Annotation of imach/src/imach.c, revision 1.98
1.98 ! brouard 1: /* $Id: imach.c,v 1.97 2004/02/20 13:25:42 lievre Exp $
1.83 lievre 2: $State: Exp $
3: $Log: imach.c,v $
1.98 ! brouard 4: Revision 1.97 2004/02/20 13:25:42 lievre
! 5: Version 0.96d. Population forecasting command line is (temporarily)
! 6: suppressed.
! 7:
1.97 lievre 8: Revision 1.96 2003/07/15 15:38:55 brouard
9: * imach.c (Repository): Errors in subdirf, 2, 3 while printing tmpout is
10: rewritten within the same printf. Workaround: many printfs.
11:
1.96 brouard 12: Revision 1.95 2003/07/08 07:54:34 brouard
13: * imach.c (Repository):
14: (Repository): Using imachwizard code to output a more meaningful covariance
15: matrix (cov(a12,c31) instead of numbers.
16:
1.95 brouard 17: Revision 1.94 2003/06/27 13:00:02 brouard
18: Just cleaning
19:
1.94 brouard 20: Revision 1.93 2003/06/25 16:33:55 brouard
21: (Module): On windows (cygwin) function asctime_r doesn't
22: exist so I changed back to asctime which exists.
23: (Module): Version 0.96b
24:
1.93 brouard 25: Revision 1.92 2003/06/25 16:30:45 brouard
26: (Module): On windows (cygwin) function asctime_r doesn't
27: exist so I changed back to asctime which exists.
28:
1.92 brouard 29: Revision 1.91 2003/06/25 15:30:29 brouard
30: * imach.c (Repository): Duplicated warning errors corrected.
31: (Repository): Elapsed time after each iteration is now output. It
32: helps to forecast when convergence will be reached. Elapsed time
33: is stamped in powell. We created a new html file for the graphs
34: concerning matrix of covariance. It has extension -cov.htm.
35:
1.91 brouard 36: Revision 1.90 2003/06/24 12:34:15 brouard
37: (Module): Some bugs corrected for windows. Also, when
38: mle=-1 a template is output in file "or"mypar.txt with the design
39: of the covariance matrix to be input.
40:
1.90 brouard 41: Revision 1.89 2003/06/24 12:30:52 brouard
42: (Module): Some bugs corrected for windows. Also, when
43: mle=-1 a template is output in file "or"mypar.txt with the design
44: of the covariance matrix to be input.
45:
1.89 brouard 46: Revision 1.88 2003/06/23 17:54:56 brouard
47: * 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.
48:
1.88 brouard 49: Revision 1.87 2003/06/18 12:26:01 brouard
50: Version 0.96
51:
1.87 brouard 52: Revision 1.86 2003/06/17 20:04:08 brouard
53: (Module): Change position of html and gnuplot routines and added
54: routine fileappend.
55:
1.86 brouard 56: Revision 1.85 2003/06/17 13:12:43 brouard
57: * imach.c (Repository): Check when date of death was earlier that
58: current date of interview. It may happen when the death was just
59: prior to the death. In this case, dh was negative and likelihood
60: was wrong (infinity). We still send an "Error" but patch by
61: assuming that the date of death was just one stepm after the
62: interview.
63: (Repository): Because some people have very long ID (first column)
64: we changed int to long in num[] and we added a new lvector for
65: memory allocation. But we also truncated to 8 characters (left
66: truncation)
67: (Repository): No more line truncation errors.
68:
1.85 brouard 69: Revision 1.84 2003/06/13 21:44:43 brouard
70: * imach.c (Repository): Replace "freqsummary" at a correct
71: place. It differs from routine "prevalence" which may be called
72: many times. Probs is memory consuming and must be used with
73: parcimony.
1.86 brouard 74: Version 0.95a3 (should output exactly the same maximization than 0.8a2)
1.85 brouard 75:
1.84 brouard 76: Revision 1.83 2003/06/10 13:39:11 lievre
77: *** empty log message ***
78:
1.83 lievre 79: Revision 1.82 2003/06/05 15:57:20 brouard
80: Add log in imach.c and fullversion number is now printed.
81:
1.82 brouard 82: */
83: /*
1.53 brouard 84: Interpolated Markov Chain
85:
86: Short summary of the programme:
87:
88: This program computes Healthy Life Expectancies from
89: cross-longitudinal data. Cross-longitudinal data consist in: -1- a
90: first survey ("cross") where individuals from different ages are
91: interviewed on their health status or degree of disability (in the
92: case of a health survey which is our main interest) -2- at least a
93: second wave of interviews ("longitudinal") which measure each change
94: (if any) in individual health status. Health expectancies are
95: computed from the time spent in each health state according to a
96: model. More health states you consider, more time is necessary to reach the
97: Maximum Likelihood of the parameters involved in the model. The
98: simplest model is the multinomial logistic model where pij is the
99: probability to be observed in state j at the second wave
100: conditional to be observed in state i at the first wave. Therefore
101: the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where
102: 'age' is age and 'sex' is a covariate. If you want to have a more
103: complex model than "constant and age", you should modify the program
104: where the markup *Covariates have to be included here again* invites
105: you to do it. More covariates you add, slower the
106: convergence.
107:
108: The advantage of this computer programme, compared to a simple
109: multinomial logistic model, is clear when the delay between waves is not
110: identical for each individual. Also, if a individual missed an
111: intermediate interview, the information is lost, but taken into
112: account using an interpolation or extrapolation.
113:
114: hPijx is the probability to be observed in state i at age x+h
115: conditional to the observed state i at age x. The delay 'h' can be
116: split into an exact number (nh*stepm) of unobserved intermediate
1.66 brouard 117: states. This elementary transition (by month, quarter,
118: semester or year) is modelled as a multinomial logistic. The hPx
1.53 brouard 119: matrix is simply the matrix product of nh*stepm elementary matrices
120: and the contribution of each individual to the likelihood is simply
121: hPijx.
122:
123: Also this programme outputs the covariance matrix of the parameters but also
1.54 brouard 124: of the life expectancies. It also computes the stable prevalence.
1.53 brouard 125:
126: Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).
127: Institut national d'études démographiques, Paris.
128: This software have been partly granted by Euro-REVES, a concerted action
129: from the European Union.
130: It is copyrighted identically to a GNU software product, ie programme and
131: software can be distributed freely for non commercial use. Latest version
132: can be accessed at http://euroreves.ined.fr/imach .
1.74 brouard 133:
134: Help to debug: LD_PRELOAD=/usr/local/lib/libnjamd.so ./imach foo.imach
135: or better on gdb : set env LD_PRELOAD=/usr/local/lib/libnjamd.so
136:
1.53 brouard 137: **********************************************************************/
1.74 brouard 138: /*
139: main
140: read parameterfile
141: read datafile
142: concatwav
1.84 brouard 143: freqsummary
1.74 brouard 144: if (mle >= 1)
145: mlikeli
146: print results files
147: if mle==1
148: computes hessian
149: read end of parameter file: agemin, agemax, bage, fage, estepm
150: begin-prev-date,...
151: open gnuplot file
152: open html file
153: stable prevalence
154: for age prevalim()
155: h Pij x
156: variance of p varprob
157: forecasting if prevfcast==1 prevforecast call prevalence()
158: health expectancies
159: Variance-covariance of DFLE
160: prevalence()
161: movingaverage()
162: varevsij()
163: if popbased==1 varevsij(,popbased)
164: total life expectancies
165: Variance of stable prevalence
166: end
167: */
168:
169:
170:
1.53 brouard 171:
172: #include <math.h>
173: #include <stdio.h>
174: #include <stdlib.h>
175: #include <unistd.h>
176:
1.86 brouard 177: #include <sys/time.h>
178: #include <time.h>
179: #include "timeval.h"
180:
1.95 brouard 181: /* #include <libintl.h> */
182: /* #define _(String) gettext (String) */
183:
1.53 brouard 184: #define MAXLINE 256
185: #define GNUPLOTPROGRAM "gnuplot"
186: /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
1.85 brouard 187: #define FILENAMELENGTH 132
1.53 brouard 188: /*#define DEBUG*/
1.85 brouard 189: /*#define windows*/
1.53 brouard 190: #define GLOCK_ERROR_NOPATH -1 /* empty path */
191: #define GLOCK_ERROR_GETCWD -2 /* cannot get cwd */
192:
193: #define MAXPARM 30 /* Maximum number of parameters for the optimization */
194: #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */
195:
196: #define NINTERVMAX 8
197: #define NLSTATEMAX 8 /* Maximum number of live states (for func) */
198: #define NDEATHMAX 8 /* Maximum number of dead states (for func) */
199: #define NCOVMAX 8 /* Maximum number of covariates */
200: #define MAXN 20000
201: #define YEARM 12. /* Number of months per year */
202: #define AGESUP 130
203: #define AGEBASE 40
1.98 ! brouard 204: #define AGEGOMP 10. /* Minimal age for Gompertz adjustment */
1.85 brouard 205: #ifdef unix
206: #define DIRSEPARATOR '/'
207: #define ODIRSEPARATOR '\\'
208: #else
1.53 brouard 209: #define DIRSEPARATOR '\\'
210: #define ODIRSEPARATOR '/'
211: #endif
212:
1.98 ! brouard 213: /* $Id: imach.c,v 1.97 2004/02/20 13:25:42 lievre Exp $ */
1.81 brouard 214: /* $State: Exp $ */
1.80 brouard 215:
1.98 ! brouard 216: char version[]="Imach version 0.70, May 2004, INED-EUROREVES ";
! 217: char fullversion[]="$Revision: 1.97 $ $Date: 2004/02/20 13:25:42 $";
1.91 brouard 218: int erreur, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings */
1.53 brouard 219: int nvar;
220: int cptcovn=0, cptcovage=0, cptcoveff=0,cptcov;
221: int npar=NPARMAX;
222: int nlstate=2; /* Number of live states */
223: int ndeath=1; /* Number of dead states */
224: int ncovmodel, ncovcol; /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
225: int popbased=0;
226:
227: int *wav; /* Number of waves for this individuual 0 is possible */
228: int maxwav; /* Maxim number of waves */
229: int jmin, jmax; /* min, max spacing between 2 waves */
1.87 brouard 230: int gipmx, gsw; /* Global variables on the number of contributions
231: to the likelihood and the sum of weights (done by funcone)*/
1.53 brouard 232: int mle, weightopt;
233: int **mw; /* mw[mi][i] is number of the mi wave for this individual */
234: int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
1.59 brouard 235: int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between
236: * wave mi and wave mi+1 is not an exact multiple of stepm. */
1.53 brouard 237: double jmean; /* Mean space between 2 waves */
238: double **oldm, **newm, **savm; /* Working pointers to matrices */
239: double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
240: FILE *fic,*ficpar, *ficparo,*ficres, *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
1.76 brouard 241: FILE *ficlog, *ficrespow;
1.85 brouard 242: int globpr; /* Global variable for printing or not */
243: double fretone; /* Only one call to likelihood */
244: long ipmx; /* Number of contributions */
245: double sw; /* Sum of weights */
1.98 ! brouard 246: char filerespow[FILENAMELENGTH];
1.85 brouard 247: char fileresilk[FILENAMELENGTH]; /* File of individual contributions to the likelihood */
248: FILE *ficresilk;
1.53 brouard 249: FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
250: FILE *ficresprobmorprev;
1.91 brouard 251: FILE *fichtm, *fichtmcov; /* Html File */
1.53 brouard 252: FILE *ficreseij;
253: char filerese[FILENAMELENGTH];
254: FILE *ficresvij;
255: char fileresv[FILENAMELENGTH];
256: FILE *ficresvpl;
257: char fileresvpl[FILENAMELENGTH];
258: char title[MAXLINE];
259: char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH], filerespl[FILENAMELENGTH];
260: char optionfilext[10], optionfilefiname[FILENAMELENGTH], plotcmd[FILENAMELENGTH];
1.96 brouard 261: char tmpout[FILENAMELENGTH], tmpout2[FILENAMELENGTH];
1.88 brouard 262: char command[FILENAMELENGTH];
263: int outcmd=0;
1.53 brouard 264:
265: char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
1.94 brouard 266:
1.53 brouard 267: char filelog[FILENAMELENGTH]; /* Log file */
268: char filerest[FILENAMELENGTH];
269: char fileregp[FILENAMELENGTH];
270: char popfile[FILENAMELENGTH];
271:
1.91 brouard 272: char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilehtmcov[FILENAMELENGTH] ;
273:
274: struct timeval start_time, end_time, curr_time, last_time, forecast_time;
275: struct timezone tzp;
276: extern int gettimeofday();
277: struct tm tmg, tm, tmf, *gmtime(), *localtime();
278: long time_value;
279: extern long time();
280: char strcurr[80], strfor[80];
1.53 brouard 281:
282: #define NR_END 1
283: #define FREE_ARG char*
284: #define FTOL 1.0e-10
285:
286: #define NRANSI
287: #define ITMAX 200
288:
289: #define TOL 2.0e-4
290:
291: #define CGOLD 0.3819660
292: #define ZEPS 1.0e-10
293: #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);
294:
295: #define GOLD 1.618034
296: #define GLIMIT 100.0
297: #define TINY 1.0e-20
298:
299: static double maxarg1,maxarg2;
300: #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
301: #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
302:
303: #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
304: #define rint(a) floor(a+0.5)
305:
306: static double sqrarg;
307: #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
308: #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}
1.98 ! brouard 309: int agegomp= AGEGOMP;
1.53 brouard 310:
311: int imx;
1.98 ! brouard 312: int stepm=1;
1.53 brouard 313: /* Stepm, step in month: minimum step interpolation*/
314:
315: int estepm;
316: /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
317:
318: int m,nb;
1.85 brouard 319: long *num;
1.98 ! brouard 320: int firstpass=0, lastpass=4,*cod, *ncodemax, *Tage,*cens;
1.53 brouard 321: double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
1.55 lievre 322: double **pmmij, ***probs;
1.98 ! brouard 323: double *ageexmed,*agecens;
1.53 brouard 324: double dateintmean=0;
325:
326: double *weight;
327: int **s; /* Status */
328: double *agedc, **covar, idx;
329: int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;
330:
331: double ftol=FTOL; /* Tolerance for computing Max Likelihood */
332: double ftolhess; /* Tolerance for computing hessian */
333:
334: /**************** split *************************/
335: static int split( char *path, char *dirc, char *name, char *ext, char *finame )
336: {
1.59 brouard 337: char *ss; /* pointer */
338: int l1, l2; /* length counters */
1.53 brouard 339:
1.59 brouard 340: l1 = strlen(path ); /* length of path */
341: if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
342: ss= strrchr( path, DIRSEPARATOR ); /* find last / */
343: if ( ss == NULL ) { /* no directory, so use current */
344: /*if(strrchr(path, ODIRSEPARATOR )==NULL)
345: printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
1.74 brouard 346: /* get current working directory */
347: /* extern char* getcwd ( char *buf , int len);*/
1.59 brouard 348: if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {
349: return( GLOCK_ERROR_GETCWD );
350: }
351: strcpy( name, path ); /* we've got it */
352: } else { /* strip direcotry from path */
353: ss++; /* after this, the filename */
354: l2 = strlen( ss ); /* length of filename */
355: if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
356: strcpy( name, ss ); /* save file name */
357: strncpy( dirc, path, l1 - l2 ); /* now the directory */
358: dirc[l1-l2] = 0; /* add zero */
359: }
360: l1 = strlen( dirc ); /* length of directory */
1.85 brouard 361: /*#ifdef windows
1.59 brouard 362: if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; }
1.53 brouard 363: #else
1.59 brouard 364: if ( dirc[l1-1] != '/' ) { dirc[l1] = '/'; dirc[l1+1] = 0; }
1.53 brouard 365: #endif
1.85 brouard 366: */
1.59 brouard 367: ss = strrchr( name, '.' ); /* find last / */
368: ss++;
369: strcpy(ext,ss); /* save extension */
370: l1= strlen( name);
371: l2= strlen(ss)+1;
372: strncpy( finame, name, l1-l2);
373: finame[l1-l2]= 0;
374: return( 0 ); /* we're done */
1.53 brouard 375: }
376:
377:
378: /******************************************/
379:
1.89 brouard 380: void replace_back_to_slash(char *s, char*t)
1.53 brouard 381: {
382: int i;
1.89 brouard 383: int lg=0;
1.53 brouard 384: i=0;
385: lg=strlen(t);
386: for(i=0; i<= lg; i++) {
387: (s[i] = t[i]);
388: if (t[i]== '\\') s[i]='/';
389: }
390: }
391:
392: int nbocc(char *s, char occ)
393: {
394: int i,j=0;
395: int lg=20;
396: i=0;
397: lg=strlen(s);
398: for(i=0; i<= lg; i++) {
399: if (s[i] == occ ) j++;
400: }
401: return j;
402: }
403:
404: void cutv(char *u,char *v, char*t, char occ)
405: {
406: /* cuts string t into u and v where u is ended by char occ excluding it
407: and v is after occ excluding it too : ex cutv(u,v,"abcdef2ghi2j",2)
408: gives u="abcedf" and v="ghi2j" */
409: int i,lg,j,p=0;
410: i=0;
411: for(j=0; j<=strlen(t)-1; j++) {
412: if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;
413: }
414:
415: lg=strlen(t);
416: for(j=0; j<p; j++) {
417: (u[j] = t[j]);
418: }
419: u[p]='\0';
420:
421: for(j=0; j<= lg; j++) {
422: if (j>=(p+1))(v[j-p-1] = t[j]);
423: }
424: }
425:
426: /********************** nrerror ********************/
427:
428: void nrerror(char error_text[])
429: {
430: fprintf(stderr,"ERREUR ...\n");
431: fprintf(stderr,"%s\n",error_text);
1.59 brouard 432: exit(EXIT_FAILURE);
1.53 brouard 433: }
434: /*********************** vector *******************/
435: double *vector(int nl, int nh)
436: {
437: double *v;
438: v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
439: if (!v) nrerror("allocation failure in vector");
440: return v-nl+NR_END;
441: }
442:
443: /************************ free vector ******************/
444: void free_vector(double*v, int nl, int nh)
445: {
446: free((FREE_ARG)(v+nl-NR_END));
447: }
448:
449: /************************ivector *******************************/
1.85 brouard 450: int *ivector(long nl,long nh)
1.76 brouard 451: {
1.85 brouard 452: int *v;
453: v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
454: if (!v) nrerror("allocation failure in ivector");
1.76 brouard 455: return v-nl+NR_END;
456: }
457:
458: /******************free ivector **************************/
1.85 brouard 459: void free_ivector(int *v, long nl, long nh)
1.76 brouard 460: {
461: free((FREE_ARG)(v+nl-NR_END));
462: }
463:
1.85 brouard 464: /************************lvector *******************************/
465: long *lvector(long nl,long nh)
1.53 brouard 466: {
1.85 brouard 467: long *v;
468: v=(long *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(long)));
1.53 brouard 469: if (!v) nrerror("allocation failure in ivector");
470: return v-nl+NR_END;
471: }
472:
1.85 brouard 473: /******************free lvector **************************/
474: void free_lvector(long *v, long nl, long nh)
1.53 brouard 475: {
476: free((FREE_ARG)(v+nl-NR_END));
477: }
478:
479: /******************* imatrix *******************************/
480: int **imatrix(long nrl, long nrh, long ncl, long nch)
481: /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */
482: {
483: long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;
484: int **m;
485:
486: /* allocate pointers to rows */
487: m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));
488: if (!m) nrerror("allocation failure 1 in matrix()");
489: m += NR_END;
490: m -= nrl;
491:
492:
493: /* allocate rows and set pointers to them */
494: m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));
495: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
496: m[nrl] += NR_END;
497: m[nrl] -= ncl;
498:
499: for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;
500:
501: /* return pointer to array of pointers to rows */
502: return m;
503: }
504:
505: /****************** free_imatrix *************************/
506: void free_imatrix(m,nrl,nrh,ncl,nch)
507: int **m;
508: long nch,ncl,nrh,nrl;
509: /* free an int matrix allocated by imatrix() */
510: {
511: free((FREE_ARG) (m[nrl]+ncl-NR_END));
512: free((FREE_ARG) (m+nrl-NR_END));
513: }
514:
515: /******************* matrix *******************************/
516: double **matrix(long nrl, long nrh, long ncl, long nch)
517: {
518: long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
519: double **m;
520:
521: m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
522: if (!m) nrerror("allocation failure 1 in matrix()");
523: m += NR_END;
524: m -= nrl;
525:
526: m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
527: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
528: m[nrl] += NR_END;
529: m[nrl] -= ncl;
530:
531: for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
532: return m;
1.85 brouard 533: /* print *(*(m+1)+70) or print m[1][70]; print m+1 or print &(m[1])
1.74 brouard 534: */
1.53 brouard 535: }
536:
537: /*************************free matrix ************************/
538: void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
539: {
540: free((FREE_ARG)(m[nrl]+ncl-NR_END));
541: free((FREE_ARG)(m+nrl-NR_END));
542: }
543:
544: /******************* ma3x *******************************/
545: double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
546: {
547: long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
548: double ***m;
549:
550: m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
551: if (!m) nrerror("allocation failure 1 in matrix()");
552: m += NR_END;
553: m -= nrl;
554:
555: m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
556: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
557: m[nrl] += NR_END;
558: m[nrl] -= ncl;
559:
560: for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
561:
562: m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
563: if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
564: m[nrl][ncl] += NR_END;
565: m[nrl][ncl] -= nll;
566: for (j=ncl+1; j<=nch; j++)
567: m[nrl][j]=m[nrl][j-1]+nlay;
568:
569: for (i=nrl+1; i<=nrh; i++) {
570: m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
571: for (j=ncl+1; j<=nch; j++)
572: m[i][j]=m[i][j-1]+nlay;
573: }
1.74 brouard 574: return m;
575: /* gdb: p *(m+1) <=> p m[1] and p (m+1) <=> p (m+1) <=> p &(m[1])
576: &(m[i][j][k]) <=> *((*(m+i) + j)+k)
577: */
1.53 brouard 578: }
579:
580: /*************************free ma3x ************************/
581: void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
582: {
583: free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
584: free((FREE_ARG)(m[nrl]+ncl-NR_END));
585: free((FREE_ARG)(m+nrl-NR_END));
586: }
587:
1.94 brouard 588: /*************** function subdirf ***********/
589: char *subdirf(char fileres[])
590: {
591: /* Caution optionfilefiname is hidden */
592: strcpy(tmpout,optionfilefiname);
593: strcat(tmpout,"/"); /* Add to the right */
594: strcat(tmpout,fileres);
595: return tmpout;
596: }
597:
598: /*************** function subdirf2 ***********/
599: char *subdirf2(char fileres[], char *preop)
600: {
601:
602: /* Caution optionfilefiname is hidden */
603: strcpy(tmpout,optionfilefiname);
604: strcat(tmpout,"/");
605: strcat(tmpout,preop);
606: strcat(tmpout,fileres);
607: return tmpout;
608: }
609:
610: /*************** function subdirf3 ***********/
611: char *subdirf3(char fileres[], char *preop, char *preop2)
612: {
613:
614: /* Caution optionfilefiname is hidden */
615: strcpy(tmpout,optionfilefiname);
616: strcat(tmpout,"/");
617: strcat(tmpout,preop);
618: strcat(tmpout,preop2);
619: strcat(tmpout,fileres);
620: return tmpout;
621: }
622:
1.53 brouard 623: /***************** f1dim *************************/
624: extern int ncom;
625: extern double *pcom,*xicom;
626: extern double (*nrfunc)(double []);
627:
628: double f1dim(double x)
629: {
630: int j;
631: double f;
632: double *xt;
633:
634: xt=vector(1,ncom);
635: for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];
636: f=(*nrfunc)(xt);
637: free_vector(xt,1,ncom);
638: return f;
639: }
640:
641: /*****************brent *************************/
642: double brent(double ax, double bx, double cx, double (*f)(double), double tol, double *xmin)
643: {
644: int iter;
645: double a,b,d,etemp;
646: double fu,fv,fw,fx;
647: double ftemp;
648: double p,q,r,tol1,tol2,u,v,w,x,xm;
649: double e=0.0;
650:
651: a=(ax < cx ? ax : cx);
652: b=(ax > cx ? ax : cx);
653: x=w=v=bx;
654: fw=fv=fx=(*f)(x);
655: for (iter=1;iter<=ITMAX;iter++) {
656: xm=0.5*(a+b);
657: tol2=2.0*(tol1=tol*fabs(x)+ZEPS);
658: /* if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
659: printf(".");fflush(stdout);
660: fprintf(ficlog,".");fflush(ficlog);
661: #ifdef DEBUG
662: 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);
663: 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);
664: /* if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
665: #endif
666: if (fabs(x-xm) <= (tol2-0.5*(b-a))){
667: *xmin=x;
668: return fx;
669: }
670: ftemp=fu;
671: if (fabs(e) > tol1) {
672: r=(x-w)*(fx-fv);
673: q=(x-v)*(fx-fw);
674: p=(x-v)*q-(x-w)*r;
675: q=2.0*(q-r);
676: if (q > 0.0) p = -p;
677: q=fabs(q);
678: etemp=e;
679: e=d;
680: if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))
681: d=CGOLD*(e=(x >= xm ? a-x : b-x));
682: else {
683: d=p/q;
684: u=x+d;
685: if (u-a < tol2 || b-u < tol2)
686: d=SIGN(tol1,xm-x);
687: }
688: } else {
689: d=CGOLD*(e=(x >= xm ? a-x : b-x));
690: }
691: u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));
692: fu=(*f)(u);
693: if (fu <= fx) {
694: if (u >= x) a=x; else b=x;
695: SHFT(v,w,x,u)
696: SHFT(fv,fw,fx,fu)
697: } else {
698: if (u < x) a=u; else b=u;
699: if (fu <= fw || w == x) {
700: v=w;
701: w=u;
702: fv=fw;
703: fw=fu;
704: } else if (fu <= fv || v == x || v == w) {
705: v=u;
706: fv=fu;
707: }
708: }
709: }
710: nrerror("Too many iterations in brent");
711: *xmin=x;
712: return fx;
713: }
714:
715: /****************** mnbrak ***********************/
716:
717: void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,
718: double (*func)(double))
719: {
720: double ulim,u,r,q, dum;
721: double fu;
722:
723: *fa=(*func)(*ax);
724: *fb=(*func)(*bx);
725: if (*fb > *fa) {
726: SHFT(dum,*ax,*bx,dum)
727: SHFT(dum,*fb,*fa,dum)
728: }
729: *cx=(*bx)+GOLD*(*bx-*ax);
730: *fc=(*func)(*cx);
731: while (*fb > *fc) {
732: r=(*bx-*ax)*(*fb-*fc);
733: q=(*bx-*cx)*(*fb-*fa);
734: u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/
735: (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r));
736: ulim=(*bx)+GLIMIT*(*cx-*bx);
737: if ((*bx-u)*(u-*cx) > 0.0) {
738: fu=(*func)(u);
739: } else if ((*cx-u)*(u-ulim) > 0.0) {
740: fu=(*func)(u);
741: if (fu < *fc) {
742: SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))
743: SHFT(*fb,*fc,fu,(*func)(u))
744: }
745: } else if ((u-ulim)*(ulim-*cx) >= 0.0) {
746: u=ulim;
747: fu=(*func)(u);
748: } else {
749: u=(*cx)+GOLD*(*cx-*bx);
750: fu=(*func)(u);
751: }
752: SHFT(*ax,*bx,*cx,u)
753: SHFT(*fa,*fb,*fc,fu)
754: }
755: }
756:
757: /*************** linmin ************************/
758:
759: int ncom;
760: double *pcom,*xicom;
761: double (*nrfunc)(double []);
762:
763: void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))
764: {
765: double brent(double ax, double bx, double cx,
766: double (*f)(double), double tol, double *xmin);
767: double f1dim(double x);
768: void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,
769: double *fc, double (*func)(double));
770: int j;
771: double xx,xmin,bx,ax;
772: double fx,fb,fa;
773:
774: ncom=n;
775: pcom=vector(1,n);
776: xicom=vector(1,n);
777: nrfunc=func;
778: for (j=1;j<=n;j++) {
779: pcom[j]=p[j];
780: xicom[j]=xi[j];
781: }
782: ax=0.0;
783: xx=1.0;
784: mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim);
785: *fret=brent(ax,xx,bx,f1dim,TOL,&xmin);
786: #ifdef DEBUG
787: printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
788: fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
789: #endif
790: for (j=1;j<=n;j++) {
791: xi[j] *= xmin;
792: p[j] += xi[j];
793: }
794: free_vector(xicom,1,n);
795: free_vector(pcom,1,n);
796: }
797:
1.91 brouard 798: char *asc_diff_time(long time_sec, char ascdiff[])
799: {
800: long sec_left, days, hours, minutes;
801: days = (time_sec) / (60*60*24);
802: sec_left = (time_sec) % (60*60*24);
803: hours = (sec_left) / (60*60) ;
804: sec_left = (sec_left) %(60*60);
805: minutes = (sec_left) /60;
806: sec_left = (sec_left) % (60);
807: sprintf(ascdiff,"%d day(s) %d hour(s) %d minute(s) %d second(s)",days, hours, minutes, sec_left);
808: return ascdiff;
809: }
810:
1.53 brouard 811: /*************** powell ************************/
812: void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,
813: double (*func)(double []))
814: {
815: void linmin(double p[], double xi[], int n, double *fret,
816: double (*func)(double []));
817: int i,ibig,j;
818: double del,t,*pt,*ptt,*xit;
819: double fp,fptt;
820: double *xits;
1.91 brouard 821: int niterf, itmp;
822:
1.53 brouard 823: pt=vector(1,n);
824: ptt=vector(1,n);
825: xit=vector(1,n);
826: xits=vector(1,n);
827: *fret=(*func)(p);
828: for (j=1;j<=n;j++) pt[j]=p[j];
829: for (*iter=1;;++(*iter)) {
830: fp=(*fret);
831: ibig=0;
832: del=0.0;
1.91 brouard 833: last_time=curr_time;
834: (void) gettimeofday(&curr_time,&tzp);
835: 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);
1.98 ! brouard 836: /* 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);
1.91 brouard 837: fprintf(ficrespow,"%d %.12f %ld",*iter,*fret,curr_time.tv_sec-start_time.tv_sec);
1.98 ! brouard 838: */
! 839: for (i=1;i<=n;i++) {
1.53 brouard 840: printf(" %d %.12f",i, p[i]);
1.76 brouard 841: fprintf(ficlog," %d %.12lf",i, p[i]);
842: fprintf(ficrespow," %.12lf", p[i]);
843: }
1.53 brouard 844: printf("\n");
845: fprintf(ficlog,"\n");
1.91 brouard 846: fprintf(ficrespow,"\n");fflush(ficrespow);
847: if(*iter <=3){
848: tm = *localtime(&curr_time.tv_sec);
1.92 brouard 849: strcpy(strcurr,asctime(&tmf));
850: /* asctime_r(&tm,strcurr); */
1.91 brouard 851: forecast_time=curr_time;
852: itmp = strlen(strcurr);
853: if(strcurr[itmp-1]=='\n')
854: strcurr[itmp-1]='\0';
855: printf("\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,curr_time.tv_sec-last_time.tv_sec);
856: fprintf(ficlog,"\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,curr_time.tv_sec-last_time.tv_sec);
857: for(niterf=10;niterf<=30;niterf+=10){
858: forecast_time.tv_sec=curr_time.tv_sec+(niterf-*iter)*(curr_time.tv_sec-last_time.tv_sec);
859: tmf = *localtime(&forecast_time.tv_sec);
1.92 brouard 860: /* asctime_r(&tmf,strfor); */
861: strcpy(strfor,asctime(&tmf));
1.91 brouard 862: itmp = strlen(strfor);
863: if(strfor[itmp-1]=='\n')
864: strfor[itmp-1]='\0';
865: 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);
866: 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);
867: }
868: }
1.53 brouard 869: for (i=1;i<=n;i++) {
870: for (j=1;j<=n;j++) xit[j]=xi[j][i];
871: fptt=(*fret);
872: #ifdef DEBUG
873: printf("fret=%lf \n",*fret);
874: fprintf(ficlog,"fret=%lf \n",*fret);
875: #endif
876: printf("%d",i);fflush(stdout);
877: fprintf(ficlog,"%d",i);fflush(ficlog);
878: linmin(p,xit,n,fret,func);
879: if (fabs(fptt-(*fret)) > del) {
880: del=fabs(fptt-(*fret));
881: ibig=i;
882: }
883: #ifdef DEBUG
884: printf("%d %.12e",i,(*fret));
885: fprintf(ficlog,"%d %.12e",i,(*fret));
886: for (j=1;j<=n;j++) {
887: xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
888: printf(" x(%d)=%.12e",j,xit[j]);
889: fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
890: }
891: for(j=1;j<=n;j++) {
892: printf(" p=%.12e",p[j]);
893: fprintf(ficlog," p=%.12e",p[j]);
894: }
895: printf("\n");
896: fprintf(ficlog,"\n");
897: #endif
898: }
899: if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {
900: #ifdef DEBUG
901: int k[2],l;
902: k[0]=1;
903: k[1]=-1;
904: printf("Max: %.12e",(*func)(p));
905: fprintf(ficlog,"Max: %.12e",(*func)(p));
906: for (j=1;j<=n;j++) {
907: printf(" %.12e",p[j]);
908: fprintf(ficlog," %.12e",p[j]);
909: }
910: printf("\n");
911: fprintf(ficlog,"\n");
912: for(l=0;l<=1;l++) {
913: for (j=1;j<=n;j++) {
914: ptt[j]=p[j]+(p[j]-pt[j])*k[l];
915: printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
916: fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
917: }
918: printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
919: fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
920: }
921: #endif
922:
923:
924: free_vector(xit,1,n);
925: free_vector(xits,1,n);
926: free_vector(ptt,1,n);
927: free_vector(pt,1,n);
928: return;
929: }
930: if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");
931: for (j=1;j<=n;j++) {
932: ptt[j]=2.0*p[j]-pt[j];
933: xit[j]=p[j]-pt[j];
934: pt[j]=p[j];
935: }
936: fptt=(*func)(ptt);
937: if (fptt < fp) {
938: t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt);
939: if (t < 0.0) {
940: linmin(p,xit,n,fret,func);
941: for (j=1;j<=n;j++) {
942: xi[j][ibig]=xi[j][n];
943: xi[j][n]=xit[j];
944: }
945: #ifdef DEBUG
946: printf("Direction changed last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
947: fprintf(ficlog,"Direction changed last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
948: for(j=1;j<=n;j++){
949: printf(" %.12e",xit[j]);
950: fprintf(ficlog," %.12e",xit[j]);
951: }
952: printf("\n");
953: fprintf(ficlog,"\n");
954: #endif
1.54 brouard 955: }
1.53 brouard 956: }
957: }
958: }
959:
1.54 brouard 960: /**** Prevalence limit (stable prevalence) ****************/
1.53 brouard 961:
962: double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)
963: {
964: /* Computes the prevalence limit in each live state at age x by left multiplying the unit
965: matrix by transitions matrix until convergence is reached */
966:
967: int i, ii,j,k;
968: double min, max, maxmin, maxmax,sumnew=0.;
969: double **matprod2();
970: double **out, cov[NCOVMAX], **pmij();
971: double **newm;
972: double agefin, delaymax=50 ; /* Max number of years to converge */
973:
974: for (ii=1;ii<=nlstate+ndeath;ii++)
975: for (j=1;j<=nlstate+ndeath;j++){
976: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
977: }
978:
979: cov[1]=1.;
980:
981: /* Even if hstepm = 1, at least one multiplication by the unit matrix */
982: for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
983: newm=savm;
984: /* Covariates have to be included here again */
985: cov[2]=agefin;
986:
987: for (k=1; k<=cptcovn;k++) {
988: cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
989: /* 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]]);*/
990: }
991: for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
992: for (k=1; k<=cptcovprod;k++)
993: cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
994:
995: /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
996: /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
997: /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
998: out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);
999:
1000: savm=oldm;
1001: oldm=newm;
1002: maxmax=0.;
1003: for(j=1;j<=nlstate;j++){
1004: min=1.;
1005: max=0.;
1006: for(i=1; i<=nlstate; i++) {
1007: sumnew=0;
1008: for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
1009: prlim[i][j]= newm[i][j]/(1-sumnew);
1010: max=FMAX(max,prlim[i][j]);
1011: min=FMIN(min,prlim[i][j]);
1012: }
1013: maxmin=max-min;
1014: maxmax=FMAX(maxmax,maxmin);
1015: }
1016: if(maxmax < ftolpl){
1017: return prlim;
1018: }
1019: }
1020: }
1021:
1022: /*************** transition probabilities ***************/
1023:
1024: double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
1025: {
1026: double s1, s2;
1027: /*double t34;*/
1028: int i,j,j1, nc, ii, jj;
1029:
1030: for(i=1; i<= nlstate; i++){
1031: for(j=1; j<i;j++){
1032: for (nc=1, s2=0.;nc <=ncovmodel; nc++){
1033: /*s2 += param[i][j][nc]*cov[nc];*/
1034: s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
1035: /*printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2);*/
1036: }
1037: ps[i][j]=s2;
1038: /*printf("s1=%.17e, s2=%.17e\n",s1,s2);*/
1039: }
1040: for(j=i+1; j<=nlstate+ndeath;j++){
1041: for (nc=1, s2=0.;nc <=ncovmodel; nc++){
1042: s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
1043: /*printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2);*/
1044: }
1045: ps[i][j]=s2;
1046: }
1047: }
1048: /*ps[3][2]=1;*/
1049:
1050: for(i=1; i<= nlstate; i++){
1051: s1=0;
1052: for(j=1; j<i; j++)
1053: s1+=exp(ps[i][j]);
1054: for(j=i+1; j<=nlstate+ndeath; j++)
1055: s1+=exp(ps[i][j]);
1056: ps[i][i]=1./(s1+1.);
1057: for(j=1; j<i; j++)
1058: ps[i][j]= exp(ps[i][j])*ps[i][i];
1059: for(j=i+1; j<=nlstate+ndeath; j++)
1060: ps[i][j]= exp(ps[i][j])*ps[i][i];
1061: /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
1062: } /* end i */
1063:
1064: for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
1065: for(jj=1; jj<= nlstate+ndeath; jj++){
1066: ps[ii][jj]=0;
1067: ps[ii][ii]=1;
1068: }
1069: }
1070:
1071:
1072: /* for(ii=1; ii<= nlstate+ndeath; ii++){
1073: for(jj=1; jj<= nlstate+ndeath; jj++){
1074: printf("%lf ",ps[ii][jj]);
1075: }
1076: printf("\n ");
1077: }
1078: printf("\n ");printf("%lf ",cov[2]);*/
1079: /*
1080: for(i=1; i<= npar; i++) printf("%f ",x[i]);
1081: goto end;*/
1082: return ps;
1083: }
1084:
1085: /**************** Product of 2 matrices ******************/
1086:
1087: double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)
1088: {
1089: /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
1090: b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
1091: /* in, b, out are matrice of pointers which should have been initialized
1092: before: only the contents of out is modified. The function returns
1093: a pointer to pointers identical to out */
1094: long i, j, k;
1095: for(i=nrl; i<= nrh; i++)
1096: for(k=ncolol; k<=ncoloh; k++)
1097: for(j=ncl,out[i][k]=0.; j<=nch; j++)
1098: out[i][k] +=in[i][j]*b[j][k];
1099:
1100: return out;
1101: }
1102:
1103:
1104: /************* Higher Matrix Product ***************/
1105:
1106: double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
1107: {
1.66 brouard 1108: /* Computes the transition matrix starting at age 'age' over
1109: 'nhstepm*hstepm*stepm' months (i.e. until
1110: age (in years) age+nhstepm*hstepm*stepm/12) by multiplying
1111: nhstepm*hstepm matrices.
1.53 brouard 1112: Output is stored in matrix po[i][j][h] for h every 'hstepm' step
1.66 brouard 1113: (typically every 2 years instead of every month which is too big
1114: for the memory).
1.53 brouard 1115: Model is determined by parameters x and covariates have to be
1116: included manually here.
1117:
1118: */
1119:
1120: int i, j, d, h, k;
1121: double **out, cov[NCOVMAX];
1122: double **newm;
1123:
1124: /* Hstepm could be zero and should return the unit matrix */
1125: for (i=1;i<=nlstate+ndeath;i++)
1126: for (j=1;j<=nlstate+ndeath;j++){
1127: oldm[i][j]=(i==j ? 1.0 : 0.0);
1128: po[i][j][0]=(i==j ? 1.0 : 0.0);
1129: }
1130: /* Even if hstepm = 1, at least one multiplication by the unit matrix */
1131: for(h=1; h <=nhstepm; h++){
1132: for(d=1; d <=hstepm; d++){
1133: newm=savm;
1134: /* Covariates have to be included here again */
1135: cov[1]=1.;
1136: cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
1137: for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
1138: for (k=1; k<=cptcovage;k++)
1139: cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
1140: for (k=1; k<=cptcovprod;k++)
1141: cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
1142:
1143:
1144: /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
1145: /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
1146: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,
1147: pmij(pmmij,cov,ncovmodel,x,nlstate));
1148: savm=oldm;
1149: oldm=newm;
1150: }
1151: for(i=1; i<=nlstate+ndeath; i++)
1152: for(j=1;j<=nlstate+ndeath;j++) {
1153: po[i][j][h]=newm[i][j];
1154: /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);
1155: */
1156: }
1157: } /* end h */
1158: return po;
1159: }
1160:
1161:
1162: /*************** log-likelihood *************/
1163: double func( double *x)
1164: {
1165: int i, ii, j, k, mi, d, kk;
1166: double l, ll[NLSTATEMAX], cov[NCOVMAX];
1167: double **out;
1168: double sw; /* Sum of weights */
1169: double lli; /* Individual log likelihood */
1.59 brouard 1170: int s1, s2;
1.68 lievre 1171: double bbh, survp;
1.53 brouard 1172: long ipmx;
1173: /*extern weight */
1174: /* We are differentiating ll according to initial status */
1175: /* for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
1176: /*for(i=1;i<imx;i++)
1177: printf(" %d\n",s[4][i]);
1178: */
1179: cov[1]=1.;
1180:
1181: for(k=1; k<=nlstate; k++) ll[k]=0.;
1.61 brouard 1182:
1183: if(mle==1){
1184: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1185: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
1186: for(mi=1; mi<= wav[i]-1; mi++){
1187: for (ii=1;ii<=nlstate+ndeath;ii++)
1188: for (j=1;j<=nlstate+ndeath;j++){
1189: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1190: savm[ii][j]=(ii==j ? 1.0 : 0.0);
1191: }
1192: for(d=0; d<dh[mi][i]; d++){
1193: newm=savm;
1194: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
1195: for (kk=1; kk<=cptcovage;kk++) {
1196: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
1197: }
1198: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1199: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1200: savm=oldm;
1201: oldm=newm;
1202: } /* end mult */
1.53 brouard 1203:
1.61 brouard 1204: /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
1205: /* But now since version 0.9 we anticipate for bias and large stepm.
1206: * If stepm is larger than one month (smallest stepm) and if the exact delay
1207: * (in months) between two waves is not a multiple of stepm, we rounded to
1208: * the nearest (and in case of equal distance, to the lowest) interval but now
1209: * we keep into memory the bias bh[mi][i] and also the previous matrix product
1210: * (i.e to dh[mi][i]-1) saved in 'savm'. The we inter(extra)polate the
1211: * probability in order to take into account the bias as a fraction of the way
1212: * from savm to out if bh is neagtive or even beyond if bh is positive. bh varies
1213: * -stepm/2 to stepm/2 .
1214: * For stepm=1 the results are the same as for previous versions of Imach.
1215: * For stepm > 1 the results are less biased than in previous versions.
1216: */
1217: s1=s[mw[mi][i]][i];
1218: s2=s[mw[mi+1][i]][i];
1.64 lievre 1219: bbh=(double)bh[mi][i]/(double)stepm;
1220: /* bias is positive if real duration
1221: * is higher than the multiple of stepm and negative otherwise.
1222: */
1223: /* 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 1224: if( s2 > nlstate){
1225: /* i.e. if s2 is a death state and if the date of death is known then the contribution
1226: to the likelihood is the probability to die between last step unit time and current
1227: step unit time, which is also the differences between probability to die before dh
1228: and probability to die before dh-stepm .
1229: In version up to 0.92 likelihood was computed
1230: as if date of death was unknown. Death was treated as any other
1231: health state: the date of the interview describes the actual state
1232: and not the date of a change in health state. The former idea was
1233: to consider that at each interview the state was recorded
1234: (healthy, disable or death) and IMaCh was corrected; but when we
1235: introduced the exact date of death then we should have modified
1236: the contribution of an exact death to the likelihood. This new
1237: contribution is smaller and very dependent of the step unit
1238: stepm. It is no more the probability to die between last interview
1239: and month of death but the probability to survive from last
1240: interview up to one month before death multiplied by the
1241: probability to die within a month. Thanks to Chris
1242: Jackson for correcting this bug. Former versions increased
1243: mortality artificially. The bad side is that we add another loop
1244: which slows down the processing. The difference can be up to 10%
1245: lower mortality.
1246: */
1247: lli=log(out[s1][s2] - savm[s1][s2]);
1248: }else{
1249: lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
1250: /* 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 */
1251: }
1.64 lievre 1252: /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
1253: /*if(lli ==000.0)*/
1254: /*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 1255: ipmx +=1;
1.64 lievre 1256: sw += weight[i];
1257: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1258: } /* end of wave */
1259: } /* end of individual */
1260: } else if(mle==2){
1261: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1262: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
1263: for(mi=1; mi<= wav[i]-1; mi++){
1264: for (ii=1;ii<=nlstate+ndeath;ii++)
1265: for (j=1;j<=nlstate+ndeath;j++){
1266: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1267: savm[ii][j]=(ii==j ? 1.0 : 0.0);
1268: }
1269: for(d=0; d<=dh[mi][i]; d++){
1270: newm=savm;
1271: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
1272: for (kk=1; kk<=cptcovage;kk++) {
1273: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
1274: }
1275: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1276: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1277: savm=oldm;
1278: oldm=newm;
1279: } /* end mult */
1280:
1281: s1=s[mw[mi][i]][i];
1282: s2=s[mw[mi+1][i]][i];
1283: bbh=(double)bh[mi][i]/(double)stepm;
1.63 lievre 1284: 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 1285: ipmx +=1;
1286: sw += weight[i];
1287: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1288: } /* end of wave */
1289: } /* end of individual */
1290: } else if(mle==3){ /* exponential inter-extrapolation */
1291: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1292: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
1293: for(mi=1; mi<= wav[i]-1; mi++){
1294: for (ii=1;ii<=nlstate+ndeath;ii++)
1295: for (j=1;j<=nlstate+ndeath;j++){
1296: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1297: savm[ii][j]=(ii==j ? 1.0 : 0.0);
1298: }
1299: for(d=0; d<dh[mi][i]; d++){
1300: newm=savm;
1301: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
1302: for (kk=1; kk<=cptcovage;kk++) {
1303: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
1304: }
1305: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1306: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1307: savm=oldm;
1308: oldm=newm;
1309: } /* end mult */
1310:
1311: s1=s[mw[mi][i]][i];
1312: s2=s[mw[mi+1][i]][i];
1313: bbh=(double)bh[mi][i]/(double)stepm;
1314: 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 1315: ipmx +=1;
1316: sw += weight[i];
1317: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1318: } /* end of wave */
1319: } /* end of individual */
1.84 brouard 1320: }else if (mle==4){ /* ml=4 no inter-extrapolation */
1.61 brouard 1321: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1322: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
1323: for(mi=1; mi<= wav[i]-1; mi++){
1324: for (ii=1;ii<=nlstate+ndeath;ii++)
1325: for (j=1;j<=nlstate+ndeath;j++){
1326: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1327: savm[ii][j]=(ii==j ? 1.0 : 0.0);
1328: }
1329: for(d=0; d<dh[mi][i]; d++){
1330: newm=savm;
1331: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
1332: for (kk=1; kk<=cptcovage;kk++) {
1333: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
1334: }
1335:
1336: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1337: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1338: savm=oldm;
1339: oldm=newm;
1340: } /* end mult */
1341:
1.84 brouard 1342: s1=s[mw[mi][i]][i];
1343: s2=s[mw[mi+1][i]][i];
1344: if( s2 > nlstate){
1345: lli=log(out[s1][s2] - savm[s1][s2]);
1346: }else{
1347: lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
1348: }
1349: ipmx +=1;
1350: sw += weight[i];
1351: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1.85 brouard 1352: /* 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 1353: } /* end of wave */
1354: } /* end of individual */
1355: }else{ /* ml=5 no inter-extrapolation no jackson =0.8a */
1356: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1357: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
1358: for(mi=1; mi<= wav[i]-1; mi++){
1359: for (ii=1;ii<=nlstate+ndeath;ii++)
1360: for (j=1;j<=nlstate+ndeath;j++){
1361: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1362: savm[ii][j]=(ii==j ? 1.0 : 0.0);
1363: }
1364: for(d=0; d<dh[mi][i]; d++){
1365: newm=savm;
1366: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
1367: for (kk=1; kk<=cptcovage;kk++) {
1368: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
1369: }
1370:
1371: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1372: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1373: savm=oldm;
1374: oldm=newm;
1375: } /* end mult */
1376:
1377: s1=s[mw[mi][i]][i];
1378: s2=s[mw[mi+1][i]][i];
1.61 brouard 1379: lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
1380: ipmx +=1;
1381: sw += weight[i];
1382: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1.84 brouard 1383: /*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 1384: } /* end of wave */
1385: } /* end of individual */
1386: } /* End of if */
1.53 brouard 1387: for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
1388: /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
1389: l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
1.85 brouard 1390: return -l;
1391: }
1392:
1393: /*************** log-likelihood *************/
1394: double funcone( double *x)
1395: {
1.87 brouard 1396: /* Same as likeli but slower because of a lot of printf and if */
1.85 brouard 1397: int i, ii, j, k, mi, d, kk;
1398: double l, ll[NLSTATEMAX], cov[NCOVMAX];
1399: double **out;
1400: double lli; /* Individual log likelihood */
1.87 brouard 1401: double llt;
1.85 brouard 1402: int s1, s2;
1403: double bbh, survp;
1404: /*extern weight */
1405: /* We are differentiating ll according to initial status */
1406: /* for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
1407: /*for(i=1;i<imx;i++)
1408: printf(" %d\n",s[4][i]);
1409: */
1410: cov[1]=1.;
1411:
1412: for(k=1; k<=nlstate; k++) ll[k]=0.;
1413:
1414: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1415: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
1416: for(mi=1; mi<= wav[i]-1; mi++){
1417: for (ii=1;ii<=nlstate+ndeath;ii++)
1418: for (j=1;j<=nlstate+ndeath;j++){
1419: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1420: savm[ii][j]=(ii==j ? 1.0 : 0.0);
1421: }
1422: for(d=0; d<dh[mi][i]; d++){
1423: newm=savm;
1424: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
1425: for (kk=1; kk<=cptcovage;kk++) {
1426: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
1427: }
1428: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1429: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1430: savm=oldm;
1431: oldm=newm;
1432: } /* end mult */
1433:
1434: s1=s[mw[mi][i]][i];
1435: s2=s[mw[mi+1][i]][i];
1436: bbh=(double)bh[mi][i]/(double)stepm;
1437: /* bias is positive if real duration
1438: * is higher than the multiple of stepm and negative otherwise.
1439: */
1440: if( s2 > nlstate && (mle <5) ){ /* Jackson */
1441: lli=log(out[s1][s2] - savm[s1][s2]);
1442: } else if (mle==1){
1443: lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
1444: } else if(mle==2){
1445: 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 */
1446: } else if(mle==3){ /* exponential inter-extrapolation */
1447: 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 */
1448: } else if (mle==4){ /* mle=4 no inter-extrapolation */
1449: lli=log(out[s1][s2]); /* Original formula */
1450: } else{ /* ml>=5 no inter-extrapolation no jackson =0.8a */
1451: lli=log(out[s1][s2]); /* Original formula */
1452: } /* End of if */
1453: ipmx +=1;
1454: sw += weight[i];
1455: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1456: /* 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]); */
1457: if(globpr){
1.88 brouard 1458: fprintf(ficresilk,"%9d %6d %1d %1d %1d %1d %3d %10.6f %6.4f\
1.86 brouard 1459: %10.6f %10.6f %10.6f ", \
1460: num[i],i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],
1461: 2*weight[i]*lli,out[s1][s2],savm[s1][s2]);
1.87 brouard 1462: for(k=1,llt=0.,l=0.; k<=nlstate; k++){
1463: llt +=ll[k]*gipmx/gsw;
1464: fprintf(ficresilk," %10.6f",-ll[k]*gipmx/gsw);
1465: }
1466: fprintf(ficresilk," %10.6f\n", -llt);
1.85 brouard 1467: }
1468: } /* end of wave */
1469: } /* end of individual */
1470: for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
1471: /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
1472: l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
1.87 brouard 1473: if(globpr==0){ /* First time we count the contributions and weights */
1474: gipmx=ipmx;
1475: gsw=sw;
1476: }
1.53 brouard 1477: return -l;
1478: }
1479:
1480:
1.94 brouard 1481: /*************** function likelione ***********/
1.87 brouard 1482: void likelione(FILE *ficres,double p[], int npar, int nlstate, int *globpri, long *ipmx, double *sw, double *fretone, double (*funcone)(double []))
1.85 brouard 1483: {
1.87 brouard 1484: /* This routine should help understanding what is done with
1485: the selection of individuals/waves and
1.85 brouard 1486: to check the exact contribution to the likelihood.
1487: Plotting could be done.
1488: */
1489: int k;
1.87 brouard 1490:
1.88 brouard 1491: if(*globpri !=0){ /* Just counts and sums, no printings */
1.85 brouard 1492: strcpy(fileresilk,"ilk");
1493: strcat(fileresilk,fileres);
1494: if((ficresilk=fopen(fileresilk,"w"))==NULL) {
1495: printf("Problem with resultfile: %s\n", fileresilk);
1496: fprintf(ficlog,"Problem with resultfile: %s\n", fileresilk);
1497: }
1.87 brouard 1498: fprintf(ficresilk, "#individual(line's_record) s1 s2 wave# effective_wave# number_of_matrices_product pij weight -2ln(pij)*weight 0pij_x 0pij_(x-stepm) cumulating_loglikeli_by_health_state(reweighted=-2ll*weightXnumber_of_contribs/sum_of_weights) and_total\n");
1.88 brouard 1499: fprintf(ficresilk, "#num_i i s1 s2 mi mw dh likeli weight 2wlli out sav ");
1.85 brouard 1500: /* i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],2*weight[i]*lli,out[s1][s2],savm[s1][s2]); */
1501: for(k=1; k<=nlstate; k++)
1.87 brouard 1502: fprintf(ficresilk," -2*gipw/gsw*weight*ll[%d]++",k);
1503: fprintf(ficresilk," -2*gipw/gsw*weight*ll(total)\n");
1.85 brouard 1504: }
1505:
1506: *fretone=(*funcone)(p);
1.87 brouard 1507: if(*globpri !=0){
1.85 brouard 1508: fclose(ficresilk);
1.88 brouard 1509: fprintf(fichtm,"\n<br>File of contributions to the likelihood: <a href=\"%s\">%s</a><br>\n",subdirf(fileresilk),subdirf(fileresilk));
1.87 brouard 1510: fflush(fichtm);
1511: }
1.85 brouard 1512: return;
1513: }
1514:
1.88 brouard 1515:
1.53 brouard 1516: /*********** Maximum Likelihood Estimation ***************/
1517:
1518: void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
1519: {
1520: int i,j, iter;
1.74 brouard 1521: double **xi;
1.53 brouard 1522: double fret;
1.85 brouard 1523: double fretone; /* Only one call to likelihood */
1.98 ! brouard 1524: /* char filerespow[FILENAMELENGTH];*/
1.53 brouard 1525: xi=matrix(1,npar,1,npar);
1526: for (i=1;i<=npar;i++)
1527: for (j=1;j<=npar;j++)
1528: xi[i][j]=(i==j ? 1.0 : 0.0);
1529: printf("Powell\n"); fprintf(ficlog,"Powell\n");
1.76 brouard 1530: strcpy(filerespow,"pow");
1531: strcat(filerespow,fileres);
1532: if((ficrespow=fopen(filerespow,"w"))==NULL) {
1533: printf("Problem with resultfile: %s\n", filerespow);
1534: fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
1535: }
1536: fprintf(ficrespow,"# Powell\n# iter -2*LL");
1537: for (i=1;i<=nlstate;i++)
1538: for(j=1;j<=nlstate+ndeath;j++)
1539: if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
1540: fprintf(ficrespow,"\n");
1.85 brouard 1541:
1.53 brouard 1542: powell(p,xi,npar,ftol,&iter,&fret,func);
1543:
1.76 brouard 1544: fclose(ficrespow);
1545: printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));
1.65 lievre 1546: fprintf(ficlog,"\n#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
1.53 brouard 1547: fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
1548:
1549: }
1550:
1551: /**** Computes Hessian and covariance matrix ***/
1552: void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
1553: {
1554: double **a,**y,*x,pd;
1555: double **hess;
1556: int i, j,jk;
1557: int *indx;
1558:
1.98 ! brouard 1559: double hessii(double p[], double delta, int theta, double delti[],double (*func)(double []),int npar);
! 1560: double hessij(double p[], double delti[], int i, int j,double (*func)(double []),int npar);
1.53 brouard 1561: void lubksb(double **a, int npar, int *indx, double b[]) ;
1562: void ludcmp(double **a, int npar, int *indx, double *d) ;
1.98 ! brouard 1563: double gompertz(double p[]);
1.53 brouard 1564: hess=matrix(1,npar,1,npar);
1565:
1566: printf("\nCalculation of the hessian matrix. Wait...\n");
1567: fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
1568: for (i=1;i<=npar;i++){
1569: printf("%d",i);fflush(stdout);
1570: fprintf(ficlog,"%d",i);fflush(ficlog);
1.98 ! brouard 1571:
! 1572: hess[i][i]=hessii(p,ftolhess,i,delti,func,npar);
! 1573:
! 1574: /* printf(" %f ",p[i]);
! 1575: printf(" %lf %lf %lf",hess[i][i],ftolhess,delti[i]);*/
1.53 brouard 1576: }
1577:
1578: for (i=1;i<=npar;i++) {
1579: for (j=1;j<=npar;j++) {
1580: if (j>i) {
1581: printf(".%d%d",i,j);fflush(stdout);
1582: fprintf(ficlog,".%d%d",i,j);fflush(ficlog);
1.98 ! brouard 1583: hess[i][j]=hessij(p,delti,i,j,func,npar);
! 1584:
1.53 brouard 1585: hess[j][i]=hess[i][j];
1586: /*printf(" %lf ",hess[i][j]);*/
1587: }
1588: }
1589: }
1590: printf("\n");
1591: fprintf(ficlog,"\n");
1592:
1593: printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
1594: fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
1595:
1596: a=matrix(1,npar,1,npar);
1597: y=matrix(1,npar,1,npar);
1598: x=vector(1,npar);
1599: indx=ivector(1,npar);
1600: for (i=1;i<=npar;i++)
1601: for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
1602: ludcmp(a,npar,indx,&pd);
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: matcov[i][j]=x[i];
1610: }
1611: }
1612:
1613: printf("\n#Hessian matrix#\n");
1614: fprintf(ficlog,"\n#Hessian matrix#\n");
1615: for (i=1;i<=npar;i++) {
1616: for (j=1;j<=npar;j++) {
1617: printf("%.3e ",hess[i][j]);
1618: fprintf(ficlog,"%.3e ",hess[i][j]);
1619: }
1620: printf("\n");
1621: fprintf(ficlog,"\n");
1622: }
1623:
1624: /* Recompute Inverse */
1625: for (i=1;i<=npar;i++)
1626: for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];
1627: ludcmp(a,npar,indx,&pd);
1628:
1629: /* printf("\n#Hessian matrix recomputed#\n");
1630:
1631: for (j=1;j<=npar;j++) {
1632: for (i=1;i<=npar;i++) x[i]=0;
1633: x[j]=1;
1634: lubksb(a,npar,indx,x);
1635: for (i=1;i<=npar;i++){
1636: y[i][j]=x[i];
1637: printf("%.3e ",y[i][j]);
1638: fprintf(ficlog,"%.3e ",y[i][j]);
1639: }
1640: printf("\n");
1641: fprintf(ficlog,"\n");
1642: }
1643: */
1644:
1645: free_matrix(a,1,npar,1,npar);
1646: free_matrix(y,1,npar,1,npar);
1647: free_vector(x,1,npar);
1648: free_ivector(indx,1,npar);
1649: free_matrix(hess,1,npar,1,npar);
1650:
1651:
1652: }
1653:
1654: /*************** hessian matrix ****************/
1.98 ! brouard 1655: double hessii(double x[], double delta, int theta, double delti[], double (*func)(double []), int npar)
1.53 brouard 1656: {
1657: int i;
1658: int l=1, lmax=20;
1659: double k1,k2;
1660: double p2[NPARMAX+1];
1661: double res;
1.98 ! brouard 1662: double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4;
1.53 brouard 1663: double fx;
1664: int k=0,kmax=10;
1665: double l1;
1666:
1667: fx=func(x);
1668: for (i=1;i<=npar;i++) p2[i]=x[i];
1669: for(l=0 ; l <=lmax; l++){
1670: l1=pow(10,l);
1671: delts=delt;
1672: for(k=1 ; k <kmax; k=k+1){
1673: delt = delta*(l1*k);
1674: p2[theta]=x[theta] +delt;
1675: k1=func(p2)-fx;
1676: p2[theta]=x[theta]-delt;
1677: k2=func(p2)-fx;
1678: /*res= (k1-2.0*fx+k2)/delt/delt; */
1679: res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */
1680:
1681: #ifdef DEBUG
1682: 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);
1683: 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);
1684: #endif
1685: /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
1686: if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
1687: k=kmax;
1688: }
1689: else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
1690: k=kmax; l=lmax*10.;
1691: }
1692: else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){
1693: delts=delt;
1694: }
1695: }
1696: }
1697: delti[theta]=delts;
1698: return res;
1699:
1700: }
1701:
1.98 ! brouard 1702: double hessij( double x[], double delti[], int thetai,int thetaj,double (*func)(double []),int npar)
1.53 brouard 1703: {
1704: int i;
1705: int l=1, l1, lmax=20;
1706: double k1,k2,k3,k4,res,fx;
1707: double p2[NPARMAX+1];
1708: int k;
1709:
1710: fx=func(x);
1711: for (k=1; k<=2; k++) {
1712: for (i=1;i<=npar;i++) p2[i]=x[i];
1713: p2[thetai]=x[thetai]+delti[thetai]/k;
1714: p2[thetaj]=x[thetaj]+delti[thetaj]/k;
1715: k1=func(p2)-fx;
1716:
1717: p2[thetai]=x[thetai]+delti[thetai]/k;
1718: p2[thetaj]=x[thetaj]-delti[thetaj]/k;
1719: k2=func(p2)-fx;
1720:
1721: p2[thetai]=x[thetai]-delti[thetai]/k;
1722: p2[thetaj]=x[thetaj]+delti[thetaj]/k;
1723: k3=func(p2)-fx;
1724:
1725: p2[thetai]=x[thetai]-delti[thetai]/k;
1726: p2[thetaj]=x[thetaj]-delti[thetaj]/k;
1727: k4=func(p2)-fx;
1728: res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */
1729: #ifdef DEBUG
1730: 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);
1731: 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);
1732: #endif
1733: }
1734: return res;
1735: }
1736:
1737: /************** Inverse of matrix **************/
1738: void ludcmp(double **a, int n, int *indx, double *d)
1739: {
1740: int i,imax,j,k;
1741: double big,dum,sum,temp;
1742: double *vv;
1743:
1744: vv=vector(1,n);
1745: *d=1.0;
1746: for (i=1;i<=n;i++) {
1747: big=0.0;
1748: for (j=1;j<=n;j++)
1749: if ((temp=fabs(a[i][j])) > big) big=temp;
1750: if (big == 0.0) nrerror("Singular matrix in routine ludcmp");
1751: vv[i]=1.0/big;
1752: }
1753: for (j=1;j<=n;j++) {
1754: for (i=1;i<j;i++) {
1755: sum=a[i][j];
1756: for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];
1757: a[i][j]=sum;
1758: }
1759: big=0.0;
1760: for (i=j;i<=n;i++) {
1761: sum=a[i][j];
1762: for (k=1;k<j;k++)
1763: sum -= a[i][k]*a[k][j];
1764: a[i][j]=sum;
1765: if ( (dum=vv[i]*fabs(sum)) >= big) {
1766: big=dum;
1767: imax=i;
1768: }
1769: }
1770: if (j != imax) {
1771: for (k=1;k<=n;k++) {
1772: dum=a[imax][k];
1773: a[imax][k]=a[j][k];
1774: a[j][k]=dum;
1775: }
1776: *d = -(*d);
1777: vv[imax]=vv[j];
1778: }
1779: indx[j]=imax;
1780: if (a[j][j] == 0.0) a[j][j]=TINY;
1781: if (j != n) {
1782: dum=1.0/(a[j][j]);
1783: for (i=j+1;i<=n;i++) a[i][j] *= dum;
1784: }
1785: }
1786: free_vector(vv,1,n); /* Doesn't work */
1787: ;
1788: }
1789:
1790: void lubksb(double **a, int n, int *indx, double b[])
1791: {
1792: int i,ii=0,ip,j;
1793: double sum;
1794:
1795: for (i=1;i<=n;i++) {
1796: ip=indx[i];
1797: sum=b[ip];
1798: b[ip]=b[i];
1799: if (ii)
1800: for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];
1801: else if (sum) ii=i;
1802: b[i]=sum;
1803: }
1804: for (i=n;i>=1;i--) {
1805: sum=b[i];
1806: for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];
1807: b[i]=sum/a[i][i];
1808: }
1809: }
1810:
1811: /************ Frequencies ********************/
1.84 brouard 1812: 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 1813: { /* Some frequencies */
1814:
1815: int i, m, jk, k1,i1, j1, bool, z1,z2,j;
1816: int first;
1817: double ***freq; /* Frequencies */
1.73 lievre 1818: double *pp, **prop;
1819: double pos,posprop, k2, dateintsum=0,k2cpt=0;
1.53 brouard 1820: FILE *ficresp;
1821: char fileresp[FILENAMELENGTH];
1822:
1823: pp=vector(1,nlstate);
1.74 brouard 1824: prop=matrix(1,nlstate,iagemin,iagemax+3);
1.53 brouard 1825: strcpy(fileresp,"p");
1826: strcat(fileresp,fileres);
1827: if((ficresp=fopen(fileresp,"w"))==NULL) {
1828: printf("Problem with prevalence resultfile: %s\n", fileresp);
1829: fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
1830: exit(0);
1831: }
1.74 brouard 1832: freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);
1.53 brouard 1833: j1=0;
1834:
1835: j=cptcoveff;
1836: if (cptcovn<1) {j=1;ncodemax[1]=1;}
1837:
1838: first=1;
1839:
1840: for(k1=1; k1<=j;k1++){
1841: for(i1=1; i1<=ncodemax[k1];i1++){
1842: j1++;
1843: /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
1844: scanf("%d", i);*/
1845: for (i=-1; i<=nlstate+ndeath; i++)
1846: for (jk=-1; jk<=nlstate+ndeath; jk++)
1.74 brouard 1847: for(m=iagemin; m <= iagemax+3; m++)
1.53 brouard 1848: freq[i][jk][m]=0;
1.73 lievre 1849:
1850: for (i=1; i<=nlstate; i++)
1.74 brouard 1851: for(m=iagemin; m <= iagemax+3; m++)
1.73 lievre 1852: prop[i][m]=0;
1.53 brouard 1853:
1854: dateintsum=0;
1855: k2cpt=0;
1856: for (i=1; i<=imx; i++) {
1857: bool=1;
1858: if (cptcovn>0) {
1859: for (z1=1; z1<=cptcoveff; z1++)
1860: if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])
1861: bool=0;
1862: }
1.58 lievre 1863: if (bool==1){
1.53 brouard 1864: for(m=firstpass; m<=lastpass; m++){
1865: k2=anint[m][i]+(mint[m][i]/12.);
1.84 brouard 1866: /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/
1.74 brouard 1867: if(agev[m][i]==0) agev[m][i]=iagemax+1;
1868: if(agev[m][i]==1) agev[m][i]=iagemax+2;
1.73 lievre 1869: if (s[m][i]>0 && s[m][i]<=nlstate) prop[s[m][i]][(int)agev[m][i]] += weight[i];
1.53 brouard 1870: if (m<lastpass) {
1871: freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
1.74 brouard 1872: freq[s[m][i]][s[m+1][i]][iagemax+3] += weight[i];
1.53 brouard 1873: }
1874:
1.74 brouard 1875: if ((agev[m][i]>1) && (agev[m][i]< (iagemax+3))) {
1.53 brouard 1876: dateintsum=dateintsum+k2;
1877: k2cpt++;
1878: }
1.84 brouard 1879: /*}*/
1.53 brouard 1880: }
1881: }
1882: }
1883:
1.84 brouard 1884: /* fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
1.53 brouard 1885:
1886: if (cptcovn>0) {
1887: fprintf(ficresp, "\n#********** Variable ");
1888: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
1889: fprintf(ficresp, "**********\n#");
1890: }
1891: for(i=1; i<=nlstate;i++)
1892: fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
1893: fprintf(ficresp, "\n");
1894:
1.74 brouard 1895: for(i=iagemin; i <= iagemax+3; i++){
1896: if(i==iagemax+3){
1.53 brouard 1897: fprintf(ficlog,"Total");
1898: }else{
1899: if(first==1){
1900: first=0;
1901: printf("See log file for details...\n");
1902: }
1903: fprintf(ficlog,"Age %d", i);
1904: }
1905: for(jk=1; jk <=nlstate ; jk++){
1906: for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
1907: pp[jk] += freq[jk][m][i];
1908: }
1909: for(jk=1; jk <=nlstate ; jk++){
1910: for(m=-1, pos=0; m <=0 ; m++)
1911: pos += freq[jk][m][i];
1912: if(pp[jk]>=1.e-10){
1913: if(first==1){
1914: printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
1915: }
1916: fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
1917: }else{
1918: if(first==1)
1919: printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
1920: fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
1921: }
1922: }
1923:
1924: for(jk=1; jk <=nlstate ; jk++){
1925: for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
1926: pp[jk] += freq[jk][m][i];
1.73 lievre 1927: }
1928: for(jk=1,pos=0,posprop=0; jk <=nlstate ; jk++){
1929: pos += pp[jk];
1930: posprop += prop[jk][i];
1.53 brouard 1931: }
1932: for(jk=1; jk <=nlstate ; jk++){
1933: if(pos>=1.e-5){
1934: if(first==1)
1935: printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
1936: fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
1937: }else{
1938: if(first==1)
1939: printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
1940: fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
1941: }
1.74 brouard 1942: if( i <= iagemax){
1.53 brouard 1943: if(pos>=1.e-5){
1.73 lievre 1944: fprintf(ficresp," %d %.5f %.0f %.0f",i,prop[jk][i]/posprop, prop[jk][i],posprop);
1.84 brouard 1945: /*probs[i][jk][j1]= pp[jk]/pos;*/
1.53 brouard 1946: /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/
1947: }
1948: else
1.73 lievre 1949: fprintf(ficresp," %d NaNq %.0f %.0f",i,prop[jk][i],posprop);
1.53 brouard 1950: }
1951: }
1952:
1.69 brouard 1953: for(jk=-1; jk <=nlstate+ndeath; jk++)
1954: for(m=-1; m <=nlstate+ndeath; m++)
1.53 brouard 1955: if(freq[jk][m][i] !=0 ) {
1956: if(first==1)
1957: printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
1958: fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
1959: }
1.74 brouard 1960: if(i <= iagemax)
1.53 brouard 1961: fprintf(ficresp,"\n");
1962: if(first==1)
1963: printf("Others in log...\n");
1964: fprintf(ficlog,"\n");
1965: }
1966: }
1967: }
1968: dateintmean=dateintsum/k2cpt;
1969:
1970: fclose(ficresp);
1.74 brouard 1971: free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);
1.53 brouard 1972: free_vector(pp,1,nlstate);
1.74 brouard 1973: free_matrix(prop,1,nlstate,iagemin, iagemax+3);
1.53 brouard 1974: /* End of Freq */
1975: }
1976:
1977: /************ Prevalence ********************/
1.84 brouard 1978: 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 1979: {
1980: /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
1981: in each health status at the date of interview (if between dateprev1 and dateprev2).
1982: We still use firstpass and lastpass as another selection.
1983: */
1.53 brouard 1984:
1985: int i, m, jk, k1, i1, j1, bool, z1,z2,j;
1986: double ***freq; /* Frequencies */
1.73 lievre 1987: double *pp, **prop;
1988: double pos,posprop;
1.69 brouard 1989: double y2; /* in fractional years */
1.74 brouard 1990: int iagemin, iagemax;
1.53 brouard 1991:
1.74 brouard 1992: iagemin= (int) agemin;
1993: iagemax= (int) agemax;
1994: /*pp=vector(1,nlstate);*/
1995: prop=matrix(1,nlstate,iagemin,iagemax+3);
1996: /* freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
1.53 brouard 1997: j1=0;
1998:
1999: j=cptcoveff;
2000: if (cptcovn<1) {j=1;ncodemax[1]=1;}
2001:
2002: for(k1=1; k1<=j;k1++){
2003: for(i1=1; i1<=ncodemax[k1];i1++){
2004: j1++;
2005:
1.73 lievre 2006: for (i=1; i<=nlstate; i++)
1.74 brouard 2007: for(m=iagemin; m <= iagemax+3; m++)
2008: prop[i][m]=0.0;
1.53 brouard 2009:
1.69 brouard 2010: for (i=1; i<=imx; i++) { /* Each individual */
1.53 brouard 2011: bool=1;
2012: if (cptcovn>0) {
2013: for (z1=1; z1<=cptcoveff; z1++)
2014: if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])
2015: bool=0;
2016: }
2017: if (bool==1) {
1.69 brouard 2018: for(m=firstpass; m<=lastpass; m++){/* Other selection (we can limit to certain interviews*/
2019: y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
2020: if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
1.74 brouard 2021: if(agev[m][i]==0) agev[m][i]=iagemax+1;
2022: if(agev[m][i]==1) agev[m][i]=iagemax+2;
2023: 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);
2024: if (s[m][i]>0 && s[m][i]<=nlstate) {
2025: /*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]]);*/
2026: prop[s[m][i]][(int)agev[m][i]] += weight[i];
2027: prop[s[m][i]][iagemax+3] += weight[i];
2028: }
1.53 brouard 2029: }
1.69 brouard 2030: } /* end selection of waves */
1.53 brouard 2031: }
2032: }
1.74 brouard 2033: for(i=iagemin; i <= iagemax+3; i++){
1.53 brouard 2034:
1.74 brouard 2035: for(jk=1,posprop=0; jk <=nlstate ; jk++) {
2036: posprop += prop[jk][i];
2037: }
2038:
2039: for(jk=1; jk <=nlstate ; jk++){
2040: if( i <= iagemax){
2041: if(posprop>=1.e-5){
2042: probs[i][jk][j1]= prop[jk][i]/posprop;
2043: }
2044: }
2045: }/* end jk */
2046: }/* end i */
1.53 brouard 2047: } /* end i1 */
2048: } /* end k1 */
2049:
1.74 brouard 2050: /* free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
2051: /*free_vector(pp,1,nlstate);*/
2052: free_matrix(prop,1,nlstate, iagemin,iagemax+3);
2053: } /* End of prevalence */
1.53 brouard 2054:
2055: /************* Waves Concatenation ***************/
2056:
1.59 brouard 2057: 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 2058: {
2059: /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
2060: Death is a valid wave (if date is known).
2061: mw[mi][i] is the mi (mi=1 to wav[i]) effective wave of individual i
1.59 brouard 2062: dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
1.53 brouard 2063: and mw[mi+1][i]. dh depends on stepm.
2064: */
2065:
2066: int i, mi, m;
2067: /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
2068: double sum=0., jmean=0.;*/
2069: int first;
2070: int j, k=0,jk, ju, jl;
2071: double sum=0.;
2072: first=0;
2073: jmin=1e+5;
2074: jmax=-1;
2075: jmean=0.;
2076: for(i=1; i<=imx; i++){
2077: mi=0;
2078: m=firstpass;
2079: while(s[m][i] <= nlstate){
1.69 brouard 2080: if(s[m][i]>=1)
1.53 brouard 2081: mw[++mi][i]=m;
2082: if(m >=lastpass)
2083: break;
2084: else
2085: m++;
2086: }/* end while */
2087: if (s[m][i] > nlstate){
2088: mi++; /* Death is another wave */
2089: /* if(mi==0) never been interviewed correctly before death */
2090: /* Only death is a correct wave */
2091: mw[mi][i]=m;
2092: }
2093:
2094: wav[i]=mi;
2095: if(mi==0){
1.91 brouard 2096: nbwarn++;
1.53 brouard 2097: if(first==0){
1.85 brouard 2098: printf("Warning! None valid information for:%ld line=%d (skipped) and may be others, see log file\n",num[i],i);
1.53 brouard 2099: first=1;
2100: }
2101: if(first==1){
1.85 brouard 2102: fprintf(ficlog,"Warning! None valid information for:%ld line=%d (skipped)\n",num[i],i);
1.53 brouard 2103: }
2104: } /* end mi==0 */
1.77 brouard 2105: } /* End individuals */
1.53 brouard 2106:
2107: for(i=1; i<=imx; i++){
2108: for(mi=1; mi<wav[i];mi++){
2109: if (stepm <=0)
2110: dh[mi][i]=1;
2111: else{
1.77 brouard 2112: if (s[mw[mi+1][i]][i] > nlstate) { /* A death */
1.53 brouard 2113: if (agedc[i] < 2*AGESUP) {
1.85 brouard 2114: j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);
2115: if(j==0) j=1; /* Survives at least one month after exam */
2116: else if(j<0){
1.91 brouard 2117: nberr++;
1.85 brouard 2118: 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 2119: j=1; /* Temporary Dangerous patch */
1.86 brouard 2120: 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 2121: 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 2122: 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);
2123: }
2124: k=k+1;
2125: if (j >= jmax) jmax=j;
2126: if (j <= jmin) jmin=j;
2127: sum=sum+j;
2128: /*if (j<0) printf("j=%d num=%d \n",j,i);*/
2129: /* printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
1.53 brouard 2130: }
2131: }
2132: else{
2133: j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
1.68 lievre 2134: /* printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
1.53 brouard 2135: k=k+1;
2136: if (j >= jmax) jmax=j;
2137: else if (j <= jmin)jmin=j;
2138: /* if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
1.73 lievre 2139: /*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 2140: if(j<0){
1.91 brouard 2141: nberr++;
1.85 brouard 2142: 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]);
2143: 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]);
2144: }
1.53 brouard 2145: sum=sum+j;
2146: }
2147: jk= j/stepm;
2148: jl= j -jk*stepm;
2149: ju= j -(jk+1)*stepm;
1.85 brouard 2150: if(mle <=1){ /* only if we use a the linear-interpoloation pseudo-likelihood */
1.64 lievre 2151: if(jl==0){
2152: dh[mi][i]=jk;
2153: bh[mi][i]=0;
2154: }else{ /* We want a negative bias in order to only have interpolation ie
2155: * at the price of an extra matrix product in likelihood */
2156: dh[mi][i]=jk+1;
2157: bh[mi][i]=ju;
2158: }
2159: }else{
2160: if(jl <= -ju){
2161: dh[mi][i]=jk;
2162: bh[mi][i]=jl; /* bias is positive if real duration
2163: * is higher than the multiple of stepm and negative otherwise.
2164: */
2165: }
2166: else{
2167: dh[mi][i]=jk+1;
2168: bh[mi][i]=ju;
2169: }
2170: if(dh[mi][i]==0){
2171: dh[mi][i]=1; /* At least one step */
2172: bh[mi][i]=ju; /* At least one step */
1.71 brouard 2173: /* 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 2174: }
1.85 brouard 2175: } /* end if mle */
2176: }
1.64 lievre 2177: } /* end wave */
1.53 brouard 2178: }
2179: jmean=sum/k;
2180: printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);
2181: fprintf(ficlog,"Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);
2182: }
2183:
2184: /*********** Tricode ****************************/
2185: void tricode(int *Tvar, int **nbcode, int imx)
2186: {
1.58 lievre 2187:
2188: int Ndum[20],ij=1, k, j, i, maxncov=19;
1.53 brouard 2189: int cptcode=0;
2190: cptcoveff=0;
2191:
1.58 lievre 2192: for (k=0; k<maxncov; k++) Ndum[k]=0;
1.53 brouard 2193: for (k=1; k<=7; k++) ncodemax[k]=0;
2194:
2195: for (j=1; j<=(cptcovn+2*cptcovprod); j++) {
1.58 lievre 2196: for (i=1; i<=imx; i++) { /*reads the data file to get the maximum
2197: modality*/
2198: ij=(int)(covar[Tvar[j]][i]); /* ij is the modality of this individual*/
2199: Ndum[ij]++; /*store the modality */
1.53 brouard 2200: /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
1.58 lievre 2201: if (ij > cptcode) cptcode=ij; /* getting the maximum of covariable
2202: Tvar[j]. If V=sex and male is 0 and
2203: female is 1, then cptcode=1.*/
1.53 brouard 2204: }
2205:
2206: for (i=0; i<=cptcode; i++) {
1.58 lievre 2207: 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 2208: }
1.58 lievre 2209:
1.53 brouard 2210: ij=1;
2211: for (i=1; i<=ncodemax[j]; i++) {
1.58 lievre 2212: for (k=0; k<= maxncov; k++) {
1.53 brouard 2213: if (Ndum[k] != 0) {
2214: nbcode[Tvar[j]][ij]=k;
1.58 lievre 2215: /* 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 2216:
2217: ij++;
2218: }
2219: if (ij > ncodemax[j]) break;
2220: }
2221: }
2222: }
2223:
1.58 lievre 2224: for (k=0; k< maxncov; k++) Ndum[k]=0;
1.53 brouard 2225:
1.58 lievre 2226: for (i=1; i<=ncovmodel-2; i++) {
2227: /* 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 2228: ij=Tvar[i];
1.58 lievre 2229: Ndum[ij]++;
1.53 brouard 2230: }
2231:
2232: ij=1;
1.58 lievre 2233: for (i=1; i<= maxncov; i++) {
1.53 brouard 2234: if((Ndum[i]!=0) && (i<=ncovcol)){
1.58 lievre 2235: Tvaraff[ij]=i; /*For printing */
1.53 brouard 2236: ij++;
2237: }
2238: }
2239:
1.58 lievre 2240: cptcoveff=ij-1; /*Number of simple covariates*/
1.53 brouard 2241: }
2242:
2243: /*********** Health Expectancies ****************/
2244:
2245: 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 )
2246:
2247: {
2248: /* Health expectancies */
2249: int i, j, nhstepm, hstepm, h, nstepm, k, cptj;
2250: double age, agelim, hf;
2251: double ***p3mat,***varhe;
2252: double **dnewm,**doldm;
2253: double *xp;
2254: double **gp, **gm;
2255: double ***gradg, ***trgradg;
2256: int theta;
2257:
1.74 brouard 2258: varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage);
1.53 brouard 2259: xp=vector(1,npar);
1.74 brouard 2260: dnewm=matrix(1,nlstate*nlstate,1,npar);
2261: doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate);
1.53 brouard 2262:
2263: fprintf(ficreseij,"# Health expectancies\n");
2264: fprintf(ficreseij,"# Age");
2265: for(i=1; i<=nlstate;i++)
2266: for(j=1; j<=nlstate;j++)
2267: fprintf(ficreseij," %1d-%1d (SE)",i,j);
2268: fprintf(ficreseij,"\n");
2269:
2270: if(estepm < stepm){
2271: printf ("Problem %d lower than %d\n",estepm, stepm);
2272: }
2273: else hstepm=estepm;
2274: /* We compute the life expectancy from trapezoids spaced every estepm months
2275: * This is mainly to measure the difference between two models: for example
2276: * if stepm=24 months pijx are given only every 2 years and by summing them
2277: * we are calculating an estimate of the Life Expectancy assuming a linear
1.66 brouard 2278: * progression in between and thus overestimating or underestimating according
1.53 brouard 2279: * to the curvature of the survival function. If, for the same date, we
2280: * estimate the model with stepm=1 month, we can keep estepm to 24 months
2281: * to compare the new estimate of Life expectancy with the same linear
2282: * hypothesis. A more precise result, taking into account a more precise
2283: * curvature will be obtained if estepm is as small as stepm. */
2284:
2285: /* For example we decided to compute the life expectancy with the smallest unit */
2286: /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
2287: nhstepm is the number of hstepm from age to agelim
2288: nstepm is the number of stepm from age to agelin.
2289: Look at hpijx to understand the reason of that which relies in memory size
2290: and note for a fixed period like estepm months */
2291: /* We decided (b) to get a life expectancy respecting the most precise curvature of the
2292: survival function given by stepm (the optimization length). Unfortunately it
2293: means that if the survival funtion is printed only each two years of age and if
2294: you sum them up and add 1 year (area under the trapezoids) you won't get the same
2295: results. So we changed our mind and took the option of the best precision.
2296: */
2297: hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
2298:
2299: agelim=AGESUP;
2300: for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
2301: /* nhstepm age range expressed in number of stepm */
2302: nstepm=(int) rint((agelim-age)*YEARM/stepm);
2303: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
2304: /* if (stepm >= YEARM) hstepm=1;*/
2305: nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
2306: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
1.74 brouard 2307: gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);
2308: gp=matrix(0,nhstepm,1,nlstate*nlstate);
2309: gm=matrix(0,nhstepm,1,nlstate*nlstate);
1.53 brouard 2310:
2311: /* Computed by stepm unit matrices, product of hstepm matrices, stored
2312: in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
2313: hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);
2314:
2315:
2316: hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
2317:
1.95 brouard 2318: /* Computing Variances of health expectancies */
1.53 brouard 2319:
2320: for(theta=1; theta <=npar; theta++){
2321: for(i=1; i<=npar; i++){
2322: xp[i] = x[i] + (i==theta ?delti[theta]:0);
2323: }
2324: hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
2325:
2326: cptj=0;
2327: for(j=1; j<= nlstate; j++){
2328: for(i=1; i<=nlstate; i++){
2329: cptj=cptj+1;
2330: for(h=0, gp[h][cptj]=0.; h<=nhstepm-1; h++){
2331: gp[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;
2332: }
2333: }
2334: }
2335:
2336:
2337: for(i=1; i<=npar; i++)
2338: xp[i] = x[i] - (i==theta ?delti[theta]:0);
2339: hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
2340:
2341: cptj=0;
2342: for(j=1; j<= nlstate; j++){
2343: for(i=1;i<=nlstate;i++){
2344: cptj=cptj+1;
2345: for(h=0, gm[h][cptj]=0.; h<=nhstepm-1; h++){
1.77 brouard 2346:
1.53 brouard 2347: gm[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;
2348: }
2349: }
2350: }
1.74 brouard 2351: for(j=1; j<= nlstate*nlstate; j++)
1.53 brouard 2352: for(h=0; h<=nhstepm-1; h++){
2353: gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
2354: }
2355: }
2356:
2357: /* End theta */
2358:
1.74 brouard 2359: trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar);
1.53 brouard 2360:
2361: for(h=0; h<=nhstepm-1; h++)
1.74 brouard 2362: for(j=1; j<=nlstate*nlstate;j++)
1.53 brouard 2363: for(theta=1; theta <=npar; theta++)
2364: trgradg[h][j][theta]=gradg[h][theta][j];
2365:
2366:
1.74 brouard 2367: for(i=1;i<=nlstate*nlstate;i++)
2368: for(j=1;j<=nlstate*nlstate;j++)
1.53 brouard 2369: varhe[i][j][(int)age] =0.;
2370:
2371: printf("%d|",(int)age);fflush(stdout);
2372: fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
2373: for(h=0;h<=nhstepm-1;h++){
2374: for(k=0;k<=nhstepm-1;k++){
1.74 brouard 2375: matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov);
2376: matprod2(doldm,dnewm,1,nlstate*nlstate,1,npar,1,nlstate*nlstate,gradg[k]);
2377: for(i=1;i<=nlstate*nlstate;i++)
2378: for(j=1;j<=nlstate*nlstate;j++)
1.53 brouard 2379: varhe[i][j][(int)age] += doldm[i][j]*hf*hf;
2380: }
2381: }
2382: /* Computing expectancies */
2383: for(i=1; i<=nlstate;i++)
2384: for(j=1; j<=nlstate;j++)
2385: for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
2386: eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
2387:
2388: /* 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]);*/
2389:
2390: }
2391:
2392: fprintf(ficreseij,"%3.0f",age );
2393: cptj=0;
2394: for(i=1; i<=nlstate;i++)
2395: for(j=1; j<=nlstate;j++){
2396: cptj++;
2397: fprintf(ficreseij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[cptj][cptj][(int)age]) );
2398: }
2399: fprintf(ficreseij,"\n");
2400:
1.74 brouard 2401: free_matrix(gm,0,nhstepm,1,nlstate*nlstate);
2402: free_matrix(gp,0,nhstepm,1,nlstate*nlstate);
2403: free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*nlstate);
2404: free_ma3x(trgradg,0,nhstepm,1,nlstate*nlstate,1,npar);
1.53 brouard 2405: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
2406: }
2407: printf("\n");
2408: fprintf(ficlog,"\n");
2409:
2410: free_vector(xp,1,npar);
1.74 brouard 2411: free_matrix(dnewm,1,nlstate*nlstate,1,npar);
2412: free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate);
2413: free_ma3x(varhe,1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int)fage);
1.53 brouard 2414: }
2415:
2416: /************ Variance ******************/
2417: 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)
2418: {
2419: /* Variance of health expectancies */
2420: /* double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
2421: /* double **newm;*/
2422: double **dnewm,**doldm;
2423: double **dnewmp,**doldmp;
2424: int i, j, nhstepm, hstepm, h, nstepm ;
2425: int k, cptcode;
2426: double *xp;
2427: double **gp, **gm; /* for var eij */
2428: double ***gradg, ***trgradg; /*for var eij */
2429: double **gradgp, **trgradgp; /* for var p point j */
2430: double *gpp, *gmp; /* for var p point j */
2431: double **varppt; /* for var p point j nlstate to nlstate+ndeath */
2432: double ***p3mat;
2433: double age,agelim, hf;
2434: double ***mobaverage;
2435: int theta;
2436: char digit[4];
1.55 lievre 2437: char digitp[25];
1.53 brouard 2438:
2439: char fileresprobmorprev[FILENAMELENGTH];
2440:
1.55 lievre 2441: if(popbased==1){
1.58 lievre 2442: if(mobilav!=0)
1.55 lievre 2443: strcpy(digitp,"-populbased-mobilav-");
2444: else strcpy(digitp,"-populbased-nomobil-");
2445: }
2446: else
1.53 brouard 2447: strcpy(digitp,"-stablbased-");
1.56 lievre 2448:
1.54 brouard 2449: if (mobilav!=0) {
1.53 brouard 2450: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
1.54 brouard 2451: if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
2452: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
2453: printf(" Error in movingaverage mobilav=%d\n",mobilav);
2454: }
1.53 brouard 2455: }
2456:
2457: strcpy(fileresprobmorprev,"prmorprev");
2458: sprintf(digit,"%-d",ij);
2459: /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
2460: strcat(fileresprobmorprev,digit); /* Tvar to be done */
2461: strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
2462: strcat(fileresprobmorprev,fileres);
2463: if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
2464: printf("Problem with resultfile: %s\n", fileresprobmorprev);
2465: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
2466: }
2467: printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
2468: fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
1.66 brouard 2469: 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 2470: fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
2471: for(j=nlstate+1; j<=(nlstate+ndeath);j++){
2472: fprintf(ficresprobmorprev," p.%-d SE",j);
2473: for(i=1; i<=nlstate;i++)
2474: fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
2475: }
2476: fprintf(ficresprobmorprev,"\n");
1.88 brouard 2477: fprintf(ficgp,"\n# Routine varevsij");
1.87 brouard 2478: 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");
2479: fprintf(fichtm,"\n<br>%s <br>\n",digitp);
2480: /* } */
1.53 brouard 2481: varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
2482:
2483: 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");
2484: fprintf(ficresvij,"# Age");
2485: for(i=1; i<=nlstate;i++)
2486: for(j=1; j<=nlstate;j++)
2487: fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);
2488: fprintf(ficresvij,"\n");
2489:
2490: xp=vector(1,npar);
2491: dnewm=matrix(1,nlstate,1,npar);
2492: doldm=matrix(1,nlstate,1,nlstate);
2493: dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
2494: doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
2495:
2496: gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
2497: gpp=vector(nlstate+1,nlstate+ndeath);
2498: gmp=vector(nlstate+1,nlstate+ndeath);
2499: trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
2500:
2501: if(estepm < stepm){
2502: printf ("Problem %d lower than %d\n",estepm, stepm);
2503: }
2504: else hstepm=estepm;
2505: /* For example we decided to compute the life expectancy with the smallest unit */
2506: /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
2507: nhstepm is the number of hstepm from age to agelim
2508: nstepm is the number of stepm from age to agelin.
2509: Look at hpijx to understand the reason of that which relies in memory size
2510: and note for a fixed period like k years */
2511: /* We decided (b) to get a life expectancy respecting the most precise curvature of the
2512: survival function given by stepm (the optimization length). Unfortunately it
1.66 brouard 2513: means that if the survival funtion is printed every two years of age and if
1.53 brouard 2514: you sum them up and add 1 year (area under the trapezoids) you won't get the same
2515: results. So we changed our mind and took the option of the best precision.
2516: */
2517: hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
2518: agelim = AGESUP;
2519: for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
2520: nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
2521: nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
2522: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
2523: gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
2524: gp=matrix(0,nhstepm,1,nlstate);
2525: gm=matrix(0,nhstepm,1,nlstate);
2526:
2527:
2528: for(theta=1; theta <=npar; theta++){
1.66 brouard 2529: for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
1.53 brouard 2530: xp[i] = x[i] + (i==theta ?delti[theta]:0);
2531: }
2532: hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
2533: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
2534:
2535: if (popbased==1) {
1.54 brouard 2536: if(mobilav ==0){
1.53 brouard 2537: for(i=1; i<=nlstate;i++)
2538: prlim[i][i]=probs[(int)age][i][ij];
1.54 brouard 2539: }else{ /* mobilav */
1.53 brouard 2540: for(i=1; i<=nlstate;i++)
2541: prlim[i][i]=mobaverage[(int)age][i][ij];
2542: }
2543: }
2544:
2545: for(j=1; j<= nlstate; j++){
2546: for(h=0; h<=nhstepm; h++){
2547: for(i=1, gp[h][j]=0.;i<=nlstate;i++)
2548: gp[h][j] += prlim[i][i]*p3mat[i][j][h];
2549: }
2550: }
1.66 brouard 2551: /* This for computing probability of death (h=1 means
2552: computed over hstepm matrices product = hstepm*stepm months)
2553: as a weighted average of prlim.
2554: */
1.69 brouard 2555: for(j=nlstate+1;j<=nlstate+ndeath;j++){
1.68 lievre 2556: for(i=1,gpp[j]=0.; i<= nlstate; i++)
1.53 brouard 2557: gpp[j] += prlim[i][i]*p3mat[i][j][1];
2558: }
1.66 brouard 2559: /* end probability of death */
1.53 brouard 2560:
1.66 brouard 2561: for(i=1; i<=npar; i++) /* Computes gradient x - delta */
1.53 brouard 2562: xp[i] = x[i] - (i==theta ?delti[theta]:0);
2563: hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
2564: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
2565:
2566: if (popbased==1) {
1.54 brouard 2567: if(mobilav ==0){
1.53 brouard 2568: for(i=1; i<=nlstate;i++)
2569: prlim[i][i]=probs[(int)age][i][ij];
1.54 brouard 2570: }else{ /* mobilav */
1.53 brouard 2571: for(i=1; i<=nlstate;i++)
2572: prlim[i][i]=mobaverage[(int)age][i][ij];
2573: }
2574: }
2575:
2576: for(j=1; j<= nlstate; j++){
2577: for(h=0; h<=nhstepm; h++){
2578: for(i=1, gm[h][j]=0.;i<=nlstate;i++)
2579: gm[h][j] += prlim[i][i]*p3mat[i][j][h];
2580: }
2581: }
1.66 brouard 2582: /* This for computing probability of death (h=1 means
2583: computed over hstepm matrices product = hstepm*stepm months)
2584: as a weighted average of prlim.
2585: */
1.69 brouard 2586: for(j=nlstate+1;j<=nlstate+ndeath;j++){
1.68 lievre 2587: for(i=1,gmp[j]=0.; i<= nlstate; i++)
2588: gmp[j] += prlim[i][i]*p3mat[i][j][1];
1.53 brouard 2589: }
1.66 brouard 2590: /* end probability of death */
1.53 brouard 2591:
2592: for(j=1; j<= nlstate; j++) /* vareij */
2593: for(h=0; h<=nhstepm; h++){
2594: gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
2595: }
1.68 lievre 2596:
1.53 brouard 2597: for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
2598: gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
2599: }
2600:
2601: } /* End theta */
2602:
2603: trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
2604:
2605: for(h=0; h<=nhstepm; h++) /* veij */
2606: for(j=1; j<=nlstate;j++)
2607: for(theta=1; theta <=npar; theta++)
2608: trgradg[h][j][theta]=gradg[h][theta][j];
2609:
2610: for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
1.69 brouard 2611: for(theta=1; theta <=npar; theta++)
1.53 brouard 2612: trgradgp[j][theta]=gradgp[theta][j];
1.69 brouard 2613:
1.53 brouard 2614:
2615: hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
2616: for(i=1;i<=nlstate;i++)
2617: for(j=1;j<=nlstate;j++)
2618: vareij[i][j][(int)age] =0.;
2619:
2620: for(h=0;h<=nhstepm;h++){
2621: for(k=0;k<=nhstepm;k++){
2622: matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
2623: matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
2624: for(i=1;i<=nlstate;i++)
2625: for(j=1;j<=nlstate;j++)
2626: vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
2627: }
2628: }
1.70 brouard 2629:
1.53 brouard 2630: /* pptj */
2631: matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
2632: matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
1.70 brouard 2633: for(j=nlstate+1;j<=nlstate+ndeath;j++)
2634: for(i=nlstate+1;i<=nlstate+ndeath;i++)
1.53 brouard 2635: varppt[j][i]=doldmp[j][i];
2636: /* end ppptj */
1.66 brouard 2637: /* x centered again */
1.53 brouard 2638: hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);
2639: prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);
2640:
2641: if (popbased==1) {
1.54 brouard 2642: if(mobilav ==0){
1.53 brouard 2643: for(i=1; i<=nlstate;i++)
2644: prlim[i][i]=probs[(int)age][i][ij];
1.54 brouard 2645: }else{ /* mobilav */
1.53 brouard 2646: for(i=1; i<=nlstate;i++)
2647: prlim[i][i]=mobaverage[(int)age][i][ij];
2648: }
2649: }
1.70 brouard 2650:
1.66 brouard 2651: /* This for computing probability of death (h=1 means
2652: computed over hstepm (estepm) matrices product = hstepm*stepm months)
2653: as a weighted average of prlim.
2654: */
1.68 lievre 2655: for(j=nlstate+1;j<=nlstate+ndeath;j++){
2656: for(i=1,gmp[j]=0.;i<= nlstate; i++)
1.53 brouard 2657: gmp[j] += prlim[i][i]*p3mat[i][j][1];
2658: }
1.66 brouard 2659: /* end probability of death */
1.53 brouard 2660:
2661: fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
2662: for(j=nlstate+1; j<=(nlstate+ndeath);j++){
2663: fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
2664: for(i=1; i<=nlstate;i++){
2665: fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
2666: }
2667: }
2668: fprintf(ficresprobmorprev,"\n");
2669:
2670: fprintf(ficresvij,"%.0f ",age );
2671: for(i=1; i<=nlstate;i++)
2672: for(j=1; j<=nlstate;j++){
2673: fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
2674: }
2675: fprintf(ficresvij,"\n");
2676: free_matrix(gp,0,nhstepm,1,nlstate);
2677: free_matrix(gm,0,nhstepm,1,nlstate);
2678: free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
2679: free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
2680: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
2681: } /* End age */
2682: free_vector(gpp,nlstate+1,nlstate+ndeath);
2683: free_vector(gmp,nlstate+1,nlstate+ndeath);
2684: free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
2685: free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
2686: fprintf(ficgp,"\nset noparametric;set nolabel; set ter png small;set size 0.65, 0.65");
2687: /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */
2688: fprintf(ficgp,"\n set log y; set nolog x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
1.67 brouard 2689: /* fprintf(ficgp,"\n plot \"%s\" u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm); */
2690: /* fprintf(ficgp,"\n replot \"%s\" u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm); */
2691: /* fprintf(ficgp,"\n replot \"%s\" u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm); */
1.88 brouard 2692: fprintf(ficgp,"\n plot \"%s\" u 1:($3) not w l 1 ",subdirf(fileresprobmorprev));
2693: fprintf(ficgp,"\n replot \"%s\" u 1:(($3+1.96*$4)) t \"95\%% interval\" w l 2 ",subdirf(fileresprobmorprev));
2694: fprintf(ficgp,"\n replot \"%s\" u 1:(($3-1.96*$4)) not w l 2 ",subdirf(fileresprobmorprev));
2695: fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",subdirf(fileresprobmorprev),subdirf(fileresprobmorprev));
2696: 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 2697: /* 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);
2698: */
1.88 brouard 2699: /* fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.png\";replot;",digitp,optionfilefiname,digit); */
1.89 brouard 2700: fprintf(ficgp,"\nset out \"%s%s.png\";replot;\n",subdirf3(optionfilefiname,"varmuptjgr",digitp),digit);
1.53 brouard 2701:
2702: free_vector(xp,1,npar);
2703: free_matrix(doldm,1,nlstate,1,nlstate);
2704: free_matrix(dnewm,1,nlstate,1,npar);
2705: free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
2706: free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
2707: free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
1.55 lievre 2708: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
1.53 brouard 2709: fclose(ficresprobmorprev);
1.88 brouard 2710: fflush(ficgp);
2711: fflush(fichtm);
1.84 brouard 2712: } /* end varevsij */
1.53 brouard 2713:
2714: /************ Variance of prevlim ******************/
2715: 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)
2716: {
2717: /* Variance of prevalence limit */
1.59 brouard 2718: /* double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
1.53 brouard 2719: double **newm;
2720: double **dnewm,**doldm;
2721: int i, j, nhstepm, hstepm;
2722: int k, cptcode;
2723: double *xp;
2724: double *gp, *gm;
2725: double **gradg, **trgradg;
2726: double age,agelim;
2727: int theta;
2728:
1.54 brouard 2729: fprintf(ficresvpl,"# Standard deviation of stable prevalences \n");
1.53 brouard 2730: fprintf(ficresvpl,"# Age");
2731: for(i=1; i<=nlstate;i++)
2732: fprintf(ficresvpl," %1d-%1d",i,i);
2733: fprintf(ficresvpl,"\n");
2734:
2735: xp=vector(1,npar);
2736: dnewm=matrix(1,nlstate,1,npar);
2737: doldm=matrix(1,nlstate,1,nlstate);
2738:
2739: hstepm=1*YEARM; /* Every year of age */
2740: hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */
2741: agelim = AGESUP;
2742: for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
2743: nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
2744: if (stepm >= YEARM) hstepm=1;
2745: nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
2746: gradg=matrix(1,npar,1,nlstate);
2747: gp=vector(1,nlstate);
2748: gm=vector(1,nlstate);
2749:
2750: for(theta=1; theta <=npar; theta++){
2751: for(i=1; i<=npar; i++){ /* Computes gradient */
2752: xp[i] = x[i] + (i==theta ?delti[theta]:0);
2753: }
2754: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
2755: for(i=1;i<=nlstate;i++)
2756: gp[i] = prlim[i][i];
2757:
2758: for(i=1; i<=npar; i++) /* Computes gradient */
2759: xp[i] = x[i] - (i==theta ?delti[theta]:0);
2760: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
2761: for(i=1;i<=nlstate;i++)
2762: gm[i] = prlim[i][i];
2763:
2764: for(i=1;i<=nlstate;i++)
2765: gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
2766: } /* End theta */
2767:
2768: trgradg =matrix(1,nlstate,1,npar);
2769:
2770: for(j=1; j<=nlstate;j++)
2771: for(theta=1; theta <=npar; theta++)
2772: trgradg[j][theta]=gradg[theta][j];
2773:
2774: for(i=1;i<=nlstate;i++)
2775: varpl[i][(int)age] =0.;
2776: matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
2777: matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
2778: for(i=1;i<=nlstate;i++)
2779: varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
2780:
2781: fprintf(ficresvpl,"%.0f ",age );
2782: for(i=1; i<=nlstate;i++)
2783: fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
2784: fprintf(ficresvpl,"\n");
2785: free_vector(gp,1,nlstate);
2786: free_vector(gm,1,nlstate);
2787: free_matrix(gradg,1,npar,1,nlstate);
2788: free_matrix(trgradg,1,nlstate,1,npar);
2789: } /* End age */
2790:
2791: free_vector(xp,1,npar);
2792: free_matrix(doldm,1,nlstate,1,npar);
2793: free_matrix(dnewm,1,nlstate,1,nlstate);
2794:
2795: }
2796:
2797: /************ Variance of one-step probabilities ******************/
2798: void varprob(char optionfilefiname[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij, int *Tvar, int **nbcode, int *ncodemax)
2799: {
2800: int i, j=0, i1, k1, l1, t, tj;
2801: int k2, l2, j1, z1;
2802: int k=0,l, cptcode;
2803: int first=1, first1;
2804: double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
2805: double **dnewm,**doldm;
2806: double *xp;
2807: double *gp, *gm;
2808: double **gradg, **trgradg;
2809: double **mu;
2810: double age,agelim, cov[NCOVMAX];
2811: double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
2812: int theta;
2813: char fileresprob[FILENAMELENGTH];
2814: char fileresprobcov[FILENAMELENGTH];
2815: char fileresprobcor[FILENAMELENGTH];
2816:
2817: double ***varpij;
2818:
2819: strcpy(fileresprob,"prob");
2820: strcat(fileresprob,fileres);
2821: if((ficresprob=fopen(fileresprob,"w"))==NULL) {
2822: printf("Problem with resultfile: %s\n", fileresprob);
2823: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
2824: }
2825: strcpy(fileresprobcov,"probcov");
2826: strcat(fileresprobcov,fileres);
2827: if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
2828: printf("Problem with resultfile: %s\n", fileresprobcov);
2829: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
2830: }
2831: strcpy(fileresprobcor,"probcor");
2832: strcat(fileresprobcor,fileres);
2833: if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
2834: printf("Problem with resultfile: %s\n", fileresprobcor);
2835: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
2836: }
2837: printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
2838: fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
2839: printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
2840: fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
2841: printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
2842: fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
2843:
2844: fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
2845: fprintf(ficresprob,"# Age");
2846: fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
2847: fprintf(ficresprobcov,"# Age");
2848: fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
2849: fprintf(ficresprobcov,"# Age");
2850:
2851:
2852: for(i=1; i<=nlstate;i++)
2853: for(j=1; j<=(nlstate+ndeath);j++){
2854: fprintf(ficresprob," p%1d-%1d (SE)",i,j);
2855: fprintf(ficresprobcov," p%1d-%1d ",i,j);
2856: fprintf(ficresprobcor," p%1d-%1d ",i,j);
2857: }
1.69 brouard 2858: /* fprintf(ficresprob,"\n");
1.53 brouard 2859: fprintf(ficresprobcov,"\n");
2860: fprintf(ficresprobcor,"\n");
1.69 brouard 2861: */
2862: xp=vector(1,npar);
1.53 brouard 2863: dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
2864: doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
2865: mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
2866: varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
2867: first=1;
1.88 brouard 2868: fprintf(ficgp,"\n# Routine varprob");
2869: fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
2870: fprintf(fichtm,"\n");
2871:
1.95 brouard 2872: fprintf(fichtm,"\n<li><h4> <a href=\"%s\">Matrix of variance-covariance of pairs of step probabilities (drawings)</a></h4></li>\n",optionfilehtmcov);
2873: fprintf(fichtmcov,"\n<h4>Matrix of variance-covariance of pairs of step probabilities</h4>\n\
1.91 brouard 2874: file %s<br>\n",optionfilehtmcov);
2875: fprintf(fichtmcov,"\nEllipsoids of confidence centered on point (p<inf>ij</inf>, p<inf>kl</inf>) are estimated\
2876: and drawn. It helps understanding how is the covariance between two incidences.\
2877: They are expressed in year<sup>-1</sup> in order to be less dependent of stepm.<br>\n");
2878: 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. \
2879: It can be understood this way: if pij and pkl where uncorrelated the (2x2) matrix of covariance \
2880: would have been (1/(var pij), 0 , 0, 1/(var pkl)), and the confidence interval would be 2 \
2881: standard deviations wide on each axis. <br>\
2882: Now, if both incidences are correlated (usual case) we diagonalised the inverse of the covariance matrix\
2883: and made the appropriate rotation to look at the uncorrelated principal directions.<br>\
2884: 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 2885:
2886: cov[1]=1;
2887: tj=cptcoveff;
2888: if (cptcovn<1) {tj=1;ncodemax[1]=1;}
2889: j1=0;
2890: for(t=1; t<=tj;t++){
2891: for(i1=1; i1<=ncodemax[t];i1++){
2892: j1++;
2893: if (cptcovn>0) {
2894: fprintf(ficresprob, "\n#********** Variable ");
2895: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
1.69 brouard 2896: fprintf(ficresprob, "**********\n#\n");
1.53 brouard 2897: fprintf(ficresprobcov, "\n#********** Variable ");
2898: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
1.69 brouard 2899: fprintf(ficresprobcov, "**********\n#\n");
1.53 brouard 2900:
2901: fprintf(ficgp, "\n#********** Variable ");
1.69 brouard 2902: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
2903: fprintf(ficgp, "**********\n#\n");
1.53 brouard 2904:
2905:
1.96 brouard 2906: fprintf(fichtmcov, "\n<hr size=\"2\" color=\"#EC5E5E\">********** Variable ");
1.53 brouard 2907: for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
1.96 brouard 2908: fprintf(fichtmcov, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
1.53 brouard 2909:
2910: fprintf(ficresprobcor, "\n#********** Variable ");
2911: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
1.69 brouard 2912: fprintf(ficresprobcor, "**********\n#");
1.53 brouard 2913: }
2914:
2915: for (age=bage; age<=fage; age ++){
2916: cov[2]=age;
2917: for (k=1; k<=cptcovn;k++) {
2918: cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];
2919: }
2920: for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
2921: for (k=1; k<=cptcovprod;k++)
2922: cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
2923:
2924: gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
2925: trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
2926: gp=vector(1,(nlstate)*(nlstate+ndeath));
2927: gm=vector(1,(nlstate)*(nlstate+ndeath));
2928:
2929: for(theta=1; theta <=npar; theta++){
2930: for(i=1; i<=npar; i++)
1.74 brouard 2931: xp[i] = x[i] + (i==theta ?delti[theta]:(double)0);
1.53 brouard 2932:
2933: pmij(pmmij,cov,ncovmodel,xp,nlstate);
2934:
2935: k=0;
2936: for(i=1; i<= (nlstate); i++){
2937: for(j=1; j<=(nlstate+ndeath);j++){
2938: k=k+1;
2939: gp[k]=pmmij[i][j];
2940: }
2941: }
2942:
2943: for(i=1; i<=npar; i++)
1.74 brouard 2944: xp[i] = x[i] - (i==theta ?delti[theta]:(double)0);
1.53 brouard 2945:
2946: pmij(pmmij,cov,ncovmodel,xp,nlstate);
2947: k=0;
2948: for(i=1; i<=(nlstate); i++){
2949: for(j=1; j<=(nlstate+ndeath);j++){
2950: k=k+1;
2951: gm[k]=pmmij[i][j];
2952: }
2953: }
2954:
2955: for(i=1; i<= (nlstate)*(nlstate+ndeath); i++)
1.74 brouard 2956: gradg[theta][i]=(gp[i]-gm[i])/(double)2./delti[theta];
1.53 brouard 2957: }
2958:
2959: for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
2960: for(theta=1; theta <=npar; theta++)
2961: trgradg[j][theta]=gradg[theta][j];
2962:
2963: matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov);
2964: matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);
1.59 brouard 2965: free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
2966: free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
2967: free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
2968: free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
2969:
1.53 brouard 2970: pmij(pmmij,cov,ncovmodel,x,nlstate);
2971:
2972: k=0;
2973: for(i=1; i<=(nlstate); i++){
2974: for(j=1; j<=(nlstate+ndeath);j++){
2975: k=k+1;
2976: mu[k][(int) age]=pmmij[i][j];
2977: }
2978: }
2979: for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
2980: for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
2981: varpij[i][j][(int)age] = doldm[i][j];
2982:
2983: /*printf("\n%d ",(int)age);
1.59 brouard 2984: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
2985: printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
2986: fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
2987: }*/
1.53 brouard 2988:
2989: fprintf(ficresprob,"\n%d ",(int)age);
2990: fprintf(ficresprobcov,"\n%d ",(int)age);
2991: fprintf(ficresprobcor,"\n%d ",(int)age);
2992:
2993: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)
2994: fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));
2995: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
2996: fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);
2997: fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
2998: }
2999: i=0;
3000: for (k=1; k<=(nlstate);k++){
3001: for (l=1; l<=(nlstate+ndeath);l++){
3002: i=i++;
3003: fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
3004: fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
3005: for (j=1; j<=i;j++){
3006: fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);
3007: fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));
3008: }
3009: }
3010: }/* end of loop for state */
3011: } /* end of loop for age */
3012:
3013: /* Confidence intervalle of pij */
3014: /*
1.59 brouard 3015: fprintf(ficgp,"\nset noparametric;unset label");
3016: fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");
3017: fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
3018: 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);
3019: fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);
3020: fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);
3021: fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);
1.53 brouard 3022: */
3023:
3024: /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
3025: first1=1;
3026: for (k2=1; k2<=(nlstate);k2++){
3027: for (l2=1; l2<=(nlstate+ndeath);l2++){
3028: if(l2==k2) continue;
3029: j=(k2-1)*(nlstate+ndeath)+l2;
3030: for (k1=1; k1<=(nlstate);k1++){
3031: for (l1=1; l1<=(nlstate+ndeath);l1++){
3032: if(l1==k1) continue;
3033: i=(k1-1)*(nlstate+ndeath)+l1;
3034: if(i<=j) continue;
3035: for (age=bage; age<=fage; age ++){
3036: if ((int)age %5==0){
3037: v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;
3038: v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;
3039: cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;
3040: mu1=mu[i][(int) age]/stepm*YEARM ;
3041: mu2=mu[j][(int) age]/stepm*YEARM;
3042: c12=cv12/sqrt(v1*v2);
3043: /* Computing eigen value of matrix of covariance */
3044: lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
3045: lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
3046: /* Eigen vectors */
3047: v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
3048: /*v21=sqrt(1.-v11*v11); *//* error */
3049: v21=(lc1-v1)/cv12*v11;
3050: v12=-v21;
3051: v22=v11;
3052: tnalp=v21/v11;
3053: if(first1==1){
3054: first1=0;
3055: 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);
3056: }
3057: 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);
3058: /*printf(fignu*/
3059: /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */
3060: /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */
3061: if(first==1){
3062: first=0;
3063: fprintf(ficgp,"\nset parametric;unset label");
3064: 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);
3065: fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
1.91 brouard 3066: fprintf(fichtmcov,"\n<br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup>\
1.88 brouard 3067: :<a href=\"%s%d%1d%1d-%1d%1d.png\">\
3068: %s%d%1d%1d-%1d%1d.png</A>, ",k1,l1,k2,l2,\
3069: subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2,\
3070: subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
1.91 brouard 3071: fprintf(fichtmcov,"\n<br><img src=\"%s%d%1d%1d-%1d%1d.png\"> ",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
3072: fprintf(fichtmcov,"\n<br> Correlation at age %d (%.3f),",(int) age, c12);
1.88 brouard 3073: fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\"",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
1.53 brouard 3074: fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
3075: fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
3076: 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",\
3077: mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
3078: mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
3079: }else{
3080: first=0;
1.91 brouard 3081: fprintf(fichtmcov," %d (%.3f),",(int) age, c12);
1.53 brouard 3082: fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
3083: fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
3084: 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",\
3085: mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
3086: mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
3087: }/* if first */
3088: } /* age mod 5 */
3089: } /* end loop age */
1.88 brouard 3090: fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\";replot;",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
1.53 brouard 3091: first=1;
3092: } /*l12 */
3093: } /* k12 */
3094: } /*l1 */
3095: }/* k1 */
3096: } /* loop covariates */
3097: }
1.59 brouard 3098: free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
3099: free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
1.53 brouard 3100: free_vector(xp,1,npar);
3101: fclose(ficresprob);
3102: fclose(ficresprobcov);
3103: fclose(ficresprobcor);
1.91 brouard 3104: fflush(ficgp);
3105: fflush(fichtmcov);
1.53 brouard 3106: }
3107:
3108:
3109: /******************* Printing html file ***********/
3110: void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \
3111: int lastpass, int stepm, int weightopt, char model[],\
3112: int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
3113: int popforecast, int estepm ,\
3114: double jprev1, double mprev1,double anprev1, \
3115: double jprev2, double mprev2,double anprev2){
3116: int jj1, k1, i1, cpt;
3117:
1.85 brouard 3118: fprintf(fichtm,"<ul><li><h4>Result files (first order: no variance)</h4>\n \
1.96 brouard 3119: - Observed prevalence in each state (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"%s\">%s</a> <br>\n ",
3120: jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirf2(fileres,"p"),subdirf2(fileres,"p"));
3121: fprintf(fichtm,"\
3122: - Estimated transition probabilities over %d (stepm) months: <a href=\"%s\">%s</a><br>\n ",
3123: stepm,subdirf2(fileres,"pij"),subdirf2(fileres,"pij"));
3124: fprintf(fichtm,"\
3125: - Stable prevalence in each health state: <a href=\"%s\">%s</a> <br>\n",
3126: subdirf2(fileres,"pl"),subdirf2(fileres,"pl"));
3127: fprintf(fichtm,"\
1.85 brouard 3128: - Life expectancies by age and initial health status (estepm=%2d months): \
1.96 brouard 3129: <a href=\"%s\">%s</a> <br>\n</li>",
1.88 brouard 3130: estepm,subdirf2(fileres,"e"),subdirf2(fileres,"e"));
1.53 brouard 3131:
3132: fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
3133:
3134: m=cptcoveff;
3135: if (cptcovn < 1) {m=1;ncodemax[1]=1;}
3136:
3137: jj1=0;
3138: for(k1=1; k1<=m;k1++){
3139: for(i1=1; i1<=ncodemax[k1];i1++){
3140: jj1++;
3141: if (cptcovn > 0) {
3142: fprintf(fichtm,"<hr size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
3143: for (cpt=1; cpt<=cptcoveff;cpt++)
3144: fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
3145: fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
3146: }
3147: /* Pij */
1.88 brouard 3148: 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> \
3149: <img src=\"%s%d1.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);
1.53 brouard 3150: /* Quasi-incidences */
1.85 brouard 3151: fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months\
1.88 brouard 3152: before but expressed in per year i.e. quasi incidences if stepm is small and probabilities too: %s%d2.png<br> \
3153: <img src=\"%s%d2.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);
1.53 brouard 3154: /* Stable prevalence in each health state */
3155: for(cpt=1; cpt<nlstate;cpt++){
1.85 brouard 3156: fprintf(fichtm,"<br>- Stable prevalence in each health state : p%s%d%d.png<br> \
1.88 brouard 3157: <img src=\"%s%d%d.png\">",subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1);
1.53 brouard 3158: }
3159: for(cpt=1; cpt<=nlstate;cpt++) {
1.88 brouard 3160: fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): %s%d%d.png <br> \
1.89 brouard 3161: <img src=\"%s%d%d.png\">",cpt,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1);
1.53 brouard 3162: }
3163: } /* end i1 */
3164: }/* End k1 */
3165: fprintf(fichtm,"</ul>");
3166:
3167:
1.96 brouard 3168: fprintf(fichtm,"\
3169: \n<br><li><h4> Result files (second order: variances)</h4>\n\
3170: - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n", rfileres,rfileres);
3171:
3172: fprintf(fichtm," - Variance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
3173: subdirf2(fileres,"prob"),subdirf2(fileres,"prob"));
3174: fprintf(fichtm,"\
3175: - Variance-covariance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
3176: subdirf2(fileres,"probcov"),subdirf2(fileres,"probcov"));
3177:
3178: fprintf(fichtm,"\
3179: - Correlation matrix of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
3180: subdirf2(fileres,"probcor"),subdirf2(fileres,"probcor"));
3181: fprintf(fichtm,"\
3182: - Variances and covariances of life expectancies by age and initial health status (estepm=%d months): <a href=\"%s\">%s</a><br>\n",
3183: estepm, subdirf2(fileres,"v"),subdirf2(fileres,"v"));
3184: fprintf(fichtm,"\
3185: - Health expectancies with their variances (no covariance): <a href=\"%s\">%s</a> <br>\n",
3186: subdirf2(fileres,"t"),subdirf2(fileres,"t"));
3187: fprintf(fichtm,"\
1.88 brouard 3188: - Standard deviation of stable prevalences: <a href=\"%s\">%s</a> <br>\n",\
3189: subdirf2(fileres,"vpl"),subdirf2(fileres,"vpl"));
1.53 brouard 3190:
1.76 brouard 3191: /* if(popforecast==1) fprintf(fichtm,"\n */
3192: /* - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n */
3193: /* - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n */
3194: /* <br>",fileres,fileres,fileres,fileres); */
3195: /* else */
3196: /* 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); */
1.96 brouard 3197: fflush(fichtm);
3198: fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
1.53 brouard 3199:
3200: m=cptcoveff;
3201: if (cptcovn < 1) {m=1;ncodemax[1]=1;}
3202:
3203: jj1=0;
3204: for(k1=1; k1<=m;k1++){
3205: for(i1=1; i1<=ncodemax[k1];i1++){
3206: jj1++;
3207: if (cptcovn > 0) {
3208: fprintf(fichtm,"<hr size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
3209: for (cpt=1; cpt<=cptcoveff;cpt++)
3210: fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
3211: fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
3212: }
3213: for(cpt=1; cpt<=nlstate;cpt++) {
1.95 brouard 3214: fprintf(fichtm,"<br>- Observed (cross-sectional) and period (incidence based) \
3215: prevalence (with 95%% confidence interval) in state (%d): %s%d%d.png <br>\
1.90 brouard 3216: <img src=\"%s%d%d.png\">",cpt,subdirf2(optionfilefiname,"v"),cpt,jj1,subdirf2(optionfilefiname,"v"),cpt,jj1);
1.53 brouard 3217: }
1.96 brouard 3218: fprintf(fichtm,"\n<br>- Total life expectancy by age and \
3219: health expectancies in states (1) and (2): %s%d.png<br>\
3220: <img src=\"%s%d.png\">",subdirf2(optionfilefiname,"e"),jj1,subdirf2(optionfilefiname,"e"),jj1);
1.53 brouard 3221: } /* end i1 */
3222: }/* End k1 */
3223: fprintf(fichtm,"</ul>");
1.87 brouard 3224: fflush(fichtm);
1.53 brouard 3225: }
3226:
3227: /******************* Gnuplot file **************/
1.89 brouard 3228: void printinggnuplot(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
1.53 brouard 3229:
1.88 brouard 3230: char dirfileres[132],optfileres[132];
1.53 brouard 3231: int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;
3232: int ng;
1.88 brouard 3233: /* if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) { */
3234: /* printf("Problem with file %s",optionfilegnuplot); */
3235: /* fprintf(ficlog,"Problem with file %s",optionfilegnuplot); */
3236: /* } */
1.53 brouard 3237:
1.54 brouard 3238: /*#ifdef windows */
1.89 brouard 3239: fprintf(ficgp,"cd \"%s\" \n",pathc);
1.54 brouard 3240: /*#endif */
1.88 brouard 3241: m=pow(2,cptcoveff);
3242:
3243: strcpy(dirfileres,optionfilefiname);
3244: strcpy(optfileres,"vpl");
1.53 brouard 3245: /* 1eme*/
3246: for (cpt=1; cpt<= nlstate ; cpt ++) {
3247: for (k1=1; k1<= m ; k1 ++) {
1.88 brouard 3248: fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"v"),cpt,k1);
3249: fprintf(ficgp,"\n#set out \"v%s%d%d.png\" \n",optionfilefiname,cpt,k1);
3250: fprintf(ficgp,"set xlabel \"Age\" \n\
3251: set ylabel \"Probability\" \n\
3252: set ter png small\n\
3253: set size 0.65,0.65\n\
3254: plot [%.f:%.f] \"%s\" every :::%d::%d u 1:2 \"\%%lf",ageminpar,fage,subdirf2(fileres,"vpl"),k1-1,k1-1);
1.53 brouard 3255:
3256: for (i=1; i<= nlstate ; i ++) {
3257: if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
3258: else fprintf(ficgp," \%%*lf (\%%*lf)");
3259: }
1.88 brouard 3260: 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 3261: for (i=1; i<= nlstate ; i ++) {
3262: if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
3263: else fprintf(ficgp," \%%*lf (\%%*lf)");
3264: }
1.88 brouard 3265: fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"%s\" every :::%d::%d u 1:($2-1.96*$3) \"\%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1);
1.53 brouard 3266: for (i=1; i<= nlstate ; i ++) {
3267: if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
3268: else fprintf(ficgp," \%%*lf (\%%*lf)");
3269: }
1.88 brouard 3270: fprintf(ficgp,"\" t\"\" w l 1,\"%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",subdirf2(fileres,"p"),k1-1,k1-1,2+4*(cpt-1));
1.53 brouard 3271: }
3272: }
3273: /*2 eme*/
3274:
3275: for (k1=1; k1<= m ; k1 ++) {
1.88 brouard 3276: fprintf(ficgp,"\nset out \"%s%d.png\" \n",subdirf2(optionfilefiname,"e"),k1);
1.53 brouard 3277: fprintf(ficgp,"set ylabel \"Years\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] ",ageminpar,fage);
3278:
3279: for (i=1; i<= nlstate+1 ; i ++) {
3280: k=2*i;
1.88 brouard 3281: fprintf(ficgp,"\"%s\" every :::%d::%d u 1:2 \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
1.53 brouard 3282: for (j=1; j<= nlstate+1 ; j ++) {
3283: if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
3284: else fprintf(ficgp," \%%*lf (\%%*lf)");
3285: }
3286: if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");
3287: else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);
1.88 brouard 3288: fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
1.53 brouard 3289: for (j=1; j<= nlstate+1 ; j ++) {
3290: if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
3291: else fprintf(ficgp," \%%*lf (\%%*lf)");
3292: }
3293: fprintf(ficgp,"\" t\"\" w l 0,");
1.88 brouard 3294: fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
1.53 brouard 3295: for (j=1; j<= nlstate+1 ; j ++) {
3296: if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
3297: else fprintf(ficgp," \%%*lf (\%%*lf)");
3298: }
3299: if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");
3300: else fprintf(ficgp,"\" t\"\" w l 0,");
3301: }
3302: }
3303:
3304: /*3eme*/
3305:
3306: for (k1=1; k1<= m ; k1 ++) {
3307: for (cpt=1; cpt<= nlstate ; cpt ++) {
3308: k=2+nlstate*(2*cpt-2);
1.88 brouard 3309: fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"exp"),cpt,k1);
3310: fprintf(ficgp,"set ter png small\n\
3311: set size 0.65,0.65\n\
3312: plot [%.f:%.f] \"%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,subdirf2(fileres,"e"),k1-1,k1-1,k,cpt);
1.53 brouard 3313: /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
3314: for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
3315: fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
3316: fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
3317: for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
3318: fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
3319:
3320: */
3321: for (i=1; i< nlstate ; i ++) {
1.88 brouard 3322: 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 3323:
3324: }
3325: }
3326: }
3327:
1.76 brouard 3328: /* CV preval stable (period) */
1.53 brouard 3329: for (k1=1; k1<= m ; k1 ++) {
1.76 brouard 3330: for (cpt=1; cpt<=nlstate ; cpt ++) {
1.53 brouard 3331: k=3;
1.88 brouard 3332: fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"p"),cpt,k1);
3333: fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\
3334: set ter png small\nset size 0.65,0.65\n\
1.89 brouard 3335: unset log y\n\
1.88 brouard 3336: plot [%.f:%.f] \"%s\" u ($1==%d ? ($3):1/0):($%d/($%d",ageminpar,agemaxpar,subdirf2(fileres,"pij"),k1,k+cpt+1,k+1);
1.53 brouard 3337:
1.83 lievre 3338: for (i=1; i< nlstate ; i ++)
1.53 brouard 3339: fprintf(ficgp,"+$%d",k+i+1);
3340: fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);
3341:
3342: l=3+(nlstate+ndeath)*cpt;
1.88 brouard 3343: fprintf(ficgp,",\"%s\" u ($1==%d ? ($3):1/0):($%d/($%d",subdirf2(fileres,"pij"),k1,l+cpt+1,l+1);
1.53 brouard 3344: for (i=1; i< nlstate ; i ++) {
3345: l=3+(nlstate+ndeath)*cpt;
3346: fprintf(ficgp,"+$%d",l+i+1);
3347: }
3348: fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);
3349: }
3350: }
3351:
3352: /* proba elementaires */
3353: for(i=1,jk=1; i <=nlstate; i++){
3354: for(k=1; k <=(nlstate+ndeath); k++){
3355: if (k != i) {
3356: for(j=1; j <=ncovmodel; j++){
3357: fprintf(ficgp,"p%d=%f ",jk,p[jk]);
3358: jk++;
3359: fprintf(ficgp,"\n");
3360: }
3361: }
3362: }
3363: }
3364:
3365: for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/
3366: for(jk=1; jk <=m; jk++) {
1.88 brouard 3367: fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"pe"),jk,ng);
1.53 brouard 3368: if (ng==2)
3369: fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
3370: else
3371: fprintf(ficgp,"\nset title \"Probability\"\n");
3372: fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65\nset log y\nplot [%.f:%.f] ",ageminpar,agemaxpar);
3373: i=1;
3374: for(k2=1; k2<=nlstate; k2++) {
3375: k3=i;
3376: for(k=1; k<=(nlstate+ndeath); k++) {
3377: if (k != k2){
3378: if(ng==2)
3379: fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);
3380: else
3381: fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
3382: ij=1;
3383: for(j=3; j <=ncovmodel; j++) {
3384: if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
3385: fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
3386: ij++;
3387: }
3388: else
3389: fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
3390: }
3391: fprintf(ficgp,")/(1");
3392:
3393: for(k1=1; k1 <=nlstate; k1++){
3394: fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);
3395: ij=1;
3396: for(j=3; j <=ncovmodel; j++){
3397: if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
3398: fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
3399: ij++;
3400: }
3401: else
3402: fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
3403: }
3404: fprintf(ficgp,")");
3405: }
3406: fprintf(ficgp,") t \"p%d%d\" ", k2,k);
3407: if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");
3408: i=i+ncovmodel;
3409: }
3410: } /* end k */
3411: } /* end k2 */
3412: } /* end jk */
3413: } /* end ng */
1.88 brouard 3414: fflush(ficgp);
1.53 brouard 3415: } /* end gnuplot */
3416:
3417:
3418: /*************** Moving average **************/
1.54 brouard 3419: int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav){
1.53 brouard 3420:
3421: int i, cpt, cptcod;
1.58 lievre 3422: int modcovmax =1;
1.54 brouard 3423: int mobilavrange, mob;
1.53 brouard 3424: double age;
1.58 lievre 3425:
3426: modcovmax=2*cptcoveff;/* Max number of modalities. We suppose
3427: a covariate has 2 modalities */
3428: if (cptcovn<1) modcovmax=1; /* At least 1 pass */
3429:
1.54 brouard 3430: if(mobilav==1||mobilav ==3 ||mobilav==5 ||mobilav== 7){
3431: if(mobilav==1) mobilavrange=5; /* default */
3432: else mobilavrange=mobilav;
3433: for (age=bage; age<=fage; age++)
3434: for (i=1; i<=nlstate;i++)
1.58 lievre 3435: for (cptcod=1;cptcod<=modcovmax;cptcod++)
1.54 brouard 3436: mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
3437: /* We keep the original values on the extreme ages bage, fage and for
3438: fage+1 and bage-1 we use a 3 terms moving average; for fage+2 bage+2
3439: we use a 5 terms etc. until the borders are no more concerned.
3440: */
3441: for (mob=3;mob <=mobilavrange;mob=mob+2){
3442: for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){
3443: for (i=1; i<=nlstate;i++){
1.58 lievre 3444: for (cptcod=1;cptcod<=modcovmax;cptcod++){
1.54 brouard 3445: mobaverage[(int)age][i][cptcod] =probs[(int)age][i][cptcod];
3446: for (cpt=1;cpt<=(mob-1)/2;cpt++){
3447: mobaverage[(int)age][i][cptcod] +=probs[(int)age-cpt][i][cptcod];
3448: mobaverage[(int)age][i][cptcod] +=probs[(int)age+cpt][i][cptcod];
3449: }
3450: mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/mob;
3451: }
1.53 brouard 3452: }
1.54 brouard 3453: }/* end age */
3454: }/* end mob */
3455: }else return -1;
3456: return 0;
3457: }/* End movingaverage */
1.53 brouard 3458:
3459:
3460: /************** Forecasting ******************/
1.70 brouard 3461: 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 3462: /* proj1, year, month, day of starting projection
3463: agemin, agemax range of age
3464: dateprev1 dateprev2 range of dates during which prevalence is computed
1.70 brouard 3465: anproj2 year of en of projection (same day and month as proj1).
1.69 brouard 3466: */
1.73 lievre 3467: int yearp, stepsize, hstepm, nhstepm, j, k, c, cptcod, i, h, i1;
1.53 brouard 3468: int *popage;
1.70 brouard 3469: double agec; /* generic age */
3470: double agelim, ppij, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
1.53 brouard 3471: double *popeffectif,*popcount;
3472: double ***p3mat;
1.55 lievre 3473: double ***mobaverage;
1.53 brouard 3474: char fileresf[FILENAMELENGTH];
3475:
1.69 brouard 3476: agelim=AGESUP;
1.84 brouard 3477: prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
1.53 brouard 3478:
3479: strcpy(fileresf,"f");
3480: strcat(fileresf,fileres);
3481: if((ficresf=fopen(fileresf,"w"))==NULL) {
3482: printf("Problem with forecast resultfile: %s\n", fileresf);
3483: fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);
3484: }
3485: printf("Computing forecasting: result on file '%s' \n", fileresf);
3486: fprintf(ficlog,"Computing forecasting: result on file '%s' \n", fileresf);
3487:
3488: if (cptcoveff==0) ncodemax[cptcoveff]=1;
3489:
1.54 brouard 3490: if (mobilav!=0) {
1.53 brouard 3491: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
1.54 brouard 3492: if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
3493: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
3494: printf(" Error in movingaverage mobilav=%d\n",mobilav);
3495: }
1.53 brouard 3496: }
3497:
3498: stepsize=(int) (stepm+YEARM-1)/YEARM;
3499: if (stepm<=12) stepsize=1;
1.74 brouard 3500: if(estepm < stepm){
3501: printf ("Problem %d lower than %d\n",estepm, stepm);
3502: }
3503: else hstepm=estepm;
3504:
1.53 brouard 3505: hstepm=hstepm/stepm;
1.69 brouard 3506: yp1=modf(dateintmean,&yp);/* extracts integral of datemean in yp and
3507: fractional in yp1 */
1.53 brouard 3508: anprojmean=yp;
3509: yp2=modf((yp1*12),&yp);
3510: mprojmean=yp;
3511: yp1=modf((yp2*30.5),&yp);
3512: jprojmean=yp;
3513: if(jprojmean==0) jprojmean=1;
3514: if(mprojmean==0) jprojmean=1;
1.73 lievre 3515:
3516: i1=cptcoveff;
3517: if (cptcovn < 1){i1=1;}
1.53 brouard 3518:
1.70 brouard 3519: fprintf(ficresf,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2);
1.53 brouard 3520:
1.70 brouard 3521: fprintf(ficresf,"#****** Routine prevforecast **\n");
1.73 lievre 3522:
1.75 brouard 3523: /* if (h==(int)(YEARM*yearp)){ */
1.73 lievre 3524: for(cptcov=1, k=0;cptcov<=i1;cptcov++){
1.53 brouard 3525: for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
3526: k=k+1;
3527: fprintf(ficresf,"\n#******");
3528: for(j=1;j<=cptcoveff;j++) {
1.70 brouard 3529: 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 3530: }
3531: fprintf(ficresf,"******\n");
1.70 brouard 3532: fprintf(ficresf,"# Covariate valuofcovar yearproj age");
3533: for(j=1; j<=nlstate+ndeath;j++){
3534: for(i=1; i<=nlstate;i++)
3535: fprintf(ficresf," p%d%d",i,j);
3536: fprintf(ficresf," p.%d",j);
3537: }
1.74 brouard 3538: for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) {
1.53 brouard 3539: fprintf(ficresf,"\n");
1.70 brouard 3540: fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+yearp);
1.53 brouard 3541:
1.71 brouard 3542: for (agec=fage; agec>=(ageminpar-1); agec--){
1.70 brouard 3543: nhstepm=(int) rint((agelim-agec)*YEARM/stepm);
1.53 brouard 3544: nhstepm = nhstepm/hstepm;
3545: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3546: oldm=oldms;savm=savms;
1.70 brouard 3547: hpxij(p3mat,nhstepm,agec,hstepm,p,nlstate,stepm,oldm,savm, k);
1.53 brouard 3548:
3549: for (h=0; h<=nhstepm; h++){
1.75 brouard 3550: if (h*hstepm/YEARM*stepm ==yearp) {
1.69 brouard 3551: fprintf(ficresf,"\n");
3552: for(j=1;j<=cptcoveff;j++)
3553: fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
1.70 brouard 3554: fprintf(ficresf,"%.f %.f ",anproj1+yearp,agec+h*hstepm/YEARM*stepm);
1.53 brouard 3555: }
3556: for(j=1; j<=nlstate+ndeath;j++) {
1.70 brouard 3557: ppij=0.;
1.71 brouard 3558: for(i=1; i<=nlstate;i++) {
1.53 brouard 3559: if (mobilav==1)
1.71 brouard 3560: ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][i][cptcod];
1.53 brouard 3561: else {
1.71 brouard 3562: ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][cptcod];
1.53 brouard 3563: }
1.75 brouard 3564: if (h*hstepm/YEARM*stepm== yearp) {
1.70 brouard 3565: fprintf(ficresf," %.3f", p3mat[i][j][h]);
1.75 brouard 3566: }
3567: } /* end i */
3568: if (h*hstepm/YEARM*stepm==yearp) {
1.70 brouard 3569: fprintf(ficresf," %.3f", ppij);
1.53 brouard 3570: }
1.75 brouard 3571: }/* end j */
3572: } /* end h */
1.53 brouard 3573: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
1.75 brouard 3574: } /* end agec */
3575: } /* end yearp */
3576: } /* end cptcod */
3577: } /* end cptcov */
1.53 brouard 3578:
1.54 brouard 3579: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
1.53 brouard 3580:
3581: fclose(ficresf);
3582: }
1.70 brouard 3583:
3584: /************** Forecasting *****not tested NB*************/
1.53 brouard 3585: 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){
3586:
3587: int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;
3588: int *popage;
1.69 brouard 3589: double calagedatem, agelim, kk1, kk2;
1.53 brouard 3590: double *popeffectif,*popcount;
3591: double ***p3mat,***tabpop,***tabpopprev;
1.55 lievre 3592: double ***mobaverage;
1.53 brouard 3593: char filerespop[FILENAMELENGTH];
3594:
3595: tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
3596: tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
3597: agelim=AGESUP;
1.69 brouard 3598: calagedatem=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;
1.53 brouard 3599:
1.84 brouard 3600: prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
1.53 brouard 3601:
3602:
3603: strcpy(filerespop,"pop");
3604: strcat(filerespop,fileres);
3605: if((ficrespop=fopen(filerespop,"w"))==NULL) {
3606: printf("Problem with forecast resultfile: %s\n", filerespop);
3607: fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop);
3608: }
3609: printf("Computing forecasting: result on file '%s' \n", filerespop);
3610: fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop);
3611:
3612: if (cptcoveff==0) ncodemax[cptcoveff]=1;
3613:
1.54 brouard 3614: if (mobilav!=0) {
1.53 brouard 3615: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
1.54 brouard 3616: if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
3617: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
3618: printf(" Error in movingaverage mobilav=%d\n",mobilav);
3619: }
1.53 brouard 3620: }
3621:
3622: stepsize=(int) (stepm+YEARM-1)/YEARM;
3623: if (stepm<=12) stepsize=1;
3624:
3625: agelim=AGESUP;
3626:
3627: hstepm=1;
3628: hstepm=hstepm/stepm;
3629:
3630: if (popforecast==1) {
3631: if((ficpop=fopen(popfile,"r"))==NULL) {
3632: printf("Problem with population file : %s\n",popfile);exit(0);
3633: fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0);
3634: }
3635: popage=ivector(0,AGESUP);
3636: popeffectif=vector(0,AGESUP);
3637: popcount=vector(0,AGESUP);
3638:
3639: i=1;
3640: while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;
3641:
3642: imx=i;
3643: for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];
3644: }
3645:
1.69 brouard 3646: for(cptcov=1,k=0;cptcov<=i2;cptcov++){
1.53 brouard 3647: for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
3648: k=k+1;
3649: fprintf(ficrespop,"\n#******");
3650: for(j=1;j<=cptcoveff;j++) {
3651: fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
3652: }
3653: fprintf(ficrespop,"******\n");
3654: fprintf(ficrespop,"# Age");
3655: for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);
3656: if (popforecast==1) fprintf(ficrespop," [Population]");
3657:
3658: for (cpt=0; cpt<=0;cpt++) {
3659: fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);
3660:
1.69 brouard 3661: for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){
1.53 brouard 3662: nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);
3663: nhstepm = nhstepm/hstepm;
3664:
3665: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3666: oldm=oldms;savm=savms;
3667: hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
3668:
3669: for (h=0; h<=nhstepm; h++){
1.69 brouard 3670: if (h==(int) (calagedatem+YEARM*cpt)) {
1.53 brouard 3671: fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
3672: }
3673: for(j=1; j<=nlstate+ndeath;j++) {
3674: kk1=0.;kk2=0;
3675: for(i=1; i<=nlstate;i++) {
3676: if (mobilav==1)
3677: kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];
3678: else {
3679: kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];
3680: }
3681: }
1.69 brouard 3682: if (h==(int)(calagedatem+12*cpt)){
1.53 brouard 3683: tabpop[(int)(agedeb)][j][cptcod]=kk1;
3684: /*fprintf(ficrespop," %.3f", kk1);
3685: if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/
3686: }
3687: }
3688: for(i=1; i<=nlstate;i++){
3689: kk1=0.;
3690: for(j=1; j<=nlstate;j++){
3691: kk1= kk1+tabpop[(int)(agedeb)][j][cptcod];
3692: }
1.69 brouard 3693: tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedatem+12*cpt)*hstepm/YEARM*stepm-1)];
1.53 brouard 3694: }
3695:
1.69 brouard 3696: if (h==(int)(calagedatem+12*cpt)) for(j=1; j<=nlstate;j++)
1.53 brouard 3697: fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);
3698: }
3699: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3700: }
3701: }
3702:
3703: /******/
3704:
3705: for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) {
3706: fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);
1.69 brouard 3707: for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){
1.53 brouard 3708: nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);
3709: nhstepm = nhstepm/hstepm;
3710:
3711: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3712: oldm=oldms;savm=savms;
3713: hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
3714: for (h=0; h<=nhstepm; h++){
1.69 brouard 3715: if (h==(int) (calagedatem+YEARM*cpt)) {
1.53 brouard 3716: fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
3717: }
3718: for(j=1; j<=nlstate+ndeath;j++) {
3719: kk1=0.;kk2=0;
3720: for(i=1; i<=nlstate;i++) {
3721: kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];
3722: }
1.69 brouard 3723: if (h==(int)(calagedatem+12*cpt)) fprintf(ficresf," %15.2f", kk1);
1.53 brouard 3724: }
3725: }
3726: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3727: }
3728: }
3729: }
3730: }
3731:
1.54 brouard 3732: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
1.53 brouard 3733:
3734: if (popforecast==1) {
3735: free_ivector(popage,0,AGESUP);
3736: free_vector(popeffectif,0,AGESUP);
3737: free_vector(popcount,0,AGESUP);
3738: }
3739: free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
3740: free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
3741: fclose(ficrespop);
1.84 brouard 3742: } /* End of popforecast */
1.53 brouard 3743:
1.87 brouard 3744: int fileappend(FILE *fichier, char *optionfich)
1.86 brouard 3745: {
1.87 brouard 3746: if((fichier=fopen(optionfich,"a"))==NULL) {
3747: printf("Problem with file: %s\n", optionfich);
3748: fprintf(ficlog,"Problem with file: %s\n", optionfich);
3749: return (0);
1.86 brouard 3750: }
1.87 brouard 3751: fflush(fichier);
3752: return (1);
1.86 brouard 3753: }
1.94 brouard 3754:
3755:
3756: /**************** function prwizard **********************/
1.88 brouard 3757: void prwizard(int ncovmodel, int nlstate, int ndeath, char model[], FILE *ficparo)
3758: {
3759:
1.94 brouard 3760: /* Wizard to print covariance matrix template */
3761:
1.88 brouard 3762: char ca[32], cb[32], cc[32];
3763: int i,j, k, l, li, lj, lk, ll, jj, npar, itimes;
3764: int numlinepar;
3765:
3766: printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
3767: fprintf(ficparo,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
3768: for(i=1; i <=nlstate; i++){
3769: jj=0;
3770: for(j=1; j <=nlstate+ndeath; j++){
3771: if(j==i) continue;
3772: jj++;
3773: /*ca[0]= k+'a'-1;ca[1]='\0';*/
3774: printf("%1d%1d",i,j);
3775: fprintf(ficparo,"%1d%1d",i,j);
3776: for(k=1; k<=ncovmodel;k++){
3777: /* printf(" %lf",param[i][j][k]); */
3778: /* fprintf(ficparo," %lf",param[i][j][k]); */
3779: printf(" 0.");
3780: fprintf(ficparo," 0.");
3781: }
3782: printf("\n");
3783: fprintf(ficparo,"\n");
3784: }
3785: }
3786: printf("# Scales (for hessian or gradient estimation)\n");
3787: fprintf(ficparo,"# Scales (for hessian or gradient estimation)\n");
3788: npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/
3789: for(i=1; i <=nlstate; i++){
3790: jj=0;
3791: for(j=1; j <=nlstate+ndeath; j++){
3792: if(j==i) continue;
3793: jj++;
3794: fprintf(ficparo,"%1d%1d",i,j);
3795: printf("%1d%1d",i,j);
3796: fflush(stdout);
3797: for(k=1; k<=ncovmodel;k++){
3798: /* printf(" %le",delti3[i][j][k]); */
3799: /* fprintf(ficparo," %le",delti3[i][j][k]); */
3800: printf(" 0.");
3801: fprintf(ficparo," 0.");
3802: }
3803: numlinepar++;
3804: printf("\n");
3805: fprintf(ficparo,"\n");
3806: }
3807: }
3808: printf("# Covariance matrix\n");
3809: /* # 121 Var(a12)\n\ */
3810: /* # 122 Cov(b12,a12) Var(b12)\n\ */
3811: /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
3812: /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
3813: /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
3814: /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
3815: /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
3816: /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
3817: fflush(stdout);
3818: fprintf(ficparo,"# Covariance matrix\n");
3819: /* # 121 Var(a12)\n\ */
3820: /* # 122 Cov(b12,a12) Var(b12)\n\ */
3821: /* # ...\n\ */
3822: /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
3823:
3824: for(itimes=1;itimes<=2;itimes++){
3825: jj=0;
3826: for(i=1; i <=nlstate; i++){
3827: for(j=1; j <=nlstate+ndeath; j++){
3828: if(j==i) continue;
3829: for(k=1; k<=ncovmodel;k++){
3830: jj++;
3831: ca[0]= k+'a'-1;ca[1]='\0';
3832: if(itimes==1){
3833: printf("#%1d%1d%d",i,j,k);
3834: fprintf(ficparo,"#%1d%1d%d",i,j,k);
3835: }else{
3836: printf("%1d%1d%d",i,j,k);
3837: fprintf(ficparo,"%1d%1d%d",i,j,k);
3838: /* printf(" %.5le",matcov[i][j]); */
3839: }
3840: ll=0;
3841: for(li=1;li <=nlstate; li++){
3842: for(lj=1;lj <=nlstate+ndeath; lj++){
3843: if(lj==li) continue;
3844: for(lk=1;lk<=ncovmodel;lk++){
3845: ll++;
3846: if(ll<=jj){
3847: cb[0]= lk +'a'-1;cb[1]='\0';
3848: if(ll<jj){
3849: if(itimes==1){
3850: printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
3851: fprintf(ficparo," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
3852: }else{
3853: printf(" 0.");
3854: fprintf(ficparo," 0.");
3855: }
3856: }else{
3857: if(itimes==1){
3858: printf(" Var(%s%1d%1d)",ca,i,j);
3859: fprintf(ficparo," Var(%s%1d%1d)",ca,i,j);
3860: }else{
3861: printf(" 0.");
3862: fprintf(ficparo," 0.");
3863: }
3864: }
3865: }
3866: } /* end lk */
3867: } /* end lj */
3868: } /* end li */
3869: printf("\n");
3870: fprintf(ficparo,"\n");
3871: numlinepar++;
3872: } /* end k*/
3873: } /*end j */
3874: } /* end i */
1.95 brouard 3875: } /* end itimes */
1.88 brouard 3876:
3877: } /* end of prwizard */
1.98 ! brouard 3878: /******************* Gompertz Likelihood ******************************/
! 3879: double gompertz(double x[])
! 3880: {
! 3881: double A,B,L=0.0,sump=0.,num=0.;
! 3882: int i,n=0; /* n is the size of the sample */
! 3883: for (i=0;i<=imx-1 ; i++) {
! 3884: sump=sump+weight[i];
! 3885: sump=sump+1;
! 3886: num=num+1;
! 3887: }
! 3888:
! 3889:
! 3890: /* for (i=1; i<=imx; i++)
! 3891: if (wav[i]>0) printf("i=%d ageex=%lf agecens=%lf agedc=%lf cens=%d %d\n" ,i,ageexmed[i],agecens[i],agedc[i],cens[i],wav[i]);*/
! 3892:
! 3893: for (i=0;i<=imx-1 ; i++)
! 3894: {
! 3895: if (cens[i]==1 & wav[i]>1)
! 3896: A=-x[1]/(x[2])*
! 3897: (exp(x[2]/YEARM*(agecens[i]*12-agegomp*12))-exp(x[2]/YEARM*(ageexmed[i]*12-agegomp*12)));
! 3898:
! 3899: if (cens[i]==0 & wav[i]>1)
! 3900: A=-x[1]/(x[2])*
! 3901: (exp(x[2]/YEARM*(agedc[i]*12-agegomp*12))-exp(x[2]/YEARM*(ageexmed[i]*12-agegomp*12)))
! 3902: +log(x[1]/YEARM)+x[2]/YEARM*(agedc[i]*12-agegomp*12)+log(YEARM);
! 3903:
! 3904: if (wav[i]>1 & agecens[i]>15) {
! 3905: L=L+A*weight[i];
! 3906: /* printf("\ni=%d A=%f L=%lf x[1]=%lf x[2]=%lf ageex=%lf agecens=%lf cens=%d agedc=%lf weight=%lf\n",i,A,L,x[1],x[2],ageexmed[i]*12,agecens[i]*12,cens[i],agedc[i]*12,weight[i]);*/
! 3907: }
! 3908: }
! 3909:
! 3910: /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/
! 3911:
! 3912: return -2*L*num/sump;
! 3913: }
! 3914:
! 3915: /******************* Printing html file ***********/
! 3916: void printinghtmlmort(char fileres[], char title[], char datafile[], int firstpass, \
! 3917: int lastpass, int stepm, int weightopt, char model[],\
! 3918: int imx, double p[],double **matcov){
! 3919: int i;
! 3920:
! 3921: fprintf(fichtm,"<ul><li><h4>Result files </h4>\n Force of mortality. Parameters of the Gompertz fit (with confidence interval in brackets):<br>");
! 3922: fprintf(fichtm," mu(age) =%lf*exp(%lf*(age-%d)) per year<br><br>",p[1],p[2],agegomp);
! 3923: for (i=1;i<=2;i++)
! 3924: fprintf(fichtm," p[%d] = %lf [%f ; %f]<br>\n",i,p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
! 3925: fprintf(fichtm,"<br><br><img src=\"graphmort.png\">");
! 3926: fprintf(fichtm,"</ul>");
! 3927: fflush(fichtm);
! 3928: }
! 3929:
! 3930: /******************* Gnuplot file **************/
! 3931: void printinggnuplotmort(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
! 3932:
! 3933: char dirfileres[132],optfileres[132];
! 3934: int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;
! 3935: int ng;
! 3936:
! 3937:
! 3938: /*#ifdef windows */
! 3939: fprintf(ficgp,"cd \"%s\" \n",pathc);
! 3940: /*#endif */
! 3941:
! 3942:
! 3943: strcpy(dirfileres,optionfilefiname);
! 3944: strcpy(optfileres,"vpl");
! 3945: fprintf(ficgp,"set out \"graphmort.png\"\n ");
! 3946: fprintf(ficgp,"set xlabel \"Age\"\n set ylabel \"Force of mortality (per year)\" \n ");
! 3947: fprintf(ficgp, "set ter png small\n set log y\n");
! 3948: fprintf(ficgp, "set size 0.65,0.65\n");
! 3949: fprintf(ficgp,"plot [%d:100] %lf*exp(%lf*(x-%d))",agegomp,p[1],p[2],agegomp);
! 3950:
! 3951: }
! 3952:
! 3953:
1.88 brouard 3954:
1.91 brouard 3955:
1.53 brouard 3956: /***********************************************/
3957: /**************** Main Program *****************/
3958: /***********************************************/
3959:
3960: int main(int argc, char *argv[])
3961: {
1.61 brouard 3962: int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav);
1.74 brouard 3963: int i,j, k, n=MAXN,iter,m,size=100,cptcode, cptcod;
1.95 brouard 3964: int jj, ll, li, lj, lk, imk;
1.85 brouard 3965: int numlinepar=0; /* Current linenumber of parameter file */
1.95 brouard 3966: int itimes;
1.98 ! brouard 3967: int NDIM=2;
1.95 brouard 3968:
3969: char ca[32], cb[32], cc[32];
1.87 brouard 3970: /* FILE *fichtm; *//* Html File */
3971: /* FILE *ficgp;*/ /*Gnuplot File */
1.53 brouard 3972: double agedeb, agefin,hf;
3973: double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;
3974:
3975: double fret;
3976: double **xi,tmp,delta;
3977:
3978: double dum; /* Dummy variable */
3979: double ***p3mat;
3980: double ***mobaverage;
3981: int *indx;
3982: char line[MAXLINE], linepar[MAXLINE];
1.88 brouard 3983: char path[MAXLINE],pathc[MAXLINE],pathcd[MAXLINE],pathtot[MAXLINE],model[MAXLINE];
3984: char pathr[MAXLINE];
1.53 brouard 3985: int firstobs=1, lastobs=10;
3986: int sdeb, sfin; /* Status at beginning and end */
3987: int c, h , cpt,l;
3988: int ju,jl, mi;
3989: int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;
1.59 brouard 3990: int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,*tab;
1.69 brouard 3991: int mobilavproj=0 , prevfcast=0 ; /* moving average of prev, If prevfcast=1 prevalence projection */
1.53 brouard 3992: int mobilav=0,popforecast=0;
3993: int hstepm, nhstepm;
1.74 brouard 3994: double jprev1=1, mprev1=1,anprev1=2000,jprev2=1, mprev2=1,anprev2=2000;
3995: double jpyram=1, mpyram=1,anpyram=2000,jpyram1=1, mpyram1=1,anpyram1=2000;
1.53 brouard 3996:
3997: double bage, fage, age, agelim, agebase;
3998: double ftolpl=FTOL;
3999: double **prlim;
4000: double *severity;
4001: double ***param; /* Matrix of parameters */
4002: double *p;
4003: double **matcov; /* Matrix of covariance */
4004: double ***delti3; /* Scale */
4005: double *delti; /* Scale */
4006: double ***eij, ***vareij;
4007: double **varpl; /* Variances of prevalence limits by age */
4008: double *epj, vepp;
4009: double kk1, kk2;
1.74 brouard 4010: double dateprev1, dateprev2,jproj1=1,mproj1=1,anproj1=2000,jproj2=1,mproj2=1,anproj2=2000;
1.98 ! brouard 4011: double **ximort;
1.53 brouard 4012: char *alph[]={"a","a","b","c","d","e"}, str[4];
1.98 ! brouard 4013: int *dcwave;
1.53 brouard 4014:
4015: char z[1]="c", occ;
1.86 brouard 4016:
1.53 brouard 4017: char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];
1.88 brouard 4018: char strstart[80], *strt, strtend[80];
1.85 brouard 4019: char *stratrunc;
4020: int lstra;
4021:
4022: long total_usecs;
1.53 brouard 4023:
1.95 brouard 4024: /* setlocale (LC_ALL, ""); */
4025: /* bindtextdomain (PACKAGE, LOCALEDIR); */
4026: /* textdomain (PACKAGE); */
4027: /* setlocale (LC_CTYPE, ""); */
4028: /* setlocale (LC_MESSAGES, ""); */
4029:
1.85 brouard 4030: /* gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */
4031: (void) gettimeofday(&start_time,&tzp);
1.91 brouard 4032: curr_time=start_time;
1.85 brouard 4033: tm = *localtime(&start_time.tv_sec);
4034: tmg = *gmtime(&start_time.tv_sec);
1.88 brouard 4035: strcpy(strstart,asctime(&tm));
1.86 brouard 4036:
1.88 brouard 4037: /* printf("Localtime (at start)=%s",strstart); */
1.85 brouard 4038: /* tp.tv_sec = tp.tv_sec +86400; */
4039: /* tm = *localtime(&start_time.tv_sec); */
4040: /* tmg.tm_year=tmg.tm_year +dsign*dyear; */
4041: /* tmg.tm_mon=tmg.tm_mon +dsign*dmonth; */
4042: /* tmg.tm_hour=tmg.tm_hour + 1; */
4043: /* tp.tv_sec = mktime(&tmg); */
4044: /* strt=asctime(&tmg); */
1.88 brouard 4045: /* printf("Time(after) =%s",strstart); */
1.85 brouard 4046: /* (void) time (&time_value);
4047: * printf("time=%d,t-=%d\n",time_value,time_value-86400);
4048: * tm = *localtime(&time_value);
1.88 brouard 4049: * strstart=asctime(&tm);
4050: * printf("tim_value=%d,asctime=%s\n",time_value,strstart);
1.85 brouard 4051: */
4052:
1.91 brouard 4053: nberr=0; /* Number of errors and warnings */
4054: nbwarn=0;
1.53 brouard 4055: getcwd(pathcd, size);
4056:
1.81 brouard 4057: printf("\n%s\n%s",version,fullversion);
1.53 brouard 4058: if(argc <=1){
4059: printf("\nEnter the parameter file name: ");
4060: scanf("%s",pathtot);
4061: }
4062: else{
4063: strcpy(pathtot,argv[1]);
4064: }
1.88 brouard 4065: /*if(getcwd(pathcd, MAXLINE)!= NULL)printf ("Error pathcd\n");*/
1.53 brouard 4066: /*cygwin_split_path(pathtot,path,optionfile);
4067: printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/
4068: /* cutv(path,optionfile,pathtot,'\\');*/
4069:
4070: split(pathtot,path,optionfile,optionfilext,optionfilefiname);
1.85 brouard 4071: printf("pathtot=%s,\npath=%s,\noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
1.53 brouard 4072: chdir(path);
1.88 brouard 4073: strcpy(command,"mkdir ");
4074: strcat(command,optionfilefiname);
4075: if((outcmd=system(command)) != 0){
4076: printf("Problem creating directory or it already exists %s%s, err=%d\n",path,optionfilefiname,outcmd);
4077: /* fprintf(ficlog,"Problem creating directory %s%s\n",path,optionfilefiname); */
4078: /* fclose(ficlog); */
4079: /* exit(1); */
4080: }
4081: /* if((imk=mkdir(optionfilefiname))<0){ */
4082: /* perror("mkdir"); */
4083: /* } */
1.53 brouard 4084:
1.59 brouard 4085: /*-------- arguments in the command line --------*/
1.53 brouard 4086:
4087: /* Log file */
4088: strcat(filelog, optionfilefiname);
4089: strcat(filelog,".log"); /* */
4090: if((ficlog=fopen(filelog,"w"))==NULL) {
4091: printf("Problem with logfile %s\n",filelog);
4092: goto end;
4093: }
4094: fprintf(ficlog,"Log filename:%s\n",filelog);
1.85 brouard 4095: fprintf(ficlog,"\n%s\n%s",version,fullversion);
1.53 brouard 4096: fprintf(ficlog,"\nEnter the parameter file name: ");
1.88 brouard 4097: fprintf(ficlog,"pathtot=%s\n\
4098: path=%s \n\
4099: optionfile=%s\n\
4100: optionfilext=%s\n\
4101: optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
1.86 brouard 4102:
1.94 brouard 4103: printf("Local time (at start):%s",strstart);
4104: fprintf(ficlog,"Local time (at start): %s",strstart);
1.53 brouard 4105: fflush(ficlog);
1.91 brouard 4106: /* (void) gettimeofday(&curr_time,&tzp); */
4107: /* printf("Elapsed time %d\n", asc_diff_time(curr_time.tv_sec-start_time.tv_sec,tmpout)); */
1.53 brouard 4108:
4109: /* */
4110: strcpy(fileres,"r");
4111: strcat(fileres, optionfilefiname);
4112: strcat(fileres,".txt"); /* Other files have txt extension */
4113:
4114: /*---------arguments file --------*/
4115:
4116: if((ficpar=fopen(optionfile,"r"))==NULL) {
4117: printf("Problem with optionfile %s\n",optionfile);
4118: fprintf(ficlog,"Problem with optionfile %s\n",optionfile);
1.85 brouard 4119: fflush(ficlog);
1.53 brouard 4120: goto end;
4121: }
4122:
1.88 brouard 4123:
4124:
1.53 brouard 4125: strcpy(filereso,"o");
4126: strcat(filereso,fileres);
1.88 brouard 4127: if((ficparo=fopen(filereso,"w"))==NULL) { /* opened on subdirectory */
1.53 brouard 4128: printf("Problem with Output resultfile: %s\n", filereso);
4129: fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso);
1.85 brouard 4130: fflush(ficlog);
1.53 brouard 4131: goto end;
4132: }
4133:
4134: /* Reads comments: lines beginning with '#' */
1.85 brouard 4135: numlinepar=0;
1.53 brouard 4136: while((c=getc(ficpar))=='#' && c!= EOF){
4137: ungetc(c,ficpar);
4138: fgets(line, MAXLINE, ficpar);
1.85 brouard 4139: numlinepar++;
1.53 brouard 4140: puts(line);
4141: fputs(line,ficparo);
1.85 brouard 4142: fputs(line,ficlog);
1.53 brouard 4143: }
4144: ungetc(c,ficpar);
4145:
4146: 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 4147: numlinepar++;
1.53 brouard 4148: 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);
4149: 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 4150: 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);
4151: fflush(ficlog);
1.59 brouard 4152: while((c=getc(ficpar))=='#' && c!= EOF){
1.53 brouard 4153: ungetc(c,ficpar);
4154: fgets(line, MAXLINE, ficpar);
1.85 brouard 4155: numlinepar++;
1.53 brouard 4156: puts(line);
4157: fputs(line,ficparo);
1.85 brouard 4158: fputs(line,ficlog);
1.53 brouard 4159: }
4160: ungetc(c,ficpar);
1.85 brouard 4161:
1.53 brouard 4162:
4163: covar=matrix(0,NCOVMAX,1,n);
1.58 lievre 4164: cptcovn=0; /*Number of covariates, i.e. number of '+' in model statement*/
1.53 brouard 4165: if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;
4166:
1.58 lievre 4167: ncovmodel=2+cptcovn; /*Number of variables = cptcovn + intercept + age */
1.53 brouard 4168: nvar=ncovmodel-1; /* Suppressing age as a basic covariate */
1.98 ! brouard 4169: npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/
! 4170:
! 4171: delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
! 4172: delti=delti3[1][1];
! 4173: /*delti=vector(1,npar); *//* Scale of each paramater (output from hesscov)*/
1.88 brouard 4174: if(mle==-1){ /* Print a wizard for help writing covariance matrix */
4175: prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
4176: printf(" You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
4177: fprintf(ficlog," You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
1.98 ! brouard 4178: free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
1.88 brouard 4179: fclose (ficparo);
4180: fclose (ficlog);
4181: exit(0);
4182: }
1.98 ! brouard 4183: else if(mle==-3) {
! 4184: prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
! 4185: printf(" You choose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
! 4186: fprintf(ficlog," You choose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
! 4187: param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
! 4188: matcov=matrix(1,npar,1,npar);
1.53 brouard 4189: }
1.98 ! brouard 4190: else{
! 4191: /* Read guess parameters */
! 4192: /* Reads comments: lines beginning with '#' */
! 4193: while((c=getc(ficpar))=='#' && c!= EOF){
! 4194: ungetc(c,ficpar);
! 4195: fgets(line, MAXLINE, ficpar);
1.85 brouard 4196: numlinepar++;
1.98 ! brouard 4197: puts(line);
! 4198: fputs(line,ficparo);
! 4199: fputs(line,ficlog);
1.53 brouard 4200: }
1.98 ! brouard 4201: ungetc(c,ficpar);
! 4202:
! 4203: param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
! 4204: for(i=1; i <=nlstate; i++){
! 4205: j=0;
! 4206: for(jj=1; jj <=nlstate+ndeath; jj++){
! 4207: if(jj==i) continue;
! 4208: j++;
! 4209: fscanf(ficpar,"%1d%1d",&i1,&j1);
! 4210: if ((i1 != i) && (j1 != j)){
! 4211: printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n",numlinepar, i,j, i1, j1);
! 4212: exit(1);
! 4213: }
! 4214: fprintf(ficparo,"%1d%1d",i1,j1);
! 4215: if(mle==1)
! 4216: printf("%1d%1d",i,j);
! 4217: fprintf(ficlog,"%1d%1d",i,j);
! 4218: for(k=1; k<=ncovmodel;k++){
! 4219: fscanf(ficpar," %lf",¶m[i][j][k]);
! 4220: if(mle==1){
! 4221: printf(" %lf",param[i][j][k]);
! 4222: fprintf(ficlog," %lf",param[i][j][k]);
! 4223: }
! 4224: else
! 4225: fprintf(ficlog," %lf",param[i][j][k]);
! 4226: fprintf(ficparo," %lf",param[i][j][k]);
! 4227: }
! 4228: fscanf(ficpar,"\n");
! 4229: numlinepar++;
! 4230: if(mle==1)
! 4231: printf("\n");
! 4232: fprintf(ficlog,"\n");
! 4233: fprintf(ficparo,"\n");
! 4234: }
! 4235: }
! 4236: fflush(ficlog);
1.85 brouard 4237:
1.53 brouard 4238:
1.98 ! brouard 4239: p=param[1][1];
! 4240:
! 4241: /* Reads comments: lines beginning with '#' */
! 4242: while((c=getc(ficpar))=='#' && c!= EOF){
! 4243: ungetc(c,ficpar);
! 4244: fgets(line, MAXLINE, ficpar);
! 4245: numlinepar++;
! 4246: puts(line);
! 4247: fputs(line,ficparo);
! 4248: fputs(line,ficlog);
! 4249: }
1.53 brouard 4250: ungetc(c,ficpar);
4251:
1.98 ! brouard 4252: for(i=1; i <=nlstate; i++){
! 4253: for(j=1; j <=nlstate+ndeath-1; j++){
! 4254: fscanf(ficpar,"%1d%1d",&i1,&j1);
! 4255: if ((i1-i)*(j1-j)!=0){
! 4256: printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n",numlinepar, i,j, i1, j1);
! 4257: exit(1);
! 4258: }
! 4259: printf("%1d%1d",i,j);
! 4260: fprintf(ficparo,"%1d%1d",i1,j1);
! 4261: fprintf(ficlog,"%1d%1d",i1,j1);
! 4262: for(k=1; k<=ncovmodel;k++){
! 4263: fscanf(ficpar,"%le",&delti3[i][j][k]);
! 4264: printf(" %le",delti3[i][j][k]);
! 4265: fprintf(ficparo," %le",delti3[i][j][k]);
! 4266: fprintf(ficlog," %le",delti3[i][j][k]);
! 4267: }
! 4268: fscanf(ficpar,"\n");
! 4269: numlinepar++;
! 4270: printf("\n");
! 4271: fprintf(ficparo,"\n");
! 4272: fprintf(ficlog,"\n");
1.85 brouard 4273: }
1.53 brouard 4274: }
1.98 ! brouard 4275: fflush(ficlog);
1.85 brouard 4276:
1.98 ! brouard 4277: delti=delti3[1][1];
1.74 brouard 4278:
4279:
1.98 ! brouard 4280: /* 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 4281:
1.98 ! brouard 4282: /* Reads comments: lines beginning with '#' */
! 4283: while((c=getc(ficpar))=='#' && c!= EOF){
! 4284: ungetc(c,ficpar);
! 4285: fgets(line, MAXLINE, ficpar);
! 4286: numlinepar++;
! 4287: puts(line);
! 4288: fputs(line,ficparo);
! 4289: fputs(line,ficlog);
! 4290: }
1.53 brouard 4291: ungetc(c,ficpar);
4292:
1.98 ! brouard 4293: matcov=matrix(1,npar,1,npar);
! 4294: for(i=1; i <=npar; i++){
! 4295: fscanf(ficpar,"%s",&str);
! 4296: if(mle==1)
! 4297: printf("%s",str);
! 4298: fprintf(ficlog,"%s",str);
! 4299: fprintf(ficparo,"%s",str);
! 4300: for(j=1; j <=i; j++){
! 4301: fscanf(ficpar," %le",&matcov[i][j]);
! 4302: if(mle==1){
! 4303: printf(" %.5le",matcov[i][j]);
! 4304: }
! 4305: fprintf(ficlog," %.5le",matcov[i][j]);
! 4306: fprintf(ficparo," %.5le",matcov[i][j]);
1.53 brouard 4307: }
1.98 ! brouard 4308: fscanf(ficpar,"\n");
! 4309: numlinepar++;
! 4310: if(mle==1)
! 4311: printf("\n");
! 4312: fprintf(ficlog,"\n");
! 4313: fprintf(ficparo,"\n");
1.53 brouard 4314: }
1.98 ! brouard 4315: for(i=1; i <=npar; i++)
! 4316: for(j=i+1;j<=npar;j++)
! 4317: matcov[i][j]=matcov[j][i];
! 4318:
1.53 brouard 4319: if(mle==1)
4320: printf("\n");
4321: fprintf(ficlog,"\n");
1.98 ! brouard 4322:
! 4323: fflush(ficlog);
! 4324:
! 4325: /*-------- Rewriting parameter file ----------*/
! 4326: strcpy(rfileres,"r"); /* "Rparameterfile */
! 4327: strcat(rfileres,optionfilefiname); /* Parameter file first name*/
! 4328: strcat(rfileres,"."); /* */
! 4329: strcat(rfileres,optionfilext); /* Other files have txt extension */
! 4330: if((ficres =fopen(rfileres,"w"))==NULL) {
! 4331: printf("Problem writing new parameter file: %s\n", fileres);goto end;
! 4332: fprintf(ficlog,"Problem writing new parameter file: %s\n", fileres);goto end;
! 4333: }
! 4334: fprintf(ficres,"#%s\n",version);
! 4335: } /* End of mle != -3 */
1.53 brouard 4336:
1.59 brouard 4337: /*-------- data file ----------*/
4338: if((fic=fopen(datafile,"r"))==NULL) {
4339: printf("Problem with datafile: %s\n", datafile);goto end;
4340: fprintf(ficlog,"Problem with datafile: %s\n", datafile);goto end;
4341: }
4342:
4343: n= lastobs;
4344: severity = vector(1,maxwav);
4345: outcome=imatrix(1,maxwav+1,1,n);
1.85 brouard 4346: num=lvector(1,n);
1.59 brouard 4347: moisnais=vector(1,n);
4348: annais=vector(1,n);
4349: moisdc=vector(1,n);
4350: andc=vector(1,n);
4351: agedc=vector(1,n);
4352: cod=ivector(1,n);
4353: weight=vector(1,n);
4354: for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */
4355: mint=matrix(1,maxwav,1,n);
4356: anint=matrix(1,maxwav,1,n);
4357: s=imatrix(1,maxwav+1,1,n);
4358: tab=ivector(1,NCOVMAX);
4359: ncodemax=ivector(1,8);
4360:
4361: i=1;
4362: while (fgets(line, MAXLINE, fic) != NULL) {
4363: if ((i >= firstobs) && (i <=lastobs)) {
1.53 brouard 4364:
1.59 brouard 4365: for (j=maxwav;j>=1;j--){
4366: cutv(stra, strb,line,' '); s[j][i]=atoi(strb);
4367: strcpy(line,stra);
4368: cutv(stra, strb,line,'/'); anint[j][i]=(double)(atoi(strb)); strcpy(line,stra);
4369: cutv(stra, strb,line,' '); mint[j][i]=(double)(atoi(strb)); strcpy(line,stra);
4370: }
1.53 brouard 4371:
1.59 brouard 4372: cutv(stra, strb,line,'/'); andc[i]=(double)(atoi(strb)); strcpy(line,stra);
4373: cutv(stra, strb,line,' '); moisdc[i]=(double)(atoi(strb)); strcpy(line,stra);
1.53 brouard 4374:
1.59 brouard 4375: cutv(stra, strb,line,'/'); annais[i]=(double)(atoi(strb)); strcpy(line,stra);
4376: cutv(stra, strb,line,' '); moisnais[i]=(double)(atoi(strb)); strcpy(line,stra);
1.53 brouard 4377:
1.59 brouard 4378: cutv(stra, strb,line,' '); weight[i]=(double)(atoi(strb)); strcpy(line,stra);
4379: for (j=ncovcol;j>=1;j--){
4380: cutv(stra, strb,line,' '); covar[j][i]=(double)(atoi(strb)); strcpy(line,stra);
4381: }
1.85 brouard 4382: lstra=strlen(stra);
4383: if(lstra > 9){ /* More than 2**32 or max of what printf can write with %ld */
4384: stratrunc = &(stra[lstra-9]);
4385: num[i]=atol(stratrunc);
4386: }
4387: else
4388: num[i]=atol(stra);
1.53 brouard 4389:
1.59 brouard 4390: /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){
1.85 brouard 4391: 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 4392:
1.59 brouard 4393: i=i+1;
4394: }
4395: }
4396: /* printf("ii=%d", ij);
4397: scanf("%d",i);*/
1.53 brouard 4398: imx=i-1; /* Number of individuals */
4399:
4400: /* for (i=1; i<=imx; i++){
4401: if ((s[1][i]==3) && (s[2][i]==2)) s[2][i]=3;
4402: if ((s[2][i]==3) && (s[3][i]==2)) s[3][i]=3;
4403: if ((s[3][i]==3) && (s[4][i]==2)) s[4][i]=3;
4404: }*/
4405: /* for (i=1; i<=imx; i++){
4406: if (s[4][i]==9) s[4][i]=-1;
1.85 brouard 4407: 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 4408:
1.71 brouard 4409: for (i=1; i<=imx; i++)
1.53 brouard 4410:
1.71 brouard 4411: /*if ((s[3][i]==3) || (s[4][i]==3)) weight[i]=0.08;
4412: else weight[i]=1;*/
4413:
1.53 brouard 4414: /* Calculation of the number of parameter from char model*/
4415: Tvar=ivector(1,15); /* stores the number n of the covariates in Vm+Vn at 1 and m at 2 */
4416: Tprod=ivector(1,15);
4417: Tvaraff=ivector(1,15);
4418: Tvard=imatrix(1,15,1,2);
4419: Tage=ivector(1,15);
4420:
1.58 lievre 4421: if (strlen(model) >1){ /* If there is at least 1 covariate */
1.53 brouard 4422: j=0, j1=0, k1=1, k2=1;
1.58 lievre 4423: j=nbocc(model,'+'); /* j=Number of '+' */
4424: j1=nbocc(model,'*'); /* j1=Number of '*' */
4425: cptcovn=j+1;
4426: cptcovprod=j1; /*Number of products */
1.53 brouard 4427:
4428: strcpy(modelsav,model);
4429: if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){
4430: printf("Error. Non available option model=%s ",model);
4431: fprintf(ficlog,"Error. Non available option model=%s ",model);
4432: goto end;
4433: }
4434:
1.59 brouard 4435: /* This loop fills the array Tvar from the string 'model'.*/
1.58 lievre 4436:
1.53 brouard 4437: for(i=(j+1); i>=1;i--){
4438: cutv(stra,strb,modelsav,'+'); /* keeps in strb after the last + */
1.59 brouard 4439: if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyzes it */
1.53 brouard 4440: /* printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/
4441: /*scanf("%d",i);*/
4442: if (strchr(strb,'*')) { /* Model includes a product */
4443: cutv(strd,strc,strb,'*'); /* strd*strc Vm*Vn (if not *age)*/
4444: if (strcmp(strc,"age")==0) { /* Vn*age */
4445: cptcovprod--;
4446: cutv(strb,stre,strd,'V');
4447: Tvar[i]=atoi(stre); /* computes n in Vn and stores in Tvar*/
4448: cptcovage++;
4449: Tage[cptcovage]=i;
4450: /*printf("stre=%s ", stre);*/
4451: }
4452: else if (strcmp(strd,"age")==0) { /* or age*Vn */
4453: cptcovprod--;
4454: cutv(strb,stre,strc,'V');
4455: Tvar[i]=atoi(stre);
4456: cptcovage++;
4457: Tage[cptcovage]=i;
4458: }
4459: else { /* Age is not in the model */
4460: cutv(strb,stre,strc,'V'); /* strc= Vn, stre is n*/
4461: Tvar[i]=ncovcol+k1;
4462: cutv(strb,strc,strd,'V'); /* strd was Vm, strc is m */
4463: Tprod[k1]=i;
4464: Tvard[k1][1]=atoi(strc); /* m*/
4465: Tvard[k1][2]=atoi(stre); /* n */
4466: Tvar[cptcovn+k2]=Tvard[k1][1];
4467: Tvar[cptcovn+k2+1]=Tvard[k1][2];
4468: for (k=1; k<=lastobs;k++)
4469: covar[ncovcol+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];
4470: k1++;
4471: k2=k2+2;
4472: }
4473: }
4474: else { /* no more sum */
4475: /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/
4476: /* scanf("%d",i);*/
4477: cutv(strd,strc,strb,'V');
4478: Tvar[i]=atoi(strc);
4479: }
4480: strcpy(modelsav,stra);
4481: /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);
4482: scanf("%d",i);*/
4483: } /* end of loop + */
4484: } /* end model */
4485:
1.58 lievre 4486: /*The number n of Vn is stored in Tvar. cptcovage =number of age covariate. Tage gives the position of age. cptcovprod= number of products.
4487: If model=V1+V1*age then Tvar[1]=1 Tvar[2]=1 cptcovage=1 Tage[1]=2 cptcovprod=0*/
4488:
1.53 brouard 4489: /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);
4490: printf("cptcovprod=%d ", cptcovprod);
4491: fprintf(ficlog,"cptcovprod=%d ", cptcovprod);
1.58 lievre 4492:
4493: scanf("%d ",i);
4494: fclose(fic);*/
1.53 brouard 4495:
4496: /* if(mle==1){*/
1.59 brouard 4497: if (weightopt != 1) { /* Maximisation without weights*/
4498: for(i=1;i<=n;i++) weight[i]=1.0;
4499: }
1.53 brouard 4500: /*-calculation of age at interview from date of interview and age at death -*/
1.59 brouard 4501: agev=matrix(1,maxwav,1,imx);
1.53 brouard 4502:
1.59 brouard 4503: for (i=1; i<=imx; i++) {
4504: for(m=2; (m<= maxwav); m++) {
1.76 brouard 4505: if (((int)mint[m][i]== 99) && (s[m][i] <= nlstate)){
1.59 brouard 4506: anint[m][i]=9999;
4507: s[m][i]=-1;
4508: }
1.76 brouard 4509: if((int)moisdc[i]==99 && (int)andc[i]==9999 && s[m][i]>nlstate){
1.91 brouard 4510: nberr++;
1.85 brouard 4511: 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);
4512: 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 4513: s[m][i]=-1;
4514: }
4515: if((int)moisdc[i]==99 && (int)andc[i]!=9999 && s[m][i]>nlstate){
1.91 brouard 4516: nberr++;
1.85 brouard 4517: 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]);
4518: 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 4519: s[m][i]=-1; /* We prefer to skip it (and to skip it in version 0.8a1 too */
1.76 brouard 4520: }
1.53 brouard 4521: }
1.59 brouard 4522: }
1.53 brouard 4523:
1.59 brouard 4524: for (i=1; i<=imx; i++) {
4525: agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);
1.71 brouard 4526: for(m=firstpass; (m<= lastpass); m++){
1.69 brouard 4527: if(s[m][i] >0){
1.59 brouard 4528: if (s[m][i] >= nlstate+1) {
4529: if(agedc[i]>0)
1.76 brouard 4530: if((int)moisdc[i]!=99 && (int)andc[i]!=9999)
1.69 brouard 4531: agev[m][i]=agedc[i];
1.59 brouard 4532: /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/
4533: else {
1.76 brouard 4534: if ((int)andc[i]!=9999){
1.91 brouard 4535: nbwarn++;
1.85 brouard 4536: printf("Warning negative age at death: %ld line:%d\n",num[i],i);
4537: fprintf(ficlog,"Warning negative age at death: %ld line:%d\n",num[i],i);
1.59 brouard 4538: agev[m][i]=-1;
1.53 brouard 4539: }
4540: }
1.70 brouard 4541: }
1.69 brouard 4542: else if(s[m][i] !=9){ /* Standard case, age in fractional
4543: years but with the precision of a
4544: month */
1.59 brouard 4545: agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);
1.76 brouard 4546: if((int)mint[m][i]==99 || (int)anint[m][i]==9999)
1.59 brouard 4547: agev[m][i]=1;
4548: else if(agev[m][i] <agemin){
4549: agemin=agev[m][i];
4550: /*printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], agemin);*/
1.53 brouard 4551: }
1.59 brouard 4552: else if(agev[m][i] >agemax){
4553: agemax=agev[m][i];
4554: /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/
1.53 brouard 4555: }
1.59 brouard 4556: /*agev[m][i]=anint[m][i]-annais[i];*/
4557: /* agev[m][i] = age[i]+2*m;*/
1.53 brouard 4558: }
1.59 brouard 4559: else { /* =9 */
1.53 brouard 4560: agev[m][i]=1;
1.59 brouard 4561: s[m][i]=-1;
4562: }
1.53 brouard 4563: }
1.59 brouard 4564: else /*= 0 Unknown */
4565: agev[m][i]=1;
4566: }
1.53 brouard 4567:
1.59 brouard 4568: }
4569: for (i=1; i<=imx; i++) {
1.71 brouard 4570: for(m=firstpass; (m<=lastpass); m++){
1.59 brouard 4571: if (s[m][i] > (nlstate+ndeath)) {
1.91 brouard 4572: nberr++;
1.59 brouard 4573: 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);
4574: 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);
4575: goto end;
1.53 brouard 4576: }
4577: }
1.59 brouard 4578: }
1.53 brouard 4579:
1.71 brouard 4580: /*for (i=1; i<=imx; i++){
4581: for (m=firstpass; (m<lastpass); m++){
1.85 brouard 4582: 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 4583: }
4584:
4585: }*/
4586:
1.97 lievre 4587:
1.59 brouard 4588: printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);
4589: fprintf(ficlog,"Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);
4590:
1.98 ! brouard 4591: agegomp=(int)agemin;
1.59 brouard 4592: free_vector(severity,1,maxwav);
4593: free_imatrix(outcome,1,maxwav+1,1,n);
4594: free_vector(moisnais,1,n);
4595: free_vector(annais,1,n);
4596: /* free_matrix(mint,1,maxwav,1,n);
4597: free_matrix(anint,1,maxwav,1,n);*/
4598: free_vector(moisdc,1,n);
4599: free_vector(andc,1,n);
1.53 brouard 4600:
4601:
1.59 brouard 4602: wav=ivector(1,imx);
4603: dh=imatrix(1,lastpass-firstpass+1,1,imx);
4604: bh=imatrix(1,lastpass-firstpass+1,1,imx);
4605: mw=imatrix(1,lastpass-firstpass+1,1,imx);
1.69 brouard 4606:
1.59 brouard 4607: /* Concatenates waves */
4608: concatwav(wav, dh, bh, mw, s, agedc, agev, firstpass, lastpass, imx, nlstate, stepm);
1.53 brouard 4609:
1.59 brouard 4610: /* Routine tricode is to calculate cptcoveff (real number of unique covariates) and to associate covariable number and modality */
1.53 brouard 4611:
1.59 brouard 4612: Tcode=ivector(1,100);
4613: nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);
4614: ncodemax[1]=1;
4615: if (cptcovn > 0) tricode(Tvar,nbcode,imx);
1.53 brouard 4616:
1.59 brouard 4617: codtab=imatrix(1,100,1,10); /* Cross tabulation to get the order of
4618: the estimations*/
4619: h=0;
4620: m=pow(2,cptcoveff);
1.53 brouard 4621:
1.59 brouard 4622: for(k=1;k<=cptcoveff; k++){
4623: for(i=1; i <=(m/pow(2,k));i++){
4624: for(j=1; j <= ncodemax[k]; j++){
4625: for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){
4626: h++;
4627: if (h>m) h=1;codtab[h][k]=j;codtab[h][Tvar[k]]=j;
4628: /* printf("h=%d k=%d j=%d codtab[h][k]=%d tvar[k]=%d \n",h, k,j,codtab[h][k],Tvar[k]);*/
4629: }
4630: }
4631: }
4632: }
4633: /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]);
4634: codtab[1][2]=1;codtab[2][2]=2; */
4635: /* for(i=1; i <=m ;i++){
4636: for(k=1; k <=cptcovn; k++){
4637: printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);
4638: }
4639: printf("\n");
1.53 brouard 4640: }
1.59 brouard 4641: scanf("%d",i);*/
1.53 brouard 4642:
1.86 brouard 4643: /*------------ gnuplot -------------*/
4644: strcpy(optionfilegnuplot,optionfilefiname);
1.98 ! brouard 4645: if(mle==-3)
! 4646: strcat(optionfilegnuplot,"-mort");
1.86 brouard 4647: strcat(optionfilegnuplot,".gp");
1.98 ! brouard 4648:
1.86 brouard 4649: if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {
4650: printf("Problem with file %s",optionfilegnuplot);
4651: }
4652: else{
4653: fprintf(ficgp,"\n# %s\n", version);
4654: fprintf(ficgp,"# %s\n", optionfilegnuplot);
4655: fprintf(ficgp,"set missing 'NaNq'\n");
4656: }
1.88 brouard 4657: /* fclose(ficgp);*/
1.86 brouard 4658: /*--------- index.htm --------*/
4659:
1.91 brouard 4660: strcpy(optionfilehtm,optionfilefiname); /* Main html file */
1.98 ! brouard 4661: if(mle==-3)
! 4662: strcat(optionfilehtm,"-mort");
1.86 brouard 4663: strcat(optionfilehtm,".htm");
4664: if((fichtm=fopen(optionfilehtm,"w"))==NULL) {
4665: printf("Problem with %s \n",optionfilehtm), exit(0);
4666: }
4667:
1.91 brouard 4668: strcpy(optionfilehtmcov,optionfilefiname); /* Only for matrix of covariance */
4669: strcat(optionfilehtmcov,"-cov.htm");
4670: if((fichtmcov=fopen(optionfilehtmcov,"w"))==NULL) {
4671: printf("Problem with %s \n",optionfilehtmcov), exit(0);
4672: }
4673: else{
4674: fprintf(fichtmcov,"<body>\n<title>IMaCh Cov %s</title>\n <font size=\"2\">%s <br> %s</font> \
4675: <hr size=\"2\" color=\"#EC5E5E\"> \n\
4676: Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n",\
4677: fileres,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);
4678: }
4679:
1.87 brouard 4680: fprintf(fichtm,"<body>\n<title>IMaCh %s</title>\n <font size=\"2\">%s <br> %s</font> \
1.86 brouard 4681: <hr size=\"2\" color=\"#EC5E5E\"> \n\
4682: Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n\
4683: \n\
4684: <hr size=\"2\" color=\"#EC5E5E\">\
4685: <ul><li><h4>Parameter files</h4>\n\
4686: - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n\
4687: - Log file of the run: <a href=\"%s\">%s</a><br>\n\
1.87 brouard 4688: - Gnuplot file name: <a href=\"%s\">%s</a><br>\n\
1.86 brouard 4689: - Date and time at start: %s</ul>\n",\
1.91 brouard 4690: fileres,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model,\
4691: fileres,fileres,\
1.88 brouard 4692: filelog,filelog,optionfilegnuplot,optionfilegnuplot,strstart);
1.87 brouard 4693: fflush(fichtm);
1.86 brouard 4694:
1.88 brouard 4695: strcpy(pathr,path);
4696: strcat(pathr,optionfilefiname);
4697: chdir(optionfilefiname); /* Move to directory named optionfile */
4698:
1.59 brouard 4699: /* Calculates basic frequencies. Computes observed prevalence at single age
4700: and prints on file fileres'p'. */
1.84 brouard 4701: freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint);
1.53 brouard 4702:
1.88 brouard 4703: fprintf(fichtm,"\n");
4704: fprintf(fichtm,"<br>Total number of observations=%d <br>\n\
1.86 brouard 4705: Youngest age at first (selected) pass %.2f, oldest age %.2f<br>\n\
4706: Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n",\
1.88 brouard 4707: imx,agemin,agemax,jmin,jmax,jmean);
4708: pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
1.60 brouard 4709: oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
4710: newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
4711: savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
4712: oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */
1.53 brouard 4713:
4714:
1.59 brouard 4715: /* For Powell, parameters are in a vector p[] starting at p[1]
4716: so we point p on param[1][1] so that p[1] maps on param[1][1][1] */
4717: p=param[1][1]; /* *(*(*(param +1)+1)+0) */
1.53 brouard 4718:
1.86 brouard 4719: globpr=0; /* To get the number ipmx of contributions and the sum of weights*/
1.98 ! brouard 4720: if (mle==-3){
! 4721: ximort=matrix(1,NDIM,1,NDIM);
! 4722: cens=ivector(1,n);
! 4723: ageexmed=vector(1,n);
! 4724: agecens=vector(1,n);
! 4725: dcwave=ivector(1,n);
! 4726:
! 4727: for (i=1; i<=imx; i++){
! 4728: dcwave[i]=-1;
! 4729: for (j=1; j<=lastpass; j++)
! 4730: if (s[j][i]>nlstate) {
! 4731: dcwave[i]=j;
! 4732: /* printf("i=%d j=%d s=%d dcwave=%d\n",i,j, s[j][i],dcwave[i]);*/
! 4733: break;
! 4734: }
! 4735: }
! 4736:
! 4737: for (i=1; i<=imx; i++) {
! 4738: if (wav[i]>0){
! 4739: ageexmed[i]=agev[mw[1][i]][i];
! 4740: j=wav[i];agecens[i]=1.;
! 4741: if (ageexmed[i]>1 & wav[i]>0) agecens[i]=agev[mw[j][i]][i];
! 4742: cens[i]=1;
! 4743:
! 4744: if (ageexmed[i]<1) cens[i]=-1;
! 4745: if (agedc[i]< AGESUP & agedc[i]>1 & dcwave[i]>firstpass & dcwave[i]<=lastpass) cens[i]=0 ;
! 4746: }
! 4747: else cens[i]=-1;
! 4748: }
! 4749:
! 4750: for (i=1;i<=NDIM;i++) {
! 4751: for (j=1;j<=NDIM;j++)
! 4752: ximort[i][j]=(i == j ? 1.0 : 0.0);
! 4753: }
! 4754:
! 4755: p[1]=0.1; p[2]=0.1;
! 4756: /*printf("%lf %lf", p[1], p[2]);*/
! 4757:
! 4758:
! 4759: printf("Powell\n"); fprintf(ficlog,"Powell\n");
! 4760: strcpy(filerespow,"pow-mort");
! 4761: strcat(filerespow,fileres);
! 4762: if((ficrespow=fopen(filerespow,"w"))==NULL) {
! 4763: printf("Problem with resultfile: %s\n", filerespow);
! 4764: fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
1.59 brouard 4765: }
1.98 ! brouard 4766: fprintf(ficrespow,"# Powell\n# iter -2*LL");
! 4767: /* for (i=1;i<=nlstate;i++)
! 4768: for(j=1;j<=nlstate+ndeath;j++)
! 4769: if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
! 4770: */
! 4771: fprintf(ficrespow,"\n");
! 4772:
! 4773: powell(p,ximort,NDIM,ftol,&iter,&fret,gompertz);
! 4774: fclose(ficrespow);
1.53 brouard 4775:
1.98 ! brouard 4776: hesscov(matcov, p, NDIM,delti, 1e-4, gompertz);
1.53 brouard 4777:
1.98 ! brouard 4778: for(i=1; i <=NDIM; i++)
! 4779: for(j=i+1;j<=NDIM;j++)
! 4780: matcov[i][j]=matcov[j][i];
! 4781:
! 4782: printf("\nCovariance matrix\n ");
! 4783: for(i=1; i <=NDIM; i++) {
! 4784: for(j=1;j<=NDIM;j++){
! 4785: printf("%f ",matcov[i][j]);
1.95 brouard 4786: }
1.98 ! brouard 4787: printf("\n ");
! 4788: }
! 4789:
! 4790: printf("iter=%d MLE=%f Eq=%lf*exp(%lf*(age-%d))\n",iter,-gompertz(p),p[1],p[2],agegomp);
! 4791: for (i=1;i<=NDIM;i++)
! 4792: printf("%f [%f ; %f]\n",p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
! 4793: replace_back_to_slash(pathc,path); /* Even gnuplot wants a / */
! 4794: printinggnuplotmort(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
! 4795:
! 4796: printinghtmlmort(fileres,title,datafile, firstpass, lastpass, \
! 4797: stepm, weightopt,\
! 4798: model,imx,p,matcov);
! 4799: } /* Endof if mle==-3 */
! 4800:
! 4801: else{ /* For mle >=1 */
! 4802:
! 4803: likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
! 4804: printf("First Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
! 4805: for (k=1; k<=npar;k++)
! 4806: printf(" %d %8.5f",k,p[k]);
! 4807: printf("\n");
! 4808: globpr=1; /* to print the contributions */
! 4809: likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
! 4810: printf("Second Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
! 4811: for (k=1; k<=npar;k++)
! 4812: printf(" %d %8.5f",k,p[k]);
! 4813: printf("\n");
! 4814: if(mle>=1){ /* Could be 1 or 2 */
! 4815: mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);
1.59 brouard 4816: }
1.98 ! brouard 4817:
! 4818: /*--------- results files --------------*/
! 4819: 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);
! 4820:
! 4821:
! 4822: fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
! 4823: printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
! 4824: fprintf(ficlog,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
! 4825: for(i=1,jk=1; i <=nlstate; i++){
! 4826: for(k=1; k <=(nlstate+ndeath); k++){
! 4827: if (k != i) {
! 4828: printf("%d%d ",i,k);
! 4829: fprintf(ficlog,"%d%d ",i,k);
! 4830: fprintf(ficres,"%1d%1d ",i,k);
! 4831: for(j=1; j <=ncovmodel; j++){
! 4832: printf("%f ",p[jk]);
! 4833: fprintf(ficlog,"%f ",p[jk]);
! 4834: fprintf(ficres,"%f ",p[jk]);
! 4835: jk++;
! 4836: }
! 4837: printf("\n");
! 4838: fprintf(ficlog,"\n");
! 4839: fprintf(ficres,"\n");
1.59 brouard 4840: }
4841: }
4842: }
1.98 ! brouard 4843: if(mle!=0){
! 4844: /* Computing hessian and covariance matrix */
! 4845: ftolhess=ftol; /* Usually correct */
! 4846: hesscov(matcov, p, npar, delti, ftolhess, func);
! 4847: }
! 4848: fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");
! 4849: printf("# Scales (for hessian or gradient estimation)\n");
! 4850: fprintf(ficlog,"# Scales (for hessian or gradient estimation)\n");
! 4851: for(i=1,jk=1; i <=nlstate; i++){
1.95 brouard 4852: for(j=1; j <=nlstate+ndeath; j++){
1.98 ! brouard 4853: if (j!=i) {
! 4854: fprintf(ficres,"%1d%1d",i,j);
! 4855: printf("%1d%1d",i,j);
! 4856: fprintf(ficlog,"%1d%1d",i,j);
! 4857: for(k=1; k<=ncovmodel;k++){
! 4858: printf(" %.5e",delti[jk]);
! 4859: fprintf(ficlog," %.5e",delti[jk]);
! 4860: fprintf(ficres," %.5e",delti[jk]);
! 4861: jk++;
1.95 brouard 4862: }
1.98 ! brouard 4863: printf("\n");
! 4864: fprintf(ficlog,"\n");
! 4865: fprintf(ficres,"\n");
! 4866: }
! 4867: }
! 4868: }
! 4869:
! 4870: 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");
! 4871: if(mle>=1)
! 4872: 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");
! 4873: 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");
! 4874: /* # 121 Var(a12)\n\ */
! 4875: /* # 122 Cov(b12,a12) Var(b12)\n\ */
! 4876: /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
! 4877: /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
! 4878: /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
! 4879: /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
! 4880: /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
! 4881: /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
! 4882:
! 4883:
! 4884: /* Just to have a covariance matrix which will be more understandable
! 4885: even is we still don't want to manage dictionary of variables
! 4886: */
! 4887: for(itimes=1;itimes<=2;itimes++){
! 4888: jj=0;
! 4889: for(i=1; i <=nlstate; i++){
! 4890: for(j=1; j <=nlstate+ndeath; j++){
! 4891: if(j==i) continue;
! 4892: for(k=1; k<=ncovmodel;k++){
! 4893: jj++;
! 4894: ca[0]= k+'a'-1;ca[1]='\0';
! 4895: if(itimes==1){
! 4896: if(mle>=1)
! 4897: printf("#%1d%1d%d",i,j,k);
! 4898: fprintf(ficlog,"#%1d%1d%d",i,j,k);
! 4899: fprintf(ficres,"#%1d%1d%d",i,j,k);
! 4900: }else{
! 4901: if(mle>=1)
! 4902: printf("%1d%1d%d",i,j,k);
! 4903: fprintf(ficlog,"%1d%1d%d",i,j,k);
! 4904: fprintf(ficres,"%1d%1d%d",i,j,k);
! 4905: }
! 4906: ll=0;
! 4907: for(li=1;li <=nlstate; li++){
! 4908: for(lj=1;lj <=nlstate+ndeath; lj++){
! 4909: if(lj==li) continue;
! 4910: for(lk=1;lk<=ncovmodel;lk++){
! 4911: ll++;
! 4912: if(ll<=jj){
! 4913: cb[0]= lk +'a'-1;cb[1]='\0';
! 4914: if(ll<jj){
! 4915: if(itimes==1){
! 4916: if(mle>=1)
! 4917: printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
! 4918: fprintf(ficlog," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
! 4919: fprintf(ficres," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
! 4920: }else{
! 4921: if(mle>=1)
! 4922: printf(" %.5e",matcov[jj][ll]);
! 4923: fprintf(ficlog," %.5e",matcov[jj][ll]);
! 4924: fprintf(ficres," %.5e",matcov[jj][ll]);
! 4925: }
1.95 brouard 4926: }else{
1.98 ! brouard 4927: if(itimes==1){
! 4928: if(mle>=1)
! 4929: printf(" Var(%s%1d%1d)",ca,i,j);
! 4930: fprintf(ficlog," Var(%s%1d%1d)",ca,i,j);
! 4931: fprintf(ficres," Var(%s%1d%1d)",ca,i,j);
! 4932: }else{
! 4933: if(mle>=1)
! 4934: printf(" %.5e",matcov[jj][ll]);
! 4935: fprintf(ficlog," %.5e",matcov[jj][ll]);
! 4936: fprintf(ficres," %.5e",matcov[jj][ll]);
! 4937: }
1.95 brouard 4938: }
4939: }
1.98 ! brouard 4940: } /* end lk */
! 4941: } /* end lj */
! 4942: } /* end li */
! 4943: if(mle>=1)
! 4944: printf("\n");
! 4945: fprintf(ficlog,"\n");
! 4946: fprintf(ficres,"\n");
! 4947: numlinepar++;
! 4948: } /* end k*/
! 4949: } /*end j */
! 4950: } /* end i */
! 4951: } /* end itimes */
! 4952:
! 4953: fflush(ficlog);
! 4954: fflush(ficres);
! 4955:
! 4956: while((c=getc(ficpar))=='#' && c!= EOF){
! 4957: ungetc(c,ficpar);
! 4958: fgets(line, MAXLINE, ficpar);
! 4959: puts(line);
! 4960: fputs(line,ficparo);
! 4961: }
1.59 brouard 4962: ungetc(c,ficpar);
1.98 ! brouard 4963:
! 4964: estepm=0;
! 4965: fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm);
! 4966: if (estepm==0 || estepm < stepm) estepm=stepm;
! 4967: if (fage <= 2) {
! 4968: bage = ageminpar;
! 4969: fage = agemaxpar;
! 4970: }
! 4971:
! 4972: fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");
! 4973: fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
! 4974: fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
! 4975:
! 4976: while((c=getc(ficpar))=='#' && c!= EOF){
! 4977: ungetc(c,ficpar);
! 4978: fgets(line, MAXLINE, ficpar);
! 4979: puts(line);
! 4980: fputs(line,ficparo);
! 4981: }
1.59 brouard 4982: ungetc(c,ficpar);
1.98 ! brouard 4983:
! 4984: 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);
! 4985: 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);
! 4986: 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);
! 4987: printf("begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
! 4988: 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);
! 4989:
! 4990: while((c=getc(ficpar))=='#' && c!= EOF){
! 4991: ungetc(c,ficpar);
! 4992: fgets(line, MAXLINE, ficpar);
! 4993: puts(line);
! 4994: fputs(line,ficparo);
! 4995: }
1.59 brouard 4996: ungetc(c,ficpar);
1.98 ! brouard 4997:
! 4998:
! 4999: dateprev1=anprev1+(mprev1-1)/12.+(jprev1-1)/365.;
! 5000: dateprev2=anprev2+(mprev2-1)/12.+(jprev2-1)/365.;
! 5001:
! 5002: fscanf(ficpar,"pop_based=%d\n",&popbased);
! 5003: fprintf(ficparo,"pop_based=%d\n",popbased);
! 5004: fprintf(ficres,"pop_based=%d\n",popbased);
! 5005:
! 5006: while((c=getc(ficpar))=='#' && c!= EOF){
! 5007: ungetc(c,ficpar);
! 5008: fgets(line, MAXLINE, ficpar);
! 5009: puts(line);
! 5010: fputs(line,ficparo);
! 5011: }
1.53 brouard 5012: ungetc(c,ficpar);
1.98 ! brouard 5013:
! 5014: 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);
! 5015: 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);
! 5016: 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);
! 5017: 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);
! 5018: 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);
! 5019: /* day and month of proj2 are not used but only year anproj2.*/
! 5020:
! 5021:
! 5022:
! 5023: /* freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint);*/
! 5024: /*,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
! 5025:
! 5026: replace_back_to_slash(pathc,path); /* Even gnuplot wants a / */
! 5027: printinggnuplot(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
! 5028:
! 5029: printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,\
! 5030: model,imx,jmin,jmax,jmean,rfileres,popforecast,estepm,\
! 5031: jprev1,mprev1,anprev1,jprev2,mprev2,anprev2);
! 5032:
! 5033: /*------------ free_vector -------------*/
! 5034: /* chdir(path); */
1.53 brouard 5035:
1.98 ! brouard 5036: free_ivector(wav,1,imx);
! 5037: free_imatrix(dh,1,lastpass-firstpass+1,1,imx);
! 5038: free_imatrix(bh,1,lastpass-firstpass+1,1,imx);
! 5039: free_imatrix(mw,1,lastpass-firstpass+1,1,imx);
! 5040: free_lvector(num,1,n);
! 5041: free_vector(agedc,1,n);
! 5042: /*free_matrix(covar,0,NCOVMAX,1,n);*/
! 5043: /*free_matrix(covar,1,NCOVMAX,1,n);*/
! 5044: fclose(ficparo);
! 5045: fclose(ficres);
! 5046:
! 5047:
! 5048: /*--------------- Prevalence limit (stable prevalence) --------------*/
! 5049:
! 5050: strcpy(filerespl,"pl");
! 5051: strcat(filerespl,fileres);
! 5052: if((ficrespl=fopen(filerespl,"w"))==NULL) {
! 5053: printf("Problem with stable prevalence resultfile: %s\n", filerespl);goto end;
! 5054: fprintf(ficlog,"Problem with stable prevalence resultfile: %s\n", filerespl);goto end;
! 5055: }
! 5056: printf("Computing stable prevalence: result on file '%s' \n", filerespl);
! 5057: fprintf(ficlog,"Computing stable prevalence: result on file '%s' \n", filerespl);
! 5058: fprintf(ficrespl,"#Stable prevalence \n");
! 5059: fprintf(ficrespl,"#Age ");
! 5060: for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);
! 5061: fprintf(ficrespl,"\n");
! 5062:
! 5063: prlim=matrix(1,nlstate,1,nlstate);
! 5064:
! 5065: agebase=ageminpar;
! 5066: agelim=agemaxpar;
! 5067: ftolpl=1.e-10;
! 5068: i1=cptcoveff;
! 5069: if (cptcovn < 1){i1=1;}
! 5070:
! 5071: for(cptcov=1,k=0;cptcov<=i1;cptcov++){
! 5072: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
! 5073: k=k+1;
! 5074: /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/
! 5075: fprintf(ficrespl,"\n#******");
! 5076: printf("\n#******");
! 5077: fprintf(ficlog,"\n#******");
! 5078: for(j=1;j<=cptcoveff;j++) {
! 5079: fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
! 5080: printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
! 5081: fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
! 5082: }
! 5083: fprintf(ficrespl,"******\n");
! 5084: printf("******\n");
! 5085: fprintf(ficlog,"******\n");
1.53 brouard 5086:
1.98 ! brouard 5087: for (age=agebase; age<=agelim; age++){
! 5088: prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
! 5089: fprintf(ficrespl,"%.0f ",age );
! 5090: for(j=1;j<=cptcoveff;j++)
! 5091: fprintf(ficrespl,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
! 5092: for(i=1; i<=nlstate;i++)
! 5093: fprintf(ficrespl," %.5f", prlim[i][i]);
! 5094: fprintf(ficrespl,"\n");
! 5095: }
1.53 brouard 5096: }
5097: }
1.98 ! brouard 5098: fclose(ficrespl);
1.53 brouard 5099:
1.98 ! brouard 5100: /*------------- h Pij x at various ages ------------*/
1.53 brouard 5101:
1.98 ! brouard 5102: strcpy(filerespij,"pij"); strcat(filerespij,fileres);
! 5103: if((ficrespij=fopen(filerespij,"w"))==NULL) {
! 5104: printf("Problem with Pij resultfile: %s\n", filerespij);goto end;
! 5105: fprintf(ficlog,"Problem with Pij resultfile: %s\n", filerespij);goto end;
! 5106: }
! 5107: printf("Computing pij: result on file '%s' \n", filerespij);
! 5108: fprintf(ficlog,"Computing pij: result on file '%s' \n", filerespij);
1.53 brouard 5109:
1.98 ! brouard 5110: stepsize=(int) (stepm+YEARM-1)/YEARM;
! 5111: /*if (stepm<=24) stepsize=2;*/
1.53 brouard 5112:
1.98 ! brouard 5113: agelim=AGESUP;
! 5114: hstepm=stepsize*YEARM; /* Every year of age */
! 5115: hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */
1.53 brouard 5116:
1.98 ! brouard 5117: /* hstepm=1; aff par mois*/
1.53 brouard 5118:
1.98 ! brouard 5119: fprintf(ficrespij,"#****** h Pij x Probability to be in state j at age x+h being in i at x ");
! 5120: for(cptcov=1,k=0;cptcov<=i1;cptcov++){
! 5121: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
! 5122: k=k+1;
! 5123: fprintf(ficrespij,"\n#****** ");
! 5124: for(j=1;j<=cptcoveff;j++)
! 5125: fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
! 5126: fprintf(ficrespij,"******\n");
1.53 brouard 5127:
1.98 ! brouard 5128: for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */
! 5129: nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
! 5130: nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
1.59 brouard 5131:
1.98 ! brouard 5132: /* nhstepm=nhstepm*YEARM; aff par mois*/
1.59 brouard 5133:
1.98 ! brouard 5134: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
! 5135: oldm=oldms;savm=savms;
! 5136: hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
! 5137: fprintf(ficrespij,"# Cov Agex agex+h hpijx with i,j=");
1.53 brouard 5138: for(i=1; i<=nlstate;i++)
5139: for(j=1; j<=nlstate+ndeath;j++)
1.98 ! brouard 5140: fprintf(ficrespij," %1d-%1d",i,j);
! 5141: fprintf(ficrespij,"\n");
! 5142: for (h=0; h<=nhstepm; h++){
! 5143: fprintf(ficrespij,"%d %3.f %3.f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );
! 5144: for(i=1; i<=nlstate;i++)
! 5145: for(j=1; j<=nlstate+ndeath;j++)
! 5146: fprintf(ficrespij," %.5f", p3mat[i][j][h]);
! 5147: fprintf(ficrespij,"\n");
! 5148: }
! 5149: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
1.53 brouard 5150: fprintf(ficrespij,"\n");
5151: }
1.59 brouard 5152: }
1.53 brouard 5153: }
5154:
1.98 ! brouard 5155: varprob(optionfilefiname, matcov, p, delti, nlstate, bage, fage,k,Tvar,nbcode, ncodemax);
1.53 brouard 5156:
1.98 ! brouard 5157: fclose(ficrespij);
1.53 brouard 5158:
1.98 ! brouard 5159: probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
! 5160: for(i=1;i<=AGESUP;i++)
! 5161: for(j=1;j<=NCOVMAX;j++)
! 5162: for(k=1;k<=NCOVMAX;k++)
! 5163: probs[i][j][k]=0.;
! 5164:
! 5165: /*---------- Forecasting ------------------*/
! 5166: /*if((stepm == 1) && (strcmp(model,".")==0)){*/
! 5167: if(prevfcast==1){
! 5168: /* if(stepm ==1){*/
1.70 brouard 5169: prevforecast(fileres, anproj1, mproj1, jproj1, agemin, agemax, dateprev1, dateprev2, mobilavproj, bage, fage, firstpass, lastpass, anproj2, p, cptcoveff);
1.74 brouard 5170: /* (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);*/
1.98 ! brouard 5171: /* } */
! 5172: /* else{ */
! 5173: /* erreur=108; */
! 5174: /* 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); */
! 5175: /* 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); */
! 5176: /* } */
! 5177: }
1.53 brouard 5178:
5179:
1.98 ! brouard 5180: /*---------- Health expectancies and variances ------------*/
1.53 brouard 5181:
1.98 ! brouard 5182: strcpy(filerest,"t");
! 5183: strcat(filerest,fileres);
! 5184: if((ficrest=fopen(filerest,"w"))==NULL) {
! 5185: printf("Problem with total LE resultfile: %s\n", filerest);goto end;
! 5186: fprintf(ficlog,"Problem with total LE resultfile: %s\n", filerest);goto end;
! 5187: }
! 5188: printf("Computing Total LEs with variances: file '%s' \n", filerest);
! 5189: fprintf(ficlog,"Computing Total LEs with variances: file '%s' \n", filerest);
1.53 brouard 5190:
5191:
1.98 ! brouard 5192: strcpy(filerese,"e");
! 5193: strcat(filerese,fileres);
! 5194: if((ficreseij=fopen(filerese,"w"))==NULL) {
! 5195: printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
! 5196: fprintf(ficlog,"Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
! 5197: }
! 5198: printf("Computing Health Expectancies: result on file '%s' \n", filerese);
! 5199: fprintf(ficlog,"Computing Health Expectancies: result on file '%s' \n", filerese);
1.68 lievre 5200:
1.98 ! brouard 5201: strcpy(fileresv,"v");
! 5202: strcat(fileresv,fileres);
! 5203: if((ficresvij=fopen(fileresv,"w"))==NULL) {
! 5204: printf("Problem with variance resultfile: %s\n", fileresv);exit(0);
! 5205: fprintf(ficlog,"Problem with variance resultfile: %s\n", fileresv);exit(0);
! 5206: }
! 5207: printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
! 5208: fprintf(ficlog,"Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
1.58 lievre 5209:
1.98 ! brouard 5210: /* Computes prevalence between agemin (i.e minimal age computed) and no more ageminpar */
! 5211: prevalence(probs, agemin, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
! 5212: /* 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",\
! 5213: ageminpar, agemax, s[lastpass][imx], agev[lastpass][imx], nlstate, imx, mint[lastpass][imx],anint[lastpass][imx], dateprev1, dateprev2, firstpass, lastpass);
! 5214: */
1.58 lievre 5215:
1.98 ! brouard 5216: if (mobilav!=0) {
! 5217: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
! 5218: if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
! 5219: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
! 5220: printf(" Error in movingaverage mobilav=%d\n",mobilav);
! 5221: }
1.54 brouard 5222: }
1.53 brouard 5223:
1.98 ! brouard 5224: for(cptcov=1,k=0;cptcov<=i1;cptcov++){
! 5225: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
! 5226: k=k+1;
! 5227: fprintf(ficrest,"\n#****** ");
! 5228: for(j=1;j<=cptcoveff;j++)
! 5229: fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
! 5230: fprintf(ficrest,"******\n");
! 5231:
! 5232: fprintf(ficreseij,"\n#****** ");
! 5233: for(j=1;j<=cptcoveff;j++)
! 5234: fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
! 5235: fprintf(ficreseij,"******\n");
! 5236:
! 5237: fprintf(ficresvij,"\n#****** ");
! 5238: for(j=1;j<=cptcoveff;j++)
! 5239: fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
! 5240: fprintf(ficresvij,"******\n");
! 5241:
! 5242: eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
! 5243: oldm=oldms;savm=savms;
! 5244: evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov);
1.53 brouard 5245:
1.98 ! brouard 5246: vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
! 5247: oldm=oldms;savm=savms;
! 5248: varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,0, mobilav);
! 5249: if(popbased==1){
! 5250: varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,popbased,mobilav);
! 5251: }
1.53 brouard 5252:
5253:
1.98 ! brouard 5254: fprintf(ficrest,"#Total LEs with variances: e.. (std) ");
! 5255: for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);
! 5256: fprintf(ficrest,"\n");
! 5257:
! 5258: epj=vector(1,nlstate+1);
! 5259: for(age=bage; age <=fage ;age++){
! 5260: prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
! 5261: if (popbased==1) {
! 5262: if(mobilav ==0){
! 5263: for(i=1; i<=nlstate;i++)
! 5264: prlim[i][i]=probs[(int)age][i][k];
! 5265: }else{ /* mobilav */
! 5266: for(i=1; i<=nlstate;i++)
! 5267: prlim[i][i]=mobaverage[(int)age][i][k];
! 5268: }
1.53 brouard 5269: }
5270:
1.98 ! brouard 5271: fprintf(ficrest," %4.0f",age);
! 5272: for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){
! 5273: for(i=1, epj[j]=0.;i <=nlstate;i++) {
! 5274: epj[j] += prlim[i][i]*eij[i][j][(int)age];
! 5275: /* printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/
! 5276: }
! 5277: epj[nlstate+1] +=epj[j];
1.53 brouard 5278: }
5279:
1.98 ! brouard 5280: for(i=1, vepp=0.;i <=nlstate;i++)
! 5281: for(j=1;j <=nlstate;j++)
! 5282: vepp += vareij[i][j][(int)age];
! 5283: fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));
! 5284: for(j=1;j <=nlstate;j++){
! 5285: fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));
! 5286: }
! 5287: fprintf(ficrest,"\n");
1.53 brouard 5288: }
1.98 ! brouard 5289: free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
! 5290: free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);
! 5291: free_vector(epj,1,nlstate+1);
! 5292: }
! 5293: }
! 5294: free_vector(weight,1,n);
! 5295: free_imatrix(Tvard,1,15,1,2);
! 5296: free_imatrix(s,1,maxwav+1,1,n);
! 5297: free_matrix(anint,1,maxwav,1,n);
! 5298: free_matrix(mint,1,maxwav,1,n);
! 5299: free_ivector(cod,1,n);
! 5300: free_ivector(tab,1,NCOVMAX);
! 5301: fclose(ficreseij);
! 5302: fclose(ficresvij);
! 5303: fclose(ficrest);
! 5304: fclose(ficpar);
! 5305:
! 5306: /*------- Variance of stable prevalence------*/
! 5307:
! 5308: strcpy(fileresvpl,"vpl");
! 5309: strcat(fileresvpl,fileres);
! 5310: if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {
! 5311: printf("Problem with variance of stable prevalence resultfile: %s\n", fileresvpl);
! 5312: exit(0);
! 5313: }
! 5314: printf("Computing Variance-covariance of stable prevalence: file '%s' \n", fileresvpl);
! 5315:
! 5316: for(cptcov=1,k=0;cptcov<=i1;cptcov++){
! 5317: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
! 5318: k=k+1;
! 5319: fprintf(ficresvpl,"\n#****** ");
! 5320: for(j=1;j<=cptcoveff;j++)
! 5321: fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
! 5322: fprintf(ficresvpl,"******\n");
! 5323:
! 5324: varpl=matrix(1,nlstate,(int) bage, (int) fage);
! 5325: oldm=oldms;savm=savms;
! 5326: varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);
! 5327: free_matrix(varpl,1,nlstate,(int) bage, (int)fage);
1.53 brouard 5328: }
1.98 ! brouard 5329: }
1.53 brouard 5330:
1.98 ! brouard 5331: fclose(ficresvpl);
1.53 brouard 5332:
1.98 ! brouard 5333: /*---------- End : free ----------------*/
! 5334: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
! 5335: free_ma3x(probs,1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
! 5336:
! 5337: } /* mle==-3 arrives here for freeing */
! 5338: free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);
! 5339: free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);
! 5340: free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);
! 5341: free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);
! 5342:
! 5343: free_matrix(covar,0,NCOVMAX,1,n);
! 5344: free_matrix(matcov,1,npar,1,npar);
! 5345: /*free_vector(delti,1,npar);*/
! 5346: free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
! 5347: free_matrix(agev,1,maxwav,1,imx);
! 5348: free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
! 5349:
! 5350: free_ivector(ncodemax,1,8);
! 5351: free_ivector(Tvar,1,15);
! 5352: free_ivector(Tprod,1,15);
! 5353: free_ivector(Tvaraff,1,15);
! 5354: free_ivector(Tage,1,15);
! 5355: free_ivector(Tcode,1,100);
1.74 brouard 5356:
1.53 brouard 5357:
1.88 brouard 5358: fflush(fichtm);
5359: fflush(ficgp);
1.53 brouard 5360:
5361:
1.91 brouard 5362: if((nberr >0) || (nbwarn>0)){
1.95 brouard 5363: printf("End of Imach with %d errors and/or %d warnings\n",nberr,nbwarn);
1.91 brouard 5364: fprintf(ficlog,"End of Imach with %d errors and/or warnings %d\n",nberr,nbwarn);
1.53 brouard 5365: }else{
1.91 brouard 5366: printf("End of Imach\n");
5367: fprintf(ficlog,"End of Imach\n");
1.53 brouard 5368: }
5369: printf("See log file on %s\n",filelog);
5370: /* gettimeofday(&end_time, (struct timezone*)0);*/ /* after time */
1.85 brouard 5371: (void) gettimeofday(&end_time,&tzp);
5372: tm = *localtime(&end_time.tv_sec);
5373: tmg = *gmtime(&end_time.tv_sec);
1.88 brouard 5374: strcpy(strtend,asctime(&tm));
1.94 brouard 5375: printf("Local time at start %s\nLocaltime at end %s",strstart, strtend);
5376: fprintf(ficlog,"Local time at start %s\nLocal time at end %s\n",strstart, strtend);
1.91 brouard 5377: printf("Total time used %s\n", asc_diff_time(end_time.tv_sec -start_time.tv_sec,tmpout));
1.85 brouard 5378:
1.91 brouard 5379: printf("Total time was %d Sec.\n", end_time.tv_sec -start_time.tv_sec);
5380: fprintf(ficlog,"Total time used %s\n", asc_diff_time(end_time.tv_sec -start_time.tv_sec,tmpout));
5381: fprintf(ficlog,"Total time was %d Sec.\n", end_time.tv_sec -start_time.tv_sec);
1.85 brouard 5382: /* printf("Total time was %d uSec.\n", total_usecs);*/
1.87 brouard 5383: /* if(fileappend(fichtm,optionfilehtm)){ */
1.88 brouard 5384: fprintf(fichtm,"<br>Local time at start %s<br>Local time at end %s<br>",strstart, strtend);
1.87 brouard 5385: fclose(fichtm);
1.91 brouard 5386: fclose(fichtmcov);
1.88 brouard 5387: fclose(ficgp);
1.91 brouard 5388: fclose(ficlog);
1.53 brouard 5389: /*------ End -----------*/
5390:
1.88 brouard 5391: chdir(path);
1.59 brouard 5392: strcpy(plotcmd,GNUPLOTPROGRAM);
5393: strcat(plotcmd," ");
5394: strcat(plotcmd,optionfilegnuplot);
1.75 brouard 5395: printf("Starting graphs with: %s",plotcmd);fflush(stdout);
1.91 brouard 5396: if((outcmd=system(plotcmd)) != 0){
5397: printf(" Problem with gnuplot\n");
5398: }
1.75 brouard 5399: printf(" Wait...");
1.53 brouard 5400: while (z[0] != 'q') {
5401: /* chdir(path); */
1.91 brouard 5402: printf("\nType e to edit output files, g to graph again and q for exiting: ");
1.53 brouard 5403: scanf("%s",z);
1.91 brouard 5404: /* if (z[0] == 'c') system("./imach"); */
5405: if (z[0] == 'e') system(optionfilehtm);
1.53 brouard 5406: else if (z[0] == 'g') system(plotcmd);
5407: else if (z[0] == 'q') exit(0);
5408: }
1.91 brouard 5409: end:
5410: while (z[0] != 'q') {
5411: printf("\nType q for exiting: ");
5412: scanf("%s",z);
5413: }
1.53 brouard 5414: }
1.88 brouard 5415:
1.53 brouard 5416:
5417:
FreeBSD-CVSweb <freebsd-cvsweb@FreeBSD.org>
![[BACK]](/icons/small/back.gif){kind=icon}
Return to imach.c CVS log ![[TXT]](/icons/small/text.gif){kind=icon}
![[DIR]](/icons/small/dir.gif){kind=icon}
Up to [Local Repository] / imach / src