1: /* $Id: imach.c,v 1.92 2003/06/25 16:30:45 brouard Exp $
2: $State: Exp $
3: $Log: imach.c,v $
4: Revision 1.92 2003/06/25 16:30:45 brouard
5: (Module): On windows (cygwin) function asctime_r doesn't
6: exist so I changed back to asctime which exists.
7:
8: Revision 1.91 2003/06/25 15:30:29 brouard
9: * imach.c (Repository): Duplicated warning errors corrected.
10: (Repository): Elapsed time after each iteration is now output. It
11: helps to forecast when convergence will be reached. Elapsed time
12: is stamped in powell. We created a new html file for the graphs
13: concerning matrix of covariance. It has extension -cov.htm.
14:
15: Revision 1.90 2003/06/24 12:34:15 brouard
16: (Module): Some bugs corrected for windows. Also, when
17: mle=-1 a template is output in file "or"mypar.txt with the design
18: of the covariance matrix to be input.
19:
20: Revision 1.89 2003/06/24 12:30:52 brouard
21: (Module): Some bugs corrected for windows. Also, when
22: mle=-1 a template is output in file "or"mypar.txt with the design
23: of the covariance matrix to be input.
24:
25: Revision 1.88 2003/06/23 17:54:56 brouard
26: * 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.
27:
28: Revision 1.87 2003/06/18 12:26:01 brouard
29: Version 0.96
30:
31: Revision 1.86 2003/06/17 20:04:08 brouard
32: (Module): Change position of html and gnuplot routines and added
33: routine fileappend.
34:
35: Revision 1.85 2003/06/17 13:12:43 brouard
36: * imach.c (Repository): Check when date of death was earlier that
37: current date of interview. It may happen when the death was just
38: prior to the death. In this case, dh was negative and likelihood
39: was wrong (infinity). We still send an "Error" but patch by
40: assuming that the date of death was just one stepm after the
41: interview.
42: (Repository): Because some people have very long ID (first column)
43: we changed int to long in num[] and we added a new lvector for
44: memory allocation. But we also truncated to 8 characters (left
45: truncation)
46: (Repository): No more line truncation errors.
47:
48: Revision 1.84 2003/06/13 21:44:43 brouard
49: * imach.c (Repository): Replace "freqsummary" at a correct
50: place. It differs from routine "prevalence" which may be called
51: many times. Probs is memory consuming and must be used with
52: parcimony.
53: Version 0.95a3 (should output exactly the same maximization than 0.8a2)
54:
55: Revision 1.83 2003/06/10 13:39:11 lievre
56: *** empty log message ***
57:
58: Revision 1.82 2003/06/05 15:57:20 brouard
59: Add log in imach.c and fullversion number is now printed.
60:
61: */
62: /*
63: Interpolated Markov Chain
64:
65: Short summary of the programme:
66:
67: This program computes Healthy Life Expectancies from
68: cross-longitudinal data. Cross-longitudinal data consist in: -1- a
69: first survey ("cross") where individuals from different ages are
70: interviewed on their health status or degree of disability (in the
71: case of a health survey which is our main interest) -2- at least a
72: second wave of interviews ("longitudinal") which measure each change
73: (if any) in individual health status. Health expectancies are
74: computed from the time spent in each health state according to a
75: model. More health states you consider, more time is necessary to reach the
76: Maximum Likelihood of the parameters involved in the model. The
77: simplest model is the multinomial logistic model where pij is the
78: probability to be observed in state j at the second wave
79: conditional to be observed in state i at the first wave. Therefore
80: the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where
81: 'age' is age and 'sex' is a covariate. If you want to have a more
82: complex model than "constant and age", you should modify the program
83: where the markup *Covariates have to be included here again* invites
84: you to do it. More covariates you add, slower the
85: convergence.
86:
87: The advantage of this computer programme, compared to a simple
88: multinomial logistic model, is clear when the delay between waves is not
89: identical for each individual. Also, if a individual missed an
90: intermediate interview, the information is lost, but taken into
91: account using an interpolation or extrapolation.
92:
93: hPijx is the probability to be observed in state i at age x+h
94: conditional to the observed state i at age x. The delay 'h' can be
95: split into an exact number (nh*stepm) of unobserved intermediate
96: states. This elementary transition (by month, quarter,
97: semester or year) is modelled as a multinomial logistic. The hPx
98: matrix is simply the matrix product of nh*stepm elementary matrices
99: and the contribution of each individual to the likelihood is simply
100: hPijx.
101:
102: Also this programme outputs the covariance matrix of the parameters but also
103: of the life expectancies. It also computes the stable prevalence.
104:
105: Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).
106: Institut national d'études démographiques, Paris.
107: This software have been partly granted by Euro-REVES, a concerted action
108: from the European Union.
109: It is copyrighted identically to a GNU software product, ie programme and
110: software can be distributed freely for non commercial use. Latest version
111: can be accessed at http://euroreves.ined.fr/imach .
112:
113: Help to debug: LD_PRELOAD=/usr/local/lib/libnjamd.so ./imach foo.imach
114: or better on gdb : set env LD_PRELOAD=/usr/local/lib/libnjamd.so
115:
116: **********************************************************************/
117: /*
118: main
119: read parameterfile
120: read datafile
121: concatwav
122: freqsummary
123: if (mle >= 1)
124: mlikeli
125: print results files
126: if mle==1
127: computes hessian
128: read end of parameter file: agemin, agemax, bage, fage, estepm
129: begin-prev-date,...
130: open gnuplot file
131: open html file
132: stable prevalence
133: for age prevalim()
134: h Pij x
135: variance of p varprob
136: forecasting if prevfcast==1 prevforecast call prevalence()
137: health expectancies
138: Variance-covariance of DFLE
139: prevalence()
140: movingaverage()
141: varevsij()
142: if popbased==1 varevsij(,popbased)
143: total life expectancies
144: Variance of stable prevalence
145: end
146: */
147:
148:
149:
150:
151: #include <math.h>
152: #include <stdio.h>
153: #include <stdlib.h>
154: #include <unistd.h>
155:
156: #include <sys/time.h>
157: #include <time.h>
158: #include "timeval.h"
159:
160: #define MAXLINE 256
161: #define GNUPLOTPROGRAM "gnuplot"
162: /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
163: #define FILENAMELENGTH 132
164: /*#define DEBUG*/
165: /*#define windows*/
166: #define GLOCK_ERROR_NOPATH -1 /* empty path */
167: #define GLOCK_ERROR_GETCWD -2 /* cannot get cwd */
168:
169: #define MAXPARM 30 /* Maximum number of parameters for the optimization */
170: #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */
171:
172: #define NINTERVMAX 8
173: #define NLSTATEMAX 8 /* Maximum number of live states (for func) */
174: #define NDEATHMAX 8 /* Maximum number of dead states (for func) */
175: #define NCOVMAX 8 /* Maximum number of covariates */
176: #define MAXN 20000
177: #define YEARM 12. /* Number of months per year */
178: #define AGESUP 130
179: #define AGEBASE 40
180: #ifdef unix
181: #define DIRSEPARATOR '/'
182: #define ODIRSEPARATOR '\\'
183: #else
184: #define DIRSEPARATOR '\\'
185: #define ODIRSEPARATOR '/'
186: #endif
187:
188: /* $Id: imach.c,v 1.92 2003/06/25 16:30:45 brouard Exp $ */
189: /* $State: Exp $ */
190:
191: char version[]="Imach version 0.96a, June 2003, INED-EUROREVES ";
192: char fullversion[]="$Revision: 1.92 $ $Date: 2003/06/25 16:30:45 $";
193: int erreur, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings */
194: int nvar;
195: int cptcovn=0, cptcovage=0, cptcoveff=0,cptcov;
196: int npar=NPARMAX;
197: int nlstate=2; /* Number of live states */
198: int ndeath=1; /* Number of dead states */
199: int ncovmodel, ncovcol; /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
200: int popbased=0;
201:
202: int *wav; /* Number of waves for this individuual 0 is possible */
203: int maxwav; /* Maxim number of waves */
204: int jmin, jmax; /* min, max spacing between 2 waves */
205: int gipmx, gsw; /* Global variables on the number of contributions
206: to the likelihood and the sum of weights (done by funcone)*/
207: int mle, weightopt;
208: int **mw; /* mw[mi][i] is number of the mi wave for this individual */
209: int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
210: int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between
211: * wave mi and wave mi+1 is not an exact multiple of stepm. */
212: double jmean; /* Mean space between 2 waves */
213: double **oldm, **newm, **savm; /* Working pointers to matrices */
214: double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
215: FILE *fic,*ficpar, *ficparo,*ficres, *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
216: FILE *ficlog, *ficrespow;
217: int globpr; /* Global variable for printing or not */
218: double fretone; /* Only one call to likelihood */
219: long ipmx; /* Number of contributions */
220: double sw; /* Sum of weights */
221: char fileresilk[FILENAMELENGTH]; /* File of individual contributions to the likelihood */
222: FILE *ficresilk;
223: FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
224: FILE *ficresprobmorprev;
225: FILE *fichtm, *fichtmcov; /* Html File */
226: FILE *ficreseij;
227: char filerese[FILENAMELENGTH];
228: FILE *ficresvij;
229: char fileresv[FILENAMELENGTH];
230: FILE *ficresvpl;
231: char fileresvpl[FILENAMELENGTH];
232: char title[MAXLINE];
233: char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH], filerespl[FILENAMELENGTH];
234: char optionfilext[10], optionfilefiname[FILENAMELENGTH], plotcmd[FILENAMELENGTH];
235: char tmpout[FILENAMELENGTH];
236: char command[FILENAMELENGTH];
237: int outcmd=0;
238:
239: char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
240: char lfileres[FILENAMELENGTH];
241: char filelog[FILENAMELENGTH]; /* Log file */
242: char filerest[FILENAMELENGTH];
243: char fileregp[FILENAMELENGTH];
244: char popfile[FILENAMELENGTH];
245:
246: char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilehtmcov[FILENAMELENGTH] ;
247:
248: struct timeval start_time, end_time, curr_time, last_time, forecast_time;
249: struct timezone tzp;
250: extern int gettimeofday();
251: struct tm tmg, tm, tmf, *gmtime(), *localtime();
252: long time_value;
253: extern long time();
254: char strcurr[80], strfor[80];
255:
256: #define NR_END 1
257: #define FREE_ARG char*
258: #define FTOL 1.0e-10
259:
260: #define NRANSI
261: #define ITMAX 200
262:
263: #define TOL 2.0e-4
264:
265: #define CGOLD 0.3819660
266: #define ZEPS 1.0e-10
267: #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);
268:
269: #define GOLD 1.618034
270: #define GLIMIT 100.0
271: #define TINY 1.0e-20
272:
273: static double maxarg1,maxarg2;
274: #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
275: #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
276:
277: #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
278: #define rint(a) floor(a+0.5)
279:
280: static double sqrarg;
281: #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
282: #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}
283:
284: int imx;
285: int stepm;
286: /* Stepm, step in month: minimum step interpolation*/
287:
288: int estepm;
289: /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
290:
291: int m,nb;
292: long *num;
293: int firstpass=0, lastpass=4,*cod, *ncodemax, *Tage;
294: double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
295: double **pmmij, ***probs;
296: double dateintmean=0;
297:
298: double *weight;
299: int **s; /* Status */
300: double *agedc, **covar, idx;
301: int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;
302:
303: double ftol=FTOL; /* Tolerance for computing Max Likelihood */
304: double ftolhess; /* Tolerance for computing hessian */
305:
306: /**************** split *************************/
307: static int split( char *path, char *dirc, char *name, char *ext, char *finame )
308: {
309: char *ss; /* pointer */
310: int l1, l2; /* length counters */
311:
312: l1 = strlen(path ); /* length of path */
313: if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
314: ss= strrchr( path, DIRSEPARATOR ); /* find last / */
315: if ( ss == NULL ) { /* no directory, so use current */
316: /*if(strrchr(path, ODIRSEPARATOR )==NULL)
317: printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
318: /* get current working directory */
319: /* extern char* getcwd ( char *buf , int len);*/
320: if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {
321: return( GLOCK_ERROR_GETCWD );
322: }
323: strcpy( name, path ); /* we've got it */
324: } else { /* strip direcotry from path */
325: ss++; /* after this, the filename */
326: l2 = strlen( ss ); /* length of filename */
327: if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
328: strcpy( name, ss ); /* save file name */
329: strncpy( dirc, path, l1 - l2 ); /* now the directory */
330: dirc[l1-l2] = 0; /* add zero */
331: }
332: l1 = strlen( dirc ); /* length of directory */
333: /*#ifdef windows
334: if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; }
335: #else
336: if ( dirc[l1-1] != '/' ) { dirc[l1] = '/'; dirc[l1+1] = 0; }
337: #endif
338: */
339: ss = strrchr( name, '.' ); /* find last / */
340: ss++;
341: strcpy(ext,ss); /* save extension */
342: l1= strlen( name);
343: l2= strlen(ss)+1;
344: strncpy( finame, name, l1-l2);
345: finame[l1-l2]= 0;
346: return( 0 ); /* we're done */
347: }
348:
349:
350: /******************************************/
351:
352: void replace_back_to_slash(char *s, char*t)
353: {
354: int i;
355: int lg=0;
356: i=0;
357: lg=strlen(t);
358: for(i=0; i<= lg; i++) {
359: (s[i] = t[i]);
360: if (t[i]== '\\') s[i]='/';
361: }
362: }
363:
364: int nbocc(char *s, char occ)
365: {
366: int i,j=0;
367: int lg=20;
368: i=0;
369: lg=strlen(s);
370: for(i=0; i<= lg; i++) {
371: if (s[i] == occ ) j++;
372: }
373: return j;
374: }
375:
376: void cutv(char *u,char *v, char*t, char occ)
377: {
378: /* cuts string t into u and v where u is ended by char occ excluding it
379: and v is after occ excluding it too : ex cutv(u,v,"abcdef2ghi2j",2)
380: gives u="abcedf" and v="ghi2j" */
381: int i,lg,j,p=0;
382: i=0;
383: for(j=0; j<=strlen(t)-1; j++) {
384: if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;
385: }
386:
387: lg=strlen(t);
388: for(j=0; j<p; j++) {
389: (u[j] = t[j]);
390: }
391: u[p]='\0';
392:
393: for(j=0; j<= lg; j++) {
394: if (j>=(p+1))(v[j-p-1] = t[j]);
395: }
396: }
397:
398: /********************** nrerror ********************/
399:
400: void nrerror(char error_text[])
401: {
402: fprintf(stderr,"ERREUR ...\n");
403: fprintf(stderr,"%s\n",error_text);
404: exit(EXIT_FAILURE);
405: }
406: /*********************** vector *******************/
407: double *vector(int nl, int nh)
408: {
409: double *v;
410: v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
411: if (!v) nrerror("allocation failure in vector");
412: return v-nl+NR_END;
413: }
414:
415: /************************ free vector ******************/
416: void free_vector(double*v, int nl, int nh)
417: {
418: free((FREE_ARG)(v+nl-NR_END));
419: }
420:
421: /************************ivector *******************************/
422: int *ivector(long nl,long nh)
423: {
424: int *v;
425: v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
426: if (!v) nrerror("allocation failure in ivector");
427: return v-nl+NR_END;
428: }
429:
430: /******************free ivector **************************/
431: void free_ivector(int *v, long nl, long nh)
432: {
433: free((FREE_ARG)(v+nl-NR_END));
434: }
435:
436: /************************lvector *******************************/
437: long *lvector(long nl,long nh)
438: {
439: long *v;
440: v=(long *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(long)));
441: if (!v) nrerror("allocation failure in ivector");
442: return v-nl+NR_END;
443: }
444:
445: /******************free lvector **************************/
446: void free_lvector(long *v, long nl, long nh)
447: {
448: free((FREE_ARG)(v+nl-NR_END));
449: }
450:
451: /******************* imatrix *******************************/
452: int **imatrix(long nrl, long nrh, long ncl, long nch)
453: /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */
454: {
455: long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;
456: int **m;
457:
458: /* allocate pointers to rows */
459: m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));
460: if (!m) nrerror("allocation failure 1 in matrix()");
461: m += NR_END;
462: m -= nrl;
463:
464:
465: /* allocate rows and set pointers to them */
466: m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));
467: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
468: m[nrl] += NR_END;
469: m[nrl] -= ncl;
470:
471: for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;
472:
473: /* return pointer to array of pointers to rows */
474: return m;
475: }
476:
477: /****************** free_imatrix *************************/
478: void free_imatrix(m,nrl,nrh,ncl,nch)
479: int **m;
480: long nch,ncl,nrh,nrl;
481: /* free an int matrix allocated by imatrix() */
482: {
483: free((FREE_ARG) (m[nrl]+ncl-NR_END));
484: free((FREE_ARG) (m+nrl-NR_END));
485: }
486:
487: /******************* matrix *******************************/
488: double **matrix(long nrl, long nrh, long ncl, long nch)
489: {
490: long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
491: double **m;
492:
493: m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
494: if (!m) nrerror("allocation failure 1 in matrix()");
495: m += NR_END;
496: m -= nrl;
497:
498: m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
499: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
500: m[nrl] += NR_END;
501: m[nrl] -= ncl;
502:
503: for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
504: return m;
505: /* print *(*(m+1)+70) or print m[1][70]; print m+1 or print &(m[1])
506: */
507: }
508:
509: /*************************free matrix ************************/
510: void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
511: {
512: free((FREE_ARG)(m[nrl]+ncl-NR_END));
513: free((FREE_ARG)(m+nrl-NR_END));
514: }
515:
516: /******************* ma3x *******************************/
517: double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
518: {
519: long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
520: double ***m;
521:
522: m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
523: if (!m) nrerror("allocation failure 1 in matrix()");
524: m += NR_END;
525: m -= nrl;
526:
527: m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
528: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
529: m[nrl] += NR_END;
530: m[nrl] -= ncl;
531:
532: for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
533:
534: m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
535: if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
536: m[nrl][ncl] += NR_END;
537: m[nrl][ncl] -= nll;
538: for (j=ncl+1; j<=nch; j++)
539: m[nrl][j]=m[nrl][j-1]+nlay;
540:
541: for (i=nrl+1; i<=nrh; i++) {
542: m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
543: for (j=ncl+1; j<=nch; j++)
544: m[i][j]=m[i][j-1]+nlay;
545: }
546: return m;
547: /* gdb: p *(m+1) <=> p m[1] and p (m+1) <=> p (m+1) <=> p &(m[1])
548: &(m[i][j][k]) <=> *((*(m+i) + j)+k)
549: */
550: }
551:
552: /*************************free ma3x ************************/
553: void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
554: {
555: free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
556: free((FREE_ARG)(m[nrl]+ncl-NR_END));
557: free((FREE_ARG)(m+nrl-NR_END));
558: }
559:
560: /***************** f1dim *************************/
561: extern int ncom;
562: extern double *pcom,*xicom;
563: extern double (*nrfunc)(double []);
564:
565: double f1dim(double x)
566: {
567: int j;
568: double f;
569: double *xt;
570:
571: xt=vector(1,ncom);
572: for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];
573: f=(*nrfunc)(xt);
574: free_vector(xt,1,ncom);
575: return f;
576: }
577:
578: /*****************brent *************************/
579: double brent(double ax, double bx, double cx, double (*f)(double), double tol, double *xmin)
580: {
581: int iter;
582: double a,b,d,etemp;
583: double fu,fv,fw,fx;
584: double ftemp;
585: double p,q,r,tol1,tol2,u,v,w,x,xm;
586: double e=0.0;
587:
588: a=(ax < cx ? ax : cx);
589: b=(ax > cx ? ax : cx);
590: x=w=v=bx;
591: fw=fv=fx=(*f)(x);
592: for (iter=1;iter<=ITMAX;iter++) {
593: xm=0.5*(a+b);
594: tol2=2.0*(tol1=tol*fabs(x)+ZEPS);
595: /* if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
596: printf(".");fflush(stdout);
597: fprintf(ficlog,".");fflush(ficlog);
598: #ifdef DEBUG
599: 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);
600: 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);
601: /* if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
602: #endif
603: if (fabs(x-xm) <= (tol2-0.5*(b-a))){
604: *xmin=x;
605: return fx;
606: }
607: ftemp=fu;
608: if (fabs(e) > tol1) {
609: r=(x-w)*(fx-fv);
610: q=(x-v)*(fx-fw);
611: p=(x-v)*q-(x-w)*r;
612: q=2.0*(q-r);
613: if (q > 0.0) p = -p;
614: q=fabs(q);
615: etemp=e;
616: e=d;
617: if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))
618: d=CGOLD*(e=(x >= xm ? a-x : b-x));
619: else {
620: d=p/q;
621: u=x+d;
622: if (u-a < tol2 || b-u < tol2)
623: d=SIGN(tol1,xm-x);
624: }
625: } else {
626: d=CGOLD*(e=(x >= xm ? a-x : b-x));
627: }
628: u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));
629: fu=(*f)(u);
630: if (fu <= fx) {
631: if (u >= x) a=x; else b=x;
632: SHFT(v,w,x,u)
633: SHFT(fv,fw,fx,fu)
634: } else {
635: if (u < x) a=u; else b=u;
636: if (fu <= fw || w == x) {
637: v=w;
638: w=u;
639: fv=fw;
640: fw=fu;
641: } else if (fu <= fv || v == x || v == w) {
642: v=u;
643: fv=fu;
644: }
645: }
646: }
647: nrerror("Too many iterations in brent");
648: *xmin=x;
649: return fx;
650: }
651:
652: /****************** mnbrak ***********************/
653:
654: void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,
655: double (*func)(double))
656: {
657: double ulim,u,r,q, dum;
658: double fu;
659:
660: *fa=(*func)(*ax);
661: *fb=(*func)(*bx);
662: if (*fb > *fa) {
663: SHFT(dum,*ax,*bx,dum)
664: SHFT(dum,*fb,*fa,dum)
665: }
666: *cx=(*bx)+GOLD*(*bx-*ax);
667: *fc=(*func)(*cx);
668: while (*fb > *fc) {
669: r=(*bx-*ax)*(*fb-*fc);
670: q=(*bx-*cx)*(*fb-*fa);
671: u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/
672: (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r));
673: ulim=(*bx)+GLIMIT*(*cx-*bx);
674: if ((*bx-u)*(u-*cx) > 0.0) {
675: fu=(*func)(u);
676: } else if ((*cx-u)*(u-ulim) > 0.0) {
677: fu=(*func)(u);
678: if (fu < *fc) {
679: SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))
680: SHFT(*fb,*fc,fu,(*func)(u))
681: }
682: } else if ((u-ulim)*(ulim-*cx) >= 0.0) {
683: u=ulim;
684: fu=(*func)(u);
685: } else {
686: u=(*cx)+GOLD*(*cx-*bx);
687: fu=(*func)(u);
688: }
689: SHFT(*ax,*bx,*cx,u)
690: SHFT(*fa,*fb,*fc,fu)
691: }
692: }
693:
694: /*************** linmin ************************/
695:
696: int ncom;
697: double *pcom,*xicom;
698: double (*nrfunc)(double []);
699:
700: void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))
701: {
702: double brent(double ax, double bx, double cx,
703: double (*f)(double), double tol, double *xmin);
704: double f1dim(double x);
705: void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,
706: double *fc, double (*func)(double));
707: int j;
708: double xx,xmin,bx,ax;
709: double fx,fb,fa;
710:
711: ncom=n;
712: pcom=vector(1,n);
713: xicom=vector(1,n);
714: nrfunc=func;
715: for (j=1;j<=n;j++) {
716: pcom[j]=p[j];
717: xicom[j]=xi[j];
718: }
719: ax=0.0;
720: xx=1.0;
721: mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim);
722: *fret=brent(ax,xx,bx,f1dim,TOL,&xmin);
723: #ifdef DEBUG
724: printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
725: fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
726: #endif
727: for (j=1;j<=n;j++) {
728: xi[j] *= xmin;
729: p[j] += xi[j];
730: }
731: free_vector(xicom,1,n);
732: free_vector(pcom,1,n);
733: }
734:
735: char *asc_diff_time(long time_sec, char ascdiff[])
736: {
737: long sec_left, days, hours, minutes;
738: days = (time_sec) / (60*60*24);
739: sec_left = (time_sec) % (60*60*24);
740: hours = (sec_left) / (60*60) ;
741: sec_left = (sec_left) %(60*60);
742: minutes = (sec_left) /60;
743: sec_left = (sec_left) % (60);
744: sprintf(ascdiff,"%d day(s) %d hour(s) %d minute(s) %d second(s)",days, hours, minutes, sec_left);
745: return ascdiff;
746: }
747:
748: /*************** powell ************************/
749: void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,
750: double (*func)(double []))
751: {
752: void linmin(double p[], double xi[], int n, double *fret,
753: double (*func)(double []));
754: int i,ibig,j;
755: double del,t,*pt,*ptt,*xit;
756: double fp,fptt;
757: double *xits;
758: int niterf, itmp;
759:
760: pt=vector(1,n);
761: ptt=vector(1,n);
762: xit=vector(1,n);
763: xits=vector(1,n);
764: *fret=(*func)(p);
765: for (j=1;j<=n;j++) pt[j]=p[j];
766: for (*iter=1;;++(*iter)) {
767: fp=(*fret);
768: ibig=0;
769: del=0.0;
770: last_time=curr_time;
771: (void) gettimeofday(&curr_time,&tzp);
772: 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);
773: 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);
774: fprintf(ficrespow,"%d %.12f %ld",*iter,*fret,curr_time.tv_sec-start_time.tv_sec);
775: for (i=1;i<=n;i++) {
776: printf(" %d %.12f",i, p[i]);
777: fprintf(ficlog," %d %.12lf",i, p[i]);
778: fprintf(ficrespow," %.12lf", p[i]);
779: }
780: printf("\n");
781: fprintf(ficlog,"\n");
782: fprintf(ficrespow,"\n");fflush(ficrespow);
783: if(*iter <=3){
784: tm = *localtime(&curr_time.tv_sec);
785: strcpy(strcurr,asctime(&tmf));
786: /* asctime_r(&tm,strcurr); */
787: forecast_time=curr_time;
788: itmp = strlen(strcurr);
789: if(strcurr[itmp-1]=='\n')
790: strcurr[itmp-1]='\0';
791: printf("\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,curr_time.tv_sec-last_time.tv_sec);
792: fprintf(ficlog,"\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,curr_time.tv_sec-last_time.tv_sec);
793: for(niterf=10;niterf<=30;niterf+=10){
794: forecast_time.tv_sec=curr_time.tv_sec+(niterf-*iter)*(curr_time.tv_sec-last_time.tv_sec);
795: tmf = *localtime(&forecast_time.tv_sec);
796: /* asctime_r(&tmf,strfor); */
797: strcpy(strfor,asctime(&tmf));
798: itmp = strlen(strfor);
799: if(strfor[itmp-1]=='\n')
800: strfor[itmp-1]='\0';
801: 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);
802: 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);
803: }
804: }
805: for (i=1;i<=n;i++) {
806: for (j=1;j<=n;j++) xit[j]=xi[j][i];
807: fptt=(*fret);
808: #ifdef DEBUG
809: printf("fret=%lf \n",*fret);
810: fprintf(ficlog,"fret=%lf \n",*fret);
811: #endif
812: printf("%d",i);fflush(stdout);
813: fprintf(ficlog,"%d",i);fflush(ficlog);
814: linmin(p,xit,n,fret,func);
815: if (fabs(fptt-(*fret)) > del) {
816: del=fabs(fptt-(*fret));
817: ibig=i;
818: }
819: #ifdef DEBUG
820: printf("%d %.12e",i,(*fret));
821: fprintf(ficlog,"%d %.12e",i,(*fret));
822: for (j=1;j<=n;j++) {
823: xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
824: printf(" x(%d)=%.12e",j,xit[j]);
825: fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
826: }
827: for(j=1;j<=n;j++) {
828: printf(" p=%.12e",p[j]);
829: fprintf(ficlog," p=%.12e",p[j]);
830: }
831: printf("\n");
832: fprintf(ficlog,"\n");
833: #endif
834: }
835: if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {
836: #ifdef DEBUG
837: int k[2],l;
838: k[0]=1;
839: k[1]=-1;
840: printf("Max: %.12e",(*func)(p));
841: fprintf(ficlog,"Max: %.12e",(*func)(p));
842: for (j=1;j<=n;j++) {
843: printf(" %.12e",p[j]);
844: fprintf(ficlog," %.12e",p[j]);
845: }
846: printf("\n");
847: fprintf(ficlog,"\n");
848: for(l=0;l<=1;l++) {
849: for (j=1;j<=n;j++) {
850: ptt[j]=p[j]+(p[j]-pt[j])*k[l];
851: printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
852: fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
853: }
854: printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
855: fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
856: }
857: #endif
858:
859:
860: free_vector(xit,1,n);
861: free_vector(xits,1,n);
862: free_vector(ptt,1,n);
863: free_vector(pt,1,n);
864: return;
865: }
866: if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");
867: for (j=1;j<=n;j++) {
868: ptt[j]=2.0*p[j]-pt[j];
869: xit[j]=p[j]-pt[j];
870: pt[j]=p[j];
871: }
872: fptt=(*func)(ptt);
873: if (fptt < fp) {
874: t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt);
875: if (t < 0.0) {
876: linmin(p,xit,n,fret,func);
877: for (j=1;j<=n;j++) {
878: xi[j][ibig]=xi[j][n];
879: xi[j][n]=xit[j];
880: }
881: #ifdef DEBUG
882: printf("Direction changed last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
883: fprintf(ficlog,"Direction changed last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
884: for(j=1;j<=n;j++){
885: printf(" %.12e",xit[j]);
886: fprintf(ficlog," %.12e",xit[j]);
887: }
888: printf("\n");
889: fprintf(ficlog,"\n");
890: #endif
891: }
892: }
893: }
894: }
895:
896: /**** Prevalence limit (stable prevalence) ****************/
897:
898: double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)
899: {
900: /* Computes the prevalence limit in each live state at age x by left multiplying the unit
901: matrix by transitions matrix until convergence is reached */
902:
903: int i, ii,j,k;
904: double min, max, maxmin, maxmax,sumnew=0.;
905: double **matprod2();
906: double **out, cov[NCOVMAX], **pmij();
907: double **newm;
908: double agefin, delaymax=50 ; /* Max number of years to converge */
909:
910: for (ii=1;ii<=nlstate+ndeath;ii++)
911: for (j=1;j<=nlstate+ndeath;j++){
912: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
913: }
914:
915: cov[1]=1.;
916:
917: /* Even if hstepm = 1, at least one multiplication by the unit matrix */
918: for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
919: newm=savm;
920: /* Covariates have to be included here again */
921: cov[2]=agefin;
922:
923: for (k=1; k<=cptcovn;k++) {
924: cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
925: /* 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]]);*/
926: }
927: for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
928: for (k=1; k<=cptcovprod;k++)
929: cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
930:
931: /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
932: /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
933: /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
934: out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);
935:
936: savm=oldm;
937: oldm=newm;
938: maxmax=0.;
939: for(j=1;j<=nlstate;j++){
940: min=1.;
941: max=0.;
942: for(i=1; i<=nlstate; i++) {
943: sumnew=0;
944: for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
945: prlim[i][j]= newm[i][j]/(1-sumnew);
946: max=FMAX(max,prlim[i][j]);
947: min=FMIN(min,prlim[i][j]);
948: }
949: maxmin=max-min;
950: maxmax=FMAX(maxmax,maxmin);
951: }
952: if(maxmax < ftolpl){
953: return prlim;
954: }
955: }
956: }
957:
958: /*************** transition probabilities ***************/
959:
960: double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
961: {
962: double s1, s2;
963: /*double t34;*/
964: int i,j,j1, nc, ii, jj;
965:
966: for(i=1; i<= nlstate; i++){
967: for(j=1; j<i;j++){
968: for (nc=1, s2=0.;nc <=ncovmodel; nc++){
969: /*s2 += param[i][j][nc]*cov[nc];*/
970: s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
971: /*printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2);*/
972: }
973: ps[i][j]=s2;
974: /*printf("s1=%.17e, s2=%.17e\n",s1,s2);*/
975: }
976: for(j=i+1; j<=nlstate+ndeath;j++){
977: for (nc=1, s2=0.;nc <=ncovmodel; nc++){
978: s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
979: /*printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2);*/
980: }
981: ps[i][j]=s2;
982: }
983: }
984: /*ps[3][2]=1;*/
985:
986: for(i=1; i<= nlstate; i++){
987: s1=0;
988: for(j=1; j<i; j++)
989: s1+=exp(ps[i][j]);
990: for(j=i+1; j<=nlstate+ndeath; j++)
991: s1+=exp(ps[i][j]);
992: ps[i][i]=1./(s1+1.);
993: for(j=1; j<i; j++)
994: ps[i][j]= exp(ps[i][j])*ps[i][i];
995: for(j=i+1; j<=nlstate+ndeath; j++)
996: ps[i][j]= exp(ps[i][j])*ps[i][i];
997: /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
998: } /* end i */
999:
1000: for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
1001: for(jj=1; jj<= nlstate+ndeath; jj++){
1002: ps[ii][jj]=0;
1003: ps[ii][ii]=1;
1004: }
1005: }
1006:
1007:
1008: /* for(ii=1; ii<= nlstate+ndeath; ii++){
1009: for(jj=1; jj<= nlstate+ndeath; jj++){
1010: printf("%lf ",ps[ii][jj]);
1011: }
1012: printf("\n ");
1013: }
1014: printf("\n ");printf("%lf ",cov[2]);*/
1015: /*
1016: for(i=1; i<= npar; i++) printf("%f ",x[i]);
1017: goto end;*/
1018: return ps;
1019: }
1020:
1021: /**************** Product of 2 matrices ******************/
1022:
1023: double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)
1024: {
1025: /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
1026: b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
1027: /* in, b, out are matrice of pointers which should have been initialized
1028: before: only the contents of out is modified. The function returns
1029: a pointer to pointers identical to out */
1030: long i, j, k;
1031: for(i=nrl; i<= nrh; i++)
1032: for(k=ncolol; k<=ncoloh; k++)
1033: for(j=ncl,out[i][k]=0.; j<=nch; j++)
1034: out[i][k] +=in[i][j]*b[j][k];
1035:
1036: return out;
1037: }
1038:
1039:
1040: /************* Higher Matrix Product ***************/
1041:
1042: double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
1043: {
1044: /* Computes the transition matrix starting at age 'age' over
1045: 'nhstepm*hstepm*stepm' months (i.e. until
1046: age (in years) age+nhstepm*hstepm*stepm/12) by multiplying
1047: nhstepm*hstepm matrices.
1048: Output is stored in matrix po[i][j][h] for h every 'hstepm' step
1049: (typically every 2 years instead of every month which is too big
1050: for the memory).
1051: Model is determined by parameters x and covariates have to be
1052: included manually here.
1053:
1054: */
1055:
1056: int i, j, d, h, k;
1057: double **out, cov[NCOVMAX];
1058: double **newm;
1059:
1060: /* Hstepm could be zero and should return the unit matrix */
1061: for (i=1;i<=nlstate+ndeath;i++)
1062: for (j=1;j<=nlstate+ndeath;j++){
1063: oldm[i][j]=(i==j ? 1.0 : 0.0);
1064: po[i][j][0]=(i==j ? 1.0 : 0.0);
1065: }
1066: /* Even if hstepm = 1, at least one multiplication by the unit matrix */
1067: for(h=1; h <=nhstepm; h++){
1068: for(d=1; d <=hstepm; d++){
1069: newm=savm;
1070: /* Covariates have to be included here again */
1071: cov[1]=1.;
1072: cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
1073: for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
1074: for (k=1; k<=cptcovage;k++)
1075: cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
1076: for (k=1; k<=cptcovprod;k++)
1077: cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
1078:
1079:
1080: /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
1081: /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
1082: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,
1083: pmij(pmmij,cov,ncovmodel,x,nlstate));
1084: savm=oldm;
1085: oldm=newm;
1086: }
1087: for(i=1; i<=nlstate+ndeath; i++)
1088: for(j=1;j<=nlstate+ndeath;j++) {
1089: po[i][j][h]=newm[i][j];
1090: /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);
1091: */
1092: }
1093: } /* end h */
1094: return po;
1095: }
1096:
1097:
1098: /*************** log-likelihood *************/
1099: double func( double *x)
1100: {
1101: int i, ii, j, k, mi, d, kk;
1102: double l, ll[NLSTATEMAX], cov[NCOVMAX];
1103: double **out;
1104: double sw; /* Sum of weights */
1105: double lli; /* Individual log likelihood */
1106: int s1, s2;
1107: double bbh, survp;
1108: long ipmx;
1109: /*extern weight */
1110: /* We are differentiating ll according to initial status */
1111: /* for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
1112: /*for(i=1;i<imx;i++)
1113: printf(" %d\n",s[4][i]);
1114: */
1115: cov[1]=1.;
1116:
1117: for(k=1; k<=nlstate; k++) ll[k]=0.;
1118:
1119: if(mle==1){
1120: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1121: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
1122: for(mi=1; mi<= wav[i]-1; mi++){
1123: for (ii=1;ii<=nlstate+ndeath;ii++)
1124: for (j=1;j<=nlstate+ndeath;j++){
1125: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1126: savm[ii][j]=(ii==j ? 1.0 : 0.0);
1127: }
1128: for(d=0; d<dh[mi][i]; d++){
1129: newm=savm;
1130: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
1131: for (kk=1; kk<=cptcovage;kk++) {
1132: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
1133: }
1134: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1135: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1136: savm=oldm;
1137: oldm=newm;
1138: } /* end mult */
1139:
1140: /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
1141: /* But now since version 0.9 we anticipate for bias and large stepm.
1142: * If stepm is larger than one month (smallest stepm) and if the exact delay
1143: * (in months) between two waves is not a multiple of stepm, we rounded to
1144: * the nearest (and in case of equal distance, to the lowest) interval but now
1145: * we keep into memory the bias bh[mi][i] and also the previous matrix product
1146: * (i.e to dh[mi][i]-1) saved in 'savm'. The we inter(extra)polate the
1147: * probability in order to take into account the bias as a fraction of the way
1148: * from savm to out if bh is neagtive or even beyond if bh is positive. bh varies
1149: * -stepm/2 to stepm/2 .
1150: * For stepm=1 the results are the same as for previous versions of Imach.
1151: * For stepm > 1 the results are less biased than in previous versions.
1152: */
1153: s1=s[mw[mi][i]][i];
1154: s2=s[mw[mi+1][i]][i];
1155: bbh=(double)bh[mi][i]/(double)stepm;
1156: /* bias is positive if real duration
1157: * is higher than the multiple of stepm and negative otherwise.
1158: */
1159: /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
1160: if( s2 > nlstate){
1161: /* i.e. if s2 is a death state and if the date of death is known then the contribution
1162: to the likelihood is the probability to die between last step unit time and current
1163: step unit time, which is also the differences between probability to die before dh
1164: and probability to die before dh-stepm .
1165: In version up to 0.92 likelihood was computed
1166: as if date of death was unknown. Death was treated as any other
1167: health state: the date of the interview describes the actual state
1168: and not the date of a change in health state. The former idea was
1169: to consider that at each interview the state was recorded
1170: (healthy, disable or death) and IMaCh was corrected; but when we
1171: introduced the exact date of death then we should have modified
1172: the contribution of an exact death to the likelihood. This new
1173: contribution is smaller and very dependent of the step unit
1174: stepm. It is no more the probability to die between last interview
1175: and month of death but the probability to survive from last
1176: interview up to one month before death multiplied by the
1177: probability to die within a month. Thanks to Chris
1178: Jackson for correcting this bug. Former versions increased
1179: mortality artificially. The bad side is that we add another loop
1180: which slows down the processing. The difference can be up to 10%
1181: lower mortality.
1182: */
1183: lli=log(out[s1][s2] - savm[s1][s2]);
1184: }else{
1185: lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
1186: /* 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 */
1187: }
1188: /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
1189: /*if(lli ==000.0)*/
1190: /*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); */
1191: ipmx +=1;
1192: sw += weight[i];
1193: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1194: } /* end of wave */
1195: } /* end of individual */
1196: } else if(mle==2){
1197: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1198: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
1199: for(mi=1; mi<= wav[i]-1; mi++){
1200: for (ii=1;ii<=nlstate+ndeath;ii++)
1201: for (j=1;j<=nlstate+ndeath;j++){
1202: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1203: savm[ii][j]=(ii==j ? 1.0 : 0.0);
1204: }
1205: for(d=0; d<=dh[mi][i]; d++){
1206: newm=savm;
1207: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
1208: for (kk=1; kk<=cptcovage;kk++) {
1209: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
1210: }
1211: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1212: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1213: savm=oldm;
1214: oldm=newm;
1215: } /* end mult */
1216:
1217: /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
1218: /* But now since version 0.9 we anticipate for bias and large stepm.
1219: * If stepm is larger than one month (smallest stepm) and if the exact delay
1220: * (in months) between two waves is not a multiple of stepm, we rounded to
1221: * the nearest (and in case of equal distance, to the lowest) interval but now
1222: * we keep into memory the bias bh[mi][i] and also the previous matrix product
1223: * (i.e to dh[mi][i]-1) saved in 'savm'. The we inter(extra)polate the
1224: * probability in order to take into account the bias as a fraction of the way
1225: * from savm to out if bh is neagtive or even beyond if bh is positive. bh varies
1226: * -stepm/2 to stepm/2 .
1227: * For stepm=1 the results are the same as for previous versions of Imach.
1228: * For stepm > 1 the results are less biased than in previous versions.
1229: */
1230: s1=s[mw[mi][i]][i];
1231: s2=s[mw[mi+1][i]][i];
1232: bbh=(double)bh[mi][i]/(double)stepm;
1233: /* bias is positive if real duration
1234: * is higher than the multiple of stepm and negative otherwise.
1235: */
1236: 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 */
1237: /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
1238: /*lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.-+bh)*out[s1][s2])); */ /* exponential interpolation */
1239: /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
1240: /*if(lli ==000.0)*/
1241: /*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); */
1242: ipmx +=1;
1243: sw += weight[i];
1244: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1245: } /* end of wave */
1246: } /* end of individual */
1247: } else if(mle==3){ /* exponential inter-extrapolation */
1248: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1249: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
1250: for(mi=1; mi<= wav[i]-1; mi++){
1251: for (ii=1;ii<=nlstate+ndeath;ii++)
1252: for (j=1;j<=nlstate+ndeath;j++){
1253: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1254: savm[ii][j]=(ii==j ? 1.0 : 0.0);
1255: }
1256: for(d=0; d<dh[mi][i]; d++){
1257: newm=savm;
1258: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
1259: for (kk=1; kk<=cptcovage;kk++) {
1260: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
1261: }
1262: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1263: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1264: savm=oldm;
1265: oldm=newm;
1266: } /* end mult */
1267:
1268: /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
1269: /* But now since version 0.9 we anticipate for bias and large stepm.
1270: * If stepm is larger than one month (smallest stepm) and if the exact delay
1271: * (in months) between two waves is not a multiple of stepm, we rounded to
1272: * the nearest (and in case of equal distance, to the lowest) interval but now
1273: * we keep into memory the bias bh[mi][i] and also the previous matrix product
1274: * (i.e to dh[mi][i]-1) saved in 'savm'. The we inter(extra)polate the
1275: * probability in order to take into account the bias as a fraction of the way
1276: * from savm to out if bh is neagtive or even beyond if bh is positive. bh varies
1277: * -stepm/2 to stepm/2 .
1278: * For stepm=1 the results are the same as for previous versions of Imach.
1279: * For stepm > 1 the results are less biased than in previous versions.
1280: */
1281: s1=s[mw[mi][i]][i];
1282: s2=s[mw[mi+1][i]][i];
1283: bbh=(double)bh[mi][i]/(double)stepm;
1284: /* bias is positive if real duration
1285: * is higher than the multiple of stepm and negative otherwise.
1286: */
1287: /* 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 */
1288: 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 */
1289: /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
1290: /*if(lli ==000.0)*/
1291: /*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); */
1292: ipmx +=1;
1293: sw += weight[i];
1294: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1295: } /* end of wave */
1296: } /* end of individual */
1297: }else if (mle==4){ /* ml=4 no inter-extrapolation */
1298: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1299: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
1300: for(mi=1; mi<= wav[i]-1; mi++){
1301: for (ii=1;ii<=nlstate+ndeath;ii++)
1302: for (j=1;j<=nlstate+ndeath;j++){
1303: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1304: savm[ii][j]=(ii==j ? 1.0 : 0.0);
1305: }
1306: for(d=0; d<dh[mi][i]; d++){
1307: newm=savm;
1308: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
1309: for (kk=1; kk<=cptcovage;kk++) {
1310: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
1311: }
1312:
1313: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1314: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1315: savm=oldm;
1316: oldm=newm;
1317: } /* end mult */
1318:
1319: s1=s[mw[mi][i]][i];
1320: s2=s[mw[mi+1][i]][i];
1321: if( s2 > nlstate){
1322: lli=log(out[s1][s2] - savm[s1][s2]);
1323: }else{
1324: lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
1325: }
1326: ipmx +=1;
1327: sw += weight[i];
1328: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1329: /* 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]); */
1330: } /* end of wave */
1331: } /* end of individual */
1332: }else{ /* ml=5 no inter-extrapolation no jackson =0.8a */
1333: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1334: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
1335: for(mi=1; mi<= wav[i]-1; mi++){
1336: for (ii=1;ii<=nlstate+ndeath;ii++)
1337: for (j=1;j<=nlstate+ndeath;j++){
1338: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1339: savm[ii][j]=(ii==j ? 1.0 : 0.0);
1340: }
1341: for(d=0; d<dh[mi][i]; d++){
1342: newm=savm;
1343: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
1344: for (kk=1; kk<=cptcovage;kk++) {
1345: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
1346: }
1347:
1348: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1349: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1350: savm=oldm;
1351: oldm=newm;
1352: } /* end mult */
1353:
1354: s1=s[mw[mi][i]][i];
1355: s2=s[mw[mi+1][i]][i];
1356: lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
1357: ipmx +=1;
1358: sw += weight[i];
1359: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1360: /*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]);*/
1361: } /* end of wave */
1362: } /* end of individual */
1363: } /* End of if */
1364: for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
1365: /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
1366: l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
1367: return -l;
1368: }
1369:
1370: /*************** log-likelihood *************/
1371: double funcone( double *x)
1372: {
1373: /* Same as likeli but slower because of a lot of printf and if */
1374: int i, ii, j, k, mi, d, kk;
1375: double l, ll[NLSTATEMAX], cov[NCOVMAX];
1376: double **out;
1377: double lli; /* Individual log likelihood */
1378: double llt;
1379: int s1, s2;
1380: double bbh, survp;
1381: /*extern weight */
1382: /* We are differentiating ll according to initial status */
1383: /* for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
1384: /*for(i=1;i<imx;i++)
1385: printf(" %d\n",s[4][i]);
1386: */
1387: cov[1]=1.;
1388:
1389: for(k=1; k<=nlstate; k++) ll[k]=0.;
1390:
1391: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1392: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
1393: for(mi=1; mi<= wav[i]-1; mi++){
1394: for (ii=1;ii<=nlstate+ndeath;ii++)
1395: for (j=1;j<=nlstate+ndeath;j++){
1396: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1397: savm[ii][j]=(ii==j ? 1.0 : 0.0);
1398: }
1399: for(d=0; d<dh[mi][i]; d++){
1400: newm=savm;
1401: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
1402: for (kk=1; kk<=cptcovage;kk++) {
1403: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
1404: }
1405: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1406: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1407: savm=oldm;
1408: oldm=newm;
1409: } /* end mult */
1410:
1411: s1=s[mw[mi][i]][i];
1412: s2=s[mw[mi+1][i]][i];
1413: bbh=(double)bh[mi][i]/(double)stepm;
1414: /* bias is positive if real duration
1415: * is higher than the multiple of stepm and negative otherwise.
1416: */
1417: if( s2 > nlstate && (mle <5) ){ /* Jackson */
1418: lli=log(out[s1][s2] - savm[s1][s2]);
1419: } else if (mle==1){
1420: lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
1421: } else if(mle==2){
1422: 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 */
1423: } else if(mle==3){ /* exponential inter-extrapolation */
1424: 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 */
1425: } else if (mle==4){ /* mle=4 no inter-extrapolation */
1426: lli=log(out[s1][s2]); /* Original formula */
1427: } else{ /* ml>=5 no inter-extrapolation no jackson =0.8a */
1428: lli=log(out[s1][s2]); /* Original formula */
1429: } /* End of if */
1430: ipmx +=1;
1431: sw += weight[i];
1432: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1433: /* 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]); */
1434: if(globpr){
1435: fprintf(ficresilk,"%9d %6d %1d %1d %1d %1d %3d %10.6f %6.4f\
1436: %10.6f %10.6f %10.6f ", \
1437: num[i],i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],
1438: 2*weight[i]*lli,out[s1][s2],savm[s1][s2]);
1439: for(k=1,llt=0.,l=0.; k<=nlstate; k++){
1440: llt +=ll[k]*gipmx/gsw;
1441: fprintf(ficresilk," %10.6f",-ll[k]*gipmx/gsw);
1442: }
1443: fprintf(ficresilk," %10.6f\n", -llt);
1444: }
1445: } /* end of wave */
1446: } /* end of individual */
1447: for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
1448: /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
1449: l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
1450: if(globpr==0){ /* First time we count the contributions and weights */
1451: gipmx=ipmx;
1452: gsw=sw;
1453: }
1454: return -l;
1455: }
1456:
1457: char *subdirf(char fileres[])
1458: {
1459: /* Caution optionfilefiname is hidden */
1460: strcpy(tmpout,optionfilefiname);
1461: strcat(tmpout,"/"); /* Add to the right */
1462: strcat(tmpout,fileres);
1463: return tmpout;
1464: }
1465:
1466: char *subdirf2(char fileres[], char *preop)
1467: {
1468:
1469: strcpy(tmpout,optionfilefiname);
1470: strcat(tmpout,"/");
1471: strcat(tmpout,preop);
1472: strcat(tmpout,fileres);
1473: return tmpout;
1474: }
1475: char *subdirf3(char fileres[], char *preop, char *preop2)
1476: {
1477:
1478: strcpy(tmpout,optionfilefiname);
1479: strcat(tmpout,"/");
1480: strcat(tmpout,preop);
1481: strcat(tmpout,preop2);
1482: strcat(tmpout,fileres);
1483: return tmpout;
1484: }
1485:
1486: void likelione(FILE *ficres,double p[], int npar, int nlstate, int *globpri, long *ipmx, double *sw, double *fretone, double (*funcone)(double []))
1487: {
1488: /* This routine should help understanding what is done with
1489: the selection of individuals/waves and
1490: to check the exact contribution to the likelihood.
1491: Plotting could be done.
1492: */
1493: int k;
1494:
1495: if(*globpri !=0){ /* Just counts and sums, no printings */
1496: strcpy(fileresilk,"ilk");
1497: strcat(fileresilk,fileres);
1498: if((ficresilk=fopen(fileresilk,"w"))==NULL) {
1499: printf("Problem with resultfile: %s\n", fileresilk);
1500: fprintf(ficlog,"Problem with resultfile: %s\n", fileresilk);
1501: }
1502: 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");
1503: fprintf(ficresilk, "#num_i i s1 s2 mi mw dh likeli weight 2wlli out sav ");
1504: /* i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],2*weight[i]*lli,out[s1][s2],savm[s1][s2]); */
1505: for(k=1; k<=nlstate; k++)
1506: fprintf(ficresilk," -2*gipw/gsw*weight*ll[%d]++",k);
1507: fprintf(ficresilk," -2*gipw/gsw*weight*ll(total)\n");
1508: }
1509:
1510: *fretone=(*funcone)(p);
1511: if(*globpri !=0){
1512: fclose(ficresilk);
1513: fprintf(fichtm,"\n<br>File of contributions to the likelihood: <a href=\"%s\">%s</a><br>\n",subdirf(fileresilk),subdirf(fileresilk));
1514: fflush(fichtm);
1515: }
1516: return;
1517: }
1518:
1519:
1520: /*********** Maximum Likelihood Estimation ***************/
1521:
1522: void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
1523: {
1524: int i,j, iter;
1525: double **xi;
1526: double fret;
1527: double fretone; /* Only one call to likelihood */
1528: char filerespow[FILENAMELENGTH];
1529: xi=matrix(1,npar,1,npar);
1530: for (i=1;i<=npar;i++)
1531: for (j=1;j<=npar;j++)
1532: xi[i][j]=(i==j ? 1.0 : 0.0);
1533: printf("Powell\n"); fprintf(ficlog,"Powell\n");
1534: strcpy(filerespow,"pow");
1535: strcat(filerespow,fileres);
1536: if((ficrespow=fopen(filerespow,"w"))==NULL) {
1537: printf("Problem with resultfile: %s\n", filerespow);
1538: fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
1539: }
1540: fprintf(ficrespow,"# Powell\n# iter -2*LL");
1541: for (i=1;i<=nlstate;i++)
1542: for(j=1;j<=nlstate+ndeath;j++)
1543: if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
1544: fprintf(ficrespow,"\n");
1545:
1546: powell(p,xi,npar,ftol,&iter,&fret,func);
1547:
1548: fclose(ficrespow);
1549: printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));
1550: fprintf(ficlog,"\n#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
1551: fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
1552:
1553: }
1554:
1555: /**** Computes Hessian and covariance matrix ***/
1556: void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
1557: {
1558: double **a,**y,*x,pd;
1559: double **hess;
1560: int i, j,jk;
1561: int *indx;
1562:
1563: double hessii(double p[], double delta, int theta, double delti[]);
1564: double hessij(double p[], double delti[], int i, int j);
1565: void lubksb(double **a, int npar, int *indx, double b[]) ;
1566: void ludcmp(double **a, int npar, int *indx, double *d) ;
1567:
1568: hess=matrix(1,npar,1,npar);
1569:
1570: printf("\nCalculation of the hessian matrix. Wait...\n");
1571: fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
1572: for (i=1;i<=npar;i++){
1573: printf("%d",i);fflush(stdout);
1574: fprintf(ficlog,"%d",i);fflush(ficlog);
1575: hess[i][i]=hessii(p,ftolhess,i,delti);
1576: /*printf(" %f ",p[i]);*/
1577: /*printf(" %lf ",hess[i][i]);*/
1578: }
1579:
1580: for (i=1;i<=npar;i++) {
1581: for (j=1;j<=npar;j++) {
1582: if (j>i) {
1583: printf(".%d%d",i,j);fflush(stdout);
1584: fprintf(ficlog,".%d%d",i,j);fflush(ficlog);
1585: hess[i][j]=hessij(p,delti,i,j);
1586: hess[j][i]=hess[i][j];
1587: /*printf(" %lf ",hess[i][j]);*/
1588: }
1589: }
1590: }
1591: printf("\n");
1592: fprintf(ficlog,"\n");
1593:
1594: printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
1595: fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
1596:
1597: a=matrix(1,npar,1,npar);
1598: y=matrix(1,npar,1,npar);
1599: x=vector(1,npar);
1600: indx=ivector(1,npar);
1601: for (i=1;i<=npar;i++)
1602: for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
1603: ludcmp(a,npar,indx,&pd);
1604:
1605: for (j=1;j<=npar;j++) {
1606: for (i=1;i<=npar;i++) x[i]=0;
1607: x[j]=1;
1608: lubksb(a,npar,indx,x);
1609: for (i=1;i<=npar;i++){
1610: matcov[i][j]=x[i];
1611: }
1612: }
1613:
1614: printf("\n#Hessian matrix#\n");
1615: fprintf(ficlog,"\n#Hessian matrix#\n");
1616: for (i=1;i<=npar;i++) {
1617: for (j=1;j<=npar;j++) {
1618: printf("%.3e ",hess[i][j]);
1619: fprintf(ficlog,"%.3e ",hess[i][j]);
1620: }
1621: printf("\n");
1622: fprintf(ficlog,"\n");
1623: }
1624:
1625: /* Recompute Inverse */
1626: for (i=1;i<=npar;i++)
1627: for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];
1628: ludcmp(a,npar,indx,&pd);
1629:
1630: /* printf("\n#Hessian matrix recomputed#\n");
1631:
1632: for (j=1;j<=npar;j++) {
1633: for (i=1;i<=npar;i++) x[i]=0;
1634: x[j]=1;
1635: lubksb(a,npar,indx,x);
1636: for (i=1;i<=npar;i++){
1637: y[i][j]=x[i];
1638: printf("%.3e ",y[i][j]);
1639: fprintf(ficlog,"%.3e ",y[i][j]);
1640: }
1641: printf("\n");
1642: fprintf(ficlog,"\n");
1643: }
1644: */
1645:
1646: free_matrix(a,1,npar,1,npar);
1647: free_matrix(y,1,npar,1,npar);
1648: free_vector(x,1,npar);
1649: free_ivector(indx,1,npar);
1650: free_matrix(hess,1,npar,1,npar);
1651:
1652:
1653: }
1654:
1655: /*************** hessian matrix ****************/
1656: double hessii( double x[], double delta, int theta, double delti[])
1657: {
1658: int i;
1659: int l=1, lmax=20;
1660: double k1,k2;
1661: double p2[NPARMAX+1];
1662: double res;
1663: double delt, delts, nkhi=10.,nkhif=1., khi=1.e-4;
1664: double fx;
1665: int k=0,kmax=10;
1666: double l1;
1667:
1668: fx=func(x);
1669: for (i=1;i<=npar;i++) p2[i]=x[i];
1670: for(l=0 ; l <=lmax; l++){
1671: l1=pow(10,l);
1672: delts=delt;
1673: for(k=1 ; k <kmax; k=k+1){
1674: delt = delta*(l1*k);
1675: p2[theta]=x[theta] +delt;
1676: k1=func(p2)-fx;
1677: p2[theta]=x[theta]-delt;
1678: k2=func(p2)-fx;
1679: /*res= (k1-2.0*fx+k2)/delt/delt; */
1680: res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */
1681:
1682: #ifdef DEBUG
1683: 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);
1684: 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);
1685: #endif
1686: /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
1687: if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
1688: k=kmax;
1689: }
1690: else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
1691: k=kmax; l=lmax*10.;
1692: }
1693: else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){
1694: delts=delt;
1695: }
1696: }
1697: }
1698: delti[theta]=delts;
1699: return res;
1700:
1701: }
1702:
1703: double hessij( double x[], double delti[], int thetai,int thetaj)
1704: {
1705: int i;
1706: int l=1, l1, lmax=20;
1707: double k1,k2,k3,k4,res,fx;
1708: double p2[NPARMAX+1];
1709: int k;
1710:
1711: fx=func(x);
1712: for (k=1; k<=2; k++) {
1713: for (i=1;i<=npar;i++) p2[i]=x[i];
1714: p2[thetai]=x[thetai]+delti[thetai]/k;
1715: p2[thetaj]=x[thetaj]+delti[thetaj]/k;
1716: k1=func(p2)-fx;
1717:
1718: p2[thetai]=x[thetai]+delti[thetai]/k;
1719: p2[thetaj]=x[thetaj]-delti[thetaj]/k;
1720: k2=func(p2)-fx;
1721:
1722: p2[thetai]=x[thetai]-delti[thetai]/k;
1723: p2[thetaj]=x[thetaj]+delti[thetaj]/k;
1724: k3=func(p2)-fx;
1725:
1726: p2[thetai]=x[thetai]-delti[thetai]/k;
1727: p2[thetaj]=x[thetaj]-delti[thetaj]/k;
1728: k4=func(p2)-fx;
1729: res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */
1730: #ifdef DEBUG
1731: 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);
1732: 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);
1733: #endif
1734: }
1735: return res;
1736: }
1737:
1738: /************** Inverse of matrix **************/
1739: void ludcmp(double **a, int n, int *indx, double *d)
1740: {
1741: int i,imax,j,k;
1742: double big,dum,sum,temp;
1743: double *vv;
1744:
1745: vv=vector(1,n);
1746: *d=1.0;
1747: for (i=1;i<=n;i++) {
1748: big=0.0;
1749: for (j=1;j<=n;j++)
1750: if ((temp=fabs(a[i][j])) > big) big=temp;
1751: if (big == 0.0) nrerror("Singular matrix in routine ludcmp");
1752: vv[i]=1.0/big;
1753: }
1754: for (j=1;j<=n;j++) {
1755: for (i=1;i<j;i++) {
1756: sum=a[i][j];
1757: for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];
1758: a[i][j]=sum;
1759: }
1760: big=0.0;
1761: for (i=j;i<=n;i++) {
1762: sum=a[i][j];
1763: for (k=1;k<j;k++)
1764: sum -= a[i][k]*a[k][j];
1765: a[i][j]=sum;
1766: if ( (dum=vv[i]*fabs(sum)) >= big) {
1767: big=dum;
1768: imax=i;
1769: }
1770: }
1771: if (j != imax) {
1772: for (k=1;k<=n;k++) {
1773: dum=a[imax][k];
1774: a[imax][k]=a[j][k];
1775: a[j][k]=dum;
1776: }
1777: *d = -(*d);
1778: vv[imax]=vv[j];
1779: }
1780: indx[j]=imax;
1781: if (a[j][j] == 0.0) a[j][j]=TINY;
1782: if (j != n) {
1783: dum=1.0/(a[j][j]);
1784: for (i=j+1;i<=n;i++) a[i][j] *= dum;
1785: }
1786: }
1787: free_vector(vv,1,n); /* Doesn't work */
1788: ;
1789: }
1790:
1791: void lubksb(double **a, int n, int *indx, double b[])
1792: {
1793: int i,ii=0,ip,j;
1794: double sum;
1795:
1796: for (i=1;i<=n;i++) {
1797: ip=indx[i];
1798: sum=b[ip];
1799: b[ip]=b[i];
1800: if (ii)
1801: for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];
1802: else if (sum) ii=i;
1803: b[i]=sum;
1804: }
1805: for (i=n;i>=1;i--) {
1806: sum=b[i];
1807: for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];
1808: b[i]=sum/a[i][i];
1809: }
1810: }
1811:
1812: /************ Frequencies ********************/
1813: 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)
1814: { /* Some frequencies */
1815:
1816: int i, m, jk, k1,i1, j1, bool, z1,z2,j;
1817: int first;
1818: double ***freq; /* Frequencies */
1819: double *pp, **prop;
1820: double pos,posprop, k2, dateintsum=0,k2cpt=0;
1821: FILE *ficresp;
1822: char fileresp[FILENAMELENGTH];
1823:
1824: pp=vector(1,nlstate);
1825: prop=matrix(1,nlstate,iagemin,iagemax+3);
1826: strcpy(fileresp,"p");
1827: strcat(fileresp,fileres);
1828: if((ficresp=fopen(fileresp,"w"))==NULL) {
1829: printf("Problem with prevalence resultfile: %s\n", fileresp);
1830: fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
1831: exit(0);
1832: }
1833: freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);
1834: j1=0;
1835:
1836: j=cptcoveff;
1837: if (cptcovn<1) {j=1;ncodemax[1]=1;}
1838:
1839: first=1;
1840:
1841: for(k1=1; k1<=j;k1++){
1842: for(i1=1; i1<=ncodemax[k1];i1++){
1843: j1++;
1844: /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
1845: scanf("%d", i);*/
1846: for (i=-1; i<=nlstate+ndeath; i++)
1847: for (jk=-1; jk<=nlstate+ndeath; jk++)
1848: for(m=iagemin; m <= iagemax+3; m++)
1849: freq[i][jk][m]=0;
1850:
1851: for (i=1; i<=nlstate; i++)
1852: for(m=iagemin; m <= iagemax+3; m++)
1853: prop[i][m]=0;
1854:
1855: dateintsum=0;
1856: k2cpt=0;
1857: for (i=1; i<=imx; i++) {
1858: bool=1;
1859: if (cptcovn>0) {
1860: for (z1=1; z1<=cptcoveff; z1++)
1861: if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])
1862: bool=0;
1863: }
1864: if (bool==1){
1865: for(m=firstpass; m<=lastpass; m++){
1866: k2=anint[m][i]+(mint[m][i]/12.);
1867: /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/
1868: if(agev[m][i]==0) agev[m][i]=iagemax+1;
1869: if(agev[m][i]==1) agev[m][i]=iagemax+2;
1870: if (s[m][i]>0 && s[m][i]<=nlstate) prop[s[m][i]][(int)agev[m][i]] += weight[i];
1871: if (m<lastpass) {
1872: freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
1873: freq[s[m][i]][s[m+1][i]][iagemax+3] += weight[i];
1874: }
1875:
1876: if ((agev[m][i]>1) && (agev[m][i]< (iagemax+3))) {
1877: dateintsum=dateintsum+k2;
1878: k2cpt++;
1879: }
1880: /*}*/
1881: }
1882: }
1883: }
1884:
1885: /* fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
1886:
1887: if (cptcovn>0) {
1888: fprintf(ficresp, "\n#********** Variable ");
1889: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
1890: fprintf(ficresp, "**********\n#");
1891: }
1892: for(i=1; i<=nlstate;i++)
1893: fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
1894: fprintf(ficresp, "\n");
1895:
1896: for(i=iagemin; i <= iagemax+3; i++){
1897: if(i==iagemax+3){
1898: fprintf(ficlog,"Total");
1899: }else{
1900: if(first==1){
1901: first=0;
1902: printf("See log file for details...\n");
1903: }
1904: fprintf(ficlog,"Age %d", i);
1905: }
1906: for(jk=1; jk <=nlstate ; jk++){
1907: for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
1908: pp[jk] += freq[jk][m][i];
1909: }
1910: for(jk=1; jk <=nlstate ; jk++){
1911: for(m=-1, pos=0; m <=0 ; m++)
1912: pos += freq[jk][m][i];
1913: if(pp[jk]>=1.e-10){
1914: if(first==1){
1915: printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
1916: }
1917: fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
1918: }else{
1919: if(first==1)
1920: printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
1921: fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
1922: }
1923: }
1924:
1925: for(jk=1; jk <=nlstate ; jk++){
1926: for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
1927: pp[jk] += freq[jk][m][i];
1928: }
1929: for(jk=1,pos=0,posprop=0; jk <=nlstate ; jk++){
1930: pos += pp[jk];
1931: posprop += prop[jk][i];
1932: }
1933: for(jk=1; jk <=nlstate ; jk++){
1934: if(pos>=1.e-5){
1935: if(first==1)
1936: printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
1937: fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
1938: }else{
1939: if(first==1)
1940: printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
1941: fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
1942: }
1943: if( i <= iagemax){
1944: if(pos>=1.e-5){
1945: fprintf(ficresp," %d %.5f %.0f %.0f",i,prop[jk][i]/posprop, prop[jk][i],posprop);
1946: /*probs[i][jk][j1]= pp[jk]/pos;*/
1947: /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/
1948: }
1949: else
1950: fprintf(ficresp," %d NaNq %.0f %.0f",i,prop[jk][i],posprop);
1951: }
1952: }
1953:
1954: for(jk=-1; jk <=nlstate+ndeath; jk++)
1955: for(m=-1; m <=nlstate+ndeath; m++)
1956: if(freq[jk][m][i] !=0 ) {
1957: if(first==1)
1958: printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
1959: fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
1960: }
1961: if(i <= iagemax)
1962: fprintf(ficresp,"\n");
1963: if(first==1)
1964: printf("Others in log...\n");
1965: fprintf(ficlog,"\n");
1966: }
1967: }
1968: }
1969: dateintmean=dateintsum/k2cpt;
1970:
1971: fclose(ficresp);
1972: free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);
1973: free_vector(pp,1,nlstate);
1974: free_matrix(prop,1,nlstate,iagemin, iagemax+3);
1975: /* End of Freq */
1976: }
1977:
1978: /************ Prevalence ********************/
1979: 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)
1980: {
1981: /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
1982: in each health status at the date of interview (if between dateprev1 and dateprev2).
1983: We still use firstpass and lastpass as another selection.
1984: */
1985:
1986: int i, m, jk, k1, i1, j1, bool, z1,z2,j;
1987: double ***freq; /* Frequencies */
1988: double *pp, **prop;
1989: double pos,posprop;
1990: double y2; /* in fractional years */
1991: int iagemin, iagemax;
1992:
1993: iagemin= (int) agemin;
1994: iagemax= (int) agemax;
1995: /*pp=vector(1,nlstate);*/
1996: prop=matrix(1,nlstate,iagemin,iagemax+3);
1997: /* freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
1998: j1=0;
1999:
2000: j=cptcoveff;
2001: if (cptcovn<1) {j=1;ncodemax[1]=1;}
2002:
2003: for(k1=1; k1<=j;k1++){
2004: for(i1=1; i1<=ncodemax[k1];i1++){
2005: j1++;
2006:
2007: for (i=1; i<=nlstate; i++)
2008: for(m=iagemin; m <= iagemax+3; m++)
2009: prop[i][m]=0.0;
2010:
2011: for (i=1; i<=imx; i++) { /* Each individual */
2012: bool=1;
2013: if (cptcovn>0) {
2014: for (z1=1; z1<=cptcoveff; z1++)
2015: if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])
2016: bool=0;
2017: }
2018: if (bool==1) {
2019: for(m=firstpass; m<=lastpass; m++){/* Other selection (we can limit to certain interviews*/
2020: y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
2021: if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
2022: if(agev[m][i]==0) agev[m][i]=iagemax+1;
2023: if(agev[m][i]==1) agev[m][i]=iagemax+2;
2024: 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);
2025: if (s[m][i]>0 && s[m][i]<=nlstate) {
2026: /*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]]);*/
2027: prop[s[m][i]][(int)agev[m][i]] += weight[i];
2028: prop[s[m][i]][iagemax+3] += weight[i];
2029: }
2030: }
2031: } /* end selection of waves */
2032: }
2033: }
2034: for(i=iagemin; i <= iagemax+3; i++){
2035:
2036: for(jk=1,posprop=0; jk <=nlstate ; jk++) {
2037: posprop += prop[jk][i];
2038: }
2039:
2040: for(jk=1; jk <=nlstate ; jk++){
2041: if( i <= iagemax){
2042: if(posprop>=1.e-5){
2043: probs[i][jk][j1]= prop[jk][i]/posprop;
2044: }
2045: }
2046: }/* end jk */
2047: }/* end i */
2048: } /* end i1 */
2049: } /* end k1 */
2050:
2051: /* free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
2052: /*free_vector(pp,1,nlstate);*/
2053: free_matrix(prop,1,nlstate, iagemin,iagemax+3);
2054: } /* End of prevalence */
2055:
2056: /************* Waves Concatenation ***************/
2057:
2058: 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)
2059: {
2060: /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
2061: Death is a valid wave (if date is known).
2062: mw[mi][i] is the mi (mi=1 to wav[i]) effective wave of individual i
2063: dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
2064: and mw[mi+1][i]. dh depends on stepm.
2065: */
2066:
2067: int i, mi, m;
2068: /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
2069: double sum=0., jmean=0.;*/
2070: int first;
2071: int j, k=0,jk, ju, jl;
2072: double sum=0.;
2073: first=0;
2074: jmin=1e+5;
2075: jmax=-1;
2076: jmean=0.;
2077: for(i=1; i<=imx; i++){
2078: mi=0;
2079: m=firstpass;
2080: while(s[m][i] <= nlstate){
2081: if(s[m][i]>=1)
2082: mw[++mi][i]=m;
2083: if(m >=lastpass)
2084: break;
2085: else
2086: m++;
2087: }/* end while */
2088: if (s[m][i] > nlstate){
2089: mi++; /* Death is another wave */
2090: /* if(mi==0) never been interviewed correctly before death */
2091: /* Only death is a correct wave */
2092: mw[mi][i]=m;
2093: }
2094:
2095: wav[i]=mi;
2096: if(mi==0){
2097: nbwarn++;
2098: if(first==0){
2099: printf("Warning! None valid information for:%ld line=%d (skipped) and may be others, see log file\n",num[i],i);
2100: first=1;
2101: }
2102: if(first==1){
2103: fprintf(ficlog,"Warning! None valid information for:%ld line=%d (skipped)\n",num[i],i);
2104: }
2105: } /* end mi==0 */
2106: } /* End individuals */
2107:
2108: for(i=1; i<=imx; i++){
2109: for(mi=1; mi<wav[i];mi++){
2110: if (stepm <=0)
2111: dh[mi][i]=1;
2112: else{
2113: if (s[mw[mi+1][i]][i] > nlstate) { /* A death */
2114: if (agedc[i] < 2*AGESUP) {
2115: j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);
2116: if(j==0) j=1; /* Survives at least one month after exam */
2117: else if(j<0){
2118: nberr++;
2119: 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]);
2120: j=1; /* Temporary Dangerous patch */
2121: 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);
2122: 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]);
2123: 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);
2124: }
2125: k=k+1;
2126: if (j >= jmax) jmax=j;
2127: if (j <= jmin) jmin=j;
2128: sum=sum+j;
2129: /*if (j<0) printf("j=%d num=%d \n",j,i);*/
2130: /* printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
2131: }
2132: }
2133: else{
2134: j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
2135: /* printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
2136: k=k+1;
2137: if (j >= jmax) jmax=j;
2138: else if (j <= jmin)jmin=j;
2139: /* if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
2140: /*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]);*/
2141: if(j<0){
2142: nberr++;
2143: 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]);
2144: 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]);
2145: }
2146: sum=sum+j;
2147: }
2148: jk= j/stepm;
2149: jl= j -jk*stepm;
2150: ju= j -(jk+1)*stepm;
2151: if(mle <=1){ /* only if we use a the linear-interpoloation pseudo-likelihood */
2152: if(jl==0){
2153: dh[mi][i]=jk;
2154: bh[mi][i]=0;
2155: }else{ /* We want a negative bias in order to only have interpolation ie
2156: * at the price of an extra matrix product in likelihood */
2157: dh[mi][i]=jk+1;
2158: bh[mi][i]=ju;
2159: }
2160: }else{
2161: if(jl <= -ju){
2162: dh[mi][i]=jk;
2163: bh[mi][i]=jl; /* bias is positive if real duration
2164: * is higher than the multiple of stepm and negative otherwise.
2165: */
2166: }
2167: else{
2168: dh[mi][i]=jk+1;
2169: bh[mi][i]=ju;
2170: }
2171: if(dh[mi][i]==0){
2172: dh[mi][i]=1; /* At least one step */
2173: bh[mi][i]=ju; /* At least one step */
2174: /* 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);*/
2175: }
2176: } /* end if mle */
2177: }
2178: } /* end wave */
2179: }
2180: jmean=sum/k;
2181: printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);
2182: fprintf(ficlog,"Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);
2183: }
2184:
2185: /*********** Tricode ****************************/
2186: void tricode(int *Tvar, int **nbcode, int imx)
2187: {
2188:
2189: int Ndum[20],ij=1, k, j, i, maxncov=19;
2190: int cptcode=0;
2191: cptcoveff=0;
2192:
2193: for (k=0; k<maxncov; k++) Ndum[k]=0;
2194: for (k=1; k<=7; k++) ncodemax[k]=0;
2195:
2196: for (j=1; j<=(cptcovn+2*cptcovprod); j++) {
2197: for (i=1; i<=imx; i++) { /*reads the data file to get the maximum
2198: modality*/
2199: ij=(int)(covar[Tvar[j]][i]); /* ij is the modality of this individual*/
2200: Ndum[ij]++; /*store the modality */
2201: /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
2202: if (ij > cptcode) cptcode=ij; /* getting the maximum of covariable
2203: Tvar[j]. If V=sex and male is 0 and
2204: female is 1, then cptcode=1.*/
2205: }
2206:
2207: for (i=0; i<=cptcode; i++) {
2208: 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 */
2209: }
2210:
2211: ij=1;
2212: for (i=1; i<=ncodemax[j]; i++) {
2213: for (k=0; k<= maxncov; k++) {
2214: if (Ndum[k] != 0) {
2215: nbcode[Tvar[j]][ij]=k;
2216: /* 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; */
2217:
2218: ij++;
2219: }
2220: if (ij > ncodemax[j]) break;
2221: }
2222: }
2223: }
2224:
2225: for (k=0; k< maxncov; k++) Ndum[k]=0;
2226:
2227: for (i=1; i<=ncovmodel-2; i++) {
2228: /* Listing of all covariables in staement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/
2229: ij=Tvar[i];
2230: Ndum[ij]++;
2231: }
2232:
2233: ij=1;
2234: for (i=1; i<= maxncov; i++) {
2235: if((Ndum[i]!=0) && (i<=ncovcol)){
2236: Tvaraff[ij]=i; /*For printing */
2237: ij++;
2238: }
2239: }
2240:
2241: cptcoveff=ij-1; /*Number of simple covariates*/
2242: }
2243:
2244: /*********** Health Expectancies ****************/
2245:
2246: 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 )
2247:
2248: {
2249: /* Health expectancies */
2250: int i, j, nhstepm, hstepm, h, nstepm, k, cptj;
2251: double age, agelim, hf;
2252: double ***p3mat,***varhe;
2253: double **dnewm,**doldm;
2254: double *xp;
2255: double **gp, **gm;
2256: double ***gradg, ***trgradg;
2257: int theta;
2258:
2259: varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage);
2260: xp=vector(1,npar);
2261: dnewm=matrix(1,nlstate*nlstate,1,npar);
2262: doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate);
2263:
2264: fprintf(ficreseij,"# Health expectancies\n");
2265: fprintf(ficreseij,"# Age");
2266: for(i=1; i<=nlstate;i++)
2267: for(j=1; j<=nlstate;j++)
2268: fprintf(ficreseij," %1d-%1d (SE)",i,j);
2269: fprintf(ficreseij,"\n");
2270:
2271: if(estepm < stepm){
2272: printf ("Problem %d lower than %d\n",estepm, stepm);
2273: }
2274: else hstepm=estepm;
2275: /* We compute the life expectancy from trapezoids spaced every estepm months
2276: * This is mainly to measure the difference between two models: for example
2277: * if stepm=24 months pijx are given only every 2 years and by summing them
2278: * we are calculating an estimate of the Life Expectancy assuming a linear
2279: * progression in between and thus overestimating or underestimating according
2280: * to the curvature of the survival function. If, for the same date, we
2281: * estimate the model with stepm=1 month, we can keep estepm to 24 months
2282: * to compare the new estimate of Life expectancy with the same linear
2283: * hypothesis. A more precise result, taking into account a more precise
2284: * curvature will be obtained if estepm is as small as stepm. */
2285:
2286: /* For example we decided to compute the life expectancy with the smallest unit */
2287: /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
2288: nhstepm is the number of hstepm from age to agelim
2289: nstepm is the number of stepm from age to agelin.
2290: Look at hpijx to understand the reason of that which relies in memory size
2291: and note for a fixed period like estepm months */
2292: /* We decided (b) to get a life expectancy respecting the most precise curvature of the
2293: survival function given by stepm (the optimization length). Unfortunately it
2294: means that if the survival funtion is printed only each two years of age and if
2295: you sum them up and add 1 year (area under the trapezoids) you won't get the same
2296: results. So we changed our mind and took the option of the best precision.
2297: */
2298: hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
2299:
2300: agelim=AGESUP;
2301: for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
2302: /* nhstepm age range expressed in number of stepm */
2303: nstepm=(int) rint((agelim-age)*YEARM/stepm);
2304: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
2305: /* if (stepm >= YEARM) hstepm=1;*/
2306: nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
2307: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
2308: gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);
2309: gp=matrix(0,nhstepm,1,nlstate*nlstate);
2310: gm=matrix(0,nhstepm,1,nlstate*nlstate);
2311:
2312: /* Computed by stepm unit matrices, product of hstepm matrices, stored
2313: in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
2314: hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);
2315:
2316:
2317: hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
2318:
2319: /* Computing Variances of health expectancies */
2320:
2321: for(theta=1; theta <=npar; theta++){
2322: for(i=1; i<=npar; i++){
2323: xp[i] = x[i] + (i==theta ?delti[theta]:0);
2324: }
2325: hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
2326:
2327: cptj=0;
2328: for(j=1; j<= nlstate; j++){
2329: for(i=1; i<=nlstate; i++){
2330: cptj=cptj+1;
2331: for(h=0, gp[h][cptj]=0.; h<=nhstepm-1; h++){
2332: gp[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;
2333: }
2334: }
2335: }
2336:
2337:
2338: for(i=1; i<=npar; i++)
2339: xp[i] = x[i] - (i==theta ?delti[theta]:0);
2340: hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
2341:
2342: cptj=0;
2343: for(j=1; j<= nlstate; j++){
2344: for(i=1;i<=nlstate;i++){
2345: cptj=cptj+1;
2346: for(h=0, gm[h][cptj]=0.; h<=nhstepm-1; h++){
2347:
2348: gm[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;
2349: }
2350: }
2351: }
2352: for(j=1; j<= nlstate*nlstate; j++)
2353: for(h=0; h<=nhstepm-1; h++){
2354: gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
2355: }
2356: }
2357:
2358: /* End theta */
2359:
2360: trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar);
2361:
2362: for(h=0; h<=nhstepm-1; h++)
2363: for(j=1; j<=nlstate*nlstate;j++)
2364: for(theta=1; theta <=npar; theta++)
2365: trgradg[h][j][theta]=gradg[h][theta][j];
2366:
2367:
2368: for(i=1;i<=nlstate*nlstate;i++)
2369: for(j=1;j<=nlstate*nlstate;j++)
2370: varhe[i][j][(int)age] =0.;
2371:
2372: printf("%d|",(int)age);fflush(stdout);
2373: fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
2374: for(h=0;h<=nhstepm-1;h++){
2375: for(k=0;k<=nhstepm-1;k++){
2376: matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov);
2377: matprod2(doldm,dnewm,1,nlstate*nlstate,1,npar,1,nlstate*nlstate,gradg[k]);
2378: for(i=1;i<=nlstate*nlstate;i++)
2379: for(j=1;j<=nlstate*nlstate;j++)
2380: varhe[i][j][(int)age] += doldm[i][j]*hf*hf;
2381: }
2382: }
2383: /* Computing expectancies */
2384: for(i=1; i<=nlstate;i++)
2385: for(j=1; j<=nlstate;j++)
2386: for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
2387: eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
2388:
2389: /* 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]);*/
2390:
2391: }
2392:
2393: fprintf(ficreseij,"%3.0f",age );
2394: cptj=0;
2395: for(i=1; i<=nlstate;i++)
2396: for(j=1; j<=nlstate;j++){
2397: cptj++;
2398: fprintf(ficreseij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[cptj][cptj][(int)age]) );
2399: }
2400: fprintf(ficreseij,"\n");
2401:
2402: free_matrix(gm,0,nhstepm,1,nlstate*nlstate);
2403: free_matrix(gp,0,nhstepm,1,nlstate*nlstate);
2404: free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*nlstate);
2405: free_ma3x(trgradg,0,nhstepm,1,nlstate*nlstate,1,npar);
2406: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
2407: }
2408: printf("\n");
2409: fprintf(ficlog,"\n");
2410:
2411: free_vector(xp,1,npar);
2412: free_matrix(dnewm,1,nlstate*nlstate,1,npar);
2413: free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate);
2414: free_ma3x(varhe,1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int)fage);
2415: }
2416:
2417: /************ Variance ******************/
2418: 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)
2419: {
2420: /* Variance of health expectancies */
2421: /* double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
2422: /* double **newm;*/
2423: double **dnewm,**doldm;
2424: double **dnewmp,**doldmp;
2425: int i, j, nhstepm, hstepm, h, nstepm ;
2426: int k, cptcode;
2427: double *xp;
2428: double **gp, **gm; /* for var eij */
2429: double ***gradg, ***trgradg; /*for var eij */
2430: double **gradgp, **trgradgp; /* for var p point j */
2431: double *gpp, *gmp; /* for var p point j */
2432: double **varppt; /* for var p point j nlstate to nlstate+ndeath */
2433: double ***p3mat;
2434: double age,agelim, hf;
2435: double ***mobaverage;
2436: int theta;
2437: char digit[4];
2438: char digitp[25];
2439:
2440: char fileresprobmorprev[FILENAMELENGTH];
2441:
2442: if(popbased==1){
2443: if(mobilav!=0)
2444: strcpy(digitp,"-populbased-mobilav-");
2445: else strcpy(digitp,"-populbased-nomobil-");
2446: }
2447: else
2448: strcpy(digitp,"-stablbased-");
2449:
2450: if (mobilav!=0) {
2451: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
2452: if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
2453: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
2454: printf(" Error in movingaverage mobilav=%d\n",mobilav);
2455: }
2456: }
2457:
2458: strcpy(fileresprobmorprev,"prmorprev");
2459: sprintf(digit,"%-d",ij);
2460: /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
2461: strcat(fileresprobmorprev,digit); /* Tvar to be done */
2462: strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
2463: strcat(fileresprobmorprev,fileres);
2464: if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
2465: printf("Problem with resultfile: %s\n", fileresprobmorprev);
2466: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
2467: }
2468: printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
2469: fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
2470: 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);
2471: fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
2472: for(j=nlstate+1; j<=(nlstate+ndeath);j++){
2473: fprintf(ficresprobmorprev," p.%-d SE",j);
2474: for(i=1; i<=nlstate;i++)
2475: fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
2476: }
2477: fprintf(ficresprobmorprev,"\n");
2478: fprintf(ficgp,"\n# Routine varevsij");
2479: 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");
2480: fprintf(fichtm,"\n<br>%s <br>\n",digitp);
2481: /* } */
2482: varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
2483:
2484: 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");
2485: fprintf(ficresvij,"# Age");
2486: for(i=1; i<=nlstate;i++)
2487: for(j=1; j<=nlstate;j++)
2488: fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);
2489: fprintf(ficresvij,"\n");
2490:
2491: xp=vector(1,npar);
2492: dnewm=matrix(1,nlstate,1,npar);
2493: doldm=matrix(1,nlstate,1,nlstate);
2494: dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
2495: doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
2496:
2497: gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
2498: gpp=vector(nlstate+1,nlstate+ndeath);
2499: gmp=vector(nlstate+1,nlstate+ndeath);
2500: trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
2501:
2502: if(estepm < stepm){
2503: printf ("Problem %d lower than %d\n",estepm, stepm);
2504: }
2505: else hstepm=estepm;
2506: /* For example we decided to compute the life expectancy with the smallest unit */
2507: /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
2508: nhstepm is the number of hstepm from age to agelim
2509: nstepm is the number of stepm from age to agelin.
2510: Look at hpijx to understand the reason of that which relies in memory size
2511: and note for a fixed period like k years */
2512: /* We decided (b) to get a life expectancy respecting the most precise curvature of the
2513: survival function given by stepm (the optimization length). Unfortunately it
2514: means that if the survival funtion is printed every two years of age and if
2515: you sum them up and add 1 year (area under the trapezoids) you won't get the same
2516: results. So we changed our mind and took the option of the best precision.
2517: */
2518: hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
2519: agelim = AGESUP;
2520: for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
2521: nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
2522: nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
2523: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
2524: gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
2525: gp=matrix(0,nhstepm,1,nlstate);
2526: gm=matrix(0,nhstepm,1,nlstate);
2527:
2528:
2529: for(theta=1; theta <=npar; theta++){
2530: for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
2531: xp[i] = x[i] + (i==theta ?delti[theta]:0);
2532: }
2533: hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
2534: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
2535:
2536: if (popbased==1) {
2537: if(mobilav ==0){
2538: for(i=1; i<=nlstate;i++)
2539: prlim[i][i]=probs[(int)age][i][ij];
2540: }else{ /* mobilav */
2541: for(i=1; i<=nlstate;i++)
2542: prlim[i][i]=mobaverage[(int)age][i][ij];
2543: }
2544: }
2545:
2546: for(j=1; j<= nlstate; j++){
2547: for(h=0; h<=nhstepm; h++){
2548: for(i=1, gp[h][j]=0.;i<=nlstate;i++)
2549: gp[h][j] += prlim[i][i]*p3mat[i][j][h];
2550: }
2551: }
2552: /* This for computing probability of death (h=1 means
2553: computed over hstepm matrices product = hstepm*stepm months)
2554: as a weighted average of prlim.
2555: */
2556: for(j=nlstate+1;j<=nlstate+ndeath;j++){
2557: for(i=1,gpp[j]=0.; i<= nlstate; i++)
2558: gpp[j] += prlim[i][i]*p3mat[i][j][1];
2559: }
2560: /* end probability of death */
2561:
2562: for(i=1; i<=npar; i++) /* Computes gradient x - delta */
2563: xp[i] = x[i] - (i==theta ?delti[theta]:0);
2564: hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
2565: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
2566:
2567: if (popbased==1) {
2568: if(mobilav ==0){
2569: for(i=1; i<=nlstate;i++)
2570: prlim[i][i]=probs[(int)age][i][ij];
2571: }else{ /* mobilav */
2572: for(i=1; i<=nlstate;i++)
2573: prlim[i][i]=mobaverage[(int)age][i][ij];
2574: }
2575: }
2576:
2577: for(j=1; j<= nlstate; j++){
2578: for(h=0; h<=nhstepm; h++){
2579: for(i=1, gm[h][j]=0.;i<=nlstate;i++)
2580: gm[h][j] += prlim[i][i]*p3mat[i][j][h];
2581: }
2582: }
2583: /* This for computing probability of death (h=1 means
2584: computed over hstepm matrices product = hstepm*stepm months)
2585: as a weighted average of prlim.
2586: */
2587: for(j=nlstate+1;j<=nlstate+ndeath;j++){
2588: for(i=1,gmp[j]=0.; i<= nlstate; i++)
2589: gmp[j] += prlim[i][i]*p3mat[i][j][1];
2590: }
2591: /* end probability of death */
2592:
2593: for(j=1; j<= nlstate; j++) /* vareij */
2594: for(h=0; h<=nhstepm; h++){
2595: gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
2596: }
2597:
2598: for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
2599: gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
2600: }
2601:
2602: } /* End theta */
2603:
2604: trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
2605:
2606: for(h=0; h<=nhstepm; h++) /* veij */
2607: for(j=1; j<=nlstate;j++)
2608: for(theta=1; theta <=npar; theta++)
2609: trgradg[h][j][theta]=gradg[h][theta][j];
2610:
2611: for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
2612: for(theta=1; theta <=npar; theta++)
2613: trgradgp[j][theta]=gradgp[theta][j];
2614:
2615:
2616: hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
2617: for(i=1;i<=nlstate;i++)
2618: for(j=1;j<=nlstate;j++)
2619: vareij[i][j][(int)age] =0.;
2620:
2621: for(h=0;h<=nhstepm;h++){
2622: for(k=0;k<=nhstepm;k++){
2623: matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
2624: matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
2625: for(i=1;i<=nlstate;i++)
2626: for(j=1;j<=nlstate;j++)
2627: vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
2628: }
2629: }
2630:
2631: /* pptj */
2632: matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
2633: matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
2634: for(j=nlstate+1;j<=nlstate+ndeath;j++)
2635: for(i=nlstate+1;i<=nlstate+ndeath;i++)
2636: varppt[j][i]=doldmp[j][i];
2637: /* end ppptj */
2638: /* x centered again */
2639: hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);
2640: prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);
2641:
2642: if (popbased==1) {
2643: if(mobilav ==0){
2644: for(i=1; i<=nlstate;i++)
2645: prlim[i][i]=probs[(int)age][i][ij];
2646: }else{ /* mobilav */
2647: for(i=1; i<=nlstate;i++)
2648: prlim[i][i]=mobaverage[(int)age][i][ij];
2649: }
2650: }
2651:
2652: /* This for computing probability of death (h=1 means
2653: computed over hstepm (estepm) matrices product = hstepm*stepm months)
2654: as a weighted average of prlim.
2655: */
2656: for(j=nlstate+1;j<=nlstate+ndeath;j++){
2657: for(i=1,gmp[j]=0.;i<= nlstate; i++)
2658: gmp[j] += prlim[i][i]*p3mat[i][j][1];
2659: }
2660: /* end probability of death */
2661:
2662: fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
2663: for(j=nlstate+1; j<=(nlstate+ndeath);j++){
2664: fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
2665: for(i=1; i<=nlstate;i++){
2666: fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
2667: }
2668: }
2669: fprintf(ficresprobmorprev,"\n");
2670:
2671: fprintf(ficresvij,"%.0f ",age );
2672: for(i=1; i<=nlstate;i++)
2673: for(j=1; j<=nlstate;j++){
2674: fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
2675: }
2676: fprintf(ficresvij,"\n");
2677: free_matrix(gp,0,nhstepm,1,nlstate);
2678: free_matrix(gm,0,nhstepm,1,nlstate);
2679: free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
2680: free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
2681: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
2682: } /* End age */
2683: free_vector(gpp,nlstate+1,nlstate+ndeath);
2684: free_vector(gmp,nlstate+1,nlstate+ndeath);
2685: free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
2686: free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
2687: fprintf(ficgp,"\nset noparametric;set nolabel; set ter png small;set size 0.65, 0.65");
2688: /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */
2689: fprintf(ficgp,"\n set log y; set nolog x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
2690: /* fprintf(ficgp,"\n plot \"%s\" u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm); */
2691: /* fprintf(ficgp,"\n replot \"%s\" u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm); */
2692: /* fprintf(ficgp,"\n replot \"%s\" u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm); */
2693: fprintf(ficgp,"\n plot \"%s\" u 1:($3) not w l 1 ",subdirf(fileresprobmorprev));
2694: fprintf(ficgp,"\n replot \"%s\" u 1:(($3+1.96*$4)) t \"95\%% interval\" w l 2 ",subdirf(fileresprobmorprev));
2695: fprintf(ficgp,"\n replot \"%s\" u 1:(($3-1.96*$4)) not w l 2 ",subdirf(fileresprobmorprev));
2696: fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",subdirf(fileresprobmorprev),subdirf(fileresprobmorprev));
2697: 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);
2698: /* 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);
2699: */
2700: /* fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.png\";replot;",digitp,optionfilefiname,digit); */
2701: fprintf(ficgp,"\nset out \"%s%s.png\";replot;\n",subdirf3(optionfilefiname,"varmuptjgr",digitp),digit);
2702:
2703: free_vector(xp,1,npar);
2704: free_matrix(doldm,1,nlstate,1,nlstate);
2705: free_matrix(dnewm,1,nlstate,1,npar);
2706: free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
2707: free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
2708: free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
2709: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
2710: fclose(ficresprobmorprev);
2711: fflush(ficgp);
2712: fflush(fichtm);
2713: } /* end varevsij */
2714:
2715: /************ Variance of prevlim ******************/
2716: 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)
2717: {
2718: /* Variance of prevalence limit */
2719: /* double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
2720: double **newm;
2721: double **dnewm,**doldm;
2722: int i, j, nhstepm, hstepm;
2723: int k, cptcode;
2724: double *xp;
2725: double *gp, *gm;
2726: double **gradg, **trgradg;
2727: double age,agelim;
2728: int theta;
2729:
2730: fprintf(ficresvpl,"# Standard deviation of stable prevalences \n");
2731: fprintf(ficresvpl,"# Age");
2732: for(i=1; i<=nlstate;i++)
2733: fprintf(ficresvpl," %1d-%1d",i,i);
2734: fprintf(ficresvpl,"\n");
2735:
2736: xp=vector(1,npar);
2737: dnewm=matrix(1,nlstate,1,npar);
2738: doldm=matrix(1,nlstate,1,nlstate);
2739:
2740: hstepm=1*YEARM; /* Every year of age */
2741: hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */
2742: agelim = AGESUP;
2743: for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
2744: nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
2745: if (stepm >= YEARM) hstepm=1;
2746: nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
2747: gradg=matrix(1,npar,1,nlstate);
2748: gp=vector(1,nlstate);
2749: gm=vector(1,nlstate);
2750:
2751: for(theta=1; theta <=npar; theta++){
2752: for(i=1; i<=npar; i++){ /* Computes gradient */
2753: xp[i] = x[i] + (i==theta ?delti[theta]:0);
2754: }
2755: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
2756: for(i=1;i<=nlstate;i++)
2757: gp[i] = prlim[i][i];
2758:
2759: for(i=1; i<=npar; i++) /* Computes gradient */
2760: xp[i] = x[i] - (i==theta ?delti[theta]:0);
2761: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
2762: for(i=1;i<=nlstate;i++)
2763: gm[i] = prlim[i][i];
2764:
2765: for(i=1;i<=nlstate;i++)
2766: gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
2767: } /* End theta */
2768:
2769: trgradg =matrix(1,nlstate,1,npar);
2770:
2771: for(j=1; j<=nlstate;j++)
2772: for(theta=1; theta <=npar; theta++)
2773: trgradg[j][theta]=gradg[theta][j];
2774:
2775: for(i=1;i<=nlstate;i++)
2776: varpl[i][(int)age] =0.;
2777: matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
2778: matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
2779: for(i=1;i<=nlstate;i++)
2780: varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
2781:
2782: fprintf(ficresvpl,"%.0f ",age );
2783: for(i=1; i<=nlstate;i++)
2784: fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
2785: fprintf(ficresvpl,"\n");
2786: free_vector(gp,1,nlstate);
2787: free_vector(gm,1,nlstate);
2788: free_matrix(gradg,1,npar,1,nlstate);
2789: free_matrix(trgradg,1,nlstate,1,npar);
2790: } /* End age */
2791:
2792: free_vector(xp,1,npar);
2793: free_matrix(doldm,1,nlstate,1,npar);
2794: free_matrix(dnewm,1,nlstate,1,nlstate);
2795:
2796: }
2797:
2798: /************ Variance of one-step probabilities ******************/
2799: void varprob(char optionfilefiname[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij, int *Tvar, int **nbcode, int *ncodemax)
2800: {
2801: int i, j=0, i1, k1, l1, t, tj;
2802: int k2, l2, j1, z1;
2803: int k=0,l, cptcode;
2804: int first=1, first1;
2805: double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
2806: double **dnewm,**doldm;
2807: double *xp;
2808: double *gp, *gm;
2809: double **gradg, **trgradg;
2810: double **mu;
2811: double age,agelim, cov[NCOVMAX];
2812: double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
2813: int theta;
2814: char fileresprob[FILENAMELENGTH];
2815: char fileresprobcov[FILENAMELENGTH];
2816: char fileresprobcor[FILENAMELENGTH];
2817:
2818: double ***varpij;
2819:
2820: strcpy(fileresprob,"prob");
2821: strcat(fileresprob,fileres);
2822: if((ficresprob=fopen(fileresprob,"w"))==NULL) {
2823: printf("Problem with resultfile: %s\n", fileresprob);
2824: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
2825: }
2826: strcpy(fileresprobcov,"probcov");
2827: strcat(fileresprobcov,fileres);
2828: if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
2829: printf("Problem with resultfile: %s\n", fileresprobcov);
2830: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
2831: }
2832: strcpy(fileresprobcor,"probcor");
2833: strcat(fileresprobcor,fileres);
2834: if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
2835: printf("Problem with resultfile: %s\n", fileresprobcor);
2836: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
2837: }
2838: printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
2839: fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
2840: printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
2841: fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
2842: printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
2843: fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
2844:
2845: fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
2846: fprintf(ficresprob,"# Age");
2847: fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
2848: fprintf(ficresprobcov,"# Age");
2849: fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
2850: fprintf(ficresprobcov,"# Age");
2851:
2852:
2853: for(i=1; i<=nlstate;i++)
2854: for(j=1; j<=(nlstate+ndeath);j++){
2855: fprintf(ficresprob," p%1d-%1d (SE)",i,j);
2856: fprintf(ficresprobcov," p%1d-%1d ",i,j);
2857: fprintf(ficresprobcor," p%1d-%1d ",i,j);
2858: }
2859: /* fprintf(ficresprob,"\n");
2860: fprintf(ficresprobcov,"\n");
2861: fprintf(ficresprobcor,"\n");
2862: */
2863: xp=vector(1,npar);
2864: dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
2865: doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
2866: mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
2867: varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
2868: first=1;
2869: fprintf(ficgp,"\n# Routine varprob");
2870: fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
2871: fprintf(fichtm,"\n");
2872:
2873: fprintf(fichtm,"\n<li><h4> <a href=\"%s\">Computing matrix of variance-covariance of step probabilities</a></h4></li>\n",optionfilehtmcov);
2874: fprintf(fichtmcov,"\n<h4>Computing matrix of variance-covariance of step probabilities</h4>\n\
2875: file %s<br>\n",optionfilehtmcov);
2876: fprintf(fichtmcov,"\nEllipsoids of confidence centered on point (p<inf>ij</inf>, p<inf>kl</inf>) are estimated\
2877: and drawn. It helps understanding how is the covariance between two incidences.\
2878: They are expressed in year<sup>-1</sup> in order to be less dependent of stepm.<br>\n");
2879: 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. \
2880: It can be understood this way: if pij and pkl where uncorrelated the (2x2) matrix of covariance \
2881: would have been (1/(var pij), 0 , 0, 1/(var pkl)), and the confidence interval would be 2 \
2882: standard deviations wide on each axis. <br>\
2883: Now, if both incidences are correlated (usual case) we diagonalised the inverse of the covariance matrix\
2884: and made the appropriate rotation to look at the uncorrelated principal directions.<br>\
2885: To be simple, these graphs help to understand the significativity of each parameter in relation to a second other one.<br> \n");
2886:
2887: cov[1]=1;
2888: tj=cptcoveff;
2889: if (cptcovn<1) {tj=1;ncodemax[1]=1;}
2890: j1=0;
2891: for(t=1; t<=tj;t++){
2892: for(i1=1; i1<=ncodemax[t];i1++){
2893: j1++;
2894: if (cptcovn>0) {
2895: fprintf(ficresprob, "\n#********** Variable ");
2896: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
2897: fprintf(ficresprob, "**********\n#\n");
2898: fprintf(ficresprobcov, "\n#********** Variable ");
2899: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
2900: fprintf(ficresprobcov, "**********\n#\n");
2901:
2902: fprintf(ficgp, "\n#********** Variable ");
2903: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
2904: fprintf(ficgp, "**********\n#\n");
2905:
2906:
2907: fprintf(fichtm, "\n<hr size=\"2\" color=\"#EC5E5E\">********** Variable ");
2908: for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
2909: fprintf(fichtm, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
2910:
2911: fprintf(ficresprobcor, "\n#********** Variable ");
2912: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
2913: fprintf(ficresprobcor, "**********\n#");
2914: }
2915:
2916: for (age=bage; age<=fage; age ++){
2917: cov[2]=age;
2918: for (k=1; k<=cptcovn;k++) {
2919: cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];
2920: }
2921: for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
2922: for (k=1; k<=cptcovprod;k++)
2923: cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
2924:
2925: gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
2926: trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
2927: gp=vector(1,(nlstate)*(nlstate+ndeath));
2928: gm=vector(1,(nlstate)*(nlstate+ndeath));
2929:
2930: for(theta=1; theta <=npar; theta++){
2931: for(i=1; i<=npar; i++)
2932: xp[i] = x[i] + (i==theta ?delti[theta]:(double)0);
2933:
2934: pmij(pmmij,cov,ncovmodel,xp,nlstate);
2935:
2936: k=0;
2937: for(i=1; i<= (nlstate); i++){
2938: for(j=1; j<=(nlstate+ndeath);j++){
2939: k=k+1;
2940: gp[k]=pmmij[i][j];
2941: }
2942: }
2943:
2944: for(i=1; i<=npar; i++)
2945: xp[i] = x[i] - (i==theta ?delti[theta]:(double)0);
2946:
2947: pmij(pmmij,cov,ncovmodel,xp,nlstate);
2948: k=0;
2949: for(i=1; i<=(nlstate); i++){
2950: for(j=1; j<=(nlstate+ndeath);j++){
2951: k=k+1;
2952: gm[k]=pmmij[i][j];
2953: }
2954: }
2955:
2956: for(i=1; i<= (nlstate)*(nlstate+ndeath); i++)
2957: gradg[theta][i]=(gp[i]-gm[i])/(double)2./delti[theta];
2958: }
2959:
2960: for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
2961: for(theta=1; theta <=npar; theta++)
2962: trgradg[j][theta]=gradg[theta][j];
2963:
2964: matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov);
2965: matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);
2966: free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
2967: free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
2968: free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
2969: free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
2970:
2971: pmij(pmmij,cov,ncovmodel,x,nlstate);
2972:
2973: k=0;
2974: for(i=1; i<=(nlstate); i++){
2975: for(j=1; j<=(nlstate+ndeath);j++){
2976: k=k+1;
2977: mu[k][(int) age]=pmmij[i][j];
2978: }
2979: }
2980: for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
2981: for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
2982: varpij[i][j][(int)age] = doldm[i][j];
2983:
2984: /*printf("\n%d ",(int)age);
2985: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
2986: printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
2987: fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
2988: }*/
2989:
2990: fprintf(ficresprob,"\n%d ",(int)age);
2991: fprintf(ficresprobcov,"\n%d ",(int)age);
2992: fprintf(ficresprobcor,"\n%d ",(int)age);
2993:
2994: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)
2995: fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));
2996: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
2997: fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);
2998: fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
2999: }
3000: i=0;
3001: for (k=1; k<=(nlstate);k++){
3002: for (l=1; l<=(nlstate+ndeath);l++){
3003: i=i++;
3004: fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
3005: fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
3006: for (j=1; j<=i;j++){
3007: fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);
3008: fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));
3009: }
3010: }
3011: }/* end of loop for state */
3012: } /* end of loop for age */
3013:
3014: /* Confidence intervalle of pij */
3015: /*
3016: fprintf(ficgp,"\nset noparametric;unset label");
3017: fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");
3018: fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
3019: 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);
3020: fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);
3021: fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);
3022: fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);
3023: */
3024:
3025: /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
3026: first1=1;
3027: for (k2=1; k2<=(nlstate);k2++){
3028: for (l2=1; l2<=(nlstate+ndeath);l2++){
3029: if(l2==k2) continue;
3030: j=(k2-1)*(nlstate+ndeath)+l2;
3031: for (k1=1; k1<=(nlstate);k1++){
3032: for (l1=1; l1<=(nlstate+ndeath);l1++){
3033: if(l1==k1) continue;
3034: i=(k1-1)*(nlstate+ndeath)+l1;
3035: if(i<=j) continue;
3036: for (age=bage; age<=fage; age ++){
3037: if ((int)age %5==0){
3038: v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;
3039: v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;
3040: cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;
3041: mu1=mu[i][(int) age]/stepm*YEARM ;
3042: mu2=mu[j][(int) age]/stepm*YEARM;
3043: c12=cv12/sqrt(v1*v2);
3044: /* Computing eigen value of matrix of covariance */
3045: lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
3046: lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
3047: /* Eigen vectors */
3048: v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
3049: /*v21=sqrt(1.-v11*v11); *//* error */
3050: v21=(lc1-v1)/cv12*v11;
3051: v12=-v21;
3052: v22=v11;
3053: tnalp=v21/v11;
3054: if(first1==1){
3055: first1=0;
3056: 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);
3057: }
3058: 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);
3059: /*printf(fignu*/
3060: /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */
3061: /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */
3062: if(first==1){
3063: first=0;
3064: fprintf(ficgp,"\nset parametric;unset label");
3065: 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);
3066: fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
3067: fprintf(fichtmcov,"\n<br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup>\
3068: :<a href=\"%s%d%1d%1d-%1d%1d.png\">\
3069: %s%d%1d%1d-%1d%1d.png</A>, ",k1,l1,k2,l2,\
3070: subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2,\
3071: subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
3072: fprintf(fichtmcov,"\n<br><img src=\"%s%d%1d%1d-%1d%1d.png\"> ",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
3073: fprintf(fichtmcov,"\n<br> Correlation at age %d (%.3f),",(int) age, c12);
3074: fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\"",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
3075: fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
3076: fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
3077: 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",\
3078: mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
3079: mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
3080: }else{
3081: first=0;
3082: fprintf(fichtmcov," %d (%.3f),",(int) age, c12);
3083: fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
3084: fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
3085: 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",\
3086: mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
3087: mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
3088: }/* if first */
3089: } /* age mod 5 */
3090: } /* end loop age */
3091: fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\";replot;",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
3092: first=1;
3093: } /*l12 */
3094: } /* k12 */
3095: } /*l1 */
3096: }/* k1 */
3097: } /* loop covariates */
3098: }
3099: free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
3100: free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
3101: free_vector(xp,1,npar);
3102: fclose(ficresprob);
3103: fclose(ficresprobcov);
3104: fclose(ficresprobcor);
3105: fflush(ficgp);
3106: fflush(fichtmcov);
3107: }
3108:
3109:
3110: /******************* Printing html file ***********/
3111: void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \
3112: int lastpass, int stepm, int weightopt, char model[],\
3113: int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
3114: int popforecast, int estepm ,\
3115: double jprev1, double mprev1,double anprev1, \
3116: double jprev2, double mprev2,double anprev2){
3117: int jj1, k1, i1, cpt;
3118: /*char optionfilehtm[FILENAMELENGTH];*/
3119: /* if((fichtm=fopen(optionfilehtm,"a"))==NULL) { */
3120: /* printf("Problem with %s \n",optionfilehtm), exit(0); */
3121: /* fprintf(ficlog,"Problem with %s \n",optionfilehtm), exit(0); */
3122: /* } */
3123:
3124: fprintf(fichtm,"<ul><li><h4>Result files (first order: no variance)</h4>\n \
3125: - Observed prevalence in each state (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"%s\">%s</a> <br>\n \
3126: - Estimated transition probabilities over %d (stepm) months: <a href=\"%s\">%s</a><br>\n \
3127: - Stable prevalence in each health state: <a href=\"%s\">%s</a> <br>\n \
3128: - Life expectancies by age and initial health status (estepm=%2d months): \
3129: <a href=\"%s\">%s</a> <br>\n</li>", \
3130: jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirf2(fileres,"p"),subdirf2(fileres,"p"),\
3131: stepm,subdirf2(fileres,"pij"),subdirf2(fileres,"pij"),\
3132: subdirf2(fileres,"pl"),subdirf2(fileres,"pl"),\
3133: estepm,subdirf2(fileres,"e"),subdirf2(fileres,"e"));
3134:
3135: fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
3136:
3137: m=cptcoveff;
3138: if (cptcovn < 1) {m=1;ncodemax[1]=1;}
3139:
3140: jj1=0;
3141: for(k1=1; k1<=m;k1++){
3142: for(i1=1; i1<=ncodemax[k1];i1++){
3143: jj1++;
3144: if (cptcovn > 0) {
3145: fprintf(fichtm,"<hr size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
3146: for (cpt=1; cpt<=cptcoveff;cpt++)
3147: fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
3148: fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
3149: }
3150: /* Pij */
3151: 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> \
3152: <img src=\"%s%d1.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);
3153: /* Quasi-incidences */
3154: fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months\
3155: before but expressed in per year i.e. quasi incidences if stepm is small and probabilities too: %s%d2.png<br> \
3156: <img src=\"%s%d2.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);
3157: /* Stable prevalence in each health state */
3158: for(cpt=1; cpt<nlstate;cpt++){
3159: fprintf(fichtm,"<br>- Stable prevalence in each health state : p%s%d%d.png<br> \
3160: <img src=\"%s%d%d.png\">",subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1);
3161: }
3162: for(cpt=1; cpt<=nlstate;cpt++) {
3163: fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): %s%d%d.png <br> \
3164: <img src=\"%s%d%d.png\">",cpt,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1);
3165: }
3166: fprintf(fichtm,"\n<br>- Total life expectancy by age and \
3167: health expectancies in states (1) and (2): %s%d.png<br>\
3168: <img src=\"%s%d.png\">",subdirf2(optionfilefiname,"e"),jj1,subdirf2(optionfilefiname,"e"),jj1);
3169: } /* end i1 */
3170: }/* End k1 */
3171: fprintf(fichtm,"</ul>");
3172:
3173:
3174: fprintf(fichtm,"\n<br><li><h4> Result files (second order: variances)</h4>\n\
3175: - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n\
3176: - Variance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n\
3177: - Variance-covariance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n\
3178: - Correlation matrix of one-step probabilities: <a href=\"%s\">%s</a> <br>\n\
3179: - Variances and covariances of life expectancies by age and initial health status (estepm=%d months): <a href=\"%s\">%s</a><br>\n\
3180: - Health expectancies with their variances (no covariance): <a href=\"%s\">%s</a> <br>\n\
3181: - Standard deviation of stable prevalences: <a href=\"%s\">%s</a> <br>\n",\
3182: rfileres,rfileres,\
3183: subdirf2(fileres,"prob"),subdirf2(fileres,"prob"),\
3184: subdirf2(fileres,"probcov"),subdirf2(fileres,"probcov"),\
3185: subdirf2(fileres,"probcor"),subdirf2(fileres,"probcor"),\
3186: estepm, subdirf2(fileres,"v"),subdirf2(fileres,"v"),\
3187: subdirf2(fileres,"t"),subdirf2(fileres,"t"),\
3188: subdirf2(fileres,"vpl"),subdirf2(fileres,"vpl"));
3189:
3190: /* if(popforecast==1) fprintf(fichtm,"\n */
3191: /* - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n */
3192: /* - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n */
3193: /* <br>",fileres,fileres,fileres,fileres); */
3194: /* else */
3195: /* 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); */
3196: fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
3197:
3198: m=cptcoveff;
3199: if (cptcovn < 1) {m=1;ncodemax[1]=1;}
3200:
3201: jj1=0;
3202: for(k1=1; k1<=m;k1++){
3203: for(i1=1; i1<=ncodemax[k1];i1++){
3204: jj1++;
3205: if (cptcovn > 0) {
3206: fprintf(fichtm,"<hr size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
3207: for (cpt=1; cpt<=cptcoveff;cpt++)
3208: fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
3209: fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
3210: }
3211: for(cpt=1; cpt<=nlstate;cpt++) {
3212: fprintf(fichtm,"<br>- Observed and period prevalence (with confident\
3213: interval) in state (%d): %s%d%d.png <br>\
3214: <img src=\"%s%d%d.png\">",cpt,subdirf2(optionfilefiname,"v"),cpt,jj1,subdirf2(optionfilefiname,"v"),cpt,jj1);
3215: }
3216: } /* end i1 */
3217: }/* End k1 */
3218: fprintf(fichtm,"</ul>");
3219: fflush(fichtm);
3220: }
3221:
3222: /******************* Gnuplot file **************/
3223: void printinggnuplot(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
3224:
3225: char dirfileres[132],optfileres[132];
3226: int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;
3227: int ng;
3228: /* if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) { */
3229: /* printf("Problem with file %s",optionfilegnuplot); */
3230: /* fprintf(ficlog,"Problem with file %s",optionfilegnuplot); */
3231: /* } */
3232:
3233: /*#ifdef windows */
3234: fprintf(ficgp,"cd \"%s\" \n",pathc);
3235: /*#endif */
3236: m=pow(2,cptcoveff);
3237:
3238: strcpy(dirfileres,optionfilefiname);
3239: strcpy(optfileres,"vpl");
3240: /* 1eme*/
3241: for (cpt=1; cpt<= nlstate ; cpt ++) {
3242: for (k1=1; k1<= m ; k1 ++) {
3243: fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"v"),cpt,k1);
3244: fprintf(ficgp,"\n#set out \"v%s%d%d.png\" \n",optionfilefiname,cpt,k1);
3245: fprintf(ficgp,"set xlabel \"Age\" \n\
3246: set ylabel \"Probability\" \n\
3247: set ter png small\n\
3248: set size 0.65,0.65\n\
3249: plot [%.f:%.f] \"%s\" every :::%d::%d u 1:2 \"\%%lf",ageminpar,fage,subdirf2(fileres,"vpl"),k1-1,k1-1);
3250:
3251: for (i=1; i<= nlstate ; i ++) {
3252: if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
3253: else fprintf(ficgp," \%%*lf (\%%*lf)");
3254: }
3255: 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);
3256: for (i=1; i<= nlstate ; i ++) {
3257: if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
3258: else fprintf(ficgp," \%%*lf (\%%*lf)");
3259: }
3260: fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"%s\" every :::%d::%d u 1:($2-1.96*$3) \"\%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1);
3261: for (i=1; i<= nlstate ; i ++) {
3262: if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
3263: else fprintf(ficgp," \%%*lf (\%%*lf)");
3264: }
3265: fprintf(ficgp,"\" t\"\" w l 1,\"%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",subdirf2(fileres,"p"),k1-1,k1-1,2+4*(cpt-1));
3266: }
3267: }
3268: /*2 eme*/
3269:
3270: for (k1=1; k1<= m ; k1 ++) {
3271: fprintf(ficgp,"\nset out \"%s%d.png\" \n",subdirf2(optionfilefiname,"e"),k1);
3272: fprintf(ficgp,"set ylabel \"Years\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] ",ageminpar,fage);
3273:
3274: for (i=1; i<= nlstate+1 ; i ++) {
3275: k=2*i;
3276: fprintf(ficgp,"\"%s\" every :::%d::%d u 1:2 \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
3277: for (j=1; j<= nlstate+1 ; j ++) {
3278: if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
3279: else fprintf(ficgp," \%%*lf (\%%*lf)");
3280: }
3281: if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");
3282: else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);
3283: fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
3284: for (j=1; j<= nlstate+1 ; j ++) {
3285: if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
3286: else fprintf(ficgp," \%%*lf (\%%*lf)");
3287: }
3288: fprintf(ficgp,"\" t\"\" w l 0,");
3289: fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
3290: for (j=1; j<= nlstate+1 ; j ++) {
3291: if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
3292: else fprintf(ficgp," \%%*lf (\%%*lf)");
3293: }
3294: if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");
3295: else fprintf(ficgp,"\" t\"\" w l 0,");
3296: }
3297: }
3298:
3299: /*3eme*/
3300:
3301: for (k1=1; k1<= m ; k1 ++) {
3302: for (cpt=1; cpt<= nlstate ; cpt ++) {
3303: k=2+nlstate*(2*cpt-2);
3304: fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"exp"),cpt,k1);
3305: fprintf(ficgp,"set ter png small\n\
3306: set size 0.65,0.65\n\
3307: plot [%.f:%.f] \"%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,subdirf2(fileres,"e"),k1-1,k1-1,k,cpt);
3308: /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
3309: for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
3310: fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
3311: fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
3312: for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
3313: fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
3314:
3315: */
3316: for (i=1; i< nlstate ; i ++) {
3317: 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);
3318:
3319: }
3320: }
3321: }
3322:
3323: /* CV preval stable (period) */
3324: for (k1=1; k1<= m ; k1 ++) {
3325: for (cpt=1; cpt<=nlstate ; cpt ++) {
3326: k=3;
3327: fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"p"),cpt,k1);
3328: fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\
3329: set ter png small\nset size 0.65,0.65\n\
3330: unset log y\n\
3331: plot [%.f:%.f] \"%s\" u ($1==%d ? ($3):1/0):($%d/($%d",ageminpar,agemaxpar,subdirf2(fileres,"pij"),k1,k+cpt+1,k+1);
3332:
3333: for (i=1; i< nlstate ; i ++)
3334: fprintf(ficgp,"+$%d",k+i+1);
3335: fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);
3336:
3337: l=3+(nlstate+ndeath)*cpt;
3338: fprintf(ficgp,",\"%s\" u ($1==%d ? ($3):1/0):($%d/($%d",subdirf2(fileres,"pij"),k1,l+cpt+1,l+1);
3339: for (i=1; i< nlstate ; i ++) {
3340: l=3+(nlstate+ndeath)*cpt;
3341: fprintf(ficgp,"+$%d",l+i+1);
3342: }
3343: fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);
3344: }
3345: }
3346:
3347: /* proba elementaires */
3348: for(i=1,jk=1; i <=nlstate; i++){
3349: for(k=1; k <=(nlstate+ndeath); k++){
3350: if (k != i) {
3351: for(j=1; j <=ncovmodel; j++){
3352: fprintf(ficgp,"p%d=%f ",jk,p[jk]);
3353: jk++;
3354: fprintf(ficgp,"\n");
3355: }
3356: }
3357: }
3358: }
3359:
3360: for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/
3361: for(jk=1; jk <=m; jk++) {
3362: fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"pe"),jk,ng);
3363: if (ng==2)
3364: fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
3365: else
3366: fprintf(ficgp,"\nset title \"Probability\"\n");
3367: fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65\nset log y\nplot [%.f:%.f] ",ageminpar,agemaxpar);
3368: i=1;
3369: for(k2=1; k2<=nlstate; k2++) {
3370: k3=i;
3371: for(k=1; k<=(nlstate+ndeath); k++) {
3372: if (k != k2){
3373: if(ng==2)
3374: fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);
3375: else
3376: fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
3377: ij=1;
3378: for(j=3; j <=ncovmodel; j++) {
3379: if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
3380: fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
3381: ij++;
3382: }
3383: else
3384: fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
3385: }
3386: fprintf(ficgp,")/(1");
3387:
3388: for(k1=1; k1 <=nlstate; k1++){
3389: fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);
3390: ij=1;
3391: for(j=3; j <=ncovmodel; j++){
3392: if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
3393: fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
3394: ij++;
3395: }
3396: else
3397: fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
3398: }
3399: fprintf(ficgp,")");
3400: }
3401: fprintf(ficgp,") t \"p%d%d\" ", k2,k);
3402: if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");
3403: i=i+ncovmodel;
3404: }
3405: } /* end k */
3406: } /* end k2 */
3407: } /* end jk */
3408: } /* end ng */
3409: fflush(ficgp);
3410: } /* end gnuplot */
3411:
3412:
3413: /*************** Moving average **************/
3414: int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav){
3415:
3416: int i, cpt, cptcod;
3417: int modcovmax =1;
3418: int mobilavrange, mob;
3419: double age;
3420:
3421: modcovmax=2*cptcoveff;/* Max number of modalities. We suppose
3422: a covariate has 2 modalities */
3423: if (cptcovn<1) modcovmax=1; /* At least 1 pass */
3424:
3425: if(mobilav==1||mobilav ==3 ||mobilav==5 ||mobilav== 7){
3426: if(mobilav==1) mobilavrange=5; /* default */
3427: else mobilavrange=mobilav;
3428: for (age=bage; age<=fage; age++)
3429: for (i=1; i<=nlstate;i++)
3430: for (cptcod=1;cptcod<=modcovmax;cptcod++)
3431: mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
3432: /* We keep the original values on the extreme ages bage, fage and for
3433: fage+1 and bage-1 we use a 3 terms moving average; for fage+2 bage+2
3434: we use a 5 terms etc. until the borders are no more concerned.
3435: */
3436: for (mob=3;mob <=mobilavrange;mob=mob+2){
3437: for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){
3438: for (i=1; i<=nlstate;i++){
3439: for (cptcod=1;cptcod<=modcovmax;cptcod++){
3440: mobaverage[(int)age][i][cptcod] =probs[(int)age][i][cptcod];
3441: for (cpt=1;cpt<=(mob-1)/2;cpt++){
3442: mobaverage[(int)age][i][cptcod] +=probs[(int)age-cpt][i][cptcod];
3443: mobaverage[(int)age][i][cptcod] +=probs[(int)age+cpt][i][cptcod];
3444: }
3445: mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/mob;
3446: }
3447: }
3448: }/* end age */
3449: }/* end mob */
3450: }else return -1;
3451: return 0;
3452: }/* End movingaverage */
3453:
3454:
3455: /************** Forecasting ******************/
3456: 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){
3457: /* proj1, year, month, day of starting projection
3458: agemin, agemax range of age
3459: dateprev1 dateprev2 range of dates during which prevalence is computed
3460: anproj2 year of en of projection (same day and month as proj1).
3461: */
3462: int yearp, stepsize, hstepm, nhstepm, j, k, c, cptcod, i, h, i1;
3463: int *popage;
3464: double agec; /* generic age */
3465: double agelim, ppij, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
3466: double *popeffectif,*popcount;
3467: double ***p3mat;
3468: double ***mobaverage;
3469: char fileresf[FILENAMELENGTH];
3470:
3471: agelim=AGESUP;
3472: prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
3473:
3474: strcpy(fileresf,"f");
3475: strcat(fileresf,fileres);
3476: if((ficresf=fopen(fileresf,"w"))==NULL) {
3477: printf("Problem with forecast resultfile: %s\n", fileresf);
3478: fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);
3479: }
3480: printf("Computing forecasting: result on file '%s' \n", fileresf);
3481: fprintf(ficlog,"Computing forecasting: result on file '%s' \n", fileresf);
3482:
3483: if (cptcoveff==0) ncodemax[cptcoveff]=1;
3484:
3485: if (mobilav!=0) {
3486: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
3487: if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
3488: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
3489: printf(" Error in movingaverage mobilav=%d\n",mobilav);
3490: }
3491: }
3492:
3493: stepsize=(int) (stepm+YEARM-1)/YEARM;
3494: if (stepm<=12) stepsize=1;
3495: if(estepm < stepm){
3496: printf ("Problem %d lower than %d\n",estepm, stepm);
3497: }
3498: else hstepm=estepm;
3499:
3500: hstepm=hstepm/stepm;
3501: yp1=modf(dateintmean,&yp);/* extracts integral of datemean in yp and
3502: fractional in yp1 */
3503: anprojmean=yp;
3504: yp2=modf((yp1*12),&yp);
3505: mprojmean=yp;
3506: yp1=modf((yp2*30.5),&yp);
3507: jprojmean=yp;
3508: if(jprojmean==0) jprojmean=1;
3509: if(mprojmean==0) jprojmean=1;
3510:
3511: i1=cptcoveff;
3512: if (cptcovn < 1){i1=1;}
3513:
3514: fprintf(ficresf,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2);
3515:
3516: fprintf(ficresf,"#****** Routine prevforecast **\n");
3517:
3518: /* if (h==(int)(YEARM*yearp)){ */
3519: for(cptcov=1, k=0;cptcov<=i1;cptcov++){
3520: for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
3521: k=k+1;
3522: fprintf(ficresf,"\n#******");
3523: for(j=1;j<=cptcoveff;j++) {
3524: 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]]);
3525: }
3526: fprintf(ficresf,"******\n");
3527: fprintf(ficresf,"# Covariate valuofcovar yearproj age");
3528: for(j=1; j<=nlstate+ndeath;j++){
3529: for(i=1; i<=nlstate;i++)
3530: fprintf(ficresf," p%d%d",i,j);
3531: fprintf(ficresf," p.%d",j);
3532: }
3533: for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) {
3534: fprintf(ficresf,"\n");
3535: fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+yearp);
3536:
3537: for (agec=fage; agec>=(ageminpar-1); agec--){
3538: nhstepm=(int) rint((agelim-agec)*YEARM/stepm);
3539: nhstepm = nhstepm/hstepm;
3540: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3541: oldm=oldms;savm=savms;
3542: hpxij(p3mat,nhstepm,agec,hstepm,p,nlstate,stepm,oldm,savm, k);
3543:
3544: for (h=0; h<=nhstepm; h++){
3545: if (h*hstepm/YEARM*stepm ==yearp) {
3546: fprintf(ficresf,"\n");
3547: for(j=1;j<=cptcoveff;j++)
3548: fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
3549: fprintf(ficresf,"%.f %.f ",anproj1+yearp,agec+h*hstepm/YEARM*stepm);
3550: }
3551: for(j=1; j<=nlstate+ndeath;j++) {
3552: ppij=0.;
3553: for(i=1; i<=nlstate;i++) {
3554: if (mobilav==1)
3555: ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][i][cptcod];
3556: else {
3557: ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][cptcod];
3558: }
3559: if (h*hstepm/YEARM*stepm== yearp) {
3560: fprintf(ficresf," %.3f", p3mat[i][j][h]);
3561: }
3562: } /* end i */
3563: if (h*hstepm/YEARM*stepm==yearp) {
3564: fprintf(ficresf," %.3f", ppij);
3565: }
3566: }/* end j */
3567: } /* end h */
3568: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3569: } /* end agec */
3570: } /* end yearp */
3571: } /* end cptcod */
3572: } /* end cptcov */
3573:
3574: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
3575:
3576: fclose(ficresf);
3577: }
3578:
3579: /************** Forecasting *****not tested NB*************/
3580: 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){
3581:
3582: int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;
3583: int *popage;
3584: double calagedatem, agelim, kk1, kk2;
3585: double *popeffectif,*popcount;
3586: double ***p3mat,***tabpop,***tabpopprev;
3587: double ***mobaverage;
3588: char filerespop[FILENAMELENGTH];
3589:
3590: tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
3591: tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
3592: agelim=AGESUP;
3593: calagedatem=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;
3594:
3595: prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
3596:
3597:
3598: strcpy(filerespop,"pop");
3599: strcat(filerespop,fileres);
3600: if((ficrespop=fopen(filerespop,"w"))==NULL) {
3601: printf("Problem with forecast resultfile: %s\n", filerespop);
3602: fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop);
3603: }
3604: printf("Computing forecasting: result on file '%s' \n", filerespop);
3605: fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop);
3606:
3607: if (cptcoveff==0) ncodemax[cptcoveff]=1;
3608:
3609: if (mobilav!=0) {
3610: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
3611: if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
3612: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
3613: printf(" Error in movingaverage mobilav=%d\n",mobilav);
3614: }
3615: }
3616:
3617: stepsize=(int) (stepm+YEARM-1)/YEARM;
3618: if (stepm<=12) stepsize=1;
3619:
3620: agelim=AGESUP;
3621:
3622: hstepm=1;
3623: hstepm=hstepm/stepm;
3624:
3625: if (popforecast==1) {
3626: if((ficpop=fopen(popfile,"r"))==NULL) {
3627: printf("Problem with population file : %s\n",popfile);exit(0);
3628: fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0);
3629: }
3630: popage=ivector(0,AGESUP);
3631: popeffectif=vector(0,AGESUP);
3632: popcount=vector(0,AGESUP);
3633:
3634: i=1;
3635: while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;
3636:
3637: imx=i;
3638: for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];
3639: }
3640:
3641: for(cptcov=1,k=0;cptcov<=i2;cptcov++){
3642: for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
3643: k=k+1;
3644: fprintf(ficrespop,"\n#******");
3645: for(j=1;j<=cptcoveff;j++) {
3646: fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
3647: }
3648: fprintf(ficrespop,"******\n");
3649: fprintf(ficrespop,"# Age");
3650: for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);
3651: if (popforecast==1) fprintf(ficrespop," [Population]");
3652:
3653: for (cpt=0; cpt<=0;cpt++) {
3654: fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);
3655:
3656: for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){
3657: nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);
3658: nhstepm = nhstepm/hstepm;
3659:
3660: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3661: oldm=oldms;savm=savms;
3662: hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
3663:
3664: for (h=0; h<=nhstepm; h++){
3665: if (h==(int) (calagedatem+YEARM*cpt)) {
3666: fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
3667: }
3668: for(j=1; j<=nlstate+ndeath;j++) {
3669: kk1=0.;kk2=0;
3670: for(i=1; i<=nlstate;i++) {
3671: if (mobilav==1)
3672: kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];
3673: else {
3674: kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];
3675: }
3676: }
3677: if (h==(int)(calagedatem+12*cpt)){
3678: tabpop[(int)(agedeb)][j][cptcod]=kk1;
3679: /*fprintf(ficrespop," %.3f", kk1);
3680: if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/
3681: }
3682: }
3683: for(i=1; i<=nlstate;i++){
3684: kk1=0.;
3685: for(j=1; j<=nlstate;j++){
3686: kk1= kk1+tabpop[(int)(agedeb)][j][cptcod];
3687: }
3688: tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedatem+12*cpt)*hstepm/YEARM*stepm-1)];
3689: }
3690:
3691: if (h==(int)(calagedatem+12*cpt)) for(j=1; j<=nlstate;j++)
3692: fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);
3693: }
3694: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3695: }
3696: }
3697:
3698: /******/
3699:
3700: for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) {
3701: fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);
3702: for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){
3703: nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);
3704: nhstepm = nhstepm/hstepm;
3705:
3706: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3707: oldm=oldms;savm=savms;
3708: hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
3709: for (h=0; h<=nhstepm; h++){
3710: if (h==(int) (calagedatem+YEARM*cpt)) {
3711: fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
3712: }
3713: for(j=1; j<=nlstate+ndeath;j++) {
3714: kk1=0.;kk2=0;
3715: for(i=1; i<=nlstate;i++) {
3716: kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];
3717: }
3718: if (h==(int)(calagedatem+12*cpt)) fprintf(ficresf," %15.2f", kk1);
3719: }
3720: }
3721: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3722: }
3723: }
3724: }
3725: }
3726:
3727: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
3728:
3729: if (popforecast==1) {
3730: free_ivector(popage,0,AGESUP);
3731: free_vector(popeffectif,0,AGESUP);
3732: free_vector(popcount,0,AGESUP);
3733: }
3734: free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
3735: free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
3736: fclose(ficrespop);
3737: } /* End of popforecast */
3738:
3739: int fileappend(FILE *fichier, char *optionfich)
3740: {
3741: if((fichier=fopen(optionfich,"a"))==NULL) {
3742: printf("Problem with file: %s\n", optionfich);
3743: fprintf(ficlog,"Problem with file: %s\n", optionfich);
3744: return (0);
3745: }
3746: fflush(fichier);
3747: return (1);
3748: }
3749: void prwizard(int ncovmodel, int nlstate, int ndeath, char model[], FILE *ficparo)
3750: {
3751:
3752: char ca[32], cb[32], cc[32];
3753: int i,j, k, l, li, lj, lk, ll, jj, npar, itimes;
3754: int numlinepar;
3755:
3756: printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
3757: fprintf(ficparo,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
3758: for(i=1; i <=nlstate; i++){
3759: jj=0;
3760: for(j=1; j <=nlstate+ndeath; j++){
3761: if(j==i) continue;
3762: jj++;
3763: /*ca[0]= k+'a'-1;ca[1]='\0';*/
3764: printf("%1d%1d",i,j);
3765: fprintf(ficparo,"%1d%1d",i,j);
3766: for(k=1; k<=ncovmodel;k++){
3767: /* printf(" %lf",param[i][j][k]); */
3768: /* fprintf(ficparo," %lf",param[i][j][k]); */
3769: printf(" 0.");
3770: fprintf(ficparo," 0.");
3771: }
3772: printf("\n");
3773: fprintf(ficparo,"\n");
3774: }
3775: }
3776: printf("# Scales (for hessian or gradient estimation)\n");
3777: fprintf(ficparo,"# Scales (for hessian or gradient estimation)\n");
3778: npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/
3779: for(i=1; i <=nlstate; i++){
3780: jj=0;
3781: for(j=1; j <=nlstate+ndeath; j++){
3782: if(j==i) continue;
3783: jj++;
3784: fprintf(ficparo,"%1d%1d",i,j);
3785: printf("%1d%1d",i,j);
3786: fflush(stdout);
3787: for(k=1; k<=ncovmodel;k++){
3788: /* printf(" %le",delti3[i][j][k]); */
3789: /* fprintf(ficparo," %le",delti3[i][j][k]); */
3790: printf(" 0.");
3791: fprintf(ficparo," 0.");
3792: }
3793: numlinepar++;
3794: printf("\n");
3795: fprintf(ficparo,"\n");
3796: }
3797: }
3798: printf("# Covariance matrix\n");
3799: /* # 121 Var(a12)\n\ */
3800: /* # 122 Cov(b12,a12) Var(b12)\n\ */
3801: /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
3802: /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
3803: /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
3804: /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
3805: /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
3806: /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
3807: fflush(stdout);
3808: fprintf(ficparo,"# Covariance matrix\n");
3809: /* # 121 Var(a12)\n\ */
3810: /* # 122 Cov(b12,a12) Var(b12)\n\ */
3811: /* # ...\n\ */
3812: /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
3813:
3814: for(itimes=1;itimes<=2;itimes++){
3815: jj=0;
3816: for(i=1; i <=nlstate; i++){
3817: for(j=1; j <=nlstate+ndeath; j++){
3818: if(j==i) continue;
3819: for(k=1; k<=ncovmodel;k++){
3820: jj++;
3821: ca[0]= k+'a'-1;ca[1]='\0';
3822: if(itimes==1){
3823: printf("#%1d%1d%d",i,j,k);
3824: fprintf(ficparo,"#%1d%1d%d",i,j,k);
3825: }else{
3826: printf("%1d%1d%d",i,j,k);
3827: fprintf(ficparo,"%1d%1d%d",i,j,k);
3828: /* printf(" %.5le",matcov[i][j]); */
3829: }
3830: ll=0;
3831: for(li=1;li <=nlstate; li++){
3832: for(lj=1;lj <=nlstate+ndeath; lj++){
3833: if(lj==li) continue;
3834: for(lk=1;lk<=ncovmodel;lk++){
3835: ll++;
3836: if(ll<=jj){
3837: cb[0]= lk +'a'-1;cb[1]='\0';
3838: if(ll<jj){
3839: if(itimes==1){
3840: printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
3841: fprintf(ficparo," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
3842: }else{
3843: printf(" 0.");
3844: fprintf(ficparo," 0.");
3845: }
3846: }else{
3847: if(itimes==1){
3848: printf(" Var(%s%1d%1d)",ca,i,j);
3849: fprintf(ficparo," Var(%s%1d%1d)",ca,i,j);
3850: }else{
3851: printf(" 0.");
3852: fprintf(ficparo," 0.");
3853: }
3854: }
3855: }
3856: } /* end lk */
3857: } /* end lj */
3858: } /* end li */
3859: printf("\n");
3860: fprintf(ficparo,"\n");
3861: numlinepar++;
3862: } /* end k*/
3863: } /*end j */
3864: } /* end i */
3865: }
3866:
3867: } /* end of prwizard */
3868:
3869:
3870: /***********************************************/
3871: /**************** Main Program *****************/
3872: /***********************************************/
3873:
3874: int main(int argc, char *argv[])
3875: {
3876: int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav);
3877: int i,j, k, n=MAXN,iter,m,size=100,cptcode, cptcod;
3878: int jj, imk;
3879: int numlinepar=0; /* Current linenumber of parameter file */
3880: /* FILE *fichtm; *//* Html File */
3881: /* FILE *ficgp;*/ /*Gnuplot File */
3882: double agedeb, agefin,hf;
3883: double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;
3884:
3885: double fret;
3886: double **xi,tmp,delta;
3887:
3888: double dum; /* Dummy variable */
3889: double ***p3mat;
3890: double ***mobaverage;
3891: int *indx;
3892: char line[MAXLINE], linepar[MAXLINE];
3893: char path[MAXLINE],pathc[MAXLINE],pathcd[MAXLINE],pathtot[MAXLINE],model[MAXLINE];
3894: char pathr[MAXLINE];
3895: int firstobs=1, lastobs=10;
3896: int sdeb, sfin; /* Status at beginning and end */
3897: int c, h , cpt,l;
3898: int ju,jl, mi;
3899: int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;
3900: int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,*tab;
3901: int mobilavproj=0 , prevfcast=0 ; /* moving average of prev, If prevfcast=1 prevalence projection */
3902: int mobilav=0,popforecast=0;
3903: int hstepm, nhstepm;
3904: double jprev1=1, mprev1=1,anprev1=2000,jprev2=1, mprev2=1,anprev2=2000;
3905: double jpyram=1, mpyram=1,anpyram=2000,jpyram1=1, mpyram1=1,anpyram1=2000;
3906:
3907: double bage, fage, age, agelim, agebase;
3908: double ftolpl=FTOL;
3909: double **prlim;
3910: double *severity;
3911: double ***param; /* Matrix of parameters */
3912: double *p;
3913: double **matcov; /* Matrix of covariance */
3914: double ***delti3; /* Scale */
3915: double *delti; /* Scale */
3916: double ***eij, ***vareij;
3917: double **varpl; /* Variances of prevalence limits by age */
3918: double *epj, vepp;
3919: double kk1, kk2;
3920: double dateprev1, dateprev2,jproj1=1,mproj1=1,anproj1=2000,jproj2=1,mproj2=1,anproj2=2000;
3921:
3922: char *alph[]={"a","a","b","c","d","e"}, str[4];
3923:
3924:
3925: char z[1]="c", occ;
3926:
3927: char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];
3928: char strstart[80], *strt, strtend[80];
3929: char *stratrunc;
3930: int lstra;
3931:
3932: long total_usecs;
3933:
3934: /* gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */
3935: (void) gettimeofday(&start_time,&tzp);
3936: curr_time=start_time;
3937: tm = *localtime(&start_time.tv_sec);
3938: tmg = *gmtime(&start_time.tv_sec);
3939: strcpy(strstart,asctime(&tm));
3940:
3941: /* printf("Localtime (at start)=%s",strstart); */
3942: /* tp.tv_sec = tp.tv_sec +86400; */
3943: /* tm = *localtime(&start_time.tv_sec); */
3944: /* tmg.tm_year=tmg.tm_year +dsign*dyear; */
3945: /* tmg.tm_mon=tmg.tm_mon +dsign*dmonth; */
3946: /* tmg.tm_hour=tmg.tm_hour + 1; */
3947: /* tp.tv_sec = mktime(&tmg); */
3948: /* strt=asctime(&tmg); */
3949: /* printf("Time(after) =%s",strstart); */
3950: /* (void) time (&time_value);
3951: * printf("time=%d,t-=%d\n",time_value,time_value-86400);
3952: * tm = *localtime(&time_value);
3953: * strstart=asctime(&tm);
3954: * printf("tim_value=%d,asctime=%s\n",time_value,strstart);
3955: */
3956:
3957: nberr=0; /* Number of errors and warnings */
3958: nbwarn=0;
3959: getcwd(pathcd, size);
3960:
3961: printf("\n%s\n%s",version,fullversion);
3962: if(argc <=1){
3963: printf("\nEnter the parameter file name: ");
3964: scanf("%s",pathtot);
3965: }
3966: else{
3967: strcpy(pathtot,argv[1]);
3968: }
3969: /*if(getcwd(pathcd, MAXLINE)!= NULL)printf ("Error pathcd\n");*/
3970: /*cygwin_split_path(pathtot,path,optionfile);
3971: printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/
3972: /* cutv(path,optionfile,pathtot,'\\');*/
3973:
3974: split(pathtot,path,optionfile,optionfilext,optionfilefiname);
3975: printf("pathtot=%s,\npath=%s,\noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
3976: chdir(path);
3977: strcpy(command,"mkdir ");
3978: strcat(command,optionfilefiname);
3979: if((outcmd=system(command)) != 0){
3980: printf("Problem creating directory or it already exists %s%s, err=%d\n",path,optionfilefiname,outcmd);
3981: /* fprintf(ficlog,"Problem creating directory %s%s\n",path,optionfilefiname); */
3982: /* fclose(ficlog); */
3983: /* exit(1); */
3984: }
3985: /* if((imk=mkdir(optionfilefiname))<0){ */
3986: /* perror("mkdir"); */
3987: /* } */
3988:
3989: /*-------- arguments in the command line --------*/
3990:
3991: /* Log file */
3992: strcat(filelog, optionfilefiname);
3993: strcat(filelog,".log"); /* */
3994: if((ficlog=fopen(filelog,"w"))==NULL) {
3995: printf("Problem with logfile %s\n",filelog);
3996: goto end;
3997: }
3998: fprintf(ficlog,"Log filename:%s\n",filelog);
3999: fprintf(ficlog,"\n%s\n%s",version,fullversion);
4000: fprintf(ficlog,"\nEnter the parameter file name: ");
4001: fprintf(ficlog,"pathtot=%s\n\
4002: path=%s \n\
4003: optionfile=%s\n\
4004: optionfilext=%s\n\
4005: optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
4006:
4007: printf("Localtime (at start):%s",strstart);
4008: fprintf(ficlog,"Localtime (at start): %s",strstart);
4009: fflush(ficlog);
4010: /* (void) gettimeofday(&curr_time,&tzp); */
4011: /* printf("Elapsed time %d\n", asc_diff_time(curr_time.tv_sec-start_time.tv_sec,tmpout)); */
4012:
4013: /* */
4014: strcpy(fileres,"r");
4015: strcat(fileres, optionfilefiname);
4016: strcat(fileres,".txt"); /* Other files have txt extension */
4017:
4018: /*---------arguments file --------*/
4019:
4020: if((ficpar=fopen(optionfile,"r"))==NULL) {
4021: printf("Problem with optionfile %s\n",optionfile);
4022: fprintf(ficlog,"Problem with optionfile %s\n",optionfile);
4023: fflush(ficlog);
4024: goto end;
4025: }
4026:
4027:
4028:
4029: strcpy(filereso,"o");
4030: strcat(filereso,fileres);
4031: if((ficparo=fopen(filereso,"w"))==NULL) { /* opened on subdirectory */
4032: printf("Problem with Output resultfile: %s\n", filereso);
4033: fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso);
4034: fflush(ficlog);
4035: goto end;
4036: }
4037:
4038: /* Reads comments: lines beginning with '#' */
4039: numlinepar=0;
4040: while((c=getc(ficpar))=='#' && c!= EOF){
4041: ungetc(c,ficpar);
4042: fgets(line, MAXLINE, ficpar);
4043: numlinepar++;
4044: puts(line);
4045: fputs(line,ficparo);
4046: fputs(line,ficlog);
4047: }
4048: ungetc(c,ficpar);
4049:
4050: 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);
4051: numlinepar++;
4052: 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);
4053: 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);
4054: 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);
4055: fflush(ficlog);
4056: while((c=getc(ficpar))=='#' && c!= EOF){
4057: ungetc(c,ficpar);
4058: fgets(line, MAXLINE, ficpar);
4059: numlinepar++;
4060: puts(line);
4061: fputs(line,ficparo);
4062: fputs(line,ficlog);
4063: }
4064: ungetc(c,ficpar);
4065:
4066:
4067: covar=matrix(0,NCOVMAX,1,n);
4068: cptcovn=0; /*Number of covariates, i.e. number of '+' in model statement*/
4069: if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;
4070:
4071: ncovmodel=2+cptcovn; /*Number of variables = cptcovn + intercept + age */
4072: nvar=ncovmodel-1; /* Suppressing age as a basic covariate */
4073:
4074: if(mle==-1){ /* Print a wizard for help writing covariance matrix */
4075: prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
4076: printf(" You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
4077: fprintf(ficlog," You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
4078: fclose (ficparo);
4079: fclose (ficlog);
4080: exit(0);
4081: }
4082: /* Read guess parameters */
4083: /* Reads comments: lines beginning with '#' */
4084: while((c=getc(ficpar))=='#' && c!= EOF){
4085: ungetc(c,ficpar);
4086: fgets(line, MAXLINE, ficpar);
4087: numlinepar++;
4088: puts(line);
4089: fputs(line,ficparo);
4090: fputs(line,ficlog);
4091: }
4092: ungetc(c,ficpar);
4093:
4094: param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
4095: for(i=1; i <=nlstate; i++){
4096: j=0;
4097: for(jj=1; jj <=nlstate+ndeath; jj++){
4098: if(jj==i) continue;
4099: j++;
4100: fscanf(ficpar,"%1d%1d",&i1,&j1);
4101: if ((i1 != i) && (j1 != j)){
4102: printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n",numlinepar, i,j, i1, j1);
4103: exit(1);
4104: }
4105: fprintf(ficparo,"%1d%1d",i1,j1);
4106: if(mle==1)
4107: printf("%1d%1d",i,j);
4108: fprintf(ficlog,"%1d%1d",i,j);
4109: for(k=1; k<=ncovmodel;k++){
4110: fscanf(ficpar," %lf",¶m[i][j][k]);
4111: if(mle==1){
4112: printf(" %lf",param[i][j][k]);
4113: fprintf(ficlog," %lf",param[i][j][k]);
4114: }
4115: else
4116: fprintf(ficlog," %lf",param[i][j][k]);
4117: fprintf(ficparo," %lf",param[i][j][k]);
4118: }
4119: fscanf(ficpar,"\n");
4120: numlinepar++;
4121: if(mle==1)
4122: printf("\n");
4123: fprintf(ficlog,"\n");
4124: fprintf(ficparo,"\n");
4125: }
4126: }
4127: fflush(ficlog);
4128:
4129: npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/
4130:
4131: p=param[1][1];
4132:
4133: /* Reads comments: lines beginning with '#' */
4134: while((c=getc(ficpar))=='#' && c!= EOF){
4135: ungetc(c,ficpar);
4136: fgets(line, MAXLINE, ficpar);
4137: numlinepar++;
4138: puts(line);
4139: fputs(line,ficparo);
4140: fputs(line,ficlog);
4141: }
4142: ungetc(c,ficpar);
4143:
4144: delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
4145: /* delti=vector(1,npar); *//* Scale of each paramater (output from hesscov) */
4146: for(i=1; i <=nlstate; i++){
4147: for(j=1; j <=nlstate+ndeath-1; j++){
4148: fscanf(ficpar,"%1d%1d",&i1,&j1);
4149: if ((i1-i)*(j1-j)!=0){
4150: printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n",numlinepar, i,j, i1, j1);
4151: exit(1);
4152: }
4153: printf("%1d%1d",i,j);
4154: fprintf(ficparo,"%1d%1d",i1,j1);
4155: fprintf(ficlog,"%1d%1d",i1,j1);
4156: for(k=1; k<=ncovmodel;k++){
4157: fscanf(ficpar,"%le",&delti3[i][j][k]);
4158: printf(" %le",delti3[i][j][k]);
4159: fprintf(ficparo," %le",delti3[i][j][k]);
4160: fprintf(ficlog," %le",delti3[i][j][k]);
4161: }
4162: fscanf(ficpar,"\n");
4163: numlinepar++;
4164: printf("\n");
4165: fprintf(ficparo,"\n");
4166: fprintf(ficlog,"\n");
4167: }
4168: }
4169: fflush(ficlog);
4170:
4171: delti=delti3[1][1];
4172:
4173:
4174: /* free_ma3x(delti3,1,nlstate,1,nlstate+ndeath-1,1,ncovmodel); */ /* Hasn't to to freed here otherwise delti is no more allocated */
4175:
4176: /* Reads comments: lines beginning with '#' */
4177: while((c=getc(ficpar))=='#' && c!= EOF){
4178: ungetc(c,ficpar);
4179: fgets(line, MAXLINE, ficpar);
4180: numlinepar++;
4181: puts(line);
4182: fputs(line,ficparo);
4183: fputs(line,ficlog);
4184: }
4185: ungetc(c,ficpar);
4186:
4187: matcov=matrix(1,npar,1,npar);
4188: for(i=1; i <=npar; i++){
4189: fscanf(ficpar,"%s",&str);
4190: if(mle==1)
4191: printf("%s",str);
4192: fprintf(ficlog,"%s",str);
4193: fprintf(ficparo,"%s",str);
4194: for(j=1; j <=i; j++){
4195: fscanf(ficpar," %le",&matcov[i][j]);
4196: if(mle==1){
4197: printf(" %.5le",matcov[i][j]);
4198: }
4199: fprintf(ficlog," %.5le",matcov[i][j]);
4200: fprintf(ficparo," %.5le",matcov[i][j]);
4201: }
4202: fscanf(ficpar,"\n");
4203: numlinepar++;
4204: if(mle==1)
4205: printf("\n");
4206: fprintf(ficlog,"\n");
4207: fprintf(ficparo,"\n");
4208: }
4209: for(i=1; i <=npar; i++)
4210: for(j=i+1;j<=npar;j++)
4211: matcov[i][j]=matcov[j][i];
4212:
4213: if(mle==1)
4214: printf("\n");
4215: fprintf(ficlog,"\n");
4216:
4217: fflush(ficlog);
4218:
4219: /*-------- Rewriting paramater file ----------*/
4220: strcpy(rfileres,"r"); /* "Rparameterfile */
4221: strcat(rfileres,optionfilefiname); /* Parameter file first name*/
4222: strcat(rfileres,"."); /* */
4223: strcat(rfileres,optionfilext); /* Other files have txt extension */
4224: if((ficres =fopen(rfileres,"w"))==NULL) {
4225: printf("Problem writing new parameter file: %s\n", fileres);goto end;
4226: fprintf(ficlog,"Problem writing new parameter file: %s\n", fileres);goto end;
4227: }
4228: fprintf(ficres,"#%s\n",version);
4229:
4230: /*-------- data file ----------*/
4231: if((fic=fopen(datafile,"r"))==NULL) {
4232: printf("Problem with datafile: %s\n", datafile);goto end;
4233: fprintf(ficlog,"Problem with datafile: %s\n", datafile);goto end;
4234: }
4235:
4236: n= lastobs;
4237: severity = vector(1,maxwav);
4238: outcome=imatrix(1,maxwav+1,1,n);
4239: num=lvector(1,n);
4240: moisnais=vector(1,n);
4241: annais=vector(1,n);
4242: moisdc=vector(1,n);
4243: andc=vector(1,n);
4244: agedc=vector(1,n);
4245: cod=ivector(1,n);
4246: weight=vector(1,n);
4247: for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */
4248: mint=matrix(1,maxwav,1,n);
4249: anint=matrix(1,maxwav,1,n);
4250: s=imatrix(1,maxwav+1,1,n);
4251: tab=ivector(1,NCOVMAX);
4252: ncodemax=ivector(1,8);
4253:
4254: i=1;
4255: while (fgets(line, MAXLINE, fic) != NULL) {
4256: if ((i >= firstobs) && (i <=lastobs)) {
4257:
4258: for (j=maxwav;j>=1;j--){
4259: cutv(stra, strb,line,' '); s[j][i]=atoi(strb);
4260: strcpy(line,stra);
4261: cutv(stra, strb,line,'/'); anint[j][i]=(double)(atoi(strb)); strcpy(line,stra);
4262: cutv(stra, strb,line,' '); mint[j][i]=(double)(atoi(strb)); strcpy(line,stra);
4263: }
4264:
4265: cutv(stra, strb,line,'/'); andc[i]=(double)(atoi(strb)); strcpy(line,stra);
4266: cutv(stra, strb,line,' '); moisdc[i]=(double)(atoi(strb)); strcpy(line,stra);
4267:
4268: cutv(stra, strb,line,'/'); annais[i]=(double)(atoi(strb)); strcpy(line,stra);
4269: cutv(stra, strb,line,' '); moisnais[i]=(double)(atoi(strb)); strcpy(line,stra);
4270:
4271: cutv(stra, strb,line,' '); weight[i]=(double)(atoi(strb)); strcpy(line,stra);
4272: for (j=ncovcol;j>=1;j--){
4273: cutv(stra, strb,line,' '); covar[j][i]=(double)(atoi(strb)); strcpy(line,stra);
4274: }
4275: lstra=strlen(stra);
4276: if(lstra > 9){ /* More than 2**32 or max of what printf can write with %ld */
4277: stratrunc = &(stra[lstra-9]);
4278: num[i]=atol(stratrunc);
4279: }
4280: else
4281: num[i]=atol(stra);
4282:
4283: /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){
4284: 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;}*/
4285:
4286: i=i+1;
4287: }
4288: }
4289: /* printf("ii=%d", ij);
4290: scanf("%d",i);*/
4291: imx=i-1; /* Number of individuals */
4292:
4293: /* for (i=1; i<=imx; i++){
4294: if ((s[1][i]==3) && (s[2][i]==2)) s[2][i]=3;
4295: if ((s[2][i]==3) && (s[3][i]==2)) s[3][i]=3;
4296: if ((s[3][i]==3) && (s[4][i]==2)) s[4][i]=3;
4297: }*/
4298: /* for (i=1; i<=imx; i++){
4299: if (s[4][i]==9) s[4][i]=-1;
4300: 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]));}*/
4301:
4302: for (i=1; i<=imx; i++)
4303:
4304: /*if ((s[3][i]==3) || (s[4][i]==3)) weight[i]=0.08;
4305: else weight[i]=1;*/
4306:
4307: /* Calculation of the number of parameter from char model*/
4308: Tvar=ivector(1,15); /* stores the number n of the covariates in Vm+Vn at 1 and m at 2 */
4309: Tprod=ivector(1,15);
4310: Tvaraff=ivector(1,15);
4311: Tvard=imatrix(1,15,1,2);
4312: Tage=ivector(1,15);
4313:
4314: if (strlen(model) >1){ /* If there is at least 1 covariate */
4315: j=0, j1=0, k1=1, k2=1;
4316: j=nbocc(model,'+'); /* j=Number of '+' */
4317: j1=nbocc(model,'*'); /* j1=Number of '*' */
4318: cptcovn=j+1;
4319: cptcovprod=j1; /*Number of products */
4320:
4321: strcpy(modelsav,model);
4322: if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){
4323: printf("Error. Non available option model=%s ",model);
4324: fprintf(ficlog,"Error. Non available option model=%s ",model);
4325: goto end;
4326: }
4327:
4328: /* This loop fills the array Tvar from the string 'model'.*/
4329:
4330: for(i=(j+1); i>=1;i--){
4331: cutv(stra,strb,modelsav,'+'); /* keeps in strb after the last + */
4332: if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyzes it */
4333: /* printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/
4334: /*scanf("%d",i);*/
4335: if (strchr(strb,'*')) { /* Model includes a product */
4336: cutv(strd,strc,strb,'*'); /* strd*strc Vm*Vn (if not *age)*/
4337: if (strcmp(strc,"age")==0) { /* Vn*age */
4338: cptcovprod--;
4339: cutv(strb,stre,strd,'V');
4340: Tvar[i]=atoi(stre); /* computes n in Vn and stores in Tvar*/
4341: cptcovage++;
4342: Tage[cptcovage]=i;
4343: /*printf("stre=%s ", stre);*/
4344: }
4345: else if (strcmp(strd,"age")==0) { /* or age*Vn */
4346: cptcovprod--;
4347: cutv(strb,stre,strc,'V');
4348: Tvar[i]=atoi(stre);
4349: cptcovage++;
4350: Tage[cptcovage]=i;
4351: }
4352: else { /* Age is not in the model */
4353: cutv(strb,stre,strc,'V'); /* strc= Vn, stre is n*/
4354: Tvar[i]=ncovcol+k1;
4355: cutv(strb,strc,strd,'V'); /* strd was Vm, strc is m */
4356: Tprod[k1]=i;
4357: Tvard[k1][1]=atoi(strc); /* m*/
4358: Tvard[k1][2]=atoi(stre); /* n */
4359: Tvar[cptcovn+k2]=Tvard[k1][1];
4360: Tvar[cptcovn+k2+1]=Tvard[k1][2];
4361: for (k=1; k<=lastobs;k++)
4362: covar[ncovcol+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];
4363: k1++;
4364: k2=k2+2;
4365: }
4366: }
4367: else { /* no more sum */
4368: /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/
4369: /* scanf("%d",i);*/
4370: cutv(strd,strc,strb,'V');
4371: Tvar[i]=atoi(strc);
4372: }
4373: strcpy(modelsav,stra);
4374: /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);
4375: scanf("%d",i);*/
4376: } /* end of loop + */
4377: } /* end model */
4378:
4379: /*The number n of Vn is stored in Tvar. cptcovage =number of age covariate. Tage gives the position of age. cptcovprod= number of products.
4380: If model=V1+V1*age then Tvar[1]=1 Tvar[2]=1 cptcovage=1 Tage[1]=2 cptcovprod=0*/
4381:
4382: /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);
4383: printf("cptcovprod=%d ", cptcovprod);
4384: fprintf(ficlog,"cptcovprod=%d ", cptcovprod);
4385:
4386: scanf("%d ",i);
4387: fclose(fic);*/
4388:
4389: /* if(mle==1){*/
4390: if (weightopt != 1) { /* Maximisation without weights*/
4391: for(i=1;i<=n;i++) weight[i]=1.0;
4392: }
4393: /*-calculation of age at interview from date of interview and age at death -*/
4394: agev=matrix(1,maxwav,1,imx);
4395:
4396: for (i=1; i<=imx; i++) {
4397: for(m=2; (m<= maxwav); m++) {
4398: if (((int)mint[m][i]== 99) && (s[m][i] <= nlstate)){
4399: anint[m][i]=9999;
4400: s[m][i]=-1;
4401: }
4402: if((int)moisdc[i]==99 && (int)andc[i]==9999 && s[m][i]>nlstate){
4403: nberr++;
4404: 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);
4405: 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);
4406: s[m][i]=-1;
4407: }
4408: if((int)moisdc[i]==99 && (int)andc[i]!=9999 && s[m][i]>nlstate){
4409: nberr++;
4410: 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]);
4411: 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]);
4412: s[m][i]=-1; /* We prefer to skip it (and to skip it in version 0.8a1 too */
4413: }
4414: }
4415: }
4416:
4417: for (i=1; i<=imx; i++) {
4418: agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);
4419: for(m=firstpass; (m<= lastpass); m++){
4420: if(s[m][i] >0){
4421: if (s[m][i] >= nlstate+1) {
4422: if(agedc[i]>0)
4423: if((int)moisdc[i]!=99 && (int)andc[i]!=9999)
4424: agev[m][i]=agedc[i];
4425: /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/
4426: else {
4427: if ((int)andc[i]!=9999){
4428: nbwarn++;
4429: printf("Warning negative age at death: %ld line:%d\n",num[i],i);
4430: fprintf(ficlog,"Warning negative age at death: %ld line:%d\n",num[i],i);
4431: agev[m][i]=-1;
4432: }
4433: }
4434: }
4435: else if(s[m][i] !=9){ /* Standard case, age in fractional
4436: years but with the precision of a
4437: month */
4438: agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);
4439: if((int)mint[m][i]==99 || (int)anint[m][i]==9999)
4440: agev[m][i]=1;
4441: else if(agev[m][i] <agemin){
4442: agemin=agev[m][i];
4443: /*printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], agemin);*/
4444: }
4445: else if(agev[m][i] >agemax){
4446: agemax=agev[m][i];
4447: /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/
4448: }
4449: /*agev[m][i]=anint[m][i]-annais[i];*/
4450: /* agev[m][i] = age[i]+2*m;*/
4451: }
4452: else { /* =9 */
4453: agev[m][i]=1;
4454: s[m][i]=-1;
4455: }
4456: }
4457: else /*= 0 Unknown */
4458: agev[m][i]=1;
4459: }
4460:
4461: }
4462: for (i=1; i<=imx; i++) {
4463: for(m=firstpass; (m<=lastpass); m++){
4464: if (s[m][i] > (nlstate+ndeath)) {
4465: nberr++;
4466: 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);
4467: 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);
4468: goto end;
4469: }
4470: }
4471: }
4472:
4473: /*for (i=1; i<=imx; i++){
4474: for (m=firstpass; (m<lastpass); m++){
4475: printf("%ld %d %.lf %d %d\n", num[i],(covar[1][i]),agev[m][i],s[m][i],s[m+1][i]);
4476: }
4477:
4478: }*/
4479:
4480: printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);
4481: fprintf(ficlog,"Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);
4482:
4483: free_vector(severity,1,maxwav);
4484: free_imatrix(outcome,1,maxwav+1,1,n);
4485: free_vector(moisnais,1,n);
4486: free_vector(annais,1,n);
4487: /* free_matrix(mint,1,maxwav,1,n);
4488: free_matrix(anint,1,maxwav,1,n);*/
4489: free_vector(moisdc,1,n);
4490: free_vector(andc,1,n);
4491:
4492:
4493: wav=ivector(1,imx);
4494: dh=imatrix(1,lastpass-firstpass+1,1,imx);
4495: bh=imatrix(1,lastpass-firstpass+1,1,imx);
4496: mw=imatrix(1,lastpass-firstpass+1,1,imx);
4497:
4498: /* Concatenates waves */
4499: concatwav(wav, dh, bh, mw, s, agedc, agev, firstpass, lastpass, imx, nlstate, stepm);
4500:
4501: /* Routine tricode is to calculate cptcoveff (real number of unique covariates) and to associate covariable number and modality */
4502:
4503: Tcode=ivector(1,100);
4504: nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);
4505: ncodemax[1]=1;
4506: if (cptcovn > 0) tricode(Tvar,nbcode,imx);
4507:
4508: codtab=imatrix(1,100,1,10); /* Cross tabulation to get the order of
4509: the estimations*/
4510: h=0;
4511: m=pow(2,cptcoveff);
4512:
4513: for(k=1;k<=cptcoveff; k++){
4514: for(i=1; i <=(m/pow(2,k));i++){
4515: for(j=1; j <= ncodemax[k]; j++){
4516: for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){
4517: h++;
4518: if (h>m) h=1;codtab[h][k]=j;codtab[h][Tvar[k]]=j;
4519: /* printf("h=%d k=%d j=%d codtab[h][k]=%d tvar[k]=%d \n",h, k,j,codtab[h][k],Tvar[k]);*/
4520: }
4521: }
4522: }
4523: }
4524: /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]);
4525: codtab[1][2]=1;codtab[2][2]=2; */
4526: /* for(i=1; i <=m ;i++){
4527: for(k=1; k <=cptcovn; k++){
4528: printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);
4529: }
4530: printf("\n");
4531: }
4532: scanf("%d",i);*/
4533:
4534: /*------------ gnuplot -------------*/
4535: strcpy(optionfilegnuplot,optionfilefiname);
4536: strcat(optionfilegnuplot,".gp");
4537: if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {
4538: printf("Problem with file %s",optionfilegnuplot);
4539: }
4540: else{
4541: fprintf(ficgp,"\n# %s\n", version);
4542: fprintf(ficgp,"# %s\n", optionfilegnuplot);
4543: fprintf(ficgp,"set missing 'NaNq'\n");
4544: }
4545: /* fclose(ficgp);*/
4546: /*--------- index.htm --------*/
4547:
4548: strcpy(optionfilehtm,optionfilefiname); /* Main html file */
4549: strcat(optionfilehtm,".htm");
4550: if((fichtm=fopen(optionfilehtm,"w"))==NULL) {
4551: printf("Problem with %s \n",optionfilehtm), exit(0);
4552: }
4553:
4554: strcpy(optionfilehtmcov,optionfilefiname); /* Only for matrix of covariance */
4555: strcat(optionfilehtmcov,"-cov.htm");
4556: if((fichtmcov=fopen(optionfilehtmcov,"w"))==NULL) {
4557: printf("Problem with %s \n",optionfilehtmcov), exit(0);
4558: }
4559: else{
4560: fprintf(fichtmcov,"<body>\n<title>IMaCh Cov %s</title>\n <font size=\"2\">%s <br> %s</font> \
4561: <hr size=\"2\" color=\"#EC5E5E\"> \n\
4562: Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n",\
4563: fileres,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);
4564: }
4565:
4566: fprintf(fichtm,"<body>\n<title>IMaCh %s</title>\n <font size=\"2\">%s <br> %s</font> \
4567: <hr size=\"2\" color=\"#EC5E5E\"> \n\
4568: Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n\
4569: \n\
4570: <hr size=\"2\" color=\"#EC5E5E\">\
4571: <ul><li><h4>Parameter files</h4>\n\
4572: - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n\
4573: - Log file of the run: <a href=\"%s\">%s</a><br>\n\
4574: - Gnuplot file name: <a href=\"%s\">%s</a><br>\n\
4575: - Date and time at start: %s</ul>\n",\
4576: fileres,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model,\
4577: fileres,fileres,\
4578: filelog,filelog,optionfilegnuplot,optionfilegnuplot,strstart);
4579: fflush(fichtm);
4580:
4581: strcpy(pathr,path);
4582: strcat(pathr,optionfilefiname);
4583: chdir(optionfilefiname); /* Move to directory named optionfile */
4584: strcpy(lfileres,fileres);
4585: strcat(lfileres,"/");
4586: strcat(lfileres,optionfilefiname);
4587:
4588: /* Calculates basic frequencies. Computes observed prevalence at single age
4589: and prints on file fileres'p'. */
4590: freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint);
4591:
4592: fprintf(fichtm,"\n");
4593: fprintf(fichtm,"<br>Total number of observations=%d <br>\n\
4594: Youngest age at first (selected) pass %.2f, oldest age %.2f<br>\n\
4595: Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n",\
4596: imx,agemin,agemax,jmin,jmax,jmean);
4597: pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
4598: oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
4599: newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
4600: savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
4601: oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */
4602:
4603:
4604: /* For Powell, parameters are in a vector p[] starting at p[1]
4605: so we point p on param[1][1] so that p[1] maps on param[1][1][1] */
4606: p=param[1][1]; /* *(*(*(param +1)+1)+0) */
4607:
4608: globpr=0; /* To get the number ipmx of contributions and the sum of weights*/
4609: likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
4610: printf("First Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
4611: for (k=1; k<=npar;k++)
4612: printf(" %d %8.5f",k,p[k]);
4613: printf("\n");
4614: globpr=1; /* to print the contributions */
4615: likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
4616: printf("Second Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
4617: for (k=1; k<=npar;k++)
4618: printf(" %d %8.5f",k,p[k]);
4619: printf("\n");
4620: if(mle>=1){ /* Could be 1 or 2 */
4621: mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);
4622: }
4623:
4624: /*--------- results files --------------*/
4625: 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);
4626:
4627:
4628: jk=1;
4629: fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
4630: printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
4631: fprintf(ficlog,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
4632: for(i=1,jk=1; i <=nlstate; i++){
4633: for(k=1; k <=(nlstate+ndeath); k++){
4634: if (k != i)
4635: {
4636: printf("%d%d ",i,k);
4637: fprintf(ficlog,"%d%d ",i,k);
4638: fprintf(ficres,"%1d%1d ",i,k);
4639: for(j=1; j <=ncovmodel; j++){
4640: printf("%f ",p[jk]);
4641: fprintf(ficlog,"%f ",p[jk]);
4642: fprintf(ficres,"%f ",p[jk]);
4643: jk++;
4644: }
4645: printf("\n");
4646: fprintf(ficlog,"\n");
4647: fprintf(ficres,"\n");
4648: }
4649: }
4650: }
4651: if(mle!=0){
4652: /* Computing hessian and covariance matrix */
4653: ftolhess=ftol; /* Usually correct */
4654: hesscov(matcov, p, npar, delti, ftolhess, func);
4655: }
4656: fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");
4657: printf("# Scales (for hessian or gradient estimation)\n");
4658: fprintf(ficlog,"# Scales (for hessian or gradient estimation)\n");
4659: for(i=1,jk=1; i <=nlstate; i++){
4660: for(j=1; j <=nlstate+ndeath; j++){
4661: if (j!=i) {
4662: fprintf(ficres,"%1d%1d",i,j);
4663: printf("%1d%1d",i,j);
4664: fprintf(ficlog,"%1d%1d",i,j);
4665: for(k=1; k<=ncovmodel;k++){
4666: printf(" %.5e",delti[jk]);
4667: fprintf(ficlog," %.5e",delti[jk]);
4668: fprintf(ficres," %.5e",delti[jk]);
4669: jk++;
4670: }
4671: printf("\n");
4672: fprintf(ficlog,"\n");
4673: fprintf(ficres,"\n");
4674: }
4675: }
4676: }
4677:
4678: 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");
4679: if(mle==1)
4680: 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");
4681: 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");
4682: for(i=1,k=1;i<=npar;i++){
4683: /* if (k>nlstate) k=1;
4684: i1=(i-1)/(ncovmodel*nlstate)+1;
4685: fprintf(ficres,"%s%d%d",alph[k],i1,tab[i]);
4686: printf("%s%d%d",alph[k],i1,tab[i]);
4687: */
4688: fprintf(ficres,"%3d",i);
4689: if(mle==1)
4690: printf("%3d",i);
4691: fprintf(ficlog,"%3d",i);
4692: for(j=1; j<=i;j++){
4693: fprintf(ficres," %.5e",matcov[i][j]);
4694: if(mle==1)
4695: printf(" %.5e",matcov[i][j]);
4696: fprintf(ficlog," %.5e",matcov[i][j]);
4697: }
4698: fprintf(ficres,"\n");
4699: if(mle==1)
4700: printf("\n");
4701: fprintf(ficlog,"\n");
4702: k++;
4703: }
4704:
4705: while((c=getc(ficpar))=='#' && c!= EOF){
4706: ungetc(c,ficpar);
4707: fgets(line, MAXLINE, ficpar);
4708: puts(line);
4709: fputs(line,ficparo);
4710: }
4711: ungetc(c,ficpar);
4712:
4713: estepm=0;
4714: fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm);
4715: if (estepm==0 || estepm < stepm) estepm=stepm;
4716: if (fage <= 2) {
4717: bage = ageminpar;
4718: fage = agemaxpar;
4719: }
4720:
4721: fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");
4722: fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
4723: fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
4724:
4725: while((c=getc(ficpar))=='#' && c!= EOF){
4726: ungetc(c,ficpar);
4727: fgets(line, MAXLINE, ficpar);
4728: puts(line);
4729: fputs(line,ficparo);
4730: }
4731: ungetc(c,ficpar);
4732:
4733: 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);
4734: 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);
4735: 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);
4736: printf("begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
4737: 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);
4738:
4739: while((c=getc(ficpar))=='#' && c!= EOF){
4740: ungetc(c,ficpar);
4741: fgets(line, MAXLINE, ficpar);
4742: puts(line);
4743: fputs(line,ficparo);
4744: }
4745: ungetc(c,ficpar);
4746:
4747:
4748: dateprev1=anprev1+(mprev1-1)/12.+(jprev1-1)/365.;
4749: dateprev2=anprev2+(mprev2-1)/12.+(jprev2-1)/365.;
4750:
4751: fscanf(ficpar,"pop_based=%d\n",&popbased);
4752: fprintf(ficparo,"pop_based=%d\n",popbased);
4753: fprintf(ficres,"pop_based=%d\n",popbased);
4754:
4755: while((c=getc(ficpar))=='#' && c!= EOF){
4756: ungetc(c,ficpar);
4757: fgets(line, MAXLINE, ficpar);
4758: puts(line);
4759: fputs(line,ficparo);
4760: }
4761: ungetc(c,ficpar);
4762:
4763: 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);
4764: 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);
4765: 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);
4766: 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);
4767: 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);
4768: /* day and month of proj2 are not used but only year anproj2.*/
4769:
4770: while((c=getc(ficpar))=='#' && c!= EOF){
4771: ungetc(c,ficpar);
4772: fgets(line, MAXLINE, ficpar);
4773: puts(line);
4774: fputs(line,ficparo);
4775: }
4776: ungetc(c,ficpar);
4777:
4778: fscanf(ficpar,"popforecast=%d popfile=%s popfiledate=%lf/%lf/%lf last-popfiledate=%lf/%lf/%lf\n",&popforecast,popfile,&jpyram,&mpyram,&anpyram,&jpyram1,&mpyram1,&anpyram1);
4779: fprintf(ficparo,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);
4780: fprintf(ficres,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);
4781:
4782: /* freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint);*/
4783: /*,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
4784:
4785: replace_back_to_slash(pathc,path); /* Even gnuplot wants a / */
4786: printinggnuplot(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
4787:
4788: printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,\
4789: model,imx,jmin,jmax,jmean,rfileres,popforecast,estepm,\
4790: jprev1,mprev1,anprev1,jprev2,mprev2,anprev2);
4791:
4792: /*------------ free_vector -------------*/
4793: /* chdir(path); */
4794:
4795: free_ivector(wav,1,imx);
4796: free_imatrix(dh,1,lastpass-firstpass+1,1,imx);
4797: free_imatrix(bh,1,lastpass-firstpass+1,1,imx);
4798: free_imatrix(mw,1,lastpass-firstpass+1,1,imx);
4799: free_lvector(num,1,n);
4800: free_vector(agedc,1,n);
4801: /*free_matrix(covar,0,NCOVMAX,1,n);*/
4802: /*free_matrix(covar,1,NCOVMAX,1,n);*/
4803: fclose(ficparo);
4804: fclose(ficres);
4805:
4806:
4807: /*--------------- Prevalence limit (stable prevalence) --------------*/
4808:
4809: strcpy(filerespl,"pl");
4810: strcat(filerespl,fileres);
4811: if((ficrespl=fopen(filerespl,"w"))==NULL) {
4812: printf("Problem with stable prevalence resultfile: %s\n", filerespl);goto end;
4813: fprintf(ficlog,"Problem with stable prevalence resultfile: %s\n", filerespl);goto end;
4814: }
4815: printf("Computing stable prevalence: result on file '%s' \n", filerespl);
4816: fprintf(ficlog,"Computing stable prevalence: result on file '%s' \n", filerespl);
4817: fprintf(ficrespl,"#Stable prevalence \n");
4818: fprintf(ficrespl,"#Age ");
4819: for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);
4820: fprintf(ficrespl,"\n");
4821:
4822: prlim=matrix(1,nlstate,1,nlstate);
4823:
4824: agebase=ageminpar;
4825: agelim=agemaxpar;
4826: ftolpl=1.e-10;
4827: i1=cptcoveff;
4828: if (cptcovn < 1){i1=1;}
4829:
4830: for(cptcov=1,k=0;cptcov<=i1;cptcov++){
4831: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
4832: k=k+1;
4833: /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/
4834: fprintf(ficrespl,"\n#******");
4835: printf("\n#******");
4836: fprintf(ficlog,"\n#******");
4837: for(j=1;j<=cptcoveff;j++) {
4838: fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
4839: printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
4840: fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
4841: }
4842: fprintf(ficrespl,"******\n");
4843: printf("******\n");
4844: fprintf(ficlog,"******\n");
4845:
4846: for (age=agebase; age<=agelim; age++){
4847: prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
4848: fprintf(ficrespl,"%.0f ",age );
4849: for(j=1;j<=cptcoveff;j++)
4850: fprintf(ficrespl,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
4851: for(i=1; i<=nlstate;i++)
4852: fprintf(ficrespl," %.5f", prlim[i][i]);
4853: fprintf(ficrespl,"\n");
4854: }
4855: }
4856: }
4857: fclose(ficrespl);
4858:
4859: /*------------- h Pij x at various ages ------------*/
4860:
4861: strcpy(filerespij,"pij"); strcat(filerespij,fileres);
4862: if((ficrespij=fopen(filerespij,"w"))==NULL) {
4863: printf("Problem with Pij resultfile: %s\n", filerespij);goto end;
4864: fprintf(ficlog,"Problem with Pij resultfile: %s\n", filerespij);goto end;
4865: }
4866: printf("Computing pij: result on file '%s' \n", filerespij);
4867: fprintf(ficlog,"Computing pij: result on file '%s' \n", filerespij);
4868:
4869: stepsize=(int) (stepm+YEARM-1)/YEARM;
4870: /*if (stepm<=24) stepsize=2;*/
4871:
4872: agelim=AGESUP;
4873: hstepm=stepsize*YEARM; /* Every year of age */
4874: hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */
4875:
4876: /* hstepm=1; aff par mois*/
4877:
4878: fprintf(ficrespij,"#****** h Pij x Probability to be in state j at age x+h being in i at x ");
4879: for(cptcov=1,k=0;cptcov<=i1;cptcov++){
4880: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
4881: k=k+1;
4882: fprintf(ficrespij,"\n#****** ");
4883: for(j=1;j<=cptcoveff;j++)
4884: fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
4885: fprintf(ficrespij,"******\n");
4886:
4887: for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */
4888: nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
4889: nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
4890:
4891: /* nhstepm=nhstepm*YEARM; aff par mois*/
4892:
4893: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4894: oldm=oldms;savm=savms;
4895: hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
4896: fprintf(ficrespij,"# Cov Agex agex+h hpijx with i,j=");
4897: for(i=1; i<=nlstate;i++)
4898: for(j=1; j<=nlstate+ndeath;j++)
4899: fprintf(ficrespij," %1d-%1d",i,j);
4900: fprintf(ficrespij,"\n");
4901: for (h=0; h<=nhstepm; h++){
4902: fprintf(ficrespij,"%d %3.f %3.f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );
4903: for(i=1; i<=nlstate;i++)
4904: for(j=1; j<=nlstate+ndeath;j++)
4905: fprintf(ficrespij," %.5f", p3mat[i][j][h]);
4906: fprintf(ficrespij,"\n");
4907: }
4908: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4909: fprintf(ficrespij,"\n");
4910: }
4911: }
4912: }
4913:
4914: varprob(optionfilefiname, matcov, p, delti, nlstate, bage, fage,k,Tvar,nbcode, ncodemax);
4915:
4916: fclose(ficrespij);
4917:
4918: probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
4919:
4920: /*---------- Forecasting ------------------*/
4921: /*if((stepm == 1) && (strcmp(model,".")==0)){*/
4922: if(prevfcast==1){
4923: /* if(stepm ==1){*/
4924: prevforecast(fileres, anproj1, mproj1, jproj1, agemin, agemax, dateprev1, dateprev2, mobilavproj, bage, fage, firstpass, lastpass, anproj2, p, cptcoveff);
4925: /* (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);*/
4926: /* } */
4927: /* else{ */
4928: /* erreur=108; */
4929: /* 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); */
4930: /* 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); */
4931: /* } */
4932: }
4933:
4934:
4935: /*---------- Health expectancies and variances ------------*/
4936:
4937: strcpy(filerest,"t");
4938: strcat(filerest,fileres);
4939: if((ficrest=fopen(filerest,"w"))==NULL) {
4940: printf("Problem with total LE resultfile: %s\n", filerest);goto end;
4941: fprintf(ficlog,"Problem with total LE resultfile: %s\n", filerest);goto end;
4942: }
4943: printf("Computing Total LEs with variances: file '%s' \n", filerest);
4944: fprintf(ficlog,"Computing Total LEs with variances: file '%s' \n", filerest);
4945:
4946:
4947: strcpy(filerese,"e");
4948: strcat(filerese,fileres);
4949: if((ficreseij=fopen(filerese,"w"))==NULL) {
4950: printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
4951: fprintf(ficlog,"Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
4952: }
4953: printf("Computing Health Expectancies: result on file '%s' \n", filerese);
4954: fprintf(ficlog,"Computing Health Expectancies: result on file '%s' \n", filerese);
4955:
4956: strcpy(fileresv,"v");
4957: strcat(fileresv,fileres);
4958: if((ficresvij=fopen(fileresv,"w"))==NULL) {
4959: printf("Problem with variance resultfile: %s\n", fileresv);exit(0);
4960: fprintf(ficlog,"Problem with variance resultfile: %s\n", fileresv);exit(0);
4961: }
4962: printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
4963: fprintf(ficlog,"Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
4964:
4965: /* Computes prevalence between agemin (i.e minimal age computed) and no more ageminpar */
4966: prevalence(probs, agemin, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
4967: /* 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",\
4968: ageminpar, agemax, s[lastpass][imx], agev[lastpass][imx], nlstate, imx, mint[lastpass][imx],anint[lastpass][imx], dateprev1, dateprev2, firstpass, lastpass);
4969: */
4970:
4971: if (mobilav!=0) {
4972: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
4973: if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
4974: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
4975: printf(" Error in movingaverage mobilav=%d\n",mobilav);
4976: }
4977: }
4978:
4979: for(cptcov=1,k=0;cptcov<=i1;cptcov++){
4980: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
4981: k=k+1;
4982: fprintf(ficrest,"\n#****** ");
4983: for(j=1;j<=cptcoveff;j++)
4984: fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
4985: fprintf(ficrest,"******\n");
4986:
4987: fprintf(ficreseij,"\n#****** ");
4988: for(j=1;j<=cptcoveff;j++)
4989: fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
4990: fprintf(ficreseij,"******\n");
4991:
4992: fprintf(ficresvij,"\n#****** ");
4993: for(j=1;j<=cptcoveff;j++)
4994: fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
4995: fprintf(ficresvij,"******\n");
4996:
4997: eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
4998: oldm=oldms;savm=savms;
4999: evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov);
5000:
5001: vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
5002: oldm=oldms;savm=savms;
5003: varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,0, mobilav);
5004: if(popbased==1){
5005: varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,popbased,mobilav);
5006: }
5007:
5008:
5009: fprintf(ficrest,"#Total LEs with variances: e.. (std) ");
5010: for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);
5011: fprintf(ficrest,"\n");
5012:
5013: epj=vector(1,nlstate+1);
5014: for(age=bage; age <=fage ;age++){
5015: prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
5016: if (popbased==1) {
5017: if(mobilav ==0){
5018: for(i=1; i<=nlstate;i++)
5019: prlim[i][i]=probs[(int)age][i][k];
5020: }else{ /* mobilav */
5021: for(i=1; i<=nlstate;i++)
5022: prlim[i][i]=mobaverage[(int)age][i][k];
5023: }
5024: }
5025:
5026: fprintf(ficrest," %4.0f",age);
5027: for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){
5028: for(i=1, epj[j]=0.;i <=nlstate;i++) {
5029: epj[j] += prlim[i][i]*eij[i][j][(int)age];
5030: /* printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/
5031: }
5032: epj[nlstate+1] +=epj[j];
5033: }
5034:
5035: for(i=1, vepp=0.;i <=nlstate;i++)
5036: for(j=1;j <=nlstate;j++)
5037: vepp += vareij[i][j][(int)age];
5038: fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));
5039: for(j=1;j <=nlstate;j++){
5040: fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));
5041: }
5042: fprintf(ficrest,"\n");
5043: }
5044: free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
5045: free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);
5046: free_vector(epj,1,nlstate+1);
5047: }
5048: }
5049: free_vector(weight,1,n);
5050: free_imatrix(Tvard,1,15,1,2);
5051: free_imatrix(s,1,maxwav+1,1,n);
5052: free_matrix(anint,1,maxwav,1,n);
5053: free_matrix(mint,1,maxwav,1,n);
5054: free_ivector(cod,1,n);
5055: free_ivector(tab,1,NCOVMAX);
5056: fclose(ficreseij);
5057: fclose(ficresvij);
5058: fclose(ficrest);
5059: fclose(ficpar);
5060:
5061: /*------- Variance of stable prevalence------*/
5062:
5063: strcpy(fileresvpl,"vpl");
5064: strcat(fileresvpl,fileres);
5065: if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {
5066: printf("Problem with variance of stable prevalence resultfile: %s\n", fileresvpl);
5067: exit(0);
5068: }
5069: printf("Computing Variance-covariance of stable prevalence: file '%s' \n", fileresvpl);
5070:
5071: for(cptcov=1,k=0;cptcov<=i1;cptcov++){
5072: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
5073: k=k+1;
5074: fprintf(ficresvpl,"\n#****** ");
5075: for(j=1;j<=cptcoveff;j++)
5076: fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
5077: fprintf(ficresvpl,"******\n");
5078:
5079: varpl=matrix(1,nlstate,(int) bage, (int) fage);
5080: oldm=oldms;savm=savms;
5081: varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);
5082: free_matrix(varpl,1,nlstate,(int) bage, (int)fage);
5083: }
5084: }
5085:
5086: fclose(ficresvpl);
5087:
5088: /*---------- End : free ----------------*/
5089: free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);
5090: free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);
5091: free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);
5092: free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);
5093:
5094: free_matrix(covar,0,NCOVMAX,1,n);
5095: free_matrix(matcov,1,npar,1,npar);
5096: /*free_vector(delti,1,npar);*/
5097: free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
5098: free_matrix(agev,1,maxwav,1,imx);
5099: free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
5100: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
5101: free_ma3x(probs,1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
5102:
5103: free_ivector(ncodemax,1,8);
5104: free_ivector(Tvar,1,15);
5105: free_ivector(Tprod,1,15);
5106: free_ivector(Tvaraff,1,15);
5107: free_ivector(Tage,1,15);
5108: free_ivector(Tcode,1,100);
5109:
5110: fflush(fichtm);
5111: fflush(ficgp);
5112:
5113:
5114: if((nberr >0) || (nbwarn>0)){
5115: printf("End of Imach with %d errors and/or warnings %d\n",nberr,nbwarn);
5116: fprintf(ficlog,"End of Imach with %d errors and/or warnings %d\n",nberr,nbwarn);
5117: }else{
5118: printf("End of Imach\n");
5119: fprintf(ficlog,"End of Imach\n");
5120: }
5121: printf("See log file on %s\n",filelog);
5122: /* gettimeofday(&end_time, (struct timezone*)0);*/ /* after time */
5123: (void) gettimeofday(&end_time,&tzp);
5124: tm = *localtime(&end_time.tv_sec);
5125: tmg = *gmtime(&end_time.tv_sec);
5126: strcpy(strtend,asctime(&tm));
5127: printf("Localtime at start %s\nLocaltime at end %s",strstart, strtend);
5128: fprintf(ficlog,"Localtime at start %s\nLocal time at end %s\n",strstart, strtend);
5129: printf("Total time used %s\n", asc_diff_time(end_time.tv_sec -start_time.tv_sec,tmpout));
5130:
5131: printf("Total time was %d Sec.\n", end_time.tv_sec -start_time.tv_sec);
5132: fprintf(ficlog,"Total time used %s\n", asc_diff_time(end_time.tv_sec -start_time.tv_sec,tmpout));
5133: fprintf(ficlog,"Total time was %d Sec.\n", end_time.tv_sec -start_time.tv_sec);
5134: /* printf("Total time was %d uSec.\n", total_usecs);*/
5135: /* if(fileappend(fichtm,optionfilehtm)){ */
5136: fprintf(fichtm,"<br>Local time at start %s<br>Local time at end %s<br>",strstart, strtend);
5137: fclose(fichtm);
5138: fclose(fichtmcov);
5139: fclose(ficgp);
5140: fclose(ficlog);
5141: /*------ End -----------*/
5142:
5143: chdir(path);
5144: strcpy(plotcmd,GNUPLOTPROGRAM);
5145: strcat(plotcmd," ");
5146: strcat(plotcmd,optionfilegnuplot);
5147: printf("Starting graphs with: %s",plotcmd);fflush(stdout);
5148: if((outcmd=system(plotcmd)) != 0){
5149: printf(" Problem with gnuplot\n");
5150: }
5151: printf(" Wait...");
5152: while (z[0] != 'q') {
5153: /* chdir(path); */
5154: printf("\nType e to edit output files, g to graph again and q for exiting: ");
5155: scanf("%s",z);
5156: /* if (z[0] == 'c') system("./imach"); */
5157: if (z[0] == 'e') system(optionfilehtm);
5158: else if (z[0] == 'g') system(plotcmd);
5159: else if (z[0] == 'q') exit(0);
5160: }
5161: end:
5162: while (z[0] != 'q') {
5163: printf("\nType q for exiting: ");
5164: scanf("%s",z);
5165: }
5166: }
5167:
5168:
5169:
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