Annotation of imach096d/src/imach.c, revision 1.89
1.89 ! brouard 1: /* $Id: imach.c,v 1.88 2003/06/23 17:54:56 brouard Exp $
1.83 lievre 2: $State: Exp $
3: $Log: imach.c,v $
1.89 ! brouard 4: Revision 1.88 2003/06/23 17:54:56 brouard
! 5: * 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.
! 6:
1.88 brouard 7: Revision 1.87 2003/06/18 12:26:01 brouard
8: Version 0.96
9:
1.87 brouard 10: Revision 1.86 2003/06/17 20:04:08 brouard
11: (Module): Change position of html and gnuplot routines and added
12: routine fileappend.
13:
1.86 brouard 14: Revision 1.85 2003/06/17 13:12:43 brouard
15: * imach.c (Repository): Check when date of death was earlier that
16: current date of interview. It may happen when the death was just
17: prior to the death. In this case, dh was negative and likelihood
18: was wrong (infinity). We still send an "Error" but patch by
19: assuming that the date of death was just one stepm after the
20: interview.
21: (Repository): Because some people have very long ID (first column)
22: we changed int to long in num[] and we added a new lvector for
23: memory allocation. But we also truncated to 8 characters (left
24: truncation)
25: (Repository): No more line truncation errors.
26:
1.85 brouard 27: Revision 1.84 2003/06/13 21:44:43 brouard
28: * imach.c (Repository): Replace "freqsummary" at a correct
29: place. It differs from routine "prevalence" which may be called
30: many times. Probs is memory consuming and must be used with
31: parcimony.
1.86 brouard 32: Version 0.95a3 (should output exactly the same maximization than 0.8a2)
1.85 brouard 33:
1.84 brouard 34: Revision 1.83 2003/06/10 13:39:11 lievre
35: *** empty log message ***
36:
1.83 lievre 37: Revision 1.82 2003/06/05 15:57:20 brouard
38: Add log in imach.c and fullversion number is now printed.
39:
1.82 brouard 40: */
41: /*
1.53 brouard 42: Interpolated Markov Chain
43:
44: Short summary of the programme:
45:
46: This program computes Healthy Life Expectancies from
47: cross-longitudinal data. Cross-longitudinal data consist in: -1- a
48: first survey ("cross") where individuals from different ages are
49: interviewed on their health status or degree of disability (in the
50: case of a health survey which is our main interest) -2- at least a
51: second wave of interviews ("longitudinal") which measure each change
52: (if any) in individual health status. Health expectancies are
53: computed from the time spent in each health state according to a
54: model. More health states you consider, more time is necessary to reach the
55: Maximum Likelihood of the parameters involved in the model. The
56: simplest model is the multinomial logistic model where pij is the
57: probability to be observed in state j at the second wave
58: conditional to be observed in state i at the first wave. Therefore
59: the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where
60: 'age' is age and 'sex' is a covariate. If you want to have a more
61: complex model than "constant and age", you should modify the program
62: where the markup *Covariates have to be included here again* invites
63: you to do it. More covariates you add, slower the
64: convergence.
65:
66: The advantage of this computer programme, compared to a simple
67: multinomial logistic model, is clear when the delay between waves is not
68: identical for each individual. Also, if a individual missed an
69: intermediate interview, the information is lost, but taken into
70: account using an interpolation or extrapolation.
71:
72: hPijx is the probability to be observed in state i at age x+h
73: conditional to the observed state i at age x. The delay 'h' can be
74: split into an exact number (nh*stepm) of unobserved intermediate
1.66 brouard 75: states. This elementary transition (by month, quarter,
76: semester or year) is modelled as a multinomial logistic. The hPx
1.53 brouard 77: matrix is simply the matrix product of nh*stepm elementary matrices
78: and the contribution of each individual to the likelihood is simply
79: hPijx.
80:
81: Also this programme outputs the covariance matrix of the parameters but also
1.54 brouard 82: of the life expectancies. It also computes the stable prevalence.
1.53 brouard 83:
84: Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).
85: Institut national d'études démographiques, Paris.
86: This software have been partly granted by Euro-REVES, a concerted action
87: from the European Union.
88: It is copyrighted identically to a GNU software product, ie programme and
89: software can be distributed freely for non commercial use. Latest version
90: can be accessed at http://euroreves.ined.fr/imach .
1.74 brouard 91:
92: Help to debug: LD_PRELOAD=/usr/local/lib/libnjamd.so ./imach foo.imach
93: or better on gdb : set env LD_PRELOAD=/usr/local/lib/libnjamd.so
94:
1.53 brouard 95: **********************************************************************/
1.74 brouard 96: /*
97: main
98: read parameterfile
99: read datafile
100: concatwav
1.84 brouard 101: freqsummary
1.74 brouard 102: if (mle >= 1)
103: mlikeli
104: print results files
105: if mle==1
106: computes hessian
107: read end of parameter file: agemin, agemax, bage, fage, estepm
108: begin-prev-date,...
109: open gnuplot file
110: open html file
111: stable prevalence
112: for age prevalim()
113: h Pij x
114: variance of p varprob
115: forecasting if prevfcast==1 prevforecast call prevalence()
116: health expectancies
117: Variance-covariance of DFLE
118: prevalence()
119: movingaverage()
120: varevsij()
121: if popbased==1 varevsij(,popbased)
122: total life expectancies
123: Variance of stable prevalence
124: end
125: */
126:
127:
128:
1.53 brouard 129:
130: #include <math.h>
131: #include <stdio.h>
132: #include <stdlib.h>
133: #include <unistd.h>
134:
1.86 brouard 135: #include <sys/time.h>
136: #include <time.h>
137: #include "timeval.h"
138:
1.53 brouard 139: #define MAXLINE 256
140: #define GNUPLOTPROGRAM "gnuplot"
141: /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
1.85 brouard 142: #define FILENAMELENGTH 132
1.53 brouard 143: /*#define DEBUG*/
1.85 brouard 144: /*#define windows*/
1.53 brouard 145: #define GLOCK_ERROR_NOPATH -1 /* empty path */
146: #define GLOCK_ERROR_GETCWD -2 /* cannot get cwd */
147:
148: #define MAXPARM 30 /* Maximum number of parameters for the optimization */
149: #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */
150:
151: #define NINTERVMAX 8
152: #define NLSTATEMAX 8 /* Maximum number of live states (for func) */
153: #define NDEATHMAX 8 /* Maximum number of dead states (for func) */
154: #define NCOVMAX 8 /* Maximum number of covariates */
155: #define MAXN 20000
156: #define YEARM 12. /* Number of months per year */
157: #define AGESUP 130
158: #define AGEBASE 40
1.85 brouard 159: #ifdef unix
160: #define DIRSEPARATOR '/'
161: #define ODIRSEPARATOR '\\'
162: #else
1.53 brouard 163: #define DIRSEPARATOR '\\'
164: #define ODIRSEPARATOR '/'
165: #endif
166:
1.89 ! brouard 167: /* $Id: imach.c,v 1.88 2003/06/23 17:54:56 brouard Exp $ */
1.81 brouard 168: /* $State: Exp $ */
1.80 brouard 169:
1.88 brouard 170: char version[]="Imach version 0.96a, June 2003, INED-EUROREVES ";
1.89 ! brouard 171: char fullversion[]="$Revision: 1.88 $ $Date: 2003/06/23 17:54:56 $";
1.53 brouard 172: int erreur; /* Error number */
173: int nvar;
174: int cptcovn=0, cptcovage=0, cptcoveff=0,cptcov;
175: int npar=NPARMAX;
176: int nlstate=2; /* Number of live states */
177: int ndeath=1; /* Number of dead states */
178: int ncovmodel, ncovcol; /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
179: int popbased=0;
180:
181: int *wav; /* Number of waves for this individuual 0 is possible */
182: int maxwav; /* Maxim number of waves */
183: int jmin, jmax; /* min, max spacing between 2 waves */
1.87 brouard 184: int gipmx, gsw; /* Global variables on the number of contributions
185: to the likelihood and the sum of weights (done by funcone)*/
1.53 brouard 186: int mle, weightopt;
187: int **mw; /* mw[mi][i] is number of the mi wave for this individual */
188: int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
1.59 brouard 189: int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between
190: * wave mi and wave mi+1 is not an exact multiple of stepm. */
1.53 brouard 191: double jmean; /* Mean space between 2 waves */
192: double **oldm, **newm, **savm; /* Working pointers to matrices */
193: double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
194: FILE *fic,*ficpar, *ficparo,*ficres, *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
1.76 brouard 195: FILE *ficlog, *ficrespow;
1.85 brouard 196: int globpr; /* Global variable for printing or not */
197: double fretone; /* Only one call to likelihood */
198: long ipmx; /* Number of contributions */
199: double sw; /* Sum of weights */
200: char fileresilk[FILENAMELENGTH]; /* File of individual contributions to the likelihood */
201: FILE *ficresilk;
1.53 brouard 202: FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
203: FILE *ficresprobmorprev;
204: FILE *fichtm; /* Html File */
205: FILE *ficreseij;
206: char filerese[FILENAMELENGTH];
207: FILE *ficresvij;
208: char fileresv[FILENAMELENGTH];
209: FILE *ficresvpl;
210: char fileresvpl[FILENAMELENGTH];
211: char title[MAXLINE];
212: char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH], filerespl[FILENAMELENGTH];
213: char optionfilext[10], optionfilefiname[FILENAMELENGTH], plotcmd[FILENAMELENGTH];
1.88 brouard 214: char tmpout[FILENAMELENGTH];
215: char command[FILENAMELENGTH];
216: int outcmd=0;
1.53 brouard 217:
218: char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
1.88 brouard 219: char lfileres[FILENAMELENGTH];
1.53 brouard 220: char filelog[FILENAMELENGTH]; /* Log file */
221: char filerest[FILENAMELENGTH];
222: char fileregp[FILENAMELENGTH];
223: char popfile[FILENAMELENGTH];
224:
225: char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH];
226:
227: #define NR_END 1
228: #define FREE_ARG char*
229: #define FTOL 1.0e-10
230:
231: #define NRANSI
232: #define ITMAX 200
233:
234: #define TOL 2.0e-4
235:
236: #define CGOLD 0.3819660
237: #define ZEPS 1.0e-10
238: #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);
239:
240: #define GOLD 1.618034
241: #define GLIMIT 100.0
242: #define TINY 1.0e-20
243:
244: static double maxarg1,maxarg2;
245: #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
246: #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
247:
248: #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
249: #define rint(a) floor(a+0.5)
250:
251: static double sqrarg;
252: #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
253: #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}
254:
255: int imx;
256: int stepm;
257: /* Stepm, step in month: minimum step interpolation*/
258:
259: int estepm;
260: /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
261:
262: int m,nb;
1.85 brouard 263: long *num;
264: int firstpass=0, lastpass=4,*cod, *ncodemax, *Tage;
1.53 brouard 265: double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
1.55 lievre 266: double **pmmij, ***probs;
1.53 brouard 267: double dateintmean=0;
268:
269: double *weight;
270: int **s; /* Status */
271: double *agedc, **covar, idx;
272: int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;
273:
274: double ftol=FTOL; /* Tolerance for computing Max Likelihood */
275: double ftolhess; /* Tolerance for computing hessian */
276:
277: /**************** split *************************/
278: static int split( char *path, char *dirc, char *name, char *ext, char *finame )
279: {
1.59 brouard 280: char *ss; /* pointer */
281: int l1, l2; /* length counters */
1.53 brouard 282:
1.59 brouard 283: l1 = strlen(path ); /* length of path */
284: if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
285: ss= strrchr( path, DIRSEPARATOR ); /* find last / */
286: if ( ss == NULL ) { /* no directory, so use current */
287: /*if(strrchr(path, ODIRSEPARATOR )==NULL)
288: printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
1.74 brouard 289: /* get current working directory */
290: /* extern char* getcwd ( char *buf , int len);*/
1.59 brouard 291: if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {
292: return( GLOCK_ERROR_GETCWD );
293: }
294: strcpy( name, path ); /* we've got it */
295: } else { /* strip direcotry from path */
296: ss++; /* after this, the filename */
297: l2 = strlen( ss ); /* length of filename */
298: if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
299: strcpy( name, ss ); /* save file name */
300: strncpy( dirc, path, l1 - l2 ); /* now the directory */
301: dirc[l1-l2] = 0; /* add zero */
302: }
303: l1 = strlen( dirc ); /* length of directory */
1.85 brouard 304: /*#ifdef windows
1.59 brouard 305: if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; }
1.53 brouard 306: #else
1.59 brouard 307: if ( dirc[l1-1] != '/' ) { dirc[l1] = '/'; dirc[l1+1] = 0; }
1.53 brouard 308: #endif
1.85 brouard 309: */
1.59 brouard 310: ss = strrchr( name, '.' ); /* find last / */
311: ss++;
312: strcpy(ext,ss); /* save extension */
313: l1= strlen( name);
314: l2= strlen(ss)+1;
315: strncpy( finame, name, l1-l2);
316: finame[l1-l2]= 0;
317: return( 0 ); /* we're done */
1.53 brouard 318: }
319:
320:
321: /******************************************/
322:
1.89 ! brouard 323: void replace_back_to_slash(char *s, char*t)
1.53 brouard 324: {
325: int i;
1.89 ! brouard 326: int lg=0;
1.53 brouard 327: i=0;
328: lg=strlen(t);
329: for(i=0; i<= lg; i++) {
330: (s[i] = t[i]);
331: if (t[i]== '\\') s[i]='/';
332: }
333: }
334:
335: int nbocc(char *s, char occ)
336: {
337: int i,j=0;
338: int lg=20;
339: i=0;
340: lg=strlen(s);
341: for(i=0; i<= lg; i++) {
342: if (s[i] == occ ) j++;
343: }
344: return j;
345: }
346:
347: void cutv(char *u,char *v, char*t, char occ)
348: {
349: /* cuts string t into u and v where u is ended by char occ excluding it
350: and v is after occ excluding it too : ex cutv(u,v,"abcdef2ghi2j",2)
351: gives u="abcedf" and v="ghi2j" */
352: int i,lg,j,p=0;
353: i=0;
354: for(j=0; j<=strlen(t)-1; j++) {
355: if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;
356: }
357:
358: lg=strlen(t);
359: for(j=0; j<p; j++) {
360: (u[j] = t[j]);
361: }
362: u[p]='\0';
363:
364: for(j=0; j<= lg; j++) {
365: if (j>=(p+1))(v[j-p-1] = t[j]);
366: }
367: }
368:
369: /********************** nrerror ********************/
370:
371: void nrerror(char error_text[])
372: {
373: fprintf(stderr,"ERREUR ...\n");
374: fprintf(stderr,"%s\n",error_text);
1.59 brouard 375: exit(EXIT_FAILURE);
1.53 brouard 376: }
377: /*********************** vector *******************/
378: double *vector(int nl, int nh)
379: {
380: double *v;
381: v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
382: if (!v) nrerror("allocation failure in vector");
383: return v-nl+NR_END;
384: }
385:
386: /************************ free vector ******************/
387: void free_vector(double*v, int nl, int nh)
388: {
389: free((FREE_ARG)(v+nl-NR_END));
390: }
391:
392: /************************ivector *******************************/
1.85 brouard 393: int *ivector(long nl,long nh)
1.76 brouard 394: {
1.85 brouard 395: int *v;
396: v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
397: if (!v) nrerror("allocation failure in ivector");
1.76 brouard 398: return v-nl+NR_END;
399: }
400:
401: /******************free ivector **************************/
1.85 brouard 402: void free_ivector(int *v, long nl, long nh)
1.76 brouard 403: {
404: free((FREE_ARG)(v+nl-NR_END));
405: }
406:
1.85 brouard 407: /************************lvector *******************************/
408: long *lvector(long nl,long nh)
1.53 brouard 409: {
1.85 brouard 410: long *v;
411: v=(long *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(long)));
1.53 brouard 412: if (!v) nrerror("allocation failure in ivector");
413: return v-nl+NR_END;
414: }
415:
1.85 brouard 416: /******************free lvector **************************/
417: void free_lvector(long *v, long nl, long nh)
1.53 brouard 418: {
419: free((FREE_ARG)(v+nl-NR_END));
420: }
421:
422: /******************* imatrix *******************************/
423: int **imatrix(long nrl, long nrh, long ncl, long nch)
424: /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */
425: {
426: long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;
427: int **m;
428:
429: /* allocate pointers to rows */
430: m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));
431: if (!m) nrerror("allocation failure 1 in matrix()");
432: m += NR_END;
433: m -= nrl;
434:
435:
436: /* allocate rows and set pointers to them */
437: m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));
438: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
439: m[nrl] += NR_END;
440: m[nrl] -= ncl;
441:
442: for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;
443:
444: /* return pointer to array of pointers to rows */
445: return m;
446: }
447:
448: /****************** free_imatrix *************************/
449: void free_imatrix(m,nrl,nrh,ncl,nch)
450: int **m;
451: long nch,ncl,nrh,nrl;
452: /* free an int matrix allocated by imatrix() */
453: {
454: free((FREE_ARG) (m[nrl]+ncl-NR_END));
455: free((FREE_ARG) (m+nrl-NR_END));
456: }
457:
458: /******************* matrix *******************************/
459: double **matrix(long nrl, long nrh, long ncl, long nch)
460: {
461: long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
462: double **m;
463:
464: m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
465: if (!m) nrerror("allocation failure 1 in matrix()");
466: m += NR_END;
467: m -= nrl;
468:
469: m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
470: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
471: m[nrl] += NR_END;
472: m[nrl] -= ncl;
473:
474: for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
475: return m;
1.85 brouard 476: /* print *(*(m+1)+70) or print m[1][70]; print m+1 or print &(m[1])
1.74 brouard 477: */
1.53 brouard 478: }
479:
480: /*************************free matrix ************************/
481: void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
482: {
483: free((FREE_ARG)(m[nrl]+ncl-NR_END));
484: free((FREE_ARG)(m+nrl-NR_END));
485: }
486:
487: /******************* ma3x *******************************/
488: double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
489: {
490: long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
491: double ***m;
492:
493: m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
494: if (!m) nrerror("allocation failure 1 in matrix()");
495: m += NR_END;
496: m -= nrl;
497:
498: m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
499: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
500: m[nrl] += NR_END;
501: m[nrl] -= ncl;
502:
503: for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
504:
505: m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
506: if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
507: m[nrl][ncl] += NR_END;
508: m[nrl][ncl] -= nll;
509: for (j=ncl+1; j<=nch; j++)
510: m[nrl][j]=m[nrl][j-1]+nlay;
511:
512: for (i=nrl+1; i<=nrh; i++) {
513: m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
514: for (j=ncl+1; j<=nch; j++)
515: m[i][j]=m[i][j-1]+nlay;
516: }
1.74 brouard 517: return m;
518: /* gdb: p *(m+1) <=> p m[1] and p (m+1) <=> p (m+1) <=> p &(m[1])
519: &(m[i][j][k]) <=> *((*(m+i) + j)+k)
520: */
1.53 brouard 521: }
522:
523: /*************************free ma3x ************************/
524: void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
525: {
526: free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
527: free((FREE_ARG)(m[nrl]+ncl-NR_END));
528: free((FREE_ARG)(m+nrl-NR_END));
529: }
530:
531: /***************** f1dim *************************/
532: extern int ncom;
533: extern double *pcom,*xicom;
534: extern double (*nrfunc)(double []);
535:
536: double f1dim(double x)
537: {
538: int j;
539: double f;
540: double *xt;
541:
542: xt=vector(1,ncom);
543: for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];
544: f=(*nrfunc)(xt);
545: free_vector(xt,1,ncom);
546: return f;
547: }
548:
549: /*****************brent *************************/
550: double brent(double ax, double bx, double cx, double (*f)(double), double tol, double *xmin)
551: {
552: int iter;
553: double a,b,d,etemp;
554: double fu,fv,fw,fx;
555: double ftemp;
556: double p,q,r,tol1,tol2,u,v,w,x,xm;
557: double e=0.0;
558:
559: a=(ax < cx ? ax : cx);
560: b=(ax > cx ? ax : cx);
561: x=w=v=bx;
562: fw=fv=fx=(*f)(x);
563: for (iter=1;iter<=ITMAX;iter++) {
564: xm=0.5*(a+b);
565: tol2=2.0*(tol1=tol*fabs(x)+ZEPS);
566: /* if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
567: printf(".");fflush(stdout);
568: fprintf(ficlog,".");fflush(ficlog);
569: #ifdef DEBUG
570: 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);
571: 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);
572: /* if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
573: #endif
574: if (fabs(x-xm) <= (tol2-0.5*(b-a))){
575: *xmin=x;
576: return fx;
577: }
578: ftemp=fu;
579: if (fabs(e) > tol1) {
580: r=(x-w)*(fx-fv);
581: q=(x-v)*(fx-fw);
582: p=(x-v)*q-(x-w)*r;
583: q=2.0*(q-r);
584: if (q > 0.0) p = -p;
585: q=fabs(q);
586: etemp=e;
587: e=d;
588: if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))
589: d=CGOLD*(e=(x >= xm ? a-x : b-x));
590: else {
591: d=p/q;
592: u=x+d;
593: if (u-a < tol2 || b-u < tol2)
594: d=SIGN(tol1,xm-x);
595: }
596: } else {
597: d=CGOLD*(e=(x >= xm ? a-x : b-x));
598: }
599: u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));
600: fu=(*f)(u);
601: if (fu <= fx) {
602: if (u >= x) a=x; else b=x;
603: SHFT(v,w,x,u)
604: SHFT(fv,fw,fx,fu)
605: } else {
606: if (u < x) a=u; else b=u;
607: if (fu <= fw || w == x) {
608: v=w;
609: w=u;
610: fv=fw;
611: fw=fu;
612: } else if (fu <= fv || v == x || v == w) {
613: v=u;
614: fv=fu;
615: }
616: }
617: }
618: nrerror("Too many iterations in brent");
619: *xmin=x;
620: return fx;
621: }
622:
623: /****************** mnbrak ***********************/
624:
625: void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,
626: double (*func)(double))
627: {
628: double ulim,u,r,q, dum;
629: double fu;
630:
631: *fa=(*func)(*ax);
632: *fb=(*func)(*bx);
633: if (*fb > *fa) {
634: SHFT(dum,*ax,*bx,dum)
635: SHFT(dum,*fb,*fa,dum)
636: }
637: *cx=(*bx)+GOLD*(*bx-*ax);
638: *fc=(*func)(*cx);
639: while (*fb > *fc) {
640: r=(*bx-*ax)*(*fb-*fc);
641: q=(*bx-*cx)*(*fb-*fa);
642: u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/
643: (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r));
644: ulim=(*bx)+GLIMIT*(*cx-*bx);
645: if ((*bx-u)*(u-*cx) > 0.0) {
646: fu=(*func)(u);
647: } else if ((*cx-u)*(u-ulim) > 0.0) {
648: fu=(*func)(u);
649: if (fu < *fc) {
650: SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))
651: SHFT(*fb,*fc,fu,(*func)(u))
652: }
653: } else if ((u-ulim)*(ulim-*cx) >= 0.0) {
654: u=ulim;
655: fu=(*func)(u);
656: } else {
657: u=(*cx)+GOLD*(*cx-*bx);
658: fu=(*func)(u);
659: }
660: SHFT(*ax,*bx,*cx,u)
661: SHFT(*fa,*fb,*fc,fu)
662: }
663: }
664:
665: /*************** linmin ************************/
666:
667: int ncom;
668: double *pcom,*xicom;
669: double (*nrfunc)(double []);
670:
671: void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))
672: {
673: double brent(double ax, double bx, double cx,
674: double (*f)(double), double tol, double *xmin);
675: double f1dim(double x);
676: void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,
677: double *fc, double (*func)(double));
678: int j;
679: double xx,xmin,bx,ax;
680: double fx,fb,fa;
681:
682: ncom=n;
683: pcom=vector(1,n);
684: xicom=vector(1,n);
685: nrfunc=func;
686: for (j=1;j<=n;j++) {
687: pcom[j]=p[j];
688: xicom[j]=xi[j];
689: }
690: ax=0.0;
691: xx=1.0;
692: mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim);
693: *fret=brent(ax,xx,bx,f1dim,TOL,&xmin);
694: #ifdef DEBUG
695: printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
696: fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
697: #endif
698: for (j=1;j<=n;j++) {
699: xi[j] *= xmin;
700: p[j] += xi[j];
701: }
702: free_vector(xicom,1,n);
703: free_vector(pcom,1,n);
704: }
705:
706: /*************** powell ************************/
707: void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,
708: double (*func)(double []))
709: {
710: void linmin(double p[], double xi[], int n, double *fret,
711: double (*func)(double []));
712: int i,ibig,j;
713: double del,t,*pt,*ptt,*xit;
714: double fp,fptt;
715: double *xits;
716: pt=vector(1,n);
717: ptt=vector(1,n);
718: xit=vector(1,n);
719: xits=vector(1,n);
720: *fret=(*func)(p);
721: for (j=1;j<=n;j++) pt[j]=p[j];
722: for (*iter=1;;++(*iter)) {
723: fp=(*fret);
724: ibig=0;
725: del=0.0;
726: printf("\nPowell iter=%d -2*LL=%.12f",*iter,*fret);
727: fprintf(ficlog,"\nPowell iter=%d -2*LL=%.12f",*iter,*fret);
1.76 brouard 728: fprintf(ficrespow,"%d %.12f",*iter,*fret);
729: for (i=1;i<=n;i++) {
1.53 brouard 730: printf(" %d %.12f",i, p[i]);
1.76 brouard 731: fprintf(ficlog," %d %.12lf",i, p[i]);
732: fprintf(ficrespow," %.12lf", p[i]);
733: }
1.53 brouard 734: printf("\n");
735: fprintf(ficlog,"\n");
1.76 brouard 736: fprintf(ficrespow,"\n");
1.53 brouard 737: for (i=1;i<=n;i++) {
738: for (j=1;j<=n;j++) xit[j]=xi[j][i];
739: fptt=(*fret);
740: #ifdef DEBUG
741: printf("fret=%lf \n",*fret);
742: fprintf(ficlog,"fret=%lf \n",*fret);
743: #endif
744: printf("%d",i);fflush(stdout);
745: fprintf(ficlog,"%d",i);fflush(ficlog);
746: linmin(p,xit,n,fret,func);
747: if (fabs(fptt-(*fret)) > del) {
748: del=fabs(fptt-(*fret));
749: ibig=i;
750: }
751: #ifdef DEBUG
752: printf("%d %.12e",i,(*fret));
753: fprintf(ficlog,"%d %.12e",i,(*fret));
754: for (j=1;j<=n;j++) {
755: xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
756: printf(" x(%d)=%.12e",j,xit[j]);
757: fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
758: }
759: for(j=1;j<=n;j++) {
760: printf(" p=%.12e",p[j]);
761: fprintf(ficlog," p=%.12e",p[j]);
762: }
763: printf("\n");
764: fprintf(ficlog,"\n");
765: #endif
766: }
767: if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {
768: #ifdef DEBUG
769: int k[2],l;
770: k[0]=1;
771: k[1]=-1;
772: printf("Max: %.12e",(*func)(p));
773: fprintf(ficlog,"Max: %.12e",(*func)(p));
774: for (j=1;j<=n;j++) {
775: printf(" %.12e",p[j]);
776: fprintf(ficlog," %.12e",p[j]);
777: }
778: printf("\n");
779: fprintf(ficlog,"\n");
780: for(l=0;l<=1;l++) {
781: for (j=1;j<=n;j++) {
782: ptt[j]=p[j]+(p[j]-pt[j])*k[l];
783: printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
784: fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
785: }
786: printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
787: fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
788: }
789: #endif
790:
791:
792: free_vector(xit,1,n);
793: free_vector(xits,1,n);
794: free_vector(ptt,1,n);
795: free_vector(pt,1,n);
796: return;
797: }
798: if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");
799: for (j=1;j<=n;j++) {
800: ptt[j]=2.0*p[j]-pt[j];
801: xit[j]=p[j]-pt[j];
802: pt[j]=p[j];
803: }
804: fptt=(*func)(ptt);
805: if (fptt < fp) {
806: t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt);
807: if (t < 0.0) {
808: linmin(p,xit,n,fret,func);
809: for (j=1;j<=n;j++) {
810: xi[j][ibig]=xi[j][n];
811: xi[j][n]=xit[j];
812: }
813: #ifdef DEBUG
814: printf("Direction changed last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
815: fprintf(ficlog,"Direction changed last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
816: for(j=1;j<=n;j++){
817: printf(" %.12e",xit[j]);
818: fprintf(ficlog," %.12e",xit[j]);
819: }
820: printf("\n");
821: fprintf(ficlog,"\n");
822: #endif
1.54 brouard 823: }
1.53 brouard 824: }
825: }
826: }
827:
1.54 brouard 828: /**** Prevalence limit (stable prevalence) ****************/
1.53 brouard 829:
830: double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)
831: {
832: /* Computes the prevalence limit in each live state at age x by left multiplying the unit
833: matrix by transitions matrix until convergence is reached */
834:
835: int i, ii,j,k;
836: double min, max, maxmin, maxmax,sumnew=0.;
837: double **matprod2();
838: double **out, cov[NCOVMAX], **pmij();
839: double **newm;
840: double agefin, delaymax=50 ; /* Max number of years to converge */
841:
842: for (ii=1;ii<=nlstate+ndeath;ii++)
843: for (j=1;j<=nlstate+ndeath;j++){
844: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
845: }
846:
847: cov[1]=1.;
848:
849: /* Even if hstepm = 1, at least one multiplication by the unit matrix */
850: for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
851: newm=savm;
852: /* Covariates have to be included here again */
853: cov[2]=agefin;
854:
855: for (k=1; k<=cptcovn;k++) {
856: cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
857: /* 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]]);*/
858: }
859: for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
860: for (k=1; k<=cptcovprod;k++)
861: cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
862:
863: /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
864: /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
865: /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
866: out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);
867:
868: savm=oldm;
869: oldm=newm;
870: maxmax=0.;
871: for(j=1;j<=nlstate;j++){
872: min=1.;
873: max=0.;
874: for(i=1; i<=nlstate; i++) {
875: sumnew=0;
876: for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
877: prlim[i][j]= newm[i][j]/(1-sumnew);
878: max=FMAX(max,prlim[i][j]);
879: min=FMIN(min,prlim[i][j]);
880: }
881: maxmin=max-min;
882: maxmax=FMAX(maxmax,maxmin);
883: }
884: if(maxmax < ftolpl){
885: return prlim;
886: }
887: }
888: }
889:
890: /*************** transition probabilities ***************/
891:
892: double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
893: {
894: double s1, s2;
895: /*double t34;*/
896: int i,j,j1, nc, ii, jj;
897:
898: for(i=1; i<= nlstate; i++){
899: for(j=1; j<i;j++){
900: for (nc=1, s2=0.;nc <=ncovmodel; nc++){
901: /*s2 += param[i][j][nc]*cov[nc];*/
902: s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
903: /*printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2);*/
904: }
905: ps[i][j]=s2;
906: /*printf("s1=%.17e, s2=%.17e\n",s1,s2);*/
907: }
908: for(j=i+1; j<=nlstate+ndeath;j++){
909: for (nc=1, s2=0.;nc <=ncovmodel; nc++){
910: s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
911: /*printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2);*/
912: }
913: ps[i][j]=s2;
914: }
915: }
916: /*ps[3][2]=1;*/
917:
918: for(i=1; i<= nlstate; i++){
919: s1=0;
920: for(j=1; j<i; j++)
921: s1+=exp(ps[i][j]);
922: for(j=i+1; j<=nlstate+ndeath; j++)
923: s1+=exp(ps[i][j]);
924: ps[i][i]=1./(s1+1.);
925: for(j=1; j<i; j++)
926: ps[i][j]= exp(ps[i][j])*ps[i][i];
927: for(j=i+1; j<=nlstate+ndeath; j++)
928: ps[i][j]= exp(ps[i][j])*ps[i][i];
929: /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
930: } /* end i */
931:
932: for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
933: for(jj=1; jj<= nlstate+ndeath; jj++){
934: ps[ii][jj]=0;
935: ps[ii][ii]=1;
936: }
937: }
938:
939:
940: /* for(ii=1; ii<= nlstate+ndeath; ii++){
941: for(jj=1; jj<= nlstate+ndeath; jj++){
942: printf("%lf ",ps[ii][jj]);
943: }
944: printf("\n ");
945: }
946: printf("\n ");printf("%lf ",cov[2]);*/
947: /*
948: for(i=1; i<= npar; i++) printf("%f ",x[i]);
949: goto end;*/
950: return ps;
951: }
952:
953: /**************** Product of 2 matrices ******************/
954:
955: double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)
956: {
957: /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
958: b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
959: /* in, b, out are matrice of pointers which should have been initialized
960: before: only the contents of out is modified. The function returns
961: a pointer to pointers identical to out */
962: long i, j, k;
963: for(i=nrl; i<= nrh; i++)
964: for(k=ncolol; k<=ncoloh; k++)
965: for(j=ncl,out[i][k]=0.; j<=nch; j++)
966: out[i][k] +=in[i][j]*b[j][k];
967:
968: return out;
969: }
970:
971:
972: /************* Higher Matrix Product ***************/
973:
974: double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
975: {
1.66 brouard 976: /* Computes the transition matrix starting at age 'age' over
977: 'nhstepm*hstepm*stepm' months (i.e. until
978: age (in years) age+nhstepm*hstepm*stepm/12) by multiplying
979: nhstepm*hstepm matrices.
1.53 brouard 980: Output is stored in matrix po[i][j][h] for h every 'hstepm' step
1.66 brouard 981: (typically every 2 years instead of every month which is too big
982: for the memory).
1.53 brouard 983: Model is determined by parameters x and covariates have to be
984: included manually here.
985:
986: */
987:
988: int i, j, d, h, k;
989: double **out, cov[NCOVMAX];
990: double **newm;
991:
992: /* Hstepm could be zero and should return the unit matrix */
993: for (i=1;i<=nlstate+ndeath;i++)
994: for (j=1;j<=nlstate+ndeath;j++){
995: oldm[i][j]=(i==j ? 1.0 : 0.0);
996: po[i][j][0]=(i==j ? 1.0 : 0.0);
997: }
998: /* Even if hstepm = 1, at least one multiplication by the unit matrix */
999: for(h=1; h <=nhstepm; h++){
1000: for(d=1; d <=hstepm; d++){
1001: newm=savm;
1002: /* Covariates have to be included here again */
1003: cov[1]=1.;
1004: cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
1005: for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
1006: for (k=1; k<=cptcovage;k++)
1007: cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
1008: for (k=1; k<=cptcovprod;k++)
1009: cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
1010:
1011:
1012: /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
1013: /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
1014: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,
1015: pmij(pmmij,cov,ncovmodel,x,nlstate));
1016: savm=oldm;
1017: oldm=newm;
1018: }
1019: for(i=1; i<=nlstate+ndeath; i++)
1020: for(j=1;j<=nlstate+ndeath;j++) {
1021: po[i][j][h]=newm[i][j];
1022: /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);
1023: */
1024: }
1025: } /* end h */
1026: return po;
1027: }
1028:
1029:
1030: /*************** log-likelihood *************/
1031: double func( double *x)
1032: {
1033: int i, ii, j, k, mi, d, kk;
1034: double l, ll[NLSTATEMAX], cov[NCOVMAX];
1035: double **out;
1036: double sw; /* Sum of weights */
1037: double lli; /* Individual log likelihood */
1.59 brouard 1038: int s1, s2;
1.68 lievre 1039: double bbh, survp;
1.53 brouard 1040: long ipmx;
1041: /*extern weight */
1042: /* We are differentiating ll according to initial status */
1043: /* for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
1044: /*for(i=1;i<imx;i++)
1045: printf(" %d\n",s[4][i]);
1046: */
1047: cov[1]=1.;
1048:
1049: for(k=1; k<=nlstate; k++) ll[k]=0.;
1.61 brouard 1050:
1051: if(mle==1){
1052: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1053: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
1054: for(mi=1; mi<= wav[i]-1; mi++){
1055: for (ii=1;ii<=nlstate+ndeath;ii++)
1056: for (j=1;j<=nlstate+ndeath;j++){
1057: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1058: savm[ii][j]=(ii==j ? 1.0 : 0.0);
1059: }
1060: for(d=0; d<dh[mi][i]; d++){
1061: newm=savm;
1062: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
1063: for (kk=1; kk<=cptcovage;kk++) {
1064: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
1065: }
1066: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1067: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1068: savm=oldm;
1069: oldm=newm;
1070: } /* end mult */
1.53 brouard 1071:
1.61 brouard 1072: /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
1073: /* But now since version 0.9 we anticipate for bias and large stepm.
1074: * If stepm is larger than one month (smallest stepm) and if the exact delay
1075: * (in months) between two waves is not a multiple of stepm, we rounded to
1076: * the nearest (and in case of equal distance, to the lowest) interval but now
1077: * we keep into memory the bias bh[mi][i] and also the previous matrix product
1078: * (i.e to dh[mi][i]-1) saved in 'savm'. The we inter(extra)polate the
1079: * probability in order to take into account the bias as a fraction of the way
1080: * from savm to out if bh is neagtive or even beyond if bh is positive. bh varies
1081: * -stepm/2 to stepm/2 .
1082: * For stepm=1 the results are the same as for previous versions of Imach.
1083: * For stepm > 1 the results are less biased than in previous versions.
1084: */
1085: s1=s[mw[mi][i]][i];
1086: s2=s[mw[mi+1][i]][i];
1.64 lievre 1087: bbh=(double)bh[mi][i]/(double)stepm;
1088: /* bias is positive if real duration
1089: * is higher than the multiple of stepm and negative otherwise.
1090: */
1091: /* 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 1092: if( s2 > nlstate){
1093: /* i.e. if s2 is a death state and if the date of death is known then the contribution
1094: to the likelihood is the probability to die between last step unit time and current
1095: step unit time, which is also the differences between probability to die before dh
1096: and probability to die before dh-stepm .
1097: In version up to 0.92 likelihood was computed
1098: as if date of death was unknown. Death was treated as any other
1099: health state: the date of the interview describes the actual state
1100: and not the date of a change in health state. The former idea was
1101: to consider that at each interview the state was recorded
1102: (healthy, disable or death) and IMaCh was corrected; but when we
1103: introduced the exact date of death then we should have modified
1104: the contribution of an exact death to the likelihood. This new
1105: contribution is smaller and very dependent of the step unit
1106: stepm. It is no more the probability to die between last interview
1107: and month of death but the probability to survive from last
1108: interview up to one month before death multiplied by the
1109: probability to die within a month. Thanks to Chris
1110: Jackson for correcting this bug. Former versions increased
1111: mortality artificially. The bad side is that we add another loop
1112: which slows down the processing. The difference can be up to 10%
1113: lower mortality.
1114: */
1115: lli=log(out[s1][s2] - savm[s1][s2]);
1116: }else{
1117: lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
1118: /* 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 */
1119: }
1.64 lievre 1120: /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
1121: /*if(lli ==000.0)*/
1122: /*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 1123: ipmx +=1;
1.64 lievre 1124: sw += weight[i];
1125: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1126: } /* end of wave */
1127: } /* end of individual */
1128: } else if(mle==2){
1129: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1130: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
1131: for(mi=1; mi<= wav[i]-1; mi++){
1132: for (ii=1;ii<=nlstate+ndeath;ii++)
1133: for (j=1;j<=nlstate+ndeath;j++){
1134: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1135: savm[ii][j]=(ii==j ? 1.0 : 0.0);
1136: }
1137: for(d=0; d<=dh[mi][i]; d++){
1138: newm=savm;
1139: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
1140: for (kk=1; kk<=cptcovage;kk++) {
1141: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
1142: }
1143: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1144: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1145: savm=oldm;
1146: oldm=newm;
1147: } /* end mult */
1148:
1149: /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
1150: /* But now since version 0.9 we anticipate for bias and large stepm.
1151: * If stepm is larger than one month (smallest stepm) and if the exact delay
1152: * (in months) between two waves is not a multiple of stepm, we rounded to
1153: * the nearest (and in case of equal distance, to the lowest) interval but now
1154: * we keep into memory the bias bh[mi][i] and also the previous matrix product
1155: * (i.e to dh[mi][i]-1) saved in 'savm'. The we inter(extra)polate the
1156: * probability in order to take into account the bias as a fraction of the way
1157: * from savm to out if bh is neagtive or even beyond if bh is positive. bh varies
1158: * -stepm/2 to stepm/2 .
1159: * For stepm=1 the results are the same as for previous versions of Imach.
1160: * For stepm > 1 the results are less biased than in previous versions.
1161: */
1162: s1=s[mw[mi][i]][i];
1163: s2=s[mw[mi+1][i]][i];
1164: bbh=(double)bh[mi][i]/(double)stepm;
1165: /* bias is positive if real duration
1166: * is higher than the multiple of stepm and negative otherwise.
1167: */
1.63 lievre 1168: 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 1169: /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
1170: /*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 */
1171: /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
1172: /*if(lli ==000.0)*/
1173: /*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); */
1174: ipmx +=1;
1175: sw += weight[i];
1176: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1177: } /* end of wave */
1178: } /* end of individual */
1179: } else if(mle==3){ /* exponential inter-extrapolation */
1180: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1181: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
1182: for(mi=1; mi<= wav[i]-1; mi++){
1183: for (ii=1;ii<=nlstate+ndeath;ii++)
1184: for (j=1;j<=nlstate+ndeath;j++){
1185: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1186: savm[ii][j]=(ii==j ? 1.0 : 0.0);
1187: }
1188: for(d=0; d<dh[mi][i]; d++){
1189: newm=savm;
1190: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
1191: for (kk=1; kk<=cptcovage;kk++) {
1192: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
1193: }
1194: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1195: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1196: savm=oldm;
1197: oldm=newm;
1198: } /* end mult */
1199:
1200: /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
1201: /* But now since version 0.9 we anticipate for bias and large stepm.
1202: * If stepm is larger than one month (smallest stepm) and if the exact delay
1203: * (in months) between two waves is not a multiple of stepm, we rounded to
1204: * the nearest (and in case of equal distance, to the lowest) interval but now
1205: * we keep into memory the bias bh[mi][i] and also the previous matrix product
1206: * (i.e to dh[mi][i]-1) saved in 'savm'. The we inter(extra)polate the
1207: * probability in order to take into account the bias as a fraction of the way
1208: * from savm to out if bh is neagtive or even beyond if bh is positive. bh varies
1209: * -stepm/2 to stepm/2 .
1210: * For stepm=1 the results are the same as for previous versions of Imach.
1211: * For stepm > 1 the results are less biased than in previous versions.
1212: */
1213: s1=s[mw[mi][i]][i];
1214: s2=s[mw[mi+1][i]][i];
1215: bbh=(double)bh[mi][i]/(double)stepm;
1216: /* bias is positive if real duration
1217: * is higher than the multiple of stepm and negative otherwise.
1218: */
1219: /* 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 */
1220: 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 1221: /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
1222: /*if(lli ==000.0)*/
1223: /*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); */
1224: ipmx +=1;
1225: sw += weight[i];
1226: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1227: } /* end of wave */
1228: } /* end of individual */
1.84 brouard 1229: }else if (mle==4){ /* ml=4 no inter-extrapolation */
1.61 brouard 1230: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1231: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
1232: for(mi=1; mi<= wav[i]-1; mi++){
1233: for (ii=1;ii<=nlstate+ndeath;ii++)
1234: for (j=1;j<=nlstate+ndeath;j++){
1235: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1236: savm[ii][j]=(ii==j ? 1.0 : 0.0);
1237: }
1238: for(d=0; d<dh[mi][i]; d++){
1239: newm=savm;
1240: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
1241: for (kk=1; kk<=cptcovage;kk++) {
1242: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
1243: }
1244:
1245: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1246: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1247: savm=oldm;
1248: oldm=newm;
1249: } /* end mult */
1250:
1.84 brouard 1251: s1=s[mw[mi][i]][i];
1252: s2=s[mw[mi+1][i]][i];
1253: if( s2 > nlstate){
1254: lli=log(out[s1][s2] - savm[s1][s2]);
1255: }else{
1256: lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
1257: }
1258: ipmx +=1;
1259: sw += weight[i];
1260: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1.85 brouard 1261: /* 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 1262: } /* end of wave */
1263: } /* end of individual */
1264: }else{ /* ml=5 no inter-extrapolation no jackson =0.8a */
1265: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1266: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
1267: for(mi=1; mi<= wav[i]-1; mi++){
1268: for (ii=1;ii<=nlstate+ndeath;ii++)
1269: for (j=1;j<=nlstate+ndeath;j++){
1270: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1271: savm[ii][j]=(ii==j ? 1.0 : 0.0);
1272: }
1273: for(d=0; d<dh[mi][i]; d++){
1274: newm=savm;
1275: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
1276: for (kk=1; kk<=cptcovage;kk++) {
1277: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
1278: }
1279:
1280: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1281: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1282: savm=oldm;
1283: oldm=newm;
1284: } /* end mult */
1285:
1286: s1=s[mw[mi][i]][i];
1287: s2=s[mw[mi+1][i]][i];
1.61 brouard 1288: lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
1289: ipmx +=1;
1290: sw += weight[i];
1291: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1.84 brouard 1292: /*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 1293: } /* end of wave */
1294: } /* end of individual */
1295: } /* End of if */
1.53 brouard 1296: for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
1297: /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
1298: l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
1.85 brouard 1299: return -l;
1300: }
1301:
1302: /*************** log-likelihood *************/
1303: double funcone( double *x)
1304: {
1.87 brouard 1305: /* Same as likeli but slower because of a lot of printf and if */
1.85 brouard 1306: int i, ii, j, k, mi, d, kk;
1307: double l, ll[NLSTATEMAX], cov[NCOVMAX];
1308: double **out;
1309: double lli; /* Individual log likelihood */
1.87 brouard 1310: double llt;
1.85 brouard 1311: int s1, s2;
1312: double bbh, survp;
1313: /*extern weight */
1314: /* We are differentiating ll according to initial status */
1315: /* for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
1316: /*for(i=1;i<imx;i++)
1317: printf(" %d\n",s[4][i]);
1318: */
1319: cov[1]=1.;
1320:
1321: for(k=1; k<=nlstate; k++) ll[k]=0.;
1322:
1323: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1324: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
1325: for(mi=1; mi<= wav[i]-1; mi++){
1326: for (ii=1;ii<=nlstate+ndeath;ii++)
1327: for (j=1;j<=nlstate+ndeath;j++){
1328: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1329: savm[ii][j]=(ii==j ? 1.0 : 0.0);
1330: }
1331: for(d=0; d<dh[mi][i]; d++){
1332: newm=savm;
1333: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
1334: for (kk=1; kk<=cptcovage;kk++) {
1335: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
1336: }
1337: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1338: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1339: savm=oldm;
1340: oldm=newm;
1341: } /* end mult */
1342:
1343: s1=s[mw[mi][i]][i];
1344: s2=s[mw[mi+1][i]][i];
1345: bbh=(double)bh[mi][i]/(double)stepm;
1346: /* bias is positive if real duration
1347: * is higher than the multiple of stepm and negative otherwise.
1348: */
1349: if( s2 > nlstate && (mle <5) ){ /* Jackson */
1350: lli=log(out[s1][s2] - savm[s1][s2]);
1351: } else if (mle==1){
1352: lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
1353: } else if(mle==2){
1354: 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 */
1355: } else if(mle==3){ /* exponential inter-extrapolation */
1356: 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 */
1357: } else if (mle==4){ /* mle=4 no inter-extrapolation */
1358: lli=log(out[s1][s2]); /* Original formula */
1359: } else{ /* ml>=5 no inter-extrapolation no jackson =0.8a */
1360: lli=log(out[s1][s2]); /* Original formula */
1361: } /* End of if */
1362: ipmx +=1;
1363: sw += weight[i];
1364: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1365: /* 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]); */
1366: if(globpr){
1.88 brouard 1367: fprintf(ficresilk,"%9d %6d %1d %1d %1d %1d %3d %10.6f %6.4f\
1.86 brouard 1368: %10.6f %10.6f %10.6f ", \
1369: num[i],i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],
1370: 2*weight[i]*lli,out[s1][s2],savm[s1][s2]);
1.87 brouard 1371: for(k=1,llt=0.,l=0.; k<=nlstate; k++){
1372: llt +=ll[k]*gipmx/gsw;
1373: fprintf(ficresilk," %10.6f",-ll[k]*gipmx/gsw);
1374: }
1375: fprintf(ficresilk," %10.6f\n", -llt);
1.85 brouard 1376: }
1377: } /* end of wave */
1378: } /* end of individual */
1379: for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
1380: /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
1381: l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
1.87 brouard 1382: if(globpr==0){ /* First time we count the contributions and weights */
1383: gipmx=ipmx;
1384: gsw=sw;
1385: }
1.53 brouard 1386: return -l;
1387: }
1388:
1.88 brouard 1389: char *subdirf(char fileres[])
1390: {
1391:
1392: strcpy(tmpout,optionfilefiname);
1393: strcat(tmpout,"/"); /* Add to the right */
1394: strcat(tmpout,fileres);
1395: return tmpout;
1396: }
1397:
1398: char *subdirf2(char fileres[], char *preop)
1399: {
1400:
1401: strcpy(tmpout,optionfilefiname);
1402: strcat(tmpout,"/");
1403: strcat(tmpout,preop);
1404: strcat(tmpout,fileres);
1405: return tmpout;
1406: }
1407: char *subdirf3(char fileres[], char *preop, char *preop2)
1408: {
1409:
1410: strcpy(tmpout,optionfilefiname);
1411: strcat(tmpout,"/");
1412: strcat(tmpout,preop);
1413: strcat(tmpout,preop2);
1414: strcat(tmpout,fileres);
1415: return tmpout;
1416: }
1.53 brouard 1417:
1.87 brouard 1418: void likelione(FILE *ficres,double p[], int npar, int nlstate, int *globpri, long *ipmx, double *sw, double *fretone, double (*funcone)(double []))
1.85 brouard 1419: {
1.87 brouard 1420: /* This routine should help understanding what is done with
1421: the selection of individuals/waves and
1.85 brouard 1422: to check the exact contribution to the likelihood.
1423: Plotting could be done.
1424: */
1425: int k;
1.87 brouard 1426:
1.88 brouard 1427: if(*globpri !=0){ /* Just counts and sums, no printings */
1.85 brouard 1428: strcpy(fileresilk,"ilk");
1429: strcat(fileresilk,fileres);
1430: if((ficresilk=fopen(fileresilk,"w"))==NULL) {
1431: printf("Problem with resultfile: %s\n", fileresilk);
1432: fprintf(ficlog,"Problem with resultfile: %s\n", fileresilk);
1433: }
1.87 brouard 1434: 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 1435: fprintf(ficresilk, "#num_i i s1 s2 mi mw dh likeli weight 2wlli out sav ");
1.85 brouard 1436: /* i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],2*weight[i]*lli,out[s1][s2],savm[s1][s2]); */
1437: for(k=1; k<=nlstate; k++)
1.87 brouard 1438: fprintf(ficresilk," -2*gipw/gsw*weight*ll[%d]++",k);
1439: fprintf(ficresilk," -2*gipw/gsw*weight*ll(total)\n");
1.85 brouard 1440: }
1441:
1442: *fretone=(*funcone)(p);
1.87 brouard 1443: if(*globpri !=0){
1.85 brouard 1444: fclose(ficresilk);
1.88 brouard 1445: fprintf(fichtm,"\n<br>File of contributions to the likelihood: <a href=\"%s\">%s</a><br>\n",subdirf(fileresilk),subdirf(fileresilk));
1.87 brouard 1446: fflush(fichtm);
1447: }
1.85 brouard 1448: return;
1449: }
1450:
1.88 brouard 1451:
1.53 brouard 1452: /*********** Maximum Likelihood Estimation ***************/
1453:
1454: void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
1455: {
1456: int i,j, iter;
1.74 brouard 1457: double **xi;
1.53 brouard 1458: double fret;
1.85 brouard 1459: double fretone; /* Only one call to likelihood */
1.76 brouard 1460: char filerespow[FILENAMELENGTH];
1.53 brouard 1461: xi=matrix(1,npar,1,npar);
1462: for (i=1;i<=npar;i++)
1463: for (j=1;j<=npar;j++)
1464: xi[i][j]=(i==j ? 1.0 : 0.0);
1465: printf("Powell\n"); fprintf(ficlog,"Powell\n");
1.76 brouard 1466: strcpy(filerespow,"pow");
1467: strcat(filerespow,fileres);
1468: if((ficrespow=fopen(filerespow,"w"))==NULL) {
1469: printf("Problem with resultfile: %s\n", filerespow);
1470: fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
1471: }
1472: fprintf(ficrespow,"# Powell\n# iter -2*LL");
1473: for (i=1;i<=nlstate;i++)
1474: for(j=1;j<=nlstate+ndeath;j++)
1475: if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
1476: fprintf(ficrespow,"\n");
1.85 brouard 1477:
1.53 brouard 1478: powell(p,xi,npar,ftol,&iter,&fret,func);
1479:
1.76 brouard 1480: fclose(ficrespow);
1481: printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));
1.65 lievre 1482: fprintf(ficlog,"\n#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
1.53 brouard 1483: fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
1484:
1485: }
1486:
1487: /**** Computes Hessian and covariance matrix ***/
1488: void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
1489: {
1490: double **a,**y,*x,pd;
1491: double **hess;
1492: int i, j,jk;
1493: int *indx;
1494:
1495: double hessii(double p[], double delta, int theta, double delti[]);
1496: double hessij(double p[], double delti[], int i, int j);
1497: void lubksb(double **a, int npar, int *indx, double b[]) ;
1498: void ludcmp(double **a, int npar, int *indx, double *d) ;
1499:
1500: hess=matrix(1,npar,1,npar);
1501:
1502: printf("\nCalculation of the hessian matrix. Wait...\n");
1503: fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
1504: for (i=1;i<=npar;i++){
1505: printf("%d",i);fflush(stdout);
1506: fprintf(ficlog,"%d",i);fflush(ficlog);
1507: hess[i][i]=hessii(p,ftolhess,i,delti);
1508: /*printf(" %f ",p[i]);*/
1509: /*printf(" %lf ",hess[i][i]);*/
1510: }
1511:
1512: for (i=1;i<=npar;i++) {
1513: for (j=1;j<=npar;j++) {
1514: if (j>i) {
1515: printf(".%d%d",i,j);fflush(stdout);
1516: fprintf(ficlog,".%d%d",i,j);fflush(ficlog);
1517: hess[i][j]=hessij(p,delti,i,j);
1518: hess[j][i]=hess[i][j];
1519: /*printf(" %lf ",hess[i][j]);*/
1520: }
1521: }
1522: }
1523: printf("\n");
1524: fprintf(ficlog,"\n");
1525:
1526: printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
1527: fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
1528:
1529: a=matrix(1,npar,1,npar);
1530: y=matrix(1,npar,1,npar);
1531: x=vector(1,npar);
1532: indx=ivector(1,npar);
1533: for (i=1;i<=npar;i++)
1534: for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
1535: ludcmp(a,npar,indx,&pd);
1536:
1537: for (j=1;j<=npar;j++) {
1538: for (i=1;i<=npar;i++) x[i]=0;
1539: x[j]=1;
1540: lubksb(a,npar,indx,x);
1541: for (i=1;i<=npar;i++){
1542: matcov[i][j]=x[i];
1543: }
1544: }
1545:
1546: printf("\n#Hessian matrix#\n");
1547: fprintf(ficlog,"\n#Hessian matrix#\n");
1548: for (i=1;i<=npar;i++) {
1549: for (j=1;j<=npar;j++) {
1550: printf("%.3e ",hess[i][j]);
1551: fprintf(ficlog,"%.3e ",hess[i][j]);
1552: }
1553: printf("\n");
1554: fprintf(ficlog,"\n");
1555: }
1556:
1557: /* Recompute Inverse */
1558: for (i=1;i<=npar;i++)
1559: for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];
1560: ludcmp(a,npar,indx,&pd);
1561:
1562: /* printf("\n#Hessian matrix recomputed#\n");
1563:
1564: for (j=1;j<=npar;j++) {
1565: for (i=1;i<=npar;i++) x[i]=0;
1566: x[j]=1;
1567: lubksb(a,npar,indx,x);
1568: for (i=1;i<=npar;i++){
1569: y[i][j]=x[i];
1570: printf("%.3e ",y[i][j]);
1571: fprintf(ficlog,"%.3e ",y[i][j]);
1572: }
1573: printf("\n");
1574: fprintf(ficlog,"\n");
1575: }
1576: */
1577:
1578: free_matrix(a,1,npar,1,npar);
1579: free_matrix(y,1,npar,1,npar);
1580: free_vector(x,1,npar);
1581: free_ivector(indx,1,npar);
1582: free_matrix(hess,1,npar,1,npar);
1583:
1584:
1585: }
1586:
1587: /*************** hessian matrix ****************/
1588: double hessii( double x[], double delta, int theta, double delti[])
1589: {
1590: int i;
1591: int l=1, lmax=20;
1592: double k1,k2;
1593: double p2[NPARMAX+1];
1594: double res;
1595: double delt, delts, nkhi=10.,nkhif=1., khi=1.e-4;
1596: double fx;
1597: int k=0,kmax=10;
1598: double l1;
1599:
1600: fx=func(x);
1601: for (i=1;i<=npar;i++) p2[i]=x[i];
1602: for(l=0 ; l <=lmax; l++){
1603: l1=pow(10,l);
1604: delts=delt;
1605: for(k=1 ; k <kmax; k=k+1){
1606: delt = delta*(l1*k);
1607: p2[theta]=x[theta] +delt;
1608: k1=func(p2)-fx;
1609: p2[theta]=x[theta]-delt;
1610: k2=func(p2)-fx;
1611: /*res= (k1-2.0*fx+k2)/delt/delt; */
1612: res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */
1613:
1614: #ifdef DEBUG
1615: 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);
1616: 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);
1617: #endif
1618: /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
1619: if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
1620: k=kmax;
1621: }
1622: else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
1623: k=kmax; l=lmax*10.;
1624: }
1625: else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){
1626: delts=delt;
1627: }
1628: }
1629: }
1630: delti[theta]=delts;
1631: return res;
1632:
1633: }
1634:
1635: double hessij( double x[], double delti[], int thetai,int thetaj)
1636: {
1637: int i;
1638: int l=1, l1, lmax=20;
1639: double k1,k2,k3,k4,res,fx;
1640: double p2[NPARMAX+1];
1641: int k;
1642:
1643: fx=func(x);
1644: for (k=1; k<=2; k++) {
1645: for (i=1;i<=npar;i++) p2[i]=x[i];
1646: p2[thetai]=x[thetai]+delti[thetai]/k;
1647: p2[thetaj]=x[thetaj]+delti[thetaj]/k;
1648: k1=func(p2)-fx;
1649:
1650: p2[thetai]=x[thetai]+delti[thetai]/k;
1651: p2[thetaj]=x[thetaj]-delti[thetaj]/k;
1652: k2=func(p2)-fx;
1653:
1654: p2[thetai]=x[thetai]-delti[thetai]/k;
1655: p2[thetaj]=x[thetaj]+delti[thetaj]/k;
1656: k3=func(p2)-fx;
1657:
1658: p2[thetai]=x[thetai]-delti[thetai]/k;
1659: p2[thetaj]=x[thetaj]-delti[thetaj]/k;
1660: k4=func(p2)-fx;
1661: res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */
1662: #ifdef DEBUG
1663: 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);
1664: 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);
1665: #endif
1666: }
1667: return res;
1668: }
1669:
1670: /************** Inverse of matrix **************/
1671: void ludcmp(double **a, int n, int *indx, double *d)
1672: {
1673: int i,imax,j,k;
1674: double big,dum,sum,temp;
1675: double *vv;
1676:
1677: vv=vector(1,n);
1678: *d=1.0;
1679: for (i=1;i<=n;i++) {
1680: big=0.0;
1681: for (j=1;j<=n;j++)
1682: if ((temp=fabs(a[i][j])) > big) big=temp;
1683: if (big == 0.0) nrerror("Singular matrix in routine ludcmp");
1684: vv[i]=1.0/big;
1685: }
1686: for (j=1;j<=n;j++) {
1687: for (i=1;i<j;i++) {
1688: sum=a[i][j];
1689: for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];
1690: a[i][j]=sum;
1691: }
1692: big=0.0;
1693: for (i=j;i<=n;i++) {
1694: sum=a[i][j];
1695: for (k=1;k<j;k++)
1696: sum -= a[i][k]*a[k][j];
1697: a[i][j]=sum;
1698: if ( (dum=vv[i]*fabs(sum)) >= big) {
1699: big=dum;
1700: imax=i;
1701: }
1702: }
1703: if (j != imax) {
1704: for (k=1;k<=n;k++) {
1705: dum=a[imax][k];
1706: a[imax][k]=a[j][k];
1707: a[j][k]=dum;
1708: }
1709: *d = -(*d);
1710: vv[imax]=vv[j];
1711: }
1712: indx[j]=imax;
1713: if (a[j][j] == 0.0) a[j][j]=TINY;
1714: if (j != n) {
1715: dum=1.0/(a[j][j]);
1716: for (i=j+1;i<=n;i++) a[i][j] *= dum;
1717: }
1718: }
1719: free_vector(vv,1,n); /* Doesn't work */
1720: ;
1721: }
1722:
1723: void lubksb(double **a, int n, int *indx, double b[])
1724: {
1725: int i,ii=0,ip,j;
1726: double sum;
1727:
1728: for (i=1;i<=n;i++) {
1729: ip=indx[i];
1730: sum=b[ip];
1731: b[ip]=b[i];
1732: if (ii)
1733: for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];
1734: else if (sum) ii=i;
1735: b[i]=sum;
1736: }
1737: for (i=n;i>=1;i--) {
1738: sum=b[i];
1739: for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];
1740: b[i]=sum/a[i][i];
1741: }
1742: }
1743:
1744: /************ Frequencies ********************/
1.84 brouard 1745: 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 1746: { /* Some frequencies */
1747:
1748: int i, m, jk, k1,i1, j1, bool, z1,z2,j;
1749: int first;
1750: double ***freq; /* Frequencies */
1.73 lievre 1751: double *pp, **prop;
1752: double pos,posprop, k2, dateintsum=0,k2cpt=0;
1.53 brouard 1753: FILE *ficresp;
1754: char fileresp[FILENAMELENGTH];
1755:
1756: pp=vector(1,nlstate);
1.74 brouard 1757: prop=matrix(1,nlstate,iagemin,iagemax+3);
1.53 brouard 1758: strcpy(fileresp,"p");
1759: strcat(fileresp,fileres);
1760: if((ficresp=fopen(fileresp,"w"))==NULL) {
1761: printf("Problem with prevalence resultfile: %s\n", fileresp);
1762: fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
1763: exit(0);
1764: }
1.74 brouard 1765: freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);
1.53 brouard 1766: j1=0;
1767:
1768: j=cptcoveff;
1769: if (cptcovn<1) {j=1;ncodemax[1]=1;}
1770:
1771: first=1;
1772:
1773: for(k1=1; k1<=j;k1++){
1774: for(i1=1; i1<=ncodemax[k1];i1++){
1775: j1++;
1776: /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
1777: scanf("%d", i);*/
1778: for (i=-1; i<=nlstate+ndeath; i++)
1779: for (jk=-1; jk<=nlstate+ndeath; jk++)
1.74 brouard 1780: for(m=iagemin; m <= iagemax+3; m++)
1.53 brouard 1781: freq[i][jk][m]=0;
1.73 lievre 1782:
1783: for (i=1; i<=nlstate; i++)
1.74 brouard 1784: for(m=iagemin; m <= iagemax+3; m++)
1.73 lievre 1785: prop[i][m]=0;
1.53 brouard 1786:
1787: dateintsum=0;
1788: k2cpt=0;
1789: for (i=1; i<=imx; i++) {
1790: bool=1;
1791: if (cptcovn>0) {
1792: for (z1=1; z1<=cptcoveff; z1++)
1793: if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])
1794: bool=0;
1795: }
1.58 lievre 1796: if (bool==1){
1.53 brouard 1797: for(m=firstpass; m<=lastpass; m++){
1798: k2=anint[m][i]+(mint[m][i]/12.);
1.84 brouard 1799: /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/
1.74 brouard 1800: if(agev[m][i]==0) agev[m][i]=iagemax+1;
1801: if(agev[m][i]==1) agev[m][i]=iagemax+2;
1.73 lievre 1802: if (s[m][i]>0 && s[m][i]<=nlstate) prop[s[m][i]][(int)agev[m][i]] += weight[i];
1.53 brouard 1803: if (m<lastpass) {
1804: freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
1.74 brouard 1805: freq[s[m][i]][s[m+1][i]][iagemax+3] += weight[i];
1.53 brouard 1806: }
1807:
1.74 brouard 1808: if ((agev[m][i]>1) && (agev[m][i]< (iagemax+3))) {
1.53 brouard 1809: dateintsum=dateintsum+k2;
1810: k2cpt++;
1811: }
1.84 brouard 1812: /*}*/
1.53 brouard 1813: }
1814: }
1815: }
1816:
1.84 brouard 1817: /* fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
1.53 brouard 1818:
1819: if (cptcovn>0) {
1820: fprintf(ficresp, "\n#********** Variable ");
1821: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
1822: fprintf(ficresp, "**********\n#");
1823: }
1824: for(i=1; i<=nlstate;i++)
1825: fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
1826: fprintf(ficresp, "\n");
1827:
1.74 brouard 1828: for(i=iagemin; i <= iagemax+3; i++){
1829: if(i==iagemax+3){
1.53 brouard 1830: fprintf(ficlog,"Total");
1831: }else{
1832: if(first==1){
1833: first=0;
1834: printf("See log file for details...\n");
1835: }
1836: fprintf(ficlog,"Age %d", i);
1837: }
1838: for(jk=1; jk <=nlstate ; jk++){
1839: for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
1840: pp[jk] += freq[jk][m][i];
1841: }
1842: for(jk=1; jk <=nlstate ; jk++){
1843: for(m=-1, pos=0; m <=0 ; m++)
1844: pos += freq[jk][m][i];
1845: if(pp[jk]>=1.e-10){
1846: if(first==1){
1847: printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
1848: }
1849: fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
1850: }else{
1851: if(first==1)
1852: printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
1853: fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
1854: }
1855: }
1856:
1857: for(jk=1; jk <=nlstate ; jk++){
1858: for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
1859: pp[jk] += freq[jk][m][i];
1.73 lievre 1860: }
1861: for(jk=1,pos=0,posprop=0; jk <=nlstate ; jk++){
1862: pos += pp[jk];
1863: posprop += prop[jk][i];
1.53 brouard 1864: }
1865: for(jk=1; jk <=nlstate ; jk++){
1866: if(pos>=1.e-5){
1867: if(first==1)
1868: printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
1869: fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
1870: }else{
1871: if(first==1)
1872: printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
1873: fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
1874: }
1.74 brouard 1875: if( i <= iagemax){
1.53 brouard 1876: if(pos>=1.e-5){
1.73 lievre 1877: fprintf(ficresp," %d %.5f %.0f %.0f",i,prop[jk][i]/posprop, prop[jk][i],posprop);
1.84 brouard 1878: /*probs[i][jk][j1]= pp[jk]/pos;*/
1.53 brouard 1879: /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/
1880: }
1881: else
1.73 lievre 1882: fprintf(ficresp," %d NaNq %.0f %.0f",i,prop[jk][i],posprop);
1.53 brouard 1883: }
1884: }
1885:
1.69 brouard 1886: for(jk=-1; jk <=nlstate+ndeath; jk++)
1887: for(m=-1; m <=nlstate+ndeath; m++)
1.53 brouard 1888: if(freq[jk][m][i] !=0 ) {
1889: if(first==1)
1890: printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
1891: fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
1892: }
1.74 brouard 1893: if(i <= iagemax)
1.53 brouard 1894: fprintf(ficresp,"\n");
1895: if(first==1)
1896: printf("Others in log...\n");
1897: fprintf(ficlog,"\n");
1898: }
1899: }
1900: }
1901: dateintmean=dateintsum/k2cpt;
1902:
1903: fclose(ficresp);
1.74 brouard 1904: free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);
1.53 brouard 1905: free_vector(pp,1,nlstate);
1.74 brouard 1906: free_matrix(prop,1,nlstate,iagemin, iagemax+3);
1.53 brouard 1907: /* End of Freq */
1908: }
1909:
1910: /************ Prevalence ********************/
1.84 brouard 1911: 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 1912: {
1913: /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
1914: in each health status at the date of interview (if between dateprev1 and dateprev2).
1915: We still use firstpass and lastpass as another selection.
1916: */
1.53 brouard 1917:
1918: int i, m, jk, k1, i1, j1, bool, z1,z2,j;
1919: double ***freq; /* Frequencies */
1.73 lievre 1920: double *pp, **prop;
1921: double pos,posprop;
1.69 brouard 1922: double y2; /* in fractional years */
1.74 brouard 1923: int iagemin, iagemax;
1.53 brouard 1924:
1.74 brouard 1925: iagemin= (int) agemin;
1926: iagemax= (int) agemax;
1927: /*pp=vector(1,nlstate);*/
1928: prop=matrix(1,nlstate,iagemin,iagemax+3);
1929: /* freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
1.53 brouard 1930: j1=0;
1931:
1932: j=cptcoveff;
1933: if (cptcovn<1) {j=1;ncodemax[1]=1;}
1934:
1935: for(k1=1; k1<=j;k1++){
1936: for(i1=1; i1<=ncodemax[k1];i1++){
1937: j1++;
1938:
1.73 lievre 1939: for (i=1; i<=nlstate; i++)
1.74 brouard 1940: for(m=iagemin; m <= iagemax+3; m++)
1941: prop[i][m]=0.0;
1.53 brouard 1942:
1.69 brouard 1943: for (i=1; i<=imx; i++) { /* Each individual */
1.53 brouard 1944: bool=1;
1945: if (cptcovn>0) {
1946: for (z1=1; z1<=cptcoveff; z1++)
1947: if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])
1948: bool=0;
1949: }
1950: if (bool==1) {
1.69 brouard 1951: for(m=firstpass; m<=lastpass; m++){/* Other selection (we can limit to certain interviews*/
1952: y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
1953: if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
1.74 brouard 1954: if(agev[m][i]==0) agev[m][i]=iagemax+1;
1955: if(agev[m][i]==1) agev[m][i]=iagemax+2;
1956: 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);
1957: if (s[m][i]>0 && s[m][i]<=nlstate) {
1958: /*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]]);*/
1959: prop[s[m][i]][(int)agev[m][i]] += weight[i];
1960: prop[s[m][i]][iagemax+3] += weight[i];
1961: }
1.53 brouard 1962: }
1.69 brouard 1963: } /* end selection of waves */
1.53 brouard 1964: }
1965: }
1.74 brouard 1966: for(i=iagemin; i <= iagemax+3; i++){
1.53 brouard 1967:
1.74 brouard 1968: for(jk=1,posprop=0; jk <=nlstate ; jk++) {
1969: posprop += prop[jk][i];
1970: }
1971:
1972: for(jk=1; jk <=nlstate ; jk++){
1973: if( i <= iagemax){
1974: if(posprop>=1.e-5){
1975: probs[i][jk][j1]= prop[jk][i]/posprop;
1976: }
1977: }
1978: }/* end jk */
1979: }/* end i */
1.53 brouard 1980: } /* end i1 */
1981: } /* end k1 */
1982:
1.74 brouard 1983: /* free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
1984: /*free_vector(pp,1,nlstate);*/
1985: free_matrix(prop,1,nlstate, iagemin,iagemax+3);
1986: } /* End of prevalence */
1.53 brouard 1987:
1988: /************* Waves Concatenation ***************/
1989:
1.59 brouard 1990: 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 1991: {
1992: /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
1993: Death is a valid wave (if date is known).
1994: mw[mi][i] is the mi (mi=1 to wav[i]) effective wave of individual i
1.59 brouard 1995: dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
1.53 brouard 1996: and mw[mi+1][i]. dh depends on stepm.
1997: */
1998:
1999: int i, mi, m;
2000: /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
2001: double sum=0., jmean=0.;*/
2002: int first;
2003: int j, k=0,jk, ju, jl;
2004: double sum=0.;
2005: first=0;
2006: jmin=1e+5;
2007: jmax=-1;
2008: jmean=0.;
2009: for(i=1; i<=imx; i++){
2010: mi=0;
2011: m=firstpass;
2012: while(s[m][i] <= nlstate){
1.69 brouard 2013: if(s[m][i]>=1)
1.53 brouard 2014: mw[++mi][i]=m;
2015: if(m >=lastpass)
2016: break;
2017: else
2018: m++;
2019: }/* end while */
2020: if (s[m][i] > nlstate){
2021: mi++; /* Death is another wave */
2022: /* if(mi==0) never been interviewed correctly before death */
2023: /* Only death is a correct wave */
2024: mw[mi][i]=m;
2025: }
2026:
2027: wav[i]=mi;
2028: if(mi==0){
2029: if(first==0){
1.85 brouard 2030: printf("Warning! None valid information for:%ld line=%d (skipped) and may be others, see log file\n",num[i],i);
1.53 brouard 2031: first=1;
2032: }
2033: if(first==1){
1.85 brouard 2034: fprintf(ficlog,"Warning! None valid information for:%ld line=%d (skipped)\n",num[i],i);
1.53 brouard 2035: }
2036: } /* end mi==0 */
1.77 brouard 2037: } /* End individuals */
1.53 brouard 2038:
2039: for(i=1; i<=imx; i++){
2040: for(mi=1; mi<wav[i];mi++){
2041: if (stepm <=0)
2042: dh[mi][i]=1;
2043: else{
1.77 brouard 2044: if (s[mw[mi+1][i]][i] > nlstate) { /* A death */
1.53 brouard 2045: if (agedc[i] < 2*AGESUP) {
1.85 brouard 2046: j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);
2047: if(j==0) j=1; /* Survives at least one month after exam */
2048: else if(j<0){
2049: 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]);
2050: j=1; /* Careful Patch */
1.86 brouard 2051: 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 2052: 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]);
2053: 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);
2054: }
2055: k=k+1;
2056: if (j >= jmax) jmax=j;
2057: if (j <= jmin) jmin=j;
2058: sum=sum+j;
2059: /*if (j<0) printf("j=%d num=%d \n",j,i);*/
2060: /* printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
1.53 brouard 2061: }
2062: }
2063: else{
2064: j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
1.68 lievre 2065: /* printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
1.53 brouard 2066: k=k+1;
2067: if (j >= jmax) jmax=j;
2068: else if (j <= jmin)jmin=j;
2069: /* if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
1.73 lievre 2070: /*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 2071: if(j<0){
2072: 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]);
2073: 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]);
2074: }
1.53 brouard 2075: sum=sum+j;
2076: }
2077: jk= j/stepm;
2078: jl= j -jk*stepm;
2079: ju= j -(jk+1)*stepm;
1.85 brouard 2080: if(mle <=1){ /* only if we use a the linear-interpoloation pseudo-likelihood */
1.64 lievre 2081: if(jl==0){
2082: dh[mi][i]=jk;
2083: bh[mi][i]=0;
2084: }else{ /* We want a negative bias in order to only have interpolation ie
2085: * at the price of an extra matrix product in likelihood */
2086: dh[mi][i]=jk+1;
2087: bh[mi][i]=ju;
2088: }
2089: }else{
2090: if(jl <= -ju){
2091: dh[mi][i]=jk;
2092: bh[mi][i]=jl; /* bias is positive if real duration
2093: * is higher than the multiple of stepm and negative otherwise.
2094: */
2095: }
2096: else{
2097: dh[mi][i]=jk+1;
2098: bh[mi][i]=ju;
2099: }
2100: if(dh[mi][i]==0){
2101: dh[mi][i]=1; /* At least one step */
2102: bh[mi][i]=ju; /* At least one step */
1.71 brouard 2103: /* 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 2104: }
1.85 brouard 2105: } /* end if mle */
2106: }
1.64 lievre 2107: } /* end wave */
1.53 brouard 2108: }
2109: jmean=sum/k;
2110: printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);
2111: fprintf(ficlog,"Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);
2112: }
2113:
2114: /*********** Tricode ****************************/
2115: void tricode(int *Tvar, int **nbcode, int imx)
2116: {
1.58 lievre 2117:
2118: int Ndum[20],ij=1, k, j, i, maxncov=19;
1.53 brouard 2119: int cptcode=0;
2120: cptcoveff=0;
2121:
1.58 lievre 2122: for (k=0; k<maxncov; k++) Ndum[k]=0;
1.53 brouard 2123: for (k=1; k<=7; k++) ncodemax[k]=0;
2124:
2125: for (j=1; j<=(cptcovn+2*cptcovprod); j++) {
1.58 lievre 2126: for (i=1; i<=imx; i++) { /*reads the data file to get the maximum
2127: modality*/
2128: ij=(int)(covar[Tvar[j]][i]); /* ij is the modality of this individual*/
2129: Ndum[ij]++; /*store the modality */
1.53 brouard 2130: /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
1.58 lievre 2131: if (ij > cptcode) cptcode=ij; /* getting the maximum of covariable
2132: Tvar[j]. If V=sex and male is 0 and
2133: female is 1, then cptcode=1.*/
1.53 brouard 2134: }
2135:
2136: for (i=0; i<=cptcode; i++) {
1.58 lievre 2137: 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 2138: }
1.58 lievre 2139:
1.53 brouard 2140: ij=1;
2141: for (i=1; i<=ncodemax[j]; i++) {
1.58 lievre 2142: for (k=0; k<= maxncov; k++) {
1.53 brouard 2143: if (Ndum[k] != 0) {
2144: nbcode[Tvar[j]][ij]=k;
1.58 lievre 2145: /* 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 2146:
2147: ij++;
2148: }
2149: if (ij > ncodemax[j]) break;
2150: }
2151: }
2152: }
2153:
1.58 lievre 2154: for (k=0; k< maxncov; k++) Ndum[k]=0;
1.53 brouard 2155:
1.58 lievre 2156: for (i=1; i<=ncovmodel-2; i++) {
2157: /* 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 2158: ij=Tvar[i];
1.58 lievre 2159: Ndum[ij]++;
1.53 brouard 2160: }
2161:
2162: ij=1;
1.58 lievre 2163: for (i=1; i<= maxncov; i++) {
1.53 brouard 2164: if((Ndum[i]!=0) && (i<=ncovcol)){
1.58 lievre 2165: Tvaraff[ij]=i; /*For printing */
1.53 brouard 2166: ij++;
2167: }
2168: }
2169:
1.58 lievre 2170: cptcoveff=ij-1; /*Number of simple covariates*/
1.53 brouard 2171: }
2172:
2173: /*********** Health Expectancies ****************/
2174:
2175: 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 )
2176:
2177: {
2178: /* Health expectancies */
2179: int i, j, nhstepm, hstepm, h, nstepm, k, cptj;
2180: double age, agelim, hf;
2181: double ***p3mat,***varhe;
2182: double **dnewm,**doldm;
2183: double *xp;
2184: double **gp, **gm;
2185: double ***gradg, ***trgradg;
2186: int theta;
2187:
1.74 brouard 2188: varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage);
1.53 brouard 2189: xp=vector(1,npar);
1.74 brouard 2190: dnewm=matrix(1,nlstate*nlstate,1,npar);
2191: doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate);
1.53 brouard 2192:
2193: fprintf(ficreseij,"# Health expectancies\n");
2194: fprintf(ficreseij,"# Age");
2195: for(i=1; i<=nlstate;i++)
2196: for(j=1; j<=nlstate;j++)
2197: fprintf(ficreseij," %1d-%1d (SE)",i,j);
2198: fprintf(ficreseij,"\n");
2199:
2200: if(estepm < stepm){
2201: printf ("Problem %d lower than %d\n",estepm, stepm);
2202: }
2203: else hstepm=estepm;
2204: /* We compute the life expectancy from trapezoids spaced every estepm months
2205: * This is mainly to measure the difference between two models: for example
2206: * if stepm=24 months pijx are given only every 2 years and by summing them
2207: * we are calculating an estimate of the Life Expectancy assuming a linear
1.66 brouard 2208: * progression in between and thus overestimating or underestimating according
1.53 brouard 2209: * to the curvature of the survival function. If, for the same date, we
2210: * estimate the model with stepm=1 month, we can keep estepm to 24 months
2211: * to compare the new estimate of Life expectancy with the same linear
2212: * hypothesis. A more precise result, taking into account a more precise
2213: * curvature will be obtained if estepm is as small as stepm. */
2214:
2215: /* For example we decided to compute the life expectancy with the smallest unit */
2216: /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
2217: nhstepm is the number of hstepm from age to agelim
2218: nstepm is the number of stepm from age to agelin.
2219: Look at hpijx to understand the reason of that which relies in memory size
2220: and note for a fixed period like estepm months */
2221: /* We decided (b) to get a life expectancy respecting the most precise curvature of the
2222: survival function given by stepm (the optimization length). Unfortunately it
2223: means that if the survival funtion is printed only each two years of age and if
2224: you sum them up and add 1 year (area under the trapezoids) you won't get the same
2225: results. So we changed our mind and took the option of the best precision.
2226: */
2227: hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
2228:
2229: agelim=AGESUP;
2230: for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
2231: /* nhstepm age range expressed in number of stepm */
2232: nstepm=(int) rint((agelim-age)*YEARM/stepm);
2233: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
2234: /* if (stepm >= YEARM) hstepm=1;*/
2235: nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
2236: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
1.74 brouard 2237: gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);
2238: gp=matrix(0,nhstepm,1,nlstate*nlstate);
2239: gm=matrix(0,nhstepm,1,nlstate*nlstate);
1.53 brouard 2240:
2241: /* Computed by stepm unit matrices, product of hstepm matrices, stored
2242: in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
2243: hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);
2244:
2245:
2246: hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
2247:
2248: /* Computing Variances of health expectancies */
2249:
2250: for(theta=1; theta <=npar; theta++){
2251: for(i=1; i<=npar; i++){
2252: xp[i] = x[i] + (i==theta ?delti[theta]:0);
2253: }
2254: hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
2255:
2256: cptj=0;
2257: for(j=1; j<= nlstate; j++){
2258: for(i=1; i<=nlstate; i++){
2259: cptj=cptj+1;
2260: for(h=0, gp[h][cptj]=0.; h<=nhstepm-1; h++){
2261: gp[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;
2262: }
2263: }
2264: }
2265:
2266:
2267: for(i=1; i<=npar; i++)
2268: xp[i] = x[i] - (i==theta ?delti[theta]:0);
2269: hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
2270:
2271: cptj=0;
2272: for(j=1; j<= nlstate; j++){
2273: for(i=1;i<=nlstate;i++){
2274: cptj=cptj+1;
2275: for(h=0, gm[h][cptj]=0.; h<=nhstepm-1; h++){
1.77 brouard 2276:
1.53 brouard 2277: gm[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;
2278: }
2279: }
2280: }
1.74 brouard 2281: for(j=1; j<= nlstate*nlstate; j++)
1.53 brouard 2282: for(h=0; h<=nhstepm-1; h++){
2283: gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
2284: }
2285: }
2286:
2287: /* End theta */
2288:
1.74 brouard 2289: trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar);
1.53 brouard 2290:
2291: for(h=0; h<=nhstepm-1; h++)
1.74 brouard 2292: for(j=1; j<=nlstate*nlstate;j++)
1.53 brouard 2293: for(theta=1; theta <=npar; theta++)
2294: trgradg[h][j][theta]=gradg[h][theta][j];
2295:
2296:
1.74 brouard 2297: for(i=1;i<=nlstate*nlstate;i++)
2298: for(j=1;j<=nlstate*nlstate;j++)
1.53 brouard 2299: varhe[i][j][(int)age] =0.;
2300:
2301: printf("%d|",(int)age);fflush(stdout);
2302: fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
2303: for(h=0;h<=nhstepm-1;h++){
2304: for(k=0;k<=nhstepm-1;k++){
1.74 brouard 2305: matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov);
2306: matprod2(doldm,dnewm,1,nlstate*nlstate,1,npar,1,nlstate*nlstate,gradg[k]);
2307: for(i=1;i<=nlstate*nlstate;i++)
2308: for(j=1;j<=nlstate*nlstate;j++)
1.53 brouard 2309: varhe[i][j][(int)age] += doldm[i][j]*hf*hf;
2310: }
2311: }
2312: /* Computing expectancies */
2313: for(i=1; i<=nlstate;i++)
2314: for(j=1; j<=nlstate;j++)
2315: for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
2316: eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
2317:
2318: /* 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]);*/
2319:
2320: }
2321:
2322: fprintf(ficreseij,"%3.0f",age );
2323: cptj=0;
2324: for(i=1; i<=nlstate;i++)
2325: for(j=1; j<=nlstate;j++){
2326: cptj++;
2327: fprintf(ficreseij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[cptj][cptj][(int)age]) );
2328: }
2329: fprintf(ficreseij,"\n");
2330:
1.74 brouard 2331: free_matrix(gm,0,nhstepm,1,nlstate*nlstate);
2332: free_matrix(gp,0,nhstepm,1,nlstate*nlstate);
2333: free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*nlstate);
2334: free_ma3x(trgradg,0,nhstepm,1,nlstate*nlstate,1,npar);
1.53 brouard 2335: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
2336: }
2337: printf("\n");
2338: fprintf(ficlog,"\n");
2339:
2340: free_vector(xp,1,npar);
1.74 brouard 2341: free_matrix(dnewm,1,nlstate*nlstate,1,npar);
2342: free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate);
2343: free_ma3x(varhe,1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int)fage);
1.53 brouard 2344: }
2345:
2346: /************ Variance ******************/
2347: 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)
2348: {
2349: /* Variance of health expectancies */
2350: /* double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
2351: /* double **newm;*/
2352: double **dnewm,**doldm;
2353: double **dnewmp,**doldmp;
2354: int i, j, nhstepm, hstepm, h, nstepm ;
2355: int k, cptcode;
2356: double *xp;
2357: double **gp, **gm; /* for var eij */
2358: double ***gradg, ***trgradg; /*for var eij */
2359: double **gradgp, **trgradgp; /* for var p point j */
2360: double *gpp, *gmp; /* for var p point j */
2361: double **varppt; /* for var p point j nlstate to nlstate+ndeath */
2362: double ***p3mat;
2363: double age,agelim, hf;
2364: double ***mobaverage;
2365: int theta;
2366: char digit[4];
1.55 lievre 2367: char digitp[25];
1.53 brouard 2368:
2369: char fileresprobmorprev[FILENAMELENGTH];
2370:
1.55 lievre 2371: if(popbased==1){
1.58 lievre 2372: if(mobilav!=0)
1.55 lievre 2373: strcpy(digitp,"-populbased-mobilav-");
2374: else strcpy(digitp,"-populbased-nomobil-");
2375: }
2376: else
1.53 brouard 2377: strcpy(digitp,"-stablbased-");
1.56 lievre 2378:
1.54 brouard 2379: if (mobilav!=0) {
1.53 brouard 2380: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
1.54 brouard 2381: if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
2382: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
2383: printf(" Error in movingaverage mobilav=%d\n",mobilav);
2384: }
1.53 brouard 2385: }
2386:
2387: strcpy(fileresprobmorprev,"prmorprev");
2388: sprintf(digit,"%-d",ij);
2389: /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
2390: strcat(fileresprobmorprev,digit); /* Tvar to be done */
2391: strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
2392: strcat(fileresprobmorprev,fileres);
2393: if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
2394: printf("Problem with resultfile: %s\n", fileresprobmorprev);
2395: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
2396: }
2397: printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
2398: fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
1.66 brouard 2399: 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 2400: fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
2401: for(j=nlstate+1; j<=(nlstate+ndeath);j++){
2402: fprintf(ficresprobmorprev," p.%-d SE",j);
2403: for(i=1; i<=nlstate;i++)
2404: fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
2405: }
2406: fprintf(ficresprobmorprev,"\n");
1.88 brouard 2407: fprintf(ficgp,"\n# Routine varevsij");
1.87 brouard 2408: 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");
2409: fprintf(fichtm,"\n<br>%s <br>\n",digitp);
2410: /* } */
1.53 brouard 2411: varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
2412:
2413: 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");
2414: fprintf(ficresvij,"# Age");
2415: for(i=1; i<=nlstate;i++)
2416: for(j=1; j<=nlstate;j++)
2417: fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);
2418: fprintf(ficresvij,"\n");
2419:
2420: xp=vector(1,npar);
2421: dnewm=matrix(1,nlstate,1,npar);
2422: doldm=matrix(1,nlstate,1,nlstate);
2423: dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
2424: doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
2425:
2426: gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
2427: gpp=vector(nlstate+1,nlstate+ndeath);
2428: gmp=vector(nlstate+1,nlstate+ndeath);
2429: trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
2430:
2431: if(estepm < stepm){
2432: printf ("Problem %d lower than %d\n",estepm, stepm);
2433: }
2434: else hstepm=estepm;
2435: /* For example we decided to compute the life expectancy with the smallest unit */
2436: /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
2437: nhstepm is the number of hstepm from age to agelim
2438: nstepm is the number of stepm from age to agelin.
2439: Look at hpijx to understand the reason of that which relies in memory size
2440: and note for a fixed period like k years */
2441: /* We decided (b) to get a life expectancy respecting the most precise curvature of the
2442: survival function given by stepm (the optimization length). Unfortunately it
1.66 brouard 2443: means that if the survival funtion is printed every two years of age and if
1.53 brouard 2444: you sum them up and add 1 year (area under the trapezoids) you won't get the same
2445: results. So we changed our mind and took the option of the best precision.
2446: */
2447: hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
2448: agelim = AGESUP;
2449: for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
2450: nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
2451: nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
2452: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
2453: gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
2454: gp=matrix(0,nhstepm,1,nlstate);
2455: gm=matrix(0,nhstepm,1,nlstate);
2456:
2457:
2458: for(theta=1; theta <=npar; theta++){
1.66 brouard 2459: for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
1.53 brouard 2460: xp[i] = x[i] + (i==theta ?delti[theta]:0);
2461: }
2462: hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
2463: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
2464:
2465: if (popbased==1) {
1.54 brouard 2466: if(mobilav ==0){
1.53 brouard 2467: for(i=1; i<=nlstate;i++)
2468: prlim[i][i]=probs[(int)age][i][ij];
1.54 brouard 2469: }else{ /* mobilav */
1.53 brouard 2470: for(i=1; i<=nlstate;i++)
2471: prlim[i][i]=mobaverage[(int)age][i][ij];
2472: }
2473: }
2474:
2475: for(j=1; j<= nlstate; j++){
2476: for(h=0; h<=nhstepm; h++){
2477: for(i=1, gp[h][j]=0.;i<=nlstate;i++)
2478: gp[h][j] += prlim[i][i]*p3mat[i][j][h];
2479: }
2480: }
1.66 brouard 2481: /* This for computing probability of death (h=1 means
2482: computed over hstepm matrices product = hstepm*stepm months)
2483: as a weighted average of prlim.
2484: */
1.69 brouard 2485: for(j=nlstate+1;j<=nlstate+ndeath;j++){
1.68 lievre 2486: for(i=1,gpp[j]=0.; i<= nlstate; i++)
1.53 brouard 2487: gpp[j] += prlim[i][i]*p3mat[i][j][1];
2488: }
1.66 brouard 2489: /* end probability of death */
1.53 brouard 2490:
1.66 brouard 2491: for(i=1; i<=npar; i++) /* Computes gradient x - delta */
1.53 brouard 2492: xp[i] = x[i] - (i==theta ?delti[theta]:0);
2493: hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
2494: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
2495:
2496: if (popbased==1) {
1.54 brouard 2497: if(mobilav ==0){
1.53 brouard 2498: for(i=1; i<=nlstate;i++)
2499: prlim[i][i]=probs[(int)age][i][ij];
1.54 brouard 2500: }else{ /* mobilav */
1.53 brouard 2501: for(i=1; i<=nlstate;i++)
2502: prlim[i][i]=mobaverage[(int)age][i][ij];
2503: }
2504: }
2505:
2506: for(j=1; j<= nlstate; j++){
2507: for(h=0; h<=nhstepm; h++){
2508: for(i=1, gm[h][j]=0.;i<=nlstate;i++)
2509: gm[h][j] += prlim[i][i]*p3mat[i][j][h];
2510: }
2511: }
1.66 brouard 2512: /* This for computing probability of death (h=1 means
2513: computed over hstepm matrices product = hstepm*stepm months)
2514: as a weighted average of prlim.
2515: */
1.69 brouard 2516: for(j=nlstate+1;j<=nlstate+ndeath;j++){
1.68 lievre 2517: for(i=1,gmp[j]=0.; i<= nlstate; i++)
2518: gmp[j] += prlim[i][i]*p3mat[i][j][1];
1.53 brouard 2519: }
1.66 brouard 2520: /* end probability of death */
1.53 brouard 2521:
2522: for(j=1; j<= nlstate; j++) /* vareij */
2523: for(h=0; h<=nhstepm; h++){
2524: gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
2525: }
1.68 lievre 2526:
1.53 brouard 2527: for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
2528: gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
2529: }
2530:
2531: } /* End theta */
2532:
2533: trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
2534:
2535: for(h=0; h<=nhstepm; h++) /* veij */
2536: for(j=1; j<=nlstate;j++)
2537: for(theta=1; theta <=npar; theta++)
2538: trgradg[h][j][theta]=gradg[h][theta][j];
2539:
2540: for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
1.69 brouard 2541: for(theta=1; theta <=npar; theta++)
1.53 brouard 2542: trgradgp[j][theta]=gradgp[theta][j];
1.69 brouard 2543:
1.53 brouard 2544:
2545: hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
2546: for(i=1;i<=nlstate;i++)
2547: for(j=1;j<=nlstate;j++)
2548: vareij[i][j][(int)age] =0.;
2549:
2550: for(h=0;h<=nhstepm;h++){
2551: for(k=0;k<=nhstepm;k++){
2552: matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
2553: matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
2554: for(i=1;i<=nlstate;i++)
2555: for(j=1;j<=nlstate;j++)
2556: vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
2557: }
2558: }
1.70 brouard 2559:
1.53 brouard 2560: /* pptj */
2561: matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
2562: matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
1.70 brouard 2563: for(j=nlstate+1;j<=nlstate+ndeath;j++)
2564: for(i=nlstate+1;i<=nlstate+ndeath;i++)
1.53 brouard 2565: varppt[j][i]=doldmp[j][i];
2566: /* end ppptj */
1.66 brouard 2567: /* x centered again */
1.53 brouard 2568: hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);
2569: prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);
2570:
2571: if (popbased==1) {
1.54 brouard 2572: if(mobilav ==0){
1.53 brouard 2573: for(i=1; i<=nlstate;i++)
2574: prlim[i][i]=probs[(int)age][i][ij];
1.54 brouard 2575: }else{ /* mobilav */
1.53 brouard 2576: for(i=1; i<=nlstate;i++)
2577: prlim[i][i]=mobaverage[(int)age][i][ij];
2578: }
2579: }
1.70 brouard 2580:
1.66 brouard 2581: /* This for computing probability of death (h=1 means
2582: computed over hstepm (estepm) matrices product = hstepm*stepm months)
2583: as a weighted average of prlim.
2584: */
1.68 lievre 2585: for(j=nlstate+1;j<=nlstate+ndeath;j++){
2586: for(i=1,gmp[j]=0.;i<= nlstate; i++)
1.53 brouard 2587: gmp[j] += prlim[i][i]*p3mat[i][j][1];
2588: }
1.66 brouard 2589: /* end probability of death */
1.53 brouard 2590:
2591: fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
2592: for(j=nlstate+1; j<=(nlstate+ndeath);j++){
2593: fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
2594: for(i=1; i<=nlstate;i++){
2595: fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
2596: }
2597: }
2598: fprintf(ficresprobmorprev,"\n");
2599:
2600: fprintf(ficresvij,"%.0f ",age );
2601: for(i=1; i<=nlstate;i++)
2602: for(j=1; j<=nlstate;j++){
2603: fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
2604: }
2605: fprintf(ficresvij,"\n");
2606: free_matrix(gp,0,nhstepm,1,nlstate);
2607: free_matrix(gm,0,nhstepm,1,nlstate);
2608: free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
2609: free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
2610: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
2611: } /* End age */
2612: free_vector(gpp,nlstate+1,nlstate+ndeath);
2613: free_vector(gmp,nlstate+1,nlstate+ndeath);
2614: free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
2615: free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
2616: fprintf(ficgp,"\nset noparametric;set nolabel; set ter png small;set size 0.65, 0.65");
2617: /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */
2618: fprintf(ficgp,"\n set log y; set nolog x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
1.67 brouard 2619: /* fprintf(ficgp,"\n plot \"%s\" u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm); */
2620: /* fprintf(ficgp,"\n replot \"%s\" u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm); */
2621: /* fprintf(ficgp,"\n replot \"%s\" u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm); */
1.88 brouard 2622: fprintf(ficgp,"\n plot \"%s\" u 1:($3) not w l 1 ",subdirf(fileresprobmorprev));
2623: fprintf(ficgp,"\n replot \"%s\" u 1:(($3+1.96*$4)) t \"95\%% interval\" w l 2 ",subdirf(fileresprobmorprev));
2624: fprintf(ficgp,"\n replot \"%s\" u 1:(($3-1.96*$4)) not w l 2 ",subdirf(fileresprobmorprev));
2625: fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",subdirf(fileresprobmorprev),subdirf(fileresprobmorprev));
2626: 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 2627: /* 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);
2628: */
1.88 brouard 2629: /* fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.png\";replot;",digitp,optionfilefiname,digit); */
1.89 ! brouard 2630: fprintf(ficgp,"\nset out \"%s%s.png\";replot;\n",subdirf3(optionfilefiname,"varmuptjgr",digitp),digit);
1.53 brouard 2631:
2632: free_vector(xp,1,npar);
2633: free_matrix(doldm,1,nlstate,1,nlstate);
2634: free_matrix(dnewm,1,nlstate,1,npar);
2635: free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
2636: free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
2637: free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
1.55 lievre 2638: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
1.53 brouard 2639: fclose(ficresprobmorprev);
1.88 brouard 2640: fflush(ficgp);
2641: fflush(fichtm);
1.84 brouard 2642: } /* end varevsij */
1.53 brouard 2643:
2644: /************ Variance of prevlim ******************/
2645: 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)
2646: {
2647: /* Variance of prevalence limit */
1.59 brouard 2648: /* double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
1.53 brouard 2649: double **newm;
2650: double **dnewm,**doldm;
2651: int i, j, nhstepm, hstepm;
2652: int k, cptcode;
2653: double *xp;
2654: double *gp, *gm;
2655: double **gradg, **trgradg;
2656: double age,agelim;
2657: int theta;
2658:
1.54 brouard 2659: fprintf(ficresvpl,"# Standard deviation of stable prevalences \n");
1.53 brouard 2660: fprintf(ficresvpl,"# Age");
2661: for(i=1; i<=nlstate;i++)
2662: fprintf(ficresvpl," %1d-%1d",i,i);
2663: fprintf(ficresvpl,"\n");
2664:
2665: xp=vector(1,npar);
2666: dnewm=matrix(1,nlstate,1,npar);
2667: doldm=matrix(1,nlstate,1,nlstate);
2668:
2669: hstepm=1*YEARM; /* Every year of age */
2670: hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */
2671: agelim = AGESUP;
2672: for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
2673: nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
2674: if (stepm >= YEARM) hstepm=1;
2675: nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
2676: gradg=matrix(1,npar,1,nlstate);
2677: gp=vector(1,nlstate);
2678: gm=vector(1,nlstate);
2679:
2680: for(theta=1; theta <=npar; theta++){
2681: for(i=1; i<=npar; i++){ /* Computes gradient */
2682: xp[i] = x[i] + (i==theta ?delti[theta]:0);
2683: }
2684: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
2685: for(i=1;i<=nlstate;i++)
2686: gp[i] = prlim[i][i];
2687:
2688: for(i=1; i<=npar; i++) /* Computes gradient */
2689: xp[i] = x[i] - (i==theta ?delti[theta]:0);
2690: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
2691: for(i=1;i<=nlstate;i++)
2692: gm[i] = prlim[i][i];
2693:
2694: for(i=1;i<=nlstate;i++)
2695: gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
2696: } /* End theta */
2697:
2698: trgradg =matrix(1,nlstate,1,npar);
2699:
2700: for(j=1; j<=nlstate;j++)
2701: for(theta=1; theta <=npar; theta++)
2702: trgradg[j][theta]=gradg[theta][j];
2703:
2704: for(i=1;i<=nlstate;i++)
2705: varpl[i][(int)age] =0.;
2706: matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
2707: matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
2708: for(i=1;i<=nlstate;i++)
2709: varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
2710:
2711: fprintf(ficresvpl,"%.0f ",age );
2712: for(i=1; i<=nlstate;i++)
2713: fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
2714: fprintf(ficresvpl,"\n");
2715: free_vector(gp,1,nlstate);
2716: free_vector(gm,1,nlstate);
2717: free_matrix(gradg,1,npar,1,nlstate);
2718: free_matrix(trgradg,1,nlstate,1,npar);
2719: } /* End age */
2720:
2721: free_vector(xp,1,npar);
2722: free_matrix(doldm,1,nlstate,1,npar);
2723: free_matrix(dnewm,1,nlstate,1,nlstate);
2724:
2725: }
2726:
2727: /************ Variance of one-step probabilities ******************/
2728: void varprob(char optionfilefiname[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij, int *Tvar, int **nbcode, int *ncodemax)
2729: {
2730: int i, j=0, i1, k1, l1, t, tj;
2731: int k2, l2, j1, z1;
2732: int k=0,l, cptcode;
2733: int first=1, first1;
2734: double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
2735: double **dnewm,**doldm;
2736: double *xp;
2737: double *gp, *gm;
2738: double **gradg, **trgradg;
2739: double **mu;
2740: double age,agelim, cov[NCOVMAX];
2741: double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
2742: int theta;
2743: char fileresprob[FILENAMELENGTH];
2744: char fileresprobcov[FILENAMELENGTH];
2745: char fileresprobcor[FILENAMELENGTH];
2746:
2747: double ***varpij;
2748:
2749: strcpy(fileresprob,"prob");
2750: strcat(fileresprob,fileres);
2751: if((ficresprob=fopen(fileresprob,"w"))==NULL) {
2752: printf("Problem with resultfile: %s\n", fileresprob);
2753: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
2754: }
2755: strcpy(fileresprobcov,"probcov");
2756: strcat(fileresprobcov,fileres);
2757: if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
2758: printf("Problem with resultfile: %s\n", fileresprobcov);
2759: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
2760: }
2761: strcpy(fileresprobcor,"probcor");
2762: strcat(fileresprobcor,fileres);
2763: if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
2764: printf("Problem with resultfile: %s\n", fileresprobcor);
2765: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
2766: }
2767: printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
2768: fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
2769: printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
2770: fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
2771: printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
2772: fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
2773:
2774: fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
2775: fprintf(ficresprob,"# Age");
2776: fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
2777: fprintf(ficresprobcov,"# Age");
2778: fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
2779: fprintf(ficresprobcov,"# Age");
2780:
2781:
2782: for(i=1; i<=nlstate;i++)
2783: for(j=1; j<=(nlstate+ndeath);j++){
2784: fprintf(ficresprob," p%1d-%1d (SE)",i,j);
2785: fprintf(ficresprobcov," p%1d-%1d ",i,j);
2786: fprintf(ficresprobcor," p%1d-%1d ",i,j);
2787: }
1.69 brouard 2788: /* fprintf(ficresprob,"\n");
1.53 brouard 2789: fprintf(ficresprobcov,"\n");
2790: fprintf(ficresprobcor,"\n");
1.69 brouard 2791: */
2792: xp=vector(1,npar);
1.53 brouard 2793: dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
2794: doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
2795: mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
2796: varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
2797: first=1;
1.88 brouard 2798: fprintf(ficgp,"\n# Routine varprob");
2799: fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
2800: fprintf(fichtm,"\n");
2801:
2802: fprintf(fichtm,"\n<li><h4> Computing matrix of variance-covariance of step probabilities</h4></li>\n");
2803: 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");
2804: 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 2805:
2806: cov[1]=1;
2807: tj=cptcoveff;
2808: if (cptcovn<1) {tj=1;ncodemax[1]=1;}
2809: j1=0;
2810: for(t=1; t<=tj;t++){
2811: for(i1=1; i1<=ncodemax[t];i1++){
2812: j1++;
2813: if (cptcovn>0) {
2814: fprintf(ficresprob, "\n#********** Variable ");
2815: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
1.69 brouard 2816: fprintf(ficresprob, "**********\n#\n");
1.53 brouard 2817: fprintf(ficresprobcov, "\n#********** Variable ");
2818: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
1.69 brouard 2819: fprintf(ficresprobcov, "**********\n#\n");
1.53 brouard 2820:
2821: fprintf(ficgp, "\n#********** Variable ");
1.69 brouard 2822: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
2823: fprintf(ficgp, "**********\n#\n");
1.53 brouard 2824:
2825:
2826: fprintf(fichtm, "\n<hr size=\"2\" color=\"#EC5E5E\">********** Variable ");
2827: for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
2828: fprintf(fichtm, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
2829:
2830: fprintf(ficresprobcor, "\n#********** Variable ");
2831: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
1.69 brouard 2832: fprintf(ficresprobcor, "**********\n#");
1.53 brouard 2833: }
2834:
2835: for (age=bage; age<=fage; age ++){
2836: cov[2]=age;
2837: for (k=1; k<=cptcovn;k++) {
2838: cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];
2839: }
2840: for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
2841: for (k=1; k<=cptcovprod;k++)
2842: cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
2843:
2844: gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
2845: trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
2846: gp=vector(1,(nlstate)*(nlstate+ndeath));
2847: gm=vector(1,(nlstate)*(nlstate+ndeath));
2848:
2849: for(theta=1; theta <=npar; theta++){
2850: for(i=1; i<=npar; i++)
1.74 brouard 2851: xp[i] = x[i] + (i==theta ?delti[theta]:(double)0);
1.53 brouard 2852:
2853: pmij(pmmij,cov,ncovmodel,xp,nlstate);
2854:
2855: k=0;
2856: for(i=1; i<= (nlstate); i++){
2857: for(j=1; j<=(nlstate+ndeath);j++){
2858: k=k+1;
2859: gp[k]=pmmij[i][j];
2860: }
2861: }
2862:
2863: for(i=1; i<=npar; i++)
1.74 brouard 2864: xp[i] = x[i] - (i==theta ?delti[theta]:(double)0);
1.53 brouard 2865:
2866: pmij(pmmij,cov,ncovmodel,xp,nlstate);
2867: k=0;
2868: for(i=1; i<=(nlstate); i++){
2869: for(j=1; j<=(nlstate+ndeath);j++){
2870: k=k+1;
2871: gm[k]=pmmij[i][j];
2872: }
2873: }
2874:
2875: for(i=1; i<= (nlstate)*(nlstate+ndeath); i++)
1.74 brouard 2876: gradg[theta][i]=(gp[i]-gm[i])/(double)2./delti[theta];
1.53 brouard 2877: }
2878:
2879: for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
2880: for(theta=1; theta <=npar; theta++)
2881: trgradg[j][theta]=gradg[theta][j];
2882:
2883: matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov);
2884: matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);
1.59 brouard 2885: free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
2886: free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
2887: free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
2888: free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
2889:
1.53 brouard 2890: pmij(pmmij,cov,ncovmodel,x,nlstate);
2891:
2892: k=0;
2893: for(i=1; i<=(nlstate); i++){
2894: for(j=1; j<=(nlstate+ndeath);j++){
2895: k=k+1;
2896: mu[k][(int) age]=pmmij[i][j];
2897: }
2898: }
2899: for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
2900: for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
2901: varpij[i][j][(int)age] = doldm[i][j];
2902:
2903: /*printf("\n%d ",(int)age);
1.59 brouard 2904: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
2905: printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
2906: fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
2907: }*/
1.53 brouard 2908:
2909: fprintf(ficresprob,"\n%d ",(int)age);
2910: fprintf(ficresprobcov,"\n%d ",(int)age);
2911: fprintf(ficresprobcor,"\n%d ",(int)age);
2912:
2913: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)
2914: fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));
2915: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
2916: fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);
2917: fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
2918: }
2919: i=0;
2920: for (k=1; k<=(nlstate);k++){
2921: for (l=1; l<=(nlstate+ndeath);l++){
2922: i=i++;
2923: fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
2924: fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
2925: for (j=1; j<=i;j++){
2926: fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);
2927: fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));
2928: }
2929: }
2930: }/* end of loop for state */
2931: } /* end of loop for age */
2932:
2933: /* Confidence intervalle of pij */
2934: /*
1.59 brouard 2935: fprintf(ficgp,"\nset noparametric;unset label");
2936: fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");
2937: fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
2938: 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);
2939: fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);
2940: fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);
2941: fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);
1.53 brouard 2942: */
2943:
2944: /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
2945: first1=1;
2946: for (k2=1; k2<=(nlstate);k2++){
2947: for (l2=1; l2<=(nlstate+ndeath);l2++){
2948: if(l2==k2) continue;
2949: j=(k2-1)*(nlstate+ndeath)+l2;
2950: for (k1=1; k1<=(nlstate);k1++){
2951: for (l1=1; l1<=(nlstate+ndeath);l1++){
2952: if(l1==k1) continue;
2953: i=(k1-1)*(nlstate+ndeath)+l1;
2954: if(i<=j) continue;
2955: for (age=bage; age<=fage; age ++){
2956: if ((int)age %5==0){
2957: v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;
2958: v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;
2959: cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;
2960: mu1=mu[i][(int) age]/stepm*YEARM ;
2961: mu2=mu[j][(int) age]/stepm*YEARM;
2962: c12=cv12/sqrt(v1*v2);
2963: /* Computing eigen value of matrix of covariance */
2964: lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
2965: lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
2966: /* Eigen vectors */
2967: v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
2968: /*v21=sqrt(1.-v11*v11); *//* error */
2969: v21=(lc1-v1)/cv12*v11;
2970: v12=-v21;
2971: v22=v11;
2972: tnalp=v21/v11;
2973: if(first1==1){
2974: first1=0;
2975: 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);
2976: }
2977: 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);
2978: /*printf(fignu*/
2979: /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */
2980: /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */
2981: if(first==1){
2982: first=0;
2983: fprintf(ficgp,"\nset parametric;unset label");
2984: 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);
2985: fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
1.88 brouard 2986: fprintf(fichtm,"\n<br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup>\
2987: :<a href=\"%s%d%1d%1d-%1d%1d.png\">\
2988: %s%d%1d%1d-%1d%1d.png</A>, ",k1,l1,k2,l2,\
2989: subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2,\
2990: subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
2991: fprintf(fichtm,"\n<br><img src=\"%s%d%1d%1d-%1d%1d.png\"> ",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
1.53 brouard 2992: fprintf(fichtm,"\n<br> Correlation at age %d (%.3f),",(int) age, c12);
1.88 brouard 2993: fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\"",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
1.53 brouard 2994: fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
2995: fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
2996: 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",\
2997: mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
2998: mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
2999: }else{
3000: first=0;
3001: fprintf(fichtm," %d (%.3f),",(int) age, c12);
3002: fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
3003: fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
3004: 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",\
3005: mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
3006: mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
3007: }/* if first */
3008: } /* age mod 5 */
3009: } /* end loop age */
1.88 brouard 3010: fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\";replot;",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
1.53 brouard 3011: first=1;
3012: } /*l12 */
3013: } /* k12 */
3014: } /*l1 */
3015: }/* k1 */
3016: } /* loop covariates */
3017: }
1.59 brouard 3018: free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
3019: free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
1.53 brouard 3020: free_vector(xp,1,npar);
3021: fclose(ficresprob);
3022: fclose(ficresprobcov);
3023: fclose(ficresprobcor);
1.88 brouard 3024: /* fclose(ficgp);*/
1.53 brouard 3025: }
3026:
3027:
3028: /******************* Printing html file ***********/
3029: void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \
3030: int lastpass, int stepm, int weightopt, char model[],\
3031: int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
3032: int popforecast, int estepm ,\
3033: double jprev1, double mprev1,double anprev1, \
3034: double jprev2, double mprev2,double anprev2){
3035: int jj1, k1, i1, cpt;
3036: /*char optionfilehtm[FILENAMELENGTH];*/
1.87 brouard 3037: /* if((fichtm=fopen(optionfilehtm,"a"))==NULL) { */
3038: /* printf("Problem with %s \n",optionfilehtm), exit(0); */
3039: /* fprintf(ficlog,"Problem with %s \n",optionfilehtm), exit(0); */
3040: /* } */
1.53 brouard 3041:
1.85 brouard 3042: fprintf(fichtm,"<ul><li><h4>Result files (first order: no variance)</h4>\n \
1.88 brouard 3043: - Observed prevalence in each state (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"%s\">%s</a> <br>\n \
3044: - Estimated transition probabilities over %d (stepm) months: <a href=\"%s\">%s</a><br>\n \
3045: - Stable prevalence in each health state: <a href=\"%s\">%s</a> <br>\n \
1.85 brouard 3046: - Life expectancies by age and initial health status (estepm=%2d months): \
1.88 brouard 3047: <a href=\"%s\">%s</a> <br>\n</li>", \
3048: jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirf2(fileres,"p"),subdirf2(fileres,"p"),\
3049: stepm,subdirf2(fileres,"pij"),subdirf2(fileres,"pij"),\
3050: subdirf2(fileres,"pl"),subdirf2(fileres,"pl"),\
3051: estepm,subdirf2(fileres,"e"),subdirf2(fileres,"e"));
1.53 brouard 3052:
3053: fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
3054:
3055: m=cptcoveff;
3056: if (cptcovn < 1) {m=1;ncodemax[1]=1;}
3057:
3058: jj1=0;
3059: for(k1=1; k1<=m;k1++){
3060: for(i1=1; i1<=ncodemax[k1];i1++){
3061: jj1++;
3062: if (cptcovn > 0) {
3063: fprintf(fichtm,"<hr size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
3064: for (cpt=1; cpt<=cptcoveff;cpt++)
3065: fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
3066: fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
3067: }
3068: /* Pij */
1.88 brouard 3069: 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> \
3070: <img src=\"%s%d1.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);
1.53 brouard 3071: /* Quasi-incidences */
1.85 brouard 3072: fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months\
1.88 brouard 3073: before but expressed in per year i.e. quasi incidences if stepm is small and probabilities too: %s%d2.png<br> \
3074: <img src=\"%s%d2.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);
1.53 brouard 3075: /* Stable prevalence in each health state */
3076: for(cpt=1; cpt<nlstate;cpt++){
1.85 brouard 3077: fprintf(fichtm,"<br>- Stable prevalence in each health state : p%s%d%d.png<br> \
1.88 brouard 3078: <img src=\"%s%d%d.png\">",subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1);
1.53 brouard 3079: }
3080: for(cpt=1; cpt<=nlstate;cpt++) {
1.88 brouard 3081: fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): %s%d%d.png <br> \
1.89 ! brouard 3082: <img src=\"%s%d%d.png\">",cpt,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1);
1.53 brouard 3083: }
1.85 brouard 3084: fprintf(fichtm,"\n<br>- Total life expectancy by age and \
1.88 brouard 3085: health expectancies in states (1) and (2): %s%d.png<br>\
3086: <img src=\"%s%d.png\">",subdirf2(optionfilefiname,"e"),jj1,subdirf2(optionfilefiname,"e"),jj1);
1.53 brouard 3087: } /* end i1 */
3088: }/* End k1 */
3089: fprintf(fichtm,"</ul>");
3090:
3091:
1.85 brouard 3092: fprintf(fichtm,"\n<br><li><h4> Result files (second order: variances)</h4>\n\
3093: - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n\
1.88 brouard 3094: - Variance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n\
3095: - Variance-covariance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n\
3096: - Correlation matrix of one-step probabilities: <a href=\"%s\">%s</a> <br>\n\
3097: - Variances and covariances of life expectancies by age and initial health status (estepm=%d months): <a href=\"%s\">%s</a><br>\n\
3098: - Health expectancies with their variances (no covariance): <a href=\"%s\">%s</a> <br>\n\
3099: - Standard deviation of stable prevalences: <a href=\"%s\">%s</a> <br>\n",\
3100: rfileres,rfileres,\
3101: subdirf2(fileres,"prob"),subdirf2(fileres,"prob"),\
3102: subdirf2(fileres,"probcov"),subdirf2(fileres,"probcov"),\
3103: subdirf2(fileres,"probcor"),subdirf2(fileres,"probcor"),\
3104: estepm, subdirf2(fileres,"v"),subdirf2(fileres,"v"),\
3105: subdirf2(fileres,"t"),subdirf2(fileres,"t"),\
3106: subdirf2(fileres,"vpl"),subdirf2(fileres,"vpl"));
1.53 brouard 3107:
1.76 brouard 3108: /* if(popforecast==1) fprintf(fichtm,"\n */
3109: /* - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n */
3110: /* - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n */
3111: /* <br>",fileres,fileres,fileres,fileres); */
3112: /* else */
3113: /* 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 3114: fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
3115:
3116: m=cptcoveff;
3117: if (cptcovn < 1) {m=1;ncodemax[1]=1;}
3118:
3119: jj1=0;
3120: for(k1=1; k1<=m;k1++){
3121: for(i1=1; i1<=ncodemax[k1];i1++){
3122: jj1++;
3123: if (cptcovn > 0) {
3124: fprintf(fichtm,"<hr size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
3125: for (cpt=1; cpt<=cptcoveff;cpt++)
3126: fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
3127: fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
3128: }
3129: for(cpt=1; cpt<=nlstate;cpt++) {
1.85 brouard 3130: fprintf(fichtm,"<br>- Observed and period prevalence (with confident\
1.88 brouard 3131: interval) in state (%d): %s%d%d.png <br>\
1.89 ! brouard 3132: <img src=\"%s%d%d.png\">",cpt,subdirf2(optionfilefiname,"vr"),cpt,jj1,subdirf2(optionfilefiname,"vr"),cpt,jj1);
1.53 brouard 3133: }
3134: } /* end i1 */
3135: }/* End k1 */
3136: fprintf(fichtm,"</ul>");
1.87 brouard 3137: fflush(fichtm);
1.53 brouard 3138: }
3139:
3140: /******************* Gnuplot file **************/
1.89 ! brouard 3141: void printinggnuplot(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
1.53 brouard 3142:
1.88 brouard 3143: char dirfileres[132],optfileres[132];
1.53 brouard 3144: int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;
3145: int ng;
1.88 brouard 3146: /* if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) { */
3147: /* printf("Problem with file %s",optionfilegnuplot); */
3148: /* fprintf(ficlog,"Problem with file %s",optionfilegnuplot); */
3149: /* } */
1.53 brouard 3150:
1.54 brouard 3151: /*#ifdef windows */
1.89 ! brouard 3152: fprintf(ficgp,"cd \"%s\" \n",pathc);
1.54 brouard 3153: /*#endif */
1.88 brouard 3154: m=pow(2,cptcoveff);
3155:
3156: strcpy(dirfileres,optionfilefiname);
3157: strcpy(optfileres,"vpl");
1.53 brouard 3158: /* 1eme*/
3159: for (cpt=1; cpt<= nlstate ; cpt ++) {
3160: for (k1=1; k1<= m ; k1 ++) {
1.88 brouard 3161: fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"v"),cpt,k1);
3162: fprintf(ficgp,"\n#set out \"v%s%d%d.png\" \n",optionfilefiname,cpt,k1);
3163: fprintf(ficgp,"set xlabel \"Age\" \n\
3164: set ylabel \"Probability\" \n\
3165: set ter png small\n\
3166: set size 0.65,0.65\n\
3167: plot [%.f:%.f] \"%s\" every :::%d::%d u 1:2 \"\%%lf",ageminpar,fage,subdirf2(fileres,"vpl"),k1-1,k1-1);
1.53 brouard 3168:
3169: for (i=1; i<= nlstate ; i ++) {
3170: if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
3171: else fprintf(ficgp," \%%*lf (\%%*lf)");
3172: }
1.88 brouard 3173: 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 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\"95\%% CI\" w l 1,\"%s\" every :::%d::%d u 1:($2-1.96*$3) \"\%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1);
1.53 brouard 3179: for (i=1; i<= nlstate ; i ++) {
3180: if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
3181: else fprintf(ficgp," \%%*lf (\%%*lf)");
3182: }
1.88 brouard 3183: fprintf(ficgp,"\" t\"\" w l 1,\"%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",subdirf2(fileres,"p"),k1-1,k1-1,2+4*(cpt-1));
1.53 brouard 3184: }
3185: }
3186: /*2 eme*/
3187:
3188: for (k1=1; k1<= m ; k1 ++) {
1.88 brouard 3189: fprintf(ficgp,"\nset out \"%s%d.png\" \n",subdirf2(optionfilefiname,"e"),k1);
1.53 brouard 3190: fprintf(ficgp,"set ylabel \"Years\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] ",ageminpar,fage);
3191:
3192: for (i=1; i<= nlstate+1 ; i ++) {
3193: k=2*i;
1.88 brouard 3194: fprintf(ficgp,"\"%s\" every :::%d::%d u 1:2 \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
1.53 brouard 3195: for (j=1; j<= nlstate+1 ; j ++) {
3196: if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
3197: else fprintf(ficgp," \%%*lf (\%%*lf)");
3198: }
3199: if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");
3200: else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);
1.88 brouard 3201: fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
1.53 brouard 3202: for (j=1; j<= nlstate+1 ; j ++) {
3203: if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
3204: else fprintf(ficgp," \%%*lf (\%%*lf)");
3205: }
3206: fprintf(ficgp,"\" t\"\" w l 0,");
1.88 brouard 3207: fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
1.53 brouard 3208: for (j=1; j<= nlstate+1 ; j ++) {
3209: if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
3210: else fprintf(ficgp," \%%*lf (\%%*lf)");
3211: }
3212: if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");
3213: else fprintf(ficgp,"\" t\"\" w l 0,");
3214: }
3215: }
3216:
3217: /*3eme*/
3218:
3219: for (k1=1; k1<= m ; k1 ++) {
3220: for (cpt=1; cpt<= nlstate ; cpt ++) {
3221: k=2+nlstate*(2*cpt-2);
1.88 brouard 3222: fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"exp"),cpt,k1);
3223: fprintf(ficgp,"set ter png small\n\
3224: set size 0.65,0.65\n\
3225: plot [%.f:%.f] \"%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,subdirf2(fileres,"e"),k1-1,k1-1,k,cpt);
1.53 brouard 3226: /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
3227: for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
3228: fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
3229: fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
3230: for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
3231: fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
3232:
3233: */
3234: for (i=1; i< nlstate ; i ++) {
1.88 brouard 3235: 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 3236:
3237: }
3238: }
3239: }
3240:
1.76 brouard 3241: /* CV preval stable (period) */
1.53 brouard 3242: for (k1=1; k1<= m ; k1 ++) {
1.76 brouard 3243: for (cpt=1; cpt<=nlstate ; cpt ++) {
1.53 brouard 3244: k=3;
1.88 brouard 3245: fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"p"),cpt,k1);
3246: fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\
3247: set ter png small\nset size 0.65,0.65\n\
1.89 ! brouard 3248: unset log y\n\
1.88 brouard 3249: plot [%.f:%.f] \"%s\" u ($1==%d ? ($3):1/0):($%d/($%d",ageminpar,agemaxpar,subdirf2(fileres,"pij"),k1,k+cpt+1,k+1);
1.53 brouard 3250:
1.83 lievre 3251: for (i=1; i< nlstate ; i ++)
1.53 brouard 3252: fprintf(ficgp,"+$%d",k+i+1);
3253: fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);
3254:
3255: l=3+(nlstate+ndeath)*cpt;
1.88 brouard 3256: fprintf(ficgp,",\"%s\" u ($1==%d ? ($3):1/0):($%d/($%d",subdirf2(fileres,"pij"),k1,l+cpt+1,l+1);
1.53 brouard 3257: for (i=1; i< nlstate ; i ++) {
3258: l=3+(nlstate+ndeath)*cpt;
3259: fprintf(ficgp,"+$%d",l+i+1);
3260: }
3261: fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);
3262: }
3263: }
3264:
3265: /* proba elementaires */
3266: for(i=1,jk=1; i <=nlstate; i++){
3267: for(k=1; k <=(nlstate+ndeath); k++){
3268: if (k != i) {
3269: for(j=1; j <=ncovmodel; j++){
3270: fprintf(ficgp,"p%d=%f ",jk,p[jk]);
3271: jk++;
3272: fprintf(ficgp,"\n");
3273: }
3274: }
3275: }
3276: }
3277:
3278: for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/
3279: for(jk=1; jk <=m; jk++) {
1.88 brouard 3280: fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"pe"),jk,ng);
1.53 brouard 3281: if (ng==2)
3282: fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
3283: else
3284: fprintf(ficgp,"\nset title \"Probability\"\n");
3285: fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65\nset log y\nplot [%.f:%.f] ",ageminpar,agemaxpar);
3286: i=1;
3287: for(k2=1; k2<=nlstate; k2++) {
3288: k3=i;
3289: for(k=1; k<=(nlstate+ndeath); k++) {
3290: if (k != k2){
3291: if(ng==2)
3292: fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);
3293: else
3294: fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
3295: ij=1;
3296: for(j=3; j <=ncovmodel; j++) {
3297: if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
3298: fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
3299: ij++;
3300: }
3301: else
3302: fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
3303: }
3304: fprintf(ficgp,")/(1");
3305:
3306: for(k1=1; k1 <=nlstate; k1++){
3307: fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);
3308: ij=1;
3309: for(j=3; j <=ncovmodel; j++){
3310: if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
3311: fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
3312: ij++;
3313: }
3314: else
3315: fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
3316: }
3317: fprintf(ficgp,")");
3318: }
3319: fprintf(ficgp,") t \"p%d%d\" ", k2,k);
3320: if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");
3321: i=i+ncovmodel;
3322: }
3323: } /* end k */
3324: } /* end k2 */
3325: } /* end jk */
3326: } /* end ng */
1.88 brouard 3327: fflush(ficgp);
1.53 brouard 3328: } /* end gnuplot */
3329:
3330:
3331: /*************** Moving average **************/
1.54 brouard 3332: int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav){
1.53 brouard 3333:
3334: int i, cpt, cptcod;
1.58 lievre 3335: int modcovmax =1;
1.54 brouard 3336: int mobilavrange, mob;
1.53 brouard 3337: double age;
1.58 lievre 3338:
3339: modcovmax=2*cptcoveff;/* Max number of modalities. We suppose
3340: a covariate has 2 modalities */
3341: if (cptcovn<1) modcovmax=1; /* At least 1 pass */
3342:
1.54 brouard 3343: if(mobilav==1||mobilav ==3 ||mobilav==5 ||mobilav== 7){
3344: if(mobilav==1) mobilavrange=5; /* default */
3345: else mobilavrange=mobilav;
3346: for (age=bage; age<=fage; age++)
3347: for (i=1; i<=nlstate;i++)
1.58 lievre 3348: for (cptcod=1;cptcod<=modcovmax;cptcod++)
1.54 brouard 3349: mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
3350: /* We keep the original values on the extreme ages bage, fage and for
3351: fage+1 and bage-1 we use a 3 terms moving average; for fage+2 bage+2
3352: we use a 5 terms etc. until the borders are no more concerned.
3353: */
3354: for (mob=3;mob <=mobilavrange;mob=mob+2){
3355: for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){
3356: for (i=1; i<=nlstate;i++){
1.58 lievre 3357: for (cptcod=1;cptcod<=modcovmax;cptcod++){
1.54 brouard 3358: mobaverage[(int)age][i][cptcod] =probs[(int)age][i][cptcod];
3359: for (cpt=1;cpt<=(mob-1)/2;cpt++){
3360: mobaverage[(int)age][i][cptcod] +=probs[(int)age-cpt][i][cptcod];
3361: mobaverage[(int)age][i][cptcod] +=probs[(int)age+cpt][i][cptcod];
3362: }
3363: mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/mob;
3364: }
1.53 brouard 3365: }
1.54 brouard 3366: }/* end age */
3367: }/* end mob */
3368: }else return -1;
3369: return 0;
3370: }/* End movingaverage */
1.53 brouard 3371:
3372:
3373: /************** Forecasting ******************/
1.70 brouard 3374: 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 3375: /* proj1, year, month, day of starting projection
3376: agemin, agemax range of age
3377: dateprev1 dateprev2 range of dates during which prevalence is computed
1.70 brouard 3378: anproj2 year of en of projection (same day and month as proj1).
1.69 brouard 3379: */
1.73 lievre 3380: int yearp, stepsize, hstepm, nhstepm, j, k, c, cptcod, i, h, i1;
1.53 brouard 3381: int *popage;
1.70 brouard 3382: double agec; /* generic age */
3383: double agelim, ppij, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
1.53 brouard 3384: double *popeffectif,*popcount;
3385: double ***p3mat;
1.55 lievre 3386: double ***mobaverage;
1.53 brouard 3387: char fileresf[FILENAMELENGTH];
3388:
1.69 brouard 3389: agelim=AGESUP;
1.84 brouard 3390: prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
1.53 brouard 3391:
3392: strcpy(fileresf,"f");
3393: strcat(fileresf,fileres);
3394: if((ficresf=fopen(fileresf,"w"))==NULL) {
3395: printf("Problem with forecast resultfile: %s\n", fileresf);
3396: fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);
3397: }
3398: printf("Computing forecasting: result on file '%s' \n", fileresf);
3399: fprintf(ficlog,"Computing forecasting: result on file '%s' \n", fileresf);
3400:
3401: if (cptcoveff==0) ncodemax[cptcoveff]=1;
3402:
1.54 brouard 3403: if (mobilav!=0) {
1.53 brouard 3404: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
1.54 brouard 3405: if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
3406: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
3407: printf(" Error in movingaverage mobilav=%d\n",mobilav);
3408: }
1.53 brouard 3409: }
3410:
3411: stepsize=(int) (stepm+YEARM-1)/YEARM;
3412: if (stepm<=12) stepsize=1;
1.74 brouard 3413: if(estepm < stepm){
3414: printf ("Problem %d lower than %d\n",estepm, stepm);
3415: }
3416: else hstepm=estepm;
3417:
1.53 brouard 3418: hstepm=hstepm/stepm;
1.69 brouard 3419: yp1=modf(dateintmean,&yp);/* extracts integral of datemean in yp and
3420: fractional in yp1 */
1.53 brouard 3421: anprojmean=yp;
3422: yp2=modf((yp1*12),&yp);
3423: mprojmean=yp;
3424: yp1=modf((yp2*30.5),&yp);
3425: jprojmean=yp;
3426: if(jprojmean==0) jprojmean=1;
3427: if(mprojmean==0) jprojmean=1;
1.73 lievre 3428:
3429: i1=cptcoveff;
3430: if (cptcovn < 1){i1=1;}
1.53 brouard 3431:
1.70 brouard 3432: fprintf(ficresf,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2);
1.53 brouard 3433:
1.70 brouard 3434: fprintf(ficresf,"#****** Routine prevforecast **\n");
1.73 lievre 3435:
1.75 brouard 3436: /* if (h==(int)(YEARM*yearp)){ */
1.73 lievre 3437: for(cptcov=1, k=0;cptcov<=i1;cptcov++){
1.53 brouard 3438: for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
3439: k=k+1;
3440: fprintf(ficresf,"\n#******");
3441: for(j=1;j<=cptcoveff;j++) {
1.70 brouard 3442: 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 3443: }
3444: fprintf(ficresf,"******\n");
1.70 brouard 3445: fprintf(ficresf,"# Covariate valuofcovar yearproj age");
3446: for(j=1; j<=nlstate+ndeath;j++){
3447: for(i=1; i<=nlstate;i++)
3448: fprintf(ficresf," p%d%d",i,j);
3449: fprintf(ficresf," p.%d",j);
3450: }
1.74 brouard 3451: for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) {
1.53 brouard 3452: fprintf(ficresf,"\n");
1.70 brouard 3453: fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+yearp);
1.53 brouard 3454:
1.71 brouard 3455: for (agec=fage; agec>=(ageminpar-1); agec--){
1.70 brouard 3456: nhstepm=(int) rint((agelim-agec)*YEARM/stepm);
1.53 brouard 3457: nhstepm = nhstepm/hstepm;
3458: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3459: oldm=oldms;savm=savms;
1.70 brouard 3460: hpxij(p3mat,nhstepm,agec,hstepm,p,nlstate,stepm,oldm,savm, k);
1.53 brouard 3461:
3462: for (h=0; h<=nhstepm; h++){
1.75 brouard 3463: if (h*hstepm/YEARM*stepm ==yearp) {
1.69 brouard 3464: fprintf(ficresf,"\n");
3465: for(j=1;j<=cptcoveff;j++)
3466: fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
1.70 brouard 3467: fprintf(ficresf,"%.f %.f ",anproj1+yearp,agec+h*hstepm/YEARM*stepm);
1.53 brouard 3468: }
3469: for(j=1; j<=nlstate+ndeath;j++) {
1.70 brouard 3470: ppij=0.;
1.71 brouard 3471: for(i=1; i<=nlstate;i++) {
1.53 brouard 3472: if (mobilav==1)
1.71 brouard 3473: ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][i][cptcod];
1.53 brouard 3474: else {
1.71 brouard 3475: ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][cptcod];
1.53 brouard 3476: }
1.75 brouard 3477: if (h*hstepm/YEARM*stepm== yearp) {
1.70 brouard 3478: fprintf(ficresf," %.3f", p3mat[i][j][h]);
1.75 brouard 3479: }
3480: } /* end i */
3481: if (h*hstepm/YEARM*stepm==yearp) {
1.70 brouard 3482: fprintf(ficresf," %.3f", ppij);
1.53 brouard 3483: }
1.75 brouard 3484: }/* end j */
3485: } /* end h */
1.53 brouard 3486: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
1.75 brouard 3487: } /* end agec */
3488: } /* end yearp */
3489: } /* end cptcod */
3490: } /* end cptcov */
1.53 brouard 3491:
1.54 brouard 3492: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
1.53 brouard 3493:
3494: fclose(ficresf);
3495: }
1.70 brouard 3496:
3497: /************** Forecasting *****not tested NB*************/
1.53 brouard 3498: 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){
3499:
3500: int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;
3501: int *popage;
1.69 brouard 3502: double calagedatem, agelim, kk1, kk2;
1.53 brouard 3503: double *popeffectif,*popcount;
3504: double ***p3mat,***tabpop,***tabpopprev;
1.55 lievre 3505: double ***mobaverage;
1.53 brouard 3506: char filerespop[FILENAMELENGTH];
3507:
3508: tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
3509: tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
3510: agelim=AGESUP;
1.69 brouard 3511: calagedatem=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;
1.53 brouard 3512:
1.84 brouard 3513: prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
1.53 brouard 3514:
3515:
3516: strcpy(filerespop,"pop");
3517: strcat(filerespop,fileres);
3518: if((ficrespop=fopen(filerespop,"w"))==NULL) {
3519: printf("Problem with forecast resultfile: %s\n", filerespop);
3520: fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop);
3521: }
3522: printf("Computing forecasting: result on file '%s' \n", filerespop);
3523: fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop);
3524:
3525: if (cptcoveff==0) ncodemax[cptcoveff]=1;
3526:
1.54 brouard 3527: if (mobilav!=0) {
1.53 brouard 3528: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
1.54 brouard 3529: if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
3530: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
3531: printf(" Error in movingaverage mobilav=%d\n",mobilav);
3532: }
1.53 brouard 3533: }
3534:
3535: stepsize=(int) (stepm+YEARM-1)/YEARM;
3536: if (stepm<=12) stepsize=1;
3537:
3538: agelim=AGESUP;
3539:
3540: hstepm=1;
3541: hstepm=hstepm/stepm;
3542:
3543: if (popforecast==1) {
3544: if((ficpop=fopen(popfile,"r"))==NULL) {
3545: printf("Problem with population file : %s\n",popfile);exit(0);
3546: fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0);
3547: }
3548: popage=ivector(0,AGESUP);
3549: popeffectif=vector(0,AGESUP);
3550: popcount=vector(0,AGESUP);
3551:
3552: i=1;
3553: while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;
3554:
3555: imx=i;
3556: for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];
3557: }
3558:
1.69 brouard 3559: for(cptcov=1,k=0;cptcov<=i2;cptcov++){
1.53 brouard 3560: for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
3561: k=k+1;
3562: fprintf(ficrespop,"\n#******");
3563: for(j=1;j<=cptcoveff;j++) {
3564: fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
3565: }
3566: fprintf(ficrespop,"******\n");
3567: fprintf(ficrespop,"# Age");
3568: for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);
3569: if (popforecast==1) fprintf(ficrespop," [Population]");
3570:
3571: for (cpt=0; cpt<=0;cpt++) {
3572: fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);
3573:
1.69 brouard 3574: for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){
1.53 brouard 3575: nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);
3576: nhstepm = nhstepm/hstepm;
3577:
3578: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3579: oldm=oldms;savm=savms;
3580: hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
3581:
3582: for (h=0; h<=nhstepm; h++){
1.69 brouard 3583: if (h==(int) (calagedatem+YEARM*cpt)) {
1.53 brouard 3584: fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
3585: }
3586: for(j=1; j<=nlstate+ndeath;j++) {
3587: kk1=0.;kk2=0;
3588: for(i=1; i<=nlstate;i++) {
3589: if (mobilav==1)
3590: kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];
3591: else {
3592: kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];
3593: }
3594: }
1.69 brouard 3595: if (h==(int)(calagedatem+12*cpt)){
1.53 brouard 3596: tabpop[(int)(agedeb)][j][cptcod]=kk1;
3597: /*fprintf(ficrespop," %.3f", kk1);
3598: if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/
3599: }
3600: }
3601: for(i=1; i<=nlstate;i++){
3602: kk1=0.;
3603: for(j=1; j<=nlstate;j++){
3604: kk1= kk1+tabpop[(int)(agedeb)][j][cptcod];
3605: }
1.69 brouard 3606: tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedatem+12*cpt)*hstepm/YEARM*stepm-1)];
1.53 brouard 3607: }
3608:
1.69 brouard 3609: if (h==(int)(calagedatem+12*cpt)) for(j=1; j<=nlstate;j++)
1.53 brouard 3610: fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);
3611: }
3612: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3613: }
3614: }
3615:
3616: /******/
3617:
3618: for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) {
3619: fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);
1.69 brouard 3620: for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){
1.53 brouard 3621: nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);
3622: nhstepm = nhstepm/hstepm;
3623:
3624: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3625: oldm=oldms;savm=savms;
3626: hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
3627: for (h=0; h<=nhstepm; h++){
1.69 brouard 3628: if (h==(int) (calagedatem+YEARM*cpt)) {
1.53 brouard 3629: fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
3630: }
3631: for(j=1; j<=nlstate+ndeath;j++) {
3632: kk1=0.;kk2=0;
3633: for(i=1; i<=nlstate;i++) {
3634: kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];
3635: }
1.69 brouard 3636: if (h==(int)(calagedatem+12*cpt)) fprintf(ficresf," %15.2f", kk1);
1.53 brouard 3637: }
3638: }
3639: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3640: }
3641: }
3642: }
3643: }
3644:
1.54 brouard 3645: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
1.53 brouard 3646:
3647: if (popforecast==1) {
3648: free_ivector(popage,0,AGESUP);
3649: free_vector(popeffectif,0,AGESUP);
3650: free_vector(popcount,0,AGESUP);
3651: }
3652: free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
3653: free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
3654: fclose(ficrespop);
1.84 brouard 3655: } /* End of popforecast */
1.53 brouard 3656:
1.87 brouard 3657: int fileappend(FILE *fichier, char *optionfich)
1.86 brouard 3658: {
1.87 brouard 3659: if((fichier=fopen(optionfich,"a"))==NULL) {
3660: printf("Problem with file: %s\n", optionfich);
3661: fprintf(ficlog,"Problem with file: %s\n", optionfich);
3662: return (0);
1.86 brouard 3663: }
1.87 brouard 3664: fflush(fichier);
3665: return (1);
1.86 brouard 3666: }
1.88 brouard 3667: void prwizard(int ncovmodel, int nlstate, int ndeath, char model[], FILE *ficparo)
3668: {
3669:
3670: char ca[32], cb[32], cc[32];
3671: int i,j, k, l, li, lj, lk, ll, jj, npar, itimes;
3672: int numlinepar;
3673:
3674: printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
3675: fprintf(ficparo,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
3676: for(i=1; i <=nlstate; i++){
3677: jj=0;
3678: for(j=1; j <=nlstate+ndeath; j++){
3679: if(j==i) continue;
3680: jj++;
3681: /*ca[0]= k+'a'-1;ca[1]='\0';*/
3682: printf("%1d%1d",i,j);
3683: fprintf(ficparo,"%1d%1d",i,j);
3684: for(k=1; k<=ncovmodel;k++){
3685: /* printf(" %lf",param[i][j][k]); */
3686: /* fprintf(ficparo," %lf",param[i][j][k]); */
3687: printf(" 0.");
3688: fprintf(ficparo," 0.");
3689: }
3690: printf("\n");
3691: fprintf(ficparo,"\n");
3692: }
3693: }
3694: printf("# Scales (for hessian or gradient estimation)\n");
3695: fprintf(ficparo,"# Scales (for hessian or gradient estimation)\n");
3696: npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/
3697: for(i=1; i <=nlstate; i++){
3698: jj=0;
3699: for(j=1; j <=nlstate+ndeath; j++){
3700: if(j==i) continue;
3701: jj++;
3702: fprintf(ficparo,"%1d%1d",i,j);
3703: printf("%1d%1d",i,j);
3704: fflush(stdout);
3705: for(k=1; k<=ncovmodel;k++){
3706: /* printf(" %le",delti3[i][j][k]); */
3707: /* fprintf(ficparo," %le",delti3[i][j][k]); */
3708: printf(" 0.");
3709: fprintf(ficparo," 0.");
3710: }
3711: numlinepar++;
3712: printf("\n");
3713: fprintf(ficparo,"\n");
3714: }
3715: }
3716: printf("# Covariance matrix\n");
3717: /* # 121 Var(a12)\n\ */
3718: /* # 122 Cov(b12,a12) Var(b12)\n\ */
3719: /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
3720: /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
3721: /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
3722: /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
3723: /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
3724: /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
3725: fflush(stdout);
3726: fprintf(ficparo,"# Covariance matrix\n");
3727: /* # 121 Var(a12)\n\ */
3728: /* # 122 Cov(b12,a12) Var(b12)\n\ */
3729: /* # ...\n\ */
3730: /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
3731:
3732: for(itimes=1;itimes<=2;itimes++){
3733: jj=0;
3734: for(i=1; i <=nlstate; i++){
3735: for(j=1; j <=nlstate+ndeath; j++){
3736: if(j==i) continue;
3737: for(k=1; k<=ncovmodel;k++){
3738: jj++;
3739: ca[0]= k+'a'-1;ca[1]='\0';
3740: if(itimes==1){
3741: printf("#%1d%1d%d",i,j,k);
3742: fprintf(ficparo,"#%1d%1d%d",i,j,k);
3743: }else{
3744: printf("%1d%1d%d",i,j,k);
3745: fprintf(ficparo,"%1d%1d%d",i,j,k);
3746: /* printf(" %.5le",matcov[i][j]); */
3747: }
3748: ll=0;
3749: for(li=1;li <=nlstate; li++){
3750: for(lj=1;lj <=nlstate+ndeath; lj++){
3751: if(lj==li) continue;
3752: for(lk=1;lk<=ncovmodel;lk++){
3753: ll++;
3754: if(ll<=jj){
3755: cb[0]= lk +'a'-1;cb[1]='\0';
3756: if(ll<jj){
3757: if(itimes==1){
3758: printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
3759: fprintf(ficparo," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
3760: }else{
3761: printf(" 0.");
3762: fprintf(ficparo," 0.");
3763: }
3764: }else{
3765: if(itimes==1){
3766: printf(" Var(%s%1d%1d)",ca,i,j);
3767: fprintf(ficparo," Var(%s%1d%1d)",ca,i,j);
3768: }else{
3769: printf(" 0.");
3770: fprintf(ficparo," 0.");
3771: }
3772: }
3773: }
3774: } /* end lk */
3775: } /* end lj */
3776: } /* end li */
3777: printf("\n");
3778: fprintf(ficparo,"\n");
3779: numlinepar++;
3780: } /* end k*/
3781: } /*end j */
3782: } /* end i */
3783: }
3784:
3785: } /* end of prwizard */
3786:
1.53 brouard 3787: /***********************************************/
3788: /**************** Main Program *****************/
3789: /***********************************************/
3790:
3791: int main(int argc, char *argv[])
3792: {
1.61 brouard 3793: int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav);
1.74 brouard 3794: int i,j, k, n=MAXN,iter,m,size=100,cptcode, cptcod;
1.88 brouard 3795: int jj, imk;
1.85 brouard 3796: int numlinepar=0; /* Current linenumber of parameter file */
1.87 brouard 3797: /* FILE *fichtm; *//* Html File */
3798: /* FILE *ficgp;*/ /*Gnuplot File */
1.53 brouard 3799: double agedeb, agefin,hf;
3800: double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;
3801:
3802: double fret;
3803: double **xi,tmp,delta;
3804:
3805: double dum; /* Dummy variable */
3806: double ***p3mat;
3807: double ***mobaverage;
3808: int *indx;
3809: char line[MAXLINE], linepar[MAXLINE];
1.88 brouard 3810: char path[MAXLINE],pathc[MAXLINE],pathcd[MAXLINE],pathtot[MAXLINE],model[MAXLINE];
3811: char pathr[MAXLINE];
1.53 brouard 3812: int firstobs=1, lastobs=10;
3813: int sdeb, sfin; /* Status at beginning and end */
3814: int c, h , cpt,l;
3815: int ju,jl, mi;
3816: int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;
1.59 brouard 3817: int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,*tab;
1.69 brouard 3818: int mobilavproj=0 , prevfcast=0 ; /* moving average of prev, If prevfcast=1 prevalence projection */
1.53 brouard 3819: int mobilav=0,popforecast=0;
3820: int hstepm, nhstepm;
1.74 brouard 3821: double jprev1=1, mprev1=1,anprev1=2000,jprev2=1, mprev2=1,anprev2=2000;
3822: double jpyram=1, mpyram=1,anpyram=2000,jpyram1=1, mpyram1=1,anpyram1=2000;
1.53 brouard 3823:
3824: double bage, fage, age, agelim, agebase;
3825: double ftolpl=FTOL;
3826: double **prlim;
3827: double *severity;
3828: double ***param; /* Matrix of parameters */
3829: double *p;
3830: double **matcov; /* Matrix of covariance */
3831: double ***delti3; /* Scale */
3832: double *delti; /* Scale */
3833: double ***eij, ***vareij;
3834: double **varpl; /* Variances of prevalence limits by age */
3835: double *epj, vepp;
3836: double kk1, kk2;
1.74 brouard 3837: double dateprev1, dateprev2,jproj1=1,mproj1=1,anproj1=2000,jproj2=1,mproj2=1,anproj2=2000;
1.53 brouard 3838:
3839: char *alph[]={"a","a","b","c","d","e"}, str[4];
3840:
3841:
3842: char z[1]="c", occ;
1.86 brouard 3843:
1.53 brouard 3844: char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];
1.88 brouard 3845: char strstart[80], *strt, strtend[80];
1.85 brouard 3846: char *stratrunc;
3847: int lstra;
3848:
3849: long total_usecs;
3850: struct timeval start_time, end_time, curr_time;
3851: struct timezone tzp;
3852: extern int gettimeofday();
3853: struct tm tmg, tm, *gmtime(), *localtime();
3854: long time_value;
3855: extern long time();
1.53 brouard 3856:
1.85 brouard 3857: /* gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */
3858: (void) gettimeofday(&start_time,&tzp);
3859: tm = *localtime(&start_time.tv_sec);
3860: tmg = *gmtime(&start_time.tv_sec);
1.88 brouard 3861: strcpy(strstart,asctime(&tm));
1.86 brouard 3862:
1.88 brouard 3863: /* printf("Localtime (at start)=%s",strstart); */
1.85 brouard 3864: /* tp.tv_sec = tp.tv_sec +86400; */
3865: /* tm = *localtime(&start_time.tv_sec); */
3866: /* tmg.tm_year=tmg.tm_year +dsign*dyear; */
3867: /* tmg.tm_mon=tmg.tm_mon +dsign*dmonth; */
3868: /* tmg.tm_hour=tmg.tm_hour + 1; */
3869: /* tp.tv_sec = mktime(&tmg); */
3870: /* strt=asctime(&tmg); */
1.88 brouard 3871: /* printf("Time(after) =%s",strstart); */
1.85 brouard 3872: /* (void) time (&time_value);
3873: * printf("time=%d,t-=%d\n",time_value,time_value-86400);
3874: * tm = *localtime(&time_value);
1.88 brouard 3875: * strstart=asctime(&tm);
3876: * printf("tim_value=%d,asctime=%s\n",time_value,strstart);
1.85 brouard 3877: */
3878:
1.53 brouard 3879: getcwd(pathcd, size);
3880:
1.81 brouard 3881: printf("\n%s\n%s",version,fullversion);
1.53 brouard 3882: if(argc <=1){
3883: printf("\nEnter the parameter file name: ");
3884: scanf("%s",pathtot);
3885: }
3886: else{
3887: strcpy(pathtot,argv[1]);
3888: }
1.88 brouard 3889: /*if(getcwd(pathcd, MAXLINE)!= NULL)printf ("Error pathcd\n");*/
1.53 brouard 3890: /*cygwin_split_path(pathtot,path,optionfile);
3891: printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/
3892: /* cutv(path,optionfile,pathtot,'\\');*/
3893:
3894: split(pathtot,path,optionfile,optionfilext,optionfilefiname);
1.85 brouard 3895: printf("pathtot=%s,\npath=%s,\noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
1.53 brouard 3896: chdir(path);
1.88 brouard 3897: strcpy(command,"mkdir ");
3898: strcat(command,optionfilefiname);
3899: if((outcmd=system(command)) != 0){
3900: printf("Problem creating directory or it already exists %s%s, err=%d\n",path,optionfilefiname,outcmd);
3901: /* fprintf(ficlog,"Problem creating directory %s%s\n",path,optionfilefiname); */
3902: /* fclose(ficlog); */
3903: /* exit(1); */
3904: }
3905: /* if((imk=mkdir(optionfilefiname))<0){ */
3906: /* perror("mkdir"); */
3907: /* } */
1.53 brouard 3908:
1.59 brouard 3909: /*-------- arguments in the command line --------*/
1.53 brouard 3910:
3911: /* Log file */
3912: strcat(filelog, optionfilefiname);
3913: strcat(filelog,".log"); /* */
3914: if((ficlog=fopen(filelog,"w"))==NULL) {
3915: printf("Problem with logfile %s\n",filelog);
3916: goto end;
3917: }
3918: fprintf(ficlog,"Log filename:%s\n",filelog);
1.85 brouard 3919: fprintf(ficlog,"\n%s\n%s",version,fullversion);
1.53 brouard 3920: fprintf(ficlog,"\nEnter the parameter file name: ");
1.88 brouard 3921: fprintf(ficlog,"pathtot=%s\n\
3922: path=%s \n\
3923: optionfile=%s\n\
3924: optionfilext=%s\n\
3925: optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
1.86 brouard 3926:
1.88 brouard 3927: printf("Localtime (at start):%s",strstart);
3928: fprintf(ficlog,"Localtime (at start): %s",strstart);
1.53 brouard 3929: fflush(ficlog);
3930:
3931: /* */
3932: strcpy(fileres,"r");
3933: strcat(fileres, optionfilefiname);
3934: strcat(fileres,".txt"); /* Other files have txt extension */
3935:
3936: /*---------arguments file --------*/
3937:
3938: if((ficpar=fopen(optionfile,"r"))==NULL) {
3939: printf("Problem with optionfile %s\n",optionfile);
3940: fprintf(ficlog,"Problem with optionfile %s\n",optionfile);
1.85 brouard 3941: fflush(ficlog);
1.53 brouard 3942: goto end;
3943: }
3944:
1.88 brouard 3945:
3946:
1.53 brouard 3947: strcpy(filereso,"o");
3948: strcat(filereso,fileres);
1.88 brouard 3949: if((ficparo=fopen(filereso,"w"))==NULL) { /* opened on subdirectory */
1.53 brouard 3950: printf("Problem with Output resultfile: %s\n", filereso);
3951: fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso);
1.85 brouard 3952: fflush(ficlog);
1.53 brouard 3953: goto end;
3954: }
3955:
3956: /* Reads comments: lines beginning with '#' */
1.85 brouard 3957: numlinepar=0;
1.53 brouard 3958: while((c=getc(ficpar))=='#' && c!= EOF){
3959: ungetc(c,ficpar);
3960: fgets(line, MAXLINE, ficpar);
1.85 brouard 3961: numlinepar++;
1.53 brouard 3962: puts(line);
3963: fputs(line,ficparo);
1.85 brouard 3964: fputs(line,ficlog);
1.53 brouard 3965: }
3966: ungetc(c,ficpar);
3967:
3968: 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 3969: numlinepar++;
1.53 brouard 3970: 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);
3971: 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 3972: 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);
3973: fflush(ficlog);
1.59 brouard 3974: while((c=getc(ficpar))=='#' && c!= EOF){
1.53 brouard 3975: ungetc(c,ficpar);
3976: fgets(line, MAXLINE, ficpar);
1.85 brouard 3977: numlinepar++;
1.53 brouard 3978: puts(line);
3979: fputs(line,ficparo);
1.85 brouard 3980: fputs(line,ficlog);
1.53 brouard 3981: }
3982: ungetc(c,ficpar);
1.85 brouard 3983:
1.53 brouard 3984:
3985: covar=matrix(0,NCOVMAX,1,n);
1.58 lievre 3986: cptcovn=0; /*Number of covariates, i.e. number of '+' in model statement*/
1.53 brouard 3987: if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;
3988:
1.58 lievre 3989: ncovmodel=2+cptcovn; /*Number of variables = cptcovn + intercept + age */
1.53 brouard 3990: nvar=ncovmodel-1; /* Suppressing age as a basic covariate */
1.88 brouard 3991:
3992: if(mle==-1){ /* Print a wizard for help writing covariance matrix */
3993: prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
3994: printf(" You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
3995: fprintf(ficlog," You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
3996: fclose (ficparo);
3997: fclose (ficlog);
3998: exit(0);
3999: }
1.53 brouard 4000: /* Read guess parameters */
4001: /* Reads comments: lines beginning with '#' */
4002: while((c=getc(ficpar))=='#' && c!= EOF){
4003: ungetc(c,ficpar);
4004: fgets(line, MAXLINE, ficpar);
1.85 brouard 4005: numlinepar++;
1.53 brouard 4006: puts(line);
4007: fputs(line,ficparo);
1.85 brouard 4008: fputs(line,ficlog);
1.53 brouard 4009: }
4010: ungetc(c,ficpar);
1.85 brouard 4011:
1.53 brouard 4012: param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
1.85 brouard 4013: for(i=1; i <=nlstate; i++){
4014: j=0;
4015: for(jj=1; jj <=nlstate+ndeath; jj++){
4016: if(jj==i) continue;
4017: j++;
1.53 brouard 4018: fscanf(ficpar,"%1d%1d",&i1,&j1);
1.85 brouard 4019: if ((i1 != i) && (j1 != j)){
4020: printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n",numlinepar, i,j, i1, j1);
4021: exit(1);
4022: }
1.53 brouard 4023: fprintf(ficparo,"%1d%1d",i1,j1);
4024: if(mle==1)
4025: printf("%1d%1d",i,j);
4026: fprintf(ficlog,"%1d%1d",i,j);
4027: for(k=1; k<=ncovmodel;k++){
4028: fscanf(ficpar," %lf",¶m[i][j][k]);
4029: if(mle==1){
4030: printf(" %lf",param[i][j][k]);
4031: fprintf(ficlog," %lf",param[i][j][k]);
4032: }
4033: else
4034: fprintf(ficlog," %lf",param[i][j][k]);
4035: fprintf(ficparo," %lf",param[i][j][k]);
4036: }
4037: fscanf(ficpar,"\n");
1.85 brouard 4038: numlinepar++;
1.53 brouard 4039: if(mle==1)
4040: printf("\n");
4041: fprintf(ficlog,"\n");
4042: fprintf(ficparo,"\n");
4043: }
1.85 brouard 4044: }
4045: fflush(ficlog);
4046:
1.59 brouard 4047: npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/
1.53 brouard 4048:
4049: p=param[1][1];
4050:
4051: /* Reads comments: lines beginning with '#' */
4052: while((c=getc(ficpar))=='#' && c!= EOF){
4053: ungetc(c,ficpar);
4054: fgets(line, MAXLINE, ficpar);
1.85 brouard 4055: numlinepar++;
1.53 brouard 4056: puts(line);
4057: fputs(line,ficparo);
1.85 brouard 4058: fputs(line,ficlog);
1.53 brouard 4059: }
4060: ungetc(c,ficpar);
4061:
4062: delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
1.74 brouard 4063: /* delti=vector(1,npar); *//* Scale of each paramater (output from hesscov) */
1.53 brouard 4064: for(i=1; i <=nlstate; i++){
4065: for(j=1; j <=nlstate+ndeath-1; j++){
4066: fscanf(ficpar,"%1d%1d",&i1,&j1);
1.85 brouard 4067: if ((i1-i)*(j1-j)!=0){
4068: printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n",numlinepar, i,j, i1, j1);
4069: exit(1);
4070: }
1.53 brouard 4071: printf("%1d%1d",i,j);
4072: fprintf(ficparo,"%1d%1d",i1,j1);
1.85 brouard 4073: fprintf(ficlog,"%1d%1d",i1,j1);
1.53 brouard 4074: for(k=1; k<=ncovmodel;k++){
4075: fscanf(ficpar,"%le",&delti3[i][j][k]);
4076: printf(" %le",delti3[i][j][k]);
4077: fprintf(ficparo," %le",delti3[i][j][k]);
1.85 brouard 4078: fprintf(ficlog," %le",delti3[i][j][k]);
1.53 brouard 4079: }
4080: fscanf(ficpar,"\n");
1.85 brouard 4081: numlinepar++;
1.53 brouard 4082: printf("\n");
4083: fprintf(ficparo,"\n");
1.85 brouard 4084: fprintf(ficlog,"\n");
1.53 brouard 4085: }
4086: }
1.85 brouard 4087: fflush(ficlog);
4088:
1.53 brouard 4089: delti=delti3[1][1];
1.74 brouard 4090:
4091:
4092: /* 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 4093:
4094: /* Reads comments: lines beginning with '#' */
4095: while((c=getc(ficpar))=='#' && c!= EOF){
4096: ungetc(c,ficpar);
4097: fgets(line, MAXLINE, ficpar);
1.85 brouard 4098: numlinepar++;
1.53 brouard 4099: puts(line);
4100: fputs(line,ficparo);
1.85 brouard 4101: fputs(line,ficlog);
1.53 brouard 4102: }
4103: ungetc(c,ficpar);
4104:
4105: matcov=matrix(1,npar,1,npar);
4106: for(i=1; i <=npar; i++){
4107: fscanf(ficpar,"%s",&str);
4108: if(mle==1)
4109: printf("%s",str);
4110: fprintf(ficlog,"%s",str);
4111: fprintf(ficparo,"%s",str);
4112: for(j=1; j <=i; j++){
4113: fscanf(ficpar," %le",&matcov[i][j]);
4114: if(mle==1){
4115: printf(" %.5le",matcov[i][j]);
4116: }
1.85 brouard 4117: fprintf(ficlog," %.5le",matcov[i][j]);
1.53 brouard 4118: fprintf(ficparo," %.5le",matcov[i][j]);
4119: }
4120: fscanf(ficpar,"\n");
1.85 brouard 4121: numlinepar++;
1.53 brouard 4122: if(mle==1)
4123: printf("\n");
4124: fprintf(ficlog,"\n");
4125: fprintf(ficparo,"\n");
4126: }
4127: for(i=1; i <=npar; i++)
4128: for(j=i+1;j<=npar;j++)
4129: matcov[i][j]=matcov[j][i];
4130:
4131: if(mle==1)
4132: printf("\n");
4133: fprintf(ficlog,"\n");
4134:
1.85 brouard 4135: fflush(ficlog);
1.53 brouard 4136:
1.59 brouard 4137: /*-------- Rewriting paramater file ----------*/
4138: strcpy(rfileres,"r"); /* "Rparameterfile */
4139: strcat(rfileres,optionfilefiname); /* Parameter file first name*/
4140: strcat(rfileres,"."); /* */
4141: strcat(rfileres,optionfilext); /* Other files have txt extension */
4142: if((ficres =fopen(rfileres,"w"))==NULL) {
4143: printf("Problem writing new parameter file: %s\n", fileres);goto end;
4144: fprintf(ficlog,"Problem writing new parameter file: %s\n", fileres);goto end;
4145: }
4146: fprintf(ficres,"#%s\n",version);
1.53 brouard 4147:
1.59 brouard 4148: /*-------- data file ----------*/
4149: if((fic=fopen(datafile,"r"))==NULL) {
4150: printf("Problem with datafile: %s\n", datafile);goto end;
4151: fprintf(ficlog,"Problem with datafile: %s\n", datafile);goto end;
4152: }
4153:
4154: n= lastobs;
4155: severity = vector(1,maxwav);
4156: outcome=imatrix(1,maxwav+1,1,n);
1.85 brouard 4157: num=lvector(1,n);
1.59 brouard 4158: moisnais=vector(1,n);
4159: annais=vector(1,n);
4160: moisdc=vector(1,n);
4161: andc=vector(1,n);
4162: agedc=vector(1,n);
4163: cod=ivector(1,n);
4164: weight=vector(1,n);
4165: for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */
4166: mint=matrix(1,maxwav,1,n);
4167: anint=matrix(1,maxwav,1,n);
4168: s=imatrix(1,maxwav+1,1,n);
4169: tab=ivector(1,NCOVMAX);
4170: ncodemax=ivector(1,8);
4171:
4172: i=1;
4173: while (fgets(line, MAXLINE, fic) != NULL) {
4174: if ((i >= firstobs) && (i <=lastobs)) {
1.53 brouard 4175:
1.59 brouard 4176: for (j=maxwav;j>=1;j--){
4177: cutv(stra, strb,line,' '); s[j][i]=atoi(strb);
4178: strcpy(line,stra);
4179: cutv(stra, strb,line,'/'); anint[j][i]=(double)(atoi(strb)); strcpy(line,stra);
4180: cutv(stra, strb,line,' '); mint[j][i]=(double)(atoi(strb)); strcpy(line,stra);
4181: }
1.53 brouard 4182:
1.59 brouard 4183: cutv(stra, strb,line,'/'); andc[i]=(double)(atoi(strb)); strcpy(line,stra);
4184: cutv(stra, strb,line,' '); moisdc[i]=(double)(atoi(strb)); strcpy(line,stra);
1.53 brouard 4185:
1.59 brouard 4186: cutv(stra, strb,line,'/'); annais[i]=(double)(atoi(strb)); strcpy(line,stra);
4187: cutv(stra, strb,line,' '); moisnais[i]=(double)(atoi(strb)); strcpy(line,stra);
1.53 brouard 4188:
1.59 brouard 4189: cutv(stra, strb,line,' '); weight[i]=(double)(atoi(strb)); strcpy(line,stra);
4190: for (j=ncovcol;j>=1;j--){
4191: cutv(stra, strb,line,' '); covar[j][i]=(double)(atoi(strb)); strcpy(line,stra);
4192: }
1.85 brouard 4193: lstra=strlen(stra);
4194: if(lstra > 9){ /* More than 2**32 or max of what printf can write with %ld */
4195: stratrunc = &(stra[lstra-9]);
4196: num[i]=atol(stratrunc);
4197: }
4198: else
4199: num[i]=atol(stra);
1.53 brouard 4200:
1.59 brouard 4201: /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){
1.85 brouard 4202: 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 4203:
1.59 brouard 4204: i=i+1;
4205: }
4206: }
4207: /* printf("ii=%d", ij);
4208: scanf("%d",i);*/
1.53 brouard 4209: imx=i-1; /* Number of individuals */
4210:
4211: /* for (i=1; i<=imx; i++){
4212: if ((s[1][i]==3) && (s[2][i]==2)) s[2][i]=3;
4213: if ((s[2][i]==3) && (s[3][i]==2)) s[3][i]=3;
4214: if ((s[3][i]==3) && (s[4][i]==2)) s[4][i]=3;
4215: }*/
4216: /* for (i=1; i<=imx; i++){
4217: if (s[4][i]==9) s[4][i]=-1;
1.85 brouard 4218: 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 4219:
1.71 brouard 4220: for (i=1; i<=imx; i++)
1.53 brouard 4221:
1.71 brouard 4222: /*if ((s[3][i]==3) || (s[4][i]==3)) weight[i]=0.08;
4223: else weight[i]=1;*/
4224:
1.53 brouard 4225: /* Calculation of the number of parameter from char model*/
4226: Tvar=ivector(1,15); /* stores the number n of the covariates in Vm+Vn at 1 and m at 2 */
4227: Tprod=ivector(1,15);
4228: Tvaraff=ivector(1,15);
4229: Tvard=imatrix(1,15,1,2);
4230: Tage=ivector(1,15);
4231:
1.58 lievre 4232: if (strlen(model) >1){ /* If there is at least 1 covariate */
1.53 brouard 4233: j=0, j1=0, k1=1, k2=1;
1.58 lievre 4234: j=nbocc(model,'+'); /* j=Number of '+' */
4235: j1=nbocc(model,'*'); /* j1=Number of '*' */
4236: cptcovn=j+1;
4237: cptcovprod=j1; /*Number of products */
1.53 brouard 4238:
4239: strcpy(modelsav,model);
4240: if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){
4241: printf("Error. Non available option model=%s ",model);
4242: fprintf(ficlog,"Error. Non available option model=%s ",model);
4243: goto end;
4244: }
4245:
1.59 brouard 4246: /* This loop fills the array Tvar from the string 'model'.*/
1.58 lievre 4247:
1.53 brouard 4248: for(i=(j+1); i>=1;i--){
4249: cutv(stra,strb,modelsav,'+'); /* keeps in strb after the last + */
1.59 brouard 4250: if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyzes it */
1.53 brouard 4251: /* printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/
4252: /*scanf("%d",i);*/
4253: if (strchr(strb,'*')) { /* Model includes a product */
4254: cutv(strd,strc,strb,'*'); /* strd*strc Vm*Vn (if not *age)*/
4255: if (strcmp(strc,"age")==0) { /* Vn*age */
4256: cptcovprod--;
4257: cutv(strb,stre,strd,'V');
4258: Tvar[i]=atoi(stre); /* computes n in Vn and stores in Tvar*/
4259: cptcovage++;
4260: Tage[cptcovage]=i;
4261: /*printf("stre=%s ", stre);*/
4262: }
4263: else if (strcmp(strd,"age")==0) { /* or age*Vn */
4264: cptcovprod--;
4265: cutv(strb,stre,strc,'V');
4266: Tvar[i]=atoi(stre);
4267: cptcovage++;
4268: Tage[cptcovage]=i;
4269: }
4270: else { /* Age is not in the model */
4271: cutv(strb,stre,strc,'V'); /* strc= Vn, stre is n*/
4272: Tvar[i]=ncovcol+k1;
4273: cutv(strb,strc,strd,'V'); /* strd was Vm, strc is m */
4274: Tprod[k1]=i;
4275: Tvard[k1][1]=atoi(strc); /* m*/
4276: Tvard[k1][2]=atoi(stre); /* n */
4277: Tvar[cptcovn+k2]=Tvard[k1][1];
4278: Tvar[cptcovn+k2+1]=Tvard[k1][2];
4279: for (k=1; k<=lastobs;k++)
4280: covar[ncovcol+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];
4281: k1++;
4282: k2=k2+2;
4283: }
4284: }
4285: else { /* no more sum */
4286: /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/
4287: /* scanf("%d",i);*/
4288: cutv(strd,strc,strb,'V');
4289: Tvar[i]=atoi(strc);
4290: }
4291: strcpy(modelsav,stra);
4292: /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);
4293: scanf("%d",i);*/
4294: } /* end of loop + */
4295: } /* end model */
4296:
1.58 lievre 4297: /*The number n of Vn is stored in Tvar. cptcovage =number of age covariate. Tage gives the position of age. cptcovprod= number of products.
4298: If model=V1+V1*age then Tvar[1]=1 Tvar[2]=1 cptcovage=1 Tage[1]=2 cptcovprod=0*/
4299:
1.53 brouard 4300: /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);
4301: printf("cptcovprod=%d ", cptcovprod);
4302: fprintf(ficlog,"cptcovprod=%d ", cptcovprod);
1.58 lievre 4303:
4304: scanf("%d ",i);
4305: fclose(fic);*/
1.53 brouard 4306:
4307: /* if(mle==1){*/
1.59 brouard 4308: if (weightopt != 1) { /* Maximisation without weights*/
4309: for(i=1;i<=n;i++) weight[i]=1.0;
4310: }
1.53 brouard 4311: /*-calculation of age at interview from date of interview and age at death -*/
1.59 brouard 4312: agev=matrix(1,maxwav,1,imx);
1.53 brouard 4313:
1.59 brouard 4314: for (i=1; i<=imx; i++) {
4315: for(m=2; (m<= maxwav); m++) {
1.76 brouard 4316: if (((int)mint[m][i]== 99) && (s[m][i] <= nlstate)){
1.59 brouard 4317: anint[m][i]=9999;
4318: s[m][i]=-1;
4319: }
1.76 brouard 4320: if((int)moisdc[i]==99 && (int)andc[i]==9999 && s[m][i]>nlstate){
1.85 brouard 4321: 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);
4322: 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 4323: s[m][i]=-1;
4324: }
4325: if((int)moisdc[i]==99 && (int)andc[i]!=9999 && s[m][i]>nlstate){
1.85 brouard 4326: 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]);
4327: 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 4328: s[m][i]=-1; /* We prefer to skip it (and to skip it in version 0.8a1 too */
1.76 brouard 4329: }
1.53 brouard 4330: }
1.59 brouard 4331: }
1.53 brouard 4332:
1.59 brouard 4333: for (i=1; i<=imx; i++) {
4334: agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);
1.71 brouard 4335: for(m=firstpass; (m<= lastpass); m++){
1.69 brouard 4336: if(s[m][i] >0){
1.59 brouard 4337: if (s[m][i] >= nlstate+1) {
4338: if(agedc[i]>0)
1.76 brouard 4339: if((int)moisdc[i]!=99 && (int)andc[i]!=9999)
1.69 brouard 4340: agev[m][i]=agedc[i];
1.59 brouard 4341: /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/
4342: else {
1.76 brouard 4343: if ((int)andc[i]!=9999){
1.85 brouard 4344: printf("Warning negative age at death: %ld line:%d\n",num[i],i);
4345: fprintf(ficlog,"Warning negative age at death: %ld line:%d\n",num[i],i);
1.59 brouard 4346: agev[m][i]=-1;
1.53 brouard 4347: }
4348: }
1.70 brouard 4349: }
1.69 brouard 4350: else if(s[m][i] !=9){ /* Standard case, age in fractional
4351: years but with the precision of a
4352: month */
1.59 brouard 4353: agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);
1.76 brouard 4354: if((int)mint[m][i]==99 || (int)anint[m][i]==9999)
1.59 brouard 4355: agev[m][i]=1;
4356: else if(agev[m][i] <agemin){
4357: agemin=agev[m][i];
4358: /*printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], agemin);*/
1.53 brouard 4359: }
1.59 brouard 4360: else if(agev[m][i] >agemax){
4361: agemax=agev[m][i];
4362: /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/
1.53 brouard 4363: }
1.59 brouard 4364: /*agev[m][i]=anint[m][i]-annais[i];*/
4365: /* agev[m][i] = age[i]+2*m;*/
1.53 brouard 4366: }
1.59 brouard 4367: else { /* =9 */
1.53 brouard 4368: agev[m][i]=1;
1.59 brouard 4369: s[m][i]=-1;
4370: }
1.53 brouard 4371: }
1.59 brouard 4372: else /*= 0 Unknown */
4373: agev[m][i]=1;
4374: }
1.53 brouard 4375:
1.59 brouard 4376: }
4377: for (i=1; i<=imx; i++) {
1.71 brouard 4378: for(m=firstpass; (m<=lastpass); m++){
1.59 brouard 4379: if (s[m][i] > (nlstate+ndeath)) {
4380: 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);
4381: 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);
4382: goto end;
1.53 brouard 4383: }
4384: }
1.59 brouard 4385: }
1.53 brouard 4386:
1.71 brouard 4387: /*for (i=1; i<=imx; i++){
4388: for (m=firstpass; (m<lastpass); m++){
1.85 brouard 4389: 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 4390: }
4391:
4392: }*/
4393:
1.59 brouard 4394: printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);
4395: fprintf(ficlog,"Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);
4396:
4397: free_vector(severity,1,maxwav);
4398: free_imatrix(outcome,1,maxwav+1,1,n);
4399: free_vector(moisnais,1,n);
4400: free_vector(annais,1,n);
4401: /* free_matrix(mint,1,maxwav,1,n);
4402: free_matrix(anint,1,maxwav,1,n);*/
4403: free_vector(moisdc,1,n);
4404: free_vector(andc,1,n);
1.53 brouard 4405:
4406:
1.59 brouard 4407: wav=ivector(1,imx);
4408: dh=imatrix(1,lastpass-firstpass+1,1,imx);
4409: bh=imatrix(1,lastpass-firstpass+1,1,imx);
4410: mw=imatrix(1,lastpass-firstpass+1,1,imx);
1.69 brouard 4411:
1.59 brouard 4412: /* Concatenates waves */
4413: concatwav(wav, dh, bh, mw, s, agedc, agev, firstpass, lastpass, imx, nlstate, stepm);
1.53 brouard 4414:
1.59 brouard 4415: /* Routine tricode is to calculate cptcoveff (real number of unique covariates) and to associate covariable number and modality */
1.53 brouard 4416:
1.59 brouard 4417: Tcode=ivector(1,100);
4418: nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);
4419: ncodemax[1]=1;
4420: if (cptcovn > 0) tricode(Tvar,nbcode,imx);
1.53 brouard 4421:
1.59 brouard 4422: codtab=imatrix(1,100,1,10); /* Cross tabulation to get the order of
4423: the estimations*/
4424: h=0;
4425: m=pow(2,cptcoveff);
1.53 brouard 4426:
1.59 brouard 4427: for(k=1;k<=cptcoveff; k++){
4428: for(i=1; i <=(m/pow(2,k));i++){
4429: for(j=1; j <= ncodemax[k]; j++){
4430: for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){
4431: h++;
4432: if (h>m) h=1;codtab[h][k]=j;codtab[h][Tvar[k]]=j;
4433: /* printf("h=%d k=%d j=%d codtab[h][k]=%d tvar[k]=%d \n",h, k,j,codtab[h][k],Tvar[k]);*/
4434: }
4435: }
4436: }
4437: }
4438: /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]);
4439: codtab[1][2]=1;codtab[2][2]=2; */
4440: /* for(i=1; i <=m ;i++){
4441: for(k=1; k <=cptcovn; k++){
4442: printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);
4443: }
4444: printf("\n");
1.53 brouard 4445: }
1.59 brouard 4446: scanf("%d",i);*/
1.53 brouard 4447:
1.86 brouard 4448: /*------------ gnuplot -------------*/
4449: strcpy(optionfilegnuplot,optionfilefiname);
4450: strcat(optionfilegnuplot,".gp");
4451: if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {
4452: printf("Problem with file %s",optionfilegnuplot);
4453: }
4454: else{
4455: fprintf(ficgp,"\n# %s\n", version);
4456: fprintf(ficgp,"# %s\n", optionfilegnuplot);
4457: fprintf(ficgp,"set missing 'NaNq'\n");
4458: }
1.88 brouard 4459: /* fclose(ficgp);*/
1.86 brouard 4460: /*--------- index.htm --------*/
4461:
1.87 brouard 4462: strcpy(optionfilehtm,optionfilefiname);
1.86 brouard 4463: strcat(optionfilehtm,".htm");
4464: if((fichtm=fopen(optionfilehtm,"w"))==NULL) {
4465: printf("Problem with %s \n",optionfilehtm), exit(0);
4466: }
4467:
1.87 brouard 4468: fprintf(fichtm,"<body>\n<title>IMaCh %s</title>\n <font size=\"2\">%s <br> %s</font> \
1.86 brouard 4469: <hr size=\"2\" color=\"#EC5E5E\"> \n\
4470: Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n\
4471: \n\
4472: <hr size=\"2\" color=\"#EC5E5E\">\
4473: <ul><li><h4>Parameter files</h4>\n\
4474: - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n\
4475: - Log file of the run: <a href=\"%s\">%s</a><br>\n\
1.87 brouard 4476: - Gnuplot file name: <a href=\"%s\">%s</a><br>\n\
1.86 brouard 4477: - Date and time at start: %s</ul>\n",\
1.87 brouard 4478: fileres,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt,\
1.86 brouard 4479: model,fileres,fileres,\
1.88 brouard 4480: filelog,filelog,optionfilegnuplot,optionfilegnuplot,strstart);
1.87 brouard 4481: /*fclose(fichtm);*/
4482: fflush(fichtm);
1.86 brouard 4483:
1.88 brouard 4484: strcpy(pathr,path);
4485: strcat(pathr,optionfilefiname);
4486: chdir(optionfilefiname); /* Move to directory named optionfile */
4487: strcpy(lfileres,fileres);
4488: strcat(lfileres,"/");
4489: strcat(lfileres,optionfilefiname);
4490:
1.59 brouard 4491: /* Calculates basic frequencies. Computes observed prevalence at single age
4492: and prints on file fileres'p'. */
1.84 brouard 4493: freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint);
1.53 brouard 4494:
1.88 brouard 4495: fprintf(fichtm,"\n");
4496: fprintf(fichtm,"<br>Total number of observations=%d <br>\n\
1.86 brouard 4497: Youngest age at first (selected) pass %.2f, oldest age %.2f<br>\n\
4498: Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n",\
1.88 brouard 4499: imx,agemin,agemax,jmin,jmax,jmean);
4500: pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
1.60 brouard 4501: oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
4502: newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
4503: savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
4504: oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */
1.53 brouard 4505:
4506:
1.59 brouard 4507: /* For Powell, parameters are in a vector p[] starting at p[1]
4508: so we point p on param[1][1] so that p[1] maps on param[1][1][1] */
4509: p=param[1][1]; /* *(*(*(param +1)+1)+0) */
1.53 brouard 4510:
1.86 brouard 4511: globpr=0; /* To get the number ipmx of contributions and the sum of weights*/
1.85 brouard 4512: likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
4513: printf("First Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
4514: for (k=1; k<=npar;k++)
4515: printf(" %d %8.5f",k,p[k]);
4516: printf("\n");
4517: globpr=1; /* to print the contributions */
4518: likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
4519: printf("Second Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
4520: for (k=1; k<=npar;k++)
4521: printf(" %d %8.5f",k,p[k]);
4522: printf("\n");
1.61 brouard 4523: if(mle>=1){ /* Could be 1 or 2 */
1.53 brouard 4524: mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);
1.59 brouard 4525: }
1.53 brouard 4526:
1.59 brouard 4527: /*--------- results files --------------*/
4528: 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 4529:
4530:
1.59 brouard 4531: jk=1;
4532: fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
4533: printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
4534: fprintf(ficlog,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
4535: for(i=1,jk=1; i <=nlstate; i++){
4536: for(k=1; k <=(nlstate+ndeath); k++){
4537: if (k != i)
4538: {
4539: printf("%d%d ",i,k);
4540: fprintf(ficlog,"%d%d ",i,k);
4541: fprintf(ficres,"%1d%1d ",i,k);
4542: for(j=1; j <=ncovmodel; j++){
4543: printf("%f ",p[jk]);
4544: fprintf(ficlog,"%f ",p[jk]);
4545: fprintf(ficres,"%f ",p[jk]);
4546: jk++;
4547: }
4548: printf("\n");
4549: fprintf(ficlog,"\n");
4550: fprintf(ficres,"\n");
4551: }
4552: }
4553: }
1.84 brouard 4554: if(mle!=0){
1.59 brouard 4555: /* Computing hessian and covariance matrix */
4556: ftolhess=ftol; /* Usually correct */
4557: hesscov(matcov, p, npar, delti, ftolhess, func);
4558: }
4559: fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");
4560: printf("# Scales (for hessian or gradient estimation)\n");
4561: fprintf(ficlog,"# Scales (for hessian or gradient estimation)\n");
4562: for(i=1,jk=1; i <=nlstate; i++){
4563: for(j=1; j <=nlstate+ndeath; j++){
4564: if (j!=i) {
4565: fprintf(ficres,"%1d%1d",i,j);
4566: printf("%1d%1d",i,j);
4567: fprintf(ficlog,"%1d%1d",i,j);
4568: for(k=1; k<=ncovmodel;k++){
4569: printf(" %.5e",delti[jk]);
4570: fprintf(ficlog," %.5e",delti[jk]);
4571: fprintf(ficres," %.5e",delti[jk]);
4572: jk++;
4573: }
4574: printf("\n");
4575: fprintf(ficlog,"\n");
4576: fprintf(ficres,"\n");
4577: }
4578: }
4579: }
1.53 brouard 4580:
1.59 brouard 4581: 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");
4582: if(mle==1)
4583: 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");
4584: 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");
4585: for(i=1,k=1;i<=npar;i++){
4586: /* if (k>nlstate) k=1;
4587: i1=(i-1)/(ncovmodel*nlstate)+1;
4588: fprintf(ficres,"%s%d%d",alph[k],i1,tab[i]);
4589: printf("%s%d%d",alph[k],i1,tab[i]);
4590: */
4591: fprintf(ficres,"%3d",i);
4592: if(mle==1)
4593: printf("%3d",i);
4594: fprintf(ficlog,"%3d",i);
4595: for(j=1; j<=i;j++){
4596: fprintf(ficres," %.5e",matcov[i][j]);
4597: if(mle==1)
4598: printf(" %.5e",matcov[i][j]);
4599: fprintf(ficlog," %.5e",matcov[i][j]);
4600: }
4601: fprintf(ficres,"\n");
4602: if(mle==1)
4603: printf("\n");
4604: fprintf(ficlog,"\n");
4605: k++;
4606: }
1.53 brouard 4607:
1.59 brouard 4608: while((c=getc(ficpar))=='#' && c!= EOF){
4609: ungetc(c,ficpar);
4610: fgets(line, MAXLINE, ficpar);
4611: puts(line);
4612: fputs(line,ficparo);
4613: }
4614: ungetc(c,ficpar);
4615:
4616: estepm=0;
4617: fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm);
4618: if (estepm==0 || estepm < stepm) estepm=stepm;
4619: if (fage <= 2) {
4620: bage = ageminpar;
4621: fage = agemaxpar;
4622: }
1.53 brouard 4623:
1.59 brouard 4624: fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");
4625: fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
4626: fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
1.53 brouard 4627:
1.59 brouard 4628: while((c=getc(ficpar))=='#' && c!= EOF){
4629: ungetc(c,ficpar);
4630: fgets(line, MAXLINE, ficpar);
4631: puts(line);
4632: fputs(line,ficparo);
4633: }
4634: ungetc(c,ficpar);
1.53 brouard 4635:
1.59 brouard 4636: 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);
4637: 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);
4638: 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 4639: printf("begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
4640: 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 4641:
1.59 brouard 4642: while((c=getc(ficpar))=='#' && c!= EOF){
4643: ungetc(c,ficpar);
4644: fgets(line, MAXLINE, ficpar);
4645: puts(line);
4646: fputs(line,ficparo);
4647: }
4648: ungetc(c,ficpar);
1.53 brouard 4649:
4650:
1.70 brouard 4651: dateprev1=anprev1+(mprev1-1)/12.+(jprev1-1)/365.;
4652: dateprev2=anprev2+(mprev2-1)/12.+(jprev2-1)/365.;
1.53 brouard 4653:
4654: fscanf(ficpar,"pop_based=%d\n",&popbased);
4655: fprintf(ficparo,"pop_based=%d\n",popbased);
4656: fprintf(ficres,"pop_based=%d\n",popbased);
4657:
4658: while((c=getc(ficpar))=='#' && c!= EOF){
4659: ungetc(c,ficpar);
4660: fgets(line, MAXLINE, ficpar);
4661: puts(line);
4662: fputs(line,ficparo);
4663: }
4664: ungetc(c,ficpar);
4665:
1.69 brouard 4666: 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 4667: 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 4668: 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);
4669: 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);
4670: 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 4671: /* day and month of proj2 are not used but only year anproj2.*/
1.53 brouard 4672:
1.59 brouard 4673: while((c=getc(ficpar))=='#' && c!= EOF){
1.53 brouard 4674: ungetc(c,ficpar);
4675: fgets(line, MAXLINE, ficpar);
4676: puts(line);
4677: fputs(line,ficparo);
4678: }
4679: ungetc(c,ficpar);
4680:
4681: fscanf(ficpar,"popforecast=%d popfile=%s popfiledate=%lf/%lf/%lf last-popfiledate=%lf/%lf/%lf\n",&popforecast,popfile,&jpyram,&mpyram,&anpyram,&jpyram1,&mpyram1,&anpyram1);
4682: fprintf(ficparo,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);
4683: fprintf(ficres,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);
4684:
1.86 brouard 4685: /* freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint);*/
1.84 brouard 4686: /*,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
1.58 lievre 4687:
1.89 ! brouard 4688: replace_back_to_slash(pathc,path); /* Even gnuplot wants a / */
! 4689: printinggnuplot(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
1.53 brouard 4690:
1.85 brouard 4691: printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,\
4692: model,imx,jmin,jmax,jmean,rfileres,popforecast,estepm,\
4693: jprev1,mprev1,anprev1,jprev2,mprev2,anprev2);
1.53 brouard 4694:
1.59 brouard 4695: /*------------ free_vector -------------*/
1.88 brouard 4696: /* chdir(path); */
1.53 brouard 4697:
1.59 brouard 4698: free_ivector(wav,1,imx);
4699: free_imatrix(dh,1,lastpass-firstpass+1,1,imx);
4700: free_imatrix(bh,1,lastpass-firstpass+1,1,imx);
4701: free_imatrix(mw,1,lastpass-firstpass+1,1,imx);
1.85 brouard 4702: free_lvector(num,1,n);
1.59 brouard 4703: free_vector(agedc,1,n);
1.65 lievre 4704: /*free_matrix(covar,0,NCOVMAX,1,n);*/
1.59 brouard 4705: /*free_matrix(covar,1,NCOVMAX,1,n);*/
4706: fclose(ficparo);
4707: fclose(ficres);
1.53 brouard 4708:
4709:
1.54 brouard 4710: /*--------------- Prevalence limit (stable prevalence) --------------*/
1.53 brouard 4711:
4712: strcpy(filerespl,"pl");
4713: strcat(filerespl,fileres);
4714: if((ficrespl=fopen(filerespl,"w"))==NULL) {
1.54 brouard 4715: printf("Problem with stable prevalence resultfile: %s\n", filerespl);goto end;
4716: fprintf(ficlog,"Problem with stable prevalence resultfile: %s\n", filerespl);goto end;
1.53 brouard 4717: }
1.54 brouard 4718: printf("Computing stable prevalence: result on file '%s' \n", filerespl);
4719: fprintf(ficlog,"Computing stable prevalence: result on file '%s' \n", filerespl);
4720: fprintf(ficrespl,"#Stable prevalence \n");
1.53 brouard 4721: fprintf(ficrespl,"#Age ");
4722: for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);
4723: fprintf(ficrespl,"\n");
4724:
4725: prlim=matrix(1,nlstate,1,nlstate);
1.59 brouard 4726:
1.53 brouard 4727: agebase=ageminpar;
4728: agelim=agemaxpar;
4729: ftolpl=1.e-10;
4730: i1=cptcoveff;
4731: if (cptcovn < 1){i1=1;}
4732:
1.59 brouard 4733: for(cptcov=1,k=0;cptcov<=i1;cptcov++){
1.53 brouard 4734: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
1.59 brouard 4735: k=k+1;
4736: /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/
4737: fprintf(ficrespl,"\n#******");
4738: printf("\n#******");
4739: fprintf(ficlog,"\n#******");
4740: for(j=1;j<=cptcoveff;j++) {
4741: fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
4742: printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
4743: fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
4744: }
4745: fprintf(ficrespl,"******\n");
4746: printf("******\n");
4747: fprintf(ficlog,"******\n");
1.53 brouard 4748:
1.59 brouard 4749: for (age=agebase; age<=agelim; age++){
4750: prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
1.69 brouard 4751: fprintf(ficrespl,"%.0f ",age );
4752: for(j=1;j<=cptcoveff;j++)
4753: fprintf(ficrespl,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
1.59 brouard 4754: for(i=1; i<=nlstate;i++)
1.53 brouard 4755: fprintf(ficrespl," %.5f", prlim[i][i]);
1.59 brouard 4756: fprintf(ficrespl,"\n");
1.53 brouard 4757: }
4758: }
1.59 brouard 4759: }
1.53 brouard 4760: fclose(ficrespl);
4761:
4762: /*------------- h Pij x at various ages ------------*/
4763:
4764: strcpy(filerespij,"pij"); strcat(filerespij,fileres);
4765: if((ficrespij=fopen(filerespij,"w"))==NULL) {
4766: printf("Problem with Pij resultfile: %s\n", filerespij);goto end;
4767: fprintf(ficlog,"Problem with Pij resultfile: %s\n", filerespij);goto end;
4768: }
4769: printf("Computing pij: result on file '%s' \n", filerespij);
4770: fprintf(ficlog,"Computing pij: result on file '%s' \n", filerespij);
4771:
4772: stepsize=(int) (stepm+YEARM-1)/YEARM;
4773: /*if (stepm<=24) stepsize=2;*/
4774:
4775: agelim=AGESUP;
4776: hstepm=stepsize*YEARM; /* Every year of age */
4777: hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */
4778:
4779: /* hstepm=1; aff par mois*/
4780:
1.70 brouard 4781: fprintf(ficrespij,"#****** h Pij x Probability to be in state j at age x+h being in i at x ");
1.59 brouard 4782: for(cptcov=1,k=0;cptcov<=i1;cptcov++){
1.53 brouard 4783: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
4784: k=k+1;
1.59 brouard 4785: fprintf(ficrespij,"\n#****** ");
4786: for(j=1;j<=cptcoveff;j++)
4787: fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
4788: fprintf(ficrespij,"******\n");
1.53 brouard 4789:
1.59 brouard 4790: for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */
4791: nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
4792: nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
4793:
4794: /* nhstepm=nhstepm*YEARM; aff par mois*/
4795:
4796: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4797: oldm=oldms;savm=savms;
4798: hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
1.70 brouard 4799: fprintf(ficrespij,"# Cov Agex agex+h hpijx with i,j=");
1.59 brouard 4800: for(i=1; i<=nlstate;i++)
4801: for(j=1; j<=nlstate+ndeath;j++)
4802: fprintf(ficrespij," %1d-%1d",i,j);
4803: fprintf(ficrespij,"\n");
4804: for (h=0; h<=nhstepm; h++){
1.70 brouard 4805: fprintf(ficrespij,"%d %3.f %3.f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );
1.53 brouard 4806: for(i=1; i<=nlstate;i++)
4807: for(j=1; j<=nlstate+ndeath;j++)
1.59 brouard 4808: fprintf(ficrespij," %.5f", p3mat[i][j][h]);
1.53 brouard 4809: fprintf(ficrespij,"\n");
4810: }
1.59 brouard 4811: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4812: fprintf(ficrespij,"\n");
4813: }
1.53 brouard 4814: }
4815: }
4816:
1.74 brouard 4817: varprob(optionfilefiname, matcov, p, delti, nlstate, bage, fage,k,Tvar,nbcode, ncodemax);
1.53 brouard 4818:
4819: fclose(ficrespij);
4820:
1.84 brouard 4821: probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
1.53 brouard 4822:
4823: /*---------- Forecasting ------------------*/
1.69 brouard 4824: /*if((stepm == 1) && (strcmp(model,".")==0)){*/
4825: if(prevfcast==1){
1.74 brouard 4826: /* if(stepm ==1){*/
1.70 brouard 4827: prevforecast(fileres, anproj1, mproj1, jproj1, agemin, agemax, dateprev1, dateprev2, mobilavproj, bage, fage, firstpass, lastpass, anproj2, p, cptcoveff);
1.74 brouard 4828: /* (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);*/
4829: /* } */
4830: /* else{ */
4831: /* erreur=108; */
4832: /* 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); */
4833: /* 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); */
4834: /* } */
1.69 brouard 4835: }
1.53 brouard 4836:
4837:
4838: /*---------- Health expectancies and variances ------------*/
4839:
4840: strcpy(filerest,"t");
4841: strcat(filerest,fileres);
4842: if((ficrest=fopen(filerest,"w"))==NULL) {
4843: printf("Problem with total LE resultfile: %s\n", filerest);goto end;
4844: fprintf(ficlog,"Problem with total LE resultfile: %s\n", filerest);goto end;
4845: }
4846: printf("Computing Total LEs with variances: file '%s' \n", filerest);
4847: fprintf(ficlog,"Computing Total LEs with variances: file '%s' \n", filerest);
4848:
4849:
4850: strcpy(filerese,"e");
4851: strcat(filerese,fileres);
4852: if((ficreseij=fopen(filerese,"w"))==NULL) {
4853: printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
4854: fprintf(ficlog,"Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
4855: }
4856: printf("Computing Health Expectancies: result on file '%s' \n", filerese);
4857: fprintf(ficlog,"Computing Health Expectancies: result on file '%s' \n", filerese);
1.68 lievre 4858:
1.53 brouard 4859: strcpy(fileresv,"v");
4860: strcat(fileresv,fileres);
4861: if((ficresvij=fopen(fileresv,"w"))==NULL) {
4862: printf("Problem with variance resultfile: %s\n", fileresv);exit(0);
4863: fprintf(ficlog,"Problem with variance resultfile: %s\n", fileresv);exit(0);
4864: }
4865: printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
4866: fprintf(ficlog,"Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
1.58 lievre 4867:
1.74 brouard 4868: /* Computes prevalence between agemin (i.e minimal age computed) and no more ageminpar */
1.84 brouard 4869: prevalence(probs, agemin, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
1.74 brouard 4870: /* 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",\
4871: ageminpar, agemax, s[lastpass][imx], agev[lastpass][imx], nlstate, imx, mint[lastpass][imx],anint[lastpass][imx], dateprev1, dateprev2, firstpass, lastpass);
4872: */
1.58 lievre 4873:
1.54 brouard 4874: if (mobilav!=0) {
1.53 brouard 4875: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
1.54 brouard 4876: if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
4877: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
4878: printf(" Error in movingaverage mobilav=%d\n",mobilav);
4879: }
1.53 brouard 4880: }
4881:
1.59 brouard 4882: for(cptcov=1,k=0;cptcov<=i1;cptcov++){
1.53 brouard 4883: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
4884: k=k+1;
4885: fprintf(ficrest,"\n#****** ");
4886: for(j=1;j<=cptcoveff;j++)
4887: fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
4888: fprintf(ficrest,"******\n");
4889:
4890: fprintf(ficreseij,"\n#****** ");
4891: for(j=1;j<=cptcoveff;j++)
4892: fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
4893: fprintf(ficreseij,"******\n");
4894:
4895: fprintf(ficresvij,"\n#****** ");
4896: for(j=1;j<=cptcoveff;j++)
4897: fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
4898: fprintf(ficresvij,"******\n");
4899:
4900: eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
4901: oldm=oldms;savm=savms;
4902: evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov);
4903:
4904: vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
4905: oldm=oldms;savm=savms;
4906: varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,0, mobilav);
4907: if(popbased==1){
4908: 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 4909: }
1.53 brouard 4910:
4911:
4912: fprintf(ficrest,"#Total LEs with variances: e.. (std) ");
4913: for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);
4914: fprintf(ficrest,"\n");
4915:
4916: epj=vector(1,nlstate+1);
4917: for(age=bage; age <=fage ;age++){
4918: prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
4919: if (popbased==1) {
1.54 brouard 4920: if(mobilav ==0){
1.53 brouard 4921: for(i=1; i<=nlstate;i++)
4922: prlim[i][i]=probs[(int)age][i][k];
1.54 brouard 4923: }else{ /* mobilav */
1.53 brouard 4924: for(i=1; i<=nlstate;i++)
4925: prlim[i][i]=mobaverage[(int)age][i][k];
4926: }
4927: }
4928:
4929: fprintf(ficrest," %4.0f",age);
4930: for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){
4931: for(i=1, epj[j]=0.;i <=nlstate;i++) {
4932: epj[j] += prlim[i][i]*eij[i][j][(int)age];
4933: /* printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/
4934: }
4935: epj[nlstate+1] +=epj[j];
4936: }
4937:
4938: for(i=1, vepp=0.;i <=nlstate;i++)
4939: for(j=1;j <=nlstate;j++)
4940: vepp += vareij[i][j][(int)age];
4941: fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));
4942: for(j=1;j <=nlstate;j++){
4943: fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));
4944: }
4945: fprintf(ficrest,"\n");
4946: }
1.59 brouard 4947: free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
4948: free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);
4949: free_vector(epj,1,nlstate+1);
1.53 brouard 4950: }
4951: }
1.59 brouard 4952: free_vector(weight,1,n);
4953: free_imatrix(Tvard,1,15,1,2);
4954: free_imatrix(s,1,maxwav+1,1,n);
4955: free_matrix(anint,1,maxwav,1,n);
4956: free_matrix(mint,1,maxwav,1,n);
4957: free_ivector(cod,1,n);
4958: free_ivector(tab,1,NCOVMAX);
1.53 brouard 4959: fclose(ficreseij);
4960: fclose(ficresvij);
4961: fclose(ficrest);
4962: fclose(ficpar);
4963:
1.54 brouard 4964: /*------- Variance of stable prevalence------*/
1.53 brouard 4965:
4966: strcpy(fileresvpl,"vpl");
4967: strcat(fileresvpl,fileres);
4968: if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {
1.54 brouard 4969: printf("Problem with variance of stable prevalence resultfile: %s\n", fileresvpl);
1.53 brouard 4970: exit(0);
4971: }
1.54 brouard 4972: printf("Computing Variance-covariance of stable prevalence: file '%s' \n", fileresvpl);
1.53 brouard 4973:
1.59 brouard 4974: for(cptcov=1,k=0;cptcov<=i1;cptcov++){
1.53 brouard 4975: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
4976: k=k+1;
4977: fprintf(ficresvpl,"\n#****** ");
4978: for(j=1;j<=cptcoveff;j++)
4979: fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
4980: fprintf(ficresvpl,"******\n");
4981:
4982: varpl=matrix(1,nlstate,(int) bage, (int) fage);
4983: oldm=oldms;savm=savms;
1.59 brouard 4984: varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);
4985: free_matrix(varpl,1,nlstate,(int) bage, (int)fage);
1.53 brouard 4986: }
1.59 brouard 4987: }
1.53 brouard 4988:
4989: fclose(ficresvpl);
4990:
4991: /*---------- End : free ----------------*/
4992: free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);
4993: free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);
4994: free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);
4995: free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);
1.65 lievre 4996:
4997: free_matrix(covar,0,NCOVMAX,1,n);
1.53 brouard 4998: free_matrix(matcov,1,npar,1,npar);
1.74 brouard 4999: /*free_vector(delti,1,npar);*/
5000: free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
1.53 brouard 5001: free_matrix(agev,1,maxwav,1,imx);
5002: free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
1.54 brouard 5003: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
1.74 brouard 5004: free_ma3x(probs,1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
5005:
1.59 brouard 5006: free_ivector(ncodemax,1,8);
5007: free_ivector(Tvar,1,15);
5008: free_ivector(Tprod,1,15);
5009: free_ivector(Tvaraff,1,15);
5010: free_ivector(Tage,1,15);
5011: free_ivector(Tcode,1,100);
1.53 brouard 5012:
1.88 brouard 5013: fflush(fichtm);
5014: fflush(ficgp);
1.53 brouard 5015:
5016:
5017: if(erreur >0){
5018: printf("End of Imach with error or warning %d\n",erreur);
5019: fprintf(ficlog,"End of Imach with error or warning %d\n",erreur);
5020: }else{
5021: printf("End of Imach\n");
5022: fprintf(ficlog,"End of Imach\n");
5023: }
5024: printf("See log file on %s\n",filelog);
5025: fclose(ficlog);
5026: /* gettimeofday(&end_time, (struct timezone*)0);*/ /* after time */
1.85 brouard 5027: (void) gettimeofday(&end_time,&tzp);
5028: tm = *localtime(&end_time.tv_sec);
5029: tmg = *gmtime(&end_time.tv_sec);
1.88 brouard 5030: strcpy(strtend,asctime(&tm));
5031: printf("Localtime at start %s\nLocaltime at end %s",strstart, strtend);
5032: fprintf(ficlog,"Localtime at start %s\nLocal time at end %s",strstart, strtend);
1.85 brouard 5033: /* printf("Total time used %d Sec\n", asc_time(end_time.tv_sec -start_time.tv_sec);*/
5034:
5035: 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);
5036: 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);
5037: /* printf("Total time was %d uSec.\n", total_usecs);*/
1.87 brouard 5038: /* if(fileappend(fichtm,optionfilehtm)){ */
1.88 brouard 5039: fprintf(fichtm,"<br>Local time at start %s<br>Local time at end %s<br>",strstart, strtend);
1.87 brouard 5040: fclose(fichtm);
1.88 brouard 5041: fclose(ficgp);
1.53 brouard 5042: /*------ End -----------*/
5043:
1.59 brouard 5044: end:
1.53 brouard 5045: #ifdef windows
5046: /* chdir(pathcd);*/
5047: #endif
1.88 brouard 5048: chdir(path);
1.53 brouard 5049: /*system("wgnuplot graph.plt");*/
5050: /*system("../gp37mgw/wgnuplot graph.plt");*/
5051: /*system("cd ../gp37mgw");*/
5052: /* system("..\\gp37mgw\\wgnuplot graph.plt");*/
1.59 brouard 5053: strcpy(plotcmd,GNUPLOTPROGRAM);
5054: strcat(plotcmd," ");
5055: strcat(plotcmd,optionfilegnuplot);
1.75 brouard 5056: printf("Starting graphs with: %s",plotcmd);fflush(stdout);
1.59 brouard 5057: system(plotcmd);
1.75 brouard 5058: printf(" Wait...");
1.53 brouard 5059:
1.54 brouard 5060: /*#ifdef windows*/
1.53 brouard 5061: while (z[0] != 'q') {
5062: /* chdir(path); */
5063: printf("\nType e to edit output files, g to graph again, c to start again, and q for exiting: ");
5064: scanf("%s",z);
5065: if (z[0] == 'c') system("./imach");
5066: else if (z[0] == 'e') system(optionfilehtm);
5067: else if (z[0] == 'g') system(plotcmd);
5068: else if (z[0] == 'q') exit(0);
5069: }
1.54 brouard 5070: /*#endif */
1.53 brouard 5071: }
1.88 brouard 5072:
1.53 brouard 5073:
5074:
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