Annotation of imach096d/src/imach.c, revision 1.92
1.92 ! brouard 1: /* $Id: imach.c,v 1.91 2003/06/25 15:30:29 brouard Exp $
1.83 lievre 2: $State: Exp $
3: $Log: imach.c,v $
1.92 ! brouard 4: Revision 1.91 2003/06/25 15:30:29 brouard
! 5: * imach.c (Repository): Duplicated warning errors corrected.
! 6: (Repository): Elapsed time after each iteration is now output. It
! 7: helps to forecast when convergence will be reached. Elapsed time
! 8: is stamped in powell. We created a new html file for the graphs
! 9: concerning matrix of covariance. It has extension -cov.htm.
! 10:
1.91 brouard 11: Revision 1.90 2003/06/24 12:34:15 brouard
12: (Module): Some bugs corrected for windows. Also, when
13: mle=-1 a template is output in file "or"mypar.txt with the design
14: of the covariance matrix to be input.
15:
1.90 brouard 16: Revision 1.89 2003/06/24 12:30:52 brouard
17: (Module): Some bugs corrected for windows. Also, when
18: mle=-1 a template is output in file "or"mypar.txt with the design
19: of the covariance matrix to be input.
20:
1.89 brouard 21: Revision 1.88 2003/06/23 17:54:56 brouard
22: * 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.
23:
1.88 brouard 24: Revision 1.87 2003/06/18 12:26:01 brouard
25: Version 0.96
26:
1.87 brouard 27: Revision 1.86 2003/06/17 20:04:08 brouard
28: (Module): Change position of html and gnuplot routines and added
29: routine fileappend.
30:
1.86 brouard 31: Revision 1.85 2003/06/17 13:12:43 brouard
32: * imach.c (Repository): Check when date of death was earlier that
33: current date of interview. It may happen when the death was just
34: prior to the death. In this case, dh was negative and likelihood
35: was wrong (infinity). We still send an "Error" but patch by
36: assuming that the date of death was just one stepm after the
37: interview.
38: (Repository): Because some people have very long ID (first column)
39: we changed int to long in num[] and we added a new lvector for
40: memory allocation. But we also truncated to 8 characters (left
41: truncation)
42: (Repository): No more line truncation errors.
43:
1.85 brouard 44: Revision 1.84 2003/06/13 21:44:43 brouard
45: * imach.c (Repository): Replace "freqsummary" at a correct
46: place. It differs from routine "prevalence" which may be called
47: many times. Probs is memory consuming and must be used with
48: parcimony.
1.86 brouard 49: Version 0.95a3 (should output exactly the same maximization than 0.8a2)
1.85 brouard 50:
1.84 brouard 51: Revision 1.83 2003/06/10 13:39:11 lievre
52: *** empty log message ***
53:
1.83 lievre 54: Revision 1.82 2003/06/05 15:57:20 brouard
55: Add log in imach.c and fullversion number is now printed.
56:
1.82 brouard 57: */
58: /*
1.53 brouard 59: Interpolated Markov Chain
60:
61: Short summary of the programme:
62:
63: This program computes Healthy Life Expectancies from
64: cross-longitudinal data. Cross-longitudinal data consist in: -1- a
65: first survey ("cross") where individuals from different ages are
66: interviewed on their health status or degree of disability (in the
67: case of a health survey which is our main interest) -2- at least a
68: second wave of interviews ("longitudinal") which measure each change
69: (if any) in individual health status. Health expectancies are
70: computed from the time spent in each health state according to a
71: model. More health states you consider, more time is necessary to reach the
72: Maximum Likelihood of the parameters involved in the model. The
73: simplest model is the multinomial logistic model where pij is the
74: probability to be observed in state j at the second wave
75: conditional to be observed in state i at the first wave. Therefore
76: the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where
77: 'age' is age and 'sex' is a covariate. If you want to have a more
78: complex model than "constant and age", you should modify the program
79: where the markup *Covariates have to be included here again* invites
80: you to do it. More covariates you add, slower the
81: convergence.
82:
83: The advantage of this computer programme, compared to a simple
84: multinomial logistic model, is clear when the delay between waves is not
85: identical for each individual. Also, if a individual missed an
86: intermediate interview, the information is lost, but taken into
87: account using an interpolation or extrapolation.
88:
89: hPijx is the probability to be observed in state i at age x+h
90: conditional to the observed state i at age x. The delay 'h' can be
91: split into an exact number (nh*stepm) of unobserved intermediate
1.66 brouard 92: states. This elementary transition (by month, quarter,
93: semester or year) is modelled as a multinomial logistic. The hPx
1.53 brouard 94: matrix is simply the matrix product of nh*stepm elementary matrices
95: and the contribution of each individual to the likelihood is simply
96: hPijx.
97:
98: Also this programme outputs the covariance matrix of the parameters but also
1.54 brouard 99: of the life expectancies. It also computes the stable prevalence.
1.53 brouard 100:
101: Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).
102: Institut national d'études démographiques, Paris.
103: This software have been partly granted by Euro-REVES, a concerted action
104: from the European Union.
105: It is copyrighted identically to a GNU software product, ie programme and
106: software can be distributed freely for non commercial use. Latest version
107: can be accessed at http://euroreves.ined.fr/imach .
1.74 brouard 108:
109: Help to debug: LD_PRELOAD=/usr/local/lib/libnjamd.so ./imach foo.imach
110: or better on gdb : set env LD_PRELOAD=/usr/local/lib/libnjamd.so
111:
1.53 brouard 112: **********************************************************************/
1.74 brouard 113: /*
114: main
115: read parameterfile
116: read datafile
117: concatwav
1.84 brouard 118: freqsummary
1.74 brouard 119: if (mle >= 1)
120: mlikeli
121: print results files
122: if mle==1
123: computes hessian
124: read end of parameter file: agemin, agemax, bage, fage, estepm
125: begin-prev-date,...
126: open gnuplot file
127: open html file
128: stable prevalence
129: for age prevalim()
130: h Pij x
131: variance of p varprob
132: forecasting if prevfcast==1 prevforecast call prevalence()
133: health expectancies
134: Variance-covariance of DFLE
135: prevalence()
136: movingaverage()
137: varevsij()
138: if popbased==1 varevsij(,popbased)
139: total life expectancies
140: Variance of stable prevalence
141: end
142: */
143:
144:
145:
1.53 brouard 146:
147: #include <math.h>
148: #include <stdio.h>
149: #include <stdlib.h>
150: #include <unistd.h>
151:
1.86 brouard 152: #include <sys/time.h>
153: #include <time.h>
154: #include "timeval.h"
155:
1.53 brouard 156: #define MAXLINE 256
157: #define GNUPLOTPROGRAM "gnuplot"
158: /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
1.85 brouard 159: #define FILENAMELENGTH 132
1.53 brouard 160: /*#define DEBUG*/
1.85 brouard 161: /*#define windows*/
1.53 brouard 162: #define GLOCK_ERROR_NOPATH -1 /* empty path */
163: #define GLOCK_ERROR_GETCWD -2 /* cannot get cwd */
164:
165: #define MAXPARM 30 /* Maximum number of parameters for the optimization */
166: #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */
167:
168: #define NINTERVMAX 8
169: #define NLSTATEMAX 8 /* Maximum number of live states (for func) */
170: #define NDEATHMAX 8 /* Maximum number of dead states (for func) */
171: #define NCOVMAX 8 /* Maximum number of covariates */
172: #define MAXN 20000
173: #define YEARM 12. /* Number of months per year */
174: #define AGESUP 130
175: #define AGEBASE 40
1.85 brouard 176: #ifdef unix
177: #define DIRSEPARATOR '/'
178: #define ODIRSEPARATOR '\\'
179: #else
1.53 brouard 180: #define DIRSEPARATOR '\\'
181: #define ODIRSEPARATOR '/'
182: #endif
183:
1.92 ! brouard 184: /* $Id: imach.c,v 1.91 2003/06/25 15:30:29 brouard Exp $ */
1.81 brouard 185: /* $State: Exp $ */
1.80 brouard 186:
1.88 brouard 187: char version[]="Imach version 0.96a, June 2003, INED-EUROREVES ";
1.92 ! brouard 188: char fullversion[]="$Revision: 1.91 $ $Date: 2003/06/25 15:30:29 $";
1.91 brouard 189: int erreur, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings */
1.53 brouard 190: int nvar;
191: int cptcovn=0, cptcovage=0, cptcoveff=0,cptcov;
192: int npar=NPARMAX;
193: int nlstate=2; /* Number of live states */
194: int ndeath=1; /* Number of dead states */
195: int ncovmodel, ncovcol; /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
196: int popbased=0;
197:
198: int *wav; /* Number of waves for this individuual 0 is possible */
199: int maxwav; /* Maxim number of waves */
200: int jmin, jmax; /* min, max spacing between 2 waves */
1.87 brouard 201: int gipmx, gsw; /* Global variables on the number of contributions
202: to the likelihood and the sum of weights (done by funcone)*/
1.53 brouard 203: int mle, weightopt;
204: int **mw; /* mw[mi][i] is number of the mi wave for this individual */
205: int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
1.59 brouard 206: int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between
207: * wave mi and wave mi+1 is not an exact multiple of stepm. */
1.53 brouard 208: double jmean; /* Mean space between 2 waves */
209: double **oldm, **newm, **savm; /* Working pointers to matrices */
210: double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
211: FILE *fic,*ficpar, *ficparo,*ficres, *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
1.76 brouard 212: FILE *ficlog, *ficrespow;
1.85 brouard 213: int globpr; /* Global variable for printing or not */
214: double fretone; /* Only one call to likelihood */
215: long ipmx; /* Number of contributions */
216: double sw; /* Sum of weights */
217: char fileresilk[FILENAMELENGTH]; /* File of individual contributions to the likelihood */
218: FILE *ficresilk;
1.53 brouard 219: FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
220: FILE *ficresprobmorprev;
1.91 brouard 221: FILE *fichtm, *fichtmcov; /* Html File */
1.53 brouard 222: FILE *ficreseij;
223: char filerese[FILENAMELENGTH];
224: FILE *ficresvij;
225: char fileresv[FILENAMELENGTH];
226: FILE *ficresvpl;
227: char fileresvpl[FILENAMELENGTH];
228: char title[MAXLINE];
229: char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH], filerespl[FILENAMELENGTH];
230: char optionfilext[10], optionfilefiname[FILENAMELENGTH], plotcmd[FILENAMELENGTH];
1.88 brouard 231: char tmpout[FILENAMELENGTH];
232: char command[FILENAMELENGTH];
233: int outcmd=0;
1.53 brouard 234:
235: char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
1.88 brouard 236: char lfileres[FILENAMELENGTH];
1.53 brouard 237: char filelog[FILENAMELENGTH]; /* Log file */
238: char filerest[FILENAMELENGTH];
239: char fileregp[FILENAMELENGTH];
240: char popfile[FILENAMELENGTH];
241:
1.91 brouard 242: char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilehtmcov[FILENAMELENGTH] ;
243:
244: struct timeval start_time, end_time, curr_time, last_time, forecast_time;
245: struct timezone tzp;
246: extern int gettimeofday();
247: struct tm tmg, tm, tmf, *gmtime(), *localtime();
248: long time_value;
249: extern long time();
250: char strcurr[80], strfor[80];
1.53 brouard 251:
252: #define NR_END 1
253: #define FREE_ARG char*
254: #define FTOL 1.0e-10
255:
256: #define NRANSI
257: #define ITMAX 200
258:
259: #define TOL 2.0e-4
260:
261: #define CGOLD 0.3819660
262: #define ZEPS 1.0e-10
263: #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);
264:
265: #define GOLD 1.618034
266: #define GLIMIT 100.0
267: #define TINY 1.0e-20
268:
269: static double maxarg1,maxarg2;
270: #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
271: #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
272:
273: #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
274: #define rint(a) floor(a+0.5)
275:
276: static double sqrarg;
277: #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
278: #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}
279:
280: int imx;
281: int stepm;
282: /* Stepm, step in month: minimum step interpolation*/
283:
284: int estepm;
285: /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
286:
287: int m,nb;
1.85 brouard 288: long *num;
289: int firstpass=0, lastpass=4,*cod, *ncodemax, *Tage;
1.53 brouard 290: double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
1.55 lievre 291: double **pmmij, ***probs;
1.53 brouard 292: double dateintmean=0;
293:
294: double *weight;
295: int **s; /* Status */
296: double *agedc, **covar, idx;
297: int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;
298:
299: double ftol=FTOL; /* Tolerance for computing Max Likelihood */
300: double ftolhess; /* Tolerance for computing hessian */
301:
302: /**************** split *************************/
303: static int split( char *path, char *dirc, char *name, char *ext, char *finame )
304: {
1.59 brouard 305: char *ss; /* pointer */
306: int l1, l2; /* length counters */
1.53 brouard 307:
1.59 brouard 308: l1 = strlen(path ); /* length of path */
309: if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
310: ss= strrchr( path, DIRSEPARATOR ); /* find last / */
311: if ( ss == NULL ) { /* no directory, so use current */
312: /*if(strrchr(path, ODIRSEPARATOR )==NULL)
313: printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
1.74 brouard 314: /* get current working directory */
315: /* extern char* getcwd ( char *buf , int len);*/
1.59 brouard 316: if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {
317: return( GLOCK_ERROR_GETCWD );
318: }
319: strcpy( name, path ); /* we've got it */
320: } else { /* strip direcotry from path */
321: ss++; /* after this, the filename */
322: l2 = strlen( ss ); /* length of filename */
323: if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
324: strcpy( name, ss ); /* save file name */
325: strncpy( dirc, path, l1 - l2 ); /* now the directory */
326: dirc[l1-l2] = 0; /* add zero */
327: }
328: l1 = strlen( dirc ); /* length of directory */
1.85 brouard 329: /*#ifdef windows
1.59 brouard 330: if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; }
1.53 brouard 331: #else
1.59 brouard 332: if ( dirc[l1-1] != '/' ) { dirc[l1] = '/'; dirc[l1+1] = 0; }
1.53 brouard 333: #endif
1.85 brouard 334: */
1.59 brouard 335: ss = strrchr( name, '.' ); /* find last / */
336: ss++;
337: strcpy(ext,ss); /* save extension */
338: l1= strlen( name);
339: l2= strlen(ss)+1;
340: strncpy( finame, name, l1-l2);
341: finame[l1-l2]= 0;
342: return( 0 ); /* we're done */
1.53 brouard 343: }
344:
345:
346: /******************************************/
347:
1.89 brouard 348: void replace_back_to_slash(char *s, char*t)
1.53 brouard 349: {
350: int i;
1.89 brouard 351: int lg=0;
1.53 brouard 352: i=0;
353: lg=strlen(t);
354: for(i=0; i<= lg; i++) {
355: (s[i] = t[i]);
356: if (t[i]== '\\') s[i]='/';
357: }
358: }
359:
360: int nbocc(char *s, char occ)
361: {
362: int i,j=0;
363: int lg=20;
364: i=0;
365: lg=strlen(s);
366: for(i=0; i<= lg; i++) {
367: if (s[i] == occ ) j++;
368: }
369: return j;
370: }
371:
372: void cutv(char *u,char *v, char*t, char occ)
373: {
374: /* cuts string t into u and v where u is ended by char occ excluding it
375: and v is after occ excluding it too : ex cutv(u,v,"abcdef2ghi2j",2)
376: gives u="abcedf" and v="ghi2j" */
377: int i,lg,j,p=0;
378: i=0;
379: for(j=0; j<=strlen(t)-1; j++) {
380: if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;
381: }
382:
383: lg=strlen(t);
384: for(j=0; j<p; j++) {
385: (u[j] = t[j]);
386: }
387: u[p]='\0';
388:
389: for(j=0; j<= lg; j++) {
390: if (j>=(p+1))(v[j-p-1] = t[j]);
391: }
392: }
393:
394: /********************** nrerror ********************/
395:
396: void nrerror(char error_text[])
397: {
398: fprintf(stderr,"ERREUR ...\n");
399: fprintf(stderr,"%s\n",error_text);
1.59 brouard 400: exit(EXIT_FAILURE);
1.53 brouard 401: }
402: /*********************** vector *******************/
403: double *vector(int nl, int nh)
404: {
405: double *v;
406: v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
407: if (!v) nrerror("allocation failure in vector");
408: return v-nl+NR_END;
409: }
410:
411: /************************ free vector ******************/
412: void free_vector(double*v, int nl, int nh)
413: {
414: free((FREE_ARG)(v+nl-NR_END));
415: }
416:
417: /************************ivector *******************************/
1.85 brouard 418: int *ivector(long nl,long nh)
1.76 brouard 419: {
1.85 brouard 420: int *v;
421: v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
422: if (!v) nrerror("allocation failure in ivector");
1.76 brouard 423: return v-nl+NR_END;
424: }
425:
426: /******************free ivector **************************/
1.85 brouard 427: void free_ivector(int *v, long nl, long nh)
1.76 brouard 428: {
429: free((FREE_ARG)(v+nl-NR_END));
430: }
431:
1.85 brouard 432: /************************lvector *******************************/
433: long *lvector(long nl,long nh)
1.53 brouard 434: {
1.85 brouard 435: long *v;
436: v=(long *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(long)));
1.53 brouard 437: if (!v) nrerror("allocation failure in ivector");
438: return v-nl+NR_END;
439: }
440:
1.85 brouard 441: /******************free lvector **************************/
442: void free_lvector(long *v, long nl, long nh)
1.53 brouard 443: {
444: free((FREE_ARG)(v+nl-NR_END));
445: }
446:
447: /******************* imatrix *******************************/
448: int **imatrix(long nrl, long nrh, long ncl, long nch)
449: /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */
450: {
451: long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;
452: int **m;
453:
454: /* allocate pointers to rows */
455: m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));
456: if (!m) nrerror("allocation failure 1 in matrix()");
457: m += NR_END;
458: m -= nrl;
459:
460:
461: /* allocate rows and set pointers to them */
462: m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));
463: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
464: m[nrl] += NR_END;
465: m[nrl] -= ncl;
466:
467: for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;
468:
469: /* return pointer to array of pointers to rows */
470: return m;
471: }
472:
473: /****************** free_imatrix *************************/
474: void free_imatrix(m,nrl,nrh,ncl,nch)
475: int **m;
476: long nch,ncl,nrh,nrl;
477: /* free an int matrix allocated by imatrix() */
478: {
479: free((FREE_ARG) (m[nrl]+ncl-NR_END));
480: free((FREE_ARG) (m+nrl-NR_END));
481: }
482:
483: /******************* matrix *******************************/
484: double **matrix(long nrl, long nrh, long ncl, long nch)
485: {
486: long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
487: double **m;
488:
489: m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
490: if (!m) nrerror("allocation failure 1 in matrix()");
491: m += NR_END;
492: m -= nrl;
493:
494: m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
495: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
496: m[nrl] += NR_END;
497: m[nrl] -= ncl;
498:
499: for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
500: return m;
1.85 brouard 501: /* print *(*(m+1)+70) or print m[1][70]; print m+1 or print &(m[1])
1.74 brouard 502: */
1.53 brouard 503: }
504:
505: /*************************free matrix ************************/
506: void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
507: {
508: free((FREE_ARG)(m[nrl]+ncl-NR_END));
509: free((FREE_ARG)(m+nrl-NR_END));
510: }
511:
512: /******************* ma3x *******************************/
513: double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
514: {
515: long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
516: double ***m;
517:
518: m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
519: if (!m) nrerror("allocation failure 1 in matrix()");
520: m += NR_END;
521: m -= nrl;
522:
523: m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
524: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
525: m[nrl] += NR_END;
526: m[nrl] -= ncl;
527:
528: for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
529:
530: m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
531: if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
532: m[nrl][ncl] += NR_END;
533: m[nrl][ncl] -= nll;
534: for (j=ncl+1; j<=nch; j++)
535: m[nrl][j]=m[nrl][j-1]+nlay;
536:
537: for (i=nrl+1; i<=nrh; i++) {
538: m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
539: for (j=ncl+1; j<=nch; j++)
540: m[i][j]=m[i][j-1]+nlay;
541: }
1.74 brouard 542: return m;
543: /* gdb: p *(m+1) <=> p m[1] and p (m+1) <=> p (m+1) <=> p &(m[1])
544: &(m[i][j][k]) <=> *((*(m+i) + j)+k)
545: */
1.53 brouard 546: }
547:
548: /*************************free ma3x ************************/
549: void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
550: {
551: free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
552: free((FREE_ARG)(m[nrl]+ncl-NR_END));
553: free((FREE_ARG)(m+nrl-NR_END));
554: }
555:
556: /***************** f1dim *************************/
557: extern int ncom;
558: extern double *pcom,*xicom;
559: extern double (*nrfunc)(double []);
560:
561: double f1dim(double x)
562: {
563: int j;
564: double f;
565: double *xt;
566:
567: xt=vector(1,ncom);
568: for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];
569: f=(*nrfunc)(xt);
570: free_vector(xt,1,ncom);
571: return f;
572: }
573:
574: /*****************brent *************************/
575: double brent(double ax, double bx, double cx, double (*f)(double), double tol, double *xmin)
576: {
577: int iter;
578: double a,b,d,etemp;
579: double fu,fv,fw,fx;
580: double ftemp;
581: double p,q,r,tol1,tol2,u,v,w,x,xm;
582: double e=0.0;
583:
584: a=(ax < cx ? ax : cx);
585: b=(ax > cx ? ax : cx);
586: x=w=v=bx;
587: fw=fv=fx=(*f)(x);
588: for (iter=1;iter<=ITMAX;iter++) {
589: xm=0.5*(a+b);
590: tol2=2.0*(tol1=tol*fabs(x)+ZEPS);
591: /* if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
592: printf(".");fflush(stdout);
593: fprintf(ficlog,".");fflush(ficlog);
594: #ifdef DEBUG
595: 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);
596: 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);
597: /* if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
598: #endif
599: if (fabs(x-xm) <= (tol2-0.5*(b-a))){
600: *xmin=x;
601: return fx;
602: }
603: ftemp=fu;
604: if (fabs(e) > tol1) {
605: r=(x-w)*(fx-fv);
606: q=(x-v)*(fx-fw);
607: p=(x-v)*q-(x-w)*r;
608: q=2.0*(q-r);
609: if (q > 0.0) p = -p;
610: q=fabs(q);
611: etemp=e;
612: e=d;
613: if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))
614: d=CGOLD*(e=(x >= xm ? a-x : b-x));
615: else {
616: d=p/q;
617: u=x+d;
618: if (u-a < tol2 || b-u < tol2)
619: d=SIGN(tol1,xm-x);
620: }
621: } else {
622: d=CGOLD*(e=(x >= xm ? a-x : b-x));
623: }
624: u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));
625: fu=(*f)(u);
626: if (fu <= fx) {
627: if (u >= x) a=x; else b=x;
628: SHFT(v,w,x,u)
629: SHFT(fv,fw,fx,fu)
630: } else {
631: if (u < x) a=u; else b=u;
632: if (fu <= fw || w == x) {
633: v=w;
634: w=u;
635: fv=fw;
636: fw=fu;
637: } else if (fu <= fv || v == x || v == w) {
638: v=u;
639: fv=fu;
640: }
641: }
642: }
643: nrerror("Too many iterations in brent");
644: *xmin=x;
645: return fx;
646: }
647:
648: /****************** mnbrak ***********************/
649:
650: void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,
651: double (*func)(double))
652: {
653: double ulim,u,r,q, dum;
654: double fu;
655:
656: *fa=(*func)(*ax);
657: *fb=(*func)(*bx);
658: if (*fb > *fa) {
659: SHFT(dum,*ax,*bx,dum)
660: SHFT(dum,*fb,*fa,dum)
661: }
662: *cx=(*bx)+GOLD*(*bx-*ax);
663: *fc=(*func)(*cx);
664: while (*fb > *fc) {
665: r=(*bx-*ax)*(*fb-*fc);
666: q=(*bx-*cx)*(*fb-*fa);
667: u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/
668: (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r));
669: ulim=(*bx)+GLIMIT*(*cx-*bx);
670: if ((*bx-u)*(u-*cx) > 0.0) {
671: fu=(*func)(u);
672: } else if ((*cx-u)*(u-ulim) > 0.0) {
673: fu=(*func)(u);
674: if (fu < *fc) {
675: SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))
676: SHFT(*fb,*fc,fu,(*func)(u))
677: }
678: } else if ((u-ulim)*(ulim-*cx) >= 0.0) {
679: u=ulim;
680: fu=(*func)(u);
681: } else {
682: u=(*cx)+GOLD*(*cx-*bx);
683: fu=(*func)(u);
684: }
685: SHFT(*ax,*bx,*cx,u)
686: SHFT(*fa,*fb,*fc,fu)
687: }
688: }
689:
690: /*************** linmin ************************/
691:
692: int ncom;
693: double *pcom,*xicom;
694: double (*nrfunc)(double []);
695:
696: void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))
697: {
698: double brent(double ax, double bx, double cx,
699: double (*f)(double), double tol, double *xmin);
700: double f1dim(double x);
701: void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,
702: double *fc, double (*func)(double));
703: int j;
704: double xx,xmin,bx,ax;
705: double fx,fb,fa;
706:
707: ncom=n;
708: pcom=vector(1,n);
709: xicom=vector(1,n);
710: nrfunc=func;
711: for (j=1;j<=n;j++) {
712: pcom[j]=p[j];
713: xicom[j]=xi[j];
714: }
715: ax=0.0;
716: xx=1.0;
717: mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim);
718: *fret=brent(ax,xx,bx,f1dim,TOL,&xmin);
719: #ifdef DEBUG
720: printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
721: fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
722: #endif
723: for (j=1;j<=n;j++) {
724: xi[j] *= xmin;
725: p[j] += xi[j];
726: }
727: free_vector(xicom,1,n);
728: free_vector(pcom,1,n);
729: }
730:
1.91 brouard 731: char *asc_diff_time(long time_sec, char ascdiff[])
732: {
733: long sec_left, days, hours, minutes;
734: days = (time_sec) / (60*60*24);
735: sec_left = (time_sec) % (60*60*24);
736: hours = (sec_left) / (60*60) ;
737: sec_left = (sec_left) %(60*60);
738: minutes = (sec_left) /60;
739: sec_left = (sec_left) % (60);
740: sprintf(ascdiff,"%d day(s) %d hour(s) %d minute(s) %d second(s)",days, hours, minutes, sec_left);
741: return ascdiff;
742: }
743:
1.53 brouard 744: /*************** powell ************************/
745: void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,
746: double (*func)(double []))
747: {
748: void linmin(double p[], double xi[], int n, double *fret,
749: double (*func)(double []));
750: int i,ibig,j;
751: double del,t,*pt,*ptt,*xit;
752: double fp,fptt;
753: double *xits;
1.91 brouard 754: int niterf, itmp;
755:
1.53 brouard 756: pt=vector(1,n);
757: ptt=vector(1,n);
758: xit=vector(1,n);
759: xits=vector(1,n);
760: *fret=(*func)(p);
761: for (j=1;j<=n;j++) pt[j]=p[j];
762: for (*iter=1;;++(*iter)) {
763: fp=(*fret);
764: ibig=0;
765: del=0.0;
1.91 brouard 766: last_time=curr_time;
767: (void) gettimeofday(&curr_time,&tzp);
768: printf("\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret, curr_time.tv_sec-last_time.tv_sec, curr_time.tv_sec-start_time.tv_sec);fflush(stdout);
769: fprintf(ficlog,"\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret, curr_time.tv_sec-last_time.tv_sec, curr_time.tv_sec-start_time.tv_sec);
770: fprintf(ficrespow,"%d %.12f %ld",*iter,*fret,curr_time.tv_sec-start_time.tv_sec);
1.76 brouard 771: for (i=1;i<=n;i++) {
1.53 brouard 772: printf(" %d %.12f",i, p[i]);
1.76 brouard 773: fprintf(ficlog," %d %.12lf",i, p[i]);
774: fprintf(ficrespow," %.12lf", p[i]);
775: }
1.53 brouard 776: printf("\n");
777: fprintf(ficlog,"\n");
1.91 brouard 778: fprintf(ficrespow,"\n");fflush(ficrespow);
779: if(*iter <=3){
780: tm = *localtime(&curr_time.tv_sec);
1.92 ! brouard 781: strcpy(strcurr,asctime(&tmf));
! 782: /* asctime_r(&tm,strcurr); */
1.91 brouard 783: forecast_time=curr_time;
784: itmp = strlen(strcurr);
785: if(strcurr[itmp-1]=='\n')
786: strcurr[itmp-1]='\0';
787: printf("\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,curr_time.tv_sec-last_time.tv_sec);
788: fprintf(ficlog,"\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,curr_time.tv_sec-last_time.tv_sec);
789: for(niterf=10;niterf<=30;niterf+=10){
790: forecast_time.tv_sec=curr_time.tv_sec+(niterf-*iter)*(curr_time.tv_sec-last_time.tv_sec);
791: tmf = *localtime(&forecast_time.tv_sec);
1.92 ! brouard 792: /* asctime_r(&tmf,strfor); */
! 793: strcpy(strfor,asctime(&tmf));
1.91 brouard 794: itmp = strlen(strfor);
795: if(strfor[itmp-1]=='\n')
796: strfor[itmp-1]='\0';
797: printf(" - if your program needs %d iterations to converge, convergence will be \n reached in %s or\n on %s (current time is %s);\n",niterf, asc_diff_time(forecast_time.tv_sec-curr_time.tv_sec,tmpout),strfor,strcurr);
798: fprintf(ficlog," - if your program needs %d iterations to converge, convergence will be \n reached in %s or\n on %s (current time is %s);\n",niterf, asc_diff_time(forecast_time.tv_sec-curr_time.tv_sec,tmpout),strfor,strcurr);
799: }
800: }
1.53 brouard 801: for (i=1;i<=n;i++) {
802: for (j=1;j<=n;j++) xit[j]=xi[j][i];
803: fptt=(*fret);
804: #ifdef DEBUG
805: printf("fret=%lf \n",*fret);
806: fprintf(ficlog,"fret=%lf \n",*fret);
807: #endif
808: printf("%d",i);fflush(stdout);
809: fprintf(ficlog,"%d",i);fflush(ficlog);
810: linmin(p,xit,n,fret,func);
811: if (fabs(fptt-(*fret)) > del) {
812: del=fabs(fptt-(*fret));
813: ibig=i;
814: }
815: #ifdef DEBUG
816: printf("%d %.12e",i,(*fret));
817: fprintf(ficlog,"%d %.12e",i,(*fret));
818: for (j=1;j<=n;j++) {
819: xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
820: printf(" x(%d)=%.12e",j,xit[j]);
821: fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
822: }
823: for(j=1;j<=n;j++) {
824: printf(" p=%.12e",p[j]);
825: fprintf(ficlog," p=%.12e",p[j]);
826: }
827: printf("\n");
828: fprintf(ficlog,"\n");
829: #endif
830: }
831: if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {
832: #ifdef DEBUG
833: int k[2],l;
834: k[0]=1;
835: k[1]=-1;
836: printf("Max: %.12e",(*func)(p));
837: fprintf(ficlog,"Max: %.12e",(*func)(p));
838: for (j=1;j<=n;j++) {
839: printf(" %.12e",p[j]);
840: fprintf(ficlog," %.12e",p[j]);
841: }
842: printf("\n");
843: fprintf(ficlog,"\n");
844: for(l=0;l<=1;l++) {
845: for (j=1;j<=n;j++) {
846: ptt[j]=p[j]+(p[j]-pt[j])*k[l];
847: printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
848: fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
849: }
850: printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
851: fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
852: }
853: #endif
854:
855:
856: free_vector(xit,1,n);
857: free_vector(xits,1,n);
858: free_vector(ptt,1,n);
859: free_vector(pt,1,n);
860: return;
861: }
862: if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");
863: for (j=1;j<=n;j++) {
864: ptt[j]=2.0*p[j]-pt[j];
865: xit[j]=p[j]-pt[j];
866: pt[j]=p[j];
867: }
868: fptt=(*func)(ptt);
869: if (fptt < fp) {
870: t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt);
871: if (t < 0.0) {
872: linmin(p,xit,n,fret,func);
873: for (j=1;j<=n;j++) {
874: xi[j][ibig]=xi[j][n];
875: xi[j][n]=xit[j];
876: }
877: #ifdef DEBUG
878: printf("Direction changed last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
879: fprintf(ficlog,"Direction changed last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
880: for(j=1;j<=n;j++){
881: printf(" %.12e",xit[j]);
882: fprintf(ficlog," %.12e",xit[j]);
883: }
884: printf("\n");
885: fprintf(ficlog,"\n");
886: #endif
1.54 brouard 887: }
1.53 brouard 888: }
889: }
890: }
891:
1.54 brouard 892: /**** Prevalence limit (stable prevalence) ****************/
1.53 brouard 893:
894: double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)
895: {
896: /* Computes the prevalence limit in each live state at age x by left multiplying the unit
897: matrix by transitions matrix until convergence is reached */
898:
899: int i, ii,j,k;
900: double min, max, maxmin, maxmax,sumnew=0.;
901: double **matprod2();
902: double **out, cov[NCOVMAX], **pmij();
903: double **newm;
904: double agefin, delaymax=50 ; /* Max number of years to converge */
905:
906: for (ii=1;ii<=nlstate+ndeath;ii++)
907: for (j=1;j<=nlstate+ndeath;j++){
908: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
909: }
910:
911: cov[1]=1.;
912:
913: /* Even if hstepm = 1, at least one multiplication by the unit matrix */
914: for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
915: newm=savm;
916: /* Covariates have to be included here again */
917: cov[2]=agefin;
918:
919: for (k=1; k<=cptcovn;k++) {
920: cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
921: /* 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]]);*/
922: }
923: for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
924: for (k=1; k<=cptcovprod;k++)
925: cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
926:
927: /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
928: /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
929: /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
930: out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);
931:
932: savm=oldm;
933: oldm=newm;
934: maxmax=0.;
935: for(j=1;j<=nlstate;j++){
936: min=1.;
937: max=0.;
938: for(i=1; i<=nlstate; i++) {
939: sumnew=0;
940: for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
941: prlim[i][j]= newm[i][j]/(1-sumnew);
942: max=FMAX(max,prlim[i][j]);
943: min=FMIN(min,prlim[i][j]);
944: }
945: maxmin=max-min;
946: maxmax=FMAX(maxmax,maxmin);
947: }
948: if(maxmax < ftolpl){
949: return prlim;
950: }
951: }
952: }
953:
954: /*************** transition probabilities ***************/
955:
956: double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
957: {
958: double s1, s2;
959: /*double t34;*/
960: int i,j,j1, nc, ii, jj;
961:
962: for(i=1; i<= nlstate; i++){
963: for(j=1; j<i;j++){
964: for (nc=1, s2=0.;nc <=ncovmodel; nc++){
965: /*s2 += param[i][j][nc]*cov[nc];*/
966: s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
967: /*printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2);*/
968: }
969: ps[i][j]=s2;
970: /*printf("s1=%.17e, s2=%.17e\n",s1,s2);*/
971: }
972: for(j=i+1; j<=nlstate+ndeath;j++){
973: for (nc=1, s2=0.;nc <=ncovmodel; nc++){
974: s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
975: /*printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2);*/
976: }
977: ps[i][j]=s2;
978: }
979: }
980: /*ps[3][2]=1;*/
981:
982: for(i=1; i<= nlstate; i++){
983: s1=0;
984: for(j=1; j<i; j++)
985: s1+=exp(ps[i][j]);
986: for(j=i+1; j<=nlstate+ndeath; j++)
987: s1+=exp(ps[i][j]);
988: ps[i][i]=1./(s1+1.);
989: for(j=1; j<i; j++)
990: ps[i][j]= exp(ps[i][j])*ps[i][i];
991: for(j=i+1; j<=nlstate+ndeath; j++)
992: ps[i][j]= exp(ps[i][j])*ps[i][i];
993: /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
994: } /* end i */
995:
996: for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
997: for(jj=1; jj<= nlstate+ndeath; jj++){
998: ps[ii][jj]=0;
999: ps[ii][ii]=1;
1000: }
1001: }
1002:
1003:
1004: /* for(ii=1; ii<= nlstate+ndeath; ii++){
1005: for(jj=1; jj<= nlstate+ndeath; jj++){
1006: printf("%lf ",ps[ii][jj]);
1007: }
1008: printf("\n ");
1009: }
1010: printf("\n ");printf("%lf ",cov[2]);*/
1011: /*
1012: for(i=1; i<= npar; i++) printf("%f ",x[i]);
1013: goto end;*/
1014: return ps;
1015: }
1016:
1017: /**************** Product of 2 matrices ******************/
1018:
1019: double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)
1020: {
1021: /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
1022: b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
1023: /* in, b, out are matrice of pointers which should have been initialized
1024: before: only the contents of out is modified. The function returns
1025: a pointer to pointers identical to out */
1026: long i, j, k;
1027: for(i=nrl; i<= nrh; i++)
1028: for(k=ncolol; k<=ncoloh; k++)
1029: for(j=ncl,out[i][k]=0.; j<=nch; j++)
1030: out[i][k] +=in[i][j]*b[j][k];
1031:
1032: return out;
1033: }
1034:
1035:
1036: /************* Higher Matrix Product ***************/
1037:
1038: double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
1039: {
1.66 brouard 1040: /* Computes the transition matrix starting at age 'age' over
1041: 'nhstepm*hstepm*stepm' months (i.e. until
1042: age (in years) age+nhstepm*hstepm*stepm/12) by multiplying
1043: nhstepm*hstepm matrices.
1.53 brouard 1044: Output is stored in matrix po[i][j][h] for h every 'hstepm' step
1.66 brouard 1045: (typically every 2 years instead of every month which is too big
1046: for the memory).
1.53 brouard 1047: Model is determined by parameters x and covariates have to be
1048: included manually here.
1049:
1050: */
1051:
1052: int i, j, d, h, k;
1053: double **out, cov[NCOVMAX];
1054: double **newm;
1055:
1056: /* Hstepm could be zero and should return the unit matrix */
1057: for (i=1;i<=nlstate+ndeath;i++)
1058: for (j=1;j<=nlstate+ndeath;j++){
1059: oldm[i][j]=(i==j ? 1.0 : 0.0);
1060: po[i][j][0]=(i==j ? 1.0 : 0.0);
1061: }
1062: /* Even if hstepm = 1, at least one multiplication by the unit matrix */
1063: for(h=1; h <=nhstepm; h++){
1064: for(d=1; d <=hstepm; d++){
1065: newm=savm;
1066: /* Covariates have to be included here again */
1067: cov[1]=1.;
1068: cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
1069: for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
1070: for (k=1; k<=cptcovage;k++)
1071: cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
1072: for (k=1; k<=cptcovprod;k++)
1073: cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
1074:
1075:
1076: /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
1077: /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
1078: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,
1079: pmij(pmmij,cov,ncovmodel,x,nlstate));
1080: savm=oldm;
1081: oldm=newm;
1082: }
1083: for(i=1; i<=nlstate+ndeath; i++)
1084: for(j=1;j<=nlstate+ndeath;j++) {
1085: po[i][j][h]=newm[i][j];
1086: /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);
1087: */
1088: }
1089: } /* end h */
1090: return po;
1091: }
1092:
1093:
1094: /*************** log-likelihood *************/
1095: double func( double *x)
1096: {
1097: int i, ii, j, k, mi, d, kk;
1098: double l, ll[NLSTATEMAX], cov[NCOVMAX];
1099: double **out;
1100: double sw; /* Sum of weights */
1101: double lli; /* Individual log likelihood */
1.59 brouard 1102: int s1, s2;
1.68 lievre 1103: double bbh, survp;
1.53 brouard 1104: long ipmx;
1105: /*extern weight */
1106: /* We are differentiating ll according to initial status */
1107: /* for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
1108: /*for(i=1;i<imx;i++)
1109: printf(" %d\n",s[4][i]);
1110: */
1111: cov[1]=1.;
1112:
1113: for(k=1; k<=nlstate; k++) ll[k]=0.;
1.61 brouard 1114:
1115: if(mle==1){
1116: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1117: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
1118: for(mi=1; mi<= wav[i]-1; mi++){
1119: for (ii=1;ii<=nlstate+ndeath;ii++)
1120: for (j=1;j<=nlstate+ndeath;j++){
1121: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1122: savm[ii][j]=(ii==j ? 1.0 : 0.0);
1123: }
1124: for(d=0; d<dh[mi][i]; d++){
1125: newm=savm;
1126: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
1127: for (kk=1; kk<=cptcovage;kk++) {
1128: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
1129: }
1130: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1131: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1132: savm=oldm;
1133: oldm=newm;
1134: } /* end mult */
1.53 brouard 1135:
1.61 brouard 1136: /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
1137: /* But now since version 0.9 we anticipate for bias and large stepm.
1138: * If stepm is larger than one month (smallest stepm) and if the exact delay
1139: * (in months) between two waves is not a multiple of stepm, we rounded to
1140: * the nearest (and in case of equal distance, to the lowest) interval but now
1141: * we keep into memory the bias bh[mi][i] and also the previous matrix product
1142: * (i.e to dh[mi][i]-1) saved in 'savm'. The we inter(extra)polate the
1143: * probability in order to take into account the bias as a fraction of the way
1144: * from savm to out if bh is neagtive or even beyond if bh is positive. bh varies
1145: * -stepm/2 to stepm/2 .
1146: * For stepm=1 the results are the same as for previous versions of Imach.
1147: * For stepm > 1 the results are less biased than in previous versions.
1148: */
1149: s1=s[mw[mi][i]][i];
1150: s2=s[mw[mi+1][i]][i];
1.64 lievre 1151: bbh=(double)bh[mi][i]/(double)stepm;
1152: /* bias is positive if real duration
1153: * is higher than the multiple of stepm and negative otherwise.
1154: */
1155: /* 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 1156: if( s2 > nlstate){
1157: /* i.e. if s2 is a death state and if the date of death is known then the contribution
1158: to the likelihood is the probability to die between last step unit time and current
1159: step unit time, which is also the differences between probability to die before dh
1160: and probability to die before dh-stepm .
1161: In version up to 0.92 likelihood was computed
1162: as if date of death was unknown. Death was treated as any other
1163: health state: the date of the interview describes the actual state
1164: and not the date of a change in health state. The former idea was
1165: to consider that at each interview the state was recorded
1166: (healthy, disable or death) and IMaCh was corrected; but when we
1167: introduced the exact date of death then we should have modified
1168: the contribution of an exact death to the likelihood. This new
1169: contribution is smaller and very dependent of the step unit
1170: stepm. It is no more the probability to die between last interview
1171: and month of death but the probability to survive from last
1172: interview up to one month before death multiplied by the
1173: probability to die within a month. Thanks to Chris
1174: Jackson for correcting this bug. Former versions increased
1175: mortality artificially. The bad side is that we add another loop
1176: which slows down the processing. The difference can be up to 10%
1177: lower mortality.
1178: */
1179: lli=log(out[s1][s2] - savm[s1][s2]);
1180: }else{
1181: lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
1182: /* 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 */
1183: }
1.64 lievre 1184: /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
1185: /*if(lli ==000.0)*/
1186: /*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 1187: ipmx +=1;
1.64 lievre 1188: sw += weight[i];
1189: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1190: } /* end of wave */
1191: } /* end of individual */
1192: } else if(mle==2){
1193: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1194: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
1195: for(mi=1; mi<= wav[i]-1; mi++){
1196: for (ii=1;ii<=nlstate+ndeath;ii++)
1197: for (j=1;j<=nlstate+ndeath;j++){
1198: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1199: savm[ii][j]=(ii==j ? 1.0 : 0.0);
1200: }
1201: for(d=0; d<=dh[mi][i]; d++){
1202: newm=savm;
1203: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
1204: for (kk=1; kk<=cptcovage;kk++) {
1205: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
1206: }
1207: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1208: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1209: savm=oldm;
1210: oldm=newm;
1211: } /* end mult */
1212:
1213: /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
1214: /* But now since version 0.9 we anticipate for bias and large stepm.
1215: * If stepm is larger than one month (smallest stepm) and if the exact delay
1216: * (in months) between two waves is not a multiple of stepm, we rounded to
1217: * the nearest (and in case of equal distance, to the lowest) interval but now
1218: * we keep into memory the bias bh[mi][i] and also the previous matrix product
1219: * (i.e to dh[mi][i]-1) saved in 'savm'. The we inter(extra)polate the
1220: * probability in order to take into account the bias as a fraction of the way
1221: * from savm to out if bh is neagtive or even beyond if bh is positive. bh varies
1222: * -stepm/2 to stepm/2 .
1223: * For stepm=1 the results are the same as for previous versions of Imach.
1224: * For stepm > 1 the results are less biased than in previous versions.
1225: */
1226: s1=s[mw[mi][i]][i];
1227: s2=s[mw[mi+1][i]][i];
1228: bbh=(double)bh[mi][i]/(double)stepm;
1229: /* bias is positive if real duration
1230: * is higher than the multiple of stepm and negative otherwise.
1231: */
1.63 lievre 1232: 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 1233: /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
1234: /*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 */
1235: /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
1236: /*if(lli ==000.0)*/
1237: /*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); */
1238: ipmx +=1;
1239: sw += weight[i];
1240: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1241: } /* end of wave */
1242: } /* end of individual */
1243: } else if(mle==3){ /* exponential inter-extrapolation */
1244: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1245: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
1246: for(mi=1; mi<= wav[i]-1; mi++){
1247: for (ii=1;ii<=nlstate+ndeath;ii++)
1248: for (j=1;j<=nlstate+ndeath;j++){
1249: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1250: savm[ii][j]=(ii==j ? 1.0 : 0.0);
1251: }
1252: for(d=0; d<dh[mi][i]; d++){
1253: newm=savm;
1254: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
1255: for (kk=1; kk<=cptcovage;kk++) {
1256: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
1257: }
1258: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1259: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1260: savm=oldm;
1261: oldm=newm;
1262: } /* end mult */
1263:
1264: /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
1265: /* But now since version 0.9 we anticipate for bias and large stepm.
1266: * If stepm is larger than one month (smallest stepm) and if the exact delay
1267: * (in months) between two waves is not a multiple of stepm, we rounded to
1268: * the nearest (and in case of equal distance, to the lowest) interval but now
1269: * we keep into memory the bias bh[mi][i] and also the previous matrix product
1270: * (i.e to dh[mi][i]-1) saved in 'savm'. The we inter(extra)polate the
1271: * probability in order to take into account the bias as a fraction of the way
1272: * from savm to out if bh is neagtive or even beyond if bh is positive. bh varies
1273: * -stepm/2 to stepm/2 .
1274: * For stepm=1 the results are the same as for previous versions of Imach.
1275: * For stepm > 1 the results are less biased than in previous versions.
1276: */
1277: s1=s[mw[mi][i]][i];
1278: s2=s[mw[mi+1][i]][i];
1279: bbh=(double)bh[mi][i]/(double)stepm;
1280: /* bias is positive if real duration
1281: * is higher than the multiple of stepm and negative otherwise.
1282: */
1283: /* 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 */
1284: 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 1285: /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
1286: /*if(lli ==000.0)*/
1287: /*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); */
1288: ipmx +=1;
1289: sw += weight[i];
1290: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1291: } /* end of wave */
1292: } /* end of individual */
1.84 brouard 1293: }else if (mle==4){ /* ml=4 no inter-extrapolation */
1.61 brouard 1294: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1295: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
1296: for(mi=1; mi<= wav[i]-1; mi++){
1297: for (ii=1;ii<=nlstate+ndeath;ii++)
1298: for (j=1;j<=nlstate+ndeath;j++){
1299: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1300: savm[ii][j]=(ii==j ? 1.0 : 0.0);
1301: }
1302: for(d=0; d<dh[mi][i]; d++){
1303: newm=savm;
1304: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
1305: for (kk=1; kk<=cptcovage;kk++) {
1306: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
1307: }
1308:
1309: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1310: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1311: savm=oldm;
1312: oldm=newm;
1313: } /* end mult */
1314:
1.84 brouard 1315: s1=s[mw[mi][i]][i];
1316: s2=s[mw[mi+1][i]][i];
1317: if( s2 > nlstate){
1318: lli=log(out[s1][s2] - savm[s1][s2]);
1319: }else{
1320: lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
1321: }
1322: ipmx +=1;
1323: sw += weight[i];
1324: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1.85 brouard 1325: /* 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 1326: } /* end of wave */
1327: } /* end of individual */
1328: }else{ /* ml=5 no inter-extrapolation no jackson =0.8a */
1329: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1330: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
1331: for(mi=1; mi<= wav[i]-1; mi++){
1332: for (ii=1;ii<=nlstate+ndeath;ii++)
1333: for (j=1;j<=nlstate+ndeath;j++){
1334: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1335: savm[ii][j]=(ii==j ? 1.0 : 0.0);
1336: }
1337: for(d=0; d<dh[mi][i]; d++){
1338: newm=savm;
1339: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
1340: for (kk=1; kk<=cptcovage;kk++) {
1341: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
1342: }
1343:
1344: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1345: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1346: savm=oldm;
1347: oldm=newm;
1348: } /* end mult */
1349:
1350: s1=s[mw[mi][i]][i];
1351: s2=s[mw[mi+1][i]][i];
1.61 brouard 1352: lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
1353: ipmx +=1;
1354: sw += weight[i];
1355: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1.84 brouard 1356: /*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 1357: } /* end of wave */
1358: } /* end of individual */
1359: } /* End of if */
1.53 brouard 1360: for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
1361: /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
1362: l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
1.85 brouard 1363: return -l;
1364: }
1365:
1366: /*************** log-likelihood *************/
1367: double funcone( double *x)
1368: {
1.87 brouard 1369: /* Same as likeli but slower because of a lot of printf and if */
1.85 brouard 1370: int i, ii, j, k, mi, d, kk;
1371: double l, ll[NLSTATEMAX], cov[NCOVMAX];
1372: double **out;
1373: double lli; /* Individual log likelihood */
1.87 brouard 1374: double llt;
1.85 brouard 1375: int s1, s2;
1376: double bbh, survp;
1377: /*extern weight */
1378: /* We are differentiating ll according to initial status */
1379: /* for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
1380: /*for(i=1;i<imx;i++)
1381: printf(" %d\n",s[4][i]);
1382: */
1383: cov[1]=1.;
1384:
1385: for(k=1; k<=nlstate; k++) ll[k]=0.;
1386:
1387: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1388: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
1389: for(mi=1; mi<= wav[i]-1; mi++){
1390: for (ii=1;ii<=nlstate+ndeath;ii++)
1391: for (j=1;j<=nlstate+ndeath;j++){
1392: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1393: savm[ii][j]=(ii==j ? 1.0 : 0.0);
1394: }
1395: for(d=0; d<dh[mi][i]; d++){
1396: newm=savm;
1397: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
1398: for (kk=1; kk<=cptcovage;kk++) {
1399: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
1400: }
1401: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1402: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1403: savm=oldm;
1404: oldm=newm;
1405: } /* end mult */
1406:
1407: s1=s[mw[mi][i]][i];
1408: s2=s[mw[mi+1][i]][i];
1409: bbh=(double)bh[mi][i]/(double)stepm;
1410: /* bias is positive if real duration
1411: * is higher than the multiple of stepm and negative otherwise.
1412: */
1413: if( s2 > nlstate && (mle <5) ){ /* Jackson */
1414: lli=log(out[s1][s2] - savm[s1][s2]);
1415: } else if (mle==1){
1416: lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
1417: } else if(mle==2){
1418: 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 */
1419: } else if(mle==3){ /* exponential inter-extrapolation */
1420: 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 */
1421: } else if (mle==4){ /* mle=4 no inter-extrapolation */
1422: lli=log(out[s1][s2]); /* Original formula */
1423: } else{ /* ml>=5 no inter-extrapolation no jackson =0.8a */
1424: lli=log(out[s1][s2]); /* Original formula */
1425: } /* End of if */
1426: ipmx +=1;
1427: sw += weight[i];
1428: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1429: /* 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]); */
1430: if(globpr){
1.88 brouard 1431: fprintf(ficresilk,"%9d %6d %1d %1d %1d %1d %3d %10.6f %6.4f\
1.86 brouard 1432: %10.6f %10.6f %10.6f ", \
1433: num[i],i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],
1434: 2*weight[i]*lli,out[s1][s2],savm[s1][s2]);
1.87 brouard 1435: for(k=1,llt=0.,l=0.; k<=nlstate; k++){
1436: llt +=ll[k]*gipmx/gsw;
1437: fprintf(ficresilk," %10.6f",-ll[k]*gipmx/gsw);
1438: }
1439: fprintf(ficresilk," %10.6f\n", -llt);
1.85 brouard 1440: }
1441: } /* end of wave */
1442: } /* end of individual */
1443: for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
1444: /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
1445: l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
1.87 brouard 1446: if(globpr==0){ /* First time we count the contributions and weights */
1447: gipmx=ipmx;
1448: gsw=sw;
1449: }
1.53 brouard 1450: return -l;
1451: }
1452:
1.88 brouard 1453: char *subdirf(char fileres[])
1454: {
1.91 brouard 1455: /* Caution optionfilefiname is hidden */
1.88 brouard 1456: strcpy(tmpout,optionfilefiname);
1457: strcat(tmpout,"/"); /* Add to the right */
1458: strcat(tmpout,fileres);
1459: return tmpout;
1460: }
1461:
1462: char *subdirf2(char fileres[], char *preop)
1463: {
1464:
1465: strcpy(tmpout,optionfilefiname);
1466: strcat(tmpout,"/");
1467: strcat(tmpout,preop);
1468: strcat(tmpout,fileres);
1469: return tmpout;
1470: }
1471: char *subdirf3(char fileres[], char *preop, char *preop2)
1472: {
1473:
1474: strcpy(tmpout,optionfilefiname);
1475: strcat(tmpout,"/");
1476: strcat(tmpout,preop);
1477: strcat(tmpout,preop2);
1478: strcat(tmpout,fileres);
1479: return tmpout;
1480: }
1.53 brouard 1481:
1.87 brouard 1482: void likelione(FILE *ficres,double p[], int npar, int nlstate, int *globpri, long *ipmx, double *sw, double *fretone, double (*funcone)(double []))
1.85 brouard 1483: {
1.87 brouard 1484: /* This routine should help understanding what is done with
1485: the selection of individuals/waves and
1.85 brouard 1486: to check the exact contribution to the likelihood.
1487: Plotting could be done.
1488: */
1489: int k;
1.87 brouard 1490:
1.88 brouard 1491: if(*globpri !=0){ /* Just counts and sums, no printings */
1.85 brouard 1492: strcpy(fileresilk,"ilk");
1493: strcat(fileresilk,fileres);
1494: if((ficresilk=fopen(fileresilk,"w"))==NULL) {
1495: printf("Problem with resultfile: %s\n", fileresilk);
1496: fprintf(ficlog,"Problem with resultfile: %s\n", fileresilk);
1497: }
1.87 brouard 1498: 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 1499: fprintf(ficresilk, "#num_i i s1 s2 mi mw dh likeli weight 2wlli out sav ");
1.85 brouard 1500: /* i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],2*weight[i]*lli,out[s1][s2],savm[s1][s2]); */
1501: for(k=1; k<=nlstate; k++)
1.87 brouard 1502: fprintf(ficresilk," -2*gipw/gsw*weight*ll[%d]++",k);
1503: fprintf(ficresilk," -2*gipw/gsw*weight*ll(total)\n");
1.85 brouard 1504: }
1505:
1506: *fretone=(*funcone)(p);
1.87 brouard 1507: if(*globpri !=0){
1.85 brouard 1508: fclose(ficresilk);
1.88 brouard 1509: fprintf(fichtm,"\n<br>File of contributions to the likelihood: <a href=\"%s\">%s</a><br>\n",subdirf(fileresilk),subdirf(fileresilk));
1.87 brouard 1510: fflush(fichtm);
1511: }
1.85 brouard 1512: return;
1513: }
1514:
1.88 brouard 1515:
1.53 brouard 1516: /*********** Maximum Likelihood Estimation ***************/
1517:
1518: void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
1519: {
1520: int i,j, iter;
1.74 brouard 1521: double **xi;
1.53 brouard 1522: double fret;
1.85 brouard 1523: double fretone; /* Only one call to likelihood */
1.76 brouard 1524: char filerespow[FILENAMELENGTH];
1.53 brouard 1525: xi=matrix(1,npar,1,npar);
1526: for (i=1;i<=npar;i++)
1527: for (j=1;j<=npar;j++)
1528: xi[i][j]=(i==j ? 1.0 : 0.0);
1529: printf("Powell\n"); fprintf(ficlog,"Powell\n");
1.76 brouard 1530: strcpy(filerespow,"pow");
1531: strcat(filerespow,fileres);
1532: if((ficrespow=fopen(filerespow,"w"))==NULL) {
1533: printf("Problem with resultfile: %s\n", filerespow);
1534: fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
1535: }
1536: fprintf(ficrespow,"# Powell\n# iter -2*LL");
1537: for (i=1;i<=nlstate;i++)
1538: for(j=1;j<=nlstate+ndeath;j++)
1539: if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
1540: fprintf(ficrespow,"\n");
1.85 brouard 1541:
1.53 brouard 1542: powell(p,xi,npar,ftol,&iter,&fret,func);
1543:
1.76 brouard 1544: fclose(ficrespow);
1545: printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));
1.65 lievre 1546: fprintf(ficlog,"\n#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
1.53 brouard 1547: fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
1548:
1549: }
1550:
1551: /**** Computes Hessian and covariance matrix ***/
1552: void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
1553: {
1554: double **a,**y,*x,pd;
1555: double **hess;
1556: int i, j,jk;
1557: int *indx;
1558:
1559: double hessii(double p[], double delta, int theta, double delti[]);
1560: double hessij(double p[], double delti[], int i, int j);
1561: void lubksb(double **a, int npar, int *indx, double b[]) ;
1562: void ludcmp(double **a, int npar, int *indx, double *d) ;
1563:
1564: hess=matrix(1,npar,1,npar);
1565:
1566: printf("\nCalculation of the hessian matrix. Wait...\n");
1567: fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
1568: for (i=1;i<=npar;i++){
1569: printf("%d",i);fflush(stdout);
1570: fprintf(ficlog,"%d",i);fflush(ficlog);
1571: hess[i][i]=hessii(p,ftolhess,i,delti);
1572: /*printf(" %f ",p[i]);*/
1573: /*printf(" %lf ",hess[i][i]);*/
1574: }
1575:
1576: for (i=1;i<=npar;i++) {
1577: for (j=1;j<=npar;j++) {
1578: if (j>i) {
1579: printf(".%d%d",i,j);fflush(stdout);
1580: fprintf(ficlog,".%d%d",i,j);fflush(ficlog);
1581: hess[i][j]=hessij(p,delti,i,j);
1582: hess[j][i]=hess[i][j];
1583: /*printf(" %lf ",hess[i][j]);*/
1584: }
1585: }
1586: }
1587: printf("\n");
1588: fprintf(ficlog,"\n");
1589:
1590: printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
1591: fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
1592:
1593: a=matrix(1,npar,1,npar);
1594: y=matrix(1,npar,1,npar);
1595: x=vector(1,npar);
1596: indx=ivector(1,npar);
1597: for (i=1;i<=npar;i++)
1598: for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
1599: ludcmp(a,npar,indx,&pd);
1600:
1601: for (j=1;j<=npar;j++) {
1602: for (i=1;i<=npar;i++) x[i]=0;
1603: x[j]=1;
1604: lubksb(a,npar,indx,x);
1605: for (i=1;i<=npar;i++){
1606: matcov[i][j]=x[i];
1607: }
1608: }
1609:
1610: printf("\n#Hessian matrix#\n");
1611: fprintf(ficlog,"\n#Hessian matrix#\n");
1612: for (i=1;i<=npar;i++) {
1613: for (j=1;j<=npar;j++) {
1614: printf("%.3e ",hess[i][j]);
1615: fprintf(ficlog,"%.3e ",hess[i][j]);
1616: }
1617: printf("\n");
1618: fprintf(ficlog,"\n");
1619: }
1620:
1621: /* Recompute Inverse */
1622: for (i=1;i<=npar;i++)
1623: for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];
1624: ludcmp(a,npar,indx,&pd);
1625:
1626: /* printf("\n#Hessian matrix recomputed#\n");
1627:
1628: for (j=1;j<=npar;j++) {
1629: for (i=1;i<=npar;i++) x[i]=0;
1630: x[j]=1;
1631: lubksb(a,npar,indx,x);
1632: for (i=1;i<=npar;i++){
1633: y[i][j]=x[i];
1634: printf("%.3e ",y[i][j]);
1635: fprintf(ficlog,"%.3e ",y[i][j]);
1636: }
1637: printf("\n");
1638: fprintf(ficlog,"\n");
1639: }
1640: */
1641:
1642: free_matrix(a,1,npar,1,npar);
1643: free_matrix(y,1,npar,1,npar);
1644: free_vector(x,1,npar);
1645: free_ivector(indx,1,npar);
1646: free_matrix(hess,1,npar,1,npar);
1647:
1648:
1649: }
1650:
1651: /*************** hessian matrix ****************/
1652: double hessii( double x[], double delta, int theta, double delti[])
1653: {
1654: int i;
1655: int l=1, lmax=20;
1656: double k1,k2;
1657: double p2[NPARMAX+1];
1658: double res;
1659: double delt, delts, nkhi=10.,nkhif=1., khi=1.e-4;
1660: double fx;
1661: int k=0,kmax=10;
1662: double l1;
1663:
1664: fx=func(x);
1665: for (i=1;i<=npar;i++) p2[i]=x[i];
1666: for(l=0 ; l <=lmax; l++){
1667: l1=pow(10,l);
1668: delts=delt;
1669: for(k=1 ; k <kmax; k=k+1){
1670: delt = delta*(l1*k);
1671: p2[theta]=x[theta] +delt;
1672: k1=func(p2)-fx;
1673: p2[theta]=x[theta]-delt;
1674: k2=func(p2)-fx;
1675: /*res= (k1-2.0*fx+k2)/delt/delt; */
1676: res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */
1677:
1678: #ifdef DEBUG
1679: 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);
1680: 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);
1681: #endif
1682: /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
1683: if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
1684: k=kmax;
1685: }
1686: else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
1687: k=kmax; l=lmax*10.;
1688: }
1689: else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){
1690: delts=delt;
1691: }
1692: }
1693: }
1694: delti[theta]=delts;
1695: return res;
1696:
1697: }
1698:
1699: double hessij( double x[], double delti[], int thetai,int thetaj)
1700: {
1701: int i;
1702: int l=1, l1, lmax=20;
1703: double k1,k2,k3,k4,res,fx;
1704: double p2[NPARMAX+1];
1705: int k;
1706:
1707: fx=func(x);
1708: for (k=1; k<=2; k++) {
1709: for (i=1;i<=npar;i++) p2[i]=x[i];
1710: p2[thetai]=x[thetai]+delti[thetai]/k;
1711: p2[thetaj]=x[thetaj]+delti[thetaj]/k;
1712: k1=func(p2)-fx;
1713:
1714: p2[thetai]=x[thetai]+delti[thetai]/k;
1715: p2[thetaj]=x[thetaj]-delti[thetaj]/k;
1716: k2=func(p2)-fx;
1717:
1718: p2[thetai]=x[thetai]-delti[thetai]/k;
1719: p2[thetaj]=x[thetaj]+delti[thetaj]/k;
1720: k3=func(p2)-fx;
1721:
1722: p2[thetai]=x[thetai]-delti[thetai]/k;
1723: p2[thetaj]=x[thetaj]-delti[thetaj]/k;
1724: k4=func(p2)-fx;
1725: res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */
1726: #ifdef DEBUG
1727: 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);
1728: 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);
1729: #endif
1730: }
1731: return res;
1732: }
1733:
1734: /************** Inverse of matrix **************/
1735: void ludcmp(double **a, int n, int *indx, double *d)
1736: {
1737: int i,imax,j,k;
1738: double big,dum,sum,temp;
1739: double *vv;
1740:
1741: vv=vector(1,n);
1742: *d=1.0;
1743: for (i=1;i<=n;i++) {
1744: big=0.0;
1745: for (j=1;j<=n;j++)
1746: if ((temp=fabs(a[i][j])) > big) big=temp;
1747: if (big == 0.0) nrerror("Singular matrix in routine ludcmp");
1748: vv[i]=1.0/big;
1749: }
1750: for (j=1;j<=n;j++) {
1751: for (i=1;i<j;i++) {
1752: sum=a[i][j];
1753: for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];
1754: a[i][j]=sum;
1755: }
1756: big=0.0;
1757: for (i=j;i<=n;i++) {
1758: sum=a[i][j];
1759: for (k=1;k<j;k++)
1760: sum -= a[i][k]*a[k][j];
1761: a[i][j]=sum;
1762: if ( (dum=vv[i]*fabs(sum)) >= big) {
1763: big=dum;
1764: imax=i;
1765: }
1766: }
1767: if (j != imax) {
1768: for (k=1;k<=n;k++) {
1769: dum=a[imax][k];
1770: a[imax][k]=a[j][k];
1771: a[j][k]=dum;
1772: }
1773: *d = -(*d);
1774: vv[imax]=vv[j];
1775: }
1776: indx[j]=imax;
1777: if (a[j][j] == 0.0) a[j][j]=TINY;
1778: if (j != n) {
1779: dum=1.0/(a[j][j]);
1780: for (i=j+1;i<=n;i++) a[i][j] *= dum;
1781: }
1782: }
1783: free_vector(vv,1,n); /* Doesn't work */
1784: ;
1785: }
1786:
1787: void lubksb(double **a, int n, int *indx, double b[])
1788: {
1789: int i,ii=0,ip,j;
1790: double sum;
1791:
1792: for (i=1;i<=n;i++) {
1793: ip=indx[i];
1794: sum=b[ip];
1795: b[ip]=b[i];
1796: if (ii)
1797: for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];
1798: else if (sum) ii=i;
1799: b[i]=sum;
1800: }
1801: for (i=n;i>=1;i--) {
1802: sum=b[i];
1803: for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];
1804: b[i]=sum/a[i][i];
1805: }
1806: }
1807:
1808: /************ Frequencies ********************/
1.84 brouard 1809: 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 1810: { /* Some frequencies */
1811:
1812: int i, m, jk, k1,i1, j1, bool, z1,z2,j;
1813: int first;
1814: double ***freq; /* Frequencies */
1.73 lievre 1815: double *pp, **prop;
1816: double pos,posprop, k2, dateintsum=0,k2cpt=0;
1.53 brouard 1817: FILE *ficresp;
1818: char fileresp[FILENAMELENGTH];
1819:
1820: pp=vector(1,nlstate);
1.74 brouard 1821: prop=matrix(1,nlstate,iagemin,iagemax+3);
1.53 brouard 1822: strcpy(fileresp,"p");
1823: strcat(fileresp,fileres);
1824: if((ficresp=fopen(fileresp,"w"))==NULL) {
1825: printf("Problem with prevalence resultfile: %s\n", fileresp);
1826: fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
1827: exit(0);
1828: }
1.74 brouard 1829: freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);
1.53 brouard 1830: j1=0;
1831:
1832: j=cptcoveff;
1833: if (cptcovn<1) {j=1;ncodemax[1]=1;}
1834:
1835: first=1;
1836:
1837: for(k1=1; k1<=j;k1++){
1838: for(i1=1; i1<=ncodemax[k1];i1++){
1839: j1++;
1840: /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
1841: scanf("%d", i);*/
1842: for (i=-1; i<=nlstate+ndeath; i++)
1843: for (jk=-1; jk<=nlstate+ndeath; jk++)
1.74 brouard 1844: for(m=iagemin; m <= iagemax+3; m++)
1.53 brouard 1845: freq[i][jk][m]=0;
1.73 lievre 1846:
1847: for (i=1; i<=nlstate; i++)
1.74 brouard 1848: for(m=iagemin; m <= iagemax+3; m++)
1.73 lievre 1849: prop[i][m]=0;
1.53 brouard 1850:
1851: dateintsum=0;
1852: k2cpt=0;
1853: for (i=1; i<=imx; i++) {
1854: bool=1;
1855: if (cptcovn>0) {
1856: for (z1=1; z1<=cptcoveff; z1++)
1857: if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])
1858: bool=0;
1859: }
1.58 lievre 1860: if (bool==1){
1.53 brouard 1861: for(m=firstpass; m<=lastpass; m++){
1862: k2=anint[m][i]+(mint[m][i]/12.);
1.84 brouard 1863: /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/
1.74 brouard 1864: if(agev[m][i]==0) agev[m][i]=iagemax+1;
1865: if(agev[m][i]==1) agev[m][i]=iagemax+2;
1.73 lievre 1866: if (s[m][i]>0 && s[m][i]<=nlstate) prop[s[m][i]][(int)agev[m][i]] += weight[i];
1.53 brouard 1867: if (m<lastpass) {
1868: freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
1.74 brouard 1869: freq[s[m][i]][s[m+1][i]][iagemax+3] += weight[i];
1.53 brouard 1870: }
1871:
1.74 brouard 1872: if ((agev[m][i]>1) && (agev[m][i]< (iagemax+3))) {
1.53 brouard 1873: dateintsum=dateintsum+k2;
1874: k2cpt++;
1875: }
1.84 brouard 1876: /*}*/
1.53 brouard 1877: }
1878: }
1879: }
1880:
1.84 brouard 1881: /* fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
1.53 brouard 1882:
1883: if (cptcovn>0) {
1884: fprintf(ficresp, "\n#********** Variable ");
1885: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
1886: fprintf(ficresp, "**********\n#");
1887: }
1888: for(i=1; i<=nlstate;i++)
1889: fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
1890: fprintf(ficresp, "\n");
1891:
1.74 brouard 1892: for(i=iagemin; i <= iagemax+3; i++){
1893: if(i==iagemax+3){
1.53 brouard 1894: fprintf(ficlog,"Total");
1895: }else{
1896: if(first==1){
1897: first=0;
1898: printf("See log file for details...\n");
1899: }
1900: fprintf(ficlog,"Age %d", i);
1901: }
1902: for(jk=1; jk <=nlstate ; jk++){
1903: for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
1904: pp[jk] += freq[jk][m][i];
1905: }
1906: for(jk=1; jk <=nlstate ; jk++){
1907: for(m=-1, pos=0; m <=0 ; m++)
1908: pos += freq[jk][m][i];
1909: if(pp[jk]>=1.e-10){
1910: if(first==1){
1911: printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
1912: }
1913: fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
1914: }else{
1915: if(first==1)
1916: printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
1917: fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
1918: }
1919: }
1920:
1921: for(jk=1; jk <=nlstate ; jk++){
1922: for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
1923: pp[jk] += freq[jk][m][i];
1.73 lievre 1924: }
1925: for(jk=1,pos=0,posprop=0; jk <=nlstate ; jk++){
1926: pos += pp[jk];
1927: posprop += prop[jk][i];
1.53 brouard 1928: }
1929: for(jk=1; jk <=nlstate ; jk++){
1930: if(pos>=1.e-5){
1931: if(first==1)
1932: printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
1933: fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
1934: }else{
1935: if(first==1)
1936: printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
1937: fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
1938: }
1.74 brouard 1939: if( i <= iagemax){
1.53 brouard 1940: if(pos>=1.e-5){
1.73 lievre 1941: fprintf(ficresp," %d %.5f %.0f %.0f",i,prop[jk][i]/posprop, prop[jk][i],posprop);
1.84 brouard 1942: /*probs[i][jk][j1]= pp[jk]/pos;*/
1.53 brouard 1943: /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/
1944: }
1945: else
1.73 lievre 1946: fprintf(ficresp," %d NaNq %.0f %.0f",i,prop[jk][i],posprop);
1.53 brouard 1947: }
1948: }
1949:
1.69 brouard 1950: for(jk=-1; jk <=nlstate+ndeath; jk++)
1951: for(m=-1; m <=nlstate+ndeath; m++)
1.53 brouard 1952: if(freq[jk][m][i] !=0 ) {
1953: if(first==1)
1954: printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
1955: fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
1956: }
1.74 brouard 1957: if(i <= iagemax)
1.53 brouard 1958: fprintf(ficresp,"\n");
1959: if(first==1)
1960: printf("Others in log...\n");
1961: fprintf(ficlog,"\n");
1962: }
1963: }
1964: }
1965: dateintmean=dateintsum/k2cpt;
1966:
1967: fclose(ficresp);
1.74 brouard 1968: free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);
1.53 brouard 1969: free_vector(pp,1,nlstate);
1.74 brouard 1970: free_matrix(prop,1,nlstate,iagemin, iagemax+3);
1.53 brouard 1971: /* End of Freq */
1972: }
1973:
1974: /************ Prevalence ********************/
1.84 brouard 1975: 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 1976: {
1977: /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
1978: in each health status at the date of interview (if between dateprev1 and dateprev2).
1979: We still use firstpass and lastpass as another selection.
1980: */
1.53 brouard 1981:
1982: int i, m, jk, k1, i1, j1, bool, z1,z2,j;
1983: double ***freq; /* Frequencies */
1.73 lievre 1984: double *pp, **prop;
1985: double pos,posprop;
1.69 brouard 1986: double y2; /* in fractional years */
1.74 brouard 1987: int iagemin, iagemax;
1.53 brouard 1988:
1.74 brouard 1989: iagemin= (int) agemin;
1990: iagemax= (int) agemax;
1991: /*pp=vector(1,nlstate);*/
1992: prop=matrix(1,nlstate,iagemin,iagemax+3);
1993: /* freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
1.53 brouard 1994: j1=0;
1995:
1996: j=cptcoveff;
1997: if (cptcovn<1) {j=1;ncodemax[1]=1;}
1998:
1999: for(k1=1; k1<=j;k1++){
2000: for(i1=1; i1<=ncodemax[k1];i1++){
2001: j1++;
2002:
1.73 lievre 2003: for (i=1; i<=nlstate; i++)
1.74 brouard 2004: for(m=iagemin; m <= iagemax+3; m++)
2005: prop[i][m]=0.0;
1.53 brouard 2006:
1.69 brouard 2007: for (i=1; i<=imx; i++) { /* Each individual */
1.53 brouard 2008: bool=1;
2009: if (cptcovn>0) {
2010: for (z1=1; z1<=cptcoveff; z1++)
2011: if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])
2012: bool=0;
2013: }
2014: if (bool==1) {
1.69 brouard 2015: for(m=firstpass; m<=lastpass; m++){/* Other selection (we can limit to certain interviews*/
2016: y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
2017: if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
1.74 brouard 2018: if(agev[m][i]==0) agev[m][i]=iagemax+1;
2019: if(agev[m][i]==1) agev[m][i]=iagemax+2;
2020: 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);
2021: if (s[m][i]>0 && s[m][i]<=nlstate) {
2022: /*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]]);*/
2023: prop[s[m][i]][(int)agev[m][i]] += weight[i];
2024: prop[s[m][i]][iagemax+3] += weight[i];
2025: }
1.53 brouard 2026: }
1.69 brouard 2027: } /* end selection of waves */
1.53 brouard 2028: }
2029: }
1.74 brouard 2030: for(i=iagemin; i <= iagemax+3; i++){
1.53 brouard 2031:
1.74 brouard 2032: for(jk=1,posprop=0; jk <=nlstate ; jk++) {
2033: posprop += prop[jk][i];
2034: }
2035:
2036: for(jk=1; jk <=nlstate ; jk++){
2037: if( i <= iagemax){
2038: if(posprop>=1.e-5){
2039: probs[i][jk][j1]= prop[jk][i]/posprop;
2040: }
2041: }
2042: }/* end jk */
2043: }/* end i */
1.53 brouard 2044: } /* end i1 */
2045: } /* end k1 */
2046:
1.74 brouard 2047: /* free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
2048: /*free_vector(pp,1,nlstate);*/
2049: free_matrix(prop,1,nlstate, iagemin,iagemax+3);
2050: } /* End of prevalence */
1.53 brouard 2051:
2052: /************* Waves Concatenation ***************/
2053:
1.59 brouard 2054: 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 2055: {
2056: /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
2057: Death is a valid wave (if date is known).
2058: mw[mi][i] is the mi (mi=1 to wav[i]) effective wave of individual i
1.59 brouard 2059: dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
1.53 brouard 2060: and mw[mi+1][i]. dh depends on stepm.
2061: */
2062:
2063: int i, mi, m;
2064: /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
2065: double sum=0., jmean=0.;*/
2066: int first;
2067: int j, k=0,jk, ju, jl;
2068: double sum=0.;
2069: first=0;
2070: jmin=1e+5;
2071: jmax=-1;
2072: jmean=0.;
2073: for(i=1; i<=imx; i++){
2074: mi=0;
2075: m=firstpass;
2076: while(s[m][i] <= nlstate){
1.69 brouard 2077: if(s[m][i]>=1)
1.53 brouard 2078: mw[++mi][i]=m;
2079: if(m >=lastpass)
2080: break;
2081: else
2082: m++;
2083: }/* end while */
2084: if (s[m][i] > nlstate){
2085: mi++; /* Death is another wave */
2086: /* if(mi==0) never been interviewed correctly before death */
2087: /* Only death is a correct wave */
2088: mw[mi][i]=m;
2089: }
2090:
2091: wav[i]=mi;
2092: if(mi==0){
1.91 brouard 2093: nbwarn++;
1.53 brouard 2094: if(first==0){
1.85 brouard 2095: printf("Warning! None valid information for:%ld line=%d (skipped) and may be others, see log file\n",num[i],i);
1.53 brouard 2096: first=1;
2097: }
2098: if(first==1){
1.85 brouard 2099: fprintf(ficlog,"Warning! None valid information for:%ld line=%d (skipped)\n",num[i],i);
1.53 brouard 2100: }
2101: } /* end mi==0 */
1.77 brouard 2102: } /* End individuals */
1.53 brouard 2103:
2104: for(i=1; i<=imx; i++){
2105: for(mi=1; mi<wav[i];mi++){
2106: if (stepm <=0)
2107: dh[mi][i]=1;
2108: else{
1.77 brouard 2109: if (s[mw[mi+1][i]][i] > nlstate) { /* A death */
1.53 brouard 2110: if (agedc[i] < 2*AGESUP) {
1.85 brouard 2111: j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);
2112: if(j==0) j=1; /* Survives at least one month after exam */
2113: else if(j<0){
1.91 brouard 2114: nberr++;
1.85 brouard 2115: 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]);
1.91 brouard 2116: j=1; /* Temporary Dangerous patch */
1.86 brouard 2117: 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);
1.91 brouard 2118: fprintf(ficlog,"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]);
1.85 brouard 2119: 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);
2120: }
2121: k=k+1;
2122: if (j >= jmax) jmax=j;
2123: if (j <= jmin) jmin=j;
2124: sum=sum+j;
2125: /*if (j<0) printf("j=%d num=%d \n",j,i);*/
2126: /* printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
1.53 brouard 2127: }
2128: }
2129: else{
2130: j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
1.68 lievre 2131: /* printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
1.53 brouard 2132: k=k+1;
2133: if (j >= jmax) jmax=j;
2134: else if (j <= jmin)jmin=j;
2135: /* if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
1.73 lievre 2136: /*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 2137: if(j<0){
1.91 brouard 2138: nberr++;
1.85 brouard 2139: 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]);
2140: 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]);
2141: }
1.53 brouard 2142: sum=sum+j;
2143: }
2144: jk= j/stepm;
2145: jl= j -jk*stepm;
2146: ju= j -(jk+1)*stepm;
1.85 brouard 2147: if(mle <=1){ /* only if we use a the linear-interpoloation pseudo-likelihood */
1.64 lievre 2148: if(jl==0){
2149: dh[mi][i]=jk;
2150: bh[mi][i]=0;
2151: }else{ /* We want a negative bias in order to only have interpolation ie
2152: * at the price of an extra matrix product in likelihood */
2153: dh[mi][i]=jk+1;
2154: bh[mi][i]=ju;
2155: }
2156: }else{
2157: if(jl <= -ju){
2158: dh[mi][i]=jk;
2159: bh[mi][i]=jl; /* bias is positive if real duration
2160: * is higher than the multiple of stepm and negative otherwise.
2161: */
2162: }
2163: else{
2164: dh[mi][i]=jk+1;
2165: bh[mi][i]=ju;
2166: }
2167: if(dh[mi][i]==0){
2168: dh[mi][i]=1; /* At least one step */
2169: bh[mi][i]=ju; /* At least one step */
1.71 brouard 2170: /* 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 2171: }
1.85 brouard 2172: } /* end if mle */
2173: }
1.64 lievre 2174: } /* end wave */
1.53 brouard 2175: }
2176: jmean=sum/k;
2177: printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);
2178: fprintf(ficlog,"Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);
2179: }
2180:
2181: /*********** Tricode ****************************/
2182: void tricode(int *Tvar, int **nbcode, int imx)
2183: {
1.58 lievre 2184:
2185: int Ndum[20],ij=1, k, j, i, maxncov=19;
1.53 brouard 2186: int cptcode=0;
2187: cptcoveff=0;
2188:
1.58 lievre 2189: for (k=0; k<maxncov; k++) Ndum[k]=0;
1.53 brouard 2190: for (k=1; k<=7; k++) ncodemax[k]=0;
2191:
2192: for (j=1; j<=(cptcovn+2*cptcovprod); j++) {
1.58 lievre 2193: for (i=1; i<=imx; i++) { /*reads the data file to get the maximum
2194: modality*/
2195: ij=(int)(covar[Tvar[j]][i]); /* ij is the modality of this individual*/
2196: Ndum[ij]++; /*store the modality */
1.53 brouard 2197: /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
1.58 lievre 2198: if (ij > cptcode) cptcode=ij; /* getting the maximum of covariable
2199: Tvar[j]. If V=sex and male is 0 and
2200: female is 1, then cptcode=1.*/
1.53 brouard 2201: }
2202:
2203: for (i=0; i<=cptcode; i++) {
1.58 lievre 2204: 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 2205: }
1.58 lievre 2206:
1.53 brouard 2207: ij=1;
2208: for (i=1; i<=ncodemax[j]; i++) {
1.58 lievre 2209: for (k=0; k<= maxncov; k++) {
1.53 brouard 2210: if (Ndum[k] != 0) {
2211: nbcode[Tvar[j]][ij]=k;
1.58 lievre 2212: /* 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 2213:
2214: ij++;
2215: }
2216: if (ij > ncodemax[j]) break;
2217: }
2218: }
2219: }
2220:
1.58 lievre 2221: for (k=0; k< maxncov; k++) Ndum[k]=0;
1.53 brouard 2222:
1.58 lievre 2223: for (i=1; i<=ncovmodel-2; i++) {
2224: /* 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 2225: ij=Tvar[i];
1.58 lievre 2226: Ndum[ij]++;
1.53 brouard 2227: }
2228:
2229: ij=1;
1.58 lievre 2230: for (i=1; i<= maxncov; i++) {
1.53 brouard 2231: if((Ndum[i]!=0) && (i<=ncovcol)){
1.58 lievre 2232: Tvaraff[ij]=i; /*For printing */
1.53 brouard 2233: ij++;
2234: }
2235: }
2236:
1.58 lievre 2237: cptcoveff=ij-1; /*Number of simple covariates*/
1.53 brouard 2238: }
2239:
2240: /*********** Health Expectancies ****************/
2241:
2242: 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 )
2243:
2244: {
2245: /* Health expectancies */
2246: int i, j, nhstepm, hstepm, h, nstepm, k, cptj;
2247: double age, agelim, hf;
2248: double ***p3mat,***varhe;
2249: double **dnewm,**doldm;
2250: double *xp;
2251: double **gp, **gm;
2252: double ***gradg, ***trgradg;
2253: int theta;
2254:
1.74 brouard 2255: varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage);
1.53 brouard 2256: xp=vector(1,npar);
1.74 brouard 2257: dnewm=matrix(1,nlstate*nlstate,1,npar);
2258: doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate);
1.53 brouard 2259:
2260: fprintf(ficreseij,"# Health expectancies\n");
2261: fprintf(ficreseij,"# Age");
2262: for(i=1; i<=nlstate;i++)
2263: for(j=1; j<=nlstate;j++)
2264: fprintf(ficreseij," %1d-%1d (SE)",i,j);
2265: fprintf(ficreseij,"\n");
2266:
2267: if(estepm < stepm){
2268: printf ("Problem %d lower than %d\n",estepm, stepm);
2269: }
2270: else hstepm=estepm;
2271: /* We compute the life expectancy from trapezoids spaced every estepm months
2272: * This is mainly to measure the difference between two models: for example
2273: * if stepm=24 months pijx are given only every 2 years and by summing them
2274: * we are calculating an estimate of the Life Expectancy assuming a linear
1.66 brouard 2275: * progression in between and thus overestimating or underestimating according
1.53 brouard 2276: * to the curvature of the survival function. If, for the same date, we
2277: * estimate the model with stepm=1 month, we can keep estepm to 24 months
2278: * to compare the new estimate of Life expectancy with the same linear
2279: * hypothesis. A more precise result, taking into account a more precise
2280: * curvature will be obtained if estepm is as small as stepm. */
2281:
2282: /* For example we decided to compute the life expectancy with the smallest unit */
2283: /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
2284: nhstepm is the number of hstepm from age to agelim
2285: nstepm is the number of stepm from age to agelin.
2286: Look at hpijx to understand the reason of that which relies in memory size
2287: and note for a fixed period like estepm months */
2288: /* We decided (b) to get a life expectancy respecting the most precise curvature of the
2289: survival function given by stepm (the optimization length). Unfortunately it
2290: means that if the survival funtion is printed only each two years of age and if
2291: you sum them up and add 1 year (area under the trapezoids) you won't get the same
2292: results. So we changed our mind and took the option of the best precision.
2293: */
2294: hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
2295:
2296: agelim=AGESUP;
2297: for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
2298: /* nhstepm age range expressed in number of stepm */
2299: nstepm=(int) rint((agelim-age)*YEARM/stepm);
2300: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
2301: /* if (stepm >= YEARM) hstepm=1;*/
2302: nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
2303: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
1.74 brouard 2304: gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);
2305: gp=matrix(0,nhstepm,1,nlstate*nlstate);
2306: gm=matrix(0,nhstepm,1,nlstate*nlstate);
1.53 brouard 2307:
2308: /* Computed by stepm unit matrices, product of hstepm matrices, stored
2309: in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
2310: hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);
2311:
2312:
2313: hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
2314:
2315: /* Computing Variances of health expectancies */
2316:
2317: for(theta=1; theta <=npar; theta++){
2318: for(i=1; i<=npar; i++){
2319: xp[i] = x[i] + (i==theta ?delti[theta]:0);
2320: }
2321: hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
2322:
2323: cptj=0;
2324: for(j=1; j<= nlstate; j++){
2325: for(i=1; i<=nlstate; i++){
2326: cptj=cptj+1;
2327: for(h=0, gp[h][cptj]=0.; h<=nhstepm-1; h++){
2328: gp[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;
2329: }
2330: }
2331: }
2332:
2333:
2334: for(i=1; i<=npar; i++)
2335: xp[i] = x[i] - (i==theta ?delti[theta]:0);
2336: hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
2337:
2338: cptj=0;
2339: for(j=1; j<= nlstate; j++){
2340: for(i=1;i<=nlstate;i++){
2341: cptj=cptj+1;
2342: for(h=0, gm[h][cptj]=0.; h<=nhstepm-1; h++){
1.77 brouard 2343:
1.53 brouard 2344: gm[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;
2345: }
2346: }
2347: }
1.74 brouard 2348: for(j=1; j<= nlstate*nlstate; j++)
1.53 brouard 2349: for(h=0; h<=nhstepm-1; h++){
2350: gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
2351: }
2352: }
2353:
2354: /* End theta */
2355:
1.74 brouard 2356: trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar);
1.53 brouard 2357:
2358: for(h=0; h<=nhstepm-1; h++)
1.74 brouard 2359: for(j=1; j<=nlstate*nlstate;j++)
1.53 brouard 2360: for(theta=1; theta <=npar; theta++)
2361: trgradg[h][j][theta]=gradg[h][theta][j];
2362:
2363:
1.74 brouard 2364: for(i=1;i<=nlstate*nlstate;i++)
2365: for(j=1;j<=nlstate*nlstate;j++)
1.53 brouard 2366: varhe[i][j][(int)age] =0.;
2367:
2368: printf("%d|",(int)age);fflush(stdout);
2369: fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
2370: for(h=0;h<=nhstepm-1;h++){
2371: for(k=0;k<=nhstepm-1;k++){
1.74 brouard 2372: matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov);
2373: matprod2(doldm,dnewm,1,nlstate*nlstate,1,npar,1,nlstate*nlstate,gradg[k]);
2374: for(i=1;i<=nlstate*nlstate;i++)
2375: for(j=1;j<=nlstate*nlstate;j++)
1.53 brouard 2376: varhe[i][j][(int)age] += doldm[i][j]*hf*hf;
2377: }
2378: }
2379: /* Computing expectancies */
2380: for(i=1; i<=nlstate;i++)
2381: for(j=1; j<=nlstate;j++)
2382: for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
2383: eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
2384:
2385: /* 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]);*/
2386:
2387: }
2388:
2389: fprintf(ficreseij,"%3.0f",age );
2390: cptj=0;
2391: for(i=1; i<=nlstate;i++)
2392: for(j=1; j<=nlstate;j++){
2393: cptj++;
2394: fprintf(ficreseij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[cptj][cptj][(int)age]) );
2395: }
2396: fprintf(ficreseij,"\n");
2397:
1.74 brouard 2398: free_matrix(gm,0,nhstepm,1,nlstate*nlstate);
2399: free_matrix(gp,0,nhstepm,1,nlstate*nlstate);
2400: free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*nlstate);
2401: free_ma3x(trgradg,0,nhstepm,1,nlstate*nlstate,1,npar);
1.53 brouard 2402: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
2403: }
2404: printf("\n");
2405: fprintf(ficlog,"\n");
2406:
2407: free_vector(xp,1,npar);
1.74 brouard 2408: free_matrix(dnewm,1,nlstate*nlstate,1,npar);
2409: free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate);
2410: free_ma3x(varhe,1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int)fage);
1.53 brouard 2411: }
2412:
2413: /************ Variance ******************/
2414: 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)
2415: {
2416: /* Variance of health expectancies */
2417: /* double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
2418: /* double **newm;*/
2419: double **dnewm,**doldm;
2420: double **dnewmp,**doldmp;
2421: int i, j, nhstepm, hstepm, h, nstepm ;
2422: int k, cptcode;
2423: double *xp;
2424: double **gp, **gm; /* for var eij */
2425: double ***gradg, ***trgradg; /*for var eij */
2426: double **gradgp, **trgradgp; /* for var p point j */
2427: double *gpp, *gmp; /* for var p point j */
2428: double **varppt; /* for var p point j nlstate to nlstate+ndeath */
2429: double ***p3mat;
2430: double age,agelim, hf;
2431: double ***mobaverage;
2432: int theta;
2433: char digit[4];
1.55 lievre 2434: char digitp[25];
1.53 brouard 2435:
2436: char fileresprobmorprev[FILENAMELENGTH];
2437:
1.55 lievre 2438: if(popbased==1){
1.58 lievre 2439: if(mobilav!=0)
1.55 lievre 2440: strcpy(digitp,"-populbased-mobilav-");
2441: else strcpy(digitp,"-populbased-nomobil-");
2442: }
2443: else
1.53 brouard 2444: strcpy(digitp,"-stablbased-");
1.56 lievre 2445:
1.54 brouard 2446: if (mobilav!=0) {
1.53 brouard 2447: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
1.54 brouard 2448: if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
2449: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
2450: printf(" Error in movingaverage mobilav=%d\n",mobilav);
2451: }
1.53 brouard 2452: }
2453:
2454: strcpy(fileresprobmorprev,"prmorprev");
2455: sprintf(digit,"%-d",ij);
2456: /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
2457: strcat(fileresprobmorprev,digit); /* Tvar to be done */
2458: strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
2459: strcat(fileresprobmorprev,fileres);
2460: if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
2461: printf("Problem with resultfile: %s\n", fileresprobmorprev);
2462: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
2463: }
2464: printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
2465: fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
1.66 brouard 2466: 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 2467: fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
2468: for(j=nlstate+1; j<=(nlstate+ndeath);j++){
2469: fprintf(ficresprobmorprev," p.%-d SE",j);
2470: for(i=1; i<=nlstate;i++)
2471: fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
2472: }
2473: fprintf(ficresprobmorprev,"\n");
1.88 brouard 2474: fprintf(ficgp,"\n# Routine varevsij");
1.87 brouard 2475: 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");
2476: fprintf(fichtm,"\n<br>%s <br>\n",digitp);
2477: /* } */
1.53 brouard 2478: varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
2479:
2480: 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");
2481: fprintf(ficresvij,"# Age");
2482: for(i=1; i<=nlstate;i++)
2483: for(j=1; j<=nlstate;j++)
2484: fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);
2485: fprintf(ficresvij,"\n");
2486:
2487: xp=vector(1,npar);
2488: dnewm=matrix(1,nlstate,1,npar);
2489: doldm=matrix(1,nlstate,1,nlstate);
2490: dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
2491: doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
2492:
2493: gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
2494: gpp=vector(nlstate+1,nlstate+ndeath);
2495: gmp=vector(nlstate+1,nlstate+ndeath);
2496: trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
2497:
2498: if(estepm < stepm){
2499: printf ("Problem %d lower than %d\n",estepm, stepm);
2500: }
2501: else hstepm=estepm;
2502: /* For example we decided to compute the life expectancy with the smallest unit */
2503: /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
2504: nhstepm is the number of hstepm from age to agelim
2505: nstepm is the number of stepm from age to agelin.
2506: Look at hpijx to understand the reason of that which relies in memory size
2507: and note for a fixed period like k years */
2508: /* We decided (b) to get a life expectancy respecting the most precise curvature of the
2509: survival function given by stepm (the optimization length). Unfortunately it
1.66 brouard 2510: means that if the survival funtion is printed every two years of age and if
1.53 brouard 2511: you sum them up and add 1 year (area under the trapezoids) you won't get the same
2512: results. So we changed our mind and took the option of the best precision.
2513: */
2514: hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
2515: agelim = AGESUP;
2516: for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
2517: nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
2518: nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
2519: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
2520: gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
2521: gp=matrix(0,nhstepm,1,nlstate);
2522: gm=matrix(0,nhstepm,1,nlstate);
2523:
2524:
2525: for(theta=1; theta <=npar; theta++){
1.66 brouard 2526: for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
1.53 brouard 2527: xp[i] = x[i] + (i==theta ?delti[theta]:0);
2528: }
2529: hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
2530: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
2531:
2532: if (popbased==1) {
1.54 brouard 2533: if(mobilav ==0){
1.53 brouard 2534: for(i=1; i<=nlstate;i++)
2535: prlim[i][i]=probs[(int)age][i][ij];
1.54 brouard 2536: }else{ /* mobilav */
1.53 brouard 2537: for(i=1; i<=nlstate;i++)
2538: prlim[i][i]=mobaverage[(int)age][i][ij];
2539: }
2540: }
2541:
2542: for(j=1; j<= nlstate; j++){
2543: for(h=0; h<=nhstepm; h++){
2544: for(i=1, gp[h][j]=0.;i<=nlstate;i++)
2545: gp[h][j] += prlim[i][i]*p3mat[i][j][h];
2546: }
2547: }
1.66 brouard 2548: /* This for computing probability of death (h=1 means
2549: computed over hstepm matrices product = hstepm*stepm months)
2550: as a weighted average of prlim.
2551: */
1.69 brouard 2552: for(j=nlstate+1;j<=nlstate+ndeath;j++){
1.68 lievre 2553: for(i=1,gpp[j]=0.; i<= nlstate; i++)
1.53 brouard 2554: gpp[j] += prlim[i][i]*p3mat[i][j][1];
2555: }
1.66 brouard 2556: /* end probability of death */
1.53 brouard 2557:
1.66 brouard 2558: for(i=1; i<=npar; i++) /* Computes gradient x - delta */
1.53 brouard 2559: xp[i] = x[i] - (i==theta ?delti[theta]:0);
2560: hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
2561: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
2562:
2563: if (popbased==1) {
1.54 brouard 2564: if(mobilav ==0){
1.53 brouard 2565: for(i=1; i<=nlstate;i++)
2566: prlim[i][i]=probs[(int)age][i][ij];
1.54 brouard 2567: }else{ /* mobilav */
1.53 brouard 2568: for(i=1; i<=nlstate;i++)
2569: prlim[i][i]=mobaverage[(int)age][i][ij];
2570: }
2571: }
2572:
2573: for(j=1; j<= nlstate; j++){
2574: for(h=0; h<=nhstepm; h++){
2575: for(i=1, gm[h][j]=0.;i<=nlstate;i++)
2576: gm[h][j] += prlim[i][i]*p3mat[i][j][h];
2577: }
2578: }
1.66 brouard 2579: /* This for computing probability of death (h=1 means
2580: computed over hstepm matrices product = hstepm*stepm months)
2581: as a weighted average of prlim.
2582: */
1.69 brouard 2583: for(j=nlstate+1;j<=nlstate+ndeath;j++){
1.68 lievre 2584: for(i=1,gmp[j]=0.; i<= nlstate; i++)
2585: gmp[j] += prlim[i][i]*p3mat[i][j][1];
1.53 brouard 2586: }
1.66 brouard 2587: /* end probability of death */
1.53 brouard 2588:
2589: for(j=1; j<= nlstate; j++) /* vareij */
2590: for(h=0; h<=nhstepm; h++){
2591: gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
2592: }
1.68 lievre 2593:
1.53 brouard 2594: for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
2595: gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
2596: }
2597:
2598: } /* End theta */
2599:
2600: trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
2601:
2602: for(h=0; h<=nhstepm; h++) /* veij */
2603: for(j=1; j<=nlstate;j++)
2604: for(theta=1; theta <=npar; theta++)
2605: trgradg[h][j][theta]=gradg[h][theta][j];
2606:
2607: for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
1.69 brouard 2608: for(theta=1; theta <=npar; theta++)
1.53 brouard 2609: trgradgp[j][theta]=gradgp[theta][j];
1.69 brouard 2610:
1.53 brouard 2611:
2612: hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
2613: for(i=1;i<=nlstate;i++)
2614: for(j=1;j<=nlstate;j++)
2615: vareij[i][j][(int)age] =0.;
2616:
2617: for(h=0;h<=nhstepm;h++){
2618: for(k=0;k<=nhstepm;k++){
2619: matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
2620: matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
2621: for(i=1;i<=nlstate;i++)
2622: for(j=1;j<=nlstate;j++)
2623: vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
2624: }
2625: }
1.70 brouard 2626:
1.53 brouard 2627: /* pptj */
2628: matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
2629: matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
1.70 brouard 2630: for(j=nlstate+1;j<=nlstate+ndeath;j++)
2631: for(i=nlstate+1;i<=nlstate+ndeath;i++)
1.53 brouard 2632: varppt[j][i]=doldmp[j][i];
2633: /* end ppptj */
1.66 brouard 2634: /* x centered again */
1.53 brouard 2635: hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);
2636: prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);
2637:
2638: if (popbased==1) {
1.54 brouard 2639: if(mobilav ==0){
1.53 brouard 2640: for(i=1; i<=nlstate;i++)
2641: prlim[i][i]=probs[(int)age][i][ij];
1.54 brouard 2642: }else{ /* mobilav */
1.53 brouard 2643: for(i=1; i<=nlstate;i++)
2644: prlim[i][i]=mobaverage[(int)age][i][ij];
2645: }
2646: }
1.70 brouard 2647:
1.66 brouard 2648: /* This for computing probability of death (h=1 means
2649: computed over hstepm (estepm) matrices product = hstepm*stepm months)
2650: as a weighted average of prlim.
2651: */
1.68 lievre 2652: for(j=nlstate+1;j<=nlstate+ndeath;j++){
2653: for(i=1,gmp[j]=0.;i<= nlstate; i++)
1.53 brouard 2654: gmp[j] += prlim[i][i]*p3mat[i][j][1];
2655: }
1.66 brouard 2656: /* end probability of death */
1.53 brouard 2657:
2658: fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
2659: for(j=nlstate+1; j<=(nlstate+ndeath);j++){
2660: fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
2661: for(i=1; i<=nlstate;i++){
2662: fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
2663: }
2664: }
2665: fprintf(ficresprobmorprev,"\n");
2666:
2667: fprintf(ficresvij,"%.0f ",age );
2668: for(i=1; i<=nlstate;i++)
2669: for(j=1; j<=nlstate;j++){
2670: fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
2671: }
2672: fprintf(ficresvij,"\n");
2673: free_matrix(gp,0,nhstepm,1,nlstate);
2674: free_matrix(gm,0,nhstepm,1,nlstate);
2675: free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
2676: free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
2677: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
2678: } /* End age */
2679: free_vector(gpp,nlstate+1,nlstate+ndeath);
2680: free_vector(gmp,nlstate+1,nlstate+ndeath);
2681: free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
2682: free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
2683: fprintf(ficgp,"\nset noparametric;set nolabel; set ter png small;set size 0.65, 0.65");
2684: /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */
2685: fprintf(ficgp,"\n set log y; set nolog x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
1.67 brouard 2686: /* fprintf(ficgp,"\n plot \"%s\" u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm); */
2687: /* fprintf(ficgp,"\n replot \"%s\" u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm); */
2688: /* fprintf(ficgp,"\n replot \"%s\" u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm); */
1.88 brouard 2689: fprintf(ficgp,"\n plot \"%s\" u 1:($3) not w l 1 ",subdirf(fileresprobmorprev));
2690: fprintf(ficgp,"\n replot \"%s\" u 1:(($3+1.96*$4)) t \"95\%% interval\" w l 2 ",subdirf(fileresprobmorprev));
2691: fprintf(ficgp,"\n replot \"%s\" u 1:(($3-1.96*$4)) not w l 2 ",subdirf(fileresprobmorprev));
2692: fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",subdirf(fileresprobmorprev),subdirf(fileresprobmorprev));
2693: 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 2694: /* 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);
2695: */
1.88 brouard 2696: /* fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.png\";replot;",digitp,optionfilefiname,digit); */
1.89 brouard 2697: fprintf(ficgp,"\nset out \"%s%s.png\";replot;\n",subdirf3(optionfilefiname,"varmuptjgr",digitp),digit);
1.53 brouard 2698:
2699: free_vector(xp,1,npar);
2700: free_matrix(doldm,1,nlstate,1,nlstate);
2701: free_matrix(dnewm,1,nlstate,1,npar);
2702: free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
2703: free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
2704: free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
1.55 lievre 2705: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
1.53 brouard 2706: fclose(ficresprobmorprev);
1.88 brouard 2707: fflush(ficgp);
2708: fflush(fichtm);
1.84 brouard 2709: } /* end varevsij */
1.53 brouard 2710:
2711: /************ Variance of prevlim ******************/
2712: 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)
2713: {
2714: /* Variance of prevalence limit */
1.59 brouard 2715: /* double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
1.53 brouard 2716: double **newm;
2717: double **dnewm,**doldm;
2718: int i, j, nhstepm, hstepm;
2719: int k, cptcode;
2720: double *xp;
2721: double *gp, *gm;
2722: double **gradg, **trgradg;
2723: double age,agelim;
2724: int theta;
2725:
1.54 brouard 2726: fprintf(ficresvpl,"# Standard deviation of stable prevalences \n");
1.53 brouard 2727: fprintf(ficresvpl,"# Age");
2728: for(i=1; i<=nlstate;i++)
2729: fprintf(ficresvpl," %1d-%1d",i,i);
2730: fprintf(ficresvpl,"\n");
2731:
2732: xp=vector(1,npar);
2733: dnewm=matrix(1,nlstate,1,npar);
2734: doldm=matrix(1,nlstate,1,nlstate);
2735:
2736: hstepm=1*YEARM; /* Every year of age */
2737: hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */
2738: agelim = AGESUP;
2739: for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
2740: nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
2741: if (stepm >= YEARM) hstepm=1;
2742: nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
2743: gradg=matrix(1,npar,1,nlstate);
2744: gp=vector(1,nlstate);
2745: gm=vector(1,nlstate);
2746:
2747: for(theta=1; theta <=npar; theta++){
2748: for(i=1; i<=npar; i++){ /* Computes gradient */
2749: xp[i] = x[i] + (i==theta ?delti[theta]:0);
2750: }
2751: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
2752: for(i=1;i<=nlstate;i++)
2753: gp[i] = prlim[i][i];
2754:
2755: for(i=1; i<=npar; i++) /* Computes gradient */
2756: xp[i] = x[i] - (i==theta ?delti[theta]:0);
2757: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
2758: for(i=1;i<=nlstate;i++)
2759: gm[i] = prlim[i][i];
2760:
2761: for(i=1;i<=nlstate;i++)
2762: gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
2763: } /* End theta */
2764:
2765: trgradg =matrix(1,nlstate,1,npar);
2766:
2767: for(j=1; j<=nlstate;j++)
2768: for(theta=1; theta <=npar; theta++)
2769: trgradg[j][theta]=gradg[theta][j];
2770:
2771: for(i=1;i<=nlstate;i++)
2772: varpl[i][(int)age] =0.;
2773: matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
2774: matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
2775: for(i=1;i<=nlstate;i++)
2776: varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
2777:
2778: fprintf(ficresvpl,"%.0f ",age );
2779: for(i=1; i<=nlstate;i++)
2780: fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
2781: fprintf(ficresvpl,"\n");
2782: free_vector(gp,1,nlstate);
2783: free_vector(gm,1,nlstate);
2784: free_matrix(gradg,1,npar,1,nlstate);
2785: free_matrix(trgradg,1,nlstate,1,npar);
2786: } /* End age */
2787:
2788: free_vector(xp,1,npar);
2789: free_matrix(doldm,1,nlstate,1,npar);
2790: free_matrix(dnewm,1,nlstate,1,nlstate);
2791:
2792: }
2793:
2794: /************ Variance of one-step probabilities ******************/
2795: void varprob(char optionfilefiname[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij, int *Tvar, int **nbcode, int *ncodemax)
2796: {
2797: int i, j=0, i1, k1, l1, t, tj;
2798: int k2, l2, j1, z1;
2799: int k=0,l, cptcode;
2800: int first=1, first1;
2801: double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
2802: double **dnewm,**doldm;
2803: double *xp;
2804: double *gp, *gm;
2805: double **gradg, **trgradg;
2806: double **mu;
2807: double age,agelim, cov[NCOVMAX];
2808: double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
2809: int theta;
2810: char fileresprob[FILENAMELENGTH];
2811: char fileresprobcov[FILENAMELENGTH];
2812: char fileresprobcor[FILENAMELENGTH];
2813:
2814: double ***varpij;
2815:
2816: strcpy(fileresprob,"prob");
2817: strcat(fileresprob,fileres);
2818: if((ficresprob=fopen(fileresprob,"w"))==NULL) {
2819: printf("Problem with resultfile: %s\n", fileresprob);
2820: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
2821: }
2822: strcpy(fileresprobcov,"probcov");
2823: strcat(fileresprobcov,fileres);
2824: if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
2825: printf("Problem with resultfile: %s\n", fileresprobcov);
2826: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
2827: }
2828: strcpy(fileresprobcor,"probcor");
2829: strcat(fileresprobcor,fileres);
2830: if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
2831: printf("Problem with resultfile: %s\n", fileresprobcor);
2832: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
2833: }
2834: printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
2835: fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
2836: printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
2837: fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
2838: printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
2839: fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
2840:
2841: fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
2842: fprintf(ficresprob,"# Age");
2843: fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
2844: fprintf(ficresprobcov,"# Age");
2845: fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
2846: fprintf(ficresprobcov,"# Age");
2847:
2848:
2849: for(i=1; i<=nlstate;i++)
2850: for(j=1; j<=(nlstate+ndeath);j++){
2851: fprintf(ficresprob," p%1d-%1d (SE)",i,j);
2852: fprintf(ficresprobcov," p%1d-%1d ",i,j);
2853: fprintf(ficresprobcor," p%1d-%1d ",i,j);
2854: }
1.69 brouard 2855: /* fprintf(ficresprob,"\n");
1.53 brouard 2856: fprintf(ficresprobcov,"\n");
2857: fprintf(ficresprobcor,"\n");
1.69 brouard 2858: */
2859: xp=vector(1,npar);
1.53 brouard 2860: dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
2861: doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
2862: mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
2863: varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
2864: first=1;
1.88 brouard 2865: fprintf(ficgp,"\n# Routine varprob");
2866: fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
2867: fprintf(fichtm,"\n");
2868:
1.91 brouard 2869: fprintf(fichtm,"\n<li><h4> <a href=\"%s\">Computing matrix of variance-covariance of step probabilities</a></h4></li>\n",optionfilehtmcov);
2870: fprintf(fichtmcov,"\n<h4>Computing matrix of variance-covariance of step probabilities</h4>\n\
2871: file %s<br>\n",optionfilehtmcov);
2872: fprintf(fichtmcov,"\nEllipsoids of confidence centered on point (p<inf>ij</inf>, p<inf>kl</inf>) are estimated\
2873: and drawn. It helps understanding how is the covariance between two incidences.\
2874: They are expressed in year<sup>-1</sup> in order to be less dependent of stepm.<br>\n");
2875: fprintf(fichtmcov,"\n<br> Contour plot corresponding to x'cov<sup>-1</sup>x = 4 (where x is the column vector (pij,pkl)) are drawn. \
2876: It can be understood this way: if pij and pkl where uncorrelated the (2x2) matrix of covariance \
2877: would have been (1/(var pij), 0 , 0, 1/(var pkl)), and the confidence interval would be 2 \
2878: standard deviations wide on each axis. <br>\
2879: Now, if both incidences are correlated (usual case) we diagonalised the inverse of the covariance matrix\
2880: and made the appropriate rotation to look at the uncorrelated principal directions.<br>\
2881: To be simple, these graphs help to understand the significativity of each parameter in relation to a second other one.<br> \n");
1.53 brouard 2882:
2883: cov[1]=1;
2884: tj=cptcoveff;
2885: if (cptcovn<1) {tj=1;ncodemax[1]=1;}
2886: j1=0;
2887: for(t=1; t<=tj;t++){
2888: for(i1=1; i1<=ncodemax[t];i1++){
2889: j1++;
2890: if (cptcovn>0) {
2891: fprintf(ficresprob, "\n#********** Variable ");
2892: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
1.69 brouard 2893: fprintf(ficresprob, "**********\n#\n");
1.53 brouard 2894: fprintf(ficresprobcov, "\n#********** Variable ");
2895: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
1.69 brouard 2896: fprintf(ficresprobcov, "**********\n#\n");
1.53 brouard 2897:
2898: fprintf(ficgp, "\n#********** Variable ");
1.69 brouard 2899: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
2900: fprintf(ficgp, "**********\n#\n");
1.53 brouard 2901:
2902:
2903: fprintf(fichtm, "\n<hr size=\"2\" color=\"#EC5E5E\">********** Variable ");
2904: for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
2905: fprintf(fichtm, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
2906:
2907: fprintf(ficresprobcor, "\n#********** Variable ");
2908: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
1.69 brouard 2909: fprintf(ficresprobcor, "**********\n#");
1.53 brouard 2910: }
2911:
2912: for (age=bage; age<=fage; age ++){
2913: cov[2]=age;
2914: for (k=1; k<=cptcovn;k++) {
2915: cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];
2916: }
2917: for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
2918: for (k=1; k<=cptcovprod;k++)
2919: cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
2920:
2921: gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
2922: trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
2923: gp=vector(1,(nlstate)*(nlstate+ndeath));
2924: gm=vector(1,(nlstate)*(nlstate+ndeath));
2925:
2926: for(theta=1; theta <=npar; theta++){
2927: for(i=1; i<=npar; i++)
1.74 brouard 2928: xp[i] = x[i] + (i==theta ?delti[theta]:(double)0);
1.53 brouard 2929:
2930: pmij(pmmij,cov,ncovmodel,xp,nlstate);
2931:
2932: k=0;
2933: for(i=1; i<= (nlstate); i++){
2934: for(j=1; j<=(nlstate+ndeath);j++){
2935: k=k+1;
2936: gp[k]=pmmij[i][j];
2937: }
2938: }
2939:
2940: for(i=1; i<=npar; i++)
1.74 brouard 2941: xp[i] = x[i] - (i==theta ?delti[theta]:(double)0);
1.53 brouard 2942:
2943: pmij(pmmij,cov,ncovmodel,xp,nlstate);
2944: k=0;
2945: for(i=1; i<=(nlstate); i++){
2946: for(j=1; j<=(nlstate+ndeath);j++){
2947: k=k+1;
2948: gm[k]=pmmij[i][j];
2949: }
2950: }
2951:
2952: for(i=1; i<= (nlstate)*(nlstate+ndeath); i++)
1.74 brouard 2953: gradg[theta][i]=(gp[i]-gm[i])/(double)2./delti[theta];
1.53 brouard 2954: }
2955:
2956: for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
2957: for(theta=1; theta <=npar; theta++)
2958: trgradg[j][theta]=gradg[theta][j];
2959:
2960: matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov);
2961: matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);
1.59 brouard 2962: free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
2963: free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
2964: free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
2965: free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
2966:
1.53 brouard 2967: pmij(pmmij,cov,ncovmodel,x,nlstate);
2968:
2969: k=0;
2970: for(i=1; i<=(nlstate); i++){
2971: for(j=1; j<=(nlstate+ndeath);j++){
2972: k=k+1;
2973: mu[k][(int) age]=pmmij[i][j];
2974: }
2975: }
2976: for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
2977: for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
2978: varpij[i][j][(int)age] = doldm[i][j];
2979:
2980: /*printf("\n%d ",(int)age);
1.59 brouard 2981: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
2982: printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
2983: fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
2984: }*/
1.53 brouard 2985:
2986: fprintf(ficresprob,"\n%d ",(int)age);
2987: fprintf(ficresprobcov,"\n%d ",(int)age);
2988: fprintf(ficresprobcor,"\n%d ",(int)age);
2989:
2990: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)
2991: fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));
2992: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
2993: fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);
2994: fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
2995: }
2996: i=0;
2997: for (k=1; k<=(nlstate);k++){
2998: for (l=1; l<=(nlstate+ndeath);l++){
2999: i=i++;
3000: fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
3001: fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
3002: for (j=1; j<=i;j++){
3003: fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);
3004: fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));
3005: }
3006: }
3007: }/* end of loop for state */
3008: } /* end of loop for age */
3009:
3010: /* Confidence intervalle of pij */
3011: /*
1.59 brouard 3012: fprintf(ficgp,"\nset noparametric;unset label");
3013: fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");
3014: fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
3015: 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);
3016: fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);
3017: fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);
3018: fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);
1.53 brouard 3019: */
3020:
3021: /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
3022: first1=1;
3023: for (k2=1; k2<=(nlstate);k2++){
3024: for (l2=1; l2<=(nlstate+ndeath);l2++){
3025: if(l2==k2) continue;
3026: j=(k2-1)*(nlstate+ndeath)+l2;
3027: for (k1=1; k1<=(nlstate);k1++){
3028: for (l1=1; l1<=(nlstate+ndeath);l1++){
3029: if(l1==k1) continue;
3030: i=(k1-1)*(nlstate+ndeath)+l1;
3031: if(i<=j) continue;
3032: for (age=bage; age<=fage; age ++){
3033: if ((int)age %5==0){
3034: v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;
3035: v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;
3036: cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;
3037: mu1=mu[i][(int) age]/stepm*YEARM ;
3038: mu2=mu[j][(int) age]/stepm*YEARM;
3039: c12=cv12/sqrt(v1*v2);
3040: /* Computing eigen value of matrix of covariance */
3041: lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
3042: lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
3043: /* Eigen vectors */
3044: v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
3045: /*v21=sqrt(1.-v11*v11); *//* error */
3046: v21=(lc1-v1)/cv12*v11;
3047: v12=-v21;
3048: v22=v11;
3049: tnalp=v21/v11;
3050: if(first1==1){
3051: first1=0;
3052: 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);
3053: }
3054: 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);
3055: /*printf(fignu*/
3056: /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */
3057: /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */
3058: if(first==1){
3059: first=0;
3060: fprintf(ficgp,"\nset parametric;unset label");
3061: 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);
3062: fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
1.91 brouard 3063: fprintf(fichtmcov,"\n<br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup>\
1.88 brouard 3064: :<a href=\"%s%d%1d%1d-%1d%1d.png\">\
3065: %s%d%1d%1d-%1d%1d.png</A>, ",k1,l1,k2,l2,\
3066: subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2,\
3067: subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
1.91 brouard 3068: fprintf(fichtmcov,"\n<br><img src=\"%s%d%1d%1d-%1d%1d.png\"> ",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
3069: fprintf(fichtmcov,"\n<br> Correlation at age %d (%.3f),",(int) age, c12);
1.88 brouard 3070: fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\"",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
1.53 brouard 3071: fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
3072: fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
3073: 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",\
3074: mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
3075: mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
3076: }else{
3077: first=0;
1.91 brouard 3078: fprintf(fichtmcov," %d (%.3f),",(int) age, c12);
1.53 brouard 3079: fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
3080: fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
3081: 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",\
3082: mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
3083: mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
3084: }/* if first */
3085: } /* age mod 5 */
3086: } /* end loop age */
1.88 brouard 3087: fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\";replot;",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
1.53 brouard 3088: first=1;
3089: } /*l12 */
3090: } /* k12 */
3091: } /*l1 */
3092: }/* k1 */
3093: } /* loop covariates */
3094: }
1.59 brouard 3095: free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
3096: free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
1.53 brouard 3097: free_vector(xp,1,npar);
3098: fclose(ficresprob);
3099: fclose(ficresprobcov);
3100: fclose(ficresprobcor);
1.91 brouard 3101: fflush(ficgp);
3102: fflush(fichtmcov);
1.53 brouard 3103: }
3104:
3105:
3106: /******************* Printing html file ***********/
3107: void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \
3108: int lastpass, int stepm, int weightopt, char model[],\
3109: int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
3110: int popforecast, int estepm ,\
3111: double jprev1, double mprev1,double anprev1, \
3112: double jprev2, double mprev2,double anprev2){
3113: int jj1, k1, i1, cpt;
3114: /*char optionfilehtm[FILENAMELENGTH];*/
1.87 brouard 3115: /* if((fichtm=fopen(optionfilehtm,"a"))==NULL) { */
3116: /* printf("Problem with %s \n",optionfilehtm), exit(0); */
3117: /* fprintf(ficlog,"Problem with %s \n",optionfilehtm), exit(0); */
3118: /* } */
1.53 brouard 3119:
1.85 brouard 3120: fprintf(fichtm,"<ul><li><h4>Result files (first order: no variance)</h4>\n \
1.88 brouard 3121: - Observed prevalence in each state (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"%s\">%s</a> <br>\n \
3122: - Estimated transition probabilities over %d (stepm) months: <a href=\"%s\">%s</a><br>\n \
3123: - Stable prevalence in each health state: <a href=\"%s\">%s</a> <br>\n \
1.85 brouard 3124: - Life expectancies by age and initial health status (estepm=%2d months): \
1.88 brouard 3125: <a href=\"%s\">%s</a> <br>\n</li>", \
3126: jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirf2(fileres,"p"),subdirf2(fileres,"p"),\
3127: stepm,subdirf2(fileres,"pij"),subdirf2(fileres,"pij"),\
3128: subdirf2(fileres,"pl"),subdirf2(fileres,"pl"),\
3129: estepm,subdirf2(fileres,"e"),subdirf2(fileres,"e"));
1.53 brouard 3130:
3131: fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
3132:
3133: m=cptcoveff;
3134: if (cptcovn < 1) {m=1;ncodemax[1]=1;}
3135:
3136: jj1=0;
3137: for(k1=1; k1<=m;k1++){
3138: for(i1=1; i1<=ncodemax[k1];i1++){
3139: jj1++;
3140: if (cptcovn > 0) {
3141: fprintf(fichtm,"<hr size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
3142: for (cpt=1; cpt<=cptcoveff;cpt++)
3143: fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
3144: fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
3145: }
3146: /* Pij */
1.88 brouard 3147: 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> \
3148: <img src=\"%s%d1.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);
1.53 brouard 3149: /* Quasi-incidences */
1.85 brouard 3150: fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months\
1.88 brouard 3151: before but expressed in per year i.e. quasi incidences if stepm is small and probabilities too: %s%d2.png<br> \
3152: <img src=\"%s%d2.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);
1.53 brouard 3153: /* Stable prevalence in each health state */
3154: for(cpt=1; cpt<nlstate;cpt++){
1.85 brouard 3155: fprintf(fichtm,"<br>- Stable prevalence in each health state : p%s%d%d.png<br> \
1.88 brouard 3156: <img src=\"%s%d%d.png\">",subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1);
1.53 brouard 3157: }
3158: for(cpt=1; cpt<=nlstate;cpt++) {
1.88 brouard 3159: fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): %s%d%d.png <br> \
1.89 brouard 3160: <img src=\"%s%d%d.png\">",cpt,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1);
1.53 brouard 3161: }
1.85 brouard 3162: fprintf(fichtm,"\n<br>- Total life expectancy by age and \
1.88 brouard 3163: health expectancies in states (1) and (2): %s%d.png<br>\
3164: <img src=\"%s%d.png\">",subdirf2(optionfilefiname,"e"),jj1,subdirf2(optionfilefiname,"e"),jj1);
1.53 brouard 3165: } /* end i1 */
3166: }/* End k1 */
3167: fprintf(fichtm,"</ul>");
3168:
3169:
1.85 brouard 3170: fprintf(fichtm,"\n<br><li><h4> Result files (second order: variances)</h4>\n\
3171: - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n\
1.88 brouard 3172: - Variance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n\
3173: - Variance-covariance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n\
3174: - Correlation matrix of one-step probabilities: <a href=\"%s\">%s</a> <br>\n\
3175: - Variances and covariances of life expectancies by age and initial health status (estepm=%d months): <a href=\"%s\">%s</a><br>\n\
3176: - Health expectancies with their variances (no covariance): <a href=\"%s\">%s</a> <br>\n\
3177: - Standard deviation of stable prevalences: <a href=\"%s\">%s</a> <br>\n",\
3178: rfileres,rfileres,\
3179: subdirf2(fileres,"prob"),subdirf2(fileres,"prob"),\
3180: subdirf2(fileres,"probcov"),subdirf2(fileres,"probcov"),\
3181: subdirf2(fileres,"probcor"),subdirf2(fileres,"probcor"),\
3182: estepm, subdirf2(fileres,"v"),subdirf2(fileres,"v"),\
3183: subdirf2(fileres,"t"),subdirf2(fileres,"t"),\
3184: subdirf2(fileres,"vpl"),subdirf2(fileres,"vpl"));
1.53 brouard 3185:
1.76 brouard 3186: /* if(popforecast==1) fprintf(fichtm,"\n */
3187: /* - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n */
3188: /* - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n */
3189: /* <br>",fileres,fileres,fileres,fileres); */
3190: /* else */
3191: /* 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 3192: fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
3193:
3194: m=cptcoveff;
3195: if (cptcovn < 1) {m=1;ncodemax[1]=1;}
3196:
3197: jj1=0;
3198: for(k1=1; k1<=m;k1++){
3199: for(i1=1; i1<=ncodemax[k1];i1++){
3200: jj1++;
3201: if (cptcovn > 0) {
3202: fprintf(fichtm,"<hr size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
3203: for (cpt=1; cpt<=cptcoveff;cpt++)
3204: fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
3205: fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
3206: }
3207: for(cpt=1; cpt<=nlstate;cpt++) {
1.85 brouard 3208: fprintf(fichtm,"<br>- Observed and period prevalence (with confident\
1.88 brouard 3209: interval) in state (%d): %s%d%d.png <br>\
1.90 brouard 3210: <img src=\"%s%d%d.png\">",cpt,subdirf2(optionfilefiname,"v"),cpt,jj1,subdirf2(optionfilefiname,"v"),cpt,jj1);
1.53 brouard 3211: }
3212: } /* end i1 */
3213: }/* End k1 */
3214: fprintf(fichtm,"</ul>");
1.87 brouard 3215: fflush(fichtm);
1.53 brouard 3216: }
3217:
3218: /******************* Gnuplot file **************/
1.89 brouard 3219: void printinggnuplot(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
1.53 brouard 3220:
1.88 brouard 3221: char dirfileres[132],optfileres[132];
1.53 brouard 3222: int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;
3223: int ng;
1.88 brouard 3224: /* if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) { */
3225: /* printf("Problem with file %s",optionfilegnuplot); */
3226: /* fprintf(ficlog,"Problem with file %s",optionfilegnuplot); */
3227: /* } */
1.53 brouard 3228:
1.54 brouard 3229: /*#ifdef windows */
1.89 brouard 3230: fprintf(ficgp,"cd \"%s\" \n",pathc);
1.54 brouard 3231: /*#endif */
1.88 brouard 3232: m=pow(2,cptcoveff);
3233:
3234: strcpy(dirfileres,optionfilefiname);
3235: strcpy(optfileres,"vpl");
1.53 brouard 3236: /* 1eme*/
3237: for (cpt=1; cpt<= nlstate ; cpt ++) {
3238: for (k1=1; k1<= m ; k1 ++) {
1.88 brouard 3239: fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"v"),cpt,k1);
3240: fprintf(ficgp,"\n#set out \"v%s%d%d.png\" \n",optionfilefiname,cpt,k1);
3241: fprintf(ficgp,"set xlabel \"Age\" \n\
3242: set ylabel \"Probability\" \n\
3243: set ter png small\n\
3244: set size 0.65,0.65\n\
3245: plot [%.f:%.f] \"%s\" every :::%d::%d u 1:2 \"\%%lf",ageminpar,fage,subdirf2(fileres,"vpl"),k1-1,k1-1);
1.53 brouard 3246:
3247: for (i=1; i<= nlstate ; i ++) {
3248: if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
3249: else fprintf(ficgp," \%%*lf (\%%*lf)");
3250: }
1.88 brouard 3251: 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 3252: for (i=1; i<= nlstate ; i ++) {
3253: if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
3254: else fprintf(ficgp," \%%*lf (\%%*lf)");
3255: }
1.88 brouard 3256: fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"%s\" every :::%d::%d u 1:($2-1.96*$3) \"\%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1);
1.53 brouard 3257: for (i=1; i<= nlstate ; i ++) {
3258: if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
3259: else fprintf(ficgp," \%%*lf (\%%*lf)");
3260: }
1.88 brouard 3261: fprintf(ficgp,"\" t\"\" w l 1,\"%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",subdirf2(fileres,"p"),k1-1,k1-1,2+4*(cpt-1));
1.53 brouard 3262: }
3263: }
3264: /*2 eme*/
3265:
3266: for (k1=1; k1<= m ; k1 ++) {
1.88 brouard 3267: fprintf(ficgp,"\nset out \"%s%d.png\" \n",subdirf2(optionfilefiname,"e"),k1);
1.53 brouard 3268: fprintf(ficgp,"set ylabel \"Years\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] ",ageminpar,fage);
3269:
3270: for (i=1; i<= nlstate+1 ; i ++) {
3271: k=2*i;
1.88 brouard 3272: fprintf(ficgp,"\"%s\" every :::%d::%d u 1:2 \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
1.53 brouard 3273: for (j=1; j<= nlstate+1 ; j ++) {
3274: if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
3275: else fprintf(ficgp," \%%*lf (\%%*lf)");
3276: }
3277: if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");
3278: else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);
1.88 brouard 3279: fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
1.53 brouard 3280: for (j=1; j<= nlstate+1 ; j ++) {
3281: if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
3282: else fprintf(ficgp," \%%*lf (\%%*lf)");
3283: }
3284: fprintf(ficgp,"\" t\"\" w l 0,");
1.88 brouard 3285: fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
1.53 brouard 3286: for (j=1; j<= nlstate+1 ; j ++) {
3287: if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
3288: else fprintf(ficgp," \%%*lf (\%%*lf)");
3289: }
3290: if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");
3291: else fprintf(ficgp,"\" t\"\" w l 0,");
3292: }
3293: }
3294:
3295: /*3eme*/
3296:
3297: for (k1=1; k1<= m ; k1 ++) {
3298: for (cpt=1; cpt<= nlstate ; cpt ++) {
3299: k=2+nlstate*(2*cpt-2);
1.88 brouard 3300: fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"exp"),cpt,k1);
3301: fprintf(ficgp,"set ter png small\n\
3302: set size 0.65,0.65\n\
3303: plot [%.f:%.f] \"%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,subdirf2(fileres,"e"),k1-1,k1-1,k,cpt);
1.53 brouard 3304: /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
3305: for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
3306: fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
3307: fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
3308: for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
3309: fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
3310:
3311: */
3312: for (i=1; i< nlstate ; i ++) {
1.88 brouard 3313: 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 3314:
3315: }
3316: }
3317: }
3318:
1.76 brouard 3319: /* CV preval stable (period) */
1.53 brouard 3320: for (k1=1; k1<= m ; k1 ++) {
1.76 brouard 3321: for (cpt=1; cpt<=nlstate ; cpt ++) {
1.53 brouard 3322: k=3;
1.88 brouard 3323: fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"p"),cpt,k1);
3324: fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\
3325: set ter png small\nset size 0.65,0.65\n\
1.89 brouard 3326: unset log y\n\
1.88 brouard 3327: plot [%.f:%.f] \"%s\" u ($1==%d ? ($3):1/0):($%d/($%d",ageminpar,agemaxpar,subdirf2(fileres,"pij"),k1,k+cpt+1,k+1);
1.53 brouard 3328:
1.83 lievre 3329: for (i=1; i< nlstate ; i ++)
1.53 brouard 3330: fprintf(ficgp,"+$%d",k+i+1);
3331: fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);
3332:
3333: l=3+(nlstate+ndeath)*cpt;
1.88 brouard 3334: fprintf(ficgp,",\"%s\" u ($1==%d ? ($3):1/0):($%d/($%d",subdirf2(fileres,"pij"),k1,l+cpt+1,l+1);
1.53 brouard 3335: for (i=1; i< nlstate ; i ++) {
3336: l=3+(nlstate+ndeath)*cpt;
3337: fprintf(ficgp,"+$%d",l+i+1);
3338: }
3339: fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);
3340: }
3341: }
3342:
3343: /* proba elementaires */
3344: for(i=1,jk=1; i <=nlstate; i++){
3345: for(k=1; k <=(nlstate+ndeath); k++){
3346: if (k != i) {
3347: for(j=1; j <=ncovmodel; j++){
3348: fprintf(ficgp,"p%d=%f ",jk,p[jk]);
3349: jk++;
3350: fprintf(ficgp,"\n");
3351: }
3352: }
3353: }
3354: }
3355:
3356: for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/
3357: for(jk=1; jk <=m; jk++) {
1.88 brouard 3358: fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"pe"),jk,ng);
1.53 brouard 3359: if (ng==2)
3360: fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
3361: else
3362: fprintf(ficgp,"\nset title \"Probability\"\n");
3363: fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65\nset log y\nplot [%.f:%.f] ",ageminpar,agemaxpar);
3364: i=1;
3365: for(k2=1; k2<=nlstate; k2++) {
3366: k3=i;
3367: for(k=1; k<=(nlstate+ndeath); k++) {
3368: if (k != k2){
3369: if(ng==2)
3370: fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);
3371: else
3372: fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
3373: ij=1;
3374: for(j=3; j <=ncovmodel; j++) {
3375: if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
3376: fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
3377: ij++;
3378: }
3379: else
3380: fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
3381: }
3382: fprintf(ficgp,")/(1");
3383:
3384: for(k1=1; k1 <=nlstate; k1++){
3385: fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);
3386: ij=1;
3387: for(j=3; j <=ncovmodel; j++){
3388: if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
3389: fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
3390: ij++;
3391: }
3392: else
3393: fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
3394: }
3395: fprintf(ficgp,")");
3396: }
3397: fprintf(ficgp,") t \"p%d%d\" ", k2,k);
3398: if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");
3399: i=i+ncovmodel;
3400: }
3401: } /* end k */
3402: } /* end k2 */
3403: } /* end jk */
3404: } /* end ng */
1.88 brouard 3405: fflush(ficgp);
1.53 brouard 3406: } /* end gnuplot */
3407:
3408:
3409: /*************** Moving average **************/
1.54 brouard 3410: int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav){
1.53 brouard 3411:
3412: int i, cpt, cptcod;
1.58 lievre 3413: int modcovmax =1;
1.54 brouard 3414: int mobilavrange, mob;
1.53 brouard 3415: double age;
1.58 lievre 3416:
3417: modcovmax=2*cptcoveff;/* Max number of modalities. We suppose
3418: a covariate has 2 modalities */
3419: if (cptcovn<1) modcovmax=1; /* At least 1 pass */
3420:
1.54 brouard 3421: if(mobilav==1||mobilav ==3 ||mobilav==5 ||mobilav== 7){
3422: if(mobilav==1) mobilavrange=5; /* default */
3423: else mobilavrange=mobilav;
3424: for (age=bage; age<=fage; age++)
3425: for (i=1; i<=nlstate;i++)
1.58 lievre 3426: for (cptcod=1;cptcod<=modcovmax;cptcod++)
1.54 brouard 3427: mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
3428: /* We keep the original values on the extreme ages bage, fage and for
3429: fage+1 and bage-1 we use a 3 terms moving average; for fage+2 bage+2
3430: we use a 5 terms etc. until the borders are no more concerned.
3431: */
3432: for (mob=3;mob <=mobilavrange;mob=mob+2){
3433: for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){
3434: for (i=1; i<=nlstate;i++){
1.58 lievre 3435: for (cptcod=1;cptcod<=modcovmax;cptcod++){
1.54 brouard 3436: mobaverage[(int)age][i][cptcod] =probs[(int)age][i][cptcod];
3437: for (cpt=1;cpt<=(mob-1)/2;cpt++){
3438: mobaverage[(int)age][i][cptcod] +=probs[(int)age-cpt][i][cptcod];
3439: mobaverage[(int)age][i][cptcod] +=probs[(int)age+cpt][i][cptcod];
3440: }
3441: mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/mob;
3442: }
1.53 brouard 3443: }
1.54 brouard 3444: }/* end age */
3445: }/* end mob */
3446: }else return -1;
3447: return 0;
3448: }/* End movingaverage */
1.53 brouard 3449:
3450:
3451: /************** Forecasting ******************/
1.70 brouard 3452: 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 3453: /* proj1, year, month, day of starting projection
3454: agemin, agemax range of age
3455: dateprev1 dateprev2 range of dates during which prevalence is computed
1.70 brouard 3456: anproj2 year of en of projection (same day and month as proj1).
1.69 brouard 3457: */
1.73 lievre 3458: int yearp, stepsize, hstepm, nhstepm, j, k, c, cptcod, i, h, i1;
1.53 brouard 3459: int *popage;
1.70 brouard 3460: double agec; /* generic age */
3461: double agelim, ppij, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
1.53 brouard 3462: double *popeffectif,*popcount;
3463: double ***p3mat;
1.55 lievre 3464: double ***mobaverage;
1.53 brouard 3465: char fileresf[FILENAMELENGTH];
3466:
1.69 brouard 3467: agelim=AGESUP;
1.84 brouard 3468: prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
1.53 brouard 3469:
3470: strcpy(fileresf,"f");
3471: strcat(fileresf,fileres);
3472: if((ficresf=fopen(fileresf,"w"))==NULL) {
3473: printf("Problem with forecast resultfile: %s\n", fileresf);
3474: fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);
3475: }
3476: printf("Computing forecasting: result on file '%s' \n", fileresf);
3477: fprintf(ficlog,"Computing forecasting: result on file '%s' \n", fileresf);
3478:
3479: if (cptcoveff==0) ncodemax[cptcoveff]=1;
3480:
1.54 brouard 3481: if (mobilav!=0) {
1.53 brouard 3482: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
1.54 brouard 3483: if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
3484: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
3485: printf(" Error in movingaverage mobilav=%d\n",mobilav);
3486: }
1.53 brouard 3487: }
3488:
3489: stepsize=(int) (stepm+YEARM-1)/YEARM;
3490: if (stepm<=12) stepsize=1;
1.74 brouard 3491: if(estepm < stepm){
3492: printf ("Problem %d lower than %d\n",estepm, stepm);
3493: }
3494: else hstepm=estepm;
3495:
1.53 brouard 3496: hstepm=hstepm/stepm;
1.69 brouard 3497: yp1=modf(dateintmean,&yp);/* extracts integral of datemean in yp and
3498: fractional in yp1 */
1.53 brouard 3499: anprojmean=yp;
3500: yp2=modf((yp1*12),&yp);
3501: mprojmean=yp;
3502: yp1=modf((yp2*30.5),&yp);
3503: jprojmean=yp;
3504: if(jprojmean==0) jprojmean=1;
3505: if(mprojmean==0) jprojmean=1;
1.73 lievre 3506:
3507: i1=cptcoveff;
3508: if (cptcovn < 1){i1=1;}
1.53 brouard 3509:
1.70 brouard 3510: fprintf(ficresf,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2);
1.53 brouard 3511:
1.70 brouard 3512: fprintf(ficresf,"#****** Routine prevforecast **\n");
1.73 lievre 3513:
1.75 brouard 3514: /* if (h==(int)(YEARM*yearp)){ */
1.73 lievre 3515: for(cptcov=1, k=0;cptcov<=i1;cptcov++){
1.53 brouard 3516: for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
3517: k=k+1;
3518: fprintf(ficresf,"\n#******");
3519: for(j=1;j<=cptcoveff;j++) {
1.70 brouard 3520: 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 3521: }
3522: fprintf(ficresf,"******\n");
1.70 brouard 3523: fprintf(ficresf,"# Covariate valuofcovar yearproj age");
3524: for(j=1; j<=nlstate+ndeath;j++){
3525: for(i=1; i<=nlstate;i++)
3526: fprintf(ficresf," p%d%d",i,j);
3527: fprintf(ficresf," p.%d",j);
3528: }
1.74 brouard 3529: for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) {
1.53 brouard 3530: fprintf(ficresf,"\n");
1.70 brouard 3531: fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+yearp);
1.53 brouard 3532:
1.71 brouard 3533: for (agec=fage; agec>=(ageminpar-1); agec--){
1.70 brouard 3534: nhstepm=(int) rint((agelim-agec)*YEARM/stepm);
1.53 brouard 3535: nhstepm = nhstepm/hstepm;
3536: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3537: oldm=oldms;savm=savms;
1.70 brouard 3538: hpxij(p3mat,nhstepm,agec,hstepm,p,nlstate,stepm,oldm,savm, k);
1.53 brouard 3539:
3540: for (h=0; h<=nhstepm; h++){
1.75 brouard 3541: if (h*hstepm/YEARM*stepm ==yearp) {
1.69 brouard 3542: fprintf(ficresf,"\n");
3543: for(j=1;j<=cptcoveff;j++)
3544: fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
1.70 brouard 3545: fprintf(ficresf,"%.f %.f ",anproj1+yearp,agec+h*hstepm/YEARM*stepm);
1.53 brouard 3546: }
3547: for(j=1; j<=nlstate+ndeath;j++) {
1.70 brouard 3548: ppij=0.;
1.71 brouard 3549: for(i=1; i<=nlstate;i++) {
1.53 brouard 3550: if (mobilav==1)
1.71 brouard 3551: ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][i][cptcod];
1.53 brouard 3552: else {
1.71 brouard 3553: ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][cptcod];
1.53 brouard 3554: }
1.75 brouard 3555: if (h*hstepm/YEARM*stepm== yearp) {
1.70 brouard 3556: fprintf(ficresf," %.3f", p3mat[i][j][h]);
1.75 brouard 3557: }
3558: } /* end i */
3559: if (h*hstepm/YEARM*stepm==yearp) {
1.70 brouard 3560: fprintf(ficresf," %.3f", ppij);
1.53 brouard 3561: }
1.75 brouard 3562: }/* end j */
3563: } /* end h */
1.53 brouard 3564: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
1.75 brouard 3565: } /* end agec */
3566: } /* end yearp */
3567: } /* end cptcod */
3568: } /* end cptcov */
1.53 brouard 3569:
1.54 brouard 3570: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
1.53 brouard 3571:
3572: fclose(ficresf);
3573: }
1.70 brouard 3574:
3575: /************** Forecasting *****not tested NB*************/
1.53 brouard 3576: 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){
3577:
3578: int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;
3579: int *popage;
1.69 brouard 3580: double calagedatem, agelim, kk1, kk2;
1.53 brouard 3581: double *popeffectif,*popcount;
3582: double ***p3mat,***tabpop,***tabpopprev;
1.55 lievre 3583: double ***mobaverage;
1.53 brouard 3584: char filerespop[FILENAMELENGTH];
3585:
3586: tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
3587: tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
3588: agelim=AGESUP;
1.69 brouard 3589: calagedatem=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;
1.53 brouard 3590:
1.84 brouard 3591: prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
1.53 brouard 3592:
3593:
3594: strcpy(filerespop,"pop");
3595: strcat(filerespop,fileres);
3596: if((ficrespop=fopen(filerespop,"w"))==NULL) {
3597: printf("Problem with forecast resultfile: %s\n", filerespop);
3598: fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop);
3599: }
3600: printf("Computing forecasting: result on file '%s' \n", filerespop);
3601: fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop);
3602:
3603: if (cptcoveff==0) ncodemax[cptcoveff]=1;
3604:
1.54 brouard 3605: if (mobilav!=0) {
1.53 brouard 3606: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
1.54 brouard 3607: if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
3608: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
3609: printf(" Error in movingaverage mobilav=%d\n",mobilav);
3610: }
1.53 brouard 3611: }
3612:
3613: stepsize=(int) (stepm+YEARM-1)/YEARM;
3614: if (stepm<=12) stepsize=1;
3615:
3616: agelim=AGESUP;
3617:
3618: hstepm=1;
3619: hstepm=hstepm/stepm;
3620:
3621: if (popforecast==1) {
3622: if((ficpop=fopen(popfile,"r"))==NULL) {
3623: printf("Problem with population file : %s\n",popfile);exit(0);
3624: fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0);
3625: }
3626: popage=ivector(0,AGESUP);
3627: popeffectif=vector(0,AGESUP);
3628: popcount=vector(0,AGESUP);
3629:
3630: i=1;
3631: while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;
3632:
3633: imx=i;
3634: for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];
3635: }
3636:
1.69 brouard 3637: for(cptcov=1,k=0;cptcov<=i2;cptcov++){
1.53 brouard 3638: for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
3639: k=k+1;
3640: fprintf(ficrespop,"\n#******");
3641: for(j=1;j<=cptcoveff;j++) {
3642: fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
3643: }
3644: fprintf(ficrespop,"******\n");
3645: fprintf(ficrespop,"# Age");
3646: for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);
3647: if (popforecast==1) fprintf(ficrespop," [Population]");
3648:
3649: for (cpt=0; cpt<=0;cpt++) {
3650: fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);
3651:
1.69 brouard 3652: for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){
1.53 brouard 3653: nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);
3654: nhstepm = nhstepm/hstepm;
3655:
3656: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3657: oldm=oldms;savm=savms;
3658: hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
3659:
3660: for (h=0; h<=nhstepm; h++){
1.69 brouard 3661: if (h==(int) (calagedatem+YEARM*cpt)) {
1.53 brouard 3662: fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
3663: }
3664: for(j=1; j<=nlstate+ndeath;j++) {
3665: kk1=0.;kk2=0;
3666: for(i=1; i<=nlstate;i++) {
3667: if (mobilav==1)
3668: kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];
3669: else {
3670: kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];
3671: }
3672: }
1.69 brouard 3673: if (h==(int)(calagedatem+12*cpt)){
1.53 brouard 3674: tabpop[(int)(agedeb)][j][cptcod]=kk1;
3675: /*fprintf(ficrespop," %.3f", kk1);
3676: if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/
3677: }
3678: }
3679: for(i=1; i<=nlstate;i++){
3680: kk1=0.;
3681: for(j=1; j<=nlstate;j++){
3682: kk1= kk1+tabpop[(int)(agedeb)][j][cptcod];
3683: }
1.69 brouard 3684: tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedatem+12*cpt)*hstepm/YEARM*stepm-1)];
1.53 brouard 3685: }
3686:
1.69 brouard 3687: if (h==(int)(calagedatem+12*cpt)) for(j=1; j<=nlstate;j++)
1.53 brouard 3688: fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);
3689: }
3690: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3691: }
3692: }
3693:
3694: /******/
3695:
3696: for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) {
3697: fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);
1.69 brouard 3698: for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){
1.53 brouard 3699: nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);
3700: nhstepm = nhstepm/hstepm;
3701:
3702: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3703: oldm=oldms;savm=savms;
3704: hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
3705: for (h=0; h<=nhstepm; h++){
1.69 brouard 3706: if (h==(int) (calagedatem+YEARM*cpt)) {
1.53 brouard 3707: fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
3708: }
3709: for(j=1; j<=nlstate+ndeath;j++) {
3710: kk1=0.;kk2=0;
3711: for(i=1; i<=nlstate;i++) {
3712: kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];
3713: }
1.69 brouard 3714: if (h==(int)(calagedatem+12*cpt)) fprintf(ficresf," %15.2f", kk1);
1.53 brouard 3715: }
3716: }
3717: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3718: }
3719: }
3720: }
3721: }
3722:
1.54 brouard 3723: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
1.53 brouard 3724:
3725: if (popforecast==1) {
3726: free_ivector(popage,0,AGESUP);
3727: free_vector(popeffectif,0,AGESUP);
3728: free_vector(popcount,0,AGESUP);
3729: }
3730: free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
3731: free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
3732: fclose(ficrespop);
1.84 brouard 3733: } /* End of popforecast */
1.53 brouard 3734:
1.87 brouard 3735: int fileappend(FILE *fichier, char *optionfich)
1.86 brouard 3736: {
1.87 brouard 3737: if((fichier=fopen(optionfich,"a"))==NULL) {
3738: printf("Problem with file: %s\n", optionfich);
3739: fprintf(ficlog,"Problem with file: %s\n", optionfich);
3740: return (0);
1.86 brouard 3741: }
1.87 brouard 3742: fflush(fichier);
3743: return (1);
1.86 brouard 3744: }
1.88 brouard 3745: void prwizard(int ncovmodel, int nlstate, int ndeath, char model[], FILE *ficparo)
3746: {
3747:
3748: char ca[32], cb[32], cc[32];
3749: int i,j, k, l, li, lj, lk, ll, jj, npar, itimes;
3750: int numlinepar;
3751:
3752: printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
3753: fprintf(ficparo,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
3754: for(i=1; i <=nlstate; i++){
3755: jj=0;
3756: for(j=1; j <=nlstate+ndeath; j++){
3757: if(j==i) continue;
3758: jj++;
3759: /*ca[0]= k+'a'-1;ca[1]='\0';*/
3760: printf("%1d%1d",i,j);
3761: fprintf(ficparo,"%1d%1d",i,j);
3762: for(k=1; k<=ncovmodel;k++){
3763: /* printf(" %lf",param[i][j][k]); */
3764: /* fprintf(ficparo," %lf",param[i][j][k]); */
3765: printf(" 0.");
3766: fprintf(ficparo," 0.");
3767: }
3768: printf("\n");
3769: fprintf(ficparo,"\n");
3770: }
3771: }
3772: printf("# Scales (for hessian or gradient estimation)\n");
3773: fprintf(ficparo,"# Scales (for hessian or gradient estimation)\n");
3774: npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/
3775: for(i=1; i <=nlstate; i++){
3776: jj=0;
3777: for(j=1; j <=nlstate+ndeath; j++){
3778: if(j==i) continue;
3779: jj++;
3780: fprintf(ficparo,"%1d%1d",i,j);
3781: printf("%1d%1d",i,j);
3782: fflush(stdout);
3783: for(k=1; k<=ncovmodel;k++){
3784: /* printf(" %le",delti3[i][j][k]); */
3785: /* fprintf(ficparo," %le",delti3[i][j][k]); */
3786: printf(" 0.");
3787: fprintf(ficparo," 0.");
3788: }
3789: numlinepar++;
3790: printf("\n");
3791: fprintf(ficparo,"\n");
3792: }
3793: }
3794: printf("# Covariance matrix\n");
3795: /* # 121 Var(a12)\n\ */
3796: /* # 122 Cov(b12,a12) Var(b12)\n\ */
3797: /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
3798: /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
3799: /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
3800: /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
3801: /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
3802: /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
3803: fflush(stdout);
3804: fprintf(ficparo,"# Covariance matrix\n");
3805: /* # 121 Var(a12)\n\ */
3806: /* # 122 Cov(b12,a12) Var(b12)\n\ */
3807: /* # ...\n\ */
3808: /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
3809:
3810: for(itimes=1;itimes<=2;itimes++){
3811: jj=0;
3812: for(i=1; i <=nlstate; i++){
3813: for(j=1; j <=nlstate+ndeath; j++){
3814: if(j==i) continue;
3815: for(k=1; k<=ncovmodel;k++){
3816: jj++;
3817: ca[0]= k+'a'-1;ca[1]='\0';
3818: if(itimes==1){
3819: printf("#%1d%1d%d",i,j,k);
3820: fprintf(ficparo,"#%1d%1d%d",i,j,k);
3821: }else{
3822: printf("%1d%1d%d",i,j,k);
3823: fprintf(ficparo,"%1d%1d%d",i,j,k);
3824: /* printf(" %.5le",matcov[i][j]); */
3825: }
3826: ll=0;
3827: for(li=1;li <=nlstate; li++){
3828: for(lj=1;lj <=nlstate+ndeath; lj++){
3829: if(lj==li) continue;
3830: for(lk=1;lk<=ncovmodel;lk++){
3831: ll++;
3832: if(ll<=jj){
3833: cb[0]= lk +'a'-1;cb[1]='\0';
3834: if(ll<jj){
3835: if(itimes==1){
3836: printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
3837: fprintf(ficparo," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
3838: }else{
3839: printf(" 0.");
3840: fprintf(ficparo," 0.");
3841: }
3842: }else{
3843: if(itimes==1){
3844: printf(" Var(%s%1d%1d)",ca,i,j);
3845: fprintf(ficparo," Var(%s%1d%1d)",ca,i,j);
3846: }else{
3847: printf(" 0.");
3848: fprintf(ficparo," 0.");
3849: }
3850: }
3851: }
3852: } /* end lk */
3853: } /* end lj */
3854: } /* end li */
3855: printf("\n");
3856: fprintf(ficparo,"\n");
3857: numlinepar++;
3858: } /* end k*/
3859: } /*end j */
3860: } /* end i */
3861: }
3862:
3863: } /* end of prwizard */
3864:
1.91 brouard 3865:
1.53 brouard 3866: /***********************************************/
3867: /**************** Main Program *****************/
3868: /***********************************************/
3869:
3870: int main(int argc, char *argv[])
3871: {
1.61 brouard 3872: int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav);
1.74 brouard 3873: int i,j, k, n=MAXN,iter,m,size=100,cptcode, cptcod;
1.88 brouard 3874: int jj, imk;
1.85 brouard 3875: int numlinepar=0; /* Current linenumber of parameter file */
1.87 brouard 3876: /* FILE *fichtm; *//* Html File */
3877: /* FILE *ficgp;*/ /*Gnuplot File */
1.53 brouard 3878: double agedeb, agefin,hf;
3879: double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;
3880:
3881: double fret;
3882: double **xi,tmp,delta;
3883:
3884: double dum; /* Dummy variable */
3885: double ***p3mat;
3886: double ***mobaverage;
3887: int *indx;
3888: char line[MAXLINE], linepar[MAXLINE];
1.88 brouard 3889: char path[MAXLINE],pathc[MAXLINE],pathcd[MAXLINE],pathtot[MAXLINE],model[MAXLINE];
3890: char pathr[MAXLINE];
1.53 brouard 3891: int firstobs=1, lastobs=10;
3892: int sdeb, sfin; /* Status at beginning and end */
3893: int c, h , cpt,l;
3894: int ju,jl, mi;
3895: int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;
1.59 brouard 3896: int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,*tab;
1.69 brouard 3897: int mobilavproj=0 , prevfcast=0 ; /* moving average of prev, If prevfcast=1 prevalence projection */
1.53 brouard 3898: int mobilav=0,popforecast=0;
3899: int hstepm, nhstepm;
1.74 brouard 3900: double jprev1=1, mprev1=1,anprev1=2000,jprev2=1, mprev2=1,anprev2=2000;
3901: double jpyram=1, mpyram=1,anpyram=2000,jpyram1=1, mpyram1=1,anpyram1=2000;
1.53 brouard 3902:
3903: double bage, fage, age, agelim, agebase;
3904: double ftolpl=FTOL;
3905: double **prlim;
3906: double *severity;
3907: double ***param; /* Matrix of parameters */
3908: double *p;
3909: double **matcov; /* Matrix of covariance */
3910: double ***delti3; /* Scale */
3911: double *delti; /* Scale */
3912: double ***eij, ***vareij;
3913: double **varpl; /* Variances of prevalence limits by age */
3914: double *epj, vepp;
3915: double kk1, kk2;
1.74 brouard 3916: double dateprev1, dateprev2,jproj1=1,mproj1=1,anproj1=2000,jproj2=1,mproj2=1,anproj2=2000;
1.53 brouard 3917:
3918: char *alph[]={"a","a","b","c","d","e"}, str[4];
3919:
3920:
3921: char z[1]="c", occ;
1.86 brouard 3922:
1.53 brouard 3923: char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];
1.88 brouard 3924: char strstart[80], *strt, strtend[80];
1.85 brouard 3925: char *stratrunc;
3926: int lstra;
3927:
3928: long total_usecs;
1.53 brouard 3929:
1.85 brouard 3930: /* gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */
3931: (void) gettimeofday(&start_time,&tzp);
1.91 brouard 3932: curr_time=start_time;
1.85 brouard 3933: tm = *localtime(&start_time.tv_sec);
3934: tmg = *gmtime(&start_time.tv_sec);
1.88 brouard 3935: strcpy(strstart,asctime(&tm));
1.86 brouard 3936:
1.88 brouard 3937: /* printf("Localtime (at start)=%s",strstart); */
1.85 brouard 3938: /* tp.tv_sec = tp.tv_sec +86400; */
3939: /* tm = *localtime(&start_time.tv_sec); */
3940: /* tmg.tm_year=tmg.tm_year +dsign*dyear; */
3941: /* tmg.tm_mon=tmg.tm_mon +dsign*dmonth; */
3942: /* tmg.tm_hour=tmg.tm_hour + 1; */
3943: /* tp.tv_sec = mktime(&tmg); */
3944: /* strt=asctime(&tmg); */
1.88 brouard 3945: /* printf("Time(after) =%s",strstart); */
1.85 brouard 3946: /* (void) time (&time_value);
3947: * printf("time=%d,t-=%d\n",time_value,time_value-86400);
3948: * tm = *localtime(&time_value);
1.88 brouard 3949: * strstart=asctime(&tm);
3950: * printf("tim_value=%d,asctime=%s\n",time_value,strstart);
1.85 brouard 3951: */
3952:
1.91 brouard 3953: nberr=0; /* Number of errors and warnings */
3954: nbwarn=0;
1.53 brouard 3955: getcwd(pathcd, size);
3956:
1.81 brouard 3957: printf("\n%s\n%s",version,fullversion);
1.53 brouard 3958: if(argc <=1){
3959: printf("\nEnter the parameter file name: ");
3960: scanf("%s",pathtot);
3961: }
3962: else{
3963: strcpy(pathtot,argv[1]);
3964: }
1.88 brouard 3965: /*if(getcwd(pathcd, MAXLINE)!= NULL)printf ("Error pathcd\n");*/
1.53 brouard 3966: /*cygwin_split_path(pathtot,path,optionfile);
3967: printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/
3968: /* cutv(path,optionfile,pathtot,'\\');*/
3969:
3970: split(pathtot,path,optionfile,optionfilext,optionfilefiname);
1.85 brouard 3971: printf("pathtot=%s,\npath=%s,\noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
1.53 brouard 3972: chdir(path);
1.88 brouard 3973: strcpy(command,"mkdir ");
3974: strcat(command,optionfilefiname);
3975: if((outcmd=system(command)) != 0){
3976: printf("Problem creating directory or it already exists %s%s, err=%d\n",path,optionfilefiname,outcmd);
3977: /* fprintf(ficlog,"Problem creating directory %s%s\n",path,optionfilefiname); */
3978: /* fclose(ficlog); */
3979: /* exit(1); */
3980: }
3981: /* if((imk=mkdir(optionfilefiname))<0){ */
3982: /* perror("mkdir"); */
3983: /* } */
1.53 brouard 3984:
1.59 brouard 3985: /*-------- arguments in the command line --------*/
1.53 brouard 3986:
3987: /* Log file */
3988: strcat(filelog, optionfilefiname);
3989: strcat(filelog,".log"); /* */
3990: if((ficlog=fopen(filelog,"w"))==NULL) {
3991: printf("Problem with logfile %s\n",filelog);
3992: goto end;
3993: }
3994: fprintf(ficlog,"Log filename:%s\n",filelog);
1.85 brouard 3995: fprintf(ficlog,"\n%s\n%s",version,fullversion);
1.53 brouard 3996: fprintf(ficlog,"\nEnter the parameter file name: ");
1.88 brouard 3997: fprintf(ficlog,"pathtot=%s\n\
3998: path=%s \n\
3999: optionfile=%s\n\
4000: optionfilext=%s\n\
4001: optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
1.86 brouard 4002:
1.88 brouard 4003: printf("Localtime (at start):%s",strstart);
4004: fprintf(ficlog,"Localtime (at start): %s",strstart);
1.53 brouard 4005: fflush(ficlog);
1.91 brouard 4006: /* (void) gettimeofday(&curr_time,&tzp); */
4007: /* printf("Elapsed time %d\n", asc_diff_time(curr_time.tv_sec-start_time.tv_sec,tmpout)); */
1.53 brouard 4008:
4009: /* */
4010: strcpy(fileres,"r");
4011: strcat(fileres, optionfilefiname);
4012: strcat(fileres,".txt"); /* Other files have txt extension */
4013:
4014: /*---------arguments file --------*/
4015:
4016: if((ficpar=fopen(optionfile,"r"))==NULL) {
4017: printf("Problem with optionfile %s\n",optionfile);
4018: fprintf(ficlog,"Problem with optionfile %s\n",optionfile);
1.85 brouard 4019: fflush(ficlog);
1.53 brouard 4020: goto end;
4021: }
4022:
1.88 brouard 4023:
4024:
1.53 brouard 4025: strcpy(filereso,"o");
4026: strcat(filereso,fileres);
1.88 brouard 4027: if((ficparo=fopen(filereso,"w"))==NULL) { /* opened on subdirectory */
1.53 brouard 4028: printf("Problem with Output resultfile: %s\n", filereso);
4029: fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso);
1.85 brouard 4030: fflush(ficlog);
1.53 brouard 4031: goto end;
4032: }
4033:
4034: /* Reads comments: lines beginning with '#' */
1.85 brouard 4035: numlinepar=0;
1.53 brouard 4036: while((c=getc(ficpar))=='#' && c!= EOF){
4037: ungetc(c,ficpar);
4038: fgets(line, MAXLINE, ficpar);
1.85 brouard 4039: numlinepar++;
1.53 brouard 4040: puts(line);
4041: fputs(line,ficparo);
1.85 brouard 4042: fputs(line,ficlog);
1.53 brouard 4043: }
4044: ungetc(c,ficpar);
4045:
4046: 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 4047: numlinepar++;
1.53 brouard 4048: 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);
4049: 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 4050: 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);
4051: fflush(ficlog);
1.59 brouard 4052: while((c=getc(ficpar))=='#' && c!= EOF){
1.53 brouard 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);
1.85 brouard 4061:
1.53 brouard 4062:
4063: covar=matrix(0,NCOVMAX,1,n);
1.58 lievre 4064: cptcovn=0; /*Number of covariates, i.e. number of '+' in model statement*/
1.53 brouard 4065: if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;
4066:
1.58 lievre 4067: ncovmodel=2+cptcovn; /*Number of variables = cptcovn + intercept + age */
1.53 brouard 4068: nvar=ncovmodel-1; /* Suppressing age as a basic covariate */
1.88 brouard 4069:
4070: if(mle==-1){ /* Print a wizard for help writing covariance matrix */
4071: prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
4072: printf(" You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
4073: fprintf(ficlog," You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
4074: fclose (ficparo);
4075: fclose (ficlog);
4076: exit(0);
4077: }
1.53 brouard 4078: /* Read guess parameters */
4079: /* Reads comments: lines beginning with '#' */
4080: while((c=getc(ficpar))=='#' && c!= EOF){
4081: ungetc(c,ficpar);
4082: fgets(line, MAXLINE, ficpar);
1.85 brouard 4083: numlinepar++;
1.53 brouard 4084: puts(line);
4085: fputs(line,ficparo);
1.85 brouard 4086: fputs(line,ficlog);
1.53 brouard 4087: }
4088: ungetc(c,ficpar);
1.85 brouard 4089:
1.53 brouard 4090: param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
1.85 brouard 4091: for(i=1; i <=nlstate; i++){
4092: j=0;
4093: for(jj=1; jj <=nlstate+ndeath; jj++){
4094: if(jj==i) continue;
4095: j++;
1.53 brouard 4096: fscanf(ficpar,"%1d%1d",&i1,&j1);
1.85 brouard 4097: if ((i1 != i) && (j1 != j)){
4098: printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n",numlinepar, i,j, i1, j1);
4099: exit(1);
4100: }
1.53 brouard 4101: fprintf(ficparo,"%1d%1d",i1,j1);
4102: if(mle==1)
4103: printf("%1d%1d",i,j);
4104: fprintf(ficlog,"%1d%1d",i,j);
4105: for(k=1; k<=ncovmodel;k++){
4106: fscanf(ficpar," %lf",¶m[i][j][k]);
4107: if(mle==1){
4108: printf(" %lf",param[i][j][k]);
4109: fprintf(ficlog," %lf",param[i][j][k]);
4110: }
4111: else
4112: fprintf(ficlog," %lf",param[i][j][k]);
4113: fprintf(ficparo," %lf",param[i][j][k]);
4114: }
4115: fscanf(ficpar,"\n");
1.85 brouard 4116: numlinepar++;
1.53 brouard 4117: if(mle==1)
4118: printf("\n");
4119: fprintf(ficlog,"\n");
4120: fprintf(ficparo,"\n");
4121: }
1.85 brouard 4122: }
4123: fflush(ficlog);
4124:
1.59 brouard 4125: npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/
1.53 brouard 4126:
4127: p=param[1][1];
4128:
4129: /* Reads comments: lines beginning with '#' */
4130: while((c=getc(ficpar))=='#' && c!= EOF){
4131: ungetc(c,ficpar);
4132: fgets(line, MAXLINE, ficpar);
1.85 brouard 4133: numlinepar++;
1.53 brouard 4134: puts(line);
4135: fputs(line,ficparo);
1.85 brouard 4136: fputs(line,ficlog);
1.53 brouard 4137: }
4138: ungetc(c,ficpar);
4139:
4140: delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
1.74 brouard 4141: /* delti=vector(1,npar); *//* Scale of each paramater (output from hesscov) */
1.53 brouard 4142: for(i=1; i <=nlstate; i++){
4143: for(j=1; j <=nlstate+ndeath-1; j++){
4144: fscanf(ficpar,"%1d%1d",&i1,&j1);
1.85 brouard 4145: if ((i1-i)*(j1-j)!=0){
4146: printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n",numlinepar, i,j, i1, j1);
4147: exit(1);
4148: }
1.53 brouard 4149: printf("%1d%1d",i,j);
4150: fprintf(ficparo,"%1d%1d",i1,j1);
1.85 brouard 4151: fprintf(ficlog,"%1d%1d",i1,j1);
1.53 brouard 4152: for(k=1; k<=ncovmodel;k++){
4153: fscanf(ficpar,"%le",&delti3[i][j][k]);
4154: printf(" %le",delti3[i][j][k]);
4155: fprintf(ficparo," %le",delti3[i][j][k]);
1.85 brouard 4156: fprintf(ficlog," %le",delti3[i][j][k]);
1.53 brouard 4157: }
4158: fscanf(ficpar,"\n");
1.85 brouard 4159: numlinepar++;
1.53 brouard 4160: printf("\n");
4161: fprintf(ficparo,"\n");
1.85 brouard 4162: fprintf(ficlog,"\n");
1.53 brouard 4163: }
4164: }
1.85 brouard 4165: fflush(ficlog);
4166:
1.53 brouard 4167: delti=delti3[1][1];
1.74 brouard 4168:
4169:
4170: /* 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 4171:
4172: /* Reads comments: lines beginning with '#' */
4173: while((c=getc(ficpar))=='#' && c!= EOF){
4174: ungetc(c,ficpar);
4175: fgets(line, MAXLINE, ficpar);
1.85 brouard 4176: numlinepar++;
1.53 brouard 4177: puts(line);
4178: fputs(line,ficparo);
1.85 brouard 4179: fputs(line,ficlog);
1.53 brouard 4180: }
4181: ungetc(c,ficpar);
4182:
4183: matcov=matrix(1,npar,1,npar);
4184: for(i=1; i <=npar; i++){
4185: fscanf(ficpar,"%s",&str);
4186: if(mle==1)
4187: printf("%s",str);
4188: fprintf(ficlog,"%s",str);
4189: fprintf(ficparo,"%s",str);
4190: for(j=1; j <=i; j++){
4191: fscanf(ficpar," %le",&matcov[i][j]);
4192: if(mle==1){
4193: printf(" %.5le",matcov[i][j]);
4194: }
1.85 brouard 4195: fprintf(ficlog," %.5le",matcov[i][j]);
1.53 brouard 4196: fprintf(ficparo," %.5le",matcov[i][j]);
4197: }
4198: fscanf(ficpar,"\n");
1.85 brouard 4199: numlinepar++;
1.53 brouard 4200: if(mle==1)
4201: printf("\n");
4202: fprintf(ficlog,"\n");
4203: fprintf(ficparo,"\n");
4204: }
4205: for(i=1; i <=npar; i++)
4206: for(j=i+1;j<=npar;j++)
4207: matcov[i][j]=matcov[j][i];
4208:
4209: if(mle==1)
4210: printf("\n");
4211: fprintf(ficlog,"\n");
4212:
1.85 brouard 4213: fflush(ficlog);
1.53 brouard 4214:
1.59 brouard 4215: /*-------- Rewriting paramater file ----------*/
4216: strcpy(rfileres,"r"); /* "Rparameterfile */
4217: strcat(rfileres,optionfilefiname); /* Parameter file first name*/
4218: strcat(rfileres,"."); /* */
4219: strcat(rfileres,optionfilext); /* Other files have txt extension */
4220: if((ficres =fopen(rfileres,"w"))==NULL) {
4221: printf("Problem writing new parameter file: %s\n", fileres);goto end;
4222: fprintf(ficlog,"Problem writing new parameter file: %s\n", fileres);goto end;
4223: }
4224: fprintf(ficres,"#%s\n",version);
1.53 brouard 4225:
1.59 brouard 4226: /*-------- data file ----------*/
4227: if((fic=fopen(datafile,"r"))==NULL) {
4228: printf("Problem with datafile: %s\n", datafile);goto end;
4229: fprintf(ficlog,"Problem with datafile: %s\n", datafile);goto end;
4230: }
4231:
4232: n= lastobs;
4233: severity = vector(1,maxwav);
4234: outcome=imatrix(1,maxwav+1,1,n);
1.85 brouard 4235: num=lvector(1,n);
1.59 brouard 4236: moisnais=vector(1,n);
4237: annais=vector(1,n);
4238: moisdc=vector(1,n);
4239: andc=vector(1,n);
4240: agedc=vector(1,n);
4241: cod=ivector(1,n);
4242: weight=vector(1,n);
4243: for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */
4244: mint=matrix(1,maxwav,1,n);
4245: anint=matrix(1,maxwav,1,n);
4246: s=imatrix(1,maxwav+1,1,n);
4247: tab=ivector(1,NCOVMAX);
4248: ncodemax=ivector(1,8);
4249:
4250: i=1;
4251: while (fgets(line, MAXLINE, fic) != NULL) {
4252: if ((i >= firstobs) && (i <=lastobs)) {
1.53 brouard 4253:
1.59 brouard 4254: for (j=maxwav;j>=1;j--){
4255: cutv(stra, strb,line,' '); s[j][i]=atoi(strb);
4256: strcpy(line,stra);
4257: cutv(stra, strb,line,'/'); anint[j][i]=(double)(atoi(strb)); strcpy(line,stra);
4258: cutv(stra, strb,line,' '); mint[j][i]=(double)(atoi(strb)); strcpy(line,stra);
4259: }
1.53 brouard 4260:
1.59 brouard 4261: cutv(stra, strb,line,'/'); andc[i]=(double)(atoi(strb)); strcpy(line,stra);
4262: cutv(stra, strb,line,' '); moisdc[i]=(double)(atoi(strb)); strcpy(line,stra);
1.53 brouard 4263:
1.59 brouard 4264: cutv(stra, strb,line,'/'); annais[i]=(double)(atoi(strb)); strcpy(line,stra);
4265: cutv(stra, strb,line,' '); moisnais[i]=(double)(atoi(strb)); strcpy(line,stra);
1.53 brouard 4266:
1.59 brouard 4267: cutv(stra, strb,line,' '); weight[i]=(double)(atoi(strb)); strcpy(line,stra);
4268: for (j=ncovcol;j>=1;j--){
4269: cutv(stra, strb,line,' '); covar[j][i]=(double)(atoi(strb)); strcpy(line,stra);
4270: }
1.85 brouard 4271: lstra=strlen(stra);
4272: if(lstra > 9){ /* More than 2**32 or max of what printf can write with %ld */
4273: stratrunc = &(stra[lstra-9]);
4274: num[i]=atol(stratrunc);
4275: }
4276: else
4277: num[i]=atol(stra);
1.53 brouard 4278:
1.59 brouard 4279: /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){
1.85 brouard 4280: 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 4281:
1.59 brouard 4282: i=i+1;
4283: }
4284: }
4285: /* printf("ii=%d", ij);
4286: scanf("%d",i);*/
1.53 brouard 4287: imx=i-1; /* Number of individuals */
4288:
4289: /* for (i=1; i<=imx; i++){
4290: if ((s[1][i]==3) && (s[2][i]==2)) s[2][i]=3;
4291: if ((s[2][i]==3) && (s[3][i]==2)) s[3][i]=3;
4292: if ((s[3][i]==3) && (s[4][i]==2)) s[4][i]=3;
4293: }*/
4294: /* for (i=1; i<=imx; i++){
4295: if (s[4][i]==9) s[4][i]=-1;
1.85 brouard 4296: 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 4297:
1.71 brouard 4298: for (i=1; i<=imx; i++)
1.53 brouard 4299:
1.71 brouard 4300: /*if ((s[3][i]==3) || (s[4][i]==3)) weight[i]=0.08;
4301: else weight[i]=1;*/
4302:
1.53 brouard 4303: /* Calculation of the number of parameter from char model*/
4304: Tvar=ivector(1,15); /* stores the number n of the covariates in Vm+Vn at 1 and m at 2 */
4305: Tprod=ivector(1,15);
4306: Tvaraff=ivector(1,15);
4307: Tvard=imatrix(1,15,1,2);
4308: Tage=ivector(1,15);
4309:
1.58 lievre 4310: if (strlen(model) >1){ /* If there is at least 1 covariate */
1.53 brouard 4311: j=0, j1=0, k1=1, k2=1;
1.58 lievre 4312: j=nbocc(model,'+'); /* j=Number of '+' */
4313: j1=nbocc(model,'*'); /* j1=Number of '*' */
4314: cptcovn=j+1;
4315: cptcovprod=j1; /*Number of products */
1.53 brouard 4316:
4317: strcpy(modelsav,model);
4318: if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){
4319: printf("Error. Non available option model=%s ",model);
4320: fprintf(ficlog,"Error. Non available option model=%s ",model);
4321: goto end;
4322: }
4323:
1.59 brouard 4324: /* This loop fills the array Tvar from the string 'model'.*/
1.58 lievre 4325:
1.53 brouard 4326: for(i=(j+1); i>=1;i--){
4327: cutv(stra,strb,modelsav,'+'); /* keeps in strb after the last + */
1.59 brouard 4328: if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyzes it */
1.53 brouard 4329: /* printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/
4330: /*scanf("%d",i);*/
4331: if (strchr(strb,'*')) { /* Model includes a product */
4332: cutv(strd,strc,strb,'*'); /* strd*strc Vm*Vn (if not *age)*/
4333: if (strcmp(strc,"age")==0) { /* Vn*age */
4334: cptcovprod--;
4335: cutv(strb,stre,strd,'V');
4336: Tvar[i]=atoi(stre); /* computes n in Vn and stores in Tvar*/
4337: cptcovage++;
4338: Tage[cptcovage]=i;
4339: /*printf("stre=%s ", stre);*/
4340: }
4341: else if (strcmp(strd,"age")==0) { /* or age*Vn */
4342: cptcovprod--;
4343: cutv(strb,stre,strc,'V');
4344: Tvar[i]=atoi(stre);
4345: cptcovage++;
4346: Tage[cptcovage]=i;
4347: }
4348: else { /* Age is not in the model */
4349: cutv(strb,stre,strc,'V'); /* strc= Vn, stre is n*/
4350: Tvar[i]=ncovcol+k1;
4351: cutv(strb,strc,strd,'V'); /* strd was Vm, strc is m */
4352: Tprod[k1]=i;
4353: Tvard[k1][1]=atoi(strc); /* m*/
4354: Tvard[k1][2]=atoi(stre); /* n */
4355: Tvar[cptcovn+k2]=Tvard[k1][1];
4356: Tvar[cptcovn+k2+1]=Tvard[k1][2];
4357: for (k=1; k<=lastobs;k++)
4358: covar[ncovcol+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];
4359: k1++;
4360: k2=k2+2;
4361: }
4362: }
4363: else { /* no more sum */
4364: /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/
4365: /* scanf("%d",i);*/
4366: cutv(strd,strc,strb,'V');
4367: Tvar[i]=atoi(strc);
4368: }
4369: strcpy(modelsav,stra);
4370: /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);
4371: scanf("%d",i);*/
4372: } /* end of loop + */
4373: } /* end model */
4374:
1.58 lievre 4375: /*The number n of Vn is stored in Tvar. cptcovage =number of age covariate. Tage gives the position of age. cptcovprod= number of products.
4376: If model=V1+V1*age then Tvar[1]=1 Tvar[2]=1 cptcovage=1 Tage[1]=2 cptcovprod=0*/
4377:
1.53 brouard 4378: /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);
4379: printf("cptcovprod=%d ", cptcovprod);
4380: fprintf(ficlog,"cptcovprod=%d ", cptcovprod);
1.58 lievre 4381:
4382: scanf("%d ",i);
4383: fclose(fic);*/
1.53 brouard 4384:
4385: /* if(mle==1){*/
1.59 brouard 4386: if (weightopt != 1) { /* Maximisation without weights*/
4387: for(i=1;i<=n;i++) weight[i]=1.0;
4388: }
1.53 brouard 4389: /*-calculation of age at interview from date of interview and age at death -*/
1.59 brouard 4390: agev=matrix(1,maxwav,1,imx);
1.53 brouard 4391:
1.59 brouard 4392: for (i=1; i<=imx; i++) {
4393: for(m=2; (m<= maxwav); m++) {
1.76 brouard 4394: if (((int)mint[m][i]== 99) && (s[m][i] <= nlstate)){
1.59 brouard 4395: anint[m][i]=9999;
4396: s[m][i]=-1;
4397: }
1.76 brouard 4398: if((int)moisdc[i]==99 && (int)andc[i]==9999 && s[m][i]>nlstate){
1.91 brouard 4399: nberr++;
1.85 brouard 4400: 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);
4401: 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 4402: s[m][i]=-1;
4403: }
4404: if((int)moisdc[i]==99 && (int)andc[i]!=9999 && s[m][i]>nlstate){
1.91 brouard 4405: nberr++;
1.85 brouard 4406: 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]);
4407: 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 4408: s[m][i]=-1; /* We prefer to skip it (and to skip it in version 0.8a1 too */
1.76 brouard 4409: }
1.53 brouard 4410: }
1.59 brouard 4411: }
1.53 brouard 4412:
1.59 brouard 4413: for (i=1; i<=imx; i++) {
4414: agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);
1.71 brouard 4415: for(m=firstpass; (m<= lastpass); m++){
1.69 brouard 4416: if(s[m][i] >0){
1.59 brouard 4417: if (s[m][i] >= nlstate+1) {
4418: if(agedc[i]>0)
1.76 brouard 4419: if((int)moisdc[i]!=99 && (int)andc[i]!=9999)
1.69 brouard 4420: agev[m][i]=agedc[i];
1.59 brouard 4421: /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/
4422: else {
1.76 brouard 4423: if ((int)andc[i]!=9999){
1.91 brouard 4424: nbwarn++;
1.85 brouard 4425: printf("Warning negative age at death: %ld line:%d\n",num[i],i);
4426: fprintf(ficlog,"Warning negative age at death: %ld line:%d\n",num[i],i);
1.59 brouard 4427: agev[m][i]=-1;
1.53 brouard 4428: }
4429: }
1.70 brouard 4430: }
1.69 brouard 4431: else if(s[m][i] !=9){ /* Standard case, age in fractional
4432: years but with the precision of a
4433: month */
1.59 brouard 4434: agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);
1.76 brouard 4435: if((int)mint[m][i]==99 || (int)anint[m][i]==9999)
1.59 brouard 4436: agev[m][i]=1;
4437: else if(agev[m][i] <agemin){
4438: agemin=agev[m][i];
4439: /*printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], agemin);*/
1.53 brouard 4440: }
1.59 brouard 4441: else if(agev[m][i] >agemax){
4442: agemax=agev[m][i];
4443: /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/
1.53 brouard 4444: }
1.59 brouard 4445: /*agev[m][i]=anint[m][i]-annais[i];*/
4446: /* agev[m][i] = age[i]+2*m;*/
1.53 brouard 4447: }
1.59 brouard 4448: else { /* =9 */
1.53 brouard 4449: agev[m][i]=1;
1.59 brouard 4450: s[m][i]=-1;
4451: }
1.53 brouard 4452: }
1.59 brouard 4453: else /*= 0 Unknown */
4454: agev[m][i]=1;
4455: }
1.53 brouard 4456:
1.59 brouard 4457: }
4458: for (i=1; i<=imx; i++) {
1.71 brouard 4459: for(m=firstpass; (m<=lastpass); m++){
1.59 brouard 4460: if (s[m][i] > (nlstate+ndeath)) {
1.91 brouard 4461: nberr++;
1.59 brouard 4462: 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);
4463: 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);
4464: goto end;
1.53 brouard 4465: }
4466: }
1.59 brouard 4467: }
1.53 brouard 4468:
1.71 brouard 4469: /*for (i=1; i<=imx; i++){
4470: for (m=firstpass; (m<lastpass); m++){
1.85 brouard 4471: 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 4472: }
4473:
4474: }*/
4475:
1.59 brouard 4476: printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);
4477: fprintf(ficlog,"Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);
4478:
4479: free_vector(severity,1,maxwav);
4480: free_imatrix(outcome,1,maxwav+1,1,n);
4481: free_vector(moisnais,1,n);
4482: free_vector(annais,1,n);
4483: /* free_matrix(mint,1,maxwav,1,n);
4484: free_matrix(anint,1,maxwav,1,n);*/
4485: free_vector(moisdc,1,n);
4486: free_vector(andc,1,n);
1.53 brouard 4487:
4488:
1.59 brouard 4489: wav=ivector(1,imx);
4490: dh=imatrix(1,lastpass-firstpass+1,1,imx);
4491: bh=imatrix(1,lastpass-firstpass+1,1,imx);
4492: mw=imatrix(1,lastpass-firstpass+1,1,imx);
1.69 brouard 4493:
1.59 brouard 4494: /* Concatenates waves */
4495: concatwav(wav, dh, bh, mw, s, agedc, agev, firstpass, lastpass, imx, nlstate, stepm);
1.53 brouard 4496:
1.59 brouard 4497: /* Routine tricode is to calculate cptcoveff (real number of unique covariates) and to associate covariable number and modality */
1.53 brouard 4498:
1.59 brouard 4499: Tcode=ivector(1,100);
4500: nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);
4501: ncodemax[1]=1;
4502: if (cptcovn > 0) tricode(Tvar,nbcode,imx);
1.53 brouard 4503:
1.59 brouard 4504: codtab=imatrix(1,100,1,10); /* Cross tabulation to get the order of
4505: the estimations*/
4506: h=0;
4507: m=pow(2,cptcoveff);
1.53 brouard 4508:
1.59 brouard 4509: for(k=1;k<=cptcoveff; k++){
4510: for(i=1; i <=(m/pow(2,k));i++){
4511: for(j=1; j <= ncodemax[k]; j++){
4512: for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){
4513: h++;
4514: if (h>m) h=1;codtab[h][k]=j;codtab[h][Tvar[k]]=j;
4515: /* printf("h=%d k=%d j=%d codtab[h][k]=%d tvar[k]=%d \n",h, k,j,codtab[h][k],Tvar[k]);*/
4516: }
4517: }
4518: }
4519: }
4520: /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]);
4521: codtab[1][2]=1;codtab[2][2]=2; */
4522: /* for(i=1; i <=m ;i++){
4523: for(k=1; k <=cptcovn; k++){
4524: printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);
4525: }
4526: printf("\n");
1.53 brouard 4527: }
1.59 brouard 4528: scanf("%d",i);*/
1.53 brouard 4529:
1.86 brouard 4530: /*------------ gnuplot -------------*/
4531: strcpy(optionfilegnuplot,optionfilefiname);
4532: strcat(optionfilegnuplot,".gp");
4533: if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {
4534: printf("Problem with file %s",optionfilegnuplot);
4535: }
4536: else{
4537: fprintf(ficgp,"\n# %s\n", version);
4538: fprintf(ficgp,"# %s\n", optionfilegnuplot);
4539: fprintf(ficgp,"set missing 'NaNq'\n");
4540: }
1.88 brouard 4541: /* fclose(ficgp);*/
1.86 brouard 4542: /*--------- index.htm --------*/
4543:
1.91 brouard 4544: strcpy(optionfilehtm,optionfilefiname); /* Main html file */
1.86 brouard 4545: strcat(optionfilehtm,".htm");
4546: if((fichtm=fopen(optionfilehtm,"w"))==NULL) {
4547: printf("Problem with %s \n",optionfilehtm), exit(0);
4548: }
4549:
1.91 brouard 4550: strcpy(optionfilehtmcov,optionfilefiname); /* Only for matrix of covariance */
4551: strcat(optionfilehtmcov,"-cov.htm");
4552: if((fichtmcov=fopen(optionfilehtmcov,"w"))==NULL) {
4553: printf("Problem with %s \n",optionfilehtmcov), exit(0);
4554: }
4555: else{
4556: fprintf(fichtmcov,"<body>\n<title>IMaCh Cov %s</title>\n <font size=\"2\">%s <br> %s</font> \
4557: <hr size=\"2\" color=\"#EC5E5E\"> \n\
4558: Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n",\
4559: fileres,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);
4560: }
4561:
1.87 brouard 4562: fprintf(fichtm,"<body>\n<title>IMaCh %s</title>\n <font size=\"2\">%s <br> %s</font> \
1.86 brouard 4563: <hr size=\"2\" color=\"#EC5E5E\"> \n\
4564: Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n\
4565: \n\
4566: <hr size=\"2\" color=\"#EC5E5E\">\
4567: <ul><li><h4>Parameter files</h4>\n\
4568: - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n\
4569: - Log file of the run: <a href=\"%s\">%s</a><br>\n\
1.87 brouard 4570: - Gnuplot file name: <a href=\"%s\">%s</a><br>\n\
1.86 brouard 4571: - Date and time at start: %s</ul>\n",\
1.91 brouard 4572: fileres,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model,\
4573: fileres,fileres,\
1.88 brouard 4574: filelog,filelog,optionfilegnuplot,optionfilegnuplot,strstart);
1.87 brouard 4575: fflush(fichtm);
1.86 brouard 4576:
1.88 brouard 4577: strcpy(pathr,path);
4578: strcat(pathr,optionfilefiname);
4579: chdir(optionfilefiname); /* Move to directory named optionfile */
4580: strcpy(lfileres,fileres);
4581: strcat(lfileres,"/");
4582: strcat(lfileres,optionfilefiname);
4583:
1.59 brouard 4584: /* Calculates basic frequencies. Computes observed prevalence at single age
4585: and prints on file fileres'p'. */
1.84 brouard 4586: freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint);
1.53 brouard 4587:
1.88 brouard 4588: fprintf(fichtm,"\n");
4589: fprintf(fichtm,"<br>Total number of observations=%d <br>\n\
1.86 brouard 4590: Youngest age at first (selected) pass %.2f, oldest age %.2f<br>\n\
4591: Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n",\
1.88 brouard 4592: imx,agemin,agemax,jmin,jmax,jmean);
4593: pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
1.60 brouard 4594: oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
4595: newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
4596: savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
4597: oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */
1.53 brouard 4598:
4599:
1.59 brouard 4600: /* For Powell, parameters are in a vector p[] starting at p[1]
4601: so we point p on param[1][1] so that p[1] maps on param[1][1][1] */
4602: p=param[1][1]; /* *(*(*(param +1)+1)+0) */
1.53 brouard 4603:
1.86 brouard 4604: globpr=0; /* To get the number ipmx of contributions and the sum of weights*/
1.85 brouard 4605: likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
4606: printf("First Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
4607: for (k=1; k<=npar;k++)
4608: printf(" %d %8.5f",k,p[k]);
4609: printf("\n");
4610: globpr=1; /* to print the contributions */
4611: likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
4612: printf("Second Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
4613: for (k=1; k<=npar;k++)
4614: printf(" %d %8.5f",k,p[k]);
4615: printf("\n");
1.61 brouard 4616: if(mle>=1){ /* Could be 1 or 2 */
1.53 brouard 4617: mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);
1.59 brouard 4618: }
1.53 brouard 4619:
1.59 brouard 4620: /*--------- results files --------------*/
4621: 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 4622:
4623:
1.59 brouard 4624: jk=1;
4625: fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
4626: printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
4627: fprintf(ficlog,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
4628: for(i=1,jk=1; i <=nlstate; i++){
4629: for(k=1; k <=(nlstate+ndeath); k++){
4630: if (k != i)
4631: {
4632: printf("%d%d ",i,k);
4633: fprintf(ficlog,"%d%d ",i,k);
4634: fprintf(ficres,"%1d%1d ",i,k);
4635: for(j=1; j <=ncovmodel; j++){
4636: printf("%f ",p[jk]);
4637: fprintf(ficlog,"%f ",p[jk]);
4638: fprintf(ficres,"%f ",p[jk]);
4639: jk++;
4640: }
4641: printf("\n");
4642: fprintf(ficlog,"\n");
4643: fprintf(ficres,"\n");
4644: }
4645: }
4646: }
1.84 brouard 4647: if(mle!=0){
1.59 brouard 4648: /* Computing hessian and covariance matrix */
4649: ftolhess=ftol; /* Usually correct */
4650: hesscov(matcov, p, npar, delti, ftolhess, func);
4651: }
4652: fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");
4653: printf("# Scales (for hessian or gradient estimation)\n");
4654: fprintf(ficlog,"# Scales (for hessian or gradient estimation)\n");
4655: for(i=1,jk=1; i <=nlstate; i++){
4656: for(j=1; j <=nlstate+ndeath; j++){
4657: if (j!=i) {
4658: fprintf(ficres,"%1d%1d",i,j);
4659: printf("%1d%1d",i,j);
4660: fprintf(ficlog,"%1d%1d",i,j);
4661: for(k=1; k<=ncovmodel;k++){
4662: printf(" %.5e",delti[jk]);
4663: fprintf(ficlog," %.5e",delti[jk]);
4664: fprintf(ficres," %.5e",delti[jk]);
4665: jk++;
4666: }
4667: printf("\n");
4668: fprintf(ficlog,"\n");
4669: fprintf(ficres,"\n");
4670: }
4671: }
4672: }
1.53 brouard 4673:
1.59 brouard 4674: 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");
4675: if(mle==1)
4676: 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");
4677: 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");
4678: for(i=1,k=1;i<=npar;i++){
4679: /* if (k>nlstate) k=1;
4680: i1=(i-1)/(ncovmodel*nlstate)+1;
4681: fprintf(ficres,"%s%d%d",alph[k],i1,tab[i]);
4682: printf("%s%d%d",alph[k],i1,tab[i]);
4683: */
4684: fprintf(ficres,"%3d",i);
4685: if(mle==1)
4686: printf("%3d",i);
4687: fprintf(ficlog,"%3d",i);
4688: for(j=1; j<=i;j++){
4689: fprintf(ficres," %.5e",matcov[i][j]);
4690: if(mle==1)
4691: printf(" %.5e",matcov[i][j]);
4692: fprintf(ficlog," %.5e",matcov[i][j]);
4693: }
4694: fprintf(ficres,"\n");
4695: if(mle==1)
4696: printf("\n");
4697: fprintf(ficlog,"\n");
4698: k++;
4699: }
1.53 brouard 4700:
1.59 brouard 4701: while((c=getc(ficpar))=='#' && c!= EOF){
4702: ungetc(c,ficpar);
4703: fgets(line, MAXLINE, ficpar);
4704: puts(line);
4705: fputs(line,ficparo);
4706: }
4707: ungetc(c,ficpar);
4708:
4709: estepm=0;
4710: fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm);
4711: if (estepm==0 || estepm < stepm) estepm=stepm;
4712: if (fage <= 2) {
4713: bage = ageminpar;
4714: fage = agemaxpar;
4715: }
1.53 brouard 4716:
1.59 brouard 4717: fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");
4718: fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
4719: fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
1.53 brouard 4720:
1.59 brouard 4721: while((c=getc(ficpar))=='#' && c!= EOF){
4722: ungetc(c,ficpar);
4723: fgets(line, MAXLINE, ficpar);
4724: puts(line);
4725: fputs(line,ficparo);
4726: }
4727: ungetc(c,ficpar);
1.53 brouard 4728:
1.59 brouard 4729: 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);
4730: 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);
4731: 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 4732: printf("begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
4733: 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 4734:
1.59 brouard 4735: while((c=getc(ficpar))=='#' && c!= EOF){
4736: ungetc(c,ficpar);
4737: fgets(line, MAXLINE, ficpar);
4738: puts(line);
4739: fputs(line,ficparo);
4740: }
4741: ungetc(c,ficpar);
1.53 brouard 4742:
4743:
1.70 brouard 4744: dateprev1=anprev1+(mprev1-1)/12.+(jprev1-1)/365.;
4745: dateprev2=anprev2+(mprev2-1)/12.+(jprev2-1)/365.;
1.53 brouard 4746:
4747: fscanf(ficpar,"pop_based=%d\n",&popbased);
4748: fprintf(ficparo,"pop_based=%d\n",popbased);
4749: fprintf(ficres,"pop_based=%d\n",popbased);
4750:
4751: while((c=getc(ficpar))=='#' && c!= EOF){
4752: ungetc(c,ficpar);
4753: fgets(line, MAXLINE, ficpar);
4754: puts(line);
4755: fputs(line,ficparo);
4756: }
4757: ungetc(c,ficpar);
4758:
1.69 brouard 4759: 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 4760: 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 4761: 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);
4762: 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);
4763: 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 4764: /* day and month of proj2 are not used but only year anproj2.*/
1.53 brouard 4765:
1.59 brouard 4766: while((c=getc(ficpar))=='#' && c!= EOF){
1.53 brouard 4767: ungetc(c,ficpar);
4768: fgets(line, MAXLINE, ficpar);
4769: puts(line);
4770: fputs(line,ficparo);
4771: }
4772: ungetc(c,ficpar);
4773:
4774: fscanf(ficpar,"popforecast=%d popfile=%s popfiledate=%lf/%lf/%lf last-popfiledate=%lf/%lf/%lf\n",&popforecast,popfile,&jpyram,&mpyram,&anpyram,&jpyram1,&mpyram1,&anpyram1);
4775: fprintf(ficparo,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);
4776: fprintf(ficres,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);
4777:
1.86 brouard 4778: /* freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint);*/
1.84 brouard 4779: /*,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
1.58 lievre 4780:
1.89 brouard 4781: replace_back_to_slash(pathc,path); /* Even gnuplot wants a / */
4782: printinggnuplot(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
1.53 brouard 4783:
1.85 brouard 4784: printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,\
4785: model,imx,jmin,jmax,jmean,rfileres,popforecast,estepm,\
4786: jprev1,mprev1,anprev1,jprev2,mprev2,anprev2);
1.53 brouard 4787:
1.59 brouard 4788: /*------------ free_vector -------------*/
1.88 brouard 4789: /* chdir(path); */
1.53 brouard 4790:
1.59 brouard 4791: free_ivector(wav,1,imx);
4792: free_imatrix(dh,1,lastpass-firstpass+1,1,imx);
4793: free_imatrix(bh,1,lastpass-firstpass+1,1,imx);
4794: free_imatrix(mw,1,lastpass-firstpass+1,1,imx);
1.85 brouard 4795: free_lvector(num,1,n);
1.59 brouard 4796: free_vector(agedc,1,n);
1.65 lievre 4797: /*free_matrix(covar,0,NCOVMAX,1,n);*/
1.59 brouard 4798: /*free_matrix(covar,1,NCOVMAX,1,n);*/
4799: fclose(ficparo);
4800: fclose(ficres);
1.53 brouard 4801:
4802:
1.54 brouard 4803: /*--------------- Prevalence limit (stable prevalence) --------------*/
1.53 brouard 4804:
4805: strcpy(filerespl,"pl");
4806: strcat(filerespl,fileres);
4807: if((ficrespl=fopen(filerespl,"w"))==NULL) {
1.54 brouard 4808: printf("Problem with stable prevalence resultfile: %s\n", filerespl);goto end;
4809: fprintf(ficlog,"Problem with stable prevalence resultfile: %s\n", filerespl);goto end;
1.53 brouard 4810: }
1.54 brouard 4811: printf("Computing stable prevalence: result on file '%s' \n", filerespl);
4812: fprintf(ficlog,"Computing stable prevalence: result on file '%s' \n", filerespl);
4813: fprintf(ficrespl,"#Stable prevalence \n");
1.53 brouard 4814: fprintf(ficrespl,"#Age ");
4815: for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);
4816: fprintf(ficrespl,"\n");
4817:
4818: prlim=matrix(1,nlstate,1,nlstate);
1.59 brouard 4819:
1.53 brouard 4820: agebase=ageminpar;
4821: agelim=agemaxpar;
4822: ftolpl=1.e-10;
4823: i1=cptcoveff;
4824: if (cptcovn < 1){i1=1;}
4825:
1.59 brouard 4826: for(cptcov=1,k=0;cptcov<=i1;cptcov++){
1.53 brouard 4827: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
1.59 brouard 4828: k=k+1;
4829: /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/
4830: fprintf(ficrespl,"\n#******");
4831: printf("\n#******");
4832: fprintf(ficlog,"\n#******");
4833: for(j=1;j<=cptcoveff;j++) {
4834: fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
4835: printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
4836: fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
4837: }
4838: fprintf(ficrespl,"******\n");
4839: printf("******\n");
4840: fprintf(ficlog,"******\n");
1.53 brouard 4841:
1.59 brouard 4842: for (age=agebase; age<=agelim; age++){
4843: prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
1.69 brouard 4844: fprintf(ficrespl,"%.0f ",age );
4845: for(j=1;j<=cptcoveff;j++)
4846: fprintf(ficrespl,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
1.59 brouard 4847: for(i=1; i<=nlstate;i++)
1.53 brouard 4848: fprintf(ficrespl," %.5f", prlim[i][i]);
1.59 brouard 4849: fprintf(ficrespl,"\n");
1.53 brouard 4850: }
4851: }
1.59 brouard 4852: }
1.53 brouard 4853: fclose(ficrespl);
4854:
4855: /*------------- h Pij x at various ages ------------*/
4856:
4857: strcpy(filerespij,"pij"); strcat(filerespij,fileres);
4858: if((ficrespij=fopen(filerespij,"w"))==NULL) {
4859: printf("Problem with Pij resultfile: %s\n", filerespij);goto end;
4860: fprintf(ficlog,"Problem with Pij resultfile: %s\n", filerespij);goto end;
4861: }
4862: printf("Computing pij: result on file '%s' \n", filerespij);
4863: fprintf(ficlog,"Computing pij: result on file '%s' \n", filerespij);
4864:
4865: stepsize=(int) (stepm+YEARM-1)/YEARM;
4866: /*if (stepm<=24) stepsize=2;*/
4867:
4868: agelim=AGESUP;
4869: hstepm=stepsize*YEARM; /* Every year of age */
4870: hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */
4871:
4872: /* hstepm=1; aff par mois*/
4873:
1.70 brouard 4874: fprintf(ficrespij,"#****** h Pij x Probability to be in state j at age x+h being in i at x ");
1.59 brouard 4875: for(cptcov=1,k=0;cptcov<=i1;cptcov++){
1.53 brouard 4876: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
4877: k=k+1;
1.59 brouard 4878: fprintf(ficrespij,"\n#****** ");
4879: for(j=1;j<=cptcoveff;j++)
4880: fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
4881: fprintf(ficrespij,"******\n");
1.53 brouard 4882:
1.59 brouard 4883: for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */
4884: nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
4885: nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
4886:
4887: /* nhstepm=nhstepm*YEARM; aff par mois*/
4888:
4889: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4890: oldm=oldms;savm=savms;
4891: hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
1.70 brouard 4892: fprintf(ficrespij,"# Cov Agex agex+h hpijx with i,j=");
1.59 brouard 4893: for(i=1; i<=nlstate;i++)
4894: for(j=1; j<=nlstate+ndeath;j++)
4895: fprintf(ficrespij," %1d-%1d",i,j);
4896: fprintf(ficrespij,"\n");
4897: for (h=0; h<=nhstepm; h++){
1.70 brouard 4898: fprintf(ficrespij,"%d %3.f %3.f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );
1.53 brouard 4899: for(i=1; i<=nlstate;i++)
4900: for(j=1; j<=nlstate+ndeath;j++)
1.59 brouard 4901: fprintf(ficrespij," %.5f", p3mat[i][j][h]);
1.53 brouard 4902: fprintf(ficrespij,"\n");
4903: }
1.59 brouard 4904: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4905: fprintf(ficrespij,"\n");
4906: }
1.53 brouard 4907: }
4908: }
4909:
1.74 brouard 4910: varprob(optionfilefiname, matcov, p, delti, nlstate, bage, fage,k,Tvar,nbcode, ncodemax);
1.53 brouard 4911:
4912: fclose(ficrespij);
4913:
1.84 brouard 4914: probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
1.53 brouard 4915:
4916: /*---------- Forecasting ------------------*/
1.69 brouard 4917: /*if((stepm == 1) && (strcmp(model,".")==0)){*/
4918: if(prevfcast==1){
1.74 brouard 4919: /* if(stepm ==1){*/
1.70 brouard 4920: prevforecast(fileres, anproj1, mproj1, jproj1, agemin, agemax, dateprev1, dateprev2, mobilavproj, bage, fage, firstpass, lastpass, anproj2, p, cptcoveff);
1.74 brouard 4921: /* (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);*/
4922: /* } */
4923: /* else{ */
4924: /* erreur=108; */
4925: /* 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); */
4926: /* 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); */
4927: /* } */
1.69 brouard 4928: }
1.53 brouard 4929:
4930:
4931: /*---------- Health expectancies and variances ------------*/
4932:
4933: strcpy(filerest,"t");
4934: strcat(filerest,fileres);
4935: if((ficrest=fopen(filerest,"w"))==NULL) {
4936: printf("Problem with total LE resultfile: %s\n", filerest);goto end;
4937: fprintf(ficlog,"Problem with total LE resultfile: %s\n", filerest);goto end;
4938: }
4939: printf("Computing Total LEs with variances: file '%s' \n", filerest);
4940: fprintf(ficlog,"Computing Total LEs with variances: file '%s' \n", filerest);
4941:
4942:
4943: strcpy(filerese,"e");
4944: strcat(filerese,fileres);
4945: if((ficreseij=fopen(filerese,"w"))==NULL) {
4946: printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
4947: fprintf(ficlog,"Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
4948: }
4949: printf("Computing Health Expectancies: result on file '%s' \n", filerese);
4950: fprintf(ficlog,"Computing Health Expectancies: result on file '%s' \n", filerese);
1.68 lievre 4951:
1.53 brouard 4952: strcpy(fileresv,"v");
4953: strcat(fileresv,fileres);
4954: if((ficresvij=fopen(fileresv,"w"))==NULL) {
4955: printf("Problem with variance resultfile: %s\n", fileresv);exit(0);
4956: fprintf(ficlog,"Problem with variance resultfile: %s\n", fileresv);exit(0);
4957: }
4958: printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
4959: fprintf(ficlog,"Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
1.58 lievre 4960:
1.74 brouard 4961: /* Computes prevalence between agemin (i.e minimal age computed) and no more ageminpar */
1.84 brouard 4962: prevalence(probs, agemin, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
1.74 brouard 4963: /* 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",\
4964: ageminpar, agemax, s[lastpass][imx], agev[lastpass][imx], nlstate, imx, mint[lastpass][imx],anint[lastpass][imx], dateprev1, dateprev2, firstpass, lastpass);
4965: */
1.58 lievre 4966:
1.54 brouard 4967: if (mobilav!=0) {
1.53 brouard 4968: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
1.54 brouard 4969: if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
4970: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
4971: printf(" Error in movingaverage mobilav=%d\n",mobilav);
4972: }
1.53 brouard 4973: }
4974:
1.59 brouard 4975: for(cptcov=1,k=0;cptcov<=i1;cptcov++){
1.53 brouard 4976: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
4977: k=k+1;
4978: fprintf(ficrest,"\n#****** ");
4979: for(j=1;j<=cptcoveff;j++)
4980: fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
4981: fprintf(ficrest,"******\n");
4982:
4983: fprintf(ficreseij,"\n#****** ");
4984: for(j=1;j<=cptcoveff;j++)
4985: fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
4986: fprintf(ficreseij,"******\n");
4987:
4988: fprintf(ficresvij,"\n#****** ");
4989: for(j=1;j<=cptcoveff;j++)
4990: fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
4991: fprintf(ficresvij,"******\n");
4992:
4993: eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
4994: oldm=oldms;savm=savms;
4995: evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov);
4996:
4997: vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
4998: oldm=oldms;savm=savms;
4999: varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,0, mobilav);
5000: if(popbased==1){
5001: 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 5002: }
1.53 brouard 5003:
5004:
5005: fprintf(ficrest,"#Total LEs with variances: e.. (std) ");
5006: for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);
5007: fprintf(ficrest,"\n");
5008:
5009: epj=vector(1,nlstate+1);
5010: for(age=bage; age <=fage ;age++){
5011: prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
5012: if (popbased==1) {
1.54 brouard 5013: if(mobilav ==0){
1.53 brouard 5014: for(i=1; i<=nlstate;i++)
5015: prlim[i][i]=probs[(int)age][i][k];
1.54 brouard 5016: }else{ /* mobilav */
1.53 brouard 5017: for(i=1; i<=nlstate;i++)
5018: prlim[i][i]=mobaverage[(int)age][i][k];
5019: }
5020: }
5021:
5022: fprintf(ficrest," %4.0f",age);
5023: for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){
5024: for(i=1, epj[j]=0.;i <=nlstate;i++) {
5025: epj[j] += prlim[i][i]*eij[i][j][(int)age];
5026: /* printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/
5027: }
5028: epj[nlstate+1] +=epj[j];
5029: }
5030:
5031: for(i=1, vepp=0.;i <=nlstate;i++)
5032: for(j=1;j <=nlstate;j++)
5033: vepp += vareij[i][j][(int)age];
5034: fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));
5035: for(j=1;j <=nlstate;j++){
5036: fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));
5037: }
5038: fprintf(ficrest,"\n");
5039: }
1.59 brouard 5040: free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
5041: free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);
5042: free_vector(epj,1,nlstate+1);
1.53 brouard 5043: }
5044: }
1.59 brouard 5045: free_vector(weight,1,n);
5046: free_imatrix(Tvard,1,15,1,2);
5047: free_imatrix(s,1,maxwav+1,1,n);
5048: free_matrix(anint,1,maxwav,1,n);
5049: free_matrix(mint,1,maxwav,1,n);
5050: free_ivector(cod,1,n);
5051: free_ivector(tab,1,NCOVMAX);
1.53 brouard 5052: fclose(ficreseij);
5053: fclose(ficresvij);
5054: fclose(ficrest);
5055: fclose(ficpar);
5056:
1.54 brouard 5057: /*------- Variance of stable prevalence------*/
1.53 brouard 5058:
5059: strcpy(fileresvpl,"vpl");
5060: strcat(fileresvpl,fileres);
5061: if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {
1.54 brouard 5062: printf("Problem with variance of stable prevalence resultfile: %s\n", fileresvpl);
1.53 brouard 5063: exit(0);
5064: }
1.54 brouard 5065: printf("Computing Variance-covariance of stable prevalence: file '%s' \n", fileresvpl);
1.53 brouard 5066:
1.59 brouard 5067: for(cptcov=1,k=0;cptcov<=i1;cptcov++){
1.53 brouard 5068: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
5069: k=k+1;
5070: fprintf(ficresvpl,"\n#****** ");
5071: for(j=1;j<=cptcoveff;j++)
5072: fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
5073: fprintf(ficresvpl,"******\n");
5074:
5075: varpl=matrix(1,nlstate,(int) bage, (int) fage);
5076: oldm=oldms;savm=savms;
1.59 brouard 5077: varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);
5078: free_matrix(varpl,1,nlstate,(int) bage, (int)fage);
1.53 brouard 5079: }
1.59 brouard 5080: }
1.53 brouard 5081:
5082: fclose(ficresvpl);
5083:
5084: /*---------- End : free ----------------*/
5085: free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);
5086: free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);
5087: free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);
5088: free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);
1.65 lievre 5089:
5090: free_matrix(covar,0,NCOVMAX,1,n);
1.53 brouard 5091: free_matrix(matcov,1,npar,1,npar);
1.74 brouard 5092: /*free_vector(delti,1,npar);*/
5093: free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
1.53 brouard 5094: free_matrix(agev,1,maxwav,1,imx);
5095: free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
1.54 brouard 5096: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
1.74 brouard 5097: free_ma3x(probs,1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
5098:
1.59 brouard 5099: free_ivector(ncodemax,1,8);
5100: free_ivector(Tvar,1,15);
5101: free_ivector(Tprod,1,15);
5102: free_ivector(Tvaraff,1,15);
5103: free_ivector(Tage,1,15);
5104: free_ivector(Tcode,1,100);
1.53 brouard 5105:
1.88 brouard 5106: fflush(fichtm);
5107: fflush(ficgp);
1.53 brouard 5108:
5109:
1.91 brouard 5110: if((nberr >0) || (nbwarn>0)){
5111: printf("End of Imach with %d errors and/or warnings %d\n",nberr,nbwarn);
5112: fprintf(ficlog,"End of Imach with %d errors and/or warnings %d\n",nberr,nbwarn);
1.53 brouard 5113: }else{
1.91 brouard 5114: printf("End of Imach\n");
5115: fprintf(ficlog,"End of Imach\n");
1.53 brouard 5116: }
5117: printf("See log file on %s\n",filelog);
5118: /* gettimeofday(&end_time, (struct timezone*)0);*/ /* after time */
1.85 brouard 5119: (void) gettimeofday(&end_time,&tzp);
5120: tm = *localtime(&end_time.tv_sec);
5121: tmg = *gmtime(&end_time.tv_sec);
1.88 brouard 5122: strcpy(strtend,asctime(&tm));
5123: printf("Localtime at start %s\nLocaltime at end %s",strstart, strtend);
1.91 brouard 5124: fprintf(ficlog,"Localtime at start %s\nLocal time at end %s\n",strstart, strtend);
5125: printf("Total time used %s\n", asc_diff_time(end_time.tv_sec -start_time.tv_sec,tmpout));
1.85 brouard 5126:
1.91 brouard 5127: printf("Total time was %d Sec.\n", end_time.tv_sec -start_time.tv_sec);
5128: fprintf(ficlog,"Total time used %s\n", asc_diff_time(end_time.tv_sec -start_time.tv_sec,tmpout));
5129: fprintf(ficlog,"Total time was %d Sec.\n", end_time.tv_sec -start_time.tv_sec);
1.85 brouard 5130: /* printf("Total time was %d uSec.\n", total_usecs);*/
1.87 brouard 5131: /* if(fileappend(fichtm,optionfilehtm)){ */
1.88 brouard 5132: fprintf(fichtm,"<br>Local time at start %s<br>Local time at end %s<br>",strstart, strtend);
1.87 brouard 5133: fclose(fichtm);
1.91 brouard 5134: fclose(fichtmcov);
1.88 brouard 5135: fclose(ficgp);
1.91 brouard 5136: fclose(ficlog);
1.53 brouard 5137: /*------ End -----------*/
5138:
1.88 brouard 5139: chdir(path);
1.59 brouard 5140: strcpy(plotcmd,GNUPLOTPROGRAM);
5141: strcat(plotcmd," ");
5142: strcat(plotcmd,optionfilegnuplot);
1.75 brouard 5143: printf("Starting graphs with: %s",plotcmd);fflush(stdout);
1.91 brouard 5144: if((outcmd=system(plotcmd)) != 0){
5145: printf(" Problem with gnuplot\n");
5146: }
1.75 brouard 5147: printf(" Wait...");
1.53 brouard 5148: while (z[0] != 'q') {
5149: /* chdir(path); */
1.91 brouard 5150: printf("\nType e to edit output files, g to graph again and q for exiting: ");
1.53 brouard 5151: scanf("%s",z);
1.91 brouard 5152: /* if (z[0] == 'c') system("./imach"); */
5153: if (z[0] == 'e') system(optionfilehtm);
1.53 brouard 5154: else if (z[0] == 'g') system(plotcmd);
5155: else if (z[0] == 'q') exit(0);
5156: }
1.91 brouard 5157: end:
5158: while (z[0] != 'q') {
5159: printf("\nType q for exiting: ");
5160: scanf("%s",z);
5161: }
1.53 brouard 5162: }
1.88 brouard 5163:
1.53 brouard 5164:
5165:
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