1: /* $Id: imach.c,v 1.102 2004/09/15 17:31:30 brouard Exp $
2: $State: Exp $
3: $Log: imach.c,v $
4: Revision 1.102 2004/09/15 17:31:30 brouard
5: Add the possibility to read data file including tab characters.
6:
7: Revision 1.101 2004/09/15 10:38:38 brouard
8: Fix on curr_time
9:
10: Revision 1.100 2004/07/12 18:29:06 brouard
11: Add version for Mac OS X. Just define UNIX in Makefile
12:
13: Revision 1.99 2004/06/05 08:57:40 brouard
14: *** empty log message ***
15:
16: Revision 1.98 2004/05/16 15:05:56 brouard
17: New version 0.97 . First attempt to estimate force of mortality
18: directly from the data i.e. without the need of knowing the health
19: state at each age, but using a Gompertz model: log u =a + b*age .
20: This is the basic analysis of mortality and should be done before any
21: other analysis, in order to test if the mortality estimated from the
22: cross-longitudinal survey is different from the mortality estimated
23: from other sources like vital statistic data.
24:
25: The same imach parameter file can be used but the option for mle should be -3.
26:
27: Agnès, who wrote this part of the code, tried to keep most of the
28: former routines in order to include the new code within the former code.
29:
30: The output is very simple: only an estimate of the intercept and of
31: the slope with 95% confident intervals.
32:
33: Current limitations:
34: A) Even if you enter covariates, i.e. with the
35: model= V1+V2 equation for example, the programm does only estimate a unique global model without covariates.
36: B) There is no computation of Life Expectancy nor Life Table.
37:
38: Revision 1.97 2004/02/20 13:25:42 lievre
39: Version 0.96d. Population forecasting command line is (temporarily)
40: suppressed.
41:
42: Revision 1.96 2003/07/15 15:38:55 brouard
43: * imach.c (Repository): Errors in subdirf, 2, 3 while printing tmpout is
44: rewritten within the same printf. Workaround: many printfs.
45:
46: Revision 1.95 2003/07/08 07:54:34 brouard
47: * imach.c (Repository):
48: (Repository): Using imachwizard code to output a more meaningful covariance
49: matrix (cov(a12,c31) instead of numbers.
50:
51: Revision 1.94 2003/06/27 13:00:02 brouard
52: Just cleaning
53:
54: Revision 1.93 2003/06/25 16:33:55 brouard
55: (Module): On windows (cygwin) function asctime_r doesn't
56: exist so I changed back to asctime which exists.
57: (Module): Version 0.96b
58:
59: Revision 1.92 2003/06/25 16:30:45 brouard
60: (Module): On windows (cygwin) function asctime_r doesn't
61: exist so I changed back to asctime which exists.
62:
63: Revision 1.91 2003/06/25 15:30:29 brouard
64: * imach.c (Repository): Duplicated warning errors corrected.
65: (Repository): Elapsed time after each iteration is now output. It
66: helps to forecast when convergence will be reached. Elapsed time
67: is stamped in powell. We created a new html file for the graphs
68: concerning matrix of covariance. It has extension -cov.htm.
69:
70: Revision 1.90 2003/06/24 12:34:15 brouard
71: (Module): Some bugs corrected for windows. Also, when
72: mle=-1 a template is output in file "or"mypar.txt with the design
73: of the covariance matrix to be input.
74:
75: Revision 1.89 2003/06/24 12:30:52 brouard
76: (Module): Some bugs corrected for windows. Also, when
77: mle=-1 a template is output in file "or"mypar.txt with the design
78: of the covariance matrix to be input.
79:
80: Revision 1.88 2003/06/23 17:54:56 brouard
81: * 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.
82:
83: Revision 1.87 2003/06/18 12:26:01 brouard
84: Version 0.96
85:
86: Revision 1.86 2003/06/17 20:04:08 brouard
87: (Module): Change position of html and gnuplot routines and added
88: routine fileappend.
89:
90: Revision 1.85 2003/06/17 13:12:43 brouard
91: * imach.c (Repository): Check when date of death was earlier that
92: current date of interview. It may happen when the death was just
93: prior to the death. In this case, dh was negative and likelihood
94: was wrong (infinity). We still send an "Error" but patch by
95: assuming that the date of death was just one stepm after the
96: interview.
97: (Repository): Because some people have very long ID (first column)
98: we changed int to long in num[] and we added a new lvector for
99: memory allocation. But we also truncated to 8 characters (left
100: truncation)
101: (Repository): No more line truncation errors.
102:
103: Revision 1.84 2003/06/13 21:44:43 brouard
104: * imach.c (Repository): Replace "freqsummary" at a correct
105: place. It differs from routine "prevalence" which may be called
106: many times. Probs is memory consuming and must be used with
107: parcimony.
108: Version 0.95a3 (should output exactly the same maximization than 0.8a2)
109:
110: Revision 1.83 2003/06/10 13:39:11 lievre
111: *** empty log message ***
112:
113: Revision 1.82 2003/06/05 15:57:20 brouard
114: Add log in imach.c and fullversion number is now printed.
115:
116: */
117: /*
118: Interpolated Markov Chain
119:
120: Short summary of the programme:
121:
122: This program computes Healthy Life Expectancies from
123: cross-longitudinal data. Cross-longitudinal data consist in: -1- a
124: first survey ("cross") where individuals from different ages are
125: interviewed on their health status or degree of disability (in the
126: case of a health survey which is our main interest) -2- at least a
127: second wave of interviews ("longitudinal") which measure each change
128: (if any) in individual health status. Health expectancies are
129: computed from the time spent in each health state according to a
130: model. More health states you consider, more time is necessary to reach the
131: Maximum Likelihood of the parameters involved in the model. The
132: simplest model is the multinomial logistic model where pij is the
133: probability to be observed in state j at the second wave
134: conditional to be observed in state i at the first wave. Therefore
135: the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where
136: 'age' is age and 'sex' is a covariate. If you want to have a more
137: complex model than "constant and age", you should modify the program
138: where the markup *Covariates have to be included here again* invites
139: you to do it. More covariates you add, slower the
140: convergence.
141:
142: The advantage of this computer programme, compared to a simple
143: multinomial logistic model, is clear when the delay between waves is not
144: identical for each individual. Also, if a individual missed an
145: intermediate interview, the information is lost, but taken into
146: account using an interpolation or extrapolation.
147:
148: hPijx is the probability to be observed in state i at age x+h
149: conditional to the observed state i at age x. The delay 'h' can be
150: split into an exact number (nh*stepm) of unobserved intermediate
151: states. This elementary transition (by month, quarter,
152: semester or year) is modelled as a multinomial logistic. The hPx
153: matrix is simply the matrix product of nh*stepm elementary matrices
154: and the contribution of each individual to the likelihood is simply
155: hPijx.
156:
157: Also this programme outputs the covariance matrix of the parameters but also
158: of the life expectancies. It also computes the stable prevalence.
159:
160: Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).
161: Institut national d'études démographiques, Paris.
162: This software have been partly granted by Euro-REVES, a concerted action
163: from the European Union.
164: It is copyrighted identically to a GNU software product, ie programme and
165: software can be distributed freely for non commercial use. Latest version
166: can be accessed at http://euroreves.ined.fr/imach .
167:
168: Help to debug: LD_PRELOAD=/usr/local/lib/libnjamd.so ./imach foo.imach
169: or better on gdb : set env LD_PRELOAD=/usr/local/lib/libnjamd.so
170:
171: **********************************************************************/
172: /*
173: main
174: read parameterfile
175: read datafile
176: concatwav
177: freqsummary
178: if (mle >= 1)
179: mlikeli
180: print results files
181: if mle==1
182: computes hessian
183: read end of parameter file: agemin, agemax, bage, fage, estepm
184: begin-prev-date,...
185: open gnuplot file
186: open html file
187: stable prevalence
188: for age prevalim()
189: h Pij x
190: variance of p varprob
191: forecasting if prevfcast==1 prevforecast call prevalence()
192: health expectancies
193: Variance-covariance of DFLE
194: prevalence()
195: movingaverage()
196: varevsij()
197: if popbased==1 varevsij(,popbased)
198: total life expectancies
199: Variance of stable prevalence
200: end
201: */
202:
203:
204:
205:
206: #include <math.h>
207: #include <stdio.h>
208: #include <stdlib.h>
209: #include <unistd.h>
210:
211: /* #include <sys/time.h> */
212: #include <time.h>
213: #include "timeval.h"
214:
215: /* #include <libintl.h> */
216: /* #define _(String) gettext (String) */
217:
218: #define MAXLINE 256
219: #define GNUPLOTPROGRAM "gnuplot"
220: /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
221: #define FILENAMELENGTH 132
222: /*#define DEBUG*/
223: /*#define windows*/
224: #define GLOCK_ERROR_NOPATH -1 /* empty path */
225: #define GLOCK_ERROR_GETCWD -2 /* cannot get cwd */
226:
227: #define MAXPARM 30 /* Maximum number of parameters for the optimization */
228: #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */
229:
230: #define NINTERVMAX 8
231: #define NLSTATEMAX 8 /* Maximum number of live states (for func) */
232: #define NDEATHMAX 8 /* Maximum number of dead states (for func) */
233: #define NCOVMAX 8 /* Maximum number of covariates */
234: #define MAXN 20000
235: #define YEARM 12. /* Number of months per year */
236: #define AGESUP 130
237: #define AGEBASE 40
238: #define AGEGOMP 10. /* Minimal age for Gompertz adjustment */
239: #ifdef UNIX
240: #define DIRSEPARATOR '/'
241: #define ODIRSEPARATOR '\\'
242: #else
243: #define DIRSEPARATOR '\\'
244: #define ODIRSEPARATOR '/'
245: #endif
246:
247: /* $Id: imach.c,v 1.102 2004/09/15 17:31:30 brouard Exp $ */
248: /* $State: Exp $ */
249:
250: char version[]="Imach version 0.97c, September 2004, INED-EUROREVES ";
251: char fullversion[]="$Revision: 1.102 $ $Date: 2004/09/15 17:31:30 $";
252: int erreur, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings */
253: int nvar;
254: int cptcovn=0, cptcovage=0, cptcoveff=0,cptcov;
255: int npar=NPARMAX;
256: int nlstate=2; /* Number of live states */
257: int ndeath=1; /* Number of dead states */
258: int ncovmodel, ncovcol; /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
259: int popbased=0;
260:
261: int *wav; /* Number of waves for this individuual 0 is possible */
262: int maxwav; /* Maxim number of waves */
263: int jmin, jmax; /* min, max spacing between 2 waves */
264: int gipmx, gsw; /* Global variables on the number of contributions
265: to the likelihood and the sum of weights (done by funcone)*/
266: int mle, weightopt;
267: int **mw; /* mw[mi][i] is number of the mi wave for this individual */
268: int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
269: int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between
270: * wave mi and wave mi+1 is not an exact multiple of stepm. */
271: double jmean; /* Mean space between 2 waves */
272: double **oldm, **newm, **savm; /* Working pointers to matrices */
273: double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
274: FILE *fic,*ficpar, *ficparo,*ficres, *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
275: FILE *ficlog, *ficrespow;
276: int globpr; /* Global variable for printing or not */
277: double fretone; /* Only one call to likelihood */
278: long ipmx; /* Number of contributions */
279: double sw; /* Sum of weights */
280: char filerespow[FILENAMELENGTH];
281: char fileresilk[FILENAMELENGTH]; /* File of individual contributions to the likelihood */
282: FILE *ficresilk;
283: FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
284: FILE *ficresprobmorprev;
285: FILE *fichtm, *fichtmcov; /* Html File */
286: FILE *ficreseij;
287: char filerese[FILENAMELENGTH];
288: FILE *ficresvij;
289: char fileresv[FILENAMELENGTH];
290: FILE *ficresvpl;
291: char fileresvpl[FILENAMELENGTH];
292: char title[MAXLINE];
293: char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH], filerespl[FILENAMELENGTH];
294: char optionfilext[10], optionfilefiname[FILENAMELENGTH], plotcmd[FILENAMELENGTH];
295: char tmpout[FILENAMELENGTH], tmpout2[FILENAMELENGTH];
296: char command[FILENAMELENGTH];
297: int outcmd=0;
298:
299: char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
300:
301: char filelog[FILENAMELENGTH]; /* Log file */
302: char filerest[FILENAMELENGTH];
303: char fileregp[FILENAMELENGTH];
304: char popfile[FILENAMELENGTH];
305:
306: char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilehtmcov[FILENAMELENGTH] ;
307:
308: struct timeval start_time, end_time, curr_time, last_time, forecast_time;
309: struct timezone tzp;
310: extern int gettimeofday();
311: struct tm tmg, tm, tmf, *gmtime(), *localtime();
312: long time_value;
313: extern long time();
314: char strcurr[80], strfor[80];
315:
316: #define NR_END 1
317: #define FREE_ARG char*
318: #define FTOL 1.0e-10
319:
320: #define NRANSI
321: #define ITMAX 200
322:
323: #define TOL 2.0e-4
324:
325: #define CGOLD 0.3819660
326: #define ZEPS 1.0e-10
327: #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);
328:
329: #define GOLD 1.618034
330: #define GLIMIT 100.0
331: #define TINY 1.0e-20
332:
333: static double maxarg1,maxarg2;
334: #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
335: #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
336:
337: #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
338: #define rint(a) floor(a+0.5)
339:
340: static double sqrarg;
341: #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
342: #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}
343: int agegomp= AGEGOMP;
344:
345: int imx;
346: int stepm=1;
347: /* Stepm, step in month: minimum step interpolation*/
348:
349: int estepm;
350: /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
351:
352: int m,nb;
353: long *num;
354: int firstpass=0, lastpass=4,*cod, *ncodemax, *Tage,*cens;
355: double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
356: double **pmmij, ***probs;
357: double *ageexmed,*agecens;
358: double dateintmean=0;
359:
360: double *weight;
361: int **s; /* Status */
362: double *agedc, **covar, idx;
363: int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;
364:
365: double ftol=FTOL; /* Tolerance for computing Max Likelihood */
366: double ftolhess; /* Tolerance for computing hessian */
367:
368: /**************** split *************************/
369: static int split( char *path, char *dirc, char *name, char *ext, char *finame )
370: {
371: /* From a file name with full path (either Unix or Windows) we extract the directory (dirc)
372: the name of the file (name), its extension only (ext) and its first part of the name (finame)
373: */
374: char *ss; /* pointer */
375: int l1, l2; /* length counters */
376:
377: l1 = strlen(path ); /* length of path */
378: if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
379: ss= strrchr( path, DIRSEPARATOR ); /* find last / */
380: if ( ss == NULL ) { /* no directory, so use current */
381: /*if(strrchr(path, ODIRSEPARATOR )==NULL)
382: printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
383: /* get current working directory */
384: /* extern char* getcwd ( char *buf , int len);*/
385: if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {
386: return( GLOCK_ERROR_GETCWD );
387: }
388: strcpy( name, path ); /* we've got it */
389: } else { /* strip direcotry from path */
390: ss++; /* after this, the filename */
391: l2 = strlen( ss ); /* length of filename */
392: if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
393: strcpy( name, ss ); /* save file name */
394: strncpy( dirc, path, l1 - l2 ); /* now the directory */
395: dirc[l1-l2] = 0; /* add zero */
396: }
397: l1 = strlen( dirc ); /* length of directory */
398: /*#ifdef windows
399: if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; }
400: #else
401: if ( dirc[l1-1] != '/' ) { dirc[l1] = '/'; dirc[l1+1] = 0; }
402: #endif
403: */
404: ss = strrchr( name, '.' ); /* find last / */
405: if (ss >0){
406: ss++;
407: strcpy(ext,ss); /* save extension */
408: l1= strlen( name);
409: l2= strlen(ss)+1;
410: strncpy( finame, name, l1-l2);
411: finame[l1-l2]= 0;
412: }
413: return( 0 ); /* we're done */
414: }
415:
416:
417: /******************************************/
418:
419: void replace_back_to_slash(char *s, char*t)
420: {
421: int i;
422: int lg=0;
423: i=0;
424: lg=strlen(t);
425: for(i=0; i<= lg; i++) {
426: (s[i] = t[i]);
427: if (t[i]== '\\') s[i]='/';
428: }
429: }
430:
431: int nbocc(char *s, char occ)
432: {
433: int i,j=0;
434: int lg=20;
435: i=0;
436: lg=strlen(s);
437: for(i=0; i<= lg; i++) {
438: if (s[i] == occ ) j++;
439: }
440: return j;
441: }
442:
443: void cutv(char *u,char *v, char*t, char occ)
444: {
445: /* cuts string t into u and v where u ends before first occurence of char 'occ'
446: and v starts after first occurence of char 'occ' : ex cutv(u,v,"abcdef2ghi2j",'2')
447: gives u="abcedf" and v="ghi2j" */
448: int i,lg,j,p=0;
449: i=0;
450: for(j=0; j<=strlen(t)-1; j++) {
451: if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;
452: }
453:
454: lg=strlen(t);
455: for(j=0; j<p; j++) {
456: (u[j] = t[j]);
457: }
458: u[p]='\0';
459:
460: for(j=0; j<= lg; j++) {
461: if (j>=(p+1))(v[j-p-1] = t[j]);
462: }
463: }
464:
465: /********************** nrerror ********************/
466:
467: void nrerror(char error_text[])
468: {
469: fprintf(stderr,"ERREUR ...\n");
470: fprintf(stderr,"%s\n",error_text);
471: exit(EXIT_FAILURE);
472: }
473: /*********************** vector *******************/
474: double *vector(int nl, int nh)
475: {
476: double *v;
477: v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
478: if (!v) nrerror("allocation failure in vector");
479: return v-nl+NR_END;
480: }
481:
482: /************************ free vector ******************/
483: void free_vector(double*v, int nl, int nh)
484: {
485: free((FREE_ARG)(v+nl-NR_END));
486: }
487:
488: /************************ivector *******************************/
489: int *ivector(long nl,long nh)
490: {
491: int *v;
492: v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
493: if (!v) nrerror("allocation failure in ivector");
494: return v-nl+NR_END;
495: }
496:
497: /******************free ivector **************************/
498: void free_ivector(int *v, long nl, long nh)
499: {
500: free((FREE_ARG)(v+nl-NR_END));
501: }
502:
503: /************************lvector *******************************/
504: long *lvector(long nl,long nh)
505: {
506: long *v;
507: v=(long *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(long)));
508: if (!v) nrerror("allocation failure in ivector");
509: return v-nl+NR_END;
510: }
511:
512: /******************free lvector **************************/
513: void free_lvector(long *v, long nl, long nh)
514: {
515: free((FREE_ARG)(v+nl-NR_END));
516: }
517:
518: /******************* imatrix *******************************/
519: int **imatrix(long nrl, long nrh, long ncl, long nch)
520: /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */
521: {
522: long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;
523: int **m;
524:
525: /* allocate pointers to rows */
526: m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));
527: if (!m) nrerror("allocation failure 1 in matrix()");
528: m += NR_END;
529: m -= nrl;
530:
531:
532: /* allocate rows and set pointers to them */
533: m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));
534: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
535: m[nrl] += NR_END;
536: m[nrl] -= ncl;
537:
538: for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;
539:
540: /* return pointer to array of pointers to rows */
541: return m;
542: }
543:
544: /****************** free_imatrix *************************/
545: void free_imatrix(m,nrl,nrh,ncl,nch)
546: int **m;
547: long nch,ncl,nrh,nrl;
548: /* free an int matrix allocated by imatrix() */
549: {
550: free((FREE_ARG) (m[nrl]+ncl-NR_END));
551: free((FREE_ARG) (m+nrl-NR_END));
552: }
553:
554: /******************* matrix *******************************/
555: double **matrix(long nrl, long nrh, long ncl, long nch)
556: {
557: long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
558: double **m;
559:
560: m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
561: if (!m) nrerror("allocation failure 1 in matrix()");
562: m += NR_END;
563: m -= nrl;
564:
565: m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
566: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
567: m[nrl] += NR_END;
568: m[nrl] -= ncl;
569:
570: for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
571: return m;
572: /* print *(*(m+1)+70) or print m[1][70]; print m+1 or print &(m[1])
573: */
574: }
575:
576: /*************************free matrix ************************/
577: void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
578: {
579: free((FREE_ARG)(m[nrl]+ncl-NR_END));
580: free((FREE_ARG)(m+nrl-NR_END));
581: }
582:
583: /******************* ma3x *******************************/
584: double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
585: {
586: long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
587: double ***m;
588:
589: m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
590: if (!m) nrerror("allocation failure 1 in matrix()");
591: m += NR_END;
592: m -= nrl;
593:
594: m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
595: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
596: m[nrl] += NR_END;
597: m[nrl] -= ncl;
598:
599: for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
600:
601: m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
602: if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
603: m[nrl][ncl] += NR_END;
604: m[nrl][ncl] -= nll;
605: for (j=ncl+1; j<=nch; j++)
606: m[nrl][j]=m[nrl][j-1]+nlay;
607:
608: for (i=nrl+1; i<=nrh; i++) {
609: m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
610: for (j=ncl+1; j<=nch; j++)
611: m[i][j]=m[i][j-1]+nlay;
612: }
613: return m;
614: /* gdb: p *(m+1) <=> p m[1] and p (m+1) <=> p (m+1) <=> p &(m[1])
615: &(m[i][j][k]) <=> *((*(m+i) + j)+k)
616: */
617: }
618:
619: /*************************free ma3x ************************/
620: void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
621: {
622: free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
623: free((FREE_ARG)(m[nrl]+ncl-NR_END));
624: free((FREE_ARG)(m+nrl-NR_END));
625: }
626:
627: /*************** function subdirf ***********/
628: char *subdirf(char fileres[])
629: {
630: /* Caution optionfilefiname is hidden */
631: strcpy(tmpout,optionfilefiname);
632: strcat(tmpout,"/"); /* Add to the right */
633: strcat(tmpout,fileres);
634: return tmpout;
635: }
636:
637: /*************** function subdirf2 ***********/
638: char *subdirf2(char fileres[], char *preop)
639: {
640:
641: /* Caution optionfilefiname is hidden */
642: strcpy(tmpout,optionfilefiname);
643: strcat(tmpout,"/");
644: strcat(tmpout,preop);
645: strcat(tmpout,fileres);
646: return tmpout;
647: }
648:
649: /*************** function subdirf3 ***********/
650: char *subdirf3(char fileres[], char *preop, char *preop2)
651: {
652:
653: /* Caution optionfilefiname is hidden */
654: strcpy(tmpout,optionfilefiname);
655: strcat(tmpout,"/");
656: strcat(tmpout,preop);
657: strcat(tmpout,preop2);
658: strcat(tmpout,fileres);
659: return tmpout;
660: }
661:
662: /***************** f1dim *************************/
663: extern int ncom;
664: extern double *pcom,*xicom;
665: extern double (*nrfunc)(double []);
666:
667: double f1dim(double x)
668: {
669: int j;
670: double f;
671: double *xt;
672:
673: xt=vector(1,ncom);
674: for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];
675: f=(*nrfunc)(xt);
676: free_vector(xt,1,ncom);
677: return f;
678: }
679:
680: /*****************brent *************************/
681: double brent(double ax, double bx, double cx, double (*f)(double), double tol, double *xmin)
682: {
683: int iter;
684: double a,b,d,etemp;
685: double fu,fv,fw,fx;
686: double ftemp;
687: double p,q,r,tol1,tol2,u,v,w,x,xm;
688: double e=0.0;
689:
690: a=(ax < cx ? ax : cx);
691: b=(ax > cx ? ax : cx);
692: x=w=v=bx;
693: fw=fv=fx=(*f)(x);
694: for (iter=1;iter<=ITMAX;iter++) {
695: xm=0.5*(a+b);
696: tol2=2.0*(tol1=tol*fabs(x)+ZEPS);
697: /* if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
698: printf(".");fflush(stdout);
699: fprintf(ficlog,".");fflush(ficlog);
700: #ifdef DEBUG
701: 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);
702: 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);
703: /* if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
704: #endif
705: if (fabs(x-xm) <= (tol2-0.5*(b-a))){
706: *xmin=x;
707: return fx;
708: }
709: ftemp=fu;
710: if (fabs(e) > tol1) {
711: r=(x-w)*(fx-fv);
712: q=(x-v)*(fx-fw);
713: p=(x-v)*q-(x-w)*r;
714: q=2.0*(q-r);
715: if (q > 0.0) p = -p;
716: q=fabs(q);
717: etemp=e;
718: e=d;
719: if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))
720: d=CGOLD*(e=(x >= xm ? a-x : b-x));
721: else {
722: d=p/q;
723: u=x+d;
724: if (u-a < tol2 || b-u < tol2)
725: d=SIGN(tol1,xm-x);
726: }
727: } else {
728: d=CGOLD*(e=(x >= xm ? a-x : b-x));
729: }
730: u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));
731: fu=(*f)(u);
732: if (fu <= fx) {
733: if (u >= x) a=x; else b=x;
734: SHFT(v,w,x,u)
735: SHFT(fv,fw,fx,fu)
736: } else {
737: if (u < x) a=u; else b=u;
738: if (fu <= fw || w == x) {
739: v=w;
740: w=u;
741: fv=fw;
742: fw=fu;
743: } else if (fu <= fv || v == x || v == w) {
744: v=u;
745: fv=fu;
746: }
747: }
748: }
749: nrerror("Too many iterations in brent");
750: *xmin=x;
751: return fx;
752: }
753:
754: /****************** mnbrak ***********************/
755:
756: void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,
757: double (*func)(double))
758: {
759: double ulim,u,r,q, dum;
760: double fu;
761:
762: *fa=(*func)(*ax);
763: *fb=(*func)(*bx);
764: if (*fb > *fa) {
765: SHFT(dum,*ax,*bx,dum)
766: SHFT(dum,*fb,*fa,dum)
767: }
768: *cx=(*bx)+GOLD*(*bx-*ax);
769: *fc=(*func)(*cx);
770: while (*fb > *fc) {
771: r=(*bx-*ax)*(*fb-*fc);
772: q=(*bx-*cx)*(*fb-*fa);
773: u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/
774: (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r));
775: ulim=(*bx)+GLIMIT*(*cx-*bx);
776: if ((*bx-u)*(u-*cx) > 0.0) {
777: fu=(*func)(u);
778: } else if ((*cx-u)*(u-ulim) > 0.0) {
779: fu=(*func)(u);
780: if (fu < *fc) {
781: SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))
782: SHFT(*fb,*fc,fu,(*func)(u))
783: }
784: } else if ((u-ulim)*(ulim-*cx) >= 0.0) {
785: u=ulim;
786: fu=(*func)(u);
787: } else {
788: u=(*cx)+GOLD*(*cx-*bx);
789: fu=(*func)(u);
790: }
791: SHFT(*ax,*bx,*cx,u)
792: SHFT(*fa,*fb,*fc,fu)
793: }
794: }
795:
796: /*************** linmin ************************/
797:
798: int ncom;
799: double *pcom,*xicom;
800: double (*nrfunc)(double []);
801:
802: void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))
803: {
804: double brent(double ax, double bx, double cx,
805: double (*f)(double), double tol, double *xmin);
806: double f1dim(double x);
807: void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,
808: double *fc, double (*func)(double));
809: int j;
810: double xx,xmin,bx,ax;
811: double fx,fb,fa;
812:
813: ncom=n;
814: pcom=vector(1,n);
815: xicom=vector(1,n);
816: nrfunc=func;
817: for (j=1;j<=n;j++) {
818: pcom[j]=p[j];
819: xicom[j]=xi[j];
820: }
821: ax=0.0;
822: xx=1.0;
823: mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim);
824: *fret=brent(ax,xx,bx,f1dim,TOL,&xmin);
825: #ifdef DEBUG
826: printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
827: fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
828: #endif
829: for (j=1;j<=n;j++) {
830: xi[j] *= xmin;
831: p[j] += xi[j];
832: }
833: free_vector(xicom,1,n);
834: free_vector(pcom,1,n);
835: }
836:
837: char *asc_diff_time(long time_sec, char ascdiff[])
838: {
839: long sec_left, days, hours, minutes;
840: days = (time_sec) / (60*60*24);
841: sec_left = (time_sec) % (60*60*24);
842: hours = (sec_left) / (60*60) ;
843: sec_left = (sec_left) %(60*60);
844: minutes = (sec_left) /60;
845: sec_left = (sec_left) % (60);
846: sprintf(ascdiff,"%d day(s) %d hour(s) %d minute(s) %d second(s)",days, hours, minutes, sec_left);
847: return ascdiff;
848: }
849:
850: /*************** powell ************************/
851: void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,
852: double (*func)(double []))
853: {
854: void linmin(double p[], double xi[], int n, double *fret,
855: double (*func)(double []));
856: int i,ibig,j;
857: double del,t,*pt,*ptt,*xit;
858: double fp,fptt;
859: double *xits;
860: int niterf, itmp;
861:
862: pt=vector(1,n);
863: ptt=vector(1,n);
864: xit=vector(1,n);
865: xits=vector(1,n);
866: *fret=(*func)(p);
867: for (j=1;j<=n;j++) pt[j]=p[j];
868: for (*iter=1;;++(*iter)) {
869: fp=(*fret);
870: ibig=0;
871: del=0.0;
872: last_time=curr_time;
873: (void) gettimeofday(&curr_time,&tzp);
874: 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);
875: /* 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);
876: fprintf(ficrespow,"%d %.12f %ld",*iter,*fret,curr_time.tv_sec-start_time.tv_sec);
877: */
878: for (i=1;i<=n;i++) {
879: printf(" %d %.12f",i, p[i]);
880: fprintf(ficlog," %d %.12lf",i, p[i]);
881: fprintf(ficrespow," %.12lf", p[i]);
882: }
883: printf("\n");
884: fprintf(ficlog,"\n");
885: fprintf(ficrespow,"\n");fflush(ficrespow);
886: if(*iter <=3){
887: tm = *localtime(&curr_time.tv_sec);
888: strcpy(strcurr,asctime(&tm));
889: /* asctime_r(&tm,strcurr); */
890: forecast_time=curr_time;
891: itmp = strlen(strcurr);
892: if(strcurr[itmp-1]=='\n') /* Windows outputs with a new line */
893: strcurr[itmp-1]='\0';
894: printf("\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,curr_time.tv_sec-last_time.tv_sec);
895: fprintf(ficlog,"\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,curr_time.tv_sec-last_time.tv_sec);
896: for(niterf=10;niterf<=30;niterf+=10){
897: forecast_time.tv_sec=curr_time.tv_sec+(niterf-*iter)*(curr_time.tv_sec-last_time.tv_sec);
898: tmf = *localtime(&forecast_time.tv_sec);
899: /* asctime_r(&tmf,strfor); */
900: strcpy(strfor,asctime(&tmf));
901: itmp = strlen(strfor);
902: if(strfor[itmp-1]=='\n')
903: strfor[itmp-1]='\0';
904: 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);
905: 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);
906: }
907: }
908: for (i=1;i<=n;i++) {
909: for (j=1;j<=n;j++) xit[j]=xi[j][i];
910: fptt=(*fret);
911: #ifdef DEBUG
912: printf("fret=%lf \n",*fret);
913: fprintf(ficlog,"fret=%lf \n",*fret);
914: #endif
915: printf("%d",i);fflush(stdout);
916: fprintf(ficlog,"%d",i);fflush(ficlog);
917: linmin(p,xit,n,fret,func);
918: if (fabs(fptt-(*fret)) > del) {
919: del=fabs(fptt-(*fret));
920: ibig=i;
921: }
922: #ifdef DEBUG
923: printf("%d %.12e",i,(*fret));
924: fprintf(ficlog,"%d %.12e",i,(*fret));
925: for (j=1;j<=n;j++) {
926: xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
927: printf(" x(%d)=%.12e",j,xit[j]);
928: fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
929: }
930: for(j=1;j<=n;j++) {
931: printf(" p=%.12e",p[j]);
932: fprintf(ficlog," p=%.12e",p[j]);
933: }
934: printf("\n");
935: fprintf(ficlog,"\n");
936: #endif
937: }
938: if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {
939: #ifdef DEBUG
940: int k[2],l;
941: k[0]=1;
942: k[1]=-1;
943: printf("Max: %.12e",(*func)(p));
944: fprintf(ficlog,"Max: %.12e",(*func)(p));
945: for (j=1;j<=n;j++) {
946: printf(" %.12e",p[j]);
947: fprintf(ficlog," %.12e",p[j]);
948: }
949: printf("\n");
950: fprintf(ficlog,"\n");
951: for(l=0;l<=1;l++) {
952: for (j=1;j<=n;j++) {
953: ptt[j]=p[j]+(p[j]-pt[j])*k[l];
954: printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
955: fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
956: }
957: printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
958: fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
959: }
960: #endif
961:
962:
963: free_vector(xit,1,n);
964: free_vector(xits,1,n);
965: free_vector(ptt,1,n);
966: free_vector(pt,1,n);
967: return;
968: }
969: if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");
970: for (j=1;j<=n;j++) {
971: ptt[j]=2.0*p[j]-pt[j];
972: xit[j]=p[j]-pt[j];
973: pt[j]=p[j];
974: }
975: fptt=(*func)(ptt);
976: if (fptt < fp) {
977: t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt);
978: if (t < 0.0) {
979: linmin(p,xit,n,fret,func);
980: for (j=1;j<=n;j++) {
981: xi[j][ibig]=xi[j][n];
982: xi[j][n]=xit[j];
983: }
984: #ifdef DEBUG
985: printf("Direction changed last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
986: fprintf(ficlog,"Direction changed last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
987: for(j=1;j<=n;j++){
988: printf(" %.12e",xit[j]);
989: fprintf(ficlog," %.12e",xit[j]);
990: }
991: printf("\n");
992: fprintf(ficlog,"\n");
993: #endif
994: }
995: }
996: }
997: }
998:
999: /**** Prevalence limit (stable prevalence) ****************/
1000:
1001: double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)
1002: {
1003: /* Computes the prevalence limit in each live state at age x by left multiplying the unit
1004: matrix by transitions matrix until convergence is reached */
1005:
1006: int i, ii,j,k;
1007: double min, max, maxmin, maxmax,sumnew=0.;
1008: double **matprod2();
1009: double **out, cov[NCOVMAX], **pmij();
1010: double **newm;
1011: double agefin, delaymax=50 ; /* Max number of years to converge */
1012:
1013: for (ii=1;ii<=nlstate+ndeath;ii++)
1014: for (j=1;j<=nlstate+ndeath;j++){
1015: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1016: }
1017:
1018: cov[1]=1.;
1019:
1020: /* Even if hstepm = 1, at least one multiplication by the unit matrix */
1021: for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
1022: newm=savm;
1023: /* Covariates have to be included here again */
1024: cov[2]=agefin;
1025:
1026: for (k=1; k<=cptcovn;k++) {
1027: cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
1028: /* 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]]);*/
1029: }
1030: for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
1031: for (k=1; k<=cptcovprod;k++)
1032: cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
1033:
1034: /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
1035: /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
1036: /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
1037: out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);
1038:
1039: savm=oldm;
1040: oldm=newm;
1041: maxmax=0.;
1042: for(j=1;j<=nlstate;j++){
1043: min=1.;
1044: max=0.;
1045: for(i=1; i<=nlstate; i++) {
1046: sumnew=0;
1047: for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
1048: prlim[i][j]= newm[i][j]/(1-sumnew);
1049: max=FMAX(max,prlim[i][j]);
1050: min=FMIN(min,prlim[i][j]);
1051: }
1052: maxmin=max-min;
1053: maxmax=FMAX(maxmax,maxmin);
1054: }
1055: if(maxmax < ftolpl){
1056: return prlim;
1057: }
1058: }
1059: }
1060:
1061: /*************** transition probabilities ***************/
1062:
1063: double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
1064: {
1065: double s1, s2;
1066: /*double t34;*/
1067: int i,j,j1, nc, ii, jj;
1068:
1069: for(i=1; i<= nlstate; i++){
1070: for(j=1; j<i;j++){
1071: for (nc=1, s2=0.;nc <=ncovmodel; nc++){
1072: /*s2 += param[i][j][nc]*cov[nc];*/
1073: s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
1074: /* printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2); */
1075: }
1076: ps[i][j]=s2;
1077: /* printf("s1=%.17e, s2=%.17e\n",s1,s2); */
1078: }
1079: for(j=i+1; j<=nlstate+ndeath;j++){
1080: for (nc=1, s2=0.;nc <=ncovmodel; nc++){
1081: s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
1082: /* printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2); */
1083: }
1084: ps[i][j]=s2;
1085: }
1086: }
1087: /*ps[3][2]=1;*/
1088:
1089: for(i=1; i<= nlstate; i++){
1090: s1=0;
1091: for(j=1; j<i; j++)
1092: s1+=exp(ps[i][j]);
1093: for(j=i+1; j<=nlstate+ndeath; j++)
1094: s1+=exp(ps[i][j]);
1095: ps[i][i]=1./(s1+1.);
1096: for(j=1; j<i; j++)
1097: ps[i][j]= exp(ps[i][j])*ps[i][i];
1098: for(j=i+1; j<=nlstate+ndeath; j++)
1099: ps[i][j]= exp(ps[i][j])*ps[i][i];
1100: /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
1101: } /* end i */
1102:
1103: for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
1104: for(jj=1; jj<= nlstate+ndeath; jj++){
1105: ps[ii][jj]=0;
1106: ps[ii][ii]=1;
1107: }
1108: }
1109:
1110:
1111: /* for(ii=1; ii<= nlstate+ndeath; ii++){ */
1112: /* for(jj=1; jj<= nlstate+ndeath; jj++){ */
1113: /* printf("ddd %lf ",ps[ii][jj]); */
1114: /* } */
1115: /* printf("\n "); */
1116: /* } */
1117: /* printf("\n ");printf("%lf ",cov[2]); */
1118: /*
1119: for(i=1; i<= npar; i++) printf("%f ",x[i]);
1120: goto end;*/
1121: return ps;
1122: }
1123:
1124: /**************** Product of 2 matrices ******************/
1125:
1126: double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)
1127: {
1128: /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
1129: b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
1130: /* in, b, out are matrice of pointers which should have been initialized
1131: before: only the contents of out is modified. The function returns
1132: a pointer to pointers identical to out */
1133: long i, j, k;
1134: for(i=nrl; i<= nrh; i++)
1135: for(k=ncolol; k<=ncoloh; k++)
1136: for(j=ncl,out[i][k]=0.; j<=nch; j++)
1137: out[i][k] +=in[i][j]*b[j][k];
1138:
1139: return out;
1140: }
1141:
1142:
1143: /************* Higher Matrix Product ***************/
1144:
1145: double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
1146: {
1147: /* Computes the transition matrix starting at age 'age' over
1148: 'nhstepm*hstepm*stepm' months (i.e. until
1149: age (in years) age+nhstepm*hstepm*stepm/12) by multiplying
1150: nhstepm*hstepm matrices.
1151: Output is stored in matrix po[i][j][h] for h every 'hstepm' step
1152: (typically every 2 years instead of every month which is too big
1153: for the memory).
1154: Model is determined by parameters x and covariates have to be
1155: included manually here.
1156:
1157: */
1158:
1159: int i, j, d, h, k;
1160: double **out, cov[NCOVMAX];
1161: double **newm;
1162:
1163: /* Hstepm could be zero and should return the unit matrix */
1164: for (i=1;i<=nlstate+ndeath;i++)
1165: for (j=1;j<=nlstate+ndeath;j++){
1166: oldm[i][j]=(i==j ? 1.0 : 0.0);
1167: po[i][j][0]=(i==j ? 1.0 : 0.0);
1168: }
1169: /* Even if hstepm = 1, at least one multiplication by the unit matrix */
1170: for(h=1; h <=nhstepm; h++){
1171: for(d=1; d <=hstepm; d++){
1172: newm=savm;
1173: /* Covariates have to be included here again */
1174: cov[1]=1.;
1175: cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
1176: for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
1177: for (k=1; k<=cptcovage;k++)
1178: cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
1179: for (k=1; k<=cptcovprod;k++)
1180: cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
1181:
1182:
1183: /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
1184: /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
1185: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,
1186: pmij(pmmij,cov,ncovmodel,x,nlstate));
1187: savm=oldm;
1188: oldm=newm;
1189: }
1190: for(i=1; i<=nlstate+ndeath; i++)
1191: for(j=1;j<=nlstate+ndeath;j++) {
1192: po[i][j][h]=newm[i][j];
1193: /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);
1194: */
1195: }
1196: } /* end h */
1197: return po;
1198: }
1199:
1200:
1201: /*************** log-likelihood *************/
1202: double func( double *x)
1203: {
1204: int i, ii, j, k, mi, d, kk;
1205: double l, ll[NLSTATEMAX], cov[NCOVMAX];
1206: double **out;
1207: double sw; /* Sum of weights */
1208: double lli; /* Individual log likelihood */
1209: int s1, s2;
1210: double bbh, survp;
1211: long ipmx;
1212: /*extern weight */
1213: /* We are differentiating ll according to initial status */
1214: /* for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
1215: /*for(i=1;i<imx;i++)
1216: printf(" %d\n",s[4][i]);
1217: */
1218: cov[1]=1.;
1219:
1220: for(k=1; k<=nlstate; k++) ll[k]=0.;
1221:
1222: if(mle==1){
1223: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1224: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
1225: for(mi=1; mi<= wav[i]-1; mi++){
1226: for (ii=1;ii<=nlstate+ndeath;ii++)
1227: for (j=1;j<=nlstate+ndeath;j++){
1228: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1229: savm[ii][j]=(ii==j ? 1.0 : 0.0);
1230: }
1231: for(d=0; d<dh[mi][i]; d++){
1232: newm=savm;
1233: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
1234: for (kk=1; kk<=cptcovage;kk++) {
1235: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
1236: }
1237: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1238: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1239: savm=oldm;
1240: oldm=newm;
1241: } /* end mult */
1242:
1243: /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
1244: /* But now since version 0.9 we anticipate for bias at large stepm.
1245: * If stepm is larger than one month (smallest stepm) and if the exact delay
1246: * (in months) between two waves is not a multiple of stepm, we rounded to
1247: * the nearest (and in case of equal distance, to the lowest) interval but now
1248: * we keep into memory the bias bh[mi][i] and also the previous matrix product
1249: * (i.e to dh[mi][i]-1) saved in 'savm'. Then we inter(extra)polate the
1250: * probability in order to take into account the bias as a fraction of the way
1251: * from savm to out if bh is negative or even beyond if bh is positive. bh varies
1252: * -stepm/2 to stepm/2 .
1253: * For stepm=1 the results are the same as for previous versions of Imach.
1254: * For stepm > 1 the results are less biased than in previous versions.
1255: */
1256: s1=s[mw[mi][i]][i];
1257: s2=s[mw[mi+1][i]][i];
1258: bbh=(double)bh[mi][i]/(double)stepm;
1259: /* bias bh is positive if real duration
1260: * is higher than the multiple of stepm and negative otherwise.
1261: */
1262: /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
1263: if( s2 > nlstate){
1264: /* i.e. if s2 is a death state and if the date of death is known then the contribution
1265: to the likelihood is the probability to die between last step unit time and current
1266: step unit time, which is also equal to probability to die before dh
1267: minus probability to die before dh-stepm .
1268: In version up to 0.92 likelihood was computed
1269: as if date of death was unknown. Death was treated as any other
1270: health state: the date of the interview describes the actual state
1271: and not the date of a change in health state. The former idea was
1272: to consider that at each interview the state was recorded
1273: (healthy, disable or death) and IMaCh was corrected; but when we
1274: introduced the exact date of death then we should have modified
1275: the contribution of an exact death to the likelihood. This new
1276: contribution is smaller and very dependent of the step unit
1277: stepm. It is no more the probability to die between last interview
1278: and month of death but the probability to survive from last
1279: interview up to one month before death multiplied by the
1280: probability to die within a month. Thanks to Chris
1281: Jackson for correcting this bug. Former versions increased
1282: mortality artificially. The bad side is that we add another loop
1283: which slows down the processing. The difference can be up to 10%
1284: lower mortality.
1285: */
1286: lli=log(out[s1][s2] - savm[s1][s2]);
1287: }else{
1288: lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
1289: /* 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 */
1290: }
1291: /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
1292: /*if(lli ==000.0)*/
1293: /*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); */
1294: ipmx +=1;
1295: sw += weight[i];
1296: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1297: } /* end of wave */
1298: } /* end of individual */
1299: } else if(mle==2){
1300: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1301: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
1302: for(mi=1; mi<= wav[i]-1; mi++){
1303: for (ii=1;ii<=nlstate+ndeath;ii++)
1304: for (j=1;j<=nlstate+ndeath;j++){
1305: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1306: savm[ii][j]=(ii==j ? 1.0 : 0.0);
1307: }
1308: for(d=0; d<=dh[mi][i]; d++){
1309: newm=savm;
1310: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
1311: for (kk=1; kk<=cptcovage;kk++) {
1312: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
1313: }
1314: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1315: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1316: savm=oldm;
1317: oldm=newm;
1318: } /* end mult */
1319:
1320: s1=s[mw[mi][i]][i];
1321: s2=s[mw[mi+1][i]][i];
1322: bbh=(double)bh[mi][i]/(double)stepm;
1323: 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 */
1324: ipmx +=1;
1325: sw += weight[i];
1326: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1327: } /* end of wave */
1328: } /* end of individual */
1329: } else if(mle==3){ /* exponential inter-extrapolation */
1330: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1331: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
1332: for(mi=1; mi<= wav[i]-1; mi++){
1333: for (ii=1;ii<=nlstate+ndeath;ii++)
1334: for (j=1;j<=nlstate+ndeath;j++){
1335: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1336: savm[ii][j]=(ii==j ? 1.0 : 0.0);
1337: }
1338: for(d=0; d<dh[mi][i]; d++){
1339: newm=savm;
1340: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
1341: for (kk=1; kk<=cptcovage;kk++) {
1342: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
1343: }
1344: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1345: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1346: savm=oldm;
1347: oldm=newm;
1348: } /* end mult */
1349:
1350: s1=s[mw[mi][i]][i];
1351: s2=s[mw[mi+1][i]][i];
1352: bbh=(double)bh[mi][i]/(double)stepm;
1353: 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 */
1354: ipmx +=1;
1355: sw += weight[i];
1356: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1357: } /* end of wave */
1358: } /* end of individual */
1359: }else if (mle==4){ /* ml=4 no inter-extrapolation */
1360: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1361: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
1362: for(mi=1; mi<= wav[i]-1; mi++){
1363: for (ii=1;ii<=nlstate+ndeath;ii++)
1364: for (j=1;j<=nlstate+ndeath;j++){
1365: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1366: savm[ii][j]=(ii==j ? 1.0 : 0.0);
1367: }
1368: for(d=0; d<dh[mi][i]; d++){
1369: newm=savm;
1370: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
1371: for (kk=1; kk<=cptcovage;kk++) {
1372: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
1373: }
1374:
1375: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1376: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1377: savm=oldm;
1378: oldm=newm;
1379: } /* end mult */
1380:
1381: s1=s[mw[mi][i]][i];
1382: s2=s[mw[mi+1][i]][i];
1383: if( s2 > nlstate){
1384: lli=log(out[s1][s2] - savm[s1][s2]);
1385: }else{
1386: lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
1387: }
1388: ipmx +=1;
1389: sw += weight[i];
1390: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1391: /* 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]); */
1392: } /* end of wave */
1393: } /* end of individual */
1394: }else{ /* ml=5 no inter-extrapolation no jackson =0.8a */
1395: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1396: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
1397: for(mi=1; mi<= wav[i]-1; mi++){
1398: for (ii=1;ii<=nlstate+ndeath;ii++)
1399: for (j=1;j<=nlstate+ndeath;j++){
1400: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1401: savm[ii][j]=(ii==j ? 1.0 : 0.0);
1402: }
1403: for(d=0; d<dh[mi][i]; d++){
1404: newm=savm;
1405: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
1406: for (kk=1; kk<=cptcovage;kk++) {
1407: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
1408: }
1409:
1410: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1411: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1412: savm=oldm;
1413: oldm=newm;
1414: } /* end mult */
1415:
1416: s1=s[mw[mi][i]][i];
1417: s2=s[mw[mi+1][i]][i];
1418: lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
1419: ipmx +=1;
1420: sw += weight[i];
1421: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1422: /*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]);*/
1423: } /* end of wave */
1424: } /* end of individual */
1425: } /* End of if */
1426: for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
1427: /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
1428: l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
1429: return -l;
1430: }
1431:
1432: /*************** log-likelihood *************/
1433: double funcone( double *x)
1434: {
1435: /* Same as likeli but slower because of a lot of printf and if */
1436: int i, ii, j, k, mi, d, kk;
1437: double l, ll[NLSTATEMAX], cov[NCOVMAX];
1438: double **out;
1439: double lli; /* Individual log likelihood */
1440: double llt;
1441: int s1, s2;
1442: double bbh, survp;
1443: /*extern weight */
1444: /* We are differentiating ll according to initial status */
1445: /* for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
1446: /*for(i=1;i<imx;i++)
1447: printf(" %d\n",s[4][i]);
1448: */
1449: cov[1]=1.;
1450:
1451: for(k=1; k<=nlstate; k++) ll[k]=0.;
1452:
1453: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1454: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
1455: for(mi=1; mi<= wav[i]-1; mi++){
1456: for (ii=1;ii<=nlstate+ndeath;ii++)
1457: for (j=1;j<=nlstate+ndeath;j++){
1458: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1459: savm[ii][j]=(ii==j ? 1.0 : 0.0);
1460: }
1461: for(d=0; d<dh[mi][i]; d++){
1462: newm=savm;
1463: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
1464: for (kk=1; kk<=cptcovage;kk++) {
1465: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
1466: }
1467: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1468: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1469: savm=oldm;
1470: oldm=newm;
1471: } /* end mult */
1472:
1473: s1=s[mw[mi][i]][i];
1474: s2=s[mw[mi+1][i]][i];
1475: bbh=(double)bh[mi][i]/(double)stepm;
1476: /* bias is positive if real duration
1477: * is higher than the multiple of stepm and negative otherwise.
1478: */
1479: if( s2 > nlstate && (mle <5) ){ /* Jackson */
1480: lli=log(out[s1][s2] - savm[s1][s2]);
1481: } else if (mle==1){
1482: lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
1483: } else if(mle==2){
1484: 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 */
1485: } else if(mle==3){ /* exponential inter-extrapolation */
1486: 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 */
1487: } else if (mle==4){ /* mle=4 no inter-extrapolation */
1488: lli=log(out[s1][s2]); /* Original formula */
1489: } else{ /* ml>=5 no inter-extrapolation no jackson =0.8a */
1490: lli=log(out[s1][s2]); /* Original formula */
1491: } /* End of if */
1492: ipmx +=1;
1493: sw += weight[i];
1494: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1495: /* 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]); */
1496: if(globpr){
1497: fprintf(ficresilk,"%9d %6d %1d %1d %1d %1d %3d %10.6f %6.4f\
1498: %10.6f %10.6f %10.6f ", \
1499: num[i],i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],
1500: 2*weight[i]*lli,out[s1][s2],savm[s1][s2]);
1501: for(k=1,llt=0.,l=0.; k<=nlstate; k++){
1502: llt +=ll[k]*gipmx/gsw;
1503: fprintf(ficresilk," %10.6f",-ll[k]*gipmx/gsw);
1504: }
1505: fprintf(ficresilk," %10.6f\n", -llt);
1506: }
1507: } /* end of wave */
1508: } /* end of individual */
1509: for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
1510: /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
1511: l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
1512: if(globpr==0){ /* First time we count the contributions and weights */
1513: gipmx=ipmx;
1514: gsw=sw;
1515: }
1516: return -l;
1517: }
1518:
1519:
1520: /*************** function likelione ***********/
1521: void likelione(FILE *ficres,double p[], int npar, int nlstate, int *globpri, long *ipmx, double *sw, double *fretone, double (*funcone)(double []))
1522: {
1523: /* This routine should help understanding what is done with
1524: the selection of individuals/waves and
1525: to check the exact contribution to the likelihood.
1526: Plotting could be done.
1527: */
1528: int k;
1529:
1530: if(*globpri !=0){ /* Just counts and sums, no printings */
1531: strcpy(fileresilk,"ilk");
1532: strcat(fileresilk,fileres);
1533: if((ficresilk=fopen(fileresilk,"w"))==NULL) {
1534: printf("Problem with resultfile: %s\n", fileresilk);
1535: fprintf(ficlog,"Problem with resultfile: %s\n", fileresilk);
1536: }
1537: 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");
1538: fprintf(ficresilk, "#num_i i s1 s2 mi mw dh likeli weight 2wlli out sav ");
1539: /* i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],2*weight[i]*lli,out[s1][s2],savm[s1][s2]); */
1540: for(k=1; k<=nlstate; k++)
1541: fprintf(ficresilk," -2*gipw/gsw*weight*ll[%d]++",k);
1542: fprintf(ficresilk," -2*gipw/gsw*weight*ll(total)\n");
1543: }
1544:
1545: *fretone=(*funcone)(p);
1546: if(*globpri !=0){
1547: fclose(ficresilk);
1548: fprintf(fichtm,"\n<br>File of contributions to the likelihood: <a href=\"%s\">%s</a><br>\n",subdirf(fileresilk),subdirf(fileresilk));
1549: fflush(fichtm);
1550: }
1551: return;
1552: }
1553:
1554:
1555: /*********** Maximum Likelihood Estimation ***************/
1556:
1557: void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
1558: {
1559: int i,j, iter;
1560: double **xi;
1561: double fret;
1562: double fretone; /* Only one call to likelihood */
1563: /* char filerespow[FILENAMELENGTH];*/
1564: xi=matrix(1,npar,1,npar);
1565: for (i=1;i<=npar;i++)
1566: for (j=1;j<=npar;j++)
1567: xi[i][j]=(i==j ? 1.0 : 0.0);
1568: printf("Powell\n"); fprintf(ficlog,"Powell\n");
1569: strcpy(filerespow,"pow");
1570: strcat(filerespow,fileres);
1571: if((ficrespow=fopen(filerespow,"w"))==NULL) {
1572: printf("Problem with resultfile: %s\n", filerespow);
1573: fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
1574: }
1575: fprintf(ficrespow,"# Powell\n# iter -2*LL");
1576: for (i=1;i<=nlstate;i++)
1577: for(j=1;j<=nlstate+ndeath;j++)
1578: if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
1579: fprintf(ficrespow,"\n");
1580:
1581: powell(p,xi,npar,ftol,&iter,&fret,func);
1582:
1583: fclose(ficrespow);
1584: printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));
1585: fprintf(ficlog,"\n#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
1586: fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
1587:
1588: }
1589:
1590: /**** Computes Hessian and covariance matrix ***/
1591: void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
1592: {
1593: double **a,**y,*x,pd;
1594: double **hess;
1595: int i, j,jk;
1596: int *indx;
1597:
1598: double hessii(double p[], double delta, int theta, double delti[],double (*func)(double []),int npar);
1599: double hessij(double p[], double delti[], int i, int j,double (*func)(double []),int npar);
1600: void lubksb(double **a, int npar, int *indx, double b[]) ;
1601: void ludcmp(double **a, int npar, int *indx, double *d) ;
1602: double gompertz(double p[]);
1603: hess=matrix(1,npar,1,npar);
1604:
1605: printf("\nCalculation of the hessian matrix. Wait...\n");
1606: fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
1607: for (i=1;i<=npar;i++){
1608: printf("%d",i);fflush(stdout);
1609: fprintf(ficlog,"%d",i);fflush(ficlog);
1610:
1611: hess[i][i]=hessii(p,ftolhess,i,delti,func,npar);
1612:
1613: /* printf(" %f ",p[i]);
1614: printf(" %lf %lf %lf",hess[i][i],ftolhess,delti[i]);*/
1615: }
1616:
1617: for (i=1;i<=npar;i++) {
1618: for (j=1;j<=npar;j++) {
1619: if (j>i) {
1620: printf(".%d%d",i,j);fflush(stdout);
1621: fprintf(ficlog,".%d%d",i,j);fflush(ficlog);
1622: hess[i][j]=hessij(p,delti,i,j,func,npar);
1623:
1624: hess[j][i]=hess[i][j];
1625: /*printf(" %lf ",hess[i][j]);*/
1626: }
1627: }
1628: }
1629: printf("\n");
1630: fprintf(ficlog,"\n");
1631:
1632: printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
1633: fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
1634:
1635: a=matrix(1,npar,1,npar);
1636: y=matrix(1,npar,1,npar);
1637: x=vector(1,npar);
1638: indx=ivector(1,npar);
1639: for (i=1;i<=npar;i++)
1640: for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
1641: ludcmp(a,npar,indx,&pd);
1642:
1643: for (j=1;j<=npar;j++) {
1644: for (i=1;i<=npar;i++) x[i]=0;
1645: x[j]=1;
1646: lubksb(a,npar,indx,x);
1647: for (i=1;i<=npar;i++){
1648: matcov[i][j]=x[i];
1649: }
1650: }
1651:
1652: printf("\n#Hessian matrix#\n");
1653: fprintf(ficlog,"\n#Hessian matrix#\n");
1654: for (i=1;i<=npar;i++) {
1655: for (j=1;j<=npar;j++) {
1656: printf("%.3e ",hess[i][j]);
1657: fprintf(ficlog,"%.3e ",hess[i][j]);
1658: }
1659: printf("\n");
1660: fprintf(ficlog,"\n");
1661: }
1662:
1663: /* Recompute Inverse */
1664: for (i=1;i<=npar;i++)
1665: for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];
1666: ludcmp(a,npar,indx,&pd);
1667:
1668: /* printf("\n#Hessian matrix recomputed#\n");
1669:
1670: for (j=1;j<=npar;j++) {
1671: for (i=1;i<=npar;i++) x[i]=0;
1672: x[j]=1;
1673: lubksb(a,npar,indx,x);
1674: for (i=1;i<=npar;i++){
1675: y[i][j]=x[i];
1676: printf("%.3e ",y[i][j]);
1677: fprintf(ficlog,"%.3e ",y[i][j]);
1678: }
1679: printf("\n");
1680: fprintf(ficlog,"\n");
1681: }
1682: */
1683:
1684: free_matrix(a,1,npar,1,npar);
1685: free_matrix(y,1,npar,1,npar);
1686: free_vector(x,1,npar);
1687: free_ivector(indx,1,npar);
1688: free_matrix(hess,1,npar,1,npar);
1689:
1690:
1691: }
1692:
1693: /*************** hessian matrix ****************/
1694: double hessii(double x[], double delta, int theta, double delti[], double (*func)(double []), int npar)
1695: {
1696: int i;
1697: int l=1, lmax=20;
1698: double k1,k2;
1699: double p2[NPARMAX+1];
1700: double res;
1701: double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4;
1702: double fx;
1703: int k=0,kmax=10;
1704: double l1;
1705:
1706: fx=func(x);
1707: for (i=1;i<=npar;i++) p2[i]=x[i];
1708: for(l=0 ; l <=lmax; l++){
1709: l1=pow(10,l);
1710: delts=delt;
1711: for(k=1 ; k <kmax; k=k+1){
1712: delt = delta*(l1*k);
1713: p2[theta]=x[theta] +delt;
1714: k1=func(p2)-fx;
1715: p2[theta]=x[theta]-delt;
1716: k2=func(p2)-fx;
1717: /*res= (k1-2.0*fx+k2)/delt/delt; */
1718: res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */
1719:
1720: #ifdef DEBUG
1721: 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);
1722: 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);
1723: #endif
1724: /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
1725: if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
1726: k=kmax;
1727: }
1728: else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
1729: k=kmax; l=lmax*10.;
1730: }
1731: else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){
1732: delts=delt;
1733: }
1734: }
1735: }
1736: delti[theta]=delts;
1737: return res;
1738:
1739: }
1740:
1741: double hessij( double x[], double delti[], int thetai,int thetaj,double (*func)(double []),int npar)
1742: {
1743: int i;
1744: int l=1, l1, lmax=20;
1745: double k1,k2,k3,k4,res,fx;
1746: double p2[NPARMAX+1];
1747: int k;
1748:
1749: fx=func(x);
1750: for (k=1; k<=2; k++) {
1751: for (i=1;i<=npar;i++) p2[i]=x[i];
1752: p2[thetai]=x[thetai]+delti[thetai]/k;
1753: p2[thetaj]=x[thetaj]+delti[thetaj]/k;
1754: k1=func(p2)-fx;
1755:
1756: p2[thetai]=x[thetai]+delti[thetai]/k;
1757: p2[thetaj]=x[thetaj]-delti[thetaj]/k;
1758: k2=func(p2)-fx;
1759:
1760: p2[thetai]=x[thetai]-delti[thetai]/k;
1761: p2[thetaj]=x[thetaj]+delti[thetaj]/k;
1762: k3=func(p2)-fx;
1763:
1764: p2[thetai]=x[thetai]-delti[thetai]/k;
1765: p2[thetaj]=x[thetaj]-delti[thetaj]/k;
1766: k4=func(p2)-fx;
1767: res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */
1768: #ifdef DEBUG
1769: 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);
1770: 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);
1771: #endif
1772: }
1773: return res;
1774: }
1775:
1776: /************** Inverse of matrix **************/
1777: void ludcmp(double **a, int n, int *indx, double *d)
1778: {
1779: int i,imax,j,k;
1780: double big,dum,sum,temp;
1781: double *vv;
1782:
1783: vv=vector(1,n);
1784: *d=1.0;
1785: for (i=1;i<=n;i++) {
1786: big=0.0;
1787: for (j=1;j<=n;j++)
1788: if ((temp=fabs(a[i][j])) > big) big=temp;
1789: if (big == 0.0) nrerror("Singular matrix in routine ludcmp");
1790: vv[i]=1.0/big;
1791: }
1792: for (j=1;j<=n;j++) {
1793: for (i=1;i<j;i++) {
1794: sum=a[i][j];
1795: for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];
1796: a[i][j]=sum;
1797: }
1798: big=0.0;
1799: for (i=j;i<=n;i++) {
1800: sum=a[i][j];
1801: for (k=1;k<j;k++)
1802: sum -= a[i][k]*a[k][j];
1803: a[i][j]=sum;
1804: if ( (dum=vv[i]*fabs(sum)) >= big) {
1805: big=dum;
1806: imax=i;
1807: }
1808: }
1809: if (j != imax) {
1810: for (k=1;k<=n;k++) {
1811: dum=a[imax][k];
1812: a[imax][k]=a[j][k];
1813: a[j][k]=dum;
1814: }
1815: *d = -(*d);
1816: vv[imax]=vv[j];
1817: }
1818: indx[j]=imax;
1819: if (a[j][j] == 0.0) a[j][j]=TINY;
1820: if (j != n) {
1821: dum=1.0/(a[j][j]);
1822: for (i=j+1;i<=n;i++) a[i][j] *= dum;
1823: }
1824: }
1825: free_vector(vv,1,n); /* Doesn't work */
1826: ;
1827: }
1828:
1829: void lubksb(double **a, int n, int *indx, double b[])
1830: {
1831: int i,ii=0,ip,j;
1832: double sum;
1833:
1834: for (i=1;i<=n;i++) {
1835: ip=indx[i];
1836: sum=b[ip];
1837: b[ip]=b[i];
1838: if (ii)
1839: for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];
1840: else if (sum) ii=i;
1841: b[i]=sum;
1842: }
1843: for (i=n;i>=1;i--) {
1844: sum=b[i];
1845: for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];
1846: b[i]=sum/a[i][i];
1847: }
1848: }
1849:
1850: /************ Frequencies ********************/
1851: 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)
1852: { /* Some frequencies */
1853:
1854: int i, m, jk, k1,i1, j1, bool, z1,z2,j;
1855: int first;
1856: double ***freq; /* Frequencies */
1857: double *pp, **prop;
1858: double pos,posprop, k2, dateintsum=0,k2cpt=0;
1859: FILE *ficresp;
1860: char fileresp[FILENAMELENGTH];
1861:
1862: pp=vector(1,nlstate);
1863: prop=matrix(1,nlstate,iagemin,iagemax+3);
1864: strcpy(fileresp,"p");
1865: strcat(fileresp,fileres);
1866: if((ficresp=fopen(fileresp,"w"))==NULL) {
1867: printf("Problem with prevalence resultfile: %s\n", fileresp);
1868: fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
1869: exit(0);
1870: }
1871: freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);
1872: j1=0;
1873:
1874: j=cptcoveff;
1875: if (cptcovn<1) {j=1;ncodemax[1]=1;}
1876:
1877: first=1;
1878:
1879: for(k1=1; k1<=j;k1++){
1880: for(i1=1; i1<=ncodemax[k1];i1++){
1881: j1++;
1882: /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
1883: scanf("%d", i);*/
1884: for (i=-1; i<=nlstate+ndeath; i++)
1885: for (jk=-1; jk<=nlstate+ndeath; jk++)
1886: for(m=iagemin; m <= iagemax+3; m++)
1887: freq[i][jk][m]=0;
1888:
1889: for (i=1; i<=nlstate; i++)
1890: for(m=iagemin; m <= iagemax+3; m++)
1891: prop[i][m]=0;
1892:
1893: dateintsum=0;
1894: k2cpt=0;
1895: for (i=1; i<=imx; i++) {
1896: bool=1;
1897: if (cptcovn>0) {
1898: for (z1=1; z1<=cptcoveff; z1++)
1899: if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])
1900: bool=0;
1901: }
1902: if (bool==1){
1903: for(m=firstpass; m<=lastpass; m++){
1904: k2=anint[m][i]+(mint[m][i]/12.);
1905: /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/
1906: if(agev[m][i]==0) agev[m][i]=iagemax+1;
1907: if(agev[m][i]==1) agev[m][i]=iagemax+2;
1908: if (s[m][i]>0 && s[m][i]<=nlstate) prop[s[m][i]][(int)agev[m][i]] += weight[i];
1909: if (m<lastpass) {
1910: freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
1911: freq[s[m][i]][s[m+1][i]][iagemax+3] += weight[i];
1912: }
1913:
1914: if ((agev[m][i]>1) && (agev[m][i]< (iagemax+3))) {
1915: dateintsum=dateintsum+k2;
1916: k2cpt++;
1917: }
1918: /*}*/
1919: }
1920: }
1921: }
1922:
1923: /* fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
1924:
1925: if (cptcovn>0) {
1926: fprintf(ficresp, "\n#********** Variable ");
1927: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
1928: fprintf(ficresp, "**********\n#");
1929: }
1930: for(i=1; i<=nlstate;i++)
1931: fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
1932: fprintf(ficresp, "\n");
1933:
1934: for(i=iagemin; i <= iagemax+3; i++){
1935: if(i==iagemax+3){
1936: fprintf(ficlog,"Total");
1937: }else{
1938: if(first==1){
1939: first=0;
1940: printf("See log file for details...\n");
1941: }
1942: fprintf(ficlog,"Age %d", i);
1943: }
1944: for(jk=1; jk <=nlstate ; jk++){
1945: for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
1946: pp[jk] += freq[jk][m][i];
1947: }
1948: for(jk=1; jk <=nlstate ; jk++){
1949: for(m=-1, pos=0; m <=0 ; m++)
1950: pos += freq[jk][m][i];
1951: if(pp[jk]>=1.e-10){
1952: if(first==1){
1953: printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
1954: }
1955: fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
1956: }else{
1957: if(first==1)
1958: printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
1959: fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
1960: }
1961: }
1962:
1963: for(jk=1; jk <=nlstate ; jk++){
1964: for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
1965: pp[jk] += freq[jk][m][i];
1966: }
1967: for(jk=1,pos=0,posprop=0; jk <=nlstate ; jk++){
1968: pos += pp[jk];
1969: posprop += prop[jk][i];
1970: }
1971: for(jk=1; jk <=nlstate ; jk++){
1972: if(pos>=1.e-5){
1973: if(first==1)
1974: printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
1975: fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
1976: }else{
1977: if(first==1)
1978: printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
1979: fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
1980: }
1981: if( i <= iagemax){
1982: if(pos>=1.e-5){
1983: fprintf(ficresp," %d %.5f %.0f %.0f",i,prop[jk][i]/posprop, prop[jk][i],posprop);
1984: /*probs[i][jk][j1]= pp[jk]/pos;*/
1985: /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/
1986: }
1987: else
1988: fprintf(ficresp," %d NaNq %.0f %.0f",i,prop[jk][i],posprop);
1989: }
1990: }
1991:
1992: for(jk=-1; jk <=nlstate+ndeath; jk++)
1993: for(m=-1; m <=nlstate+ndeath; m++)
1994: if(freq[jk][m][i] !=0 ) {
1995: if(first==1)
1996: printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
1997: fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
1998: }
1999: if(i <= iagemax)
2000: fprintf(ficresp,"\n");
2001: if(first==1)
2002: printf("Others in log...\n");
2003: fprintf(ficlog,"\n");
2004: }
2005: }
2006: }
2007: dateintmean=dateintsum/k2cpt;
2008:
2009: fclose(ficresp);
2010: free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);
2011: free_vector(pp,1,nlstate);
2012: free_matrix(prop,1,nlstate,iagemin, iagemax+3);
2013: /* End of Freq */
2014: }
2015:
2016: /************ Prevalence ********************/
2017: 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)
2018: {
2019: /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
2020: in each health status at the date of interview (if between dateprev1 and dateprev2).
2021: We still use firstpass and lastpass as another selection.
2022: */
2023:
2024: int i, m, jk, k1, i1, j1, bool, z1,z2,j;
2025: double ***freq; /* Frequencies */
2026: double *pp, **prop;
2027: double pos,posprop;
2028: double y2; /* in fractional years */
2029: int iagemin, iagemax;
2030:
2031: iagemin= (int) agemin;
2032: iagemax= (int) agemax;
2033: /*pp=vector(1,nlstate);*/
2034: prop=matrix(1,nlstate,iagemin,iagemax+3);
2035: /* freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
2036: j1=0;
2037:
2038: j=cptcoveff;
2039: if (cptcovn<1) {j=1;ncodemax[1]=1;}
2040:
2041: for(k1=1; k1<=j;k1++){
2042: for(i1=1; i1<=ncodemax[k1];i1++){
2043: j1++;
2044:
2045: for (i=1; i<=nlstate; i++)
2046: for(m=iagemin; m <= iagemax+3; m++)
2047: prop[i][m]=0.0;
2048:
2049: for (i=1; i<=imx; i++) { /* Each individual */
2050: bool=1;
2051: if (cptcovn>0) {
2052: for (z1=1; z1<=cptcoveff; z1++)
2053: if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])
2054: bool=0;
2055: }
2056: if (bool==1) {
2057: for(m=firstpass; m<=lastpass; m++){/* Other selection (we can limit to certain interviews*/
2058: y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
2059: if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
2060: if(agev[m][i]==0) agev[m][i]=iagemax+1;
2061: if(agev[m][i]==1) agev[m][i]=iagemax+2;
2062: 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);
2063: if (s[m][i]>0 && s[m][i]<=nlstate) {
2064: /*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]]);*/
2065: prop[s[m][i]][(int)agev[m][i]] += weight[i];
2066: prop[s[m][i]][iagemax+3] += weight[i];
2067: }
2068: }
2069: } /* end selection of waves */
2070: }
2071: }
2072: for(i=iagemin; i <= iagemax+3; i++){
2073:
2074: for(jk=1,posprop=0; jk <=nlstate ; jk++) {
2075: posprop += prop[jk][i];
2076: }
2077:
2078: for(jk=1; jk <=nlstate ; jk++){
2079: if( i <= iagemax){
2080: if(posprop>=1.e-5){
2081: probs[i][jk][j1]= prop[jk][i]/posprop;
2082: }
2083: }
2084: }/* end jk */
2085: }/* end i */
2086: } /* end i1 */
2087: } /* end k1 */
2088:
2089: /* free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
2090: /*free_vector(pp,1,nlstate);*/
2091: free_matrix(prop,1,nlstate, iagemin,iagemax+3);
2092: } /* End of prevalence */
2093:
2094: /************* Waves Concatenation ***************/
2095:
2096: 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)
2097: {
2098: /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
2099: Death is a valid wave (if date is known).
2100: mw[mi][i] is the mi (mi=1 to wav[i]) effective wave of individual i
2101: dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
2102: and mw[mi+1][i]. dh depends on stepm.
2103: */
2104:
2105: int i, mi, m;
2106: /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
2107: double sum=0., jmean=0.;*/
2108: int first;
2109: int j, k=0,jk, ju, jl;
2110: double sum=0.;
2111: first=0;
2112: jmin=1e+5;
2113: jmax=-1;
2114: jmean=0.;
2115: for(i=1; i<=imx; i++){
2116: mi=0;
2117: m=firstpass;
2118: while(s[m][i] <= nlstate){
2119: if(s[m][i]>=1)
2120: mw[++mi][i]=m;
2121: if(m >=lastpass)
2122: break;
2123: else
2124: m++;
2125: }/* end while */
2126: if (s[m][i] > nlstate){
2127: mi++; /* Death is another wave */
2128: /* if(mi==0) never been interviewed correctly before death */
2129: /* Only death is a correct wave */
2130: mw[mi][i]=m;
2131: }
2132:
2133: wav[i]=mi;
2134: if(mi==0){
2135: nbwarn++;
2136: if(first==0){
2137: printf("Warning! None valid information for:%ld line=%d (skipped) and may be others, see log file\n",num[i],i);
2138: first=1;
2139: }
2140: if(first==1){
2141: fprintf(ficlog,"Warning! None valid information for:%ld line=%d (skipped)\n",num[i],i);
2142: }
2143: } /* end mi==0 */
2144: } /* End individuals */
2145:
2146: for(i=1; i<=imx; i++){
2147: for(mi=1; mi<wav[i];mi++){
2148: if (stepm <=0)
2149: dh[mi][i]=1;
2150: else{
2151: if (s[mw[mi+1][i]][i] > nlstate) { /* A death */
2152: if (agedc[i] < 2*AGESUP) {
2153: j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);
2154: if(j==0) j=1; /* Survives at least one month after exam */
2155: else if(j<0){
2156: nberr++;
2157: 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]);
2158: j=1; /* Temporary Dangerous patch */
2159: 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);
2160: 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]);
2161: 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);
2162: }
2163: k=k+1;
2164: if (j >= jmax) jmax=j;
2165: if (j <= jmin) jmin=j;
2166: sum=sum+j;
2167: /*if (j<0) printf("j=%d num=%d \n",j,i);*/
2168: /* printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
2169: }
2170: }
2171: else{
2172: j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
2173: /* printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
2174: k=k+1;
2175: if (j >= jmax) jmax=j;
2176: else if (j <= jmin)jmin=j;
2177: /* if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
2178: /*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]);*/
2179: if(j<0){
2180: nberr++;
2181: 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]);
2182: 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]);
2183: }
2184: sum=sum+j;
2185: }
2186: jk= j/stepm;
2187: jl= j -jk*stepm;
2188: ju= j -(jk+1)*stepm;
2189: if(mle <=1){ /* only if we use a the linear-interpoloation pseudo-likelihood */
2190: if(jl==0){
2191: dh[mi][i]=jk;
2192: bh[mi][i]=0;
2193: }else{ /* We want a negative bias in order to only have interpolation ie
2194: * at the price of an extra matrix product in likelihood */
2195: dh[mi][i]=jk+1;
2196: bh[mi][i]=ju;
2197: }
2198: }else{
2199: if(jl <= -ju){
2200: dh[mi][i]=jk;
2201: bh[mi][i]=jl; /* bias is positive if real duration
2202: * is higher than the multiple of stepm and negative otherwise.
2203: */
2204: }
2205: else{
2206: dh[mi][i]=jk+1;
2207: bh[mi][i]=ju;
2208: }
2209: if(dh[mi][i]==0){
2210: dh[mi][i]=1; /* At least one step */
2211: bh[mi][i]=ju; /* At least one step */
2212: /* 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);*/
2213: }
2214: } /* end if mle */
2215: }
2216: } /* end wave */
2217: }
2218: jmean=sum/k;
2219: printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);
2220: fprintf(ficlog,"Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);
2221: }
2222:
2223: /*********** Tricode ****************************/
2224: void tricode(int *Tvar, int **nbcode, int imx)
2225: {
2226:
2227: int Ndum[20],ij=1, k, j, i, maxncov=19;
2228: int cptcode=0;
2229: cptcoveff=0;
2230:
2231: for (k=0; k<maxncov; k++) Ndum[k]=0;
2232: for (k=1; k<=7; k++) ncodemax[k]=0;
2233:
2234: for (j=1; j<=(cptcovn+2*cptcovprod); j++) {
2235: for (i=1; i<=imx; i++) { /*reads the data file to get the maximum
2236: modality*/
2237: ij=(int)(covar[Tvar[j]][i]); /* ij is the modality of this individual*/
2238: Ndum[ij]++; /*store the modality */
2239: /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
2240: if (ij > cptcode) cptcode=ij; /* getting the maximum of covariable
2241: Tvar[j]. If V=sex and male is 0 and
2242: female is 1, then cptcode=1.*/
2243: }
2244:
2245: for (i=0; i<=cptcode; i++) {
2246: 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 */
2247: }
2248:
2249: ij=1;
2250: for (i=1; i<=ncodemax[j]; i++) {
2251: for (k=0; k<= maxncov; k++) {
2252: if (Ndum[k] != 0) {
2253: nbcode[Tvar[j]][ij]=k;
2254: /* 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; */
2255:
2256: ij++;
2257: }
2258: if (ij > ncodemax[j]) break;
2259: }
2260: }
2261: }
2262:
2263: for (k=0; k< maxncov; k++) Ndum[k]=0;
2264:
2265: for (i=1; i<=ncovmodel-2; i++) {
2266: /* Listing of all covariables in staement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/
2267: ij=Tvar[i];
2268: Ndum[ij]++;
2269: }
2270:
2271: ij=1;
2272: for (i=1; i<= maxncov; i++) {
2273: if((Ndum[i]!=0) && (i<=ncovcol)){
2274: Tvaraff[ij]=i; /*For printing */
2275: ij++;
2276: }
2277: }
2278:
2279: cptcoveff=ij-1; /*Number of simple covariates*/
2280: }
2281:
2282: /*********** Health Expectancies ****************/
2283:
2284: 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 )
2285:
2286: {
2287: /* Health expectancies */
2288: int i, j, nhstepm, hstepm, h, nstepm, k, cptj;
2289: double age, agelim, hf;
2290: double ***p3mat,***varhe;
2291: double **dnewm,**doldm;
2292: double *xp;
2293: double **gp, **gm;
2294: double ***gradg, ***trgradg;
2295: int theta;
2296:
2297: varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage);
2298: xp=vector(1,npar);
2299: dnewm=matrix(1,nlstate*nlstate,1,npar);
2300: doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate);
2301:
2302: fprintf(ficreseij,"# Health expectancies\n");
2303: fprintf(ficreseij,"# Age");
2304: for(i=1; i<=nlstate;i++)
2305: for(j=1; j<=nlstate;j++)
2306: fprintf(ficreseij," %1d-%1d (SE)",i,j);
2307: fprintf(ficreseij,"\n");
2308:
2309: if(estepm < stepm){
2310: printf ("Problem %d lower than %d\n",estepm, stepm);
2311: }
2312: else hstepm=estepm;
2313: /* We compute the life expectancy from trapezoids spaced every estepm months
2314: * This is mainly to measure the difference between two models: for example
2315: * if stepm=24 months pijx are given only every 2 years and by summing them
2316: * we are calculating an estimate of the Life Expectancy assuming a linear
2317: * progression in between and thus overestimating or underestimating according
2318: * to the curvature of the survival function. If, for the same date, we
2319: * estimate the model with stepm=1 month, we can keep estepm to 24 months
2320: * to compare the new estimate of Life expectancy with the same linear
2321: * hypothesis. A more precise result, taking into account a more precise
2322: * curvature will be obtained if estepm is as small as stepm. */
2323:
2324: /* For example we decided to compute the life expectancy with the smallest unit */
2325: /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
2326: nhstepm is the number of hstepm from age to agelim
2327: nstepm is the number of stepm from age to agelin.
2328: Look at hpijx to understand the reason of that which relies in memory size
2329: and note for a fixed period like estepm months */
2330: /* We decided (b) to get a life expectancy respecting the most precise curvature of the
2331: survival function given by stepm (the optimization length). Unfortunately it
2332: means that if the survival funtion is printed only each two years of age and if
2333: you sum them up and add 1 year (area under the trapezoids) you won't get the same
2334: results. So we changed our mind and took the option of the best precision.
2335: */
2336: hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
2337:
2338: agelim=AGESUP;
2339: for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
2340: /* nhstepm age range expressed in number of stepm */
2341: nstepm=(int) rint((agelim-age)*YEARM/stepm);
2342: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
2343: /* if (stepm >= YEARM) hstepm=1;*/
2344: nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
2345: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
2346: gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);
2347: gp=matrix(0,nhstepm,1,nlstate*nlstate);
2348: gm=matrix(0,nhstepm,1,nlstate*nlstate);
2349:
2350: /* Computed by stepm unit matrices, product of hstepm matrices, stored
2351: in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
2352: hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);
2353:
2354:
2355: hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
2356:
2357: /* Computing Variances of health expectancies */
2358:
2359: for(theta=1; theta <=npar; theta++){
2360: for(i=1; i<=npar; i++){
2361: xp[i] = x[i] + (i==theta ?delti[theta]:0);
2362: }
2363: hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
2364:
2365: cptj=0;
2366: for(j=1; j<= nlstate; j++){
2367: for(i=1; i<=nlstate; i++){
2368: cptj=cptj+1;
2369: for(h=0, gp[h][cptj]=0.; h<=nhstepm-1; h++){
2370: gp[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;
2371: }
2372: }
2373: }
2374:
2375:
2376: for(i=1; i<=npar; i++)
2377: xp[i] = x[i] - (i==theta ?delti[theta]:0);
2378: hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
2379:
2380: cptj=0;
2381: for(j=1; j<= nlstate; j++){
2382: for(i=1;i<=nlstate;i++){
2383: cptj=cptj+1;
2384: for(h=0, gm[h][cptj]=0.; h<=nhstepm-1; h++){
2385:
2386: gm[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;
2387: }
2388: }
2389: }
2390: for(j=1; j<= nlstate*nlstate; j++)
2391: for(h=0; h<=nhstepm-1; h++){
2392: gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
2393: }
2394: }
2395:
2396: /* End theta */
2397:
2398: trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar);
2399:
2400: for(h=0; h<=nhstepm-1; h++)
2401: for(j=1; j<=nlstate*nlstate;j++)
2402: for(theta=1; theta <=npar; theta++)
2403: trgradg[h][j][theta]=gradg[h][theta][j];
2404:
2405:
2406: for(i=1;i<=nlstate*nlstate;i++)
2407: for(j=1;j<=nlstate*nlstate;j++)
2408: varhe[i][j][(int)age] =0.;
2409:
2410: printf("%d|",(int)age);fflush(stdout);
2411: fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
2412: for(h=0;h<=nhstepm-1;h++){
2413: for(k=0;k<=nhstepm-1;k++){
2414: matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov);
2415: matprod2(doldm,dnewm,1,nlstate*nlstate,1,npar,1,nlstate*nlstate,gradg[k]);
2416: for(i=1;i<=nlstate*nlstate;i++)
2417: for(j=1;j<=nlstate*nlstate;j++)
2418: varhe[i][j][(int)age] += doldm[i][j]*hf*hf;
2419: }
2420: }
2421: /* Computing expectancies */
2422: for(i=1; i<=nlstate;i++)
2423: for(j=1; j<=nlstate;j++)
2424: for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
2425: eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
2426:
2427: /* 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]);*/
2428:
2429: }
2430:
2431: fprintf(ficreseij,"%3.0f",age );
2432: cptj=0;
2433: for(i=1; i<=nlstate;i++)
2434: for(j=1; j<=nlstate;j++){
2435: cptj++;
2436: fprintf(ficreseij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[cptj][cptj][(int)age]) );
2437: }
2438: fprintf(ficreseij,"\n");
2439:
2440: free_matrix(gm,0,nhstepm,1,nlstate*nlstate);
2441: free_matrix(gp,0,nhstepm,1,nlstate*nlstate);
2442: free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*nlstate);
2443: free_ma3x(trgradg,0,nhstepm,1,nlstate*nlstate,1,npar);
2444: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
2445: }
2446: printf("\n");
2447: fprintf(ficlog,"\n");
2448:
2449: free_vector(xp,1,npar);
2450: free_matrix(dnewm,1,nlstate*nlstate,1,npar);
2451: free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate);
2452: free_ma3x(varhe,1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int)fage);
2453: }
2454:
2455: /************ Variance ******************/
2456: 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)
2457: {
2458: /* Variance of health expectancies */
2459: /* double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
2460: /* double **newm;*/
2461: double **dnewm,**doldm;
2462: double **dnewmp,**doldmp;
2463: int i, j, nhstepm, hstepm, h, nstepm ;
2464: int k, cptcode;
2465: double *xp;
2466: double **gp, **gm; /* for var eij */
2467: double ***gradg, ***trgradg; /*for var eij */
2468: double **gradgp, **trgradgp; /* for var p point j */
2469: double *gpp, *gmp; /* for var p point j */
2470: double **varppt; /* for var p point j nlstate to nlstate+ndeath */
2471: double ***p3mat;
2472: double age,agelim, hf;
2473: double ***mobaverage;
2474: int theta;
2475: char digit[4];
2476: char digitp[25];
2477:
2478: char fileresprobmorprev[FILENAMELENGTH];
2479:
2480: if(popbased==1){
2481: if(mobilav!=0)
2482: strcpy(digitp,"-populbased-mobilav-");
2483: else strcpy(digitp,"-populbased-nomobil-");
2484: }
2485: else
2486: strcpy(digitp,"-stablbased-");
2487:
2488: if (mobilav!=0) {
2489: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
2490: if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
2491: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
2492: printf(" Error in movingaverage mobilav=%d\n",mobilav);
2493: }
2494: }
2495:
2496: strcpy(fileresprobmorprev,"prmorprev");
2497: sprintf(digit,"%-d",ij);
2498: /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
2499: strcat(fileresprobmorprev,digit); /* Tvar to be done */
2500: strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
2501: strcat(fileresprobmorprev,fileres);
2502: if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
2503: printf("Problem with resultfile: %s\n", fileresprobmorprev);
2504: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
2505: }
2506: printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
2507: fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
2508: 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);
2509: fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
2510: for(j=nlstate+1; j<=(nlstate+ndeath);j++){
2511: fprintf(ficresprobmorprev," p.%-d SE",j);
2512: for(i=1; i<=nlstate;i++)
2513: fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
2514: }
2515: fprintf(ficresprobmorprev,"\n");
2516: fprintf(ficgp,"\n# Routine varevsij");
2517: 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");
2518: fprintf(fichtm,"\n<br>%s <br>\n",digitp);
2519: /* } */
2520: varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
2521:
2522: 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");
2523: fprintf(ficresvij,"# Age");
2524: for(i=1; i<=nlstate;i++)
2525: for(j=1; j<=nlstate;j++)
2526: fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);
2527: fprintf(ficresvij,"\n");
2528:
2529: xp=vector(1,npar);
2530: dnewm=matrix(1,nlstate,1,npar);
2531: doldm=matrix(1,nlstate,1,nlstate);
2532: dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
2533: doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
2534:
2535: gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
2536: gpp=vector(nlstate+1,nlstate+ndeath);
2537: gmp=vector(nlstate+1,nlstate+ndeath);
2538: trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
2539:
2540: if(estepm < stepm){
2541: printf ("Problem %d lower than %d\n",estepm, stepm);
2542: }
2543: else hstepm=estepm;
2544: /* For example we decided to compute the life expectancy with the smallest unit */
2545: /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
2546: nhstepm is the number of hstepm from age to agelim
2547: nstepm is the number of stepm from age to agelin.
2548: Look at hpijx to understand the reason of that which relies in memory size
2549: and note for a fixed period like k years */
2550: /* We decided (b) to get a life expectancy respecting the most precise curvature of the
2551: survival function given by stepm (the optimization length). Unfortunately it
2552: means that if the survival funtion is printed every two years of age and if
2553: you sum them up and add 1 year (area under the trapezoids) you won't get the same
2554: results. So we changed our mind and took the option of the best precision.
2555: */
2556: hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
2557: agelim = AGESUP;
2558: for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
2559: nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
2560: nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
2561: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
2562: gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
2563: gp=matrix(0,nhstepm,1,nlstate);
2564: gm=matrix(0,nhstepm,1,nlstate);
2565:
2566:
2567: for(theta=1; theta <=npar; theta++){
2568: for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
2569: xp[i] = x[i] + (i==theta ?delti[theta]:0);
2570: }
2571: hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
2572: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
2573:
2574: if (popbased==1) {
2575: if(mobilav ==0){
2576: for(i=1; i<=nlstate;i++)
2577: prlim[i][i]=probs[(int)age][i][ij];
2578: }else{ /* mobilav */
2579: for(i=1; i<=nlstate;i++)
2580: prlim[i][i]=mobaverage[(int)age][i][ij];
2581: }
2582: }
2583:
2584: for(j=1; j<= nlstate; j++){
2585: for(h=0; h<=nhstepm; h++){
2586: for(i=1, gp[h][j]=0.;i<=nlstate;i++)
2587: gp[h][j] += prlim[i][i]*p3mat[i][j][h];
2588: }
2589: }
2590: /* This for computing probability of death (h=1 means
2591: computed over hstepm matrices product = hstepm*stepm months)
2592: as a weighted average of prlim.
2593: */
2594: for(j=nlstate+1;j<=nlstate+ndeath;j++){
2595: for(i=1,gpp[j]=0.; i<= nlstate; i++)
2596: gpp[j] += prlim[i][i]*p3mat[i][j][1];
2597: }
2598: /* end probability of death */
2599:
2600: for(i=1; i<=npar; i++) /* Computes gradient x - delta */
2601: xp[i] = x[i] - (i==theta ?delti[theta]:0);
2602: hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
2603: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
2604:
2605: if (popbased==1) {
2606: if(mobilav ==0){
2607: for(i=1; i<=nlstate;i++)
2608: prlim[i][i]=probs[(int)age][i][ij];
2609: }else{ /* mobilav */
2610: for(i=1; i<=nlstate;i++)
2611: prlim[i][i]=mobaverage[(int)age][i][ij];
2612: }
2613: }
2614:
2615: for(j=1; j<= nlstate; j++){
2616: for(h=0; h<=nhstepm; h++){
2617: for(i=1, gm[h][j]=0.;i<=nlstate;i++)
2618: gm[h][j] += prlim[i][i]*p3mat[i][j][h];
2619: }
2620: }
2621: /* This for computing probability of death (h=1 means
2622: computed over hstepm matrices product = hstepm*stepm months)
2623: as a weighted average of prlim.
2624: */
2625: for(j=nlstate+1;j<=nlstate+ndeath;j++){
2626: for(i=1,gmp[j]=0.; i<= nlstate; i++)
2627: gmp[j] += prlim[i][i]*p3mat[i][j][1];
2628: }
2629: /* end probability of death */
2630:
2631: for(j=1; j<= nlstate; j++) /* vareij */
2632: for(h=0; h<=nhstepm; h++){
2633: gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
2634: }
2635:
2636: for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
2637: gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
2638: }
2639:
2640: } /* End theta */
2641:
2642: trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
2643:
2644: for(h=0; h<=nhstepm; h++) /* veij */
2645: for(j=1; j<=nlstate;j++)
2646: for(theta=1; theta <=npar; theta++)
2647: trgradg[h][j][theta]=gradg[h][theta][j];
2648:
2649: for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
2650: for(theta=1; theta <=npar; theta++)
2651: trgradgp[j][theta]=gradgp[theta][j];
2652:
2653:
2654: hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
2655: for(i=1;i<=nlstate;i++)
2656: for(j=1;j<=nlstate;j++)
2657: vareij[i][j][(int)age] =0.;
2658:
2659: for(h=0;h<=nhstepm;h++){
2660: for(k=0;k<=nhstepm;k++){
2661: matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
2662: matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
2663: for(i=1;i<=nlstate;i++)
2664: for(j=1;j<=nlstate;j++)
2665: vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
2666: }
2667: }
2668:
2669: /* pptj */
2670: matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
2671: matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
2672: for(j=nlstate+1;j<=nlstate+ndeath;j++)
2673: for(i=nlstate+1;i<=nlstate+ndeath;i++)
2674: varppt[j][i]=doldmp[j][i];
2675: /* end ppptj */
2676: /* x centered again */
2677: hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);
2678: prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);
2679:
2680: if (popbased==1) {
2681: if(mobilav ==0){
2682: for(i=1; i<=nlstate;i++)
2683: prlim[i][i]=probs[(int)age][i][ij];
2684: }else{ /* mobilav */
2685: for(i=1; i<=nlstate;i++)
2686: prlim[i][i]=mobaverage[(int)age][i][ij];
2687: }
2688: }
2689:
2690: /* This for computing probability of death (h=1 means
2691: computed over hstepm (estepm) matrices product = hstepm*stepm months)
2692: as a weighted average of prlim.
2693: */
2694: for(j=nlstate+1;j<=nlstate+ndeath;j++){
2695: for(i=1,gmp[j]=0.;i<= nlstate; i++)
2696: gmp[j] += prlim[i][i]*p3mat[i][j][1];
2697: }
2698: /* end probability of death */
2699:
2700: fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
2701: for(j=nlstate+1; j<=(nlstate+ndeath);j++){
2702: fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
2703: for(i=1; i<=nlstate;i++){
2704: fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
2705: }
2706: }
2707: fprintf(ficresprobmorprev,"\n");
2708:
2709: fprintf(ficresvij,"%.0f ",age );
2710: for(i=1; i<=nlstate;i++)
2711: for(j=1; j<=nlstate;j++){
2712: fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
2713: }
2714: fprintf(ficresvij,"\n");
2715: free_matrix(gp,0,nhstepm,1,nlstate);
2716: free_matrix(gm,0,nhstepm,1,nlstate);
2717: free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
2718: free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
2719: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
2720: } /* End age */
2721: free_vector(gpp,nlstate+1,nlstate+ndeath);
2722: free_vector(gmp,nlstate+1,nlstate+ndeath);
2723: free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
2724: free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
2725: fprintf(ficgp,"\nset noparametric;set nolabel; set ter png small;set size 0.65, 0.65");
2726: /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */
2727: fprintf(ficgp,"\n set log y; set nolog x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
2728: /* fprintf(ficgp,"\n plot \"%s\" u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm); */
2729: /* fprintf(ficgp,"\n replot \"%s\" u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm); */
2730: /* fprintf(ficgp,"\n replot \"%s\" u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm); */
2731: fprintf(ficgp,"\n plot \"%s\" u 1:($3) not w l 1 ",subdirf(fileresprobmorprev));
2732: fprintf(ficgp,"\n replot \"%s\" u 1:(($3+1.96*$4)) t \"95\%% interval\" w l 2 ",subdirf(fileresprobmorprev));
2733: fprintf(ficgp,"\n replot \"%s\" u 1:(($3-1.96*$4)) not w l 2 ",subdirf(fileresprobmorprev));
2734: fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",subdirf(fileresprobmorprev),subdirf(fileresprobmorprev));
2735: 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);
2736: /* 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);
2737: */
2738: /* fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.png\";replot;",digitp,optionfilefiname,digit); */
2739: fprintf(ficgp,"\nset out \"%s%s.png\";replot;\n",subdirf3(optionfilefiname,"varmuptjgr",digitp),digit);
2740:
2741: free_vector(xp,1,npar);
2742: free_matrix(doldm,1,nlstate,1,nlstate);
2743: free_matrix(dnewm,1,nlstate,1,npar);
2744: free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
2745: free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
2746: free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
2747: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
2748: fclose(ficresprobmorprev);
2749: fflush(ficgp);
2750: fflush(fichtm);
2751: } /* end varevsij */
2752:
2753: /************ Variance of prevlim ******************/
2754: 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)
2755: {
2756: /* Variance of prevalence limit */
2757: /* double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
2758: double **newm;
2759: double **dnewm,**doldm;
2760: int i, j, nhstepm, hstepm;
2761: int k, cptcode;
2762: double *xp;
2763: double *gp, *gm;
2764: double **gradg, **trgradg;
2765: double age,agelim;
2766: int theta;
2767:
2768: fprintf(ficresvpl,"# Standard deviation of stable prevalences \n");
2769: fprintf(ficresvpl,"# Age");
2770: for(i=1; i<=nlstate;i++)
2771: fprintf(ficresvpl," %1d-%1d",i,i);
2772: fprintf(ficresvpl,"\n");
2773:
2774: xp=vector(1,npar);
2775: dnewm=matrix(1,nlstate,1,npar);
2776: doldm=matrix(1,nlstate,1,nlstate);
2777:
2778: hstepm=1*YEARM; /* Every year of age */
2779: hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */
2780: agelim = AGESUP;
2781: for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
2782: nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
2783: if (stepm >= YEARM) hstepm=1;
2784: nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
2785: gradg=matrix(1,npar,1,nlstate);
2786: gp=vector(1,nlstate);
2787: gm=vector(1,nlstate);
2788:
2789: for(theta=1; theta <=npar; theta++){
2790: for(i=1; i<=npar; i++){ /* Computes gradient */
2791: xp[i] = x[i] + (i==theta ?delti[theta]:0);
2792: }
2793: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
2794: for(i=1;i<=nlstate;i++)
2795: gp[i] = prlim[i][i];
2796:
2797: for(i=1; i<=npar; i++) /* Computes gradient */
2798: xp[i] = x[i] - (i==theta ?delti[theta]:0);
2799: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
2800: for(i=1;i<=nlstate;i++)
2801: gm[i] = prlim[i][i];
2802:
2803: for(i=1;i<=nlstate;i++)
2804: gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
2805: } /* End theta */
2806:
2807: trgradg =matrix(1,nlstate,1,npar);
2808:
2809: for(j=1; j<=nlstate;j++)
2810: for(theta=1; theta <=npar; theta++)
2811: trgradg[j][theta]=gradg[theta][j];
2812:
2813: for(i=1;i<=nlstate;i++)
2814: varpl[i][(int)age] =0.;
2815: matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
2816: matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
2817: for(i=1;i<=nlstate;i++)
2818: varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
2819:
2820: fprintf(ficresvpl,"%.0f ",age );
2821: for(i=1; i<=nlstate;i++)
2822: fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
2823: fprintf(ficresvpl,"\n");
2824: free_vector(gp,1,nlstate);
2825: free_vector(gm,1,nlstate);
2826: free_matrix(gradg,1,npar,1,nlstate);
2827: free_matrix(trgradg,1,nlstate,1,npar);
2828: } /* End age */
2829:
2830: free_vector(xp,1,npar);
2831: free_matrix(doldm,1,nlstate,1,npar);
2832: free_matrix(dnewm,1,nlstate,1,nlstate);
2833:
2834: }
2835:
2836: /************ Variance of one-step probabilities ******************/
2837: void varprob(char optionfilefiname[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij, int *Tvar, int **nbcode, int *ncodemax)
2838: {
2839: int i, j=0, i1, k1, l1, t, tj;
2840: int k2, l2, j1, z1;
2841: int k=0,l, cptcode;
2842: int first=1, first1;
2843: double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
2844: double **dnewm,**doldm;
2845: double *xp;
2846: double *gp, *gm;
2847: double **gradg, **trgradg;
2848: double **mu;
2849: double age,agelim, cov[NCOVMAX];
2850: double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
2851: int theta;
2852: char fileresprob[FILENAMELENGTH];
2853: char fileresprobcov[FILENAMELENGTH];
2854: char fileresprobcor[FILENAMELENGTH];
2855:
2856: double ***varpij;
2857:
2858: strcpy(fileresprob,"prob");
2859: strcat(fileresprob,fileres);
2860: if((ficresprob=fopen(fileresprob,"w"))==NULL) {
2861: printf("Problem with resultfile: %s\n", fileresprob);
2862: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
2863: }
2864: strcpy(fileresprobcov,"probcov");
2865: strcat(fileresprobcov,fileres);
2866: if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
2867: printf("Problem with resultfile: %s\n", fileresprobcov);
2868: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
2869: }
2870: strcpy(fileresprobcor,"probcor");
2871: strcat(fileresprobcor,fileres);
2872: if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
2873: printf("Problem with resultfile: %s\n", fileresprobcor);
2874: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
2875: }
2876: printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
2877: fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
2878: printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
2879: fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
2880: printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
2881: fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
2882:
2883: fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
2884: fprintf(ficresprob,"# Age");
2885: fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
2886: fprintf(ficresprobcov,"# Age");
2887: fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
2888: fprintf(ficresprobcov,"# Age");
2889:
2890:
2891: for(i=1; i<=nlstate;i++)
2892: for(j=1; j<=(nlstate+ndeath);j++){
2893: fprintf(ficresprob," p%1d-%1d (SE)",i,j);
2894: fprintf(ficresprobcov," p%1d-%1d ",i,j);
2895: fprintf(ficresprobcor," p%1d-%1d ",i,j);
2896: }
2897: /* fprintf(ficresprob,"\n");
2898: fprintf(ficresprobcov,"\n");
2899: fprintf(ficresprobcor,"\n");
2900: */
2901: xp=vector(1,npar);
2902: dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
2903: doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
2904: mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
2905: varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
2906: first=1;
2907: fprintf(ficgp,"\n# Routine varprob");
2908: fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
2909: fprintf(fichtm,"\n");
2910:
2911: fprintf(fichtm,"\n<li><h4> <a href=\"%s\">Matrix of variance-covariance of pairs of step probabilities (drawings)</a></h4></li>\n",optionfilehtmcov);
2912: fprintf(fichtmcov,"\n<h4>Matrix of variance-covariance of pairs of step probabilities</h4>\n\
2913: file %s<br>\n",optionfilehtmcov);
2914: fprintf(fichtmcov,"\nEllipsoids of confidence centered on point (p<inf>ij</inf>, p<inf>kl</inf>) are estimated\
2915: and drawn. It helps understanding how is the covariance between two incidences.\
2916: They are expressed in year<sup>-1</sup> in order to be less dependent of stepm.<br>\n");
2917: 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. \
2918: It can be understood this way: if pij and pkl where uncorrelated the (2x2) matrix of covariance \
2919: would have been (1/(var pij), 0 , 0, 1/(var pkl)), and the confidence interval would be 2 \
2920: standard deviations wide on each axis. <br>\
2921: Now, if both incidences are correlated (usual case) we diagonalised the inverse of the covariance matrix\
2922: and made the appropriate rotation to look at the uncorrelated principal directions.<br>\
2923: To be simple, these graphs help to understand the significativity of each parameter in relation to a second other one.<br> \n");
2924:
2925: cov[1]=1;
2926: tj=cptcoveff;
2927: if (cptcovn<1) {tj=1;ncodemax[1]=1;}
2928: j1=0;
2929: for(t=1; t<=tj;t++){
2930: for(i1=1; i1<=ncodemax[t];i1++){
2931: j1++;
2932: if (cptcovn>0) {
2933: fprintf(ficresprob, "\n#********** Variable ");
2934: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
2935: fprintf(ficresprob, "**********\n#\n");
2936: fprintf(ficresprobcov, "\n#********** Variable ");
2937: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
2938: fprintf(ficresprobcov, "**********\n#\n");
2939:
2940: fprintf(ficgp, "\n#********** Variable ");
2941: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
2942: fprintf(ficgp, "**********\n#\n");
2943:
2944:
2945: fprintf(fichtmcov, "\n<hr size=\"2\" color=\"#EC5E5E\">********** Variable ");
2946: for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
2947: fprintf(fichtmcov, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
2948:
2949: fprintf(ficresprobcor, "\n#********** Variable ");
2950: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
2951: fprintf(ficresprobcor, "**********\n#");
2952: }
2953:
2954: for (age=bage; age<=fage; age ++){
2955: cov[2]=age;
2956: for (k=1; k<=cptcovn;k++) {
2957: cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];
2958: }
2959: for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
2960: for (k=1; k<=cptcovprod;k++)
2961: cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
2962:
2963: gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
2964: trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
2965: gp=vector(1,(nlstate)*(nlstate+ndeath));
2966: gm=vector(1,(nlstate)*(nlstate+ndeath));
2967:
2968: for(theta=1; theta <=npar; theta++){
2969: for(i=1; i<=npar; i++)
2970: xp[i] = x[i] + (i==theta ?delti[theta]:(double)0);
2971:
2972: pmij(pmmij,cov,ncovmodel,xp,nlstate);
2973:
2974: k=0;
2975: for(i=1; i<= (nlstate); i++){
2976: for(j=1; j<=(nlstate+ndeath);j++){
2977: k=k+1;
2978: gp[k]=pmmij[i][j];
2979: }
2980: }
2981:
2982: for(i=1; i<=npar; i++)
2983: xp[i] = x[i] - (i==theta ?delti[theta]:(double)0);
2984:
2985: pmij(pmmij,cov,ncovmodel,xp,nlstate);
2986: k=0;
2987: for(i=1; i<=(nlstate); i++){
2988: for(j=1; j<=(nlstate+ndeath);j++){
2989: k=k+1;
2990: gm[k]=pmmij[i][j];
2991: }
2992: }
2993:
2994: for(i=1; i<= (nlstate)*(nlstate+ndeath); i++)
2995: gradg[theta][i]=(gp[i]-gm[i])/(double)2./delti[theta];
2996: }
2997:
2998: for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
2999: for(theta=1; theta <=npar; theta++)
3000: trgradg[j][theta]=gradg[theta][j];
3001:
3002: matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov);
3003: matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);
3004: free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
3005: free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
3006: free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
3007: free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
3008:
3009: pmij(pmmij,cov,ncovmodel,x,nlstate);
3010:
3011: k=0;
3012: for(i=1; i<=(nlstate); i++){
3013: for(j=1; j<=(nlstate+ndeath);j++){
3014: k=k+1;
3015: mu[k][(int) age]=pmmij[i][j];
3016: }
3017: }
3018: for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
3019: for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
3020: varpij[i][j][(int)age] = doldm[i][j];
3021:
3022: /*printf("\n%d ",(int)age);
3023: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
3024: printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
3025: fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
3026: }*/
3027:
3028: fprintf(ficresprob,"\n%d ",(int)age);
3029: fprintf(ficresprobcov,"\n%d ",(int)age);
3030: fprintf(ficresprobcor,"\n%d ",(int)age);
3031:
3032: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)
3033: fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));
3034: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
3035: fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);
3036: fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
3037: }
3038: i=0;
3039: for (k=1; k<=(nlstate);k++){
3040: for (l=1; l<=(nlstate+ndeath);l++){
3041: i=i++;
3042: fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
3043: fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
3044: for (j=1; j<=i;j++){
3045: fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);
3046: fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));
3047: }
3048: }
3049: }/* end of loop for state */
3050: } /* end of loop for age */
3051:
3052: /* Confidence intervalle of pij */
3053: /*
3054: fprintf(ficgp,"\nset noparametric;unset label");
3055: fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");
3056: fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
3057: 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);
3058: fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);
3059: fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);
3060: fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);
3061: */
3062:
3063: /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
3064: first1=1;
3065: for (k2=1; k2<=(nlstate);k2++){
3066: for (l2=1; l2<=(nlstate+ndeath);l2++){
3067: if(l2==k2) continue;
3068: j=(k2-1)*(nlstate+ndeath)+l2;
3069: for (k1=1; k1<=(nlstate);k1++){
3070: for (l1=1; l1<=(nlstate+ndeath);l1++){
3071: if(l1==k1) continue;
3072: i=(k1-1)*(nlstate+ndeath)+l1;
3073: if(i<=j) continue;
3074: for (age=bage; age<=fage; age ++){
3075: if ((int)age %5==0){
3076: v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;
3077: v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;
3078: cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;
3079: mu1=mu[i][(int) age]/stepm*YEARM ;
3080: mu2=mu[j][(int) age]/stepm*YEARM;
3081: c12=cv12/sqrt(v1*v2);
3082: /* Computing eigen value of matrix of covariance */
3083: lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
3084: lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
3085: /* Eigen vectors */
3086: v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
3087: /*v21=sqrt(1.-v11*v11); *//* error */
3088: v21=(lc1-v1)/cv12*v11;
3089: v12=-v21;
3090: v22=v11;
3091: tnalp=v21/v11;
3092: if(first1==1){
3093: first1=0;
3094: 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);
3095: }
3096: 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);
3097: /*printf(fignu*/
3098: /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */
3099: /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */
3100: if(first==1){
3101: first=0;
3102: fprintf(ficgp,"\nset parametric;unset label");
3103: 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);
3104: fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
3105: fprintf(fichtmcov,"\n<br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup>\
3106: :<a href=\"%s%d%1d%1d-%1d%1d.png\">\
3107: %s%d%1d%1d-%1d%1d.png</A>, ",k1,l1,k2,l2,\
3108: subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2,\
3109: subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
3110: fprintf(fichtmcov,"\n<br><img src=\"%s%d%1d%1d-%1d%1d.png\"> ",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
3111: fprintf(fichtmcov,"\n<br> Correlation at age %d (%.3f),",(int) age, c12);
3112: fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\"",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
3113: fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
3114: fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
3115: 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",\
3116: mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
3117: mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
3118: }else{
3119: first=0;
3120: fprintf(fichtmcov," %d (%.3f),",(int) age, c12);
3121: fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
3122: fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
3123: 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",\
3124: mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
3125: mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
3126: }/* if first */
3127: } /* age mod 5 */
3128: } /* end loop age */
3129: fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\";replot;",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
3130: first=1;
3131: } /*l12 */
3132: } /* k12 */
3133: } /*l1 */
3134: }/* k1 */
3135: } /* loop covariates */
3136: }
3137: free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
3138: free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
3139: free_vector(xp,1,npar);
3140: fclose(ficresprob);
3141: fclose(ficresprobcov);
3142: fclose(ficresprobcor);
3143: fflush(ficgp);
3144: fflush(fichtmcov);
3145: }
3146:
3147:
3148: /******************* Printing html file ***********/
3149: void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \
3150: int lastpass, int stepm, int weightopt, char model[],\
3151: int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
3152: int popforecast, int estepm ,\
3153: double jprev1, double mprev1,double anprev1, \
3154: double jprev2, double mprev2,double anprev2){
3155: int jj1, k1, i1, cpt;
3156:
3157: fprintf(fichtm,"<ul><li><h4>Result files (first order: no variance)</h4>\n \
3158: - Observed prevalence in each state (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"%s\">%s</a> <br>\n ",
3159: jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirf2(fileres,"p"),subdirf2(fileres,"p"));
3160: fprintf(fichtm,"\
3161: - Estimated transition probabilities over %d (stepm) months: <a href=\"%s\">%s</a><br>\n ",
3162: stepm,subdirf2(fileres,"pij"),subdirf2(fileres,"pij"));
3163: fprintf(fichtm,"\
3164: - Stable prevalence in each health state: <a href=\"%s\">%s</a> <br>\n",
3165: subdirf2(fileres,"pl"),subdirf2(fileres,"pl"));
3166: fprintf(fichtm,"\
3167: - Life expectancies by age and initial health status (estepm=%2d months): \
3168: <a href=\"%s\">%s</a> <br>\n</li>",
3169: estepm,subdirf2(fileres,"e"),subdirf2(fileres,"e"));
3170:
3171: fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
3172:
3173: m=cptcoveff;
3174: if (cptcovn < 1) {m=1;ncodemax[1]=1;}
3175:
3176: jj1=0;
3177: for(k1=1; k1<=m;k1++){
3178: for(i1=1; i1<=ncodemax[k1];i1++){
3179: jj1++;
3180: if (cptcovn > 0) {
3181: fprintf(fichtm,"<hr size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
3182: for (cpt=1; cpt<=cptcoveff;cpt++)
3183: fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
3184: fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
3185: }
3186: /* Pij */
3187: 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> \
3188: <img src=\"%s%d1.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);
3189: /* Quasi-incidences */
3190: fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months\
3191: before but expressed in per year i.e. quasi incidences if stepm is small and probabilities too: %s%d2.png<br> \
3192: <img src=\"%s%d2.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);
3193: /* Stable prevalence in each health state */
3194: for(cpt=1; cpt<nlstate;cpt++){
3195: fprintf(fichtm,"<br>- Stable prevalence in each health state : p%s%d%d.png<br> \
3196: <img src=\"%s%d%d.png\">",subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1);
3197: }
3198: for(cpt=1; cpt<=nlstate;cpt++) {
3199: fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): %s%d%d.png <br> \
3200: <img src=\"%s%d%d.png\">",cpt,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1);
3201: }
3202: } /* end i1 */
3203: }/* End k1 */
3204: fprintf(fichtm,"</ul>");
3205:
3206:
3207: fprintf(fichtm,"\
3208: \n<br><li><h4> Result files (second order: variances)</h4>\n\
3209: - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n", rfileres,rfileres);
3210:
3211: fprintf(fichtm," - Variance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
3212: subdirf2(fileres,"prob"),subdirf2(fileres,"prob"));
3213: fprintf(fichtm,"\
3214: - Variance-covariance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
3215: subdirf2(fileres,"probcov"),subdirf2(fileres,"probcov"));
3216:
3217: fprintf(fichtm,"\
3218: - Correlation matrix of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
3219: subdirf2(fileres,"probcor"),subdirf2(fileres,"probcor"));
3220: fprintf(fichtm,"\
3221: - Variances and covariances of life expectancies by age and initial health status (estepm=%d months): <a href=\"%s\">%s</a><br>\n",
3222: estepm, subdirf2(fileres,"v"),subdirf2(fileres,"v"));
3223: fprintf(fichtm,"\
3224: - Health expectancies with their variances (no covariance): <a href=\"%s\">%s</a> <br>\n",
3225: subdirf2(fileres,"t"),subdirf2(fileres,"t"));
3226: fprintf(fichtm,"\
3227: - Standard deviation of stable prevalences: <a href=\"%s\">%s</a> <br>\n",\
3228: subdirf2(fileres,"vpl"),subdirf2(fileres,"vpl"));
3229:
3230: /* if(popforecast==1) fprintf(fichtm,"\n */
3231: /* - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n */
3232: /* - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n */
3233: /* <br>",fileres,fileres,fileres,fileres); */
3234: /* else */
3235: /* 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); */
3236: fflush(fichtm);
3237: fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
3238:
3239: m=cptcoveff;
3240: if (cptcovn < 1) {m=1;ncodemax[1]=1;}
3241:
3242: jj1=0;
3243: for(k1=1; k1<=m;k1++){
3244: for(i1=1; i1<=ncodemax[k1];i1++){
3245: jj1++;
3246: if (cptcovn > 0) {
3247: fprintf(fichtm,"<hr size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
3248: for (cpt=1; cpt<=cptcoveff;cpt++)
3249: fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
3250: fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
3251: }
3252: for(cpt=1; cpt<=nlstate;cpt++) {
3253: fprintf(fichtm,"<br>- Observed (cross-sectional) and period (incidence based) \
3254: prevalence (with 95%% confidence interval) in state (%d): %s%d%d.png <br>\
3255: <img src=\"%s%d%d.png\">",cpt,subdirf2(optionfilefiname,"v"),cpt,jj1,subdirf2(optionfilefiname,"v"),cpt,jj1);
3256: }
3257: fprintf(fichtm,"\n<br>- Total life expectancy by age and \
3258: health expectancies in states (1) and (2): %s%d.png<br>\
3259: <img src=\"%s%d.png\">",subdirf2(optionfilefiname,"e"),jj1,subdirf2(optionfilefiname,"e"),jj1);
3260: } /* end i1 */
3261: }/* End k1 */
3262: fprintf(fichtm,"</ul>");
3263: fflush(fichtm);
3264: }
3265:
3266: /******************* Gnuplot file **************/
3267: void printinggnuplot(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
3268:
3269: char dirfileres[132],optfileres[132];
3270: int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;
3271: int ng;
3272: /* if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) { */
3273: /* printf("Problem with file %s",optionfilegnuplot); */
3274: /* fprintf(ficlog,"Problem with file %s",optionfilegnuplot); */
3275: /* } */
3276:
3277: /*#ifdef windows */
3278: fprintf(ficgp,"cd \"%s\" \n",pathc);
3279: /*#endif */
3280: m=pow(2,cptcoveff);
3281:
3282: strcpy(dirfileres,optionfilefiname);
3283: strcpy(optfileres,"vpl");
3284: /* 1eme*/
3285: for (cpt=1; cpt<= nlstate ; cpt ++) {
3286: for (k1=1; k1<= m ; k1 ++) {
3287: fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"v"),cpt,k1);
3288: fprintf(ficgp,"\n#set out \"v%s%d%d.png\" \n",optionfilefiname,cpt,k1);
3289: fprintf(ficgp,"set xlabel \"Age\" \n\
3290: set ylabel \"Probability\" \n\
3291: set ter png small\n\
3292: set size 0.65,0.65\n\
3293: plot [%.f:%.f] \"%s\" every :::%d::%d u 1:2 \"\%%lf",ageminpar,fage,subdirf2(fileres,"vpl"),k1-1,k1-1);
3294:
3295: for (i=1; i<= nlstate ; i ++) {
3296: if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
3297: else fprintf(ficgp," \%%*lf (\%%*lf)");
3298: }
3299: 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);
3300: for (i=1; i<= nlstate ; i ++) {
3301: if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
3302: else fprintf(ficgp," \%%*lf (\%%*lf)");
3303: }
3304: fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"%s\" every :::%d::%d u 1:($2-1.96*$3) \"\%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1);
3305: for (i=1; i<= nlstate ; i ++) {
3306: if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
3307: else fprintf(ficgp," \%%*lf (\%%*lf)");
3308: }
3309: fprintf(ficgp,"\" t\"\" w l 1,\"%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",subdirf2(fileres,"p"),k1-1,k1-1,2+4*(cpt-1));
3310: }
3311: }
3312: /*2 eme*/
3313:
3314: for (k1=1; k1<= m ; k1 ++) {
3315: fprintf(ficgp,"\nset out \"%s%d.png\" \n",subdirf2(optionfilefiname,"e"),k1);
3316: fprintf(ficgp,"set ylabel \"Years\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] ",ageminpar,fage);
3317:
3318: for (i=1; i<= nlstate+1 ; i ++) {
3319: k=2*i;
3320: fprintf(ficgp,"\"%s\" every :::%d::%d u 1:2 \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
3321: for (j=1; j<= nlstate+1 ; j ++) {
3322: if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
3323: else fprintf(ficgp," \%%*lf (\%%*lf)");
3324: }
3325: if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");
3326: else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);
3327: fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
3328: for (j=1; j<= nlstate+1 ; j ++) {
3329: if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
3330: else fprintf(ficgp," \%%*lf (\%%*lf)");
3331: }
3332: fprintf(ficgp,"\" t\"\" w l 0,");
3333: fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
3334: for (j=1; j<= nlstate+1 ; j ++) {
3335: if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
3336: else fprintf(ficgp," \%%*lf (\%%*lf)");
3337: }
3338: if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");
3339: else fprintf(ficgp,"\" t\"\" w l 0,");
3340: }
3341: }
3342:
3343: /*3eme*/
3344:
3345: for (k1=1; k1<= m ; k1 ++) {
3346: for (cpt=1; cpt<= nlstate ; cpt ++) {
3347: k=2+nlstate*(2*cpt-2);
3348: fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"exp"),cpt,k1);
3349: fprintf(ficgp,"set ter png small\n\
3350: set size 0.65,0.65\n\
3351: plot [%.f:%.f] \"%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,subdirf2(fileres,"e"),k1-1,k1-1,k,cpt);
3352: /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
3353: for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
3354: fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
3355: fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
3356: for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
3357: fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
3358:
3359: */
3360: for (i=1; i< nlstate ; i ++) {
3361: 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);
3362:
3363: }
3364: }
3365: }
3366:
3367: /* CV preval stable (period) */
3368: for (k1=1; k1<= m ; k1 ++) {
3369: for (cpt=1; cpt<=nlstate ; cpt ++) {
3370: k=3;
3371: fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"p"),cpt,k1);
3372: fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\
3373: set ter png small\nset size 0.65,0.65\n\
3374: unset log y\n\
3375: plot [%.f:%.f] \"%s\" u ($1==%d ? ($3):1/0):($%d/($%d",ageminpar,agemaxpar,subdirf2(fileres,"pij"),k1,k+cpt+1,k+1);
3376:
3377: for (i=1; i< nlstate ; i ++)
3378: fprintf(ficgp,"+$%d",k+i+1);
3379: fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);
3380:
3381: l=3+(nlstate+ndeath)*cpt;
3382: fprintf(ficgp,",\"%s\" u ($1==%d ? ($3):1/0):($%d/($%d",subdirf2(fileres,"pij"),k1,l+cpt+1,l+1);
3383: for (i=1; i< nlstate ; i ++) {
3384: l=3+(nlstate+ndeath)*cpt;
3385: fprintf(ficgp,"+$%d",l+i+1);
3386: }
3387: fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);
3388: }
3389: }
3390:
3391: /* proba elementaires */
3392: for(i=1,jk=1; i <=nlstate; i++){
3393: for(k=1; k <=(nlstate+ndeath); k++){
3394: if (k != i) {
3395: for(j=1; j <=ncovmodel; j++){
3396: fprintf(ficgp,"p%d=%f ",jk,p[jk]);
3397: jk++;
3398: fprintf(ficgp,"\n");
3399: }
3400: }
3401: }
3402: }
3403:
3404: for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/
3405: for(jk=1; jk <=m; jk++) {
3406: fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"pe"),jk,ng);
3407: if (ng==2)
3408: fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
3409: else
3410: fprintf(ficgp,"\nset title \"Probability\"\n");
3411: fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65\nset log y\nplot [%.f:%.f] ",ageminpar,agemaxpar);
3412: i=1;
3413: for(k2=1; k2<=nlstate; k2++) {
3414: k3=i;
3415: for(k=1; k<=(nlstate+ndeath); k++) {
3416: if (k != k2){
3417: if(ng==2)
3418: fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);
3419: else
3420: fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
3421: ij=1;
3422: for(j=3; j <=ncovmodel; j++) {
3423: if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
3424: fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
3425: ij++;
3426: }
3427: else
3428: fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
3429: }
3430: fprintf(ficgp,")/(1");
3431:
3432: for(k1=1; k1 <=nlstate; k1++){
3433: fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);
3434: ij=1;
3435: for(j=3; j <=ncovmodel; j++){
3436: if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
3437: fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
3438: ij++;
3439: }
3440: else
3441: fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
3442: }
3443: fprintf(ficgp,")");
3444: }
3445: fprintf(ficgp,") t \"p%d%d\" ", k2,k);
3446: if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");
3447: i=i+ncovmodel;
3448: }
3449: } /* end k */
3450: } /* end k2 */
3451: } /* end jk */
3452: } /* end ng */
3453: fflush(ficgp);
3454: } /* end gnuplot */
3455:
3456:
3457: /*************** Moving average **************/
3458: int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav){
3459:
3460: int i, cpt, cptcod;
3461: int modcovmax =1;
3462: int mobilavrange, mob;
3463: double age;
3464:
3465: modcovmax=2*cptcoveff;/* Max number of modalities. We suppose
3466: a covariate has 2 modalities */
3467: if (cptcovn<1) modcovmax=1; /* At least 1 pass */
3468:
3469: if(mobilav==1||mobilav ==3 ||mobilav==5 ||mobilav== 7){
3470: if(mobilav==1) mobilavrange=5; /* default */
3471: else mobilavrange=mobilav;
3472: for (age=bage; age<=fage; age++)
3473: for (i=1; i<=nlstate;i++)
3474: for (cptcod=1;cptcod<=modcovmax;cptcod++)
3475: mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
3476: /* We keep the original values on the extreme ages bage, fage and for
3477: fage+1 and bage-1 we use a 3 terms moving average; for fage+2 bage+2
3478: we use a 5 terms etc. until the borders are no more concerned.
3479: */
3480: for (mob=3;mob <=mobilavrange;mob=mob+2){
3481: for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){
3482: for (i=1; i<=nlstate;i++){
3483: for (cptcod=1;cptcod<=modcovmax;cptcod++){
3484: mobaverage[(int)age][i][cptcod] =probs[(int)age][i][cptcod];
3485: for (cpt=1;cpt<=(mob-1)/2;cpt++){
3486: mobaverage[(int)age][i][cptcod] +=probs[(int)age-cpt][i][cptcod];
3487: mobaverage[(int)age][i][cptcod] +=probs[(int)age+cpt][i][cptcod];
3488: }
3489: mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/mob;
3490: }
3491: }
3492: }/* end age */
3493: }/* end mob */
3494: }else return -1;
3495: return 0;
3496: }/* End movingaverage */
3497:
3498:
3499: /************** Forecasting ******************/
3500: 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){
3501: /* proj1, year, month, day of starting projection
3502: agemin, agemax range of age
3503: dateprev1 dateprev2 range of dates during which prevalence is computed
3504: anproj2 year of en of projection (same day and month as proj1).
3505: */
3506: int yearp, stepsize, hstepm, nhstepm, j, k, c, cptcod, i, h, i1;
3507: int *popage;
3508: double agec; /* generic age */
3509: double agelim, ppij, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
3510: double *popeffectif,*popcount;
3511: double ***p3mat;
3512: double ***mobaverage;
3513: char fileresf[FILENAMELENGTH];
3514:
3515: agelim=AGESUP;
3516: prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
3517:
3518: strcpy(fileresf,"f");
3519: strcat(fileresf,fileres);
3520: if((ficresf=fopen(fileresf,"w"))==NULL) {
3521: printf("Problem with forecast resultfile: %s\n", fileresf);
3522: fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);
3523: }
3524: printf("Computing forecasting: result on file '%s' \n", fileresf);
3525: fprintf(ficlog,"Computing forecasting: result on file '%s' \n", fileresf);
3526:
3527: if (cptcoveff==0) ncodemax[cptcoveff]=1;
3528:
3529: if (mobilav!=0) {
3530: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
3531: if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
3532: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
3533: printf(" Error in movingaverage mobilav=%d\n",mobilav);
3534: }
3535: }
3536:
3537: stepsize=(int) (stepm+YEARM-1)/YEARM;
3538: if (stepm<=12) stepsize=1;
3539: if(estepm < stepm){
3540: printf ("Problem %d lower than %d\n",estepm, stepm);
3541: }
3542: else hstepm=estepm;
3543:
3544: hstepm=hstepm/stepm;
3545: yp1=modf(dateintmean,&yp);/* extracts integral of datemean in yp and
3546: fractional in yp1 */
3547: anprojmean=yp;
3548: yp2=modf((yp1*12),&yp);
3549: mprojmean=yp;
3550: yp1=modf((yp2*30.5),&yp);
3551: jprojmean=yp;
3552: if(jprojmean==0) jprojmean=1;
3553: if(mprojmean==0) jprojmean=1;
3554:
3555: i1=cptcoveff;
3556: if (cptcovn < 1){i1=1;}
3557:
3558: fprintf(ficresf,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2);
3559:
3560: fprintf(ficresf,"#****** Routine prevforecast **\n");
3561:
3562: /* if (h==(int)(YEARM*yearp)){ */
3563: for(cptcov=1, k=0;cptcov<=i1;cptcov++){
3564: for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
3565: k=k+1;
3566: fprintf(ficresf,"\n#******");
3567: for(j=1;j<=cptcoveff;j++) {
3568: 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]]);
3569: }
3570: fprintf(ficresf,"******\n");
3571: fprintf(ficresf,"# Covariate valuofcovar yearproj age");
3572: for(j=1; j<=nlstate+ndeath;j++){
3573: for(i=1; i<=nlstate;i++)
3574: fprintf(ficresf," p%d%d",i,j);
3575: fprintf(ficresf," p.%d",j);
3576: }
3577: for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) {
3578: fprintf(ficresf,"\n");
3579: fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+yearp);
3580:
3581: for (agec=fage; agec>=(ageminpar-1); agec--){
3582: nhstepm=(int) rint((agelim-agec)*YEARM/stepm);
3583: nhstepm = nhstepm/hstepm;
3584: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3585: oldm=oldms;savm=savms;
3586: hpxij(p3mat,nhstepm,agec,hstepm,p,nlstate,stepm,oldm,savm, k);
3587:
3588: for (h=0; h<=nhstepm; h++){
3589: if (h*hstepm/YEARM*stepm ==yearp) {
3590: fprintf(ficresf,"\n");
3591: for(j=1;j<=cptcoveff;j++)
3592: fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
3593: fprintf(ficresf,"%.f %.f ",anproj1+yearp,agec+h*hstepm/YEARM*stepm);
3594: }
3595: for(j=1; j<=nlstate+ndeath;j++) {
3596: ppij=0.;
3597: for(i=1; i<=nlstate;i++) {
3598: if (mobilav==1)
3599: ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][i][cptcod];
3600: else {
3601: ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][cptcod];
3602: }
3603: if (h*hstepm/YEARM*stepm== yearp) {
3604: fprintf(ficresf," %.3f", p3mat[i][j][h]);
3605: }
3606: } /* end i */
3607: if (h*hstepm/YEARM*stepm==yearp) {
3608: fprintf(ficresf," %.3f", ppij);
3609: }
3610: }/* end j */
3611: } /* end h */
3612: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3613: } /* end agec */
3614: } /* end yearp */
3615: } /* end cptcod */
3616: } /* end cptcov */
3617:
3618: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
3619:
3620: fclose(ficresf);
3621: }
3622:
3623: /************** Forecasting *****not tested NB*************/
3624: 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){
3625:
3626: int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;
3627: int *popage;
3628: double calagedatem, agelim, kk1, kk2;
3629: double *popeffectif,*popcount;
3630: double ***p3mat,***tabpop,***tabpopprev;
3631: double ***mobaverage;
3632: char filerespop[FILENAMELENGTH];
3633:
3634: tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
3635: tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
3636: agelim=AGESUP;
3637: calagedatem=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;
3638:
3639: prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
3640:
3641:
3642: strcpy(filerespop,"pop");
3643: strcat(filerespop,fileres);
3644: if((ficrespop=fopen(filerespop,"w"))==NULL) {
3645: printf("Problem with forecast resultfile: %s\n", filerespop);
3646: fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop);
3647: }
3648: printf("Computing forecasting: result on file '%s' \n", filerespop);
3649: fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop);
3650:
3651: if (cptcoveff==0) ncodemax[cptcoveff]=1;
3652:
3653: if (mobilav!=0) {
3654: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
3655: if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
3656: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
3657: printf(" Error in movingaverage mobilav=%d\n",mobilav);
3658: }
3659: }
3660:
3661: stepsize=(int) (stepm+YEARM-1)/YEARM;
3662: if (stepm<=12) stepsize=1;
3663:
3664: agelim=AGESUP;
3665:
3666: hstepm=1;
3667: hstepm=hstepm/stepm;
3668:
3669: if (popforecast==1) {
3670: if((ficpop=fopen(popfile,"r"))==NULL) {
3671: printf("Problem with population file : %s\n",popfile);exit(0);
3672: fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0);
3673: }
3674: popage=ivector(0,AGESUP);
3675: popeffectif=vector(0,AGESUP);
3676: popcount=vector(0,AGESUP);
3677:
3678: i=1;
3679: while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;
3680:
3681: imx=i;
3682: for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];
3683: }
3684:
3685: for(cptcov=1,k=0;cptcov<=i2;cptcov++){
3686: for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
3687: k=k+1;
3688: fprintf(ficrespop,"\n#******");
3689: for(j=1;j<=cptcoveff;j++) {
3690: fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
3691: }
3692: fprintf(ficrespop,"******\n");
3693: fprintf(ficrespop,"# Age");
3694: for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);
3695: if (popforecast==1) fprintf(ficrespop," [Population]");
3696:
3697: for (cpt=0; cpt<=0;cpt++) {
3698: fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);
3699:
3700: for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){
3701: nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);
3702: nhstepm = nhstepm/hstepm;
3703:
3704: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3705: oldm=oldms;savm=savms;
3706: hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
3707:
3708: for (h=0; h<=nhstepm; h++){
3709: if (h==(int) (calagedatem+YEARM*cpt)) {
3710: fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
3711: }
3712: for(j=1; j<=nlstate+ndeath;j++) {
3713: kk1=0.;kk2=0;
3714: for(i=1; i<=nlstate;i++) {
3715: if (mobilav==1)
3716: kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];
3717: else {
3718: kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];
3719: }
3720: }
3721: if (h==(int)(calagedatem+12*cpt)){
3722: tabpop[(int)(agedeb)][j][cptcod]=kk1;
3723: /*fprintf(ficrespop," %.3f", kk1);
3724: if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/
3725: }
3726: }
3727: for(i=1; i<=nlstate;i++){
3728: kk1=0.;
3729: for(j=1; j<=nlstate;j++){
3730: kk1= kk1+tabpop[(int)(agedeb)][j][cptcod];
3731: }
3732: tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedatem+12*cpt)*hstepm/YEARM*stepm-1)];
3733: }
3734:
3735: if (h==(int)(calagedatem+12*cpt)) for(j=1; j<=nlstate;j++)
3736: fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);
3737: }
3738: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3739: }
3740: }
3741:
3742: /******/
3743:
3744: for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) {
3745: fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);
3746: for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){
3747: nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);
3748: nhstepm = nhstepm/hstepm;
3749:
3750: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3751: oldm=oldms;savm=savms;
3752: hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
3753: for (h=0; h<=nhstepm; h++){
3754: if (h==(int) (calagedatem+YEARM*cpt)) {
3755: fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
3756: }
3757: for(j=1; j<=nlstate+ndeath;j++) {
3758: kk1=0.;kk2=0;
3759: for(i=1; i<=nlstate;i++) {
3760: kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];
3761: }
3762: if (h==(int)(calagedatem+12*cpt)) fprintf(ficresf," %15.2f", kk1);
3763: }
3764: }
3765: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3766: }
3767: }
3768: }
3769: }
3770:
3771: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
3772:
3773: if (popforecast==1) {
3774: free_ivector(popage,0,AGESUP);
3775: free_vector(popeffectif,0,AGESUP);
3776: free_vector(popcount,0,AGESUP);
3777: }
3778: free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
3779: free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
3780: fclose(ficrespop);
3781: } /* End of popforecast */
3782:
3783: int fileappend(FILE *fichier, char *optionfich)
3784: {
3785: if((fichier=fopen(optionfich,"a"))==NULL) {
3786: printf("Problem with file: %s\n", optionfich);
3787: fprintf(ficlog,"Problem with file: %s\n", optionfich);
3788: return (0);
3789: }
3790: fflush(fichier);
3791: return (1);
3792: }
3793:
3794:
3795: /**************** function prwizard **********************/
3796: void prwizard(int ncovmodel, int nlstate, int ndeath, char model[], FILE *ficparo)
3797: {
3798:
3799: /* Wizard to print covariance matrix template */
3800:
3801: char ca[32], cb[32], cc[32];
3802: int i,j, k, l, li, lj, lk, ll, jj, npar, itimes;
3803: int numlinepar;
3804:
3805: printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
3806: fprintf(ficparo,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
3807: for(i=1; i <=nlstate; i++){
3808: jj=0;
3809: for(j=1; j <=nlstate+ndeath; j++){
3810: if(j==i) continue;
3811: jj++;
3812: /*ca[0]= k+'a'-1;ca[1]='\0';*/
3813: printf("%1d%1d",i,j);
3814: fprintf(ficparo,"%1d%1d",i,j);
3815: for(k=1; k<=ncovmodel;k++){
3816: /* printf(" %lf",param[i][j][k]); */
3817: /* fprintf(ficparo," %lf",param[i][j][k]); */
3818: printf(" 0.");
3819: fprintf(ficparo," 0.");
3820: }
3821: printf("\n");
3822: fprintf(ficparo,"\n");
3823: }
3824: }
3825: printf("# Scales (for hessian or gradient estimation)\n");
3826: fprintf(ficparo,"# Scales (for hessian or gradient estimation)\n");
3827: npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/
3828: for(i=1; i <=nlstate; i++){
3829: jj=0;
3830: for(j=1; j <=nlstate+ndeath; j++){
3831: if(j==i) continue;
3832: jj++;
3833: fprintf(ficparo,"%1d%1d",i,j);
3834: printf("%1d%1d",i,j);
3835: fflush(stdout);
3836: for(k=1; k<=ncovmodel;k++){
3837: /* printf(" %le",delti3[i][j][k]); */
3838: /* fprintf(ficparo," %le",delti3[i][j][k]); */
3839: printf(" 0.");
3840: fprintf(ficparo," 0.");
3841: }
3842: numlinepar++;
3843: printf("\n");
3844: fprintf(ficparo,"\n");
3845: }
3846: }
3847: printf("# Covariance matrix\n");
3848: /* # 121 Var(a12)\n\ */
3849: /* # 122 Cov(b12,a12) Var(b12)\n\ */
3850: /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
3851: /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
3852: /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
3853: /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
3854: /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
3855: /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
3856: fflush(stdout);
3857: fprintf(ficparo,"# Covariance matrix\n");
3858: /* # 121 Var(a12)\n\ */
3859: /* # 122 Cov(b12,a12) Var(b12)\n\ */
3860: /* # ...\n\ */
3861: /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
3862:
3863: for(itimes=1;itimes<=2;itimes++){
3864: jj=0;
3865: for(i=1; i <=nlstate; i++){
3866: for(j=1; j <=nlstate+ndeath; j++){
3867: if(j==i) continue;
3868: for(k=1; k<=ncovmodel;k++){
3869: jj++;
3870: ca[0]= k+'a'-1;ca[1]='\0';
3871: if(itimes==1){
3872: printf("#%1d%1d%d",i,j,k);
3873: fprintf(ficparo,"#%1d%1d%d",i,j,k);
3874: }else{
3875: printf("%1d%1d%d",i,j,k);
3876: fprintf(ficparo,"%1d%1d%d",i,j,k);
3877: /* printf(" %.5le",matcov[i][j]); */
3878: }
3879: ll=0;
3880: for(li=1;li <=nlstate; li++){
3881: for(lj=1;lj <=nlstate+ndeath; lj++){
3882: if(lj==li) continue;
3883: for(lk=1;lk<=ncovmodel;lk++){
3884: ll++;
3885: if(ll<=jj){
3886: cb[0]= lk +'a'-1;cb[1]='\0';
3887: if(ll<jj){
3888: if(itimes==1){
3889: printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
3890: fprintf(ficparo," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
3891: }else{
3892: printf(" 0.");
3893: fprintf(ficparo," 0.");
3894: }
3895: }else{
3896: if(itimes==1){
3897: printf(" Var(%s%1d%1d)",ca,i,j);
3898: fprintf(ficparo," Var(%s%1d%1d)",ca,i,j);
3899: }else{
3900: printf(" 0.");
3901: fprintf(ficparo," 0.");
3902: }
3903: }
3904: }
3905: } /* end lk */
3906: } /* end lj */
3907: } /* end li */
3908: printf("\n");
3909: fprintf(ficparo,"\n");
3910: numlinepar++;
3911: } /* end k*/
3912: } /*end j */
3913: } /* end i */
3914: } /* end itimes */
3915:
3916: } /* end of prwizard */
3917: /******************* Gompertz Likelihood ******************************/
3918: double gompertz(double x[])
3919: {
3920: double A,B,L=0.0,sump=0.,num=0.;
3921: int i,n=0; /* n is the size of the sample */
3922: for (i=0;i<=imx-1 ; i++) {
3923: sump=sump+weight[i];
3924: sump=sump+1;
3925: num=num+1;
3926: }
3927:
3928:
3929: /* for (i=1; i<=imx; i++)
3930: 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]);*/
3931:
3932: for (i=0;i<=imx-1 ; i++)
3933: {
3934: if (cens[i]==1 & wav[i]>1)
3935: A=-x[1]/(x[2])*
3936: (exp(x[2]/YEARM*(agecens[i]*12-agegomp*12))-exp(x[2]/YEARM*(ageexmed[i]*12-agegomp*12)));
3937:
3938: if (cens[i]==0 & wav[i]>1)
3939: A=-x[1]/(x[2])*
3940: (exp(x[2]/YEARM*(agedc[i]*12-agegomp*12))-exp(x[2]/YEARM*(ageexmed[i]*12-agegomp*12)))
3941: +log(x[1]/YEARM)+x[2]/YEARM*(agedc[i]*12-agegomp*12)+log(YEARM);
3942:
3943: if (wav[i]>1 & agecens[i]>15) {
3944: L=L+A*weight[i];
3945: /* 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]);*/
3946: }
3947: }
3948:
3949: /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/
3950:
3951: return -2*L*num/sump;
3952: }
3953:
3954: /******************* Printing html file ***********/
3955: void printinghtmlmort(char fileres[], char title[], char datafile[], int firstpass, \
3956: int lastpass, int stepm, int weightopt, char model[],\
3957: int imx, double p[],double **matcov){
3958: int i;
3959:
3960: fprintf(fichtm,"<ul><li><h4>Result files </h4>\n Force of mortality. Parameters of the Gompertz fit (with confidence interval in brackets):<br>");
3961: fprintf(fichtm," mu(age) =%lf*exp(%lf*(age-%d)) per year<br><br>",p[1],p[2],agegomp);
3962: for (i=1;i<=2;i++)
3963: 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]));
3964: fprintf(fichtm,"<br><br><img src=\"graphmort.png\">");
3965: fprintf(fichtm,"</ul>");
3966: fflush(fichtm);
3967: }
3968:
3969: /******************* Gnuplot file **************/
3970: void printinggnuplotmort(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
3971:
3972: char dirfileres[132],optfileres[132];
3973: int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;
3974: int ng;
3975:
3976:
3977: /*#ifdef windows */
3978: fprintf(ficgp,"cd \"%s\" \n",pathc);
3979: /*#endif */
3980:
3981:
3982: strcpy(dirfileres,optionfilefiname);
3983: strcpy(optfileres,"vpl");
3984: fprintf(ficgp,"set out \"graphmort.png\"\n ");
3985: fprintf(ficgp,"set xlabel \"Age\"\n set ylabel \"Force of mortality (per year)\" \n ");
3986: fprintf(ficgp, "set ter png small\n set log y\n");
3987: fprintf(ficgp, "set size 0.65,0.65\n");
3988: fprintf(ficgp,"plot [%d:100] %lf*exp(%lf*(x-%d))",agegomp,p[1],p[2],agegomp);
3989:
3990: }
3991:
3992:
3993:
3994:
3995: /***********************************************/
3996: /**************** Main Program *****************/
3997: /***********************************************/
3998:
3999: int main(int argc, char *argv[])
4000: {
4001: int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav);
4002: int i,j, k, n=MAXN,iter,m,size=100,cptcode, cptcod;
4003: int jj, ll, li, lj, lk, imk;
4004: int numlinepar=0; /* Current linenumber of parameter file */
4005: int itimes;
4006: int NDIM=2;
4007:
4008: char ca[32], cb[32], cc[32];
4009: /* FILE *fichtm; *//* Html File */
4010: /* FILE *ficgp;*/ /*Gnuplot File */
4011: double agedeb, agefin,hf;
4012: double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;
4013:
4014: double fret;
4015: double **xi,tmp,delta;
4016:
4017: double dum; /* Dummy variable */
4018: double ***p3mat;
4019: double ***mobaverage;
4020: int *indx;
4021: char line[MAXLINE], linepar[MAXLINE];
4022: char path[MAXLINE],pathc[MAXLINE],pathcd[MAXLINE],pathtot[MAXLINE],model[MAXLINE];
4023: char pathr[MAXLINE], pathimach[MAXLINE];
4024: int firstobs=1, lastobs=10;
4025: int sdeb, sfin; /* Status at beginning and end */
4026: int c, h , cpt,l;
4027: int ju,jl, mi;
4028: int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;
4029: int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,*tab;
4030: int mobilavproj=0 , prevfcast=0 ; /* moving average of prev, If prevfcast=1 prevalence projection */
4031: int mobilav=0,popforecast=0;
4032: int hstepm, nhstepm;
4033: double jprev1=1, mprev1=1,anprev1=2000,jprev2=1, mprev2=1,anprev2=2000;
4034: double jpyram=1, mpyram=1,anpyram=2000,jpyram1=1, mpyram1=1,anpyram1=2000;
4035:
4036: double bage, fage, age, agelim, agebase;
4037: double ftolpl=FTOL;
4038: double **prlim;
4039: double *severity;
4040: double ***param; /* Matrix of parameters */
4041: double *p;
4042: double **matcov; /* Matrix of covariance */
4043: double ***delti3; /* Scale */
4044: double *delti; /* Scale */
4045: double ***eij, ***vareij;
4046: double **varpl; /* Variances of prevalence limits by age */
4047: double *epj, vepp;
4048: double kk1, kk2;
4049: double dateprev1, dateprev2,jproj1=1,mproj1=1,anproj1=2000,jproj2=1,mproj2=1,anproj2=2000;
4050: double **ximort;
4051: char *alph[]={"a","a","b","c","d","e"}, str[4];
4052: int *dcwave;
4053:
4054: char z[1]="c", occ;
4055:
4056: char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];
4057: char strstart[80], *strt, strtend[80];
4058: char *stratrunc;
4059: int lstra;
4060:
4061: long total_usecs;
4062:
4063: /* setlocale (LC_ALL, ""); */
4064: /* bindtextdomain (PACKAGE, LOCALEDIR); */
4065: /* textdomain (PACKAGE); */
4066: /* setlocale (LC_CTYPE, ""); */
4067: /* setlocale (LC_MESSAGES, ""); */
4068:
4069: /* gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */
4070: (void) gettimeofday(&start_time,&tzp);
4071: curr_time=start_time;
4072: tm = *localtime(&start_time.tv_sec);
4073: tmg = *gmtime(&start_time.tv_sec);
4074: strcpy(strstart,asctime(&tm));
4075:
4076: /* printf("Localtime (at start)=%s",strstart); */
4077: /* tp.tv_sec = tp.tv_sec +86400; */
4078: /* tm = *localtime(&start_time.tv_sec); */
4079: /* tmg.tm_year=tmg.tm_year +dsign*dyear; */
4080: /* tmg.tm_mon=tmg.tm_mon +dsign*dmonth; */
4081: /* tmg.tm_hour=tmg.tm_hour + 1; */
4082: /* tp.tv_sec = mktime(&tmg); */
4083: /* strt=asctime(&tmg); */
4084: /* printf("Time(after) =%s",strstart); */
4085: /* (void) time (&time_value);
4086: * printf("time=%d,t-=%d\n",time_value,time_value-86400);
4087: * tm = *localtime(&time_value);
4088: * strstart=asctime(&tm);
4089: * printf("tim_value=%d,asctime=%s\n",time_value,strstart);
4090: */
4091:
4092: nberr=0; /* Number of errors and warnings */
4093: nbwarn=0;
4094: getcwd(pathcd, size);
4095:
4096: printf("\n%s\n%s",version,fullversion);
4097: if(argc <=1){
4098: printf("\nEnter the parameter file name: ");
4099: scanf("%s",pathtot);
4100: }
4101: else{
4102: strcpy(pathtot,argv[1]);
4103: }
4104: /*if(getcwd(pathcd, MAXLINE)!= NULL)printf ("Error pathcd\n");*/
4105: /*cygwin_split_path(pathtot,path,optionfile);
4106: printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/
4107: /* cutv(path,optionfile,pathtot,'\\');*/
4108:
4109: split(argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
4110: /* strcpy(pathimach,argv[0]); */
4111: split(pathtot,path,optionfile,optionfilext,optionfilefiname);
4112: printf("pathimach=%s, pathtot=%s,\npath=%s,\noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",pathimach,pathtot,path,optionfile,optionfilext,optionfilefiname);
4113: chdir(path);
4114: strcpy(command,"mkdir ");
4115: strcat(command,optionfilefiname);
4116: if((outcmd=system(command)) != 0){
4117: printf("Problem creating directory or it already exists %s%s, err=%d\n",path,optionfilefiname,outcmd);
4118: /* fprintf(ficlog,"Problem creating directory %s%s\n",path,optionfilefiname); */
4119: /* fclose(ficlog); */
4120: /* exit(1); */
4121: }
4122: /* if((imk=mkdir(optionfilefiname))<0){ */
4123: /* perror("mkdir"); */
4124: /* } */
4125:
4126: /*-------- arguments in the command line --------*/
4127:
4128: /* Log file */
4129: strcat(filelog, optionfilefiname);
4130: strcat(filelog,".log"); /* */
4131: if((ficlog=fopen(filelog,"w"))==NULL) {
4132: printf("Problem with logfile %s\n",filelog);
4133: goto end;
4134: }
4135: fprintf(ficlog,"Log filename:%s\n",filelog);
4136: fprintf(ficlog,"\n%s\n%s",version,fullversion);
4137: fprintf(ficlog,"\nEnter the parameter file name: \n");
4138: fprintf(ficlog,"pathimach=%s\npathtot=%s\n\
4139: path=%s \n\
4140: optionfile=%s\n\
4141: optionfilext=%s\n\
4142: optionfilefiname=%s\n",pathimach,pathtot,path,optionfile,optionfilext,optionfilefiname);
4143:
4144: printf("Local time (at start):%s",strstart);
4145: fprintf(ficlog,"Local time (at start): %s",strstart);
4146: fflush(ficlog);
4147: /* (void) gettimeofday(&curr_time,&tzp); */
4148: /* printf("Elapsed time %d\n", asc_diff_time(curr_time.tv_sec-start_time.tv_sec,tmpout)); */
4149:
4150: /* */
4151: strcpy(fileres,"r");
4152: strcat(fileres, optionfilefiname);
4153: strcat(fileres,".txt"); /* Other files have txt extension */
4154:
4155: /*---------arguments file --------*/
4156:
4157: if((ficpar=fopen(optionfile,"r"))==NULL) {
4158: printf("Problem with optionfile %s\n",optionfile);
4159: fprintf(ficlog,"Problem with optionfile %s\n",optionfile);
4160: fflush(ficlog);
4161: goto end;
4162: }
4163:
4164:
4165:
4166: strcpy(filereso,"o");
4167: strcat(filereso,fileres);
4168: if((ficparo=fopen(filereso,"w"))==NULL) { /* opened on subdirectory */
4169: printf("Problem with Output resultfile: %s\n", filereso);
4170: fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso);
4171: fflush(ficlog);
4172: goto end;
4173: }
4174:
4175: /* Reads comments: lines beginning with '#' */
4176: numlinepar=0;
4177: while((c=getc(ficpar))=='#' && c!= EOF){
4178: ungetc(c,ficpar);
4179: fgets(line, MAXLINE, ficpar);
4180: numlinepar++;
4181: puts(line);
4182: fputs(line,ficparo);
4183: fputs(line,ficlog);
4184: }
4185: ungetc(c,ficpar);
4186:
4187: 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);
4188: numlinepar++;
4189: 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);
4190: 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);
4191: 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);
4192: fflush(ficlog);
4193: while((c=getc(ficpar))=='#' && c!= EOF){
4194: ungetc(c,ficpar);
4195: fgets(line, MAXLINE, ficpar);
4196: numlinepar++;
4197: puts(line);
4198: fputs(line,ficparo);
4199: fputs(line,ficlog);
4200: }
4201: ungetc(c,ficpar);
4202:
4203:
4204: covar=matrix(0,NCOVMAX,1,n);
4205: cptcovn=0; /*Number of covariates, i.e. number of '+' in model statement*/
4206: if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;
4207:
4208: ncovmodel=2+cptcovn; /*Number of variables = cptcovn + intercept + age */
4209: nvar=ncovmodel-1; /* Suppressing age as a basic covariate */
4210: npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/
4211:
4212: delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
4213: delti=delti3[1][1];
4214: /*delti=vector(1,npar); *//* Scale of each paramater (output from hesscov)*/
4215: if(mle==-1){ /* Print a wizard for help writing covariance matrix */
4216: prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
4217: printf(" You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
4218: fprintf(ficlog," You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
4219: free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
4220: fclose (ficparo);
4221: fclose (ficlog);
4222: exit(0);
4223: }
4224: else if(mle==-3) {
4225: prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
4226: printf(" You choose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
4227: fprintf(ficlog," You choose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
4228: param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
4229: matcov=matrix(1,npar,1,npar);
4230: }
4231: else{
4232: /* Read guess parameters */
4233: /* Reads comments: lines beginning with '#' */
4234: while((c=getc(ficpar))=='#' && c!= EOF){
4235: ungetc(c,ficpar);
4236: fgets(line, MAXLINE, ficpar);
4237: numlinepar++;
4238: puts(line);
4239: fputs(line,ficparo);
4240: fputs(line,ficlog);
4241: }
4242: ungetc(c,ficpar);
4243:
4244: param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
4245: for(i=1; i <=nlstate; i++){
4246: j=0;
4247: for(jj=1; jj <=nlstate+ndeath; jj++){
4248: if(jj==i) continue;
4249: j++;
4250: fscanf(ficpar,"%1d%1d",&i1,&j1);
4251: if ((i1 != i) && (j1 != j)){
4252: printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n",numlinepar, i,j, i1, j1);
4253: exit(1);
4254: }
4255: fprintf(ficparo,"%1d%1d",i1,j1);
4256: if(mle==1)
4257: printf("%1d%1d",i,j);
4258: fprintf(ficlog,"%1d%1d",i,j);
4259: for(k=1; k<=ncovmodel;k++){
4260: fscanf(ficpar," %lf",¶m[i][j][k]);
4261: if(mle==1){
4262: printf(" %lf",param[i][j][k]);
4263: fprintf(ficlog," %lf",param[i][j][k]);
4264: }
4265: else
4266: fprintf(ficlog," %lf",param[i][j][k]);
4267: fprintf(ficparo," %lf",param[i][j][k]);
4268: }
4269: fscanf(ficpar,"\n");
4270: numlinepar++;
4271: if(mle==1)
4272: printf("\n");
4273: fprintf(ficlog,"\n");
4274: fprintf(ficparo,"\n");
4275: }
4276: }
4277: fflush(ficlog);
4278:
4279:
4280: p=param[1][1];
4281:
4282: /* Reads comments: lines beginning with '#' */
4283: while((c=getc(ficpar))=='#' && c!= EOF){
4284: ungetc(c,ficpar);
4285: fgets(line, MAXLINE, ficpar);
4286: numlinepar++;
4287: puts(line);
4288: fputs(line,ficparo);
4289: fputs(line,ficlog);
4290: }
4291: ungetc(c,ficpar);
4292:
4293: for(i=1; i <=nlstate; i++){
4294: for(j=1; j <=nlstate+ndeath-1; j++){
4295: fscanf(ficpar,"%1d%1d",&i1,&j1);
4296: if ((i1-i)*(j1-j)!=0){
4297: printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n",numlinepar, i,j, i1, j1);
4298: exit(1);
4299: }
4300: printf("%1d%1d",i,j);
4301: fprintf(ficparo,"%1d%1d",i1,j1);
4302: fprintf(ficlog,"%1d%1d",i1,j1);
4303: for(k=1; k<=ncovmodel;k++){
4304: fscanf(ficpar,"%le",&delti3[i][j][k]);
4305: printf(" %le",delti3[i][j][k]);
4306: fprintf(ficparo," %le",delti3[i][j][k]);
4307: fprintf(ficlog," %le",delti3[i][j][k]);
4308: }
4309: fscanf(ficpar,"\n");
4310: numlinepar++;
4311: printf("\n");
4312: fprintf(ficparo,"\n");
4313: fprintf(ficlog,"\n");
4314: }
4315: }
4316: fflush(ficlog);
4317:
4318: delti=delti3[1][1];
4319:
4320:
4321: /* free_ma3x(delti3,1,nlstate,1,nlstate+ndeath-1,1,ncovmodel); */ /* Hasn't to to freed here otherwise delti is no more allocated */
4322:
4323: /* Reads comments: lines beginning with '#' */
4324: while((c=getc(ficpar))=='#' && c!= EOF){
4325: ungetc(c,ficpar);
4326: fgets(line, MAXLINE, ficpar);
4327: numlinepar++;
4328: puts(line);
4329: fputs(line,ficparo);
4330: fputs(line,ficlog);
4331: }
4332: ungetc(c,ficpar);
4333:
4334: matcov=matrix(1,npar,1,npar);
4335: for(i=1; i <=npar; i++){
4336: fscanf(ficpar,"%s",&str);
4337: if(mle==1)
4338: printf("%s",str);
4339: fprintf(ficlog,"%s",str);
4340: fprintf(ficparo,"%s",str);
4341: for(j=1; j <=i; j++){
4342: fscanf(ficpar," %le",&matcov[i][j]);
4343: if(mle==1){
4344: printf(" %.5le",matcov[i][j]);
4345: }
4346: fprintf(ficlog," %.5le",matcov[i][j]);
4347: fprintf(ficparo," %.5le",matcov[i][j]);
4348: }
4349: fscanf(ficpar,"\n");
4350: numlinepar++;
4351: if(mle==1)
4352: printf("\n");
4353: fprintf(ficlog,"\n");
4354: fprintf(ficparo,"\n");
4355: }
4356: for(i=1; i <=npar; i++)
4357: for(j=i+1;j<=npar;j++)
4358: matcov[i][j]=matcov[j][i];
4359:
4360: if(mle==1)
4361: printf("\n");
4362: fprintf(ficlog,"\n");
4363:
4364: fflush(ficlog);
4365:
4366: /*-------- Rewriting parameter file ----------*/
4367: strcpy(rfileres,"r"); /* "Rparameterfile */
4368: strcat(rfileres,optionfilefiname); /* Parameter file first name*/
4369: strcat(rfileres,"."); /* */
4370: strcat(rfileres,optionfilext); /* Other files have txt extension */
4371: if((ficres =fopen(rfileres,"w"))==NULL) {
4372: printf("Problem writing new parameter file: %s\n", fileres);goto end;
4373: fprintf(ficlog,"Problem writing new parameter file: %s\n", fileres);goto end;
4374: }
4375: fprintf(ficres,"#%s\n",version);
4376: } /* End of mle != -3 */
4377:
4378: /*-------- data file ----------*/
4379: if((fic=fopen(datafile,"r"))==NULL) {
4380: printf("Problem with datafile: %s\n", datafile);goto end;
4381: fprintf(ficlog,"Problem with datafile: %s\n", datafile);goto end;
4382: }
4383:
4384: n= lastobs;
4385: severity = vector(1,maxwav);
4386: outcome=imatrix(1,maxwav+1,1,n);
4387: num=lvector(1,n);
4388: moisnais=vector(1,n);
4389: annais=vector(1,n);
4390: moisdc=vector(1,n);
4391: andc=vector(1,n);
4392: agedc=vector(1,n);
4393: cod=ivector(1,n);
4394: weight=vector(1,n);
4395: for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */
4396: mint=matrix(1,maxwav,1,n);
4397: anint=matrix(1,maxwav,1,n);
4398: s=imatrix(1,maxwav+1,1,n);
4399: tab=ivector(1,NCOVMAX);
4400: ncodemax=ivector(1,8);
4401:
4402: i=1;
4403: while (fgets(line, MAXLINE, fic) != NULL) {
4404: if ((i >= firstobs) && (i <=lastobs)) {
4405: for(j=0; line[j] != '\n';j++){ /* Untabifies line */
4406: if(line[j] == '\t')
4407: line[j] = ' ';
4408: }
4409: for (j=maxwav;j>=1;j--){
4410: cutv(stra, strb,line,' '); s[j][i]=atoi(strb);
4411: strcpy(line,stra);
4412: cutv(stra, strb,line,'/'); anint[j][i]=(double)(atoi(strb)); strcpy(line,stra);
4413: cutv(stra, strb,line,' '); mint[j][i]=(double)(atoi(strb)); strcpy(line,stra);
4414: }
4415:
4416: cutv(stra, strb,line,'/'); andc[i]=(double)(atoi(strb)); strcpy(line,stra);
4417: cutv(stra, strb,line,' '); moisdc[i]=(double)(atoi(strb)); strcpy(line,stra);
4418:
4419: cutv(stra, strb,line,'/'); annais[i]=(double)(atoi(strb)); strcpy(line,stra);
4420: cutv(stra, strb,line,' '); moisnais[i]=(double)(atoi(strb)); strcpy(line,stra);
4421:
4422: cutv(stra, strb,line,' '); weight[i]=(double)(atoi(strb)); strcpy(line,stra);
4423: for (j=ncovcol;j>=1;j--){
4424: cutv(stra, strb,line,' '); covar[j][i]=(double)(atoi(strb)); strcpy(line,stra);
4425: }
4426: lstra=strlen(stra);
4427: if(lstra > 9){ /* More than 2**32 or max of what printf can write with %ld */
4428: stratrunc = &(stra[lstra-9]);
4429: num[i]=atol(stratrunc);
4430: }
4431: else
4432: num[i]=atol(stra);
4433:
4434: /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){
4435: 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;}*/
4436:
4437: i=i+1;
4438: }
4439: }
4440: /* printf("ii=%d", ij);
4441: scanf("%d",i);*/
4442: imx=i-1; /* Number of individuals */
4443:
4444: /* for (i=1; i<=imx; i++){
4445: if ((s[1][i]==3) && (s[2][i]==2)) s[2][i]=3;
4446: if ((s[2][i]==3) && (s[3][i]==2)) s[3][i]=3;
4447: if ((s[3][i]==3) && (s[4][i]==2)) s[4][i]=3;
4448: }*/
4449: /* for (i=1; i<=imx; i++){
4450: if (s[4][i]==9) s[4][i]=-1;
4451: 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]));}*/
4452:
4453: for (i=1; i<=imx; i++)
4454:
4455: /*if ((s[3][i]==3) || (s[4][i]==3)) weight[i]=0.08;
4456: else weight[i]=1;*/
4457:
4458: /* Calculation of the number of parameter from char model*/
4459: Tvar=ivector(1,15); /* stores the number n of the covariates in Vm+Vn at 1 and m at 2 */
4460: Tprod=ivector(1,15);
4461: Tvaraff=ivector(1,15);
4462: Tvard=imatrix(1,15,1,2);
4463: Tage=ivector(1,15);
4464:
4465: if (strlen(model) >1){ /* If there is at least 1 covariate */
4466: j=0, j1=0, k1=1, k2=1;
4467: j=nbocc(model,'+'); /* j=Number of '+' */
4468: j1=nbocc(model,'*'); /* j1=Number of '*' */
4469: cptcovn=j+1;
4470: cptcovprod=j1; /*Number of products */
4471:
4472: strcpy(modelsav,model);
4473: if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){
4474: printf("Error. Non available option model=%s ",model);
4475: fprintf(ficlog,"Error. Non available option model=%s ",model);
4476: goto end;
4477: }
4478:
4479: /* This loop fills the array Tvar from the string 'model'.*/
4480:
4481: for(i=(j+1); i>=1;i--){
4482: cutv(stra,strb,modelsav,'+'); /* keeps in strb after the last + */
4483: if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyzes it */
4484: /* printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/
4485: /*scanf("%d",i);*/
4486: if (strchr(strb,'*')) { /* Model includes a product */
4487: cutv(strd,strc,strb,'*'); /* strd*strc Vm*Vn (if not *age)*/
4488: if (strcmp(strc,"age")==0) { /* Vn*age */
4489: cptcovprod--;
4490: cutv(strb,stre,strd,'V');
4491: Tvar[i]=atoi(stre); /* computes n in Vn and stores in Tvar*/
4492: cptcovage++;
4493: Tage[cptcovage]=i;
4494: /*printf("stre=%s ", stre);*/
4495: }
4496: else if (strcmp(strd,"age")==0) { /* or age*Vn */
4497: cptcovprod--;
4498: cutv(strb,stre,strc,'V');
4499: Tvar[i]=atoi(stre);
4500: cptcovage++;
4501: Tage[cptcovage]=i;
4502: }
4503: else { /* Age is not in the model */
4504: cutv(strb,stre,strc,'V'); /* strc= Vn, stre is n*/
4505: Tvar[i]=ncovcol+k1;
4506: cutv(strb,strc,strd,'V'); /* strd was Vm, strc is m */
4507: Tprod[k1]=i;
4508: Tvard[k1][1]=atoi(strc); /* m*/
4509: Tvard[k1][2]=atoi(stre); /* n */
4510: Tvar[cptcovn+k2]=Tvard[k1][1];
4511: Tvar[cptcovn+k2+1]=Tvard[k1][2];
4512: for (k=1; k<=lastobs;k++)
4513: covar[ncovcol+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];
4514: k1++;
4515: k2=k2+2;
4516: }
4517: }
4518: else { /* no more sum */
4519: /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/
4520: /* scanf("%d",i);*/
4521: cutv(strd,strc,strb,'V');
4522: Tvar[i]=atoi(strc);
4523: }
4524: strcpy(modelsav,stra);
4525: /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);
4526: scanf("%d",i);*/
4527: } /* end of loop + */
4528: } /* end model */
4529:
4530: /*The number n of Vn is stored in Tvar. cptcovage =number of age covariate. Tage gives the position of age. cptcovprod= number of products.
4531: If model=V1+V1*age then Tvar[1]=1 Tvar[2]=1 cptcovage=1 Tage[1]=2 cptcovprod=0*/
4532:
4533: /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);
4534: printf("cptcovprod=%d ", cptcovprod);
4535: fprintf(ficlog,"cptcovprod=%d ", cptcovprod);
4536:
4537: scanf("%d ",i);
4538: fclose(fic);*/
4539:
4540: /* if(mle==1){*/
4541: if (weightopt != 1) { /* Maximisation without weights*/
4542: for(i=1;i<=n;i++) weight[i]=1.0;
4543: }
4544: /*-calculation of age at interview from date of interview and age at death -*/
4545: agev=matrix(1,maxwav,1,imx);
4546:
4547: for (i=1; i<=imx; i++) {
4548: for(m=2; (m<= maxwav); m++) {
4549: if (((int)mint[m][i]== 99) && (s[m][i] <= nlstate)){
4550: anint[m][i]=9999;
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! 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);
4556: 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);
4557: s[m][i]=-1;
4558: }
4559: if((int)moisdc[i]==99 && (int)andc[i]!=9999 && s[m][i]>nlstate){
4560: nberr++;
4561: 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]);
4562: 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]);
4563: s[m][i]=-1; /* We prefer to skip it (and to skip it in version 0.8a1 too */
4564: }
4565: }
4566: }
4567:
4568: for (i=1; i<=imx; i++) {
4569: agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);
4570: for(m=firstpass; (m<= lastpass); m++){
4571: if(s[m][i] >0){
4572: if (s[m][i] >= nlstate+1) {
4573: if(agedc[i]>0)
4574: if((int)moisdc[i]!=99 && (int)andc[i]!=9999)
4575: agev[m][i]=agedc[i];
4576: /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/
4577: else {
4578: if ((int)andc[i]!=9999){
4579: nbwarn++;
4580: printf("Warning negative age at death: %ld line:%d\n",num[i],i);
4581: fprintf(ficlog,"Warning negative age at death: %ld line:%d\n",num[i],i);
4582: agev[m][i]=-1;
4583: }
4584: }
4585: }
4586: else if(s[m][i] !=9){ /* Standard case, age in fractional
4587: years but with the precision of a
4588: month */
4589: agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);
4590: if((int)mint[m][i]==99 || (int)anint[m][i]==9999)
4591: agev[m][i]=1;
4592: else if(agev[m][i] <agemin){
4593: agemin=agev[m][i];
4594: /*printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], agemin);*/
4595: }
4596: else if(agev[m][i] >agemax){
4597: agemax=agev[m][i];
4598: /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/
4599: }
4600: /*agev[m][i]=anint[m][i]-annais[i];*/
4601: /* agev[m][i] = age[i]+2*m;*/
4602: }
4603: else { /* =9 */
4604: agev[m][i]=1;
4605: s[m][i]=-1;
4606: }
4607: }
4608: else /*= 0 Unknown */
4609: agev[m][i]=1;
4610: }
4611:
4612: }
4613: for (i=1; i<=imx; i++) {
4614: for(m=firstpass; (m<=lastpass); m++){
4615: if (s[m][i] > (nlstate+ndeath)) {
4616: nberr++;
4617: 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);
4618: 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);
4619: goto end;
4620: }
4621: }
4622: }
4623:
4624: /*for (i=1; i<=imx; i++){
4625: for (m=firstpass; (m<lastpass); m++){
4626: printf("%ld %d %.lf %d %d\n", num[i],(covar[1][i]),agev[m][i],s[m][i],s[m+1][i]);
4627: }
4628:
4629: }*/
4630:
4631:
4632: printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);
4633: fprintf(ficlog,"Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);
4634:
4635: agegomp=(int)agemin;
4636: free_vector(severity,1,maxwav);
4637: free_imatrix(outcome,1,maxwav+1,1,n);
4638: free_vector(moisnais,1,n);
4639: free_vector(annais,1,n);
4640: /* free_matrix(mint,1,maxwav,1,n);
4641: free_matrix(anint,1,maxwav,1,n);*/
4642: free_vector(moisdc,1,n);
4643: free_vector(andc,1,n);
4644:
4645:
4646: wav=ivector(1,imx);
4647: dh=imatrix(1,lastpass-firstpass+1,1,imx);
4648: bh=imatrix(1,lastpass-firstpass+1,1,imx);
4649: mw=imatrix(1,lastpass-firstpass+1,1,imx);
4650:
4651: /* Concatenates waves */
4652: concatwav(wav, dh, bh, mw, s, agedc, agev, firstpass, lastpass, imx, nlstate, stepm);
4653:
4654: /* Routine tricode is to calculate cptcoveff (real number of unique covariates) and to associate covariable number and modality */
4655:
4656: Tcode=ivector(1,100);
4657: nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);
4658: ncodemax[1]=1;
4659: if (cptcovn > 0) tricode(Tvar,nbcode,imx);
4660:
4661: codtab=imatrix(1,100,1,10); /* Cross tabulation to get the order of
4662: the estimations*/
4663: h=0;
4664: m=pow(2,cptcoveff);
4665:
4666: for(k=1;k<=cptcoveff; k++){
4667: for(i=1; i <=(m/pow(2,k));i++){
4668: for(j=1; j <= ncodemax[k]; j++){
4669: for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){
4670: h++;
4671: if (h>m) h=1;codtab[h][k]=j;codtab[h][Tvar[k]]=j;
4672: /* printf("h=%d k=%d j=%d codtab[h][k]=%d tvar[k]=%d \n",h, k,j,codtab[h][k],Tvar[k]);*/
4673: }
4674: }
4675: }
4676: }
4677: /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]);
4678: codtab[1][2]=1;codtab[2][2]=2; */
4679: /* for(i=1; i <=m ;i++){
4680: for(k=1; k <=cptcovn; k++){
4681: printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);
4682: }
4683: printf("\n");
4684: }
4685: scanf("%d",i);*/
4686:
4687: /*------------ gnuplot -------------*/
4688: strcpy(optionfilegnuplot,optionfilefiname);
4689: if(mle==-3)
4690: strcat(optionfilegnuplot,"-mort");
4691: strcat(optionfilegnuplot,".gp");
4692:
4693: if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {
4694: printf("Problem with file %s",optionfilegnuplot);
4695: }
4696: else{
4697: fprintf(ficgp,"\n# %s\n", version);
4698: fprintf(ficgp,"# %s\n", optionfilegnuplot);
4699: fprintf(ficgp,"set missing 'NaNq'\n");
4700: }
4701: /* fclose(ficgp);*/
4702: /*--------- index.htm --------*/
4703:
4704: strcpy(optionfilehtm,optionfilefiname); /* Main html file */
4705: if(mle==-3)
4706: strcat(optionfilehtm,"-mort");
4707: strcat(optionfilehtm,".htm");
4708: if((fichtm=fopen(optionfilehtm,"w"))==NULL) {
4709: printf("Problem with %s \n",optionfilehtm), exit(0);
4710: }
4711:
4712: strcpy(optionfilehtmcov,optionfilefiname); /* Only for matrix of covariance */
4713: strcat(optionfilehtmcov,"-cov.htm");
4714: if((fichtmcov=fopen(optionfilehtmcov,"w"))==NULL) {
4715: printf("Problem with %s \n",optionfilehtmcov), exit(0);
4716: }
4717: else{
4718: fprintf(fichtmcov,"<body>\n<title>IMaCh Cov %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: fileres,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);
4722: }
4723:
4724: fprintf(fichtm,"<body>\n<title>IMaCh %s</title>\n <font size=\"2\">%s <br> %s</font> \
4725: <hr size=\"2\" color=\"#EC5E5E\"> \n\
4726: Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n\
4727: \n\
4728: <hr size=\"2\" color=\"#EC5E5E\">\
4729: <ul><li><h4>Parameter files</h4>\n\
4730: - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n\
4731: - Log file of the run: <a href=\"%s\">%s</a><br>\n\
4732: - Gnuplot file name: <a href=\"%s\">%s</a><br>\n\
4733: - Date and time at start: %s</ul>\n",\
4734: fileres,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model,\
4735: fileres,fileres,\
4736: filelog,filelog,optionfilegnuplot,optionfilegnuplot,strstart);
4737: fflush(fichtm);
4738:
4739: strcpy(pathr,path);
4740: strcat(pathr,optionfilefiname);
4741: chdir(optionfilefiname); /* Move to directory named optionfile */
4742:
4743: /* Calculates basic frequencies. Computes observed prevalence at single age
4744: and prints on file fileres'p'. */
4745: freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint);
4746:
4747: fprintf(fichtm,"\n");
4748: fprintf(fichtm,"<br>Total number of observations=%d <br>\n\
4749: Youngest age at first (selected) pass %.2f, oldest age %.2f<br>\n\
4750: Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n",\
4751: imx,agemin,agemax,jmin,jmax,jmean);
4752: pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
4753: oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
4754: newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
4755: savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
4756: oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */
4757:
4758:
4759: /* For Powell, parameters are in a vector p[] starting at p[1]
4760: so we point p on param[1][1] so that p[1] maps on param[1][1][1] */
4761: p=param[1][1]; /* *(*(*(param +1)+1)+0) */
4762:
4763: globpr=0; /* To get the number ipmx of contributions and the sum of weights*/
4764: if (mle==-3){
4765: ximort=matrix(1,NDIM,1,NDIM);
4766: cens=ivector(1,n);
4767: ageexmed=vector(1,n);
4768: agecens=vector(1,n);
4769: dcwave=ivector(1,n);
4770:
4771: for (i=1; i<=imx; i++){
4772: dcwave[i]=-1;
4773: for (j=1; j<=lastpass; j++)
4774: if (s[j][i]>nlstate) {
4775: dcwave[i]=j;
4776: /* printf("i=%d j=%d s=%d dcwave=%d\n",i,j, s[j][i],dcwave[i]);*/
4777: break;
4778: }
4779: }
4780:
4781: for (i=1; i<=imx; i++) {
4782: if (wav[i]>0){
4783: ageexmed[i]=agev[mw[1][i]][i];
4784: j=wav[i];agecens[i]=1.;
4785: if (ageexmed[i]>1 & wav[i]>0) agecens[i]=agev[mw[j][i]][i];
4786: cens[i]=1;
4787:
4788: if (ageexmed[i]<1) cens[i]=-1;
4789: if (agedc[i]< AGESUP & agedc[i]>1 & dcwave[i]>firstpass & dcwave[i]<=lastpass) cens[i]=0 ;
4790: }
4791: else cens[i]=-1;
4792: }
4793:
4794: for (i=1;i<=NDIM;i++) {
4795: for (j=1;j<=NDIM;j++)
4796: ximort[i][j]=(i == j ? 1.0 : 0.0);
4797: }
4798:
4799: p[1]=0.1; p[2]=0.1;
4800: /*printf("%lf %lf", p[1], p[2]);*/
4801:
4802:
4803: printf("Powell\n"); fprintf(ficlog,"Powell\n");
4804: strcpy(filerespow,"pow-mort");
4805: strcat(filerespow,fileres);
4806: if((ficrespow=fopen(filerespow,"w"))==NULL) {
4807: printf("Problem with resultfile: %s\n", filerespow);
4808: fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
4809: }
4810: fprintf(ficrespow,"# Powell\n# iter -2*LL");
4811: /* for (i=1;i<=nlstate;i++)
4812: for(j=1;j<=nlstate+ndeath;j++)
4813: if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
4814: */
4815: fprintf(ficrespow,"\n");
4816:
4817: powell(p,ximort,NDIM,ftol,&iter,&fret,gompertz);
4818: fclose(ficrespow);
4819:
4820: hesscov(matcov, p, NDIM,delti, 1e-4, gompertz);
4821:
4822: for(i=1; i <=NDIM; i++)
4823: for(j=i+1;j<=NDIM;j++)
4824: matcov[i][j]=matcov[j][i];
4825:
4826: printf("\nCovariance matrix\n ");
4827: for(i=1; i <=NDIM; i++) {
4828: for(j=1;j<=NDIM;j++){
4829: printf("%f ",matcov[i][j]);
4830: }
4831: printf("\n ");
4832: }
4833:
4834: printf("iter=%d MLE=%f Eq=%lf*exp(%lf*(age-%d))\n",iter,-gompertz(p),p[1],p[2],agegomp);
4835: for (i=1;i<=NDIM;i++)
4836: printf("%f [%f ; %f]\n",p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
4837: replace_back_to_slash(pathc,path); /* Even gnuplot wants a / */
4838: printinggnuplotmort(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
4839:
4840: printinghtmlmort(fileres,title,datafile, firstpass, lastpass, \
4841: stepm, weightopt,\
4842: model,imx,p,matcov);
4843: } /* Endof if mle==-3 */
4844:
4845: else{ /* For mle >=1 */
4846:
4847: likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
4848: printf("First 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: globpr=1; /* to print the contributions */
4853: likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
4854: printf("Second Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
4855: for (k=1; k<=npar;k++)
4856: printf(" %d %8.5f",k,p[k]);
4857: printf("\n");
4858: if(mle>=1){ /* Could be 1 or 2 */
4859: mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);
4860: }
4861:
4862: /*--------- results files --------------*/
4863: 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);
4864:
4865:
4866: fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
4867: printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
4868: fprintf(ficlog,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
4869: for(i=1,jk=1; i <=nlstate; i++){
4870: for(k=1; k <=(nlstate+ndeath); k++){
4871: if (k != i) {
4872: printf("%d%d ",i,k);
4873: fprintf(ficlog,"%d%d ",i,k);
4874: fprintf(ficres,"%1d%1d ",i,k);
4875: for(j=1; j <=ncovmodel; j++){
4876: printf("%f ",p[jk]);
4877: fprintf(ficlog,"%f ",p[jk]);
4878: fprintf(ficres,"%f ",p[jk]);
4879: jk++;
4880: }
4881: printf("\n");
4882: fprintf(ficlog,"\n");
4883: fprintf(ficres,"\n");
4884: }
4885: }
4886: }
4887: if(mle!=0){
4888: /* Computing hessian and covariance matrix */
4889: ftolhess=ftol; /* Usually correct */
4890: hesscov(matcov, p, npar, delti, ftolhess, func);
4891: }
4892: fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");
4893: printf("# Scales (for hessian or gradient estimation)\n");
4894: fprintf(ficlog,"# Scales (for hessian or gradient estimation)\n");
4895: for(i=1,jk=1; i <=nlstate; i++){
4896: for(j=1; j <=nlstate+ndeath; j++){
4897: if (j!=i) {
4898: fprintf(ficres,"%1d%1d",i,j);
4899: printf("%1d%1d",i,j);
4900: fprintf(ficlog,"%1d%1d",i,j);
4901: for(k=1; k<=ncovmodel;k++){
4902: printf(" %.5e",delti[jk]);
4903: fprintf(ficlog," %.5e",delti[jk]);
4904: fprintf(ficres," %.5e",delti[jk]);
4905: jk++;
4906: }
4907: printf("\n");
4908: fprintf(ficlog,"\n");
4909: fprintf(ficres,"\n");
4910: }
4911: }
4912: }
4913:
4914: 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");
4915: if(mle>=1)
4916: 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");
4917: 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");
4918: /* # 121 Var(a12)\n\ */
4919: /* # 122 Cov(b12,a12) Var(b12)\n\ */
4920: /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
4921: /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
4922: /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
4923: /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
4924: /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
4925: /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
4926:
4927:
4928: /* Just to have a covariance matrix which will be more understandable
4929: even is we still don't want to manage dictionary of variables
4930: */
4931: for(itimes=1;itimes<=2;itimes++){
4932: jj=0;
4933: for(i=1; i <=nlstate; i++){
4934: for(j=1; j <=nlstate+ndeath; j++){
4935: if(j==i) continue;
4936: for(k=1; k<=ncovmodel;k++){
4937: jj++;
4938: ca[0]= k+'a'-1;ca[1]='\0';
4939: if(itimes==1){
4940: if(mle>=1)
4941: printf("#%1d%1d%d",i,j,k);
4942: fprintf(ficlog,"#%1d%1d%d",i,j,k);
4943: fprintf(ficres,"#%1d%1d%d",i,j,k);
4944: }else{
4945: if(mle>=1)
4946: printf("%1d%1d%d",i,j,k);
4947: fprintf(ficlog,"%1d%1d%d",i,j,k);
4948: fprintf(ficres,"%1d%1d%d",i,j,k);
4949: }
4950: ll=0;
4951: for(li=1;li <=nlstate; li++){
4952: for(lj=1;lj <=nlstate+ndeath; lj++){
4953: if(lj==li) continue;
4954: for(lk=1;lk<=ncovmodel;lk++){
4955: ll++;
4956: if(ll<=jj){
4957: cb[0]= lk +'a'-1;cb[1]='\0';
4958: if(ll<jj){
4959: if(itimes==1){
4960: if(mle>=1)
4961: printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
4962: fprintf(ficlog," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
4963: fprintf(ficres," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
4964: }else{
4965: if(mle>=1)
4966: printf(" %.5e",matcov[jj][ll]);
4967: fprintf(ficlog," %.5e",matcov[jj][ll]);
4968: fprintf(ficres," %.5e",matcov[jj][ll]);
4969: }
4970: }else{
4971: if(itimes==1){
4972: if(mle>=1)
4973: printf(" Var(%s%1d%1d)",ca,i,j);
4974: fprintf(ficlog," Var(%s%1d%1d)",ca,i,j);
4975: fprintf(ficres," Var(%s%1d%1d)",ca,i,j);
4976: }else{
4977: if(mle>=1)
4978: printf(" %.5e",matcov[jj][ll]);
4979: fprintf(ficlog," %.5e",matcov[jj][ll]);
4980: fprintf(ficres," %.5e",matcov[jj][ll]);
4981: }
4982: }
4983: }
4984: } /* end lk */
4985: } /* end lj */
4986: } /* end li */
4987: if(mle>=1)
4988: printf("\n");
4989: fprintf(ficlog,"\n");
4990: fprintf(ficres,"\n");
4991: numlinepar++;
4992: } /* end k*/
4993: } /*end j */
4994: } /* end i */
4995: } /* end itimes */
4996:
4997: fflush(ficlog);
4998: fflush(ficres);
4999:
5000: while((c=getc(ficpar))=='#' && c!= EOF){
5001: ungetc(c,ficpar);
5002: fgets(line, MAXLINE, ficpar);
5003: puts(line);
5004: fputs(line,ficparo);
5005: }
5006: ungetc(c,ficpar);
5007:
5008: estepm=0;
5009: fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm);
5010: if (estepm==0 || estepm < stepm) estepm=stepm;
5011: if (fage <= 2) {
5012: bage = ageminpar;
5013: fage = agemaxpar;
5014: }
5015:
5016: fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");
5017: fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
5018: fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
5019:
5020: while((c=getc(ficpar))=='#' && c!= EOF){
5021: ungetc(c,ficpar);
5022: fgets(line, MAXLINE, ficpar);
5023: puts(line);
5024: fputs(line,ficparo);
5025: }
5026: ungetc(c,ficpar);
5027:
5028: 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);
5029: 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);
5030: 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);
5031: printf("begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
5032: 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);
5033:
5034: while((c=getc(ficpar))=='#' && c!= EOF){
5035: ungetc(c,ficpar);
5036: fgets(line, MAXLINE, ficpar);
5037: puts(line);
5038: fputs(line,ficparo);
5039: }
5040: ungetc(c,ficpar);
5041:
5042:
5043: dateprev1=anprev1+(mprev1-1)/12.+(jprev1-1)/365.;
5044: dateprev2=anprev2+(mprev2-1)/12.+(jprev2-1)/365.;
5045:
5046: fscanf(ficpar,"pop_based=%d\n",&popbased);
5047: fprintf(ficparo,"pop_based=%d\n",popbased);
5048: fprintf(ficres,"pop_based=%d\n",popbased);
5049:
5050: while((c=getc(ficpar))=='#' && c!= EOF){
5051: ungetc(c,ficpar);
5052: fgets(line, MAXLINE, ficpar);
5053: puts(line);
5054: fputs(line,ficparo);
5055: }
5056: ungetc(c,ficpar);
5057:
5058: 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);
5059: 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);
5060: 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);
5061: 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);
5062: 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);
5063: /* day and month of proj2 are not used but only year anproj2.*/
5064:
5065:
5066:
5067: /* freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint);*/
5068: /*,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
5069:
5070: replace_back_to_slash(pathc,path); /* Even gnuplot wants a / */
5071: printinggnuplot(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
5072:
5073: printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,\
5074: model,imx,jmin,jmax,jmean,rfileres,popforecast,estepm,\
5075: jprev1,mprev1,anprev1,jprev2,mprev2,anprev2);
5076:
5077: /*------------ free_vector -------------*/
5078: /* chdir(path); */
5079:
5080: free_ivector(wav,1,imx);
5081: free_imatrix(dh,1,lastpass-firstpass+1,1,imx);
5082: free_imatrix(bh,1,lastpass-firstpass+1,1,imx);
5083: free_imatrix(mw,1,lastpass-firstpass+1,1,imx);
5084: free_lvector(num,1,n);
5085: free_vector(agedc,1,n);
5086: /*free_matrix(covar,0,NCOVMAX,1,n);*/
5087: /*free_matrix(covar,1,NCOVMAX,1,n);*/
5088: fclose(ficparo);
5089: fclose(ficres);
5090:
5091:
5092: /*--------------- Prevalence limit (stable prevalence) --------------*/
5093:
5094: strcpy(filerespl,"pl");
5095: strcat(filerespl,fileres);
5096: if((ficrespl=fopen(filerespl,"w"))==NULL) {
5097: printf("Problem with stable prevalence resultfile: %s\n", filerespl);goto end;
5098: fprintf(ficlog,"Problem with stable prevalence resultfile: %s\n", filerespl);goto end;
5099: }
5100: printf("Computing stable prevalence: result on file '%s' \n", filerespl);
5101: fprintf(ficlog,"Computing stable prevalence: result on file '%s' \n", filerespl);
5102: fprintf(ficrespl,"#Stable prevalence \n");
5103: fprintf(ficrespl,"#Age ");
5104: for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);
5105: fprintf(ficrespl,"\n");
5106:
5107: prlim=matrix(1,nlstate,1,nlstate);
5108:
5109: agebase=ageminpar;
5110: agelim=agemaxpar;
5111: ftolpl=1.e-10;
5112: i1=cptcoveff;
5113: if (cptcovn < 1){i1=1;}
5114:
5115: for(cptcov=1,k=0;cptcov<=i1;cptcov++){
5116: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
5117: k=k+1;
5118: /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/
5119: fprintf(ficrespl,"\n#******");
5120: printf("\n#******");
5121: fprintf(ficlog,"\n#******");
5122: for(j=1;j<=cptcoveff;j++) {
5123: fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
5124: printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
5125: fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
5126: }
5127: fprintf(ficrespl,"******\n");
5128: printf("******\n");
5129: fprintf(ficlog,"******\n");
5130:
5131: for (age=agebase; age<=agelim; age++){
5132: prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
5133: fprintf(ficrespl,"%.0f ",age );
5134: for(j=1;j<=cptcoveff;j++)
5135: fprintf(ficrespl,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
5136: for(i=1; i<=nlstate;i++)
5137: fprintf(ficrespl," %.5f", prlim[i][i]);
5138: fprintf(ficrespl,"\n");
5139: }
5140: }
5141: }
5142: fclose(ficrespl);
5143:
5144: /*------------- h Pij x at various ages ------------*/
5145:
5146: strcpy(filerespij,"pij"); strcat(filerespij,fileres);
5147: if((ficrespij=fopen(filerespij,"w"))==NULL) {
5148: printf("Problem with Pij resultfile: %s\n", filerespij);goto end;
5149: fprintf(ficlog,"Problem with Pij resultfile: %s\n", filerespij);goto end;
5150: }
5151: printf("Computing pij: result on file '%s' \n", filerespij);
5152: fprintf(ficlog,"Computing pij: result on file '%s' \n", filerespij);
5153:
5154: stepsize=(int) (stepm+YEARM-1)/YEARM;
5155: /*if (stepm<=24) stepsize=2;*/
5156:
5157: agelim=AGESUP;
5158: hstepm=stepsize*YEARM; /* Every year of age */
5159: hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */
5160:
5161: /* hstepm=1; aff par mois*/
5162:
5163: fprintf(ficrespij,"#****** h Pij x Probability to be in state j at age x+h being in i at x ");
5164: for(cptcov=1,k=0;cptcov<=i1;cptcov++){
5165: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
5166: k=k+1;
5167: fprintf(ficrespij,"\n#****** ");
5168: for(j=1;j<=cptcoveff;j++)
5169: fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
5170: fprintf(ficrespij,"******\n");
5171:
5172: for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */
5173: nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
5174: nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
5175:
5176: /* nhstepm=nhstepm*YEARM; aff par mois*/
5177:
5178: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
5179: oldm=oldms;savm=savms;
5180: hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
5181: fprintf(ficrespij,"# Cov Agex agex+h hpijx with i,j=");
5182: for(i=1; i<=nlstate;i++)
5183: for(j=1; j<=nlstate+ndeath;j++)
5184: fprintf(ficrespij," %1d-%1d",i,j);
5185: fprintf(ficrespij,"\n");
5186: for (h=0; h<=nhstepm; h++){
5187: fprintf(ficrespij,"%d %3.f %3.f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );
5188: for(i=1; i<=nlstate;i++)
5189: for(j=1; j<=nlstate+ndeath;j++)
5190: fprintf(ficrespij," %.5f", p3mat[i][j][h]);
5191: fprintf(ficrespij,"\n");
5192: }
5193: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
5194: fprintf(ficrespij,"\n");
5195: }
5196: }
5197: }
5198:
5199: varprob(optionfilefiname, matcov, p, delti, nlstate, bage, fage,k,Tvar,nbcode, ncodemax);
5200:
5201: fclose(ficrespij);
5202:
5203: probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
5204: for(i=1;i<=AGESUP;i++)
5205: for(j=1;j<=NCOVMAX;j++)
5206: for(k=1;k<=NCOVMAX;k++)
5207: probs[i][j][k]=0.;
5208:
5209: /*---------- Forecasting ------------------*/
5210: /*if((stepm == 1) && (strcmp(model,".")==0)){*/
5211: if(prevfcast==1){
5212: /* if(stepm ==1){*/
5213: prevforecast(fileres, anproj1, mproj1, jproj1, agemin, agemax, dateprev1, dateprev2, mobilavproj, bage, fage, firstpass, lastpass, anproj2, p, cptcoveff);
5214: /* (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);*/
5215: /* } */
5216: /* else{ */
5217: /* erreur=108; */
5218: /* 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); */
5219: /* 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); */
5220: /* } */
5221: }
5222:
5223:
5224: /*---------- Health expectancies and variances ------------*/
5225:
5226: strcpy(filerest,"t");
5227: strcat(filerest,fileres);
5228: if((ficrest=fopen(filerest,"w"))==NULL) {
5229: printf("Problem with total LE resultfile: %s\n", filerest);goto end;
5230: fprintf(ficlog,"Problem with total LE resultfile: %s\n", filerest);goto end;
5231: }
5232: printf("Computing Total LEs with variances: file '%s' \n", filerest);
5233: fprintf(ficlog,"Computing Total LEs with variances: file '%s' \n", filerest);
5234:
5235:
5236: strcpy(filerese,"e");
5237: strcat(filerese,fileres);
5238: if((ficreseij=fopen(filerese,"w"))==NULL) {
5239: printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
5240: fprintf(ficlog,"Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
5241: }
5242: printf("Computing Health Expectancies: result on file '%s' \n", filerese);
5243: fprintf(ficlog,"Computing Health Expectancies: result on file '%s' \n", filerese);
5244:
5245: strcpy(fileresv,"v");
5246: strcat(fileresv,fileres);
5247: if((ficresvij=fopen(fileresv,"w"))==NULL) {
5248: printf("Problem with variance resultfile: %s\n", fileresv);exit(0);
5249: fprintf(ficlog,"Problem with variance resultfile: %s\n", fileresv);exit(0);
5250: }
5251: printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
5252: fprintf(ficlog,"Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
5253:
5254: /* Computes prevalence between agemin (i.e minimal age computed) and no more ageminpar */
5255: prevalence(probs, agemin, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
5256: /* 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",\
5257: ageminpar, agemax, s[lastpass][imx], agev[lastpass][imx], nlstate, imx, mint[lastpass][imx],anint[lastpass][imx], dateprev1, dateprev2, firstpass, lastpass);
5258: */
5259:
5260: if (mobilav!=0) {
5261: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
5262: if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
5263: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
5264: printf(" Error in movingaverage mobilav=%d\n",mobilav);
5265: }
5266: }
5267:
5268: for(cptcov=1,k=0;cptcov<=i1;cptcov++){
5269: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
5270: k=k+1;
5271: fprintf(ficrest,"\n#****** ");
5272: for(j=1;j<=cptcoveff;j++)
5273: fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
5274: fprintf(ficrest,"******\n");
5275:
5276: fprintf(ficreseij,"\n#****** ");
5277: for(j=1;j<=cptcoveff;j++)
5278: fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
5279: fprintf(ficreseij,"******\n");
5280:
5281: fprintf(ficresvij,"\n#****** ");
5282: for(j=1;j<=cptcoveff;j++)
5283: fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
5284: fprintf(ficresvij,"******\n");
5285:
5286: eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
5287: oldm=oldms;savm=savms;
5288: evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov);
5289:
5290: vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
5291: oldm=oldms;savm=savms;
5292: varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,0, mobilav);
5293: if(popbased==1){
5294: varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,popbased,mobilav);
5295: }
5296:
5297:
5298: fprintf(ficrest,"#Total LEs with variances: e.. (std) ");
5299: for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);
5300: fprintf(ficrest,"\n");
5301:
5302: epj=vector(1,nlstate+1);
5303: for(age=bage; age <=fage ;age++){
5304: prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
5305: if (popbased==1) {
5306: if(mobilav ==0){
5307: for(i=1; i<=nlstate;i++)
5308: prlim[i][i]=probs[(int)age][i][k];
5309: }else{ /* mobilav */
5310: for(i=1; i<=nlstate;i++)
5311: prlim[i][i]=mobaverage[(int)age][i][k];
5312: }
5313: }
5314:
5315: fprintf(ficrest," %4.0f",age);
5316: for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){
5317: for(i=1, epj[j]=0.;i <=nlstate;i++) {
5318: epj[j] += prlim[i][i]*eij[i][j][(int)age];
5319: /* printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/
5320: }
5321: epj[nlstate+1] +=epj[j];
5322: }
5323:
5324: for(i=1, vepp=0.;i <=nlstate;i++)
5325: for(j=1;j <=nlstate;j++)
5326: vepp += vareij[i][j][(int)age];
5327: fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));
5328: for(j=1;j <=nlstate;j++){
5329: fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));
5330: }
5331: fprintf(ficrest,"\n");
5332: }
5333: free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
5334: free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);
5335: free_vector(epj,1,nlstate+1);
5336: }
5337: }
5338: free_vector(weight,1,n);
5339: free_imatrix(Tvard,1,15,1,2);
5340: free_imatrix(s,1,maxwav+1,1,n);
5341: free_matrix(anint,1,maxwav,1,n);
5342: free_matrix(mint,1,maxwav,1,n);
5343: free_ivector(cod,1,n);
5344: free_ivector(tab,1,NCOVMAX);
5345: fclose(ficreseij);
5346: fclose(ficresvij);
5347: fclose(ficrest);
5348: fclose(ficpar);
5349:
5350: /*------- Variance of stable prevalence------*/
5351:
5352: strcpy(fileresvpl,"vpl");
5353: strcat(fileresvpl,fileres);
5354: if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {
5355: printf("Problem with variance of stable prevalence resultfile: %s\n", fileresvpl);
5356: exit(0);
5357: }
5358: printf("Computing Variance-covariance of stable prevalence: file '%s' \n", fileresvpl);
5359:
5360: for(cptcov=1,k=0;cptcov<=i1;cptcov++){
5361: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
5362: k=k+1;
5363: fprintf(ficresvpl,"\n#****** ");
5364: for(j=1;j<=cptcoveff;j++)
5365: fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
5366: fprintf(ficresvpl,"******\n");
5367:
5368: varpl=matrix(1,nlstate,(int) bage, (int) fage);
5369: oldm=oldms;savm=savms;
5370: varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);
5371: free_matrix(varpl,1,nlstate,(int) bage, (int)fage);
5372: }
5373: }
5374:
5375: fclose(ficresvpl);
5376:
5377: /*---------- End : free ----------------*/
5378: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
5379: free_ma3x(probs,1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
5380:
5381: } /* mle==-3 arrives here for freeing */
5382: free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);
5383: free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);
5384: free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);
5385: free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);
5386:
5387: free_matrix(covar,0,NCOVMAX,1,n);
5388: free_matrix(matcov,1,npar,1,npar);
5389: /*free_vector(delti,1,npar);*/
5390: free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
5391: free_matrix(agev,1,maxwav,1,imx);
5392: free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
5393:
5394: free_ivector(ncodemax,1,8);
5395: free_ivector(Tvar,1,15);
5396: free_ivector(Tprod,1,15);
5397: free_ivector(Tvaraff,1,15);
5398: free_ivector(Tage,1,15);
5399: free_ivector(Tcode,1,100);
5400:
5401:
5402: fflush(fichtm);
5403: fflush(ficgp);
5404:
5405:
5406: if((nberr >0) || (nbwarn>0)){
5407: printf("End of Imach with %d errors and/or %d warnings\n",nberr,nbwarn);
5408: fprintf(ficlog,"End of Imach with %d errors and/or warnings %d\n",nberr,nbwarn);
5409: }else{
5410: printf("End of Imach\n");
5411: fprintf(ficlog,"End of Imach\n");
5412: }
5413: printf("See log file on %s\n",filelog);
5414: /* gettimeofday(&end_time, (struct timezone*)0);*/ /* after time */
5415: (void) gettimeofday(&end_time,&tzp);
5416: tm = *localtime(&end_time.tv_sec);
5417: tmg = *gmtime(&end_time.tv_sec);
5418: strcpy(strtend,asctime(&tm));
5419: printf("Local time at start %s\nLocaltime at end %s",strstart, strtend);
5420: fprintf(ficlog,"Local time at start %s\nLocal time at end %s\n",strstart, strtend);
5421: printf("Total time used %s\n", asc_diff_time(end_time.tv_sec -start_time.tv_sec,tmpout));
5422:
5423: printf("Total time was %d Sec.\n", end_time.tv_sec -start_time.tv_sec);
5424: fprintf(ficlog,"Total time used %s\n", asc_diff_time(end_time.tv_sec -start_time.tv_sec,tmpout));
5425: fprintf(ficlog,"Total time was %d Sec.\n", end_time.tv_sec -start_time.tv_sec);
5426: /* printf("Total time was %d uSec.\n", total_usecs);*/
5427: /* if(fileappend(fichtm,optionfilehtm)){ */
5428: fprintf(fichtm,"<br>Local time at start %s<br>Local time at end %s<br>",strstart, strtend);
5429: fclose(fichtm);
5430: fclose(fichtmcov);
5431: fclose(ficgp);
5432: fclose(ficlog);
5433: /*------ End -----------*/
5434:
5435: chdir(path);
5436: strcpy(plotcmd,"\"");
5437: strcat(plotcmd,pathimach);
5438: strcat(plotcmd,GNUPLOTPROGRAM);
5439: strcat(plotcmd,"\"");
5440: strcat(plotcmd," ");
5441: strcat(plotcmd,optionfilegnuplot);
5442: printf("Starting graphs with: %s",plotcmd);fflush(stdout);
5443: if((outcmd=system(plotcmd)) != 0){
5444: printf(" Problem with gnuplot\n");
5445: }
5446: printf(" Wait...");
5447: while (z[0] != 'q') {
5448: /* chdir(path); */
5449: printf("\nType e to edit output files, g to graph again and q for exiting: ");
5450: scanf("%s",z);
5451: /* if (z[0] == 'c') system("./imach"); */
5452: if (z[0] == 'e') {
5453: printf("Starting browser with: %s",optionfilehtm);fflush(stdout);
5454: system(optionfilehtm);
5455: }
5456: else if (z[0] == 'g') system(plotcmd);
5457: else if (z[0] == 'q') exit(0);
5458: }
5459: end:
5460: while (z[0] != 'q') {
5461: printf("\nType q for exiting: ");
5462: scanf("%s",z);
5463: }
5464: }
5465:
5466:
5467:
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