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