Annotation of imach/src/imach.c, revision 1.91
1.91 ! brouard 1: /* $Id: imach.c,v 1.90 2003/06/24 12:34:15 brouard Exp $
1.83 lievre 2: $State: Exp $
3: $Log: imach.c,v $
1.91 ! brouard 4: Revision 1.90 2003/06/24 12:34:15 brouard
! 5: (Module): Some bugs corrected for windows. Also, when
! 6: mle=-1 a template is output in file "or"mypar.txt with the design
! 7: of the covariance matrix to be input.
! 8:
1.90 brouard 9: Revision 1.89 2003/06/24 12:30:52 brouard
10: (Module): Some bugs corrected for windows. Also, when
11: mle=-1 a template is output in file "or"mypar.txt with the design
12: of the covariance matrix to be input.
13:
1.89 brouard 14: Revision 1.88 2003/06/23 17:54:56 brouard
15: * 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.
16:
1.88 brouard 17: Revision 1.87 2003/06/18 12:26:01 brouard
18: Version 0.96
19:
1.87 brouard 20: Revision 1.86 2003/06/17 20:04:08 brouard
21: (Module): Change position of html and gnuplot routines and added
22: routine fileappend.
23:
1.86 brouard 24: Revision 1.85 2003/06/17 13:12:43 brouard
25: * imach.c (Repository): Check when date of death was earlier that
26: current date of interview. It may happen when the death was just
27: prior to the death. In this case, dh was negative and likelihood
28: was wrong (infinity). We still send an "Error" but patch by
29: assuming that the date of death was just one stepm after the
30: interview.
31: (Repository): Because some people have very long ID (first column)
32: we changed int to long in num[] and we added a new lvector for
33: memory allocation. But we also truncated to 8 characters (left
34: truncation)
35: (Repository): No more line truncation errors.
36:
1.85 brouard 37: Revision 1.84 2003/06/13 21:44:43 brouard
38: * imach.c (Repository): Replace "freqsummary" at a correct
39: place. It differs from routine "prevalence" which may be called
40: many times. Probs is memory consuming and must be used with
41: parcimony.
1.86 brouard 42: Version 0.95a3 (should output exactly the same maximization than 0.8a2)
1.85 brouard 43:
1.84 brouard 44: Revision 1.83 2003/06/10 13:39:11 lievre
45: *** empty log message ***
46:
1.83 lievre 47: Revision 1.82 2003/06/05 15:57:20 brouard
48: Add log in imach.c and fullversion number is now printed.
49:
1.82 brouard 50: */
51: /*
1.53 brouard 52: Interpolated Markov Chain
53:
54: Short summary of the programme:
55:
56: This program computes Healthy Life Expectancies from
57: cross-longitudinal data. Cross-longitudinal data consist in: -1- a
58: first survey ("cross") where individuals from different ages are
59: interviewed on their health status or degree of disability (in the
60: case of a health survey which is our main interest) -2- at least a
61: second wave of interviews ("longitudinal") which measure each change
62: (if any) in individual health status. Health expectancies are
63: computed from the time spent in each health state according to a
64: model. More health states you consider, more time is necessary to reach the
65: Maximum Likelihood of the parameters involved in the model. The
66: simplest model is the multinomial logistic model where pij is the
67: probability to be observed in state j at the second wave
68: conditional to be observed in state i at the first wave. Therefore
69: the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where
70: 'age' is age and 'sex' is a covariate. If you want to have a more
71: complex model than "constant and age", you should modify the program
72: where the markup *Covariates have to be included here again* invites
73: you to do it. More covariates you add, slower the
74: convergence.
75:
76: The advantage of this computer programme, compared to a simple
77: multinomial logistic model, is clear when the delay between waves is not
78: identical for each individual. Also, if a individual missed an
79: intermediate interview, the information is lost, but taken into
80: account using an interpolation or extrapolation.
81:
82: hPijx is the probability to be observed in state i at age x+h
83: conditional to the observed state i at age x. The delay 'h' can be
84: split into an exact number (nh*stepm) of unobserved intermediate
1.66 brouard 85: states. This elementary transition (by month, quarter,
86: semester or year) is modelled as a multinomial logistic. The hPx
1.53 brouard 87: matrix is simply the matrix product of nh*stepm elementary matrices
88: and the contribution of each individual to the likelihood is simply
89: hPijx.
90:
91: Also this programme outputs the covariance matrix of the parameters but also
1.54 brouard 92: of the life expectancies. It also computes the stable prevalence.
1.53 brouard 93:
94: Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).
95: Institut national d'études démographiques, Paris.
96: This software have been partly granted by Euro-REVES, a concerted action
97: from the European Union.
98: It is copyrighted identically to a GNU software product, ie programme and
99: software can be distributed freely for non commercial use. Latest version
100: can be accessed at http://euroreves.ined.fr/imach .
1.74 brouard 101:
102: Help to debug: LD_PRELOAD=/usr/local/lib/libnjamd.so ./imach foo.imach
103: or better on gdb : set env LD_PRELOAD=/usr/local/lib/libnjamd.so
104:
1.53 brouard 105: **********************************************************************/
1.74 brouard 106: /*
107: main
108: read parameterfile
109: read datafile
110: concatwav
1.84 brouard 111: freqsummary
1.74 brouard 112: if (mle >= 1)
113: mlikeli
114: print results files
115: if mle==1
116: computes hessian
117: read end of parameter file: agemin, agemax, bage, fage, estepm
118: begin-prev-date,...
119: open gnuplot file
120: open html file
121: stable prevalence
122: for age prevalim()
123: h Pij x
124: variance of p varprob
125: forecasting if prevfcast==1 prevforecast call prevalence()
126: health expectancies
127: Variance-covariance of DFLE
128: prevalence()
129: movingaverage()
130: varevsij()
131: if popbased==1 varevsij(,popbased)
132: total life expectancies
133: Variance of stable prevalence
134: end
135: */
136:
137:
138:
1.53 brouard 139:
140: #include <math.h>
141: #include <stdio.h>
142: #include <stdlib.h>
143: #include <unistd.h>
144:
1.86 brouard 145: #include <sys/time.h>
146: #include <time.h>
147: #include "timeval.h"
148:
1.53 brouard 149: #define MAXLINE 256
150: #define GNUPLOTPROGRAM "gnuplot"
151: /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
1.85 brouard 152: #define FILENAMELENGTH 132
1.53 brouard 153: /*#define DEBUG*/
1.85 brouard 154: /*#define windows*/
1.53 brouard 155: #define GLOCK_ERROR_NOPATH -1 /* empty path */
156: #define GLOCK_ERROR_GETCWD -2 /* cannot get cwd */
157:
158: #define MAXPARM 30 /* Maximum number of parameters for the optimization */
159: #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */
160:
161: #define NINTERVMAX 8
162: #define NLSTATEMAX 8 /* Maximum number of live states (for func) */
163: #define NDEATHMAX 8 /* Maximum number of dead states (for func) */
164: #define NCOVMAX 8 /* Maximum number of covariates */
165: #define MAXN 20000
166: #define YEARM 12. /* Number of months per year */
167: #define AGESUP 130
168: #define AGEBASE 40
1.85 brouard 169: #ifdef unix
170: #define DIRSEPARATOR '/'
171: #define ODIRSEPARATOR '\\'
172: #else
1.53 brouard 173: #define DIRSEPARATOR '\\'
174: #define ODIRSEPARATOR '/'
175: #endif
176:
1.91 ! brouard 177: /* $Id: imach.c,v 1.90 2003/06/24 12:34:15 brouard Exp $ */
1.81 brouard 178: /* $State: Exp $ */
1.80 brouard 179:
1.88 brouard 180: char version[]="Imach version 0.96a, June 2003, INED-EUROREVES ";
1.91 ! brouard 181: char fullversion[]="$Revision: 1.90 $ $Date: 2003/06/24 12:34:15 $";
! 182: int erreur, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings */
1.53 brouard 183: int nvar;
184: int cptcovn=0, cptcovage=0, cptcoveff=0,cptcov;
185: int npar=NPARMAX;
186: int nlstate=2; /* Number of live states */
187: int ndeath=1; /* Number of dead states */
188: int ncovmodel, ncovcol; /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
189: int popbased=0;
190:
191: int *wav; /* Number of waves for this individuual 0 is possible */
192: int maxwav; /* Maxim number of waves */
193: int jmin, jmax; /* min, max spacing between 2 waves */
1.87 brouard 194: int gipmx, gsw; /* Global variables on the number of contributions
195: to the likelihood and the sum of weights (done by funcone)*/
1.53 brouard 196: int mle, weightopt;
197: int **mw; /* mw[mi][i] is number of the mi wave for this individual */
198: int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
1.59 brouard 199: int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between
200: * wave mi and wave mi+1 is not an exact multiple of stepm. */
1.53 brouard 201: double jmean; /* Mean space between 2 waves */
202: double **oldm, **newm, **savm; /* Working pointers to matrices */
203: double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
204: FILE *fic,*ficpar, *ficparo,*ficres, *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
1.76 brouard 205: FILE *ficlog, *ficrespow;
1.85 brouard 206: int globpr; /* Global variable for printing or not */
207: double fretone; /* Only one call to likelihood */
208: long ipmx; /* Number of contributions */
209: double sw; /* Sum of weights */
210: char fileresilk[FILENAMELENGTH]; /* File of individual contributions to the likelihood */
211: FILE *ficresilk;
1.53 brouard 212: FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
213: FILE *ficresprobmorprev;
1.91 ! brouard 214: FILE *fichtm, *fichtmcov; /* Html File */
1.53 brouard 215: FILE *ficreseij;
216: char filerese[FILENAMELENGTH];
217: FILE *ficresvij;
218: char fileresv[FILENAMELENGTH];
219: FILE *ficresvpl;
220: char fileresvpl[FILENAMELENGTH];
221: char title[MAXLINE];
222: char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH], filerespl[FILENAMELENGTH];
223: char optionfilext[10], optionfilefiname[FILENAMELENGTH], plotcmd[FILENAMELENGTH];
1.88 brouard 224: char tmpout[FILENAMELENGTH];
225: char command[FILENAMELENGTH];
226: int outcmd=0;
1.53 brouard 227:
228: char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
1.88 brouard 229: char lfileres[FILENAMELENGTH];
1.53 brouard 230: char filelog[FILENAMELENGTH]; /* Log file */
231: char filerest[FILENAMELENGTH];
232: char fileregp[FILENAMELENGTH];
233: char popfile[FILENAMELENGTH];
234:
1.91 ! brouard 235: char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilehtmcov[FILENAMELENGTH] ;
! 236:
! 237: struct timeval start_time, end_time, curr_time, last_time, forecast_time;
! 238: struct timezone tzp;
! 239: extern int gettimeofday();
! 240: struct tm tmg, tm, tmf, *gmtime(), *localtime();
! 241: long time_value;
! 242: extern long time();
! 243: char strcurr[80], strfor[80];
1.53 brouard 244:
245: #define NR_END 1
246: #define FREE_ARG char*
247: #define FTOL 1.0e-10
248:
249: #define NRANSI
250: #define ITMAX 200
251:
252: #define TOL 2.0e-4
253:
254: #define CGOLD 0.3819660
255: #define ZEPS 1.0e-10
256: #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);
257:
258: #define GOLD 1.618034
259: #define GLIMIT 100.0
260: #define TINY 1.0e-20
261:
262: static double maxarg1,maxarg2;
263: #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
264: #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
265:
266: #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
267: #define rint(a) floor(a+0.5)
268:
269: static double sqrarg;
270: #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
271: #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}
272:
273: int imx;
274: int stepm;
275: /* Stepm, step in month: minimum step interpolation*/
276:
277: int estepm;
278: /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
279:
280: int m,nb;
1.85 brouard 281: long *num;
282: int firstpass=0, lastpass=4,*cod, *ncodemax, *Tage;
1.53 brouard 283: double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
1.55 lievre 284: double **pmmij, ***probs;
1.53 brouard 285: double dateintmean=0;
286:
287: double *weight;
288: int **s; /* Status */
289: double *agedc, **covar, idx;
290: int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;
291:
292: double ftol=FTOL; /* Tolerance for computing Max Likelihood */
293: double ftolhess; /* Tolerance for computing hessian */
294:
295: /**************** split *************************/
296: static int split( char *path, char *dirc, char *name, char *ext, char *finame )
297: {
1.59 brouard 298: char *ss; /* pointer */
299: int l1, l2; /* length counters */
1.53 brouard 300:
1.59 brouard 301: l1 = strlen(path ); /* length of path */
302: if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
303: ss= strrchr( path, DIRSEPARATOR ); /* find last / */
304: if ( ss == NULL ) { /* no directory, so use current */
305: /*if(strrchr(path, ODIRSEPARATOR )==NULL)
306: printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
1.74 brouard 307: /* get current working directory */
308: /* extern char* getcwd ( char *buf , int len);*/
1.59 brouard 309: if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {
310: return( GLOCK_ERROR_GETCWD );
311: }
312: strcpy( name, path ); /* we've got it */
313: } else { /* strip direcotry from path */
314: ss++; /* after this, the filename */
315: l2 = strlen( ss ); /* length of filename */
316: if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
317: strcpy( name, ss ); /* save file name */
318: strncpy( dirc, path, l1 - l2 ); /* now the directory */
319: dirc[l1-l2] = 0; /* add zero */
320: }
321: l1 = strlen( dirc ); /* length of directory */
1.85 brouard 322: /*#ifdef windows
1.59 brouard 323: if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; }
1.53 brouard 324: #else
1.59 brouard 325: if ( dirc[l1-1] != '/' ) { dirc[l1] = '/'; dirc[l1+1] = 0; }
1.53 brouard 326: #endif
1.85 brouard 327: */
1.59 brouard 328: ss = strrchr( name, '.' ); /* find last / */
329: ss++;
330: strcpy(ext,ss); /* save extension */
331: l1= strlen( name);
332: l2= strlen(ss)+1;
333: strncpy( finame, name, l1-l2);
334: finame[l1-l2]= 0;
335: return( 0 ); /* we're done */
1.53 brouard 336: }
337:
338:
339: /******************************************/
340:
1.89 brouard 341: void replace_back_to_slash(char *s, char*t)
1.53 brouard 342: {
343: int i;
1.89 brouard 344: int lg=0;
1.53 brouard 345: i=0;
346: lg=strlen(t);
347: for(i=0; i<= lg; i++) {
348: (s[i] = t[i]);
349: if (t[i]== '\\') s[i]='/';
350: }
351: }
352:
353: int nbocc(char *s, char occ)
354: {
355: int i,j=0;
356: int lg=20;
357: i=0;
358: lg=strlen(s);
359: for(i=0; i<= lg; i++) {
360: if (s[i] == occ ) j++;
361: }
362: return j;
363: }
364:
365: void cutv(char *u,char *v, char*t, char occ)
366: {
367: /* cuts string t into u and v where u is ended by char occ excluding it
368: and v is after occ excluding it too : ex cutv(u,v,"abcdef2ghi2j",2)
369: gives u="abcedf" and v="ghi2j" */
370: int i,lg,j,p=0;
371: i=0;
372: for(j=0; j<=strlen(t)-1; j++) {
373: if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;
374: }
375:
376: lg=strlen(t);
377: for(j=0; j<p; j++) {
378: (u[j] = t[j]);
379: }
380: u[p]='\0';
381:
382: for(j=0; j<= lg; j++) {
383: if (j>=(p+1))(v[j-p-1] = t[j]);
384: }
385: }
386:
387: /********************** nrerror ********************/
388:
389: void nrerror(char error_text[])
390: {
391: fprintf(stderr,"ERREUR ...\n");
392: fprintf(stderr,"%s\n",error_text);
1.59 brouard 393: exit(EXIT_FAILURE);
1.53 brouard 394: }
395: /*********************** vector *******************/
396: double *vector(int nl, int nh)
397: {
398: double *v;
399: v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
400: if (!v) nrerror("allocation failure in vector");
401: return v-nl+NR_END;
402: }
403:
404: /************************ free vector ******************/
405: void free_vector(double*v, int nl, int nh)
406: {
407: free((FREE_ARG)(v+nl-NR_END));
408: }
409:
410: /************************ivector *******************************/
1.85 brouard 411: int *ivector(long nl,long nh)
1.76 brouard 412: {
1.85 brouard 413: int *v;
414: v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
415: if (!v) nrerror("allocation failure in ivector");
1.76 brouard 416: return v-nl+NR_END;
417: }
418:
419: /******************free ivector **************************/
1.85 brouard 420: void free_ivector(int *v, long nl, long nh)
1.76 brouard 421: {
422: free((FREE_ARG)(v+nl-NR_END));
423: }
424:
1.85 brouard 425: /************************lvector *******************************/
426: long *lvector(long nl,long nh)
1.53 brouard 427: {
1.85 brouard 428: long *v;
429: v=(long *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(long)));
1.53 brouard 430: if (!v) nrerror("allocation failure in ivector");
431: return v-nl+NR_END;
432: }
433:
1.85 brouard 434: /******************free lvector **************************/
435: void free_lvector(long *v, long nl, long nh)
1.53 brouard 436: {
437: free((FREE_ARG)(v+nl-NR_END));
438: }
439:
440: /******************* imatrix *******************************/
441: int **imatrix(long nrl, long nrh, long ncl, long nch)
442: /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */
443: {
444: long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;
445: int **m;
446:
447: /* allocate pointers to rows */
448: m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));
449: if (!m) nrerror("allocation failure 1 in matrix()");
450: m += NR_END;
451: m -= nrl;
452:
453:
454: /* allocate rows and set pointers to them */
455: m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));
456: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
457: m[nrl] += NR_END;
458: m[nrl] -= ncl;
459:
460: for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;
461:
462: /* return pointer to array of pointers to rows */
463: return m;
464: }
465:
466: /****************** free_imatrix *************************/
467: void free_imatrix(m,nrl,nrh,ncl,nch)
468: int **m;
469: long nch,ncl,nrh,nrl;
470: /* free an int matrix allocated by imatrix() */
471: {
472: free((FREE_ARG) (m[nrl]+ncl-NR_END));
473: free((FREE_ARG) (m+nrl-NR_END));
474: }
475:
476: /******************* matrix *******************************/
477: double **matrix(long nrl, long nrh, long ncl, long nch)
478: {
479: long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
480: double **m;
481:
482: m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
483: if (!m) nrerror("allocation failure 1 in matrix()");
484: m += NR_END;
485: m -= nrl;
486:
487: m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
488: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
489: m[nrl] += NR_END;
490: m[nrl] -= ncl;
491:
492: for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
493: return m;
1.85 brouard 494: /* print *(*(m+1)+70) or print m[1][70]; print m+1 or print &(m[1])
1.74 brouard 495: */
1.53 brouard 496: }
497:
498: /*************************free matrix ************************/
499: void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
500: {
501: free((FREE_ARG)(m[nrl]+ncl-NR_END));
502: free((FREE_ARG)(m+nrl-NR_END));
503: }
504:
505: /******************* ma3x *******************************/
506: double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
507: {
508: long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
509: double ***m;
510:
511: m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
512: if (!m) nrerror("allocation failure 1 in matrix()");
513: m += NR_END;
514: m -= nrl;
515:
516: m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
517: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
518: m[nrl] += NR_END;
519: m[nrl] -= ncl;
520:
521: for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
522:
523: m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
524: if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
525: m[nrl][ncl] += NR_END;
526: m[nrl][ncl] -= nll;
527: for (j=ncl+1; j<=nch; j++)
528: m[nrl][j]=m[nrl][j-1]+nlay;
529:
530: for (i=nrl+1; i<=nrh; i++) {
531: m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
532: for (j=ncl+1; j<=nch; j++)
533: m[i][j]=m[i][j-1]+nlay;
534: }
1.74 brouard 535: return m;
536: /* gdb: p *(m+1) <=> p m[1] and p (m+1) <=> p (m+1) <=> p &(m[1])
537: &(m[i][j][k]) <=> *((*(m+i) + j)+k)
538: */
1.53 brouard 539: }
540:
541: /*************************free ma3x ************************/
542: void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
543: {
544: free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
545: free((FREE_ARG)(m[nrl]+ncl-NR_END));
546: free((FREE_ARG)(m+nrl-NR_END));
547: }
548:
549: /***************** f1dim *************************/
550: extern int ncom;
551: extern double *pcom,*xicom;
552: extern double (*nrfunc)(double []);
553:
554: double f1dim(double x)
555: {
556: int j;
557: double f;
558: double *xt;
559:
560: xt=vector(1,ncom);
561: for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];
562: f=(*nrfunc)(xt);
563: free_vector(xt,1,ncom);
564: return f;
565: }
566:
567: /*****************brent *************************/
568: double brent(double ax, double bx, double cx, double (*f)(double), double tol, double *xmin)
569: {
570: int iter;
571: double a,b,d,etemp;
572: double fu,fv,fw,fx;
573: double ftemp;
574: double p,q,r,tol1,tol2,u,v,w,x,xm;
575: double e=0.0;
576:
577: a=(ax < cx ? ax : cx);
578: b=(ax > cx ? ax : cx);
579: x=w=v=bx;
580: fw=fv=fx=(*f)(x);
581: for (iter=1;iter<=ITMAX;iter++) {
582: xm=0.5*(a+b);
583: tol2=2.0*(tol1=tol*fabs(x)+ZEPS);
584: /* if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
585: printf(".");fflush(stdout);
586: fprintf(ficlog,".");fflush(ficlog);
587: #ifdef DEBUG
588: 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);
589: 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);
590: /* if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
591: #endif
592: if (fabs(x-xm) <= (tol2-0.5*(b-a))){
593: *xmin=x;
594: return fx;
595: }
596: ftemp=fu;
597: if (fabs(e) > tol1) {
598: r=(x-w)*(fx-fv);
599: q=(x-v)*(fx-fw);
600: p=(x-v)*q-(x-w)*r;
601: q=2.0*(q-r);
602: if (q > 0.0) p = -p;
603: q=fabs(q);
604: etemp=e;
605: e=d;
606: if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))
607: d=CGOLD*(e=(x >= xm ? a-x : b-x));
608: else {
609: d=p/q;
610: u=x+d;
611: if (u-a < tol2 || b-u < tol2)
612: d=SIGN(tol1,xm-x);
613: }
614: } else {
615: d=CGOLD*(e=(x >= xm ? a-x : b-x));
616: }
617: u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));
618: fu=(*f)(u);
619: if (fu <= fx) {
620: if (u >= x) a=x; else b=x;
621: SHFT(v,w,x,u)
622: SHFT(fv,fw,fx,fu)
623: } else {
624: if (u < x) a=u; else b=u;
625: if (fu <= fw || w == x) {
626: v=w;
627: w=u;
628: fv=fw;
629: fw=fu;
630: } else if (fu <= fv || v == x || v == w) {
631: v=u;
632: fv=fu;
633: }
634: }
635: }
636: nrerror("Too many iterations in brent");
637: *xmin=x;
638: return fx;
639: }
640:
641: /****************** mnbrak ***********************/
642:
643: void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,
644: double (*func)(double))
645: {
646: double ulim,u,r,q, dum;
647: double fu;
648:
649: *fa=(*func)(*ax);
650: *fb=(*func)(*bx);
651: if (*fb > *fa) {
652: SHFT(dum,*ax,*bx,dum)
653: SHFT(dum,*fb,*fa,dum)
654: }
655: *cx=(*bx)+GOLD*(*bx-*ax);
656: *fc=(*func)(*cx);
657: while (*fb > *fc) {
658: r=(*bx-*ax)*(*fb-*fc);
659: q=(*bx-*cx)*(*fb-*fa);
660: u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/
661: (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r));
662: ulim=(*bx)+GLIMIT*(*cx-*bx);
663: if ((*bx-u)*(u-*cx) > 0.0) {
664: fu=(*func)(u);
665: } else if ((*cx-u)*(u-ulim) > 0.0) {
666: fu=(*func)(u);
667: if (fu < *fc) {
668: SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))
669: SHFT(*fb,*fc,fu,(*func)(u))
670: }
671: } else if ((u-ulim)*(ulim-*cx) >= 0.0) {
672: u=ulim;
673: fu=(*func)(u);
674: } else {
675: u=(*cx)+GOLD*(*cx-*bx);
676: fu=(*func)(u);
677: }
678: SHFT(*ax,*bx,*cx,u)
679: SHFT(*fa,*fb,*fc,fu)
680: }
681: }
682:
683: /*************** linmin ************************/
684:
685: int ncom;
686: double *pcom,*xicom;
687: double (*nrfunc)(double []);
688:
689: void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))
690: {
691: double brent(double ax, double bx, double cx,
692: double (*f)(double), double tol, double *xmin);
693: double f1dim(double x);
694: void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,
695: double *fc, double (*func)(double));
696: int j;
697: double xx,xmin,bx,ax;
698: double fx,fb,fa;
699:
700: ncom=n;
701: pcom=vector(1,n);
702: xicom=vector(1,n);
703: nrfunc=func;
704: for (j=1;j<=n;j++) {
705: pcom[j]=p[j];
706: xicom[j]=xi[j];
707: }
708: ax=0.0;
709: xx=1.0;
710: mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim);
711: *fret=brent(ax,xx,bx,f1dim,TOL,&xmin);
712: #ifdef DEBUG
713: printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
714: fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
715: #endif
716: for (j=1;j<=n;j++) {
717: xi[j] *= xmin;
718: p[j] += xi[j];
719: }
720: free_vector(xicom,1,n);
721: free_vector(pcom,1,n);
722: }
723:
1.91 ! brouard 724: char *asc_diff_time(long time_sec, char ascdiff[])
! 725: {
! 726: long sec_left, days, hours, minutes;
! 727: days = (time_sec) / (60*60*24);
! 728: sec_left = (time_sec) % (60*60*24);
! 729: hours = (sec_left) / (60*60) ;
! 730: sec_left = (sec_left) %(60*60);
! 731: minutes = (sec_left) /60;
! 732: sec_left = (sec_left) % (60);
! 733: sprintf(ascdiff,"%d day(s) %d hour(s) %d minute(s) %d second(s)",days, hours, minutes, sec_left);
! 734: return ascdiff;
! 735: }
! 736:
1.53 brouard 737: /*************** powell ************************/
738: void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,
739: double (*func)(double []))
740: {
741: void linmin(double p[], double xi[], int n, double *fret,
742: double (*func)(double []));
743: int i,ibig,j;
744: double del,t,*pt,*ptt,*xit;
745: double fp,fptt;
746: double *xits;
1.91 ! brouard 747: int niterf, itmp;
! 748:
1.53 brouard 749: pt=vector(1,n);
750: ptt=vector(1,n);
751: xit=vector(1,n);
752: xits=vector(1,n);
753: *fret=(*func)(p);
754: for (j=1;j<=n;j++) pt[j]=p[j];
755: for (*iter=1;;++(*iter)) {
756: fp=(*fret);
757: ibig=0;
758: del=0.0;
1.91 ! brouard 759: last_time=curr_time;
! 760: (void) gettimeofday(&curr_time,&tzp);
! 761: 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);
! 762: 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);
! 763: fprintf(ficrespow,"%d %.12f %ld",*iter,*fret,curr_time.tv_sec-start_time.tv_sec);
1.76 brouard 764: for (i=1;i<=n;i++) {
1.53 brouard 765: printf(" %d %.12f",i, p[i]);
1.76 brouard 766: fprintf(ficlog," %d %.12lf",i, p[i]);
767: fprintf(ficrespow," %.12lf", p[i]);
768: }
1.53 brouard 769: printf("\n");
770: fprintf(ficlog,"\n");
1.91 ! brouard 771: fprintf(ficrespow,"\n");fflush(ficrespow);
! 772: if(*iter <=3){
! 773: tm = *localtime(&curr_time.tv_sec);
! 774: asctime_r(&tm,strcurr);
! 775: forecast_time=curr_time;
! 776: itmp = strlen(strcurr);
! 777: if(strcurr[itmp-1]=='\n')
! 778: strcurr[itmp-1]='\0';
! 779: printf("\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,curr_time.tv_sec-last_time.tv_sec);
! 780: fprintf(ficlog,"\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,curr_time.tv_sec-last_time.tv_sec);
! 781: for(niterf=10;niterf<=30;niterf+=10){
! 782: forecast_time.tv_sec=curr_time.tv_sec+(niterf-*iter)*(curr_time.tv_sec-last_time.tv_sec);
! 783: tmf = *localtime(&forecast_time.tv_sec);
! 784: asctime_r(&tmf,strfor);
! 785: /* strcpy(strfor,asctime(&tmf)); */
! 786: itmp = strlen(strfor);
! 787: if(strfor[itmp-1]=='\n')
! 788: strfor[itmp-1]='\0';
! 789: 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);
! 790: 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);
! 791: }
! 792: }
1.53 brouard 793: for (i=1;i<=n;i++) {
794: for (j=1;j<=n;j++) xit[j]=xi[j][i];
795: fptt=(*fret);
796: #ifdef DEBUG
797: printf("fret=%lf \n",*fret);
798: fprintf(ficlog,"fret=%lf \n",*fret);
799: #endif
800: printf("%d",i);fflush(stdout);
801: fprintf(ficlog,"%d",i);fflush(ficlog);
802: linmin(p,xit,n,fret,func);
803: if (fabs(fptt-(*fret)) > del) {
804: del=fabs(fptt-(*fret));
805: ibig=i;
806: }
807: #ifdef DEBUG
808: printf("%d %.12e",i,(*fret));
809: fprintf(ficlog,"%d %.12e",i,(*fret));
810: for (j=1;j<=n;j++) {
811: xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
812: printf(" x(%d)=%.12e",j,xit[j]);
813: fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
814: }
815: for(j=1;j<=n;j++) {
816: printf(" p=%.12e",p[j]);
817: fprintf(ficlog," p=%.12e",p[j]);
818: }
819: printf("\n");
820: fprintf(ficlog,"\n");
821: #endif
822: }
823: if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {
824: #ifdef DEBUG
825: int k[2],l;
826: k[0]=1;
827: k[1]=-1;
828: printf("Max: %.12e",(*func)(p));
829: fprintf(ficlog,"Max: %.12e",(*func)(p));
830: for (j=1;j<=n;j++) {
831: printf(" %.12e",p[j]);
832: fprintf(ficlog," %.12e",p[j]);
833: }
834: printf("\n");
835: fprintf(ficlog,"\n");
836: for(l=0;l<=1;l++) {
837: for (j=1;j<=n;j++) {
838: ptt[j]=p[j]+(p[j]-pt[j])*k[l];
839: printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
840: fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
841: }
842: printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
843: fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
844: }
845: #endif
846:
847:
848: free_vector(xit,1,n);
849: free_vector(xits,1,n);
850: free_vector(ptt,1,n);
851: free_vector(pt,1,n);
852: return;
853: }
854: if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");
855: for (j=1;j<=n;j++) {
856: ptt[j]=2.0*p[j]-pt[j];
857: xit[j]=p[j]-pt[j];
858: pt[j]=p[j];
859: }
860: fptt=(*func)(ptt);
861: if (fptt < fp) {
862: t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt);
863: if (t < 0.0) {
864: linmin(p,xit,n,fret,func);
865: for (j=1;j<=n;j++) {
866: xi[j][ibig]=xi[j][n];
867: xi[j][n]=xit[j];
868: }
869: #ifdef DEBUG
870: printf("Direction changed last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
871: fprintf(ficlog,"Direction changed last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
872: for(j=1;j<=n;j++){
873: printf(" %.12e",xit[j]);
874: fprintf(ficlog," %.12e",xit[j]);
875: }
876: printf("\n");
877: fprintf(ficlog,"\n");
878: #endif
1.54 brouard 879: }
1.53 brouard 880: }
881: }
882: }
883:
1.54 brouard 884: /**** Prevalence limit (stable prevalence) ****************/
1.53 brouard 885:
886: double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)
887: {
888: /* Computes the prevalence limit in each live state at age x by left multiplying the unit
889: matrix by transitions matrix until convergence is reached */
890:
891: int i, ii,j,k;
892: double min, max, maxmin, maxmax,sumnew=0.;
893: double **matprod2();
894: double **out, cov[NCOVMAX], **pmij();
895: double **newm;
896: double agefin, delaymax=50 ; /* Max number of years to converge */
897:
898: for (ii=1;ii<=nlstate+ndeath;ii++)
899: for (j=1;j<=nlstate+ndeath;j++){
900: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
901: }
902:
903: cov[1]=1.;
904:
905: /* Even if hstepm = 1, at least one multiplication by the unit matrix */
906: for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
907: newm=savm;
908: /* Covariates have to be included here again */
909: cov[2]=agefin;
910:
911: for (k=1; k<=cptcovn;k++) {
912: cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
913: /* 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]]);*/
914: }
915: for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
916: for (k=1; k<=cptcovprod;k++)
917: cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
918:
919: /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
920: /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
921: /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
922: out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);
923:
924: savm=oldm;
925: oldm=newm;
926: maxmax=0.;
927: for(j=1;j<=nlstate;j++){
928: min=1.;
929: max=0.;
930: for(i=1; i<=nlstate; i++) {
931: sumnew=0;
932: for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
933: prlim[i][j]= newm[i][j]/(1-sumnew);
934: max=FMAX(max,prlim[i][j]);
935: min=FMIN(min,prlim[i][j]);
936: }
937: maxmin=max-min;
938: maxmax=FMAX(maxmax,maxmin);
939: }
940: if(maxmax < ftolpl){
941: return prlim;
942: }
943: }
944: }
945:
946: /*************** transition probabilities ***************/
947:
948: double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
949: {
950: double s1, s2;
951: /*double t34;*/
952: int i,j,j1, nc, ii, jj;
953:
954: for(i=1; i<= nlstate; i++){
955: for(j=1; j<i;j++){
956: for (nc=1, s2=0.;nc <=ncovmodel; nc++){
957: /*s2 += param[i][j][nc]*cov[nc];*/
958: s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
959: /*printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2);*/
960: }
961: ps[i][j]=s2;
962: /*printf("s1=%.17e, s2=%.17e\n",s1,s2);*/
963: }
964: for(j=i+1; j<=nlstate+ndeath;j++){
965: for (nc=1, s2=0.;nc <=ncovmodel; nc++){
966: s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
967: /*printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2);*/
968: }
969: ps[i][j]=s2;
970: }
971: }
972: /*ps[3][2]=1;*/
973:
974: for(i=1; i<= nlstate; i++){
975: s1=0;
976: for(j=1; j<i; j++)
977: s1+=exp(ps[i][j]);
978: for(j=i+1; j<=nlstate+ndeath; j++)
979: s1+=exp(ps[i][j]);
980: ps[i][i]=1./(s1+1.);
981: for(j=1; j<i; j++)
982: ps[i][j]= exp(ps[i][j])*ps[i][i];
983: for(j=i+1; j<=nlstate+ndeath; j++)
984: ps[i][j]= exp(ps[i][j])*ps[i][i];
985: /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
986: } /* end i */
987:
988: for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
989: for(jj=1; jj<= nlstate+ndeath; jj++){
990: ps[ii][jj]=0;
991: ps[ii][ii]=1;
992: }
993: }
994:
995:
996: /* for(ii=1; ii<= nlstate+ndeath; ii++){
997: for(jj=1; jj<= nlstate+ndeath; jj++){
998: printf("%lf ",ps[ii][jj]);
999: }
1000: printf("\n ");
1001: }
1002: printf("\n ");printf("%lf ",cov[2]);*/
1003: /*
1004: for(i=1; i<= npar; i++) printf("%f ",x[i]);
1005: goto end;*/
1006: return ps;
1007: }
1008:
1009: /**************** Product of 2 matrices ******************/
1010:
1011: double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)
1012: {
1013: /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
1014: b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
1015: /* in, b, out are matrice of pointers which should have been initialized
1016: before: only the contents of out is modified. The function returns
1017: a pointer to pointers identical to out */
1018: long i, j, k;
1019: for(i=nrl; i<= nrh; i++)
1020: for(k=ncolol; k<=ncoloh; k++)
1021: for(j=ncl,out[i][k]=0.; j<=nch; j++)
1022: out[i][k] +=in[i][j]*b[j][k];
1023:
1024: return out;
1025: }
1026:
1027:
1028: /************* Higher Matrix Product ***************/
1029:
1030: double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
1031: {
1.66 brouard 1032: /* Computes the transition matrix starting at age 'age' over
1033: 'nhstepm*hstepm*stepm' months (i.e. until
1034: age (in years) age+nhstepm*hstepm*stepm/12) by multiplying
1035: nhstepm*hstepm matrices.
1.53 brouard 1036: Output is stored in matrix po[i][j][h] for h every 'hstepm' step
1.66 brouard 1037: (typically every 2 years instead of every month which is too big
1038: for the memory).
1.53 brouard 1039: Model is determined by parameters x and covariates have to be
1040: included manually here.
1041:
1042: */
1043:
1044: int i, j, d, h, k;
1045: double **out, cov[NCOVMAX];
1046: double **newm;
1047:
1048: /* Hstepm could be zero and should return the unit matrix */
1049: for (i=1;i<=nlstate+ndeath;i++)
1050: for (j=1;j<=nlstate+ndeath;j++){
1051: oldm[i][j]=(i==j ? 1.0 : 0.0);
1052: po[i][j][0]=(i==j ? 1.0 : 0.0);
1053: }
1054: /* Even if hstepm = 1, at least one multiplication by the unit matrix */
1055: for(h=1; h <=nhstepm; h++){
1056: for(d=1; d <=hstepm; d++){
1057: newm=savm;
1058: /* Covariates have to be included here again */
1059: cov[1]=1.;
1060: cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
1061: for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
1062: for (k=1; k<=cptcovage;k++)
1063: cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
1064: for (k=1; k<=cptcovprod;k++)
1065: cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
1066:
1067:
1068: /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
1069: /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
1070: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,
1071: pmij(pmmij,cov,ncovmodel,x,nlstate));
1072: savm=oldm;
1073: oldm=newm;
1074: }
1075: for(i=1; i<=nlstate+ndeath; i++)
1076: for(j=1;j<=nlstate+ndeath;j++) {
1077: po[i][j][h]=newm[i][j];
1078: /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);
1079: */
1080: }
1081: } /* end h */
1082: return po;
1083: }
1084:
1085:
1086: /*************** log-likelihood *************/
1087: double func( double *x)
1088: {
1089: int i, ii, j, k, mi, d, kk;
1090: double l, ll[NLSTATEMAX], cov[NCOVMAX];
1091: double **out;
1092: double sw; /* Sum of weights */
1093: double lli; /* Individual log likelihood */
1.59 brouard 1094: int s1, s2;
1.68 lievre 1095: double bbh, survp;
1.53 brouard 1096: long ipmx;
1097: /*extern weight */
1098: /* We are differentiating ll according to initial status */
1099: /* for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
1100: /*for(i=1;i<imx;i++)
1101: printf(" %d\n",s[4][i]);
1102: */
1103: cov[1]=1.;
1104:
1105: for(k=1; k<=nlstate; k++) ll[k]=0.;
1.61 brouard 1106:
1107: if(mle==1){
1108: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1109: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
1110: for(mi=1; mi<= wav[i]-1; mi++){
1111: for (ii=1;ii<=nlstate+ndeath;ii++)
1112: for (j=1;j<=nlstate+ndeath;j++){
1113: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1114: savm[ii][j]=(ii==j ? 1.0 : 0.0);
1115: }
1116: for(d=0; d<dh[mi][i]; d++){
1117: newm=savm;
1118: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
1119: for (kk=1; kk<=cptcovage;kk++) {
1120: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
1121: }
1122: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1123: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1124: savm=oldm;
1125: oldm=newm;
1126: } /* end mult */
1.53 brouard 1127:
1.61 brouard 1128: /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
1129: /* But now since version 0.9 we anticipate for bias and large stepm.
1130: * If stepm is larger than one month (smallest stepm) and if the exact delay
1131: * (in months) between two waves is not a multiple of stepm, we rounded to
1132: * the nearest (and in case of equal distance, to the lowest) interval but now
1133: * we keep into memory the bias bh[mi][i] and also the previous matrix product
1134: * (i.e to dh[mi][i]-1) saved in 'savm'. The we inter(extra)polate the
1135: * probability in order to take into account the bias as a fraction of the way
1136: * from savm to out if bh is neagtive or even beyond if bh is positive. bh varies
1137: * -stepm/2 to stepm/2 .
1138: * For stepm=1 the results are the same as for previous versions of Imach.
1139: * For stepm > 1 the results are less biased than in previous versions.
1140: */
1141: s1=s[mw[mi][i]][i];
1142: s2=s[mw[mi+1][i]][i];
1.64 lievre 1143: bbh=(double)bh[mi][i]/(double)stepm;
1144: /* bias is positive if real duration
1145: * is higher than the multiple of stepm and negative otherwise.
1146: */
1147: /* 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 1148: if( s2 > nlstate){
1149: /* i.e. if s2 is a death state and if the date of death is known then the contribution
1150: to the likelihood is the probability to die between last step unit time and current
1151: step unit time, which is also the differences between probability to die before dh
1152: and probability to die before dh-stepm .
1153: In version up to 0.92 likelihood was computed
1154: as if date of death was unknown. Death was treated as any other
1155: health state: the date of the interview describes the actual state
1156: and not the date of a change in health state. The former idea was
1157: to consider that at each interview the state was recorded
1158: (healthy, disable or death) and IMaCh was corrected; but when we
1159: introduced the exact date of death then we should have modified
1160: the contribution of an exact death to the likelihood. This new
1161: contribution is smaller and very dependent of the step unit
1162: stepm. It is no more the probability to die between last interview
1163: and month of death but the probability to survive from last
1164: interview up to one month before death multiplied by the
1165: probability to die within a month. Thanks to Chris
1166: Jackson for correcting this bug. Former versions increased
1167: mortality artificially. The bad side is that we add another loop
1168: which slows down the processing. The difference can be up to 10%
1169: lower mortality.
1170: */
1171: lli=log(out[s1][s2] - savm[s1][s2]);
1172: }else{
1173: lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
1174: /* 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 */
1175: }
1.64 lievre 1176: /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
1177: /*if(lli ==000.0)*/
1178: /*printf("bbh= %f lli=%f savm=%f out=%f %d\n",bbh,lli,savm[s1][s2], out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]],i); */
1.71 brouard 1179: ipmx +=1;
1.64 lievre 1180: sw += weight[i];
1181: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1182: } /* end of wave */
1183: } /* end of individual */
1184: } else if(mle==2){
1185: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1186: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
1187: for(mi=1; mi<= wav[i]-1; mi++){
1188: for (ii=1;ii<=nlstate+ndeath;ii++)
1189: for (j=1;j<=nlstate+ndeath;j++){
1190: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1191: savm[ii][j]=(ii==j ? 1.0 : 0.0);
1192: }
1193: for(d=0; d<=dh[mi][i]; d++){
1194: newm=savm;
1195: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
1196: for (kk=1; kk<=cptcovage;kk++) {
1197: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
1198: }
1199: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1200: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1201: savm=oldm;
1202: oldm=newm;
1203: } /* end mult */
1204:
1205: /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
1206: /* But now since version 0.9 we anticipate for bias and large stepm.
1207: * If stepm is larger than one month (smallest stepm) and if the exact delay
1208: * (in months) between two waves is not a multiple of stepm, we rounded to
1209: * the nearest (and in case of equal distance, to the lowest) interval but now
1210: * we keep into memory the bias bh[mi][i] and also the previous matrix product
1211: * (i.e to dh[mi][i]-1) saved in 'savm'. The we inter(extra)polate the
1212: * probability in order to take into account the bias as a fraction of the way
1213: * from savm to out if bh is neagtive or even beyond if bh is positive. bh varies
1214: * -stepm/2 to stepm/2 .
1215: * For stepm=1 the results are the same as for previous versions of Imach.
1216: * For stepm > 1 the results are less biased than in previous versions.
1217: */
1218: s1=s[mw[mi][i]][i];
1219: s2=s[mw[mi+1][i]][i];
1220: bbh=(double)bh[mi][i]/(double)stepm;
1221: /* bias is positive if real duration
1222: * is higher than the multiple of stepm and negative otherwise.
1223: */
1.63 lievre 1224: lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*(savm[s1][s2])):log((1.+bbh)*out[s1][s2])); /* linear interpolation */
1.64 lievre 1225: /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
1226: /*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 */
1227: /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
1228: /*if(lli ==000.0)*/
1229: /*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); */
1230: ipmx +=1;
1231: sw += weight[i];
1232: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1233: } /* end of wave */
1234: } /* end of individual */
1235: } else if(mle==3){ /* exponential inter-extrapolation */
1236: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1237: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
1238: for(mi=1; mi<= wav[i]-1; mi++){
1239: for (ii=1;ii<=nlstate+ndeath;ii++)
1240: for (j=1;j<=nlstate+ndeath;j++){
1241: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1242: savm[ii][j]=(ii==j ? 1.0 : 0.0);
1243: }
1244: for(d=0; d<dh[mi][i]; d++){
1245: newm=savm;
1246: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
1247: for (kk=1; kk<=cptcovage;kk++) {
1248: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
1249: }
1250: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1251: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1252: savm=oldm;
1253: oldm=newm;
1254: } /* end mult */
1255:
1256: /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
1257: /* But now since version 0.9 we anticipate for bias and large stepm.
1258: * If stepm is larger than one month (smallest stepm) and if the exact delay
1259: * (in months) between two waves is not a multiple of stepm, we rounded to
1260: * the nearest (and in case of equal distance, to the lowest) interval but now
1261: * we keep into memory the bias bh[mi][i] and also the previous matrix product
1262: * (i.e to dh[mi][i]-1) saved in 'savm'. The we inter(extra)polate the
1263: * probability in order to take into account the bias as a fraction of the way
1264: * from savm to out if bh is neagtive or even beyond if bh is positive. bh varies
1265: * -stepm/2 to stepm/2 .
1266: * For stepm=1 the results are the same as for previous versions of Imach.
1267: * For stepm > 1 the results are less biased than in previous versions.
1268: */
1269: s1=s[mw[mi][i]][i];
1270: s2=s[mw[mi+1][i]][i];
1271: bbh=(double)bh[mi][i]/(double)stepm;
1272: /* bias is positive if real duration
1273: * is higher than the multiple of stepm and negative otherwise.
1274: */
1275: /* 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 */
1276: 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 1277: /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
1278: /*if(lli ==000.0)*/
1279: /*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); */
1280: ipmx +=1;
1281: sw += weight[i];
1282: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1283: } /* end of wave */
1284: } /* end of individual */
1.84 brouard 1285: }else if (mle==4){ /* ml=4 no inter-extrapolation */
1.61 brouard 1286: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1287: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
1288: for(mi=1; mi<= wav[i]-1; mi++){
1289: for (ii=1;ii<=nlstate+ndeath;ii++)
1290: for (j=1;j<=nlstate+ndeath;j++){
1291: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1292: savm[ii][j]=(ii==j ? 1.0 : 0.0);
1293: }
1294: for(d=0; d<dh[mi][i]; d++){
1295: newm=savm;
1296: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
1297: for (kk=1; kk<=cptcovage;kk++) {
1298: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
1299: }
1300:
1301: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1302: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1303: savm=oldm;
1304: oldm=newm;
1305: } /* end mult */
1306:
1.84 brouard 1307: s1=s[mw[mi][i]][i];
1308: s2=s[mw[mi+1][i]][i];
1309: if( s2 > nlstate){
1310: lli=log(out[s1][s2] - savm[s1][s2]);
1311: }else{
1312: lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
1313: }
1314: ipmx +=1;
1315: sw += weight[i];
1316: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1.85 brouard 1317: /* 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 1318: } /* end of wave */
1319: } /* end of individual */
1320: }else{ /* ml=5 no inter-extrapolation no jackson =0.8a */
1321: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1322: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
1323: for(mi=1; mi<= wav[i]-1; mi++){
1324: for (ii=1;ii<=nlstate+ndeath;ii++)
1325: for (j=1;j<=nlstate+ndeath;j++){
1326: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1327: savm[ii][j]=(ii==j ? 1.0 : 0.0);
1328: }
1329: for(d=0; d<dh[mi][i]; d++){
1330: newm=savm;
1331: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
1332: for (kk=1; kk<=cptcovage;kk++) {
1333: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
1334: }
1335:
1336: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1337: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1338: savm=oldm;
1339: oldm=newm;
1340: } /* end mult */
1341:
1342: s1=s[mw[mi][i]][i];
1343: s2=s[mw[mi+1][i]][i];
1.61 brouard 1344: lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
1345: ipmx +=1;
1346: sw += weight[i];
1347: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1.84 brouard 1348: /*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 1349: } /* end of wave */
1350: } /* end of individual */
1351: } /* End of if */
1.53 brouard 1352: for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
1353: /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
1354: l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
1.85 brouard 1355: return -l;
1356: }
1357:
1358: /*************** log-likelihood *************/
1359: double funcone( double *x)
1360: {
1.87 brouard 1361: /* Same as likeli but slower because of a lot of printf and if */
1.85 brouard 1362: int i, ii, j, k, mi, d, kk;
1363: double l, ll[NLSTATEMAX], cov[NCOVMAX];
1364: double **out;
1365: double lli; /* Individual log likelihood */
1.87 brouard 1366: double llt;
1.85 brouard 1367: int s1, s2;
1368: double bbh, survp;
1369: /*extern weight */
1370: /* We are differentiating ll according to initial status */
1371: /* for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
1372: /*for(i=1;i<imx;i++)
1373: printf(" %d\n",s[4][i]);
1374: */
1375: cov[1]=1.;
1376:
1377: for(k=1; k<=nlstate; k++) ll[k]=0.;
1378:
1379: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1380: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
1381: for(mi=1; mi<= wav[i]-1; mi++){
1382: for (ii=1;ii<=nlstate+ndeath;ii++)
1383: for (j=1;j<=nlstate+ndeath;j++){
1384: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1385: savm[ii][j]=(ii==j ? 1.0 : 0.0);
1386: }
1387: for(d=0; d<dh[mi][i]; d++){
1388: newm=savm;
1389: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
1390: for (kk=1; kk<=cptcovage;kk++) {
1391: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
1392: }
1393: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1394: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1395: savm=oldm;
1396: oldm=newm;
1397: } /* end mult */
1398:
1399: s1=s[mw[mi][i]][i];
1400: s2=s[mw[mi+1][i]][i];
1401: bbh=(double)bh[mi][i]/(double)stepm;
1402: /* bias is positive if real duration
1403: * is higher than the multiple of stepm and negative otherwise.
1404: */
1405: if( s2 > nlstate && (mle <5) ){ /* Jackson */
1406: lli=log(out[s1][s2] - savm[s1][s2]);
1407: } else if (mle==1){
1408: lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
1409: } else if(mle==2){
1410: 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 */
1411: } else if(mle==3){ /* exponential inter-extrapolation */
1412: 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 */
1413: } else if (mle==4){ /* mle=4 no inter-extrapolation */
1414: lli=log(out[s1][s2]); /* Original formula */
1415: } else{ /* ml>=5 no inter-extrapolation no jackson =0.8a */
1416: lli=log(out[s1][s2]); /* Original formula */
1417: } /* End of if */
1418: ipmx +=1;
1419: sw += weight[i];
1420: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1421: /* 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]); */
1422: if(globpr){
1.88 brouard 1423: fprintf(ficresilk,"%9d %6d %1d %1d %1d %1d %3d %10.6f %6.4f\
1.86 brouard 1424: %10.6f %10.6f %10.6f ", \
1425: num[i],i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],
1426: 2*weight[i]*lli,out[s1][s2],savm[s1][s2]);
1.87 brouard 1427: for(k=1,llt=0.,l=0.; k<=nlstate; k++){
1428: llt +=ll[k]*gipmx/gsw;
1429: fprintf(ficresilk," %10.6f",-ll[k]*gipmx/gsw);
1430: }
1431: fprintf(ficresilk," %10.6f\n", -llt);
1.85 brouard 1432: }
1433: } /* end of wave */
1434: } /* end of individual */
1435: for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
1436: /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
1437: l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
1.87 brouard 1438: if(globpr==0){ /* First time we count the contributions and weights */
1439: gipmx=ipmx;
1440: gsw=sw;
1441: }
1.53 brouard 1442: return -l;
1443: }
1444:
1.88 brouard 1445: char *subdirf(char fileres[])
1446: {
1.91 ! brouard 1447: /* Caution optionfilefiname is hidden */
1.88 brouard 1448: strcpy(tmpout,optionfilefiname);
1449: strcat(tmpout,"/"); /* Add to the right */
1450: strcat(tmpout,fileres);
1451: return tmpout;
1452: }
1453:
1454: char *subdirf2(char fileres[], char *preop)
1455: {
1456:
1457: strcpy(tmpout,optionfilefiname);
1458: strcat(tmpout,"/");
1459: strcat(tmpout,preop);
1460: strcat(tmpout,fileres);
1461: return tmpout;
1462: }
1463: char *subdirf3(char fileres[], char *preop, char *preop2)
1464: {
1465:
1466: strcpy(tmpout,optionfilefiname);
1467: strcat(tmpout,"/");
1468: strcat(tmpout,preop);
1469: strcat(tmpout,preop2);
1470: strcat(tmpout,fileres);
1471: return tmpout;
1472: }
1.53 brouard 1473:
1.87 brouard 1474: void likelione(FILE *ficres,double p[], int npar, int nlstate, int *globpri, long *ipmx, double *sw, double *fretone, double (*funcone)(double []))
1.85 brouard 1475: {
1.87 brouard 1476: /* This routine should help understanding what is done with
1477: the selection of individuals/waves and
1.85 brouard 1478: to check the exact contribution to the likelihood.
1479: Plotting could be done.
1480: */
1481: int k;
1.87 brouard 1482:
1.88 brouard 1483: if(*globpri !=0){ /* Just counts and sums, no printings */
1.85 brouard 1484: strcpy(fileresilk,"ilk");
1485: strcat(fileresilk,fileres);
1486: if((ficresilk=fopen(fileresilk,"w"))==NULL) {
1487: printf("Problem with resultfile: %s\n", fileresilk);
1488: fprintf(ficlog,"Problem with resultfile: %s\n", fileresilk);
1489: }
1.87 brouard 1490: 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 1491: fprintf(ficresilk, "#num_i i s1 s2 mi mw dh likeli weight 2wlli out sav ");
1.85 brouard 1492: /* i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],2*weight[i]*lli,out[s1][s2],savm[s1][s2]); */
1493: for(k=1; k<=nlstate; k++)
1.87 brouard 1494: fprintf(ficresilk," -2*gipw/gsw*weight*ll[%d]++",k);
1495: fprintf(ficresilk," -2*gipw/gsw*weight*ll(total)\n");
1.85 brouard 1496: }
1497:
1498: *fretone=(*funcone)(p);
1.87 brouard 1499: if(*globpri !=0){
1.85 brouard 1500: fclose(ficresilk);
1.88 brouard 1501: fprintf(fichtm,"\n<br>File of contributions to the likelihood: <a href=\"%s\">%s</a><br>\n",subdirf(fileresilk),subdirf(fileresilk));
1.87 brouard 1502: fflush(fichtm);
1503: }
1.85 brouard 1504: return;
1505: }
1506:
1.88 brouard 1507:
1.53 brouard 1508: /*********** Maximum Likelihood Estimation ***************/
1509:
1510: void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
1511: {
1512: int i,j, iter;
1.74 brouard 1513: double **xi;
1.53 brouard 1514: double fret;
1.85 brouard 1515: double fretone; /* Only one call to likelihood */
1.76 brouard 1516: char filerespow[FILENAMELENGTH];
1.53 brouard 1517: xi=matrix(1,npar,1,npar);
1518: for (i=1;i<=npar;i++)
1519: for (j=1;j<=npar;j++)
1520: xi[i][j]=(i==j ? 1.0 : 0.0);
1521: printf("Powell\n"); fprintf(ficlog,"Powell\n");
1.76 brouard 1522: strcpy(filerespow,"pow");
1523: strcat(filerespow,fileres);
1524: if((ficrespow=fopen(filerespow,"w"))==NULL) {
1525: printf("Problem with resultfile: %s\n", filerespow);
1526: fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
1527: }
1528: fprintf(ficrespow,"# Powell\n# iter -2*LL");
1529: for (i=1;i<=nlstate;i++)
1530: for(j=1;j<=nlstate+ndeath;j++)
1531: if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
1532: fprintf(ficrespow,"\n");
1.85 brouard 1533:
1.53 brouard 1534: powell(p,xi,npar,ftol,&iter,&fret,func);
1535:
1.76 brouard 1536: fclose(ficrespow);
1537: printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));
1.65 lievre 1538: fprintf(ficlog,"\n#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
1.53 brouard 1539: fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
1540:
1541: }
1542:
1543: /**** Computes Hessian and covariance matrix ***/
1544: void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
1545: {
1546: double **a,**y,*x,pd;
1547: double **hess;
1548: int i, j,jk;
1549: int *indx;
1550:
1551: double hessii(double p[], double delta, int theta, double delti[]);
1552: double hessij(double p[], double delti[], int i, int j);
1553: void lubksb(double **a, int npar, int *indx, double b[]) ;
1554: void ludcmp(double **a, int npar, int *indx, double *d) ;
1555:
1556: hess=matrix(1,npar,1,npar);
1557:
1558: printf("\nCalculation of the hessian matrix. Wait...\n");
1559: fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
1560: for (i=1;i<=npar;i++){
1561: printf("%d",i);fflush(stdout);
1562: fprintf(ficlog,"%d",i);fflush(ficlog);
1563: hess[i][i]=hessii(p,ftolhess,i,delti);
1564: /*printf(" %f ",p[i]);*/
1565: /*printf(" %lf ",hess[i][i]);*/
1566: }
1567:
1568: for (i=1;i<=npar;i++) {
1569: for (j=1;j<=npar;j++) {
1570: if (j>i) {
1571: printf(".%d%d",i,j);fflush(stdout);
1572: fprintf(ficlog,".%d%d",i,j);fflush(ficlog);
1573: hess[i][j]=hessij(p,delti,i,j);
1574: hess[j][i]=hess[i][j];
1575: /*printf(" %lf ",hess[i][j]);*/
1576: }
1577: }
1578: }
1579: printf("\n");
1580: fprintf(ficlog,"\n");
1581:
1582: printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
1583: fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
1584:
1585: a=matrix(1,npar,1,npar);
1586: y=matrix(1,npar,1,npar);
1587: x=vector(1,npar);
1588: indx=ivector(1,npar);
1589: for (i=1;i<=npar;i++)
1590: for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
1591: ludcmp(a,npar,indx,&pd);
1592:
1593: for (j=1;j<=npar;j++) {
1594: for (i=1;i<=npar;i++) x[i]=0;
1595: x[j]=1;
1596: lubksb(a,npar,indx,x);
1597: for (i=1;i<=npar;i++){
1598: matcov[i][j]=x[i];
1599: }
1600: }
1601:
1602: printf("\n#Hessian matrix#\n");
1603: fprintf(ficlog,"\n#Hessian matrix#\n");
1604: for (i=1;i<=npar;i++) {
1605: for (j=1;j<=npar;j++) {
1606: printf("%.3e ",hess[i][j]);
1607: fprintf(ficlog,"%.3e ",hess[i][j]);
1608: }
1609: printf("\n");
1610: fprintf(ficlog,"\n");
1611: }
1612:
1613: /* Recompute Inverse */
1614: for (i=1;i<=npar;i++)
1615: for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];
1616: ludcmp(a,npar,indx,&pd);
1617:
1618: /* printf("\n#Hessian matrix recomputed#\n");
1619:
1620: for (j=1;j<=npar;j++) {
1621: for (i=1;i<=npar;i++) x[i]=0;
1622: x[j]=1;
1623: lubksb(a,npar,indx,x);
1624: for (i=1;i<=npar;i++){
1625: y[i][j]=x[i];
1626: printf("%.3e ",y[i][j]);
1627: fprintf(ficlog,"%.3e ",y[i][j]);
1628: }
1629: printf("\n");
1630: fprintf(ficlog,"\n");
1631: }
1632: */
1633:
1634: free_matrix(a,1,npar,1,npar);
1635: free_matrix(y,1,npar,1,npar);
1636: free_vector(x,1,npar);
1637: free_ivector(indx,1,npar);
1638: free_matrix(hess,1,npar,1,npar);
1639:
1640:
1641: }
1642:
1643: /*************** hessian matrix ****************/
1644: double hessii( double x[], double delta, int theta, double delti[])
1645: {
1646: int i;
1647: int l=1, lmax=20;
1648: double k1,k2;
1649: double p2[NPARMAX+1];
1650: double res;
1651: double delt, delts, nkhi=10.,nkhif=1., khi=1.e-4;
1652: double fx;
1653: int k=0,kmax=10;
1654: double l1;
1655:
1656: fx=func(x);
1657: for (i=1;i<=npar;i++) p2[i]=x[i];
1658: for(l=0 ; l <=lmax; l++){
1659: l1=pow(10,l);
1660: delts=delt;
1661: for(k=1 ; k <kmax; k=k+1){
1662: delt = delta*(l1*k);
1663: p2[theta]=x[theta] +delt;
1664: k1=func(p2)-fx;
1665: p2[theta]=x[theta]-delt;
1666: k2=func(p2)-fx;
1667: /*res= (k1-2.0*fx+k2)/delt/delt; */
1668: res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */
1669:
1670: #ifdef DEBUG
1671: 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);
1672: 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);
1673: #endif
1674: /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
1675: if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
1676: k=kmax;
1677: }
1678: else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
1679: k=kmax; l=lmax*10.;
1680: }
1681: else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){
1682: delts=delt;
1683: }
1684: }
1685: }
1686: delti[theta]=delts;
1687: return res;
1688:
1689: }
1690:
1691: double hessij( double x[], double delti[], int thetai,int thetaj)
1692: {
1693: int i;
1694: int l=1, l1, lmax=20;
1695: double k1,k2,k3,k4,res,fx;
1696: double p2[NPARMAX+1];
1697: int k;
1698:
1699: fx=func(x);
1700: for (k=1; k<=2; k++) {
1701: for (i=1;i<=npar;i++) p2[i]=x[i];
1702: p2[thetai]=x[thetai]+delti[thetai]/k;
1703: p2[thetaj]=x[thetaj]+delti[thetaj]/k;
1704: k1=func(p2)-fx;
1705:
1706: p2[thetai]=x[thetai]+delti[thetai]/k;
1707: p2[thetaj]=x[thetaj]-delti[thetaj]/k;
1708: k2=func(p2)-fx;
1709:
1710: p2[thetai]=x[thetai]-delti[thetai]/k;
1711: p2[thetaj]=x[thetaj]+delti[thetaj]/k;
1712: k3=func(p2)-fx;
1713:
1714: p2[thetai]=x[thetai]-delti[thetai]/k;
1715: p2[thetaj]=x[thetaj]-delti[thetaj]/k;
1716: k4=func(p2)-fx;
1717: res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */
1718: #ifdef DEBUG
1719: 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);
1720: 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);
1721: #endif
1722: }
1723: return res;
1724: }
1725:
1726: /************** Inverse of matrix **************/
1727: void ludcmp(double **a, int n, int *indx, double *d)
1728: {
1729: int i,imax,j,k;
1730: double big,dum,sum,temp;
1731: double *vv;
1732:
1733: vv=vector(1,n);
1734: *d=1.0;
1735: for (i=1;i<=n;i++) {
1736: big=0.0;
1737: for (j=1;j<=n;j++)
1738: if ((temp=fabs(a[i][j])) > big) big=temp;
1739: if (big == 0.0) nrerror("Singular matrix in routine ludcmp");
1740: vv[i]=1.0/big;
1741: }
1742: for (j=1;j<=n;j++) {
1743: for (i=1;i<j;i++) {
1744: sum=a[i][j];
1745: for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];
1746: a[i][j]=sum;
1747: }
1748: big=0.0;
1749: for (i=j;i<=n;i++) {
1750: sum=a[i][j];
1751: for (k=1;k<j;k++)
1752: sum -= a[i][k]*a[k][j];
1753: a[i][j]=sum;
1754: if ( (dum=vv[i]*fabs(sum)) >= big) {
1755: big=dum;
1756: imax=i;
1757: }
1758: }
1759: if (j != imax) {
1760: for (k=1;k<=n;k++) {
1761: dum=a[imax][k];
1762: a[imax][k]=a[j][k];
1763: a[j][k]=dum;
1764: }
1765: *d = -(*d);
1766: vv[imax]=vv[j];
1767: }
1768: indx[j]=imax;
1769: if (a[j][j] == 0.0) a[j][j]=TINY;
1770: if (j != n) {
1771: dum=1.0/(a[j][j]);
1772: for (i=j+1;i<=n;i++) a[i][j] *= dum;
1773: }
1774: }
1775: free_vector(vv,1,n); /* Doesn't work */
1776: ;
1777: }
1778:
1779: void lubksb(double **a, int n, int *indx, double b[])
1780: {
1781: int i,ii=0,ip,j;
1782: double sum;
1783:
1784: for (i=1;i<=n;i++) {
1785: ip=indx[i];
1786: sum=b[ip];
1787: b[ip]=b[i];
1788: if (ii)
1789: for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];
1790: else if (sum) ii=i;
1791: b[i]=sum;
1792: }
1793: for (i=n;i>=1;i--) {
1794: sum=b[i];
1795: for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];
1796: b[i]=sum/a[i][i];
1797: }
1798: }
1799:
1800: /************ Frequencies ********************/
1.84 brouard 1801: 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 1802: { /* Some frequencies */
1803:
1804: int i, m, jk, k1,i1, j1, bool, z1,z2,j;
1805: int first;
1806: double ***freq; /* Frequencies */
1.73 lievre 1807: double *pp, **prop;
1808: double pos,posprop, k2, dateintsum=0,k2cpt=0;
1.53 brouard 1809: FILE *ficresp;
1810: char fileresp[FILENAMELENGTH];
1811:
1812: pp=vector(1,nlstate);
1.74 brouard 1813: prop=matrix(1,nlstate,iagemin,iagemax+3);
1.53 brouard 1814: strcpy(fileresp,"p");
1815: strcat(fileresp,fileres);
1816: if((ficresp=fopen(fileresp,"w"))==NULL) {
1817: printf("Problem with prevalence resultfile: %s\n", fileresp);
1818: fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
1819: exit(0);
1820: }
1.74 brouard 1821: freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);
1.53 brouard 1822: j1=0;
1823:
1824: j=cptcoveff;
1825: if (cptcovn<1) {j=1;ncodemax[1]=1;}
1826:
1827: first=1;
1828:
1829: for(k1=1; k1<=j;k1++){
1830: for(i1=1; i1<=ncodemax[k1];i1++){
1831: j1++;
1832: /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
1833: scanf("%d", i);*/
1834: for (i=-1; i<=nlstate+ndeath; i++)
1835: for (jk=-1; jk<=nlstate+ndeath; jk++)
1.74 brouard 1836: for(m=iagemin; m <= iagemax+3; m++)
1.53 brouard 1837: freq[i][jk][m]=0;
1.73 lievre 1838:
1839: for (i=1; i<=nlstate; i++)
1.74 brouard 1840: for(m=iagemin; m <= iagemax+3; m++)
1.73 lievre 1841: prop[i][m]=0;
1.53 brouard 1842:
1843: dateintsum=0;
1844: k2cpt=0;
1845: for (i=1; i<=imx; i++) {
1846: bool=1;
1847: if (cptcovn>0) {
1848: for (z1=1; z1<=cptcoveff; z1++)
1849: if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])
1850: bool=0;
1851: }
1.58 lievre 1852: if (bool==1){
1.53 brouard 1853: for(m=firstpass; m<=lastpass; m++){
1854: k2=anint[m][i]+(mint[m][i]/12.);
1.84 brouard 1855: /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/
1.74 brouard 1856: if(agev[m][i]==0) agev[m][i]=iagemax+1;
1857: if(agev[m][i]==1) agev[m][i]=iagemax+2;
1.73 lievre 1858: if (s[m][i]>0 && s[m][i]<=nlstate) prop[s[m][i]][(int)agev[m][i]] += weight[i];
1.53 brouard 1859: if (m<lastpass) {
1860: freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
1.74 brouard 1861: freq[s[m][i]][s[m+1][i]][iagemax+3] += weight[i];
1.53 brouard 1862: }
1863:
1.74 brouard 1864: if ((agev[m][i]>1) && (agev[m][i]< (iagemax+3))) {
1.53 brouard 1865: dateintsum=dateintsum+k2;
1866: k2cpt++;
1867: }
1.84 brouard 1868: /*}*/
1.53 brouard 1869: }
1870: }
1871: }
1872:
1.84 brouard 1873: /* fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
1.53 brouard 1874:
1875: if (cptcovn>0) {
1876: fprintf(ficresp, "\n#********** Variable ");
1877: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
1878: fprintf(ficresp, "**********\n#");
1879: }
1880: for(i=1; i<=nlstate;i++)
1881: fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
1882: fprintf(ficresp, "\n");
1883:
1.74 brouard 1884: for(i=iagemin; i <= iagemax+3; i++){
1885: if(i==iagemax+3){
1.53 brouard 1886: fprintf(ficlog,"Total");
1887: }else{
1888: if(first==1){
1889: first=0;
1890: printf("See log file for details...\n");
1891: }
1892: fprintf(ficlog,"Age %d", i);
1893: }
1894: for(jk=1; jk <=nlstate ; jk++){
1895: for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
1896: pp[jk] += freq[jk][m][i];
1897: }
1898: for(jk=1; jk <=nlstate ; jk++){
1899: for(m=-1, pos=0; m <=0 ; m++)
1900: pos += freq[jk][m][i];
1901: if(pp[jk]>=1.e-10){
1902: if(first==1){
1903: printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
1904: }
1905: fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
1906: }else{
1907: if(first==1)
1908: printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
1909: fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
1910: }
1911: }
1912:
1913: for(jk=1; jk <=nlstate ; jk++){
1914: for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
1915: pp[jk] += freq[jk][m][i];
1.73 lievre 1916: }
1917: for(jk=1,pos=0,posprop=0; jk <=nlstate ; jk++){
1918: pos += pp[jk];
1919: posprop += prop[jk][i];
1.53 brouard 1920: }
1921: for(jk=1; jk <=nlstate ; jk++){
1922: if(pos>=1.e-5){
1923: if(first==1)
1924: printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
1925: fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
1926: }else{
1927: if(first==1)
1928: printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
1929: fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
1930: }
1.74 brouard 1931: if( i <= iagemax){
1.53 brouard 1932: if(pos>=1.e-5){
1.73 lievre 1933: fprintf(ficresp," %d %.5f %.0f %.0f",i,prop[jk][i]/posprop, prop[jk][i],posprop);
1.84 brouard 1934: /*probs[i][jk][j1]= pp[jk]/pos;*/
1.53 brouard 1935: /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/
1936: }
1937: else
1.73 lievre 1938: fprintf(ficresp," %d NaNq %.0f %.0f",i,prop[jk][i],posprop);
1.53 brouard 1939: }
1940: }
1941:
1.69 brouard 1942: for(jk=-1; jk <=nlstate+ndeath; jk++)
1943: for(m=-1; m <=nlstate+ndeath; m++)
1.53 brouard 1944: if(freq[jk][m][i] !=0 ) {
1945: if(first==1)
1946: printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
1947: fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
1948: }
1.74 brouard 1949: if(i <= iagemax)
1.53 brouard 1950: fprintf(ficresp,"\n");
1951: if(first==1)
1952: printf("Others in log...\n");
1953: fprintf(ficlog,"\n");
1954: }
1955: }
1956: }
1957: dateintmean=dateintsum/k2cpt;
1958:
1959: fclose(ficresp);
1.74 brouard 1960: free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);
1.53 brouard 1961: free_vector(pp,1,nlstate);
1.74 brouard 1962: free_matrix(prop,1,nlstate,iagemin, iagemax+3);
1.53 brouard 1963: /* End of Freq */
1964: }
1965:
1966: /************ Prevalence ********************/
1.84 brouard 1967: 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 1968: {
1969: /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
1970: in each health status at the date of interview (if between dateprev1 and dateprev2).
1971: We still use firstpass and lastpass as another selection.
1972: */
1.53 brouard 1973:
1974: int i, m, jk, k1, i1, j1, bool, z1,z2,j;
1975: double ***freq; /* Frequencies */
1.73 lievre 1976: double *pp, **prop;
1977: double pos,posprop;
1.69 brouard 1978: double y2; /* in fractional years */
1.74 brouard 1979: int iagemin, iagemax;
1.53 brouard 1980:
1.74 brouard 1981: iagemin= (int) agemin;
1982: iagemax= (int) agemax;
1983: /*pp=vector(1,nlstate);*/
1984: prop=matrix(1,nlstate,iagemin,iagemax+3);
1985: /* freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
1.53 brouard 1986: j1=0;
1987:
1988: j=cptcoveff;
1989: if (cptcovn<1) {j=1;ncodemax[1]=1;}
1990:
1991: for(k1=1; k1<=j;k1++){
1992: for(i1=1; i1<=ncodemax[k1];i1++){
1993: j1++;
1994:
1.73 lievre 1995: for (i=1; i<=nlstate; i++)
1.74 brouard 1996: for(m=iagemin; m <= iagemax+3; m++)
1997: prop[i][m]=0.0;
1.53 brouard 1998:
1.69 brouard 1999: for (i=1; i<=imx; i++) { /* Each individual */
1.53 brouard 2000: bool=1;
2001: if (cptcovn>0) {
2002: for (z1=1; z1<=cptcoveff; z1++)
2003: if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])
2004: bool=0;
2005: }
2006: if (bool==1) {
1.69 brouard 2007: for(m=firstpass; m<=lastpass; m++){/* Other selection (we can limit to certain interviews*/
2008: y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
2009: if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
1.74 brouard 2010: if(agev[m][i]==0) agev[m][i]=iagemax+1;
2011: if(agev[m][i]==1) agev[m][i]=iagemax+2;
2012: 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);
2013: if (s[m][i]>0 && s[m][i]<=nlstate) {
2014: /*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]]);*/
2015: prop[s[m][i]][(int)agev[m][i]] += weight[i];
2016: prop[s[m][i]][iagemax+3] += weight[i];
2017: }
1.53 brouard 2018: }
1.69 brouard 2019: } /* end selection of waves */
1.53 brouard 2020: }
2021: }
1.74 brouard 2022: for(i=iagemin; i <= iagemax+3; i++){
1.53 brouard 2023:
1.74 brouard 2024: for(jk=1,posprop=0; jk <=nlstate ; jk++) {
2025: posprop += prop[jk][i];
2026: }
2027:
2028: for(jk=1; jk <=nlstate ; jk++){
2029: if( i <= iagemax){
2030: if(posprop>=1.e-5){
2031: probs[i][jk][j1]= prop[jk][i]/posprop;
2032: }
2033: }
2034: }/* end jk */
2035: }/* end i */
1.53 brouard 2036: } /* end i1 */
2037: } /* end k1 */
2038:
1.74 brouard 2039: /* free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
2040: /*free_vector(pp,1,nlstate);*/
2041: free_matrix(prop,1,nlstate, iagemin,iagemax+3);
2042: } /* End of prevalence */
1.53 brouard 2043:
2044: /************* Waves Concatenation ***************/
2045:
1.59 brouard 2046: 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 2047: {
2048: /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
2049: Death is a valid wave (if date is known).
2050: mw[mi][i] is the mi (mi=1 to wav[i]) effective wave of individual i
1.59 brouard 2051: dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
1.53 brouard 2052: and mw[mi+1][i]. dh depends on stepm.
2053: */
2054:
2055: int i, mi, m;
2056: /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
2057: double sum=0., jmean=0.;*/
2058: int first;
2059: int j, k=0,jk, ju, jl;
2060: double sum=0.;
2061: first=0;
2062: jmin=1e+5;
2063: jmax=-1;
2064: jmean=0.;
2065: for(i=1; i<=imx; i++){
2066: mi=0;
2067: m=firstpass;
2068: while(s[m][i] <= nlstate){
1.69 brouard 2069: if(s[m][i]>=1)
1.53 brouard 2070: mw[++mi][i]=m;
2071: if(m >=lastpass)
2072: break;
2073: else
2074: m++;
2075: }/* end while */
2076: if (s[m][i] > nlstate){
2077: mi++; /* Death is another wave */
2078: /* if(mi==0) never been interviewed correctly before death */
2079: /* Only death is a correct wave */
2080: mw[mi][i]=m;
2081: }
2082:
2083: wav[i]=mi;
2084: if(mi==0){
1.91 ! brouard 2085: nbwarn++;
1.53 brouard 2086: if(first==0){
1.85 brouard 2087: printf("Warning! None valid information for:%ld line=%d (skipped) and may be others, see log file\n",num[i],i);
1.53 brouard 2088: first=1;
2089: }
2090: if(first==1){
1.85 brouard 2091: fprintf(ficlog,"Warning! None valid information for:%ld line=%d (skipped)\n",num[i],i);
1.53 brouard 2092: }
2093: } /* end mi==0 */
1.77 brouard 2094: } /* End individuals */
1.53 brouard 2095:
2096: for(i=1; i<=imx; i++){
2097: for(mi=1; mi<wav[i];mi++){
2098: if (stepm <=0)
2099: dh[mi][i]=1;
2100: else{
1.77 brouard 2101: if (s[mw[mi+1][i]][i] > nlstate) { /* A death */
1.53 brouard 2102: if (agedc[i] < 2*AGESUP) {
1.85 brouard 2103: j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);
2104: if(j==0) j=1; /* Survives at least one month after exam */
2105: else if(j<0){
1.91 ! brouard 2106: nberr++;
1.85 brouard 2107: 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 2108: j=1; /* Temporary Dangerous patch */
1.86 brouard 2109: 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 2110: 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 2111: 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);
2112: }
2113: k=k+1;
2114: if (j >= jmax) jmax=j;
2115: if (j <= jmin) jmin=j;
2116: sum=sum+j;
2117: /*if (j<0) printf("j=%d num=%d \n",j,i);*/
2118: /* printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
1.53 brouard 2119: }
2120: }
2121: else{
2122: j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
1.68 lievre 2123: /* printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
1.53 brouard 2124: k=k+1;
2125: if (j >= jmax) jmax=j;
2126: else if (j <= jmin)jmin=j;
2127: /* if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
1.73 lievre 2128: /*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 2129: if(j<0){
1.91 ! brouard 2130: nberr++;
1.85 brouard 2131: 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]);
2132: 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]);
2133: }
1.53 brouard 2134: sum=sum+j;
2135: }
2136: jk= j/stepm;
2137: jl= j -jk*stepm;
2138: ju= j -(jk+1)*stepm;
1.85 brouard 2139: if(mle <=1){ /* only if we use a the linear-interpoloation pseudo-likelihood */
1.64 lievre 2140: if(jl==0){
2141: dh[mi][i]=jk;
2142: bh[mi][i]=0;
2143: }else{ /* We want a negative bias in order to only have interpolation ie
2144: * at the price of an extra matrix product in likelihood */
2145: dh[mi][i]=jk+1;
2146: bh[mi][i]=ju;
2147: }
2148: }else{
2149: if(jl <= -ju){
2150: dh[mi][i]=jk;
2151: bh[mi][i]=jl; /* bias is positive if real duration
2152: * is higher than the multiple of stepm and negative otherwise.
2153: */
2154: }
2155: else{
2156: dh[mi][i]=jk+1;
2157: bh[mi][i]=ju;
2158: }
2159: if(dh[mi][i]==0){
2160: dh[mi][i]=1; /* At least one step */
2161: bh[mi][i]=ju; /* At least one step */
1.71 brouard 2162: /* 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 2163: }
1.85 brouard 2164: } /* end if mle */
2165: }
1.64 lievre 2166: } /* end wave */
1.53 brouard 2167: }
2168: jmean=sum/k;
2169: printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);
2170: fprintf(ficlog,"Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);
2171: }
2172:
2173: /*********** Tricode ****************************/
2174: void tricode(int *Tvar, int **nbcode, int imx)
2175: {
1.58 lievre 2176:
2177: int Ndum[20],ij=1, k, j, i, maxncov=19;
1.53 brouard 2178: int cptcode=0;
2179: cptcoveff=0;
2180:
1.58 lievre 2181: for (k=0; k<maxncov; k++) Ndum[k]=0;
1.53 brouard 2182: for (k=1; k<=7; k++) ncodemax[k]=0;
2183:
2184: for (j=1; j<=(cptcovn+2*cptcovprod); j++) {
1.58 lievre 2185: for (i=1; i<=imx; i++) { /*reads the data file to get the maximum
2186: modality*/
2187: ij=(int)(covar[Tvar[j]][i]); /* ij is the modality of this individual*/
2188: Ndum[ij]++; /*store the modality */
1.53 brouard 2189: /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
1.58 lievre 2190: if (ij > cptcode) cptcode=ij; /* getting the maximum of covariable
2191: Tvar[j]. If V=sex and male is 0 and
2192: female is 1, then cptcode=1.*/
1.53 brouard 2193: }
2194:
2195: for (i=0; i<=cptcode; i++) {
1.58 lievre 2196: 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 2197: }
1.58 lievre 2198:
1.53 brouard 2199: ij=1;
2200: for (i=1; i<=ncodemax[j]; i++) {
1.58 lievre 2201: for (k=0; k<= maxncov; k++) {
1.53 brouard 2202: if (Ndum[k] != 0) {
2203: nbcode[Tvar[j]][ij]=k;
1.58 lievre 2204: /* 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 2205:
2206: ij++;
2207: }
2208: if (ij > ncodemax[j]) break;
2209: }
2210: }
2211: }
2212:
1.58 lievre 2213: for (k=0; k< maxncov; k++) Ndum[k]=0;
1.53 brouard 2214:
1.58 lievre 2215: for (i=1; i<=ncovmodel-2; i++) {
2216: /* 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 2217: ij=Tvar[i];
1.58 lievre 2218: Ndum[ij]++;
1.53 brouard 2219: }
2220:
2221: ij=1;
1.58 lievre 2222: for (i=1; i<= maxncov; i++) {
1.53 brouard 2223: if((Ndum[i]!=0) && (i<=ncovcol)){
1.58 lievre 2224: Tvaraff[ij]=i; /*For printing */
1.53 brouard 2225: ij++;
2226: }
2227: }
2228:
1.58 lievre 2229: cptcoveff=ij-1; /*Number of simple covariates*/
1.53 brouard 2230: }
2231:
2232: /*********** Health Expectancies ****************/
2233:
2234: 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 )
2235:
2236: {
2237: /* Health expectancies */
2238: int i, j, nhstepm, hstepm, h, nstepm, k, cptj;
2239: double age, agelim, hf;
2240: double ***p3mat,***varhe;
2241: double **dnewm,**doldm;
2242: double *xp;
2243: double **gp, **gm;
2244: double ***gradg, ***trgradg;
2245: int theta;
2246:
1.74 brouard 2247: varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage);
1.53 brouard 2248: xp=vector(1,npar);
1.74 brouard 2249: dnewm=matrix(1,nlstate*nlstate,1,npar);
2250: doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate);
1.53 brouard 2251:
2252: fprintf(ficreseij,"# Health expectancies\n");
2253: fprintf(ficreseij,"# Age");
2254: for(i=1; i<=nlstate;i++)
2255: for(j=1; j<=nlstate;j++)
2256: fprintf(ficreseij," %1d-%1d (SE)",i,j);
2257: fprintf(ficreseij,"\n");
2258:
2259: if(estepm < stepm){
2260: printf ("Problem %d lower than %d\n",estepm, stepm);
2261: }
2262: else hstepm=estepm;
2263: /* We compute the life expectancy from trapezoids spaced every estepm months
2264: * This is mainly to measure the difference between two models: for example
2265: * if stepm=24 months pijx are given only every 2 years and by summing them
2266: * we are calculating an estimate of the Life Expectancy assuming a linear
1.66 brouard 2267: * progression in between and thus overestimating or underestimating according
1.53 brouard 2268: * to the curvature of the survival function. If, for the same date, we
2269: * estimate the model with stepm=1 month, we can keep estepm to 24 months
2270: * to compare the new estimate of Life expectancy with the same linear
2271: * hypothesis. A more precise result, taking into account a more precise
2272: * curvature will be obtained if estepm is as small as stepm. */
2273:
2274: /* For example we decided to compute the life expectancy with the smallest unit */
2275: /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
2276: nhstepm is the number of hstepm from age to agelim
2277: nstepm is the number of stepm from age to agelin.
2278: Look at hpijx to understand the reason of that which relies in memory size
2279: and note for a fixed period like estepm months */
2280: /* We decided (b) to get a life expectancy respecting the most precise curvature of the
2281: survival function given by stepm (the optimization length). Unfortunately it
2282: means that if the survival funtion is printed only each two years of age and if
2283: you sum them up and add 1 year (area under the trapezoids) you won't get the same
2284: results. So we changed our mind and took the option of the best precision.
2285: */
2286: hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
2287:
2288: agelim=AGESUP;
2289: for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
2290: /* nhstepm age range expressed in number of stepm */
2291: nstepm=(int) rint((agelim-age)*YEARM/stepm);
2292: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
2293: /* if (stepm >= YEARM) hstepm=1;*/
2294: nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
2295: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
1.74 brouard 2296: gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);
2297: gp=matrix(0,nhstepm,1,nlstate*nlstate);
2298: gm=matrix(0,nhstepm,1,nlstate*nlstate);
1.53 brouard 2299:
2300: /* Computed by stepm unit matrices, product of hstepm matrices, stored
2301: in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
2302: hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);
2303:
2304:
2305: hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
2306:
2307: /* Computing Variances of health expectancies */
2308:
2309: for(theta=1; theta <=npar; theta++){
2310: for(i=1; i<=npar; i++){
2311: xp[i] = x[i] + (i==theta ?delti[theta]:0);
2312: }
2313: hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
2314:
2315: cptj=0;
2316: for(j=1; j<= nlstate; j++){
2317: for(i=1; i<=nlstate; i++){
2318: cptj=cptj+1;
2319: for(h=0, gp[h][cptj]=0.; h<=nhstepm-1; h++){
2320: gp[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;
2321: }
2322: }
2323: }
2324:
2325:
2326: for(i=1; i<=npar; i++)
2327: xp[i] = x[i] - (i==theta ?delti[theta]:0);
2328: hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
2329:
2330: cptj=0;
2331: for(j=1; j<= nlstate; j++){
2332: for(i=1;i<=nlstate;i++){
2333: cptj=cptj+1;
2334: for(h=0, gm[h][cptj]=0.; h<=nhstepm-1; h++){
1.77 brouard 2335:
1.53 brouard 2336: gm[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;
2337: }
2338: }
2339: }
1.74 brouard 2340: for(j=1; j<= nlstate*nlstate; j++)
1.53 brouard 2341: for(h=0; h<=nhstepm-1; h++){
2342: gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
2343: }
2344: }
2345:
2346: /* End theta */
2347:
1.74 brouard 2348: trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar);
1.53 brouard 2349:
2350: for(h=0; h<=nhstepm-1; h++)
1.74 brouard 2351: for(j=1; j<=nlstate*nlstate;j++)
1.53 brouard 2352: for(theta=1; theta <=npar; theta++)
2353: trgradg[h][j][theta]=gradg[h][theta][j];
2354:
2355:
1.74 brouard 2356: for(i=1;i<=nlstate*nlstate;i++)
2357: for(j=1;j<=nlstate*nlstate;j++)
1.53 brouard 2358: varhe[i][j][(int)age] =0.;
2359:
2360: printf("%d|",(int)age);fflush(stdout);
2361: fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
2362: for(h=0;h<=nhstepm-1;h++){
2363: for(k=0;k<=nhstepm-1;k++){
1.74 brouard 2364: matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov);
2365: matprod2(doldm,dnewm,1,nlstate*nlstate,1,npar,1,nlstate*nlstate,gradg[k]);
2366: for(i=1;i<=nlstate*nlstate;i++)
2367: for(j=1;j<=nlstate*nlstate;j++)
1.53 brouard 2368: varhe[i][j][(int)age] += doldm[i][j]*hf*hf;
2369: }
2370: }
2371: /* Computing expectancies */
2372: for(i=1; i<=nlstate;i++)
2373: for(j=1; j<=nlstate;j++)
2374: for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
2375: eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
2376:
2377: /* 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]);*/
2378:
2379: }
2380:
2381: fprintf(ficreseij,"%3.0f",age );
2382: cptj=0;
2383: for(i=1; i<=nlstate;i++)
2384: for(j=1; j<=nlstate;j++){
2385: cptj++;
2386: fprintf(ficreseij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[cptj][cptj][(int)age]) );
2387: }
2388: fprintf(ficreseij,"\n");
2389:
1.74 brouard 2390: free_matrix(gm,0,nhstepm,1,nlstate*nlstate);
2391: free_matrix(gp,0,nhstepm,1,nlstate*nlstate);
2392: free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*nlstate);
2393: free_ma3x(trgradg,0,nhstepm,1,nlstate*nlstate,1,npar);
1.53 brouard 2394: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
2395: }
2396: printf("\n");
2397: fprintf(ficlog,"\n");
2398:
2399: free_vector(xp,1,npar);
1.74 brouard 2400: free_matrix(dnewm,1,nlstate*nlstate,1,npar);
2401: free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate);
2402: free_ma3x(varhe,1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int)fage);
1.53 brouard 2403: }
2404:
2405: /************ Variance ******************/
2406: 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)
2407: {
2408: /* Variance of health expectancies */
2409: /* double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
2410: /* double **newm;*/
2411: double **dnewm,**doldm;
2412: double **dnewmp,**doldmp;
2413: int i, j, nhstepm, hstepm, h, nstepm ;
2414: int k, cptcode;
2415: double *xp;
2416: double **gp, **gm; /* for var eij */
2417: double ***gradg, ***trgradg; /*for var eij */
2418: double **gradgp, **trgradgp; /* for var p point j */
2419: double *gpp, *gmp; /* for var p point j */
2420: double **varppt; /* for var p point j nlstate to nlstate+ndeath */
2421: double ***p3mat;
2422: double age,agelim, hf;
2423: double ***mobaverage;
2424: int theta;
2425: char digit[4];
1.55 lievre 2426: char digitp[25];
1.53 brouard 2427:
2428: char fileresprobmorprev[FILENAMELENGTH];
2429:
1.55 lievre 2430: if(popbased==1){
1.58 lievre 2431: if(mobilav!=0)
1.55 lievre 2432: strcpy(digitp,"-populbased-mobilav-");
2433: else strcpy(digitp,"-populbased-nomobil-");
2434: }
2435: else
1.53 brouard 2436: strcpy(digitp,"-stablbased-");
1.56 lievre 2437:
1.54 brouard 2438: if (mobilav!=0) {
1.53 brouard 2439: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
1.54 brouard 2440: if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
2441: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
2442: printf(" Error in movingaverage mobilav=%d\n",mobilav);
2443: }
1.53 brouard 2444: }
2445:
2446: strcpy(fileresprobmorprev,"prmorprev");
2447: sprintf(digit,"%-d",ij);
2448: /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
2449: strcat(fileresprobmorprev,digit); /* Tvar to be done */
2450: strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
2451: strcat(fileresprobmorprev,fileres);
2452: if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
2453: printf("Problem with resultfile: %s\n", fileresprobmorprev);
2454: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
2455: }
2456: printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
2457: fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
1.66 brouard 2458: 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 2459: fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
2460: for(j=nlstate+1; j<=(nlstate+ndeath);j++){
2461: fprintf(ficresprobmorprev," p.%-d SE",j);
2462: for(i=1; i<=nlstate;i++)
2463: fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
2464: }
2465: fprintf(ficresprobmorprev,"\n");
1.88 brouard 2466: fprintf(ficgp,"\n# Routine varevsij");
1.87 brouard 2467: 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");
2468: fprintf(fichtm,"\n<br>%s <br>\n",digitp);
2469: /* } */
1.53 brouard 2470: varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
2471:
2472: 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");
2473: fprintf(ficresvij,"# Age");
2474: for(i=1; i<=nlstate;i++)
2475: for(j=1; j<=nlstate;j++)
2476: fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);
2477: fprintf(ficresvij,"\n");
2478:
2479: xp=vector(1,npar);
2480: dnewm=matrix(1,nlstate,1,npar);
2481: doldm=matrix(1,nlstate,1,nlstate);
2482: dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
2483: doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
2484:
2485: gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
2486: gpp=vector(nlstate+1,nlstate+ndeath);
2487: gmp=vector(nlstate+1,nlstate+ndeath);
2488: trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
2489:
2490: if(estepm < stepm){
2491: printf ("Problem %d lower than %d\n",estepm, stepm);
2492: }
2493: else hstepm=estepm;
2494: /* For example we decided to compute the life expectancy with the smallest unit */
2495: /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
2496: nhstepm is the number of hstepm from age to agelim
2497: nstepm is the number of stepm from age to agelin.
2498: Look at hpijx to understand the reason of that which relies in memory size
2499: and note for a fixed period like k years */
2500: /* We decided (b) to get a life expectancy respecting the most precise curvature of the
2501: survival function given by stepm (the optimization length). Unfortunately it
1.66 brouard 2502: means that if the survival funtion is printed every two years of age and if
1.53 brouard 2503: you sum them up and add 1 year (area under the trapezoids) you won't get the same
2504: results. So we changed our mind and took the option of the best precision.
2505: */
2506: hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
2507: agelim = AGESUP;
2508: for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
2509: nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
2510: nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
2511: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
2512: gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
2513: gp=matrix(0,nhstepm,1,nlstate);
2514: gm=matrix(0,nhstepm,1,nlstate);
2515:
2516:
2517: for(theta=1; theta <=npar; theta++){
1.66 brouard 2518: for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
1.53 brouard 2519: xp[i] = x[i] + (i==theta ?delti[theta]:0);
2520: }
2521: hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
2522: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
2523:
2524: if (popbased==1) {
1.54 brouard 2525: if(mobilav ==0){
1.53 brouard 2526: for(i=1; i<=nlstate;i++)
2527: prlim[i][i]=probs[(int)age][i][ij];
1.54 brouard 2528: }else{ /* mobilav */
1.53 brouard 2529: for(i=1; i<=nlstate;i++)
2530: prlim[i][i]=mobaverage[(int)age][i][ij];
2531: }
2532: }
2533:
2534: for(j=1; j<= nlstate; j++){
2535: for(h=0; h<=nhstepm; h++){
2536: for(i=1, gp[h][j]=0.;i<=nlstate;i++)
2537: gp[h][j] += prlim[i][i]*p3mat[i][j][h];
2538: }
2539: }
1.66 brouard 2540: /* This for computing probability of death (h=1 means
2541: computed over hstepm matrices product = hstepm*stepm months)
2542: as a weighted average of prlim.
2543: */
1.69 brouard 2544: for(j=nlstate+1;j<=nlstate+ndeath;j++){
1.68 lievre 2545: for(i=1,gpp[j]=0.; i<= nlstate; i++)
1.53 brouard 2546: gpp[j] += prlim[i][i]*p3mat[i][j][1];
2547: }
1.66 brouard 2548: /* end probability of death */
1.53 brouard 2549:
1.66 brouard 2550: for(i=1; i<=npar; i++) /* Computes gradient x - delta */
1.53 brouard 2551: xp[i] = x[i] - (i==theta ?delti[theta]:0);
2552: hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
2553: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
2554:
2555: if (popbased==1) {
1.54 brouard 2556: if(mobilav ==0){
1.53 brouard 2557: for(i=1; i<=nlstate;i++)
2558: prlim[i][i]=probs[(int)age][i][ij];
1.54 brouard 2559: }else{ /* mobilav */
1.53 brouard 2560: for(i=1; i<=nlstate;i++)
2561: prlim[i][i]=mobaverage[(int)age][i][ij];
2562: }
2563: }
2564:
2565: for(j=1; j<= nlstate; j++){
2566: for(h=0; h<=nhstepm; h++){
2567: for(i=1, gm[h][j]=0.;i<=nlstate;i++)
2568: gm[h][j] += prlim[i][i]*p3mat[i][j][h];
2569: }
2570: }
1.66 brouard 2571: /* This for computing probability of death (h=1 means
2572: computed over hstepm matrices product = hstepm*stepm months)
2573: as a weighted average of prlim.
2574: */
1.69 brouard 2575: for(j=nlstate+1;j<=nlstate+ndeath;j++){
1.68 lievre 2576: for(i=1,gmp[j]=0.; i<= nlstate; i++)
2577: gmp[j] += prlim[i][i]*p3mat[i][j][1];
1.53 brouard 2578: }
1.66 brouard 2579: /* end probability of death */
1.53 brouard 2580:
2581: for(j=1; j<= nlstate; j++) /* vareij */
2582: for(h=0; h<=nhstepm; h++){
2583: gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
2584: }
1.68 lievre 2585:
1.53 brouard 2586: for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
2587: gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
2588: }
2589:
2590: } /* End theta */
2591:
2592: trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
2593:
2594: for(h=0; h<=nhstepm; h++) /* veij */
2595: for(j=1; j<=nlstate;j++)
2596: for(theta=1; theta <=npar; theta++)
2597: trgradg[h][j][theta]=gradg[h][theta][j];
2598:
2599: for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
1.69 brouard 2600: for(theta=1; theta <=npar; theta++)
1.53 brouard 2601: trgradgp[j][theta]=gradgp[theta][j];
1.69 brouard 2602:
1.53 brouard 2603:
2604: hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
2605: for(i=1;i<=nlstate;i++)
2606: for(j=1;j<=nlstate;j++)
2607: vareij[i][j][(int)age] =0.;
2608:
2609: for(h=0;h<=nhstepm;h++){
2610: for(k=0;k<=nhstepm;k++){
2611: matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
2612: matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
2613: for(i=1;i<=nlstate;i++)
2614: for(j=1;j<=nlstate;j++)
2615: vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
2616: }
2617: }
1.70 brouard 2618:
1.53 brouard 2619: /* pptj */
2620: matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
2621: matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
1.70 brouard 2622: for(j=nlstate+1;j<=nlstate+ndeath;j++)
2623: for(i=nlstate+1;i<=nlstate+ndeath;i++)
1.53 brouard 2624: varppt[j][i]=doldmp[j][i];
2625: /* end ppptj */
1.66 brouard 2626: /* x centered again */
1.53 brouard 2627: hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);
2628: prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);
2629:
2630: if (popbased==1) {
1.54 brouard 2631: if(mobilav ==0){
1.53 brouard 2632: for(i=1; i<=nlstate;i++)
2633: prlim[i][i]=probs[(int)age][i][ij];
1.54 brouard 2634: }else{ /* mobilav */
1.53 brouard 2635: for(i=1; i<=nlstate;i++)
2636: prlim[i][i]=mobaverage[(int)age][i][ij];
2637: }
2638: }
1.70 brouard 2639:
1.66 brouard 2640: /* This for computing probability of death (h=1 means
2641: computed over hstepm (estepm) matrices product = hstepm*stepm months)
2642: as a weighted average of prlim.
2643: */
1.68 lievre 2644: for(j=nlstate+1;j<=nlstate+ndeath;j++){
2645: for(i=1,gmp[j]=0.;i<= nlstate; i++)
1.53 brouard 2646: gmp[j] += prlim[i][i]*p3mat[i][j][1];
2647: }
1.66 brouard 2648: /* end probability of death */
1.53 brouard 2649:
2650: fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
2651: for(j=nlstate+1; j<=(nlstate+ndeath);j++){
2652: fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
2653: for(i=1; i<=nlstate;i++){
2654: fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
2655: }
2656: }
2657: fprintf(ficresprobmorprev,"\n");
2658:
2659: fprintf(ficresvij,"%.0f ",age );
2660: for(i=1; i<=nlstate;i++)
2661: for(j=1; j<=nlstate;j++){
2662: fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
2663: }
2664: fprintf(ficresvij,"\n");
2665: free_matrix(gp,0,nhstepm,1,nlstate);
2666: free_matrix(gm,0,nhstepm,1,nlstate);
2667: free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
2668: free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
2669: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
2670: } /* End age */
2671: free_vector(gpp,nlstate+1,nlstate+ndeath);
2672: free_vector(gmp,nlstate+1,nlstate+ndeath);
2673: free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
2674: free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
2675: fprintf(ficgp,"\nset noparametric;set nolabel; set ter png small;set size 0.65, 0.65");
2676: /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */
2677: fprintf(ficgp,"\n set log y; set nolog x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
1.67 brouard 2678: /* fprintf(ficgp,"\n plot \"%s\" u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm); */
2679: /* fprintf(ficgp,"\n replot \"%s\" u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm); */
2680: /* fprintf(ficgp,"\n replot \"%s\" u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm); */
1.88 brouard 2681: fprintf(ficgp,"\n plot \"%s\" u 1:($3) not w l 1 ",subdirf(fileresprobmorprev));
2682: fprintf(ficgp,"\n replot \"%s\" u 1:(($3+1.96*$4)) t \"95\%% interval\" w l 2 ",subdirf(fileresprobmorprev));
2683: fprintf(ficgp,"\n replot \"%s\" u 1:(($3-1.96*$4)) not w l 2 ",subdirf(fileresprobmorprev));
2684: fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",subdirf(fileresprobmorprev),subdirf(fileresprobmorprev));
2685: 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 2686: /* 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);
2687: */
1.88 brouard 2688: /* fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.png\";replot;",digitp,optionfilefiname,digit); */
1.89 brouard 2689: fprintf(ficgp,"\nset out \"%s%s.png\";replot;\n",subdirf3(optionfilefiname,"varmuptjgr",digitp),digit);
1.53 brouard 2690:
2691: free_vector(xp,1,npar);
2692: free_matrix(doldm,1,nlstate,1,nlstate);
2693: free_matrix(dnewm,1,nlstate,1,npar);
2694: free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
2695: free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
2696: free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
1.55 lievre 2697: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
1.53 brouard 2698: fclose(ficresprobmorprev);
1.88 brouard 2699: fflush(ficgp);
2700: fflush(fichtm);
1.84 brouard 2701: } /* end varevsij */
1.53 brouard 2702:
2703: /************ Variance of prevlim ******************/
2704: 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)
2705: {
2706: /* Variance of prevalence limit */
1.59 brouard 2707: /* double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
1.53 brouard 2708: double **newm;
2709: double **dnewm,**doldm;
2710: int i, j, nhstepm, hstepm;
2711: int k, cptcode;
2712: double *xp;
2713: double *gp, *gm;
2714: double **gradg, **trgradg;
2715: double age,agelim;
2716: int theta;
2717:
1.54 brouard 2718: fprintf(ficresvpl,"# Standard deviation of stable prevalences \n");
1.53 brouard 2719: fprintf(ficresvpl,"# Age");
2720: for(i=1; i<=nlstate;i++)
2721: fprintf(ficresvpl," %1d-%1d",i,i);
2722: fprintf(ficresvpl,"\n");
2723:
2724: xp=vector(1,npar);
2725: dnewm=matrix(1,nlstate,1,npar);
2726: doldm=matrix(1,nlstate,1,nlstate);
2727:
2728: hstepm=1*YEARM; /* Every year of age */
2729: hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */
2730: agelim = AGESUP;
2731: for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
2732: nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
2733: if (stepm >= YEARM) hstepm=1;
2734: nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
2735: gradg=matrix(1,npar,1,nlstate);
2736: gp=vector(1,nlstate);
2737: gm=vector(1,nlstate);
2738:
2739: for(theta=1; theta <=npar; theta++){
2740: for(i=1; i<=npar; i++){ /* Computes gradient */
2741: xp[i] = x[i] + (i==theta ?delti[theta]:0);
2742: }
2743: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
2744: for(i=1;i<=nlstate;i++)
2745: gp[i] = prlim[i][i];
2746:
2747: for(i=1; i<=npar; i++) /* Computes gradient */
2748: xp[i] = x[i] - (i==theta ?delti[theta]:0);
2749: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
2750: for(i=1;i<=nlstate;i++)
2751: gm[i] = prlim[i][i];
2752:
2753: for(i=1;i<=nlstate;i++)
2754: gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
2755: } /* End theta */
2756:
2757: trgradg =matrix(1,nlstate,1,npar);
2758:
2759: for(j=1; j<=nlstate;j++)
2760: for(theta=1; theta <=npar; theta++)
2761: trgradg[j][theta]=gradg[theta][j];
2762:
2763: for(i=1;i<=nlstate;i++)
2764: varpl[i][(int)age] =0.;
2765: matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
2766: matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
2767: for(i=1;i<=nlstate;i++)
2768: varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
2769:
2770: fprintf(ficresvpl,"%.0f ",age );
2771: for(i=1; i<=nlstate;i++)
2772: fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
2773: fprintf(ficresvpl,"\n");
2774: free_vector(gp,1,nlstate);
2775: free_vector(gm,1,nlstate);
2776: free_matrix(gradg,1,npar,1,nlstate);
2777: free_matrix(trgradg,1,nlstate,1,npar);
2778: } /* End age */
2779:
2780: free_vector(xp,1,npar);
2781: free_matrix(doldm,1,nlstate,1,npar);
2782: free_matrix(dnewm,1,nlstate,1,nlstate);
2783:
2784: }
2785:
2786: /************ Variance of one-step probabilities ******************/
2787: void varprob(char optionfilefiname[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij, int *Tvar, int **nbcode, int *ncodemax)
2788: {
2789: int i, j=0, i1, k1, l1, t, tj;
2790: int k2, l2, j1, z1;
2791: int k=0,l, cptcode;
2792: int first=1, first1;
2793: double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
2794: double **dnewm,**doldm;
2795: double *xp;
2796: double *gp, *gm;
2797: double **gradg, **trgradg;
2798: double **mu;
2799: double age,agelim, cov[NCOVMAX];
2800: double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
2801: int theta;
2802: char fileresprob[FILENAMELENGTH];
2803: char fileresprobcov[FILENAMELENGTH];
2804: char fileresprobcor[FILENAMELENGTH];
2805:
2806: double ***varpij;
2807:
2808: strcpy(fileresprob,"prob");
2809: strcat(fileresprob,fileres);
2810: if((ficresprob=fopen(fileresprob,"w"))==NULL) {
2811: printf("Problem with resultfile: %s\n", fileresprob);
2812: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
2813: }
2814: strcpy(fileresprobcov,"probcov");
2815: strcat(fileresprobcov,fileres);
2816: if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
2817: printf("Problem with resultfile: %s\n", fileresprobcov);
2818: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
2819: }
2820: strcpy(fileresprobcor,"probcor");
2821: strcat(fileresprobcor,fileres);
2822: if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
2823: printf("Problem with resultfile: %s\n", fileresprobcor);
2824: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
2825: }
2826: printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
2827: fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
2828: printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
2829: fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
2830: printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
2831: fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
2832:
2833: fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
2834: fprintf(ficresprob,"# Age");
2835: fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
2836: fprintf(ficresprobcov,"# Age");
2837: fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
2838: fprintf(ficresprobcov,"# Age");
2839:
2840:
2841: for(i=1; i<=nlstate;i++)
2842: for(j=1; j<=(nlstate+ndeath);j++){
2843: fprintf(ficresprob," p%1d-%1d (SE)",i,j);
2844: fprintf(ficresprobcov," p%1d-%1d ",i,j);
2845: fprintf(ficresprobcor," p%1d-%1d ",i,j);
2846: }
1.69 brouard 2847: /* fprintf(ficresprob,"\n");
1.53 brouard 2848: fprintf(ficresprobcov,"\n");
2849: fprintf(ficresprobcor,"\n");
1.69 brouard 2850: */
2851: xp=vector(1,npar);
1.53 brouard 2852: dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
2853: doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
2854: mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
2855: varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
2856: first=1;
1.88 brouard 2857: fprintf(ficgp,"\n# Routine varprob");
2858: fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
2859: fprintf(fichtm,"\n");
2860:
1.91 ! brouard 2861: fprintf(fichtm,"\n<li><h4> <a href=\"%s\">Computing matrix of variance-covariance of step probabilities</a></h4></li>\n",optionfilehtmcov);
! 2862: fprintf(fichtmcov,"\n<h4>Computing matrix of variance-covariance of step probabilities</h4>\n\
! 2863: file %s<br>\n",optionfilehtmcov);
! 2864: fprintf(fichtmcov,"\nEllipsoids of confidence centered on point (p<inf>ij</inf>, p<inf>kl</inf>) are estimated\
! 2865: and drawn. It helps understanding how is the covariance between two incidences.\
! 2866: They are expressed in year<sup>-1</sup> in order to be less dependent of stepm.<br>\n");
! 2867: 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. \
! 2868: It can be understood this way: if pij and pkl where uncorrelated the (2x2) matrix of covariance \
! 2869: would have been (1/(var pij), 0 , 0, 1/(var pkl)), and the confidence interval would be 2 \
! 2870: standard deviations wide on each axis. <br>\
! 2871: Now, if both incidences are correlated (usual case) we diagonalised the inverse of the covariance matrix\
! 2872: and made the appropriate rotation to look at the uncorrelated principal directions.<br>\
! 2873: 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 2874:
2875: cov[1]=1;
2876: tj=cptcoveff;
2877: if (cptcovn<1) {tj=1;ncodemax[1]=1;}
2878: j1=0;
2879: for(t=1; t<=tj;t++){
2880: for(i1=1; i1<=ncodemax[t];i1++){
2881: j1++;
2882: if (cptcovn>0) {
2883: fprintf(ficresprob, "\n#********** Variable ");
2884: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
1.69 brouard 2885: fprintf(ficresprob, "**********\n#\n");
1.53 brouard 2886: fprintf(ficresprobcov, "\n#********** Variable ");
2887: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
1.69 brouard 2888: fprintf(ficresprobcov, "**********\n#\n");
1.53 brouard 2889:
2890: fprintf(ficgp, "\n#********** Variable ");
1.69 brouard 2891: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
2892: fprintf(ficgp, "**********\n#\n");
1.53 brouard 2893:
2894:
2895: fprintf(fichtm, "\n<hr size=\"2\" color=\"#EC5E5E\">********** Variable ");
2896: for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
2897: fprintf(fichtm, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
2898:
2899: fprintf(ficresprobcor, "\n#********** Variable ");
2900: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
1.69 brouard 2901: fprintf(ficresprobcor, "**********\n#");
1.53 brouard 2902: }
2903:
2904: for (age=bage; age<=fage; age ++){
2905: cov[2]=age;
2906: for (k=1; k<=cptcovn;k++) {
2907: cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];
2908: }
2909: for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
2910: for (k=1; k<=cptcovprod;k++)
2911: cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
2912:
2913: gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
2914: trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
2915: gp=vector(1,(nlstate)*(nlstate+ndeath));
2916: gm=vector(1,(nlstate)*(nlstate+ndeath));
2917:
2918: for(theta=1; theta <=npar; theta++){
2919: for(i=1; i<=npar; i++)
1.74 brouard 2920: xp[i] = x[i] + (i==theta ?delti[theta]:(double)0);
1.53 brouard 2921:
2922: pmij(pmmij,cov,ncovmodel,xp,nlstate);
2923:
2924: k=0;
2925: for(i=1; i<= (nlstate); i++){
2926: for(j=1; j<=(nlstate+ndeath);j++){
2927: k=k+1;
2928: gp[k]=pmmij[i][j];
2929: }
2930: }
2931:
2932: for(i=1; i<=npar; i++)
1.74 brouard 2933: xp[i] = x[i] - (i==theta ?delti[theta]:(double)0);
1.53 brouard 2934:
2935: pmij(pmmij,cov,ncovmodel,xp,nlstate);
2936: k=0;
2937: for(i=1; i<=(nlstate); i++){
2938: for(j=1; j<=(nlstate+ndeath);j++){
2939: k=k+1;
2940: gm[k]=pmmij[i][j];
2941: }
2942: }
2943:
2944: for(i=1; i<= (nlstate)*(nlstate+ndeath); i++)
1.74 brouard 2945: gradg[theta][i]=(gp[i]-gm[i])/(double)2./delti[theta];
1.53 brouard 2946: }
2947:
2948: for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
2949: for(theta=1; theta <=npar; theta++)
2950: trgradg[j][theta]=gradg[theta][j];
2951:
2952: matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov);
2953: matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);
1.59 brouard 2954: free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
2955: free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
2956: free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
2957: free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
2958:
1.53 brouard 2959: pmij(pmmij,cov,ncovmodel,x,nlstate);
2960:
2961: k=0;
2962: for(i=1; i<=(nlstate); i++){
2963: for(j=1; j<=(nlstate+ndeath);j++){
2964: k=k+1;
2965: mu[k][(int) age]=pmmij[i][j];
2966: }
2967: }
2968: for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
2969: for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
2970: varpij[i][j][(int)age] = doldm[i][j];
2971:
2972: /*printf("\n%d ",(int)age);
1.59 brouard 2973: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
2974: printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
2975: fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
2976: }*/
1.53 brouard 2977:
2978: fprintf(ficresprob,"\n%d ",(int)age);
2979: fprintf(ficresprobcov,"\n%d ",(int)age);
2980: fprintf(ficresprobcor,"\n%d ",(int)age);
2981:
2982: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)
2983: fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));
2984: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
2985: fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);
2986: fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
2987: }
2988: i=0;
2989: for (k=1; k<=(nlstate);k++){
2990: for (l=1; l<=(nlstate+ndeath);l++){
2991: i=i++;
2992: fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
2993: fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
2994: for (j=1; j<=i;j++){
2995: fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);
2996: fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));
2997: }
2998: }
2999: }/* end of loop for state */
3000: } /* end of loop for age */
3001:
3002: /* Confidence intervalle of pij */
3003: /*
1.59 brouard 3004: fprintf(ficgp,"\nset noparametric;unset label");
3005: fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");
3006: fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
3007: 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);
3008: fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);
3009: fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);
3010: fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);
1.53 brouard 3011: */
3012:
3013: /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
3014: first1=1;
3015: for (k2=1; k2<=(nlstate);k2++){
3016: for (l2=1; l2<=(nlstate+ndeath);l2++){
3017: if(l2==k2) continue;
3018: j=(k2-1)*(nlstate+ndeath)+l2;
3019: for (k1=1; k1<=(nlstate);k1++){
3020: for (l1=1; l1<=(nlstate+ndeath);l1++){
3021: if(l1==k1) continue;
3022: i=(k1-1)*(nlstate+ndeath)+l1;
3023: if(i<=j) continue;
3024: for (age=bage; age<=fage; age ++){
3025: if ((int)age %5==0){
3026: v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;
3027: v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;
3028: cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;
3029: mu1=mu[i][(int) age]/stepm*YEARM ;
3030: mu2=mu[j][(int) age]/stepm*YEARM;
3031: c12=cv12/sqrt(v1*v2);
3032: /* Computing eigen value of matrix of covariance */
3033: lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
3034: lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
3035: /* Eigen vectors */
3036: v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
3037: /*v21=sqrt(1.-v11*v11); *//* error */
3038: v21=(lc1-v1)/cv12*v11;
3039: v12=-v21;
3040: v22=v11;
3041: tnalp=v21/v11;
3042: if(first1==1){
3043: first1=0;
3044: 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);
3045: }
3046: 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);
3047: /*printf(fignu*/
3048: /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */
3049: /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */
3050: if(first==1){
3051: first=0;
3052: fprintf(ficgp,"\nset parametric;unset label");
3053: 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);
3054: fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
1.91 ! brouard 3055: fprintf(fichtmcov,"\n<br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup>\
1.88 brouard 3056: :<a href=\"%s%d%1d%1d-%1d%1d.png\">\
3057: %s%d%1d%1d-%1d%1d.png</A>, ",k1,l1,k2,l2,\
3058: subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2,\
3059: subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
1.91 ! brouard 3060: fprintf(fichtmcov,"\n<br><img src=\"%s%d%1d%1d-%1d%1d.png\"> ",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
! 3061: fprintf(fichtmcov,"\n<br> Correlation at age %d (%.3f),",(int) age, c12);
1.88 brouard 3062: fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\"",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
1.53 brouard 3063: fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
3064: fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
3065: 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",\
3066: mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
3067: mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
3068: }else{
3069: first=0;
1.91 ! brouard 3070: fprintf(fichtmcov," %d (%.3f),",(int) age, c12);
1.53 brouard 3071: fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
3072: fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
3073: 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",\
3074: mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
3075: mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
3076: }/* if first */
3077: } /* age mod 5 */
3078: } /* end loop age */
1.88 brouard 3079: fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\";replot;",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
1.53 brouard 3080: first=1;
3081: } /*l12 */
3082: } /* k12 */
3083: } /*l1 */
3084: }/* k1 */
3085: } /* loop covariates */
3086: }
1.59 brouard 3087: free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
3088: free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
1.53 brouard 3089: free_vector(xp,1,npar);
3090: fclose(ficresprob);
3091: fclose(ficresprobcov);
3092: fclose(ficresprobcor);
1.91 ! brouard 3093: fflush(ficgp);
! 3094: fflush(fichtmcov);
1.53 brouard 3095: }
3096:
3097:
3098: /******************* Printing html file ***********/
3099: void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \
3100: int lastpass, int stepm, int weightopt, char model[],\
3101: int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
3102: int popforecast, int estepm ,\
3103: double jprev1, double mprev1,double anprev1, \
3104: double jprev2, double mprev2,double anprev2){
3105: int jj1, k1, i1, cpt;
3106: /*char optionfilehtm[FILENAMELENGTH];*/
1.87 brouard 3107: /* if((fichtm=fopen(optionfilehtm,"a"))==NULL) { */
3108: /* printf("Problem with %s \n",optionfilehtm), exit(0); */
3109: /* fprintf(ficlog,"Problem with %s \n",optionfilehtm), exit(0); */
3110: /* } */
1.53 brouard 3111:
1.85 brouard 3112: fprintf(fichtm,"<ul><li><h4>Result files (first order: no variance)</h4>\n \
1.88 brouard 3113: - Observed prevalence in each state (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"%s\">%s</a> <br>\n \
3114: - Estimated transition probabilities over %d (stepm) months: <a href=\"%s\">%s</a><br>\n \
3115: - Stable prevalence in each health state: <a href=\"%s\">%s</a> <br>\n \
1.85 brouard 3116: - Life expectancies by age and initial health status (estepm=%2d months): \
1.88 brouard 3117: <a href=\"%s\">%s</a> <br>\n</li>", \
3118: jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirf2(fileres,"p"),subdirf2(fileres,"p"),\
3119: stepm,subdirf2(fileres,"pij"),subdirf2(fileres,"pij"),\
3120: subdirf2(fileres,"pl"),subdirf2(fileres,"pl"),\
3121: estepm,subdirf2(fileres,"e"),subdirf2(fileres,"e"));
1.53 brouard 3122:
3123: fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
3124:
3125: m=cptcoveff;
3126: if (cptcovn < 1) {m=1;ncodemax[1]=1;}
3127:
3128: jj1=0;
3129: for(k1=1; k1<=m;k1++){
3130: for(i1=1; i1<=ncodemax[k1];i1++){
3131: jj1++;
3132: if (cptcovn > 0) {
3133: fprintf(fichtm,"<hr size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
3134: for (cpt=1; cpt<=cptcoveff;cpt++)
3135: fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
3136: fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
3137: }
3138: /* Pij */
1.88 brouard 3139: 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> \
3140: <img src=\"%s%d1.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);
1.53 brouard 3141: /* Quasi-incidences */
1.85 brouard 3142: fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months\
1.88 brouard 3143: before but expressed in per year i.e. quasi incidences if stepm is small and probabilities too: %s%d2.png<br> \
3144: <img src=\"%s%d2.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);
1.53 brouard 3145: /* Stable prevalence in each health state */
3146: for(cpt=1; cpt<nlstate;cpt++){
1.85 brouard 3147: fprintf(fichtm,"<br>- Stable prevalence in each health state : p%s%d%d.png<br> \
1.88 brouard 3148: <img src=\"%s%d%d.png\">",subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1);
1.53 brouard 3149: }
3150: for(cpt=1; cpt<=nlstate;cpt++) {
1.88 brouard 3151: fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): %s%d%d.png <br> \
1.89 brouard 3152: <img src=\"%s%d%d.png\">",cpt,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1);
1.53 brouard 3153: }
1.85 brouard 3154: fprintf(fichtm,"\n<br>- Total life expectancy by age and \
1.88 brouard 3155: health expectancies in states (1) and (2): %s%d.png<br>\
3156: <img src=\"%s%d.png\">",subdirf2(optionfilefiname,"e"),jj1,subdirf2(optionfilefiname,"e"),jj1);
1.53 brouard 3157: } /* end i1 */
3158: }/* End k1 */
3159: fprintf(fichtm,"</ul>");
3160:
3161:
1.85 brouard 3162: fprintf(fichtm,"\n<br><li><h4> Result files (second order: variances)</h4>\n\
3163: - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n\
1.88 brouard 3164: - Variance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n\
3165: - Variance-covariance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n\
3166: - Correlation matrix of one-step probabilities: <a href=\"%s\">%s</a> <br>\n\
3167: - Variances and covariances of life expectancies by age and initial health status (estepm=%d months): <a href=\"%s\">%s</a><br>\n\
3168: - Health expectancies with their variances (no covariance): <a href=\"%s\">%s</a> <br>\n\
3169: - Standard deviation of stable prevalences: <a href=\"%s\">%s</a> <br>\n",\
3170: rfileres,rfileres,\
3171: subdirf2(fileres,"prob"),subdirf2(fileres,"prob"),\
3172: subdirf2(fileres,"probcov"),subdirf2(fileres,"probcov"),\
3173: subdirf2(fileres,"probcor"),subdirf2(fileres,"probcor"),\
3174: estepm, subdirf2(fileres,"v"),subdirf2(fileres,"v"),\
3175: subdirf2(fileres,"t"),subdirf2(fileres,"t"),\
3176: subdirf2(fileres,"vpl"),subdirf2(fileres,"vpl"));
1.53 brouard 3177:
1.76 brouard 3178: /* if(popforecast==1) fprintf(fichtm,"\n */
3179: /* - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n */
3180: /* - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n */
3181: /* <br>",fileres,fileres,fileres,fileres); */
3182: /* else */
3183: /* 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 3184: fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
3185:
3186: m=cptcoveff;
3187: if (cptcovn < 1) {m=1;ncodemax[1]=1;}
3188:
3189: jj1=0;
3190: for(k1=1; k1<=m;k1++){
3191: for(i1=1; i1<=ncodemax[k1];i1++){
3192: jj1++;
3193: if (cptcovn > 0) {
3194: fprintf(fichtm,"<hr size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
3195: for (cpt=1; cpt<=cptcoveff;cpt++)
3196: fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
3197: fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
3198: }
3199: for(cpt=1; cpt<=nlstate;cpt++) {
1.85 brouard 3200: fprintf(fichtm,"<br>- Observed and period prevalence (with confident\
1.88 brouard 3201: interval) in state (%d): %s%d%d.png <br>\
1.90 brouard 3202: <img src=\"%s%d%d.png\">",cpt,subdirf2(optionfilefiname,"v"),cpt,jj1,subdirf2(optionfilefiname,"v"),cpt,jj1);
1.53 brouard 3203: }
3204: } /* end i1 */
3205: }/* End k1 */
3206: fprintf(fichtm,"</ul>");
1.87 brouard 3207: fflush(fichtm);
1.53 brouard 3208: }
3209:
3210: /******************* Gnuplot file **************/
1.89 brouard 3211: void printinggnuplot(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
1.53 brouard 3212:
1.88 brouard 3213: char dirfileres[132],optfileres[132];
1.53 brouard 3214: int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;
3215: int ng;
1.88 brouard 3216: /* if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) { */
3217: /* printf("Problem with file %s",optionfilegnuplot); */
3218: /* fprintf(ficlog,"Problem with file %s",optionfilegnuplot); */
3219: /* } */
1.53 brouard 3220:
1.54 brouard 3221: /*#ifdef windows */
1.89 brouard 3222: fprintf(ficgp,"cd \"%s\" \n",pathc);
1.54 brouard 3223: /*#endif */
1.88 brouard 3224: m=pow(2,cptcoveff);
3225:
3226: strcpy(dirfileres,optionfilefiname);
3227: strcpy(optfileres,"vpl");
1.53 brouard 3228: /* 1eme*/
3229: for (cpt=1; cpt<= nlstate ; cpt ++) {
3230: for (k1=1; k1<= m ; k1 ++) {
1.88 brouard 3231: fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"v"),cpt,k1);
3232: fprintf(ficgp,"\n#set out \"v%s%d%d.png\" \n",optionfilefiname,cpt,k1);
3233: fprintf(ficgp,"set xlabel \"Age\" \n\
3234: set ylabel \"Probability\" \n\
3235: set ter png small\n\
3236: set size 0.65,0.65\n\
3237: plot [%.f:%.f] \"%s\" every :::%d::%d u 1:2 \"\%%lf",ageminpar,fage,subdirf2(fileres,"vpl"),k1-1,k1-1);
1.53 brouard 3238:
3239: for (i=1; i<= nlstate ; i ++) {
3240: if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
3241: else fprintf(ficgp," \%%*lf (\%%*lf)");
3242: }
1.88 brouard 3243: 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 3244: for (i=1; i<= nlstate ; i ++) {
3245: if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
3246: else fprintf(ficgp," \%%*lf (\%%*lf)");
3247: }
1.88 brouard 3248: fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"%s\" every :::%d::%d u 1:($2-1.96*$3) \"\%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1);
1.53 brouard 3249: for (i=1; i<= nlstate ; i ++) {
3250: if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
3251: else fprintf(ficgp," \%%*lf (\%%*lf)");
3252: }
1.88 brouard 3253: fprintf(ficgp,"\" t\"\" w l 1,\"%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",subdirf2(fileres,"p"),k1-1,k1-1,2+4*(cpt-1));
1.53 brouard 3254: }
3255: }
3256: /*2 eme*/
3257:
3258: for (k1=1; k1<= m ; k1 ++) {
1.88 brouard 3259: fprintf(ficgp,"\nset out \"%s%d.png\" \n",subdirf2(optionfilefiname,"e"),k1);
1.53 brouard 3260: fprintf(ficgp,"set ylabel \"Years\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] ",ageminpar,fage);
3261:
3262: for (i=1; i<= nlstate+1 ; i ++) {
3263: k=2*i;
1.88 brouard 3264: fprintf(ficgp,"\"%s\" every :::%d::%d u 1:2 \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
1.53 brouard 3265: for (j=1; j<= nlstate+1 ; j ++) {
3266: if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
3267: else fprintf(ficgp," \%%*lf (\%%*lf)");
3268: }
3269: if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");
3270: else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);
1.88 brouard 3271: fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
1.53 brouard 3272: for (j=1; j<= nlstate+1 ; j ++) {
3273: if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
3274: else fprintf(ficgp," \%%*lf (\%%*lf)");
3275: }
3276: fprintf(ficgp,"\" t\"\" w l 0,");
1.88 brouard 3277: fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
1.53 brouard 3278: for (j=1; j<= nlstate+1 ; j ++) {
3279: if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
3280: else fprintf(ficgp," \%%*lf (\%%*lf)");
3281: }
3282: if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");
3283: else fprintf(ficgp,"\" t\"\" w l 0,");
3284: }
3285: }
3286:
3287: /*3eme*/
3288:
3289: for (k1=1; k1<= m ; k1 ++) {
3290: for (cpt=1; cpt<= nlstate ; cpt ++) {
3291: k=2+nlstate*(2*cpt-2);
1.88 brouard 3292: fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"exp"),cpt,k1);
3293: fprintf(ficgp,"set ter png small\n\
3294: set size 0.65,0.65\n\
3295: plot [%.f:%.f] \"%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,subdirf2(fileres,"e"),k1-1,k1-1,k,cpt);
1.53 brouard 3296: /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
3297: for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
3298: fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
3299: fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
3300: for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
3301: fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
3302:
3303: */
3304: for (i=1; i< nlstate ; i ++) {
1.88 brouard 3305: 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 3306:
3307: }
3308: }
3309: }
3310:
1.76 brouard 3311: /* CV preval stable (period) */
1.53 brouard 3312: for (k1=1; k1<= m ; k1 ++) {
1.76 brouard 3313: for (cpt=1; cpt<=nlstate ; cpt ++) {
1.53 brouard 3314: k=3;
1.88 brouard 3315: fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"p"),cpt,k1);
3316: fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\
3317: set ter png small\nset size 0.65,0.65\n\
1.89 brouard 3318: unset log y\n\
1.88 brouard 3319: plot [%.f:%.f] \"%s\" u ($1==%d ? ($3):1/0):($%d/($%d",ageminpar,agemaxpar,subdirf2(fileres,"pij"),k1,k+cpt+1,k+1);
1.53 brouard 3320:
1.83 lievre 3321: for (i=1; i< nlstate ; i ++)
1.53 brouard 3322: fprintf(ficgp,"+$%d",k+i+1);
3323: fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);
3324:
3325: l=3+(nlstate+ndeath)*cpt;
1.88 brouard 3326: fprintf(ficgp,",\"%s\" u ($1==%d ? ($3):1/0):($%d/($%d",subdirf2(fileres,"pij"),k1,l+cpt+1,l+1);
1.53 brouard 3327: for (i=1; i< nlstate ; i ++) {
3328: l=3+(nlstate+ndeath)*cpt;
3329: fprintf(ficgp,"+$%d",l+i+1);
3330: }
3331: fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);
3332: }
3333: }
3334:
3335: /* proba elementaires */
3336: for(i=1,jk=1; i <=nlstate; i++){
3337: for(k=1; k <=(nlstate+ndeath); k++){
3338: if (k != i) {
3339: for(j=1; j <=ncovmodel; j++){
3340: fprintf(ficgp,"p%d=%f ",jk,p[jk]);
3341: jk++;
3342: fprintf(ficgp,"\n");
3343: }
3344: }
3345: }
3346: }
3347:
3348: for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/
3349: for(jk=1; jk <=m; jk++) {
1.88 brouard 3350: fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"pe"),jk,ng);
1.53 brouard 3351: if (ng==2)
3352: fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
3353: else
3354: fprintf(ficgp,"\nset title \"Probability\"\n");
3355: fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65\nset log y\nplot [%.f:%.f] ",ageminpar,agemaxpar);
3356: i=1;
3357: for(k2=1; k2<=nlstate; k2++) {
3358: k3=i;
3359: for(k=1; k<=(nlstate+ndeath); k++) {
3360: if (k != k2){
3361: if(ng==2)
3362: fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);
3363: else
3364: fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
3365: ij=1;
3366: for(j=3; j <=ncovmodel; j++) {
3367: if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
3368: fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
3369: ij++;
3370: }
3371: else
3372: fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
3373: }
3374: fprintf(ficgp,")/(1");
3375:
3376: for(k1=1; k1 <=nlstate; k1++){
3377: fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);
3378: ij=1;
3379: for(j=3; j <=ncovmodel; j++){
3380: if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
3381: fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
3382: ij++;
3383: }
3384: else
3385: fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
3386: }
3387: fprintf(ficgp,")");
3388: }
3389: fprintf(ficgp,") t \"p%d%d\" ", k2,k);
3390: if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");
3391: i=i+ncovmodel;
3392: }
3393: } /* end k */
3394: } /* end k2 */
3395: } /* end jk */
3396: } /* end ng */
1.88 brouard 3397: fflush(ficgp);
1.53 brouard 3398: } /* end gnuplot */
3399:
3400:
3401: /*************** Moving average **************/
1.54 brouard 3402: int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav){
1.53 brouard 3403:
3404: int i, cpt, cptcod;
1.58 lievre 3405: int modcovmax =1;
1.54 brouard 3406: int mobilavrange, mob;
1.53 brouard 3407: double age;
1.58 lievre 3408:
3409: modcovmax=2*cptcoveff;/* Max number of modalities. We suppose
3410: a covariate has 2 modalities */
3411: if (cptcovn<1) modcovmax=1; /* At least 1 pass */
3412:
1.54 brouard 3413: if(mobilav==1||mobilav ==3 ||mobilav==5 ||mobilav== 7){
3414: if(mobilav==1) mobilavrange=5; /* default */
3415: else mobilavrange=mobilav;
3416: for (age=bage; age<=fage; age++)
3417: for (i=1; i<=nlstate;i++)
1.58 lievre 3418: for (cptcod=1;cptcod<=modcovmax;cptcod++)
1.54 brouard 3419: mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
3420: /* We keep the original values on the extreme ages bage, fage and for
3421: fage+1 and bage-1 we use a 3 terms moving average; for fage+2 bage+2
3422: we use a 5 terms etc. until the borders are no more concerned.
3423: */
3424: for (mob=3;mob <=mobilavrange;mob=mob+2){
3425: for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){
3426: for (i=1; i<=nlstate;i++){
1.58 lievre 3427: for (cptcod=1;cptcod<=modcovmax;cptcod++){
1.54 brouard 3428: mobaverage[(int)age][i][cptcod] =probs[(int)age][i][cptcod];
3429: for (cpt=1;cpt<=(mob-1)/2;cpt++){
3430: mobaverage[(int)age][i][cptcod] +=probs[(int)age-cpt][i][cptcod];
3431: mobaverage[(int)age][i][cptcod] +=probs[(int)age+cpt][i][cptcod];
3432: }
3433: mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/mob;
3434: }
1.53 brouard 3435: }
1.54 brouard 3436: }/* end age */
3437: }/* end mob */
3438: }else return -1;
3439: return 0;
3440: }/* End movingaverage */
1.53 brouard 3441:
3442:
3443: /************** Forecasting ******************/
1.70 brouard 3444: 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 3445: /* proj1, year, month, day of starting projection
3446: agemin, agemax range of age
3447: dateprev1 dateprev2 range of dates during which prevalence is computed
1.70 brouard 3448: anproj2 year of en of projection (same day and month as proj1).
1.69 brouard 3449: */
1.73 lievre 3450: int yearp, stepsize, hstepm, nhstepm, j, k, c, cptcod, i, h, i1;
1.53 brouard 3451: int *popage;
1.70 brouard 3452: double agec; /* generic age */
3453: double agelim, ppij, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
1.53 brouard 3454: double *popeffectif,*popcount;
3455: double ***p3mat;
1.55 lievre 3456: double ***mobaverage;
1.53 brouard 3457: char fileresf[FILENAMELENGTH];
3458:
1.69 brouard 3459: agelim=AGESUP;
1.84 brouard 3460: prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
1.53 brouard 3461:
3462: strcpy(fileresf,"f");
3463: strcat(fileresf,fileres);
3464: if((ficresf=fopen(fileresf,"w"))==NULL) {
3465: printf("Problem with forecast resultfile: %s\n", fileresf);
3466: fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);
3467: }
3468: printf("Computing forecasting: result on file '%s' \n", fileresf);
3469: fprintf(ficlog,"Computing forecasting: result on file '%s' \n", fileresf);
3470:
3471: if (cptcoveff==0) ncodemax[cptcoveff]=1;
3472:
1.54 brouard 3473: if (mobilav!=0) {
1.53 brouard 3474: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
1.54 brouard 3475: if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
3476: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
3477: printf(" Error in movingaverage mobilav=%d\n",mobilav);
3478: }
1.53 brouard 3479: }
3480:
3481: stepsize=(int) (stepm+YEARM-1)/YEARM;
3482: if (stepm<=12) stepsize=1;
1.74 brouard 3483: if(estepm < stepm){
3484: printf ("Problem %d lower than %d\n",estepm, stepm);
3485: }
3486: else hstepm=estepm;
3487:
1.53 brouard 3488: hstepm=hstepm/stepm;
1.69 brouard 3489: yp1=modf(dateintmean,&yp);/* extracts integral of datemean in yp and
3490: fractional in yp1 */
1.53 brouard 3491: anprojmean=yp;
3492: yp2=modf((yp1*12),&yp);
3493: mprojmean=yp;
3494: yp1=modf((yp2*30.5),&yp);
3495: jprojmean=yp;
3496: if(jprojmean==0) jprojmean=1;
3497: if(mprojmean==0) jprojmean=1;
1.73 lievre 3498:
3499: i1=cptcoveff;
3500: if (cptcovn < 1){i1=1;}
1.53 brouard 3501:
1.70 brouard 3502: fprintf(ficresf,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2);
1.53 brouard 3503:
1.70 brouard 3504: fprintf(ficresf,"#****** Routine prevforecast **\n");
1.73 lievre 3505:
1.75 brouard 3506: /* if (h==(int)(YEARM*yearp)){ */
1.73 lievre 3507: for(cptcov=1, k=0;cptcov<=i1;cptcov++){
1.53 brouard 3508: for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
3509: k=k+1;
3510: fprintf(ficresf,"\n#******");
3511: for(j=1;j<=cptcoveff;j++) {
1.70 brouard 3512: 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 3513: }
3514: fprintf(ficresf,"******\n");
1.70 brouard 3515: fprintf(ficresf,"# Covariate valuofcovar yearproj age");
3516: for(j=1; j<=nlstate+ndeath;j++){
3517: for(i=1; i<=nlstate;i++)
3518: fprintf(ficresf," p%d%d",i,j);
3519: fprintf(ficresf," p.%d",j);
3520: }
1.74 brouard 3521: for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) {
1.53 brouard 3522: fprintf(ficresf,"\n");
1.70 brouard 3523: fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+yearp);
1.53 brouard 3524:
1.71 brouard 3525: for (agec=fage; agec>=(ageminpar-1); agec--){
1.70 brouard 3526: nhstepm=(int) rint((agelim-agec)*YEARM/stepm);
1.53 brouard 3527: nhstepm = nhstepm/hstepm;
3528: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3529: oldm=oldms;savm=savms;
1.70 brouard 3530: hpxij(p3mat,nhstepm,agec,hstepm,p,nlstate,stepm,oldm,savm, k);
1.53 brouard 3531:
3532: for (h=0; h<=nhstepm; h++){
1.75 brouard 3533: if (h*hstepm/YEARM*stepm ==yearp) {
1.69 brouard 3534: fprintf(ficresf,"\n");
3535: for(j=1;j<=cptcoveff;j++)
3536: fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
1.70 brouard 3537: fprintf(ficresf,"%.f %.f ",anproj1+yearp,agec+h*hstepm/YEARM*stepm);
1.53 brouard 3538: }
3539: for(j=1; j<=nlstate+ndeath;j++) {
1.70 brouard 3540: ppij=0.;
1.71 brouard 3541: for(i=1; i<=nlstate;i++) {
1.53 brouard 3542: if (mobilav==1)
1.71 brouard 3543: ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][i][cptcod];
1.53 brouard 3544: else {
1.71 brouard 3545: ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][cptcod];
1.53 brouard 3546: }
1.75 brouard 3547: if (h*hstepm/YEARM*stepm== yearp) {
1.70 brouard 3548: fprintf(ficresf," %.3f", p3mat[i][j][h]);
1.75 brouard 3549: }
3550: } /* end i */
3551: if (h*hstepm/YEARM*stepm==yearp) {
1.70 brouard 3552: fprintf(ficresf," %.3f", ppij);
1.53 brouard 3553: }
1.75 brouard 3554: }/* end j */
3555: } /* end h */
1.53 brouard 3556: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
1.75 brouard 3557: } /* end agec */
3558: } /* end yearp */
3559: } /* end cptcod */
3560: } /* end cptcov */
1.53 brouard 3561:
1.54 brouard 3562: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
1.53 brouard 3563:
3564: fclose(ficresf);
3565: }
1.70 brouard 3566:
3567: /************** Forecasting *****not tested NB*************/
1.53 brouard 3568: 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){
3569:
3570: int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;
3571: int *popage;
1.69 brouard 3572: double calagedatem, agelim, kk1, kk2;
1.53 brouard 3573: double *popeffectif,*popcount;
3574: double ***p3mat,***tabpop,***tabpopprev;
1.55 lievre 3575: double ***mobaverage;
1.53 brouard 3576: char filerespop[FILENAMELENGTH];
3577:
3578: tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
3579: tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
3580: agelim=AGESUP;
1.69 brouard 3581: calagedatem=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;
1.53 brouard 3582:
1.84 brouard 3583: prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
1.53 brouard 3584:
3585:
3586: strcpy(filerespop,"pop");
3587: strcat(filerespop,fileres);
3588: if((ficrespop=fopen(filerespop,"w"))==NULL) {
3589: printf("Problem with forecast resultfile: %s\n", filerespop);
3590: fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop);
3591: }
3592: printf("Computing forecasting: result on file '%s' \n", filerespop);
3593: fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop);
3594:
3595: if (cptcoveff==0) ncodemax[cptcoveff]=1;
3596:
1.54 brouard 3597: if (mobilav!=0) {
1.53 brouard 3598: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
1.54 brouard 3599: if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
3600: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
3601: printf(" Error in movingaverage mobilav=%d\n",mobilav);
3602: }
1.53 brouard 3603: }
3604:
3605: stepsize=(int) (stepm+YEARM-1)/YEARM;
3606: if (stepm<=12) stepsize=1;
3607:
3608: agelim=AGESUP;
3609:
3610: hstepm=1;
3611: hstepm=hstepm/stepm;
3612:
3613: if (popforecast==1) {
3614: if((ficpop=fopen(popfile,"r"))==NULL) {
3615: printf("Problem with population file : %s\n",popfile);exit(0);
3616: fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0);
3617: }
3618: popage=ivector(0,AGESUP);
3619: popeffectif=vector(0,AGESUP);
3620: popcount=vector(0,AGESUP);
3621:
3622: i=1;
3623: while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;
3624:
3625: imx=i;
3626: for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];
3627: }
3628:
1.69 brouard 3629: for(cptcov=1,k=0;cptcov<=i2;cptcov++){
1.53 brouard 3630: for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
3631: k=k+1;
3632: fprintf(ficrespop,"\n#******");
3633: for(j=1;j<=cptcoveff;j++) {
3634: fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
3635: }
3636: fprintf(ficrespop,"******\n");
3637: fprintf(ficrespop,"# Age");
3638: for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);
3639: if (popforecast==1) fprintf(ficrespop," [Population]");
3640:
3641: for (cpt=0; cpt<=0;cpt++) {
3642: fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);
3643:
1.69 brouard 3644: for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){
1.53 brouard 3645: nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);
3646: nhstepm = nhstepm/hstepm;
3647:
3648: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3649: oldm=oldms;savm=savms;
3650: hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
3651:
3652: for (h=0; h<=nhstepm; h++){
1.69 brouard 3653: if (h==(int) (calagedatem+YEARM*cpt)) {
1.53 brouard 3654: fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
3655: }
3656: for(j=1; j<=nlstate+ndeath;j++) {
3657: kk1=0.;kk2=0;
3658: for(i=1; i<=nlstate;i++) {
3659: if (mobilav==1)
3660: kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];
3661: else {
3662: kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];
3663: }
3664: }
1.69 brouard 3665: if (h==(int)(calagedatem+12*cpt)){
1.53 brouard 3666: tabpop[(int)(agedeb)][j][cptcod]=kk1;
3667: /*fprintf(ficrespop," %.3f", kk1);
3668: if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/
3669: }
3670: }
3671: for(i=1; i<=nlstate;i++){
3672: kk1=0.;
3673: for(j=1; j<=nlstate;j++){
3674: kk1= kk1+tabpop[(int)(agedeb)][j][cptcod];
3675: }
1.69 brouard 3676: tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedatem+12*cpt)*hstepm/YEARM*stepm-1)];
1.53 brouard 3677: }
3678:
1.69 brouard 3679: if (h==(int)(calagedatem+12*cpt)) for(j=1; j<=nlstate;j++)
1.53 brouard 3680: fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);
3681: }
3682: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3683: }
3684: }
3685:
3686: /******/
3687:
3688: for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) {
3689: fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);
1.69 brouard 3690: for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){
1.53 brouard 3691: nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);
3692: nhstepm = nhstepm/hstepm;
3693:
3694: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3695: oldm=oldms;savm=savms;
3696: hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
3697: for (h=0; h<=nhstepm; h++){
1.69 brouard 3698: if (h==(int) (calagedatem+YEARM*cpt)) {
1.53 brouard 3699: fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
3700: }
3701: for(j=1; j<=nlstate+ndeath;j++) {
3702: kk1=0.;kk2=0;
3703: for(i=1; i<=nlstate;i++) {
3704: kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];
3705: }
1.69 brouard 3706: if (h==(int)(calagedatem+12*cpt)) fprintf(ficresf," %15.2f", kk1);
1.53 brouard 3707: }
3708: }
3709: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3710: }
3711: }
3712: }
3713: }
3714:
1.54 brouard 3715: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
1.53 brouard 3716:
3717: if (popforecast==1) {
3718: free_ivector(popage,0,AGESUP);
3719: free_vector(popeffectif,0,AGESUP);
3720: free_vector(popcount,0,AGESUP);
3721: }
3722: free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
3723: free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
3724: fclose(ficrespop);
1.84 brouard 3725: } /* End of popforecast */
1.53 brouard 3726:
1.87 brouard 3727: int fileappend(FILE *fichier, char *optionfich)
1.86 brouard 3728: {
1.87 brouard 3729: if((fichier=fopen(optionfich,"a"))==NULL) {
3730: printf("Problem with file: %s\n", optionfich);
3731: fprintf(ficlog,"Problem with file: %s\n", optionfich);
3732: return (0);
1.86 brouard 3733: }
1.87 brouard 3734: fflush(fichier);
3735: return (1);
1.86 brouard 3736: }
1.88 brouard 3737: void prwizard(int ncovmodel, int nlstate, int ndeath, char model[], FILE *ficparo)
3738: {
3739:
3740: char ca[32], cb[32], cc[32];
3741: int i,j, k, l, li, lj, lk, ll, jj, npar, itimes;
3742: int numlinepar;
3743:
3744: printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
3745: fprintf(ficparo,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
3746: for(i=1; i <=nlstate; i++){
3747: jj=0;
3748: for(j=1; j <=nlstate+ndeath; j++){
3749: if(j==i) continue;
3750: jj++;
3751: /*ca[0]= k+'a'-1;ca[1]='\0';*/
3752: printf("%1d%1d",i,j);
3753: fprintf(ficparo,"%1d%1d",i,j);
3754: for(k=1; k<=ncovmodel;k++){
3755: /* printf(" %lf",param[i][j][k]); */
3756: /* fprintf(ficparo," %lf",param[i][j][k]); */
3757: printf(" 0.");
3758: fprintf(ficparo," 0.");
3759: }
3760: printf("\n");
3761: fprintf(ficparo,"\n");
3762: }
3763: }
3764: printf("# Scales (for hessian or gradient estimation)\n");
3765: fprintf(ficparo,"# Scales (for hessian or gradient estimation)\n");
3766: npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/
3767: for(i=1; i <=nlstate; i++){
3768: jj=0;
3769: for(j=1; j <=nlstate+ndeath; j++){
3770: if(j==i) continue;
3771: jj++;
3772: fprintf(ficparo,"%1d%1d",i,j);
3773: printf("%1d%1d",i,j);
3774: fflush(stdout);
3775: for(k=1; k<=ncovmodel;k++){
3776: /* printf(" %le",delti3[i][j][k]); */
3777: /* fprintf(ficparo," %le",delti3[i][j][k]); */
3778: printf(" 0.");
3779: fprintf(ficparo," 0.");
3780: }
3781: numlinepar++;
3782: printf("\n");
3783: fprintf(ficparo,"\n");
3784: }
3785: }
3786: printf("# Covariance matrix\n");
3787: /* # 121 Var(a12)\n\ */
3788: /* # 122 Cov(b12,a12) Var(b12)\n\ */
3789: /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
3790: /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
3791: /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
3792: /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
3793: /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
3794: /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
3795: fflush(stdout);
3796: fprintf(ficparo,"# Covariance matrix\n");
3797: /* # 121 Var(a12)\n\ */
3798: /* # 122 Cov(b12,a12) Var(b12)\n\ */
3799: /* # ...\n\ */
3800: /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
3801:
3802: for(itimes=1;itimes<=2;itimes++){
3803: jj=0;
3804: for(i=1; i <=nlstate; i++){
3805: for(j=1; j <=nlstate+ndeath; j++){
3806: if(j==i) continue;
3807: for(k=1; k<=ncovmodel;k++){
3808: jj++;
3809: ca[0]= k+'a'-1;ca[1]='\0';
3810: if(itimes==1){
3811: printf("#%1d%1d%d",i,j,k);
3812: fprintf(ficparo,"#%1d%1d%d",i,j,k);
3813: }else{
3814: printf("%1d%1d%d",i,j,k);
3815: fprintf(ficparo,"%1d%1d%d",i,j,k);
3816: /* printf(" %.5le",matcov[i][j]); */
3817: }
3818: ll=0;
3819: for(li=1;li <=nlstate; li++){
3820: for(lj=1;lj <=nlstate+ndeath; lj++){
3821: if(lj==li) continue;
3822: for(lk=1;lk<=ncovmodel;lk++){
3823: ll++;
3824: if(ll<=jj){
3825: cb[0]= lk +'a'-1;cb[1]='\0';
3826: if(ll<jj){
3827: if(itimes==1){
3828: printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
3829: fprintf(ficparo," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
3830: }else{
3831: printf(" 0.");
3832: fprintf(ficparo," 0.");
3833: }
3834: }else{
3835: if(itimes==1){
3836: printf(" Var(%s%1d%1d)",ca,i,j);
3837: fprintf(ficparo," Var(%s%1d%1d)",ca,i,j);
3838: }else{
3839: printf(" 0.");
3840: fprintf(ficparo," 0.");
3841: }
3842: }
3843: }
3844: } /* end lk */
3845: } /* end lj */
3846: } /* end li */
3847: printf("\n");
3848: fprintf(ficparo,"\n");
3849: numlinepar++;
3850: } /* end k*/
3851: } /*end j */
3852: } /* end i */
3853: }
3854:
3855: } /* end of prwizard */
3856:
1.91 ! brouard 3857:
1.53 brouard 3858: /***********************************************/
3859: /**************** Main Program *****************/
3860: /***********************************************/
3861:
3862: int main(int argc, char *argv[])
3863: {
1.61 brouard 3864: int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav);
1.74 brouard 3865: int i,j, k, n=MAXN,iter,m,size=100,cptcode, cptcod;
1.88 brouard 3866: int jj, imk;
1.85 brouard 3867: int numlinepar=0; /* Current linenumber of parameter file */
1.87 brouard 3868: /* FILE *fichtm; *//* Html File */
3869: /* FILE *ficgp;*/ /*Gnuplot File */
1.53 brouard 3870: double agedeb, agefin,hf;
3871: double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;
3872:
3873: double fret;
3874: double **xi,tmp,delta;
3875:
3876: double dum; /* Dummy variable */
3877: double ***p3mat;
3878: double ***mobaverage;
3879: int *indx;
3880: char line[MAXLINE], linepar[MAXLINE];
1.88 brouard 3881: char path[MAXLINE],pathc[MAXLINE],pathcd[MAXLINE],pathtot[MAXLINE],model[MAXLINE];
3882: char pathr[MAXLINE];
1.53 brouard 3883: int firstobs=1, lastobs=10;
3884: int sdeb, sfin; /* Status at beginning and end */
3885: int c, h , cpt,l;
3886: int ju,jl, mi;
3887: int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;
1.59 brouard 3888: int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,*tab;
1.69 brouard 3889: int mobilavproj=0 , prevfcast=0 ; /* moving average of prev, If prevfcast=1 prevalence projection */
1.53 brouard 3890: int mobilav=0,popforecast=0;
3891: int hstepm, nhstepm;
1.74 brouard 3892: double jprev1=1, mprev1=1,anprev1=2000,jprev2=1, mprev2=1,anprev2=2000;
3893: double jpyram=1, mpyram=1,anpyram=2000,jpyram1=1, mpyram1=1,anpyram1=2000;
1.53 brouard 3894:
3895: double bage, fage, age, agelim, agebase;
3896: double ftolpl=FTOL;
3897: double **prlim;
3898: double *severity;
3899: double ***param; /* Matrix of parameters */
3900: double *p;
3901: double **matcov; /* Matrix of covariance */
3902: double ***delti3; /* Scale */
3903: double *delti; /* Scale */
3904: double ***eij, ***vareij;
3905: double **varpl; /* Variances of prevalence limits by age */
3906: double *epj, vepp;
3907: double kk1, kk2;
1.74 brouard 3908: double dateprev1, dateprev2,jproj1=1,mproj1=1,anproj1=2000,jproj2=1,mproj2=1,anproj2=2000;
1.53 brouard 3909:
3910: char *alph[]={"a","a","b","c","d","e"}, str[4];
3911:
3912:
3913: char z[1]="c", occ;
1.86 brouard 3914:
1.53 brouard 3915: char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];
1.88 brouard 3916: char strstart[80], *strt, strtend[80];
1.85 brouard 3917: char *stratrunc;
3918: int lstra;
3919:
3920: long total_usecs;
1.53 brouard 3921:
1.85 brouard 3922: /* gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */
3923: (void) gettimeofday(&start_time,&tzp);
1.91 ! brouard 3924: curr_time=start_time;
1.85 brouard 3925: tm = *localtime(&start_time.tv_sec);
3926: tmg = *gmtime(&start_time.tv_sec);
1.88 brouard 3927: strcpy(strstart,asctime(&tm));
1.86 brouard 3928:
1.88 brouard 3929: /* printf("Localtime (at start)=%s",strstart); */
1.85 brouard 3930: /* tp.tv_sec = tp.tv_sec +86400; */
3931: /* tm = *localtime(&start_time.tv_sec); */
3932: /* tmg.tm_year=tmg.tm_year +dsign*dyear; */
3933: /* tmg.tm_mon=tmg.tm_mon +dsign*dmonth; */
3934: /* tmg.tm_hour=tmg.tm_hour + 1; */
3935: /* tp.tv_sec = mktime(&tmg); */
3936: /* strt=asctime(&tmg); */
1.88 brouard 3937: /* printf("Time(after) =%s",strstart); */
1.85 brouard 3938: /* (void) time (&time_value);
3939: * printf("time=%d,t-=%d\n",time_value,time_value-86400);
3940: * tm = *localtime(&time_value);
1.88 brouard 3941: * strstart=asctime(&tm);
3942: * printf("tim_value=%d,asctime=%s\n",time_value,strstart);
1.85 brouard 3943: */
3944:
1.91 ! brouard 3945: nberr=0; /* Number of errors and warnings */
! 3946: nbwarn=0;
1.53 brouard 3947: getcwd(pathcd, size);
3948:
1.81 brouard 3949: printf("\n%s\n%s",version,fullversion);
1.53 brouard 3950: if(argc <=1){
3951: printf("\nEnter the parameter file name: ");
3952: scanf("%s",pathtot);
3953: }
3954: else{
3955: strcpy(pathtot,argv[1]);
3956: }
1.88 brouard 3957: /*if(getcwd(pathcd, MAXLINE)!= NULL)printf ("Error pathcd\n");*/
1.53 brouard 3958: /*cygwin_split_path(pathtot,path,optionfile);
3959: printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/
3960: /* cutv(path,optionfile,pathtot,'\\');*/
3961:
3962: split(pathtot,path,optionfile,optionfilext,optionfilefiname);
1.85 brouard 3963: printf("pathtot=%s,\npath=%s,\noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
1.53 brouard 3964: chdir(path);
1.88 brouard 3965: strcpy(command,"mkdir ");
3966: strcat(command,optionfilefiname);
3967: if((outcmd=system(command)) != 0){
3968: printf("Problem creating directory or it already exists %s%s, err=%d\n",path,optionfilefiname,outcmd);
3969: /* fprintf(ficlog,"Problem creating directory %s%s\n",path,optionfilefiname); */
3970: /* fclose(ficlog); */
3971: /* exit(1); */
3972: }
3973: /* if((imk=mkdir(optionfilefiname))<0){ */
3974: /* perror("mkdir"); */
3975: /* } */
1.53 brouard 3976:
1.59 brouard 3977: /*-------- arguments in the command line --------*/
1.53 brouard 3978:
3979: /* Log file */
3980: strcat(filelog, optionfilefiname);
3981: strcat(filelog,".log"); /* */
3982: if((ficlog=fopen(filelog,"w"))==NULL) {
3983: printf("Problem with logfile %s\n",filelog);
3984: goto end;
3985: }
3986: fprintf(ficlog,"Log filename:%s\n",filelog);
1.85 brouard 3987: fprintf(ficlog,"\n%s\n%s",version,fullversion);
1.53 brouard 3988: fprintf(ficlog,"\nEnter the parameter file name: ");
1.88 brouard 3989: fprintf(ficlog,"pathtot=%s\n\
3990: path=%s \n\
3991: optionfile=%s\n\
3992: optionfilext=%s\n\
3993: optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
1.86 brouard 3994:
1.88 brouard 3995: printf("Localtime (at start):%s",strstart);
3996: fprintf(ficlog,"Localtime (at start): %s",strstart);
1.53 brouard 3997: fflush(ficlog);
1.91 ! brouard 3998: /* (void) gettimeofday(&curr_time,&tzp); */
! 3999: /* printf("Elapsed time %d\n", asc_diff_time(curr_time.tv_sec-start_time.tv_sec,tmpout)); */
1.53 brouard 4000:
4001: /* */
4002: strcpy(fileres,"r");
4003: strcat(fileres, optionfilefiname);
4004: strcat(fileres,".txt"); /* Other files have txt extension */
4005:
4006: /*---------arguments file --------*/
4007:
4008: if((ficpar=fopen(optionfile,"r"))==NULL) {
4009: printf("Problem with optionfile %s\n",optionfile);
4010: fprintf(ficlog,"Problem with optionfile %s\n",optionfile);
1.85 brouard 4011: fflush(ficlog);
1.53 brouard 4012: goto end;
4013: }
4014:
1.88 brouard 4015:
4016:
1.53 brouard 4017: strcpy(filereso,"o");
4018: strcat(filereso,fileres);
1.88 brouard 4019: if((ficparo=fopen(filereso,"w"))==NULL) { /* opened on subdirectory */
1.53 brouard 4020: printf("Problem with Output resultfile: %s\n", filereso);
4021: fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso);
1.85 brouard 4022: fflush(ficlog);
1.53 brouard 4023: goto end;
4024: }
4025:
4026: /* Reads comments: lines beginning with '#' */
1.85 brouard 4027: numlinepar=0;
1.53 brouard 4028: while((c=getc(ficpar))=='#' && c!= EOF){
4029: ungetc(c,ficpar);
4030: fgets(line, MAXLINE, ficpar);
1.85 brouard 4031: numlinepar++;
1.53 brouard 4032: puts(line);
4033: fputs(line,ficparo);
1.85 brouard 4034: fputs(line,ficlog);
1.53 brouard 4035: }
4036: ungetc(c,ficpar);
4037:
4038: 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 4039: numlinepar++;
1.53 brouard 4040: 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);
4041: 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 4042: 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);
4043: fflush(ficlog);
1.59 brouard 4044: while((c=getc(ficpar))=='#' && c!= EOF){
1.53 brouard 4045: ungetc(c,ficpar);
4046: fgets(line, MAXLINE, ficpar);
1.85 brouard 4047: numlinepar++;
1.53 brouard 4048: puts(line);
4049: fputs(line,ficparo);
1.85 brouard 4050: fputs(line,ficlog);
1.53 brouard 4051: }
4052: ungetc(c,ficpar);
1.85 brouard 4053:
1.53 brouard 4054:
4055: covar=matrix(0,NCOVMAX,1,n);
1.58 lievre 4056: cptcovn=0; /*Number of covariates, i.e. number of '+' in model statement*/
1.53 brouard 4057: if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;
4058:
1.58 lievre 4059: ncovmodel=2+cptcovn; /*Number of variables = cptcovn + intercept + age */
1.53 brouard 4060: nvar=ncovmodel-1; /* Suppressing age as a basic covariate */
1.88 brouard 4061:
4062: if(mle==-1){ /* Print a wizard for help writing covariance matrix */
4063: prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
4064: printf(" You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
4065: fprintf(ficlog," You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
4066: fclose (ficparo);
4067: fclose (ficlog);
4068: exit(0);
4069: }
1.53 brouard 4070: /* Read guess parameters */
4071: /* Reads comments: lines beginning with '#' */
4072: while((c=getc(ficpar))=='#' && c!= EOF){
4073: ungetc(c,ficpar);
4074: fgets(line, MAXLINE, ficpar);
1.85 brouard 4075: numlinepar++;
1.53 brouard 4076: puts(line);
4077: fputs(line,ficparo);
1.85 brouard 4078: fputs(line,ficlog);
1.53 brouard 4079: }
4080: ungetc(c,ficpar);
1.85 brouard 4081:
1.53 brouard 4082: param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
1.85 brouard 4083: for(i=1; i <=nlstate; i++){
4084: j=0;
4085: for(jj=1; jj <=nlstate+ndeath; jj++){
4086: if(jj==i) continue;
4087: j++;
1.53 brouard 4088: fscanf(ficpar,"%1d%1d",&i1,&j1);
1.85 brouard 4089: if ((i1 != i) && (j1 != j)){
4090: printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n",numlinepar, i,j, i1, j1);
4091: exit(1);
4092: }
1.53 brouard 4093: fprintf(ficparo,"%1d%1d",i1,j1);
4094: if(mle==1)
4095: printf("%1d%1d",i,j);
4096: fprintf(ficlog,"%1d%1d",i,j);
4097: for(k=1; k<=ncovmodel;k++){
4098: fscanf(ficpar," %lf",¶m[i][j][k]);
4099: if(mle==1){
4100: printf(" %lf",param[i][j][k]);
4101: fprintf(ficlog," %lf",param[i][j][k]);
4102: }
4103: else
4104: fprintf(ficlog," %lf",param[i][j][k]);
4105: fprintf(ficparo," %lf",param[i][j][k]);
4106: }
4107: fscanf(ficpar,"\n");
1.85 brouard 4108: numlinepar++;
1.53 brouard 4109: if(mle==1)
4110: printf("\n");
4111: fprintf(ficlog,"\n");
4112: fprintf(ficparo,"\n");
4113: }
1.85 brouard 4114: }
4115: fflush(ficlog);
4116:
1.59 brouard 4117: npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/
1.53 brouard 4118:
4119: p=param[1][1];
4120:
4121: /* Reads comments: lines beginning with '#' */
4122: while((c=getc(ficpar))=='#' && c!= EOF){
4123: ungetc(c,ficpar);
4124: fgets(line, MAXLINE, ficpar);
1.85 brouard 4125: numlinepar++;
1.53 brouard 4126: puts(line);
4127: fputs(line,ficparo);
1.85 brouard 4128: fputs(line,ficlog);
1.53 brouard 4129: }
4130: ungetc(c,ficpar);
4131:
4132: delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
1.74 brouard 4133: /* delti=vector(1,npar); *//* Scale of each paramater (output from hesscov) */
1.53 brouard 4134: for(i=1; i <=nlstate; i++){
4135: for(j=1; j <=nlstate+ndeath-1; j++){
4136: fscanf(ficpar,"%1d%1d",&i1,&j1);
1.85 brouard 4137: if ((i1-i)*(j1-j)!=0){
4138: printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n",numlinepar, i,j, i1, j1);
4139: exit(1);
4140: }
1.53 brouard 4141: printf("%1d%1d",i,j);
4142: fprintf(ficparo,"%1d%1d",i1,j1);
1.85 brouard 4143: fprintf(ficlog,"%1d%1d",i1,j1);
1.53 brouard 4144: for(k=1; k<=ncovmodel;k++){
4145: fscanf(ficpar,"%le",&delti3[i][j][k]);
4146: printf(" %le",delti3[i][j][k]);
4147: fprintf(ficparo," %le",delti3[i][j][k]);
1.85 brouard 4148: fprintf(ficlog," %le",delti3[i][j][k]);
1.53 brouard 4149: }
4150: fscanf(ficpar,"\n");
1.85 brouard 4151: numlinepar++;
1.53 brouard 4152: printf("\n");
4153: fprintf(ficparo,"\n");
1.85 brouard 4154: fprintf(ficlog,"\n");
1.53 brouard 4155: }
4156: }
1.85 brouard 4157: fflush(ficlog);
4158:
1.53 brouard 4159: delti=delti3[1][1];
1.74 brouard 4160:
4161:
4162: /* 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 4163:
4164: /* Reads comments: lines beginning with '#' */
4165: while((c=getc(ficpar))=='#' && c!= EOF){
4166: ungetc(c,ficpar);
4167: fgets(line, MAXLINE, ficpar);
1.85 brouard 4168: numlinepar++;
1.53 brouard 4169: puts(line);
4170: fputs(line,ficparo);
1.85 brouard 4171: fputs(line,ficlog);
1.53 brouard 4172: }
4173: ungetc(c,ficpar);
4174:
4175: matcov=matrix(1,npar,1,npar);
4176: for(i=1; i <=npar; i++){
4177: fscanf(ficpar,"%s",&str);
4178: if(mle==1)
4179: printf("%s",str);
4180: fprintf(ficlog,"%s",str);
4181: fprintf(ficparo,"%s",str);
4182: for(j=1; j <=i; j++){
4183: fscanf(ficpar," %le",&matcov[i][j]);
4184: if(mle==1){
4185: printf(" %.5le",matcov[i][j]);
4186: }
1.85 brouard 4187: fprintf(ficlog," %.5le",matcov[i][j]);
1.53 brouard 4188: fprintf(ficparo," %.5le",matcov[i][j]);
4189: }
4190: fscanf(ficpar,"\n");
1.85 brouard 4191: numlinepar++;
1.53 brouard 4192: if(mle==1)
4193: printf("\n");
4194: fprintf(ficlog,"\n");
4195: fprintf(ficparo,"\n");
4196: }
4197: for(i=1; i <=npar; i++)
4198: for(j=i+1;j<=npar;j++)
4199: matcov[i][j]=matcov[j][i];
4200:
4201: if(mle==1)
4202: printf("\n");
4203: fprintf(ficlog,"\n");
4204:
1.85 brouard 4205: fflush(ficlog);
1.53 brouard 4206:
1.59 brouard 4207: /*-------- Rewriting paramater file ----------*/
4208: strcpy(rfileres,"r"); /* "Rparameterfile */
4209: strcat(rfileres,optionfilefiname); /* Parameter file first name*/
4210: strcat(rfileres,"."); /* */
4211: strcat(rfileres,optionfilext); /* Other files have txt extension */
4212: if((ficres =fopen(rfileres,"w"))==NULL) {
4213: printf("Problem writing new parameter file: %s\n", fileres);goto end;
4214: fprintf(ficlog,"Problem writing new parameter file: %s\n", fileres);goto end;
4215: }
4216: fprintf(ficres,"#%s\n",version);
1.53 brouard 4217:
1.59 brouard 4218: /*-------- data file ----------*/
4219: if((fic=fopen(datafile,"r"))==NULL) {
4220: printf("Problem with datafile: %s\n", datafile);goto end;
4221: fprintf(ficlog,"Problem with datafile: %s\n", datafile);goto end;
4222: }
4223:
4224: n= lastobs;
4225: severity = vector(1,maxwav);
4226: outcome=imatrix(1,maxwav+1,1,n);
1.85 brouard 4227: num=lvector(1,n);
1.59 brouard 4228: moisnais=vector(1,n);
4229: annais=vector(1,n);
4230: moisdc=vector(1,n);
4231: andc=vector(1,n);
4232: agedc=vector(1,n);
4233: cod=ivector(1,n);
4234: weight=vector(1,n);
4235: for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */
4236: mint=matrix(1,maxwav,1,n);
4237: anint=matrix(1,maxwav,1,n);
4238: s=imatrix(1,maxwav+1,1,n);
4239: tab=ivector(1,NCOVMAX);
4240: ncodemax=ivector(1,8);
4241:
4242: i=1;
4243: while (fgets(line, MAXLINE, fic) != NULL) {
4244: if ((i >= firstobs) && (i <=lastobs)) {
1.53 brouard 4245:
1.59 brouard 4246: for (j=maxwav;j>=1;j--){
4247: cutv(stra, strb,line,' '); s[j][i]=atoi(strb);
4248: strcpy(line,stra);
4249: cutv(stra, strb,line,'/'); anint[j][i]=(double)(atoi(strb)); strcpy(line,stra);
4250: cutv(stra, strb,line,' '); mint[j][i]=(double)(atoi(strb)); strcpy(line,stra);
4251: }
1.53 brouard 4252:
1.59 brouard 4253: cutv(stra, strb,line,'/'); andc[i]=(double)(atoi(strb)); strcpy(line,stra);
4254: cutv(stra, strb,line,' '); moisdc[i]=(double)(atoi(strb)); strcpy(line,stra);
1.53 brouard 4255:
1.59 brouard 4256: cutv(stra, strb,line,'/'); annais[i]=(double)(atoi(strb)); strcpy(line,stra);
4257: cutv(stra, strb,line,' '); moisnais[i]=(double)(atoi(strb)); strcpy(line,stra);
1.53 brouard 4258:
1.59 brouard 4259: cutv(stra, strb,line,' '); weight[i]=(double)(atoi(strb)); strcpy(line,stra);
4260: for (j=ncovcol;j>=1;j--){
4261: cutv(stra, strb,line,' '); covar[j][i]=(double)(atoi(strb)); strcpy(line,stra);
4262: }
1.85 brouard 4263: lstra=strlen(stra);
4264: if(lstra > 9){ /* More than 2**32 or max of what printf can write with %ld */
4265: stratrunc = &(stra[lstra-9]);
4266: num[i]=atol(stratrunc);
4267: }
4268: else
4269: num[i]=atol(stra);
1.53 brouard 4270:
1.59 brouard 4271: /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){
1.85 brouard 4272: 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 4273:
1.59 brouard 4274: i=i+1;
4275: }
4276: }
4277: /* printf("ii=%d", ij);
4278: scanf("%d",i);*/
1.53 brouard 4279: imx=i-1; /* Number of individuals */
4280:
4281: /* for (i=1; i<=imx; i++){
4282: if ((s[1][i]==3) && (s[2][i]==2)) s[2][i]=3;
4283: if ((s[2][i]==3) && (s[3][i]==2)) s[3][i]=3;
4284: if ((s[3][i]==3) && (s[4][i]==2)) s[4][i]=3;
4285: }*/
4286: /* for (i=1; i<=imx; i++){
4287: if (s[4][i]==9) s[4][i]=-1;
1.85 brouard 4288: 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 4289:
1.71 brouard 4290: for (i=1; i<=imx; i++)
1.53 brouard 4291:
1.71 brouard 4292: /*if ((s[3][i]==3) || (s[4][i]==3)) weight[i]=0.08;
4293: else weight[i]=1;*/
4294:
1.53 brouard 4295: /* Calculation of the number of parameter from char model*/
4296: Tvar=ivector(1,15); /* stores the number n of the covariates in Vm+Vn at 1 and m at 2 */
4297: Tprod=ivector(1,15);
4298: Tvaraff=ivector(1,15);
4299: Tvard=imatrix(1,15,1,2);
4300: Tage=ivector(1,15);
4301:
1.58 lievre 4302: if (strlen(model) >1){ /* If there is at least 1 covariate */
1.53 brouard 4303: j=0, j1=0, k1=1, k2=1;
1.58 lievre 4304: j=nbocc(model,'+'); /* j=Number of '+' */
4305: j1=nbocc(model,'*'); /* j1=Number of '*' */
4306: cptcovn=j+1;
4307: cptcovprod=j1; /*Number of products */
1.53 brouard 4308:
4309: strcpy(modelsav,model);
4310: if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){
4311: printf("Error. Non available option model=%s ",model);
4312: fprintf(ficlog,"Error. Non available option model=%s ",model);
4313: goto end;
4314: }
4315:
1.59 brouard 4316: /* This loop fills the array Tvar from the string 'model'.*/
1.58 lievre 4317:
1.53 brouard 4318: for(i=(j+1); i>=1;i--){
4319: cutv(stra,strb,modelsav,'+'); /* keeps in strb after the last + */
1.59 brouard 4320: if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyzes it */
1.53 brouard 4321: /* printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/
4322: /*scanf("%d",i);*/
4323: if (strchr(strb,'*')) { /* Model includes a product */
4324: cutv(strd,strc,strb,'*'); /* strd*strc Vm*Vn (if not *age)*/
4325: if (strcmp(strc,"age")==0) { /* Vn*age */
4326: cptcovprod--;
4327: cutv(strb,stre,strd,'V');
4328: Tvar[i]=atoi(stre); /* computes n in Vn and stores in Tvar*/
4329: cptcovage++;
4330: Tage[cptcovage]=i;
4331: /*printf("stre=%s ", stre);*/
4332: }
4333: else if (strcmp(strd,"age")==0) { /* or age*Vn */
4334: cptcovprod--;
4335: cutv(strb,stre,strc,'V');
4336: Tvar[i]=atoi(stre);
4337: cptcovage++;
4338: Tage[cptcovage]=i;
4339: }
4340: else { /* Age is not in the model */
4341: cutv(strb,stre,strc,'V'); /* strc= Vn, stre is n*/
4342: Tvar[i]=ncovcol+k1;
4343: cutv(strb,strc,strd,'V'); /* strd was Vm, strc is m */
4344: Tprod[k1]=i;
4345: Tvard[k1][1]=atoi(strc); /* m*/
4346: Tvard[k1][2]=atoi(stre); /* n */
4347: Tvar[cptcovn+k2]=Tvard[k1][1];
4348: Tvar[cptcovn+k2+1]=Tvard[k1][2];
4349: for (k=1; k<=lastobs;k++)
4350: covar[ncovcol+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];
4351: k1++;
4352: k2=k2+2;
4353: }
4354: }
4355: else { /* no more sum */
4356: /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/
4357: /* scanf("%d",i);*/
4358: cutv(strd,strc,strb,'V');
4359: Tvar[i]=atoi(strc);
4360: }
4361: strcpy(modelsav,stra);
4362: /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);
4363: scanf("%d",i);*/
4364: } /* end of loop + */
4365: } /* end model */
4366:
1.58 lievre 4367: /*The number n of Vn is stored in Tvar. cptcovage =number of age covariate. Tage gives the position of age. cptcovprod= number of products.
4368: If model=V1+V1*age then Tvar[1]=1 Tvar[2]=1 cptcovage=1 Tage[1]=2 cptcovprod=0*/
4369:
1.53 brouard 4370: /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);
4371: printf("cptcovprod=%d ", cptcovprod);
4372: fprintf(ficlog,"cptcovprod=%d ", cptcovprod);
1.58 lievre 4373:
4374: scanf("%d ",i);
4375: fclose(fic);*/
1.53 brouard 4376:
4377: /* if(mle==1){*/
1.59 brouard 4378: if (weightopt != 1) { /* Maximisation without weights*/
4379: for(i=1;i<=n;i++) weight[i]=1.0;
4380: }
1.53 brouard 4381: /*-calculation of age at interview from date of interview and age at death -*/
1.59 brouard 4382: agev=matrix(1,maxwav,1,imx);
1.53 brouard 4383:
1.59 brouard 4384: for (i=1; i<=imx; i++) {
4385: for(m=2; (m<= maxwav); m++) {
1.76 brouard 4386: if (((int)mint[m][i]== 99) && (s[m][i] <= nlstate)){
1.59 brouard 4387: anint[m][i]=9999;
4388: s[m][i]=-1;
4389: }
1.76 brouard 4390: if((int)moisdc[i]==99 && (int)andc[i]==9999 && s[m][i]>nlstate){
1.91 ! brouard 4391: nberr++;
1.85 brouard 4392: 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);
4393: 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 4394: s[m][i]=-1;
4395: }
4396: if((int)moisdc[i]==99 && (int)andc[i]!=9999 && s[m][i]>nlstate){
1.91 ! brouard 4397: nberr++;
1.85 brouard 4398: 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]);
4399: 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 4400: s[m][i]=-1; /* We prefer to skip it (and to skip it in version 0.8a1 too */
1.76 brouard 4401: }
1.53 brouard 4402: }
1.59 brouard 4403: }
1.53 brouard 4404:
1.59 brouard 4405: for (i=1; i<=imx; i++) {
4406: agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);
1.71 brouard 4407: for(m=firstpass; (m<= lastpass); m++){
1.69 brouard 4408: if(s[m][i] >0){
1.59 brouard 4409: if (s[m][i] >= nlstate+1) {
4410: if(agedc[i]>0)
1.76 brouard 4411: if((int)moisdc[i]!=99 && (int)andc[i]!=9999)
1.69 brouard 4412: agev[m][i]=agedc[i];
1.59 brouard 4413: /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/
4414: else {
1.76 brouard 4415: if ((int)andc[i]!=9999){
1.91 ! brouard 4416: nbwarn++;
1.85 brouard 4417: printf("Warning negative age at death: %ld line:%d\n",num[i],i);
4418: fprintf(ficlog,"Warning negative age at death: %ld line:%d\n",num[i],i);
1.59 brouard 4419: agev[m][i]=-1;
1.53 brouard 4420: }
4421: }
1.70 brouard 4422: }
1.69 brouard 4423: else if(s[m][i] !=9){ /* Standard case, age in fractional
4424: years but with the precision of a
4425: month */
1.59 brouard 4426: agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);
1.76 brouard 4427: if((int)mint[m][i]==99 || (int)anint[m][i]==9999)
1.59 brouard 4428: agev[m][i]=1;
4429: else if(agev[m][i] <agemin){
4430: agemin=agev[m][i];
4431: /*printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], agemin);*/
1.53 brouard 4432: }
1.59 brouard 4433: else if(agev[m][i] >agemax){
4434: agemax=agev[m][i];
4435: /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/
1.53 brouard 4436: }
1.59 brouard 4437: /*agev[m][i]=anint[m][i]-annais[i];*/
4438: /* agev[m][i] = age[i]+2*m;*/
1.53 brouard 4439: }
1.59 brouard 4440: else { /* =9 */
1.53 brouard 4441: agev[m][i]=1;
1.59 brouard 4442: s[m][i]=-1;
4443: }
1.53 brouard 4444: }
1.59 brouard 4445: else /*= 0 Unknown */
4446: agev[m][i]=1;
4447: }
1.53 brouard 4448:
1.59 brouard 4449: }
4450: for (i=1; i<=imx; i++) {
1.71 brouard 4451: for(m=firstpass; (m<=lastpass); m++){
1.59 brouard 4452: if (s[m][i] > (nlstate+ndeath)) {
1.91 ! brouard 4453: nberr++;
1.59 brouard 4454: 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);
4455: 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);
4456: goto end;
1.53 brouard 4457: }
4458: }
1.59 brouard 4459: }
1.53 brouard 4460:
1.71 brouard 4461: /*for (i=1; i<=imx; i++){
4462: for (m=firstpass; (m<lastpass); m++){
1.85 brouard 4463: 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 4464: }
4465:
4466: }*/
4467:
1.59 brouard 4468: printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);
4469: fprintf(ficlog,"Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);
4470:
4471: free_vector(severity,1,maxwav);
4472: free_imatrix(outcome,1,maxwav+1,1,n);
4473: free_vector(moisnais,1,n);
4474: free_vector(annais,1,n);
4475: /* free_matrix(mint,1,maxwav,1,n);
4476: free_matrix(anint,1,maxwav,1,n);*/
4477: free_vector(moisdc,1,n);
4478: free_vector(andc,1,n);
1.53 brouard 4479:
4480:
1.59 brouard 4481: wav=ivector(1,imx);
4482: dh=imatrix(1,lastpass-firstpass+1,1,imx);
4483: bh=imatrix(1,lastpass-firstpass+1,1,imx);
4484: mw=imatrix(1,lastpass-firstpass+1,1,imx);
1.69 brouard 4485:
1.59 brouard 4486: /* Concatenates waves */
4487: concatwav(wav, dh, bh, mw, s, agedc, agev, firstpass, lastpass, imx, nlstate, stepm);
1.53 brouard 4488:
1.59 brouard 4489: /* Routine tricode is to calculate cptcoveff (real number of unique covariates) and to associate covariable number and modality */
1.53 brouard 4490:
1.59 brouard 4491: Tcode=ivector(1,100);
4492: nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);
4493: ncodemax[1]=1;
4494: if (cptcovn > 0) tricode(Tvar,nbcode,imx);
1.53 brouard 4495:
1.59 brouard 4496: codtab=imatrix(1,100,1,10); /* Cross tabulation to get the order of
4497: the estimations*/
4498: h=0;
4499: m=pow(2,cptcoveff);
1.53 brouard 4500:
1.59 brouard 4501: for(k=1;k<=cptcoveff; k++){
4502: for(i=1; i <=(m/pow(2,k));i++){
4503: for(j=1; j <= ncodemax[k]; j++){
4504: for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){
4505: h++;
4506: if (h>m) h=1;codtab[h][k]=j;codtab[h][Tvar[k]]=j;
4507: /* printf("h=%d k=%d j=%d codtab[h][k]=%d tvar[k]=%d \n",h, k,j,codtab[h][k],Tvar[k]);*/
4508: }
4509: }
4510: }
4511: }
4512: /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]);
4513: codtab[1][2]=1;codtab[2][2]=2; */
4514: /* for(i=1; i <=m ;i++){
4515: for(k=1; k <=cptcovn; k++){
4516: printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);
4517: }
4518: printf("\n");
1.53 brouard 4519: }
1.59 brouard 4520: scanf("%d",i);*/
1.53 brouard 4521:
1.86 brouard 4522: /*------------ gnuplot -------------*/
4523: strcpy(optionfilegnuplot,optionfilefiname);
4524: strcat(optionfilegnuplot,".gp");
4525: if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {
4526: printf("Problem with file %s",optionfilegnuplot);
4527: }
4528: else{
4529: fprintf(ficgp,"\n# %s\n", version);
4530: fprintf(ficgp,"# %s\n", optionfilegnuplot);
4531: fprintf(ficgp,"set missing 'NaNq'\n");
4532: }
1.88 brouard 4533: /* fclose(ficgp);*/
1.86 brouard 4534: /*--------- index.htm --------*/
4535:
1.91 ! brouard 4536: strcpy(optionfilehtm,optionfilefiname); /* Main html file */
1.86 brouard 4537: strcat(optionfilehtm,".htm");
4538: if((fichtm=fopen(optionfilehtm,"w"))==NULL) {
4539: printf("Problem with %s \n",optionfilehtm), exit(0);
4540: }
4541:
1.91 ! brouard 4542: strcpy(optionfilehtmcov,optionfilefiname); /* Only for matrix of covariance */
! 4543: strcat(optionfilehtmcov,"-cov.htm");
! 4544: if((fichtmcov=fopen(optionfilehtmcov,"w"))==NULL) {
! 4545: printf("Problem with %s \n",optionfilehtmcov), exit(0);
! 4546: }
! 4547: else{
! 4548: fprintf(fichtmcov,"<body>\n<title>IMaCh Cov %s</title>\n <font size=\"2\">%s <br> %s</font> \
! 4549: <hr size=\"2\" color=\"#EC5E5E\"> \n\
! 4550: Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n",\
! 4551: fileres,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);
! 4552: }
! 4553:
1.87 brouard 4554: fprintf(fichtm,"<body>\n<title>IMaCh %s</title>\n <font size=\"2\">%s <br> %s</font> \
1.86 brouard 4555: <hr size=\"2\" color=\"#EC5E5E\"> \n\
4556: Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n\
4557: \n\
4558: <hr size=\"2\" color=\"#EC5E5E\">\
4559: <ul><li><h4>Parameter files</h4>\n\
4560: - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n\
4561: - Log file of the run: <a href=\"%s\">%s</a><br>\n\
1.87 brouard 4562: - Gnuplot file name: <a href=\"%s\">%s</a><br>\n\
1.86 brouard 4563: - Date and time at start: %s</ul>\n",\
1.91 ! brouard 4564: fileres,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model,\
! 4565: fileres,fileres,\
1.88 brouard 4566: filelog,filelog,optionfilegnuplot,optionfilegnuplot,strstart);
1.87 brouard 4567: fflush(fichtm);
1.86 brouard 4568:
1.88 brouard 4569: strcpy(pathr,path);
4570: strcat(pathr,optionfilefiname);
4571: chdir(optionfilefiname); /* Move to directory named optionfile */
4572: strcpy(lfileres,fileres);
4573: strcat(lfileres,"/");
4574: strcat(lfileres,optionfilefiname);
4575:
1.59 brouard 4576: /* Calculates basic frequencies. Computes observed prevalence at single age
4577: and prints on file fileres'p'. */
1.84 brouard 4578: freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint);
1.53 brouard 4579:
1.88 brouard 4580: fprintf(fichtm,"\n");
4581: fprintf(fichtm,"<br>Total number of observations=%d <br>\n\
1.86 brouard 4582: Youngest age at first (selected) pass %.2f, oldest age %.2f<br>\n\
4583: Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n",\
1.88 brouard 4584: imx,agemin,agemax,jmin,jmax,jmean);
4585: pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
1.60 brouard 4586: oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
4587: newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
4588: savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
4589: oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */
1.53 brouard 4590:
4591:
1.59 brouard 4592: /* For Powell, parameters are in a vector p[] starting at p[1]
4593: so we point p on param[1][1] so that p[1] maps on param[1][1][1] */
4594: p=param[1][1]; /* *(*(*(param +1)+1)+0) */
1.53 brouard 4595:
1.86 brouard 4596: globpr=0; /* To get the number ipmx of contributions and the sum of weights*/
1.85 brouard 4597: likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
4598: printf("First Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
4599: for (k=1; k<=npar;k++)
4600: printf(" %d %8.5f",k,p[k]);
4601: printf("\n");
4602: globpr=1; /* to print the contributions */
4603: likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
4604: printf("Second Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
4605: for (k=1; k<=npar;k++)
4606: printf(" %d %8.5f",k,p[k]);
4607: printf("\n");
1.61 brouard 4608: if(mle>=1){ /* Could be 1 or 2 */
1.53 brouard 4609: mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);
1.59 brouard 4610: }
1.53 brouard 4611:
1.59 brouard 4612: /*--------- results files --------------*/
4613: 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 4614:
4615:
1.59 brouard 4616: jk=1;
4617: fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
4618: printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
4619: fprintf(ficlog,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
4620: for(i=1,jk=1; i <=nlstate; i++){
4621: for(k=1; k <=(nlstate+ndeath); k++){
4622: if (k != i)
4623: {
4624: printf("%d%d ",i,k);
4625: fprintf(ficlog,"%d%d ",i,k);
4626: fprintf(ficres,"%1d%1d ",i,k);
4627: for(j=1; j <=ncovmodel; j++){
4628: printf("%f ",p[jk]);
4629: fprintf(ficlog,"%f ",p[jk]);
4630: fprintf(ficres,"%f ",p[jk]);
4631: jk++;
4632: }
4633: printf("\n");
4634: fprintf(ficlog,"\n");
4635: fprintf(ficres,"\n");
4636: }
4637: }
4638: }
1.84 brouard 4639: if(mle!=0){
1.59 brouard 4640: /* Computing hessian and covariance matrix */
4641: ftolhess=ftol; /* Usually correct */
4642: hesscov(matcov, p, npar, delti, ftolhess, func);
4643: }
4644: fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");
4645: printf("# Scales (for hessian or gradient estimation)\n");
4646: fprintf(ficlog,"# Scales (for hessian or gradient estimation)\n");
4647: for(i=1,jk=1; i <=nlstate; i++){
4648: for(j=1; j <=nlstate+ndeath; j++){
4649: if (j!=i) {
4650: fprintf(ficres,"%1d%1d",i,j);
4651: printf("%1d%1d",i,j);
4652: fprintf(ficlog,"%1d%1d",i,j);
4653: for(k=1; k<=ncovmodel;k++){
4654: printf(" %.5e",delti[jk]);
4655: fprintf(ficlog," %.5e",delti[jk]);
4656: fprintf(ficres," %.5e",delti[jk]);
4657: jk++;
4658: }
4659: printf("\n");
4660: fprintf(ficlog,"\n");
4661: fprintf(ficres,"\n");
4662: }
4663: }
4664: }
1.53 brouard 4665:
1.59 brouard 4666: 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");
4667: if(mle==1)
4668: 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");
4669: 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");
4670: for(i=1,k=1;i<=npar;i++){
4671: /* if (k>nlstate) k=1;
4672: i1=(i-1)/(ncovmodel*nlstate)+1;
4673: fprintf(ficres,"%s%d%d",alph[k],i1,tab[i]);
4674: printf("%s%d%d",alph[k],i1,tab[i]);
4675: */
4676: fprintf(ficres,"%3d",i);
4677: if(mle==1)
4678: printf("%3d",i);
4679: fprintf(ficlog,"%3d",i);
4680: for(j=1; j<=i;j++){
4681: fprintf(ficres," %.5e",matcov[i][j]);
4682: if(mle==1)
4683: printf(" %.5e",matcov[i][j]);
4684: fprintf(ficlog," %.5e",matcov[i][j]);
4685: }
4686: fprintf(ficres,"\n");
4687: if(mle==1)
4688: printf("\n");
4689: fprintf(ficlog,"\n");
4690: k++;
4691: }
1.53 brouard 4692:
1.59 brouard 4693: while((c=getc(ficpar))=='#' && c!= EOF){
4694: ungetc(c,ficpar);
4695: fgets(line, MAXLINE, ficpar);
4696: puts(line);
4697: fputs(line,ficparo);
4698: }
4699: ungetc(c,ficpar);
4700:
4701: estepm=0;
4702: fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm);
4703: if (estepm==0 || estepm < stepm) estepm=stepm;
4704: if (fage <= 2) {
4705: bage = ageminpar;
4706: fage = agemaxpar;
4707: }
1.53 brouard 4708:
1.59 brouard 4709: fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");
4710: fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
4711: fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
1.53 brouard 4712:
1.59 brouard 4713: while((c=getc(ficpar))=='#' && c!= EOF){
4714: ungetc(c,ficpar);
4715: fgets(line, MAXLINE, ficpar);
4716: puts(line);
4717: fputs(line,ficparo);
4718: }
4719: ungetc(c,ficpar);
1.53 brouard 4720:
1.59 brouard 4721: 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);
4722: 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);
4723: 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 4724: printf("begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
4725: 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 4726:
1.59 brouard 4727: while((c=getc(ficpar))=='#' && c!= EOF){
4728: ungetc(c,ficpar);
4729: fgets(line, MAXLINE, ficpar);
4730: puts(line);
4731: fputs(line,ficparo);
4732: }
4733: ungetc(c,ficpar);
1.53 brouard 4734:
4735:
1.70 brouard 4736: dateprev1=anprev1+(mprev1-1)/12.+(jprev1-1)/365.;
4737: dateprev2=anprev2+(mprev2-1)/12.+(jprev2-1)/365.;
1.53 brouard 4738:
4739: fscanf(ficpar,"pop_based=%d\n",&popbased);
4740: fprintf(ficparo,"pop_based=%d\n",popbased);
4741: fprintf(ficres,"pop_based=%d\n",popbased);
4742:
4743: while((c=getc(ficpar))=='#' && c!= EOF){
4744: ungetc(c,ficpar);
4745: fgets(line, MAXLINE, ficpar);
4746: puts(line);
4747: fputs(line,ficparo);
4748: }
4749: ungetc(c,ficpar);
4750:
1.69 brouard 4751: 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 4752: 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 4753: 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);
4754: 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);
4755: 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 4756: /* day and month of proj2 are not used but only year anproj2.*/
1.53 brouard 4757:
1.59 brouard 4758: while((c=getc(ficpar))=='#' && c!= EOF){
1.53 brouard 4759: ungetc(c,ficpar);
4760: fgets(line, MAXLINE, ficpar);
4761: puts(line);
4762: fputs(line,ficparo);
4763: }
4764: ungetc(c,ficpar);
4765:
4766: fscanf(ficpar,"popforecast=%d popfile=%s popfiledate=%lf/%lf/%lf last-popfiledate=%lf/%lf/%lf\n",&popforecast,popfile,&jpyram,&mpyram,&anpyram,&jpyram1,&mpyram1,&anpyram1);
4767: fprintf(ficparo,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);
4768: fprintf(ficres,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);
4769:
1.86 brouard 4770: /* freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint);*/
1.84 brouard 4771: /*,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
1.58 lievre 4772:
1.89 brouard 4773: replace_back_to_slash(pathc,path); /* Even gnuplot wants a / */
4774: printinggnuplot(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
1.53 brouard 4775:
1.85 brouard 4776: printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,\
4777: model,imx,jmin,jmax,jmean,rfileres,popforecast,estepm,\
4778: jprev1,mprev1,anprev1,jprev2,mprev2,anprev2);
1.53 brouard 4779:
1.59 brouard 4780: /*------------ free_vector -------------*/
1.88 brouard 4781: /* chdir(path); */
1.53 brouard 4782:
1.59 brouard 4783: free_ivector(wav,1,imx);
4784: free_imatrix(dh,1,lastpass-firstpass+1,1,imx);
4785: free_imatrix(bh,1,lastpass-firstpass+1,1,imx);
4786: free_imatrix(mw,1,lastpass-firstpass+1,1,imx);
1.85 brouard 4787: free_lvector(num,1,n);
1.59 brouard 4788: free_vector(agedc,1,n);
1.65 lievre 4789: /*free_matrix(covar,0,NCOVMAX,1,n);*/
1.59 brouard 4790: /*free_matrix(covar,1,NCOVMAX,1,n);*/
4791: fclose(ficparo);
4792: fclose(ficres);
1.53 brouard 4793:
4794:
1.54 brouard 4795: /*--------------- Prevalence limit (stable prevalence) --------------*/
1.53 brouard 4796:
4797: strcpy(filerespl,"pl");
4798: strcat(filerespl,fileres);
4799: if((ficrespl=fopen(filerespl,"w"))==NULL) {
1.54 brouard 4800: printf("Problem with stable prevalence resultfile: %s\n", filerespl);goto end;
4801: fprintf(ficlog,"Problem with stable prevalence resultfile: %s\n", filerespl);goto end;
1.53 brouard 4802: }
1.54 brouard 4803: printf("Computing stable prevalence: result on file '%s' \n", filerespl);
4804: fprintf(ficlog,"Computing stable prevalence: result on file '%s' \n", filerespl);
4805: fprintf(ficrespl,"#Stable prevalence \n");
1.53 brouard 4806: fprintf(ficrespl,"#Age ");
4807: for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);
4808: fprintf(ficrespl,"\n");
4809:
4810: prlim=matrix(1,nlstate,1,nlstate);
1.59 brouard 4811:
1.53 brouard 4812: agebase=ageminpar;
4813: agelim=agemaxpar;
4814: ftolpl=1.e-10;
4815: i1=cptcoveff;
4816: if (cptcovn < 1){i1=1;}
4817:
1.59 brouard 4818: for(cptcov=1,k=0;cptcov<=i1;cptcov++){
1.53 brouard 4819: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
1.59 brouard 4820: k=k+1;
4821: /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/
4822: fprintf(ficrespl,"\n#******");
4823: printf("\n#******");
4824: fprintf(ficlog,"\n#******");
4825: for(j=1;j<=cptcoveff;j++) {
4826: fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
4827: printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
4828: fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
4829: }
4830: fprintf(ficrespl,"******\n");
4831: printf("******\n");
4832: fprintf(ficlog,"******\n");
1.53 brouard 4833:
1.59 brouard 4834: for (age=agebase; age<=agelim; age++){
4835: prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
1.69 brouard 4836: fprintf(ficrespl,"%.0f ",age );
4837: for(j=1;j<=cptcoveff;j++)
4838: fprintf(ficrespl,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
1.59 brouard 4839: for(i=1; i<=nlstate;i++)
1.53 brouard 4840: fprintf(ficrespl," %.5f", prlim[i][i]);
1.59 brouard 4841: fprintf(ficrespl,"\n");
1.53 brouard 4842: }
4843: }
1.59 brouard 4844: }
1.53 brouard 4845: fclose(ficrespl);
4846:
4847: /*------------- h Pij x at various ages ------------*/
4848:
4849: strcpy(filerespij,"pij"); strcat(filerespij,fileres);
4850: if((ficrespij=fopen(filerespij,"w"))==NULL) {
4851: printf("Problem with Pij resultfile: %s\n", filerespij);goto end;
4852: fprintf(ficlog,"Problem with Pij resultfile: %s\n", filerespij);goto end;
4853: }
4854: printf("Computing pij: result on file '%s' \n", filerespij);
4855: fprintf(ficlog,"Computing pij: result on file '%s' \n", filerespij);
4856:
4857: stepsize=(int) (stepm+YEARM-1)/YEARM;
4858: /*if (stepm<=24) stepsize=2;*/
4859:
4860: agelim=AGESUP;
4861: hstepm=stepsize*YEARM; /* Every year of age */
4862: hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */
4863:
4864: /* hstepm=1; aff par mois*/
4865:
1.70 brouard 4866: fprintf(ficrespij,"#****** h Pij x Probability to be in state j at age x+h being in i at x ");
1.59 brouard 4867: for(cptcov=1,k=0;cptcov<=i1;cptcov++){
1.53 brouard 4868: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
4869: k=k+1;
1.59 brouard 4870: fprintf(ficrespij,"\n#****** ");
4871: for(j=1;j<=cptcoveff;j++)
4872: fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
4873: fprintf(ficrespij,"******\n");
1.53 brouard 4874:
1.59 brouard 4875: for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */
4876: nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
4877: nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
4878:
4879: /* nhstepm=nhstepm*YEARM; aff par mois*/
4880:
4881: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4882: oldm=oldms;savm=savms;
4883: hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
1.70 brouard 4884: fprintf(ficrespij,"# Cov Agex agex+h hpijx with i,j=");
1.59 brouard 4885: for(i=1; i<=nlstate;i++)
4886: for(j=1; j<=nlstate+ndeath;j++)
4887: fprintf(ficrespij," %1d-%1d",i,j);
4888: fprintf(ficrespij,"\n");
4889: for (h=0; h<=nhstepm; h++){
1.70 brouard 4890: fprintf(ficrespij,"%d %3.f %3.f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );
1.53 brouard 4891: for(i=1; i<=nlstate;i++)
4892: for(j=1; j<=nlstate+ndeath;j++)
1.59 brouard 4893: fprintf(ficrespij," %.5f", p3mat[i][j][h]);
1.53 brouard 4894: fprintf(ficrespij,"\n");
4895: }
1.59 brouard 4896: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4897: fprintf(ficrespij,"\n");
4898: }
1.53 brouard 4899: }
4900: }
4901:
1.74 brouard 4902: varprob(optionfilefiname, matcov, p, delti, nlstate, bage, fage,k,Tvar,nbcode, ncodemax);
1.53 brouard 4903:
4904: fclose(ficrespij);
4905:
1.84 brouard 4906: probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
1.53 brouard 4907:
4908: /*---------- Forecasting ------------------*/
1.69 brouard 4909: /*if((stepm == 1) && (strcmp(model,".")==0)){*/
4910: if(prevfcast==1){
1.74 brouard 4911: /* if(stepm ==1){*/
1.70 brouard 4912: prevforecast(fileres, anproj1, mproj1, jproj1, agemin, agemax, dateprev1, dateprev2, mobilavproj, bage, fage, firstpass, lastpass, anproj2, p, cptcoveff);
1.74 brouard 4913: /* (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);*/
4914: /* } */
4915: /* else{ */
4916: /* erreur=108; */
4917: /* 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); */
4918: /* 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); */
4919: /* } */
1.69 brouard 4920: }
1.53 brouard 4921:
4922:
4923: /*---------- Health expectancies and variances ------------*/
4924:
4925: strcpy(filerest,"t");
4926: strcat(filerest,fileres);
4927: if((ficrest=fopen(filerest,"w"))==NULL) {
4928: printf("Problem with total LE resultfile: %s\n", filerest);goto end;
4929: fprintf(ficlog,"Problem with total LE resultfile: %s\n", filerest);goto end;
4930: }
4931: printf("Computing Total LEs with variances: file '%s' \n", filerest);
4932: fprintf(ficlog,"Computing Total LEs with variances: file '%s' \n", filerest);
4933:
4934:
4935: strcpy(filerese,"e");
4936: strcat(filerese,fileres);
4937: if((ficreseij=fopen(filerese,"w"))==NULL) {
4938: printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
4939: fprintf(ficlog,"Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
4940: }
4941: printf("Computing Health Expectancies: result on file '%s' \n", filerese);
4942: fprintf(ficlog,"Computing Health Expectancies: result on file '%s' \n", filerese);
1.68 lievre 4943:
1.53 brouard 4944: strcpy(fileresv,"v");
4945: strcat(fileresv,fileres);
4946: if((ficresvij=fopen(fileresv,"w"))==NULL) {
4947: printf("Problem with variance resultfile: %s\n", fileresv);exit(0);
4948: fprintf(ficlog,"Problem with variance resultfile: %s\n", fileresv);exit(0);
4949: }
4950: printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
4951: fprintf(ficlog,"Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
1.58 lievre 4952:
1.74 brouard 4953: /* Computes prevalence between agemin (i.e minimal age computed) and no more ageminpar */
1.84 brouard 4954: prevalence(probs, agemin, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
1.74 brouard 4955: /* 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",\
4956: ageminpar, agemax, s[lastpass][imx], agev[lastpass][imx], nlstate, imx, mint[lastpass][imx],anint[lastpass][imx], dateprev1, dateprev2, firstpass, lastpass);
4957: */
1.58 lievre 4958:
1.54 brouard 4959: if (mobilav!=0) {
1.53 brouard 4960: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
1.54 brouard 4961: if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
4962: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
4963: printf(" Error in movingaverage mobilav=%d\n",mobilav);
4964: }
1.53 brouard 4965: }
4966:
1.59 brouard 4967: for(cptcov=1,k=0;cptcov<=i1;cptcov++){
1.53 brouard 4968: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
4969: k=k+1;
4970: fprintf(ficrest,"\n#****** ");
4971: for(j=1;j<=cptcoveff;j++)
4972: fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
4973: fprintf(ficrest,"******\n");
4974:
4975: fprintf(ficreseij,"\n#****** ");
4976: for(j=1;j<=cptcoveff;j++)
4977: fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
4978: fprintf(ficreseij,"******\n");
4979:
4980: fprintf(ficresvij,"\n#****** ");
4981: for(j=1;j<=cptcoveff;j++)
4982: fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
4983: fprintf(ficresvij,"******\n");
4984:
4985: eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
4986: oldm=oldms;savm=savms;
4987: evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov);
4988:
4989: vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
4990: oldm=oldms;savm=savms;
4991: varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,0, mobilav);
4992: if(popbased==1){
4993: 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 4994: }
1.53 brouard 4995:
4996:
4997: fprintf(ficrest,"#Total LEs with variances: e.. (std) ");
4998: for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);
4999: fprintf(ficrest,"\n");
5000:
5001: epj=vector(1,nlstate+1);
5002: for(age=bage; age <=fage ;age++){
5003: prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
5004: if (popbased==1) {
1.54 brouard 5005: if(mobilav ==0){
1.53 brouard 5006: for(i=1; i<=nlstate;i++)
5007: prlim[i][i]=probs[(int)age][i][k];
1.54 brouard 5008: }else{ /* mobilav */
1.53 brouard 5009: for(i=1; i<=nlstate;i++)
5010: prlim[i][i]=mobaverage[(int)age][i][k];
5011: }
5012: }
5013:
5014: fprintf(ficrest," %4.0f",age);
5015: for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){
5016: for(i=1, epj[j]=0.;i <=nlstate;i++) {
5017: epj[j] += prlim[i][i]*eij[i][j][(int)age];
5018: /* printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/
5019: }
5020: epj[nlstate+1] +=epj[j];
5021: }
5022:
5023: for(i=1, vepp=0.;i <=nlstate;i++)
5024: for(j=1;j <=nlstate;j++)
5025: vepp += vareij[i][j][(int)age];
5026: fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));
5027: for(j=1;j <=nlstate;j++){
5028: fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));
5029: }
5030: fprintf(ficrest,"\n");
5031: }
1.59 brouard 5032: free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
5033: free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);
5034: free_vector(epj,1,nlstate+1);
1.53 brouard 5035: }
5036: }
1.59 brouard 5037: free_vector(weight,1,n);
5038: free_imatrix(Tvard,1,15,1,2);
5039: free_imatrix(s,1,maxwav+1,1,n);
5040: free_matrix(anint,1,maxwav,1,n);
5041: free_matrix(mint,1,maxwav,1,n);
5042: free_ivector(cod,1,n);
5043: free_ivector(tab,1,NCOVMAX);
1.53 brouard 5044: fclose(ficreseij);
5045: fclose(ficresvij);
5046: fclose(ficrest);
5047: fclose(ficpar);
5048:
1.54 brouard 5049: /*------- Variance of stable prevalence------*/
1.53 brouard 5050:
5051: strcpy(fileresvpl,"vpl");
5052: strcat(fileresvpl,fileres);
5053: if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {
1.54 brouard 5054: printf("Problem with variance of stable prevalence resultfile: %s\n", fileresvpl);
1.53 brouard 5055: exit(0);
5056: }
1.54 brouard 5057: printf("Computing Variance-covariance of stable prevalence: file '%s' \n", fileresvpl);
1.53 brouard 5058:
1.59 brouard 5059: for(cptcov=1,k=0;cptcov<=i1;cptcov++){
1.53 brouard 5060: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
5061: k=k+1;
5062: fprintf(ficresvpl,"\n#****** ");
5063: for(j=1;j<=cptcoveff;j++)
5064: fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
5065: fprintf(ficresvpl,"******\n");
5066:
5067: varpl=matrix(1,nlstate,(int) bage, (int) fage);
5068: oldm=oldms;savm=savms;
1.59 brouard 5069: varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);
5070: free_matrix(varpl,1,nlstate,(int) bage, (int)fage);
1.53 brouard 5071: }
1.59 brouard 5072: }
1.53 brouard 5073:
5074: fclose(ficresvpl);
5075:
5076: /*---------- End : free ----------------*/
5077: free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);
5078: free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);
5079: free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);
5080: free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);
1.65 lievre 5081:
5082: free_matrix(covar,0,NCOVMAX,1,n);
1.53 brouard 5083: free_matrix(matcov,1,npar,1,npar);
1.74 brouard 5084: /*free_vector(delti,1,npar);*/
5085: free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
1.53 brouard 5086: free_matrix(agev,1,maxwav,1,imx);
5087: free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
1.54 brouard 5088: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
1.74 brouard 5089: free_ma3x(probs,1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
5090:
1.59 brouard 5091: free_ivector(ncodemax,1,8);
5092: free_ivector(Tvar,1,15);
5093: free_ivector(Tprod,1,15);
5094: free_ivector(Tvaraff,1,15);
5095: free_ivector(Tage,1,15);
5096: free_ivector(Tcode,1,100);
1.53 brouard 5097:
1.88 brouard 5098: fflush(fichtm);
5099: fflush(ficgp);
1.53 brouard 5100:
5101:
1.91 ! brouard 5102: if((nberr >0) || (nbwarn>0)){
! 5103: printf("End of Imach with %d errors and/or warnings %d\n",nberr,nbwarn);
! 5104: fprintf(ficlog,"End of Imach with %d errors and/or warnings %d\n",nberr,nbwarn);
1.53 brouard 5105: }else{
1.91 ! brouard 5106: printf("End of Imach\n");
! 5107: fprintf(ficlog,"End of Imach\n");
1.53 brouard 5108: }
5109: printf("See log file on %s\n",filelog);
5110: /* gettimeofday(&end_time, (struct timezone*)0);*/ /* after time */
1.85 brouard 5111: (void) gettimeofday(&end_time,&tzp);
5112: tm = *localtime(&end_time.tv_sec);
5113: tmg = *gmtime(&end_time.tv_sec);
1.88 brouard 5114: strcpy(strtend,asctime(&tm));
5115: printf("Localtime at start %s\nLocaltime at end %s",strstart, strtend);
1.91 ! brouard 5116: fprintf(ficlog,"Localtime at start %s\nLocal time at end %s\n",strstart, strtend);
! 5117: printf("Total time used %s\n", asc_diff_time(end_time.tv_sec -start_time.tv_sec,tmpout));
1.85 brouard 5118:
1.91 ! brouard 5119: printf("Total time was %d Sec.\n", end_time.tv_sec -start_time.tv_sec);
! 5120: fprintf(ficlog,"Total time used %s\n", asc_diff_time(end_time.tv_sec -start_time.tv_sec,tmpout));
! 5121: fprintf(ficlog,"Total time was %d Sec.\n", end_time.tv_sec -start_time.tv_sec);
1.85 brouard 5122: /* printf("Total time was %d uSec.\n", total_usecs);*/
1.87 brouard 5123: /* if(fileappend(fichtm,optionfilehtm)){ */
1.88 brouard 5124: fprintf(fichtm,"<br>Local time at start %s<br>Local time at end %s<br>",strstart, strtend);
1.87 brouard 5125: fclose(fichtm);
1.91 ! brouard 5126: fclose(fichtmcov);
1.88 brouard 5127: fclose(ficgp);
1.91 ! brouard 5128: fclose(ficlog);
1.53 brouard 5129: /*------ End -----------*/
5130:
1.88 brouard 5131: chdir(path);
1.59 brouard 5132: strcpy(plotcmd,GNUPLOTPROGRAM);
5133: strcat(plotcmd," ");
5134: strcat(plotcmd,optionfilegnuplot);
1.75 brouard 5135: printf("Starting graphs with: %s",plotcmd);fflush(stdout);
1.91 ! brouard 5136: if((outcmd=system(plotcmd)) != 0){
! 5137: printf(" Problem with gnuplot\n");
! 5138: }
1.75 brouard 5139: printf(" Wait...");
1.53 brouard 5140: while (z[0] != 'q') {
5141: /* chdir(path); */
1.91 ! brouard 5142: printf("\nType e to edit output files, g to graph again and q for exiting: ");
1.53 brouard 5143: scanf("%s",z);
1.91 ! brouard 5144: /* if (z[0] == 'c') system("./imach"); */
! 5145: if (z[0] == 'e') system(optionfilehtm);
1.53 brouard 5146: else if (z[0] == 'g') system(plotcmd);
5147: else if (z[0] == 'q') exit(0);
5148: }
1.91 ! brouard 5149: end:
! 5150: while (z[0] != 'q') {
! 5151: printf("\nType q for exiting: ");
! 5152: scanf("%s",z);
! 5153: }
1.53 brouard 5154: }
1.88 brouard 5155:
1.53 brouard 5156:
5157:
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