1.77 brouard 2281:
1.53 brouard 2282: gm[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;
2283: }
2284: }
2285: }
1.74 brouard 2286: for(j=1; j<= nlstate*nlstate; j++)
1.53 brouard 2287: for(h=0; h<=nhstepm-1; h++){
2288: gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
2289: }
2290: }
2291:
2292: /* End theta */
2293:
1.74 brouard 2294: trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar);
1.53 brouard 2295:
2296: for(h=0; h<=nhstepm-1; h++)
1.74 brouard 2297: for(j=1; j<=nlstate*nlstate;j++)
1.53 brouard 2298: for(theta=1; theta <=npar; theta++)
2299: trgradg[h][j][theta]=gradg[h][theta][j];
2300:
2301:
1.74 brouard 2302: for(i=1;i<=nlstate*nlstate;i++)
2303: for(j=1;j<=nlstate*nlstate;j++)
1.53 brouard 2304: varhe[i][j][(int)age] =0.;
2305:
2306: printf("%d|",(int)age);fflush(stdout);
2307: fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
2308: for(h=0;h<=nhstepm-1;h++){
2309: for(k=0;k<=nhstepm-1;k++){
1.74 brouard 2310: matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov);
2311: matprod2(doldm,dnewm,1,nlstate*nlstate,1,npar,1,nlstate*nlstate,gradg[k]);
2312: for(i=1;i<=nlstate*nlstate;i++)
2313: for(j=1;j<=nlstate*nlstate;j++)
1.53 brouard 2314: varhe[i][j][(int)age] += doldm[i][j]*hf*hf;
2315: }
2316: }
2317: /* Computing expectancies */
2318: for(i=1; i<=nlstate;i++)
2319: for(j=1; j<=nlstate;j++)
2320: for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
2321: eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
2322:
2323: /* 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]);*/
2324:
2325: }
2326:
2327: fprintf(ficreseij,"%3.0f",age );
2328: cptj=0;
2329: for(i=1; i<=nlstate;i++)
2330: for(j=1; j<=nlstate;j++){
2331: cptj++;
2332: fprintf(ficreseij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[cptj][cptj][(int)age]) );
2333: }
2334: fprintf(ficreseij,"\n");
2335:
1.74 brouard 2336: free_matrix(gm,0,nhstepm,1,nlstate*nlstate);
2337: free_matrix(gp,0,nhstepm,1,nlstate*nlstate);
2338: free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*nlstate);
2339: free_ma3x(trgradg,0,nhstepm,1,nlstate*nlstate,1,npar);
1.53 brouard 2340: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
2341: }
2342: printf("\n");
2343: fprintf(ficlog,"\n");
2344:
2345: free_vector(xp,1,npar);
1.74 brouard 2346: free_matrix(dnewm,1,nlstate*nlstate,1,npar);
2347: free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate);
2348: free_ma3x(varhe,1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int)fage);
1.53 brouard 2349: }
2350:
2351: /************ Variance ******************/
2352: 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)
2353: {
2354: /* Variance of health expectancies */
2355: /* double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
2356: /* double **newm;*/
2357: double **dnewm,**doldm;
2358: double **dnewmp,**doldmp;
2359: int i, j, nhstepm, hstepm, h, nstepm ;
2360: int k, cptcode;
2361: double *xp;
2362: double **gp, **gm; /* for var eij */
2363: double ***gradg, ***trgradg; /*for var eij */
2364: double **gradgp, **trgradgp; /* for var p point j */
2365: double *gpp, *gmp; /* for var p point j */
2366: double **varppt; /* for var p point j nlstate to nlstate+ndeath */
2367: double ***p3mat;
2368: double age,agelim, hf;
2369: double ***mobaverage;
2370: int theta;
2371: char digit[4];
1.55 lievre 2372: char digitp[25];
1.53 brouard 2373:
2374: char fileresprobmorprev[FILENAMELENGTH];
2375:
1.55 lievre 2376: if(popbased==1){
1.58 lievre 2377: if(mobilav!=0)
1.55 lievre 2378: strcpy(digitp,"-populbased-mobilav-");
2379: else strcpy(digitp,"-populbased-nomobil-");
2380: }
2381: else
1.53 brouard 2382: strcpy(digitp,"-stablbased-");
1.56 lievre 2383:
1.54 brouard 2384: if (mobilav!=0) {
1.53 brouard 2385: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
1.54 brouard 2386: if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
2387: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
2388: printf(" Error in movingaverage mobilav=%d\n",mobilav);
2389: }
1.53 brouard 2390: }
2391:
2392: strcpy(fileresprobmorprev,"prmorprev");
2393: sprintf(digit,"%-d",ij);
2394: /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
2395: strcat(fileresprobmorprev,digit); /* Tvar to be done */
2396: strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
2397: strcat(fileresprobmorprev,fileres);
2398: if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
2399: printf("Problem with resultfile: %s\n", fileresprobmorprev);
2400: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
2401: }
2402: printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
2403: fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
1.66 brouard 2404: 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 2405: fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
2406: for(j=nlstate+1; j<=(nlstate+ndeath);j++){
2407: fprintf(ficresprobmorprev," p.%-d SE",j);
2408: for(i=1; i<=nlstate;i++)
2409: fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
2410: }
2411: fprintf(ficresprobmorprev,"\n");
1.88 brouard 2412: fprintf(ficgp,"\n# Routine varevsij");
1.87 brouard 2413: 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");
2414: fprintf(fichtm,"\n<br>%s <br>\n",digitp);
2415: /* } */
1.53 brouard 2416: varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
2417:
2418: 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");
2419: fprintf(ficresvij,"# Age");
2420: for(i=1; i<=nlstate;i++)
2421: for(j=1; j<=nlstate;j++)
2422: fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);
2423: fprintf(ficresvij,"\n");
2424:
2425: xp=vector(1,npar);
2426: dnewm=matrix(1,nlstate,1,npar);
2427: doldm=matrix(1,nlstate,1,nlstate);
2428: dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
2429: doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
2430:
2431: gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
2432: gpp=vector(nlstate+1,nlstate+ndeath);
2433: gmp=vector(nlstate+1,nlstate+ndeath);
2434: trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
2435:
2436: if(estepm < stepm){
2437: printf ("Problem %d lower than %d\n",estepm, stepm);
2438: }
2439: else hstepm=estepm;
2440: /* For example we decided to compute the life expectancy with the smallest unit */
2441: /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
2442: nhstepm is the number of hstepm from age to agelim
2443: nstepm is the number of stepm from age to agelin.
2444: Look at hpijx to understand the reason of that which relies in memory size
2445: and note for a fixed period like k years */
2446: /* We decided (b) to get a life expectancy respecting the most precise curvature of the
2447: survival function given by stepm (the optimization length). Unfortunately it
1.66 brouard 2448: means that if the survival funtion is printed every two years of age and if
1.53 brouard 2449: you sum them up and add 1 year (area under the trapezoids) you won't get the same
2450: results. So we changed our mind and took the option of the best precision.
2451: */
2452: hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
2453: agelim = AGESUP;
2454: for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
2455: nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
2456: nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
2457: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
2458: gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
2459: gp=matrix(0,nhstepm,1,nlstate);
2460: gm=matrix(0,nhstepm,1,nlstate);
2461:
2462:
2463: for(theta=1; theta <=npar; theta++){
1.66 brouard 2464: for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
1.53 brouard 2465: xp[i] = x[i] + (i==theta ?delti[theta]:0);
2466: }
2467: hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
2468: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
2469:
2470: if (popbased==1) {
1.54 brouard 2471: if(mobilav ==0){
1.53 brouard 2472: for(i=1; i<=nlstate;i++)
2473: prlim[i][i]=probs[(int)age][i][ij];
1.54 brouard 2474: }else{ /* mobilav */
1.53 brouard 2475: for(i=1; i<=nlstate;i++)
2476: prlim[i][i]=mobaverage[(int)age][i][ij];
2477: }
2478: }
2479:
2480: for(j=1; j<= nlstate; j++){
2481: for(h=0; h<=nhstepm; h++){
2482: for(i=1, gp[h][j]=0.;i<=nlstate;i++)
2483: gp[h][j] += prlim[i][i]*p3mat[i][j][h];
2484: }
2485: }
1.66 brouard 2486: /* This for computing probability of death (h=1 means
2487: computed over hstepm matrices product = hstepm*stepm months)
2488: as a weighted average of prlim.
2489: */
1.69 brouard 2490: for(j=nlstate+1;j<=nlstate+ndeath;j++){
1.68 lievre 2491: for(i=1,gpp[j]=0.; i<= nlstate; i++)
1.53 brouard 2492: gpp[j] += prlim[i][i]*p3mat[i][j][1];
2493: }
1.66 brouard 2494: /* end probability of death */
1.53 brouard 2495:
1.66 brouard 2496: for(i=1; i<=npar; i++) /* Computes gradient x - delta */
1.53 brouard 2497: xp[i] = x[i] - (i==theta ?delti[theta]:0);
2498: hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
2499: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
2500:
2501: if (popbased==1) {
1.54 brouard 2502: if(mobilav ==0){
1.53 brouard 2503: for(i=1; i<=nlstate;i++)
2504: prlim[i][i]=probs[(int)age][i][ij];
1.54 brouard 2505: }else{ /* mobilav */
1.53 brouard 2506: for(i=1; i<=nlstate;i++)
2507: prlim[i][i]=mobaverage[(int)age][i][ij];
2508: }
2509: }
2510:
2511: for(j=1; j<= nlstate; j++){
2512: for(h=0; h<=nhstepm; h++){
2513: for(i=1, gm[h][j]=0.;i<=nlstate;i++)
2514: gm[h][j] += prlim[i][i]*p3mat[i][j][h];
2515: }
2516: }
1.66 brouard 2517: /* This for computing probability of death (h=1 means
2518: computed over hstepm matrices product = hstepm*stepm months)
2519: as a weighted average of prlim.
2520: */
1.69 brouard 2521: for(j=nlstate+1;j<=nlstate+ndeath;j++){
1.68 lievre 2522: for(i=1,gmp[j]=0.; i<= nlstate; i++)
2523: gmp[j] += prlim[i][i]*p3mat[i][j][1];
1.53 brouard 2524: }
1.66 brouard 2525: /* end probability of death */
1.53 brouard 2526:
2527: for(j=1; j<= nlstate; j++) /* vareij */
2528: for(h=0; h<=nhstepm; h++){
2529: gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
2530: }
1.68 lievre 2531:
1.53 brouard 2532: for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
2533: gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
2534: }
2535:
2536: } /* End theta */
2537:
2538: trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
2539:
2540: for(h=0; h<=nhstepm; h++) /* veij */
2541: for(j=1; j<=nlstate;j++)
2542: for(theta=1; theta <=npar; theta++)
2543: trgradg[h][j][theta]=gradg[h][theta][j];
2544:
2545: for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
1.69 brouard 2546: for(theta=1; theta <=npar; theta++)
1.53 brouard 2547: trgradgp[j][theta]=gradgp[theta][j];
1.69 brouard 2548:
1.53 brouard 2549:
2550: hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
2551: for(i=1;i<=nlstate;i++)
2552: for(j=1;j<=nlstate;j++)
2553: vareij[i][j][(int)age] =0.;
2554:
2555: for(h=0;h<=nhstepm;h++){
2556: for(k=0;k<=nhstepm;k++){
2557: matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
2558: matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
2559: for(i=1;i<=nlstate;i++)
2560: for(j=1;j<=nlstate;j++)
2561: vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
2562: }
2563: }
1.70 brouard 2564:
1.53 brouard 2565: /* pptj */
2566: matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
2567: matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
1.70 brouard 2568: for(j=nlstate+1;j<=nlstate+ndeath;j++)
2569: for(i=nlstate+1;i<=nlstate+ndeath;i++)
1.53 brouard 2570: varppt[j][i]=doldmp[j][i];
2571: /* end ppptj */
1.66 brouard 2572: /* x centered again */
1.53 brouard 2573: hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);
2574: prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);
2575:
2576: if (popbased==1) {
1.54 brouard 2577: if(mobilav ==0){
1.53 brouard 2578: for(i=1; i<=nlstate;i++)
2579: prlim[i][i]=probs[(int)age][i][ij];
1.54 brouard 2580: }else{ /* mobilav */
1.53 brouard 2581: for(i=1; i<=nlstate;i++)
2582: prlim[i][i]=mobaverage[(int)age][i][ij];
2583: }
2584: }
1.70 brouard 2585:
1.66 brouard 2586: /* This for computing probability of death (h=1 means
2587: computed over hstepm (estepm) matrices product = hstepm*stepm months)
2588: as a weighted average of prlim.
2589: */
1.68 lievre 2590: for(j=nlstate+1;j<=nlstate+ndeath;j++){
2591: for(i=1,gmp[j]=0.;i<= nlstate; i++)
1.53 brouard 2592: gmp[j] += prlim[i][i]*p3mat[i][j][1];
2593: }
1.66 brouard 2594: /* end probability of death */
1.53 brouard 2595:
2596: fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
2597: for(j=nlstate+1; j<=(nlstate+ndeath);j++){
2598: fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
2599: for(i=1; i<=nlstate;i++){
2600: fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
2601: }
2602: }
2603: fprintf(ficresprobmorprev,"\n");
2604:
2605: fprintf(ficresvij,"%.0f ",age );
2606: for(i=1; i<=nlstate;i++)
2607: for(j=1; j<=nlstate;j++){
2608: fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
2609: }
2610: fprintf(ficresvij,"\n");
2611: free_matrix(gp,0,nhstepm,1,nlstate);
2612: free_matrix(gm,0,nhstepm,1,nlstate);
2613: free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
2614: free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
2615: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
2616: } /* End age */
2617: free_vector(gpp,nlstate+1,nlstate+ndeath);
2618: free_vector(gmp,nlstate+1,nlstate+ndeath);
2619: free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
2620: free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
2621: fprintf(ficgp,"\nset noparametric;set nolabel; set ter png small;set size 0.65, 0.65");
2622: /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */
2623: fprintf(ficgp,"\n set log y; set nolog x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
1.67 brouard 2624: /* fprintf(ficgp,"\n plot \"%s\" u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm); */
2625: /* fprintf(ficgp,"\n replot \"%s\" u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm); */
2626: /* fprintf(ficgp,"\n replot \"%s\" u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm); */
1.88 brouard 2627: fprintf(ficgp,"\n plot \"%s\" u 1:($3) not w l 1 ",subdirf(fileresprobmorprev));
2628: fprintf(ficgp,"\n replot \"%s\" u 1:(($3+1.96*$4)) t \"95\%% interval\" w l 2 ",subdirf(fileresprobmorprev));
2629: fprintf(ficgp,"\n replot \"%s\" u 1:(($3-1.96*$4)) not w l 2 ",subdirf(fileresprobmorprev));
2630: fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",subdirf(fileresprobmorprev),subdirf(fileresprobmorprev));
2631: fprintf(fichtm,"\n<br> Probability is computed over estepm=%d months. <br> <img src=\"%s%s.png\"> <br>\n", estepm,subdirf3(optionfilefiname,"varmuptjgr",digitp),digit);
1.53 brouard 2632: /* 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);
2633: */
1.88 brouard 2634: /* fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.png\";replot;",digitp,optionfilefiname,digit); */
1.89 brouard 2635: fprintf(ficgp,"\nset out \"%s%s.png\";replot;\n",subdirf3(optionfilefiname,"varmuptjgr",digitp),digit);
1.53 brouard 2636:
2637: free_vector(xp,1,npar);
2638: free_matrix(doldm,1,nlstate,1,nlstate);
2639: free_matrix(dnewm,1,nlstate,1,npar);
2640: free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
2641: free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
2642: free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
1.55 lievre 2643: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
1.53 brouard 2644: fclose(ficresprobmorprev);
1.88 brouard 2645: fflush(ficgp);
2646: fflush(fichtm);
1.84 brouard 2647: } /* end varevsij */
1.53 brouard 2648:
2649: /************ Variance of prevlim ******************/
2650: 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)
2651: {
2652: /* Variance of prevalence limit */
1.59 brouard 2653: /* double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
1.53 brouard 2654: double **newm;
2655: double **dnewm,**doldm;
2656: int i, j, nhstepm, hstepm;
2657: int k, cptcode;
2658: double *xp;
2659: double *gp, *gm;
2660: double **gradg, **trgradg;
2661: double age,agelim;
2662: int theta;
2663:
1.54 brouard 2664: fprintf(ficresvpl,"# Standard deviation of stable prevalences \n");
1.53 brouard 2665: fprintf(ficresvpl,"# Age");
2666: for(i=1; i<=nlstate;i++)
2667: fprintf(ficresvpl," %1d-%1d",i,i);
2668: fprintf(ficresvpl,"\n");
2669:
2670: xp=vector(1,npar);
2671: dnewm=matrix(1,nlstate,1,npar);
2672: doldm=matrix(1,nlstate,1,nlstate);
2673:
2674: hstepm=1*YEARM; /* Every year of age */
2675: hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */
2676: agelim = AGESUP;
2677: for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
2678: nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
2679: if (stepm >= YEARM) hstepm=1;
2680: nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
2681: gradg=matrix(1,npar,1,nlstate);
2682: gp=vector(1,nlstate);
2683: gm=vector(1,nlstate);
2684:
2685: for(theta=1; theta <=npar; theta++){
2686: for(i=1; i<=npar; i++){ /* Computes gradient */
2687: xp[i] = x[i] + (i==theta ?delti[theta]:0);
2688: }
2689: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
2690: for(i=1;i<=nlstate;i++)
2691: gp[i] = prlim[i][i];
2692:
2693: for(i=1; i<=npar; i++) /* Computes gradient */
2694: xp[i] = x[i] - (i==theta ?delti[theta]:0);
2695: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
2696: for(i=1;i<=nlstate;i++)
2697: gm[i] = prlim[i][i];
2698:
2699: for(i=1;i<=nlstate;i++)
2700: gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
2701: } /* End theta */
2702:
2703: trgradg =matrix(1,nlstate,1,npar);
2704:
2705: for(j=1; j<=nlstate;j++)
2706: for(theta=1; theta <=npar; theta++)
2707: trgradg[j][theta]=gradg[theta][j];
2708:
2709: for(i=1;i<=nlstate;i++)
2710: varpl[i][(int)age] =0.;
2711: matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
2712: matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
2713: for(i=1;i<=nlstate;i++)
2714: varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
2715:
2716: fprintf(ficresvpl,"%.0f ",age );
2717: for(i=1; i<=nlstate;i++)
2718: fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
2719: fprintf(ficresvpl,"\n");
2720: free_vector(gp,1,nlstate);
2721: free_vector(gm,1,nlstate);
2722: free_matrix(gradg,1,npar,1,nlstate);
2723: free_matrix(trgradg,1,nlstate,1,npar);
2724: } /* End age */
2725:
2726: free_vector(xp,1,npar);
2727: free_matrix(doldm,1,nlstate,1,npar);
2728: free_matrix(dnewm,1,nlstate,1,nlstate);
2729:
2730: }
2731:
2732: /************ Variance of one-step probabilities ******************/
2733: void varprob(char optionfilefiname[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij, int *Tvar, int **nbcode, int *ncodemax)
2734: {
2735: int i, j=0, i1, k1, l1, t, tj;
2736: int k2, l2, j1, z1;
2737: int k=0,l, cptcode;
2738: int first=1, first1;
2739: double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
2740: double **dnewm,**doldm;
2741: double *xp;
2742: double *gp, *gm;
2743: double **gradg, **trgradg;
2744: double **mu;
2745: double age,agelim, cov[NCOVMAX];
2746: double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
2747: int theta;
2748: char fileresprob[FILENAMELENGTH];
2749: char fileresprobcov[FILENAMELENGTH];
2750: char fileresprobcor[FILENAMELENGTH];
2751:
2752: double ***varpij;
2753:
2754: strcpy(fileresprob,"prob");
2755: strcat(fileresprob,fileres);
2756: if((ficresprob=fopen(fileresprob,"w"))==NULL) {
2757: printf("Problem with resultfile: %s\n", fileresprob);
2758: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
2759: }
2760: strcpy(fileresprobcov,"probcov");
2761: strcat(fileresprobcov,fileres);
2762: if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
2763: printf("Problem with resultfile: %s\n", fileresprobcov);
2764: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
2765: }
2766: strcpy(fileresprobcor,"probcor");
2767: strcat(fileresprobcor,fileres);
2768: if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
2769: printf("Problem with resultfile: %s\n", fileresprobcor);
2770: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
2771: }
2772: printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
2773: fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
2774: printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
2775: fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
2776: printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
2777: fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
2778:
2779: fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
2780: fprintf(ficresprob,"# Age");
2781: fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
2782: fprintf(ficresprobcov,"# Age");
2783: fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
2784: fprintf(ficresprobcov,"# Age");
2785:
2786:
2787: for(i=1; i<=nlstate;i++)
2788: for(j=1; j<=(nlstate+ndeath);j++){
2789: fprintf(ficresprob," p%1d-%1d (SE)",i,j);
2790: fprintf(ficresprobcov," p%1d-%1d ",i,j);
2791: fprintf(ficresprobcor," p%1d-%1d ",i,j);
2792: }
1.69 brouard 2793: /* fprintf(ficresprob,"\n");
1.53 brouard 2794: fprintf(ficresprobcov,"\n");
2795: fprintf(ficresprobcor,"\n");
1.69 brouard 2796: */
2797: xp=vector(1,npar);
1.53 brouard 2798: dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
2799: doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
2800: mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
2801: varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
2802: first=1;
1.88 brouard 2803: fprintf(ficgp,"\n# Routine varprob");
2804: fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
2805: fprintf(fichtm,"\n");
2806:
2807: fprintf(fichtm,"\n<li><h4> Computing matrix of variance-covariance of step probabilities</h4></li>\n");
2808: 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");
2809: 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");
1.53 brouard 2810:
2811: cov[1]=1;
2812: tj=cptcoveff;
2813: if (cptcovn<1) {tj=1;ncodemax[1]=1;}
2814: j1=0;
2815: for(t=1; t<=tj;t++){
2816: for(i1=1; i1<=ncodemax[t];i1++){
2817: j1++;
2818: if (cptcovn>0) {
2819: fprintf(ficresprob, "\n#********** Variable ");
2820: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
1.69 brouard 2821: fprintf(ficresprob, "**********\n#\n");
1.53 brouard 2822: fprintf(ficresprobcov, "\n#********** Variable ");
2823: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
1.69 brouard 2824: fprintf(ficresprobcov, "**********\n#\n");
1.53 brouard 2825:
2826: fprintf(ficgp, "\n#********** Variable ");
1.69 brouard 2827: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
2828: fprintf(ficgp, "**********\n#\n");
1.53 brouard 2829:
2830:
2831: fprintf(fichtm, "\n<hr size=\"2\" color=\"#EC5E5E\">********** Variable ");
2832: for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
2833: fprintf(fichtm, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
2834:
2835: fprintf(ficresprobcor, "\n#********** Variable ");
2836: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
1.69 brouard 2837: fprintf(ficresprobcor, "**********\n#");
1.53 brouard 2838: }
2839:
2840: for (age=bage; age<=fage; age ++){
2841: cov[2]=age;
2842: for (k=1; k<=cptcovn;k++) {
2843: cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];
2844: }
2845: for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
2846: for (k=1; k<=cptcovprod;k++)
2847: cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
2848:
2849: gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
2850: trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
2851: gp=vector(1,(nlstate)*(nlstate+ndeath));
2852: gm=vector(1,(nlstate)*(nlstate+ndeath));
2853:
2854: for(theta=1; theta <=npar; theta++){
2855: for(i=1; i<=npar; i++)
1.74 brouard 2856: xp[i] = x[i] + (i==theta ?delti[theta]:(double)0);
1.53 brouard 2857:
2858: pmij(pmmij,cov,ncovmodel,xp,nlstate);
2859:
2860: k=0;
2861: for(i=1; i<= (nlstate); i++){
2862: for(j=1; j<=(nlstate+ndeath);j++){
2863: k=k+1;
2864: gp[k]=pmmij[i][j];
2865: }
2866: }
2867:
2868: for(i=1; i<=npar; i++)
1.74 brouard 2869: xp[i] = x[i] - (i==theta ?delti[theta]:(double)0);
1.53 brouard 2870:
2871: pmij(pmmij,cov,ncovmodel,xp,nlstate);
2872: k=0;
2873: for(i=1; i<=(nlstate); i++){
2874: for(j=1; j<=(nlstate+ndeath);j++){
2875: k=k+1;
2876: gm[k]=pmmij[i][j];
2877: }
2878: }
2879:
2880: for(i=1; i<= (nlstate)*(nlstate+ndeath); i++)
1.74 brouard 2881: gradg[theta][i]=(gp[i]-gm[i])/(double)2./delti[theta];
1.53 brouard 2882: }
2883:
2884: for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
2885: for(theta=1; theta <=npar; theta++)
2886: trgradg[j][theta]=gradg[theta][j];
2887:
2888: matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov);
2889: matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);
1.59 brouard 2890: free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
2891: free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
2892: free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
2893: free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
2894:
1.53 brouard 2895: pmij(pmmij,cov,ncovmodel,x,nlstate);
2896:
2897: k=0;
2898: for(i=1; i<=(nlstate); i++){
2899: for(j=1; j<=(nlstate+ndeath);j++){
2900: k=k+1;
2901: mu[k][(int) age]=pmmij[i][j];
2902: }
2903: }
2904: for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
2905: for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
2906: varpij[i][j][(int)age] = doldm[i][j];
2907:
2908: /*printf("\n%d ",(int)age);
1.59 brouard 2909: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
2910: printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
2911: fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
2912: }*/
1.53 brouard 2913:
2914: fprintf(ficresprob,"\n%d ",(int)age);
2915: fprintf(ficresprobcov,"\n%d ",(int)age);
2916: fprintf(ficresprobcor,"\n%d ",(int)age);
2917:
2918: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)
2919: fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));
2920: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
2921: fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);
2922: fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
2923: }
2924: i=0;
2925: for (k=1; k<=(nlstate);k++){
2926: for (l=1; l<=(nlstate+ndeath);l++){
2927: i=i++;
2928: fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
2929: fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
2930: for (j=1; j<=i;j++){
2931: fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);
2932: fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));
2933: }
2934: }
2935: }/* end of loop for state */
2936: } /* end of loop for age */
2937:
2938: /* Confidence intervalle of pij */
2939: /*
1.59 brouard 2940: fprintf(ficgp,"\nset noparametric;unset label");
2941: fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");
2942: fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
2943: 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);
2944: fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);
2945: fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);
2946: fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);
1.53 brouard 2947: */
2948:
2949: /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
2950: first1=1;
2951: for (k2=1; k2<=(nlstate);k2++){
2952: for (l2=1; l2<=(nlstate+ndeath);l2++){
2953: if(l2==k2) continue;
2954: j=(k2-1)*(nlstate+ndeath)+l2;
2955: for (k1=1; k1<=(nlstate);k1++){
2956: for (l1=1; l1<=(nlstate+ndeath);l1++){
2957: if(l1==k1) continue;
2958: i=(k1-1)*(nlstate+ndeath)+l1;
2959: if(i<=j) continue;
2960: for (age=bage; age<=fage; age ++){
2961: if ((int)age %5==0){
2962: v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;
2963: v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;
2964: cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;
2965: mu1=mu[i][(int) age]/stepm*YEARM ;
2966: mu2=mu[j][(int) age]/stepm*YEARM;
2967: c12=cv12/sqrt(v1*v2);
2968: /* Computing eigen value of matrix of covariance */
2969: lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
2970: lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
2971: /* Eigen vectors */
2972: v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
2973: /*v21=sqrt(1.-v11*v11); *//* error */
2974: v21=(lc1-v1)/cv12*v11;
2975: v12=-v21;
2976: v22=v11;
2977: tnalp=v21/v11;
2978: if(first1==1){
2979: first1=0;
2980: 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);
2981: }
2982: 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);
2983: /*printf(fignu*/
2984: /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */
2985: /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */
2986: if(first==1){
2987: first=0;
2988: fprintf(ficgp,"\nset parametric;unset label");
2989: 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);
2990: fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
1.88 brouard 2991: fprintf(fichtm,"\n<br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup>\
2992: :<a href=\"%s%d%1d%1d-%1d%1d.png\">\
2993: %s%d%1d%1d-%1d%1d.png</A>, ",k1,l1,k2,l2,\
2994: subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2,\
2995: subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
2996: fprintf(fichtm,"\n<br><img src=\"%s%d%1d%1d-%1d%1d.png\"> ",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
1.53 brouard 2997: fprintf(fichtm,"\n<br> Correlation at age %d (%.3f),",(int) age, c12);
1.88 brouard 2998: fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\"",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
1.53 brouard 2999: fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
3000: fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
3001: 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",\
3002: mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
3003: mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
3004: }else{
3005: first=0;
3006: fprintf(fichtm," %d (%.3f),",(int) age, c12);
3007: fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
3008: fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
3009: 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",\
3010: mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
3011: mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
3012: }/* if first */
3013: } /* age mod 5 */
3014: } /* end loop age */
1.88 brouard 3015: fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\";replot;",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
1.53 brouard 3016: first=1;
3017: } /*l12 */
3018: } /* k12 */
3019: } /*l1 */
3020: }/* k1 */
3021: } /* loop covariates */
3022: }
1.59 brouard 3023: free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
3024: free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
1.53 brouard 3025: free_vector(xp,1,npar);
3026: fclose(ficresprob);
3027: fclose(ficresprobcov);
3028: fclose(ficresprobcor);
1.88 brouard 3029: /* fclose(ficgp);*/
1.53 brouard 3030: }
3031:
3032:
3033: /******************* Printing html file ***********/
3034: void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \
3035: int lastpass, int stepm, int weightopt, char model[],\
3036: int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
3037: int popforecast, int estepm ,\
3038: double jprev1, double mprev1,double anprev1, \
3039: double jprev2, double mprev2,double anprev2){
3040: int jj1, k1, i1, cpt;
3041: /*char optionfilehtm[FILENAMELENGTH];*/
1.87 brouard 3042: /* if((fichtm=fopen(optionfilehtm,"a"))==NULL) { */
3043: /* printf("Problem with %s \n",optionfilehtm), exit(0); */
3044: /* fprintf(ficlog,"Problem with %s \n",optionfilehtm), exit(0); */
3045: /* } */
1.53 brouard 3046:
1.85 brouard 3047: fprintf(fichtm,"<ul><li><h4>Result files (first order: no variance)</h4>\n \
1.88 brouard 3048: - Observed prevalence in each state (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"%s\">%s</a> <br>\n \
3049: - Estimated transition probabilities over %d (stepm) months: <a href=\"%s\">%s</a><br>\n \
3050: - Stable prevalence in each health state: <a href=\"%s\">%s</a> <br>\n \
1.85 brouard 3051: - Life expectancies by age and initial health status (estepm=%2d months): \
1.88 brouard 3052: <a href=\"%s\">%s</a> <br>\n</li>", \
3053: jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirf2(fileres,"p"),subdirf2(fileres,"p"),\
3054: stepm,subdirf2(fileres,"pij"),subdirf2(fileres,"pij"),\
3055: subdirf2(fileres,"pl"),subdirf2(fileres,"pl"),\
3056: estepm,subdirf2(fileres,"e"),subdirf2(fileres,"e"));
1.53 brouard 3057:
3058: fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
3059:
3060: m=cptcoveff;
3061: if (cptcovn < 1) {m=1;ncodemax[1]=1;}
3062:
3063: jj1=0;
3064: for(k1=1; k1<=m;k1++){
3065: for(i1=1; i1<=ncodemax[k1];i1++){
3066: jj1++;
3067: if (cptcovn > 0) {
3068: fprintf(fichtm,"<hr size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
3069: for (cpt=1; cpt<=cptcoveff;cpt++)
3070: fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
3071: fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
3072: }
3073: /* Pij */
1.88 brouard 3074: fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i, %d (stepm) months before: %s%d1.png<br> \
3075: <img src=\"%s%d1.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);
1.53 brouard 3076: /* Quasi-incidences */
1.85 brouard 3077: fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months\
1.88 brouard 3078: before but expressed in per year i.e. quasi incidences if stepm is small and probabilities too: %s%d2.png<br> \
3079: <img src=\"%s%d2.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);
1.53 brouard 3080: /* Stable prevalence in each health state */
3081: for(cpt=1; cpt<nlstate;cpt++){
1.85 brouard 3082: fprintf(fichtm,"<br>- Stable prevalence in each health state : p%s%d%d.png<br> \
1.88 brouard 3083: <img src=\"%s%d%d.png\">",subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1);
1.53 brouard 3084: }
3085: for(cpt=1; cpt<=nlstate;cpt++) {
1.88 brouard 3086: fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): %s%d%d.png <br> \
1.89 brouard 3087: <img src=\"%s%d%d.png\">",cpt,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1);
1.53 brouard 3088: }
1.85 brouard 3089: fprintf(fichtm,"\n<br>- Total life expectancy by age and \
1.88 brouard 3090: health expectancies in states (1) and (2): %s%d.png<br>\
3091: <img src=\"%s%d.png\">",subdirf2(optionfilefiname,"e"),jj1,subdirf2(optionfilefiname,"e"),jj1);
1.53 brouard 3092: } /* end i1 */
3093: }/* End k1 */
3094: fprintf(fichtm,"</ul>");
3095:
3096:
1.85 brouard 3097: fprintf(fichtm,"\n<br><li><h4> Result files (second order: variances)</h4>\n\
3098: - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n\
1.88 brouard 3099: - Variance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n\
3100: - Variance-covariance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n\
3101: - Correlation matrix of one-step probabilities: <a href=\"%s\">%s</a> <br>\n\
3102: - Variances and covariances of life expectancies by age and initial health status (estepm=%d months): <a href=\"%s\">%s</a><br>\n\
3103: - Health expectancies with their variances (no covariance): <a href=\"%s\">%s</a> <br>\n\
3104: - Standard deviation of stable prevalences: <a href=\"%s\">%s</a> <br>\n",\
3105: rfileres,rfileres,\
3106: subdirf2(fileres,"prob"),subdirf2(fileres,"prob"),\
3107: subdirf2(fileres,"probcov"),subdirf2(fileres,"probcov"),\
3108: subdirf2(fileres,"probcor"),subdirf2(fileres,"probcor"),\
3109: estepm, subdirf2(fileres,"v"),subdirf2(fileres,"v"),\
3110: subdirf2(fileres,"t"),subdirf2(fileres,"t"),\
3111: subdirf2(fileres,"vpl"),subdirf2(fileres,"vpl"));
1.53 brouard 3112:
1.76 brouard 3113: /* if(popforecast==1) fprintf(fichtm,"\n */
3114: /* - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n */
3115: /* - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n */
3116: /* <br>",fileres,fileres,fileres,fileres); */
3117: /* else */
3118: /* 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 3119: fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
3120:
3121: m=cptcoveff;
3122: if (cptcovn < 1) {m=1;ncodemax[1]=1;}
3123:
3124: jj1=0;
3125: for(k1=1; k1<=m;k1++){
3126: for(i1=1; i1<=ncodemax[k1];i1++){
3127: jj1++;
3128: if (cptcovn > 0) {
3129: fprintf(fichtm,"<hr size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
3130: for (cpt=1; cpt<=cptcoveff;cpt++)
3131: fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
3132: fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
3133: }
3134: for(cpt=1; cpt<=nlstate;cpt++) {
1.85 brouard 3135: fprintf(fichtm,"<br>- Observed and period prevalence (with confident\
1.88 brouard 3136: interval) in state (%d): %s%d%d.png <br>\
1.90 ! brouard 3137: <img src=\"%s%d%d.png\">",cpt,subdirf2(optionfilefiname,"v"),cpt,jj1,subdirf2(optionfilefiname,"v"),cpt,jj1);
1.53 brouard 3138: }
3139: } /* end i1 */
3140: }/* End k1 */
3141: fprintf(fichtm,"</ul>");
1.87 brouard 3142: fflush(fichtm);
1.53 brouard 3143: }
3144:
3145: /******************* Gnuplot file **************/
1.89 brouard 3146: void printinggnuplot(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
1.53 brouard 3147:
1.88 brouard 3148: char dirfileres[132],optfileres[132];
1.53 brouard 3149: int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;
3150: int ng;
1.88 brouard 3151: /* if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) { */
3152: /* printf("Problem with file %s",optionfilegnuplot); */
3153: /* fprintf(ficlog,"Problem with file %s",optionfilegnuplot); */
3154: /* } */
1.53 brouard 3155:
1.54 brouard 3156: /*#ifdef windows */
1.89 brouard 3157: fprintf(ficgp,"cd \"%s\" \n",pathc);
1.54 brouard 3158: /*#endif */
1.88 brouard 3159: m=pow(2,cptcoveff);
3160:
3161: strcpy(dirfileres,optionfilefiname);
3162: strcpy(optfileres,"vpl");
1.53 brouard 3163: /* 1eme*/
3164: for (cpt=1; cpt<= nlstate ; cpt ++) {
3165: for (k1=1; k1<= m ; k1 ++) {
1.88 brouard 3166: fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"v"),cpt,k1);
3167: fprintf(ficgp,"\n#set out \"v%s%d%d.png\" \n",optionfilefiname,cpt,k1);
3168: fprintf(ficgp,"set xlabel \"Age\" \n\
3169: set ylabel \"Probability\" \n\
3170: set ter png small\n\
3171: set size 0.65,0.65\n\
3172: plot [%.f:%.f] \"%s\" every :::%d::%d u 1:2 \"\%%lf",ageminpar,fage,subdirf2(fileres,"vpl"),k1-1,k1-1);
1.53 brouard 3173:
3174: for (i=1; i<= nlstate ; i ++) {
3175: if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
3176: else fprintf(ficgp," \%%*lf (\%%*lf)");
3177: }
1.88 brouard 3178: fprintf(ficgp,"\" t\"Stable prevalence\" w l 0,\"%s\" every :::%d::%d u 1:($2+1.96*$3) \"\%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1);
1.53 brouard 3179: for (i=1; i<= nlstate ; i ++) {
3180: if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
3181: else fprintf(ficgp," \%%*lf (\%%*lf)");
3182: }
1.88 brouard 3183: fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"%s\" every :::%d::%d u 1:($2-1.96*$3) \"\%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1);
1.53 brouard 3184: for (i=1; i<= nlstate ; i ++) {
3185: if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
3186: else fprintf(ficgp," \%%*lf (\%%*lf)");
3187: }
1.88 brouard 3188: fprintf(ficgp,"\" t\"\" w l 1,\"%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",subdirf2(fileres,"p"),k1-1,k1-1,2+4*(cpt-1));
1.53 brouard 3189: }
3190: }
3191: /*2 eme*/
3192:
3193: for (k1=1; k1<= m ; k1 ++) {
1.88 brouard 3194: fprintf(ficgp,"\nset out \"%s%d.png\" \n",subdirf2(optionfilefiname,"e"),k1);
1.53 brouard 3195: fprintf(ficgp,"set ylabel \"Years\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] ",ageminpar,fage);
3196:
3197: for (i=1; i<= nlstate+1 ; i ++) {
3198: k=2*i;
1.88 brouard 3199: fprintf(ficgp,"\"%s\" every :::%d::%d u 1:2 \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
1.53 brouard 3200: for (j=1; j<= nlstate+1 ; j ++) {
3201: if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
3202: else fprintf(ficgp," \%%*lf (\%%*lf)");
3203: }
3204: if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");
3205: else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);
1.88 brouard 3206: fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
1.53 brouard 3207: for (j=1; j<= nlstate+1 ; j ++) {
3208: if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
3209: else fprintf(ficgp," \%%*lf (\%%*lf)");
3210: }
3211: fprintf(ficgp,"\" t\"\" w l 0,");
1.88 brouard 3212: fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
1.53 brouard 3213: for (j=1; j<= nlstate+1 ; j ++) {
3214: if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
3215: else fprintf(ficgp," \%%*lf (\%%*lf)");
3216: }
3217: if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");
3218: else fprintf(ficgp,"\" t\"\" w l 0,");
3219: }
3220: }
3221:
3222: /*3eme*/
3223:
3224: for (k1=1; k1<= m ; k1 ++) {
3225: for (cpt=1; cpt<= nlstate ; cpt ++) {
3226: k=2+nlstate*(2*cpt-2);
1.88 brouard 3227: fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"exp"),cpt,k1);
3228: fprintf(ficgp,"set ter png small\n\
3229: set size 0.65,0.65\n\
3230: plot [%.f:%.f] \"%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,subdirf2(fileres,"e"),k1-1,k1-1,k,cpt);
1.53 brouard 3231: /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
3232: for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
3233: fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
3234: fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
3235: for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
3236: fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
3237:
3238: */
3239: for (i=1; i< nlstate ; i ++) {
1.88 brouard 3240: fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+2*i,cpt,i+1);
1.53 brouard 3241:
3242: }
3243: }
3244: }
3245:
1.76 brouard 3246: /* CV preval stable (period) */
1.53 brouard 3247: for (k1=1; k1<= m ; k1 ++) {
1.76 brouard 3248: for (cpt=1; cpt<=nlstate ; cpt ++) {
1.53 brouard 3249: k=3;
1.88 brouard 3250: fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"p"),cpt,k1);
3251: fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\
3252: set ter png small\nset size 0.65,0.65\n\
1.89 brouard 3253: unset log y\n\
1.88 brouard 3254: plot [%.f:%.f] \"%s\" u ($1==%d ? ($3):1/0):($%d/($%d",ageminpar,agemaxpar,subdirf2(fileres,"pij"),k1,k+cpt+1,k+1);
1.53 brouard 3255:
1.83 lievre 3256: for (i=1; i< nlstate ; i ++)
1.53 brouard 3257: fprintf(ficgp,"+$%d",k+i+1);
3258: fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);
3259:
3260: l=3+(nlstate+ndeath)*cpt;
1.88 brouard 3261: fprintf(ficgp,",\"%s\" u ($1==%d ? ($3):1/0):($%d/($%d",subdirf2(fileres,"pij"),k1,l+cpt+1,l+1);
1.53 brouard 3262: for (i=1; i< nlstate ; i ++) {
3263: l=3+(nlstate+ndeath)*cpt;
3264: fprintf(ficgp,"+$%d",l+i+1);
3265: }
3266: fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);
3267: }
3268: }
3269:
3270: /* proba elementaires */
3271: for(i=1,jk=1; i <=nlstate; i++){
3272: for(k=1; k <=(nlstate+ndeath); k++){
3273: if (k != i) {
3274: for(j=1; j <=ncovmodel; j++){
3275: fprintf(ficgp,"p%d=%f ",jk,p[jk]);
3276: jk++;
3277: fprintf(ficgp,"\n");
3278: }
3279: }
3280: }
3281: }
3282:
3283: for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/
3284: for(jk=1; jk <=m; jk++) {
1.88 brouard 3285: fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"pe"),jk,ng);
1.53 brouard 3286: if (ng==2)
3287: fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
3288: else
3289: fprintf(ficgp,"\nset title \"Probability\"\n");
3290: fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65\nset log y\nplot [%.f:%.f] ",ageminpar,agemaxpar);
3291: i=1;
3292: for(k2=1; k2<=nlstate; k2++) {
3293: k3=i;
3294: for(k=1; k<=(nlstate+ndeath); k++) {
3295: if (k != k2){
3296: if(ng==2)
3297: fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);
3298: else
3299: fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
3300: ij=1;
3301: for(j=3; j <=ncovmodel; j++) {
3302: if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
3303: fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
3304: ij++;
3305: }
3306: else
3307: fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
3308: }
3309: fprintf(ficgp,")/(1");
3310:
3311: for(k1=1; k1 <=nlstate; k1++){
3312: fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);
3313: ij=1;
3314: for(j=3; j <=ncovmodel; j++){
3315: if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
3316: fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
3317: ij++;
3318: }
3319: else
3320: fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
3321: }
3322: fprintf(ficgp,")");
3323: }
3324: fprintf(ficgp,") t \"p%d%d\" ", k2,k);
3325: if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");
3326: i=i+ncovmodel;
3327: }
3328: } /* end k */
3329: } /* end k2 */
3330: } /* end jk */
3331: } /* end ng */
1.88 brouard 3332: fflush(ficgp);
1.53 brouard 3333: } /* end gnuplot */
3334:
3335:
3336: /*************** Moving average **************/
1.54 brouard 3337: int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav){
1.53 brouard 3338:
3339: int i, cpt, cptcod;
1.58 lievre 3340: int modcovmax =1;
1.54 brouard 3341: int mobilavrange, mob;
1.53 brouard 3342: double age;
1.58 lievre 3343:
3344: modcovmax=2*cptcoveff;/* Max number of modalities. We suppose
3345: a covariate has 2 modalities */
3346: if (cptcovn<1) modcovmax=1; /* At least 1 pass */
3347:
1.54 brouard 3348: if(mobilav==1||mobilav ==3 ||mobilav==5 ||mobilav== 7){
3349: if(mobilav==1) mobilavrange=5; /* default */
3350: else mobilavrange=mobilav;
3351: for (age=bage; age<=fage; age++)
3352: for (i=1; i<=nlstate;i++)
1.58 lievre 3353: for (cptcod=1;cptcod<=modcovmax;cptcod++)
1.54 brouard 3354: mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
3355: /* We keep the original values on the extreme ages bage, fage and for
3356: fage+1 and bage-1 we use a 3 terms moving average; for fage+2 bage+2
3357: we use a 5 terms etc. until the borders are no more concerned.
3358: */
3359: for (mob=3;mob <=mobilavrange;mob=mob+2){
3360: for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){
3361: for (i=1; i<=nlstate;i++){
1.58 lievre 3362: for (cptcod=1;cptcod<=modcovmax;cptcod++){
1.54 brouard 3363: mobaverage[(int)age][i][cptcod] =probs[(int)age][i][cptcod];
3364: for (cpt=1;cpt<=(mob-1)/2;cpt++){
3365: mobaverage[(int)age][i][cptcod] +=probs[(int)age-cpt][i][cptcod];
3366: mobaverage[(int)age][i][cptcod] +=probs[(int)age+cpt][i][cptcod];
3367: }
3368: mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/mob;
3369: }
1.53 brouard 3370: }
1.54 brouard 3371: }/* end age */
3372: }/* end mob */
3373: }else return -1;
3374: return 0;
3375: }/* End movingaverage */
1.53 brouard 3376:
3377:
3378: /************** Forecasting ******************/
1.70 brouard 3379: 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 3380: /* proj1, year, month, day of starting projection
3381: agemin, agemax range of age
3382: dateprev1 dateprev2 range of dates during which prevalence is computed
1.70 brouard 3383: anproj2 year of en of projection (same day and month as proj1).
1.69 brouard 3384: */
1.73 lievre 3385: int yearp, stepsize, hstepm, nhstepm, j, k, c, cptcod, i, h, i1;
1.53 brouard 3386: int *popage;
1.70 brouard 3387: double agec; /* generic age */
3388: double agelim, ppij, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
1.53 brouard 3389: double *popeffectif,*popcount;
3390: double ***p3mat;
1.55 lievre 3391: double ***mobaverage;
1.53 brouard 3392: char fileresf[FILENAMELENGTH];
3393:
1.69 brouard 3394: agelim=AGESUP;
1.84 brouard 3395: prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
1.53 brouard 3396:
3397: strcpy(fileresf,"f");
3398: strcat(fileresf,fileres);
3399: if((ficresf=fopen(fileresf,"w"))==NULL) {
3400: printf("Problem with forecast resultfile: %s\n", fileresf);
3401: fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);
3402: }
3403: printf("Computing forecasting: result on file '%s' \n", fileresf);
3404: fprintf(ficlog,"Computing forecasting: result on file '%s' \n", fileresf);
3405:
3406: if (cptcoveff==0) ncodemax[cptcoveff]=1;
3407:
1.54 brouard 3408: if (mobilav!=0) {
1.53 brouard 3409: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
1.54 brouard 3410: if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
3411: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
3412: printf(" Error in movingaverage mobilav=%d\n",mobilav);
3413: }
1.53 brouard 3414: }
3415:
3416: stepsize=(int) (stepm+YEARM-1)/YEARM;
3417: if (stepm<=12) stepsize=1;
1.74 brouard 3418: if(estepm < stepm){
3419: printf ("Problem %d lower than %d\n",estepm, stepm);
3420: }
3421: else hstepm=estepm;
3422:
1.53 brouard 3423: hstepm=hstepm/stepm;
1.69 brouard 3424: yp1=modf(dateintmean,&yp);/* extracts integral of datemean in yp and
3425: fractional in yp1 */
1.53 brouard 3426: anprojmean=yp;
3427: yp2=modf((yp1*12),&yp);
3428: mprojmean=yp;
3429: yp1=modf((yp2*30.5),&yp);
3430: jprojmean=yp;
3431: if(jprojmean==0) jprojmean=1;
3432: if(mprojmean==0) jprojmean=1;
1.73 lievre 3433:
3434: i1=cptcoveff;
3435: if (cptcovn < 1){i1=1;}
1.53 brouard 3436:
1.70 brouard 3437: fprintf(ficresf,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2);
1.53 brouard 3438:
1.70 brouard 3439: fprintf(ficresf,"#****** Routine prevforecast **\n");
1.73 lievre 3440:
1.75 brouard 3441: /* if (h==(int)(YEARM*yearp)){ */
1.73 lievre 3442: for(cptcov=1, k=0;cptcov<=i1;cptcov++){
1.53 brouard 3443: for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
3444: k=k+1;
3445: fprintf(ficresf,"\n#******");
3446: for(j=1;j<=cptcoveff;j++) {
1.70 brouard 3447: 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 3448: }
3449: fprintf(ficresf,"******\n");
1.70 brouard 3450: fprintf(ficresf,"# Covariate valuofcovar yearproj age");
3451: for(j=1; j<=nlstate+ndeath;j++){
3452: for(i=1; i<=nlstate;i++)
3453: fprintf(ficresf," p%d%d",i,j);
3454: fprintf(ficresf," p.%d",j);
3455: }
1.74 brouard 3456: for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) {
1.53 brouard 3457: fprintf(ficresf,"\n");
1.70 brouard 3458: fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+yearp);
1.53 brouard 3459:
1.71 brouard 3460: for (agec=fage; agec>=(ageminpar-1); agec--){
1.70 brouard 3461: nhstepm=(int) rint((agelim-agec)*YEARM/stepm);
1.53 brouard 3462: nhstepm = nhstepm/hstepm;
3463: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3464: oldm=oldms;savm=savms;
1.70 brouard 3465: hpxij(p3mat,nhstepm,agec,hstepm,p,nlstate,stepm,oldm,savm, k);
1.53 brouard 3466:
3467: for (h=0; h<=nhstepm; h++){
1.75 brouard 3468: if (h*hstepm/YEARM*stepm ==yearp) {
1.69 brouard 3469: fprintf(ficresf,"\n");
3470: for(j=1;j<=cptcoveff;j++)
3471: fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
1.70 brouard 3472: fprintf(ficresf,"%.f %.f ",anproj1+yearp,agec+h*hstepm/YEARM*stepm);
1.53 brouard 3473: }
3474: for(j=1; j<=nlstate+ndeath;j++) {
1.70 brouard 3475: ppij=0.;
1.71 brouard 3476: for(i=1; i<=nlstate;i++) {
1.53 brouard 3477: if (mobilav==1)
1.71 brouard 3478: ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][i][cptcod];
1.53 brouard 3479: else {
1.71 brouard 3480: ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][cptcod];
1.53 brouard 3481: }
1.75 brouard 3482: if (h*hstepm/YEARM*stepm== yearp) {
1.70 brouard 3483: fprintf(ficresf," %.3f", p3mat[i][j][h]);
1.75 brouard 3484: }
3485: } /* end i */
3486: if (h*hstepm/YEARM*stepm==yearp) {
1.70 brouard 3487: fprintf(ficresf," %.3f", ppij);
1.53 brouard 3488: }
1.75 brouard 3489: }/* end j */
3490: } /* end h */
1.53 brouard 3491: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
1.75 brouard 3492: } /* end agec */
3493: } /* end yearp */
3494: } /* end cptcod */
3495: } /* end cptcov */
1.53 brouard 3496:
1.54 brouard 3497: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
1.53 brouard 3498:
3499: fclose(ficresf);
3500: }
1.70 brouard 3501:
3502: /************** Forecasting *****not tested NB*************/
1.53 brouard 3503: 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){
3504:
3505: int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;
3506: int *popage;
1.69 brouard 3507: double calagedatem, agelim, kk1, kk2;
1.53 brouard 3508: double *popeffectif,*popcount;
3509: double ***p3mat,***tabpop,***tabpopprev;
1.55 lievre 3510: double ***mobaverage;
1.53 brouard 3511: char filerespop[FILENAMELENGTH];
3512:
3513: tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
3514: tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
3515: agelim=AGESUP;
1.69 brouard 3516: calagedatem=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;
1.53 brouard 3517:
1.84 brouard 3518: prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
1.53 brouard 3519:
3520:
3521: strcpy(filerespop,"pop");
3522: strcat(filerespop,fileres);
3523: if((ficrespop=fopen(filerespop,"w"))==NULL) {
3524: printf("Problem with forecast resultfile: %s\n", filerespop);
3525: fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop);
3526: }
3527: printf("Computing forecasting: result on file '%s' \n", filerespop);
3528: fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop);
3529:
3530: if (cptcoveff==0) ncodemax[cptcoveff]=1;
3531:
1.54 brouard 3532: if (mobilav!=0) {
1.53 brouard 3533: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
1.54 brouard 3534: if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
3535: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
3536: printf(" Error in movingaverage mobilav=%d\n",mobilav);
3537: }
1.53 brouard 3538: }
3539:
3540: stepsize=(int) (stepm+YEARM-1)/YEARM;
3541: if (stepm<=12) stepsize=1;
3542:
3543: agelim=AGESUP;
3544:
3545: hstepm=1;
3546: hstepm=hstepm/stepm;
3547:
3548: if (popforecast==1) {
3549: if((ficpop=fopen(popfile,"r"))==NULL) {
3550: printf("Problem with population file : %s\n",popfile);exit(0);
3551: fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0);
3552: }
3553: popage=ivector(0,AGESUP);
3554: popeffectif=vector(0,AGESUP);
3555: popcount=vector(0,AGESUP);
3556:
3557: i=1;
3558: while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;
3559:
3560: imx=i;
3561: for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];
3562: }
3563:
1.69 brouard 3564: for(cptcov=1,k=0;cptcov<=i2;cptcov++){
1.53 brouard 3565: for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
3566: k=k+1;
3567: fprintf(ficrespop,"\n#******");
3568: for(j=1;j<=cptcoveff;j++) {
3569: fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
3570: }
3571: fprintf(ficrespop,"******\n");
3572: fprintf(ficrespop,"# Age");
3573: for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);
3574: if (popforecast==1) fprintf(ficrespop," [Population]");
3575:
3576: for (cpt=0; cpt<=0;cpt++) {
3577: fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);
3578:
1.69 brouard 3579: for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){
1.53 brouard 3580: nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);
3581: nhstepm = nhstepm/hstepm;
3582:
3583: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3584: oldm=oldms;savm=savms;
3585: hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
3586:
3587: for (h=0; h<=nhstepm; h++){
1.69 brouard 3588: if (h==(int) (calagedatem+YEARM*cpt)) {
1.53 brouard 3589: fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
3590: }
3591: for(j=1; j<=nlstate+ndeath;j++) {
3592: kk1=0.;kk2=0;
3593: for(i=1; i<=nlstate;i++) {
3594: if (mobilav==1)
3595: kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];
3596: else {
3597: kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];
3598: }
3599: }
1.69 brouard 3600: if (h==(int)(calagedatem+12*cpt)){
1.53 brouard 3601: tabpop[(int)(agedeb)][j][cptcod]=kk1;
3602: /*fprintf(ficrespop," %.3f", kk1);
3603: if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/
3604: }
3605: }
3606: for(i=1; i<=nlstate;i++){
3607: kk1=0.;
3608: for(j=1; j<=nlstate;j++){
3609: kk1= kk1+tabpop[(int)(agedeb)][j][cptcod];
3610: }
1.69 brouard 3611: tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedatem+12*cpt)*hstepm/YEARM*stepm-1)];
1.53 brouard 3612: }
3613:
1.69 brouard 3614: if (h==(int)(calagedatem+12*cpt)) for(j=1; j<=nlstate;j++)
1.53 brouard 3615: fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);
3616: }
3617: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3618: }
3619: }
3620:
3621: /******/
3622:
3623: for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) {
3624: fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);
1.69 brouard 3625: for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){
1.53 brouard 3626: nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);
3627: nhstepm = nhstepm/hstepm;
3628:
3629: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3630: oldm=oldms;savm=savms;
3631: hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
3632: for (h=0; h<=nhstepm; h++){
1.69 brouard 3633: if (h==(int) (calagedatem+YEARM*cpt)) {
1.53 brouard 3634: fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
3635: }
3636: for(j=1; j<=nlstate+ndeath;j++) {
3637: kk1=0.;kk2=0;
3638: for(i=1; i<=nlstate;i++) {
3639: kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];
3640: }
1.69 brouard 3641: if (h==(int)(calagedatem+12*cpt)) fprintf(ficresf," %15.2f", kk1);
1.53 brouard 3642: }
3643: }
3644: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3645: }
3646: }
3647: }
3648: }
3649:
1.54 brouard 3650: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
1.53 brouard 3651:
3652: if (popforecast==1) {
3653: free_ivector(popage,0,AGESUP);
3654: free_vector(popeffectif,0,AGESUP);
3655: free_vector(popcount,0,AGESUP);
3656: }
3657: free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
3658: free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
3659: fclose(ficrespop);
1.84 brouard 3660: } /* End of popforecast */
1.53 brouard 3661:
1.87 brouard 3662: int fileappend(FILE *fichier, char *optionfich)
1.86 brouard 3663: {
1.87 brouard 3664: if((fichier=fopen(optionfich,"a"))==NULL) {
3665: printf("Problem with file: %s\n", optionfich);
3666: fprintf(ficlog,"Problem with file: %s\n", optionfich);
3667: return (0);
1.86 brouard 3668: }
1.87 brouard 3669: fflush(fichier);
3670: return (1);
1.86 brouard 3671: }
1.88 brouard 3672: void prwizard(int ncovmodel, int nlstate, int ndeath, char model[], FILE *ficparo)
3673: {
3674:
3675: char ca[32], cb[32], cc[32];
3676: int i,j, k, l, li, lj, lk, ll, jj, npar, itimes;
3677: int numlinepar;
3678:
3679: printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
3680: fprintf(ficparo,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
3681: for(i=1; i <=nlstate; i++){
3682: jj=0;
3683: for(j=1; j <=nlstate+ndeath; j++){
3684: if(j==i) continue;
3685: jj++;
3686: /*ca[0]= k+'a'-1;ca[1]='\0';*/
3687: printf("%1d%1d",i,j);
3688: fprintf(ficparo,"%1d%1d",i,j);
3689: for(k=1; k<=ncovmodel;k++){
3690: /* printf(" %lf",param[i][j][k]); */
3691: /* fprintf(ficparo," %lf",param[i][j][k]); */
3692: printf(" 0.");
3693: fprintf(ficparo," 0.");
3694: }
3695: printf("\n");
3696: fprintf(ficparo,"\n");
3697: }
3698: }
3699: printf("# Scales (for hessian or gradient estimation)\n");
3700: fprintf(ficparo,"# Scales (for hessian or gradient estimation)\n");
3701: npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/
3702: for(i=1; i <=nlstate; i++){
3703: jj=0;
3704: for(j=1; j <=nlstate+ndeath; j++){
3705: if(j==i) continue;
3706: jj++;
3707: fprintf(ficparo,"%1d%1d",i,j);
3708: printf("%1d%1d",i,j);
3709: fflush(stdout);
3710: for(k=1; k<=ncovmodel;k++){
3711: /* printf(" %le",delti3[i][j][k]); */
3712: /* fprintf(ficparo," %le",delti3[i][j][k]); */
3713: printf(" 0.");
3714: fprintf(ficparo," 0.");
3715: }
3716: numlinepar++;
3717: printf("\n");
3718: fprintf(ficparo,"\n");
3719: }
3720: }
3721: printf("# Covariance matrix\n");
3722: /* # 121 Var(a12)\n\ */
3723: /* # 122 Cov(b12,a12) Var(b12)\n\ */
3724: /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
3725: /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
3726: /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
3727: /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
3728: /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
3729: /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
3730: fflush(stdout);
3731: fprintf(ficparo,"# Covariance matrix\n");
3732: /* # 121 Var(a12)\n\ */
3733: /* # 122 Cov(b12,a12) Var(b12)\n\ */
3734: /* # ...\n\ */
3735: /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
3736:
3737: for(itimes=1;itimes<=2;itimes++){
3738: jj=0;
3739: for(i=1; i <=nlstate; i++){
3740: for(j=1; j <=nlstate+ndeath; j++){
3741: if(j==i) continue;
3742: for(k=1; k<=ncovmodel;k++){
3743: jj++;
3744: ca[0]= k+'a'-1;ca[1]='\0';
3745: if(itimes==1){
3746: printf("#%1d%1d%d",i,j,k);
3747: fprintf(ficparo,"#%1d%1d%d",i,j,k);
3748: }else{
3749: printf("%1d%1d%d",i,j,k);
3750: fprintf(ficparo,"%1d%1d%d",i,j,k);
3751: /* printf(" %.5le",matcov[i][j]); */
3752: }
3753: ll=0;
3754: for(li=1;li <=nlstate; li++){
3755: for(lj=1;lj <=nlstate+ndeath; lj++){
3756: if(lj==li) continue;
3757: for(lk=1;lk<=ncovmodel;lk++){
3758: ll++;
3759: if(ll<=jj){
3760: cb[0]= lk +'a'-1;cb[1]='\0';
3761: if(ll<jj){
3762: if(itimes==1){
3763: printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
3764: fprintf(ficparo," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
3765: }else{
3766: printf(" 0.");
3767: fprintf(ficparo," 0.");
3768: }
3769: }else{
3770: if(itimes==1){
3771: printf(" Var(%s%1d%1d)",ca,i,j);
3772: fprintf(ficparo," Var(%s%1d%1d)",ca,i,j);
3773: }else{
3774: printf(" 0.");
3775: fprintf(ficparo," 0.");
3776: }
3777: }
3778: }
3779: } /* end lk */
3780: } /* end lj */
3781: } /* end li */
3782: printf("\n");
3783: fprintf(ficparo,"\n");
3784: numlinepar++;
3785: } /* end k*/
3786: } /*end j */
3787: } /* end i */
3788: }
3789:
3790: } /* end of prwizard */
3791:
1.53 brouard 3792: /***********************************************/
3793: /**************** Main Program *****************/
3794: /***********************************************/
3795:
3796: int main(int argc, char *argv[])
3797: {
1.61 brouard 3798: int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav);
1.74 brouard 3799: int i,j, k, n=MAXN,iter,m,size=100,cptcode, cptcod;
1.88 brouard 3800: int jj, imk;
1.85 brouard 3801: int numlinepar=0; /* Current linenumber of parameter file */
1.87 brouard 3802: /* FILE *fichtm; *//* Html File */
3803: /* FILE *ficgp;*/ /*Gnuplot File */
1.53 brouard 3804: double agedeb, agefin,hf;
3805: double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;
3806:
3807: double fret;
3808: double **xi,tmp,delta;
3809:
3810: double dum; /* Dummy variable */
3811: double ***p3mat;
3812: double ***mobaverage;
3813: int *indx;
3814: char line[MAXLINE], linepar[MAXLINE];
1.88 brouard 3815: char path[MAXLINE],pathc[MAXLINE],pathcd[MAXLINE],pathtot[MAXLINE],model[MAXLINE];
3816: char pathr[MAXLINE];
1.53 brouard 3817: int firstobs=1, lastobs=10;
3818: int sdeb, sfin; /* Status at beginning and end */
3819: int c, h , cpt,l;
3820: int ju,jl, mi;
3821: int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;
1.59 brouard 3822: int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,*tab;
1.69 brouard 3823: int mobilavproj=0 , prevfcast=0 ; /* moving average of prev, If prevfcast=1 prevalence projection */
1.53 brouard 3824: int mobilav=0,popforecast=0;
3825: int hstepm, nhstepm;
1.74 brouard 3826: double jprev1=1, mprev1=1,anprev1=2000,jprev2=1, mprev2=1,anprev2=2000;
3827: double jpyram=1, mpyram=1,anpyram=2000,jpyram1=1, mpyram1=1,anpyram1=2000;
1.53 brouard 3828:
3829: double bage, fage, age, agelim, agebase;
3830: double ftolpl=FTOL;
3831: double **prlim;
3832: double *severity;
3833: double ***param; /* Matrix of parameters */
3834: double *p;
3835: double **matcov; /* Matrix of covariance */
3836: double ***delti3; /* Scale */
3837: double *delti; /* Scale */
3838: double ***eij, ***vareij;
3839: double **varpl; /* Variances of prevalence limits by age */
3840: double *epj, vepp;
3841: double kk1, kk2;
1.74 brouard 3842: double dateprev1, dateprev2,jproj1=1,mproj1=1,anproj1=2000,jproj2=1,mproj2=1,anproj2=2000;
1.53 brouard 3843:
3844: char *alph[]={"a","a","b","c","d","e"}, str[4];
3845:
3846:
3847: char z[1]="c", occ;
1.86 brouard 3848:
1.53 brouard 3849: char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];
1.88 brouard 3850: char strstart[80], *strt, strtend[80];
1.85 brouard 3851: char *stratrunc;
3852: int lstra;
3853:
3854: long total_usecs;
3855: struct timeval start_time, end_time, curr_time;
3856: struct timezone tzp;
3857: extern int gettimeofday();
3858: struct tm tmg, tm, *gmtime(), *localtime();
3859: long time_value;
3860: extern long time();
1.53 brouard 3861:
1.85 brouard 3862: /* gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */
3863: (void) gettimeofday(&start_time,&tzp);
3864: tm = *localtime(&start_time.tv_sec);
3865: tmg = *gmtime(&start_time.tv_sec);
1.88 brouard 3866: strcpy(strstart,asctime(&tm));
1.86 brouard 3867:
1.88 brouard 3868: /* printf("Localtime (at start)=%s",strstart); */
1.85 brouard 3869: /* tp.tv_sec = tp.tv_sec +86400; */
3870: /* tm = *localtime(&start_time.tv_sec); */
3871: /* tmg.tm_year=tmg.tm_year +dsign*dyear; */
3872: /* tmg.tm_mon=tmg.tm_mon +dsign*dmonth; */
3873: /* tmg.tm_hour=tmg.tm_hour + 1; */
3874: /* tp.tv_sec = mktime(&tmg); */
3875: /* strt=asctime(&tmg); */
1.88 brouard 3876: /* printf("Time(after) =%s",strstart); */
1.85 brouard 3877: /* (void) time (&time_value);
3878: * printf("time=%d,t-=%d\n",time_value,time_value-86400);
3879: * tm = *localtime(&time_value);
1.88 brouard 3880: * strstart=asctime(&tm);
3881: * printf("tim_value=%d,asctime=%s\n",time_value,strstart);
1.85 brouard 3882: */
3883:
1.53 brouard 3884: getcwd(pathcd, size);
3885:
1.81 brouard 3886: printf("\n%s\n%s",version,fullversion);
1.53 brouard 3887: if(argc <=1){
3888: printf("\nEnter the parameter file name: ");
3889: scanf("%s",pathtot);
3890: }
3891: else{
3892: strcpy(pathtot,argv[1]);
3893: }
1.88 brouard 3894: /*if(getcwd(pathcd, MAXLINE)!= NULL)printf ("Error pathcd\n");*/
1.53 brouard 3895: /*cygwin_split_path(pathtot,path,optionfile);
3896: printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/
3897: /* cutv(path,optionfile,pathtot,'\\');*/
3898:
3899: split(pathtot,path,optionfile,optionfilext,optionfilefiname);
1.85 brouard 3900: printf("pathtot=%s,\npath=%s,\noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
1.53 brouard 3901: chdir(path);
1.88 brouard 3902: strcpy(command,"mkdir ");
3903: strcat(command,optionfilefiname);
3904: if((outcmd=system(command)) != 0){
3905: printf("Problem creating directory or it already exists %s%s, err=%d\n",path,optionfilefiname,outcmd);
3906: /* fprintf(ficlog,"Problem creating directory %s%s\n",path,optionfilefiname); */
3907: /* fclose(ficlog); */
3908: /* exit(1); */
3909: }
3910: /* if((imk=mkdir(optionfilefiname))<0){ */
3911: /* perror("mkdir"); */
3912: /* } */
1.53 brouard 3913:
1.59 brouard 3914: /*-------- arguments in the command line --------*/
1.53 brouard 3915:
3916: /* Log file */
3917: strcat(filelog, optionfilefiname);
3918: strcat(filelog,".log"); /* */
3919: if((ficlog=fopen(filelog,"w"))==NULL) {
3920: printf("Problem with logfile %s\n",filelog);
3921: goto end;
3922: }
3923: fprintf(ficlog,"Log filename:%s\n",filelog);
1.85 brouard 3924: fprintf(ficlog,"\n%s\n%s",version,fullversion);
1.53 brouard 3925: fprintf(ficlog,"\nEnter the parameter file name: ");
1.88 brouard 3926: fprintf(ficlog,"pathtot=%s\n\
3927: path=%s \n\
3928: optionfile=%s\n\
3929: optionfilext=%s\n\
3930: optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
1.86 brouard 3931:
1.88 brouard 3932: printf("Localtime (at start):%s",strstart);
3933: fprintf(ficlog,"Localtime (at start): %s",strstart);
1.53 brouard 3934: fflush(ficlog);
3935:
3936: /* */
3937: strcpy(fileres,"r");
3938: strcat(fileres, optionfilefiname);
3939: strcat(fileres,".txt"); /* Other files have txt extension */
3940:
3941: /*---------arguments file --------*/
3942:
3943: if((ficpar=fopen(optionfile,"r"))==NULL) {
3944: printf("Problem with optionfile %s\n",optionfile);
3945: fprintf(ficlog,"Problem with optionfile %s\n",optionfile);
1.85 brouard 3946: fflush(ficlog);
1.53 brouard 3947: goto end;
3948: }
3949:
1.88 brouard 3950:
3951:
1.53 brouard 3952: strcpy(filereso,"o");
3953: strcat(filereso,fileres);
1.88 brouard 3954: if((ficparo=fopen(filereso,"w"))==NULL) { /* opened on subdirectory */
1.53 brouard 3955: printf("Problem with Output resultfile: %s\n", filereso);
3956: fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso);
1.85 brouard 3957: fflush(ficlog);
1.53 brouard 3958: goto end;
3959: }
3960:
3961: /* Reads comments: lines beginning with '#' */
1.85 brouard 3962: numlinepar=0;
1.53 brouard 3963: while((c=getc(ficpar))=='#' && c!= EOF){
3964: ungetc(c,ficpar);
3965: fgets(line, MAXLINE, ficpar);
1.85 brouard 3966: numlinepar++;
1.53 brouard 3967: puts(line);
3968: fputs(line,ficparo);
1.85 brouard 3969: fputs(line,ficlog);
1.53 brouard 3970: }
3971: ungetc(c,ficpar);
3972:
3973: 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 3974: numlinepar++;
1.53 brouard 3975: 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);
3976: 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 3977: 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);
3978: fflush(ficlog);
1.59 brouard 3979: while((c=getc(ficpar))=='#' && c!= EOF){
1.53 brouard 3980: ungetc(c,ficpar);
3981: fgets(line, MAXLINE, ficpar);
1.85 brouard 3982: numlinepar++;
1.53 brouard 3983: puts(line);
3984: fputs(line,ficparo);
1.85 brouard 3985: fputs(line,ficlog);
1.53 brouard 3986: }
3987: ungetc(c,ficpar);
1.85 brouard 3988:
1.53 brouard 3989:
3990: covar=matrix(0,NCOVMAX,1,n);
1.58 lievre 3991: cptcovn=0; /*Number of covariates, i.e. number of '+' in model statement*/
1.53 brouard 3992: if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;
3993:
1.58 lievre 3994: ncovmodel=2+cptcovn; /*Number of variables = cptcovn + intercept + age */
1.53 brouard 3995: nvar=ncovmodel-1; /* Suppressing age as a basic covariate */
1.88 brouard 3996:
3997: if(mle==-1){ /* Print a wizard for help writing covariance matrix */
3998: prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
3999: printf(" You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
4000: fprintf(ficlog," You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
4001: fclose (ficparo);
4002: fclose (ficlog);
4003: exit(0);
4004: }
1.53 brouard 4005: /* Read guess parameters */
4006: /* Reads comments: lines beginning with '#' */
4007: while((c=getc(ficpar))=='#' && c!= EOF){
4008: ungetc(c,ficpar);
4009: fgets(line, MAXLINE, ficpar);
1.85 brouard 4010: numlinepar++;
1.53 brouard 4011: puts(line);
4012: fputs(line,ficparo);
1.85 brouard 4013: fputs(line,ficlog);
1.53 brouard 4014: }
4015: ungetc(c,ficpar);
1.85 brouard 4016:
1.53 brouard 4017: param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
1.85 brouard 4018: for(i=1; i <=nlstate; i++){
4019: j=0;
4020: for(jj=1; jj <=nlstate+ndeath; jj++){
4021: if(jj==i) continue;
4022: j++;
1.53 brouard 4023: fscanf(ficpar,"%1d%1d",&i1,&j1);
1.85 brouard 4024: if ((i1 != i) && (j1 != j)){
4025: printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n",numlinepar, i,j, i1, j1);
4026: exit(1);
4027: }
1.53 brouard 4028: fprintf(ficparo,"%1d%1d",i1,j1);
4029: if(mle==1)
4030: printf("%1d%1d",i,j);
4031: fprintf(ficlog,"%1d%1d",i,j);
4032: for(k=1; k<=ncovmodel;k++){
4033: fscanf(ficpar," %lf",¶m[i][j][k]);
4034: if(mle==1){
4035: printf(" %lf",param[i][j][k]);
4036: fprintf(ficlog," %lf",param[i][j][k]);
4037: }
4038: else
4039: fprintf(ficlog," %lf",param[i][j][k]);
4040: fprintf(ficparo," %lf",param[i][j][k]);
4041: }
4042: fscanf(ficpar,"\n");
1.85 brouard 4043: numlinepar++;
1.53 brouard 4044: if(mle==1)
4045: printf("\n");
4046: fprintf(ficlog,"\n");
4047: fprintf(ficparo,"\n");
4048: }
1.85 brouard 4049: }
4050: fflush(ficlog);
4051:
1.59 brouard 4052: npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/
1.53 brouard 4053:
4054: p=param[1][1];
4055:
4056: /* Reads comments: lines beginning with '#' */
4057: while((c=getc(ficpar))=='#' && c!= EOF){
4058: ungetc(c,ficpar);
4059: fgets(line, MAXLINE, ficpar);
1.85 brouard 4060: numlinepar++;
1.53 brouard 4061: puts(line);
4062: fputs(line,ficparo);
1.85 brouard 4063: fputs(line,ficlog);
1.53 brouard 4064: }
4065: ungetc(c,ficpar);
4066:
4067: delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
1.74 brouard 4068: /* delti=vector(1,npar); *//* Scale of each paramater (output from hesscov) */
1.53 brouard 4069: for(i=1; i <=nlstate; i++){
4070: for(j=1; j <=nlstate+ndeath-1; j++){
4071: fscanf(ficpar,"%1d%1d",&i1,&j1);
1.85 brouard 4072: if ((i1-i)*(j1-j)!=0){
4073: printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n",numlinepar, i,j, i1, j1);
4074: exit(1);
4075: }
1.53 brouard 4076: printf("%1d%1d",i,j);
4077: fprintf(ficparo,"%1d%1d",i1,j1);
1.85 brouard 4078: fprintf(ficlog,"%1d%1d",i1,j1);
1.53 brouard 4079: for(k=1; k<=ncovmodel;k++){
4080: fscanf(ficpar,"%le",&delti3[i][j][k]);
4081: printf(" %le",delti3[i][j][k]);
4082: fprintf(ficparo," %le",delti3[i][j][k]);
1.85 brouard 4083: fprintf(ficlog," %le",delti3[i][j][k]);
1.53 brouard 4084: }
4085: fscanf(ficpar,"\n");
1.85 brouard 4086: numlinepar++;
1.53 brouard 4087: printf("\n");
4088: fprintf(ficparo,"\n");
1.85 brouard 4089: fprintf(ficlog,"\n");
1.53 brouard 4090: }
4091: }
1.85 brouard 4092: fflush(ficlog);
4093:
1.53 brouard 4094: delti=delti3[1][1];
1.74 brouard 4095:
4096:
4097: /* 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 4098:
4099: /* Reads comments: lines beginning with '#' */
4100: while((c=getc(ficpar))=='#' && c!= EOF){
4101: ungetc(c,ficpar);
4102: fgets(line, MAXLINE, ficpar);
1.85 brouard 4103: numlinepar++;
1.53 brouard 4104: puts(line);
4105: fputs(line,ficparo);
1.85 brouard 4106: fputs(line,ficlog);
1.53 brouard 4107: }
4108: ungetc(c,ficpar);
4109:
4110: matcov=matrix(1,npar,1,npar);
4111: for(i=1; i <=npar; i++){
4112: fscanf(ficpar,"%s",&str);
4113: if(mle==1)
4114: printf("%s",str);
4115: fprintf(ficlog,"%s",str);
4116: fprintf(ficparo,"%s",str);
4117: for(j=1; j <=i; j++){
4118: fscanf(ficpar," %le",&matcov[i][j]);
4119: if(mle==1){
4120: printf(" %.5le",matcov[i][j]);
4121: }
1.85 brouard 4122: fprintf(ficlog," %.5le",matcov[i][j]);
1.53 brouard 4123: fprintf(ficparo," %.5le",matcov[i][j]);
4124: }
4125: fscanf(ficpar,"\n");
1.85 brouard 4126: numlinepar++;
1.53 brouard 4127: if(mle==1)
4128: printf("\n");
4129: fprintf(ficlog,"\n");
4130: fprintf(ficparo,"\n");
4131: }
4132: for(i=1; i <=npar; i++)
4133: for(j=i+1;j<=npar;j++)
4134: matcov[i][j]=matcov[j][i];
4135:
4136: if(mle==1)
4137: printf("\n");
4138: fprintf(ficlog,"\n");
4139:
1.85 brouard 4140: fflush(ficlog);
1.53 brouard 4141:
1.59 brouard 4142: /*-------- Rewriting paramater file ----------*/
4143: strcpy(rfileres,"r"); /* "Rparameterfile */
4144: strcat(rfileres,optionfilefiname); /* Parameter file first name*/
4145: strcat(rfileres,"."); /* */
4146: strcat(rfileres,optionfilext); /* Other files have txt extension */
4147: if((ficres =fopen(rfileres,"w"))==NULL) {
4148: printf("Problem writing new parameter file: %s\n", fileres);goto end;
4149: fprintf(ficlog,"Problem writing new parameter file: %s\n", fileres);goto end;
4150: }
4151: fprintf(ficres,"#%s\n",version);
1.53 brouard 4152:
1.59 brouard 4153: /*-------- data file ----------*/
4154: if((fic=fopen(datafile,"r"))==NULL) {
4155: printf("Problem with datafile: %s\n", datafile);goto end;
4156: fprintf(ficlog,"Problem with datafile: %s\n", datafile);goto end;
4157: }
4158:
4159: n= lastobs;
4160: severity = vector(1,maxwav);
4161: outcome=imatrix(1,maxwav+1,1,n);
1.85 brouard 4162: num=lvector(1,n);
1.59 brouard 4163: moisnais=vector(1,n);
4164: annais=vector(1,n);
4165: moisdc=vector(1,n);
4166: andc=vector(1,n);
4167: agedc=vector(1,n);
4168: cod=ivector(1,n);
4169: weight=vector(1,n);
4170: for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */
4171: mint=matrix(1,maxwav,1,n);
4172: anint=matrix(1,maxwav,1,n);
4173: s=imatrix(1,maxwav+1,1,n);
4174: tab=ivector(1,NCOVMAX);
4175: ncodemax=ivector(1,8);
4176:
4177: i=1;
4178: while (fgets(line, MAXLINE, fic) != NULL) {
4179: if ((i >= firstobs) && (i <=lastobs)) {
1.53 brouard 4180:
1.59 brouard 4181: for (j=maxwav;j>=1;j--){
4182: cutv(stra, strb,line,' '); s[j][i]=atoi(strb);
4183: strcpy(line,stra);
4184: cutv(stra, strb,line,'/'); anint[j][i]=(double)(atoi(strb)); strcpy(line,stra);
4185: cutv(stra, strb,line,' '); mint[j][i]=(double)(atoi(strb)); strcpy(line,stra);
4186: }
1.53 brouard 4187:
1.59 brouard 4188: cutv(stra, strb,line,'/'); andc[i]=(double)(atoi(strb)); strcpy(line,stra);
4189: cutv(stra, strb,line,' '); moisdc[i]=(double)(atoi(strb)); strcpy(line,stra);
1.53 brouard 4190:
1.59 brouard 4191: cutv(stra, strb,line,'/'); annais[i]=(double)(atoi(strb)); strcpy(line,stra);
4192: cutv(stra, strb,line,' '); moisnais[i]=(double)(atoi(strb)); strcpy(line,stra);
1.53 brouard 4193:
1.59 brouard 4194: cutv(stra, strb,line,' '); weight[i]=(double)(atoi(strb)); strcpy(line,stra);
4195: for (j=ncovcol;j>=1;j--){
4196: cutv(stra, strb,line,' '); covar[j][i]=(double)(atoi(strb)); strcpy(line,stra);
4197: }
1.85 brouard 4198: lstra=strlen(stra);
4199: if(lstra > 9){ /* More than 2**32 or max of what printf can write with %ld */
4200: stratrunc = &(stra[lstra-9]);
4201: num[i]=atol(stratrunc);
4202: }
4203: else
4204: num[i]=atol(stra);
1.53 brouard 4205:
1.59 brouard 4206: /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){
1.85 brouard 4207: 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 4208:
1.59 brouard 4209: i=i+1;
4210: }
4211: }
4212: /* printf("ii=%d", ij);
4213: scanf("%d",i);*/
1.53 brouard 4214: imx=i-1; /* Number of individuals */
4215:
4216: /* for (i=1; i<=imx; i++){
4217: if ((s[1][i]==3) && (s[2][i]==2)) s[2][i]=3;
4218: if ((s[2][i]==3) && (s[3][i]==2)) s[3][i]=3;
4219: if ((s[3][i]==3) && (s[4][i]==2)) s[4][i]=3;
4220: }*/
4221: /* for (i=1; i<=imx; i++){
4222: if (s[4][i]==9) s[4][i]=-1;
1.85 brouard 4223: 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 4224:
1.71 brouard 4225: for (i=1; i<=imx; i++)
1.53 brouard 4226:
1.71 brouard 4227: /*if ((s[3][i]==3) || (s[4][i]==3)) weight[i]=0.08;
4228: else weight[i]=1;*/
4229:
1.53 brouard 4230: /* Calculation of the number of parameter from char model*/
4231: Tvar=ivector(1,15); /* stores the number n of the covariates in Vm+Vn at 1 and m at 2 */
4232: Tprod=ivector(1,15);
4233: Tvaraff=ivector(1,15);
4234: Tvard=imatrix(1,15,1,2);
4235: Tage=ivector(1,15);
4236:
1.58 lievre 4237: if (strlen(model) >1){ /* If there is at least 1 covariate */
1.53 brouard 4238: j=0, j1=0, k1=1, k2=1;
1.58 lievre 4239: j=nbocc(model,'+'); /* j=Number of '+' */
4240: j1=nbocc(model,'*'); /* j1=Number of '*' */
4241: cptcovn=j+1;
4242: cptcovprod=j1; /*Number of products */
1.53 brouard 4243:
4244: strcpy(modelsav,model);
4245: if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){
4246: printf("Error. Non available option model=%s ",model);
4247: fprintf(ficlog,"Error. Non available option model=%s ",model);
4248: goto end;
4249: }
4250:
1.59 brouard 4251: /* This loop fills the array Tvar from the string 'model'.*/
1.58 lievre 4252:
1.53 brouard 4253: for(i=(j+1); i>=1;i--){
4254: cutv(stra,strb,modelsav,'+'); /* keeps in strb after the last + */
1.59 brouard 4255: if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyzes it */
1.53 brouard 4256: /* printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/
4257: /*scanf("%d",i);*/
4258: if (strchr(strb,'*')) { /* Model includes a product */
4259: cutv(strd,strc,strb,'*'); /* strd*strc Vm*Vn (if not *age)*/
4260: if (strcmp(strc,"age")==0) { /* Vn*age */
4261: cptcovprod--;
4262: cutv(strb,stre,strd,'V');
4263: Tvar[i]=atoi(stre); /* computes n in Vn and stores in Tvar*/
4264: cptcovage++;
4265: Tage[cptcovage]=i;
4266: /*printf("stre=%s ", stre);*/
4267: }
4268: else if (strcmp(strd,"age")==0) { /* or age*Vn */
4269: cptcovprod--;
4270: cutv(strb,stre,strc,'V');
4271: Tvar[i]=atoi(stre);
4272: cptcovage++;
4273: Tage[cptcovage]=i;
4274: }
4275: else { /* Age is not in the model */
4276: cutv(strb,stre,strc,'V'); /* strc= Vn, stre is n*/
4277: Tvar[i]=ncovcol+k1;
4278: cutv(strb,strc,strd,'V'); /* strd was Vm, strc is m */
4279: Tprod[k1]=i;
4280: Tvard[k1][1]=atoi(strc); /* m*/
4281: Tvard[k1][2]=atoi(stre); /* n */
4282: Tvar[cptcovn+k2]=Tvard[k1][1];
4283: Tvar[cptcovn+k2+1]=Tvard[k1][2];
4284: for (k=1; k<=lastobs;k++)
4285: covar[ncovcol+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];
4286: k1++;
4287: k2=k2+2;
4288: }
4289: }
4290: else { /* no more sum */
4291: /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/
4292: /* scanf("%d",i);*/
4293: cutv(strd,strc,strb,'V');
4294: Tvar[i]=atoi(strc);
4295: }
4296: strcpy(modelsav,stra);
4297: /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);
4298: scanf("%d",i);*/
4299: } /* end of loop + */
4300: } /* end model */
4301:
1.58 lievre 4302: /*The number n of Vn is stored in Tvar. cptcovage =number of age covariate. Tage gives the position of age. cptcovprod= number of products.
4303: If model=V1+V1*age then Tvar[1]=1 Tvar[2]=1 cptcovage=1 Tage[1]=2 cptcovprod=0*/
4304:
1.53 brouard 4305: /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);
4306: printf("cptcovprod=%d ", cptcovprod);
4307: fprintf(ficlog,"cptcovprod=%d ", cptcovprod);
1.58 lievre 4308:
4309: scanf("%d ",i);
4310: fclose(fic);*/
1.53 brouard 4311:
4312: /* if(mle==1){*/
1.59 brouard 4313: if (weightopt != 1) { /* Maximisation without weights*/
4314: for(i=1;i<=n;i++) weight[i]=1.0;
4315: }
1.53 brouard 4316: /*-calculation of age at interview from date of interview and age at death -*/
1.59 brouard 4317: agev=matrix(1,maxwav,1,imx);
1.53 brouard 4318:
1.59 brouard 4319: for (i=1; i<=imx; i++) {
4320: for(m=2; (m<= maxwav); m++) {
1.76 brouard 4321: if (((int)mint[m][i]== 99) && (s[m][i] <= nlstate)){
1.59 brouard 4322: anint[m][i]=9999;
4323: s[m][i]=-1;
4324: }
1.76 brouard 4325: if((int)moisdc[i]==99 && (int)andc[i]==9999 && s[m][i]>nlstate){
1.85 brouard 4326: 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);
4327: 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 4328: s[m][i]=-1;
4329: }
4330: if((int)moisdc[i]==99 && (int)andc[i]!=9999 && s[m][i]>nlstate){
1.85 brouard 4331: 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]);
4332: 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 4333: s[m][i]=-1; /* We prefer to skip it (and to skip it in version 0.8a1 too */
1.76 brouard 4334: }
1.53 brouard 4335: }
1.59 brouard 4336: }
1.53 brouard 4337:
1.59 brouard 4338: for (i=1; i<=imx; i++) {
4339: agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);
1.71 brouard 4340: for(m=firstpass; (m<= lastpass); m++){
1.69 brouard 4341: if(s[m][i] >0){
1.59 brouard 4342: if (s[m][i] >= nlstate+1) {
4343: if(agedc[i]>0)
1.76 brouard 4344: if((int)moisdc[i]!=99 && (int)andc[i]!=9999)
1.69 brouard 4345: agev[m][i]=agedc[i];
1.59 brouard 4346: /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/
4347: else {
1.76 brouard 4348: if ((int)andc[i]!=9999){
1.85 brouard 4349: printf("Warning negative age at death: %ld line:%d\n",num[i],i);
4350: fprintf(ficlog,"Warning negative age at death: %ld line:%d\n",num[i],i);
1.59 brouard 4351: agev[m][i]=-1;
1.53 brouard 4352: }
4353: }
1.70 brouard 4354: }
1.69 brouard 4355: else if(s[m][i] !=9){ /* Standard case, age in fractional
4356: years but with the precision of a
4357: month */
1.59 brouard 4358: agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);
1.76 brouard 4359: if((int)mint[m][i]==99 || (int)anint[m][i]==9999)
1.59 brouard 4360: agev[m][i]=1;
4361: else if(agev[m][i] <agemin){
4362: agemin=agev[m][i];
4363: /*printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], agemin);*/
1.53 brouard 4364: }
1.59 brouard 4365: else if(agev[m][i] >agemax){
4366: agemax=agev[m][i];
4367: /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/
1.53 brouard 4368: }
1.59 brouard 4369: /*agev[m][i]=anint[m][i]-annais[i];*/
4370: /* agev[m][i] = age[i]+2*m;*/
1.53 brouard 4371: }
1.59 brouard 4372: else { /* =9 */
1.53 brouard 4373: agev[m][i]=1;
1.59 brouard 4374: s[m][i]=-1;
4375: }
1.53 brouard 4376: }
1.59 brouard 4377: else /*= 0 Unknown */
4378: agev[m][i]=1;
4379: }
1.53 brouard 4380:
1.59 brouard 4381: }
4382: for (i=1; i<=imx; i++) {
1.71 brouard 4383: for(m=firstpass; (m<=lastpass); m++){
1.59 brouard 4384: if (s[m][i] > (nlstate+ndeath)) {
4385: 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);
4386: 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);
4387: goto end;
1.53 brouard 4388: }
4389: }
1.59 brouard 4390: }
1.53 brouard 4391:
1.71 brouard 4392: /*for (i=1; i<=imx; i++){
4393: for (m=firstpass; (m<lastpass); m++){
1.85 brouard 4394: 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 4395: }
4396:
4397: }*/
4398:
1.59 brouard 4399: printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);
4400: fprintf(ficlog,"Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);
4401:
4402: free_vector(severity,1,maxwav);
4403: free_imatrix(outcome,1,maxwav+1,1,n);
4404: free_vector(moisnais,1,n);
4405: free_vector(annais,1,n);
4406: /* free_matrix(mint,1,maxwav,1,n);
4407: free_matrix(anint,1,maxwav,1,n);*/
4408: free_vector(moisdc,1,n);
4409: free_vector(andc,1,n);
1.53 brouard 4410:
4411:
1.59 brouard 4412: wav=ivector(1,imx);
4413: dh=imatrix(1,lastpass-firstpass+1,1,imx);
4414: bh=imatrix(1,lastpass-firstpass+1,1,imx);
4415: mw=imatrix(1,lastpass-firstpass+1,1,imx);
1.69 brouard 4416:
1.59 brouard 4417: /* Concatenates waves */
4418: concatwav(wav, dh, bh, mw, s, agedc, agev, firstpass, lastpass, imx, nlstate, stepm);
1.53 brouard 4419:
1.59 brouard 4420: /* Routine tricode is to calculate cptcoveff (real number of unique covariates) and to associate covariable number and modality */
1.53 brouard 4421:
1.59 brouard 4422: Tcode=ivector(1,100);
4423: nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);
4424: ncodemax[1]=1;
4425: if (cptcovn > 0) tricode(Tvar,nbcode,imx);
1.53 brouard 4426:
1.59 brouard 4427: codtab=imatrix(1,100,1,10); /* Cross tabulation to get the order of
4428: the estimations*/
4429: h=0;
4430: m=pow(2,cptcoveff);
1.53 brouard 4431:
1.59 brouard 4432: for(k=1;k<=cptcoveff; k++){
4433: for(i=1; i <=(m/pow(2,k));i++){
4434: for(j=1; j <= ncodemax[k]; j++){
4435: for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){
4436: h++;
4437: if (h>m) h=1;codtab[h][k]=j;codtab[h][Tvar[k]]=j;
4438: /* printf("h=%d k=%d j=%d codtab[h][k]=%d tvar[k]=%d \n",h, k,j,codtab[h][k],Tvar[k]);*/
4439: }
4440: }
4441: }
4442: }
4443: /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]);
4444: codtab[1][2]=1;codtab[2][2]=2; */
4445: /* for(i=1; i <=m ;i++){
4446: for(k=1; k <=cptcovn; k++){
4447: printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);
4448: }
4449: printf("\n");
1.53 brouard 4450: }
1.59 brouard 4451: scanf("%d",i);*/
1.53 brouard 4452:
1.86 brouard 4453: /*------------ gnuplot -------------*/
4454: strcpy(optionfilegnuplot,optionfilefiname);
4455: strcat(optionfilegnuplot,".gp");
4456: if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {
4457: printf("Problem with file %s",optionfilegnuplot);
4458: }
4459: else{
4460: fprintf(ficgp,"\n# %s\n", version);
4461: fprintf(ficgp,"# %s\n", optionfilegnuplot);
4462: fprintf(ficgp,"set missing 'NaNq'\n");
4463: }
1.88 brouard 4464: /* fclose(ficgp);*/
1.86 brouard 4465: /*--------- index.htm --------*/
4466:
1.87 brouard 4467: strcpy(optionfilehtm,optionfilefiname);
1.86 brouard 4468: strcat(optionfilehtm,".htm");
4469: if((fichtm=fopen(optionfilehtm,"w"))==NULL) {
4470: printf("Problem with %s \n",optionfilehtm), exit(0);
4471: }
4472:
1.87 brouard 4473: fprintf(fichtm,"<body>\n<title>IMaCh %s</title>\n <font size=\"2\">%s <br> %s</font> \
1.86 brouard 4474: <hr size=\"2\" color=\"#EC5E5E\"> \n\
4475: Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n\
4476: \n\
4477: <hr size=\"2\" color=\"#EC5E5E\">\
4478: <ul><li><h4>Parameter files</h4>\n\
4479: - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n\
4480: - Log file of the run: <a href=\"%s\">%s</a><br>\n\
1.87 brouard 4481: - Gnuplot file name: <a href=\"%s\">%s</a><br>\n\
1.86 brouard 4482: - Date and time at start: %s</ul>\n",\
1.87 brouard 4483: fileres,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt,\
1.86 brouard 4484: model,fileres,fileres,\
1.88 brouard 4485: filelog,filelog,optionfilegnuplot,optionfilegnuplot,strstart);
1.87 brouard 4486: /*fclose(fichtm);*/
4487: fflush(fichtm);
1.86 brouard 4488:
1.88 brouard 4489: strcpy(pathr,path);
4490: strcat(pathr,optionfilefiname);
4491: chdir(optionfilefiname); /* Move to directory named optionfile */
4492: strcpy(lfileres,fileres);
4493: strcat(lfileres,"/");
4494: strcat(lfileres,optionfilefiname);
4495:
1.59 brouard 4496: /* Calculates basic frequencies. Computes observed prevalence at single age
4497: and prints on file fileres'p'. */
1.84 brouard 4498: freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint);
1.53 brouard 4499:
1.88 brouard 4500: fprintf(fichtm,"\n");
4501: fprintf(fichtm,"<br>Total number of observations=%d <br>\n\
1.86 brouard 4502: Youngest age at first (selected) pass %.2f, oldest age %.2f<br>\n\
4503: Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n",\
1.88 brouard 4504: imx,agemin,agemax,jmin,jmax,jmean);
4505: pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
1.60 brouard 4506: oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
4507: newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
4508: savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
4509: oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */
1.53 brouard 4510:
4511:
1.59 brouard 4512: /* For Powell, parameters are in a vector p[] starting at p[1]
4513: so we point p on param[1][1] so that p[1] maps on param[1][1][1] */
4514: p=param[1][1]; /* *(*(*(param +1)+1)+0) */
1.53 brouard 4515:
1.86 brouard 4516: globpr=0; /* To get the number ipmx of contributions and the sum of weights*/
1.85 brouard 4517: likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
4518: printf("First Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
4519: for (k=1; k<=npar;k++)
4520: printf(" %d %8.5f",k,p[k]);
4521: printf("\n");
4522: globpr=1; /* to print the contributions */
4523: likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
4524: printf("Second Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
4525: for (k=1; k<=npar;k++)
4526: printf(" %d %8.5f",k,p[k]);
4527: printf("\n");
1.61 brouard 4528: if(mle>=1){ /* Could be 1 or 2 */
1.53 brouard 4529: mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);
1.59 brouard 4530: }
1.53 brouard 4531:
1.59 brouard 4532: /*--------- results files --------------*/
4533: 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 4534:
4535:
1.59 brouard 4536: jk=1;
4537: fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
4538: printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
4539: fprintf(ficlog,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
4540: for(i=1,jk=1; i <=nlstate; i++){
4541: for(k=1; k <=(nlstate+ndeath); k++){
4542: if (k != i)
4543: {
4544: printf("%d%d ",i,k);
4545: fprintf(ficlog,"%d%d ",i,k);
4546: fprintf(ficres,"%1d%1d ",i,k);
4547: for(j=1; j <=ncovmodel; j++){
4548: printf("%f ",p[jk]);
4549: fprintf(ficlog,"%f ",p[jk]);
4550: fprintf(ficres,"%f ",p[jk]);
4551: jk++;
4552: }
4553: printf("\n");
4554: fprintf(ficlog,"\n");
4555: fprintf(ficres,"\n");
4556: }
4557: }
4558: }
1.84 brouard 4559: if(mle!=0){
1.59 brouard 4560: /* Computing hessian and covariance matrix */
4561: ftolhess=ftol; /* Usually correct */
4562: hesscov(matcov, p, npar, delti, ftolhess, func);
4563: }
4564: fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");
4565: printf("# Scales (for hessian or gradient estimation)\n");
4566: fprintf(ficlog,"# Scales (for hessian or gradient estimation)\n");
4567: for(i=1,jk=1; i <=nlstate; i++){
4568: for(j=1; j <=nlstate+ndeath; j++){
4569: if (j!=i) {
4570: fprintf(ficres,"%1d%1d",i,j);
4571: printf("%1d%1d",i,j);
4572: fprintf(ficlog,"%1d%1d",i,j);
4573: for(k=1; k<=ncovmodel;k++){
4574: printf(" %.5e",delti[jk]);
4575: fprintf(ficlog," %.5e",delti[jk]);
4576: fprintf(ficres," %.5e",delti[jk]);
4577: jk++;
4578: }
4579: printf("\n");
4580: fprintf(ficlog,"\n");
4581: fprintf(ficres,"\n");
4582: }
4583: }
4584: }
1.53 brouard 4585:
1.59 brouard 4586: 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");
4587: if(mle==1)
4588: 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");
4589: 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");
4590: for(i=1,k=1;i<=npar;i++){
4591: /* if (k>nlstate) k=1;
4592: i1=(i-1)/(ncovmodel*nlstate)+1;
4593: fprintf(ficres,"%s%d%d",alph[k],i1,tab[i]);
4594: printf("%s%d%d",alph[k],i1,tab[i]);
4595: */
4596: fprintf(ficres,"%3d",i);
4597: if(mle==1)
4598: printf("%3d",i);
4599: fprintf(ficlog,"%3d",i);
4600: for(j=1; j<=i;j++){
4601: fprintf(ficres," %.5e",matcov[i][j]);
4602: if(mle==1)
4603: printf(" %.5e",matcov[i][j]);
4604: fprintf(ficlog," %.5e",matcov[i][j]);
4605: }
4606: fprintf(ficres,"\n");
4607: if(mle==1)
4608: printf("\n");
4609: fprintf(ficlog,"\n");
4610: k++;
4611: }
1.53 brouard 4612:
1.59 brouard 4613: while((c=getc(ficpar))=='#' && c!= EOF){
4614: ungetc(c,ficpar);
4615: fgets(line, MAXLINE, ficpar);
4616: puts(line);
4617: fputs(line,ficparo);
4618: }
4619: ungetc(c,ficpar);
4620:
4621: estepm=0;
4622: fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm);
4623: if (estepm==0 || estepm < stepm) estepm=stepm;
4624: if (fage <= 2) {
4625: bage = ageminpar;
4626: fage = agemaxpar;
4627: }
1.53 brouard 4628:
1.59 brouard 4629: fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");
4630: fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
4631: fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
1.53 brouard 4632:
1.59 brouard 4633: while((c=getc(ficpar))=='#' && c!= EOF){
4634: ungetc(c,ficpar);
4635: fgets(line, MAXLINE, ficpar);
4636: puts(line);
4637: fputs(line,ficparo);
4638: }
4639: ungetc(c,ficpar);
1.53 brouard 4640:
1.59 brouard 4641: 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);
4642: 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);
4643: 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 4644: printf("begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
4645: 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 4646:
1.59 brouard 4647: while((c=getc(ficpar))=='#' && c!= EOF){
4648: ungetc(c,ficpar);
4649: fgets(line, MAXLINE, ficpar);
4650: puts(line);
4651: fputs(line,ficparo);
4652: }
4653: ungetc(c,ficpar);
1.53 brouard 4654:
4655:
1.70 brouard 4656: dateprev1=anprev1+(mprev1-1)/12.+(jprev1-1)/365.;
4657: dateprev2=anprev2+(mprev2-1)/12.+(jprev2-1)/365.;
1.53 brouard 4658:
4659: fscanf(ficpar,"pop_based=%d\n",&popbased);
4660: fprintf(ficparo,"pop_based=%d\n",popbased);
4661: fprintf(ficres,"pop_based=%d\n",popbased);
4662:
4663: while((c=getc(ficpar))=='#' && c!= EOF){
4664: ungetc(c,ficpar);
4665: fgets(line, MAXLINE, ficpar);
4666: puts(line);
4667: fputs(line,ficparo);
4668: }
4669: ungetc(c,ficpar);
4670:
1.69 brouard 4671: 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 4672: 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 4673: 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);
4674: 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);
4675: 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 4676: /* day and month of proj2 are not used but only year anproj2.*/
1.53 brouard 4677:
1.59 brouard 4678: while((c=getc(ficpar))=='#' && c!= EOF){
1.53 brouard 4679: ungetc(c,ficpar);
4680: fgets(line, MAXLINE, ficpar);
4681: puts(line);
4682: fputs(line,ficparo);
4683: }
4684: ungetc(c,ficpar);
4685:
4686: fscanf(ficpar,"popforecast=%d popfile=%s popfiledate=%lf/%lf/%lf last-popfiledate=%lf/%lf/%lf\n",&popforecast,popfile,&jpyram,&mpyram,&anpyram,&jpyram1,&mpyram1,&anpyram1);
4687: fprintf(ficparo,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);
4688: fprintf(ficres,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);
4689:
1.86 brouard 4690: /* freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint);*/
1.84 brouard 4691: /*,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
1.58 lievre 4692:
1.89 brouard 4693: replace_back_to_slash(pathc,path); /* Even gnuplot wants a / */
4694: printinggnuplot(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
1.53 brouard 4695:
1.85 brouard 4696: printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,\
4697: model,imx,jmin,jmax,jmean,rfileres,popforecast,estepm,\
4698: jprev1,mprev1,anprev1,jprev2,mprev2,anprev2);
1.53 brouard 4699:
1.59 brouard 4700: /*------------ free_vector -------------*/
1.88 brouard 4701: /* chdir(path); */
1.53 brouard 4702:
1.59 brouard 4703: free_ivector(wav,1,imx);
4704: free_imatrix(dh,1,lastpass-firstpass+1,1,imx);
4705: free_imatrix(bh,1,lastpass-firstpass+1,1,imx);
4706: free_imatrix(mw,1,lastpass-firstpass+1,1,imx);
1.85 brouard 4707: free_lvector(num,1,n);
1.59 brouard 4708: free_vector(agedc,1,n);
1.65 lievre 4709: /*free_matrix(covar,0,NCOVMAX,1,n);*/
1.59 brouard 4710: /*free_matrix(covar,1,NCOVMAX,1,n);*/
4711: fclose(ficparo);
4712: fclose(ficres);
1.53 brouard 4713:
4714:
1.54 brouard 4715: /*--------------- Prevalence limit (stable prevalence) --------------*/
1.53 brouard 4716:
4717: strcpy(filerespl,"pl");
4718: strcat(filerespl,fileres);
4719: if((ficrespl=fopen(filerespl,"w"))==NULL) {
1.54 brouard 4720: printf("Problem with stable prevalence resultfile: %s\n", filerespl);goto end;
4721: fprintf(ficlog,"Problem with stable prevalence resultfile: %s\n", filerespl);goto end;
1.53 brouard 4722: }
1.54 brouard 4723: printf("Computing stable prevalence: result on file '%s' \n", filerespl);
4724: fprintf(ficlog,"Computing stable prevalence: result on file '%s' \n", filerespl);
4725: fprintf(ficrespl,"#Stable prevalence \n");
1.53 brouard 4726: fprintf(ficrespl,"#Age ");
4727: for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);
4728: fprintf(ficrespl,"\n");
4729:
4730: prlim=matrix(1,nlstate,1,nlstate);
1.59 brouard 4731:
1.53 brouard 4732: agebase=ageminpar;
4733: agelim=agemaxpar;
4734: ftolpl=1.e-10;
4735: i1=cptcoveff;
4736: if (cptcovn < 1){i1=1;}
4737:
1.59 brouard 4738: for(cptcov=1,k=0;cptcov<=i1;cptcov++){
1.53 brouard 4739: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
1.59 brouard 4740: k=k+1;
4741: /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/
4742: fprintf(ficrespl,"\n#******");
4743: printf("\n#******");
4744: fprintf(ficlog,"\n#******");
4745: for(j=1;j<=cptcoveff;j++) {
4746: fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
4747: printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
4748: fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
4749: }
4750: fprintf(ficrespl,"******\n");
4751: printf("******\n");
4752: fprintf(ficlog,"******\n");
1.53 brouard 4753:
1.59 brouard 4754: for (age=agebase; age<=agelim; age++){
4755: prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
1.69 brouard 4756: fprintf(ficrespl,"%.0f ",age );
4757: for(j=1;j<=cptcoveff;j++)
4758: fprintf(ficrespl,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
1.59 brouard 4759: for(i=1; i<=nlstate;i++)
1.53 brouard 4760: fprintf(ficrespl," %.5f", prlim[i][i]);
1.59 brouard 4761: fprintf(ficrespl,"\n");
1.53 brouard 4762: }
4763: }
1.59 brouard 4764: }
1.53 brouard 4765: fclose(ficrespl);
4766:
4767: /*------------- h Pij x at various ages ------------*/
4768:
4769: strcpy(filerespij,"pij"); strcat(filerespij,fileres);
4770: if((ficrespij=fopen(filerespij,"w"))==NULL) {
4771: printf("Problem with Pij resultfile: %s\n", filerespij);goto end;
4772: fprintf(ficlog,"Problem with Pij resultfile: %s\n", filerespij);goto end;
4773: }
4774: printf("Computing pij: result on file '%s' \n", filerespij);
4775: fprintf(ficlog,"Computing pij: result on file '%s' \n", filerespij);
4776:
4777: stepsize=(int) (stepm+YEARM-1)/YEARM;
4778: /*if (stepm<=24) stepsize=2;*/
4779:
4780: agelim=AGESUP;
4781: hstepm=stepsize*YEARM; /* Every year of age */
4782: hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */
4783:
4784: /* hstepm=1; aff par mois*/
4785:
1.70 brouard 4786: fprintf(ficrespij,"#****** h Pij x Probability to be in state j at age x+h being in i at x ");
1.59 brouard 4787: for(cptcov=1,k=0;cptcov<=i1;cptcov++){
1.53 brouard 4788: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
4789: k=k+1;
1.59 brouard 4790: fprintf(ficrespij,"\n#****** ");
4791: for(j=1;j<=cptcoveff;j++)
4792: fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
4793: fprintf(ficrespij,"******\n");
1.53 brouard 4794:
1.59 brouard 4795: for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */
4796: nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
4797: nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
4798:
4799: /* nhstepm=nhstepm*YEARM; aff par mois*/
4800:
4801: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4802: oldm=oldms;savm=savms;
4803: hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
1.70 brouard 4804: fprintf(ficrespij,"# Cov Agex agex+h hpijx with i,j=");
1.59 brouard 4805: for(i=1; i<=nlstate;i++)
4806: for(j=1; j<=nlstate+ndeath;j++)
4807: fprintf(ficrespij," %1d-%1d",i,j);
4808: fprintf(ficrespij,"\n");
4809: for (h=0; h<=nhstepm; h++){
1.70 brouard 4810: fprintf(ficrespij,"%d %3.f %3.f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );
1.53 brouard 4811: for(i=1; i<=nlstate;i++)
4812: for(j=1; j<=nlstate+ndeath;j++)
1.59 brouard 4813: fprintf(ficrespij," %.5f", p3mat[i][j][h]);
1.53 brouard 4814: fprintf(ficrespij,"\n");
4815: }
1.59 brouard 4816: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4817: fprintf(ficrespij,"\n");
4818: }
1.53 brouard 4819: }
4820: }
4821:
1.74 brouard 4822: varprob(optionfilefiname, matcov, p, delti, nlstate, bage, fage,k,Tvar,nbcode, ncodemax);
1.53 brouard 4823:
4824: fclose(ficrespij);
4825:
1.84 brouard 4826: probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
1.53 brouard 4827:
4828: /*---------- Forecasting ------------------*/
1.69 brouard 4829: /*if((stepm == 1) && (strcmp(model,".")==0)){*/
4830: if(prevfcast==1){
1.74 brouard 4831: /* if(stepm ==1){*/
1.70 brouard 4832: prevforecast(fileres, anproj1, mproj1, jproj1, agemin, agemax, dateprev1, dateprev2, mobilavproj, bage, fage, firstpass, lastpass, anproj2, p, cptcoveff);
1.74 brouard 4833: /* (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);*/
4834: /* } */
4835: /* else{ */
4836: /* erreur=108; */
4837: /* 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); */
4838: /* 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); */
4839: /* } */
1.69 brouard 4840: }
1.53 brouard 4841:
4842:
4843: /*---------- Health expectancies and variances ------------*/
4844:
4845: strcpy(filerest,"t");
4846: strcat(filerest,fileres);
4847: if((ficrest=fopen(filerest,"w"))==NULL) {
4848: printf("Problem with total LE resultfile: %s\n", filerest);goto end;
4849: fprintf(ficlog,"Problem with total LE resultfile: %s\n", filerest);goto end;
4850: }
4851: printf("Computing Total LEs with variances: file '%s' \n", filerest);
4852: fprintf(ficlog,"Computing Total LEs with variances: file '%s' \n", filerest);
4853:
4854:
4855: strcpy(filerese,"e");
4856: strcat(filerese,fileres);
4857: if((ficreseij=fopen(filerese,"w"))==NULL) {
4858: printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
4859: fprintf(ficlog,"Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
4860: }
4861: printf("Computing Health Expectancies: result on file '%s' \n", filerese);
4862: fprintf(ficlog,"Computing Health Expectancies: result on file '%s' \n", filerese);
1.68 lievre 4863:
1.53 brouard 4864: strcpy(fileresv,"v");
4865: strcat(fileresv,fileres);
4866: if((ficresvij=fopen(fileresv,"w"))==NULL) {
4867: printf("Problem with variance resultfile: %s\n", fileresv);exit(0);
4868: fprintf(ficlog,"Problem with variance resultfile: %s\n", fileresv);exit(0);
4869: }
4870: printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
4871: fprintf(ficlog,"Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
1.58 lievre 4872:
1.74 brouard 4873: /* Computes prevalence between agemin (i.e minimal age computed) and no more ageminpar */
1.84 brouard 4874: prevalence(probs, agemin, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
1.74 brouard 4875: /* 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",\
4876: ageminpar, agemax, s[lastpass][imx], agev[lastpass][imx], nlstate, imx, mint[lastpass][imx],anint[lastpass][imx], dateprev1, dateprev2, firstpass, lastpass);
4877: */
1.58 lievre 4878:
1.54 brouard 4879: if (mobilav!=0) {
1.53 brouard 4880: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
1.54 brouard 4881: if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
4882: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
4883: printf(" Error in movingaverage mobilav=%d\n",mobilav);
4884: }
1.53 brouard 4885: }
4886:
1.59 brouard 4887: for(cptcov=1,k=0;cptcov<=i1;cptcov++){
1.53 brouard 4888: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
4889: k=k+1;
4890: fprintf(ficrest,"\n#****** ");
4891: for(j=1;j<=cptcoveff;j++)
4892: fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
4893: fprintf(ficrest,"******\n");
4894:
4895: fprintf(ficreseij,"\n#****** ");
4896: for(j=1;j<=cptcoveff;j++)
4897: fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
4898: fprintf(ficreseij,"******\n");
4899:
4900: fprintf(ficresvij,"\n#****** ");
4901: for(j=1;j<=cptcoveff;j++)
4902: fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
4903: fprintf(ficresvij,"******\n");
4904:
4905: eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
4906: oldm=oldms;savm=savms;
4907: evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov);
4908:
4909: vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
4910: oldm=oldms;savm=savms;
4911: varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,0, mobilav);
4912: if(popbased==1){
4913: 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 4914: }
1.53 brouard 4915:
4916:
4917: fprintf(ficrest,"#Total LEs with variances: e.. (std) ");
4918: for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);
4919: fprintf(ficrest,"\n");
4920:
4921: epj=vector(1,nlstate+1);
4922: for(age=bage; age <=fage ;age++){
4923: prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
4924: if (popbased==1) {
1.54 brouard 4925: if(mobilav ==0){
1.53 brouard 4926: for(i=1; i<=nlstate;i++)
4927: prlim[i][i]=probs[(int)age][i][k];
1.54 brouard 4928: }else{ /* mobilav */
1.53 brouard 4929: for(i=1; i<=nlstate;i++)
4930: prlim[i][i]=mobaverage[(int)age][i][k];
4931: }
4932: }
4933:
4934: fprintf(ficrest," %4.0f",age);
4935: for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){
4936: for(i=1, epj[j]=0.;i <=nlstate;i++) {
4937: epj[j] += prlim[i][i]*eij[i][j][(int)age];
4938: /* printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/
4939: }
4940: epj[nlstate+1] +=epj[j];
4941: }
4942:
4943: for(i=1, vepp=0.;i <=nlstate;i++)
4944: for(j=1;j <=nlstate;j++)
4945: vepp += vareij[i][j][(int)age];
4946: fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));
4947: for(j=1;j <=nlstate;j++){
4948: fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));
4949: }
4950: fprintf(ficrest,"\n");
4951: }
1.59 brouard 4952: free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
4953: free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);
4954: free_vector(epj,1,nlstate+1);
1.53 brouard 4955: }
4956: }
1.59 brouard 4957: free_vector(weight,1,n);
4958: free_imatrix(Tvard,1,15,1,2);
4959: free_imatrix(s,1,maxwav+1,1,n);
4960: free_matrix(anint,1,maxwav,1,n);
4961: free_matrix(mint,1,maxwav,1,n);
4962: free_ivector(cod,1,n);
4963: free_ivector(tab,1,NCOVMAX);
1.53 brouard 4964: fclose(ficreseij);
4965: fclose(ficresvij);
4966: fclose(ficrest);
4967: fclose(ficpar);
4968:
1.54 brouard 4969: /*------- Variance of stable prevalence------*/
1.53 brouard 4970:
4971: strcpy(fileresvpl,"vpl");
4972: strcat(fileresvpl,fileres);
4973: if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {
1.54 brouard 4974: printf("Problem with variance of stable prevalence resultfile: %s\n", fileresvpl);
1.53 brouard 4975: exit(0);
4976: }
1.54 brouard 4977: printf("Computing Variance-covariance of stable prevalence: file '%s' \n", fileresvpl);
1.53 brouard 4978:
1.59 brouard 4979: for(cptcov=1,k=0;cptcov<=i1;cptcov++){
1.53 brouard 4980: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
4981: k=k+1;
4982: fprintf(ficresvpl,"\n#****** ");
4983: for(j=1;j<=cptcoveff;j++)
4984: fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
4985: fprintf(ficresvpl,"******\n");
4986:
4987: varpl=matrix(1,nlstate,(int) bage, (int) fage);
4988: oldm=oldms;savm=savms;
1.59 brouard 4989: varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);
4990: free_matrix(varpl,1,nlstate,(int) bage, (int)fage);
1.53 brouard 4991: }
1.59 brouard 4992: }
1.53 brouard 4993:
4994: fclose(ficresvpl);
4995:
4996: /*---------- End : free ----------------*/
4997: free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);
4998: free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);
4999: free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);
5000: free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);
1.65 lievre 5001:
5002: free_matrix(covar,0,NCOVMAX,1,n);
1.53 brouard 5003: free_matrix(matcov,1,npar,1,npar);
1.74 brouard 5004: /*free_vector(delti,1,npar);*/
5005: free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
1.53 brouard 5006: free_matrix(agev,1,maxwav,1,imx);
5007: free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
1.54 brouard 5008: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
1.74 brouard 5009: free_ma3x(probs,1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
5010:
1.59 brouard 5011: free_ivector(ncodemax,1,8);
5012: free_ivector(Tvar,1,15);
5013: free_ivector(Tprod,1,15);
5014: free_ivector(Tvaraff,1,15);
5015: free_ivector(Tage,1,15);
5016: free_ivector(Tcode,1,100);
1.53 brouard 5017:
1.88 brouard 5018: fflush(fichtm);
5019: fflush(ficgp);
1.53 brouard 5020:
5021:
5022: if(erreur >0){
5023: printf("End of Imach with error or warning %d\n",erreur);
5024: fprintf(ficlog,"End of Imach with error or warning %d\n",erreur);
5025: }else{
5026: printf("End of Imach\n");
5027: fprintf(ficlog,"End of Imach\n");
5028: }
5029: printf("See log file on %s\n",filelog);
5030: fclose(ficlog);
5031: /* gettimeofday(&end_time, (struct timezone*)0);*/ /* after time */
1.85 brouard 5032: (void) gettimeofday(&end_time,&tzp);
5033: tm = *localtime(&end_time.tv_sec);
5034: tmg = *gmtime(&end_time.tv_sec);
1.88 brouard 5035: strcpy(strtend,asctime(&tm));
5036: printf("Localtime at start %s\nLocaltime at end %s",strstart, strtend);
5037: fprintf(ficlog,"Localtime at start %s\nLocal time at end %s",strstart, strtend);
1.85 brouard 5038: /* printf("Total time used %d Sec\n", asc_time(end_time.tv_sec -start_time.tv_sec);*/
5039:
5040: 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);
5041: 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);
5042: /* printf("Total time was %d uSec.\n", total_usecs);*/
1.87 brouard 5043: /* if(fileappend(fichtm,optionfilehtm)){ */
1.88 brouard 5044: fprintf(fichtm,"<br>Local time at start %s<br>Local time at end %s<br>",strstart, strtend);
1.87 brouard 5045: fclose(fichtm);
1.88 brouard 5046: fclose(ficgp);
1.53 brouard 5047: /*------ End -----------*/
5048:
1.59 brouard 5049: end:
1.53 brouard 5050: #ifdef windows
5051: /* chdir(pathcd);*/
5052: #endif
1.88 brouard 5053: chdir(path);
1.53 brouard 5054: /*system("wgnuplot graph.plt");*/
5055: /*system("../gp37mgw/wgnuplot graph.plt");*/
5056: /*system("cd ../gp37mgw");*/
5057: /* system("..\\gp37mgw\\wgnuplot graph.plt");*/
1.59 brouard 5058: strcpy(plotcmd,GNUPLOTPROGRAM);
5059: strcat(plotcmd," ");
5060: strcat(plotcmd,optionfilegnuplot);
1.75 brouard 5061: printf("Starting graphs with: %s",plotcmd);fflush(stdout);
1.59 brouard 5062: system(plotcmd);
1.75 brouard 5063: printf(" Wait...");
1.53 brouard 5064:
1.54 brouard 5065: /*#ifdef windows*/
1.53 brouard 5066: while (z[0] != 'q') {
5067: /* chdir(path); */
5068: printf("\nType e to edit output files, g to graph again, c to start again, and q for exiting: ");
5069: scanf("%s",z);
5070: if (z[0] == 'c') system("./imach");
5071: else if (z[0] == 'e') system(optionfilehtm);
5072: else if (z[0] == 'g') system(plotcmd);
5073: else if (z[0] == 'q') exit(0);
5074: }
1.54 brouard 5075: /*#endif */
1.53 brouard 5076: }
1.88 brouard 5077:
1.53 brouard 5078:
5079:
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