1: /* $Id: imach.c,v 1.101 2004/09/15 10:38:38 brouard Exp $
2: $State: Exp $
3: $Log: imach.c,v $
4: Revision 1.101 2004/09/15 10:38:38 brouard
5: Fix on curr_time
6:
7: Revision 1.100 2004/07/12 18:29:06 brouard
8: Add version for Mac OS X. Just define UNIX in Makefile
9:
10: Revision 1.99 2004/06/05 08:57:40 brouard
11: *** empty log message ***
12:
13: Revision 1.98 2004/05/16 15:05:56 brouard
14: New version 0.97 . First attempt to estimate force of mortality
15: directly from the data i.e. without the need of knowing the health
16: state at each age, but using a Gompertz model: log u =a + b*age .
17: This is the basic analysis of mortality and should be done before any
18: other analysis, in order to test if the mortality estimated from the
19: cross-longitudinal survey is different from the mortality estimated
20: from other sources like vital statistic data.
21:
22: The same imach parameter file can be used but the option for mle should be -3.
23:
24: Agnès, who wrote this part of the code, tried to keep most of the
25: former routines in order to include the new code within the former code.
26:
27: The output is very simple: only an estimate of the intercept and of
28: the slope with 95% confident intervals.
29:
30: Current limitations:
31: A) Even if you enter covariates, i.e. with the
32: model= V1+V2 equation for example, the programm does only estimate a unique global model without covariates.
33: B) There is no computation of Life Expectancy nor Life Table.
34:
35: Revision 1.97 2004/02/20 13:25:42 lievre
36: Version 0.96d. Population forecasting command line is (temporarily)
37: suppressed.
38:
39: Revision 1.96 2003/07/15 15:38:55 brouard
40: * imach.c (Repository): Errors in subdirf, 2, 3 while printing tmpout is
41: rewritten within the same printf. Workaround: many printfs.
42:
43: Revision 1.95 2003/07/08 07:54:34 brouard
44: * imach.c (Repository):
45: (Repository): Using imachwizard code to output a more meaningful covariance
46: matrix (cov(a12,c31) instead of numbers.
47:
48: Revision 1.94 2003/06/27 13:00:02 brouard
49: Just cleaning
50:
51: Revision 1.93 2003/06/25 16:33:55 brouard
52: (Module): On windows (cygwin) function asctime_r doesn't
53: exist so I changed back to asctime which exists.
54: (Module): Version 0.96b
55:
56: Revision 1.92 2003/06/25 16:30:45 brouard
57: (Module): On windows (cygwin) function asctime_r doesn't
58: exist so I changed back to asctime which exists.
59:
60: Revision 1.91 2003/06/25 15:30:29 brouard
61: * imach.c (Repository): Duplicated warning errors corrected.
62: (Repository): Elapsed time after each iteration is now output. It
63: helps to forecast when convergence will be reached. Elapsed time
64: is stamped in powell. We created a new html file for the graphs
65: concerning matrix of covariance. It has extension -cov.htm.
66:
67: Revision 1.90 2003/06/24 12:34:15 brouard
68: (Module): Some bugs corrected for windows. Also, when
69: mle=-1 a template is output in file "or"mypar.txt with the design
70: of the covariance matrix to be input.
71:
72: Revision 1.89 2003/06/24 12:30:52 brouard
73: (Module): Some bugs corrected for windows. Also, when
74: mle=-1 a template is output in file "or"mypar.txt with the design
75: of the covariance matrix to be input.
76:
77: Revision 1.88 2003/06/23 17:54:56 brouard
78: * 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.
79:
80: Revision 1.87 2003/06/18 12:26:01 brouard
81: Version 0.96
82:
83: Revision 1.86 2003/06/17 20:04:08 brouard
84: (Module): Change position of html and gnuplot routines and added
85: routine fileappend.
86:
87: Revision 1.85 2003/06/17 13:12:43 brouard
88: * imach.c (Repository): Check when date of death was earlier that
89: current date of interview. It may happen when the death was just
90: prior to the death. In this case, dh was negative and likelihood
91: was wrong (infinity). We still send an "Error" but patch by
92: assuming that the date of death was just one stepm after the
93: interview.
94: (Repository): Because some people have very long ID (first column)
95: we changed int to long in num[] and we added a new lvector for
96: memory allocation. But we also truncated to 8 characters (left
97: truncation)
98: (Repository): No more line truncation errors.
99:
100: Revision 1.84 2003/06/13 21:44:43 brouard
101: * imach.c (Repository): Replace "freqsummary" at a correct
102: place. It differs from routine "prevalence" which may be called
103: many times. Probs is memory consuming and must be used with
104: parcimony.
105: Version 0.95a3 (should output exactly the same maximization than 0.8a2)
106:
107: Revision 1.83 2003/06/10 13:39:11 lievre
108: *** empty log message ***
109:
110: Revision 1.82 2003/06/05 15:57:20 brouard
111: Add log in imach.c and fullversion number is now printed.
112:
113: */
114: /*
115: Interpolated Markov Chain
116:
117: Short summary of the programme:
118:
119: This program computes Healthy Life Expectancies from
120: cross-longitudinal data. Cross-longitudinal data consist in: -1- a
121: first survey ("cross") where individuals from different ages are
122: interviewed on their health status or degree of disability (in the
123: case of a health survey which is our main interest) -2- at least a
124: second wave of interviews ("longitudinal") which measure each change
125: (if any) in individual health status. Health expectancies are
126: computed from the time spent in each health state according to a
127: model. More health states you consider, more time is necessary to reach the
128: Maximum Likelihood of the parameters involved in the model. The
129: simplest model is the multinomial logistic model where pij is the
130: probability to be observed in state j at the second wave
131: conditional to be observed in state i at the first wave. Therefore
132: the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where
133: 'age' is age and 'sex' is a covariate. If you want to have a more
134: complex model than "constant and age", you should modify the program
135: where the markup *Covariates have to be included here again* invites
136: you to do it. More covariates you add, slower the
137: convergence.
138:
139: The advantage of this computer programme, compared to a simple
140: multinomial logistic model, is clear when the delay between waves is not
141: identical for each individual. Also, if a individual missed an
142: intermediate interview, the information is lost, but taken into
143: account using an interpolation or extrapolation.
144:
145: hPijx is the probability to be observed in state i at age x+h
146: conditional to the observed state i at age x. The delay 'h' can be
147: split into an exact number (nh*stepm) of unobserved intermediate
148: states. This elementary transition (by month, quarter,
149: semester or year) is modelled as a multinomial logistic. The hPx
150: matrix is simply the matrix product of nh*stepm elementary matrices
151: and the contribution of each individual to the likelihood is simply
152: hPijx.
153:
154: Also this programme outputs the covariance matrix of the parameters but also
155: of the life expectancies. It also computes the stable prevalence.
156:
157: Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).
158: Institut national d'études démographiques, Paris.
159: This software have been partly granted by Euro-REVES, a concerted action
160: from the European Union.
161: It is copyrighted identically to a GNU software product, ie programme and
162: software can be distributed freely for non commercial use. Latest version
163: can be accessed at http://euroreves.ined.fr/imach .
164:
165: Help to debug: LD_PRELOAD=/usr/local/lib/libnjamd.so ./imach foo.imach
166: or better on gdb : set env LD_PRELOAD=/usr/local/lib/libnjamd.so
167:
168: **********************************************************************/
169: /*
170: main
171: read parameterfile
172: read datafile
173: concatwav
174: freqsummary
175: if (mle >= 1)
176: mlikeli
177: print results files
178: if mle==1
179: computes hessian
180: read end of parameter file: agemin, agemax, bage, fage, estepm
181: begin-prev-date,...
182: open gnuplot file
183: open html file
184: stable prevalence
185: for age prevalim()
186: h Pij x
187: variance of p varprob
188: forecasting if prevfcast==1 prevforecast call prevalence()
189: health expectancies
190: Variance-covariance of DFLE
191: prevalence()
192: movingaverage()
193: varevsij()
194: if popbased==1 varevsij(,popbased)
195: total life expectancies
196: Variance of stable prevalence
197: end
198: */
199:
200:
201:
202:
203: #include <math.h>
204: #include <stdio.h>
205: #include <stdlib.h>
206: #include <unistd.h>
207:
208: /* #include <sys/time.h> */
209: #include <time.h>
210: #include "timeval.h"
211:
212: /* #include <libintl.h> */
213: /* #define _(String) gettext (String) */
214:
215: #define MAXLINE 256
216: #define GNUPLOTPROGRAM "gnuplot"
217: /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
218: #define FILENAMELENGTH 132
219: /*#define DEBUG*/
220: /*#define windows*/
221: #define GLOCK_ERROR_NOPATH -1 /* empty path */
222: #define GLOCK_ERROR_GETCWD -2 /* cannot get cwd */
223:
224: #define MAXPARM 30 /* Maximum number of parameters for the optimization */
225: #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */
226:
227: #define NINTERVMAX 8
228: #define NLSTATEMAX 8 /* Maximum number of live states (for func) */
229: #define NDEATHMAX 8 /* Maximum number of dead states (for func) */
230: #define NCOVMAX 8 /* Maximum number of covariates */
231: #define MAXN 20000
232: #define YEARM 12. /* Number of months per year */
233: #define AGESUP 130
234: #define AGEBASE 40
235: #define AGEGOMP 10. /* Minimal age for Gompertz adjustment */
236: #ifdef UNIX
237: #define DIRSEPARATOR '/'
238: #define ODIRSEPARATOR '\\'
239: #else
240: #define DIRSEPARATOR '\\'
241: #define ODIRSEPARATOR '/'
242: #endif
243:
244: /* $Id: imach.c,v 1.101 2004/09/15 10:38:38 brouard Exp $ */
245: /* $State: Exp $ */
246:
247: char version[]="Imach version 0.97b, May 2004, INED-EUROREVES ";
248: char fullversion[]="$Revision: 1.101 $ $Date: 2004/09/15 10:38:38 $";
249: int erreur, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings */
250: int nvar;
251: int cptcovn=0, cptcovage=0, cptcoveff=0,cptcov;
252: int npar=NPARMAX;
253: int nlstate=2; /* Number of live states */
254: int ndeath=1; /* Number of dead states */
255: int ncovmodel, ncovcol; /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
256: int popbased=0;
257:
258: int *wav; /* Number of waves for this individuual 0 is possible */
259: int maxwav; /* Maxim number of waves */
260: int jmin, jmax; /* min, max spacing between 2 waves */
261: int gipmx, gsw; /* Global variables on the number of contributions
262: to the likelihood and the sum of weights (done by funcone)*/
263: int mle, weightopt;
264: int **mw; /* mw[mi][i] is number of the mi wave for this individual */
265: int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
266: int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between
267: * wave mi and wave mi+1 is not an exact multiple of stepm. */
268: double jmean; /* Mean space between 2 waves */
269: double **oldm, **newm, **savm; /* Working pointers to matrices */
270: double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
271: FILE *fic,*ficpar, *ficparo,*ficres, *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
272: FILE *ficlog, *ficrespow;
273: int globpr; /* Global variable for printing or not */
274: double fretone; /* Only one call to likelihood */
275: long ipmx; /* Number of contributions */
276: double sw; /* Sum of weights */
277: char filerespow[FILENAMELENGTH];
278: char fileresilk[FILENAMELENGTH]; /* File of individual contributions to the likelihood */
279: FILE *ficresilk;
280: FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
281: FILE *ficresprobmorprev;
282: FILE *fichtm, *fichtmcov; /* Html File */
283: FILE *ficreseij;
284: char filerese[FILENAMELENGTH];
285: FILE *ficresvij;
286: char fileresv[FILENAMELENGTH];
287: FILE *ficresvpl;
288: char fileresvpl[FILENAMELENGTH];
289: char title[MAXLINE];
290: char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH], filerespl[FILENAMELENGTH];
291: char optionfilext[10], optionfilefiname[FILENAMELENGTH], plotcmd[FILENAMELENGTH];
292: char tmpout[FILENAMELENGTH], tmpout2[FILENAMELENGTH];
293: char command[FILENAMELENGTH];
294: int outcmd=0;
295:
296: char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
297:
298: char filelog[FILENAMELENGTH]; /* Log file */
299: char filerest[FILENAMELENGTH];
300: char fileregp[FILENAMELENGTH];
301: char popfile[FILENAMELENGTH];
302:
303: char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilehtmcov[FILENAMELENGTH] ;
304:
305: struct timeval start_time, end_time, curr_time, last_time, forecast_time;
306: struct timezone tzp;
307: extern int gettimeofday();
308: struct tm tmg, tm, tmf, *gmtime(), *localtime();
309: long time_value;
310: extern long time();
311: char strcurr[80], strfor[80];
312:
313: #define NR_END 1
314: #define FREE_ARG char*
315: #define FTOL 1.0e-10
316:
317: #define NRANSI
318: #define ITMAX 200
319:
320: #define TOL 2.0e-4
321:
322: #define CGOLD 0.3819660
323: #define ZEPS 1.0e-10
324: #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);
325:
326: #define GOLD 1.618034
327: #define GLIMIT 100.0
328: #define TINY 1.0e-20
329:
330: static double maxarg1,maxarg2;
331: #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
332: #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
333:
334: #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
335: #define rint(a) floor(a+0.5)
336:
337: static double sqrarg;
338: #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
339: #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}
340: int agegomp= AGEGOMP;
341:
342: int imx;
343: int stepm=1;
344: /* Stepm, step in month: minimum step interpolation*/
345:
346: int estepm;
347: /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
348:
349: int m,nb;
350: long *num;
351: int firstpass=0, lastpass=4,*cod, *ncodemax, *Tage,*cens;
352: double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
353: double **pmmij, ***probs;
354: double *ageexmed,*agecens;
355: double dateintmean=0;
356:
357: double *weight;
358: int **s; /* Status */
359: double *agedc, **covar, idx;
360: int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;
361:
362: double ftol=FTOL; /* Tolerance for computing Max Likelihood */
363: double ftolhess; /* Tolerance for computing hessian */
364:
365: /**************** split *************************/
366: static int split( char *path, char *dirc, char *name, char *ext, char *finame )
367: {
368: /* From a file name with full path (either Unix or Windows) we extract the directory (dirc)
369: the name of the file (name), its extension only (ext) and its first part of the name (finame)
370: */
371: char *ss; /* pointer */
372: int l1, l2; /* length counters */
373:
374: l1 = strlen(path ); /* length of path */
375: if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
376: ss= strrchr( path, DIRSEPARATOR ); /* find last / */
377: if ( ss == NULL ) { /* no directory, so use current */
378: /*if(strrchr(path, ODIRSEPARATOR )==NULL)
379: printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
380: /* get current working directory */
381: /* extern char* getcwd ( char *buf , int len);*/
382: if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {
383: return( GLOCK_ERROR_GETCWD );
384: }
385: strcpy( name, path ); /* we've got it */
386: } else { /* strip direcotry from path */
387: ss++; /* after this, the filename */
388: l2 = strlen( ss ); /* length of filename */
389: if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
390: strcpy( name, ss ); /* save file name */
391: strncpy( dirc, path, l1 - l2 ); /* now the directory */
392: dirc[l1-l2] = 0; /* add zero */
393: }
394: l1 = strlen( dirc ); /* length of directory */
395: /*#ifdef windows
396: if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; }
397: #else
398: if ( dirc[l1-1] != '/' ) { dirc[l1] = '/'; dirc[l1+1] = 0; }
399: #endif
400: */
401: ss = strrchr( name, '.' ); /* find last / */
402: if (ss >0){
403: ss++;
404: strcpy(ext,ss); /* save extension */
405: l1= strlen( name);
406: l2= strlen(ss)+1;
407: strncpy( finame, name, l1-l2);
408: finame[l1-l2]= 0;
409: }
410: return( 0 ); /* we're done */
411: }
412:
413:
414: /******************************************/
415:
416: void replace_back_to_slash(char *s, char*t)
417: {
418: int i;
419: int lg=0;
420: i=0;
421: lg=strlen(t);
422: for(i=0; i<= lg; i++) {
423: (s[i] = t[i]);
424: if (t[i]== '\\') s[i]='/';
425: }
426: }
427:
428: int nbocc(char *s, char occ)
429: {
430: int i,j=0;
431: int lg=20;
432: i=0;
433: lg=strlen(s);
434: for(i=0; i<= lg; i++) {
435: if (s[i] == occ ) j++;
436: }
437: return j;
438: }
439:
440: void cutv(char *u,char *v, char*t, char occ)
441: {
442: /* cuts string t into u and v where u is ended by char occ excluding it
443: and v is after occ excluding it too : ex cutv(u,v,"abcdef2ghi2j",2)
444: gives u="abcedf" and v="ghi2j" */
445: int i,lg,j,p=0;
446: i=0;
447: for(j=0; j<=strlen(t)-1; j++) {
448: if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;
449: }
450:
451: lg=strlen(t);
452: for(j=0; j<p; j++) {
453: (u[j] = t[j]);
454: }
455: u[p]='\0';
456:
457: for(j=0; j<= lg; j++) {
458: if (j>=(p+1))(v[j-p-1] = t[j]);
459: }
460: }
461:
462: /********************** nrerror ********************/
463:
464: void nrerror(char error_text[])
465: {
466: fprintf(stderr,"ERREUR ...\n");
467: fprintf(stderr,"%s\n",error_text);
468: exit(EXIT_FAILURE);
469: }
470: /*********************** vector *******************/
471: double *vector(int nl, int nh)
472: {
473: double *v;
474: v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
475: if (!v) nrerror("allocation failure in vector");
476: return v-nl+NR_END;
477: }
478:
479: /************************ free vector ******************/
480: void free_vector(double*v, int nl, int nh)
481: {
482: free((FREE_ARG)(v+nl-NR_END));
483: }
484:
485: /************************ivector *******************************/
486: int *ivector(long nl,long nh)
487: {
488: int *v;
489: v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
490: if (!v) nrerror("allocation failure in ivector");
491: return v-nl+NR_END;
492: }
493:
494: /******************free ivector **************************/
495: void free_ivector(int *v, long nl, long nh)
496: {
497: free((FREE_ARG)(v+nl-NR_END));
498: }
499:
500: /************************lvector *******************************/
501: long *lvector(long nl,long nh)
502: {
503: long *v;
504: v=(long *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(long)));
505: if (!v) nrerror("allocation failure in ivector");
506: return v-nl+NR_END;
507: }
508:
509: /******************free lvector **************************/
510: void free_lvector(long *v, long nl, long nh)
511: {
512: free((FREE_ARG)(v+nl-NR_END));
513: }
514:
515: /******************* imatrix *******************************/
516: int **imatrix(long nrl, long nrh, long ncl, long nch)
517: /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */
518: {
519: long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;
520: int **m;
521:
522: /* allocate pointers to rows */
523: m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));
524: if (!m) nrerror("allocation failure 1 in matrix()");
525: m += NR_END;
526: m -= nrl;
527:
528:
529: /* allocate rows and set pointers to them */
530: m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));
531: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
532: m[nrl] += NR_END;
533: m[nrl] -= ncl;
534:
535: for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;
536:
537: /* return pointer to array of pointers to rows */
538: return m;
539: }
540:
541: /****************** free_imatrix *************************/
542: void free_imatrix(m,nrl,nrh,ncl,nch)
543: int **m;
544: long nch,ncl,nrh,nrl;
545: /* free an int matrix allocated by imatrix() */
546: {
547: free((FREE_ARG) (m[nrl]+ncl-NR_END));
548: free((FREE_ARG) (m+nrl-NR_END));
549: }
550:
551: /******************* matrix *******************************/
552: double **matrix(long nrl, long nrh, long ncl, long nch)
553: {
554: long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
555: double **m;
556:
557: m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
558: if (!m) nrerror("allocation failure 1 in matrix()");
559: m += NR_END;
560: m -= nrl;
561:
562: m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
563: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
564: m[nrl] += NR_END;
565: m[nrl] -= ncl;
566:
567: for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
568: return m;
569: /* print *(*(m+1)+70) or print m[1][70]; print m+1 or print &(m[1])
570: */
571: }
572:
573: /*************************free matrix ************************/
574: void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
575: {
576: free((FREE_ARG)(m[nrl]+ncl-NR_END));
577: free((FREE_ARG)(m+nrl-NR_END));
578: }
579:
580: /******************* ma3x *******************************/
581: double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
582: {
583: long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
584: double ***m;
585:
586: m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
587: if (!m) nrerror("allocation failure 1 in matrix()");
588: m += NR_END;
589: m -= nrl;
590:
591: m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
592: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
593: m[nrl] += NR_END;
594: m[nrl] -= ncl;
595:
596: for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
597:
598: m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
599: if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
600: m[nrl][ncl] += NR_END;
601: m[nrl][ncl] -= nll;
602: for (j=ncl+1; j<=nch; j++)
603: m[nrl][j]=m[nrl][j-1]+nlay;
604:
605: for (i=nrl+1; i<=nrh; i++) {
606: m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
607: for (j=ncl+1; j<=nch; j++)
608: m[i][j]=m[i][j-1]+nlay;
609: }
610: return m;
611: /* gdb: p *(m+1) <=> p m[1] and p (m+1) <=> p (m+1) <=> p &(m[1])
612: &(m[i][j][k]) <=> *((*(m+i) + j)+k)
613: */
614: }
615:
616: /*************************free ma3x ************************/
617: void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
618: {
619: free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
620: free((FREE_ARG)(m[nrl]+ncl-NR_END));
621: free((FREE_ARG)(m+nrl-NR_END));
622: }
623:
624: /*************** function subdirf ***********/
625: char *subdirf(char fileres[])
626: {
627: /* Caution optionfilefiname is hidden */
628: strcpy(tmpout,optionfilefiname);
629: strcat(tmpout,"/"); /* Add to the right */
630: strcat(tmpout,fileres);
631: return tmpout;
632: }
633:
634: /*************** function subdirf2 ***********/
635: char *subdirf2(char fileres[], char *preop)
636: {
637:
638: /* Caution optionfilefiname is hidden */
639: strcpy(tmpout,optionfilefiname);
640: strcat(tmpout,"/");
641: strcat(tmpout,preop);
642: strcat(tmpout,fileres);
643: return tmpout;
644: }
645:
646: /*************** function subdirf3 ***********/
647: char *subdirf3(char fileres[], char *preop, char *preop2)
648: {
649:
650: /* Caution optionfilefiname is hidden */
651: strcpy(tmpout,optionfilefiname);
652: strcat(tmpout,"/");
653: strcat(tmpout,preop);
654: strcat(tmpout,preop2);
655: strcat(tmpout,fileres);
656: return tmpout;
657: }
658:
659: /***************** f1dim *************************/
660: extern int ncom;
661: extern double *pcom,*xicom;
662: extern double (*nrfunc)(double []);
663:
664: double f1dim(double x)
665: {
666: int j;
667: double f;
668: double *xt;
669:
670: xt=vector(1,ncom);
671: for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];
672: f=(*nrfunc)(xt);
673: free_vector(xt,1,ncom);
674: return f;
675: }
676:
677: /*****************brent *************************/
678: double brent(double ax, double bx, double cx, double (*f)(double), double tol, double *xmin)
679: {
680: int iter;
681: double a,b,d,etemp;
682: double fu,fv,fw,fx;
683: double ftemp;
684: double p,q,r,tol1,tol2,u,v,w,x,xm;
685: double e=0.0;
686:
687: a=(ax < cx ? ax : cx);
688: b=(ax > cx ? ax : cx);
689: x=w=v=bx;
690: fw=fv=fx=(*f)(x);
691: for (iter=1;iter<=ITMAX;iter++) {
692: xm=0.5*(a+b);
693: tol2=2.0*(tol1=tol*fabs(x)+ZEPS);
694: /* if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
695: printf(".");fflush(stdout);
696: fprintf(ficlog,".");fflush(ficlog);
697: #ifdef DEBUG
698: 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);
699: 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);
700: /* if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
701: #endif
702: if (fabs(x-xm) <= (tol2-0.5*(b-a))){
703: *xmin=x;
704: return fx;
705: }
706: ftemp=fu;
707: if (fabs(e) > tol1) {
708: r=(x-w)*(fx-fv);
709: q=(x-v)*(fx-fw);
710: p=(x-v)*q-(x-w)*r;
711: q=2.0*(q-r);
712: if (q > 0.0) p = -p;
713: q=fabs(q);
714: etemp=e;
715: e=d;
716: if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))
717: d=CGOLD*(e=(x >= xm ? a-x : b-x));
718: else {
719: d=p/q;
720: u=x+d;
721: if (u-a < tol2 || b-u < tol2)
722: d=SIGN(tol1,xm-x);
723: }
724: } else {
725: d=CGOLD*(e=(x >= xm ? a-x : b-x));
726: }
727: u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));
728: fu=(*f)(u);
729: if (fu <= fx) {
730: if (u >= x) a=x; else b=x;
731: SHFT(v,w,x,u)
732: SHFT(fv,fw,fx,fu)
733: } else {
734: if (u < x) a=u; else b=u;
735: if (fu <= fw || w == x) {
736: v=w;
737: w=u;
738: fv=fw;
739: fw=fu;
740: } else if (fu <= fv || v == x || v == w) {
741: v=u;
742: fv=fu;
743: }
744: }
745: }
746: nrerror("Too many iterations in brent");
747: *xmin=x;
748: return fx;
749: }
750:
751: /****************** mnbrak ***********************/
752:
753: void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,
754: double (*func)(double))
755: {
756: double ulim,u,r,q, dum;
757: double fu;
758:
759: *fa=(*func)(*ax);
760: *fb=(*func)(*bx);
761: if (*fb > *fa) {
762: SHFT(dum,*ax,*bx,dum)
763: SHFT(dum,*fb,*fa,dum)
764: }
765: *cx=(*bx)+GOLD*(*bx-*ax);
766: *fc=(*func)(*cx);
767: while (*fb > *fc) {
768: r=(*bx-*ax)*(*fb-*fc);
769: q=(*bx-*cx)*(*fb-*fa);
770: u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/
771: (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r));
772: ulim=(*bx)+GLIMIT*(*cx-*bx);
773: if ((*bx-u)*(u-*cx) > 0.0) {
774: fu=(*func)(u);
775: } else if ((*cx-u)*(u-ulim) > 0.0) {
776: fu=(*func)(u);
777: if (fu < *fc) {
778: SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))
779: SHFT(*fb,*fc,fu,(*func)(u))
780: }
781: } else if ((u-ulim)*(ulim-*cx) >= 0.0) {
782: u=ulim;
783: fu=(*func)(u);
784: } else {
785: u=(*cx)+GOLD*(*cx-*bx);
786: fu=(*func)(u);
787: }
788: SHFT(*ax,*bx,*cx,u)
789: SHFT(*fa,*fb,*fc,fu)
790: }
791: }
792:
793: /*************** linmin ************************/
794:
795: int ncom;
796: double *pcom,*xicom;
797: double (*nrfunc)(double []);
798:
799: void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))
800: {
801: double brent(double ax, double bx, double cx,
802: double (*f)(double), double tol, double *xmin);
803: double f1dim(double x);
804: void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,
805: double *fc, double (*func)(double));
806: int j;
807: double xx,xmin,bx,ax;
808: double fx,fb,fa;
809:
810: ncom=n;
811: pcom=vector(1,n);
812: xicom=vector(1,n);
813: nrfunc=func;
814: for (j=1;j<=n;j++) {
815: pcom[j]=p[j];
816: xicom[j]=xi[j];
817: }
818: ax=0.0;
819: xx=1.0;
820: mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim);
821: *fret=brent(ax,xx,bx,f1dim,TOL,&xmin);
822: #ifdef DEBUG
823: printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
824: fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
825: #endif
826: for (j=1;j<=n;j++) {
827: xi[j] *= xmin;
828: p[j] += xi[j];
829: }
830: free_vector(xicom,1,n);
831: free_vector(pcom,1,n);
832: }
833:
834: char *asc_diff_time(long time_sec, char ascdiff[])
835: {
836: long sec_left, days, hours, minutes;
837: days = (time_sec) / (60*60*24);
838: sec_left = (time_sec) % (60*60*24);
839: hours = (sec_left) / (60*60) ;
840: sec_left = (sec_left) %(60*60);
841: minutes = (sec_left) /60;
842: sec_left = (sec_left) % (60);
843: sprintf(ascdiff,"%d day(s) %d hour(s) %d minute(s) %d second(s)",days, hours, minutes, sec_left);
844: return ascdiff;
845: }
846:
847: /*************** powell ************************/
848: void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,
849: double (*func)(double []))
850: {
851: void linmin(double p[], double xi[], int n, double *fret,
852: double (*func)(double []));
853: int i,ibig,j;
854: double del,t,*pt,*ptt,*xit;
855: double fp,fptt;
856: double *xits;
857: int niterf, itmp;
858:
859: pt=vector(1,n);
860: ptt=vector(1,n);
861: xit=vector(1,n);
862: xits=vector(1,n);
863: *fret=(*func)(p);
864: for (j=1;j<=n;j++) pt[j]=p[j];
865: for (*iter=1;;++(*iter)) {
866: fp=(*fret);
867: ibig=0;
868: del=0.0;
869: last_time=curr_time;
870: (void) gettimeofday(&curr_time,&tzp);
871: 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);
872: /* 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);
873: fprintf(ficrespow,"%d %.12f %ld",*iter,*fret,curr_time.tv_sec-start_time.tv_sec);
874: */
875: for (i=1;i<=n;i++) {
876: printf(" %d %.12f",i, p[i]);
877: fprintf(ficlog," %d %.12lf",i, p[i]);
878: fprintf(ficrespow," %.12lf", p[i]);
879: }
880: printf("\n");
881: fprintf(ficlog,"\n");
882: fprintf(ficrespow,"\n");fflush(ficrespow);
883: if(*iter <=3){
884: tm = *localtime(&curr_time.tv_sec);
885: strcpy(strcurr,asctime(&tm));
886: /* asctime_r(&tm,strcurr); */
887: forecast_time=curr_time;
888: itmp = strlen(strcurr);
889: if(strcurr[itmp-1]=='\n') /* Windows outputs with a new line */
890: strcurr[itmp-1]='\0';
891: printf("\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,curr_time.tv_sec-last_time.tv_sec);
892: fprintf(ficlog,"\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,curr_time.tv_sec-last_time.tv_sec);
893: for(niterf=10;niterf<=30;niterf+=10){
894: forecast_time.tv_sec=curr_time.tv_sec+(niterf-*iter)*(curr_time.tv_sec-last_time.tv_sec);
895: tmf = *localtime(&forecast_time.tv_sec);
896: /* asctime_r(&tmf,strfor); */
897: strcpy(strfor,asctime(&tmf));
898: itmp = strlen(strfor);
899: if(strfor[itmp-1]=='\n')
900: strfor[itmp-1]='\0';
901: printf(" - if your program needs %d iterations to converge, convergence will be \n reached in %s i.e.\n on %s (current time is %s);\n",niterf, asc_diff_time(forecast_time.tv_sec-curr_time.tv_sec,tmpout),strfor,strcurr);
902: fprintf(ficlog," - if your program needs %d iterations to converge, convergence will be \n reached in %s i.e.\n on %s (current time is %s);\n",niterf, asc_diff_time(forecast_time.tv_sec-curr_time.tv_sec,tmpout),strfor,strcurr);
903: }
904: }
905: for (i=1;i<=n;i++) {
906: for (j=1;j<=n;j++) xit[j]=xi[j][i];
907: fptt=(*fret);
908: #ifdef DEBUG
909: printf("fret=%lf \n",*fret);
910: fprintf(ficlog,"fret=%lf \n",*fret);
911: #endif
912: printf("%d",i);fflush(stdout);
913: fprintf(ficlog,"%d",i);fflush(ficlog);
914: linmin(p,xit,n,fret,func);
915: if (fabs(fptt-(*fret)) > del) {
916: del=fabs(fptt-(*fret));
917: ibig=i;
918: }
919: #ifdef DEBUG
920: printf("%d %.12e",i,(*fret));
921: fprintf(ficlog,"%d %.12e",i,(*fret));
922: for (j=1;j<=n;j++) {
923: xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
924: printf(" x(%d)=%.12e",j,xit[j]);
925: fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
926: }
927: for(j=1;j<=n;j++) {
928: printf(" p=%.12e",p[j]);
929: fprintf(ficlog," p=%.12e",p[j]);
930: }
931: printf("\n");
932: fprintf(ficlog,"\n");
933: #endif
934: }
935: if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {
936: #ifdef DEBUG
937: int k[2],l;
938: k[0]=1;
939: k[1]=-1;
940: printf("Max: %.12e",(*func)(p));
941: fprintf(ficlog,"Max: %.12e",(*func)(p));
942: for (j=1;j<=n;j++) {
943: printf(" %.12e",p[j]);
944: fprintf(ficlog," %.12e",p[j]);
945: }
946: printf("\n");
947: fprintf(ficlog,"\n");
948: for(l=0;l<=1;l++) {
949: for (j=1;j<=n;j++) {
950: ptt[j]=p[j]+(p[j]-pt[j])*k[l];
951: printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
952: fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
953: }
954: printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
955: fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
956: }
957: #endif
958:
959:
960: free_vector(xit,1,n);
961: free_vector(xits,1,n);
962: free_vector(ptt,1,n);
963: free_vector(pt,1,n);
964: return;
965: }
966: if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");
967: for (j=1;j<=n;j++) {
968: ptt[j]=2.0*p[j]-pt[j];
969: xit[j]=p[j]-pt[j];
970: pt[j]=p[j];
971: }
972: fptt=(*func)(ptt);
973: if (fptt < fp) {
974: t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt);
975: if (t < 0.0) {
976: linmin(p,xit,n,fret,func);
977: for (j=1;j<=n;j++) {
978: xi[j][ibig]=xi[j][n];
979: xi[j][n]=xit[j];
980: }
981: #ifdef DEBUG
982: printf("Direction changed last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
983: fprintf(ficlog,"Direction changed last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
984: for(j=1;j<=n;j++){
985: printf(" %.12e",xit[j]);
986: fprintf(ficlog," %.12e",xit[j]);
987: }
988: printf("\n");
989: fprintf(ficlog,"\n");
990: #endif
991: }
992: }
993: }
994: }
995:
996: /**** Prevalence limit (stable prevalence) ****************/
997:
998: double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)
999: {
1000: /* Computes the prevalence limit in each live state at age x by left multiplying the unit
1001: matrix by transitions matrix until convergence is reached */
1002:
1003: int i, ii,j,k;
1004: double min, max, maxmin, maxmax,sumnew=0.;
1005: double **matprod2();
1006: double **out, cov[NCOVMAX], **pmij();
1007: double **newm;
1008: double agefin, delaymax=50 ; /* Max number of years to converge */
1009:
1010: for (ii=1;ii<=nlstate+ndeath;ii++)
1011: for (j=1;j<=nlstate+ndeath;j++){
1012: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1013: }
1014:
1015: cov[1]=1.;
1016:
1017: /* Even if hstepm = 1, at least one multiplication by the unit matrix */
1018: for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
1019: newm=savm;
1020: /* Covariates have to be included here again */
1021: cov[2]=agefin;
1022:
1023: for (k=1; k<=cptcovn;k++) {
1024: cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
1025: /* 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]]);*/
1026: }
1027: for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
1028: for (k=1; k<=cptcovprod;k++)
1029: cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
1030:
1031: /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
1032: /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
1033: /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
1034: out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);
1035:
1036: savm=oldm;
1037: oldm=newm;
1038: maxmax=0.;
1039: for(j=1;j<=nlstate;j++){
1040: min=1.;
1041: max=0.;
1042: for(i=1; i<=nlstate; i++) {
1043: sumnew=0;
1044: for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
1045: prlim[i][j]= newm[i][j]/(1-sumnew);
1046: max=FMAX(max,prlim[i][j]);
1047: min=FMIN(min,prlim[i][j]);
1048: }
1049: maxmin=max-min;
1050: maxmax=FMAX(maxmax,maxmin);
1051: }
1052: if(maxmax < ftolpl){
1053: return prlim;
1054: }
1055: }
1056: }
1057:
1058: /*************** transition probabilities ***************/
1059:
1060: double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
1061: {
1062: double s1, s2;
1063: /*double t34;*/
1064: int i,j,j1, nc, ii, jj;
1065:
1066: for(i=1; i<= nlstate; i++){
1067: for(j=1; j<i;j++){
1068: for (nc=1, s2=0.;nc <=ncovmodel; nc++){
1069: /*s2 += param[i][j][nc]*cov[nc];*/
1070: s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
1071: /* printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2); */
1072: }
1073: ps[i][j]=s2;
1074: /* printf("s1=%.17e, s2=%.17e\n",s1,s2); */
1075: }
1076: for(j=i+1; j<=nlstate+ndeath;j++){
1077: for (nc=1, s2=0.;nc <=ncovmodel; nc++){
1078: s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
1079: /* printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2); */
1080: }
1081: ps[i][j]=s2;
1082: }
1083: }
1084: /*ps[3][2]=1;*/
1085:
1086: for(i=1; i<= nlstate; i++){
1087: s1=0;
1088: for(j=1; j<i; j++)
1089: s1+=exp(ps[i][j]);
1090: for(j=i+1; j<=nlstate+ndeath; j++)
1091: s1+=exp(ps[i][j]);
1092: ps[i][i]=1./(s1+1.);
1093: for(j=1; j<i; j++)
1094: ps[i][j]= exp(ps[i][j])*ps[i][i];
1095: for(j=i+1; j<=nlstate+ndeath; j++)
1096: ps[i][j]= exp(ps[i][j])*ps[i][i];
1097: /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
1098: } /* end i */
1099:
1100: for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
1101: for(jj=1; jj<= nlstate+ndeath; jj++){
1102: ps[ii][jj]=0;
1103: ps[ii][ii]=1;
1104: }
1105: }
1106:
1107:
1108: /* for(ii=1; ii<= nlstate+ndeath; ii++){ */
1109: /* for(jj=1; jj<= nlstate+ndeath; jj++){ */
1110: /* printf("ddd %lf ",ps[ii][jj]); */
1111: /* } */
1112: /* printf("\n "); */
1113: /* } */
1114: /* printf("\n ");printf("%lf ",cov[2]); */
1115: /*
1116: for(i=1; i<= npar; i++) printf("%f ",x[i]);
1117: goto end;*/
1118: return ps;
1119: }
1120:
1121: /**************** Product of 2 matrices ******************/
1122:
1123: double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)
1124: {
1125: /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
1126: b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
1127: /* in, b, out are matrice of pointers which should have been initialized
1128: before: only the contents of out is modified. The function returns
1129: a pointer to pointers identical to out */
1130: long i, j, k;
1131: for(i=nrl; i<= nrh; i++)
1132: for(k=ncolol; k<=ncoloh; k++)
1133: for(j=ncl,out[i][k]=0.; j<=nch; j++)
1134: out[i][k] +=in[i][j]*b[j][k];
1135:
1136: return out;
1137: }
1138:
1139:
1140: /************* Higher Matrix Product ***************/
1141:
1142: double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
1143: {
1144: /* Computes the transition matrix starting at age 'age' over
1145: 'nhstepm*hstepm*stepm' months (i.e. until
1146: age (in years) age+nhstepm*hstepm*stepm/12) by multiplying
1147: nhstepm*hstepm matrices.
1148: Output is stored in matrix po[i][j][h] for h every 'hstepm' step
1149: (typically every 2 years instead of every month which is too big
1150: for the memory).
1151: Model is determined by parameters x and covariates have to be
1152: included manually here.
1153:
1154: */
1155:
1156: int i, j, d, h, k;
1157: double **out, cov[NCOVMAX];
1158: double **newm;
1159:
1160: /* Hstepm could be zero and should return the unit matrix */
1161: for (i=1;i<=nlstate+ndeath;i++)
1162: for (j=1;j<=nlstate+ndeath;j++){
1163: oldm[i][j]=(i==j ? 1.0 : 0.0);
1164: po[i][j][0]=(i==j ? 1.0 : 0.0);
1165: }
1166: /* Even if hstepm = 1, at least one multiplication by the unit matrix */
1167: for(h=1; h <=nhstepm; h++){
1168: for(d=1; d <=hstepm; d++){
1169: newm=savm;
1170: /* Covariates have to be included here again */
1171: cov[1]=1.;
1172: cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
1173: for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
1174: for (k=1; k<=cptcovage;k++)
1175: cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
1176: for (k=1; k<=cptcovprod;k++)
1177: cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
1178:
1179:
1180: /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
1181: /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
1182: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,
1183: pmij(pmmij,cov,ncovmodel,x,nlstate));
1184: savm=oldm;
1185: oldm=newm;
1186: }
1187: for(i=1; i<=nlstate+ndeath; i++)
1188: for(j=1;j<=nlstate+ndeath;j++) {
1189: po[i][j][h]=newm[i][j];
1190: /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);
1191: */
1192: }
1193: } /* end h */
1194: return po;
1195: }
1196:
1197:
1198: /*************** log-likelihood *************/
1199: double func( double *x)
1200: {
1201: int i, ii, j, k, mi, d, kk;
1202: double l, ll[NLSTATEMAX], cov[NCOVMAX];
1203: double **out;
1204: double sw; /* Sum of weights */
1205: double lli; /* Individual log likelihood */
1206: int s1, s2;
1207: double bbh, survp;
1208: long ipmx;
1209: /*extern weight */
1210: /* We are differentiating ll according to initial status */
1211: /* for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
1212: /*for(i=1;i<imx;i++)
1213: printf(" %d\n",s[4][i]);
1214: */
1215: cov[1]=1.;
1216:
1217: for(k=1; k<=nlstate; k++) ll[k]=0.;
1218:
1219: if(mle==1){
1220: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1221: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
1222: for(mi=1; mi<= wav[i]-1; mi++){
1223: for (ii=1;ii<=nlstate+ndeath;ii++)
1224: for (j=1;j<=nlstate+ndeath;j++){
1225: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1226: savm[ii][j]=(ii==j ? 1.0 : 0.0);
1227: }
1228: for(d=0; d<dh[mi][i]; d++){
1229: newm=savm;
1230: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
1231: for (kk=1; kk<=cptcovage;kk++) {
1232: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
1233: }
1234: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1235: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1236: savm=oldm;
1237: oldm=newm;
1238: } /* end mult */
1239:
1240: /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
1241: /* But now since version 0.9 we anticipate for bias at large stepm.
1242: * If stepm is larger than one month (smallest stepm) and if the exact delay
1243: * (in months) between two waves is not a multiple of stepm, we rounded to
1244: * the nearest (and in case of equal distance, to the lowest) interval but now
1245: * we keep into memory the bias bh[mi][i] and also the previous matrix product
1246: * (i.e to dh[mi][i]-1) saved in 'savm'. Then we inter(extra)polate the
1247: * probability in order to take into account the bias as a fraction of the way
1248: * from savm to out if bh is negative or even beyond if bh is positive. bh varies
1249: * -stepm/2 to stepm/2 .
1250: * For stepm=1 the results are the same as for previous versions of Imach.
1251: * For stepm > 1 the results are less biased than in previous versions.
1252: */
1253: s1=s[mw[mi][i]][i];
1254: s2=s[mw[mi+1][i]][i];
1255: bbh=(double)bh[mi][i]/(double)stepm;
1256: /* bias bh is positive if real duration
1257: * is higher than the multiple of stepm and negative otherwise.
1258: */
1259: /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
1260: if( s2 > nlstate){
1261: /* i.e. if s2 is a death state and if the date of death is known then the contribution
1262: to the likelihood is the probability to die between last step unit time and current
1263: step unit time, which is also equal to probability to die before dh
1264: minus probability to die before dh-stepm .
1265: In version up to 0.92 likelihood was computed
1266: as if date of death was unknown. Death was treated as any other
1267: health state: the date of the interview describes the actual state
1268: and not the date of a change in health state. The former idea was
1269: to consider that at each interview the state was recorded
1270: (healthy, disable or death) and IMaCh was corrected; but when we
1271: introduced the exact date of death then we should have modified
1272: the contribution of an exact death to the likelihood. This new
1273: contribution is smaller and very dependent of the step unit
1274: stepm. It is no more the probability to die between last interview
1275: and month of death but the probability to survive from last
1276: interview up to one month before death multiplied by the
1277: probability to die within a month. Thanks to Chris
1278: Jackson for correcting this bug. Former versions increased
1279: mortality artificially. The bad side is that we add another loop
1280: which slows down the processing. The difference can be up to 10%
1281: lower mortality.
1282: */
1283: lli=log(out[s1][s2] - savm[s1][s2]);
1284: }else{
1285: lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
1286: /* 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 */
1287: }
1288: /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
1289: /*if(lli ==000.0)*/
1290: /*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); */
1291: ipmx +=1;
1292: sw += weight[i];
1293: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1294: } /* end of wave */
1295: } /* end of individual */
1296: } else if(mle==2){
1297: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1298: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
1299: for(mi=1; mi<= wav[i]-1; mi++){
1300: for (ii=1;ii<=nlstate+ndeath;ii++)
1301: for (j=1;j<=nlstate+ndeath;j++){
1302: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1303: savm[ii][j]=(ii==j ? 1.0 : 0.0);
1304: }
1305: for(d=0; d<=dh[mi][i]; d++){
1306: newm=savm;
1307: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
1308: for (kk=1; kk<=cptcovage;kk++) {
1309: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
1310: }
1311: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1312: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1313: savm=oldm;
1314: oldm=newm;
1315: } /* end mult */
1316:
1317: s1=s[mw[mi][i]][i];
1318: s2=s[mw[mi+1][i]][i];
1319: bbh=(double)bh[mi][i]/(double)stepm;
1320: 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 */
1321: ipmx +=1;
1322: sw += weight[i];
1323: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1324: } /* end of wave */
1325: } /* end of individual */
1326: } else if(mle==3){ /* exponential inter-extrapolation */
1327: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1328: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
1329: for(mi=1; mi<= wav[i]-1; mi++){
1330: for (ii=1;ii<=nlstate+ndeath;ii++)
1331: for (j=1;j<=nlstate+ndeath;j++){
1332: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1333: savm[ii][j]=(ii==j ? 1.0 : 0.0);
1334: }
1335: for(d=0; d<dh[mi][i]; d++){
1336: newm=savm;
1337: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
1338: for (kk=1; kk<=cptcovage;kk++) {
1339: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
1340: }
1341: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1342: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1343: savm=oldm;
1344: oldm=newm;
1345: } /* end mult */
1346:
1347: s1=s[mw[mi][i]][i];
1348: s2=s[mw[mi+1][i]][i];
1349: bbh=(double)bh[mi][i]/(double)stepm;
1350: 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 */
1351: ipmx +=1;
1352: sw += weight[i];
1353: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1354: } /* end of wave */
1355: } /* end of individual */
1356: }else if (mle==4){ /* ml=4 no inter-extrapolation */
1357: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1358: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
1359: for(mi=1; mi<= wav[i]-1; mi++){
1360: for (ii=1;ii<=nlstate+ndeath;ii++)
1361: for (j=1;j<=nlstate+ndeath;j++){
1362: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1363: savm[ii][j]=(ii==j ? 1.0 : 0.0);
1364: }
1365: for(d=0; d<dh[mi][i]; d++){
1366: newm=savm;
1367: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
1368: for (kk=1; kk<=cptcovage;kk++) {
1369: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
1370: }
1371:
1372: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1373: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1374: savm=oldm;
1375: oldm=newm;
1376: } /* end mult */
1377:
1378: s1=s[mw[mi][i]][i];
1379: s2=s[mw[mi+1][i]][i];
1380: if( s2 > nlstate){
1381: lli=log(out[s1][s2] - savm[s1][s2]);
1382: }else{
1383: lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
1384: }
1385: ipmx +=1;
1386: sw += weight[i];
1387: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1388: /* 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]); */
1389: } /* end of wave */
1390: } /* end of individual */
1391: }else{ /* ml=5 no inter-extrapolation no jackson =0.8a */
1392: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1393: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
1394: for(mi=1; mi<= wav[i]-1; mi++){
1395: for (ii=1;ii<=nlstate+ndeath;ii++)
1396: for (j=1;j<=nlstate+ndeath;j++){
1397: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1398: savm[ii][j]=(ii==j ? 1.0 : 0.0);
1399: }
1400: for(d=0; d<dh[mi][i]; d++){
1401: newm=savm;
1402: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
1403: for (kk=1; kk<=cptcovage;kk++) {
1404: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
1405: }
1406:
1407: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1408: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1409: savm=oldm;
1410: oldm=newm;
1411: } /* end mult */
1412:
1413: s1=s[mw[mi][i]][i];
1414: s2=s[mw[mi+1][i]][i];
1415: lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
1416: ipmx +=1;
1417: sw += weight[i];
1418: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1419: /*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]);*/
1420: } /* end of wave */
1421: } /* end of individual */
1422: } /* End of if */
1423: for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
1424: /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
1425: l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
1426: return -l;
1427: }
1428:
1429: /*************** log-likelihood *************/
1430: double funcone( double *x)
1431: {
1432: /* Same as likeli but slower because of a lot of printf and if */
1433: int i, ii, j, k, mi, d, kk;
1434: double l, ll[NLSTATEMAX], cov[NCOVMAX];
1435: double **out;
1436: double lli; /* Individual log likelihood */
1437: double llt;
1438: int s1, s2;
1439: double bbh, survp;
1440: /*extern weight */
1441: /* We are differentiating ll according to initial status */
1442: /* for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
1443: /*for(i=1;i<imx;i++)
1444: printf(" %d\n",s[4][i]);
1445: */
1446: cov[1]=1.;
1447:
1448: for(k=1; k<=nlstate; k++) ll[k]=0.;
1449:
1450: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1451: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
1452: for(mi=1; mi<= wav[i]-1; mi++){
1453: for (ii=1;ii<=nlstate+ndeath;ii++)
1454: for (j=1;j<=nlstate+ndeath;j++){
1455: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1456: savm[ii][j]=(ii==j ? 1.0 : 0.0);
1457: }
1458: for(d=0; d<dh[mi][i]; d++){
1459: newm=savm;
1460: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
1461: for (kk=1; kk<=cptcovage;kk++) {
1462: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
1463: }
1464: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1465: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1466: savm=oldm;
1467: oldm=newm;
1468: } /* end mult */
1469:
1470: s1=s[mw[mi][i]][i];
1471: s2=s[mw[mi+1][i]][i];
1472: bbh=(double)bh[mi][i]/(double)stepm;
1473: /* bias is positive if real duration
1474: * is higher than the multiple of stepm and negative otherwise.
1475: */
1476: if( s2 > nlstate && (mle <5) ){ /* Jackson */
1477: lli=log(out[s1][s2] - savm[s1][s2]);
1478: } else if (mle==1){
1479: lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
1480: } else if(mle==2){
1481: 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 */
1482: } else if(mle==3){ /* exponential inter-extrapolation */
1483: 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 */
1484: } else if (mle==4){ /* mle=4 no inter-extrapolation */
1485: lli=log(out[s1][s2]); /* Original formula */
1486: } else{ /* ml>=5 no inter-extrapolation no jackson =0.8a */
1487: lli=log(out[s1][s2]); /* Original formula */
1488: } /* End of if */
1489: ipmx +=1;
1490: sw += weight[i];
1491: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1492: /* 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]); */
1493: if(globpr){
1494: fprintf(ficresilk,"%9d %6d %1d %1d %1d %1d %3d %10.6f %6.4f\
1495: %10.6f %10.6f %10.6f ", \
1496: num[i],i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],
1497: 2*weight[i]*lli,out[s1][s2],savm[s1][s2]);
1498: for(k=1,llt=0.,l=0.; k<=nlstate; k++){
1499: llt +=ll[k]*gipmx/gsw;
1500: fprintf(ficresilk," %10.6f",-ll[k]*gipmx/gsw);
1501: }
1502: fprintf(ficresilk," %10.6f\n", -llt);
1503: }
1504: } /* end of wave */
1505: } /* end of individual */
1506: for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
1507: /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
1508: l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
1509: if(globpr==0){ /* First time we count the contributions and weights */
1510: gipmx=ipmx;
1511: gsw=sw;
1512: }
1513: return -l;
1514: }
1515:
1516:
1517: /*************** function likelione ***********/
1518: void likelione(FILE *ficres,double p[], int npar, int nlstate, int *globpri, long *ipmx, double *sw, double *fretone, double (*funcone)(double []))
1519: {
1520: /* This routine should help understanding what is done with
1521: the selection of individuals/waves and
1522: to check the exact contribution to the likelihood.
1523: Plotting could be done.
1524: */
1525: int k;
1526:
1527: if(*globpri !=0){ /* Just counts and sums, no printings */
1528: strcpy(fileresilk,"ilk");
1529: strcat(fileresilk,fileres);
1530: if((ficresilk=fopen(fileresilk,"w"))==NULL) {
1531: printf("Problem with resultfile: %s\n", fileresilk);
1532: fprintf(ficlog,"Problem with resultfile: %s\n", fileresilk);
1533: }
1534: 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");
1535: fprintf(ficresilk, "#num_i i s1 s2 mi mw dh likeli weight 2wlli out sav ");
1536: /* i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],2*weight[i]*lli,out[s1][s2],savm[s1][s2]); */
1537: for(k=1; k<=nlstate; k++)
1538: fprintf(ficresilk," -2*gipw/gsw*weight*ll[%d]++",k);
1539: fprintf(ficresilk," -2*gipw/gsw*weight*ll(total)\n");
1540: }
1541:
1542: *fretone=(*funcone)(p);
1543: if(*globpri !=0){
1544: fclose(ficresilk);
1545: fprintf(fichtm,"\n<br>File of contributions to the likelihood: <a href=\"%s\">%s</a><br>\n",subdirf(fileresilk),subdirf(fileresilk));
1546: fflush(fichtm);
1547: }
1548: return;
1549: }
1550:
1551:
1552: /*********** Maximum Likelihood Estimation ***************/
1553:
1554: void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
1555: {
1556: int i,j, iter;
1557: double **xi;
1558: double fret;
1559: double fretone; /* Only one call to likelihood */
1560: /* char filerespow[FILENAMELENGTH];*/
1561: xi=matrix(1,npar,1,npar);
1562: for (i=1;i<=npar;i++)
1563: for (j=1;j<=npar;j++)
1564: xi[i][j]=(i==j ? 1.0 : 0.0);
1565: printf("Powell\n"); fprintf(ficlog,"Powell\n");
1566: strcpy(filerespow,"pow");
1567: strcat(filerespow,fileres);
1568: if((ficrespow=fopen(filerespow,"w"))==NULL) {
1569: printf("Problem with resultfile: %s\n", filerespow);
1570: fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
1571: }
1572: fprintf(ficrespow,"# Powell\n# iter -2*LL");
1573: for (i=1;i<=nlstate;i++)
1574: for(j=1;j<=nlstate+ndeath;j++)
1575: if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
1576: fprintf(ficrespow,"\n");
1577:
1578: powell(p,xi,npar,ftol,&iter,&fret,func);
1579:
1580: fclose(ficrespow);
1581: printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));
1582: fprintf(ficlog,"\n#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
1583: fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
1584:
1585: }
1586:
1587: /**** Computes Hessian and covariance matrix ***/
1588: void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
1589: {
1590: double **a,**y,*x,pd;
1591: double **hess;
1592: int i, j,jk;
1593: int *indx;
1594:
1595: double hessii(double p[], double delta, int theta, double delti[],double (*func)(double []),int npar);
1596: double hessij(double p[], double delti[], int i, int j,double (*func)(double []),int npar);
1597: void lubksb(double **a, int npar, int *indx, double b[]) ;
1598: void ludcmp(double **a, int npar, int *indx, double *d) ;
1599: double gompertz(double p[]);
1600: hess=matrix(1,npar,1,npar);
1601:
1602: printf("\nCalculation of the hessian matrix. Wait...\n");
1603: fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
1604: for (i=1;i<=npar;i++){
1605: printf("%d",i);fflush(stdout);
1606: fprintf(ficlog,"%d",i);fflush(ficlog);
1607:
1608: hess[i][i]=hessii(p,ftolhess,i,delti,func,npar);
1609:
1610: /* printf(" %f ",p[i]);
1611: printf(" %lf %lf %lf",hess[i][i],ftolhess,delti[i]);*/
1612: }
1613:
1614: for (i=1;i<=npar;i++) {
1615: for (j=1;j<=npar;j++) {
1616: if (j>i) {
1617: printf(".%d%d",i,j);fflush(stdout);
1618: fprintf(ficlog,".%d%d",i,j);fflush(ficlog);
1619: hess[i][j]=hessij(p,delti,i,j,func,npar);
1620:
1621: hess[j][i]=hess[i][j];
1622: /*printf(" %lf ",hess[i][j]);*/
1623: }
1624: }
1625: }
1626: printf("\n");
1627: fprintf(ficlog,"\n");
1628:
1629: printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
1630: fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
1631:
1632: a=matrix(1,npar,1,npar);
1633: y=matrix(1,npar,1,npar);
1634: x=vector(1,npar);
1635: indx=ivector(1,npar);
1636: for (i=1;i<=npar;i++)
1637: for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
1638: ludcmp(a,npar,indx,&pd);
1639:
1640: for (j=1;j<=npar;j++) {
1641: for (i=1;i<=npar;i++) x[i]=0;
1642: x[j]=1;
1643: lubksb(a,npar,indx,x);
1644: for (i=1;i<=npar;i++){
1645: matcov[i][j]=x[i];
1646: }
1647: }
1648:
1649: printf("\n#Hessian matrix#\n");
1650: fprintf(ficlog,"\n#Hessian matrix#\n");
1651: for (i=1;i<=npar;i++) {
1652: for (j=1;j<=npar;j++) {
1653: printf("%.3e ",hess[i][j]);
1654: fprintf(ficlog,"%.3e ",hess[i][j]);
1655: }
1656: printf("\n");
1657: fprintf(ficlog,"\n");
1658: }
1659:
1660: /* Recompute Inverse */
1661: for (i=1;i<=npar;i++)
1662: for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];
1663: ludcmp(a,npar,indx,&pd);
1664:
1665: /* printf("\n#Hessian matrix recomputed#\n");
1666:
1667: for (j=1;j<=npar;j++) {
1668: for (i=1;i<=npar;i++) x[i]=0;
1669: x[j]=1;
1670: lubksb(a,npar,indx,x);
1671: for (i=1;i<=npar;i++){
1672: y[i][j]=x[i];
1673: printf("%.3e ",y[i][j]);
1674: fprintf(ficlog,"%.3e ",y[i][j]);
1675: }
1676: printf("\n");
1677: fprintf(ficlog,"\n");
1678: }
1679: */
1680:
1681: free_matrix(a,1,npar,1,npar);
1682: free_matrix(y,1,npar,1,npar);
1683: free_vector(x,1,npar);
1684: free_ivector(indx,1,npar);
1685: free_matrix(hess,1,npar,1,npar);
1686:
1687:
1688: }
1689:
1690: /*************** hessian matrix ****************/
1691: double hessii(double x[], double delta, int theta, double delti[], double (*func)(double []), int npar)
1692: {
1693: int i;
1694: int l=1, lmax=20;
1695: double k1,k2;
1696: double p2[NPARMAX+1];
1697: double res;
1698: double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4;
1699: double fx;
1700: int k=0,kmax=10;
1701: double l1;
1702:
1703: fx=func(x);
1704: for (i=1;i<=npar;i++) p2[i]=x[i];
1705: for(l=0 ; l <=lmax; l++){
1706: l1=pow(10,l);
1707: delts=delt;
1708: for(k=1 ; k <kmax; k=k+1){
1709: delt = delta*(l1*k);
1710: p2[theta]=x[theta] +delt;
1711: k1=func(p2)-fx;
1712: p2[theta]=x[theta]-delt;
1713: k2=func(p2)-fx;
1714: /*res= (k1-2.0*fx+k2)/delt/delt; */
1715: res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */
1716:
1717: #ifdef DEBUG
1718: 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);
1719: 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);
1720: #endif
1721: /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
1722: if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
1723: k=kmax;
1724: }
1725: else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
1726: k=kmax; l=lmax*10.;
1727: }
1728: else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){
1729: delts=delt;
1730: }
1731: }
1732: }
1733: delti[theta]=delts;
1734: return res;
1735:
1736: }
1737:
1738: double hessij( double x[], double delti[], int thetai,int thetaj,double (*func)(double []),int npar)
1739: {
1740: int i;
1741: int l=1, l1, lmax=20;
1742: double k1,k2,k3,k4,res,fx;
1743: double p2[NPARMAX+1];
1744: int k;
1745:
1746: fx=func(x);
1747: for (k=1; k<=2; k++) {
1748: for (i=1;i<=npar;i++) p2[i]=x[i];
1749: p2[thetai]=x[thetai]+delti[thetai]/k;
1750: p2[thetaj]=x[thetaj]+delti[thetaj]/k;
1751: k1=func(p2)-fx;
1752:
1753: p2[thetai]=x[thetai]+delti[thetai]/k;
1754: p2[thetaj]=x[thetaj]-delti[thetaj]/k;
1755: k2=func(p2)-fx;
1756:
1757: p2[thetai]=x[thetai]-delti[thetai]/k;
1758: p2[thetaj]=x[thetaj]+delti[thetaj]/k;
1759: k3=func(p2)-fx;
1760:
1761: p2[thetai]=x[thetai]-delti[thetai]/k;
1762: p2[thetaj]=x[thetaj]-delti[thetaj]/k;
1763: k4=func(p2)-fx;
1764: res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */
1765: #ifdef DEBUG
1766: 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);
1767: 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);
1768: #endif
1769: }
1770: return res;
1771: }
1772:
1773: /************** Inverse of matrix **************/
1774: void ludcmp(double **a, int n, int *indx, double *d)
1775: {
1776: int i,imax,j,k;
1777: double big,dum,sum,temp;
1778: double *vv;
1779:
1780: vv=vector(1,n);
1781: *d=1.0;
1782: for (i=1;i<=n;i++) {
1783: big=0.0;
1784: for (j=1;j<=n;j++)
1785: if ((temp=fabs(a[i][j])) > big) big=temp;
1786: if (big == 0.0) nrerror("Singular matrix in routine ludcmp");
1787: vv[i]=1.0/big;
1788: }
1789: for (j=1;j<=n;j++) {
1790: for (i=1;i<j;i++) {
1791: sum=a[i][j];
1792: for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];
1793: a[i][j]=sum;
1794: }
1795: big=0.0;
1796: for (i=j;i<=n;i++) {
1797: sum=a[i][j];
1798: for (k=1;k<j;k++)
1799: sum -= a[i][k]*a[k][j];
1800: a[i][j]=sum;
1801: if ( (dum=vv[i]*fabs(sum)) >= big) {
1802: big=dum;
1803: imax=i;
1804: }
1805: }
1806: if (j != imax) {
1807: for (k=1;k<=n;k++) {
1808: dum=a[imax][k];
1809: a[imax][k]=a[j][k];
1810: a[j][k]=dum;
1811: }
1812: *d = -(*d);
1813: vv[imax]=vv[j];
1814: }
1815: indx[j]=imax;
1816: if (a[j][j] == 0.0) a[j][j]=TINY;
1817: if (j != n) {
1818: dum=1.0/(a[j][j]);
1819: for (i=j+1;i<=n;i++) a[i][j] *= dum;
1820: }
1821: }
1822: free_vector(vv,1,n); /* Doesn't work */
1823: ;
1824: }
1825:
1826: void lubksb(double **a, int n, int *indx, double b[])
1827: {
1828: int i,ii=0,ip,j;
1829: double sum;
1830:
1831: for (i=1;i<=n;i++) {
1832: ip=indx[i];
1833: sum=b[ip];
1834: b[ip]=b[i];
1835: if (ii)
1836: for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];
1837: else if (sum) ii=i;
1838: b[i]=sum;
1839: }
1840: for (i=n;i>=1;i--) {
1841: sum=b[i];
1842: for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];
1843: b[i]=sum/a[i][i];
1844: }
1845: }
1846:
1847: /************ Frequencies ********************/
1848: 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)
1849: { /* Some frequencies */
1850:
1851: int i, m, jk, k1,i1, j1, bool, z1,z2,j;
1852: int first;
1853: double ***freq; /* Frequencies */
1854: double *pp, **prop;
1855: double pos,posprop, k2, dateintsum=0,k2cpt=0;
1856: FILE *ficresp;
1857: char fileresp[FILENAMELENGTH];
1858:
1859: pp=vector(1,nlstate);
1860: prop=matrix(1,nlstate,iagemin,iagemax+3);
1861: strcpy(fileresp,"p");
1862: strcat(fileresp,fileres);
1863: if((ficresp=fopen(fileresp,"w"))==NULL) {
1864: printf("Problem with prevalence resultfile: %s\n", fileresp);
1865: fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
1866: exit(0);
1867: }
1868: freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);
1869: j1=0;
1870:
1871: j=cptcoveff;
1872: if (cptcovn<1) {j=1;ncodemax[1]=1;}
1873:
1874: first=1;
1875:
1876: for(k1=1; k1<=j;k1++){
1877: for(i1=1; i1<=ncodemax[k1];i1++){
1878: j1++;
1879: /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
1880: scanf("%d", i);*/
1881: for (i=-1; i<=nlstate+ndeath; i++)
1882: for (jk=-1; jk<=nlstate+ndeath; jk++)
1883: for(m=iagemin; m <= iagemax+3; m++)
1884: freq[i][jk][m]=0;
1885:
1886: for (i=1; i<=nlstate; i++)
1887: for(m=iagemin; m <= iagemax+3; m++)
1888: prop[i][m]=0;
1889:
1890: dateintsum=0;
1891: k2cpt=0;
1892: for (i=1; i<=imx; i++) {
1893: bool=1;
1894: if (cptcovn>0) {
1895: for (z1=1; z1<=cptcoveff; z1++)
1896: if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])
1897: bool=0;
1898: }
1899: if (bool==1){
1900: for(m=firstpass; m<=lastpass; m++){
1901: k2=anint[m][i]+(mint[m][i]/12.);
1902: /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/
1903: if(agev[m][i]==0) agev[m][i]=iagemax+1;
1904: if(agev[m][i]==1) agev[m][i]=iagemax+2;
1905: if (s[m][i]>0 && s[m][i]<=nlstate) prop[s[m][i]][(int)agev[m][i]] += weight[i];
1906: if (m<lastpass) {
1907: freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
1908: freq[s[m][i]][s[m+1][i]][iagemax+3] += weight[i];
1909: }
1910:
1911: if ((agev[m][i]>1) && (agev[m][i]< (iagemax+3))) {
1912: dateintsum=dateintsum+k2;
1913: k2cpt++;
1914: }
1915: /*}*/
1916: }
1917: }
1918: }
1919:
1920: /* fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
1921:
1922: if (cptcovn>0) {
1923: fprintf(ficresp, "\n#********** Variable ");
1924: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
1925: fprintf(ficresp, "**********\n#");
1926: }
1927: for(i=1; i<=nlstate;i++)
1928: fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
1929: fprintf(ficresp, "\n");
1930:
1931: for(i=iagemin; i <= iagemax+3; i++){
1932: if(i==iagemax+3){
1933: fprintf(ficlog,"Total");
1934: }else{
1935: if(first==1){
1936: first=0;
1937: printf("See log file for details...\n");
1938: }
1939: fprintf(ficlog,"Age %d", i);
1940: }
1941: for(jk=1; jk <=nlstate ; jk++){
1942: for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
1943: pp[jk] += freq[jk][m][i];
1944: }
1945: for(jk=1; jk <=nlstate ; jk++){
1946: for(m=-1, pos=0; m <=0 ; m++)
1947: pos += freq[jk][m][i];
1948: if(pp[jk]>=1.e-10){
1949: if(first==1){
1950: printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
1951: }
1952: fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
1953: }else{
1954: if(first==1)
1955: printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
1956: fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
1957: }
1958: }
1959:
1960: for(jk=1; jk <=nlstate ; jk++){
1961: for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
1962: pp[jk] += freq[jk][m][i];
1963: }
1964: for(jk=1,pos=0,posprop=0; jk <=nlstate ; jk++){
1965: pos += pp[jk];
1966: posprop += prop[jk][i];
1967: }
1968: for(jk=1; jk <=nlstate ; jk++){
1969: if(pos>=1.e-5){
1970: if(first==1)
1971: printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
1972: fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
1973: }else{
1974: if(first==1)
1975: printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
1976: fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
1977: }
1978: if( i <= iagemax){
1979: if(pos>=1.e-5){
1980: fprintf(ficresp," %d %.5f %.0f %.0f",i,prop[jk][i]/posprop, prop[jk][i],posprop);
1981: /*probs[i][jk][j1]= pp[jk]/pos;*/
1982: /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/
1983: }
1984: else
1985: fprintf(ficresp," %d NaNq %.0f %.0f",i,prop[jk][i],posprop);
1986: }
1987: }
1988:
1989: for(jk=-1; jk <=nlstate+ndeath; jk++)
1990: for(m=-1; m <=nlstate+ndeath; m++)
1991: if(freq[jk][m][i] !=0 ) {
1992: if(first==1)
1993: printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
1994: fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
1995: }
1996: if(i <= iagemax)
1997: fprintf(ficresp,"\n");
1998: if(first==1)
1999: printf("Others in log...\n");
2000: fprintf(ficlog,"\n");
2001: }
2002: }
2003: }
2004: dateintmean=dateintsum/k2cpt;
2005:
2006: fclose(ficresp);
2007: free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);
2008: free_vector(pp,1,nlstate);
2009: free_matrix(prop,1,nlstate,iagemin, iagemax+3);
2010: /* End of Freq */
2011: }
2012:
2013: /************ Prevalence ********************/
2014: 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)
2015: {
2016: /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
2017: in each health status at the date of interview (if between dateprev1 and dateprev2).
2018: We still use firstpass and lastpass as another selection.
2019: */
2020:
2021: int i, m, jk, k1, i1, j1, bool, z1,z2,j;
2022: double ***freq; /* Frequencies */
2023: double *pp, **prop;
2024: double pos,posprop;
2025: double y2; /* in fractional years */
2026: int iagemin, iagemax;
2027:
2028: iagemin= (int) agemin;
2029: iagemax= (int) agemax;
2030: /*pp=vector(1,nlstate);*/
2031: prop=matrix(1,nlstate,iagemin,iagemax+3);
2032: /* freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
2033: j1=0;
2034:
2035: j=cptcoveff;
2036: if (cptcovn<1) {j=1;ncodemax[1]=1;}
2037:
2038: for(k1=1; k1<=j;k1++){
2039: for(i1=1; i1<=ncodemax[k1];i1++){
2040: j1++;
2041:
2042: for (i=1; i<=nlstate; i++)
2043: for(m=iagemin; m <= iagemax+3; m++)
2044: prop[i][m]=0.0;
2045:
2046: for (i=1; i<=imx; i++) { /* Each individual */
2047: bool=1;
2048: if (cptcovn>0) {
2049: for (z1=1; z1<=cptcoveff; z1++)
2050: if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])
2051: bool=0;
2052: }
2053: if (bool==1) {
2054: for(m=firstpass; m<=lastpass; m++){/* Other selection (we can limit to certain interviews*/
2055: y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
2056: if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
2057: if(agev[m][i]==0) agev[m][i]=iagemax+1;
2058: if(agev[m][i]==1) agev[m][i]=iagemax+2;
2059: 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);
2060: if (s[m][i]>0 && s[m][i]<=nlstate) {
2061: /*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]]);*/
2062: prop[s[m][i]][(int)agev[m][i]] += weight[i];
2063: prop[s[m][i]][iagemax+3] += weight[i];
2064: }
2065: }
2066: } /* end selection of waves */
2067: }
2068: }
2069: for(i=iagemin; i <= iagemax+3; i++){
2070:
2071: for(jk=1,posprop=0; jk <=nlstate ; jk++) {
2072: posprop += prop[jk][i];
2073: }
2074:
2075: for(jk=1; jk <=nlstate ; jk++){
2076: if( i <= iagemax){
2077: if(posprop>=1.e-5){
2078: probs[i][jk][j1]= prop[jk][i]/posprop;
2079: }
2080: }
2081: }/* end jk */
2082: }/* end i */
2083: } /* end i1 */
2084: } /* end k1 */
2085:
2086: /* free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
2087: /*free_vector(pp,1,nlstate);*/
2088: free_matrix(prop,1,nlstate, iagemin,iagemax+3);
2089: } /* End of prevalence */
2090:
2091: /************* Waves Concatenation ***************/
2092:
2093: 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)
2094: {
2095: /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
2096: Death is a valid wave (if date is known).
2097: mw[mi][i] is the mi (mi=1 to wav[i]) effective wave of individual i
2098: dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
2099: and mw[mi+1][i]. dh depends on stepm.
2100: */
2101:
2102: int i, mi, m;
2103: /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
2104: double sum=0., jmean=0.;*/
2105: int first;
2106: int j, k=0,jk, ju, jl;
2107: double sum=0.;
2108: first=0;
2109: jmin=1e+5;
2110: jmax=-1;
2111: jmean=0.;
2112: for(i=1; i<=imx; i++){
2113: mi=0;
2114: m=firstpass;
2115: while(s[m][i] <= nlstate){
2116: if(s[m][i]>=1)
2117: mw[++mi][i]=m;
2118: if(m >=lastpass)
2119: break;
2120: else
2121: m++;
2122: }/* end while */
2123: if (s[m][i] > nlstate){
2124: mi++; /* Death is another wave */
2125: /* if(mi==0) never been interviewed correctly before death */
2126: /* Only death is a correct wave */
2127: mw[mi][i]=m;
2128: }
2129:
2130: wav[i]=mi;
2131: if(mi==0){
2132: nbwarn++;
2133: if(first==0){
2134: printf("Warning! None valid information for:%ld line=%d (skipped) and may be others, see log file\n",num[i],i);
2135: first=1;
2136: }
2137: if(first==1){
2138: fprintf(ficlog,"Warning! None valid information for:%ld line=%d (skipped)\n",num[i],i);
2139: }
2140: } /* end mi==0 */
2141: } /* End individuals */
2142:
2143: for(i=1; i<=imx; i++){
2144: for(mi=1; mi<wav[i];mi++){
2145: if (stepm <=0)
2146: dh[mi][i]=1;
2147: else{
2148: if (s[mw[mi+1][i]][i] > nlstate) { /* A death */
2149: if (agedc[i] < 2*AGESUP) {
2150: j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);
2151: if(j==0) j=1; /* Survives at least one month after exam */
2152: else if(j<0){
2153: nberr++;
2154: 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]);
2155: j=1; /* Temporary Dangerous patch */
2156: 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);
2157: 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]);
2158: 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);
2159: }
2160: k=k+1;
2161: if (j >= jmax) jmax=j;
2162: if (j <= jmin) jmin=j;
2163: sum=sum+j;
2164: /*if (j<0) printf("j=%d num=%d \n",j,i);*/
2165: /* printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
2166: }
2167: }
2168: else{
2169: j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
2170: /* printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
2171: k=k+1;
2172: if (j >= jmax) jmax=j;
2173: else if (j <= jmin)jmin=j;
2174: /* if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
2175: /*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]);*/
2176: if(j<0){
2177: nberr++;
2178: 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]);
2179: 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]);
2180: }
2181: sum=sum+j;
2182: }
2183: jk= j/stepm;
2184: jl= j -jk*stepm;
2185: ju= j -(jk+1)*stepm;
2186: if(mle <=1){ /* only if we use a the linear-interpoloation pseudo-likelihood */
2187: if(jl==0){
2188: dh[mi][i]=jk;
2189: bh[mi][i]=0;
2190: }else{ /* We want a negative bias in order to only have interpolation ie
2191: * at the price of an extra matrix product in likelihood */
2192: dh[mi][i]=jk+1;
2193: bh[mi][i]=ju;
2194: }
2195: }else{
2196: if(jl <= -ju){
2197: dh[mi][i]=jk;
2198: bh[mi][i]=jl; /* bias is positive if real duration
2199: * is higher than the multiple of stepm and negative otherwise.
2200: */
2201: }
2202: else{
2203: dh[mi][i]=jk+1;
2204: bh[mi][i]=ju;
2205: }
2206: if(dh[mi][i]==0){
2207: dh[mi][i]=1; /* At least one step */
2208: bh[mi][i]=ju; /* At least one step */
2209: /* 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);*/
2210: }
2211: } /* end if mle */
2212: }
2213: } /* end wave */
2214: }
2215: jmean=sum/k;
2216: printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);
2217: fprintf(ficlog,"Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);
2218: }
2219:
2220: /*********** Tricode ****************************/
2221: void tricode(int *Tvar, int **nbcode, int imx)
2222: {
2223:
2224: int Ndum[20],ij=1, k, j, i, maxncov=19;
2225: int cptcode=0;
2226: cptcoveff=0;
2227:
2228: for (k=0; k<maxncov; k++) Ndum[k]=0;
2229: for (k=1; k<=7; k++) ncodemax[k]=0;
2230:
2231: for (j=1; j<=(cptcovn+2*cptcovprod); j++) {
2232: for (i=1; i<=imx; i++) { /*reads the data file to get the maximum
2233: modality*/
2234: ij=(int)(covar[Tvar[j]][i]); /* ij is the modality of this individual*/
2235: Ndum[ij]++; /*store the modality */
2236: /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
2237: if (ij > cptcode) cptcode=ij; /* getting the maximum of covariable
2238: Tvar[j]. If V=sex and male is 0 and
2239: female is 1, then cptcode=1.*/
2240: }
2241:
2242: for (i=0; i<=cptcode; i++) {
2243: 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 */
2244: }
2245:
2246: ij=1;
2247: for (i=1; i<=ncodemax[j]; i++) {
2248: for (k=0; k<= maxncov; k++) {
2249: if (Ndum[k] != 0) {
2250: nbcode[Tvar[j]][ij]=k;
2251: /* 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; */
2252:
2253: ij++;
2254: }
2255: if (ij > ncodemax[j]) break;
2256: }
2257: }
2258: }
2259:
2260: for (k=0; k< maxncov; k++) Ndum[k]=0;
2261:
2262: for (i=1; i<=ncovmodel-2; i++) {
2263: /* Listing of all covariables in staement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/
2264: ij=Tvar[i];
2265: Ndum[ij]++;
2266: }
2267:
2268: ij=1;
2269: for (i=1; i<= maxncov; i++) {
2270: if((Ndum[i]!=0) && (i<=ncovcol)){
2271: Tvaraff[ij]=i; /*For printing */
2272: ij++;
2273: }
2274: }
2275:
2276: cptcoveff=ij-1; /*Number of simple covariates*/
2277: }
2278:
2279: /*********** Health Expectancies ****************/
2280:
2281: 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 )
2282:
2283: {
2284: /* Health expectancies */
2285: int i, j, nhstepm, hstepm, h, nstepm, k, cptj;
2286: double age, agelim, hf;
2287: double ***p3mat,***varhe;
2288: double **dnewm,**doldm;
2289: double *xp;
2290: double **gp, **gm;
2291: double ***gradg, ***trgradg;
2292: int theta;
2293:
2294: varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage);
2295: xp=vector(1,npar);
2296: dnewm=matrix(1,nlstate*nlstate,1,npar);
2297: doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate);
2298:
2299: fprintf(ficreseij,"# Health expectancies\n");
2300: fprintf(ficreseij,"# Age");
2301: for(i=1; i<=nlstate;i++)
2302: for(j=1; j<=nlstate;j++)
2303: fprintf(ficreseij," %1d-%1d (SE)",i,j);
2304: fprintf(ficreseij,"\n");
2305:
2306: if(estepm < stepm){
2307: printf ("Problem %d lower than %d\n",estepm, stepm);
2308: }
2309: else hstepm=estepm;
2310: /* We compute the life expectancy from trapezoids spaced every estepm months
2311: * This is mainly to measure the difference between two models: for example
2312: * if stepm=24 months pijx are given only every 2 years and by summing them
2313: * we are calculating an estimate of the Life Expectancy assuming a linear
2314: * progression in between and thus overestimating or underestimating according
2315: * to the curvature of the survival function. If, for the same date, we
2316: * estimate the model with stepm=1 month, we can keep estepm to 24 months
2317: * to compare the new estimate of Life expectancy with the same linear
2318: * hypothesis. A more precise result, taking into account a more precise
2319: * curvature will be obtained if estepm is as small as stepm. */
2320:
2321: /* For example we decided to compute the life expectancy with the smallest unit */
2322: /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
2323: nhstepm is the number of hstepm from age to agelim
2324: nstepm is the number of stepm from age to agelin.
2325: Look at hpijx to understand the reason of that which relies in memory size
2326: and note for a fixed period like estepm months */
2327: /* We decided (b) to get a life expectancy respecting the most precise curvature of the
2328: survival function given by stepm (the optimization length). Unfortunately it
2329: means that if the survival funtion is printed only each two years of age and if
2330: you sum them up and add 1 year (area under the trapezoids) you won't get the same
2331: results. So we changed our mind and took the option of the best precision.
2332: */
2333: hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
2334:
2335: agelim=AGESUP;
2336: for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
2337: /* nhstepm age range expressed in number of stepm */
2338: nstepm=(int) rint((agelim-age)*YEARM/stepm);
2339: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
2340: /* if (stepm >= YEARM) hstepm=1;*/
2341: nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
2342: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
2343: gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);
2344: gp=matrix(0,nhstepm,1,nlstate*nlstate);
2345: gm=matrix(0,nhstepm,1,nlstate*nlstate);
2346:
2347: /* Computed by stepm unit matrices, product of hstepm matrices, stored
2348: in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
2349: hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);
2350:
2351:
2352: hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
2353:
2354: /* Computing Variances of health expectancies */
2355:
2356: for(theta=1; theta <=npar; theta++){
2357: for(i=1; i<=npar; i++){
2358: xp[i] = x[i] + (i==theta ?delti[theta]:0);
2359: }
2360: hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
2361:
2362: cptj=0;
2363: for(j=1; j<= nlstate; j++){
2364: for(i=1; i<=nlstate; i++){
2365: cptj=cptj+1;
2366: for(h=0, gp[h][cptj]=0.; h<=nhstepm-1; h++){
2367: gp[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;
2368: }
2369: }
2370: }
2371:
2372:
2373: for(i=1; i<=npar; i++)
2374: xp[i] = x[i] - (i==theta ?delti[theta]:0);
2375: hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
2376:
2377: cptj=0;
2378: for(j=1; j<= nlstate; j++){
2379: for(i=1;i<=nlstate;i++){
2380: cptj=cptj+1;
2381: for(h=0, gm[h][cptj]=0.; h<=nhstepm-1; h++){
2382:
2383: gm[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;
2384: }
2385: }
2386: }
2387: for(j=1; j<= nlstate*nlstate; j++)
2388: for(h=0; h<=nhstepm-1; h++){
2389: gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
2390: }
2391: }
2392:
2393: /* End theta */
2394:
2395: trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar);
2396:
2397: for(h=0; h<=nhstepm-1; h++)
2398: for(j=1; j<=nlstate*nlstate;j++)
2399: for(theta=1; theta <=npar; theta++)
2400: trgradg[h][j][theta]=gradg[h][theta][j];
2401:
2402:
2403: for(i=1;i<=nlstate*nlstate;i++)
2404: for(j=1;j<=nlstate*nlstate;j++)
2405: varhe[i][j][(int)age] =0.;
2406:
2407: printf("%d|",(int)age);fflush(stdout);
2408: fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
2409: for(h=0;h<=nhstepm-1;h++){
2410: for(k=0;k<=nhstepm-1;k++){
2411: matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov);
2412: matprod2(doldm,dnewm,1,nlstate*nlstate,1,npar,1,nlstate*nlstate,gradg[k]);
2413: for(i=1;i<=nlstate*nlstate;i++)
2414: for(j=1;j<=nlstate*nlstate;j++)
2415: varhe[i][j][(int)age] += doldm[i][j]*hf*hf;
2416: }
2417: }
2418: /* Computing expectancies */
2419: for(i=1; i<=nlstate;i++)
2420: for(j=1; j<=nlstate;j++)
2421: for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
2422: eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
2423:
2424: /* 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]);*/
2425:
2426: }
2427:
2428: fprintf(ficreseij,"%3.0f",age );
2429: cptj=0;
2430: for(i=1; i<=nlstate;i++)
2431: for(j=1; j<=nlstate;j++){
2432: cptj++;
2433: fprintf(ficreseij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[cptj][cptj][(int)age]) );
2434: }
2435: fprintf(ficreseij,"\n");
2436:
2437: free_matrix(gm,0,nhstepm,1,nlstate*nlstate);
2438: free_matrix(gp,0,nhstepm,1,nlstate*nlstate);
2439: free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*nlstate);
2440: free_ma3x(trgradg,0,nhstepm,1,nlstate*nlstate,1,npar);
2441: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
2442: }
2443: printf("\n");
2444: fprintf(ficlog,"\n");
2445:
2446: free_vector(xp,1,npar);
2447: free_matrix(dnewm,1,nlstate*nlstate,1,npar);
2448: free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate);
2449: free_ma3x(varhe,1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int)fage);
2450: }
2451:
2452: /************ Variance ******************/
2453: 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)
2454: {
2455: /* Variance of health expectancies */
2456: /* double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
2457: /* double **newm;*/
2458: double **dnewm,**doldm;
2459: double **dnewmp,**doldmp;
2460: int i, j, nhstepm, hstepm, h, nstepm ;
2461: int k, cptcode;
2462: double *xp;
2463: double **gp, **gm; /* for var eij */
2464: double ***gradg, ***trgradg; /*for var eij */
2465: double **gradgp, **trgradgp; /* for var p point j */
2466: double *gpp, *gmp; /* for var p point j */
2467: double **varppt; /* for var p point j nlstate to nlstate+ndeath */
2468: double ***p3mat;
2469: double age,agelim, hf;
2470: double ***mobaverage;
2471: int theta;
2472: char digit[4];
2473: char digitp[25];
2474:
2475: char fileresprobmorprev[FILENAMELENGTH];
2476:
2477: if(popbased==1){
2478: if(mobilav!=0)
2479: strcpy(digitp,"-populbased-mobilav-");
2480: else strcpy(digitp,"-populbased-nomobil-");
2481: }
2482: else
2483: strcpy(digitp,"-stablbased-");
2484:
2485: if (mobilav!=0) {
2486: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
2487: if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
2488: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
2489: printf(" Error in movingaverage mobilav=%d\n",mobilav);
2490: }
2491: }
2492:
2493: strcpy(fileresprobmorprev,"prmorprev");
2494: sprintf(digit,"%-d",ij);
2495: /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
2496: strcat(fileresprobmorprev,digit); /* Tvar to be done */
2497: strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
2498: strcat(fileresprobmorprev,fileres);
2499: if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
2500: printf("Problem with resultfile: %s\n", fileresprobmorprev);
2501: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
2502: }
2503: printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
2504: fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
2505: 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);
2506: fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
2507: for(j=nlstate+1; j<=(nlstate+ndeath);j++){
2508: fprintf(ficresprobmorprev," p.%-d SE",j);
2509: for(i=1; i<=nlstate;i++)
2510: fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
2511: }
2512: fprintf(ficresprobmorprev,"\n");
2513: fprintf(ficgp,"\n# Routine varevsij");
2514: 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");
2515: fprintf(fichtm,"\n<br>%s <br>\n",digitp);
2516: /* } */
2517: varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
2518:
2519: 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");
2520: fprintf(ficresvij,"# Age");
2521: for(i=1; i<=nlstate;i++)
2522: for(j=1; j<=nlstate;j++)
2523: fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);
2524: fprintf(ficresvij,"\n");
2525:
2526: xp=vector(1,npar);
2527: dnewm=matrix(1,nlstate,1,npar);
2528: doldm=matrix(1,nlstate,1,nlstate);
2529: dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
2530: doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
2531:
2532: gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
2533: gpp=vector(nlstate+1,nlstate+ndeath);
2534: gmp=vector(nlstate+1,nlstate+ndeath);
2535: trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
2536:
2537: if(estepm < stepm){
2538: printf ("Problem %d lower than %d\n",estepm, stepm);
2539: }
2540: else hstepm=estepm;
2541: /* For example we decided to compute the life expectancy with the smallest unit */
2542: /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
2543: nhstepm is the number of hstepm from age to agelim
2544: nstepm is the number of stepm from age to agelin.
2545: Look at hpijx to understand the reason of that which relies in memory size
2546: and note for a fixed period like k years */
2547: /* We decided (b) to get a life expectancy respecting the most precise curvature of the
2548: survival function given by stepm (the optimization length). Unfortunately it
2549: means that if the survival funtion is printed every two years of age and if
2550: you sum them up and add 1 year (area under the trapezoids) you won't get the same
2551: results. So we changed our mind and took the option of the best precision.
2552: */
2553: hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
2554: agelim = AGESUP;
2555: for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
2556: nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
2557: nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
2558: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
2559: gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
2560: gp=matrix(0,nhstepm,1,nlstate);
2561: gm=matrix(0,nhstepm,1,nlstate);
2562:
2563:
2564: for(theta=1; theta <=npar; theta++){
2565: for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
2566: xp[i] = x[i] + (i==theta ?delti[theta]:0);
2567: }
2568: hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
2569: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
2570:
2571: if (popbased==1) {
2572: if(mobilav ==0){
2573: for(i=1; i<=nlstate;i++)
2574: prlim[i][i]=probs[(int)age][i][ij];
2575: }else{ /* mobilav */
2576: for(i=1; i<=nlstate;i++)
2577: prlim[i][i]=mobaverage[(int)age][i][ij];
2578: }
2579: }
2580:
2581: for(j=1; j<= nlstate; j++){
2582: for(h=0; h<=nhstepm; h++){
2583: for(i=1, gp[h][j]=0.;i<=nlstate;i++)
2584: gp[h][j] += prlim[i][i]*p3mat[i][j][h];
2585: }
2586: }
2587: /* This for computing probability of death (h=1 means
2588: computed over hstepm matrices product = hstepm*stepm months)
2589: as a weighted average of prlim.
2590: */
2591: for(j=nlstate+1;j<=nlstate+ndeath;j++){
2592: for(i=1,gpp[j]=0.; i<= nlstate; i++)
2593: gpp[j] += prlim[i][i]*p3mat[i][j][1];
2594: }
2595: /* end probability of death */
2596:
2597: for(i=1; i<=npar; i++) /* Computes gradient x - delta */
2598: xp[i] = x[i] - (i==theta ?delti[theta]:0);
2599: hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
2600: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
2601:
2602: if (popbased==1) {
2603: if(mobilav ==0){
2604: for(i=1; i<=nlstate;i++)
2605: prlim[i][i]=probs[(int)age][i][ij];
2606: }else{ /* mobilav */
2607: for(i=1; i<=nlstate;i++)
2608: prlim[i][i]=mobaverage[(int)age][i][ij];
2609: }
2610: }
2611:
2612: for(j=1; j<= nlstate; j++){
2613: for(h=0; h<=nhstepm; h++){
2614: for(i=1, gm[h][j]=0.;i<=nlstate;i++)
2615: gm[h][j] += prlim[i][i]*p3mat[i][j][h];
2616: }
2617: }
2618: /* This for computing probability of death (h=1 means
2619: computed over hstepm matrices product = hstepm*stepm months)
2620: as a weighted average of prlim.
2621: */
2622: for(j=nlstate+1;j<=nlstate+ndeath;j++){
2623: for(i=1,gmp[j]=0.; i<= nlstate; i++)
2624: gmp[j] += prlim[i][i]*p3mat[i][j][1];
2625: }
2626: /* end probability of death */
2627:
2628: for(j=1; j<= nlstate; j++) /* vareij */
2629: for(h=0; h<=nhstepm; h++){
2630: gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
2631: }
2632:
2633: for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
2634: gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
2635: }
2636:
2637: } /* End theta */
2638:
2639: trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
2640:
2641: for(h=0; h<=nhstepm; h++) /* veij */
2642: for(j=1; j<=nlstate;j++)
2643: for(theta=1; theta <=npar; theta++)
2644: trgradg[h][j][theta]=gradg[h][theta][j];
2645:
2646: for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
2647: for(theta=1; theta <=npar; theta++)
2648: trgradgp[j][theta]=gradgp[theta][j];
2649:
2650:
2651: hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
2652: for(i=1;i<=nlstate;i++)
2653: for(j=1;j<=nlstate;j++)
2654: vareij[i][j][(int)age] =0.;
2655:
2656: for(h=0;h<=nhstepm;h++){
2657: for(k=0;k<=nhstepm;k++){
2658: matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
2659: matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
2660: for(i=1;i<=nlstate;i++)
2661: for(j=1;j<=nlstate;j++)
2662: vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
2663: }
2664: }
2665:
2666: /* pptj */
2667: matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
2668: matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
2669: for(j=nlstate+1;j<=nlstate+ndeath;j++)
2670: for(i=nlstate+1;i<=nlstate+ndeath;i++)
2671: varppt[j][i]=doldmp[j][i];
2672: /* end ppptj */
2673: /* x centered again */
2674: hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);
2675: prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);
2676:
2677: if (popbased==1) {
2678: if(mobilav ==0){
2679: for(i=1; i<=nlstate;i++)
2680: prlim[i][i]=probs[(int)age][i][ij];
2681: }else{ /* mobilav */
2682: for(i=1; i<=nlstate;i++)
2683: prlim[i][i]=mobaverage[(int)age][i][ij];
2684: }
2685: }
2686:
2687: /* This for computing probability of death (h=1 means
2688: computed over hstepm (estepm) matrices product = hstepm*stepm months)
2689: as a weighted average of prlim.
2690: */
2691: for(j=nlstate+1;j<=nlstate+ndeath;j++){
2692: for(i=1,gmp[j]=0.;i<= nlstate; i++)
2693: gmp[j] += prlim[i][i]*p3mat[i][j][1];
2694: }
2695: /* end probability of death */
2696:
2697: fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
2698: for(j=nlstate+1; j<=(nlstate+ndeath);j++){
2699: fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
2700: for(i=1; i<=nlstate;i++){
2701: fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
2702: }
2703: }
2704: fprintf(ficresprobmorprev,"\n");
2705:
2706: fprintf(ficresvij,"%.0f ",age );
2707: for(i=1; i<=nlstate;i++)
2708: for(j=1; j<=nlstate;j++){
2709: fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
2710: }
2711: fprintf(ficresvij,"\n");
2712: free_matrix(gp,0,nhstepm,1,nlstate);
2713: free_matrix(gm,0,nhstepm,1,nlstate);
2714: free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
2715: free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
2716: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
2717: } /* End age */
2718: free_vector(gpp,nlstate+1,nlstate+ndeath);
2719: free_vector(gmp,nlstate+1,nlstate+ndeath);
2720: free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
2721: free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
2722: fprintf(ficgp,"\nset noparametric;set nolabel; set ter png small;set size 0.65, 0.65");
2723: /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */
2724: fprintf(ficgp,"\n set log y; set nolog x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
2725: /* fprintf(ficgp,"\n plot \"%s\" u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm); */
2726: /* fprintf(ficgp,"\n replot \"%s\" u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm); */
2727: /* fprintf(ficgp,"\n replot \"%s\" u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm); */
2728: fprintf(ficgp,"\n plot \"%s\" u 1:($3) not w l 1 ",subdirf(fileresprobmorprev));
2729: fprintf(ficgp,"\n replot \"%s\" u 1:(($3+1.96*$4)) t \"95\%% interval\" w l 2 ",subdirf(fileresprobmorprev));
2730: fprintf(ficgp,"\n replot \"%s\" u 1:(($3-1.96*$4)) not w l 2 ",subdirf(fileresprobmorprev));
2731: fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",subdirf(fileresprobmorprev),subdirf(fileresprobmorprev));
2732: 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);
2733: /* 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);
2734: */
2735: /* fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.png\";replot;",digitp,optionfilefiname,digit); */
2736: fprintf(ficgp,"\nset out \"%s%s.png\";replot;\n",subdirf3(optionfilefiname,"varmuptjgr",digitp),digit);
2737:
2738: free_vector(xp,1,npar);
2739: free_matrix(doldm,1,nlstate,1,nlstate);
2740: free_matrix(dnewm,1,nlstate,1,npar);
2741: free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
2742: free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
2743: free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
2744: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
2745: fclose(ficresprobmorprev);
2746: fflush(ficgp);
2747: fflush(fichtm);
2748: } /* end varevsij */
2749:
2750: /************ Variance of prevlim ******************/
2751: 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)
2752: {
2753: /* Variance of prevalence limit */
2754: /* double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
2755: double **newm;
2756: double **dnewm,**doldm;
2757: int i, j, nhstepm, hstepm;
2758: int k, cptcode;
2759: double *xp;
2760: double *gp, *gm;
2761: double **gradg, **trgradg;
2762: double age,agelim;
2763: int theta;
2764:
2765: fprintf(ficresvpl,"# Standard deviation of stable prevalences \n");
2766: fprintf(ficresvpl,"# Age");
2767: for(i=1; i<=nlstate;i++)
2768: fprintf(ficresvpl," %1d-%1d",i,i);
2769: fprintf(ficresvpl,"\n");
2770:
2771: xp=vector(1,npar);
2772: dnewm=matrix(1,nlstate,1,npar);
2773: doldm=matrix(1,nlstate,1,nlstate);
2774:
2775: hstepm=1*YEARM; /* Every year of age */
2776: hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */
2777: agelim = AGESUP;
2778: for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
2779: nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
2780: if (stepm >= YEARM) hstepm=1;
2781: nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
2782: gradg=matrix(1,npar,1,nlstate);
2783: gp=vector(1,nlstate);
2784: gm=vector(1,nlstate);
2785:
2786: for(theta=1; theta <=npar; theta++){
2787: for(i=1; i<=npar; i++){ /* Computes gradient */
2788: xp[i] = x[i] + (i==theta ?delti[theta]:0);
2789: }
2790: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
2791: for(i=1;i<=nlstate;i++)
2792: gp[i] = prlim[i][i];
2793:
2794: for(i=1; i<=npar; i++) /* Computes gradient */
2795: xp[i] = x[i] - (i==theta ?delti[theta]:0);
2796: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
2797: for(i=1;i<=nlstate;i++)
2798: gm[i] = prlim[i][i];
2799:
2800: for(i=1;i<=nlstate;i++)
2801: gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
2802: } /* End theta */
2803:
2804: trgradg =matrix(1,nlstate,1,npar);
2805:
2806: for(j=1; j<=nlstate;j++)
2807: for(theta=1; theta <=npar; theta++)
2808: trgradg[j][theta]=gradg[theta][j];
2809:
2810: for(i=1;i<=nlstate;i++)
2811: varpl[i][(int)age] =0.;
2812: matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
2813: matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
2814: for(i=1;i<=nlstate;i++)
2815: varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
2816:
2817: fprintf(ficresvpl,"%.0f ",age );
2818: for(i=1; i<=nlstate;i++)
2819: fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
2820: fprintf(ficresvpl,"\n");
2821: free_vector(gp,1,nlstate);
2822: free_vector(gm,1,nlstate);
2823: free_matrix(gradg,1,npar,1,nlstate);
2824: free_matrix(trgradg,1,nlstate,1,npar);
2825: } /* End age */
2826:
2827: free_vector(xp,1,npar);
2828: free_matrix(doldm,1,nlstate,1,npar);
2829: free_matrix(dnewm,1,nlstate,1,nlstate);
2830:
2831: }
2832:
2833: /************ Variance of one-step probabilities ******************/
2834: void varprob(char optionfilefiname[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij, int *Tvar, int **nbcode, int *ncodemax)
2835: {
2836: int i, j=0, i1, k1, l1, t, tj;
2837: int k2, l2, j1, z1;
2838: int k=0,l, cptcode;
2839: int first=1, first1;
2840: double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
2841: double **dnewm,**doldm;
2842: double *xp;
2843: double *gp, *gm;
2844: double **gradg, **trgradg;
2845: double **mu;
2846: double age,agelim, cov[NCOVMAX];
2847: double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
2848: int theta;
2849: char fileresprob[FILENAMELENGTH];
2850: char fileresprobcov[FILENAMELENGTH];
2851: char fileresprobcor[FILENAMELENGTH];
2852:
2853: double ***varpij;
2854:
2855: strcpy(fileresprob,"prob");
2856: strcat(fileresprob,fileres);
2857: if((ficresprob=fopen(fileresprob,"w"))==NULL) {
2858: printf("Problem with resultfile: %s\n", fileresprob);
2859: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
2860: }
2861: strcpy(fileresprobcov,"probcov");
2862: strcat(fileresprobcov,fileres);
2863: if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
2864: printf("Problem with resultfile: %s\n", fileresprobcov);
2865: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
2866: }
2867: strcpy(fileresprobcor,"probcor");
2868: strcat(fileresprobcor,fileres);
2869: if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
2870: printf("Problem with resultfile: %s\n", fileresprobcor);
2871: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
2872: }
2873: printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
2874: fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
2875: printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
2876: fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
2877: printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
2878: fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
2879:
2880: fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
2881: fprintf(ficresprob,"# Age");
2882: fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
2883: fprintf(ficresprobcov,"# Age");
2884: fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
2885: fprintf(ficresprobcov,"# Age");
2886:
2887:
2888: for(i=1; i<=nlstate;i++)
2889: for(j=1; j<=(nlstate+ndeath);j++){
2890: fprintf(ficresprob," p%1d-%1d (SE)",i,j);
2891: fprintf(ficresprobcov," p%1d-%1d ",i,j);
2892: fprintf(ficresprobcor," p%1d-%1d ",i,j);
2893: }
2894: /* fprintf(ficresprob,"\n");
2895: fprintf(ficresprobcov,"\n");
2896: fprintf(ficresprobcor,"\n");
2897: */
2898: xp=vector(1,npar);
2899: dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
2900: doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
2901: mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
2902: varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
2903: first=1;
2904: fprintf(ficgp,"\n# Routine varprob");
2905: fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
2906: fprintf(fichtm,"\n");
2907:
2908: fprintf(fichtm,"\n<li><h4> <a href=\"%s\">Matrix of variance-covariance of pairs of step probabilities (drawings)</a></h4></li>\n",optionfilehtmcov);
2909: fprintf(fichtmcov,"\n<h4>Matrix of variance-covariance of pairs of step probabilities</h4>\n\
2910: file %s<br>\n",optionfilehtmcov);
2911: fprintf(fichtmcov,"\nEllipsoids of confidence centered on point (p<inf>ij</inf>, p<inf>kl</inf>) are estimated\
2912: and drawn. It helps understanding how is the covariance between two incidences.\
2913: They are expressed in year<sup>-1</sup> in order to be less dependent of stepm.<br>\n");
2914: 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. \
2915: It can be understood this way: if pij and pkl where uncorrelated the (2x2) matrix of covariance \
2916: would have been (1/(var pij), 0 , 0, 1/(var pkl)), and the confidence interval would be 2 \
2917: standard deviations wide on each axis. <br>\
2918: Now, if both incidences are correlated (usual case) we diagonalised the inverse of the covariance matrix\
2919: and made the appropriate rotation to look at the uncorrelated principal directions.<br>\
2920: To be simple, these graphs help to understand the significativity of each parameter in relation to a second other one.<br> \n");
2921:
2922: cov[1]=1;
2923: tj=cptcoveff;
2924: if (cptcovn<1) {tj=1;ncodemax[1]=1;}
2925: j1=0;
2926: for(t=1; t<=tj;t++){
2927: for(i1=1; i1<=ncodemax[t];i1++){
2928: j1++;
2929: if (cptcovn>0) {
2930: fprintf(ficresprob, "\n#********** Variable ");
2931: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
2932: fprintf(ficresprob, "**********\n#\n");
2933: fprintf(ficresprobcov, "\n#********** Variable ");
2934: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
2935: fprintf(ficresprobcov, "**********\n#\n");
2936:
2937: fprintf(ficgp, "\n#********** Variable ");
2938: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
2939: fprintf(ficgp, "**********\n#\n");
2940:
2941:
2942: fprintf(fichtmcov, "\n<hr size=\"2\" color=\"#EC5E5E\">********** Variable ");
2943: for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
2944: fprintf(fichtmcov, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
2945:
2946: fprintf(ficresprobcor, "\n#********** Variable ");
2947: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
2948: fprintf(ficresprobcor, "**********\n#");
2949: }
2950:
2951: for (age=bage; age<=fage; age ++){
2952: cov[2]=age;
2953: for (k=1; k<=cptcovn;k++) {
2954: cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];
2955: }
2956: for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
2957: for (k=1; k<=cptcovprod;k++)
2958: cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
2959:
2960: gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
2961: trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
2962: gp=vector(1,(nlstate)*(nlstate+ndeath));
2963: gm=vector(1,(nlstate)*(nlstate+ndeath));
2964:
2965: for(theta=1; theta <=npar; theta++){
2966: for(i=1; i<=npar; i++)
2967: xp[i] = x[i] + (i==theta ?delti[theta]:(double)0);
2968:
2969: pmij(pmmij,cov,ncovmodel,xp,nlstate);
2970:
2971: k=0;
2972: for(i=1; i<= (nlstate); i++){
2973: for(j=1; j<=(nlstate+ndeath);j++){
2974: k=k+1;
2975: gp[k]=pmmij[i][j];
2976: }
2977: }
2978:
2979: for(i=1; i<=npar; i++)
2980: xp[i] = x[i] - (i==theta ?delti[theta]:(double)0);
2981:
2982: pmij(pmmij,cov,ncovmodel,xp,nlstate);
2983: k=0;
2984: for(i=1; i<=(nlstate); i++){
2985: for(j=1; j<=(nlstate+ndeath);j++){
2986: k=k+1;
2987: gm[k]=pmmij[i][j];
2988: }
2989: }
2990:
2991: for(i=1; i<= (nlstate)*(nlstate+ndeath); i++)
2992: gradg[theta][i]=(gp[i]-gm[i])/(double)2./delti[theta];
2993: }
2994:
2995: for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
2996: for(theta=1; theta <=npar; theta++)
2997: trgradg[j][theta]=gradg[theta][j];
2998:
2999: matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov);
3000: matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);
3001: free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
3002: free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
3003: free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
3004: free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
3005:
3006: pmij(pmmij,cov,ncovmodel,x,nlstate);
3007:
3008: k=0;
3009: for(i=1; i<=(nlstate); i++){
3010: for(j=1; j<=(nlstate+ndeath);j++){
3011: k=k+1;
3012: mu[k][(int) age]=pmmij[i][j];
3013: }
3014: }
3015: for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
3016: for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
3017: varpij[i][j][(int)age] = doldm[i][j];
3018:
3019: /*printf("\n%d ",(int)age);
3020: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
3021: printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
3022: fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
3023: }*/
3024:
3025: fprintf(ficresprob,"\n%d ",(int)age);
3026: fprintf(ficresprobcov,"\n%d ",(int)age);
3027: fprintf(ficresprobcor,"\n%d ",(int)age);
3028:
3029: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)
3030: fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));
3031: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
3032: fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);
3033: fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
3034: }
3035: i=0;
3036: for (k=1; k<=(nlstate);k++){
3037: for (l=1; l<=(nlstate+ndeath);l++){
3038: i=i++;
3039: fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
3040: fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
3041: for (j=1; j<=i;j++){
3042: fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);
3043: fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));
3044: }
3045: }
3046: }/* end of loop for state */
3047: } /* end of loop for age */
3048:
3049: /* Confidence intervalle of pij */
3050: /*
3051: fprintf(ficgp,"\nset noparametric;unset label");
3052: fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");
3053: fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
3054: 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);
3055: fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);
3056: fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);
3057: fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);
3058: */
3059:
3060: /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
3061: first1=1;
3062: for (k2=1; k2<=(nlstate);k2++){
3063: for (l2=1; l2<=(nlstate+ndeath);l2++){
3064: if(l2==k2) continue;
3065: j=(k2-1)*(nlstate+ndeath)+l2;
3066: for (k1=1; k1<=(nlstate);k1++){
3067: for (l1=1; l1<=(nlstate+ndeath);l1++){
3068: if(l1==k1) continue;
3069: i=(k1-1)*(nlstate+ndeath)+l1;
3070: if(i<=j) continue;
3071: for (age=bage; age<=fage; age ++){
3072: if ((int)age %5==0){
3073: v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;
3074: v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;
3075: cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;
3076: mu1=mu[i][(int) age]/stepm*YEARM ;
3077: mu2=mu[j][(int) age]/stepm*YEARM;
3078: c12=cv12/sqrt(v1*v2);
3079: /* Computing eigen value of matrix of covariance */
3080: lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
3081: lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
3082: /* Eigen vectors */
3083: v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
3084: /*v21=sqrt(1.-v11*v11); *//* error */
3085: v21=(lc1-v1)/cv12*v11;
3086: v12=-v21;
3087: v22=v11;
3088: tnalp=v21/v11;
3089: if(first1==1){
3090: first1=0;
3091: 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);
3092: }
3093: 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);
3094: /*printf(fignu*/
3095: /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */
3096: /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */
3097: if(first==1){
3098: first=0;
3099: fprintf(ficgp,"\nset parametric;unset label");
3100: 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);
3101: fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
3102: fprintf(fichtmcov,"\n<br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup>\
3103: :<a href=\"%s%d%1d%1d-%1d%1d.png\">\
3104: %s%d%1d%1d-%1d%1d.png</A>, ",k1,l1,k2,l2,\
3105: subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2,\
3106: subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
3107: fprintf(fichtmcov,"\n<br><img src=\"%s%d%1d%1d-%1d%1d.png\"> ",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
3108: fprintf(fichtmcov,"\n<br> Correlation at age %d (%.3f),",(int) age, c12);
3109: fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\"",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
3110: fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
3111: fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
3112: 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",\
3113: mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
3114: mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
3115: }else{
3116: first=0;
3117: fprintf(fichtmcov," %d (%.3f),",(int) age, c12);
3118: fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
3119: fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
3120: 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",\
3121: mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
3122: mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
3123: }/* if first */
3124: } /* age mod 5 */
3125: } /* end loop age */
3126: fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\";replot;",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
3127: first=1;
3128: } /*l12 */
3129: } /* k12 */
3130: } /*l1 */
3131: }/* k1 */
3132: } /* loop covariates */
3133: }
3134: free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
3135: free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
3136: free_vector(xp,1,npar);
3137: fclose(ficresprob);
3138: fclose(ficresprobcov);
3139: fclose(ficresprobcor);
3140: fflush(ficgp);
3141: fflush(fichtmcov);
3142: }
3143:
3144:
3145: /******************* Printing html file ***********/
3146: void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \
3147: int lastpass, int stepm, int weightopt, char model[],\
3148: int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
3149: int popforecast, int estepm ,\
3150: double jprev1, double mprev1,double anprev1, \
3151: double jprev2, double mprev2,double anprev2){
3152: int jj1, k1, i1, cpt;
3153:
3154: fprintf(fichtm,"<ul><li><h4>Result files (first order: no variance)</h4>\n \
3155: - Observed prevalence in each state (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"%s\">%s</a> <br>\n ",
3156: jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirf2(fileres,"p"),subdirf2(fileres,"p"));
3157: fprintf(fichtm,"\
3158: - Estimated transition probabilities over %d (stepm) months: <a href=\"%s\">%s</a><br>\n ",
3159: stepm,subdirf2(fileres,"pij"),subdirf2(fileres,"pij"));
3160: fprintf(fichtm,"\
3161: - Stable prevalence in each health state: <a href=\"%s\">%s</a> <br>\n",
3162: subdirf2(fileres,"pl"),subdirf2(fileres,"pl"));
3163: fprintf(fichtm,"\
3164: - Life expectancies by age and initial health status (estepm=%2d months): \
3165: <a href=\"%s\">%s</a> <br>\n</li>",
3166: estepm,subdirf2(fileres,"e"),subdirf2(fileres,"e"));
3167:
3168: fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
3169:
3170: m=cptcoveff;
3171: if (cptcovn < 1) {m=1;ncodemax[1]=1;}
3172:
3173: jj1=0;
3174: for(k1=1; k1<=m;k1++){
3175: for(i1=1; i1<=ncodemax[k1];i1++){
3176: jj1++;
3177: if (cptcovn > 0) {
3178: fprintf(fichtm,"<hr size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
3179: for (cpt=1; cpt<=cptcoveff;cpt++)
3180: fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
3181: fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
3182: }
3183: /* Pij */
3184: 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> \
3185: <img src=\"%s%d1.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);
3186: /* Quasi-incidences */
3187: fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months\
3188: before but expressed in per year i.e. quasi incidences if stepm is small and probabilities too: %s%d2.png<br> \
3189: <img src=\"%s%d2.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);
3190: /* Stable prevalence in each health state */
3191: for(cpt=1; cpt<nlstate;cpt++){
3192: fprintf(fichtm,"<br>- Stable prevalence in each health state : p%s%d%d.png<br> \
3193: <img src=\"%s%d%d.png\">",subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1);
3194: }
3195: for(cpt=1; cpt<=nlstate;cpt++) {
3196: fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): %s%d%d.png <br> \
3197: <img src=\"%s%d%d.png\">",cpt,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1);
3198: }
3199: } /* end i1 */
3200: }/* End k1 */
3201: fprintf(fichtm,"</ul>");
3202:
3203:
3204: fprintf(fichtm,"\
3205: \n<br><li><h4> Result files (second order: variances)</h4>\n\
3206: - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n", rfileres,rfileres);
3207:
3208: fprintf(fichtm," - Variance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
3209: subdirf2(fileres,"prob"),subdirf2(fileres,"prob"));
3210: fprintf(fichtm,"\
3211: - Variance-covariance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
3212: subdirf2(fileres,"probcov"),subdirf2(fileres,"probcov"));
3213:
3214: fprintf(fichtm,"\
3215: - Correlation matrix of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
3216: subdirf2(fileres,"probcor"),subdirf2(fileres,"probcor"));
3217: fprintf(fichtm,"\
3218: - Variances and covariances of life expectancies by age and initial health status (estepm=%d months): <a href=\"%s\">%s</a><br>\n",
3219: estepm, subdirf2(fileres,"v"),subdirf2(fileres,"v"));
3220: fprintf(fichtm,"\
3221: - Health expectancies with their variances (no covariance): <a href=\"%s\">%s</a> <br>\n",
3222: subdirf2(fileres,"t"),subdirf2(fileres,"t"));
3223: fprintf(fichtm,"\
3224: - Standard deviation of stable prevalences: <a href=\"%s\">%s</a> <br>\n",\
3225: subdirf2(fileres,"vpl"),subdirf2(fileres,"vpl"));
3226:
3227: /* if(popforecast==1) fprintf(fichtm,"\n */
3228: /* - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n */
3229: /* - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n */
3230: /* <br>",fileres,fileres,fileres,fileres); */
3231: /* else */
3232: /* 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); */
3233: fflush(fichtm);
3234: fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
3235:
3236: m=cptcoveff;
3237: if (cptcovn < 1) {m=1;ncodemax[1]=1;}
3238:
3239: jj1=0;
3240: for(k1=1; k1<=m;k1++){
3241: for(i1=1; i1<=ncodemax[k1];i1++){
3242: jj1++;
3243: if (cptcovn > 0) {
3244: fprintf(fichtm,"<hr size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
3245: for (cpt=1; cpt<=cptcoveff;cpt++)
3246: fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
3247: fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
3248: }
3249: for(cpt=1; cpt<=nlstate;cpt++) {
3250: fprintf(fichtm,"<br>- Observed (cross-sectional) and period (incidence based) \
3251: prevalence (with 95%% confidence interval) in state (%d): %s%d%d.png <br>\
3252: <img src=\"%s%d%d.png\">",cpt,subdirf2(optionfilefiname,"v"),cpt,jj1,subdirf2(optionfilefiname,"v"),cpt,jj1);
3253: }
3254: fprintf(fichtm,"\n<br>- Total life expectancy by age and \
3255: health expectancies in states (1) and (2): %s%d.png<br>\
3256: <img src=\"%s%d.png\">",subdirf2(optionfilefiname,"e"),jj1,subdirf2(optionfilefiname,"e"),jj1);
3257: } /* end i1 */
3258: }/* End k1 */
3259: fprintf(fichtm,"</ul>");
3260: fflush(fichtm);
3261: }
3262:
3263: /******************* Gnuplot file **************/
3264: void printinggnuplot(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
3265:
3266: char dirfileres[132],optfileres[132];
3267: int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;
3268: int ng;
3269: /* if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) { */
3270: /* printf("Problem with file %s",optionfilegnuplot); */
3271: /* fprintf(ficlog,"Problem with file %s",optionfilegnuplot); */
3272: /* } */
3273:
3274: /*#ifdef windows */
3275: fprintf(ficgp,"cd \"%s\" \n",pathc);
3276: /*#endif */
3277: m=pow(2,cptcoveff);
3278:
3279: strcpy(dirfileres,optionfilefiname);
3280: strcpy(optfileres,"vpl");
3281: /* 1eme*/
3282: for (cpt=1; cpt<= nlstate ; cpt ++) {
3283: for (k1=1; k1<= m ; k1 ++) {
3284: fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"v"),cpt,k1);
3285: fprintf(ficgp,"\n#set out \"v%s%d%d.png\" \n",optionfilefiname,cpt,k1);
3286: fprintf(ficgp,"set xlabel \"Age\" \n\
3287: set ylabel \"Probability\" \n\
3288: set ter png small\n\
3289: set size 0.65,0.65\n\
3290: plot [%.f:%.f] \"%s\" every :::%d::%d u 1:2 \"\%%lf",ageminpar,fage,subdirf2(fileres,"vpl"),k1-1,k1-1);
3291:
3292: for (i=1; i<= nlstate ; i ++) {
3293: if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
3294: else fprintf(ficgp," \%%*lf (\%%*lf)");
3295: }
3296: 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);
3297: for (i=1; i<= nlstate ; i ++) {
3298: if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
3299: else fprintf(ficgp," \%%*lf (\%%*lf)");
3300: }
3301: fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"%s\" every :::%d::%d u 1:($2-1.96*$3) \"\%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1);
3302: for (i=1; i<= nlstate ; i ++) {
3303: if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
3304: else fprintf(ficgp," \%%*lf (\%%*lf)");
3305: }
3306: fprintf(ficgp,"\" t\"\" w l 1,\"%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",subdirf2(fileres,"p"),k1-1,k1-1,2+4*(cpt-1));
3307: }
3308: }
3309: /*2 eme*/
3310:
3311: for (k1=1; k1<= m ; k1 ++) {
3312: fprintf(ficgp,"\nset out \"%s%d.png\" \n",subdirf2(optionfilefiname,"e"),k1);
3313: fprintf(ficgp,"set ylabel \"Years\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] ",ageminpar,fage);
3314:
3315: for (i=1; i<= nlstate+1 ; i ++) {
3316: k=2*i;
3317: fprintf(ficgp,"\"%s\" every :::%d::%d u 1:2 \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
3318: for (j=1; j<= nlstate+1 ; j ++) {
3319: if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
3320: else fprintf(ficgp," \%%*lf (\%%*lf)");
3321: }
3322: if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");
3323: else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);
3324: fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
3325: for (j=1; j<= nlstate+1 ; j ++) {
3326: if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
3327: else fprintf(ficgp," \%%*lf (\%%*lf)");
3328: }
3329: fprintf(ficgp,"\" t\"\" w l 0,");
3330: fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
3331: for (j=1; j<= nlstate+1 ; j ++) {
3332: if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
3333: else fprintf(ficgp," \%%*lf (\%%*lf)");
3334: }
3335: if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");
3336: else fprintf(ficgp,"\" t\"\" w l 0,");
3337: }
3338: }
3339:
3340: /*3eme*/
3341:
3342: for (k1=1; k1<= m ; k1 ++) {
3343: for (cpt=1; cpt<= nlstate ; cpt ++) {
3344: k=2+nlstate*(2*cpt-2);
3345: fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"exp"),cpt,k1);
3346: fprintf(ficgp,"set ter png small\n\
3347: set size 0.65,0.65\n\
3348: plot [%.f:%.f] \"%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,subdirf2(fileres,"e"),k1-1,k1-1,k,cpt);
3349: /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
3350: for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
3351: fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
3352: fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
3353: for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
3354: fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
3355:
3356: */
3357: for (i=1; i< nlstate ; i ++) {
3358: 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);
3359:
3360: }
3361: }
3362: }
3363:
3364: /* CV preval stable (period) */
3365: for (k1=1; k1<= m ; k1 ++) {
3366: for (cpt=1; cpt<=nlstate ; cpt ++) {
3367: k=3;
3368: fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"p"),cpt,k1);
3369: fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\
3370: set ter png small\nset size 0.65,0.65\n\
3371: unset log y\n\
3372: plot [%.f:%.f] \"%s\" u ($1==%d ? ($3):1/0):($%d/($%d",ageminpar,agemaxpar,subdirf2(fileres,"pij"),k1,k+cpt+1,k+1);
3373:
3374: for (i=1; i< nlstate ; i ++)
3375: fprintf(ficgp,"+$%d",k+i+1);
3376: fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);
3377:
3378: l=3+(nlstate+ndeath)*cpt;
3379: fprintf(ficgp,",\"%s\" u ($1==%d ? ($3):1/0):($%d/($%d",subdirf2(fileres,"pij"),k1,l+cpt+1,l+1);
3380: for (i=1; i< nlstate ; i ++) {
3381: l=3+(nlstate+ndeath)*cpt;
3382: fprintf(ficgp,"+$%d",l+i+1);
3383: }
3384: fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);
3385: }
3386: }
3387:
3388: /* proba elementaires */
3389: for(i=1,jk=1; i <=nlstate; i++){
3390: for(k=1; k <=(nlstate+ndeath); k++){
3391: if (k != i) {
3392: for(j=1; j <=ncovmodel; j++){
3393: fprintf(ficgp,"p%d=%f ",jk,p[jk]);
3394: jk++;
3395: fprintf(ficgp,"\n");
3396: }
3397: }
3398: }
3399: }
3400:
3401: for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/
3402: for(jk=1; jk <=m; jk++) {
3403: fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"pe"),jk,ng);
3404: if (ng==2)
3405: fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
3406: else
3407: fprintf(ficgp,"\nset title \"Probability\"\n");
3408: fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65\nset log y\nplot [%.f:%.f] ",ageminpar,agemaxpar);
3409: i=1;
3410: for(k2=1; k2<=nlstate; k2++) {
3411: k3=i;
3412: for(k=1; k<=(nlstate+ndeath); k++) {
3413: if (k != k2){
3414: if(ng==2)
3415: fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);
3416: else
3417: fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
3418: ij=1;
3419: for(j=3; j <=ncovmodel; j++) {
3420: if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
3421: fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
3422: ij++;
3423: }
3424: else
3425: fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
3426: }
3427: fprintf(ficgp,")/(1");
3428:
3429: for(k1=1; k1 <=nlstate; k1++){
3430: fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);
3431: ij=1;
3432: for(j=3; j <=ncovmodel; j++){
3433: if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
3434: fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
3435: ij++;
3436: }
3437: else
3438: fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
3439: }
3440: fprintf(ficgp,")");
3441: }
3442: fprintf(ficgp,") t \"p%d%d\" ", k2,k);
3443: if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");
3444: i=i+ncovmodel;
3445: }
3446: } /* end k */
3447: } /* end k2 */
3448: } /* end jk */
3449: } /* end ng */
3450: fflush(ficgp);
3451: } /* end gnuplot */
3452:
3453:
3454: /*************** Moving average **************/
3455: int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav){
3456:
3457: int i, cpt, cptcod;
3458: int modcovmax =1;
3459: int mobilavrange, mob;
3460: double age;
3461:
3462: modcovmax=2*cptcoveff;/* Max number of modalities. We suppose
3463: a covariate has 2 modalities */
3464: if (cptcovn<1) modcovmax=1; /* At least 1 pass */
3465:
3466: if(mobilav==1||mobilav ==3 ||mobilav==5 ||mobilav== 7){
3467: if(mobilav==1) mobilavrange=5; /* default */
3468: else mobilavrange=mobilav;
3469: for (age=bage; age<=fage; age++)
3470: for (i=1; i<=nlstate;i++)
3471: for (cptcod=1;cptcod<=modcovmax;cptcod++)
3472: mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
3473: /* We keep the original values on the extreme ages bage, fage and for
3474: fage+1 and bage-1 we use a 3 terms moving average; for fage+2 bage+2
3475: we use a 5 terms etc. until the borders are no more concerned.
3476: */
3477: for (mob=3;mob <=mobilavrange;mob=mob+2){
3478: for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){
3479: for (i=1; i<=nlstate;i++){
3480: for (cptcod=1;cptcod<=modcovmax;cptcod++){
3481: mobaverage[(int)age][i][cptcod] =probs[(int)age][i][cptcod];
3482: for (cpt=1;cpt<=(mob-1)/2;cpt++){
3483: mobaverage[(int)age][i][cptcod] +=probs[(int)age-cpt][i][cptcod];
3484: mobaverage[(int)age][i][cptcod] +=probs[(int)age+cpt][i][cptcod];
3485: }
3486: mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/mob;
3487: }
3488: }
3489: }/* end age */
3490: }/* end mob */
3491: }else return -1;
3492: return 0;
3493: }/* End movingaverage */
3494:
3495:
3496: /************** Forecasting ******************/
3497: 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){
3498: /* proj1, year, month, day of starting projection
3499: agemin, agemax range of age
3500: dateprev1 dateprev2 range of dates during which prevalence is computed
3501: anproj2 year of en of projection (same day and month as proj1).
3502: */
3503: int yearp, stepsize, hstepm, nhstepm, j, k, c, cptcod, i, h, i1;
3504: int *popage;
3505: double agec; /* generic age */
3506: double agelim, ppij, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
3507: double *popeffectif,*popcount;
3508: double ***p3mat;
3509: double ***mobaverage;
3510: char fileresf[FILENAMELENGTH];
3511:
3512: agelim=AGESUP;
3513: prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
3514:
3515: strcpy(fileresf,"f");
3516: strcat(fileresf,fileres);
3517: if((ficresf=fopen(fileresf,"w"))==NULL) {
3518: printf("Problem with forecast resultfile: %s\n", fileresf);
3519: fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);
3520: }
3521: printf("Computing forecasting: result on file '%s' \n", fileresf);
3522: fprintf(ficlog,"Computing forecasting: result on file '%s' \n", fileresf);
3523:
3524: if (cptcoveff==0) ncodemax[cptcoveff]=1;
3525:
3526: if (mobilav!=0) {
3527: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
3528: if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
3529: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
3530: printf(" Error in movingaverage mobilav=%d\n",mobilav);
3531: }
3532: }
3533:
3534: stepsize=(int) (stepm+YEARM-1)/YEARM;
3535: if (stepm<=12) stepsize=1;
3536: if(estepm < stepm){
3537: printf ("Problem %d lower than %d\n",estepm, stepm);
3538: }
3539: else hstepm=estepm;
3540:
3541: hstepm=hstepm/stepm;
3542: yp1=modf(dateintmean,&yp);/* extracts integral of datemean in yp and
3543: fractional in yp1 */
3544: anprojmean=yp;
3545: yp2=modf((yp1*12),&yp);
3546: mprojmean=yp;
3547: yp1=modf((yp2*30.5),&yp);
3548: jprojmean=yp;
3549: if(jprojmean==0) jprojmean=1;
3550: if(mprojmean==0) jprojmean=1;
3551:
3552: i1=cptcoveff;
3553: if (cptcovn < 1){i1=1;}
3554:
3555: fprintf(ficresf,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2);
3556:
3557: fprintf(ficresf,"#****** Routine prevforecast **\n");
3558:
3559: /* if (h==(int)(YEARM*yearp)){ */
3560: for(cptcov=1, k=0;cptcov<=i1;cptcov++){
3561: for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
3562: k=k+1;
3563: fprintf(ficresf,"\n#******");
3564: for(j=1;j<=cptcoveff;j++) {
3565: 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]]);
3566: }
3567: fprintf(ficresf,"******\n");
3568: fprintf(ficresf,"# Covariate valuofcovar yearproj age");
3569: for(j=1; j<=nlstate+ndeath;j++){
3570: for(i=1; i<=nlstate;i++)
3571: fprintf(ficresf," p%d%d",i,j);
3572: fprintf(ficresf," p.%d",j);
3573: }
3574: for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) {
3575: fprintf(ficresf,"\n");
3576: fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+yearp);
3577:
3578: for (agec=fage; agec>=(ageminpar-1); agec--){
3579: nhstepm=(int) rint((agelim-agec)*YEARM/stepm);
3580: nhstepm = nhstepm/hstepm;
3581: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3582: oldm=oldms;savm=savms;
3583: hpxij(p3mat,nhstepm,agec,hstepm,p,nlstate,stepm,oldm,savm, k);
3584:
3585: for (h=0; h<=nhstepm; h++){
3586: if (h*hstepm/YEARM*stepm ==yearp) {
3587: fprintf(ficresf,"\n");
3588: for(j=1;j<=cptcoveff;j++)
3589: fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
3590: fprintf(ficresf,"%.f %.f ",anproj1+yearp,agec+h*hstepm/YEARM*stepm);
3591: }
3592: for(j=1; j<=nlstate+ndeath;j++) {
3593: ppij=0.;
3594: for(i=1; i<=nlstate;i++) {
3595: if (mobilav==1)
3596: ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][i][cptcod];
3597: else {
3598: ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][cptcod];
3599: }
3600: if (h*hstepm/YEARM*stepm== yearp) {
3601: fprintf(ficresf," %.3f", p3mat[i][j][h]);
3602: }
3603: } /* end i */
3604: if (h*hstepm/YEARM*stepm==yearp) {
3605: fprintf(ficresf," %.3f", ppij);
3606: }
3607: }/* end j */
3608: } /* end h */
3609: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3610: } /* end agec */
3611: } /* end yearp */
3612: } /* end cptcod */
3613: } /* end cptcov */
3614:
3615: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
3616:
3617: fclose(ficresf);
3618: }
3619:
3620: /************** Forecasting *****not tested NB*************/
3621: 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){
3622:
3623: int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;
3624: int *popage;
3625: double calagedatem, agelim, kk1, kk2;
3626: double *popeffectif,*popcount;
3627: double ***p3mat,***tabpop,***tabpopprev;
3628: double ***mobaverage;
3629: char filerespop[FILENAMELENGTH];
3630:
3631: tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
3632: tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
3633: agelim=AGESUP;
3634: calagedatem=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;
3635:
3636: prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
3637:
3638:
3639: strcpy(filerespop,"pop");
3640: strcat(filerespop,fileres);
3641: if((ficrespop=fopen(filerespop,"w"))==NULL) {
3642: printf("Problem with forecast resultfile: %s\n", filerespop);
3643: fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop);
3644: }
3645: printf("Computing forecasting: result on file '%s' \n", filerespop);
3646: fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop);
3647:
3648: if (cptcoveff==0) ncodemax[cptcoveff]=1;
3649:
3650: if (mobilav!=0) {
3651: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
3652: if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
3653: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
3654: printf(" Error in movingaverage mobilav=%d\n",mobilav);
3655: }
3656: }
3657:
3658: stepsize=(int) (stepm+YEARM-1)/YEARM;
3659: if (stepm<=12) stepsize=1;
3660:
3661: agelim=AGESUP;
3662:
3663: hstepm=1;
3664: hstepm=hstepm/stepm;
3665:
3666: if (popforecast==1) {
3667: if((ficpop=fopen(popfile,"r"))==NULL) {
3668: printf("Problem with population file : %s\n",popfile);exit(0);
3669: fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0);
3670: }
3671: popage=ivector(0,AGESUP);
3672: popeffectif=vector(0,AGESUP);
3673: popcount=vector(0,AGESUP);
3674:
3675: i=1;
3676: while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;
3677:
3678: imx=i;
3679: for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];
3680: }
3681:
3682: for(cptcov=1,k=0;cptcov<=i2;cptcov++){
3683: for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
3684: k=k+1;
3685: fprintf(ficrespop,"\n#******");
3686: for(j=1;j<=cptcoveff;j++) {
3687: fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
3688: }
3689: fprintf(ficrespop,"******\n");
3690: fprintf(ficrespop,"# Age");
3691: for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);
3692: if (popforecast==1) fprintf(ficrespop," [Population]");
3693:
3694: for (cpt=0; cpt<=0;cpt++) {
3695: fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);
3696:
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:
3705: for (h=0; h<=nhstepm; h++){
3706: if (h==(int) (calagedatem+YEARM*cpt)) {
3707: fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
3708: }
3709: for(j=1; j<=nlstate+ndeath;j++) {
3710: kk1=0.;kk2=0;
3711: for(i=1; i<=nlstate;i++) {
3712: if (mobilav==1)
3713: kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];
3714: else {
3715: kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];
3716: }
3717: }
3718: if (h==(int)(calagedatem+12*cpt)){
3719: tabpop[(int)(agedeb)][j][cptcod]=kk1;
3720: /*fprintf(ficrespop," %.3f", kk1);
3721: if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/
3722: }
3723: }
3724: for(i=1; i<=nlstate;i++){
3725: kk1=0.;
3726: for(j=1; j<=nlstate;j++){
3727: kk1= kk1+tabpop[(int)(agedeb)][j][cptcod];
3728: }
3729: tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedatem+12*cpt)*hstepm/YEARM*stepm-1)];
3730: }
3731:
3732: if (h==(int)(calagedatem+12*cpt)) for(j=1; j<=nlstate;j++)
3733: fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);
3734: }
3735: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3736: }
3737: }
3738:
3739: /******/
3740:
3741: for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) {
3742: fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);
3743: for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){
3744: nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);
3745: nhstepm = nhstepm/hstepm;
3746:
3747: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3748: oldm=oldms;savm=savms;
3749: hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
3750: for (h=0; h<=nhstepm; h++){
3751: if (h==(int) (calagedatem+YEARM*cpt)) {
3752: fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
3753: }
3754: for(j=1; j<=nlstate+ndeath;j++) {
3755: kk1=0.;kk2=0;
3756: for(i=1; i<=nlstate;i++) {
3757: kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];
3758: }
3759: if (h==(int)(calagedatem+12*cpt)) fprintf(ficresf," %15.2f", kk1);
3760: }
3761: }
3762: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3763: }
3764: }
3765: }
3766: }
3767:
3768: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
3769:
3770: if (popforecast==1) {
3771: free_ivector(popage,0,AGESUP);
3772: free_vector(popeffectif,0,AGESUP);
3773: free_vector(popcount,0,AGESUP);
3774: }
3775: free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
3776: free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
3777: fclose(ficrespop);
3778: } /* End of popforecast */
3779:
3780: int fileappend(FILE *fichier, char *optionfich)
3781: {
3782: if((fichier=fopen(optionfich,"a"))==NULL) {
3783: printf("Problem with file: %s\n", optionfich);
3784: fprintf(ficlog,"Problem with file: %s\n", optionfich);
3785: return (0);
3786: }
3787: fflush(fichier);
3788: return (1);
3789: }
3790:
3791:
3792: /**************** function prwizard **********************/
3793: void prwizard(int ncovmodel, int nlstate, int ndeath, char model[], FILE *ficparo)
3794: {
3795:
3796: /* Wizard to print covariance matrix template */
3797:
3798: char ca[32], cb[32], cc[32];
3799: int i,j, k, l, li, lj, lk, ll, jj, npar, itimes;
3800: int numlinepar;
3801:
3802: printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
3803: fprintf(ficparo,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
3804: for(i=1; i <=nlstate; i++){
3805: jj=0;
3806: for(j=1; j <=nlstate+ndeath; j++){
3807: if(j==i) continue;
3808: jj++;
3809: /*ca[0]= k+'a'-1;ca[1]='\0';*/
3810: printf("%1d%1d",i,j);
3811: fprintf(ficparo,"%1d%1d",i,j);
3812: for(k=1; k<=ncovmodel;k++){
3813: /* printf(" %lf",param[i][j][k]); */
3814: /* fprintf(ficparo," %lf",param[i][j][k]); */
3815: printf(" 0.");
3816: fprintf(ficparo," 0.");
3817: }
3818: printf("\n");
3819: fprintf(ficparo,"\n");
3820: }
3821: }
3822: printf("# Scales (for hessian or gradient estimation)\n");
3823: fprintf(ficparo,"# Scales (for hessian or gradient estimation)\n");
3824: npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/
3825: for(i=1; i <=nlstate; i++){
3826: jj=0;
3827: for(j=1; j <=nlstate+ndeath; j++){
3828: if(j==i) continue;
3829: jj++;
3830: fprintf(ficparo,"%1d%1d",i,j);
3831: printf("%1d%1d",i,j);
3832: fflush(stdout);
3833: for(k=1; k<=ncovmodel;k++){
3834: /* printf(" %le",delti3[i][j][k]); */
3835: /* fprintf(ficparo," %le",delti3[i][j][k]); */
3836: printf(" 0.");
3837: fprintf(ficparo," 0.");
3838: }
3839: numlinepar++;
3840: printf("\n");
3841: fprintf(ficparo,"\n");
3842: }
3843: }
3844: printf("# Covariance matrix\n");
3845: /* # 121 Var(a12)\n\ */
3846: /* # 122 Cov(b12,a12) Var(b12)\n\ */
3847: /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
3848: /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
3849: /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
3850: /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
3851: /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
3852: /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
3853: fflush(stdout);
3854: fprintf(ficparo,"# Covariance matrix\n");
3855: /* # 121 Var(a12)\n\ */
3856: /* # 122 Cov(b12,a12) Var(b12)\n\ */
3857: /* # ...\n\ */
3858: /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
3859:
3860: for(itimes=1;itimes<=2;itimes++){
3861: jj=0;
3862: for(i=1; i <=nlstate; i++){
3863: for(j=1; j <=nlstate+ndeath; j++){
3864: if(j==i) continue;
3865: for(k=1; k<=ncovmodel;k++){
3866: jj++;
3867: ca[0]= k+'a'-1;ca[1]='\0';
3868: if(itimes==1){
3869: printf("#%1d%1d%d",i,j,k);
3870: fprintf(ficparo,"#%1d%1d%d",i,j,k);
3871: }else{
3872: printf("%1d%1d%d",i,j,k);
3873: fprintf(ficparo,"%1d%1d%d",i,j,k);
3874: /* printf(" %.5le",matcov[i][j]); */
3875: }
3876: ll=0;
3877: for(li=1;li <=nlstate; li++){
3878: for(lj=1;lj <=nlstate+ndeath; lj++){
3879: if(lj==li) continue;
3880: for(lk=1;lk<=ncovmodel;lk++){
3881: ll++;
3882: if(ll<=jj){
3883: cb[0]= lk +'a'-1;cb[1]='\0';
3884: if(ll<jj){
3885: if(itimes==1){
3886: printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
3887: fprintf(ficparo," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
3888: }else{
3889: printf(" 0.");
3890: fprintf(ficparo," 0.");
3891: }
3892: }else{
3893: if(itimes==1){
3894: printf(" Var(%s%1d%1d)",ca,i,j);
3895: fprintf(ficparo," Var(%s%1d%1d)",ca,i,j);
3896: }else{
3897: printf(" 0.");
3898: fprintf(ficparo," 0.");
3899: }
3900: }
3901: }
3902: } /* end lk */
3903: } /* end lj */
3904: } /* end li */
3905: printf("\n");
3906: fprintf(ficparo,"\n");
3907: numlinepar++;
3908: } /* end k*/
3909: } /*end j */
3910: } /* end i */
3911: } /* end itimes */
3912:
3913: } /* end of prwizard */
3914: /******************* Gompertz Likelihood ******************************/
3915: double gompertz(double x[])
3916: {
3917: double A,B,L=0.0,sump=0.,num=0.;
3918: int i,n=0; /* n is the size of the sample */
3919: for (i=0;i<=imx-1 ; i++) {
3920: sump=sump+weight[i];
3921: sump=sump+1;
3922: num=num+1;
3923: }
3924:
3925:
3926: /* for (i=1; i<=imx; i++)
3927: if (wav[i]>0) printf("i=%d ageex=%lf agecens=%lf agedc=%lf cens=%d %d\n" ,i,ageexmed[i],agecens[i],agedc[i],cens[i],wav[i]);*/
3928:
3929: for (i=0;i<=imx-1 ; i++)
3930: {
3931: if (cens[i]==1 & wav[i]>1)
3932: A=-x[1]/(x[2])*
3933: (exp(x[2]/YEARM*(agecens[i]*12-agegomp*12))-exp(x[2]/YEARM*(ageexmed[i]*12-agegomp*12)));
3934:
3935: if (cens[i]==0 & wav[i]>1)
3936: A=-x[1]/(x[2])*
3937: (exp(x[2]/YEARM*(agedc[i]*12-agegomp*12))-exp(x[2]/YEARM*(ageexmed[i]*12-agegomp*12)))
3938: +log(x[1]/YEARM)+x[2]/YEARM*(agedc[i]*12-agegomp*12)+log(YEARM);
3939:
3940: if (wav[i]>1 & agecens[i]>15) {
3941: L=L+A*weight[i];
3942: /* printf("\ni=%d A=%f L=%lf x[1]=%lf x[2]=%lf ageex=%lf agecens=%lf cens=%d agedc=%lf weight=%lf\n",i,A,L,x[1],x[2],ageexmed[i]*12,agecens[i]*12,cens[i],agedc[i]*12,weight[i]);*/
3943: }
3944: }
3945:
3946: /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/
3947:
3948: return -2*L*num/sump;
3949: }
3950:
3951: /******************* Printing html file ***********/
3952: void printinghtmlmort(char fileres[], char title[], char datafile[], int firstpass, \
3953: int lastpass, int stepm, int weightopt, char model[],\
3954: int imx, double p[],double **matcov){
3955: int i;
3956:
3957: fprintf(fichtm,"<ul><li><h4>Result files </h4>\n Force of mortality. Parameters of the Gompertz fit (with confidence interval in brackets):<br>");
3958: fprintf(fichtm," mu(age) =%lf*exp(%lf*(age-%d)) per year<br><br>",p[1],p[2],agegomp);
3959: for (i=1;i<=2;i++)
3960: fprintf(fichtm," p[%d] = %lf [%f ; %f]<br>\n",i,p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
3961: fprintf(fichtm,"<br><br><img src=\"graphmort.png\">");
3962: fprintf(fichtm,"</ul>");
3963: fflush(fichtm);
3964: }
3965:
3966: /******************* Gnuplot file **************/
3967: void printinggnuplotmort(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
3968:
3969: char dirfileres[132],optfileres[132];
3970: int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;
3971: int ng;
3972:
3973:
3974: /*#ifdef windows */
3975: fprintf(ficgp,"cd \"%s\" \n",pathc);
3976: /*#endif */
3977:
3978:
3979: strcpy(dirfileres,optionfilefiname);
3980: strcpy(optfileres,"vpl");
3981: fprintf(ficgp,"set out \"graphmort.png\"\n ");
3982: fprintf(ficgp,"set xlabel \"Age\"\n set ylabel \"Force of mortality (per year)\" \n ");
3983: fprintf(ficgp, "set ter png small\n set log y\n");
3984: fprintf(ficgp, "set size 0.65,0.65\n");
3985: fprintf(ficgp,"plot [%d:100] %lf*exp(%lf*(x-%d))",agegomp,p[1],p[2],agegomp);
3986:
3987: }
3988:
3989:
3990:
3991:
3992: /***********************************************/
3993: /**************** Main Program *****************/
3994: /***********************************************/
3995:
3996: int main(int argc, char *argv[])
3997: {
3998: int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav);
3999: int i,j, k, n=MAXN,iter,m,size=100,cptcode, cptcod;
4000: int jj, ll, li, lj, lk, imk;
4001: int numlinepar=0; /* Current linenumber of parameter file */
4002: int itimes;
4003: int NDIM=2;
4004:
4005: char ca[32], cb[32], cc[32];
4006: /* FILE *fichtm; *//* Html File */
4007: /* FILE *ficgp;*/ /*Gnuplot File */
4008: double agedeb, agefin,hf;
4009: double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;
4010:
4011: double fret;
4012: double **xi,tmp,delta;
4013:
4014: double dum; /* Dummy variable */
4015: double ***p3mat;
4016: double ***mobaverage;
4017: int *indx;
4018: char line[MAXLINE], linepar[MAXLINE];
4019: char path[MAXLINE],pathc[MAXLINE],pathcd[MAXLINE],pathtot[MAXLINE],model[MAXLINE];
4020: char pathr[MAXLINE], pathimach[MAXLINE];
4021: int firstobs=1, lastobs=10;
4022: int sdeb, sfin; /* Status at beginning and end */
4023: int c, h , cpt,l;
4024: int ju,jl, mi;
4025: int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;
4026: int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,*tab;
4027: int mobilavproj=0 , prevfcast=0 ; /* moving average of prev, If prevfcast=1 prevalence projection */
4028: int mobilav=0,popforecast=0;
4029: int hstepm, nhstepm;
4030: double jprev1=1, mprev1=1,anprev1=2000,jprev2=1, mprev2=1,anprev2=2000;
4031: double jpyram=1, mpyram=1,anpyram=2000,jpyram1=1, mpyram1=1,anpyram1=2000;
4032:
4033: double bage, fage, age, agelim, agebase;
4034: double ftolpl=FTOL;
4035: double **prlim;
4036: double *severity;
4037: double ***param; /* Matrix of parameters */
4038: double *p;
4039: double **matcov; /* Matrix of covariance */
4040: double ***delti3; /* Scale */
4041: double *delti; /* Scale */
4042: double ***eij, ***vareij;
4043: double **varpl; /* Variances of prevalence limits by age */
4044: double *epj, vepp;
4045: double kk1, kk2;
4046: double dateprev1, dateprev2,jproj1=1,mproj1=1,anproj1=2000,jproj2=1,mproj2=1,anproj2=2000;
4047: double **ximort;
4048: char *alph[]={"a","a","b","c","d","e"}, str[4];
4049: int *dcwave;
4050:
4051: char z[1]="c", occ;
4052:
4053: char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];
4054: char strstart[80], *strt, strtend[80];
4055: char *stratrunc;
4056: int lstra;
4057:
4058: long total_usecs;
4059:
4060: /* setlocale (LC_ALL, ""); */
4061: /* bindtextdomain (PACKAGE, LOCALEDIR); */
4062: /* textdomain (PACKAGE); */
4063: /* setlocale (LC_CTYPE, ""); */
4064: /* setlocale (LC_MESSAGES, ""); */
4065:
4066: /* gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */
4067: (void) gettimeofday(&start_time,&tzp);
4068: curr_time=start_time;
4069: tm = *localtime(&start_time.tv_sec);
4070: tmg = *gmtime(&start_time.tv_sec);
4071: strcpy(strstart,asctime(&tm));
4072:
4073: /* printf("Localtime (at start)=%s",strstart); */
4074: /* tp.tv_sec = tp.tv_sec +86400; */
4075: /* tm = *localtime(&start_time.tv_sec); */
4076: /* tmg.tm_year=tmg.tm_year +dsign*dyear; */
4077: /* tmg.tm_mon=tmg.tm_mon +dsign*dmonth; */
4078: /* tmg.tm_hour=tmg.tm_hour + 1; */
4079: /* tp.tv_sec = mktime(&tmg); */
4080: /* strt=asctime(&tmg); */
4081: /* printf("Time(after) =%s",strstart); */
4082: /* (void) time (&time_value);
4083: * printf("time=%d,t-=%d\n",time_value,time_value-86400);
4084: * tm = *localtime(&time_value);
4085: * strstart=asctime(&tm);
4086: * printf("tim_value=%d,asctime=%s\n",time_value,strstart);
4087: */
4088:
4089: nberr=0; /* Number of errors and warnings */
4090: nbwarn=0;
4091: getcwd(pathcd, size);
4092:
4093: printf("\n%s\n%s",version,fullversion);
4094: if(argc <=1){
4095: printf("\nEnter the parameter file name: ");
4096: scanf("%s",pathtot);
4097: }
4098: else{
4099: strcpy(pathtot,argv[1]);
4100: }
4101: /*if(getcwd(pathcd, MAXLINE)!= NULL)printf ("Error pathcd\n");*/
4102: /*cygwin_split_path(pathtot,path,optionfile);
4103: printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/
4104: /* cutv(path,optionfile,pathtot,'\\');*/
4105:
4106: split(argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
4107: /* strcpy(pathimach,argv[0]); */
4108: split(pathtot,path,optionfile,optionfilext,optionfilefiname);
4109: printf("pathimach=%s, pathtot=%s,\npath=%s,\noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",pathimach,pathtot,path,optionfile,optionfilext,optionfilefiname);
4110: chdir(path);
4111: strcpy(command,"mkdir ");
4112: strcat(command,optionfilefiname);
4113: if((outcmd=system(command)) != 0){
4114: printf("Problem creating directory or it already exists %s%s, err=%d\n",path,optionfilefiname,outcmd);
4115: /* fprintf(ficlog,"Problem creating directory %s%s\n",path,optionfilefiname); */
4116: /* fclose(ficlog); */
4117: /* exit(1); */
4118: }
4119: /* if((imk=mkdir(optionfilefiname))<0){ */
4120: /* perror("mkdir"); */
4121: /* } */
4122:
4123: /*-------- arguments in the command line --------*/
4124:
4125: /* Log file */
4126: strcat(filelog, optionfilefiname);
4127: strcat(filelog,".log"); /* */
4128: if((ficlog=fopen(filelog,"w"))==NULL) {
4129: printf("Problem with logfile %s\n",filelog);
4130: goto end;
4131: }
4132: fprintf(ficlog,"Log filename:%s\n",filelog);
4133: fprintf(ficlog,"\n%s\n%s",version,fullversion);
4134: fprintf(ficlog,"\nEnter the parameter file name: \n");
4135: fprintf(ficlog,"pathimach=%s\npathtot=%s\n\
4136: path=%s \n\
4137: optionfile=%s\n\
4138: optionfilext=%s\n\
4139: optionfilefiname=%s\n",pathimach,pathtot,path,optionfile,optionfilext,optionfilefiname);
4140:
4141: printf("Local time (at start):%s",strstart);
4142: fprintf(ficlog,"Local time (at start): %s",strstart);
4143: fflush(ficlog);
4144: /* (void) gettimeofday(&curr_time,&tzp); */
4145: /* printf("Elapsed time %d\n", asc_diff_time(curr_time.tv_sec-start_time.tv_sec,tmpout)); */
4146:
4147: /* */
4148: strcpy(fileres,"r");
4149: strcat(fileres, optionfilefiname);
4150: strcat(fileres,".txt"); /* Other files have txt extension */
4151:
4152: /*---------arguments file --------*/
4153:
4154: if((ficpar=fopen(optionfile,"r"))==NULL) {
4155: printf("Problem with optionfile %s\n",optionfile);
4156: fprintf(ficlog,"Problem with optionfile %s\n",optionfile);
4157: fflush(ficlog);
4158: goto end;
4159: }
4160:
4161:
4162:
4163: strcpy(filereso,"o");
4164: strcat(filereso,fileres);
4165: if((ficparo=fopen(filereso,"w"))==NULL) { /* opened on subdirectory */
4166: printf("Problem with Output resultfile: %s\n", filereso);
4167: fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso);
4168: fflush(ficlog);
4169: goto end;
4170: }
4171:
4172: /* Reads comments: lines beginning with '#' */
4173: numlinepar=0;
4174: while((c=getc(ficpar))=='#' && c!= EOF){
4175: ungetc(c,ficpar);
4176: fgets(line, MAXLINE, ficpar);
4177: numlinepar++;
4178: puts(line);
4179: fputs(line,ficparo);
4180: fputs(line,ficlog);
4181: }
4182: ungetc(c,ficpar);
4183:
4184: 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);
4185: numlinepar++;
4186: 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);
4187: 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);
4188: 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);
4189: fflush(ficlog);
4190: while((c=getc(ficpar))=='#' && c!= EOF){
4191: ungetc(c,ficpar);
4192: fgets(line, MAXLINE, ficpar);
4193: numlinepar++;
4194: puts(line);
4195: fputs(line,ficparo);
4196: fputs(line,ficlog);
4197: }
4198: ungetc(c,ficpar);
4199:
4200:
4201: covar=matrix(0,NCOVMAX,1,n);
4202: cptcovn=0; /*Number of covariates, i.e. number of '+' in model statement*/
4203: if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;
4204:
4205: ncovmodel=2+cptcovn; /*Number of variables = cptcovn + intercept + age */
4206: nvar=ncovmodel-1; /* Suppressing age as a basic covariate */
4207: npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/
4208:
4209: delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
4210: delti=delti3[1][1];
4211: /*delti=vector(1,npar); *//* Scale of each paramater (output from hesscov)*/
4212: if(mle==-1){ /* Print a wizard for help writing covariance matrix */
4213: prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
4214: printf(" You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
4215: fprintf(ficlog," You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
4216: free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
4217: fclose (ficparo);
4218: fclose (ficlog);
4219: exit(0);
4220: }
4221: else if(mle==-3) {
4222: prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
4223: printf(" You choose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
4224: fprintf(ficlog," You choose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
4225: param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
4226: matcov=matrix(1,npar,1,npar);
4227: }
4228: else{
4229: /* Read guess parameters */
4230: /* Reads comments: lines beginning with '#' */
4231: while((c=getc(ficpar))=='#' && c!= EOF){
4232: ungetc(c,ficpar);
4233: fgets(line, MAXLINE, ficpar);
4234: numlinepar++;
4235: puts(line);
4236: fputs(line,ficparo);
4237: fputs(line,ficlog);
4238: }
4239: ungetc(c,ficpar);
4240:
4241: param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
4242: for(i=1; i <=nlstate; i++){
4243: j=0;
4244: for(jj=1; jj <=nlstate+ndeath; jj++){
4245: if(jj==i) continue;
4246: j++;
4247: fscanf(ficpar,"%1d%1d",&i1,&j1);
4248: if ((i1 != i) && (j1 != j)){
4249: printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n",numlinepar, i,j, i1, j1);
4250: exit(1);
4251: }
4252: fprintf(ficparo,"%1d%1d",i1,j1);
4253: if(mle==1)
4254: printf("%1d%1d",i,j);
4255: fprintf(ficlog,"%1d%1d",i,j);
4256: for(k=1; k<=ncovmodel;k++){
4257: fscanf(ficpar," %lf",¶m[i][j][k]);
4258: if(mle==1){
4259: printf(" %lf",param[i][j][k]);
4260: fprintf(ficlog," %lf",param[i][j][k]);
4261: }
4262: else
4263: fprintf(ficlog," %lf",param[i][j][k]);
4264: fprintf(ficparo," %lf",param[i][j][k]);
4265: }
4266: fscanf(ficpar,"\n");
4267: numlinepar++;
4268: if(mle==1)
4269: printf("\n");
4270: fprintf(ficlog,"\n");
4271: fprintf(ficparo,"\n");
4272: }
4273: }
4274: fflush(ficlog);
4275:
4276:
4277: p=param[1][1];
4278:
4279: /* Reads comments: lines beginning with '#' */
4280: while((c=getc(ficpar))=='#' && c!= EOF){
4281: ungetc(c,ficpar);
4282: fgets(line, MAXLINE, ficpar);
4283: numlinepar++;
4284: puts(line);
4285: fputs(line,ficparo);
4286: fputs(line,ficlog);
4287: }
4288: ungetc(c,ficpar);
4289:
4290: for(i=1; i <=nlstate; i++){
4291: for(j=1; j <=nlstate+ndeath-1; j++){
4292: fscanf(ficpar,"%1d%1d",&i1,&j1);
4293: if ((i1-i)*(j1-j)!=0){
4294: printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n",numlinepar, i,j, i1, j1);
4295: exit(1);
4296: }
4297: printf("%1d%1d",i,j);
4298: fprintf(ficparo,"%1d%1d",i1,j1);
4299: fprintf(ficlog,"%1d%1d",i1,j1);
4300: for(k=1; k<=ncovmodel;k++){
4301: fscanf(ficpar,"%le",&delti3[i][j][k]);
4302: printf(" %le",delti3[i][j][k]);
4303: fprintf(ficparo," %le",delti3[i][j][k]);
4304: fprintf(ficlog," %le",delti3[i][j][k]);
4305: }
4306: fscanf(ficpar,"\n");
4307: numlinepar++;
4308: printf("\n");
4309: fprintf(ficparo,"\n");
4310: fprintf(ficlog,"\n");
4311: }
4312: }
4313: fflush(ficlog);
4314:
4315: delti=delti3[1][1];
4316:
4317:
4318: /* free_ma3x(delti3,1,nlstate,1,nlstate+ndeath-1,1,ncovmodel); */ /* Hasn't to to freed here otherwise delti is no more allocated */
4319:
4320: /* Reads comments: lines beginning with '#' */
4321: while((c=getc(ficpar))=='#' && c!= EOF){
4322: ungetc(c,ficpar);
4323: fgets(line, MAXLINE, ficpar);
4324: numlinepar++;
4325: puts(line);
4326: fputs(line,ficparo);
4327: fputs(line,ficlog);
4328: }
4329: ungetc(c,ficpar);
4330:
4331: matcov=matrix(1,npar,1,npar);
4332: for(i=1; i <=npar; i++){
4333: fscanf(ficpar,"%s",&str);
4334: if(mle==1)
4335: printf("%s",str);
4336: fprintf(ficlog,"%s",str);
4337: fprintf(ficparo,"%s",str);
4338: for(j=1; j <=i; j++){
4339: fscanf(ficpar," %le",&matcov[i][j]);
4340: if(mle==1){
4341: printf(" %.5le",matcov[i][j]);
4342: }
4343: fprintf(ficlog," %.5le",matcov[i][j]);
4344: fprintf(ficparo," %.5le",matcov[i][j]);
4345: }
4346: fscanf(ficpar,"\n");
4347: numlinepar++;
4348: if(mle==1)
4349: printf("\n");
4350: fprintf(ficlog,"\n");
4351: fprintf(ficparo,"\n");
4352: }
4353: for(i=1; i <=npar; i++)
4354: for(j=i+1;j<=npar;j++)
4355: matcov[i][j]=matcov[j][i];
4356:
4357: if(mle==1)
4358: printf("\n");
4359: fprintf(ficlog,"\n");
4360:
4361: fflush(ficlog);
4362:
4363: /*-------- Rewriting parameter file ----------*/
4364: strcpy(rfileres,"r"); /* "Rparameterfile */
4365: strcat(rfileres,optionfilefiname); /* Parameter file first name*/
4366: strcat(rfileres,"."); /* */
4367: strcat(rfileres,optionfilext); /* Other files have txt extension */
4368: if((ficres =fopen(rfileres,"w"))==NULL) {
4369: printf("Problem writing new parameter file: %s\n", fileres);goto end;
4370: fprintf(ficlog,"Problem writing new parameter file: %s\n", fileres);goto end;
4371: }
4372: fprintf(ficres,"#%s\n",version);
4373: } /* End of mle != -3 */
4374:
4375: /*-------- data file ----------*/
4376: if((fic=fopen(datafile,"r"))==NULL) {
4377: printf("Problem with datafile: %s\n", datafile);goto end;
4378: fprintf(ficlog,"Problem with datafile: %s\n", datafile);goto end;
4379: }
4380:
4381: n= lastobs;
4382: severity = vector(1,maxwav);
4383: outcome=imatrix(1,maxwav+1,1,n);
4384: num=lvector(1,n);
4385: moisnais=vector(1,n);
4386: annais=vector(1,n);
4387: moisdc=vector(1,n);
4388: andc=vector(1,n);
4389: agedc=vector(1,n);
4390: cod=ivector(1,n);
4391: weight=vector(1,n);
4392: for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */
4393: mint=matrix(1,maxwav,1,n);
4394: anint=matrix(1,maxwav,1,n);
4395: s=imatrix(1,maxwav+1,1,n);
4396: tab=ivector(1,NCOVMAX);
4397: ncodemax=ivector(1,8);
4398:
4399: i=1;
4400: while (fgets(line, MAXLINE, fic) != NULL) {
4401: if ((i >= firstobs) && (i <=lastobs)) {
4402:
4403: for (j=maxwav;j>=1;j--){
4404: cutv(stra, strb,line,' '); s[j][i]=atoi(strb);
4405: strcpy(line,stra);
4406: cutv(stra, strb,line,'/'); anint[j][i]=(double)(atoi(strb)); strcpy(line,stra);
4407: cutv(stra, strb,line,' '); mint[j][i]=(double)(atoi(strb)); strcpy(line,stra);
4408: }
4409:
4410: cutv(stra, strb,line,'/'); andc[i]=(double)(atoi(strb)); strcpy(line,stra);
4411: cutv(stra, strb,line,' '); moisdc[i]=(double)(atoi(strb)); strcpy(line,stra);
4412:
4413: cutv(stra, strb,line,'/'); annais[i]=(double)(atoi(strb)); strcpy(line,stra);
4414: cutv(stra, strb,line,' '); moisnais[i]=(double)(atoi(strb)); strcpy(line,stra);
4415:
4416: cutv(stra, strb,line,' '); weight[i]=(double)(atoi(strb)); strcpy(line,stra);
4417: for (j=ncovcol;j>=1;j--){
4418: cutv(stra, strb,line,' '); covar[j][i]=(double)(atoi(strb)); strcpy(line,stra);
4419: }
4420: lstra=strlen(stra);
4421: if(lstra > 9){ /* More than 2**32 or max of what printf can write with %ld */
4422: stratrunc = &(stra[lstra-9]);
4423: num[i]=atol(stratrunc);
4424: }
4425: else
4426: num[i]=atol(stra);
4427:
4428: /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){
4429: 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;}*/
4430:
4431: i=i+1;
4432: }
4433: }
4434: /* printf("ii=%d", ij);
4435: scanf("%d",i);*/
4436: imx=i-1; /* Number of individuals */
4437:
4438: /* for (i=1; i<=imx; i++){
4439: if ((s[1][i]==3) && (s[2][i]==2)) s[2][i]=3;
4440: if ((s[2][i]==3) && (s[3][i]==2)) s[3][i]=3;
4441: if ((s[3][i]==3) && (s[4][i]==2)) s[4][i]=3;
4442: }*/
4443: /* for (i=1; i<=imx; i++){
4444: if (s[4][i]==9) s[4][i]=-1;
4445: 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]));}*/
4446:
4447: for (i=1; i<=imx; i++)
4448:
4449: /*if ((s[3][i]==3) || (s[4][i]==3)) weight[i]=0.08;
4450: else weight[i]=1;*/
4451:
4452: /* Calculation of the number of parameter from char model*/
4453: Tvar=ivector(1,15); /* stores the number n of the covariates in Vm+Vn at 1 and m at 2 */
4454: Tprod=ivector(1,15);
4455: Tvaraff=ivector(1,15);
4456: Tvard=imatrix(1,15,1,2);
4457: Tage=ivector(1,15);
4458:
4459: if (strlen(model) >1){ /* If there is at least 1 covariate */
4460: j=0, j1=0, k1=1, k2=1;
4461: j=nbocc(model,'+'); /* j=Number of '+' */
4462: j1=nbocc(model,'*'); /* j1=Number of '*' */
4463: cptcovn=j+1;
4464: cptcovprod=j1; /*Number of products */
4465:
4466: strcpy(modelsav,model);
4467: if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){
4468: printf("Error. Non available option model=%s ",model);
4469: fprintf(ficlog,"Error. Non available option model=%s ",model);
4470: goto end;
4471: }
4472:
4473: /* This loop fills the array Tvar from the string 'model'.*/
4474:
4475: for(i=(j+1); i>=1;i--){
4476: cutv(stra,strb,modelsav,'+'); /* keeps in strb after the last + */
4477: if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyzes it */
4478: /* printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/
4479: /*scanf("%d",i);*/
4480: if (strchr(strb,'*')) { /* Model includes a product */
4481: cutv(strd,strc,strb,'*'); /* strd*strc Vm*Vn (if not *age)*/
4482: if (strcmp(strc,"age")==0) { /* Vn*age */
4483: cptcovprod--;
4484: cutv(strb,stre,strd,'V');
4485: Tvar[i]=atoi(stre); /* computes n in Vn and stores in Tvar*/
4486: cptcovage++;
4487: Tage[cptcovage]=i;
4488: /*printf("stre=%s ", stre);*/
4489: }
4490: else if (strcmp(strd,"age")==0) { /* or age*Vn */
4491: cptcovprod--;
4492: cutv(strb,stre,strc,'V');
4493: Tvar[i]=atoi(stre);
4494: cptcovage++;
4495: Tage[cptcovage]=i;
4496: }
4497: else { /* Age is not in the model */
4498: cutv(strb,stre,strc,'V'); /* strc= Vn, stre is n*/
4499: Tvar[i]=ncovcol+k1;
4500: cutv(strb,strc,strd,'V'); /* strd was Vm, strc is m */
4501: Tprod[k1]=i;
4502: Tvard[k1][1]=atoi(strc); /* m*/
4503: Tvard[k1][2]=atoi(stre); /* n */
4504: Tvar[cptcovn+k2]=Tvard[k1][1];
4505: Tvar[cptcovn+k2+1]=Tvard[k1][2];
4506: for (k=1; k<=lastobs;k++)
4507: covar[ncovcol+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];
4508: k1++;
4509: k2=k2+2;
4510: }
4511: }
4512: else { /* no more sum */
4513: /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/
4514: /* scanf("%d",i);*/
4515: cutv(strd,strc,strb,'V');
4516: Tvar[i]=atoi(strc);
4517: }
4518: strcpy(modelsav,stra);
4519: /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);
4520: scanf("%d",i);*/
4521: } /* end of loop + */
4522: } /* end model */
4523:
4524: /*The number n of Vn is stored in Tvar. cptcovage =number of age covariate. Tage gives the position of age. cptcovprod= number of products.
4525: If model=V1+V1*age then Tvar[1]=1 Tvar[2]=1 cptcovage=1 Tage[1]=2 cptcovprod=0*/
4526:
4527: /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);
4528: printf("cptcovprod=%d ", cptcovprod);
4529: fprintf(ficlog,"cptcovprod=%d ", cptcovprod);
4530:
4531: scanf("%d ",i);
4532: fclose(fic);*/
4533:
4534: /* if(mle==1){*/
4535: if (weightopt != 1) { /* Maximisation without weights*/
4536: for(i=1;i<=n;i++) weight[i]=1.0;
4537: }
4538: /*-calculation of age at interview from date of interview and age at death -*/
4539: agev=matrix(1,maxwav,1,imx);
4540:
4541: for (i=1; i<=imx; i++) {
4542: for(m=2; (m<= maxwav); m++) {
4543: if (((int)mint[m][i]== 99) && (s[m][i] <= nlstate)){
4544: anint[m][i]=9999;
4545: s[m][i]=-1;
4546: }
4547: if((int)moisdc[i]==99 && (int)andc[i]==9999 && s[m][i]>nlstate){
4548: nberr++;
4549: 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);
4550: 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);
4551: s[m][i]=-1;
4552: }
4553: if((int)moisdc[i]==99 && (int)andc[i]!=9999 && s[m][i]>nlstate){
4554: nberr++;
4555: 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]);
4556: 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]);
4557: s[m][i]=-1; /* We prefer to skip it (and to skip it in version 0.8a1 too */
4558: }
4559: }
4560: }
4561:
4562: for (i=1; i<=imx; i++) {
4563: agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);
4564: for(m=firstpass; (m<= lastpass); m++){
4565: if(s[m][i] >0){
4566: if (s[m][i] >= nlstate+1) {
4567: if(agedc[i]>0)
4568: if((int)moisdc[i]!=99 && (int)andc[i]!=9999)
4569: agev[m][i]=agedc[i];
4570: /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/
4571: else {
4572: if ((int)andc[i]!=9999){
4573: nbwarn++;
4574: printf("Warning negative age at death: %ld line:%d\n",num[i],i);
4575: fprintf(ficlog,"Warning negative age at death: %ld line:%d\n",num[i],i);
4576: agev[m][i]=-1;
4577: }
4578: }
4579: }
4580: else if(s[m][i] !=9){ /* Standard case, age in fractional
4581: years but with the precision of a
4582: month */
4583: agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);
4584: if((int)mint[m][i]==99 || (int)anint[m][i]==9999)
4585: agev[m][i]=1;
4586: else if(agev[m][i] <agemin){
4587: agemin=agev[m][i];
4588: /*printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], agemin);*/
4589: }
4590: else if(agev[m][i] >agemax){
4591: agemax=agev[m][i];
4592: /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/
4593: }
4594: /*agev[m][i]=anint[m][i]-annais[i];*/
4595: /* agev[m][i] = age[i]+2*m;*/
4596: }
4597: else { /* =9 */
4598: agev[m][i]=1;
4599: s[m][i]=-1;
4600: }
4601: }
4602: else /*= 0 Unknown */
4603: agev[m][i]=1;
4604: }
4605:
4606: }
4607: for (i=1; i<=imx; i++) {
4608: for(m=firstpass; (m<=lastpass); m++){
4609: if (s[m][i] > (nlstate+ndeath)) {
4610: nberr++;
4611: 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);
4612: 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);
4613: goto end;
4614: }
4615: }
4616: }
4617:
4618: /*for (i=1; i<=imx; i++){
4619: for (m=firstpass; (m<lastpass); m++){
4620: printf("%ld %d %.lf %d %d\n", num[i],(covar[1][i]),agev[m][i],s[m][i],s[m+1][i]);
4621: }
4622:
4623: }*/
4624:
4625:
4626: printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);
4627: fprintf(ficlog,"Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);
4628:
4629: agegomp=(int)agemin;
4630: free_vector(severity,1,maxwav);
4631: free_imatrix(outcome,1,maxwav+1,1,n);
4632: free_vector(moisnais,1,n);
4633: free_vector(annais,1,n);
4634: /* free_matrix(mint,1,maxwav,1,n);
4635: free_matrix(anint,1,maxwav,1,n);*/
4636: free_vector(moisdc,1,n);
4637: free_vector(andc,1,n);
4638:
4639:
4640: wav=ivector(1,imx);
4641: dh=imatrix(1,lastpass-firstpass+1,1,imx);
4642: bh=imatrix(1,lastpass-firstpass+1,1,imx);
4643: mw=imatrix(1,lastpass-firstpass+1,1,imx);
4644:
4645: /* Concatenates waves */
4646: concatwav(wav, dh, bh, mw, s, agedc, agev, firstpass, lastpass, imx, nlstate, stepm);
4647:
4648: /* Routine tricode is to calculate cptcoveff (real number of unique covariates) and to associate covariable number and modality */
4649:
4650: Tcode=ivector(1,100);
4651: nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);
4652: ncodemax[1]=1;
4653: if (cptcovn > 0) tricode(Tvar,nbcode,imx);
4654:
4655: codtab=imatrix(1,100,1,10); /* Cross tabulation to get the order of
4656: the estimations*/
4657: h=0;
4658: m=pow(2,cptcoveff);
4659:
4660: for(k=1;k<=cptcoveff; k++){
4661: for(i=1; i <=(m/pow(2,k));i++){
4662: for(j=1; j <= ncodemax[k]; j++){
4663: for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){
4664: h++;
4665: if (h>m) h=1;codtab[h][k]=j;codtab[h][Tvar[k]]=j;
4666: /* printf("h=%d k=%d j=%d codtab[h][k]=%d tvar[k]=%d \n",h, k,j,codtab[h][k],Tvar[k]);*/
4667: }
4668: }
4669: }
4670: }
4671: /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]);
4672: codtab[1][2]=1;codtab[2][2]=2; */
4673: /* for(i=1; i <=m ;i++){
4674: for(k=1; k <=cptcovn; k++){
4675: printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);
4676: }
4677: printf("\n");
4678: }
4679: scanf("%d",i);*/
4680:
4681: /*------------ gnuplot -------------*/
4682: strcpy(optionfilegnuplot,optionfilefiname);
4683: if(mle==-3)
4684: strcat(optionfilegnuplot,"-mort");
4685: strcat(optionfilegnuplot,".gp");
4686:
4687: if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {
4688: printf("Problem with file %s",optionfilegnuplot);
4689: }
4690: else{
4691: fprintf(ficgp,"\n# %s\n", version);
4692: fprintf(ficgp,"# %s\n", optionfilegnuplot);
4693: fprintf(ficgp,"set missing 'NaNq'\n");
4694: }
4695: /* fclose(ficgp);*/
4696: /*--------- index.htm --------*/
4697:
4698: strcpy(optionfilehtm,optionfilefiname); /* Main html file */
4699: if(mle==-3)
4700: strcat(optionfilehtm,"-mort");
4701: strcat(optionfilehtm,".htm");
4702: if((fichtm=fopen(optionfilehtm,"w"))==NULL) {
4703: printf("Problem with %s \n",optionfilehtm), exit(0);
4704: }
4705:
4706: strcpy(optionfilehtmcov,optionfilefiname); /* Only for matrix of covariance */
4707: strcat(optionfilehtmcov,"-cov.htm");
4708: if((fichtmcov=fopen(optionfilehtmcov,"w"))==NULL) {
4709: printf("Problem with %s \n",optionfilehtmcov), exit(0);
4710: }
4711: else{
4712: fprintf(fichtmcov,"<body>\n<title>IMaCh Cov %s</title>\n <font size=\"2\">%s <br> %s</font> \
4713: <hr size=\"2\" color=\"#EC5E5E\"> \n\
4714: Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n",\
4715: fileres,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);
4716: }
4717:
4718: fprintf(fichtm,"<body>\n<title>IMaCh %s</title>\n <font size=\"2\">%s <br> %s</font> \
4719: <hr size=\"2\" color=\"#EC5E5E\"> \n\
4720: Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n\
4721: \n\
4722: <hr size=\"2\" color=\"#EC5E5E\">\
4723: <ul><li><h4>Parameter files</h4>\n\
4724: - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n\
4725: - Log file of the run: <a href=\"%s\">%s</a><br>\n\
4726: - Gnuplot file name: <a href=\"%s\">%s</a><br>\n\
4727: - Date and time at start: %s</ul>\n",\
4728: fileres,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model,\
4729: fileres,fileres,\
4730: filelog,filelog,optionfilegnuplot,optionfilegnuplot,strstart);
4731: fflush(fichtm);
4732:
4733: strcpy(pathr,path);
4734: strcat(pathr,optionfilefiname);
4735: chdir(optionfilefiname); /* Move to directory named optionfile */
4736:
4737: /* Calculates basic frequencies. Computes observed prevalence at single age
4738: and prints on file fileres'p'. */
4739: freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint);
4740:
4741: fprintf(fichtm,"\n");
4742: fprintf(fichtm,"<br>Total number of observations=%d <br>\n\
4743: Youngest age at first (selected) pass %.2f, oldest age %.2f<br>\n\
4744: Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n",\
4745: imx,agemin,agemax,jmin,jmax,jmean);
4746: pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
4747: oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
4748: newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
4749: savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
4750: oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */
4751:
4752:
4753: /* For Powell, parameters are in a vector p[] starting at p[1]
4754: so we point p on param[1][1] so that p[1] maps on param[1][1][1] */
4755: p=param[1][1]; /* *(*(*(param +1)+1)+0) */
4756:
4757: globpr=0; /* To get the number ipmx of contributions and the sum of weights*/
4758: if (mle==-3){
4759: ximort=matrix(1,NDIM,1,NDIM);
4760: cens=ivector(1,n);
4761: ageexmed=vector(1,n);
4762: agecens=vector(1,n);
4763: dcwave=ivector(1,n);
4764:
4765: for (i=1; i<=imx; i++){
4766: dcwave[i]=-1;
4767: for (j=1; j<=lastpass; j++)
4768: if (s[j][i]>nlstate) {
4769: dcwave[i]=j;
4770: /* printf("i=%d j=%d s=%d dcwave=%d\n",i,j, s[j][i],dcwave[i]);*/
4771: break;
4772: }
4773: }
4774:
4775: for (i=1; i<=imx; i++) {
4776: if (wav[i]>0){
4777: ageexmed[i]=agev[mw[1][i]][i];
4778: j=wav[i];agecens[i]=1.;
4779: if (ageexmed[i]>1 & wav[i]>0) agecens[i]=agev[mw[j][i]][i];
4780: cens[i]=1;
4781:
4782: if (ageexmed[i]<1) cens[i]=-1;
4783: if (agedc[i]< AGESUP & agedc[i]>1 & dcwave[i]>firstpass & dcwave[i]<=lastpass) cens[i]=0 ;
4784: }
4785: else cens[i]=-1;
4786: }
4787:
4788: for (i=1;i<=NDIM;i++) {
4789: for (j=1;j<=NDIM;j++)
4790: ximort[i][j]=(i == j ? 1.0 : 0.0);
4791: }
4792:
4793: p[1]=0.1; p[2]=0.1;
4794: /*printf("%lf %lf", p[1], p[2]);*/
4795:
4796:
4797: printf("Powell\n"); fprintf(ficlog,"Powell\n");
4798: strcpy(filerespow,"pow-mort");
4799: strcat(filerespow,fileres);
4800: if((ficrespow=fopen(filerespow,"w"))==NULL) {
4801: printf("Problem with resultfile: %s\n", filerespow);
4802: fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
4803: }
4804: fprintf(ficrespow,"# Powell\n# iter -2*LL");
4805: /* for (i=1;i<=nlstate;i++)
4806: for(j=1;j<=nlstate+ndeath;j++)
4807: if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
4808: */
4809: fprintf(ficrespow,"\n");
4810:
4811: powell(p,ximort,NDIM,ftol,&iter,&fret,gompertz);
4812: fclose(ficrespow);
4813:
4814: hesscov(matcov, p, NDIM,delti, 1e-4, gompertz);
4815:
4816: for(i=1; i <=NDIM; i++)
4817: for(j=i+1;j<=NDIM;j++)
4818: matcov[i][j]=matcov[j][i];
4819:
4820: printf("\nCovariance matrix\n ");
4821: for(i=1; i <=NDIM; i++) {
4822: for(j=1;j<=NDIM;j++){
4823: printf("%f ",matcov[i][j]);
4824: }
4825: printf("\n ");
4826: }
4827:
4828: printf("iter=%d MLE=%f Eq=%lf*exp(%lf*(age-%d))\n",iter,-gompertz(p),p[1],p[2],agegomp);
4829: for (i=1;i<=NDIM;i++)
4830: printf("%f [%f ; %f]\n",p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
4831: replace_back_to_slash(pathc,path); /* Even gnuplot wants a / */
4832: printinggnuplotmort(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
4833:
4834: printinghtmlmort(fileres,title,datafile, firstpass, lastpass, \
4835: stepm, weightopt,\
4836: model,imx,p,matcov);
4837: } /* Endof if mle==-3 */
4838:
4839: else{ /* For mle >=1 */
4840:
4841: likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
4842: printf("First Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
4843: for (k=1; k<=npar;k++)
4844: printf(" %d %8.5f",k,p[k]);
4845: printf("\n");
4846: globpr=1; /* to print the contributions */
4847: likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
4848: printf("Second Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
4849: for (k=1; k<=npar;k++)
4850: printf(" %d %8.5f",k,p[k]);
4851: printf("\n");
4852: if(mle>=1){ /* Could be 1 or 2 */
4853: mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);
4854: }
4855:
4856: /*--------- results files --------------*/
4857: 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);
4858:
4859:
4860: fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
4861: printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
4862: fprintf(ficlog,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
4863: for(i=1,jk=1; i <=nlstate; i++){
4864: for(k=1; k <=(nlstate+ndeath); k++){
4865: if (k != i) {
4866: printf("%d%d ",i,k);
4867: fprintf(ficlog,"%d%d ",i,k);
4868: fprintf(ficres,"%1d%1d ",i,k);
4869: for(j=1; j <=ncovmodel; j++){
4870: printf("%f ",p[jk]);
4871: fprintf(ficlog,"%f ",p[jk]);
4872: fprintf(ficres,"%f ",p[jk]);
4873: jk++;
4874: }
4875: printf("\n");
4876: fprintf(ficlog,"\n");
4877: fprintf(ficres,"\n");
4878: }
4879: }
4880: }
4881: if(mle!=0){
4882: /* Computing hessian and covariance matrix */
4883: ftolhess=ftol; /* Usually correct */
4884: hesscov(matcov, p, npar, delti, ftolhess, func);
4885: }
4886: fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");
4887: printf("# Scales (for hessian or gradient estimation)\n");
4888: fprintf(ficlog,"# Scales (for hessian or gradient estimation)\n");
4889: for(i=1,jk=1; i <=nlstate; i++){
4890: for(j=1; j <=nlstate+ndeath; j++){
4891: if (j!=i) {
4892: fprintf(ficres,"%1d%1d",i,j);
4893: printf("%1d%1d",i,j);
4894: fprintf(ficlog,"%1d%1d",i,j);
4895: for(k=1; k<=ncovmodel;k++){
4896: printf(" %.5e",delti[jk]);
4897: fprintf(ficlog," %.5e",delti[jk]);
4898: fprintf(ficres," %.5e",delti[jk]);
4899: jk++;
4900: }
4901: printf("\n");
4902: fprintf(ficlog,"\n");
4903: fprintf(ficres,"\n");
4904: }
4905: }
4906: }
4907:
4908: 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");
4909: if(mle>=1)
4910: 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");
4911: 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");
4912: /* # 121 Var(a12)\n\ */
4913: /* # 122 Cov(b12,a12) Var(b12)\n\ */
4914: /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
4915: /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
4916: /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
4917: /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
4918: /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
4919: /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
4920:
4921:
4922: /* Just to have a covariance matrix which will be more understandable
4923: even is we still don't want to manage dictionary of variables
4924: */
4925: for(itimes=1;itimes<=2;itimes++){
4926: jj=0;
4927: for(i=1; i <=nlstate; i++){
4928: for(j=1; j <=nlstate+ndeath; j++){
4929: if(j==i) continue;
4930: for(k=1; k<=ncovmodel;k++){
4931: jj++;
4932: ca[0]= k+'a'-1;ca[1]='\0';
4933: if(itimes==1){
4934: if(mle>=1)
4935: printf("#%1d%1d%d",i,j,k);
4936: fprintf(ficlog,"#%1d%1d%d",i,j,k);
4937: fprintf(ficres,"#%1d%1d%d",i,j,k);
4938: }else{
4939: if(mle>=1)
4940: printf("%1d%1d%d",i,j,k);
4941: fprintf(ficlog,"%1d%1d%d",i,j,k);
4942: fprintf(ficres,"%1d%1d%d",i,j,k);
4943: }
4944: ll=0;
4945: for(li=1;li <=nlstate; li++){
4946: for(lj=1;lj <=nlstate+ndeath; lj++){
4947: if(lj==li) continue;
4948: for(lk=1;lk<=ncovmodel;lk++){
4949: ll++;
4950: if(ll<=jj){
4951: cb[0]= lk +'a'-1;cb[1]='\0';
4952: if(ll<jj){
4953: if(itimes==1){
4954: if(mle>=1)
4955: printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
4956: fprintf(ficlog," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
4957: fprintf(ficres," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
4958: }else{
4959: if(mle>=1)
4960: printf(" %.5e",matcov[jj][ll]);
4961: fprintf(ficlog," %.5e",matcov[jj][ll]);
4962: fprintf(ficres," %.5e",matcov[jj][ll]);
4963: }
4964: }else{
4965: if(itimes==1){
4966: if(mle>=1)
4967: printf(" Var(%s%1d%1d)",ca,i,j);
4968: fprintf(ficlog," Var(%s%1d%1d)",ca,i,j);
4969: fprintf(ficres," Var(%s%1d%1d)",ca,i,j);
4970: }else{
4971: if(mle>=1)
4972: printf(" %.5e",matcov[jj][ll]);
4973: fprintf(ficlog," %.5e",matcov[jj][ll]);
4974: fprintf(ficres," %.5e",matcov[jj][ll]);
4975: }
4976: }
4977: }
4978: } /* end lk */
4979: } /* end lj */
4980: } /* end li */
4981: if(mle>=1)
4982: printf("\n");
4983: fprintf(ficlog,"\n");
4984: fprintf(ficres,"\n");
4985: numlinepar++;
4986: } /* end k*/
4987: } /*end j */
4988: } /* end i */
4989: } /* end itimes */
4990:
4991: fflush(ficlog);
4992: fflush(ficres);
4993:
4994: while((c=getc(ficpar))=='#' && c!= EOF){
4995: ungetc(c,ficpar);
4996: fgets(line, MAXLINE, ficpar);
4997: puts(line);
4998: fputs(line,ficparo);
4999: }
5000: ungetc(c,ficpar);
5001:
5002: estepm=0;
5003: fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm);
5004: if (estepm==0 || estepm < stepm) estepm=stepm;
5005: if (fage <= 2) {
5006: bage = ageminpar;
5007: fage = agemaxpar;
5008: }
5009:
5010: fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");
5011: fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
5012: fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
5013:
5014: while((c=getc(ficpar))=='#' && c!= EOF){
5015: ungetc(c,ficpar);
5016: fgets(line, MAXLINE, ficpar);
5017: puts(line);
5018: fputs(line,ficparo);
5019: }
5020: ungetc(c,ficpar);
5021:
5022: 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);
5023: 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);
5024: 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);
5025: printf("begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
5026: 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);
5027:
5028: while((c=getc(ficpar))=='#' && c!= EOF){
5029: ungetc(c,ficpar);
5030: fgets(line, MAXLINE, ficpar);
5031: puts(line);
5032: fputs(line,ficparo);
5033: }
5034: ungetc(c,ficpar);
5035:
5036:
5037: dateprev1=anprev1+(mprev1-1)/12.+(jprev1-1)/365.;
5038: dateprev2=anprev2+(mprev2-1)/12.+(jprev2-1)/365.;
5039:
5040: fscanf(ficpar,"pop_based=%d\n",&popbased);
5041: fprintf(ficparo,"pop_based=%d\n",popbased);
5042: fprintf(ficres,"pop_based=%d\n",popbased);
5043:
5044: while((c=getc(ficpar))=='#' && c!= EOF){
5045: ungetc(c,ficpar);
5046: fgets(line, MAXLINE, ficpar);
5047: puts(line);
5048: fputs(line,ficparo);
5049: }
5050: ungetc(c,ficpar);
5051:
5052: 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);
5053: 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);
5054: 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);
5055: 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);
5056: 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);
5057: /* day and month of proj2 are not used but only year anproj2.*/
5058:
5059:
5060:
5061: /* freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint);*/
5062: /*,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
5063:
5064: replace_back_to_slash(pathc,path); /* Even gnuplot wants a / */
5065: printinggnuplot(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
5066:
5067: printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,\
5068: model,imx,jmin,jmax,jmean,rfileres,popforecast,estepm,\
5069: jprev1,mprev1,anprev1,jprev2,mprev2,anprev2);
5070:
5071: /*------------ free_vector -------------*/
5072: /* chdir(path); */
5073:
5074: free_ivector(wav,1,imx);
5075: free_imatrix(dh,1,lastpass-firstpass+1,1,imx);
5076: free_imatrix(bh,1,lastpass-firstpass+1,1,imx);
5077: free_imatrix(mw,1,lastpass-firstpass+1,1,imx);
5078: free_lvector(num,1,n);
5079: free_vector(agedc,1,n);
5080: /*free_matrix(covar,0,NCOVMAX,1,n);*/
5081: /*free_matrix(covar,1,NCOVMAX,1,n);*/
5082: fclose(ficparo);
5083: fclose(ficres);
5084:
5085:
5086: /*--------------- Prevalence limit (stable prevalence) --------------*/
5087:
5088: strcpy(filerespl,"pl");
5089: strcat(filerespl,fileres);
5090: if((ficrespl=fopen(filerespl,"w"))==NULL) {
5091: printf("Problem with stable prevalence resultfile: %s\n", filerespl);goto end;
5092: fprintf(ficlog,"Problem with stable prevalence resultfile: %s\n", filerespl);goto end;
5093: }
5094: printf("Computing stable prevalence: result on file '%s' \n", filerespl);
5095: fprintf(ficlog,"Computing stable prevalence: result on file '%s' \n", filerespl);
5096: fprintf(ficrespl,"#Stable prevalence \n");
5097: fprintf(ficrespl,"#Age ");
5098: for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);
5099: fprintf(ficrespl,"\n");
5100:
5101: prlim=matrix(1,nlstate,1,nlstate);
5102:
5103: agebase=ageminpar;
5104: agelim=agemaxpar;
5105: ftolpl=1.e-10;
5106: i1=cptcoveff;
5107: if (cptcovn < 1){i1=1;}
5108:
5109: for(cptcov=1,k=0;cptcov<=i1;cptcov++){
5110: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
5111: k=k+1;
5112: /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/
5113: fprintf(ficrespl,"\n#******");
5114: printf("\n#******");
5115: fprintf(ficlog,"\n#******");
5116: for(j=1;j<=cptcoveff;j++) {
5117: fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
5118: printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
5119: fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
5120: }
5121: fprintf(ficrespl,"******\n");
5122: printf("******\n");
5123: fprintf(ficlog,"******\n");
5124:
5125: for (age=agebase; age<=agelim; age++){
5126: prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
5127: fprintf(ficrespl,"%.0f ",age );
5128: for(j=1;j<=cptcoveff;j++)
5129: fprintf(ficrespl,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
5130: for(i=1; i<=nlstate;i++)
5131: fprintf(ficrespl," %.5f", prlim[i][i]);
5132: fprintf(ficrespl,"\n");
5133: }
5134: }
5135: }
5136: fclose(ficrespl);
5137:
5138: /*------------- h Pij x at various ages ------------*/
5139:
5140: strcpy(filerespij,"pij"); strcat(filerespij,fileres);
5141: if((ficrespij=fopen(filerespij,"w"))==NULL) {
5142: printf("Problem with Pij resultfile: %s\n", filerespij);goto end;
5143: fprintf(ficlog,"Problem with Pij resultfile: %s\n", filerespij);goto end;
5144: }
5145: printf("Computing pij: result on file '%s' \n", filerespij);
5146: fprintf(ficlog,"Computing pij: result on file '%s' \n", filerespij);
5147:
5148: stepsize=(int) (stepm+YEARM-1)/YEARM;
5149: /*if (stepm<=24) stepsize=2;*/
5150:
5151: agelim=AGESUP;
5152: hstepm=stepsize*YEARM; /* Every year of age */
5153: hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */
5154:
5155: /* hstepm=1; aff par mois*/
5156:
5157: fprintf(ficrespij,"#****** h Pij x Probability to be in state j at age x+h being in i at x ");
5158: for(cptcov=1,k=0;cptcov<=i1;cptcov++){
5159: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
5160: k=k+1;
5161: fprintf(ficrespij,"\n#****** ");
5162: for(j=1;j<=cptcoveff;j++)
5163: fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
5164: fprintf(ficrespij,"******\n");
5165:
5166: for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */
5167: nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
5168: nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
5169:
5170: /* nhstepm=nhstepm*YEARM; aff par mois*/
5171:
5172: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
5173: oldm=oldms;savm=savms;
5174: hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
5175: fprintf(ficrespij,"# Cov Agex agex+h hpijx with i,j=");
5176: for(i=1; i<=nlstate;i++)
5177: for(j=1; j<=nlstate+ndeath;j++)
5178: fprintf(ficrespij," %1d-%1d",i,j);
5179: fprintf(ficrespij,"\n");
5180: for (h=0; h<=nhstepm; h++){
5181: fprintf(ficrespij,"%d %3.f %3.f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );
5182: for(i=1; i<=nlstate;i++)
5183: for(j=1; j<=nlstate+ndeath;j++)
5184: fprintf(ficrespij," %.5f", p3mat[i][j][h]);
5185: fprintf(ficrespij,"\n");
5186: }
5187: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
5188: fprintf(ficrespij,"\n");
5189: }
5190: }
5191: }
5192:
5193: varprob(optionfilefiname, matcov, p, delti, nlstate, bage, fage,k,Tvar,nbcode, ncodemax);
5194:
5195: fclose(ficrespij);
5196:
5197: probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
5198: for(i=1;i<=AGESUP;i++)
5199: for(j=1;j<=NCOVMAX;j++)
5200: for(k=1;k<=NCOVMAX;k++)
5201: probs[i][j][k]=0.;
5202:
5203: /*---------- Forecasting ------------------*/
5204: /*if((stepm == 1) && (strcmp(model,".")==0)){*/
5205: if(prevfcast==1){
5206: /* if(stepm ==1){*/
5207: prevforecast(fileres, anproj1, mproj1, jproj1, agemin, agemax, dateprev1, dateprev2, mobilavproj, bage, fage, firstpass, lastpass, anproj2, p, cptcoveff);
5208: /* (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);*/
5209: /* } */
5210: /* else{ */
5211: /* erreur=108; */
5212: /* 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); */
5213: /* 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); */
5214: /* } */
5215: }
5216:
5217:
5218: /*---------- Health expectancies and variances ------------*/
5219:
5220: strcpy(filerest,"t");
5221: strcat(filerest,fileres);
5222: if((ficrest=fopen(filerest,"w"))==NULL) {
5223: printf("Problem with total LE resultfile: %s\n", filerest);goto end;
5224: fprintf(ficlog,"Problem with total LE resultfile: %s\n", filerest);goto end;
5225: }
5226: printf("Computing Total LEs with variances: file '%s' \n", filerest);
5227: fprintf(ficlog,"Computing Total LEs with variances: file '%s' \n", filerest);
5228:
5229:
5230: strcpy(filerese,"e");
5231: strcat(filerese,fileres);
5232: if((ficreseij=fopen(filerese,"w"))==NULL) {
5233: printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
5234: fprintf(ficlog,"Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
5235: }
5236: printf("Computing Health Expectancies: result on file '%s' \n", filerese);
5237: fprintf(ficlog,"Computing Health Expectancies: result on file '%s' \n", filerese);
5238:
5239: strcpy(fileresv,"v");
5240: strcat(fileresv,fileres);
5241: if((ficresvij=fopen(fileresv,"w"))==NULL) {
5242: printf("Problem with variance resultfile: %s\n", fileresv);exit(0);
5243: fprintf(ficlog,"Problem with variance resultfile: %s\n", fileresv);exit(0);
5244: }
5245: printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
5246: fprintf(ficlog,"Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
5247:
5248: /* Computes prevalence between agemin (i.e minimal age computed) and no more ageminpar */
5249: prevalence(probs, agemin, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
5250: /* 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",\
5251: ageminpar, agemax, s[lastpass][imx], agev[lastpass][imx], nlstate, imx, mint[lastpass][imx],anint[lastpass][imx], dateprev1, dateprev2, firstpass, lastpass);
5252: */
5253:
5254: if (mobilav!=0) {
5255: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
5256: if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
5257: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
5258: printf(" Error in movingaverage mobilav=%d\n",mobilav);
5259: }
5260: }
5261:
5262: for(cptcov=1,k=0;cptcov<=i1;cptcov++){
5263: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
5264: k=k+1;
5265: fprintf(ficrest,"\n#****** ");
5266: for(j=1;j<=cptcoveff;j++)
5267: fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
5268: fprintf(ficrest,"******\n");
5269:
5270: fprintf(ficreseij,"\n#****** ");
5271: for(j=1;j<=cptcoveff;j++)
5272: fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
5273: fprintf(ficreseij,"******\n");
5274:
5275: fprintf(ficresvij,"\n#****** ");
5276: for(j=1;j<=cptcoveff;j++)
5277: fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
5278: fprintf(ficresvij,"******\n");
5279:
5280: eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
5281: oldm=oldms;savm=savms;
5282: evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov);
5283:
5284: vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
5285: oldm=oldms;savm=savms;
5286: varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,0, mobilav);
5287: if(popbased==1){
5288: varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,popbased,mobilav);
5289: }
5290:
5291:
5292: fprintf(ficrest,"#Total LEs with variances: e.. (std) ");
5293: for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);
5294: fprintf(ficrest,"\n");
5295:
5296: epj=vector(1,nlstate+1);
5297: for(age=bage; age <=fage ;age++){
5298: prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
5299: if (popbased==1) {
5300: if(mobilav ==0){
5301: for(i=1; i<=nlstate;i++)
5302: prlim[i][i]=probs[(int)age][i][k];
5303: }else{ /* mobilav */
5304: for(i=1; i<=nlstate;i++)
5305: prlim[i][i]=mobaverage[(int)age][i][k];
5306: }
5307: }
5308:
5309: fprintf(ficrest," %4.0f",age);
5310: for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){
5311: for(i=1, epj[j]=0.;i <=nlstate;i++) {
5312: epj[j] += prlim[i][i]*eij[i][j][(int)age];
5313: /* printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/
5314: }
5315: epj[nlstate+1] +=epj[j];
5316: }
5317:
5318: for(i=1, vepp=0.;i <=nlstate;i++)
5319: for(j=1;j <=nlstate;j++)
5320: vepp += vareij[i][j][(int)age];
5321: fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));
5322: for(j=1;j <=nlstate;j++){
5323: fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));
5324: }
5325: fprintf(ficrest,"\n");
5326: }
5327: free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
5328: free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);
5329: free_vector(epj,1,nlstate+1);
5330: }
5331: }
5332: free_vector(weight,1,n);
5333: free_imatrix(Tvard,1,15,1,2);
5334: free_imatrix(s,1,maxwav+1,1,n);
5335: free_matrix(anint,1,maxwav,1,n);
5336: free_matrix(mint,1,maxwav,1,n);
5337: free_ivector(cod,1,n);
5338: free_ivector(tab,1,NCOVMAX);
5339: fclose(ficreseij);
5340: fclose(ficresvij);
5341: fclose(ficrest);
5342: fclose(ficpar);
5343:
5344: /*------- Variance of stable prevalence------*/
5345:
5346: strcpy(fileresvpl,"vpl");
5347: strcat(fileresvpl,fileres);
5348: if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {
5349: printf("Problem with variance of stable prevalence resultfile: %s\n", fileresvpl);
5350: exit(0);
5351: }
5352: printf("Computing Variance-covariance of stable prevalence: file '%s' \n", fileresvpl);
5353:
5354: for(cptcov=1,k=0;cptcov<=i1;cptcov++){
5355: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
5356: k=k+1;
5357: fprintf(ficresvpl,"\n#****** ");
5358: for(j=1;j<=cptcoveff;j++)
5359: fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
5360: fprintf(ficresvpl,"******\n");
5361:
5362: varpl=matrix(1,nlstate,(int) bage, (int) fage);
5363: oldm=oldms;savm=savms;
5364: varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);
5365: free_matrix(varpl,1,nlstate,(int) bage, (int)fage);
5366: }
5367: }
5368:
5369: fclose(ficresvpl);
5370:
5371: /*---------- End : free ----------------*/
5372: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
5373: free_ma3x(probs,1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
5374:
5375: } /* mle==-3 arrives here for freeing */
5376: free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);
5377: free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);
5378: free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);
5379: free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);
5380:
5381: free_matrix(covar,0,NCOVMAX,1,n);
5382: free_matrix(matcov,1,npar,1,npar);
5383: /*free_vector(delti,1,npar);*/
5384: free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
5385: free_matrix(agev,1,maxwav,1,imx);
5386: free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
5387:
5388: free_ivector(ncodemax,1,8);
5389: free_ivector(Tvar,1,15);
5390: free_ivector(Tprod,1,15);
5391: free_ivector(Tvaraff,1,15);
5392: free_ivector(Tage,1,15);
5393: free_ivector(Tcode,1,100);
5394:
5395:
5396: fflush(fichtm);
5397: fflush(ficgp);
5398:
5399:
5400: if((nberr >0) || (nbwarn>0)){
5401: printf("End of Imach with %d errors and/or %d warnings\n",nberr,nbwarn);
5402: fprintf(ficlog,"End of Imach with %d errors and/or warnings %d\n",nberr,nbwarn);
5403: }else{
5404: printf("End of Imach\n");
5405: fprintf(ficlog,"End of Imach\n");
5406: }
5407: printf("See log file on %s\n",filelog);
5408: /* gettimeofday(&end_time, (struct timezone*)0);*/ /* after time */
5409: (void) gettimeofday(&end_time,&tzp);
5410: tm = *localtime(&end_time.tv_sec);
5411: tmg = *gmtime(&end_time.tv_sec);
5412: strcpy(strtend,asctime(&tm));
5413: printf("Local time at start %s\nLocaltime at end %s",strstart, strtend);
5414: fprintf(ficlog,"Local time at start %s\nLocal time at end %s\n",strstart, strtend);
5415: printf("Total time used %s\n", asc_diff_time(end_time.tv_sec -start_time.tv_sec,tmpout));
5416:
5417: printf("Total time was %d Sec.\n", end_time.tv_sec -start_time.tv_sec);
5418: fprintf(ficlog,"Total time used %s\n", asc_diff_time(end_time.tv_sec -start_time.tv_sec,tmpout));
5419: fprintf(ficlog,"Total time was %d Sec.\n", end_time.tv_sec -start_time.tv_sec);
5420: /* printf("Total time was %d uSec.\n", total_usecs);*/
5421: /* if(fileappend(fichtm,optionfilehtm)){ */
5422: fprintf(fichtm,"<br>Local time at start %s<br>Local time at end %s<br>",strstart, strtend);
5423: fclose(fichtm);
5424: fclose(fichtmcov);
5425: fclose(ficgp);
5426: fclose(ficlog);
5427: /*------ End -----------*/
5428:
5429: chdir(path);
5430: strcpy(plotcmd,"\"");
5431: strcat(plotcmd,pathimach);
5432: strcat(plotcmd,GNUPLOTPROGRAM);
5433: strcat(plotcmd,"\"");
5434: strcat(plotcmd," ");
5435: strcat(plotcmd,optionfilegnuplot);
5436: printf("Starting graphs with: %s",plotcmd);fflush(stdout);
5437: if((outcmd=system(plotcmd)) != 0){
5438: printf(" Problem with gnuplot\n");
5439: }
5440: printf(" Wait...");
5441: while (z[0] != 'q') {
5442: /* chdir(path); */
5443: printf("\nType e to edit output files, g to graph again and q for exiting: ");
5444: scanf("%s",z);
5445: /* if (z[0] == 'c') system("./imach"); */
5446: if (z[0] == 'e') {
5447: printf("Starting browser with: %s",optionfilehtm);fflush(stdout);
5448: system(optionfilehtm);
5449: }
5450: else if (z[0] == 'g') system(plotcmd);
5451: else if (z[0] == 'q') exit(0);
5452: }
5453: end:
5454: while (z[0] != 'q') {
5455: printf("\nType q for exiting: ");
5456: scanf("%s",z);
5457: }
5458: }
5459:
5460:
5461:
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