Annotation of imach/src/imach.c, revision 1.94
1.94 ! brouard 1: /* $Id: imach.c,v 1.93 2003/06/25 16:33:55 brouard Exp $
1.83 lievre 2: $State: Exp $
3: $Log: imach.c,v $
1.94 ! brouard 4: Revision 1.93 2003/06/25 16:33:55 brouard
! 5: (Module): On windows (cygwin) function asctime_r doesn't
! 6: exist so I changed back to asctime which exists.
! 7: (Module): Version 0.96b
! 8:
1.93 brouard 9: Revision 1.92 2003/06/25 16:30:45 brouard
10: (Module): On windows (cygwin) function asctime_r doesn't
11: exist so I changed back to asctime which exists.
12:
1.92 brouard 13: Revision 1.91 2003/06/25 15:30:29 brouard
14: * imach.c (Repository): Duplicated warning errors corrected.
15: (Repository): Elapsed time after each iteration is now output. It
16: helps to forecast when convergence will be reached. Elapsed time
17: is stamped in powell. We created a new html file for the graphs
18: concerning matrix of covariance. It has extension -cov.htm.
19:
1.91 brouard 20: Revision 1.90 2003/06/24 12:34:15 brouard
21: (Module): Some bugs corrected for windows. Also, when
22: mle=-1 a template is output in file "or"mypar.txt with the design
23: of the covariance matrix to be input.
24:
1.90 brouard 25: Revision 1.89 2003/06/24 12:30:52 brouard
26: (Module): Some bugs corrected for windows. Also, when
27: mle=-1 a template is output in file "or"mypar.txt with the design
28: of the covariance matrix to be input.
29:
1.89 brouard 30: Revision 1.88 2003/06/23 17:54:56 brouard
31: * 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.
32:
1.88 brouard 33: Revision 1.87 2003/06/18 12:26:01 brouard
34: Version 0.96
35:
1.87 brouard 36: Revision 1.86 2003/06/17 20:04:08 brouard
37: (Module): Change position of html and gnuplot routines and added
38: routine fileappend.
39:
1.86 brouard 40: Revision 1.85 2003/06/17 13:12:43 brouard
41: * imach.c (Repository): Check when date of death was earlier that
42: current date of interview. It may happen when the death was just
43: prior to the death. In this case, dh was negative and likelihood
44: was wrong (infinity). We still send an "Error" but patch by
45: assuming that the date of death was just one stepm after the
46: interview.
47: (Repository): Because some people have very long ID (first column)
48: we changed int to long in num[] and we added a new lvector for
49: memory allocation. But we also truncated to 8 characters (left
50: truncation)
51: (Repository): No more line truncation errors.
52:
1.85 brouard 53: Revision 1.84 2003/06/13 21:44:43 brouard
54: * imach.c (Repository): Replace "freqsummary" at a correct
55: place. It differs from routine "prevalence" which may be called
56: many times. Probs is memory consuming and must be used with
57: parcimony.
1.86 brouard 58: Version 0.95a3 (should output exactly the same maximization than 0.8a2)
1.85 brouard 59:
1.84 brouard 60: Revision 1.83 2003/06/10 13:39:11 lievre
61: *** empty log message ***
62:
1.83 lievre 63: Revision 1.82 2003/06/05 15:57:20 brouard
64: Add log in imach.c and fullversion number is now printed.
65:
1.82 brouard 66: */
67: /*
1.53 brouard 68: Interpolated Markov Chain
69:
70: Short summary of the programme:
71:
72: This program computes Healthy Life Expectancies from
73: cross-longitudinal data. Cross-longitudinal data consist in: -1- a
74: first survey ("cross") where individuals from different ages are
75: interviewed on their health status or degree of disability (in the
76: case of a health survey which is our main interest) -2- at least a
77: second wave of interviews ("longitudinal") which measure each change
78: (if any) in individual health status. Health expectancies are
79: computed from the time spent in each health state according to a
80: model. More health states you consider, more time is necessary to reach the
81: Maximum Likelihood of the parameters involved in the model. The
82: simplest model is the multinomial logistic model where pij is the
83: probability to be observed in state j at the second wave
84: conditional to be observed in state i at the first wave. Therefore
85: the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where
86: 'age' is age and 'sex' is a covariate. If you want to have a more
87: complex model than "constant and age", you should modify the program
88: where the markup *Covariates have to be included here again* invites
89: you to do it. More covariates you add, slower the
90: convergence.
91:
92: The advantage of this computer programme, compared to a simple
93: multinomial logistic model, is clear when the delay between waves is not
94: identical for each individual. Also, if a individual missed an
95: intermediate interview, the information is lost, but taken into
96: account using an interpolation or extrapolation.
97:
98: hPijx is the probability to be observed in state i at age x+h
99: conditional to the observed state i at age x. The delay 'h' can be
100: split into an exact number (nh*stepm) of unobserved intermediate
1.66 brouard 101: states. This elementary transition (by month, quarter,
102: semester or year) is modelled as a multinomial logistic. The hPx
1.53 brouard 103: matrix is simply the matrix product of nh*stepm elementary matrices
104: and the contribution of each individual to the likelihood is simply
105: hPijx.
106:
107: Also this programme outputs the covariance matrix of the parameters but also
1.54 brouard 108: of the life expectancies. It also computes the stable prevalence.
1.53 brouard 109:
110: Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).
111: Institut national d'études démographiques, Paris.
112: This software have been partly granted by Euro-REVES, a concerted action
113: from the European Union.
114: It is copyrighted identically to a GNU software product, ie programme and
115: software can be distributed freely for non commercial use. Latest version
116: can be accessed at http://euroreves.ined.fr/imach .
1.74 brouard 117:
118: Help to debug: LD_PRELOAD=/usr/local/lib/libnjamd.so ./imach foo.imach
119: or better on gdb : set env LD_PRELOAD=/usr/local/lib/libnjamd.so
120:
1.53 brouard 121: **********************************************************************/
1.74 brouard 122: /*
123: main
124: read parameterfile
125: read datafile
126: concatwav
1.84 brouard 127: freqsummary
1.74 brouard 128: if (mle >= 1)
129: mlikeli
130: print results files
131: if mle==1
132: computes hessian
133: read end of parameter file: agemin, agemax, bage, fage, estepm
134: begin-prev-date,...
135: open gnuplot file
136: open html file
137: stable prevalence
138: for age prevalim()
139: h Pij x
140: variance of p varprob
141: forecasting if prevfcast==1 prevforecast call prevalence()
142: health expectancies
143: Variance-covariance of DFLE
144: prevalence()
145: movingaverage()
146: varevsij()
147: if popbased==1 varevsij(,popbased)
148: total life expectancies
149: Variance of stable prevalence
150: end
151: */
152:
153:
154:
1.53 brouard 155:
156: #include <math.h>
157: #include <stdio.h>
158: #include <stdlib.h>
159: #include <unistd.h>
160:
1.86 brouard 161: #include <sys/time.h>
162: #include <time.h>
163: #include "timeval.h"
164:
1.53 brouard 165: #define MAXLINE 256
166: #define GNUPLOTPROGRAM "gnuplot"
167: /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
1.85 brouard 168: #define FILENAMELENGTH 132
1.53 brouard 169: /*#define DEBUG*/
1.85 brouard 170: /*#define windows*/
1.53 brouard 171: #define GLOCK_ERROR_NOPATH -1 /* empty path */
172: #define GLOCK_ERROR_GETCWD -2 /* cannot get cwd */
173:
174: #define MAXPARM 30 /* Maximum number of parameters for the optimization */
175: #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */
176:
177: #define NINTERVMAX 8
178: #define NLSTATEMAX 8 /* Maximum number of live states (for func) */
179: #define NDEATHMAX 8 /* Maximum number of dead states (for func) */
180: #define NCOVMAX 8 /* Maximum number of covariates */
181: #define MAXN 20000
182: #define YEARM 12. /* Number of months per year */
183: #define AGESUP 130
184: #define AGEBASE 40
1.85 brouard 185: #ifdef unix
186: #define DIRSEPARATOR '/'
187: #define ODIRSEPARATOR '\\'
188: #else
1.53 brouard 189: #define DIRSEPARATOR '\\'
190: #define ODIRSEPARATOR '/'
191: #endif
192:
1.94 ! brouard 193: /* $Id: imach.c,v 1.93 2003/06/25 16:33:55 brouard Exp $ */
1.81 brouard 194: /* $State: Exp $ */
1.80 brouard 195:
1.93 brouard 196: char version[]="Imach version 0.96b, June 2003, INED-EUROREVES ";
1.94 ! brouard 197: char fullversion[]="$Revision: 1.93 $ $Date: 2003/06/25 16:33:55 $";
1.91 brouard 198: int erreur, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings */
1.53 brouard 199: int nvar;
200: int cptcovn=0, cptcovage=0, cptcoveff=0,cptcov;
201: int npar=NPARMAX;
202: int nlstate=2; /* Number of live states */
203: int ndeath=1; /* Number of dead states */
204: int ncovmodel, ncovcol; /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
205: int popbased=0;
206:
207: int *wav; /* Number of waves for this individuual 0 is possible */
208: int maxwav; /* Maxim number of waves */
209: int jmin, jmax; /* min, max spacing between 2 waves */
1.87 brouard 210: int gipmx, gsw; /* Global variables on the number of contributions
211: to the likelihood and the sum of weights (done by funcone)*/
1.53 brouard 212: int mle, weightopt;
213: int **mw; /* mw[mi][i] is number of the mi wave for this individual */
214: int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
1.59 brouard 215: int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between
216: * wave mi and wave mi+1 is not an exact multiple of stepm. */
1.53 brouard 217: double jmean; /* Mean space between 2 waves */
218: double **oldm, **newm, **savm; /* Working pointers to matrices */
219: double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
220: FILE *fic,*ficpar, *ficparo,*ficres, *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
1.76 brouard 221: FILE *ficlog, *ficrespow;
1.85 brouard 222: int globpr; /* Global variable for printing or not */
223: double fretone; /* Only one call to likelihood */
224: long ipmx; /* Number of contributions */
225: double sw; /* Sum of weights */
226: char fileresilk[FILENAMELENGTH]; /* File of individual contributions to the likelihood */
227: FILE *ficresilk;
1.53 brouard 228: FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
229: FILE *ficresprobmorprev;
1.91 brouard 230: FILE *fichtm, *fichtmcov; /* Html File */
1.53 brouard 231: FILE *ficreseij;
232: char filerese[FILENAMELENGTH];
233: FILE *ficresvij;
234: char fileresv[FILENAMELENGTH];
235: FILE *ficresvpl;
236: char fileresvpl[FILENAMELENGTH];
237: char title[MAXLINE];
238: char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH], filerespl[FILENAMELENGTH];
239: char optionfilext[10], optionfilefiname[FILENAMELENGTH], plotcmd[FILENAMELENGTH];
1.88 brouard 240: char tmpout[FILENAMELENGTH];
241: char command[FILENAMELENGTH];
242: int outcmd=0;
1.53 brouard 243:
244: char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
1.94 ! brouard 245:
1.53 brouard 246: char filelog[FILENAMELENGTH]; /* Log file */
247: char filerest[FILENAMELENGTH];
248: char fileregp[FILENAMELENGTH];
249: char popfile[FILENAMELENGTH];
250:
1.91 brouard 251: char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilehtmcov[FILENAMELENGTH] ;
252:
253: struct timeval start_time, end_time, curr_time, last_time, forecast_time;
254: struct timezone tzp;
255: extern int gettimeofday();
256: struct tm tmg, tm, tmf, *gmtime(), *localtime();
257: long time_value;
258: extern long time();
259: char strcurr[80], strfor[80];
1.53 brouard 260:
261: #define NR_END 1
262: #define FREE_ARG char*
263: #define FTOL 1.0e-10
264:
265: #define NRANSI
266: #define ITMAX 200
267:
268: #define TOL 2.0e-4
269:
270: #define CGOLD 0.3819660
271: #define ZEPS 1.0e-10
272: #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);
273:
274: #define GOLD 1.618034
275: #define GLIMIT 100.0
276: #define TINY 1.0e-20
277:
278: static double maxarg1,maxarg2;
279: #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
280: #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
281:
282: #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
283: #define rint(a) floor(a+0.5)
284:
285: static double sqrarg;
286: #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
287: #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}
288:
289: int imx;
290: int stepm;
291: /* Stepm, step in month: minimum step interpolation*/
292:
293: int estepm;
294: /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
295:
296: int m,nb;
1.85 brouard 297: long *num;
298: int firstpass=0, lastpass=4,*cod, *ncodemax, *Tage;
1.53 brouard 299: double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
1.55 lievre 300: double **pmmij, ***probs;
1.53 brouard 301: double dateintmean=0;
302:
303: double *weight;
304: int **s; /* Status */
305: double *agedc, **covar, idx;
306: int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;
307:
308: double ftol=FTOL; /* Tolerance for computing Max Likelihood */
309: double ftolhess; /* Tolerance for computing hessian */
310:
311: /**************** split *************************/
312: static int split( char *path, char *dirc, char *name, char *ext, char *finame )
313: {
1.59 brouard 314: char *ss; /* pointer */
315: int l1, l2; /* length counters */
1.53 brouard 316:
1.59 brouard 317: l1 = strlen(path ); /* length of path */
318: if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
319: ss= strrchr( path, DIRSEPARATOR ); /* find last / */
320: if ( ss == NULL ) { /* no directory, so use current */
321: /*if(strrchr(path, ODIRSEPARATOR )==NULL)
322: printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
1.74 brouard 323: /* get current working directory */
324: /* extern char* getcwd ( char *buf , int len);*/
1.59 brouard 325: if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {
326: return( GLOCK_ERROR_GETCWD );
327: }
328: strcpy( name, path ); /* we've got it */
329: } else { /* strip direcotry from path */
330: ss++; /* after this, the filename */
331: l2 = strlen( ss ); /* length of filename */
332: if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
333: strcpy( name, ss ); /* save file name */
334: strncpy( dirc, path, l1 - l2 ); /* now the directory */
335: dirc[l1-l2] = 0; /* add zero */
336: }
337: l1 = strlen( dirc ); /* length of directory */
1.85 brouard 338: /*#ifdef windows
1.59 brouard 339: if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; }
1.53 brouard 340: #else
1.59 brouard 341: if ( dirc[l1-1] != '/' ) { dirc[l1] = '/'; dirc[l1+1] = 0; }
1.53 brouard 342: #endif
1.85 brouard 343: */
1.59 brouard 344: ss = strrchr( name, '.' ); /* find last / */
345: ss++;
346: strcpy(ext,ss); /* save extension */
347: l1= strlen( name);
348: l2= strlen(ss)+1;
349: strncpy( finame, name, l1-l2);
350: finame[l1-l2]= 0;
351: return( 0 ); /* we're done */
1.53 brouard 352: }
353:
354:
355: /******************************************/
356:
1.89 brouard 357: void replace_back_to_slash(char *s, char*t)
1.53 brouard 358: {
359: int i;
1.89 brouard 360: int lg=0;
1.53 brouard 361: i=0;
362: lg=strlen(t);
363: for(i=0; i<= lg; i++) {
364: (s[i] = t[i]);
365: if (t[i]== '\\') s[i]='/';
366: }
367: }
368:
369: int nbocc(char *s, char occ)
370: {
371: int i,j=0;
372: int lg=20;
373: i=0;
374: lg=strlen(s);
375: for(i=0; i<= lg; i++) {
376: if (s[i] == occ ) j++;
377: }
378: return j;
379: }
380:
381: void cutv(char *u,char *v, char*t, char occ)
382: {
383: /* cuts string t into u and v where u is ended by char occ excluding it
384: and v is after occ excluding it too : ex cutv(u,v,"abcdef2ghi2j",2)
385: gives u="abcedf" and v="ghi2j" */
386: int i,lg,j,p=0;
387: i=0;
388: for(j=0; j<=strlen(t)-1; j++) {
389: if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;
390: }
391:
392: lg=strlen(t);
393: for(j=0; j<p; j++) {
394: (u[j] = t[j]);
395: }
396: u[p]='\0';
397:
398: for(j=0; j<= lg; j++) {
399: if (j>=(p+1))(v[j-p-1] = t[j]);
400: }
401: }
402:
403: /********************** nrerror ********************/
404:
405: void nrerror(char error_text[])
406: {
407: fprintf(stderr,"ERREUR ...\n");
408: fprintf(stderr,"%s\n",error_text);
1.59 brouard 409: exit(EXIT_FAILURE);
1.53 brouard 410: }
411: /*********************** vector *******************/
412: double *vector(int nl, int nh)
413: {
414: double *v;
415: v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
416: if (!v) nrerror("allocation failure in vector");
417: return v-nl+NR_END;
418: }
419:
420: /************************ free vector ******************/
421: void free_vector(double*v, int nl, int nh)
422: {
423: free((FREE_ARG)(v+nl-NR_END));
424: }
425:
426: /************************ivector *******************************/
1.85 brouard 427: int *ivector(long nl,long nh)
1.76 brouard 428: {
1.85 brouard 429: int *v;
430: v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
431: if (!v) nrerror("allocation failure in ivector");
1.76 brouard 432: return v-nl+NR_END;
433: }
434:
435: /******************free ivector **************************/
1.85 brouard 436: void free_ivector(int *v, long nl, long nh)
1.76 brouard 437: {
438: free((FREE_ARG)(v+nl-NR_END));
439: }
440:
1.85 brouard 441: /************************lvector *******************************/
442: long *lvector(long nl,long nh)
1.53 brouard 443: {
1.85 brouard 444: long *v;
445: v=(long *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(long)));
1.53 brouard 446: if (!v) nrerror("allocation failure in ivector");
447: return v-nl+NR_END;
448: }
449:
1.85 brouard 450: /******************free lvector **************************/
451: void free_lvector(long *v, long nl, long nh)
1.53 brouard 452: {
453: free((FREE_ARG)(v+nl-NR_END));
454: }
455:
456: /******************* imatrix *******************************/
457: int **imatrix(long nrl, long nrh, long ncl, long nch)
458: /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */
459: {
460: long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;
461: int **m;
462:
463: /* allocate pointers to rows */
464: m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));
465: if (!m) nrerror("allocation failure 1 in matrix()");
466: m += NR_END;
467: m -= nrl;
468:
469:
470: /* allocate rows and set pointers to them */
471: m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));
472: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
473: m[nrl] += NR_END;
474: m[nrl] -= ncl;
475:
476: for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;
477:
478: /* return pointer to array of pointers to rows */
479: return m;
480: }
481:
482: /****************** free_imatrix *************************/
483: void free_imatrix(m,nrl,nrh,ncl,nch)
484: int **m;
485: long nch,ncl,nrh,nrl;
486: /* free an int matrix allocated by imatrix() */
487: {
488: free((FREE_ARG) (m[nrl]+ncl-NR_END));
489: free((FREE_ARG) (m+nrl-NR_END));
490: }
491:
492: /******************* matrix *******************************/
493: double **matrix(long nrl, long nrh, long ncl, long nch)
494: {
495: long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
496: double **m;
497:
498: m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
499: if (!m) nrerror("allocation failure 1 in matrix()");
500: m += NR_END;
501: m -= nrl;
502:
503: m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
504: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
505: m[nrl] += NR_END;
506: m[nrl] -= ncl;
507:
508: for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
509: return m;
1.85 brouard 510: /* print *(*(m+1)+70) or print m[1][70]; print m+1 or print &(m[1])
1.74 brouard 511: */
1.53 brouard 512: }
513:
514: /*************************free matrix ************************/
515: void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
516: {
517: free((FREE_ARG)(m[nrl]+ncl-NR_END));
518: free((FREE_ARG)(m+nrl-NR_END));
519: }
520:
521: /******************* ma3x *******************************/
522: double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
523: {
524: long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
525: double ***m;
526:
527: m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
528: if (!m) nrerror("allocation failure 1 in matrix()");
529: m += NR_END;
530: m -= nrl;
531:
532: m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
533: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
534: m[nrl] += NR_END;
535: m[nrl] -= ncl;
536:
537: for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
538:
539: m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
540: if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
541: m[nrl][ncl] += NR_END;
542: m[nrl][ncl] -= nll;
543: for (j=ncl+1; j<=nch; j++)
544: m[nrl][j]=m[nrl][j-1]+nlay;
545:
546: for (i=nrl+1; i<=nrh; i++) {
547: m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
548: for (j=ncl+1; j<=nch; j++)
549: m[i][j]=m[i][j-1]+nlay;
550: }
1.74 brouard 551: return m;
552: /* gdb: p *(m+1) <=> p m[1] and p (m+1) <=> p (m+1) <=> p &(m[1])
553: &(m[i][j][k]) <=> *((*(m+i) + j)+k)
554: */
1.53 brouard 555: }
556:
557: /*************************free ma3x ************************/
558: void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
559: {
560: free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
561: free((FREE_ARG)(m[nrl]+ncl-NR_END));
562: free((FREE_ARG)(m+nrl-NR_END));
563: }
564:
1.94 ! brouard 565: /*************** function subdirf ***********/
! 566: char *subdirf(char fileres[])
! 567: {
! 568: /* Caution optionfilefiname is hidden */
! 569: strcpy(tmpout,optionfilefiname);
! 570: strcat(tmpout,"/"); /* Add to the right */
! 571: strcat(tmpout,fileres);
! 572: return tmpout;
! 573: }
! 574:
! 575: /*************** function subdirf2 ***********/
! 576: char *subdirf2(char fileres[], char *preop)
! 577: {
! 578:
! 579: /* Caution optionfilefiname is hidden */
! 580: strcpy(tmpout,optionfilefiname);
! 581: strcat(tmpout,"/");
! 582: strcat(tmpout,preop);
! 583: strcat(tmpout,fileres);
! 584: return tmpout;
! 585: }
! 586:
! 587: /*************** function subdirf3 ***********/
! 588: char *subdirf3(char fileres[], char *preop, char *preop2)
! 589: {
! 590:
! 591: /* Caution optionfilefiname is hidden */
! 592: strcpy(tmpout,optionfilefiname);
! 593: strcat(tmpout,"/");
! 594: strcat(tmpout,preop);
! 595: strcat(tmpout,preop2);
! 596: strcat(tmpout,fileres);
! 597: return tmpout;
! 598: }
! 599:
1.53 brouard 600: /***************** f1dim *************************/
601: extern int ncom;
602: extern double *pcom,*xicom;
603: extern double (*nrfunc)(double []);
604:
605: double f1dim(double x)
606: {
607: int j;
608: double f;
609: double *xt;
610:
611: xt=vector(1,ncom);
612: for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];
613: f=(*nrfunc)(xt);
614: free_vector(xt,1,ncom);
615: return f;
616: }
617:
618: /*****************brent *************************/
619: double brent(double ax, double bx, double cx, double (*f)(double), double tol, double *xmin)
620: {
621: int iter;
622: double a,b,d,etemp;
623: double fu,fv,fw,fx;
624: double ftemp;
625: double p,q,r,tol1,tol2,u,v,w,x,xm;
626: double e=0.0;
627:
628: a=(ax < cx ? ax : cx);
629: b=(ax > cx ? ax : cx);
630: x=w=v=bx;
631: fw=fv=fx=(*f)(x);
632: for (iter=1;iter<=ITMAX;iter++) {
633: xm=0.5*(a+b);
634: tol2=2.0*(tol1=tol*fabs(x)+ZEPS);
635: /* if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
636: printf(".");fflush(stdout);
637: fprintf(ficlog,".");fflush(ficlog);
638: #ifdef DEBUG
639: 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);
640: 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);
641: /* if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
642: #endif
643: if (fabs(x-xm) <= (tol2-0.5*(b-a))){
644: *xmin=x;
645: return fx;
646: }
647: ftemp=fu;
648: if (fabs(e) > tol1) {
649: r=(x-w)*(fx-fv);
650: q=(x-v)*(fx-fw);
651: p=(x-v)*q-(x-w)*r;
652: q=2.0*(q-r);
653: if (q > 0.0) p = -p;
654: q=fabs(q);
655: etemp=e;
656: e=d;
657: if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))
658: d=CGOLD*(e=(x >= xm ? a-x : b-x));
659: else {
660: d=p/q;
661: u=x+d;
662: if (u-a < tol2 || b-u < tol2)
663: d=SIGN(tol1,xm-x);
664: }
665: } else {
666: d=CGOLD*(e=(x >= xm ? a-x : b-x));
667: }
668: u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));
669: fu=(*f)(u);
670: if (fu <= fx) {
671: if (u >= x) a=x; else b=x;
672: SHFT(v,w,x,u)
673: SHFT(fv,fw,fx,fu)
674: } else {
675: if (u < x) a=u; else b=u;
676: if (fu <= fw || w == x) {
677: v=w;
678: w=u;
679: fv=fw;
680: fw=fu;
681: } else if (fu <= fv || v == x || v == w) {
682: v=u;
683: fv=fu;
684: }
685: }
686: }
687: nrerror("Too many iterations in brent");
688: *xmin=x;
689: return fx;
690: }
691:
692: /****************** mnbrak ***********************/
693:
694: void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,
695: double (*func)(double))
696: {
697: double ulim,u,r,q, dum;
698: double fu;
699:
700: *fa=(*func)(*ax);
701: *fb=(*func)(*bx);
702: if (*fb > *fa) {
703: SHFT(dum,*ax,*bx,dum)
704: SHFT(dum,*fb,*fa,dum)
705: }
706: *cx=(*bx)+GOLD*(*bx-*ax);
707: *fc=(*func)(*cx);
708: while (*fb > *fc) {
709: r=(*bx-*ax)*(*fb-*fc);
710: q=(*bx-*cx)*(*fb-*fa);
711: u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/
712: (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r));
713: ulim=(*bx)+GLIMIT*(*cx-*bx);
714: if ((*bx-u)*(u-*cx) > 0.0) {
715: fu=(*func)(u);
716: } else if ((*cx-u)*(u-ulim) > 0.0) {
717: fu=(*func)(u);
718: if (fu < *fc) {
719: SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))
720: SHFT(*fb,*fc,fu,(*func)(u))
721: }
722: } else if ((u-ulim)*(ulim-*cx) >= 0.0) {
723: u=ulim;
724: fu=(*func)(u);
725: } else {
726: u=(*cx)+GOLD*(*cx-*bx);
727: fu=(*func)(u);
728: }
729: SHFT(*ax,*bx,*cx,u)
730: SHFT(*fa,*fb,*fc,fu)
731: }
732: }
733:
734: /*************** linmin ************************/
735:
736: int ncom;
737: double *pcom,*xicom;
738: double (*nrfunc)(double []);
739:
740: void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))
741: {
742: double brent(double ax, double bx, double cx,
743: double (*f)(double), double tol, double *xmin);
744: double f1dim(double x);
745: void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,
746: double *fc, double (*func)(double));
747: int j;
748: double xx,xmin,bx,ax;
749: double fx,fb,fa;
750:
751: ncom=n;
752: pcom=vector(1,n);
753: xicom=vector(1,n);
754: nrfunc=func;
755: for (j=1;j<=n;j++) {
756: pcom[j]=p[j];
757: xicom[j]=xi[j];
758: }
759: ax=0.0;
760: xx=1.0;
761: mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim);
762: *fret=brent(ax,xx,bx,f1dim,TOL,&xmin);
763: #ifdef DEBUG
764: printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
765: fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
766: #endif
767: for (j=1;j<=n;j++) {
768: xi[j] *= xmin;
769: p[j] += xi[j];
770: }
771: free_vector(xicom,1,n);
772: free_vector(pcom,1,n);
773: }
774:
1.91 brouard 775: char *asc_diff_time(long time_sec, char ascdiff[])
776: {
777: long sec_left, days, hours, minutes;
778: days = (time_sec) / (60*60*24);
779: sec_left = (time_sec) % (60*60*24);
780: hours = (sec_left) / (60*60) ;
781: sec_left = (sec_left) %(60*60);
782: minutes = (sec_left) /60;
783: sec_left = (sec_left) % (60);
784: sprintf(ascdiff,"%d day(s) %d hour(s) %d minute(s) %d second(s)",days, hours, minutes, sec_left);
785: return ascdiff;
786: }
787:
1.53 brouard 788: /*************** powell ************************/
789: void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,
790: double (*func)(double []))
791: {
792: void linmin(double p[], double xi[], int n, double *fret,
793: double (*func)(double []));
794: int i,ibig,j;
795: double del,t,*pt,*ptt,*xit;
796: double fp,fptt;
797: double *xits;
1.91 brouard 798: int niterf, itmp;
799:
1.53 brouard 800: pt=vector(1,n);
801: ptt=vector(1,n);
802: xit=vector(1,n);
803: xits=vector(1,n);
804: *fret=(*func)(p);
805: for (j=1;j<=n;j++) pt[j]=p[j];
806: for (*iter=1;;++(*iter)) {
807: fp=(*fret);
808: ibig=0;
809: del=0.0;
1.91 brouard 810: last_time=curr_time;
811: (void) gettimeofday(&curr_time,&tzp);
812: 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);
813: 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);
814: fprintf(ficrespow,"%d %.12f %ld",*iter,*fret,curr_time.tv_sec-start_time.tv_sec);
1.76 brouard 815: for (i=1;i<=n;i++) {
1.53 brouard 816: printf(" %d %.12f",i, p[i]);
1.76 brouard 817: fprintf(ficlog," %d %.12lf",i, p[i]);
818: fprintf(ficrespow," %.12lf", p[i]);
819: }
1.53 brouard 820: printf("\n");
821: fprintf(ficlog,"\n");
1.91 brouard 822: fprintf(ficrespow,"\n");fflush(ficrespow);
823: if(*iter <=3){
824: tm = *localtime(&curr_time.tv_sec);
1.92 brouard 825: strcpy(strcurr,asctime(&tmf));
826: /* asctime_r(&tm,strcurr); */
1.91 brouard 827: forecast_time=curr_time;
828: itmp = strlen(strcurr);
829: if(strcurr[itmp-1]=='\n')
830: strcurr[itmp-1]='\0';
831: printf("\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,curr_time.tv_sec-last_time.tv_sec);
832: fprintf(ficlog,"\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,curr_time.tv_sec-last_time.tv_sec);
833: for(niterf=10;niterf<=30;niterf+=10){
834: forecast_time.tv_sec=curr_time.tv_sec+(niterf-*iter)*(curr_time.tv_sec-last_time.tv_sec);
835: tmf = *localtime(&forecast_time.tv_sec);
1.92 brouard 836: /* asctime_r(&tmf,strfor); */
837: strcpy(strfor,asctime(&tmf));
1.91 brouard 838: itmp = strlen(strfor);
839: if(strfor[itmp-1]=='\n')
840: strfor[itmp-1]='\0';
841: 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);
842: 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);
843: }
844: }
1.53 brouard 845: for (i=1;i<=n;i++) {
846: for (j=1;j<=n;j++) xit[j]=xi[j][i];
847: fptt=(*fret);
848: #ifdef DEBUG
849: printf("fret=%lf \n",*fret);
850: fprintf(ficlog,"fret=%lf \n",*fret);
851: #endif
852: printf("%d",i);fflush(stdout);
853: fprintf(ficlog,"%d",i);fflush(ficlog);
854: linmin(p,xit,n,fret,func);
855: if (fabs(fptt-(*fret)) > del) {
856: del=fabs(fptt-(*fret));
857: ibig=i;
858: }
859: #ifdef DEBUG
860: printf("%d %.12e",i,(*fret));
861: fprintf(ficlog,"%d %.12e",i,(*fret));
862: for (j=1;j<=n;j++) {
863: xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
864: printf(" x(%d)=%.12e",j,xit[j]);
865: fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
866: }
867: for(j=1;j<=n;j++) {
868: printf(" p=%.12e",p[j]);
869: fprintf(ficlog," p=%.12e",p[j]);
870: }
871: printf("\n");
872: fprintf(ficlog,"\n");
873: #endif
874: }
875: if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {
876: #ifdef DEBUG
877: int k[2],l;
878: k[0]=1;
879: k[1]=-1;
880: printf("Max: %.12e",(*func)(p));
881: fprintf(ficlog,"Max: %.12e",(*func)(p));
882: for (j=1;j<=n;j++) {
883: printf(" %.12e",p[j]);
884: fprintf(ficlog," %.12e",p[j]);
885: }
886: printf("\n");
887: fprintf(ficlog,"\n");
888: for(l=0;l<=1;l++) {
889: for (j=1;j<=n;j++) {
890: ptt[j]=p[j]+(p[j]-pt[j])*k[l];
891: printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
892: fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
893: }
894: printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
895: fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
896: }
897: #endif
898:
899:
900: free_vector(xit,1,n);
901: free_vector(xits,1,n);
902: free_vector(ptt,1,n);
903: free_vector(pt,1,n);
904: return;
905: }
906: if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");
907: for (j=1;j<=n;j++) {
908: ptt[j]=2.0*p[j]-pt[j];
909: xit[j]=p[j]-pt[j];
910: pt[j]=p[j];
911: }
912: fptt=(*func)(ptt);
913: if (fptt < fp) {
914: t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt);
915: if (t < 0.0) {
916: linmin(p,xit,n,fret,func);
917: for (j=1;j<=n;j++) {
918: xi[j][ibig]=xi[j][n];
919: xi[j][n]=xit[j];
920: }
921: #ifdef DEBUG
922: printf("Direction changed last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
923: fprintf(ficlog,"Direction changed last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
924: for(j=1;j<=n;j++){
925: printf(" %.12e",xit[j]);
926: fprintf(ficlog," %.12e",xit[j]);
927: }
928: printf("\n");
929: fprintf(ficlog,"\n");
930: #endif
1.54 brouard 931: }
1.53 brouard 932: }
933: }
934: }
935:
1.54 brouard 936: /**** Prevalence limit (stable prevalence) ****************/
1.53 brouard 937:
938: double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)
939: {
940: /* Computes the prevalence limit in each live state at age x by left multiplying the unit
941: matrix by transitions matrix until convergence is reached */
942:
943: int i, ii,j,k;
944: double min, max, maxmin, maxmax,sumnew=0.;
945: double **matprod2();
946: double **out, cov[NCOVMAX], **pmij();
947: double **newm;
948: double agefin, delaymax=50 ; /* Max number of years to converge */
949:
950: for (ii=1;ii<=nlstate+ndeath;ii++)
951: for (j=1;j<=nlstate+ndeath;j++){
952: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
953: }
954:
955: cov[1]=1.;
956:
957: /* Even if hstepm = 1, at least one multiplication by the unit matrix */
958: for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
959: newm=savm;
960: /* Covariates have to be included here again */
961: cov[2]=agefin;
962:
963: for (k=1; k<=cptcovn;k++) {
964: cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
965: /* 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]]);*/
966: }
967: for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
968: for (k=1; k<=cptcovprod;k++)
969: cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
970:
971: /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
972: /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
973: /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
974: out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);
975:
976: savm=oldm;
977: oldm=newm;
978: maxmax=0.;
979: for(j=1;j<=nlstate;j++){
980: min=1.;
981: max=0.;
982: for(i=1; i<=nlstate; i++) {
983: sumnew=0;
984: for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
985: prlim[i][j]= newm[i][j]/(1-sumnew);
986: max=FMAX(max,prlim[i][j]);
987: min=FMIN(min,prlim[i][j]);
988: }
989: maxmin=max-min;
990: maxmax=FMAX(maxmax,maxmin);
991: }
992: if(maxmax < ftolpl){
993: return prlim;
994: }
995: }
996: }
997:
998: /*************** transition probabilities ***************/
999:
1000: double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
1001: {
1002: double s1, s2;
1003: /*double t34;*/
1004: int i,j,j1, nc, ii, jj;
1005:
1006: for(i=1; i<= nlstate; i++){
1007: for(j=1; j<i;j++){
1008: for (nc=1, s2=0.;nc <=ncovmodel; nc++){
1009: /*s2 += param[i][j][nc]*cov[nc];*/
1010: s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
1011: /*printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2);*/
1012: }
1013: ps[i][j]=s2;
1014: /*printf("s1=%.17e, s2=%.17e\n",s1,s2);*/
1015: }
1016: for(j=i+1; j<=nlstate+ndeath;j++){
1017: for (nc=1, s2=0.;nc <=ncovmodel; nc++){
1018: s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
1019: /*printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2);*/
1020: }
1021: ps[i][j]=s2;
1022: }
1023: }
1024: /*ps[3][2]=1;*/
1025:
1026: for(i=1; i<= nlstate; i++){
1027: s1=0;
1028: for(j=1; j<i; j++)
1029: s1+=exp(ps[i][j]);
1030: for(j=i+1; j<=nlstate+ndeath; j++)
1031: s1+=exp(ps[i][j]);
1032: ps[i][i]=1./(s1+1.);
1033: for(j=1; j<i; j++)
1034: ps[i][j]= exp(ps[i][j])*ps[i][i];
1035: for(j=i+1; j<=nlstate+ndeath; j++)
1036: ps[i][j]= exp(ps[i][j])*ps[i][i];
1037: /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
1038: } /* end i */
1039:
1040: for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
1041: for(jj=1; jj<= nlstate+ndeath; jj++){
1042: ps[ii][jj]=0;
1043: ps[ii][ii]=1;
1044: }
1045: }
1046:
1047:
1048: /* for(ii=1; ii<= nlstate+ndeath; ii++){
1049: for(jj=1; jj<= nlstate+ndeath; jj++){
1050: printf("%lf ",ps[ii][jj]);
1051: }
1052: printf("\n ");
1053: }
1054: printf("\n ");printf("%lf ",cov[2]);*/
1055: /*
1056: for(i=1; i<= npar; i++) printf("%f ",x[i]);
1057: goto end;*/
1058: return ps;
1059: }
1060:
1061: /**************** Product of 2 matrices ******************/
1062:
1063: double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)
1064: {
1065: /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
1066: b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
1067: /* in, b, out are matrice of pointers which should have been initialized
1068: before: only the contents of out is modified. The function returns
1069: a pointer to pointers identical to out */
1070: long i, j, k;
1071: for(i=nrl; i<= nrh; i++)
1072: for(k=ncolol; k<=ncoloh; k++)
1073: for(j=ncl,out[i][k]=0.; j<=nch; j++)
1074: out[i][k] +=in[i][j]*b[j][k];
1075:
1076: return out;
1077: }
1078:
1079:
1080: /************* Higher Matrix Product ***************/
1081:
1082: double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
1083: {
1.66 brouard 1084: /* Computes the transition matrix starting at age 'age' over
1085: 'nhstepm*hstepm*stepm' months (i.e. until
1086: age (in years) age+nhstepm*hstepm*stepm/12) by multiplying
1087: nhstepm*hstepm matrices.
1.53 brouard 1088: Output is stored in matrix po[i][j][h] for h every 'hstepm' step
1.66 brouard 1089: (typically every 2 years instead of every month which is too big
1090: for the memory).
1.53 brouard 1091: Model is determined by parameters x and covariates have to be
1092: included manually here.
1093:
1094: */
1095:
1096: int i, j, d, h, k;
1097: double **out, cov[NCOVMAX];
1098: double **newm;
1099:
1100: /* Hstepm could be zero and should return the unit matrix */
1101: for (i=1;i<=nlstate+ndeath;i++)
1102: for (j=1;j<=nlstate+ndeath;j++){
1103: oldm[i][j]=(i==j ? 1.0 : 0.0);
1104: po[i][j][0]=(i==j ? 1.0 : 0.0);
1105: }
1106: /* Even if hstepm = 1, at least one multiplication by the unit matrix */
1107: for(h=1; h <=nhstepm; h++){
1108: for(d=1; d <=hstepm; d++){
1109: newm=savm;
1110: /* Covariates have to be included here again */
1111: cov[1]=1.;
1112: cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
1113: for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
1114: for (k=1; k<=cptcovage;k++)
1115: cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
1116: for (k=1; k<=cptcovprod;k++)
1117: cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
1118:
1119:
1120: /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
1121: /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
1122: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,
1123: pmij(pmmij,cov,ncovmodel,x,nlstate));
1124: savm=oldm;
1125: oldm=newm;
1126: }
1127: for(i=1; i<=nlstate+ndeath; i++)
1128: for(j=1;j<=nlstate+ndeath;j++) {
1129: po[i][j][h]=newm[i][j];
1130: /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);
1131: */
1132: }
1133: } /* end h */
1134: return po;
1135: }
1136:
1137:
1138: /*************** log-likelihood *************/
1139: double func( double *x)
1140: {
1141: int i, ii, j, k, mi, d, kk;
1142: double l, ll[NLSTATEMAX], cov[NCOVMAX];
1143: double **out;
1144: double sw; /* Sum of weights */
1145: double lli; /* Individual log likelihood */
1.59 brouard 1146: int s1, s2;
1.68 lievre 1147: double bbh, survp;
1.53 brouard 1148: long ipmx;
1149: /*extern weight */
1150: /* We are differentiating ll according to initial status */
1151: /* for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
1152: /*for(i=1;i<imx;i++)
1153: printf(" %d\n",s[4][i]);
1154: */
1155: cov[1]=1.;
1156:
1157: for(k=1; k<=nlstate; k++) ll[k]=0.;
1.61 brouard 1158:
1159: if(mle==1){
1160: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1161: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
1162: for(mi=1; mi<= wav[i]-1; mi++){
1163: for (ii=1;ii<=nlstate+ndeath;ii++)
1164: for (j=1;j<=nlstate+ndeath;j++){
1165: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1166: savm[ii][j]=(ii==j ? 1.0 : 0.0);
1167: }
1168: for(d=0; d<dh[mi][i]; d++){
1169: newm=savm;
1170: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
1171: for (kk=1; kk<=cptcovage;kk++) {
1172: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
1173: }
1174: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1175: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1176: savm=oldm;
1177: oldm=newm;
1178: } /* end mult */
1.53 brouard 1179:
1.61 brouard 1180: /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
1181: /* But now since version 0.9 we anticipate for bias and large stepm.
1182: * If stepm is larger than one month (smallest stepm) and if the exact delay
1183: * (in months) between two waves is not a multiple of stepm, we rounded to
1184: * the nearest (and in case of equal distance, to the lowest) interval but now
1185: * we keep into memory the bias bh[mi][i] and also the previous matrix product
1186: * (i.e to dh[mi][i]-1) saved in 'savm'. The we inter(extra)polate the
1187: * probability in order to take into account the bias as a fraction of the way
1188: * from savm to out if bh is neagtive or even beyond if bh is positive. bh varies
1189: * -stepm/2 to stepm/2 .
1190: * For stepm=1 the results are the same as for previous versions of Imach.
1191: * For stepm > 1 the results are less biased than in previous versions.
1192: */
1193: s1=s[mw[mi][i]][i];
1194: s2=s[mw[mi+1][i]][i];
1.64 lievre 1195: bbh=(double)bh[mi][i]/(double)stepm;
1196: /* bias is positive if real duration
1197: * is higher than the multiple of stepm and negative otherwise.
1198: */
1199: /* 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 1200: if( s2 > nlstate){
1201: /* i.e. if s2 is a death state and if the date of death is known then the contribution
1202: to the likelihood is the probability to die between last step unit time and current
1203: step unit time, which is also the differences between probability to die before dh
1204: and probability to die before dh-stepm .
1205: In version up to 0.92 likelihood was computed
1206: as if date of death was unknown. Death was treated as any other
1207: health state: the date of the interview describes the actual state
1208: and not the date of a change in health state. The former idea was
1209: to consider that at each interview the state was recorded
1210: (healthy, disable or death) and IMaCh was corrected; but when we
1211: introduced the exact date of death then we should have modified
1212: the contribution of an exact death to the likelihood. This new
1213: contribution is smaller and very dependent of the step unit
1214: stepm. It is no more the probability to die between last interview
1215: and month of death but the probability to survive from last
1216: interview up to one month before death multiplied by the
1217: probability to die within a month. Thanks to Chris
1218: Jackson for correcting this bug. Former versions increased
1219: mortality artificially. The bad side is that we add another loop
1220: which slows down the processing. The difference can be up to 10%
1221: lower mortality.
1222: */
1223: lli=log(out[s1][s2] - savm[s1][s2]);
1224: }else{
1225: lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
1226: /* 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 */
1227: }
1.64 lievre 1228: /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
1229: /*if(lli ==000.0)*/
1230: /*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 1231: ipmx +=1;
1.64 lievre 1232: sw += weight[i];
1233: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1234: } /* end of wave */
1235: } /* end of individual */
1236: } else if(mle==2){
1237: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1238: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
1239: for(mi=1; mi<= wav[i]-1; mi++){
1240: for (ii=1;ii<=nlstate+ndeath;ii++)
1241: for (j=1;j<=nlstate+ndeath;j++){
1242: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1243: savm[ii][j]=(ii==j ? 1.0 : 0.0);
1244: }
1245: for(d=0; d<=dh[mi][i]; d++){
1246: newm=savm;
1247: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
1248: for (kk=1; kk<=cptcovage;kk++) {
1249: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
1250: }
1251: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1252: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1253: savm=oldm;
1254: oldm=newm;
1255: } /* end mult */
1256:
1257: s1=s[mw[mi][i]][i];
1258: s2=s[mw[mi+1][i]][i];
1259: bbh=(double)bh[mi][i]/(double)stepm;
1.63 lievre 1260: 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 1261: ipmx +=1;
1262: sw += weight[i];
1263: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1264: } /* end of wave */
1265: } /* end of individual */
1266: } else if(mle==3){ /* exponential inter-extrapolation */
1267: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1268: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
1269: for(mi=1; mi<= wav[i]-1; mi++){
1270: for (ii=1;ii<=nlstate+ndeath;ii++)
1271: for (j=1;j<=nlstate+ndeath;j++){
1272: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1273: savm[ii][j]=(ii==j ? 1.0 : 0.0);
1274: }
1275: for(d=0; d<dh[mi][i]; d++){
1276: newm=savm;
1277: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
1278: for (kk=1; kk<=cptcovage;kk++) {
1279: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
1280: }
1281: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1282: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1283: savm=oldm;
1284: oldm=newm;
1285: } /* end mult */
1286:
1287: s1=s[mw[mi][i]][i];
1288: s2=s[mw[mi+1][i]][i];
1289: bbh=(double)bh[mi][i]/(double)stepm;
1290: 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 1291: ipmx +=1;
1292: sw += weight[i];
1293: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1294: } /* end of wave */
1295: } /* end of individual */
1.84 brouard 1296: }else if (mle==4){ /* ml=4 no inter-extrapolation */
1.61 brouard 1297: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1298: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
1299: for(mi=1; mi<= wav[i]-1; mi++){
1300: for (ii=1;ii<=nlstate+ndeath;ii++)
1301: for (j=1;j<=nlstate+ndeath;j++){
1302: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1303: savm[ii][j]=(ii==j ? 1.0 : 0.0);
1304: }
1305: for(d=0; d<dh[mi][i]; d++){
1306: newm=savm;
1307: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
1308: for (kk=1; kk<=cptcovage;kk++) {
1309: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
1310: }
1311:
1312: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1313: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1314: savm=oldm;
1315: oldm=newm;
1316: } /* end mult */
1317:
1.84 brouard 1318: s1=s[mw[mi][i]][i];
1319: s2=s[mw[mi+1][i]][i];
1320: if( s2 > nlstate){
1321: lli=log(out[s1][s2] - savm[s1][s2]);
1322: }else{
1323: lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
1324: }
1325: ipmx +=1;
1326: sw += weight[i];
1327: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1.85 brouard 1328: /* 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 1329: } /* end of wave */
1330: } /* end of individual */
1331: }else{ /* ml=5 no inter-extrapolation no jackson =0.8a */
1332: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1333: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
1334: for(mi=1; mi<= wav[i]-1; mi++){
1335: for (ii=1;ii<=nlstate+ndeath;ii++)
1336: for (j=1;j<=nlstate+ndeath;j++){
1337: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1338: savm[ii][j]=(ii==j ? 1.0 : 0.0);
1339: }
1340: for(d=0; d<dh[mi][i]; d++){
1341: newm=savm;
1342: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
1343: for (kk=1; kk<=cptcovage;kk++) {
1344: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
1345: }
1346:
1347: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1348: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1349: savm=oldm;
1350: oldm=newm;
1351: } /* end mult */
1352:
1353: s1=s[mw[mi][i]][i];
1354: s2=s[mw[mi+1][i]][i];
1.61 brouard 1355: lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
1356: ipmx +=1;
1357: sw += weight[i];
1358: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1.84 brouard 1359: /*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 1360: } /* end of wave */
1361: } /* end of individual */
1362: } /* End of if */
1.53 brouard 1363: for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
1364: /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
1365: l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
1.85 brouard 1366: return -l;
1367: }
1368:
1369: /*************** log-likelihood *************/
1370: double funcone( double *x)
1371: {
1.87 brouard 1372: /* Same as likeli but slower because of a lot of printf and if */
1.85 brouard 1373: int i, ii, j, k, mi, d, kk;
1374: double l, ll[NLSTATEMAX], cov[NCOVMAX];
1375: double **out;
1376: double lli; /* Individual log likelihood */
1.87 brouard 1377: double llt;
1.85 brouard 1378: int s1, s2;
1379: double bbh, survp;
1380: /*extern weight */
1381: /* We are differentiating ll according to initial status */
1382: /* for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
1383: /*for(i=1;i<imx;i++)
1384: printf(" %d\n",s[4][i]);
1385: */
1386: cov[1]=1.;
1387:
1388: for(k=1; k<=nlstate; k++) ll[k]=0.;
1389:
1390: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1391: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
1392: for(mi=1; mi<= wav[i]-1; mi++){
1393: for (ii=1;ii<=nlstate+ndeath;ii++)
1394: for (j=1;j<=nlstate+ndeath;j++){
1395: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1396: savm[ii][j]=(ii==j ? 1.0 : 0.0);
1397: }
1398: for(d=0; d<dh[mi][i]; d++){
1399: newm=savm;
1400: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
1401: for (kk=1; kk<=cptcovage;kk++) {
1402: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
1403: }
1404: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1405: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1406: savm=oldm;
1407: oldm=newm;
1408: } /* end mult */
1409:
1410: s1=s[mw[mi][i]][i];
1411: s2=s[mw[mi+1][i]][i];
1412: bbh=(double)bh[mi][i]/(double)stepm;
1413: /* bias is positive if real duration
1414: * is higher than the multiple of stepm and negative otherwise.
1415: */
1416: if( s2 > nlstate && (mle <5) ){ /* Jackson */
1417: lli=log(out[s1][s2] - savm[s1][s2]);
1418: } else if (mle==1){
1419: lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
1420: } else if(mle==2){
1421: 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 */
1422: } else if(mle==3){ /* exponential inter-extrapolation */
1423: 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 */
1424: } else if (mle==4){ /* mle=4 no inter-extrapolation */
1425: lli=log(out[s1][s2]); /* Original formula */
1426: } else{ /* ml>=5 no inter-extrapolation no jackson =0.8a */
1427: lli=log(out[s1][s2]); /* Original formula */
1428: } /* End of if */
1429: ipmx +=1;
1430: sw += weight[i];
1431: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1432: /* 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]); */
1433: if(globpr){
1.88 brouard 1434: fprintf(ficresilk,"%9d %6d %1d %1d %1d %1d %3d %10.6f %6.4f\
1.86 brouard 1435: %10.6f %10.6f %10.6f ", \
1436: num[i],i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],
1437: 2*weight[i]*lli,out[s1][s2],savm[s1][s2]);
1.87 brouard 1438: for(k=1,llt=0.,l=0.; k<=nlstate; k++){
1439: llt +=ll[k]*gipmx/gsw;
1440: fprintf(ficresilk," %10.6f",-ll[k]*gipmx/gsw);
1441: }
1442: fprintf(ficresilk," %10.6f\n", -llt);
1.85 brouard 1443: }
1444: } /* end of wave */
1445: } /* end of individual */
1446: for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
1447: /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
1448: l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
1.87 brouard 1449: if(globpr==0){ /* First time we count the contributions and weights */
1450: gipmx=ipmx;
1451: gsw=sw;
1452: }
1.53 brouard 1453: return -l;
1454: }
1455:
1456:
1.94 ! brouard 1457: /*************** function likelione ***********/
1.87 brouard 1458: void likelione(FILE *ficres,double p[], int npar, int nlstate, int *globpri, long *ipmx, double *sw, double *fretone, double (*funcone)(double []))
1.85 brouard 1459: {
1.87 brouard 1460: /* This routine should help understanding what is done with
1461: the selection of individuals/waves and
1.85 brouard 1462: to check the exact contribution to the likelihood.
1463: Plotting could be done.
1464: */
1465: int k;
1.87 brouard 1466:
1.88 brouard 1467: if(*globpri !=0){ /* Just counts and sums, no printings */
1.85 brouard 1468: strcpy(fileresilk,"ilk");
1469: strcat(fileresilk,fileres);
1470: if((ficresilk=fopen(fileresilk,"w"))==NULL) {
1471: printf("Problem with resultfile: %s\n", fileresilk);
1472: fprintf(ficlog,"Problem with resultfile: %s\n", fileresilk);
1473: }
1.87 brouard 1474: 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 1475: fprintf(ficresilk, "#num_i i s1 s2 mi mw dh likeli weight 2wlli out sav ");
1.85 brouard 1476: /* i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],2*weight[i]*lli,out[s1][s2],savm[s1][s2]); */
1477: for(k=1; k<=nlstate; k++)
1.87 brouard 1478: fprintf(ficresilk," -2*gipw/gsw*weight*ll[%d]++",k);
1479: fprintf(ficresilk," -2*gipw/gsw*weight*ll(total)\n");
1.85 brouard 1480: }
1481:
1482: *fretone=(*funcone)(p);
1.87 brouard 1483: if(*globpri !=0){
1.85 brouard 1484: fclose(ficresilk);
1.88 brouard 1485: fprintf(fichtm,"\n<br>File of contributions to the likelihood: <a href=\"%s\">%s</a><br>\n",subdirf(fileresilk),subdirf(fileresilk));
1.87 brouard 1486: fflush(fichtm);
1487: }
1.85 brouard 1488: return;
1489: }
1490:
1.88 brouard 1491:
1.53 brouard 1492: /*********** Maximum Likelihood Estimation ***************/
1493:
1494: void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
1495: {
1496: int i,j, iter;
1.74 brouard 1497: double **xi;
1.53 brouard 1498: double fret;
1.85 brouard 1499: double fretone; /* Only one call to likelihood */
1.76 brouard 1500: char filerespow[FILENAMELENGTH];
1.53 brouard 1501: xi=matrix(1,npar,1,npar);
1502: for (i=1;i<=npar;i++)
1503: for (j=1;j<=npar;j++)
1504: xi[i][j]=(i==j ? 1.0 : 0.0);
1505: printf("Powell\n"); fprintf(ficlog,"Powell\n");
1.76 brouard 1506: strcpy(filerespow,"pow");
1507: strcat(filerespow,fileres);
1508: if((ficrespow=fopen(filerespow,"w"))==NULL) {
1509: printf("Problem with resultfile: %s\n", filerespow);
1510: fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
1511: }
1512: fprintf(ficrespow,"# Powell\n# iter -2*LL");
1513: for (i=1;i<=nlstate;i++)
1514: for(j=1;j<=nlstate+ndeath;j++)
1515: if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
1516: fprintf(ficrespow,"\n");
1.85 brouard 1517:
1.53 brouard 1518: powell(p,xi,npar,ftol,&iter,&fret,func);
1519:
1.76 brouard 1520: fclose(ficrespow);
1521: printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));
1.65 lievre 1522: fprintf(ficlog,"\n#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
1.53 brouard 1523: fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
1524:
1525: }
1526:
1527: /**** Computes Hessian and covariance matrix ***/
1528: void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
1529: {
1530: double **a,**y,*x,pd;
1531: double **hess;
1532: int i, j,jk;
1533: int *indx;
1534:
1535: double hessii(double p[], double delta, int theta, double delti[]);
1536: double hessij(double p[], double delti[], int i, int j);
1537: void lubksb(double **a, int npar, int *indx, double b[]) ;
1538: void ludcmp(double **a, int npar, int *indx, double *d) ;
1539:
1540: hess=matrix(1,npar,1,npar);
1541:
1542: printf("\nCalculation of the hessian matrix. Wait...\n");
1543: fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
1544: for (i=1;i<=npar;i++){
1545: printf("%d",i);fflush(stdout);
1546: fprintf(ficlog,"%d",i);fflush(ficlog);
1547: hess[i][i]=hessii(p,ftolhess,i,delti);
1548: /*printf(" %f ",p[i]);*/
1549: /*printf(" %lf ",hess[i][i]);*/
1550: }
1551:
1552: for (i=1;i<=npar;i++) {
1553: for (j=1;j<=npar;j++) {
1554: if (j>i) {
1555: printf(".%d%d",i,j);fflush(stdout);
1556: fprintf(ficlog,".%d%d",i,j);fflush(ficlog);
1557: hess[i][j]=hessij(p,delti,i,j);
1558: hess[j][i]=hess[i][j];
1559: /*printf(" %lf ",hess[i][j]);*/
1560: }
1561: }
1562: }
1563: printf("\n");
1564: fprintf(ficlog,"\n");
1565:
1566: printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
1567: fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
1568:
1569: a=matrix(1,npar,1,npar);
1570: y=matrix(1,npar,1,npar);
1571: x=vector(1,npar);
1572: indx=ivector(1,npar);
1573: for (i=1;i<=npar;i++)
1574: for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
1575: ludcmp(a,npar,indx,&pd);
1576:
1577: for (j=1;j<=npar;j++) {
1578: for (i=1;i<=npar;i++) x[i]=0;
1579: x[j]=1;
1580: lubksb(a,npar,indx,x);
1581: for (i=1;i<=npar;i++){
1582: matcov[i][j]=x[i];
1583: }
1584: }
1585:
1586: printf("\n#Hessian matrix#\n");
1587: fprintf(ficlog,"\n#Hessian matrix#\n");
1588: for (i=1;i<=npar;i++) {
1589: for (j=1;j<=npar;j++) {
1590: printf("%.3e ",hess[i][j]);
1591: fprintf(ficlog,"%.3e ",hess[i][j]);
1592: }
1593: printf("\n");
1594: fprintf(ficlog,"\n");
1595: }
1596:
1597: /* Recompute Inverse */
1598: for (i=1;i<=npar;i++)
1599: for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];
1600: ludcmp(a,npar,indx,&pd);
1601:
1602: /* printf("\n#Hessian matrix recomputed#\n");
1603:
1604: for (j=1;j<=npar;j++) {
1605: for (i=1;i<=npar;i++) x[i]=0;
1606: x[j]=1;
1607: lubksb(a,npar,indx,x);
1608: for (i=1;i<=npar;i++){
1609: y[i][j]=x[i];
1610: printf("%.3e ",y[i][j]);
1611: fprintf(ficlog,"%.3e ",y[i][j]);
1612: }
1613: printf("\n");
1614: fprintf(ficlog,"\n");
1615: }
1616: */
1617:
1618: free_matrix(a,1,npar,1,npar);
1619: free_matrix(y,1,npar,1,npar);
1620: free_vector(x,1,npar);
1621: free_ivector(indx,1,npar);
1622: free_matrix(hess,1,npar,1,npar);
1623:
1624:
1625: }
1626:
1627: /*************** hessian matrix ****************/
1628: double hessii( double x[], double delta, int theta, double delti[])
1629: {
1630: int i;
1631: int l=1, lmax=20;
1632: double k1,k2;
1633: double p2[NPARMAX+1];
1634: double res;
1635: double delt, delts, nkhi=10.,nkhif=1., khi=1.e-4;
1636: double fx;
1637: int k=0,kmax=10;
1638: double l1;
1639:
1640: fx=func(x);
1641: for (i=1;i<=npar;i++) p2[i]=x[i];
1642: for(l=0 ; l <=lmax; l++){
1643: l1=pow(10,l);
1644: delts=delt;
1645: for(k=1 ; k <kmax; k=k+1){
1646: delt = delta*(l1*k);
1647: p2[theta]=x[theta] +delt;
1648: k1=func(p2)-fx;
1649: p2[theta]=x[theta]-delt;
1650: k2=func(p2)-fx;
1651: /*res= (k1-2.0*fx+k2)/delt/delt; */
1652: res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */
1653:
1654: #ifdef DEBUG
1655: 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);
1656: 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);
1657: #endif
1658: /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
1659: if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
1660: k=kmax;
1661: }
1662: else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
1663: k=kmax; l=lmax*10.;
1664: }
1665: else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){
1666: delts=delt;
1667: }
1668: }
1669: }
1670: delti[theta]=delts;
1671: return res;
1672:
1673: }
1674:
1675: double hessij( double x[], double delti[], int thetai,int thetaj)
1676: {
1677: int i;
1678: int l=1, l1, lmax=20;
1679: double k1,k2,k3,k4,res,fx;
1680: double p2[NPARMAX+1];
1681: int k;
1682:
1683: fx=func(x);
1684: for (k=1; k<=2; k++) {
1685: for (i=1;i<=npar;i++) p2[i]=x[i];
1686: p2[thetai]=x[thetai]+delti[thetai]/k;
1687: p2[thetaj]=x[thetaj]+delti[thetaj]/k;
1688: k1=func(p2)-fx;
1689:
1690: p2[thetai]=x[thetai]+delti[thetai]/k;
1691: p2[thetaj]=x[thetaj]-delti[thetaj]/k;
1692: k2=func(p2)-fx;
1693:
1694: p2[thetai]=x[thetai]-delti[thetai]/k;
1695: p2[thetaj]=x[thetaj]+delti[thetaj]/k;
1696: k3=func(p2)-fx;
1697:
1698: p2[thetai]=x[thetai]-delti[thetai]/k;
1699: p2[thetaj]=x[thetaj]-delti[thetaj]/k;
1700: k4=func(p2)-fx;
1701: res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */
1702: #ifdef DEBUG
1703: 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);
1704: 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);
1705: #endif
1706: }
1707: return res;
1708: }
1709:
1710: /************** Inverse of matrix **************/
1711: void ludcmp(double **a, int n, int *indx, double *d)
1712: {
1713: int i,imax,j,k;
1714: double big,dum,sum,temp;
1715: double *vv;
1716:
1717: vv=vector(1,n);
1718: *d=1.0;
1719: for (i=1;i<=n;i++) {
1720: big=0.0;
1721: for (j=1;j<=n;j++)
1722: if ((temp=fabs(a[i][j])) > big) big=temp;
1723: if (big == 0.0) nrerror("Singular matrix in routine ludcmp");
1724: vv[i]=1.0/big;
1725: }
1726: for (j=1;j<=n;j++) {
1727: for (i=1;i<j;i++) {
1728: sum=a[i][j];
1729: for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];
1730: a[i][j]=sum;
1731: }
1732: big=0.0;
1733: for (i=j;i<=n;i++) {
1734: sum=a[i][j];
1735: for (k=1;k<j;k++)
1736: sum -= a[i][k]*a[k][j];
1737: a[i][j]=sum;
1738: if ( (dum=vv[i]*fabs(sum)) >= big) {
1739: big=dum;
1740: imax=i;
1741: }
1742: }
1743: if (j != imax) {
1744: for (k=1;k<=n;k++) {
1745: dum=a[imax][k];
1746: a[imax][k]=a[j][k];
1747: a[j][k]=dum;
1748: }
1749: *d = -(*d);
1750: vv[imax]=vv[j];
1751: }
1752: indx[j]=imax;
1753: if (a[j][j] == 0.0) a[j][j]=TINY;
1754: if (j != n) {
1755: dum=1.0/(a[j][j]);
1756: for (i=j+1;i<=n;i++) a[i][j] *= dum;
1757: }
1758: }
1759: free_vector(vv,1,n); /* Doesn't work */
1760: ;
1761: }
1762:
1763: void lubksb(double **a, int n, int *indx, double b[])
1764: {
1765: int i,ii=0,ip,j;
1766: double sum;
1767:
1768: for (i=1;i<=n;i++) {
1769: ip=indx[i];
1770: sum=b[ip];
1771: b[ip]=b[i];
1772: if (ii)
1773: for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];
1774: else if (sum) ii=i;
1775: b[i]=sum;
1776: }
1777: for (i=n;i>=1;i--) {
1778: sum=b[i];
1779: for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];
1780: b[i]=sum/a[i][i];
1781: }
1782: }
1783:
1784: /************ Frequencies ********************/
1.84 brouard 1785: 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 1786: { /* Some frequencies */
1787:
1788: int i, m, jk, k1,i1, j1, bool, z1,z2,j;
1789: int first;
1790: double ***freq; /* Frequencies */
1.73 lievre 1791: double *pp, **prop;
1792: double pos,posprop, k2, dateintsum=0,k2cpt=0;
1.53 brouard 1793: FILE *ficresp;
1794: char fileresp[FILENAMELENGTH];
1795:
1796: pp=vector(1,nlstate);
1.74 brouard 1797: prop=matrix(1,nlstate,iagemin,iagemax+3);
1.53 brouard 1798: strcpy(fileresp,"p");
1799: strcat(fileresp,fileres);
1800: if((ficresp=fopen(fileresp,"w"))==NULL) {
1801: printf("Problem with prevalence resultfile: %s\n", fileresp);
1802: fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
1803: exit(0);
1804: }
1.74 brouard 1805: freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);
1.53 brouard 1806: j1=0;
1807:
1808: j=cptcoveff;
1809: if (cptcovn<1) {j=1;ncodemax[1]=1;}
1810:
1811: first=1;
1812:
1813: for(k1=1; k1<=j;k1++){
1814: for(i1=1; i1<=ncodemax[k1];i1++){
1815: j1++;
1816: /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
1817: scanf("%d", i);*/
1818: for (i=-1; i<=nlstate+ndeath; i++)
1819: for (jk=-1; jk<=nlstate+ndeath; jk++)
1.74 brouard 1820: for(m=iagemin; m <= iagemax+3; m++)
1.53 brouard 1821: freq[i][jk][m]=0;
1.73 lievre 1822:
1823: for (i=1; i<=nlstate; i++)
1.74 brouard 1824: for(m=iagemin; m <= iagemax+3; m++)
1.73 lievre 1825: prop[i][m]=0;
1.53 brouard 1826:
1827: dateintsum=0;
1828: k2cpt=0;
1829: for (i=1; i<=imx; i++) {
1830: bool=1;
1831: if (cptcovn>0) {
1832: for (z1=1; z1<=cptcoveff; z1++)
1833: if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])
1834: bool=0;
1835: }
1.58 lievre 1836: if (bool==1){
1.53 brouard 1837: for(m=firstpass; m<=lastpass; m++){
1838: k2=anint[m][i]+(mint[m][i]/12.);
1.84 brouard 1839: /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/
1.74 brouard 1840: if(agev[m][i]==0) agev[m][i]=iagemax+1;
1841: if(agev[m][i]==1) agev[m][i]=iagemax+2;
1.73 lievre 1842: if (s[m][i]>0 && s[m][i]<=nlstate) prop[s[m][i]][(int)agev[m][i]] += weight[i];
1.53 brouard 1843: if (m<lastpass) {
1844: freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
1.74 brouard 1845: freq[s[m][i]][s[m+1][i]][iagemax+3] += weight[i];
1.53 brouard 1846: }
1847:
1.74 brouard 1848: if ((agev[m][i]>1) && (agev[m][i]< (iagemax+3))) {
1.53 brouard 1849: dateintsum=dateintsum+k2;
1850: k2cpt++;
1851: }
1.84 brouard 1852: /*}*/
1.53 brouard 1853: }
1854: }
1855: }
1856:
1.84 brouard 1857: /* fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
1.53 brouard 1858:
1859: if (cptcovn>0) {
1860: fprintf(ficresp, "\n#********** Variable ");
1861: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
1862: fprintf(ficresp, "**********\n#");
1863: }
1864: for(i=1; i<=nlstate;i++)
1865: fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
1866: fprintf(ficresp, "\n");
1867:
1.74 brouard 1868: for(i=iagemin; i <= iagemax+3; i++){
1869: if(i==iagemax+3){
1.53 brouard 1870: fprintf(ficlog,"Total");
1871: }else{
1872: if(first==1){
1873: first=0;
1874: printf("See log file for details...\n");
1875: }
1876: fprintf(ficlog,"Age %d", i);
1877: }
1878: for(jk=1; jk <=nlstate ; jk++){
1879: for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
1880: pp[jk] += freq[jk][m][i];
1881: }
1882: for(jk=1; jk <=nlstate ; jk++){
1883: for(m=-1, pos=0; m <=0 ; m++)
1884: pos += freq[jk][m][i];
1885: if(pp[jk]>=1.e-10){
1886: if(first==1){
1887: printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
1888: }
1889: fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
1890: }else{
1891: if(first==1)
1892: printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
1893: fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
1894: }
1895: }
1896:
1897: for(jk=1; jk <=nlstate ; jk++){
1898: for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
1899: pp[jk] += freq[jk][m][i];
1.73 lievre 1900: }
1901: for(jk=1,pos=0,posprop=0; jk <=nlstate ; jk++){
1902: pos += pp[jk];
1903: posprop += prop[jk][i];
1.53 brouard 1904: }
1905: for(jk=1; jk <=nlstate ; jk++){
1906: if(pos>=1.e-5){
1907: if(first==1)
1908: printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
1909: fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
1910: }else{
1911: if(first==1)
1912: printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
1913: fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
1914: }
1.74 brouard 1915: if( i <= iagemax){
1.53 brouard 1916: if(pos>=1.e-5){
1.73 lievre 1917: fprintf(ficresp," %d %.5f %.0f %.0f",i,prop[jk][i]/posprop, prop[jk][i],posprop);
1.84 brouard 1918: /*probs[i][jk][j1]= pp[jk]/pos;*/
1.53 brouard 1919: /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/
1920: }
1921: else
1.73 lievre 1922: fprintf(ficresp," %d NaNq %.0f %.0f",i,prop[jk][i],posprop);
1.53 brouard 1923: }
1924: }
1925:
1.69 brouard 1926: for(jk=-1; jk <=nlstate+ndeath; jk++)
1927: for(m=-1; m <=nlstate+ndeath; m++)
1.53 brouard 1928: if(freq[jk][m][i] !=0 ) {
1929: if(first==1)
1930: printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
1931: fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
1932: }
1.74 brouard 1933: if(i <= iagemax)
1.53 brouard 1934: fprintf(ficresp,"\n");
1935: if(first==1)
1936: printf("Others in log...\n");
1937: fprintf(ficlog,"\n");
1938: }
1939: }
1940: }
1941: dateintmean=dateintsum/k2cpt;
1942:
1943: fclose(ficresp);
1.74 brouard 1944: free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);
1.53 brouard 1945: free_vector(pp,1,nlstate);
1.74 brouard 1946: free_matrix(prop,1,nlstate,iagemin, iagemax+3);
1.53 brouard 1947: /* End of Freq */
1948: }
1949:
1950: /************ Prevalence ********************/
1.84 brouard 1951: 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 1952: {
1953: /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
1954: in each health status at the date of interview (if between dateprev1 and dateprev2).
1955: We still use firstpass and lastpass as another selection.
1956: */
1.53 brouard 1957:
1958: int i, m, jk, k1, i1, j1, bool, z1,z2,j;
1959: double ***freq; /* Frequencies */
1.73 lievre 1960: double *pp, **prop;
1961: double pos,posprop;
1.69 brouard 1962: double y2; /* in fractional years */
1.74 brouard 1963: int iagemin, iagemax;
1.53 brouard 1964:
1.74 brouard 1965: iagemin= (int) agemin;
1966: iagemax= (int) agemax;
1967: /*pp=vector(1,nlstate);*/
1968: prop=matrix(1,nlstate,iagemin,iagemax+3);
1969: /* freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
1.53 brouard 1970: j1=0;
1971:
1972: j=cptcoveff;
1973: if (cptcovn<1) {j=1;ncodemax[1]=1;}
1974:
1975: for(k1=1; k1<=j;k1++){
1976: for(i1=1; i1<=ncodemax[k1];i1++){
1977: j1++;
1978:
1.73 lievre 1979: for (i=1; i<=nlstate; i++)
1.74 brouard 1980: for(m=iagemin; m <= iagemax+3; m++)
1981: prop[i][m]=0.0;
1.53 brouard 1982:
1.69 brouard 1983: for (i=1; i<=imx; i++) { /* Each individual */
1.53 brouard 1984: bool=1;
1985: if (cptcovn>0) {
1986: for (z1=1; z1<=cptcoveff; z1++)
1987: if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])
1988: bool=0;
1989: }
1990: if (bool==1) {
1.69 brouard 1991: for(m=firstpass; m<=lastpass; m++){/* Other selection (we can limit to certain interviews*/
1992: y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
1993: if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
1.74 brouard 1994: if(agev[m][i]==0) agev[m][i]=iagemax+1;
1995: if(agev[m][i]==1) agev[m][i]=iagemax+2;
1996: 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);
1997: if (s[m][i]>0 && s[m][i]<=nlstate) {
1998: /*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]]);*/
1999: prop[s[m][i]][(int)agev[m][i]] += weight[i];
2000: prop[s[m][i]][iagemax+3] += weight[i];
2001: }
1.53 brouard 2002: }
1.69 brouard 2003: } /* end selection of waves */
1.53 brouard 2004: }
2005: }
1.74 brouard 2006: for(i=iagemin; i <= iagemax+3; i++){
1.53 brouard 2007:
1.74 brouard 2008: for(jk=1,posprop=0; jk <=nlstate ; jk++) {
2009: posprop += prop[jk][i];
2010: }
2011:
2012: for(jk=1; jk <=nlstate ; jk++){
2013: if( i <= iagemax){
2014: if(posprop>=1.e-5){
2015: probs[i][jk][j1]= prop[jk][i]/posprop;
2016: }
2017: }
2018: }/* end jk */
2019: }/* end i */
1.53 brouard 2020: } /* end i1 */
2021: } /* end k1 */
2022:
1.74 brouard 2023: /* free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
2024: /*free_vector(pp,1,nlstate);*/
2025: free_matrix(prop,1,nlstate, iagemin,iagemax+3);
2026: } /* End of prevalence */
1.53 brouard 2027:
2028: /************* Waves Concatenation ***************/
2029:
1.59 brouard 2030: 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 2031: {
2032: /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
2033: Death is a valid wave (if date is known).
2034: mw[mi][i] is the mi (mi=1 to wav[i]) effective wave of individual i
1.59 brouard 2035: dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
1.53 brouard 2036: and mw[mi+1][i]. dh depends on stepm.
2037: */
2038:
2039: int i, mi, m;
2040: /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
2041: double sum=0., jmean=0.;*/
2042: int first;
2043: int j, k=0,jk, ju, jl;
2044: double sum=0.;
2045: first=0;
2046: jmin=1e+5;
2047: jmax=-1;
2048: jmean=0.;
2049: for(i=1; i<=imx; i++){
2050: mi=0;
2051: m=firstpass;
2052: while(s[m][i] <= nlstate){
1.69 brouard 2053: if(s[m][i]>=1)
1.53 brouard 2054: mw[++mi][i]=m;
2055: if(m >=lastpass)
2056: break;
2057: else
2058: m++;
2059: }/* end while */
2060: if (s[m][i] > nlstate){
2061: mi++; /* Death is another wave */
2062: /* if(mi==0) never been interviewed correctly before death */
2063: /* Only death is a correct wave */
2064: mw[mi][i]=m;
2065: }
2066:
2067: wav[i]=mi;
2068: if(mi==0){
1.91 brouard 2069: nbwarn++;
1.53 brouard 2070: if(first==0){
1.85 brouard 2071: printf("Warning! None valid information for:%ld line=%d (skipped) and may be others, see log file\n",num[i],i);
1.53 brouard 2072: first=1;
2073: }
2074: if(first==1){
1.85 brouard 2075: fprintf(ficlog,"Warning! None valid information for:%ld line=%d (skipped)\n",num[i],i);
1.53 brouard 2076: }
2077: } /* end mi==0 */
1.77 brouard 2078: } /* End individuals */
1.53 brouard 2079:
2080: for(i=1; i<=imx; i++){
2081: for(mi=1; mi<wav[i];mi++){
2082: if (stepm <=0)
2083: dh[mi][i]=1;
2084: else{
1.77 brouard 2085: if (s[mw[mi+1][i]][i] > nlstate) { /* A death */
1.53 brouard 2086: if (agedc[i] < 2*AGESUP) {
1.85 brouard 2087: j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);
2088: if(j==0) j=1; /* Survives at least one month after exam */
2089: else if(j<0){
1.91 brouard 2090: nberr++;
1.85 brouard 2091: 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 2092: j=1; /* Temporary Dangerous patch */
1.86 brouard 2093: 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 2094: 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 2095: 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);
2096: }
2097: k=k+1;
2098: if (j >= jmax) jmax=j;
2099: if (j <= jmin) jmin=j;
2100: sum=sum+j;
2101: /*if (j<0) printf("j=%d num=%d \n",j,i);*/
2102: /* printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
1.53 brouard 2103: }
2104: }
2105: else{
2106: j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
1.68 lievre 2107: /* printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
1.53 brouard 2108: k=k+1;
2109: if (j >= jmax) jmax=j;
2110: else if (j <= jmin)jmin=j;
2111: /* if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
1.73 lievre 2112: /*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 2113: if(j<0){
1.91 brouard 2114: nberr++;
1.85 brouard 2115: 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]);
2116: 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]);
2117: }
1.53 brouard 2118: sum=sum+j;
2119: }
2120: jk= j/stepm;
2121: jl= j -jk*stepm;
2122: ju= j -(jk+1)*stepm;
1.85 brouard 2123: if(mle <=1){ /* only if we use a the linear-interpoloation pseudo-likelihood */
1.64 lievre 2124: if(jl==0){
2125: dh[mi][i]=jk;
2126: bh[mi][i]=0;
2127: }else{ /* We want a negative bias in order to only have interpolation ie
2128: * at the price of an extra matrix product in likelihood */
2129: dh[mi][i]=jk+1;
2130: bh[mi][i]=ju;
2131: }
2132: }else{
2133: if(jl <= -ju){
2134: dh[mi][i]=jk;
2135: bh[mi][i]=jl; /* bias is positive if real duration
2136: * is higher than the multiple of stepm and negative otherwise.
2137: */
2138: }
2139: else{
2140: dh[mi][i]=jk+1;
2141: bh[mi][i]=ju;
2142: }
2143: if(dh[mi][i]==0){
2144: dh[mi][i]=1; /* At least one step */
2145: bh[mi][i]=ju; /* At least one step */
1.71 brouard 2146: /* 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 2147: }
1.85 brouard 2148: } /* end if mle */
2149: }
1.64 lievre 2150: } /* end wave */
1.53 brouard 2151: }
2152: jmean=sum/k;
2153: printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);
2154: fprintf(ficlog,"Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);
2155: }
2156:
2157: /*********** Tricode ****************************/
2158: void tricode(int *Tvar, int **nbcode, int imx)
2159: {
1.58 lievre 2160:
2161: int Ndum[20],ij=1, k, j, i, maxncov=19;
1.53 brouard 2162: int cptcode=0;
2163: cptcoveff=0;
2164:
1.58 lievre 2165: for (k=0; k<maxncov; k++) Ndum[k]=0;
1.53 brouard 2166: for (k=1; k<=7; k++) ncodemax[k]=0;
2167:
2168: for (j=1; j<=(cptcovn+2*cptcovprod); j++) {
1.58 lievre 2169: for (i=1; i<=imx; i++) { /*reads the data file to get the maximum
2170: modality*/
2171: ij=(int)(covar[Tvar[j]][i]); /* ij is the modality of this individual*/
2172: Ndum[ij]++; /*store the modality */
1.53 brouard 2173: /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
1.58 lievre 2174: if (ij > cptcode) cptcode=ij; /* getting the maximum of covariable
2175: Tvar[j]. If V=sex and male is 0 and
2176: female is 1, then cptcode=1.*/
1.53 brouard 2177: }
2178:
2179: for (i=0; i<=cptcode; i++) {
1.58 lievre 2180: 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 2181: }
1.58 lievre 2182:
1.53 brouard 2183: ij=1;
2184: for (i=1; i<=ncodemax[j]; i++) {
1.58 lievre 2185: for (k=0; k<= maxncov; k++) {
1.53 brouard 2186: if (Ndum[k] != 0) {
2187: nbcode[Tvar[j]][ij]=k;
1.58 lievre 2188: /* 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 2189:
2190: ij++;
2191: }
2192: if (ij > ncodemax[j]) break;
2193: }
2194: }
2195: }
2196:
1.58 lievre 2197: for (k=0; k< maxncov; k++) Ndum[k]=0;
1.53 brouard 2198:
1.58 lievre 2199: for (i=1; i<=ncovmodel-2; i++) {
2200: /* 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 2201: ij=Tvar[i];
1.58 lievre 2202: Ndum[ij]++;
1.53 brouard 2203: }
2204:
2205: ij=1;
1.58 lievre 2206: for (i=1; i<= maxncov; i++) {
1.53 brouard 2207: if((Ndum[i]!=0) && (i<=ncovcol)){
1.58 lievre 2208: Tvaraff[ij]=i; /*For printing */
1.53 brouard 2209: ij++;
2210: }
2211: }
2212:
1.58 lievre 2213: cptcoveff=ij-1; /*Number of simple covariates*/
1.53 brouard 2214: }
2215:
2216: /*********** Health Expectancies ****************/
2217:
2218: 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 )
2219:
2220: {
2221: /* Health expectancies */
2222: int i, j, nhstepm, hstepm, h, nstepm, k, cptj;
2223: double age, agelim, hf;
2224: double ***p3mat,***varhe;
2225: double **dnewm,**doldm;
2226: double *xp;
2227: double **gp, **gm;
2228: double ***gradg, ***trgradg;
2229: int theta;
2230:
1.74 brouard 2231: varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage);
1.53 brouard 2232: xp=vector(1,npar);
1.74 brouard 2233: dnewm=matrix(1,nlstate*nlstate,1,npar);
2234: doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate);
1.53 brouard 2235:
2236: fprintf(ficreseij,"# Health expectancies\n");
2237: fprintf(ficreseij,"# Age");
2238: for(i=1; i<=nlstate;i++)
2239: for(j=1; j<=nlstate;j++)
2240: fprintf(ficreseij," %1d-%1d (SE)",i,j);
2241: fprintf(ficreseij,"\n");
2242:
2243: if(estepm < stepm){
2244: printf ("Problem %d lower than %d\n",estepm, stepm);
2245: }
2246: else hstepm=estepm;
2247: /* We compute the life expectancy from trapezoids spaced every estepm months
2248: * This is mainly to measure the difference between two models: for example
2249: * if stepm=24 months pijx are given only every 2 years and by summing them
2250: * we are calculating an estimate of the Life Expectancy assuming a linear
1.66 brouard 2251: * progression in between and thus overestimating or underestimating according
1.53 brouard 2252: * to the curvature of the survival function. If, for the same date, we
2253: * estimate the model with stepm=1 month, we can keep estepm to 24 months
2254: * to compare the new estimate of Life expectancy with the same linear
2255: * hypothesis. A more precise result, taking into account a more precise
2256: * curvature will be obtained if estepm is as small as stepm. */
2257:
2258: /* For example we decided to compute the life expectancy with the smallest unit */
2259: /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
2260: nhstepm is the number of hstepm from age to agelim
2261: nstepm is the number of stepm from age to agelin.
2262: Look at hpijx to understand the reason of that which relies in memory size
2263: and note for a fixed period like estepm months */
2264: /* We decided (b) to get a life expectancy respecting the most precise curvature of the
2265: survival function given by stepm (the optimization length). Unfortunately it
2266: means that if the survival funtion is printed only each two years of age and if
2267: you sum them up and add 1 year (area under the trapezoids) you won't get the same
2268: results. So we changed our mind and took the option of the best precision.
2269: */
2270: hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
2271:
2272: agelim=AGESUP;
2273: for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
2274: /* nhstepm age range expressed in number of stepm */
2275: nstepm=(int) rint((agelim-age)*YEARM/stepm);
2276: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
2277: /* if (stepm >= YEARM) hstepm=1;*/
2278: nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
2279: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
1.74 brouard 2280: gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);
2281: gp=matrix(0,nhstepm,1,nlstate*nlstate);
2282: gm=matrix(0,nhstepm,1,nlstate*nlstate);
1.53 brouard 2283:
2284: /* Computed by stepm unit matrices, product of hstepm matrices, stored
2285: in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
2286: hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);
2287:
2288:
2289: hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
2290:
2291: /* Computing Variances of health expectancies */
2292:
2293: for(theta=1; theta <=npar; theta++){
2294: for(i=1; i<=npar; i++){
2295: xp[i] = x[i] + (i==theta ?delti[theta]:0);
2296: }
2297: hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
2298:
2299: cptj=0;
2300: for(j=1; j<= nlstate; j++){
2301: for(i=1; i<=nlstate; i++){
2302: cptj=cptj+1;
2303: for(h=0, gp[h][cptj]=0.; h<=nhstepm-1; h++){
2304: gp[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;
2305: }
2306: }
2307: }
2308:
2309:
2310: for(i=1; i<=npar; i++)
2311: xp[i] = x[i] - (i==theta ?delti[theta]:0);
2312: hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
2313:
2314: cptj=0;
2315: for(j=1; j<= nlstate; j++){
2316: for(i=1;i<=nlstate;i++){
2317: cptj=cptj+1;
2318: for(h=0, gm[h][cptj]=0.; h<=nhstepm-1; h++){
1.77 brouard 2319:
1.53 brouard 2320: gm[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;
2321: }
2322: }
2323: }
1.74 brouard 2324: for(j=1; j<= nlstate*nlstate; j++)
1.53 brouard 2325: for(h=0; h<=nhstepm-1; h++){
2326: gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
2327: }
2328: }
2329:
2330: /* End theta */
2331:
1.74 brouard 2332: trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar);
1.53 brouard 2333:
2334: for(h=0; h<=nhstepm-1; h++)
1.74 brouard 2335: for(j=1; j<=nlstate*nlstate;j++)
1.53 brouard 2336: for(theta=1; theta <=npar; theta++)
2337: trgradg[h][j][theta]=gradg[h][theta][j];
2338:
2339:
1.74 brouard 2340: for(i=1;i<=nlstate*nlstate;i++)
2341: for(j=1;j<=nlstate*nlstate;j++)
1.53 brouard 2342: varhe[i][j][(int)age] =0.;
2343:
2344: printf("%d|",(int)age);fflush(stdout);
2345: fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
2346: for(h=0;h<=nhstepm-1;h++){
2347: for(k=0;k<=nhstepm-1;k++){
1.74 brouard 2348: matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov);
2349: matprod2(doldm,dnewm,1,nlstate*nlstate,1,npar,1,nlstate*nlstate,gradg[k]);
2350: for(i=1;i<=nlstate*nlstate;i++)
2351: for(j=1;j<=nlstate*nlstate;j++)
1.53 brouard 2352: varhe[i][j][(int)age] += doldm[i][j]*hf*hf;
2353: }
2354: }
2355: /* Computing expectancies */
2356: for(i=1; i<=nlstate;i++)
2357: for(j=1; j<=nlstate;j++)
2358: for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
2359: eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
2360:
2361: /* 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]);*/
2362:
2363: }
2364:
2365: fprintf(ficreseij,"%3.0f",age );
2366: cptj=0;
2367: for(i=1; i<=nlstate;i++)
2368: for(j=1; j<=nlstate;j++){
2369: cptj++;
2370: fprintf(ficreseij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[cptj][cptj][(int)age]) );
2371: }
2372: fprintf(ficreseij,"\n");
2373:
1.74 brouard 2374: free_matrix(gm,0,nhstepm,1,nlstate*nlstate);
2375: free_matrix(gp,0,nhstepm,1,nlstate*nlstate);
2376: free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*nlstate);
2377: free_ma3x(trgradg,0,nhstepm,1,nlstate*nlstate,1,npar);
1.53 brouard 2378: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
2379: }
2380: printf("\n");
2381: fprintf(ficlog,"\n");
2382:
2383: free_vector(xp,1,npar);
1.74 brouard 2384: free_matrix(dnewm,1,nlstate*nlstate,1,npar);
2385: free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate);
2386: free_ma3x(varhe,1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int)fage);
1.53 brouard 2387: }
2388:
2389: /************ Variance ******************/
2390: 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)
2391: {
2392: /* Variance of health expectancies */
2393: /* double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
2394: /* double **newm;*/
2395: double **dnewm,**doldm;
2396: double **dnewmp,**doldmp;
2397: int i, j, nhstepm, hstepm, h, nstepm ;
2398: int k, cptcode;
2399: double *xp;
2400: double **gp, **gm; /* for var eij */
2401: double ***gradg, ***trgradg; /*for var eij */
2402: double **gradgp, **trgradgp; /* for var p point j */
2403: double *gpp, *gmp; /* for var p point j */
2404: double **varppt; /* for var p point j nlstate to nlstate+ndeath */
2405: double ***p3mat;
2406: double age,agelim, hf;
2407: double ***mobaverage;
2408: int theta;
2409: char digit[4];
1.55 lievre 2410: char digitp[25];
1.53 brouard 2411:
2412: char fileresprobmorprev[FILENAMELENGTH];
2413:
1.55 lievre 2414: if(popbased==1){
1.58 lievre 2415: if(mobilav!=0)
1.55 lievre 2416: strcpy(digitp,"-populbased-mobilav-");
2417: else strcpy(digitp,"-populbased-nomobil-");
2418: }
2419: else
1.53 brouard 2420: strcpy(digitp,"-stablbased-");
1.56 lievre 2421:
1.54 brouard 2422: if (mobilav!=0) {
1.53 brouard 2423: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
1.54 brouard 2424: if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
2425: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
2426: printf(" Error in movingaverage mobilav=%d\n",mobilav);
2427: }
1.53 brouard 2428: }
2429:
2430: strcpy(fileresprobmorprev,"prmorprev");
2431: sprintf(digit,"%-d",ij);
2432: /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
2433: strcat(fileresprobmorprev,digit); /* Tvar to be done */
2434: strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
2435: strcat(fileresprobmorprev,fileres);
2436: if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
2437: printf("Problem with resultfile: %s\n", fileresprobmorprev);
2438: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
2439: }
2440: printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
2441: fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
1.66 brouard 2442: 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 2443: fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
2444: for(j=nlstate+1; j<=(nlstate+ndeath);j++){
2445: fprintf(ficresprobmorprev," p.%-d SE",j);
2446: for(i=1; i<=nlstate;i++)
2447: fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
2448: }
2449: fprintf(ficresprobmorprev,"\n");
1.88 brouard 2450: fprintf(ficgp,"\n# Routine varevsij");
1.87 brouard 2451: 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");
2452: fprintf(fichtm,"\n<br>%s <br>\n",digitp);
2453: /* } */
1.53 brouard 2454: varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
2455:
2456: 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");
2457: fprintf(ficresvij,"# Age");
2458: for(i=1; i<=nlstate;i++)
2459: for(j=1; j<=nlstate;j++)
2460: fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);
2461: fprintf(ficresvij,"\n");
2462:
2463: xp=vector(1,npar);
2464: dnewm=matrix(1,nlstate,1,npar);
2465: doldm=matrix(1,nlstate,1,nlstate);
2466: dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
2467: doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
2468:
2469: gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
2470: gpp=vector(nlstate+1,nlstate+ndeath);
2471: gmp=vector(nlstate+1,nlstate+ndeath);
2472: trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
2473:
2474: if(estepm < stepm){
2475: printf ("Problem %d lower than %d\n",estepm, stepm);
2476: }
2477: else hstepm=estepm;
2478: /* For example we decided to compute the life expectancy with the smallest unit */
2479: /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
2480: nhstepm is the number of hstepm from age to agelim
2481: nstepm is the number of stepm from age to agelin.
2482: Look at hpijx to understand the reason of that which relies in memory size
2483: and note for a fixed period like k years */
2484: /* We decided (b) to get a life expectancy respecting the most precise curvature of the
2485: survival function given by stepm (the optimization length). Unfortunately it
1.66 brouard 2486: means that if the survival funtion is printed every two years of age and if
1.53 brouard 2487: you sum them up and add 1 year (area under the trapezoids) you won't get the same
2488: results. So we changed our mind and took the option of the best precision.
2489: */
2490: hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
2491: agelim = AGESUP;
2492: for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
2493: nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
2494: nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
2495: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
2496: gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
2497: gp=matrix(0,nhstepm,1,nlstate);
2498: gm=matrix(0,nhstepm,1,nlstate);
2499:
2500:
2501: for(theta=1; theta <=npar; theta++){
1.66 brouard 2502: for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
1.53 brouard 2503: xp[i] = x[i] + (i==theta ?delti[theta]:0);
2504: }
2505: hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
2506: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
2507:
2508: if (popbased==1) {
1.54 brouard 2509: if(mobilav ==0){
1.53 brouard 2510: for(i=1; i<=nlstate;i++)
2511: prlim[i][i]=probs[(int)age][i][ij];
1.54 brouard 2512: }else{ /* mobilav */
1.53 brouard 2513: for(i=1; i<=nlstate;i++)
2514: prlim[i][i]=mobaverage[(int)age][i][ij];
2515: }
2516: }
2517:
2518: for(j=1; j<= nlstate; j++){
2519: for(h=0; h<=nhstepm; h++){
2520: for(i=1, gp[h][j]=0.;i<=nlstate;i++)
2521: gp[h][j] += prlim[i][i]*p3mat[i][j][h];
2522: }
2523: }
1.66 brouard 2524: /* This for computing probability of death (h=1 means
2525: computed over hstepm matrices product = hstepm*stepm months)
2526: as a weighted average of prlim.
2527: */
1.69 brouard 2528: for(j=nlstate+1;j<=nlstate+ndeath;j++){
1.68 lievre 2529: for(i=1,gpp[j]=0.; i<= nlstate; i++)
1.53 brouard 2530: gpp[j] += prlim[i][i]*p3mat[i][j][1];
2531: }
1.66 brouard 2532: /* end probability of death */
1.53 brouard 2533:
1.66 brouard 2534: for(i=1; i<=npar; i++) /* Computes gradient x - delta */
1.53 brouard 2535: xp[i] = x[i] - (i==theta ?delti[theta]:0);
2536: hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
2537: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
2538:
2539: if (popbased==1) {
1.54 brouard 2540: if(mobilav ==0){
1.53 brouard 2541: for(i=1; i<=nlstate;i++)
2542: prlim[i][i]=probs[(int)age][i][ij];
1.54 brouard 2543: }else{ /* mobilav */
1.53 brouard 2544: for(i=1; i<=nlstate;i++)
2545: prlim[i][i]=mobaverage[(int)age][i][ij];
2546: }
2547: }
2548:
2549: for(j=1; j<= nlstate; j++){
2550: for(h=0; h<=nhstepm; h++){
2551: for(i=1, gm[h][j]=0.;i<=nlstate;i++)
2552: gm[h][j] += prlim[i][i]*p3mat[i][j][h];
2553: }
2554: }
1.66 brouard 2555: /* This for computing probability of death (h=1 means
2556: computed over hstepm matrices product = hstepm*stepm months)
2557: as a weighted average of prlim.
2558: */
1.69 brouard 2559: for(j=nlstate+1;j<=nlstate+ndeath;j++){
1.68 lievre 2560: for(i=1,gmp[j]=0.; i<= nlstate; i++)
2561: gmp[j] += prlim[i][i]*p3mat[i][j][1];
1.53 brouard 2562: }
1.66 brouard 2563: /* end probability of death */
1.53 brouard 2564:
2565: for(j=1; j<= nlstate; j++) /* vareij */
2566: for(h=0; h<=nhstepm; h++){
2567: gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
2568: }
1.68 lievre 2569:
1.53 brouard 2570: for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
2571: gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
2572: }
2573:
2574: } /* End theta */
2575:
2576: trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
2577:
2578: for(h=0; h<=nhstepm; h++) /* veij */
2579: for(j=1; j<=nlstate;j++)
2580: for(theta=1; theta <=npar; theta++)
2581: trgradg[h][j][theta]=gradg[h][theta][j];
2582:
2583: for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
1.69 brouard 2584: for(theta=1; theta <=npar; theta++)
1.53 brouard 2585: trgradgp[j][theta]=gradgp[theta][j];
1.69 brouard 2586:
1.53 brouard 2587:
2588: hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
2589: for(i=1;i<=nlstate;i++)
2590: for(j=1;j<=nlstate;j++)
2591: vareij[i][j][(int)age] =0.;
2592:
2593: for(h=0;h<=nhstepm;h++){
2594: for(k=0;k<=nhstepm;k++){
2595: matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
2596: matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
2597: for(i=1;i<=nlstate;i++)
2598: for(j=1;j<=nlstate;j++)
2599: vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
2600: }
2601: }
1.70 brouard 2602:
1.53 brouard 2603: /* pptj */
2604: matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
2605: matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
1.70 brouard 2606: for(j=nlstate+1;j<=nlstate+ndeath;j++)
2607: for(i=nlstate+1;i<=nlstate+ndeath;i++)
1.53 brouard 2608: varppt[j][i]=doldmp[j][i];
2609: /* end ppptj */
1.66 brouard 2610: /* x centered again */
1.53 brouard 2611: hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);
2612: prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);
2613:
2614: if (popbased==1) {
1.54 brouard 2615: if(mobilav ==0){
1.53 brouard 2616: for(i=1; i<=nlstate;i++)
2617: prlim[i][i]=probs[(int)age][i][ij];
1.54 brouard 2618: }else{ /* mobilav */
1.53 brouard 2619: for(i=1; i<=nlstate;i++)
2620: prlim[i][i]=mobaverage[(int)age][i][ij];
2621: }
2622: }
1.70 brouard 2623:
1.66 brouard 2624: /* This for computing probability of death (h=1 means
2625: computed over hstepm (estepm) matrices product = hstepm*stepm months)
2626: as a weighted average of prlim.
2627: */
1.68 lievre 2628: for(j=nlstate+1;j<=nlstate+ndeath;j++){
2629: for(i=1,gmp[j]=0.;i<= nlstate; i++)
1.53 brouard 2630: gmp[j] += prlim[i][i]*p3mat[i][j][1];
2631: }
1.66 brouard 2632: /* end probability of death */
1.53 brouard 2633:
2634: fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
2635: for(j=nlstate+1; j<=(nlstate+ndeath);j++){
2636: fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
2637: for(i=1; i<=nlstate;i++){
2638: fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
2639: }
2640: }
2641: fprintf(ficresprobmorprev,"\n");
2642:
2643: fprintf(ficresvij,"%.0f ",age );
2644: for(i=1; i<=nlstate;i++)
2645: for(j=1; j<=nlstate;j++){
2646: fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
2647: }
2648: fprintf(ficresvij,"\n");
2649: free_matrix(gp,0,nhstepm,1,nlstate);
2650: free_matrix(gm,0,nhstepm,1,nlstate);
2651: free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
2652: free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
2653: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
2654: } /* End age */
2655: free_vector(gpp,nlstate+1,nlstate+ndeath);
2656: free_vector(gmp,nlstate+1,nlstate+ndeath);
2657: free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
2658: free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
2659: fprintf(ficgp,"\nset noparametric;set nolabel; set ter png small;set size 0.65, 0.65");
2660: /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */
2661: fprintf(ficgp,"\n set log y; set nolog x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
1.67 brouard 2662: /* fprintf(ficgp,"\n plot \"%s\" u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm); */
2663: /* fprintf(ficgp,"\n replot \"%s\" u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm); */
2664: /* fprintf(ficgp,"\n replot \"%s\" u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm); */
1.88 brouard 2665: fprintf(ficgp,"\n plot \"%s\" u 1:($3) not w l 1 ",subdirf(fileresprobmorprev));
2666: fprintf(ficgp,"\n replot \"%s\" u 1:(($3+1.96*$4)) t \"95\%% interval\" w l 2 ",subdirf(fileresprobmorprev));
2667: fprintf(ficgp,"\n replot \"%s\" u 1:(($3-1.96*$4)) not w l 2 ",subdirf(fileresprobmorprev));
2668: fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",subdirf(fileresprobmorprev),subdirf(fileresprobmorprev));
2669: 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 2670: /* 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);
2671: */
1.88 brouard 2672: /* fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.png\";replot;",digitp,optionfilefiname,digit); */
1.89 brouard 2673: fprintf(ficgp,"\nset out \"%s%s.png\";replot;\n",subdirf3(optionfilefiname,"varmuptjgr",digitp),digit);
1.53 brouard 2674:
2675: free_vector(xp,1,npar);
2676: free_matrix(doldm,1,nlstate,1,nlstate);
2677: free_matrix(dnewm,1,nlstate,1,npar);
2678: free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
2679: free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
2680: free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
1.55 lievre 2681: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
1.53 brouard 2682: fclose(ficresprobmorprev);
1.88 brouard 2683: fflush(ficgp);
2684: fflush(fichtm);
1.84 brouard 2685: } /* end varevsij */
1.53 brouard 2686:
2687: /************ Variance of prevlim ******************/
2688: 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)
2689: {
2690: /* Variance of prevalence limit */
1.59 brouard 2691: /* double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
1.53 brouard 2692: double **newm;
2693: double **dnewm,**doldm;
2694: int i, j, nhstepm, hstepm;
2695: int k, cptcode;
2696: double *xp;
2697: double *gp, *gm;
2698: double **gradg, **trgradg;
2699: double age,agelim;
2700: int theta;
2701:
1.54 brouard 2702: fprintf(ficresvpl,"# Standard deviation of stable prevalences \n");
1.53 brouard 2703: fprintf(ficresvpl,"# Age");
2704: for(i=1; i<=nlstate;i++)
2705: fprintf(ficresvpl," %1d-%1d",i,i);
2706: fprintf(ficresvpl,"\n");
2707:
2708: xp=vector(1,npar);
2709: dnewm=matrix(1,nlstate,1,npar);
2710: doldm=matrix(1,nlstate,1,nlstate);
2711:
2712: hstepm=1*YEARM; /* Every year of age */
2713: hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */
2714: agelim = AGESUP;
2715: for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
2716: nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
2717: if (stepm >= YEARM) hstepm=1;
2718: nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
2719: gradg=matrix(1,npar,1,nlstate);
2720: gp=vector(1,nlstate);
2721: gm=vector(1,nlstate);
2722:
2723: for(theta=1; theta <=npar; theta++){
2724: for(i=1; i<=npar; i++){ /* Computes gradient */
2725: xp[i] = x[i] + (i==theta ?delti[theta]:0);
2726: }
2727: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
2728: for(i=1;i<=nlstate;i++)
2729: gp[i] = prlim[i][i];
2730:
2731: for(i=1; i<=npar; i++) /* Computes gradient */
2732: xp[i] = x[i] - (i==theta ?delti[theta]:0);
2733: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
2734: for(i=1;i<=nlstate;i++)
2735: gm[i] = prlim[i][i];
2736:
2737: for(i=1;i<=nlstate;i++)
2738: gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
2739: } /* End theta */
2740:
2741: trgradg =matrix(1,nlstate,1,npar);
2742:
2743: for(j=1; j<=nlstate;j++)
2744: for(theta=1; theta <=npar; theta++)
2745: trgradg[j][theta]=gradg[theta][j];
2746:
2747: for(i=1;i<=nlstate;i++)
2748: varpl[i][(int)age] =0.;
2749: matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
2750: matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
2751: for(i=1;i<=nlstate;i++)
2752: varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
2753:
2754: fprintf(ficresvpl,"%.0f ",age );
2755: for(i=1; i<=nlstate;i++)
2756: fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
2757: fprintf(ficresvpl,"\n");
2758: free_vector(gp,1,nlstate);
2759: free_vector(gm,1,nlstate);
2760: free_matrix(gradg,1,npar,1,nlstate);
2761: free_matrix(trgradg,1,nlstate,1,npar);
2762: } /* End age */
2763:
2764: free_vector(xp,1,npar);
2765: free_matrix(doldm,1,nlstate,1,npar);
2766: free_matrix(dnewm,1,nlstate,1,nlstate);
2767:
2768: }
2769:
2770: /************ Variance of one-step probabilities ******************/
2771: void varprob(char optionfilefiname[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij, int *Tvar, int **nbcode, int *ncodemax)
2772: {
2773: int i, j=0, i1, k1, l1, t, tj;
2774: int k2, l2, j1, z1;
2775: int k=0,l, cptcode;
2776: int first=1, first1;
2777: double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
2778: double **dnewm,**doldm;
2779: double *xp;
2780: double *gp, *gm;
2781: double **gradg, **trgradg;
2782: double **mu;
2783: double age,agelim, cov[NCOVMAX];
2784: double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
2785: int theta;
2786: char fileresprob[FILENAMELENGTH];
2787: char fileresprobcov[FILENAMELENGTH];
2788: char fileresprobcor[FILENAMELENGTH];
2789:
2790: double ***varpij;
2791:
2792: strcpy(fileresprob,"prob");
2793: strcat(fileresprob,fileres);
2794: if((ficresprob=fopen(fileresprob,"w"))==NULL) {
2795: printf("Problem with resultfile: %s\n", fileresprob);
2796: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
2797: }
2798: strcpy(fileresprobcov,"probcov");
2799: strcat(fileresprobcov,fileres);
2800: if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
2801: printf("Problem with resultfile: %s\n", fileresprobcov);
2802: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
2803: }
2804: strcpy(fileresprobcor,"probcor");
2805: strcat(fileresprobcor,fileres);
2806: if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
2807: printf("Problem with resultfile: %s\n", fileresprobcor);
2808: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
2809: }
2810: printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
2811: fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
2812: printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
2813: fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
2814: printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
2815: fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
2816:
2817: fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
2818: fprintf(ficresprob,"# Age");
2819: fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
2820: fprintf(ficresprobcov,"# Age");
2821: fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
2822: fprintf(ficresprobcov,"# Age");
2823:
2824:
2825: for(i=1; i<=nlstate;i++)
2826: for(j=1; j<=(nlstate+ndeath);j++){
2827: fprintf(ficresprob," p%1d-%1d (SE)",i,j);
2828: fprintf(ficresprobcov," p%1d-%1d ",i,j);
2829: fprintf(ficresprobcor," p%1d-%1d ",i,j);
2830: }
1.69 brouard 2831: /* fprintf(ficresprob,"\n");
1.53 brouard 2832: fprintf(ficresprobcov,"\n");
2833: fprintf(ficresprobcor,"\n");
1.69 brouard 2834: */
2835: xp=vector(1,npar);
1.53 brouard 2836: dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
2837: doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
2838: mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
2839: varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
2840: first=1;
1.88 brouard 2841: fprintf(ficgp,"\n# Routine varprob");
2842: fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
2843: fprintf(fichtm,"\n");
2844:
1.91 brouard 2845: fprintf(fichtm,"\n<li><h4> <a href=\"%s\">Computing matrix of variance-covariance of step probabilities</a></h4></li>\n",optionfilehtmcov);
2846: fprintf(fichtmcov,"\n<h4>Computing matrix of variance-covariance of step probabilities</h4>\n\
2847: file %s<br>\n",optionfilehtmcov);
2848: fprintf(fichtmcov,"\nEllipsoids of confidence centered on point (p<inf>ij</inf>, p<inf>kl</inf>) are estimated\
2849: and drawn. It helps understanding how is the covariance between two incidences.\
2850: They are expressed in year<sup>-1</sup> in order to be less dependent of stepm.<br>\n");
2851: 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. \
2852: It can be understood this way: if pij and pkl where uncorrelated the (2x2) matrix of covariance \
2853: would have been (1/(var pij), 0 , 0, 1/(var pkl)), and the confidence interval would be 2 \
2854: standard deviations wide on each axis. <br>\
2855: Now, if both incidences are correlated (usual case) we diagonalised the inverse of the covariance matrix\
2856: and made the appropriate rotation to look at the uncorrelated principal directions.<br>\
2857: 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 2858:
2859: cov[1]=1;
2860: tj=cptcoveff;
2861: if (cptcovn<1) {tj=1;ncodemax[1]=1;}
2862: j1=0;
2863: for(t=1; t<=tj;t++){
2864: for(i1=1; i1<=ncodemax[t];i1++){
2865: j1++;
2866: if (cptcovn>0) {
2867: fprintf(ficresprob, "\n#********** Variable ");
2868: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
1.69 brouard 2869: fprintf(ficresprob, "**********\n#\n");
1.53 brouard 2870: fprintf(ficresprobcov, "\n#********** Variable ");
2871: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
1.69 brouard 2872: fprintf(ficresprobcov, "**********\n#\n");
1.53 brouard 2873:
2874: fprintf(ficgp, "\n#********** Variable ");
1.69 brouard 2875: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
2876: fprintf(ficgp, "**********\n#\n");
1.53 brouard 2877:
2878:
2879: fprintf(fichtm, "\n<hr size=\"2\" color=\"#EC5E5E\">********** Variable ");
2880: for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
2881: fprintf(fichtm, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
2882:
2883: fprintf(ficresprobcor, "\n#********** Variable ");
2884: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
1.69 brouard 2885: fprintf(ficresprobcor, "**********\n#");
1.53 brouard 2886: }
2887:
2888: for (age=bage; age<=fage; age ++){
2889: cov[2]=age;
2890: for (k=1; k<=cptcovn;k++) {
2891: cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];
2892: }
2893: for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
2894: for (k=1; k<=cptcovprod;k++)
2895: cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
2896:
2897: gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
2898: trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
2899: gp=vector(1,(nlstate)*(nlstate+ndeath));
2900: gm=vector(1,(nlstate)*(nlstate+ndeath));
2901:
2902: for(theta=1; theta <=npar; theta++){
2903: for(i=1; i<=npar; i++)
1.74 brouard 2904: xp[i] = x[i] + (i==theta ?delti[theta]:(double)0);
1.53 brouard 2905:
2906: pmij(pmmij,cov,ncovmodel,xp,nlstate);
2907:
2908: k=0;
2909: for(i=1; i<= (nlstate); i++){
2910: for(j=1; j<=(nlstate+ndeath);j++){
2911: k=k+1;
2912: gp[k]=pmmij[i][j];
2913: }
2914: }
2915:
2916: for(i=1; i<=npar; i++)
1.74 brouard 2917: xp[i] = x[i] - (i==theta ?delti[theta]:(double)0);
1.53 brouard 2918:
2919: pmij(pmmij,cov,ncovmodel,xp,nlstate);
2920: k=0;
2921: for(i=1; i<=(nlstate); i++){
2922: for(j=1; j<=(nlstate+ndeath);j++){
2923: k=k+1;
2924: gm[k]=pmmij[i][j];
2925: }
2926: }
2927:
2928: for(i=1; i<= (nlstate)*(nlstate+ndeath); i++)
1.74 brouard 2929: gradg[theta][i]=(gp[i]-gm[i])/(double)2./delti[theta];
1.53 brouard 2930: }
2931:
2932: for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
2933: for(theta=1; theta <=npar; theta++)
2934: trgradg[j][theta]=gradg[theta][j];
2935:
2936: matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov);
2937: matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);
1.59 brouard 2938: free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
2939: free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
2940: free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
2941: free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
2942:
1.53 brouard 2943: pmij(pmmij,cov,ncovmodel,x,nlstate);
2944:
2945: k=0;
2946: for(i=1; i<=(nlstate); i++){
2947: for(j=1; j<=(nlstate+ndeath);j++){
2948: k=k+1;
2949: mu[k][(int) age]=pmmij[i][j];
2950: }
2951: }
2952: for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
2953: for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
2954: varpij[i][j][(int)age] = doldm[i][j];
2955:
2956: /*printf("\n%d ",(int)age);
1.59 brouard 2957: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
2958: printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
2959: fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
2960: }*/
1.53 brouard 2961:
2962: fprintf(ficresprob,"\n%d ",(int)age);
2963: fprintf(ficresprobcov,"\n%d ",(int)age);
2964: fprintf(ficresprobcor,"\n%d ",(int)age);
2965:
2966: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)
2967: fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));
2968: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
2969: fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);
2970: fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
2971: }
2972: i=0;
2973: for (k=1; k<=(nlstate);k++){
2974: for (l=1; l<=(nlstate+ndeath);l++){
2975: i=i++;
2976: fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
2977: fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
2978: for (j=1; j<=i;j++){
2979: fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);
2980: fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));
2981: }
2982: }
2983: }/* end of loop for state */
2984: } /* end of loop for age */
2985:
2986: /* Confidence intervalle of pij */
2987: /*
1.59 brouard 2988: fprintf(ficgp,"\nset noparametric;unset label");
2989: fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");
2990: fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
2991: 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);
2992: fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);
2993: fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);
2994: fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);
1.53 brouard 2995: */
2996:
2997: /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
2998: first1=1;
2999: for (k2=1; k2<=(nlstate);k2++){
3000: for (l2=1; l2<=(nlstate+ndeath);l2++){
3001: if(l2==k2) continue;
3002: j=(k2-1)*(nlstate+ndeath)+l2;
3003: for (k1=1; k1<=(nlstate);k1++){
3004: for (l1=1; l1<=(nlstate+ndeath);l1++){
3005: if(l1==k1) continue;
3006: i=(k1-1)*(nlstate+ndeath)+l1;
3007: if(i<=j) continue;
3008: for (age=bage; age<=fage; age ++){
3009: if ((int)age %5==0){
3010: v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;
3011: v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;
3012: cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;
3013: mu1=mu[i][(int) age]/stepm*YEARM ;
3014: mu2=mu[j][(int) age]/stepm*YEARM;
3015: c12=cv12/sqrt(v1*v2);
3016: /* Computing eigen value of matrix of covariance */
3017: lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
3018: lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
3019: /* Eigen vectors */
3020: v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
3021: /*v21=sqrt(1.-v11*v11); *//* error */
3022: v21=(lc1-v1)/cv12*v11;
3023: v12=-v21;
3024: v22=v11;
3025: tnalp=v21/v11;
3026: if(first1==1){
3027: first1=0;
3028: 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);
3029: }
3030: 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);
3031: /*printf(fignu*/
3032: /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */
3033: /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */
3034: if(first==1){
3035: first=0;
3036: fprintf(ficgp,"\nset parametric;unset label");
3037: 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);
3038: fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
1.91 brouard 3039: fprintf(fichtmcov,"\n<br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup>\
1.88 brouard 3040: :<a href=\"%s%d%1d%1d-%1d%1d.png\">\
3041: %s%d%1d%1d-%1d%1d.png</A>, ",k1,l1,k2,l2,\
3042: subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2,\
3043: subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
1.91 brouard 3044: fprintf(fichtmcov,"\n<br><img src=\"%s%d%1d%1d-%1d%1d.png\"> ",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
3045: fprintf(fichtmcov,"\n<br> Correlation at age %d (%.3f),",(int) age, c12);
1.88 brouard 3046: fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\"",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
1.53 brouard 3047: fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
3048: fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
3049: 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",\
3050: mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
3051: mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
3052: }else{
3053: first=0;
1.91 brouard 3054: fprintf(fichtmcov," %d (%.3f),",(int) age, c12);
1.53 brouard 3055: fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
3056: fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
3057: 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",\
3058: mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
3059: mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
3060: }/* if first */
3061: } /* age mod 5 */
3062: } /* end loop age */
1.88 brouard 3063: fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\";replot;",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
1.53 brouard 3064: first=1;
3065: } /*l12 */
3066: } /* k12 */
3067: } /*l1 */
3068: }/* k1 */
3069: } /* loop covariates */
3070: }
1.59 brouard 3071: free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
3072: free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
1.53 brouard 3073: free_vector(xp,1,npar);
3074: fclose(ficresprob);
3075: fclose(ficresprobcov);
3076: fclose(ficresprobcor);
1.91 brouard 3077: fflush(ficgp);
3078: fflush(fichtmcov);
1.53 brouard 3079: }
3080:
3081:
3082: /******************* Printing html file ***********/
3083: void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \
3084: int lastpass, int stepm, int weightopt, char model[],\
3085: int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
3086: int popforecast, int estepm ,\
3087: double jprev1, double mprev1,double anprev1, \
3088: double jprev2, double mprev2,double anprev2){
3089: int jj1, k1, i1, cpt;
3090: /*char optionfilehtm[FILENAMELENGTH];*/
1.87 brouard 3091: /* if((fichtm=fopen(optionfilehtm,"a"))==NULL) { */
3092: /* printf("Problem with %s \n",optionfilehtm), exit(0); */
3093: /* fprintf(ficlog,"Problem with %s \n",optionfilehtm), exit(0); */
3094: /* } */
1.53 brouard 3095:
1.85 brouard 3096: fprintf(fichtm,"<ul><li><h4>Result files (first order: no variance)</h4>\n \
1.88 brouard 3097: - Observed prevalence in each state (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"%s\">%s</a> <br>\n \
3098: - Estimated transition probabilities over %d (stepm) months: <a href=\"%s\">%s</a><br>\n \
3099: - Stable prevalence in each health state: <a href=\"%s\">%s</a> <br>\n \
1.85 brouard 3100: - Life expectancies by age and initial health status (estepm=%2d months): \
1.88 brouard 3101: <a href=\"%s\">%s</a> <br>\n</li>", \
3102: jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirf2(fileres,"p"),subdirf2(fileres,"p"),\
3103: stepm,subdirf2(fileres,"pij"),subdirf2(fileres,"pij"),\
3104: subdirf2(fileres,"pl"),subdirf2(fileres,"pl"),\
3105: estepm,subdirf2(fileres,"e"),subdirf2(fileres,"e"));
1.53 brouard 3106:
3107: fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
3108:
3109: m=cptcoveff;
3110: if (cptcovn < 1) {m=1;ncodemax[1]=1;}
3111:
3112: jj1=0;
3113: for(k1=1; k1<=m;k1++){
3114: for(i1=1; i1<=ncodemax[k1];i1++){
3115: jj1++;
3116: if (cptcovn > 0) {
3117: fprintf(fichtm,"<hr size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
3118: for (cpt=1; cpt<=cptcoveff;cpt++)
3119: fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
3120: fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
3121: }
3122: /* Pij */
1.88 brouard 3123: 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> \
3124: <img src=\"%s%d1.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);
1.53 brouard 3125: /* Quasi-incidences */
1.85 brouard 3126: fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months\
1.88 brouard 3127: before but expressed in per year i.e. quasi incidences if stepm is small and probabilities too: %s%d2.png<br> \
3128: <img src=\"%s%d2.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);
1.53 brouard 3129: /* Stable prevalence in each health state */
3130: for(cpt=1; cpt<nlstate;cpt++){
1.85 brouard 3131: fprintf(fichtm,"<br>- Stable prevalence in each health state : p%s%d%d.png<br> \
1.88 brouard 3132: <img src=\"%s%d%d.png\">",subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1);
1.53 brouard 3133: }
3134: for(cpt=1; cpt<=nlstate;cpt++) {
1.88 brouard 3135: fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): %s%d%d.png <br> \
1.89 brouard 3136: <img src=\"%s%d%d.png\">",cpt,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1);
1.53 brouard 3137: }
1.85 brouard 3138: fprintf(fichtm,"\n<br>- Total life expectancy by age and \
1.88 brouard 3139: health expectancies in states (1) and (2): %s%d.png<br>\
3140: <img src=\"%s%d.png\">",subdirf2(optionfilefiname,"e"),jj1,subdirf2(optionfilefiname,"e"),jj1);
1.53 brouard 3141: } /* end i1 */
3142: }/* End k1 */
3143: fprintf(fichtm,"</ul>");
3144:
3145:
1.85 brouard 3146: fprintf(fichtm,"\n<br><li><h4> Result files (second order: variances)</h4>\n\
3147: - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n\
1.88 brouard 3148: - Variance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n\
3149: - Variance-covariance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n\
3150: - Correlation matrix of one-step probabilities: <a href=\"%s\">%s</a> <br>\n\
3151: - Variances and covariances of life expectancies by age and initial health status (estepm=%d months): <a href=\"%s\">%s</a><br>\n\
3152: - Health expectancies with their variances (no covariance): <a href=\"%s\">%s</a> <br>\n\
3153: - Standard deviation of stable prevalences: <a href=\"%s\">%s</a> <br>\n",\
3154: rfileres,rfileres,\
3155: subdirf2(fileres,"prob"),subdirf2(fileres,"prob"),\
3156: subdirf2(fileres,"probcov"),subdirf2(fileres,"probcov"),\
3157: subdirf2(fileres,"probcor"),subdirf2(fileres,"probcor"),\
3158: estepm, subdirf2(fileres,"v"),subdirf2(fileres,"v"),\
3159: subdirf2(fileres,"t"),subdirf2(fileres,"t"),\
3160: subdirf2(fileres,"vpl"),subdirf2(fileres,"vpl"));
1.53 brouard 3161:
1.76 brouard 3162: /* if(popforecast==1) fprintf(fichtm,"\n */
3163: /* - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n */
3164: /* - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n */
3165: /* <br>",fileres,fileres,fileres,fileres); */
3166: /* else */
3167: /* 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 3168: fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
3169:
3170: m=cptcoveff;
3171: if (cptcovn < 1) {m=1;ncodemax[1]=1;}
3172:
3173: jj1=0;
3174: for(k1=1; k1<=m;k1++){
3175: for(i1=1; i1<=ncodemax[k1];i1++){
3176: jj1++;
3177: if (cptcovn > 0) {
3178: fprintf(fichtm,"<hr size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
3179: for (cpt=1; cpt<=cptcoveff;cpt++)
3180: fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
3181: fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
3182: }
3183: for(cpt=1; cpt<=nlstate;cpt++) {
1.85 brouard 3184: fprintf(fichtm,"<br>- Observed and period prevalence (with confident\
1.88 brouard 3185: interval) in state (%d): %s%d%d.png <br>\
1.90 brouard 3186: <img src=\"%s%d%d.png\">",cpt,subdirf2(optionfilefiname,"v"),cpt,jj1,subdirf2(optionfilefiname,"v"),cpt,jj1);
1.53 brouard 3187: }
3188: } /* end i1 */
3189: }/* End k1 */
3190: fprintf(fichtm,"</ul>");
1.87 brouard 3191: fflush(fichtm);
1.53 brouard 3192: }
3193:
3194: /******************* Gnuplot file **************/
1.89 brouard 3195: void printinggnuplot(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
1.53 brouard 3196:
1.88 brouard 3197: char dirfileres[132],optfileres[132];
1.53 brouard 3198: int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;
3199: int ng;
1.88 brouard 3200: /* if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) { */
3201: /* printf("Problem with file %s",optionfilegnuplot); */
3202: /* fprintf(ficlog,"Problem with file %s",optionfilegnuplot); */
3203: /* } */
1.53 brouard 3204:
1.54 brouard 3205: /*#ifdef windows */
1.89 brouard 3206: fprintf(ficgp,"cd \"%s\" \n",pathc);
1.54 brouard 3207: /*#endif */
1.88 brouard 3208: m=pow(2,cptcoveff);
3209:
3210: strcpy(dirfileres,optionfilefiname);
3211: strcpy(optfileres,"vpl");
1.53 brouard 3212: /* 1eme*/
3213: for (cpt=1; cpt<= nlstate ; cpt ++) {
3214: for (k1=1; k1<= m ; k1 ++) {
1.88 brouard 3215: fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"v"),cpt,k1);
3216: fprintf(ficgp,"\n#set out \"v%s%d%d.png\" \n",optionfilefiname,cpt,k1);
3217: fprintf(ficgp,"set xlabel \"Age\" \n\
3218: set ylabel \"Probability\" \n\
3219: set ter png small\n\
3220: set size 0.65,0.65\n\
3221: plot [%.f:%.f] \"%s\" every :::%d::%d u 1:2 \"\%%lf",ageminpar,fage,subdirf2(fileres,"vpl"),k1-1,k1-1);
1.53 brouard 3222:
3223: for (i=1; i<= nlstate ; i ++) {
3224: if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
3225: else fprintf(ficgp," \%%*lf (\%%*lf)");
3226: }
1.88 brouard 3227: 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 3228: for (i=1; i<= nlstate ; i ++) {
3229: if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
3230: else fprintf(ficgp," \%%*lf (\%%*lf)");
3231: }
1.88 brouard 3232: fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"%s\" every :::%d::%d u 1:($2-1.96*$3) \"\%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1);
1.53 brouard 3233: for (i=1; i<= nlstate ; i ++) {
3234: if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
3235: else fprintf(ficgp," \%%*lf (\%%*lf)");
3236: }
1.88 brouard 3237: fprintf(ficgp,"\" t\"\" w l 1,\"%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",subdirf2(fileres,"p"),k1-1,k1-1,2+4*(cpt-1));
1.53 brouard 3238: }
3239: }
3240: /*2 eme*/
3241:
3242: for (k1=1; k1<= m ; k1 ++) {
1.88 brouard 3243: fprintf(ficgp,"\nset out \"%s%d.png\" \n",subdirf2(optionfilefiname,"e"),k1);
1.53 brouard 3244: fprintf(ficgp,"set ylabel \"Years\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] ",ageminpar,fage);
3245:
3246: for (i=1; i<= nlstate+1 ; i ++) {
3247: k=2*i;
1.88 brouard 3248: fprintf(ficgp,"\"%s\" every :::%d::%d u 1:2 \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
1.53 brouard 3249: for (j=1; j<= nlstate+1 ; j ++) {
3250: if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
3251: else fprintf(ficgp," \%%*lf (\%%*lf)");
3252: }
3253: if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");
3254: else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);
1.88 brouard 3255: fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
1.53 brouard 3256: for (j=1; j<= nlstate+1 ; j ++) {
3257: if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
3258: else fprintf(ficgp," \%%*lf (\%%*lf)");
3259: }
3260: fprintf(ficgp,"\" t\"\" w l 0,");
1.88 brouard 3261: fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
1.53 brouard 3262: for (j=1; j<= nlstate+1 ; j ++) {
3263: if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
3264: else fprintf(ficgp," \%%*lf (\%%*lf)");
3265: }
3266: if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");
3267: else fprintf(ficgp,"\" t\"\" w l 0,");
3268: }
3269: }
3270:
3271: /*3eme*/
3272:
3273: for (k1=1; k1<= m ; k1 ++) {
3274: for (cpt=1; cpt<= nlstate ; cpt ++) {
3275: k=2+nlstate*(2*cpt-2);
1.88 brouard 3276: fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"exp"),cpt,k1);
3277: fprintf(ficgp,"set ter png small\n\
3278: set size 0.65,0.65\n\
3279: plot [%.f:%.f] \"%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,subdirf2(fileres,"e"),k1-1,k1-1,k,cpt);
1.53 brouard 3280: /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
3281: for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
3282: fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
3283: fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
3284: for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
3285: fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
3286:
3287: */
3288: for (i=1; i< nlstate ; i ++) {
1.88 brouard 3289: 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 3290:
3291: }
3292: }
3293: }
3294:
1.76 brouard 3295: /* CV preval stable (period) */
1.53 brouard 3296: for (k1=1; k1<= m ; k1 ++) {
1.76 brouard 3297: for (cpt=1; cpt<=nlstate ; cpt ++) {
1.53 brouard 3298: k=3;
1.88 brouard 3299: fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"p"),cpt,k1);
3300: fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\
3301: set ter png small\nset size 0.65,0.65\n\
1.89 brouard 3302: unset log y\n\
1.88 brouard 3303: plot [%.f:%.f] \"%s\" u ($1==%d ? ($3):1/0):($%d/($%d",ageminpar,agemaxpar,subdirf2(fileres,"pij"),k1,k+cpt+1,k+1);
1.53 brouard 3304:
1.83 lievre 3305: for (i=1; i< nlstate ; i ++)
1.53 brouard 3306: fprintf(ficgp,"+$%d",k+i+1);
3307: fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);
3308:
3309: l=3+(nlstate+ndeath)*cpt;
1.88 brouard 3310: fprintf(ficgp,",\"%s\" u ($1==%d ? ($3):1/0):($%d/($%d",subdirf2(fileres,"pij"),k1,l+cpt+1,l+1);
1.53 brouard 3311: for (i=1; i< nlstate ; i ++) {
3312: l=3+(nlstate+ndeath)*cpt;
3313: fprintf(ficgp,"+$%d",l+i+1);
3314: }
3315: fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);
3316: }
3317: }
3318:
3319: /* proba elementaires */
3320: for(i=1,jk=1; i <=nlstate; i++){
3321: for(k=1; k <=(nlstate+ndeath); k++){
3322: if (k != i) {
3323: for(j=1; j <=ncovmodel; j++){
3324: fprintf(ficgp,"p%d=%f ",jk,p[jk]);
3325: jk++;
3326: fprintf(ficgp,"\n");
3327: }
3328: }
3329: }
3330: }
3331:
3332: for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/
3333: for(jk=1; jk <=m; jk++) {
1.88 brouard 3334: fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"pe"),jk,ng);
1.53 brouard 3335: if (ng==2)
3336: fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
3337: else
3338: fprintf(ficgp,"\nset title \"Probability\"\n");
3339: fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65\nset log y\nplot [%.f:%.f] ",ageminpar,agemaxpar);
3340: i=1;
3341: for(k2=1; k2<=nlstate; k2++) {
3342: k3=i;
3343: for(k=1; k<=(nlstate+ndeath); k++) {
3344: if (k != k2){
3345: if(ng==2)
3346: fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);
3347: else
3348: fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
3349: ij=1;
3350: for(j=3; j <=ncovmodel; j++) {
3351: if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
3352: fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
3353: ij++;
3354: }
3355: else
3356: fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
3357: }
3358: fprintf(ficgp,")/(1");
3359:
3360: for(k1=1; k1 <=nlstate; k1++){
3361: fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);
3362: ij=1;
3363: for(j=3; j <=ncovmodel; j++){
3364: if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
3365: fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
3366: ij++;
3367: }
3368: else
3369: fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
3370: }
3371: fprintf(ficgp,")");
3372: }
3373: fprintf(ficgp,") t \"p%d%d\" ", k2,k);
3374: if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");
3375: i=i+ncovmodel;
3376: }
3377: } /* end k */
3378: } /* end k2 */
3379: } /* end jk */
3380: } /* end ng */
1.88 brouard 3381: fflush(ficgp);
1.53 brouard 3382: } /* end gnuplot */
3383:
3384:
3385: /*************** Moving average **************/
1.54 brouard 3386: int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav){
1.53 brouard 3387:
3388: int i, cpt, cptcod;
1.58 lievre 3389: int modcovmax =1;
1.54 brouard 3390: int mobilavrange, mob;
1.53 brouard 3391: double age;
1.58 lievre 3392:
3393: modcovmax=2*cptcoveff;/* Max number of modalities. We suppose
3394: a covariate has 2 modalities */
3395: if (cptcovn<1) modcovmax=1; /* At least 1 pass */
3396:
1.54 brouard 3397: if(mobilav==1||mobilav ==3 ||mobilav==5 ||mobilav== 7){
3398: if(mobilav==1) mobilavrange=5; /* default */
3399: else mobilavrange=mobilav;
3400: for (age=bage; age<=fage; age++)
3401: for (i=1; i<=nlstate;i++)
1.58 lievre 3402: for (cptcod=1;cptcod<=modcovmax;cptcod++)
1.54 brouard 3403: mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
3404: /* We keep the original values on the extreme ages bage, fage and for
3405: fage+1 and bage-1 we use a 3 terms moving average; for fage+2 bage+2
3406: we use a 5 terms etc. until the borders are no more concerned.
3407: */
3408: for (mob=3;mob <=mobilavrange;mob=mob+2){
3409: for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){
3410: for (i=1; i<=nlstate;i++){
1.58 lievre 3411: for (cptcod=1;cptcod<=modcovmax;cptcod++){
1.54 brouard 3412: mobaverage[(int)age][i][cptcod] =probs[(int)age][i][cptcod];
3413: for (cpt=1;cpt<=(mob-1)/2;cpt++){
3414: mobaverage[(int)age][i][cptcod] +=probs[(int)age-cpt][i][cptcod];
3415: mobaverage[(int)age][i][cptcod] +=probs[(int)age+cpt][i][cptcod];
3416: }
3417: mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/mob;
3418: }
1.53 brouard 3419: }
1.54 brouard 3420: }/* end age */
3421: }/* end mob */
3422: }else return -1;
3423: return 0;
3424: }/* End movingaverage */
1.53 brouard 3425:
3426:
3427: /************** Forecasting ******************/
1.70 brouard 3428: 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 3429: /* proj1, year, month, day of starting projection
3430: agemin, agemax range of age
3431: dateprev1 dateprev2 range of dates during which prevalence is computed
1.70 brouard 3432: anproj2 year of en of projection (same day and month as proj1).
1.69 brouard 3433: */
1.73 lievre 3434: int yearp, stepsize, hstepm, nhstepm, j, k, c, cptcod, i, h, i1;
1.53 brouard 3435: int *popage;
1.70 brouard 3436: double agec; /* generic age */
3437: double agelim, ppij, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
1.53 brouard 3438: double *popeffectif,*popcount;
3439: double ***p3mat;
1.55 lievre 3440: double ***mobaverage;
1.53 brouard 3441: char fileresf[FILENAMELENGTH];
3442:
1.69 brouard 3443: agelim=AGESUP;
1.84 brouard 3444: prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
1.53 brouard 3445:
3446: strcpy(fileresf,"f");
3447: strcat(fileresf,fileres);
3448: if((ficresf=fopen(fileresf,"w"))==NULL) {
3449: printf("Problem with forecast resultfile: %s\n", fileresf);
3450: fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);
3451: }
3452: printf("Computing forecasting: result on file '%s' \n", fileresf);
3453: fprintf(ficlog,"Computing forecasting: result on file '%s' \n", fileresf);
3454:
3455: if (cptcoveff==0) ncodemax[cptcoveff]=1;
3456:
1.54 brouard 3457: if (mobilav!=0) {
1.53 brouard 3458: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
1.54 brouard 3459: if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
3460: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
3461: printf(" Error in movingaverage mobilav=%d\n",mobilav);
3462: }
1.53 brouard 3463: }
3464:
3465: stepsize=(int) (stepm+YEARM-1)/YEARM;
3466: if (stepm<=12) stepsize=1;
1.74 brouard 3467: if(estepm < stepm){
3468: printf ("Problem %d lower than %d\n",estepm, stepm);
3469: }
3470: else hstepm=estepm;
3471:
1.53 brouard 3472: hstepm=hstepm/stepm;
1.69 brouard 3473: yp1=modf(dateintmean,&yp);/* extracts integral of datemean in yp and
3474: fractional in yp1 */
1.53 brouard 3475: anprojmean=yp;
3476: yp2=modf((yp1*12),&yp);
3477: mprojmean=yp;
3478: yp1=modf((yp2*30.5),&yp);
3479: jprojmean=yp;
3480: if(jprojmean==0) jprojmean=1;
3481: if(mprojmean==0) jprojmean=1;
1.73 lievre 3482:
3483: i1=cptcoveff;
3484: if (cptcovn < 1){i1=1;}
1.53 brouard 3485:
1.70 brouard 3486: fprintf(ficresf,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2);
1.53 brouard 3487:
1.70 brouard 3488: fprintf(ficresf,"#****** Routine prevforecast **\n");
1.73 lievre 3489:
1.75 brouard 3490: /* if (h==(int)(YEARM*yearp)){ */
1.73 lievre 3491: for(cptcov=1, k=0;cptcov<=i1;cptcov++){
1.53 brouard 3492: for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
3493: k=k+1;
3494: fprintf(ficresf,"\n#******");
3495: for(j=1;j<=cptcoveff;j++) {
1.70 brouard 3496: 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 3497: }
3498: fprintf(ficresf,"******\n");
1.70 brouard 3499: fprintf(ficresf,"# Covariate valuofcovar yearproj age");
3500: for(j=1; j<=nlstate+ndeath;j++){
3501: for(i=1; i<=nlstate;i++)
3502: fprintf(ficresf," p%d%d",i,j);
3503: fprintf(ficresf," p.%d",j);
3504: }
1.74 brouard 3505: for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) {
1.53 brouard 3506: fprintf(ficresf,"\n");
1.70 brouard 3507: fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+yearp);
1.53 brouard 3508:
1.71 brouard 3509: for (agec=fage; agec>=(ageminpar-1); agec--){
1.70 brouard 3510: nhstepm=(int) rint((agelim-agec)*YEARM/stepm);
1.53 brouard 3511: nhstepm = nhstepm/hstepm;
3512: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3513: oldm=oldms;savm=savms;
1.70 brouard 3514: hpxij(p3mat,nhstepm,agec,hstepm,p,nlstate,stepm,oldm,savm, k);
1.53 brouard 3515:
3516: for (h=0; h<=nhstepm; h++){
1.75 brouard 3517: if (h*hstepm/YEARM*stepm ==yearp) {
1.69 brouard 3518: fprintf(ficresf,"\n");
3519: for(j=1;j<=cptcoveff;j++)
3520: fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
1.70 brouard 3521: fprintf(ficresf,"%.f %.f ",anproj1+yearp,agec+h*hstepm/YEARM*stepm);
1.53 brouard 3522: }
3523: for(j=1; j<=nlstate+ndeath;j++) {
1.70 brouard 3524: ppij=0.;
1.71 brouard 3525: for(i=1; i<=nlstate;i++) {
1.53 brouard 3526: if (mobilav==1)
1.71 brouard 3527: ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][i][cptcod];
1.53 brouard 3528: else {
1.71 brouard 3529: ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][cptcod];
1.53 brouard 3530: }
1.75 brouard 3531: if (h*hstepm/YEARM*stepm== yearp) {
1.70 brouard 3532: fprintf(ficresf," %.3f", p3mat[i][j][h]);
1.75 brouard 3533: }
3534: } /* end i */
3535: if (h*hstepm/YEARM*stepm==yearp) {
1.70 brouard 3536: fprintf(ficresf," %.3f", ppij);
1.53 brouard 3537: }
1.75 brouard 3538: }/* end j */
3539: } /* end h */
1.53 brouard 3540: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
1.75 brouard 3541: } /* end agec */
3542: } /* end yearp */
3543: } /* end cptcod */
3544: } /* end cptcov */
1.53 brouard 3545:
1.54 brouard 3546: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
1.53 brouard 3547:
3548: fclose(ficresf);
3549: }
1.70 brouard 3550:
3551: /************** Forecasting *****not tested NB*************/
1.53 brouard 3552: 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){
3553:
3554: int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;
3555: int *popage;
1.69 brouard 3556: double calagedatem, agelim, kk1, kk2;
1.53 brouard 3557: double *popeffectif,*popcount;
3558: double ***p3mat,***tabpop,***tabpopprev;
1.55 lievre 3559: double ***mobaverage;
1.53 brouard 3560: char filerespop[FILENAMELENGTH];
3561:
3562: tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
3563: tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
3564: agelim=AGESUP;
1.69 brouard 3565: calagedatem=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;
1.53 brouard 3566:
1.84 brouard 3567: prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
1.53 brouard 3568:
3569:
3570: strcpy(filerespop,"pop");
3571: strcat(filerespop,fileres);
3572: if((ficrespop=fopen(filerespop,"w"))==NULL) {
3573: printf("Problem with forecast resultfile: %s\n", filerespop);
3574: fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop);
3575: }
3576: printf("Computing forecasting: result on file '%s' \n", filerespop);
3577: fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop);
3578:
3579: if (cptcoveff==0) ncodemax[cptcoveff]=1;
3580:
1.54 brouard 3581: if (mobilav!=0) {
1.53 brouard 3582: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
1.54 brouard 3583: if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
3584: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
3585: printf(" Error in movingaverage mobilav=%d\n",mobilav);
3586: }
1.53 brouard 3587: }
3588:
3589: stepsize=(int) (stepm+YEARM-1)/YEARM;
3590: if (stepm<=12) stepsize=1;
3591:
3592: agelim=AGESUP;
3593:
3594: hstepm=1;
3595: hstepm=hstepm/stepm;
3596:
3597: if (popforecast==1) {
3598: if((ficpop=fopen(popfile,"r"))==NULL) {
3599: printf("Problem with population file : %s\n",popfile);exit(0);
3600: fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0);
3601: }
3602: popage=ivector(0,AGESUP);
3603: popeffectif=vector(0,AGESUP);
3604: popcount=vector(0,AGESUP);
3605:
3606: i=1;
3607: while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;
3608:
3609: imx=i;
3610: for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];
3611: }
3612:
1.69 brouard 3613: for(cptcov=1,k=0;cptcov<=i2;cptcov++){
1.53 brouard 3614: for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
3615: k=k+1;
3616: fprintf(ficrespop,"\n#******");
3617: for(j=1;j<=cptcoveff;j++) {
3618: fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
3619: }
3620: fprintf(ficrespop,"******\n");
3621: fprintf(ficrespop,"# Age");
3622: for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);
3623: if (popforecast==1) fprintf(ficrespop," [Population]");
3624:
3625: for (cpt=0; cpt<=0;cpt++) {
3626: fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);
3627:
1.69 brouard 3628: for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){
1.53 brouard 3629: nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);
3630: nhstepm = nhstepm/hstepm;
3631:
3632: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3633: oldm=oldms;savm=savms;
3634: hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
3635:
3636: for (h=0; h<=nhstepm; h++){
1.69 brouard 3637: if (h==(int) (calagedatem+YEARM*cpt)) {
1.53 brouard 3638: fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
3639: }
3640: for(j=1; j<=nlstate+ndeath;j++) {
3641: kk1=0.;kk2=0;
3642: for(i=1; i<=nlstate;i++) {
3643: if (mobilav==1)
3644: kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];
3645: else {
3646: kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];
3647: }
3648: }
1.69 brouard 3649: if (h==(int)(calagedatem+12*cpt)){
1.53 brouard 3650: tabpop[(int)(agedeb)][j][cptcod]=kk1;
3651: /*fprintf(ficrespop," %.3f", kk1);
3652: if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/
3653: }
3654: }
3655: for(i=1; i<=nlstate;i++){
3656: kk1=0.;
3657: for(j=1; j<=nlstate;j++){
3658: kk1= kk1+tabpop[(int)(agedeb)][j][cptcod];
3659: }
1.69 brouard 3660: tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedatem+12*cpt)*hstepm/YEARM*stepm-1)];
1.53 brouard 3661: }
3662:
1.69 brouard 3663: if (h==(int)(calagedatem+12*cpt)) for(j=1; j<=nlstate;j++)
1.53 brouard 3664: fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);
3665: }
3666: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3667: }
3668: }
3669:
3670: /******/
3671:
3672: for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) {
3673: fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);
1.69 brouard 3674: for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){
1.53 brouard 3675: nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);
3676: nhstepm = nhstepm/hstepm;
3677:
3678: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3679: oldm=oldms;savm=savms;
3680: hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
3681: for (h=0; h<=nhstepm; h++){
1.69 brouard 3682: if (h==(int) (calagedatem+YEARM*cpt)) {
1.53 brouard 3683: fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
3684: }
3685: for(j=1; j<=nlstate+ndeath;j++) {
3686: kk1=0.;kk2=0;
3687: for(i=1; i<=nlstate;i++) {
3688: kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];
3689: }
1.69 brouard 3690: if (h==(int)(calagedatem+12*cpt)) fprintf(ficresf," %15.2f", kk1);
1.53 brouard 3691: }
3692: }
3693: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3694: }
3695: }
3696: }
3697: }
3698:
1.54 brouard 3699: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
1.53 brouard 3700:
3701: if (popforecast==1) {
3702: free_ivector(popage,0,AGESUP);
3703: free_vector(popeffectif,0,AGESUP);
3704: free_vector(popcount,0,AGESUP);
3705: }
3706: free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
3707: free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
3708: fclose(ficrespop);
1.84 brouard 3709: } /* End of popforecast */
1.53 brouard 3710:
1.87 brouard 3711: int fileappend(FILE *fichier, char *optionfich)
1.86 brouard 3712: {
1.87 brouard 3713: if((fichier=fopen(optionfich,"a"))==NULL) {
3714: printf("Problem with file: %s\n", optionfich);
3715: fprintf(ficlog,"Problem with file: %s\n", optionfich);
3716: return (0);
1.86 brouard 3717: }
1.87 brouard 3718: fflush(fichier);
3719: return (1);
1.86 brouard 3720: }
1.94 ! brouard 3721:
! 3722:
! 3723: /**************** function prwizard **********************/
1.88 brouard 3724: void prwizard(int ncovmodel, int nlstate, int ndeath, char model[], FILE *ficparo)
3725: {
3726:
1.94 ! brouard 3727: /* Wizard to print covariance matrix template */
! 3728:
1.88 brouard 3729: char ca[32], cb[32], cc[32];
3730: int i,j, k, l, li, lj, lk, ll, jj, npar, itimes;
3731: int numlinepar;
3732:
3733: printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
3734: fprintf(ficparo,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
3735: for(i=1; i <=nlstate; i++){
3736: jj=0;
3737: for(j=1; j <=nlstate+ndeath; j++){
3738: if(j==i) continue;
3739: jj++;
3740: /*ca[0]= k+'a'-1;ca[1]='\0';*/
3741: printf("%1d%1d",i,j);
3742: fprintf(ficparo,"%1d%1d",i,j);
3743: for(k=1; k<=ncovmodel;k++){
3744: /* printf(" %lf",param[i][j][k]); */
3745: /* fprintf(ficparo," %lf",param[i][j][k]); */
3746: printf(" 0.");
3747: fprintf(ficparo," 0.");
3748: }
3749: printf("\n");
3750: fprintf(ficparo,"\n");
3751: }
3752: }
3753: printf("# Scales (for hessian or gradient estimation)\n");
3754: fprintf(ficparo,"# Scales (for hessian or gradient estimation)\n");
3755: npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/
3756: for(i=1; i <=nlstate; i++){
3757: jj=0;
3758: for(j=1; j <=nlstate+ndeath; j++){
3759: if(j==i) continue;
3760: jj++;
3761: fprintf(ficparo,"%1d%1d",i,j);
3762: printf("%1d%1d",i,j);
3763: fflush(stdout);
3764: for(k=1; k<=ncovmodel;k++){
3765: /* printf(" %le",delti3[i][j][k]); */
3766: /* fprintf(ficparo," %le",delti3[i][j][k]); */
3767: printf(" 0.");
3768: fprintf(ficparo," 0.");
3769: }
3770: numlinepar++;
3771: printf("\n");
3772: fprintf(ficparo,"\n");
3773: }
3774: }
3775: printf("# Covariance matrix\n");
3776: /* # 121 Var(a12)\n\ */
3777: /* # 122 Cov(b12,a12) Var(b12)\n\ */
3778: /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
3779: /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
3780: /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
3781: /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
3782: /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
3783: /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
3784: fflush(stdout);
3785: fprintf(ficparo,"# Covariance matrix\n");
3786: /* # 121 Var(a12)\n\ */
3787: /* # 122 Cov(b12,a12) Var(b12)\n\ */
3788: /* # ...\n\ */
3789: /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
3790:
3791: for(itimes=1;itimes<=2;itimes++){
3792: jj=0;
3793: for(i=1; i <=nlstate; i++){
3794: for(j=1; j <=nlstate+ndeath; j++){
3795: if(j==i) continue;
3796: for(k=1; k<=ncovmodel;k++){
3797: jj++;
3798: ca[0]= k+'a'-1;ca[1]='\0';
3799: if(itimes==1){
3800: printf("#%1d%1d%d",i,j,k);
3801: fprintf(ficparo,"#%1d%1d%d",i,j,k);
3802: }else{
3803: printf("%1d%1d%d",i,j,k);
3804: fprintf(ficparo,"%1d%1d%d",i,j,k);
3805: /* printf(" %.5le",matcov[i][j]); */
3806: }
3807: ll=0;
3808: for(li=1;li <=nlstate; li++){
3809: for(lj=1;lj <=nlstate+ndeath; lj++){
3810: if(lj==li) continue;
3811: for(lk=1;lk<=ncovmodel;lk++){
3812: ll++;
3813: if(ll<=jj){
3814: cb[0]= lk +'a'-1;cb[1]='\0';
3815: if(ll<jj){
3816: if(itimes==1){
3817: printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
3818: fprintf(ficparo," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
3819: }else{
3820: printf(" 0.");
3821: fprintf(ficparo," 0.");
3822: }
3823: }else{
3824: if(itimes==1){
3825: printf(" Var(%s%1d%1d)",ca,i,j);
3826: fprintf(ficparo," Var(%s%1d%1d)",ca,i,j);
3827: }else{
3828: printf(" 0.");
3829: fprintf(ficparo," 0.");
3830: }
3831: }
3832: }
3833: } /* end lk */
3834: } /* end lj */
3835: } /* end li */
3836: printf("\n");
3837: fprintf(ficparo,"\n");
3838: numlinepar++;
3839: } /* end k*/
3840: } /*end j */
3841: } /* end i */
3842: }
3843:
3844: } /* end of prwizard */
3845:
1.91 brouard 3846:
1.53 brouard 3847: /***********************************************/
3848: /**************** Main Program *****************/
3849: /***********************************************/
3850:
3851: int main(int argc, char *argv[])
3852: {
1.61 brouard 3853: int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav);
1.74 brouard 3854: int i,j, k, n=MAXN,iter,m,size=100,cptcode, cptcod;
1.88 brouard 3855: int jj, imk;
1.85 brouard 3856: int numlinepar=0; /* Current linenumber of parameter file */
1.87 brouard 3857: /* FILE *fichtm; *//* Html File */
3858: /* FILE *ficgp;*/ /*Gnuplot File */
1.53 brouard 3859: double agedeb, agefin,hf;
3860: double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;
3861:
3862: double fret;
3863: double **xi,tmp,delta;
3864:
3865: double dum; /* Dummy variable */
3866: double ***p3mat;
3867: double ***mobaverage;
3868: int *indx;
3869: char line[MAXLINE], linepar[MAXLINE];
1.88 brouard 3870: char path[MAXLINE],pathc[MAXLINE],pathcd[MAXLINE],pathtot[MAXLINE],model[MAXLINE];
3871: char pathr[MAXLINE];
1.53 brouard 3872: int firstobs=1, lastobs=10;
3873: int sdeb, sfin; /* Status at beginning and end */
3874: int c, h , cpt,l;
3875: int ju,jl, mi;
3876: int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;
1.59 brouard 3877: int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,*tab;
1.69 brouard 3878: int mobilavproj=0 , prevfcast=0 ; /* moving average of prev, If prevfcast=1 prevalence projection */
1.53 brouard 3879: int mobilav=0,popforecast=0;
3880: int hstepm, nhstepm;
1.74 brouard 3881: double jprev1=1, mprev1=1,anprev1=2000,jprev2=1, mprev2=1,anprev2=2000;
3882: double jpyram=1, mpyram=1,anpyram=2000,jpyram1=1, mpyram1=1,anpyram1=2000;
1.53 brouard 3883:
3884: double bage, fage, age, agelim, agebase;
3885: double ftolpl=FTOL;
3886: double **prlim;
3887: double *severity;
3888: double ***param; /* Matrix of parameters */
3889: double *p;
3890: double **matcov; /* Matrix of covariance */
3891: double ***delti3; /* Scale */
3892: double *delti; /* Scale */
3893: double ***eij, ***vareij;
3894: double **varpl; /* Variances of prevalence limits by age */
3895: double *epj, vepp;
3896: double kk1, kk2;
1.74 brouard 3897: double dateprev1, dateprev2,jproj1=1,mproj1=1,anproj1=2000,jproj2=1,mproj2=1,anproj2=2000;
1.53 brouard 3898:
3899: char *alph[]={"a","a","b","c","d","e"}, str[4];
3900:
3901:
3902: char z[1]="c", occ;
1.86 brouard 3903:
1.53 brouard 3904: char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];
1.88 brouard 3905: char strstart[80], *strt, strtend[80];
1.85 brouard 3906: char *stratrunc;
3907: int lstra;
3908:
3909: long total_usecs;
1.53 brouard 3910:
1.85 brouard 3911: /* gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */
3912: (void) gettimeofday(&start_time,&tzp);
1.91 brouard 3913: curr_time=start_time;
1.85 brouard 3914: tm = *localtime(&start_time.tv_sec);
3915: tmg = *gmtime(&start_time.tv_sec);
1.88 brouard 3916: strcpy(strstart,asctime(&tm));
1.86 brouard 3917:
1.88 brouard 3918: /* printf("Localtime (at start)=%s",strstart); */
1.85 brouard 3919: /* tp.tv_sec = tp.tv_sec +86400; */
3920: /* tm = *localtime(&start_time.tv_sec); */
3921: /* tmg.tm_year=tmg.tm_year +dsign*dyear; */
3922: /* tmg.tm_mon=tmg.tm_mon +dsign*dmonth; */
3923: /* tmg.tm_hour=tmg.tm_hour + 1; */
3924: /* tp.tv_sec = mktime(&tmg); */
3925: /* strt=asctime(&tmg); */
1.88 brouard 3926: /* printf("Time(after) =%s",strstart); */
1.85 brouard 3927: /* (void) time (&time_value);
3928: * printf("time=%d,t-=%d\n",time_value,time_value-86400);
3929: * tm = *localtime(&time_value);
1.88 brouard 3930: * strstart=asctime(&tm);
3931: * printf("tim_value=%d,asctime=%s\n",time_value,strstart);
1.85 brouard 3932: */
3933:
1.91 brouard 3934: nberr=0; /* Number of errors and warnings */
3935: nbwarn=0;
1.53 brouard 3936: getcwd(pathcd, size);
3937:
1.81 brouard 3938: printf("\n%s\n%s",version,fullversion);
1.53 brouard 3939: if(argc <=1){
3940: printf("\nEnter the parameter file name: ");
3941: scanf("%s",pathtot);
3942: }
3943: else{
3944: strcpy(pathtot,argv[1]);
3945: }
1.88 brouard 3946: /*if(getcwd(pathcd, MAXLINE)!= NULL)printf ("Error pathcd\n");*/
1.53 brouard 3947: /*cygwin_split_path(pathtot,path,optionfile);
3948: printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/
3949: /* cutv(path,optionfile,pathtot,'\\');*/
3950:
3951: split(pathtot,path,optionfile,optionfilext,optionfilefiname);
1.85 brouard 3952: printf("pathtot=%s,\npath=%s,\noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
1.53 brouard 3953: chdir(path);
1.88 brouard 3954: strcpy(command,"mkdir ");
3955: strcat(command,optionfilefiname);
3956: if((outcmd=system(command)) != 0){
3957: printf("Problem creating directory or it already exists %s%s, err=%d\n",path,optionfilefiname,outcmd);
3958: /* fprintf(ficlog,"Problem creating directory %s%s\n",path,optionfilefiname); */
3959: /* fclose(ficlog); */
3960: /* exit(1); */
3961: }
3962: /* if((imk=mkdir(optionfilefiname))<0){ */
3963: /* perror("mkdir"); */
3964: /* } */
1.53 brouard 3965:
1.59 brouard 3966: /*-------- arguments in the command line --------*/
1.53 brouard 3967:
3968: /* Log file */
3969: strcat(filelog, optionfilefiname);
3970: strcat(filelog,".log"); /* */
3971: if((ficlog=fopen(filelog,"w"))==NULL) {
3972: printf("Problem with logfile %s\n",filelog);
3973: goto end;
3974: }
3975: fprintf(ficlog,"Log filename:%s\n",filelog);
1.85 brouard 3976: fprintf(ficlog,"\n%s\n%s",version,fullversion);
1.53 brouard 3977: fprintf(ficlog,"\nEnter the parameter file name: ");
1.88 brouard 3978: fprintf(ficlog,"pathtot=%s\n\
3979: path=%s \n\
3980: optionfile=%s\n\
3981: optionfilext=%s\n\
3982: optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
1.86 brouard 3983:
1.94 ! brouard 3984: printf("Local time (at start):%s",strstart);
! 3985: fprintf(ficlog,"Local time (at start): %s",strstart);
1.53 brouard 3986: fflush(ficlog);
1.91 brouard 3987: /* (void) gettimeofday(&curr_time,&tzp); */
3988: /* printf("Elapsed time %d\n", asc_diff_time(curr_time.tv_sec-start_time.tv_sec,tmpout)); */
1.53 brouard 3989:
3990: /* */
3991: strcpy(fileres,"r");
3992: strcat(fileres, optionfilefiname);
3993: strcat(fileres,".txt"); /* Other files have txt extension */
3994:
3995: /*---------arguments file --------*/
3996:
3997: if((ficpar=fopen(optionfile,"r"))==NULL) {
3998: printf("Problem with optionfile %s\n",optionfile);
3999: fprintf(ficlog,"Problem with optionfile %s\n",optionfile);
1.85 brouard 4000: fflush(ficlog);
1.53 brouard 4001: goto end;
4002: }
4003:
1.88 brouard 4004:
4005:
1.53 brouard 4006: strcpy(filereso,"o");
4007: strcat(filereso,fileres);
1.88 brouard 4008: if((ficparo=fopen(filereso,"w"))==NULL) { /* opened on subdirectory */
1.53 brouard 4009: printf("Problem with Output resultfile: %s\n", filereso);
4010: fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso);
1.85 brouard 4011: fflush(ficlog);
1.53 brouard 4012: goto end;
4013: }
4014:
4015: /* Reads comments: lines beginning with '#' */
1.85 brouard 4016: numlinepar=0;
1.53 brouard 4017: while((c=getc(ficpar))=='#' && c!= EOF){
4018: ungetc(c,ficpar);
4019: fgets(line, MAXLINE, ficpar);
1.85 brouard 4020: numlinepar++;
1.53 brouard 4021: puts(line);
4022: fputs(line,ficparo);
1.85 brouard 4023: fputs(line,ficlog);
1.53 brouard 4024: }
4025: ungetc(c,ficpar);
4026:
4027: 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 4028: numlinepar++;
1.53 brouard 4029: 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);
4030: 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 4031: 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);
4032: fflush(ficlog);
1.59 brouard 4033: while((c=getc(ficpar))=='#' && c!= EOF){
1.53 brouard 4034: ungetc(c,ficpar);
4035: fgets(line, MAXLINE, ficpar);
1.85 brouard 4036: numlinepar++;
1.53 brouard 4037: puts(line);
4038: fputs(line,ficparo);
1.85 brouard 4039: fputs(line,ficlog);
1.53 brouard 4040: }
4041: ungetc(c,ficpar);
1.85 brouard 4042:
1.53 brouard 4043:
4044: covar=matrix(0,NCOVMAX,1,n);
1.58 lievre 4045: cptcovn=0; /*Number of covariates, i.e. number of '+' in model statement*/
1.53 brouard 4046: if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;
4047:
1.58 lievre 4048: ncovmodel=2+cptcovn; /*Number of variables = cptcovn + intercept + age */
1.53 brouard 4049: nvar=ncovmodel-1; /* Suppressing age as a basic covariate */
1.88 brouard 4050:
4051: if(mle==-1){ /* Print a wizard for help writing covariance matrix */
4052: prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
4053: printf(" You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
4054: fprintf(ficlog," You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
4055: fclose (ficparo);
4056: fclose (ficlog);
4057: exit(0);
4058: }
1.53 brouard 4059: /* Read guess parameters */
4060: /* Reads comments: lines beginning with '#' */
4061: while((c=getc(ficpar))=='#' && c!= EOF){
4062: ungetc(c,ficpar);
4063: fgets(line, MAXLINE, ficpar);
1.85 brouard 4064: numlinepar++;
1.53 brouard 4065: puts(line);
4066: fputs(line,ficparo);
1.85 brouard 4067: fputs(line,ficlog);
1.53 brouard 4068: }
4069: ungetc(c,ficpar);
1.85 brouard 4070:
1.53 brouard 4071: param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
1.85 brouard 4072: for(i=1; i <=nlstate; i++){
4073: j=0;
4074: for(jj=1; jj <=nlstate+ndeath; jj++){
4075: if(jj==i) continue;
4076: j++;
1.53 brouard 4077: fscanf(ficpar,"%1d%1d",&i1,&j1);
1.85 brouard 4078: if ((i1 != i) && (j1 != j)){
4079: printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n",numlinepar, i,j, i1, j1);
4080: exit(1);
4081: }
1.53 brouard 4082: fprintf(ficparo,"%1d%1d",i1,j1);
4083: if(mle==1)
4084: printf("%1d%1d",i,j);
4085: fprintf(ficlog,"%1d%1d",i,j);
4086: for(k=1; k<=ncovmodel;k++){
4087: fscanf(ficpar," %lf",¶m[i][j][k]);
4088: if(mle==1){
4089: printf(" %lf",param[i][j][k]);
4090: fprintf(ficlog," %lf",param[i][j][k]);
4091: }
4092: else
4093: fprintf(ficlog," %lf",param[i][j][k]);
4094: fprintf(ficparo," %lf",param[i][j][k]);
4095: }
4096: fscanf(ficpar,"\n");
1.85 brouard 4097: numlinepar++;
1.53 brouard 4098: if(mle==1)
4099: printf("\n");
4100: fprintf(ficlog,"\n");
4101: fprintf(ficparo,"\n");
4102: }
1.85 brouard 4103: }
4104: fflush(ficlog);
4105:
1.59 brouard 4106: npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/
1.53 brouard 4107:
4108: p=param[1][1];
4109:
4110: /* Reads comments: lines beginning with '#' */
4111: while((c=getc(ficpar))=='#' && c!= EOF){
4112: ungetc(c,ficpar);
4113: fgets(line, MAXLINE, ficpar);
1.85 brouard 4114: numlinepar++;
1.53 brouard 4115: puts(line);
4116: fputs(line,ficparo);
1.85 brouard 4117: fputs(line,ficlog);
1.53 brouard 4118: }
4119: ungetc(c,ficpar);
4120:
4121: delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
1.74 brouard 4122: /* delti=vector(1,npar); *//* Scale of each paramater (output from hesscov) */
1.53 brouard 4123: for(i=1; i <=nlstate; i++){
4124: for(j=1; j <=nlstate+ndeath-1; j++){
4125: fscanf(ficpar,"%1d%1d",&i1,&j1);
1.85 brouard 4126: if ((i1-i)*(j1-j)!=0){
4127: printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n",numlinepar, i,j, i1, j1);
4128: exit(1);
4129: }
1.53 brouard 4130: printf("%1d%1d",i,j);
4131: fprintf(ficparo,"%1d%1d",i1,j1);
1.85 brouard 4132: fprintf(ficlog,"%1d%1d",i1,j1);
1.53 brouard 4133: for(k=1; k<=ncovmodel;k++){
4134: fscanf(ficpar,"%le",&delti3[i][j][k]);
4135: printf(" %le",delti3[i][j][k]);
4136: fprintf(ficparo," %le",delti3[i][j][k]);
1.85 brouard 4137: fprintf(ficlog," %le",delti3[i][j][k]);
1.53 brouard 4138: }
4139: fscanf(ficpar,"\n");
1.85 brouard 4140: numlinepar++;
1.53 brouard 4141: printf("\n");
4142: fprintf(ficparo,"\n");
1.85 brouard 4143: fprintf(ficlog,"\n");
1.53 brouard 4144: }
4145: }
1.85 brouard 4146: fflush(ficlog);
4147:
1.53 brouard 4148: delti=delti3[1][1];
1.74 brouard 4149:
4150:
4151: /* 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 4152:
4153: /* Reads comments: lines beginning with '#' */
4154: while((c=getc(ficpar))=='#' && c!= EOF){
4155: ungetc(c,ficpar);
4156: fgets(line, MAXLINE, ficpar);
1.85 brouard 4157: numlinepar++;
1.53 brouard 4158: puts(line);
4159: fputs(line,ficparo);
1.85 brouard 4160: fputs(line,ficlog);
1.53 brouard 4161: }
4162: ungetc(c,ficpar);
4163:
4164: matcov=matrix(1,npar,1,npar);
4165: for(i=1; i <=npar; i++){
4166: fscanf(ficpar,"%s",&str);
4167: if(mle==1)
4168: printf("%s",str);
4169: fprintf(ficlog,"%s",str);
4170: fprintf(ficparo,"%s",str);
4171: for(j=1; j <=i; j++){
4172: fscanf(ficpar," %le",&matcov[i][j]);
4173: if(mle==1){
4174: printf(" %.5le",matcov[i][j]);
4175: }
1.85 brouard 4176: fprintf(ficlog," %.5le",matcov[i][j]);
1.53 brouard 4177: fprintf(ficparo," %.5le",matcov[i][j]);
4178: }
4179: fscanf(ficpar,"\n");
1.85 brouard 4180: numlinepar++;
1.53 brouard 4181: if(mle==1)
4182: printf("\n");
4183: fprintf(ficlog,"\n");
4184: fprintf(ficparo,"\n");
4185: }
4186: for(i=1; i <=npar; i++)
4187: for(j=i+1;j<=npar;j++)
4188: matcov[i][j]=matcov[j][i];
4189:
4190: if(mle==1)
4191: printf("\n");
4192: fprintf(ficlog,"\n");
4193:
1.85 brouard 4194: fflush(ficlog);
1.53 brouard 4195:
1.59 brouard 4196: /*-------- Rewriting paramater file ----------*/
4197: strcpy(rfileres,"r"); /* "Rparameterfile */
4198: strcat(rfileres,optionfilefiname); /* Parameter file first name*/
4199: strcat(rfileres,"."); /* */
4200: strcat(rfileres,optionfilext); /* Other files have txt extension */
4201: if((ficres =fopen(rfileres,"w"))==NULL) {
4202: printf("Problem writing new parameter file: %s\n", fileres);goto end;
4203: fprintf(ficlog,"Problem writing new parameter file: %s\n", fileres);goto end;
4204: }
4205: fprintf(ficres,"#%s\n",version);
1.53 brouard 4206:
1.59 brouard 4207: /*-------- data file ----------*/
4208: if((fic=fopen(datafile,"r"))==NULL) {
4209: printf("Problem with datafile: %s\n", datafile);goto end;
4210: fprintf(ficlog,"Problem with datafile: %s\n", datafile);goto end;
4211: }
4212:
4213: n= lastobs;
4214: severity = vector(1,maxwav);
4215: outcome=imatrix(1,maxwav+1,1,n);
1.85 brouard 4216: num=lvector(1,n);
1.59 brouard 4217: moisnais=vector(1,n);
4218: annais=vector(1,n);
4219: moisdc=vector(1,n);
4220: andc=vector(1,n);
4221: agedc=vector(1,n);
4222: cod=ivector(1,n);
4223: weight=vector(1,n);
4224: for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */
4225: mint=matrix(1,maxwav,1,n);
4226: anint=matrix(1,maxwav,1,n);
4227: s=imatrix(1,maxwav+1,1,n);
4228: tab=ivector(1,NCOVMAX);
4229: ncodemax=ivector(1,8);
4230:
4231: i=1;
4232: while (fgets(line, MAXLINE, fic) != NULL) {
4233: if ((i >= firstobs) && (i <=lastobs)) {
1.53 brouard 4234:
1.59 brouard 4235: for (j=maxwav;j>=1;j--){
4236: cutv(stra, strb,line,' '); s[j][i]=atoi(strb);
4237: strcpy(line,stra);
4238: cutv(stra, strb,line,'/'); anint[j][i]=(double)(atoi(strb)); strcpy(line,stra);
4239: cutv(stra, strb,line,' '); mint[j][i]=(double)(atoi(strb)); strcpy(line,stra);
4240: }
1.53 brouard 4241:
1.59 brouard 4242: cutv(stra, strb,line,'/'); andc[i]=(double)(atoi(strb)); strcpy(line,stra);
4243: cutv(stra, strb,line,' '); moisdc[i]=(double)(atoi(strb)); strcpy(line,stra);
1.53 brouard 4244:
1.59 brouard 4245: cutv(stra, strb,line,'/'); annais[i]=(double)(atoi(strb)); strcpy(line,stra);
4246: cutv(stra, strb,line,' '); moisnais[i]=(double)(atoi(strb)); strcpy(line,stra);
1.53 brouard 4247:
1.59 brouard 4248: cutv(stra, strb,line,' '); weight[i]=(double)(atoi(strb)); strcpy(line,stra);
4249: for (j=ncovcol;j>=1;j--){
4250: cutv(stra, strb,line,' '); covar[j][i]=(double)(atoi(strb)); strcpy(line,stra);
4251: }
1.85 brouard 4252: lstra=strlen(stra);
4253: if(lstra > 9){ /* More than 2**32 or max of what printf can write with %ld */
4254: stratrunc = &(stra[lstra-9]);
4255: num[i]=atol(stratrunc);
4256: }
4257: else
4258: num[i]=atol(stra);
1.53 brouard 4259:
1.59 brouard 4260: /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){
1.85 brouard 4261: 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 4262:
1.59 brouard 4263: i=i+1;
4264: }
4265: }
4266: /* printf("ii=%d", ij);
4267: scanf("%d",i);*/
1.53 brouard 4268: imx=i-1; /* Number of individuals */
4269:
4270: /* for (i=1; i<=imx; i++){
4271: if ((s[1][i]==3) && (s[2][i]==2)) s[2][i]=3;
4272: if ((s[2][i]==3) && (s[3][i]==2)) s[3][i]=3;
4273: if ((s[3][i]==3) && (s[4][i]==2)) s[4][i]=3;
4274: }*/
4275: /* for (i=1; i<=imx; i++){
4276: if (s[4][i]==9) s[4][i]=-1;
1.85 brouard 4277: 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 4278:
1.71 brouard 4279: for (i=1; i<=imx; i++)
1.53 brouard 4280:
1.71 brouard 4281: /*if ((s[3][i]==3) || (s[4][i]==3)) weight[i]=0.08;
4282: else weight[i]=1;*/
4283:
1.53 brouard 4284: /* Calculation of the number of parameter from char model*/
4285: Tvar=ivector(1,15); /* stores the number n of the covariates in Vm+Vn at 1 and m at 2 */
4286: Tprod=ivector(1,15);
4287: Tvaraff=ivector(1,15);
4288: Tvard=imatrix(1,15,1,2);
4289: Tage=ivector(1,15);
4290:
1.58 lievre 4291: if (strlen(model) >1){ /* If there is at least 1 covariate */
1.53 brouard 4292: j=0, j1=0, k1=1, k2=1;
1.58 lievre 4293: j=nbocc(model,'+'); /* j=Number of '+' */
4294: j1=nbocc(model,'*'); /* j1=Number of '*' */
4295: cptcovn=j+1;
4296: cptcovprod=j1; /*Number of products */
1.53 brouard 4297:
4298: strcpy(modelsav,model);
4299: if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){
4300: printf("Error. Non available option model=%s ",model);
4301: fprintf(ficlog,"Error. Non available option model=%s ",model);
4302: goto end;
4303: }
4304:
1.59 brouard 4305: /* This loop fills the array Tvar from the string 'model'.*/
1.58 lievre 4306:
1.53 brouard 4307: for(i=(j+1); i>=1;i--){
4308: cutv(stra,strb,modelsav,'+'); /* keeps in strb after the last + */
1.59 brouard 4309: if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyzes it */
1.53 brouard 4310: /* printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/
4311: /*scanf("%d",i);*/
4312: if (strchr(strb,'*')) { /* Model includes a product */
4313: cutv(strd,strc,strb,'*'); /* strd*strc Vm*Vn (if not *age)*/
4314: if (strcmp(strc,"age")==0) { /* Vn*age */
4315: cptcovprod--;
4316: cutv(strb,stre,strd,'V');
4317: Tvar[i]=atoi(stre); /* computes n in Vn and stores in Tvar*/
4318: cptcovage++;
4319: Tage[cptcovage]=i;
4320: /*printf("stre=%s ", stre);*/
4321: }
4322: else if (strcmp(strd,"age")==0) { /* or age*Vn */
4323: cptcovprod--;
4324: cutv(strb,stre,strc,'V');
4325: Tvar[i]=atoi(stre);
4326: cptcovage++;
4327: Tage[cptcovage]=i;
4328: }
4329: else { /* Age is not in the model */
4330: cutv(strb,stre,strc,'V'); /* strc= Vn, stre is n*/
4331: Tvar[i]=ncovcol+k1;
4332: cutv(strb,strc,strd,'V'); /* strd was Vm, strc is m */
4333: Tprod[k1]=i;
4334: Tvard[k1][1]=atoi(strc); /* m*/
4335: Tvard[k1][2]=atoi(stre); /* n */
4336: Tvar[cptcovn+k2]=Tvard[k1][1];
4337: Tvar[cptcovn+k2+1]=Tvard[k1][2];
4338: for (k=1; k<=lastobs;k++)
4339: covar[ncovcol+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];
4340: k1++;
4341: k2=k2+2;
4342: }
4343: }
4344: else { /* no more sum */
4345: /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/
4346: /* scanf("%d",i);*/
4347: cutv(strd,strc,strb,'V');
4348: Tvar[i]=atoi(strc);
4349: }
4350: strcpy(modelsav,stra);
4351: /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);
4352: scanf("%d",i);*/
4353: } /* end of loop + */
4354: } /* end model */
4355:
1.58 lievre 4356: /*The number n of Vn is stored in Tvar. cptcovage =number of age covariate. Tage gives the position of age. cptcovprod= number of products.
4357: If model=V1+V1*age then Tvar[1]=1 Tvar[2]=1 cptcovage=1 Tage[1]=2 cptcovprod=0*/
4358:
1.53 brouard 4359: /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);
4360: printf("cptcovprod=%d ", cptcovprod);
4361: fprintf(ficlog,"cptcovprod=%d ", cptcovprod);
1.58 lievre 4362:
4363: scanf("%d ",i);
4364: fclose(fic);*/
1.53 brouard 4365:
4366: /* if(mle==1){*/
1.59 brouard 4367: if (weightopt != 1) { /* Maximisation without weights*/
4368: for(i=1;i<=n;i++) weight[i]=1.0;
4369: }
1.53 brouard 4370: /*-calculation of age at interview from date of interview and age at death -*/
1.59 brouard 4371: agev=matrix(1,maxwav,1,imx);
1.53 brouard 4372:
1.59 brouard 4373: for (i=1; i<=imx; i++) {
4374: for(m=2; (m<= maxwav); m++) {
1.76 brouard 4375: if (((int)mint[m][i]== 99) && (s[m][i] <= nlstate)){
1.59 brouard 4376: anint[m][i]=9999;
4377: s[m][i]=-1;
4378: }
1.76 brouard 4379: if((int)moisdc[i]==99 && (int)andc[i]==9999 && s[m][i]>nlstate){
1.91 brouard 4380: nberr++;
1.85 brouard 4381: 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);
4382: 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 4383: s[m][i]=-1;
4384: }
4385: if((int)moisdc[i]==99 && (int)andc[i]!=9999 && s[m][i]>nlstate){
1.91 brouard 4386: nberr++;
1.85 brouard 4387: 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]);
4388: 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 4389: s[m][i]=-1; /* We prefer to skip it (and to skip it in version 0.8a1 too */
1.76 brouard 4390: }
1.53 brouard 4391: }
1.59 brouard 4392: }
1.53 brouard 4393:
1.59 brouard 4394: for (i=1; i<=imx; i++) {
4395: agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);
1.71 brouard 4396: for(m=firstpass; (m<= lastpass); m++){
1.69 brouard 4397: if(s[m][i] >0){
1.59 brouard 4398: if (s[m][i] >= nlstate+1) {
4399: if(agedc[i]>0)
1.76 brouard 4400: if((int)moisdc[i]!=99 && (int)andc[i]!=9999)
1.69 brouard 4401: agev[m][i]=agedc[i];
1.59 brouard 4402: /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/
4403: else {
1.76 brouard 4404: if ((int)andc[i]!=9999){
1.91 brouard 4405: nbwarn++;
1.85 brouard 4406: printf("Warning negative age at death: %ld line:%d\n",num[i],i);
4407: fprintf(ficlog,"Warning negative age at death: %ld line:%d\n",num[i],i);
1.59 brouard 4408: agev[m][i]=-1;
1.53 brouard 4409: }
4410: }
1.70 brouard 4411: }
1.69 brouard 4412: else if(s[m][i] !=9){ /* Standard case, age in fractional
4413: years but with the precision of a
4414: month */
1.59 brouard 4415: agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);
1.76 brouard 4416: if((int)mint[m][i]==99 || (int)anint[m][i]==9999)
1.59 brouard 4417: agev[m][i]=1;
4418: else if(agev[m][i] <agemin){
4419: agemin=agev[m][i];
4420: /*printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], agemin);*/
1.53 brouard 4421: }
1.59 brouard 4422: else if(agev[m][i] >agemax){
4423: agemax=agev[m][i];
4424: /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/
1.53 brouard 4425: }
1.59 brouard 4426: /*agev[m][i]=anint[m][i]-annais[i];*/
4427: /* agev[m][i] = age[i]+2*m;*/
1.53 brouard 4428: }
1.59 brouard 4429: else { /* =9 */
1.53 brouard 4430: agev[m][i]=1;
1.59 brouard 4431: s[m][i]=-1;
4432: }
1.53 brouard 4433: }
1.59 brouard 4434: else /*= 0 Unknown */
4435: agev[m][i]=1;
4436: }
1.53 brouard 4437:
1.59 brouard 4438: }
4439: for (i=1; i<=imx; i++) {
1.71 brouard 4440: for(m=firstpass; (m<=lastpass); m++){
1.59 brouard 4441: if (s[m][i] > (nlstate+ndeath)) {
1.91 brouard 4442: nberr++;
1.59 brouard 4443: 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);
4444: 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);
4445: goto end;
1.53 brouard 4446: }
4447: }
1.59 brouard 4448: }
1.53 brouard 4449:
1.71 brouard 4450: /*for (i=1; i<=imx; i++){
4451: for (m=firstpass; (m<lastpass); m++){
1.85 brouard 4452: 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 4453: }
4454:
4455: }*/
4456:
1.59 brouard 4457: printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);
4458: fprintf(ficlog,"Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);
4459:
4460: free_vector(severity,1,maxwav);
4461: free_imatrix(outcome,1,maxwav+1,1,n);
4462: free_vector(moisnais,1,n);
4463: free_vector(annais,1,n);
4464: /* free_matrix(mint,1,maxwav,1,n);
4465: free_matrix(anint,1,maxwav,1,n);*/
4466: free_vector(moisdc,1,n);
4467: free_vector(andc,1,n);
1.53 brouard 4468:
4469:
1.59 brouard 4470: wav=ivector(1,imx);
4471: dh=imatrix(1,lastpass-firstpass+1,1,imx);
4472: bh=imatrix(1,lastpass-firstpass+1,1,imx);
4473: mw=imatrix(1,lastpass-firstpass+1,1,imx);
1.69 brouard 4474:
1.59 brouard 4475: /* Concatenates waves */
4476: concatwav(wav, dh, bh, mw, s, agedc, agev, firstpass, lastpass, imx, nlstate, stepm);
1.53 brouard 4477:
1.59 brouard 4478: /* Routine tricode is to calculate cptcoveff (real number of unique covariates) and to associate covariable number and modality */
1.53 brouard 4479:
1.59 brouard 4480: Tcode=ivector(1,100);
4481: nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);
4482: ncodemax[1]=1;
4483: if (cptcovn > 0) tricode(Tvar,nbcode,imx);
1.53 brouard 4484:
1.59 brouard 4485: codtab=imatrix(1,100,1,10); /* Cross tabulation to get the order of
4486: the estimations*/
4487: h=0;
4488: m=pow(2,cptcoveff);
1.53 brouard 4489:
1.59 brouard 4490: for(k=1;k<=cptcoveff; k++){
4491: for(i=1; i <=(m/pow(2,k));i++){
4492: for(j=1; j <= ncodemax[k]; j++){
4493: for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){
4494: h++;
4495: if (h>m) h=1;codtab[h][k]=j;codtab[h][Tvar[k]]=j;
4496: /* printf("h=%d k=%d j=%d codtab[h][k]=%d tvar[k]=%d \n",h, k,j,codtab[h][k],Tvar[k]);*/
4497: }
4498: }
4499: }
4500: }
4501: /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]);
4502: codtab[1][2]=1;codtab[2][2]=2; */
4503: /* for(i=1; i <=m ;i++){
4504: for(k=1; k <=cptcovn; k++){
4505: printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);
4506: }
4507: printf("\n");
1.53 brouard 4508: }
1.59 brouard 4509: scanf("%d",i);*/
1.53 brouard 4510:
1.86 brouard 4511: /*------------ gnuplot -------------*/
4512: strcpy(optionfilegnuplot,optionfilefiname);
4513: strcat(optionfilegnuplot,".gp");
4514: if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {
4515: printf("Problem with file %s",optionfilegnuplot);
4516: }
4517: else{
4518: fprintf(ficgp,"\n# %s\n", version);
4519: fprintf(ficgp,"# %s\n", optionfilegnuplot);
4520: fprintf(ficgp,"set missing 'NaNq'\n");
4521: }
1.88 brouard 4522: /* fclose(ficgp);*/
1.86 brouard 4523: /*--------- index.htm --------*/
4524:
1.91 brouard 4525: strcpy(optionfilehtm,optionfilefiname); /* Main html file */
1.86 brouard 4526: strcat(optionfilehtm,".htm");
4527: if((fichtm=fopen(optionfilehtm,"w"))==NULL) {
4528: printf("Problem with %s \n",optionfilehtm), exit(0);
4529: }
4530:
1.91 brouard 4531: strcpy(optionfilehtmcov,optionfilefiname); /* Only for matrix of covariance */
4532: strcat(optionfilehtmcov,"-cov.htm");
4533: if((fichtmcov=fopen(optionfilehtmcov,"w"))==NULL) {
4534: printf("Problem with %s \n",optionfilehtmcov), exit(0);
4535: }
4536: else{
4537: fprintf(fichtmcov,"<body>\n<title>IMaCh Cov %s</title>\n <font size=\"2\">%s <br> %s</font> \
4538: <hr size=\"2\" color=\"#EC5E5E\"> \n\
4539: Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n",\
4540: fileres,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);
4541: }
4542:
1.87 brouard 4543: fprintf(fichtm,"<body>\n<title>IMaCh %s</title>\n <font size=\"2\">%s <br> %s</font> \
1.86 brouard 4544: <hr size=\"2\" color=\"#EC5E5E\"> \n\
4545: Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n\
4546: \n\
4547: <hr size=\"2\" color=\"#EC5E5E\">\
4548: <ul><li><h4>Parameter files</h4>\n\
4549: - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n\
4550: - Log file of the run: <a href=\"%s\">%s</a><br>\n\
1.87 brouard 4551: - Gnuplot file name: <a href=\"%s\">%s</a><br>\n\
1.86 brouard 4552: - Date and time at start: %s</ul>\n",\
1.91 brouard 4553: fileres,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model,\
4554: fileres,fileres,\
1.88 brouard 4555: filelog,filelog,optionfilegnuplot,optionfilegnuplot,strstart);
1.87 brouard 4556: fflush(fichtm);
1.86 brouard 4557:
1.88 brouard 4558: strcpy(pathr,path);
4559: strcat(pathr,optionfilefiname);
4560: chdir(optionfilefiname); /* Move to directory named optionfile */
4561:
1.59 brouard 4562: /* Calculates basic frequencies. Computes observed prevalence at single age
4563: and prints on file fileres'p'. */
1.84 brouard 4564: freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint);
1.53 brouard 4565:
1.88 brouard 4566: fprintf(fichtm,"\n");
4567: fprintf(fichtm,"<br>Total number of observations=%d <br>\n\
1.86 brouard 4568: Youngest age at first (selected) pass %.2f, oldest age %.2f<br>\n\
4569: Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n",\
1.88 brouard 4570: imx,agemin,agemax,jmin,jmax,jmean);
4571: pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
1.60 brouard 4572: oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
4573: newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
4574: savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
4575: oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */
1.53 brouard 4576:
4577:
1.59 brouard 4578: /* For Powell, parameters are in a vector p[] starting at p[1]
4579: so we point p on param[1][1] so that p[1] maps on param[1][1][1] */
4580: p=param[1][1]; /* *(*(*(param +1)+1)+0) */
1.53 brouard 4581:
1.86 brouard 4582: globpr=0; /* To get the number ipmx of contributions and the sum of weights*/
1.85 brouard 4583: likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
4584: printf("First Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
4585: for (k=1; k<=npar;k++)
4586: printf(" %d %8.5f",k,p[k]);
4587: printf("\n");
4588: globpr=1; /* to print the contributions */
4589: likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
4590: printf("Second Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
4591: for (k=1; k<=npar;k++)
4592: printf(" %d %8.5f",k,p[k]);
4593: printf("\n");
1.61 brouard 4594: if(mle>=1){ /* Could be 1 or 2 */
1.53 brouard 4595: mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);
1.59 brouard 4596: }
1.53 brouard 4597:
1.59 brouard 4598: /*--------- results files --------------*/
4599: 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 4600:
4601:
1.59 brouard 4602: jk=1;
4603: fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
4604: printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
4605: fprintf(ficlog,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
4606: for(i=1,jk=1; i <=nlstate; i++){
4607: for(k=1; k <=(nlstate+ndeath); k++){
4608: if (k != i)
4609: {
4610: printf("%d%d ",i,k);
4611: fprintf(ficlog,"%d%d ",i,k);
4612: fprintf(ficres,"%1d%1d ",i,k);
4613: for(j=1; j <=ncovmodel; j++){
4614: printf("%f ",p[jk]);
4615: fprintf(ficlog,"%f ",p[jk]);
4616: fprintf(ficres,"%f ",p[jk]);
4617: jk++;
4618: }
4619: printf("\n");
4620: fprintf(ficlog,"\n");
4621: fprintf(ficres,"\n");
4622: }
4623: }
4624: }
1.84 brouard 4625: if(mle!=0){
1.59 brouard 4626: /* Computing hessian and covariance matrix */
4627: ftolhess=ftol; /* Usually correct */
4628: hesscov(matcov, p, npar, delti, ftolhess, func);
4629: }
4630: fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");
4631: printf("# Scales (for hessian or gradient estimation)\n");
4632: fprintf(ficlog,"# Scales (for hessian or gradient estimation)\n");
4633: for(i=1,jk=1; i <=nlstate; i++){
4634: for(j=1; j <=nlstate+ndeath; j++){
4635: if (j!=i) {
4636: fprintf(ficres,"%1d%1d",i,j);
4637: printf("%1d%1d",i,j);
4638: fprintf(ficlog,"%1d%1d",i,j);
4639: for(k=1; k<=ncovmodel;k++){
4640: printf(" %.5e",delti[jk]);
4641: fprintf(ficlog," %.5e",delti[jk]);
4642: fprintf(ficres," %.5e",delti[jk]);
4643: jk++;
4644: }
4645: printf("\n");
4646: fprintf(ficlog,"\n");
4647: fprintf(ficres,"\n");
4648: }
4649: }
4650: }
1.53 brouard 4651:
1.59 brouard 4652: 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");
4653: if(mle==1)
4654: 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");
4655: 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");
4656: for(i=1,k=1;i<=npar;i++){
4657: /* if (k>nlstate) k=1;
4658: i1=(i-1)/(ncovmodel*nlstate)+1;
4659: fprintf(ficres,"%s%d%d",alph[k],i1,tab[i]);
4660: printf("%s%d%d",alph[k],i1,tab[i]);
4661: */
4662: fprintf(ficres,"%3d",i);
4663: if(mle==1)
4664: printf("%3d",i);
4665: fprintf(ficlog,"%3d",i);
4666: for(j=1; j<=i;j++){
4667: fprintf(ficres," %.5e",matcov[i][j]);
4668: if(mle==1)
4669: printf(" %.5e",matcov[i][j]);
4670: fprintf(ficlog," %.5e",matcov[i][j]);
4671: }
4672: fprintf(ficres,"\n");
4673: if(mle==1)
4674: printf("\n");
4675: fprintf(ficlog,"\n");
4676: k++;
4677: }
1.53 brouard 4678:
1.59 brouard 4679: while((c=getc(ficpar))=='#' && c!= EOF){
4680: ungetc(c,ficpar);
4681: fgets(line, MAXLINE, ficpar);
4682: puts(line);
4683: fputs(line,ficparo);
4684: }
4685: ungetc(c,ficpar);
4686:
4687: estepm=0;
4688: fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm);
4689: if (estepm==0 || estepm < stepm) estepm=stepm;
4690: if (fage <= 2) {
4691: bage = ageminpar;
4692: fage = agemaxpar;
4693: }
1.53 brouard 4694:
1.59 brouard 4695: fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");
4696: fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
4697: fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
1.53 brouard 4698:
1.59 brouard 4699: while((c=getc(ficpar))=='#' && c!= EOF){
4700: ungetc(c,ficpar);
4701: fgets(line, MAXLINE, ficpar);
4702: puts(line);
4703: fputs(line,ficparo);
4704: }
4705: ungetc(c,ficpar);
1.53 brouard 4706:
1.59 brouard 4707: 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);
4708: 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);
4709: 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 4710: printf("begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
4711: 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 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:
4721:
1.70 brouard 4722: dateprev1=anprev1+(mprev1-1)/12.+(jprev1-1)/365.;
4723: dateprev2=anprev2+(mprev2-1)/12.+(jprev2-1)/365.;
1.53 brouard 4724:
4725: fscanf(ficpar,"pop_based=%d\n",&popbased);
4726: fprintf(ficparo,"pop_based=%d\n",popbased);
4727: fprintf(ficres,"pop_based=%d\n",popbased);
4728:
4729: while((c=getc(ficpar))=='#' && c!= EOF){
4730: ungetc(c,ficpar);
4731: fgets(line, MAXLINE, ficpar);
4732: puts(line);
4733: fputs(line,ficparo);
4734: }
4735: ungetc(c,ficpar);
4736:
1.69 brouard 4737: 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 4738: 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 4739: 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);
4740: 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);
4741: 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 4742: /* day and month of proj2 are not used but only year anproj2.*/
1.53 brouard 4743:
1.59 brouard 4744: while((c=getc(ficpar))=='#' && c!= EOF){
1.53 brouard 4745: ungetc(c,ficpar);
4746: fgets(line, MAXLINE, ficpar);
4747: puts(line);
4748: fputs(line,ficparo);
4749: }
4750: ungetc(c,ficpar);
4751:
4752: fscanf(ficpar,"popforecast=%d popfile=%s popfiledate=%lf/%lf/%lf last-popfiledate=%lf/%lf/%lf\n",&popforecast,popfile,&jpyram,&mpyram,&anpyram,&jpyram1,&mpyram1,&anpyram1);
4753: fprintf(ficparo,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);
4754: fprintf(ficres,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);
4755:
1.86 brouard 4756: /* freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint);*/
1.84 brouard 4757: /*,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
1.58 lievre 4758:
1.89 brouard 4759: replace_back_to_slash(pathc,path); /* Even gnuplot wants a / */
4760: printinggnuplot(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
1.53 brouard 4761:
1.85 brouard 4762: printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,\
4763: model,imx,jmin,jmax,jmean,rfileres,popforecast,estepm,\
4764: jprev1,mprev1,anprev1,jprev2,mprev2,anprev2);
1.53 brouard 4765:
1.59 brouard 4766: /*------------ free_vector -------------*/
1.88 brouard 4767: /* chdir(path); */
1.53 brouard 4768:
1.59 brouard 4769: free_ivector(wav,1,imx);
4770: free_imatrix(dh,1,lastpass-firstpass+1,1,imx);
4771: free_imatrix(bh,1,lastpass-firstpass+1,1,imx);
4772: free_imatrix(mw,1,lastpass-firstpass+1,1,imx);
1.85 brouard 4773: free_lvector(num,1,n);
1.59 brouard 4774: free_vector(agedc,1,n);
1.65 lievre 4775: /*free_matrix(covar,0,NCOVMAX,1,n);*/
1.59 brouard 4776: /*free_matrix(covar,1,NCOVMAX,1,n);*/
4777: fclose(ficparo);
4778: fclose(ficres);
1.53 brouard 4779:
4780:
1.54 brouard 4781: /*--------------- Prevalence limit (stable prevalence) --------------*/
1.53 brouard 4782:
4783: strcpy(filerespl,"pl");
4784: strcat(filerespl,fileres);
4785: if((ficrespl=fopen(filerespl,"w"))==NULL) {
1.54 brouard 4786: printf("Problem with stable prevalence resultfile: %s\n", filerespl);goto end;
4787: fprintf(ficlog,"Problem with stable prevalence resultfile: %s\n", filerespl);goto end;
1.53 brouard 4788: }
1.54 brouard 4789: printf("Computing stable prevalence: result on file '%s' \n", filerespl);
4790: fprintf(ficlog,"Computing stable prevalence: result on file '%s' \n", filerespl);
4791: fprintf(ficrespl,"#Stable prevalence \n");
1.53 brouard 4792: fprintf(ficrespl,"#Age ");
4793: for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);
4794: fprintf(ficrespl,"\n");
4795:
4796: prlim=matrix(1,nlstate,1,nlstate);
1.59 brouard 4797:
1.53 brouard 4798: agebase=ageminpar;
4799: agelim=agemaxpar;
4800: ftolpl=1.e-10;
4801: i1=cptcoveff;
4802: if (cptcovn < 1){i1=1;}
4803:
1.59 brouard 4804: for(cptcov=1,k=0;cptcov<=i1;cptcov++){
1.53 brouard 4805: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
1.59 brouard 4806: k=k+1;
4807: /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/
4808: fprintf(ficrespl,"\n#******");
4809: printf("\n#******");
4810: fprintf(ficlog,"\n#******");
4811: for(j=1;j<=cptcoveff;j++) {
4812: fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
4813: printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
4814: fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
4815: }
4816: fprintf(ficrespl,"******\n");
4817: printf("******\n");
4818: fprintf(ficlog,"******\n");
1.53 brouard 4819:
1.59 brouard 4820: for (age=agebase; age<=agelim; age++){
4821: prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
1.69 brouard 4822: fprintf(ficrespl,"%.0f ",age );
4823: for(j=1;j<=cptcoveff;j++)
4824: fprintf(ficrespl,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
1.59 brouard 4825: for(i=1; i<=nlstate;i++)
1.53 brouard 4826: fprintf(ficrespl," %.5f", prlim[i][i]);
1.59 brouard 4827: fprintf(ficrespl,"\n");
1.53 brouard 4828: }
4829: }
1.59 brouard 4830: }
1.53 brouard 4831: fclose(ficrespl);
4832:
4833: /*------------- h Pij x at various ages ------------*/
4834:
4835: strcpy(filerespij,"pij"); strcat(filerespij,fileres);
4836: if((ficrespij=fopen(filerespij,"w"))==NULL) {
4837: printf("Problem with Pij resultfile: %s\n", filerespij);goto end;
4838: fprintf(ficlog,"Problem with Pij resultfile: %s\n", filerespij);goto end;
4839: }
4840: printf("Computing pij: result on file '%s' \n", filerespij);
4841: fprintf(ficlog,"Computing pij: result on file '%s' \n", filerespij);
4842:
4843: stepsize=(int) (stepm+YEARM-1)/YEARM;
4844: /*if (stepm<=24) stepsize=2;*/
4845:
4846: agelim=AGESUP;
4847: hstepm=stepsize*YEARM; /* Every year of age */
4848: hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */
4849:
4850: /* hstepm=1; aff par mois*/
4851:
1.70 brouard 4852: fprintf(ficrespij,"#****** h Pij x Probability to be in state j at age x+h being in i at x ");
1.59 brouard 4853: for(cptcov=1,k=0;cptcov<=i1;cptcov++){
1.53 brouard 4854: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
4855: k=k+1;
1.59 brouard 4856: fprintf(ficrespij,"\n#****** ");
4857: for(j=1;j<=cptcoveff;j++)
4858: fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
4859: fprintf(ficrespij,"******\n");
1.53 brouard 4860:
1.59 brouard 4861: for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */
4862: nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
4863: nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
4864:
4865: /* nhstepm=nhstepm*YEARM; aff par mois*/
4866:
4867: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4868: oldm=oldms;savm=savms;
4869: hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
1.70 brouard 4870: fprintf(ficrespij,"# Cov Agex agex+h hpijx with i,j=");
1.59 brouard 4871: for(i=1; i<=nlstate;i++)
4872: for(j=1; j<=nlstate+ndeath;j++)
4873: fprintf(ficrespij," %1d-%1d",i,j);
4874: fprintf(ficrespij,"\n");
4875: for (h=0; h<=nhstepm; h++){
1.70 brouard 4876: fprintf(ficrespij,"%d %3.f %3.f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );
1.53 brouard 4877: for(i=1; i<=nlstate;i++)
4878: for(j=1; j<=nlstate+ndeath;j++)
1.59 brouard 4879: fprintf(ficrespij," %.5f", p3mat[i][j][h]);
1.53 brouard 4880: fprintf(ficrespij,"\n");
4881: }
1.59 brouard 4882: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4883: fprintf(ficrespij,"\n");
4884: }
1.53 brouard 4885: }
4886: }
4887:
1.74 brouard 4888: varprob(optionfilefiname, matcov, p, delti, nlstate, bage, fage,k,Tvar,nbcode, ncodemax);
1.53 brouard 4889:
4890: fclose(ficrespij);
4891:
1.84 brouard 4892: probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
1.53 brouard 4893:
4894: /*---------- Forecasting ------------------*/
1.69 brouard 4895: /*if((stepm == 1) && (strcmp(model,".")==0)){*/
4896: if(prevfcast==1){
1.74 brouard 4897: /* if(stepm ==1){*/
1.70 brouard 4898: prevforecast(fileres, anproj1, mproj1, jproj1, agemin, agemax, dateprev1, dateprev2, mobilavproj, bage, fage, firstpass, lastpass, anproj2, p, cptcoveff);
1.74 brouard 4899: /* (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);*/
4900: /* } */
4901: /* else{ */
4902: /* erreur=108; */
4903: /* 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); */
4904: /* 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); */
4905: /* } */
1.69 brouard 4906: }
1.53 brouard 4907:
4908:
4909: /*---------- Health expectancies and variances ------------*/
4910:
4911: strcpy(filerest,"t");
4912: strcat(filerest,fileres);
4913: if((ficrest=fopen(filerest,"w"))==NULL) {
4914: printf("Problem with total LE resultfile: %s\n", filerest);goto end;
4915: fprintf(ficlog,"Problem with total LE resultfile: %s\n", filerest);goto end;
4916: }
4917: printf("Computing Total LEs with variances: file '%s' \n", filerest);
4918: fprintf(ficlog,"Computing Total LEs with variances: file '%s' \n", filerest);
4919:
4920:
4921: strcpy(filerese,"e");
4922: strcat(filerese,fileres);
4923: if((ficreseij=fopen(filerese,"w"))==NULL) {
4924: printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
4925: fprintf(ficlog,"Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
4926: }
4927: printf("Computing Health Expectancies: result on file '%s' \n", filerese);
4928: fprintf(ficlog,"Computing Health Expectancies: result on file '%s' \n", filerese);
1.68 lievre 4929:
1.53 brouard 4930: strcpy(fileresv,"v");
4931: strcat(fileresv,fileres);
4932: if((ficresvij=fopen(fileresv,"w"))==NULL) {
4933: printf("Problem with variance resultfile: %s\n", fileresv);exit(0);
4934: fprintf(ficlog,"Problem with variance resultfile: %s\n", fileresv);exit(0);
4935: }
4936: printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
4937: fprintf(ficlog,"Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
1.58 lievre 4938:
1.74 brouard 4939: /* Computes prevalence between agemin (i.e minimal age computed) and no more ageminpar */
1.84 brouard 4940: prevalence(probs, agemin, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
1.74 brouard 4941: /* 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",\
4942: ageminpar, agemax, s[lastpass][imx], agev[lastpass][imx], nlstate, imx, mint[lastpass][imx],anint[lastpass][imx], dateprev1, dateprev2, firstpass, lastpass);
4943: */
1.58 lievre 4944:
1.54 brouard 4945: if (mobilav!=0) {
1.53 brouard 4946: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
1.54 brouard 4947: if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
4948: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
4949: printf(" Error in movingaverage mobilav=%d\n",mobilav);
4950: }
1.53 brouard 4951: }
4952:
1.59 brouard 4953: for(cptcov=1,k=0;cptcov<=i1;cptcov++){
1.53 brouard 4954: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
4955: k=k+1;
4956: fprintf(ficrest,"\n#****** ");
4957: for(j=1;j<=cptcoveff;j++)
4958: fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
4959: fprintf(ficrest,"******\n");
4960:
4961: fprintf(ficreseij,"\n#****** ");
4962: for(j=1;j<=cptcoveff;j++)
4963: fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
4964: fprintf(ficreseij,"******\n");
4965:
4966: fprintf(ficresvij,"\n#****** ");
4967: for(j=1;j<=cptcoveff;j++)
4968: fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
4969: fprintf(ficresvij,"******\n");
4970:
4971: eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
4972: oldm=oldms;savm=savms;
4973: evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov);
4974:
4975: vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
4976: oldm=oldms;savm=savms;
4977: varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,0, mobilav);
4978: if(popbased==1){
4979: 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 4980: }
1.53 brouard 4981:
4982:
4983: fprintf(ficrest,"#Total LEs with variances: e.. (std) ");
4984: for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);
4985: fprintf(ficrest,"\n");
4986:
4987: epj=vector(1,nlstate+1);
4988: for(age=bage; age <=fage ;age++){
4989: prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
4990: if (popbased==1) {
1.54 brouard 4991: if(mobilav ==0){
1.53 brouard 4992: for(i=1; i<=nlstate;i++)
4993: prlim[i][i]=probs[(int)age][i][k];
1.54 brouard 4994: }else{ /* mobilav */
1.53 brouard 4995: for(i=1; i<=nlstate;i++)
4996: prlim[i][i]=mobaverage[(int)age][i][k];
4997: }
4998: }
4999:
5000: fprintf(ficrest," %4.0f",age);
5001: for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){
5002: for(i=1, epj[j]=0.;i <=nlstate;i++) {
5003: epj[j] += prlim[i][i]*eij[i][j][(int)age];
5004: /* printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/
5005: }
5006: epj[nlstate+1] +=epj[j];
5007: }
5008:
5009: for(i=1, vepp=0.;i <=nlstate;i++)
5010: for(j=1;j <=nlstate;j++)
5011: vepp += vareij[i][j][(int)age];
5012: fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));
5013: for(j=1;j <=nlstate;j++){
5014: fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));
5015: }
5016: fprintf(ficrest,"\n");
5017: }
1.59 brouard 5018: free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
5019: free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);
5020: free_vector(epj,1,nlstate+1);
1.53 brouard 5021: }
5022: }
1.59 brouard 5023: free_vector(weight,1,n);
5024: free_imatrix(Tvard,1,15,1,2);
5025: free_imatrix(s,1,maxwav+1,1,n);
5026: free_matrix(anint,1,maxwav,1,n);
5027: free_matrix(mint,1,maxwav,1,n);
5028: free_ivector(cod,1,n);
5029: free_ivector(tab,1,NCOVMAX);
1.53 brouard 5030: fclose(ficreseij);
5031: fclose(ficresvij);
5032: fclose(ficrest);
5033: fclose(ficpar);
5034:
1.54 brouard 5035: /*------- Variance of stable prevalence------*/
1.53 brouard 5036:
5037: strcpy(fileresvpl,"vpl");
5038: strcat(fileresvpl,fileres);
5039: if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {
1.54 brouard 5040: printf("Problem with variance of stable prevalence resultfile: %s\n", fileresvpl);
1.53 brouard 5041: exit(0);
5042: }
1.54 brouard 5043: printf("Computing Variance-covariance of stable prevalence: file '%s' \n", fileresvpl);
1.53 brouard 5044:
1.59 brouard 5045: for(cptcov=1,k=0;cptcov<=i1;cptcov++){
1.53 brouard 5046: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
5047: k=k+1;
5048: fprintf(ficresvpl,"\n#****** ");
5049: for(j=1;j<=cptcoveff;j++)
5050: fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
5051: fprintf(ficresvpl,"******\n");
5052:
5053: varpl=matrix(1,nlstate,(int) bage, (int) fage);
5054: oldm=oldms;savm=savms;
1.59 brouard 5055: varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);
5056: free_matrix(varpl,1,nlstate,(int) bage, (int)fage);
1.53 brouard 5057: }
1.59 brouard 5058: }
1.53 brouard 5059:
5060: fclose(ficresvpl);
5061:
5062: /*---------- End : free ----------------*/
5063: free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);
5064: free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);
5065: free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);
5066: free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);
1.65 lievre 5067:
5068: free_matrix(covar,0,NCOVMAX,1,n);
1.53 brouard 5069: free_matrix(matcov,1,npar,1,npar);
1.74 brouard 5070: /*free_vector(delti,1,npar);*/
5071: free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
1.53 brouard 5072: free_matrix(agev,1,maxwav,1,imx);
5073: free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
1.54 brouard 5074: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
1.74 brouard 5075: free_ma3x(probs,1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
5076:
1.59 brouard 5077: free_ivector(ncodemax,1,8);
5078: free_ivector(Tvar,1,15);
5079: free_ivector(Tprod,1,15);
5080: free_ivector(Tvaraff,1,15);
5081: free_ivector(Tage,1,15);
5082: free_ivector(Tcode,1,100);
1.53 brouard 5083:
1.88 brouard 5084: fflush(fichtm);
5085: fflush(ficgp);
1.53 brouard 5086:
5087:
1.91 brouard 5088: if((nberr >0) || (nbwarn>0)){
5089: printf("End of Imach with %d errors and/or warnings %d\n",nberr,nbwarn);
5090: fprintf(ficlog,"End of Imach with %d errors and/or warnings %d\n",nberr,nbwarn);
1.53 brouard 5091: }else{
1.91 brouard 5092: printf("End of Imach\n");
5093: fprintf(ficlog,"End of Imach\n");
1.53 brouard 5094: }
5095: printf("See log file on %s\n",filelog);
5096: /* gettimeofday(&end_time, (struct timezone*)0);*/ /* after time */
1.85 brouard 5097: (void) gettimeofday(&end_time,&tzp);
5098: tm = *localtime(&end_time.tv_sec);
5099: tmg = *gmtime(&end_time.tv_sec);
1.88 brouard 5100: strcpy(strtend,asctime(&tm));
1.94 ! brouard 5101: printf("Local time at start %s\nLocaltime at end %s",strstart, strtend);
! 5102: fprintf(ficlog,"Local time at start %s\nLocal time at end %s\n",strstart, strtend);
1.91 brouard 5103: printf("Total time used %s\n", asc_diff_time(end_time.tv_sec -start_time.tv_sec,tmpout));
1.85 brouard 5104:
1.91 brouard 5105: printf("Total time was %d Sec.\n", end_time.tv_sec -start_time.tv_sec);
5106: fprintf(ficlog,"Total time used %s\n", asc_diff_time(end_time.tv_sec -start_time.tv_sec,tmpout));
5107: fprintf(ficlog,"Total time was %d Sec.\n", end_time.tv_sec -start_time.tv_sec);
1.85 brouard 5108: /* printf("Total time was %d uSec.\n", total_usecs);*/
1.87 brouard 5109: /* if(fileappend(fichtm,optionfilehtm)){ */
1.88 brouard 5110: fprintf(fichtm,"<br>Local time at start %s<br>Local time at end %s<br>",strstart, strtend);
1.87 brouard 5111: fclose(fichtm);
1.91 brouard 5112: fclose(fichtmcov);
1.88 brouard 5113: fclose(ficgp);
1.91 brouard 5114: fclose(ficlog);
1.53 brouard 5115: /*------ End -----------*/
5116:
1.88 brouard 5117: chdir(path);
1.59 brouard 5118: strcpy(plotcmd,GNUPLOTPROGRAM);
5119: strcat(plotcmd," ");
5120: strcat(plotcmd,optionfilegnuplot);
1.75 brouard 5121: printf("Starting graphs with: %s",plotcmd);fflush(stdout);
1.91 brouard 5122: if((outcmd=system(plotcmd)) != 0){
5123: printf(" Problem with gnuplot\n");
5124: }
1.75 brouard 5125: printf(" Wait...");
1.53 brouard 5126: while (z[0] != 'q') {
5127: /* chdir(path); */
1.91 brouard 5128: printf("\nType e to edit output files, g to graph again and q for exiting: ");
1.53 brouard 5129: scanf("%s",z);
1.91 brouard 5130: /* if (z[0] == 'c') system("./imach"); */
5131: if (z[0] == 'e') system(optionfilehtm);
1.53 brouard 5132: else if (z[0] == 'g') system(plotcmd);
5133: else if (z[0] == 'q') exit(0);
5134: }
1.91 brouard 5135: end:
5136: while (z[0] != 'q') {
5137: printf("\nType q for exiting: ");
5138: scanf("%s",z);
5139: }
1.53 brouard 5140: }
1.88 brouard 5141:
1.53 brouard 5142:
5143:
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