1: /* $Id: imach.c,v 1.116 2006/03/06 10:29:27 brouard Exp $
2: $State: Exp $
3: $Log: imach.c,v $
4: Revision 1.116 2006/03/06 10:29:27 brouard
5: (Module): Variance-covariance wrong links and
6: varian-covariance of ej. is needed (Saito).
7:
8: Revision 1.115 2006/02/27 12:17:45 brouard
9: (Module): One freematrix added in mlikeli! 0.98c
10:
11: Revision 1.114 2006/02/26 12:57:58 brouard
12: (Module): Some improvements in processing parameter
13: filename with strsep.
14:
15: Revision 1.113 2006/02/24 14:20:24 brouard
16: (Module): Memory leaks checks with valgrind and:
17: datafile was not closed, some imatrix were not freed and on matrix
18: allocation too.
19:
20: Revision 1.112 2006/01/30 09:55:26 brouard
21: (Module): Back to gnuplot.exe instead of wgnuplot.exe
22:
23: Revision 1.111 2006/01/25 20:38:18 brouard
24: (Module): Lots of cleaning and bugs added (Gompertz)
25: (Module): Comments can be added in data file. Missing date values
26: can be a simple dot '.'.
27:
28: Revision 1.110 2006/01/25 00:51:50 brouard
29: (Module): Lots of cleaning and bugs added (Gompertz)
30:
31: Revision 1.109 2006/01/24 19:37:15 brouard
32: (Module): Comments (lines starting with a #) are allowed in data.
33:
34: Revision 1.108 2006/01/19 18:05:42 lievre
35: Gnuplot problem appeared...
36: To be fixed
37:
38: Revision 1.107 2006/01/19 16:20:37 brouard
39: Test existence of gnuplot in imach path
40:
41: Revision 1.106 2006/01/19 13:24:36 brouard
42: Some cleaning and links added in html output
43:
44: Revision 1.105 2006/01/05 20:23:19 lievre
45: *** empty log message ***
46:
47: Revision 1.104 2005/09/30 16:11:43 lievre
48: (Module): sump fixed, loop imx fixed, and simplifications.
49: (Module): If the status is missing at the last wave but we know
50: that the person is alive, then we can code his/her status as -2
51: (instead of missing=-1 in earlier versions) and his/her
52: contributions to the likelihood is 1 - Prob of dying from last
53: health status (= 1-p13= p11+p12 in the easiest case of somebody in
54: the healthy state at last known wave). Version is 0.98
55:
56: Revision 1.103 2005/09/30 15:54:49 lievre
57: (Module): sump fixed, loop imx fixed, and simplifications.
58:
59: Revision 1.102 2004/09/15 17:31:30 brouard
60: Add the possibility to read data file including tab characters.
61:
62: Revision 1.101 2004/09/15 10:38:38 brouard
63: Fix on curr_time
64:
65: Revision 1.100 2004/07/12 18:29:06 brouard
66: Add version for Mac OS X. Just define UNIX in Makefile
67:
68: Revision 1.99 2004/06/05 08:57:40 brouard
69: *** empty log message ***
70:
71: Revision 1.98 2004/05/16 15:05:56 brouard
72: New version 0.97 . First attempt to estimate force of mortality
73: directly from the data i.e. without the need of knowing the health
74: state at each age, but using a Gompertz model: log u =a + b*age .
75: This is the basic analysis of mortality and should be done before any
76: other analysis, in order to test if the mortality estimated from the
77: cross-longitudinal survey is different from the mortality estimated
78: from other sources like vital statistic data.
79:
80: The same imach parameter file can be used but the option for mle should be -3.
81:
82: Agnès, who wrote this part of the code, tried to keep most of the
83: former routines in order to include the new code within the former code.
84:
85: The output is very simple: only an estimate of the intercept and of
86: the slope with 95% confident intervals.
87:
88: Current limitations:
89: A) Even if you enter covariates, i.e. with the
90: model= V1+V2 equation for example, the programm does only estimate a unique global model without covariates.
91: B) There is no computation of Life Expectancy nor Life Table.
92:
93: Revision 1.97 2004/02/20 13:25:42 lievre
94: Version 0.96d. Population forecasting command line is (temporarily)
95: suppressed.
96:
97: Revision 1.96 2003/07/15 15:38:55 brouard
98: * imach.c (Repository): Errors in subdirf, 2, 3 while printing tmpout is
99: rewritten within the same printf. Workaround: many printfs.
100:
101: Revision 1.95 2003/07/08 07:54:34 brouard
102: * imach.c (Repository):
103: (Repository): Using imachwizard code to output a more meaningful covariance
104: matrix (cov(a12,c31) instead of numbers.
105:
106: Revision 1.94 2003/06/27 13:00:02 brouard
107: Just cleaning
108:
109: Revision 1.93 2003/06/25 16:33:55 brouard
110: (Module): On windows (cygwin) function asctime_r doesn't
111: exist so I changed back to asctime which exists.
112: (Module): Version 0.96b
113:
114: Revision 1.92 2003/06/25 16:30:45 brouard
115: (Module): On windows (cygwin) function asctime_r doesn't
116: exist so I changed back to asctime which exists.
117:
118: Revision 1.91 2003/06/25 15:30:29 brouard
119: * imach.c (Repository): Duplicated warning errors corrected.
120: (Repository): Elapsed time after each iteration is now output. It
121: helps to forecast when convergence will be reached. Elapsed time
122: is stamped in powell. We created a new html file for the graphs
123: concerning matrix of covariance. It has extension -cov.htm.
124:
125: Revision 1.90 2003/06/24 12:34:15 brouard
126: (Module): Some bugs corrected for windows. Also, when
127: mle=-1 a template is output in file "or"mypar.txt with the design
128: of the covariance matrix to be input.
129:
130: Revision 1.89 2003/06/24 12:30:52 brouard
131: (Module): Some bugs corrected for windows. Also, when
132: mle=-1 a template is output in file "or"mypar.txt with the design
133: of the covariance matrix to be input.
134:
135: Revision 1.88 2003/06/23 17:54:56 brouard
136: * 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.
137:
138: Revision 1.87 2003/06/18 12:26:01 brouard
139: Version 0.96
140:
141: Revision 1.86 2003/06/17 20:04:08 brouard
142: (Module): Change position of html and gnuplot routines and added
143: routine fileappend.
144:
145: Revision 1.85 2003/06/17 13:12:43 brouard
146: * imach.c (Repository): Check when date of death was earlier that
147: current date of interview. It may happen when the death was just
148: prior to the death. In this case, dh was negative and likelihood
149: was wrong (infinity). We still send an "Error" but patch by
150: assuming that the date of death was just one stepm after the
151: interview.
152: (Repository): Because some people have very long ID (first column)
153: we changed int to long in num[] and we added a new lvector for
154: memory allocation. But we also truncated to 8 characters (left
155: truncation)
156: (Repository): No more line truncation errors.
157:
158: Revision 1.84 2003/06/13 21:44:43 brouard
159: * imach.c (Repository): Replace "freqsummary" at a correct
160: place. It differs from routine "prevalence" which may be called
161: many times. Probs is memory consuming and must be used with
162: parcimony.
163: Version 0.95a3 (should output exactly the same maximization than 0.8a2)
164:
165: Revision 1.83 2003/06/10 13:39:11 lievre
166: *** empty log message ***
167:
168: Revision 1.82 2003/06/05 15:57:20 brouard
169: Add log in imach.c and fullversion number is now printed.
170:
171: */
172: /*
173: Interpolated Markov Chain
174:
175: Short summary of the programme:
176:
177: This program computes Healthy Life Expectancies from
178: cross-longitudinal data. Cross-longitudinal data consist in: -1- a
179: first survey ("cross") where individuals from different ages are
180: interviewed on their health status or degree of disability (in the
181: case of a health survey which is our main interest) -2- at least a
182: second wave of interviews ("longitudinal") which measure each change
183: (if any) in individual health status. Health expectancies are
184: computed from the time spent in each health state according to a
185: model. More health states you consider, more time is necessary to reach the
186: Maximum Likelihood of the parameters involved in the model. The
187: simplest model is the multinomial logistic model where pij is the
188: probability to be observed in state j at the second wave
189: conditional to be observed in state i at the first wave. Therefore
190: the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where
191: 'age' is age and 'sex' is a covariate. If you want to have a more
192: complex model than "constant and age", you should modify the program
193: where the markup *Covariates have to be included here again* invites
194: you to do it. More covariates you add, slower the
195: convergence.
196:
197: The advantage of this computer programme, compared to a simple
198: multinomial logistic model, is clear when the delay between waves is not
199: identical for each individual. Also, if a individual missed an
200: intermediate interview, the information is lost, but taken into
201: account using an interpolation or extrapolation.
202:
203: hPijx is the probability to be observed in state i at age x+h
204: conditional to the observed state i at age x. The delay 'h' can be
205: split into an exact number (nh*stepm) of unobserved intermediate
206: states. This elementary transition (by month, quarter,
207: semester or year) is modelled as a multinomial logistic. The hPx
208: matrix is simply the matrix product of nh*stepm elementary matrices
209: and the contribution of each individual to the likelihood is simply
210: hPijx.
211:
212: Also this programme outputs the covariance matrix of the parameters but also
213: of the life expectancies. It also computes the stable prevalence.
214:
215: Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).
216: Institut national d'études démographiques, Paris.
217: This software have been partly granted by Euro-REVES, a concerted action
218: from the European Union.
219: It is copyrighted identically to a GNU software product, ie programme and
220: software can be distributed freely for non commercial use. Latest version
221: can be accessed at http://euroreves.ined.fr/imach .
222:
223: Help to debug: LD_PRELOAD=/usr/local/lib/libnjamd.so ./imach foo.imach
224: or better on gdb : set env LD_PRELOAD=/usr/local/lib/libnjamd.so
225:
226: **********************************************************************/
227: /*
228: main
229: read parameterfile
230: read datafile
231: concatwav
232: freqsummary
233: if (mle >= 1)
234: mlikeli
235: print results files
236: if mle==1
237: computes hessian
238: read end of parameter file: agemin, agemax, bage, fage, estepm
239: begin-prev-date,...
240: open gnuplot file
241: open html file
242: stable prevalence
243: for age prevalim()
244: h Pij x
245: variance of p varprob
246: forecasting if prevfcast==1 prevforecast call prevalence()
247: health expectancies
248: Variance-covariance of DFLE
249: prevalence()
250: movingaverage()
251: varevsij()
252: if popbased==1 varevsij(,popbased)
253: total life expectancies
254: Variance of stable prevalence
255: end
256: */
257:
258:
259:
260:
261: #include <math.h>
262: #include <stdio.h>
263: #include <stdlib.h>
264: #include <string.h>
265: #include <unistd.h>
266:
267: #include <limits.h>
268: #include <sys/types.h>
269: #include <sys/stat.h>
270: #include <errno.h>
271: extern int errno;
272:
273: /* #include <sys/time.h> */
274: #include <time.h>
275: #include "timeval.h"
276:
277: /* #include <libintl.h> */
278: /* #define _(String) gettext (String) */
279:
280: #define MAXLINE 256
281:
282: #define GNUPLOTPROGRAM "gnuplot"
283: /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
284: #define FILENAMELENGTH 132
285:
286: #define GLOCK_ERROR_NOPATH -1 /* empty path */
287: #define GLOCK_ERROR_GETCWD -2 /* cannot get cwd */
288:
289: #define MAXPARM 30 /* Maximum number of parameters for the optimization */
290: #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */
291:
292: #define NINTERVMAX 8
293: #define NLSTATEMAX 8 /* Maximum number of live states (for func) */
294: #define NDEATHMAX 8 /* Maximum number of dead states (for func) */
295: #define NCOVMAX 8 /* Maximum number of covariates */
296: #define MAXN 20000
297: #define YEARM 12. /* Number of months per year */
298: #define AGESUP 130
299: #define AGEBASE 40
300: #define AGEGOMP 10. /* Minimal age for Gompertz adjustment */
301: #ifdef UNIX
302: #define DIRSEPARATOR '/'
303: #define CHARSEPARATOR "/"
304: #define ODIRSEPARATOR '\\'
305: #else
306: #define DIRSEPARATOR '\\'
307: #define CHARSEPARATOR "\\"
308: #define ODIRSEPARATOR '/'
309: #endif
310:
311: /* $Id: imach.c,v 1.116 2006/03/06 10:29:27 brouard Exp $ */
312: /* $State: Exp $ */
313:
314: char version[]="Imach version 0.98c, February 2006, INED-EUROREVES ";
315: char fullversion[]="$Revision: 1.116 $ $Date: 2006/03/06 10:29:27 $";
316: int erreur, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings */
317: int nvar;
318: int cptcovn=0, cptcovage=0, cptcoveff=0,cptcov;
319: int npar=NPARMAX;
320: int nlstate=2; /* Number of live states */
321: int ndeath=1; /* Number of dead states */
322: int ncovmodel, ncovcol; /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
323: int popbased=0;
324:
325: int *wav; /* Number of waves for this individuual 0 is possible */
326: int maxwav; /* Maxim number of waves */
327: int jmin, jmax; /* min, max spacing between 2 waves */
328: int ijmin, ijmax; /* Individuals having jmin and jmax */
329: int gipmx, gsw; /* Global variables on the number of contributions
330: to the likelihood and the sum of weights (done by funcone)*/
331: int mle, weightopt;
332: int **mw; /* mw[mi][i] is number of the mi wave for this individual */
333: int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
334: int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between
335: * wave mi and wave mi+1 is not an exact multiple of stepm. */
336: double jmean; /* Mean space between 2 waves */
337: double **oldm, **newm, **savm; /* Working pointers to matrices */
338: double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
339: FILE *fic,*ficpar, *ficparo,*ficres, *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
340: FILE *ficlog, *ficrespow;
341: int globpr; /* Global variable for printing or not */
342: double fretone; /* Only one call to likelihood */
343: long ipmx; /* Number of contributions */
344: double sw; /* Sum of weights */
345: char filerespow[FILENAMELENGTH];
346: char fileresilk[FILENAMELENGTH]; /* File of individual contributions to the likelihood */
347: FILE *ficresilk;
348: FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
349: FILE *ficresprobmorprev;
350: FILE *fichtm, *fichtmcov; /* Html File */
351: FILE *ficreseij;
352: char filerese[FILENAMELENGTH];
353: FILE *ficresvij;
354: char fileresv[FILENAMELENGTH];
355: FILE *ficresvpl;
356: char fileresvpl[FILENAMELENGTH];
357: char title[MAXLINE];
358: char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH], filerespl[FILENAMELENGTH];
359: char optionfilext[10], optionfilefiname[FILENAMELENGTH], plotcmd[FILENAMELENGTH], pplotcmd[FILENAMELENGTH];
360: char tmpout[FILENAMELENGTH], tmpout2[FILENAMELENGTH];
361: char command[FILENAMELENGTH];
362: int outcmd=0;
363:
364: char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
365:
366: char filelog[FILENAMELENGTH]; /* Log file */
367: char filerest[FILENAMELENGTH];
368: char fileregp[FILENAMELENGTH];
369: char popfile[FILENAMELENGTH];
370:
371: char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilehtmcov[FILENAMELENGTH] ;
372:
373: struct timeval start_time, end_time, curr_time, last_time, forecast_time;
374: struct timezone tzp;
375: extern int gettimeofday();
376: struct tm tmg, tm, tmf, *gmtime(), *localtime();
377: long time_value;
378: extern long time();
379: char strcurr[80], strfor[80];
380:
381: char *endptr;
382: long lval;
383:
384: #define NR_END 1
385: #define FREE_ARG char*
386: #define FTOL 1.0e-10
387:
388: #define NRANSI
389: #define ITMAX 200
390:
391: #define TOL 2.0e-4
392:
393: #define CGOLD 0.3819660
394: #define ZEPS 1.0e-10
395: #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);
396:
397: #define GOLD 1.618034
398: #define GLIMIT 100.0
399: #define TINY 1.0e-20
400:
401: static double maxarg1,maxarg2;
402: #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
403: #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
404:
405: #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
406: #define rint(a) floor(a+0.5)
407:
408: static double sqrarg;
409: #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
410: #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}
411: int agegomp= AGEGOMP;
412:
413: int imx;
414: int stepm=1;
415: /* Stepm, step in month: minimum step interpolation*/
416:
417: int estepm;
418: /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
419:
420: int m,nb;
421: long *num;
422: int firstpass=0, lastpass=4,*cod, *ncodemax, *Tage,*cens;
423: double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
424: double **pmmij, ***probs;
425: double *ageexmed,*agecens;
426: double dateintmean=0;
427:
428: double *weight;
429: int **s; /* Status */
430: double *agedc, **covar, idx;
431: int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;
432: double *lsurv, *lpop, *tpop;
433:
434: double ftol=FTOL; /* Tolerance for computing Max Likelihood */
435: double ftolhess; /* Tolerance for computing hessian */
436:
437: /**************** split *************************/
438: static int split( char *path, char *dirc, char *name, char *ext, char *finame )
439: {
440: /* From a file name with (full) path (either Unix or Windows) we extract the directory (dirc)
441: the name of the file (name), its extension only (ext) and its first part of the name (finame)
442: */
443: char *ss; /* pointer */
444: int l1, l2; /* length counters */
445:
446: l1 = strlen(path ); /* length of path */
447: if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
448: ss= strrchr( path, DIRSEPARATOR ); /* find last / */
449: if ( ss == NULL ) { /* no directory, so determine current directory */
450: strcpy( name, path ); /* we got the fullname name because no directory */
451: /*if(strrchr(path, ODIRSEPARATOR )==NULL)
452: printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
453: /* get current working directory */
454: /* extern char* getcwd ( char *buf , int len);*/
455: if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {
456: return( GLOCK_ERROR_GETCWD );
457: }
458: /* got dirc from getcwd*/
459: printf(" DIRC = %s \n",dirc);
460: } else { /* strip direcotry from path */
461: ss++; /* after this, the filename */
462: l2 = strlen( ss ); /* length of filename */
463: if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
464: strcpy( name, ss ); /* save file name */
465: strncpy( dirc, path, l1 - l2 ); /* now the directory */
466: dirc[l1-l2] = 0; /* add zero */
467: printf(" DIRC2 = %s \n",dirc);
468: }
469: /* We add a separator at the end of dirc if not exists */
470: l1 = strlen( dirc ); /* length of directory */
471: if( dirc[l1-1] != DIRSEPARATOR ){
472: dirc[l1] = DIRSEPARATOR;
473: dirc[l1+1] = 0;
474: printf(" DIRC3 = %s \n",dirc);
475: }
476: ss = strrchr( name, '.' ); /* find last / */
477: if (ss >0){
478: ss++;
479: strcpy(ext,ss); /* save extension */
480: l1= strlen( name);
481: l2= strlen(ss)+1;
482: strncpy( finame, name, l1-l2);
483: finame[l1-l2]= 0;
484: }
485:
486: return( 0 ); /* we're done */
487: }
488:
489:
490: /******************************************/
491:
492: void replace_back_to_slash(char *s, char*t)
493: {
494: int i;
495: int lg=0;
496: i=0;
497: lg=strlen(t);
498: for(i=0; i<= lg; i++) {
499: (s[i] = t[i]);
500: if (t[i]== '\\') s[i]='/';
501: }
502: }
503:
504: int nbocc(char *s, char occ)
505: {
506: int i,j=0;
507: int lg=20;
508: i=0;
509: lg=strlen(s);
510: for(i=0; i<= lg; i++) {
511: if (s[i] == occ ) j++;
512: }
513: return j;
514: }
515:
516: void cutv(char *u,char *v, char*t, char occ)
517: {
518: /* cuts string t into u and v where u ends before first occurence of char 'occ'
519: and v starts after first occurence of char 'occ' : ex cutv(u,v,"abcdef2ghi2j",'2')
520: gives u="abcedf" and v="ghi2j" */
521: int i,lg,j,p=0;
522: i=0;
523: for(j=0; j<=strlen(t)-1; j++) {
524: if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;
525: }
526:
527: lg=strlen(t);
528: for(j=0; j<p; j++) {
529: (u[j] = t[j]);
530: }
531: u[p]='\0';
532:
533: for(j=0; j<= lg; j++) {
534: if (j>=(p+1))(v[j-p-1] = t[j]);
535: }
536: }
537:
538: /********************** nrerror ********************/
539:
540: void nrerror(char error_text[])
541: {
542: fprintf(stderr,"ERREUR ...\n");
543: fprintf(stderr,"%s\n",error_text);
544: exit(EXIT_FAILURE);
545: }
546: /*********************** vector *******************/
547: double *vector(int nl, int nh)
548: {
549: double *v;
550: v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
551: if (!v) nrerror("allocation failure in vector");
552: return v-nl+NR_END;
553: }
554:
555: /************************ free vector ******************/
556: void free_vector(double*v, int nl, int nh)
557: {
558: free((FREE_ARG)(v+nl-NR_END));
559: }
560:
561: /************************ivector *******************************/
562: int *ivector(long nl,long nh)
563: {
564: int *v;
565: v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
566: if (!v) nrerror("allocation failure in ivector");
567: return v-nl+NR_END;
568: }
569:
570: /******************free ivector **************************/
571: void free_ivector(int *v, long nl, long nh)
572: {
573: free((FREE_ARG)(v+nl-NR_END));
574: }
575:
576: /************************lvector *******************************/
577: long *lvector(long nl,long nh)
578: {
579: long *v;
580: v=(long *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(long)));
581: if (!v) nrerror("allocation failure in ivector");
582: return v-nl+NR_END;
583: }
584:
585: /******************free lvector **************************/
586: void free_lvector(long *v, long nl, long nh)
587: {
588: free((FREE_ARG)(v+nl-NR_END));
589: }
590:
591: /******************* imatrix *******************************/
592: int **imatrix(long nrl, long nrh, long ncl, long nch)
593: /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */
594: {
595: long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;
596: int **m;
597:
598: /* allocate pointers to rows */
599: m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));
600: if (!m) nrerror("allocation failure 1 in matrix()");
601: m += NR_END;
602: m -= nrl;
603:
604:
605: /* allocate rows and set pointers to them */
606: m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));
607: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
608: m[nrl] += NR_END;
609: m[nrl] -= ncl;
610:
611: for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;
612:
613: /* return pointer to array of pointers to rows */
614: return m;
615: }
616:
617: /****************** free_imatrix *************************/
618: void free_imatrix(m,nrl,nrh,ncl,nch)
619: int **m;
620: long nch,ncl,nrh,nrl;
621: /* free an int matrix allocated by imatrix() */
622: {
623: free((FREE_ARG) (m[nrl]+ncl-NR_END));
624: free((FREE_ARG) (m+nrl-NR_END));
625: }
626:
627: /******************* matrix *******************************/
628: double **matrix(long nrl, long nrh, long ncl, long nch)
629: {
630: long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
631: double **m;
632:
633: m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
634: if (!m) nrerror("allocation failure 1 in matrix()");
635: m += NR_END;
636: m -= nrl;
637:
638: m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
639: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
640: m[nrl] += NR_END;
641: m[nrl] -= ncl;
642:
643: for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
644: return m;
645: /* print *(*(m+1)+70) or print m[1][70]; print m+1 or print &(m[1])
646: */
647: }
648:
649: /*************************free matrix ************************/
650: void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
651: {
652: free((FREE_ARG)(m[nrl]+ncl-NR_END));
653: free((FREE_ARG)(m+nrl-NR_END));
654: }
655:
656: /******************* ma3x *******************************/
657: double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
658: {
659: long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
660: double ***m;
661:
662: m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
663: if (!m) nrerror("allocation failure 1 in matrix()");
664: m += NR_END;
665: m -= nrl;
666:
667: m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
668: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
669: m[nrl] += NR_END;
670: m[nrl] -= ncl;
671:
672: for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
673:
674: m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
675: if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
676: m[nrl][ncl] += NR_END;
677: m[nrl][ncl] -= nll;
678: for (j=ncl+1; j<=nch; j++)
679: m[nrl][j]=m[nrl][j-1]+nlay;
680:
681: for (i=nrl+1; i<=nrh; i++) {
682: m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
683: for (j=ncl+1; j<=nch; j++)
684: m[i][j]=m[i][j-1]+nlay;
685: }
686: return m;
687: /* gdb: p *(m+1) <=> p m[1] and p (m+1) <=> p (m+1) <=> p &(m[1])
688: &(m[i][j][k]) <=> *((*(m+i) + j)+k)
689: */
690: }
691:
692: /*************************free ma3x ************************/
693: void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
694: {
695: free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
696: free((FREE_ARG)(m[nrl]+ncl-NR_END));
697: free((FREE_ARG)(m+nrl-NR_END));
698: }
699:
700: /*************** function subdirf ***********/
701: char *subdirf(char fileres[])
702: {
703: /* Caution optionfilefiname is hidden */
704: strcpy(tmpout,optionfilefiname);
705: strcat(tmpout,"/"); /* Add to the right */
706: strcat(tmpout,fileres);
707: return tmpout;
708: }
709:
710: /*************** function subdirf2 ***********/
711: char *subdirf2(char fileres[], char *preop)
712: {
713:
714: /* Caution optionfilefiname is hidden */
715: strcpy(tmpout,optionfilefiname);
716: strcat(tmpout,"/");
717: strcat(tmpout,preop);
718: strcat(tmpout,fileres);
719: return tmpout;
720: }
721:
722: /*************** function subdirf3 ***********/
723: char *subdirf3(char fileres[], char *preop, char *preop2)
724: {
725:
726: /* Caution optionfilefiname is hidden */
727: strcpy(tmpout,optionfilefiname);
728: strcat(tmpout,"/");
729: strcat(tmpout,preop);
730: strcat(tmpout,preop2);
731: strcat(tmpout,fileres);
732: return tmpout;
733: }
734:
735: /***************** f1dim *************************/
736: extern int ncom;
737: extern double *pcom,*xicom;
738: extern double (*nrfunc)(double []);
739:
740: double f1dim(double x)
741: {
742: int j;
743: double f;
744: double *xt;
745:
746: xt=vector(1,ncom);
747: for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];
748: f=(*nrfunc)(xt);
749: free_vector(xt,1,ncom);
750: return f;
751: }
752:
753: /*****************brent *************************/
754: double brent(double ax, double bx, double cx, double (*f)(double), double tol, double *xmin)
755: {
756: int iter;
757: double a,b,d,etemp;
758: double fu,fv,fw,fx;
759: double ftemp;
760: double p,q,r,tol1,tol2,u,v,w,x,xm;
761: double e=0.0;
762:
763: a=(ax < cx ? ax : cx);
764: b=(ax > cx ? ax : cx);
765: x=w=v=bx;
766: fw=fv=fx=(*f)(x);
767: for (iter=1;iter<=ITMAX;iter++) {
768: xm=0.5*(a+b);
769: tol2=2.0*(tol1=tol*fabs(x)+ZEPS);
770: /* if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
771: printf(".");fflush(stdout);
772: fprintf(ficlog,".");fflush(ficlog);
773: #ifdef DEBUG
774: 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);
775: 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);
776: /* if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
777: #endif
778: if (fabs(x-xm) <= (tol2-0.5*(b-a))){
779: *xmin=x;
780: return fx;
781: }
782: ftemp=fu;
783: if (fabs(e) > tol1) {
784: r=(x-w)*(fx-fv);
785: q=(x-v)*(fx-fw);
786: p=(x-v)*q-(x-w)*r;
787: q=2.0*(q-r);
788: if (q > 0.0) p = -p;
789: q=fabs(q);
790: etemp=e;
791: e=d;
792: if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))
793: d=CGOLD*(e=(x >= xm ? a-x : b-x));
794: else {
795: d=p/q;
796: u=x+d;
797: if (u-a < tol2 || b-u < tol2)
798: d=SIGN(tol1,xm-x);
799: }
800: } else {
801: d=CGOLD*(e=(x >= xm ? a-x : b-x));
802: }
803: u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));
804: fu=(*f)(u);
805: if (fu <= fx) {
806: if (u >= x) a=x; else b=x;
807: SHFT(v,w,x,u)
808: SHFT(fv,fw,fx,fu)
809: } else {
810: if (u < x) a=u; else b=u;
811: if (fu <= fw || w == x) {
812: v=w;
813: w=u;
814: fv=fw;
815: fw=fu;
816: } else if (fu <= fv || v == x || v == w) {
817: v=u;
818: fv=fu;
819: }
820: }
821: }
822: nrerror("Too many iterations in brent");
823: *xmin=x;
824: return fx;
825: }
826:
827: /****************** mnbrak ***********************/
828:
829: void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,
830: double (*func)(double))
831: {
832: double ulim,u,r,q, dum;
833: double fu;
834:
835: *fa=(*func)(*ax);
836: *fb=(*func)(*bx);
837: if (*fb > *fa) {
838: SHFT(dum,*ax,*bx,dum)
839: SHFT(dum,*fb,*fa,dum)
840: }
841: *cx=(*bx)+GOLD*(*bx-*ax);
842: *fc=(*func)(*cx);
843: while (*fb > *fc) {
844: r=(*bx-*ax)*(*fb-*fc);
845: q=(*bx-*cx)*(*fb-*fa);
846: u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/
847: (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r));
848: ulim=(*bx)+GLIMIT*(*cx-*bx);
849: if ((*bx-u)*(u-*cx) > 0.0) {
850: fu=(*func)(u);
851: } else if ((*cx-u)*(u-ulim) > 0.0) {
852: fu=(*func)(u);
853: if (fu < *fc) {
854: SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))
855: SHFT(*fb,*fc,fu,(*func)(u))
856: }
857: } else if ((u-ulim)*(ulim-*cx) >= 0.0) {
858: u=ulim;
859: fu=(*func)(u);
860: } else {
861: u=(*cx)+GOLD*(*cx-*bx);
862: fu=(*func)(u);
863: }
864: SHFT(*ax,*bx,*cx,u)
865: SHFT(*fa,*fb,*fc,fu)
866: }
867: }
868:
869: /*************** linmin ************************/
870:
871: int ncom;
872: double *pcom,*xicom;
873: double (*nrfunc)(double []);
874:
875: void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))
876: {
877: double brent(double ax, double bx, double cx,
878: double (*f)(double), double tol, double *xmin);
879: double f1dim(double x);
880: void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,
881: double *fc, double (*func)(double));
882: int j;
883: double xx,xmin,bx,ax;
884: double fx,fb,fa;
885:
886: ncom=n;
887: pcom=vector(1,n);
888: xicom=vector(1,n);
889: nrfunc=func;
890: for (j=1;j<=n;j++) {
891: pcom[j]=p[j];
892: xicom[j]=xi[j];
893: }
894: ax=0.0;
895: xx=1.0;
896: mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim);
897: *fret=brent(ax,xx,bx,f1dim,TOL,&xmin);
898: #ifdef DEBUG
899: printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
900: fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
901: #endif
902: for (j=1;j<=n;j++) {
903: xi[j] *= xmin;
904: p[j] += xi[j];
905: }
906: free_vector(xicom,1,n);
907: free_vector(pcom,1,n);
908: }
909:
910: char *asc_diff_time(long time_sec, char ascdiff[])
911: {
912: long sec_left, days, hours, minutes;
913: days = (time_sec) / (60*60*24);
914: sec_left = (time_sec) % (60*60*24);
915: hours = (sec_left) / (60*60) ;
916: sec_left = (sec_left) %(60*60);
917: minutes = (sec_left) /60;
918: sec_left = (sec_left) % (60);
919: sprintf(ascdiff,"%d day(s) %d hour(s) %d minute(s) %d second(s)",days, hours, minutes, sec_left);
920: return ascdiff;
921: }
922:
923: /*************** powell ************************/
924: void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,
925: double (*func)(double []))
926: {
927: void linmin(double p[], double xi[], int n, double *fret,
928: double (*func)(double []));
929: int i,ibig,j;
930: double del,t,*pt,*ptt,*xit;
931: double fp,fptt;
932: double *xits;
933: int niterf, itmp;
934:
935: pt=vector(1,n);
936: ptt=vector(1,n);
937: xit=vector(1,n);
938: xits=vector(1,n);
939: *fret=(*func)(p);
940: for (j=1;j<=n;j++) pt[j]=p[j];
941: for (*iter=1;;++(*iter)) {
942: fp=(*fret);
943: ibig=0;
944: del=0.0;
945: last_time=curr_time;
946: (void) gettimeofday(&curr_time,&tzp);
947: 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);
948: /* 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);
949: fprintf(ficrespow,"%d %.12f %ld",*iter,*fret,curr_time.tv_sec-start_time.tv_sec);
950: */
951: for (i=1;i<=n;i++) {
952: printf(" %d %.12f",i, p[i]);
953: fprintf(ficlog," %d %.12lf",i, p[i]);
954: fprintf(ficrespow," %.12lf", p[i]);
955: }
956: printf("\n");
957: fprintf(ficlog,"\n");
958: fprintf(ficrespow,"\n");fflush(ficrespow);
959: if(*iter <=3){
960: tm = *localtime(&curr_time.tv_sec);
961: strcpy(strcurr,asctime(&tm));
962: /* asctime_r(&tm,strcurr); */
963: forecast_time=curr_time;
964: itmp = strlen(strcurr);
965: if(strcurr[itmp-1]=='\n') /* Windows outputs with a new line */
966: strcurr[itmp-1]='\0';
967: printf("\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,curr_time.tv_sec-last_time.tv_sec);
968: fprintf(ficlog,"\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,curr_time.tv_sec-last_time.tv_sec);
969: for(niterf=10;niterf<=30;niterf+=10){
970: forecast_time.tv_sec=curr_time.tv_sec+(niterf-*iter)*(curr_time.tv_sec-last_time.tv_sec);
971: tmf = *localtime(&forecast_time.tv_sec);
972: /* asctime_r(&tmf,strfor); */
973: strcpy(strfor,asctime(&tmf));
974: itmp = strlen(strfor);
975: if(strfor[itmp-1]=='\n')
976: strfor[itmp-1]='\0';
977: 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);
978: 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);
979: }
980: }
981: for (i=1;i<=n;i++) {
982: for (j=1;j<=n;j++) xit[j]=xi[j][i];
983: fptt=(*fret);
984: #ifdef DEBUG
985: printf("fret=%lf \n",*fret);
986: fprintf(ficlog,"fret=%lf \n",*fret);
987: #endif
988: printf("%d",i);fflush(stdout);
989: fprintf(ficlog,"%d",i);fflush(ficlog);
990: linmin(p,xit,n,fret,func);
991: if (fabs(fptt-(*fret)) > del) {
992: del=fabs(fptt-(*fret));
993: ibig=i;
994: }
995: #ifdef DEBUG
996: printf("%d %.12e",i,(*fret));
997: fprintf(ficlog,"%d %.12e",i,(*fret));
998: for (j=1;j<=n;j++) {
999: xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
1000: printf(" x(%d)=%.12e",j,xit[j]);
1001: fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
1002: }
1003: for(j=1;j<=n;j++) {
1004: printf(" p=%.12e",p[j]);
1005: fprintf(ficlog," p=%.12e",p[j]);
1006: }
1007: printf("\n");
1008: fprintf(ficlog,"\n");
1009: #endif
1010: }
1011: if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {
1012: #ifdef DEBUG
1013: int k[2],l;
1014: k[0]=1;
1015: k[1]=-1;
1016: printf("Max: %.12e",(*func)(p));
1017: fprintf(ficlog,"Max: %.12e",(*func)(p));
1018: for (j=1;j<=n;j++) {
1019: printf(" %.12e",p[j]);
1020: fprintf(ficlog," %.12e",p[j]);
1021: }
1022: printf("\n");
1023: fprintf(ficlog,"\n");
1024: for(l=0;l<=1;l++) {
1025: for (j=1;j<=n;j++) {
1026: ptt[j]=p[j]+(p[j]-pt[j])*k[l];
1027: printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
1028: fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
1029: }
1030: printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
1031: fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
1032: }
1033: #endif
1034:
1035:
1036: free_vector(xit,1,n);
1037: free_vector(xits,1,n);
1038: free_vector(ptt,1,n);
1039: free_vector(pt,1,n);
1040: return;
1041: }
1042: if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");
1043: for (j=1;j<=n;j++) {
1044: ptt[j]=2.0*p[j]-pt[j];
1045: xit[j]=p[j]-pt[j];
1046: pt[j]=p[j];
1047: }
1048: fptt=(*func)(ptt);
1049: if (fptt < fp) {
1050: t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt);
1051: if (t < 0.0) {
1052: linmin(p,xit,n,fret,func);
1053: for (j=1;j<=n;j++) {
1054: xi[j][ibig]=xi[j][n];
1055: xi[j][n]=xit[j];
1056: }
1057: #ifdef DEBUG
1058: printf("Direction changed last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
1059: fprintf(ficlog,"Direction changed last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
1060: for(j=1;j<=n;j++){
1061: printf(" %.12e",xit[j]);
1062: fprintf(ficlog," %.12e",xit[j]);
1063: }
1064: printf("\n");
1065: fprintf(ficlog,"\n");
1066: #endif
1067: }
1068: }
1069: }
1070: }
1071:
1072: /**** Prevalence limit (stable prevalence) ****************/
1073:
1074: double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)
1075: {
1076: /* Computes the prevalence limit in each live state at age x by left multiplying the unit
1077: matrix by transitions matrix until convergence is reached */
1078:
1079: int i, ii,j,k;
1080: double min, max, maxmin, maxmax,sumnew=0.;
1081: double **matprod2();
1082: double **out, cov[NCOVMAX], **pmij();
1083: double **newm;
1084: double agefin, delaymax=50 ; /* Max number of years to converge */
1085:
1086: for (ii=1;ii<=nlstate+ndeath;ii++)
1087: for (j=1;j<=nlstate+ndeath;j++){
1088: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1089: }
1090:
1091: cov[1]=1.;
1092:
1093: /* Even if hstepm = 1, at least one multiplication by the unit matrix */
1094: for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
1095: newm=savm;
1096: /* Covariates have to be included here again */
1097: cov[2]=agefin;
1098:
1099: for (k=1; k<=cptcovn;k++) {
1100: cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
1101: /* 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]]);*/
1102: }
1103: for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
1104: for (k=1; k<=cptcovprod;k++)
1105: cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
1106:
1107: /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
1108: /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
1109: /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
1110: out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);
1111:
1112: savm=oldm;
1113: oldm=newm;
1114: maxmax=0.;
1115: for(j=1;j<=nlstate;j++){
1116: min=1.;
1117: max=0.;
1118: for(i=1; i<=nlstate; i++) {
1119: sumnew=0;
1120: for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
1121: prlim[i][j]= newm[i][j]/(1-sumnew);
1122: max=FMAX(max,prlim[i][j]);
1123: min=FMIN(min,prlim[i][j]);
1124: }
1125: maxmin=max-min;
1126: maxmax=FMAX(maxmax,maxmin);
1127: }
1128: if(maxmax < ftolpl){
1129: return prlim;
1130: }
1131: }
1132: }
1133:
1134: /*************** transition probabilities ***************/
1135:
1136: double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
1137: {
1138: double s1, s2;
1139: /*double t34;*/
1140: int i,j,j1, nc, ii, jj;
1141:
1142: for(i=1; i<= nlstate; i++){
1143: for(j=1; j<i;j++){
1144: for (nc=1, s2=0.;nc <=ncovmodel; nc++){
1145: /*s2 += param[i][j][nc]*cov[nc];*/
1146: s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
1147: /* printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2); */
1148: }
1149: ps[i][j]=s2;
1150: /* printf("s1=%.17e, s2=%.17e\n",s1,s2); */
1151: }
1152: for(j=i+1; j<=nlstate+ndeath;j++){
1153: for (nc=1, s2=0.;nc <=ncovmodel; nc++){
1154: s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
1155: /* printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2); */
1156: }
1157: ps[i][j]=s2;
1158: }
1159: }
1160: /*ps[3][2]=1;*/
1161:
1162: for(i=1; i<= nlstate; i++){
1163: s1=0;
1164: for(j=1; j<i; j++)
1165: s1+=exp(ps[i][j]);
1166: for(j=i+1; j<=nlstate+ndeath; j++)
1167: s1+=exp(ps[i][j]);
1168: ps[i][i]=1./(s1+1.);
1169: for(j=1; j<i; j++)
1170: ps[i][j]= exp(ps[i][j])*ps[i][i];
1171: for(j=i+1; j<=nlstate+ndeath; j++)
1172: ps[i][j]= exp(ps[i][j])*ps[i][i];
1173: /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
1174: } /* end i */
1175:
1176: for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
1177: for(jj=1; jj<= nlstate+ndeath; jj++){
1178: ps[ii][jj]=0;
1179: ps[ii][ii]=1;
1180: }
1181: }
1182:
1183:
1184: /* for(ii=1; ii<= nlstate+ndeath; ii++){ */
1185: /* for(jj=1; jj<= nlstate+ndeath; jj++){ */
1186: /* printf("ddd %lf ",ps[ii][jj]); */
1187: /* } */
1188: /* printf("\n "); */
1189: /* } */
1190: /* printf("\n ");printf("%lf ",cov[2]); */
1191: /*
1192: for(i=1; i<= npar; i++) printf("%f ",x[i]);
1193: goto end;*/
1194: return ps;
1195: }
1196:
1197: /**************** Product of 2 matrices ******************/
1198:
1199: double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)
1200: {
1201: /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
1202: b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
1203: /* in, b, out are matrice of pointers which should have been initialized
1204: before: only the contents of out is modified. The function returns
1205: a pointer to pointers identical to out */
1206: long i, j, k;
1207: for(i=nrl; i<= nrh; i++)
1208: for(k=ncolol; k<=ncoloh; k++)
1209: for(j=ncl,out[i][k]=0.; j<=nch; j++)
1210: out[i][k] +=in[i][j]*b[j][k];
1211:
1212: return out;
1213: }
1214:
1215:
1216: /************* Higher Matrix Product ***************/
1217:
1218: double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
1219: {
1220: /* Computes the transition matrix starting at age 'age' over
1221: 'nhstepm*hstepm*stepm' months (i.e. until
1222: age (in years) age+nhstepm*hstepm*stepm/12) by multiplying
1223: nhstepm*hstepm matrices.
1224: Output is stored in matrix po[i][j][h] for h every 'hstepm' step
1225: (typically every 2 years instead of every month which is too big
1226: for the memory).
1227: Model is determined by parameters x and covariates have to be
1228: included manually here.
1229:
1230: */
1231:
1232: int i, j, d, h, k;
1233: double **out, cov[NCOVMAX];
1234: double **newm;
1235:
1236: /* Hstepm could be zero and should return the unit matrix */
1237: for (i=1;i<=nlstate+ndeath;i++)
1238: for (j=1;j<=nlstate+ndeath;j++){
1239: oldm[i][j]=(i==j ? 1.0 : 0.0);
1240: po[i][j][0]=(i==j ? 1.0 : 0.0);
1241: }
1242: /* Even if hstepm = 1, at least one multiplication by the unit matrix */
1243: for(h=1; h <=nhstepm; h++){
1244: for(d=1; d <=hstepm; d++){
1245: newm=savm;
1246: /* Covariates have to be included here again */
1247: cov[1]=1.;
1248: cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
1249: for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
1250: for (k=1; k<=cptcovage;k++)
1251: cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
1252: for (k=1; k<=cptcovprod;k++)
1253: cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
1254:
1255:
1256: /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
1257: /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
1258: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,
1259: pmij(pmmij,cov,ncovmodel,x,nlstate));
1260: savm=oldm;
1261: oldm=newm;
1262: }
1263: for(i=1; i<=nlstate+ndeath; i++)
1264: for(j=1;j<=nlstate+ndeath;j++) {
1265: po[i][j][h]=newm[i][j];
1266: /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);
1267: */
1268: }
1269: } /* end h */
1270: return po;
1271: }
1272:
1273:
1274: /*************** log-likelihood *************/
1275: double func( double *x)
1276: {
1277: int i, ii, j, k, mi, d, kk;
1278: double l, ll[NLSTATEMAX], cov[NCOVMAX];
1279: double **out;
1280: double sw; /* Sum of weights */
1281: double lli; /* Individual log likelihood */
1282: int s1, s2;
1283: double bbh, survp;
1284: long ipmx;
1285: /*extern weight */
1286: /* We are differentiating ll according to initial status */
1287: /* for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
1288: /*for(i=1;i<imx;i++)
1289: printf(" %d\n",s[4][i]);
1290: */
1291: cov[1]=1.;
1292:
1293: for(k=1; k<=nlstate; k++) ll[k]=0.;
1294:
1295: if(mle==1){
1296: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1297: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
1298: for(mi=1; mi<= wav[i]-1; mi++){
1299: for (ii=1;ii<=nlstate+ndeath;ii++)
1300: for (j=1;j<=nlstate+ndeath;j++){
1301: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1302: savm[ii][j]=(ii==j ? 1.0 : 0.0);
1303: }
1304: for(d=0; d<dh[mi][i]; d++){
1305: newm=savm;
1306: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
1307: for (kk=1; kk<=cptcovage;kk++) {
1308: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
1309: }
1310: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1311: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1312: savm=oldm;
1313: oldm=newm;
1314: } /* end mult */
1315:
1316: /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
1317: /* But now since version 0.9 we anticipate for bias at large stepm.
1318: * If stepm is larger than one month (smallest stepm) and if the exact delay
1319: * (in months) between two waves is not a multiple of stepm, we rounded to
1320: * the nearest (and in case of equal distance, to the lowest) interval but now
1321: * we keep into memory the bias bh[mi][i] and also the previous matrix product
1322: * (i.e to dh[mi][i]-1) saved in 'savm'. Then we inter(extra)polate the
1323: * probability in order to take into account the bias as a fraction of the way
1324: * from savm to out if bh is negative or even beyond if bh is positive. bh varies
1325: * -stepm/2 to stepm/2 .
1326: * For stepm=1 the results are the same as for previous versions of Imach.
1327: * For stepm > 1 the results are less biased than in previous versions.
1328: */
1329: s1=s[mw[mi][i]][i];
1330: s2=s[mw[mi+1][i]][i];
1331: bbh=(double)bh[mi][i]/(double)stepm;
1332: /* bias bh is positive if real duration
1333: * is higher than the multiple of stepm and negative otherwise.
1334: */
1335: /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
1336: if( s2 > nlstate){
1337: /* i.e. if s2 is a death state and if the date of death is known
1338: then the contribution to the likelihood is the probability to
1339: die between last step unit time and current step unit time,
1340: which is also equal to probability to die before dh
1341: minus probability to die before dh-stepm .
1342: In version up to 0.92 likelihood was computed
1343: as if date of death was unknown. Death was treated as any other
1344: health state: the date of the interview describes the actual state
1345: and not the date of a change in health state. The former idea was
1346: to consider that at each interview the state was recorded
1347: (healthy, disable or death) and IMaCh was corrected; but when we
1348: introduced the exact date of death then we should have modified
1349: the contribution of an exact death to the likelihood. This new
1350: contribution is smaller and very dependent of the step unit
1351: stepm. It is no more the probability to die between last interview
1352: and month of death but the probability to survive from last
1353: interview up to one month before death multiplied by the
1354: probability to die within a month. Thanks to Chris
1355: Jackson for correcting this bug. Former versions increased
1356: mortality artificially. The bad side is that we add another loop
1357: which slows down the processing. The difference can be up to 10%
1358: lower mortality.
1359: */
1360: lli=log(out[s1][s2] - savm[s1][s2]);
1361:
1362:
1363: } else if (s2==-2) {
1364: for (j=1,survp=0. ; j<=nlstate; j++)
1365: survp += out[s1][j];
1366: lli= survp;
1367: }
1368:
1369: else if (s2==-4) {
1370: for (j=3,survp=0. ; j<=nlstate; j++)
1371: survp += out[s1][j];
1372: lli= survp;
1373: }
1374:
1375: else if (s2==-5) {
1376: for (j=1,survp=0. ; j<=2; j++)
1377: survp += out[s1][j];
1378: lli= survp;
1379: }
1380:
1381:
1382: else{
1383: lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
1384: /* 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 */
1385: }
1386: /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
1387: /*if(lli ==000.0)*/
1388: /*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); */
1389: ipmx +=1;
1390: sw += weight[i];
1391: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1392: } /* end of wave */
1393: } /* end of individual */
1394: } else if(mle==2){
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: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1410: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1411: savm=oldm;
1412: oldm=newm;
1413: } /* end mult */
1414:
1415: s1=s[mw[mi][i]][i];
1416: s2=s[mw[mi+1][i]][i];
1417: bbh=(double)bh[mi][i]/(double)stepm;
1418: 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 */
1419: ipmx +=1;
1420: sw += weight[i];
1421: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1422: } /* end of wave */
1423: } /* end of individual */
1424: } else if(mle==3){ /* exponential inter-extrapolation */
1425: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1426: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
1427: for(mi=1; mi<= wav[i]-1; mi++){
1428: for (ii=1;ii<=nlstate+ndeath;ii++)
1429: for (j=1;j<=nlstate+ndeath;j++){
1430: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1431: savm[ii][j]=(ii==j ? 1.0 : 0.0);
1432: }
1433: for(d=0; d<dh[mi][i]; d++){
1434: newm=savm;
1435: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
1436: for (kk=1; kk<=cptcovage;kk++) {
1437: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
1438: }
1439: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1440: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1441: savm=oldm;
1442: oldm=newm;
1443: } /* end mult */
1444:
1445: s1=s[mw[mi][i]][i];
1446: s2=s[mw[mi+1][i]][i];
1447: bbh=(double)bh[mi][i]/(double)stepm;
1448: 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 */
1449: ipmx +=1;
1450: sw += weight[i];
1451: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1452: } /* end of wave */
1453: } /* end of individual */
1454: }else if (mle==4){ /* ml=4 no inter-extrapolation */
1455: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1456: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
1457: for(mi=1; mi<= wav[i]-1; mi++){
1458: for (ii=1;ii<=nlstate+ndeath;ii++)
1459: for (j=1;j<=nlstate+ndeath;j++){
1460: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1461: savm[ii][j]=(ii==j ? 1.0 : 0.0);
1462: }
1463: for(d=0; d<dh[mi][i]; d++){
1464: newm=savm;
1465: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
1466: for (kk=1; kk<=cptcovage;kk++) {
1467: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
1468: }
1469:
1470: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1471: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1472: savm=oldm;
1473: oldm=newm;
1474: } /* end mult */
1475:
1476: s1=s[mw[mi][i]][i];
1477: s2=s[mw[mi+1][i]][i];
1478: if( s2 > nlstate){
1479: lli=log(out[s1][s2] - savm[s1][s2]);
1480: }else{
1481: lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
1482: }
1483: ipmx +=1;
1484: sw += weight[i];
1485: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1486: /* 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]); */
1487: } /* end of wave */
1488: } /* end of individual */
1489: }else{ /* ml=5 no inter-extrapolation no jackson =0.8a */
1490: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1491: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
1492: for(mi=1; mi<= wav[i]-1; mi++){
1493: for (ii=1;ii<=nlstate+ndeath;ii++)
1494: for (j=1;j<=nlstate+ndeath;j++){
1495: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1496: savm[ii][j]=(ii==j ? 1.0 : 0.0);
1497: }
1498: for(d=0; d<dh[mi][i]; d++){
1499: newm=savm;
1500: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
1501: for (kk=1; kk<=cptcovage;kk++) {
1502: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
1503: }
1504:
1505: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1506: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1507: savm=oldm;
1508: oldm=newm;
1509: } /* end mult */
1510:
1511: s1=s[mw[mi][i]][i];
1512: s2=s[mw[mi+1][i]][i];
1513: lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
1514: ipmx +=1;
1515: sw += weight[i];
1516: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1517: /*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]);*/
1518: } /* end of wave */
1519: } /* end of individual */
1520: } /* End of if */
1521: for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
1522: /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
1523: l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
1524: return -l;
1525: }
1526:
1527: /*************** log-likelihood *************/
1528: double funcone( double *x)
1529: {
1530: /* Same as likeli but slower because of a lot of printf and if */
1531: int i, ii, j, k, mi, d, kk;
1532: double l, ll[NLSTATEMAX], cov[NCOVMAX];
1533: double **out;
1534: double lli; /* Individual log likelihood */
1535: double llt;
1536: int s1, s2;
1537: double bbh, survp;
1538: /*extern weight */
1539: /* We are differentiating ll according to initial status */
1540: /* for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
1541: /*for(i=1;i<imx;i++)
1542: printf(" %d\n",s[4][i]);
1543: */
1544: cov[1]=1.;
1545:
1546: for(k=1; k<=nlstate; k++) ll[k]=0.;
1547:
1548: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1549: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
1550: for(mi=1; mi<= wav[i]-1; mi++){
1551: for (ii=1;ii<=nlstate+ndeath;ii++)
1552: for (j=1;j<=nlstate+ndeath;j++){
1553: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1554: savm[ii][j]=(ii==j ? 1.0 : 0.0);
1555: }
1556: for(d=0; d<dh[mi][i]; d++){
1557: newm=savm;
1558: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
1559: for (kk=1; kk<=cptcovage;kk++) {
1560: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
1561: }
1562: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1563: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1564: savm=oldm;
1565: oldm=newm;
1566: } /* end mult */
1567:
1568: s1=s[mw[mi][i]][i];
1569: s2=s[mw[mi+1][i]][i];
1570: bbh=(double)bh[mi][i]/(double)stepm;
1571: /* bias is positive if real duration
1572: * is higher than the multiple of stepm and negative otherwise.
1573: */
1574: if( s2 > nlstate && (mle <5) ){ /* Jackson */
1575: lli=log(out[s1][s2] - savm[s1][s2]);
1576: } else if (mle==1){
1577: lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
1578: } else if(mle==2){
1579: 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 */
1580: } else if(mle==3){ /* exponential inter-extrapolation */
1581: 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 */
1582: } else if (mle==4){ /* mle=4 no inter-extrapolation */
1583: lli=log(out[s1][s2]); /* Original formula */
1584: } else{ /* ml>=5 no inter-extrapolation no jackson =0.8a */
1585: lli=log(out[s1][s2]); /* Original formula */
1586: } /* End of if */
1587: ipmx +=1;
1588: sw += weight[i];
1589: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1590: /* 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]); */
1591: if(globpr){
1592: fprintf(ficresilk,"%9d %6d %1d %1d %1d %1d %3d %10.6f %6.4f\
1593: %10.6f %10.6f %10.6f ", \
1594: num[i],i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],
1595: 2*weight[i]*lli,out[s1][s2],savm[s1][s2]);
1596: for(k=1,llt=0.,l=0.; k<=nlstate; k++){
1597: llt +=ll[k]*gipmx/gsw;
1598: fprintf(ficresilk," %10.6f",-ll[k]*gipmx/gsw);
1599: }
1600: fprintf(ficresilk," %10.6f\n", -llt);
1601: }
1602: } /* end of wave */
1603: } /* end of individual */
1604: for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
1605: /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
1606: l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
1607: if(globpr==0){ /* First time we count the contributions and weights */
1608: gipmx=ipmx;
1609: gsw=sw;
1610: }
1611: return -l;
1612: }
1613:
1614:
1615: /*************** function likelione ***********/
1616: void likelione(FILE *ficres,double p[], int npar, int nlstate, int *globpri, long *ipmx, double *sw, double *fretone, double (*funcone)(double []))
1617: {
1618: /* This routine should help understanding what is done with
1619: the selection of individuals/waves and
1620: to check the exact contribution to the likelihood.
1621: Plotting could be done.
1622: */
1623: int k;
1624:
1625: if(*globpri !=0){ /* Just counts and sums, no printings */
1626: strcpy(fileresilk,"ilk");
1627: strcat(fileresilk,fileres);
1628: if((ficresilk=fopen(fileresilk,"w"))==NULL) {
1629: printf("Problem with resultfile: %s\n", fileresilk);
1630: fprintf(ficlog,"Problem with resultfile: %s\n", fileresilk);
1631: }
1632: 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");
1633: fprintf(ficresilk, "#num_i i s1 s2 mi mw dh likeli weight 2wlli out sav ");
1634: /* i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],2*weight[i]*lli,out[s1][s2],savm[s1][s2]); */
1635: for(k=1; k<=nlstate; k++)
1636: fprintf(ficresilk," -2*gipw/gsw*weight*ll[%d]++",k);
1637: fprintf(ficresilk," -2*gipw/gsw*weight*ll(total)\n");
1638: }
1639:
1640: *fretone=(*funcone)(p);
1641: if(*globpri !=0){
1642: fclose(ficresilk);
1643: fprintf(fichtm,"\n<br>File of contributions to the likelihood: <a href=\"%s\">%s</a><br>\n",subdirf(fileresilk),subdirf(fileresilk));
1644: fflush(fichtm);
1645: }
1646: return;
1647: }
1648:
1649:
1650: /*********** Maximum Likelihood Estimation ***************/
1651:
1652: void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
1653: {
1654: int i,j, iter;
1655: double **xi;
1656: double fret;
1657: double fretone; /* Only one call to likelihood */
1658: /* char filerespow[FILENAMELENGTH];*/
1659: xi=matrix(1,npar,1,npar);
1660: for (i=1;i<=npar;i++)
1661: for (j=1;j<=npar;j++)
1662: xi[i][j]=(i==j ? 1.0 : 0.0);
1663: printf("Powell\n"); fprintf(ficlog,"Powell\n");
1664: strcpy(filerespow,"pow");
1665: strcat(filerespow,fileres);
1666: if((ficrespow=fopen(filerespow,"w"))==NULL) {
1667: printf("Problem with resultfile: %s\n", filerespow);
1668: fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
1669: }
1670: fprintf(ficrespow,"# Powell\n# iter -2*LL");
1671: for (i=1;i<=nlstate;i++)
1672: for(j=1;j<=nlstate+ndeath;j++)
1673: if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
1674: fprintf(ficrespow,"\n");
1675:
1676: powell(p,xi,npar,ftol,&iter,&fret,func);
1677:
1678: free_matrix(xi,1,npar,1,npar);
1679: fclose(ficrespow);
1680: printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));
1681: fprintf(ficlog,"\n#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
1682: fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
1683:
1684: }
1685:
1686: /**** Computes Hessian and covariance matrix ***/
1687: void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
1688: {
1689: double **a,**y,*x,pd;
1690: double **hess;
1691: int i, j,jk;
1692: int *indx;
1693:
1694: double hessii(double p[], double delta, int theta, double delti[],double (*func)(double []),int npar);
1695: double hessij(double p[], double delti[], int i, int j,double (*func)(double []),int npar);
1696: void lubksb(double **a, int npar, int *indx, double b[]) ;
1697: void ludcmp(double **a, int npar, int *indx, double *d) ;
1698: double gompertz(double p[]);
1699: hess=matrix(1,npar,1,npar);
1700:
1701: printf("\nCalculation of the hessian matrix. Wait...\n");
1702: fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
1703: for (i=1;i<=npar;i++){
1704: printf("%d",i);fflush(stdout);
1705: fprintf(ficlog,"%d",i);fflush(ficlog);
1706:
1707: hess[i][i]=hessii(p,ftolhess,i,delti,func,npar);
1708:
1709: /* printf(" %f ",p[i]);
1710: printf(" %lf %lf %lf",hess[i][i],ftolhess,delti[i]);*/
1711: }
1712:
1713: for (i=1;i<=npar;i++) {
1714: for (j=1;j<=npar;j++) {
1715: if (j>i) {
1716: printf(".%d%d",i,j);fflush(stdout);
1717: fprintf(ficlog,".%d%d",i,j);fflush(ficlog);
1718: hess[i][j]=hessij(p,delti,i,j,func,npar);
1719:
1720: hess[j][i]=hess[i][j];
1721: /*printf(" %lf ",hess[i][j]);*/
1722: }
1723: }
1724: }
1725: printf("\n");
1726: fprintf(ficlog,"\n");
1727:
1728: printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
1729: fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
1730:
1731: a=matrix(1,npar,1,npar);
1732: y=matrix(1,npar,1,npar);
1733: x=vector(1,npar);
1734: indx=ivector(1,npar);
1735: for (i=1;i<=npar;i++)
1736: for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
1737: ludcmp(a,npar,indx,&pd);
1738:
1739: for (j=1;j<=npar;j++) {
1740: for (i=1;i<=npar;i++) x[i]=0;
1741: x[j]=1;
1742: lubksb(a,npar,indx,x);
1743: for (i=1;i<=npar;i++){
1744: matcov[i][j]=x[i];
1745: }
1746: }
1747:
1748: printf("\n#Hessian matrix#\n");
1749: fprintf(ficlog,"\n#Hessian matrix#\n");
1750: for (i=1;i<=npar;i++) {
1751: for (j=1;j<=npar;j++) {
1752: printf("%.3e ",hess[i][j]);
1753: fprintf(ficlog,"%.3e ",hess[i][j]);
1754: }
1755: printf("\n");
1756: fprintf(ficlog,"\n");
1757: }
1758:
1759: /* Recompute Inverse */
1760: for (i=1;i<=npar;i++)
1761: for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];
1762: ludcmp(a,npar,indx,&pd);
1763:
1764: /* printf("\n#Hessian matrix recomputed#\n");
1765:
1766: for (j=1;j<=npar;j++) {
1767: for (i=1;i<=npar;i++) x[i]=0;
1768: x[j]=1;
1769: lubksb(a,npar,indx,x);
1770: for (i=1;i<=npar;i++){
1771: y[i][j]=x[i];
1772: printf("%.3e ",y[i][j]);
1773: fprintf(ficlog,"%.3e ",y[i][j]);
1774: }
1775: printf("\n");
1776: fprintf(ficlog,"\n");
1777: }
1778: */
1779:
1780: free_matrix(a,1,npar,1,npar);
1781: free_matrix(y,1,npar,1,npar);
1782: free_vector(x,1,npar);
1783: free_ivector(indx,1,npar);
1784: free_matrix(hess,1,npar,1,npar);
1785:
1786:
1787: }
1788:
1789: /*************** hessian matrix ****************/
1790: double hessii(double x[], double delta, int theta, double delti[], double (*func)(double []), int npar)
1791: {
1792: int i;
1793: int l=1, lmax=20;
1794: double k1,k2;
1795: double p2[NPARMAX+1];
1796: double res;
1797: double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4;
1798: double fx;
1799: int k=0,kmax=10;
1800: double l1;
1801:
1802: fx=func(x);
1803: for (i=1;i<=npar;i++) p2[i]=x[i];
1804: for(l=0 ; l <=lmax; l++){
1805: l1=pow(10,l);
1806: delts=delt;
1807: for(k=1 ; k <kmax; k=k+1){
1808: delt = delta*(l1*k);
1809: p2[theta]=x[theta] +delt;
1810: k1=func(p2)-fx;
1811: p2[theta]=x[theta]-delt;
1812: k2=func(p2)-fx;
1813: /*res= (k1-2.0*fx+k2)/delt/delt; */
1814: res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */
1815:
1816: #ifdef DEBUG
1817: 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);
1818: 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);
1819: #endif
1820: /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
1821: if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
1822: k=kmax;
1823: }
1824: else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
1825: k=kmax; l=lmax*10.;
1826: }
1827: else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){
1828: delts=delt;
1829: }
1830: }
1831: }
1832: delti[theta]=delts;
1833: return res;
1834:
1835: }
1836:
1837: double hessij( double x[], double delti[], int thetai,int thetaj,double (*func)(double []),int npar)
1838: {
1839: int i;
1840: int l=1, l1, lmax=20;
1841: double k1,k2,k3,k4,res,fx;
1842: double p2[NPARMAX+1];
1843: int k;
1844:
1845: fx=func(x);
1846: for (k=1; k<=2; k++) {
1847: for (i=1;i<=npar;i++) p2[i]=x[i];
1848: p2[thetai]=x[thetai]+delti[thetai]/k;
1849: p2[thetaj]=x[thetaj]+delti[thetaj]/k;
1850: k1=func(p2)-fx;
1851:
1852: p2[thetai]=x[thetai]+delti[thetai]/k;
1853: p2[thetaj]=x[thetaj]-delti[thetaj]/k;
1854: k2=func(p2)-fx;
1855:
1856: p2[thetai]=x[thetai]-delti[thetai]/k;
1857: p2[thetaj]=x[thetaj]+delti[thetaj]/k;
1858: k3=func(p2)-fx;
1859:
1860: p2[thetai]=x[thetai]-delti[thetai]/k;
1861: p2[thetaj]=x[thetaj]-delti[thetaj]/k;
1862: k4=func(p2)-fx;
1863: res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */
1864: #ifdef DEBUG
1865: 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);
1866: 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);
1867: #endif
1868: }
1869: return res;
1870: }
1871:
1872: /************** Inverse of matrix **************/
1873: void ludcmp(double **a, int n, int *indx, double *d)
1874: {
1875: int i,imax,j,k;
1876: double big,dum,sum,temp;
1877: double *vv;
1878:
1879: vv=vector(1,n);
1880: *d=1.0;
1881: for (i=1;i<=n;i++) {
1882: big=0.0;
1883: for (j=1;j<=n;j++)
1884: if ((temp=fabs(a[i][j])) > big) big=temp;
1885: if (big == 0.0) nrerror("Singular matrix in routine ludcmp");
1886: vv[i]=1.0/big;
1887: }
1888: for (j=1;j<=n;j++) {
1889: for (i=1;i<j;i++) {
1890: sum=a[i][j];
1891: for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];
1892: a[i][j]=sum;
1893: }
1894: big=0.0;
1895: for (i=j;i<=n;i++) {
1896: sum=a[i][j];
1897: for (k=1;k<j;k++)
1898: sum -= a[i][k]*a[k][j];
1899: a[i][j]=sum;
1900: if ( (dum=vv[i]*fabs(sum)) >= big) {
1901: big=dum;
1902: imax=i;
1903: }
1904: }
1905: if (j != imax) {
1906: for (k=1;k<=n;k++) {
1907: dum=a[imax][k];
1908: a[imax][k]=a[j][k];
1909: a[j][k]=dum;
1910: }
1911: *d = -(*d);
1912: vv[imax]=vv[j];
1913: }
1914: indx[j]=imax;
1915: if (a[j][j] == 0.0) a[j][j]=TINY;
1916: if (j != n) {
1917: dum=1.0/(a[j][j]);
1918: for (i=j+1;i<=n;i++) a[i][j] *= dum;
1919: }
1920: }
1921: free_vector(vv,1,n); /* Doesn't work */
1922: ;
1923: }
1924:
1925: void lubksb(double **a, int n, int *indx, double b[])
1926: {
1927: int i,ii=0,ip,j;
1928: double sum;
1929:
1930: for (i=1;i<=n;i++) {
1931: ip=indx[i];
1932: sum=b[ip];
1933: b[ip]=b[i];
1934: if (ii)
1935: for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];
1936: else if (sum) ii=i;
1937: b[i]=sum;
1938: }
1939: for (i=n;i>=1;i--) {
1940: sum=b[i];
1941: for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];
1942: b[i]=sum/a[i][i];
1943: }
1944: }
1945:
1946: /************ Frequencies ********************/
1947: 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, char strstart[])
1948: { /* Some frequencies */
1949:
1950: int i, m, jk, k1,i1, j1, bool, z1,z2,j;
1951: int first;
1952: double ***freq; /* Frequencies */
1953: double *pp, **prop;
1954: double pos,posprop, k2, dateintsum=0,k2cpt=0;
1955: FILE *ficresp;
1956: char fileresp[FILENAMELENGTH];
1957:
1958: pp=vector(1,nlstate);
1959: prop=matrix(1,nlstate,iagemin,iagemax+3);
1960: strcpy(fileresp,"p");
1961: strcat(fileresp,fileres);
1962: if((ficresp=fopen(fileresp,"w"))==NULL) {
1963: printf("Problem with prevalence resultfile: %s\n", fileresp);
1964: fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
1965: exit(0);
1966: }
1967: freq= ma3x(-5,nlstate+ndeath,-5,nlstate+ndeath,iagemin,iagemax+3);
1968: j1=0;
1969:
1970: j=cptcoveff;
1971: if (cptcovn<1) {j=1;ncodemax[1]=1;}
1972:
1973: first=1;
1974:
1975: for(k1=1; k1<=j;k1++){
1976: for(i1=1; i1<=ncodemax[k1];i1++){
1977: j1++;
1978: /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
1979: scanf("%d", i);*/
1980: for (i=-5; i<=nlstate+ndeath; i++)
1981: for (jk=-5; jk<=nlstate+ndeath; jk++)
1982: for(m=iagemin; m <= iagemax+3; m++)
1983: freq[i][jk][m]=0;
1984:
1985: for (i=1; i<=nlstate; i++)
1986: for(m=iagemin; m <= iagemax+3; m++)
1987: prop[i][m]=0;
1988:
1989: dateintsum=0;
1990: k2cpt=0;
1991: for (i=1; i<=imx; i++) {
1992: bool=1;
1993: if (cptcovn>0) {
1994: for (z1=1; z1<=cptcoveff; z1++)
1995: if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])
1996: bool=0;
1997: }
1998: if (bool==1){
1999: for(m=firstpass; m<=lastpass; m++){
2000: k2=anint[m][i]+(mint[m][i]/12.);
2001: /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/
2002: if(agev[m][i]==0) agev[m][i]=iagemax+1;
2003: if(agev[m][i]==1) agev[m][i]=iagemax+2;
2004: if (s[m][i]>0 && s[m][i]<=nlstate) prop[s[m][i]][(int)agev[m][i]] += weight[i];
2005: if (m<lastpass) {
2006: freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
2007: freq[s[m][i]][s[m+1][i]][iagemax+3] += weight[i];
2008: }
2009:
2010: if ((agev[m][i]>1) && (agev[m][i]< (iagemax+3))) {
2011: dateintsum=dateintsum+k2;
2012: k2cpt++;
2013: }
2014: /*}*/
2015: }
2016: }
2017: }
2018:
2019: /* fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
2020: fprintf(ficresp, "#Local time at start: %s", strstart);
2021: if (cptcovn>0) {
2022: fprintf(ficresp, "\n#********** Variable ");
2023: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
2024: fprintf(ficresp, "**********\n#");
2025: }
2026: for(i=1; i<=nlstate;i++)
2027: fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
2028: fprintf(ficresp, "\n");
2029:
2030: for(i=iagemin; i <= iagemax+3; i++){
2031: if(i==iagemax+3){
2032: fprintf(ficlog,"Total");
2033: }else{
2034: if(first==1){
2035: first=0;
2036: printf("See log file for details...\n");
2037: }
2038: fprintf(ficlog,"Age %d", i);
2039: }
2040: for(jk=1; jk <=nlstate ; jk++){
2041: for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
2042: pp[jk] += freq[jk][m][i];
2043: }
2044: for(jk=1; jk <=nlstate ; jk++){
2045: for(m=-1, pos=0; m <=0 ; m++)
2046: pos += freq[jk][m][i];
2047: if(pp[jk]>=1.e-10){
2048: if(first==1){
2049: printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
2050: }
2051: fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
2052: }else{
2053: if(first==1)
2054: printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
2055: fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
2056: }
2057: }
2058:
2059: for(jk=1; jk <=nlstate ; jk++){
2060: for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
2061: pp[jk] += freq[jk][m][i];
2062: }
2063: for(jk=1,pos=0,posprop=0; jk <=nlstate ; jk++){
2064: pos += pp[jk];
2065: posprop += prop[jk][i];
2066: }
2067: for(jk=1; jk <=nlstate ; jk++){
2068: if(pos>=1.e-5){
2069: if(first==1)
2070: printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
2071: fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
2072: }else{
2073: if(first==1)
2074: printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
2075: fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
2076: }
2077: if( i <= iagemax){
2078: if(pos>=1.e-5){
2079: fprintf(ficresp," %d %.5f %.0f %.0f",i,prop[jk][i]/posprop, prop[jk][i],posprop);
2080: /*probs[i][jk][j1]= pp[jk]/pos;*/
2081: /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/
2082: }
2083: else
2084: fprintf(ficresp," %d NaNq %.0f %.0f",i,prop[jk][i],posprop);
2085: }
2086: }
2087:
2088: for(jk=-1; jk <=nlstate+ndeath; jk++)
2089: for(m=-1; m <=nlstate+ndeath; m++)
2090: if(freq[jk][m][i] !=0 ) {
2091: if(first==1)
2092: printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
2093: fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
2094: }
2095: if(i <= iagemax)
2096: fprintf(ficresp,"\n");
2097: if(first==1)
2098: printf("Others in log...\n");
2099: fprintf(ficlog,"\n");
2100: }
2101: }
2102: }
2103: dateintmean=dateintsum/k2cpt;
2104:
2105: fclose(ficresp);
2106: free_ma3x(freq,-5,nlstate+ndeath,-5,nlstate+ndeath, iagemin, iagemax+3);
2107: free_vector(pp,1,nlstate);
2108: free_matrix(prop,1,nlstate,iagemin, iagemax+3);
2109: /* End of Freq */
2110: }
2111:
2112: /************ Prevalence ********************/
2113: 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)
2114: {
2115: /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
2116: in each health status at the date of interview (if between dateprev1 and dateprev2).
2117: We still use firstpass and lastpass as another selection.
2118: */
2119:
2120: int i, m, jk, k1, i1, j1, bool, z1,z2,j;
2121: double ***freq; /* Frequencies */
2122: double *pp, **prop;
2123: double pos,posprop;
2124: double y2; /* in fractional years */
2125: int iagemin, iagemax;
2126:
2127: iagemin= (int) agemin;
2128: iagemax= (int) agemax;
2129: /*pp=vector(1,nlstate);*/
2130: prop=matrix(1,nlstate,iagemin,iagemax+3);
2131: /* freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
2132: j1=0;
2133:
2134: j=cptcoveff;
2135: if (cptcovn<1) {j=1;ncodemax[1]=1;}
2136:
2137: for(k1=1; k1<=j;k1++){
2138: for(i1=1; i1<=ncodemax[k1];i1++){
2139: j1++;
2140:
2141: for (i=1; i<=nlstate; i++)
2142: for(m=iagemin; m <= iagemax+3; m++)
2143: prop[i][m]=0.0;
2144:
2145: for (i=1; i<=imx; i++) { /* Each individual */
2146: bool=1;
2147: if (cptcovn>0) {
2148: for (z1=1; z1<=cptcoveff; z1++)
2149: if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])
2150: bool=0;
2151: }
2152: if (bool==1) {
2153: for(m=firstpass; m<=lastpass; m++){/* Other selection (we can limit to certain interviews*/
2154: y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
2155: if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
2156: if(agev[m][i]==0) agev[m][i]=iagemax+1;
2157: if(agev[m][i]==1) agev[m][i]=iagemax+2;
2158: 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);
2159: if (s[m][i]>0 && s[m][i]<=nlstate) {
2160: /*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]]);*/
2161: prop[s[m][i]][(int)agev[m][i]] += weight[i];
2162: prop[s[m][i]][iagemax+3] += weight[i];
2163: }
2164: }
2165: } /* end selection of waves */
2166: }
2167: }
2168: for(i=iagemin; i <= iagemax+3; i++){
2169:
2170: for(jk=1,posprop=0; jk <=nlstate ; jk++) {
2171: posprop += prop[jk][i];
2172: }
2173:
2174: for(jk=1; jk <=nlstate ; jk++){
2175: if( i <= iagemax){
2176: if(posprop>=1.e-5){
2177: probs[i][jk][j1]= prop[jk][i]/posprop;
2178: }
2179: }
2180: }/* end jk */
2181: }/* end i */
2182: } /* end i1 */
2183: } /* end k1 */
2184:
2185: /* free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
2186: /*free_vector(pp,1,nlstate);*/
2187: free_matrix(prop,1,nlstate, iagemin,iagemax+3);
2188: } /* End of prevalence */
2189:
2190: /************* Waves Concatenation ***************/
2191:
2192: 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)
2193: {
2194: /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
2195: Death is a valid wave (if date is known).
2196: mw[mi][i] is the mi (mi=1 to wav[i]) effective wave of individual i
2197: dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
2198: and mw[mi+1][i]. dh depends on stepm.
2199: */
2200:
2201: int i, mi, m;
2202: /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
2203: double sum=0., jmean=0.;*/
2204: int first;
2205: int j, k=0,jk, ju, jl;
2206: double sum=0.;
2207: first=0;
2208: jmin=1e+5;
2209: jmax=-1;
2210: jmean=0.;
2211: for(i=1; i<=imx; i++){
2212: mi=0;
2213: m=firstpass;
2214: while(s[m][i] <= nlstate){
2215: if(s[m][i]>=1 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5)
2216: mw[++mi][i]=m;
2217: if(m >=lastpass)
2218: break;
2219: else
2220: m++;
2221: }/* end while */
2222: if (s[m][i] > nlstate){
2223: mi++; /* Death is another wave */
2224: /* if(mi==0) never been interviewed correctly before death */
2225: /* Only death is a correct wave */
2226: mw[mi][i]=m;
2227: }
2228:
2229: wav[i]=mi;
2230: if(mi==0){
2231: nbwarn++;
2232: if(first==0){
2233: printf("Warning! No valid information for individual %ld line=%d (skipped) and may be others, see log file\n",num[i],i);
2234: first=1;
2235: }
2236: if(first==1){
2237: fprintf(ficlog,"Warning! No valid information for individual %ld line=%d (skipped)\n",num[i],i);
2238: }
2239: } /* end mi==0 */
2240: } /* End individuals */
2241:
2242: for(i=1; i<=imx; i++){
2243: for(mi=1; mi<wav[i];mi++){
2244: if (stepm <=0)
2245: dh[mi][i]=1;
2246: else{
2247: if (s[mw[mi+1][i]][i] > nlstate) { /* A death */
2248: if (agedc[i] < 2*AGESUP) {
2249: j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);
2250: if(j==0) j=1; /* Survives at least one month after exam */
2251: else if(j<0){
2252: nberr++;
2253: 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]);
2254: j=1; /* Temporary Dangerous patch */
2255: 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. You MUST fix the contradiction between dates.\n",stepm);
2256: 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]);
2257: 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. You MUST fix the contradiction between dates.\n",stepm);
2258: }
2259: k=k+1;
2260: if (j >= jmax){
2261: jmax=j;
2262: ijmax=i;
2263: }
2264: if (j <= jmin){
2265: jmin=j;
2266: ijmin=i;
2267: }
2268: sum=sum+j;
2269: /*if (j<0) printf("j=%d num=%d \n",j,i);*/
2270: /* printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
2271: }
2272: }
2273: else{
2274: j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
2275: /* if (j<0) printf("%d %lf %lf %d %d %d\n", i,agev[mw[mi+1][i]][i], agev[mw[mi][i]][i],j,s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]); */
2276:
2277: k=k+1;
2278: if (j >= jmax) {
2279: jmax=j;
2280: ijmax=i;
2281: }
2282: else if (j <= jmin){
2283: jmin=j;
2284: ijmin=i;
2285: }
2286: /* if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
2287: /*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]);*/
2288: if(j<0){
2289: nberr++;
2290: 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]);
2291: 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]);
2292: }
2293: sum=sum+j;
2294: }
2295: jk= j/stepm;
2296: jl= j -jk*stepm;
2297: ju= j -(jk+1)*stepm;
2298: if(mle <=1){ /* only if we use a the linear-interpoloation pseudo-likelihood */
2299: if(jl==0){
2300: dh[mi][i]=jk;
2301: bh[mi][i]=0;
2302: }else{ /* We want a negative bias in order to only have interpolation ie
2303: * at the price of an extra matrix product in likelihood */
2304: dh[mi][i]=jk+1;
2305: bh[mi][i]=ju;
2306: }
2307: }else{
2308: if(jl <= -ju){
2309: dh[mi][i]=jk;
2310: bh[mi][i]=jl; /* bias is positive if real duration
2311: * is higher than the multiple of stepm and negative otherwise.
2312: */
2313: }
2314: else{
2315: dh[mi][i]=jk+1;
2316: bh[mi][i]=ju;
2317: }
2318: if(dh[mi][i]==0){
2319: dh[mi][i]=1; /* At least one step */
2320: bh[mi][i]=ju; /* At least one step */
2321: /* 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);*/
2322: }
2323: } /* end if mle */
2324: }
2325: } /* end wave */
2326: }
2327: jmean=sum/k;
2328: printf("Delay (in months) between two waves Min=%d (for indiviudal %ld) Max=%d (%ld) Mean=%f\n\n ",jmin, num[ijmin], jmax, num[ijmax], jmean);
2329: fprintf(ficlog,"Delay (in months) between two waves Min=%d (for indiviudal %ld) Max=%d (%ld) Mean=%f\n\n ",jmin, ijmin, jmax, ijmax, jmean);
2330: }
2331:
2332: /*********** Tricode ****************************/
2333: void tricode(int *Tvar, int **nbcode, int imx)
2334: {
2335:
2336: int Ndum[20],ij=1, k, j, i, maxncov=19;
2337: int cptcode=0;
2338: cptcoveff=0;
2339:
2340: for (k=0; k<maxncov; k++) Ndum[k]=0;
2341: for (k=1; k<=7; k++) ncodemax[k]=0;
2342:
2343: for (j=1; j<=(cptcovn+2*cptcovprod); j++) {
2344: for (i=1; i<=imx; i++) { /*reads the data file to get the maximum
2345: modality*/
2346: ij=(int)(covar[Tvar[j]][i]); /* ij is the modality of this individual*/
2347: Ndum[ij]++; /*store the modality */
2348: /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
2349: if (ij > cptcode) cptcode=ij; /* getting the maximum of covariable
2350: Tvar[j]. If V=sex and male is 0 and
2351: female is 1, then cptcode=1.*/
2352: }
2353:
2354: for (i=0; i<=cptcode; i++) {
2355: 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 */
2356: }
2357:
2358: ij=1;
2359: for (i=1; i<=ncodemax[j]; i++) {
2360: for (k=0; k<= maxncov; k++) {
2361: if (Ndum[k] != 0) {
2362: nbcode[Tvar[j]][ij]=k;
2363: /* 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; */
2364:
2365: ij++;
2366: }
2367: if (ij > ncodemax[j]) break;
2368: }
2369: }
2370: }
2371:
2372: for (k=0; k< maxncov; k++) Ndum[k]=0;
2373:
2374: for (i=1; i<=ncovmodel-2; i++) {
2375: /* Listing of all covariables in statement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/
2376: ij=Tvar[i];
2377: Ndum[ij]++;
2378: }
2379:
2380: ij=1;
2381: for (i=1; i<= maxncov; i++) {
2382: if((Ndum[i]!=0) && (i<=ncovcol)){
2383: Tvaraff[ij]=i; /*For printing */
2384: ij++;
2385: }
2386: }
2387:
2388: cptcoveff=ij-1; /*Number of simple covariates*/
2389: }
2390:
2391: /*********** Health Expectancies ****************/
2392:
2393: 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,char strstart[] )
2394:
2395: {
2396: /* Health expectancies */
2397: int i, j, nhstepm, hstepm, h, nstepm, k, cptj;
2398: double age, agelim, hf;
2399: double ***p3mat,***varhe;
2400: double **dnewm,**doldm;
2401: double *xp;
2402: double **gp, **gm;
2403: double ***gradg, ***trgradg;
2404: int theta;
2405:
2406: varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage);
2407: xp=vector(1,npar);
2408: dnewm=matrix(1,nlstate*nlstate,1,npar);
2409: doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate);
2410:
2411: fprintf(ficreseij,"# Local time at start: %s", strstart);
2412: fprintf(ficreseij,"# Health expectancies\n");
2413: fprintf(ficreseij,"# Age");
2414: for(i=1; i<=nlstate;i++)
2415: for(j=1; j<=nlstate;j++)
2416: fprintf(ficreseij," %1d-%1d (SE)",i,j);
2417: fprintf(ficreseij,"\n");
2418:
2419: if(estepm < stepm){
2420: printf ("Problem %d lower than %d\n",estepm, stepm);
2421: }
2422: else hstepm=estepm;
2423: /* We compute the life expectancy from trapezoids spaced every estepm months
2424: * This is mainly to measure the difference between two models: for example
2425: * if stepm=24 months pijx are given only every 2 years and by summing them
2426: * we are calculating an estimate of the Life Expectancy assuming a linear
2427: * progression in between and thus overestimating or underestimating according
2428: * to the curvature of the survival function. If, for the same date, we
2429: * estimate the model with stepm=1 month, we can keep estepm to 24 months
2430: * to compare the new estimate of Life expectancy with the same linear
2431: * hypothesis. A more precise result, taking into account a more precise
2432: * curvature will be obtained if estepm is as small as stepm. */
2433:
2434: /* For example we decided to compute the life expectancy with the smallest unit */
2435: /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
2436: nhstepm is the number of hstepm from age to agelim
2437: nstepm is the number of stepm from age to agelin.
2438: Look at hpijx to understand the reason of that which relies in memory size
2439: and note for a fixed period like estepm months */
2440: /* We decided (b) to get a life expectancy respecting the most precise curvature of the
2441: survival function given by stepm (the optimization length). Unfortunately it
2442: means that if the survival funtion is printed only each two years of age and if
2443: you sum them up and add 1 year (area under the trapezoids) you won't get the same
2444: results. So we changed our mind and took the option of the best precision.
2445: */
2446: hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
2447:
2448: agelim=AGESUP;
2449: for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
2450: /* nhstepm age range expressed in number of stepm */
2451: nstepm=(int) rint((agelim-age)*YEARM/stepm);
2452: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
2453: /* if (stepm >= YEARM) hstepm=1;*/
2454: nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
2455: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
2456: gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);
2457: gp=matrix(0,nhstepm,1,nlstate*nlstate);
2458: gm=matrix(0,nhstepm,1,nlstate*nlstate);
2459:
2460: /* Computed by stepm unit matrices, product of hstepm matrices, stored
2461: in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
2462: hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);
2463:
2464:
2465: hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
2466:
2467: /* Computing Variances of health expectancies */
2468:
2469: for(theta=1; theta <=npar; theta++){
2470: for(i=1; i<=npar; i++){
2471: xp[i] = x[i] + (i==theta ?delti[theta]:0);
2472: }
2473: hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
2474:
2475: cptj=0;
2476: for(j=1; j<= nlstate; j++){
2477: for(i=1; i<=nlstate; i++){
2478: cptj=cptj+1;
2479: for(h=0, gp[h][cptj]=0.; h<=nhstepm-1; h++){
2480: gp[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;
2481: }
2482: }
2483: }
2484:
2485:
2486: for(i=1; i<=npar; i++)
2487: xp[i] = x[i] - (i==theta ?delti[theta]:0);
2488: hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
2489:
2490: cptj=0;
2491: for(j=1; j<= nlstate; j++){
2492: for(i=1;i<=nlstate;i++){
2493: cptj=cptj+1;
2494: for(h=0, gm[h][cptj]=0.; h<=nhstepm-1; h++){
2495:
2496: gm[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;
2497: }
2498: }
2499: }
2500: for(j=1; j<= nlstate*nlstate; j++)
2501: for(h=0; h<=nhstepm-1; h++){
2502: gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
2503: }
2504: }
2505:
2506: /* End theta */
2507:
2508: trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar);
2509:
2510: for(h=0; h<=nhstepm-1; h++)
2511: for(j=1; j<=nlstate*nlstate;j++)
2512: for(theta=1; theta <=npar; theta++)
2513: trgradg[h][j][theta]=gradg[h][theta][j];
2514:
2515:
2516: for(i=1;i<=nlstate*nlstate;i++)
2517: for(j=1;j<=nlstate*nlstate;j++)
2518: varhe[i][j][(int)age] =0.;
2519:
2520: printf("%d|",(int)age);fflush(stdout);
2521: fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
2522: for(h=0;h<=nhstepm-1;h++){
2523: for(k=0;k<=nhstepm-1;k++){
2524: matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov);
2525: matprod2(doldm,dnewm,1,nlstate*nlstate,1,npar,1,nlstate*nlstate,gradg[k]);
2526: for(i=1;i<=nlstate*nlstate;i++)
2527: for(j=1;j<=nlstate*nlstate;j++)
2528: varhe[i][j][(int)age] += doldm[i][j]*hf*hf;
2529: }
2530: }
2531: /* Computing expectancies */
2532: for(i=1; i<=nlstate;i++)
2533: for(j=1; j<=nlstate;j++)
2534: for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
2535: eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
2536:
2537: /* 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]);*/
2538:
2539: }
2540:
2541: fprintf(ficreseij,"%3.0f",age );
2542: cptj=0;
2543: for(i=1; i<=nlstate;i++)
2544: for(j=1; j<=nlstate;j++){
2545: cptj++;
2546: fprintf(ficreseij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[cptj][cptj][(int)age]) );
2547: }
2548: fprintf(ficreseij,"\n");
2549:
2550: free_matrix(gm,0,nhstepm,1,nlstate*nlstate);
2551: free_matrix(gp,0,nhstepm,1,nlstate*nlstate);
2552: free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*nlstate);
2553: free_ma3x(trgradg,0,nhstepm,1,nlstate*nlstate,1,npar);
2554: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
2555: }
2556: printf("\n");
2557: fprintf(ficlog,"\n");
2558:
2559: free_vector(xp,1,npar);
2560: free_matrix(dnewm,1,nlstate*nlstate,1,npar);
2561: free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate);
2562: free_ma3x(varhe,1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int)fage);
2563: }
2564:
2565: /************ Variance ******************/
2566: 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, char strstart[])
2567: {
2568: /* Variance of health expectancies */
2569: /* double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
2570: /* double **newm;*/
2571: double **dnewm,**doldm;
2572: double **dnewmp,**doldmp;
2573: int i, j, nhstepm, hstepm, h, nstepm ;
2574: int k, cptcode;
2575: double *xp;
2576: double **gp, **gm; /* for var eij */
2577: double ***gradg, ***trgradg; /*for var eij */
2578: double **gradgp, **trgradgp; /* for var p point j */
2579: double *gpp, *gmp; /* for var p point j */
2580: double **varppt; /* for var p point j nlstate to nlstate+ndeath */
2581: double ***p3mat;
2582: double age,agelim, hf;
2583: double ***mobaverage;
2584: int theta;
2585: char digit[4];
2586: char digitp[25];
2587:
2588: char fileresprobmorprev[FILENAMELENGTH];
2589:
2590: if(popbased==1){
2591: if(mobilav!=0)
2592: strcpy(digitp,"-populbased-mobilav-");
2593: else strcpy(digitp,"-populbased-nomobil-");
2594: }
2595: else
2596: strcpy(digitp,"-stablbased-");
2597:
2598: if (mobilav!=0) {
2599: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
2600: if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
2601: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
2602: printf(" Error in movingaverage mobilav=%d\n",mobilav);
2603: }
2604: }
2605:
2606: strcpy(fileresprobmorprev,"prmorprev");
2607: sprintf(digit,"%-d",ij);
2608: /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
2609: strcat(fileresprobmorprev,digit); /* Tvar to be done */
2610: strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
2611: strcat(fileresprobmorprev,fileres);
2612: if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
2613: printf("Problem with resultfile: %s\n", fileresprobmorprev);
2614: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
2615: }
2616: printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
2617:
2618: fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
2619: fprintf(ficresprobmorprev, "#Local time at start: %s", strstart);
2620: 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);
2621: fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
2622: for(j=nlstate+1; j<=(nlstate+ndeath);j++){
2623: fprintf(ficresprobmorprev," p.%-d SE",j);
2624: for(i=1; i<=nlstate;i++)
2625: fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
2626: }
2627: fprintf(ficresprobmorprev,"\n");
2628: fprintf(ficgp,"\n# Routine varevsij");
2629: /* fprintf(fichtm, "#Local time at start: %s", strstart);*/
2630: 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");
2631: fprintf(fichtm,"\n<br>%s <br>\n",digitp);
2632: /* } */
2633: varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
2634: fprintf(ficresvij, "#Local time at start: %s", strstart);
2635: 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");
2636: fprintf(ficresvij,"# Age");
2637: for(i=1; i<=nlstate;i++)
2638: for(j=1; j<=nlstate;j++)
2639: fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);
2640: fprintf(ficresvij,"\n");
2641:
2642: xp=vector(1,npar);
2643: dnewm=matrix(1,nlstate,1,npar);
2644: doldm=matrix(1,nlstate,1,nlstate);
2645: dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
2646: doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
2647:
2648: gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
2649: gpp=vector(nlstate+1,nlstate+ndeath);
2650: gmp=vector(nlstate+1,nlstate+ndeath);
2651: trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
2652:
2653: if(estepm < stepm){
2654: printf ("Problem %d lower than %d\n",estepm, stepm);
2655: }
2656: else hstepm=estepm;
2657: /* For example we decided to compute the life expectancy with the smallest unit */
2658: /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
2659: nhstepm is the number of hstepm from age to agelim
2660: nstepm is the number of stepm from age to agelin.
2661: Look at hpijx to understand the reason of that which relies in memory size
2662: and note for a fixed period like k years */
2663: /* We decided (b) to get a life expectancy respecting the most precise curvature of the
2664: survival function given by stepm (the optimization length). Unfortunately it
2665: means that if the survival funtion is printed every two years of age and if
2666: you sum them up and add 1 year (area under the trapezoids) you won't get the same
2667: results. So we changed our mind and took the option of the best precision.
2668: */
2669: hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
2670: agelim = AGESUP;
2671: for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
2672: nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
2673: nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
2674: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
2675: gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
2676: gp=matrix(0,nhstepm,1,nlstate);
2677: gm=matrix(0,nhstepm,1,nlstate);
2678:
2679:
2680: for(theta=1; theta <=npar; theta++){
2681: for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
2682: xp[i] = x[i] + (i==theta ?delti[theta]:0);
2683: }
2684: hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
2685: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
2686:
2687: if (popbased==1) {
2688: if(mobilav ==0){
2689: for(i=1; i<=nlstate;i++)
2690: prlim[i][i]=probs[(int)age][i][ij];
2691: }else{ /* mobilav */
2692: for(i=1; i<=nlstate;i++)
2693: prlim[i][i]=mobaverage[(int)age][i][ij];
2694: }
2695: }
2696:
2697: for(j=1; j<= nlstate; j++){
2698: for(h=0; h<=nhstepm; h++){
2699: for(i=1, gp[h][j]=0.;i<=nlstate;i++)
2700: gp[h][j] += prlim[i][i]*p3mat[i][j][h];
2701: }
2702: }
2703: /* This for computing probability of death (h=1 means
2704: computed over hstepm matrices product = hstepm*stepm months)
2705: as a weighted average of prlim.
2706: */
2707: for(j=nlstate+1;j<=nlstate+ndeath;j++){
2708: for(i=1,gpp[j]=0.; i<= nlstate; i++)
2709: gpp[j] += prlim[i][i]*p3mat[i][j][1];
2710: }
2711: /* end probability of death */
2712:
2713: for(i=1; i<=npar; i++) /* Computes gradient x - delta */
2714: xp[i] = x[i] - (i==theta ?delti[theta]:0);
2715: hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
2716: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
2717:
2718: if (popbased==1) {
2719: if(mobilav ==0){
2720: for(i=1; i<=nlstate;i++)
2721: prlim[i][i]=probs[(int)age][i][ij];
2722: }else{ /* mobilav */
2723: for(i=1; i<=nlstate;i++)
2724: prlim[i][i]=mobaverage[(int)age][i][ij];
2725: }
2726: }
2727:
2728: for(j=1; j<= nlstate; j++){
2729: for(h=0; h<=nhstepm; h++){
2730: for(i=1, gm[h][j]=0.;i<=nlstate;i++)
2731: gm[h][j] += prlim[i][i]*p3mat[i][j][h];
2732: }
2733: }
2734: /* This for computing probability of death (h=1 means
2735: computed over hstepm matrices product = hstepm*stepm months)
2736: as a weighted average of prlim.
2737: */
2738: for(j=nlstate+1;j<=nlstate+ndeath;j++){
2739: for(i=1,gmp[j]=0.; i<= nlstate; i++)
2740: gmp[j] += prlim[i][i]*p3mat[i][j][1];
2741: }
2742: /* end probability of death */
2743:
2744: for(j=1; j<= nlstate; j++) /* vareij */
2745: for(h=0; h<=nhstepm; h++){
2746: gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
2747: }
2748:
2749: for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
2750: gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
2751: }
2752:
2753: } /* End theta */
2754:
2755: trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
2756:
2757: for(h=0; h<=nhstepm; h++) /* veij */
2758: for(j=1; j<=nlstate;j++)
2759: for(theta=1; theta <=npar; theta++)
2760: trgradg[h][j][theta]=gradg[h][theta][j];
2761:
2762: for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
2763: for(theta=1; theta <=npar; theta++)
2764: trgradgp[j][theta]=gradgp[theta][j];
2765:
2766:
2767: hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
2768: for(i=1;i<=nlstate;i++)
2769: for(j=1;j<=nlstate;j++)
2770: vareij[i][j][(int)age] =0.;
2771:
2772: for(h=0;h<=nhstepm;h++){
2773: for(k=0;k<=nhstepm;k++){
2774: matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
2775: matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
2776: for(i=1;i<=nlstate;i++)
2777: for(j=1;j<=nlstate;j++)
2778: vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
2779: }
2780: }
2781:
2782: /* pptj */
2783: matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
2784: matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
2785: for(j=nlstate+1;j<=nlstate+ndeath;j++)
2786: for(i=nlstate+1;i<=nlstate+ndeath;i++)
2787: varppt[j][i]=doldmp[j][i];
2788: /* end ppptj */
2789: /* x centered again */
2790: hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);
2791: prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);
2792:
2793: if (popbased==1) {
2794: if(mobilav ==0){
2795: for(i=1; i<=nlstate;i++)
2796: prlim[i][i]=probs[(int)age][i][ij];
2797: }else{ /* mobilav */
2798: for(i=1; i<=nlstate;i++)
2799: prlim[i][i]=mobaverage[(int)age][i][ij];
2800: }
2801: }
2802:
2803: /* This for computing probability of death (h=1 means
2804: computed over hstepm (estepm) matrices product = hstepm*stepm months)
2805: as a weighted average of prlim.
2806: */
2807: for(j=nlstate+1;j<=nlstate+ndeath;j++){
2808: for(i=1,gmp[j]=0.;i<= nlstate; i++)
2809: gmp[j] += prlim[i][i]*p3mat[i][j][1];
2810: }
2811: /* end probability of death */
2812:
2813: fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
2814: for(j=nlstate+1; j<=(nlstate+ndeath);j++){
2815: fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
2816: for(i=1; i<=nlstate;i++){
2817: fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
2818: }
2819: }
2820: fprintf(ficresprobmorprev,"\n");
2821:
2822: fprintf(ficresvij,"%.0f ",age );
2823: for(i=1; i<=nlstate;i++)
2824: for(j=1; j<=nlstate;j++){
2825: fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
2826: }
2827: fprintf(ficresvij,"\n");
2828: free_matrix(gp,0,nhstepm,1,nlstate);
2829: free_matrix(gm,0,nhstepm,1,nlstate);
2830: free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
2831: free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
2832: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
2833: } /* End age */
2834: free_vector(gpp,nlstate+1,nlstate+ndeath);
2835: free_vector(gmp,nlstate+1,nlstate+ndeath);
2836: free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
2837: free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
2838: fprintf(ficgp,"\nset noparametric;set nolabel; set ter png small;set size 0.65, 0.65");
2839: /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */
2840: fprintf(ficgp,"\n set log y; set nolog x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
2841: /* fprintf(ficgp,"\n plot \"%s\" u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm); */
2842: /* fprintf(ficgp,"\n replot \"%s\" u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm); */
2843: /* fprintf(ficgp,"\n replot \"%s\" u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm); */
2844: fprintf(ficgp,"\n plot \"%s\" u 1:($3) not w l 1 ",subdirf(fileresprobmorprev));
2845: fprintf(ficgp,"\n replot \"%s\" u 1:(($3+1.96*$4)) t \"95\%% interval\" w l 2 ",subdirf(fileresprobmorprev));
2846: fprintf(ficgp,"\n replot \"%s\" u 1:(($3-1.96*$4)) not w l 2 ",subdirf(fileresprobmorprev));
2847: fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",subdirf(fileresprobmorprev),subdirf(fileresprobmorprev));
2848: 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);
2849: /* 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);
2850: */
2851: /* fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.png\";replot;",digitp,optionfilefiname,digit); */
2852: fprintf(ficgp,"\nset out \"%s%s.png\";replot;\n",subdirf3(optionfilefiname,"varmuptjgr",digitp),digit);
2853:
2854: free_vector(xp,1,npar);
2855: free_matrix(doldm,1,nlstate,1,nlstate);
2856: free_matrix(dnewm,1,nlstate,1,npar);
2857: free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
2858: free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
2859: free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
2860: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
2861: fclose(ficresprobmorprev);
2862: fflush(ficgp);
2863: fflush(fichtm);
2864: } /* end varevsij */
2865:
2866: /************ Variance of prevlim ******************/
2867: 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, char strstart[])
2868: {
2869: /* Variance of prevalence limit */
2870: /* double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
2871: double **newm;
2872: double **dnewm,**doldm;
2873: int i, j, nhstepm, hstepm;
2874: int k, cptcode;
2875: double *xp;
2876: double *gp, *gm;
2877: double **gradg, **trgradg;
2878: double age,agelim;
2879: int theta;
2880: fprintf(ficresvpl, "#Local time at start: %s", strstart);
2881: fprintf(ficresvpl,"# Standard deviation of stable prevalences \n");
2882: fprintf(ficresvpl,"# Age");
2883: for(i=1; i<=nlstate;i++)
2884: fprintf(ficresvpl," %1d-%1d",i,i);
2885: fprintf(ficresvpl,"\n");
2886:
2887: xp=vector(1,npar);
2888: dnewm=matrix(1,nlstate,1,npar);
2889: doldm=matrix(1,nlstate,1,nlstate);
2890:
2891: hstepm=1*YEARM; /* Every year of age */
2892: hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */
2893: agelim = AGESUP;
2894: for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
2895: nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
2896: if (stepm >= YEARM) hstepm=1;
2897: nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
2898: gradg=matrix(1,npar,1,nlstate);
2899: gp=vector(1,nlstate);
2900: gm=vector(1,nlstate);
2901:
2902: for(theta=1; theta <=npar; theta++){
2903: for(i=1; i<=npar; i++){ /* Computes gradient */
2904: xp[i] = x[i] + (i==theta ?delti[theta]:0);
2905: }
2906: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
2907: for(i=1;i<=nlstate;i++)
2908: gp[i] = prlim[i][i];
2909:
2910: for(i=1; i<=npar; i++) /* Computes gradient */
2911: xp[i] = x[i] - (i==theta ?delti[theta]:0);
2912: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
2913: for(i=1;i<=nlstate;i++)
2914: gm[i] = prlim[i][i];
2915:
2916: for(i=1;i<=nlstate;i++)
2917: gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
2918: } /* End theta */
2919:
2920: trgradg =matrix(1,nlstate,1,npar);
2921:
2922: for(j=1; j<=nlstate;j++)
2923: for(theta=1; theta <=npar; theta++)
2924: trgradg[j][theta]=gradg[theta][j];
2925:
2926: for(i=1;i<=nlstate;i++)
2927: varpl[i][(int)age] =0.;
2928: matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
2929: matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
2930: for(i=1;i<=nlstate;i++)
2931: varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
2932:
2933: fprintf(ficresvpl,"%.0f ",age );
2934: for(i=1; i<=nlstate;i++)
2935: fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
2936: fprintf(ficresvpl,"\n");
2937: free_vector(gp,1,nlstate);
2938: free_vector(gm,1,nlstate);
2939: free_matrix(gradg,1,npar,1,nlstate);
2940: free_matrix(trgradg,1,nlstate,1,npar);
2941: } /* End age */
2942:
2943: free_vector(xp,1,npar);
2944: free_matrix(doldm,1,nlstate,1,npar);
2945: free_matrix(dnewm,1,nlstate,1,nlstate);
2946:
2947: }
2948:
2949: /************ Variance of one-step probabilities ******************/
2950: void varprob(char optionfilefiname[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij, int *Tvar, int **nbcode, int *ncodemax, char strstart[])
2951: {
2952: int i, j=0, i1, k1, l1, t, tj;
2953: int k2, l2, j1, z1;
2954: int k=0,l, cptcode;
2955: int first=1, first1;
2956: double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
2957: double **dnewm,**doldm;
2958: double *xp;
2959: double *gp, *gm;
2960: double **gradg, **trgradg;
2961: double **mu;
2962: double age,agelim, cov[NCOVMAX];
2963: double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
2964: int theta;
2965: char fileresprob[FILENAMELENGTH];
2966: char fileresprobcov[FILENAMELENGTH];
2967: char fileresprobcor[FILENAMELENGTH];
2968:
2969: double ***varpij;
2970:
2971: strcpy(fileresprob,"prob");
2972: strcat(fileresprob,fileres);
2973: if((ficresprob=fopen(fileresprob,"w"))==NULL) {
2974: printf("Problem with resultfile: %s\n", fileresprob);
2975: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
2976: }
2977: strcpy(fileresprobcov,"probcov");
2978: strcat(fileresprobcov,fileres);
2979: if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
2980: printf("Problem with resultfile: %s\n", fileresprobcov);
2981: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
2982: }
2983: strcpy(fileresprobcor,"probcor");
2984: strcat(fileresprobcor,fileres);
2985: if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
2986: printf("Problem with resultfile: %s\n", fileresprobcor);
2987: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
2988: }
2989: printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
2990: fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
2991: printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
2992: fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
2993: printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
2994: fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
2995: fprintf(ficresprob, "#Local time at start: %s", strstart);
2996: fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
2997: fprintf(ficresprob,"# Age");
2998: fprintf(ficresprobcov, "#Local time at start: %s", strstart);
2999: fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
3000: fprintf(ficresprobcov,"# Age");
3001: fprintf(ficresprobcor, "#Local time at start: %s", strstart);
3002: fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
3003: fprintf(ficresprobcov,"# Age");
3004:
3005:
3006: for(i=1; i<=nlstate;i++)
3007: for(j=1; j<=(nlstate+ndeath);j++){
3008: fprintf(ficresprob," p%1d-%1d (SE)",i,j);
3009: fprintf(ficresprobcov," p%1d-%1d ",i,j);
3010: fprintf(ficresprobcor," p%1d-%1d ",i,j);
3011: }
3012: /* fprintf(ficresprob,"\n");
3013: fprintf(ficresprobcov,"\n");
3014: fprintf(ficresprobcor,"\n");
3015: */
3016: xp=vector(1,npar);
3017: dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
3018: doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
3019: mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
3020: varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
3021: first=1;
3022: fprintf(ficgp,"\n# Routine varprob");
3023: fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
3024: fprintf(fichtm,"\n");
3025:
3026: fprintf(fichtm,"\n<li><h4> <a href=\"%s\">Matrix of variance-covariance of pairs of step probabilities (drawings)</a></h4></li>\n",optionfilehtmcov);
3027: fprintf(fichtmcov,"\n<h4>Matrix of variance-covariance of pairs of step probabilities</h4>\n\
3028: file %s<br>\n",optionfilehtmcov);
3029: fprintf(fichtmcov,"\nEllipsoids of confidence centered on point (p<inf>ij</inf>, p<inf>kl</inf>) are estimated\
3030: and drawn. It helps understanding how is the covariance between two incidences.\
3031: They are expressed in year<sup>-1</sup> in order to be less dependent of stepm.<br>\n");
3032: 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. \
3033: It can be understood this way: if pij and pkl where uncorrelated the (2x2) matrix of covariance \
3034: would have been (1/(var pij), 0 , 0, 1/(var pkl)), and the confidence interval would be 2 \
3035: standard deviations wide on each axis. <br>\
3036: Now, if both incidences are correlated (usual case) we diagonalised the inverse of the covariance matrix\
3037: and made the appropriate rotation to look at the uncorrelated principal directions.<br>\
3038: To be simple, these graphs help to understand the significativity of each parameter in relation to a second other one.<br> \n");
3039:
3040: cov[1]=1;
3041: tj=cptcoveff;
3042: if (cptcovn<1) {tj=1;ncodemax[1]=1;}
3043: j1=0;
3044: for(t=1; t<=tj;t++){
3045: for(i1=1; i1<=ncodemax[t];i1++){
3046: j1++;
3047: if (cptcovn>0) {
3048: fprintf(ficresprob, "\n#********** Variable ");
3049: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
3050: fprintf(ficresprob, "**********\n#\n");
3051: fprintf(ficresprobcov, "\n#********** Variable ");
3052: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
3053: fprintf(ficresprobcov, "**********\n#\n");
3054:
3055: fprintf(ficgp, "\n#********** Variable ");
3056: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
3057: fprintf(ficgp, "**********\n#\n");
3058:
3059:
3060: fprintf(fichtmcov, "\n<hr size=\"2\" color=\"#EC5E5E\">********** Variable ");
3061: for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
3062: fprintf(fichtmcov, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
3063:
3064: fprintf(ficresprobcor, "\n#********** Variable ");
3065: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
3066: fprintf(ficresprobcor, "**********\n#");
3067: }
3068:
3069: for (age=bage; age<=fage; age ++){
3070: cov[2]=age;
3071: for (k=1; k<=cptcovn;k++) {
3072: cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];
3073: }
3074: for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
3075: for (k=1; k<=cptcovprod;k++)
3076: cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
3077:
3078: gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
3079: trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
3080: gp=vector(1,(nlstate)*(nlstate+ndeath));
3081: gm=vector(1,(nlstate)*(nlstate+ndeath));
3082:
3083: for(theta=1; theta <=npar; theta++){
3084: for(i=1; i<=npar; i++)
3085: xp[i] = x[i] + (i==theta ?delti[theta]:(double)0);
3086:
3087: pmij(pmmij,cov,ncovmodel,xp,nlstate);
3088:
3089: k=0;
3090: for(i=1; i<= (nlstate); i++){
3091: for(j=1; j<=(nlstate+ndeath);j++){
3092: k=k+1;
3093: gp[k]=pmmij[i][j];
3094: }
3095: }
3096:
3097: for(i=1; i<=npar; i++)
3098: xp[i] = x[i] - (i==theta ?delti[theta]:(double)0);
3099:
3100: pmij(pmmij,cov,ncovmodel,xp,nlstate);
3101: k=0;
3102: for(i=1; i<=(nlstate); i++){
3103: for(j=1; j<=(nlstate+ndeath);j++){
3104: k=k+1;
3105: gm[k]=pmmij[i][j];
3106: }
3107: }
3108:
3109: for(i=1; i<= (nlstate)*(nlstate+ndeath); i++)
3110: gradg[theta][i]=(gp[i]-gm[i])/(double)2./delti[theta];
3111: }
3112:
3113: for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
3114: for(theta=1; theta <=npar; theta++)
3115: trgradg[j][theta]=gradg[theta][j];
3116:
3117: matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov);
3118: matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);
3119: free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
3120: free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
3121: free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
3122: free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
3123:
3124: pmij(pmmij,cov,ncovmodel,x,nlstate);
3125:
3126: k=0;
3127: for(i=1; i<=(nlstate); i++){
3128: for(j=1; j<=(nlstate+ndeath);j++){
3129: k=k+1;
3130: mu[k][(int) age]=pmmij[i][j];
3131: }
3132: }
3133: for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
3134: for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
3135: varpij[i][j][(int)age] = doldm[i][j];
3136:
3137: /*printf("\n%d ",(int)age);
3138: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
3139: printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
3140: fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
3141: }*/
3142:
3143: fprintf(ficresprob,"\n%d ",(int)age);
3144: fprintf(ficresprobcov,"\n%d ",(int)age);
3145: fprintf(ficresprobcor,"\n%d ",(int)age);
3146:
3147: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)
3148: fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));
3149: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
3150: fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);
3151: fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
3152: }
3153: i=0;
3154: for (k=1; k<=(nlstate);k++){
3155: for (l=1; l<=(nlstate+ndeath);l++){
3156: i=i++;
3157: fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
3158: fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
3159: for (j=1; j<=i;j++){
3160: fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);
3161: fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));
3162: }
3163: }
3164: }/* end of loop for state */
3165: } /* end of loop for age */
3166:
3167: /* Confidence intervalle of pij */
3168: /*
3169: fprintf(ficgp,"\nset noparametric;unset label");
3170: fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");
3171: fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
3172: 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);
3173: fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);
3174: fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);
3175: fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);
3176: */
3177:
3178: /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
3179: first1=1;
3180: for (k2=1; k2<=(nlstate);k2++){
3181: for (l2=1; l2<=(nlstate+ndeath);l2++){
3182: if(l2==k2) continue;
3183: j=(k2-1)*(nlstate+ndeath)+l2;
3184: for (k1=1; k1<=(nlstate);k1++){
3185: for (l1=1; l1<=(nlstate+ndeath);l1++){
3186: if(l1==k1) continue;
3187: i=(k1-1)*(nlstate+ndeath)+l1;
3188: if(i<=j) continue;
3189: for (age=bage; age<=fage; age ++){
3190: if ((int)age %5==0){
3191: v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;
3192: v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;
3193: cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;
3194: mu1=mu[i][(int) age]/stepm*YEARM ;
3195: mu2=mu[j][(int) age]/stepm*YEARM;
3196: c12=cv12/sqrt(v1*v2);
3197: /* Computing eigen value of matrix of covariance */
3198: lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
3199: lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
3200: /* Eigen vectors */
3201: v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
3202: /*v21=sqrt(1.-v11*v11); *//* error */
3203: v21=(lc1-v1)/cv12*v11;
3204: v12=-v21;
3205: v22=v11;
3206: tnalp=v21/v11;
3207: if(first1==1){
3208: first1=0;
3209: 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);
3210: }
3211: 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);
3212: /*printf(fignu*/
3213: /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */
3214: /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */
3215: if(first==1){
3216: first=0;
3217: fprintf(ficgp,"\nset parametric;unset label");
3218: 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);
3219: fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
3220: fprintf(fichtmcov,"\n<br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup>\
3221: :<a href=\"%s%d%1d%1d-%1d%1d.png\">\
3222: %s%d%1d%1d-%1d%1d.png</A>, ",k1,l1,k2,l2,\
3223: subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2,\
3224: subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
3225: fprintf(fichtmcov,"\n<br><img src=\"%s%d%1d%1d-%1d%1d.png\"> ",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
3226: fprintf(fichtmcov,"\n<br> Correlation at age %d (%.3f),",(int) age, c12);
3227: fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\"",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
3228: fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
3229: fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
3230: 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",\
3231: mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
3232: mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
3233: }else{
3234: first=0;
3235: fprintf(fichtmcov," %d (%.3f),",(int) age, c12);
3236: fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
3237: fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
3238: 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",\
3239: mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
3240: mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
3241: }/* if first */
3242: } /* age mod 5 */
3243: } /* end loop age */
3244: fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\";replot;",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
3245: first=1;
3246: } /*l12 */
3247: } /* k12 */
3248: } /*l1 */
3249: }/* k1 */
3250: } /* loop covariates */
3251: }
3252: free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
3253: free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
3254: free_matrix(doldm,1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
3255: free_matrix(dnewm,1,(nlstate)*(nlstate+ndeath),1,npar);
3256: free_vector(xp,1,npar);
3257: fclose(ficresprob);
3258: fclose(ficresprobcov);
3259: fclose(ficresprobcor);
3260: fflush(ficgp);
3261: fflush(fichtmcov);
3262: }
3263:
3264:
3265: /******************* Printing html file ***********/
3266: void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \
3267: int lastpass, int stepm, int weightopt, char model[],\
3268: int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
3269: int popforecast, int estepm ,\
3270: double jprev1, double mprev1,double anprev1, \
3271: double jprev2, double mprev2,double anprev2){
3272: int jj1, k1, i1, cpt;
3273:
3274: fprintf(fichtm,"<ul><li><a href='#firstorder'>Result files (first order: no variance)</a>\n \
3275: <li><a href='#secondorder'>Result files (second order (variance)</a>\n \
3276: </ul>");
3277: fprintf(fichtm,"<ul><li><h4><a name='firstorder'>Result files (first order: no variance)</a></h4>\n \
3278: - Observed prevalence in each state (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"%s\">%s</a> <br>\n ",
3279: jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirf2(fileres,"p"),subdirf2(fileres,"p"));
3280: fprintf(fichtm,"\
3281: - Estimated transition probabilities over %d (stepm) months: <a href=\"%s\">%s</a><br>\n ",
3282: stepm,subdirf2(fileres,"pij"),subdirf2(fileres,"pij"));
3283: fprintf(fichtm,"\
3284: - Stable prevalence in each health state: <a href=\"%s\">%s</a> <br>\n",
3285: subdirf2(fileres,"pl"),subdirf2(fileres,"pl"));
3286: fprintf(fichtm,"\
3287: - Life expectancies by age and initial health status (estepm=%2d months) WRONG LINK (to be made): \
3288: <a href=\"%s\">%s</a> <br>\n</li>",
3289: estepm,subdirf2(fileres,"le"),subdirf2(fileres,"le"));
3290: fprintf(fichtm,"\
3291: - Health expectancies by age and initial health status with standard errors (estepm=%2d months): \
3292: <a href=\"%s\">%s</a> <br>\n</li>",
3293: estepm,subdirf2(fileres,"e"),subdirf2(fileres,"e"));
3294: fprintf(fichtm,"\
3295: - Variances and covariances of health expectancies by age and initial health status (estepm=%2d months) TO BE MADE: \
3296: <a href=\"%s\">%s</a> <br>\n</li>",
3297: estepm,subdirf2(fileres,"vch"),subdirf2(fileres,"vch"));
3298:
3299:
3300: fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
3301:
3302: m=cptcoveff;
3303: if (cptcovn < 1) {m=1;ncodemax[1]=1;}
3304:
3305: jj1=0;
3306: for(k1=1; k1<=m;k1++){
3307: for(i1=1; i1<=ncodemax[k1];i1++){
3308: jj1++;
3309: if (cptcovn > 0) {
3310: fprintf(fichtm,"<hr size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
3311: for (cpt=1; cpt<=cptcoveff;cpt++)
3312: fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
3313: fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
3314: }
3315: /* Pij */
3316: 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> \
3317: <img src=\"%s%d1.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);
3318: /* Quasi-incidences */
3319: fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months\
3320: before but expressed in per year i.e. quasi incidences if stepm is small and probabilities too: %s%d2.png<br> \
3321: <img src=\"%s%d2.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);
3322: /* Stable prevalence in each health state */
3323: for(cpt=1; cpt<nlstate;cpt++){
3324: fprintf(fichtm,"<br>- Stable prevalence in each health state : p%s%d%d.png<br> \
3325: <img src=\"%s%d%d.png\">",subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1);
3326: }
3327: for(cpt=1; cpt<=nlstate;cpt++) {
3328: fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): %s%d%d.png <br> \
3329: <img src=\"%s%d%d.png\">",cpt,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1);
3330: }
3331: } /* end i1 */
3332: }/* End k1 */
3333: fprintf(fichtm,"</ul>");
3334:
3335:
3336: fprintf(fichtm,"\
3337: \n<br><li><h4> <a name='secondorder'>Result files (second order: variances)</a></h4>\n\
3338: - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n", rfileres,rfileres);
3339:
3340: fprintf(fichtm," - Variance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
3341: subdirf2(fileres,"prob"),subdirf2(fileres,"prob"));
3342: fprintf(fichtm,"\
3343: - Variance-covariance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
3344: subdirf2(fileres,"probcov"),subdirf2(fileres,"probcov"));
3345:
3346: fprintf(fichtm,"\
3347: - Correlation matrix of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
3348: subdirf2(fileres,"probcor"),subdirf2(fileres,"probcor"));
3349: fprintf(fichtm,"\
3350: - Variances and covariances of health expectancies by age (estepm=%d months): <a href=\"%s\">%s</a><br>\n",
3351: estepm, subdirf2(fileres,"v"),subdirf2(fileres,"v"));
3352: fprintf(fichtm,"\
3353: - Life and health expectancies with their standard errors: <a href=\"%s\">%s</a> <br>\n",
3354: subdirf2(fileres,"t"),subdirf2(fileres,"t"));
3355: fprintf(fichtm,"\
3356: - Standard deviation of stable prevalences: <a href=\"%s\">%s</a> <br>\n",\
3357: subdirf2(fileres,"vpl"),subdirf2(fileres,"vpl"));
3358:
3359: /* if(popforecast==1) fprintf(fichtm,"\n */
3360: /* - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n */
3361: /* - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n */
3362: /* <br>",fileres,fileres,fileres,fileres); */
3363: /* else */
3364: /* 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); */
3365: fflush(fichtm);
3366: fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
3367:
3368: m=cptcoveff;
3369: if (cptcovn < 1) {m=1;ncodemax[1]=1;}
3370:
3371: jj1=0;
3372: for(k1=1; k1<=m;k1++){
3373: for(i1=1; i1<=ncodemax[k1];i1++){
3374: jj1++;
3375: if (cptcovn > 0) {
3376: fprintf(fichtm,"<hr size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
3377: for (cpt=1; cpt<=cptcoveff;cpt++)
3378: fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
3379: fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
3380: }
3381: for(cpt=1; cpt<=nlstate;cpt++) {
3382: fprintf(fichtm,"<br>- Observed (cross-sectional) and period (incidence based) \
3383: prevalence (with 95%% confidence interval) in state (%d): %s%d%d.png <br>\
3384: <img src=\"%s%d%d.png\">",cpt,subdirf2(optionfilefiname,"v"),cpt,jj1,subdirf2(optionfilefiname,"v"),cpt,jj1);
3385: }
3386: fprintf(fichtm,"\n<br>- Total life expectancy by age and \
3387: health expectancies in states (1) and (2): %s%d.png<br>\
3388: <img src=\"%s%d.png\">",subdirf2(optionfilefiname,"e"),jj1,subdirf2(optionfilefiname,"e"),jj1);
3389: } /* end i1 */
3390: }/* End k1 */
3391: fprintf(fichtm,"</ul>");
3392: fflush(fichtm);
3393: }
3394:
3395: /******************* Gnuplot file **************/
3396: void printinggnuplot(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
3397:
3398: char dirfileres[132],optfileres[132];
3399: int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;
3400: int ng;
3401: /* if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) { */
3402: /* printf("Problem with file %s",optionfilegnuplot); */
3403: /* fprintf(ficlog,"Problem with file %s",optionfilegnuplot); */
3404: /* } */
3405:
3406: /*#ifdef windows */
3407: fprintf(ficgp,"cd \"%s\" \n",pathc);
3408: /*#endif */
3409: m=pow(2,cptcoveff);
3410:
3411: strcpy(dirfileres,optionfilefiname);
3412: strcpy(optfileres,"vpl");
3413: /* 1eme*/
3414: for (cpt=1; cpt<= nlstate ; cpt ++) {
3415: for (k1=1; k1<= m ; k1 ++) {
3416: fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"v"),cpt,k1);
3417: fprintf(ficgp,"\n#set out \"v%s%d%d.png\" \n",optionfilefiname,cpt,k1);
3418: fprintf(ficgp,"set xlabel \"Age\" \n\
3419: set ylabel \"Probability\" \n\
3420: set ter png small\n\
3421: set size 0.65,0.65\n\
3422: plot [%.f:%.f] \"%s\" every :::%d::%d u 1:2 \"\%%lf",ageminpar,fage,subdirf2(fileres,"vpl"),k1-1,k1-1);
3423:
3424: for (i=1; i<= nlstate ; i ++) {
3425: if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
3426: else fprintf(ficgp," \%%*lf (\%%*lf)");
3427: }
3428: 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);
3429: for (i=1; i<= nlstate ; i ++) {
3430: if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
3431: else fprintf(ficgp," \%%*lf (\%%*lf)");
3432: }
3433: fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"%s\" every :::%d::%d u 1:($2-1.96*$3) \"\%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1);
3434: for (i=1; i<= nlstate ; i ++) {
3435: if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
3436: else fprintf(ficgp," \%%*lf (\%%*lf)");
3437: }
3438: fprintf(ficgp,"\" t\"\" w l 1,\"%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",subdirf2(fileres,"p"),k1-1,k1-1,2+4*(cpt-1));
3439: }
3440: }
3441: /*2 eme*/
3442:
3443: for (k1=1; k1<= m ; k1 ++) {
3444: fprintf(ficgp,"\nset out \"%s%d.png\" \n",subdirf2(optionfilefiname,"e"),k1);
3445: fprintf(ficgp,"set ylabel \"Years\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] ",ageminpar,fage);
3446:
3447: for (i=1; i<= nlstate+1 ; i ++) {
3448: k=2*i;
3449: fprintf(ficgp,"\"%s\" every :::%d::%d u 1:2 \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
3450: for (j=1; j<= nlstate+1 ; j ++) {
3451: if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
3452: else fprintf(ficgp," \%%*lf (\%%*lf)");
3453: }
3454: if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");
3455: else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);
3456: fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
3457: for (j=1; j<= nlstate+1 ; j ++) {
3458: if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
3459: else fprintf(ficgp," \%%*lf (\%%*lf)");
3460: }
3461: fprintf(ficgp,"\" t\"\" w l 0,");
3462: fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
3463: for (j=1; j<= nlstate+1 ; j ++) {
3464: if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
3465: else fprintf(ficgp," \%%*lf (\%%*lf)");
3466: }
3467: if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");
3468: else fprintf(ficgp,"\" t\"\" w l 0,");
3469: }
3470: }
3471:
3472: /*3eme*/
3473:
3474: for (k1=1; k1<= m ; k1 ++) {
3475: for (cpt=1; cpt<= nlstate ; cpt ++) {
3476: k=2+nlstate*(2*cpt-2);
3477: fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"exp"),cpt,k1);
3478: fprintf(ficgp,"set ter png small\n\
3479: set size 0.65,0.65\n\
3480: plot [%.f:%.f] \"%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,subdirf2(fileres,"e"),k1-1,k1-1,k,cpt);
3481: /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
3482: for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
3483: fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
3484: fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
3485: for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
3486: fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
3487:
3488: */
3489: for (i=1; i< nlstate ; i ++) {
3490: 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);
3491:
3492: }
3493: }
3494: }
3495:
3496: /* CV preval stable (period) */
3497: for (k1=1; k1<= m ; k1 ++) {
3498: for (cpt=1; cpt<=nlstate ; cpt ++) {
3499: k=3;
3500: fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"p"),cpt,k1);
3501: fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\
3502: set ter png small\nset size 0.65,0.65\n\
3503: unset log y\n\
3504: plot [%.f:%.f] \"%s\" u ($1==%d ? ($3):1/0):($%d/($%d",ageminpar,agemaxpar,subdirf2(fileres,"pij"),k1,k+cpt+1,k+1);
3505:
3506: for (i=1; i< nlstate ; i ++)
3507: fprintf(ficgp,"+$%d",k+i+1);
3508: fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);
3509:
3510: l=3+(nlstate+ndeath)*cpt;
3511: fprintf(ficgp,",\"%s\" u ($1==%d ? ($3):1/0):($%d/($%d",subdirf2(fileres,"pij"),k1,l+cpt+1,l+1);
3512: for (i=1; i< nlstate ; i ++) {
3513: l=3+(nlstate+ndeath)*cpt;
3514: fprintf(ficgp,"+$%d",l+i+1);
3515: }
3516: fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);
3517: }
3518: }
3519:
3520: /* proba elementaires */
3521: for(i=1,jk=1; i <=nlstate; i++){
3522: for(k=1; k <=(nlstate+ndeath); k++){
3523: if (k != i) {
3524: for(j=1; j <=ncovmodel; j++){
3525: fprintf(ficgp,"p%d=%f ",jk,p[jk]);
3526: jk++;
3527: fprintf(ficgp,"\n");
3528: }
3529: }
3530: }
3531: }
3532:
3533: for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/
3534: for(jk=1; jk <=m; jk++) {
3535: fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"pe"),jk,ng);
3536: if (ng==2)
3537: fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
3538: else
3539: fprintf(ficgp,"\nset title \"Probability\"\n");
3540: fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65\nset log y\nplot [%.f:%.f] ",ageminpar,agemaxpar);
3541: i=1;
3542: for(k2=1; k2<=nlstate; k2++) {
3543: k3=i;
3544: for(k=1; k<=(nlstate+ndeath); k++) {
3545: if (k != k2){
3546: if(ng==2)
3547: fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);
3548: else
3549: fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
3550: ij=1;
3551: for(j=3; j <=ncovmodel; j++) {
3552: if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
3553: fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
3554: ij++;
3555: }
3556: else
3557: fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
3558: }
3559: fprintf(ficgp,")/(1");
3560:
3561: for(k1=1; k1 <=nlstate; k1++){
3562: fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);
3563: ij=1;
3564: for(j=3; j <=ncovmodel; j++){
3565: if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
3566: fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
3567: ij++;
3568: }
3569: else
3570: fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
3571: }
3572: fprintf(ficgp,")");
3573: }
3574: fprintf(ficgp,") t \"p%d%d\" ", k2,k);
3575: if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");
3576: i=i+ncovmodel;
3577: }
3578: } /* end k */
3579: } /* end k2 */
3580: } /* end jk */
3581: } /* end ng */
3582: fflush(ficgp);
3583: } /* end gnuplot */
3584:
3585:
3586: /*************** Moving average **************/
3587: int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav){
3588:
3589: int i, cpt, cptcod;
3590: int modcovmax =1;
3591: int mobilavrange, mob;
3592: double age;
3593:
3594: modcovmax=2*cptcoveff;/* Max number of modalities. We suppose
3595: a covariate has 2 modalities */
3596: if (cptcovn<1) modcovmax=1; /* At least 1 pass */
3597:
3598: if(mobilav==1||mobilav ==3 ||mobilav==5 ||mobilav== 7){
3599: if(mobilav==1) mobilavrange=5; /* default */
3600: else mobilavrange=mobilav;
3601: for (age=bage; age<=fage; age++)
3602: for (i=1; i<=nlstate;i++)
3603: for (cptcod=1;cptcod<=modcovmax;cptcod++)
3604: mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
3605: /* We keep the original values on the extreme ages bage, fage and for
3606: fage+1 and bage-1 we use a 3 terms moving average; for fage+2 bage+2
3607: we use a 5 terms etc. until the borders are no more concerned.
3608: */
3609: for (mob=3;mob <=mobilavrange;mob=mob+2){
3610: for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){
3611: for (i=1; i<=nlstate;i++){
3612: for (cptcod=1;cptcod<=modcovmax;cptcod++){
3613: mobaverage[(int)age][i][cptcod] =probs[(int)age][i][cptcod];
3614: for (cpt=1;cpt<=(mob-1)/2;cpt++){
3615: mobaverage[(int)age][i][cptcod] +=probs[(int)age-cpt][i][cptcod];
3616: mobaverage[(int)age][i][cptcod] +=probs[(int)age+cpt][i][cptcod];
3617: }
3618: mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/mob;
3619: }
3620: }
3621: }/* end age */
3622: }/* end mob */
3623: }else return -1;
3624: return 0;
3625: }/* End movingaverage */
3626:
3627:
3628: /************** Forecasting ******************/
3629: 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){
3630: /* proj1, year, month, day of starting projection
3631: agemin, agemax range of age
3632: dateprev1 dateprev2 range of dates during which prevalence is computed
3633: anproj2 year of en of projection (same day and month as proj1).
3634: */
3635: int yearp, stepsize, hstepm, nhstepm, j, k, c, cptcod, i, h, i1;
3636: int *popage;
3637: double agec; /* generic age */
3638: double agelim, ppij, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
3639: double *popeffectif,*popcount;
3640: double ***p3mat;
3641: double ***mobaverage;
3642: char fileresf[FILENAMELENGTH];
3643:
3644: agelim=AGESUP;
3645: prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
3646:
3647: strcpy(fileresf,"f");
3648: strcat(fileresf,fileres);
3649: if((ficresf=fopen(fileresf,"w"))==NULL) {
3650: printf("Problem with forecast resultfile: %s\n", fileresf);
3651: fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);
3652: }
3653: printf("Computing forecasting: result on file '%s' \n", fileresf);
3654: fprintf(ficlog,"Computing forecasting: result on file '%s' \n", fileresf);
3655:
3656: if (cptcoveff==0) ncodemax[cptcoveff]=1;
3657:
3658: if (mobilav!=0) {
3659: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
3660: if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
3661: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
3662: printf(" Error in movingaverage mobilav=%d\n",mobilav);
3663: }
3664: }
3665:
3666: stepsize=(int) (stepm+YEARM-1)/YEARM;
3667: if (stepm<=12) stepsize=1;
3668: if(estepm < stepm){
3669: printf ("Problem %d lower than %d\n",estepm, stepm);
3670: }
3671: else hstepm=estepm;
3672:
3673: hstepm=hstepm/stepm;
3674: yp1=modf(dateintmean,&yp);/* extracts integral of datemean in yp and
3675: fractional in yp1 */
3676: anprojmean=yp;
3677: yp2=modf((yp1*12),&yp);
3678: mprojmean=yp;
3679: yp1=modf((yp2*30.5),&yp);
3680: jprojmean=yp;
3681: if(jprojmean==0) jprojmean=1;
3682: if(mprojmean==0) jprojmean=1;
3683:
3684: i1=cptcoveff;
3685: if (cptcovn < 1){i1=1;}
3686:
3687: fprintf(ficresf,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2);
3688:
3689: fprintf(ficresf,"#****** Routine prevforecast **\n");
3690:
3691: /* if (h==(int)(YEARM*yearp)){ */
3692: for(cptcov=1, k=0;cptcov<=i1;cptcov++){
3693: for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
3694: k=k+1;
3695: fprintf(ficresf,"\n#******");
3696: for(j=1;j<=cptcoveff;j++) {
3697: 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]]);
3698: }
3699: fprintf(ficresf,"******\n");
3700: fprintf(ficresf,"# Covariate valuofcovar yearproj age");
3701: for(j=1; j<=nlstate+ndeath;j++){
3702: for(i=1; i<=nlstate;i++)
3703: fprintf(ficresf," p%d%d",i,j);
3704: fprintf(ficresf," p.%d",j);
3705: }
3706: for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) {
3707: fprintf(ficresf,"\n");
3708: fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+yearp);
3709:
3710: for (agec=fage; agec>=(ageminpar-1); agec--){
3711: nhstepm=(int) rint((agelim-agec)*YEARM/stepm);
3712: nhstepm = nhstepm/hstepm;
3713: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3714: oldm=oldms;savm=savms;
3715: hpxij(p3mat,nhstepm,agec,hstepm,p,nlstate,stepm,oldm,savm, k);
3716:
3717: for (h=0; h<=nhstepm; h++){
3718: if (h*hstepm/YEARM*stepm ==yearp) {
3719: fprintf(ficresf,"\n");
3720: for(j=1;j<=cptcoveff;j++)
3721: fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
3722: fprintf(ficresf,"%.f %.f ",anproj1+yearp,agec+h*hstepm/YEARM*stepm);
3723: }
3724: for(j=1; j<=nlstate+ndeath;j++) {
3725: ppij=0.;
3726: for(i=1; i<=nlstate;i++) {
3727: if (mobilav==1)
3728: ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][i][cptcod];
3729: else {
3730: ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][cptcod];
3731: }
3732: if (h*hstepm/YEARM*stepm== yearp) {
3733: fprintf(ficresf," %.3f", p3mat[i][j][h]);
3734: }
3735: } /* end i */
3736: if (h*hstepm/YEARM*stepm==yearp) {
3737: fprintf(ficresf," %.3f", ppij);
3738: }
3739: }/* end j */
3740: } /* end h */
3741: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3742: } /* end agec */
3743: } /* end yearp */
3744: } /* end cptcod */
3745: } /* end cptcov */
3746:
3747: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
3748:
3749: fclose(ficresf);
3750: }
3751:
3752: /************** Forecasting *****not tested NB*************/
3753: 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){
3754:
3755: int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;
3756: int *popage;
3757: double calagedatem, agelim, kk1, kk2;
3758: double *popeffectif,*popcount;
3759: double ***p3mat,***tabpop,***tabpopprev;
3760: double ***mobaverage;
3761: char filerespop[FILENAMELENGTH];
3762:
3763: tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
3764: tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
3765: agelim=AGESUP;
3766: calagedatem=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;
3767:
3768: prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
3769:
3770:
3771: strcpy(filerespop,"pop");
3772: strcat(filerespop,fileres);
3773: if((ficrespop=fopen(filerespop,"w"))==NULL) {
3774: printf("Problem with forecast resultfile: %s\n", filerespop);
3775: fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop);
3776: }
3777: printf("Computing forecasting: result on file '%s' \n", filerespop);
3778: fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop);
3779:
3780: if (cptcoveff==0) ncodemax[cptcoveff]=1;
3781:
3782: if (mobilav!=0) {
3783: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
3784: if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
3785: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
3786: printf(" Error in movingaverage mobilav=%d\n",mobilav);
3787: }
3788: }
3789:
3790: stepsize=(int) (stepm+YEARM-1)/YEARM;
3791: if (stepm<=12) stepsize=1;
3792:
3793: agelim=AGESUP;
3794:
3795: hstepm=1;
3796: hstepm=hstepm/stepm;
3797:
3798: if (popforecast==1) {
3799: if((ficpop=fopen(popfile,"r"))==NULL) {
3800: printf("Problem with population file : %s\n",popfile);exit(0);
3801: fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0);
3802: }
3803: popage=ivector(0,AGESUP);
3804: popeffectif=vector(0,AGESUP);
3805: popcount=vector(0,AGESUP);
3806:
3807: i=1;
3808: while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;
3809:
3810: imx=i;
3811: for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];
3812: }
3813:
3814: for(cptcov=1,k=0;cptcov<=i2;cptcov++){
3815: for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
3816: k=k+1;
3817: fprintf(ficrespop,"\n#******");
3818: for(j=1;j<=cptcoveff;j++) {
3819: fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
3820: }
3821: fprintf(ficrespop,"******\n");
3822: fprintf(ficrespop,"# Age");
3823: for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);
3824: if (popforecast==1) fprintf(ficrespop," [Population]");
3825:
3826: for (cpt=0; cpt<=0;cpt++) {
3827: fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);
3828:
3829: for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){
3830: nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);
3831: nhstepm = nhstepm/hstepm;
3832:
3833: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3834: oldm=oldms;savm=savms;
3835: hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
3836:
3837: for (h=0; h<=nhstepm; h++){
3838: if (h==(int) (calagedatem+YEARM*cpt)) {
3839: fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
3840: }
3841: for(j=1; j<=nlstate+ndeath;j++) {
3842: kk1=0.;kk2=0;
3843: for(i=1; i<=nlstate;i++) {
3844: if (mobilav==1)
3845: kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];
3846: else {
3847: kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];
3848: }
3849: }
3850: if (h==(int)(calagedatem+12*cpt)){
3851: tabpop[(int)(agedeb)][j][cptcod]=kk1;
3852: /*fprintf(ficrespop," %.3f", kk1);
3853: if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/
3854: }
3855: }
3856: for(i=1; i<=nlstate;i++){
3857: kk1=0.;
3858: for(j=1; j<=nlstate;j++){
3859: kk1= kk1+tabpop[(int)(agedeb)][j][cptcod];
3860: }
3861: tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedatem+12*cpt)*hstepm/YEARM*stepm-1)];
3862: }
3863:
3864: if (h==(int)(calagedatem+12*cpt)) for(j=1; j<=nlstate;j++)
3865: fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);
3866: }
3867: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3868: }
3869: }
3870:
3871: /******/
3872:
3873: for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) {
3874: fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);
3875: for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){
3876: nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);
3877: nhstepm = nhstepm/hstepm;
3878:
3879: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3880: oldm=oldms;savm=savms;
3881: hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
3882: for (h=0; h<=nhstepm; h++){
3883: if (h==(int) (calagedatem+YEARM*cpt)) {
3884: fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
3885: }
3886: for(j=1; j<=nlstate+ndeath;j++) {
3887: kk1=0.;kk2=0;
3888: for(i=1; i<=nlstate;i++) {
3889: kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];
3890: }
3891: if (h==(int)(calagedatem+12*cpt)) fprintf(ficresf," %15.2f", kk1);
3892: }
3893: }
3894: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3895: }
3896: }
3897: }
3898: }
3899:
3900: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
3901:
3902: if (popforecast==1) {
3903: free_ivector(popage,0,AGESUP);
3904: free_vector(popeffectif,0,AGESUP);
3905: free_vector(popcount,0,AGESUP);
3906: }
3907: free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
3908: free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
3909: fclose(ficrespop);
3910: } /* End of popforecast */
3911:
3912: int fileappend(FILE *fichier, char *optionfich)
3913: {
3914: if((fichier=fopen(optionfich,"a"))==NULL) {
3915: printf("Problem with file: %s\n", optionfich);
3916: fprintf(ficlog,"Problem with file: %s\n", optionfich);
3917: return (0);
3918: }
3919: fflush(fichier);
3920: return (1);
3921: }
3922:
3923:
3924: /**************** function prwizard **********************/
3925: void prwizard(int ncovmodel, int nlstate, int ndeath, char model[], FILE *ficparo)
3926: {
3927:
3928: /* Wizard to print covariance matrix template */
3929:
3930: char ca[32], cb[32], cc[32];
3931: int i,j, k, l, li, lj, lk, ll, jj, npar, itimes;
3932: int numlinepar;
3933:
3934: printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
3935: fprintf(ficparo,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
3936: for(i=1; i <=nlstate; i++){
3937: jj=0;
3938: for(j=1; j <=nlstate+ndeath; j++){
3939: if(j==i) continue;
3940: jj++;
3941: /*ca[0]= k+'a'-1;ca[1]='\0';*/
3942: printf("%1d%1d",i,j);
3943: fprintf(ficparo,"%1d%1d",i,j);
3944: for(k=1; k<=ncovmodel;k++){
3945: /* printf(" %lf",param[i][j][k]); */
3946: /* fprintf(ficparo," %lf",param[i][j][k]); */
3947: printf(" 0.");
3948: fprintf(ficparo," 0.");
3949: }
3950: printf("\n");
3951: fprintf(ficparo,"\n");
3952: }
3953: }
3954: printf("# Scales (for hessian or gradient estimation)\n");
3955: fprintf(ficparo,"# Scales (for hessian or gradient estimation)\n");
3956: npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/
3957: for(i=1; i <=nlstate; i++){
3958: jj=0;
3959: for(j=1; j <=nlstate+ndeath; j++){
3960: if(j==i) continue;
3961: jj++;
3962: fprintf(ficparo,"%1d%1d",i,j);
3963: printf("%1d%1d",i,j);
3964: fflush(stdout);
3965: for(k=1; k<=ncovmodel;k++){
3966: /* printf(" %le",delti3[i][j][k]); */
3967: /* fprintf(ficparo," %le",delti3[i][j][k]); */
3968: printf(" 0.");
3969: fprintf(ficparo," 0.");
3970: }
3971: numlinepar++;
3972: printf("\n");
3973: fprintf(ficparo,"\n");
3974: }
3975: }
3976: printf("# Covariance matrix\n");
3977: /* # 121 Var(a12)\n\ */
3978: /* # 122 Cov(b12,a12) Var(b12)\n\ */
3979: /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
3980: /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
3981: /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
3982: /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
3983: /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
3984: /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
3985: fflush(stdout);
3986: fprintf(ficparo,"# Covariance matrix\n");
3987: /* # 121 Var(a12)\n\ */
3988: /* # 122 Cov(b12,a12) Var(b12)\n\ */
3989: /* # ...\n\ */
3990: /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
3991:
3992: for(itimes=1;itimes<=2;itimes++){
3993: jj=0;
3994: for(i=1; i <=nlstate; i++){
3995: for(j=1; j <=nlstate+ndeath; j++){
3996: if(j==i) continue;
3997: for(k=1; k<=ncovmodel;k++){
3998: jj++;
3999: ca[0]= k+'a'-1;ca[1]='\0';
4000: if(itimes==1){
4001: printf("#%1d%1d%d",i,j,k);
4002: fprintf(ficparo,"#%1d%1d%d",i,j,k);
4003: }else{
4004: printf("%1d%1d%d",i,j,k);
4005: fprintf(ficparo,"%1d%1d%d",i,j,k);
4006: /* printf(" %.5le",matcov[i][j]); */
4007: }
4008: ll=0;
4009: for(li=1;li <=nlstate; li++){
4010: for(lj=1;lj <=nlstate+ndeath; lj++){
4011: if(lj==li) continue;
4012: for(lk=1;lk<=ncovmodel;lk++){
4013: ll++;
4014: if(ll<=jj){
4015: cb[0]= lk +'a'-1;cb[1]='\0';
4016: if(ll<jj){
4017: if(itimes==1){
4018: printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
4019: fprintf(ficparo," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
4020: }else{
4021: printf(" 0.");
4022: fprintf(ficparo," 0.");
4023: }
4024: }else{
4025: if(itimes==1){
4026: printf(" Var(%s%1d%1d)",ca,i,j);
4027: fprintf(ficparo," Var(%s%1d%1d)",ca,i,j);
4028: }else{
4029: printf(" 0.");
4030: fprintf(ficparo," 0.");
4031: }
4032: }
4033: }
4034: } /* end lk */
4035: } /* end lj */
4036: } /* end li */
4037: printf("\n");
4038: fprintf(ficparo,"\n");
4039: numlinepar++;
4040: } /* end k*/
4041: } /*end j */
4042: } /* end i */
4043: } /* end itimes */
4044:
4045: } /* end of prwizard */
4046: /******************* Gompertz Likelihood ******************************/
4047: double gompertz(double x[])
4048: {
4049: double A,B,L=0.0,sump=0.,num=0.;
4050: int i,n=0; /* n is the size of the sample */
4051:
4052: for (i=0;i<=imx-1 ; i++) {
4053: sump=sump+weight[i];
4054: /* sump=sump+1;*/
4055: num=num+1;
4056: }
4057:
4058:
4059: /* for (i=0; i<=imx; i++)
4060: 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]);*/
4061:
4062: for (i=1;i<=imx ; i++)
4063: {
4064: if (cens[i] == 1 && wav[i]>1)
4065: A=-x[1]/(x[2])*(exp(x[2]*(agecens[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)));
4066:
4067: if (cens[i] == 0 && wav[i]>1)
4068: A=-x[1]/(x[2])*(exp(x[2]*(agedc[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)))
4069: +log(x[1]/YEARM)+x[2]*(agedc[i]-agegomp)+log(YEARM);
4070:
4071: /*if (wav[i] > 1 && agecens[i] > 15) {*/ /* ??? */
4072: if (wav[i] > 1 ) { /* ??? */
4073: L=L+A*weight[i];
4074: /* 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]);*/
4075: }
4076: }
4077:
4078: /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/
4079:
4080: return -2*L*num/sump;
4081: }
4082:
4083: /******************* Printing html file ***********/
4084: void printinghtmlmort(char fileres[], char title[], char datafile[], int firstpass, \
4085: int lastpass, int stepm, int weightopt, char model[],\
4086: int imx, double p[],double **matcov,double agemortsup){
4087: int i,k;
4088:
4089: fprintf(fichtm,"<ul><li><h4>Result files </h4>\n Force of mortality. Parameters of the Gompertz fit (with confidence interval in brackets):<br>");
4090: fprintf(fichtm," mu(age) =%lf*exp(%lf*(age-%d)) per year<br><br>",p[1],p[2],agegomp);
4091: for (i=1;i<=2;i++)
4092: 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]));
4093: fprintf(fichtm,"<br><br><img src=\"graphmort.png\">");
4094: fprintf(fichtm,"</ul>");
4095:
4096: fprintf(fichtm,"<ul><li><h4>Life table</h4>\n <br>");
4097:
4098: fprintf(fichtm,"\nAge l<inf>x</inf> q<inf>x</inf> d(x,x+1) L<inf>x</inf> T<inf>x</inf> e<infx</inf><br>");
4099:
4100: for (k=agegomp;k<(agemortsup-2);k++)
4101: fprintf(fichtm,"%d %.0lf %lf %.0lf %.0lf %.0lf %lf<br>\n",k,lsurv[k],p[1]*exp(p[2]*(k-agegomp)),(p[1]*exp(p[2]*(k-agegomp)))*lsurv[k],lpop[k],tpop[k],tpop[k]/lsurv[k]);
4102:
4103:
4104: fflush(fichtm);
4105: }
4106:
4107: /******************* Gnuplot file **************/
4108: void printinggnuplotmort(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
4109:
4110: char dirfileres[132],optfileres[132];
4111: int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;
4112: int ng;
4113:
4114:
4115: /*#ifdef windows */
4116: fprintf(ficgp,"cd \"%s\" \n",pathc);
4117: /*#endif */
4118:
4119:
4120: strcpy(dirfileres,optionfilefiname);
4121: strcpy(optfileres,"vpl");
4122: fprintf(ficgp,"set out \"graphmort.png\"\n ");
4123: fprintf(ficgp,"set xlabel \"Age\"\n set ylabel \"Force of mortality (per year)\" \n ");
4124: fprintf(ficgp, "set ter png small\n set log y\n");
4125: fprintf(ficgp, "set size 0.65,0.65\n");
4126: fprintf(ficgp,"plot [%d:100] %lf*exp(%lf*(x-%d))",agegomp,p[1],p[2],agegomp);
4127:
4128: }
4129:
4130:
4131:
4132:
4133: /***********************************************/
4134: /**************** Main Program *****************/
4135: /***********************************************/
4136:
4137: int main(int argc, char *argv[])
4138: {
4139: int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav);
4140: int i,j, k, n=MAXN,iter,m,size=100,cptcode, cptcod;
4141: int linei, month, year,iout;
4142: int jj, ll, li, lj, lk, imk;
4143: int numlinepar=0; /* Current linenumber of parameter file */
4144: int itimes;
4145: int NDIM=2;
4146:
4147: char ca[32], cb[32], cc[32];
4148: char dummy[]=" ";
4149: /* FILE *fichtm; *//* Html File */
4150: /* FILE *ficgp;*/ /*Gnuplot File */
4151: struct stat info;
4152: double agedeb, agefin,hf;
4153: double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;
4154:
4155: double fret;
4156: double **xi,tmp,delta;
4157:
4158: double dum; /* Dummy variable */
4159: double ***p3mat;
4160: double ***mobaverage;
4161: int *indx;
4162: char line[MAXLINE], linepar[MAXLINE];
4163: char path[MAXLINE],pathc[MAXLINE],pathcd[MAXLINE],pathtot[MAXLINE],model[MAXLINE];
4164: char pathr[MAXLINE], pathimach[MAXLINE];
4165: char **bp, *tok, *val; /* pathtot */
4166: int firstobs=1, lastobs=10;
4167: int sdeb, sfin; /* Status at beginning and end */
4168: int c, h , cpt,l;
4169: int ju,jl, mi;
4170: int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;
4171: int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,*tab;
4172: int mobilavproj=0 , prevfcast=0 ; /* moving average of prev, If prevfcast=1 prevalence projection */
4173: int mobilav=0,popforecast=0;
4174: int hstepm, nhstepm;
4175: int agemortsup;
4176: float sumlpop=0.;
4177: double jprev1=1, mprev1=1,anprev1=2000,jprev2=1, mprev2=1,anprev2=2000;
4178: double jpyram=1, mpyram=1,anpyram=2000,jpyram1=1, mpyram1=1,anpyram1=2000;
4179:
4180: double bage, fage, age, agelim, agebase;
4181: double ftolpl=FTOL;
4182: double **prlim;
4183: double *severity;
4184: double ***param; /* Matrix of parameters */
4185: double *p;
4186: double **matcov; /* Matrix of covariance */
4187: double ***delti3; /* Scale */
4188: double *delti; /* Scale */
4189: double ***eij, ***vareij;
4190: double **varpl; /* Variances of prevalence limits by age */
4191: double *epj, vepp;
4192: double kk1, kk2;
4193: double dateprev1, dateprev2,jproj1=1,mproj1=1,anproj1=2000,jproj2=1,mproj2=1,anproj2=2000;
4194: double **ximort;
4195: char *alph[]={"a","a","b","c","d","e"}, str[4];
4196: int *dcwave;
4197:
4198: char z[1]="c", occ;
4199:
4200: char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];
4201: char strstart[80], *strt, strtend[80];
4202: char *stratrunc;
4203: int lstra;
4204:
4205: long total_usecs;
4206:
4207: /* setlocale (LC_ALL, ""); */
4208: /* bindtextdomain (PACKAGE, LOCALEDIR); */
4209: /* textdomain (PACKAGE); */
4210: /* setlocale (LC_CTYPE, ""); */
4211: /* setlocale (LC_MESSAGES, ""); */
4212:
4213: /* gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */
4214: (void) gettimeofday(&start_time,&tzp);
4215: curr_time=start_time;
4216: tm = *localtime(&start_time.tv_sec);
4217: tmg = *gmtime(&start_time.tv_sec);
4218: strcpy(strstart,asctime(&tm));
4219:
4220: /* printf("Localtime (at start)=%s",strstart); */
4221: /* tp.tv_sec = tp.tv_sec +86400; */
4222: /* tm = *localtime(&start_time.tv_sec); */
4223: /* tmg.tm_year=tmg.tm_year +dsign*dyear; */
4224: /* tmg.tm_mon=tmg.tm_mon +dsign*dmonth; */
4225: /* tmg.tm_hour=tmg.tm_hour + 1; */
4226: /* tp.tv_sec = mktime(&tmg); */
4227: /* strt=asctime(&tmg); */
4228: /* printf("Time(after) =%s",strstart); */
4229: /* (void) time (&time_value);
4230: * printf("time=%d,t-=%d\n",time_value,time_value-86400);
4231: * tm = *localtime(&time_value);
4232: * strstart=asctime(&tm);
4233: * printf("tim_value=%d,asctime=%s\n",time_value,strstart);
4234: */
4235:
4236: nberr=0; /* Number of errors and warnings */
4237: nbwarn=0;
4238: getcwd(pathcd, size);
4239:
4240: printf("\n%s\n%s",version,fullversion);
4241: if(argc <=1){
4242: printf("\nEnter the parameter file name: ");
4243: fgets(pathr,FILENAMELENGTH,stdin);
4244: i=strlen(pathr);
4245: if(pathr[i-1]=='\n')
4246: pathr[i-1]='\0';
4247: for (tok = pathr; tok != NULL; ){
4248: printf("Pathr |%s|\n",pathr);
4249: while ((val = strsep(&tok, "\"" )) != NULL && *val == '\0');
4250: printf("val= |%s| pathr=%s\n",val,pathr);
4251: strcpy (pathtot, val);
4252: if(pathr[0] == '\0') break; /* Un peu sale */
4253: }
4254: }
4255: else{
4256: strcpy(pathtot,argv[1]);
4257: }
4258: /*if(getcwd(pathcd, MAXLINE)!= NULL)printf ("Error pathcd\n");*/
4259: /*cygwin_split_path(pathtot,path,optionfile);
4260: printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/
4261: /* cutv(path,optionfile,pathtot,'\\');*/
4262:
4263: /* Split argv[0], imach program to get pathimach */
4264: printf("\nargv[0]=%s argv[1]=%s, \n",argv[0],argv[1]);
4265: split(argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
4266: printf("\nargv[0]=%s pathimach=%s, \noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
4267: /* strcpy(pathimach,argv[0]); */
4268: /* Split argv[1]=pathtot, parameter file name to get path, optionfile, extension and name */
4269: split(pathtot,path,optionfile,optionfilext,optionfilefiname);
4270: printf("\npathtot=%s,\npath=%s,\noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
4271: chdir(path);
4272: strcpy(command,"mkdir ");
4273: strcat(command,optionfilefiname);
4274: if((outcmd=system(command)) != 0){
4275: printf("Problem creating directory or it already exists %s%s, err=%d\n",path,optionfilefiname,outcmd);
4276: /* fprintf(ficlog,"Problem creating directory %s%s\n",path,optionfilefiname); */
4277: /* fclose(ficlog); */
4278: /* exit(1); */
4279: }
4280: /* if((imk=mkdir(optionfilefiname))<0){ */
4281: /* perror("mkdir"); */
4282: /* } */
4283:
4284: /*-------- arguments in the command line --------*/
4285:
4286: /* Log file */
4287: strcat(filelog, optionfilefiname);
4288: strcat(filelog,".log"); /* */
4289: if((ficlog=fopen(filelog,"w"))==NULL) {
4290: printf("Problem with logfile %s\n",filelog);
4291: goto end;
4292: }
4293: fprintf(ficlog,"Log filename:%s\n",filelog);
4294: fprintf(ficlog,"\n%s\n%s",version,fullversion);
4295: fprintf(ficlog,"\nEnter the parameter file name: \n");
4296: fprintf(ficlog,"pathimach=%s\npathtot=%s\n\
4297: path=%s \n\
4298: optionfile=%s\n\
4299: optionfilext=%s\n\
4300: optionfilefiname=%s\n",pathimach,pathtot,path,optionfile,optionfilext,optionfilefiname);
4301:
4302: printf("Local time (at start):%s",strstart);
4303: fprintf(ficlog,"Local time (at start): %s",strstart);
4304: fflush(ficlog);
4305: /* (void) gettimeofday(&curr_time,&tzp); */
4306: /* printf("Elapsed time %d\n", asc_diff_time(curr_time.tv_sec-start_time.tv_sec,tmpout)); */
4307:
4308: /* */
4309: strcpy(fileres,"r");
4310: strcat(fileres, optionfilefiname);
4311: strcat(fileres,".txt"); /* Other files have txt extension */
4312:
4313: /*---------arguments file --------*/
4314:
4315: if((ficpar=fopen(optionfile,"r"))==NULL) {
4316: printf("Problem with optionfile %s\n",optionfile);
4317: fprintf(ficlog,"Problem with optionfile %s\n",optionfile);
4318: fflush(ficlog);
4319: goto end;
4320: }
4321:
4322:
4323:
4324: strcpy(filereso,"o");
4325: strcat(filereso,fileres);
4326: if((ficparo=fopen(filereso,"w"))==NULL) { /* opened on subdirectory */
4327: printf("Problem with Output resultfile: %s\n", filereso);
4328: fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso);
4329: fflush(ficlog);
4330: goto end;
4331: }
4332:
4333: /* Reads comments: lines beginning with '#' */
4334: numlinepar=0;
4335: while((c=getc(ficpar))=='#' && c!= EOF){
4336: ungetc(c,ficpar);
4337: fgets(line, MAXLINE, ficpar);
4338: numlinepar++;
4339: puts(line);
4340: fputs(line,ficparo);
4341: fputs(line,ficlog);
4342: }
4343: ungetc(c,ficpar);
4344:
4345: 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);
4346: numlinepar++;
4347: 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);
4348: 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);
4349: 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);
4350: fflush(ficlog);
4351: while((c=getc(ficpar))=='#' && c!= EOF){
4352: ungetc(c,ficpar);
4353: fgets(line, MAXLINE, ficpar);
4354: numlinepar++;
4355: puts(line);
4356: fputs(line,ficparo);
4357: fputs(line,ficlog);
4358: }
4359: ungetc(c,ficpar);
4360:
4361:
4362: covar=matrix(0,NCOVMAX,1,n);
4363: cptcovn=0; /*Number of covariates, i.e. number of '+' in model statement*/
4364: if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;
4365:
4366: ncovmodel=2+cptcovn; /*Number of variables = cptcovn + intercept + age */
4367: nvar=ncovmodel-1; /* Suppressing age as a basic covariate */
4368: npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/
4369:
4370: delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
4371: delti=delti3[1][1];
4372: /*delti=vector(1,npar); *//* Scale of each paramater (output from hesscov)*/
4373: if(mle==-1){ /* Print a wizard for help writing covariance matrix */
4374: prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
4375: printf(" You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
4376: fprintf(ficlog," You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
4377: free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
4378: fclose (ficparo);
4379: fclose (ficlog);
4380: exit(0);
4381: }
4382: else if(mle==-3) {
4383: prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
4384: printf(" You choose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
4385: fprintf(ficlog," You choose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
4386: param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
4387: matcov=matrix(1,npar,1,npar);
4388: }
4389: else{
4390: /* Read guess parameters */
4391: /* Reads comments: lines beginning with '#' */
4392: while((c=getc(ficpar))=='#' && c!= EOF){
4393: ungetc(c,ficpar);
4394: fgets(line, MAXLINE, ficpar);
4395: numlinepar++;
4396: puts(line);
4397: fputs(line,ficparo);
4398: fputs(line,ficlog);
4399: }
4400: ungetc(c,ficpar);
4401:
4402: param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
4403: for(i=1; i <=nlstate; i++){
4404: j=0;
4405: for(jj=1; jj <=nlstate+ndeath; jj++){
4406: if(jj==i) continue;
4407: j++;
4408: fscanf(ficpar,"%1d%1d",&i1,&j1);
4409: if ((i1 != i) && (j1 != j)){
4410: printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n",numlinepar, i,j, i1, j1);
4411: exit(1);
4412: }
4413: fprintf(ficparo,"%1d%1d",i1,j1);
4414: if(mle==1)
4415: printf("%1d%1d",i,j);
4416: fprintf(ficlog,"%1d%1d",i,j);
4417: for(k=1; k<=ncovmodel;k++){
4418: fscanf(ficpar," %lf",¶m[i][j][k]);
4419: if(mle==1){
4420: printf(" %lf",param[i][j][k]);
4421: fprintf(ficlog," %lf",param[i][j][k]);
4422: }
4423: else
4424: fprintf(ficlog," %lf",param[i][j][k]);
4425: fprintf(ficparo," %lf",param[i][j][k]);
4426: }
4427: fscanf(ficpar,"\n");
4428: numlinepar++;
4429: if(mle==1)
4430: printf("\n");
4431: fprintf(ficlog,"\n");
4432: fprintf(ficparo,"\n");
4433: }
4434: }
4435: fflush(ficlog);
4436:
4437: p=param[1][1];
4438:
4439: /* Reads comments: lines beginning with '#' */
4440: while((c=getc(ficpar))=='#' && c!= EOF){
4441: ungetc(c,ficpar);
4442: fgets(line, MAXLINE, ficpar);
4443: numlinepar++;
4444: puts(line);
4445: fputs(line,ficparo);
4446: fputs(line,ficlog);
4447: }
4448: ungetc(c,ficpar);
4449:
4450: for(i=1; i <=nlstate; i++){
4451: for(j=1; j <=nlstate+ndeath-1; j++){
4452: fscanf(ficpar,"%1d%1d",&i1,&j1);
4453: if ((i1-i)*(j1-j)!=0){
4454: printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n",numlinepar, i,j, i1, j1);
4455: exit(1);
4456: }
4457: printf("%1d%1d",i,j);
4458: fprintf(ficparo,"%1d%1d",i1,j1);
4459: fprintf(ficlog,"%1d%1d",i1,j1);
4460: for(k=1; k<=ncovmodel;k++){
4461: fscanf(ficpar,"%le",&delti3[i][j][k]);
4462: printf(" %le",delti3[i][j][k]);
4463: fprintf(ficparo," %le",delti3[i][j][k]);
4464: fprintf(ficlog," %le",delti3[i][j][k]);
4465: }
4466: fscanf(ficpar,"\n");
4467: numlinepar++;
4468: printf("\n");
4469: fprintf(ficparo,"\n");
4470: fprintf(ficlog,"\n");
4471: }
4472: }
4473: fflush(ficlog);
4474:
4475: delti=delti3[1][1];
4476:
4477:
4478: /* free_ma3x(delti3,1,nlstate,1,nlstate+ndeath-1,1,ncovmodel); */ /* Hasn't to to freed here otherwise delti is no more allocated */
4479:
4480: /* Reads comments: lines beginning with '#' */
4481: while((c=getc(ficpar))=='#' && c!= EOF){
4482: ungetc(c,ficpar);
4483: fgets(line, MAXLINE, ficpar);
4484: numlinepar++;
4485: puts(line);
4486: fputs(line,ficparo);
4487: fputs(line,ficlog);
4488: }
4489: ungetc(c,ficpar);
4490:
4491: matcov=matrix(1,npar,1,npar);
4492: for(i=1; i <=npar; i++){
4493: fscanf(ficpar,"%s",&str);
4494: if(mle==1)
4495: printf("%s",str);
4496: fprintf(ficlog,"%s",str);
4497: fprintf(ficparo,"%s",str);
4498: for(j=1; j <=i; j++){
4499: fscanf(ficpar," %le",&matcov[i][j]);
4500: if(mle==1){
4501: printf(" %.5le",matcov[i][j]);
4502: }
4503: fprintf(ficlog," %.5le",matcov[i][j]);
4504: fprintf(ficparo," %.5le",matcov[i][j]);
4505: }
4506: fscanf(ficpar,"\n");
4507: numlinepar++;
4508: if(mle==1)
4509: printf("\n");
4510: fprintf(ficlog,"\n");
4511: fprintf(ficparo,"\n");
4512: }
4513: for(i=1; i <=npar; i++)
4514: for(j=i+1;j<=npar;j++)
4515: matcov[i][j]=matcov[j][i];
4516:
4517: if(mle==1)
4518: printf("\n");
4519: fprintf(ficlog,"\n");
4520:
4521: fflush(ficlog);
4522:
4523: /*-------- Rewriting parameter file ----------*/
4524: strcpy(rfileres,"r"); /* "Rparameterfile */
4525: strcat(rfileres,optionfilefiname); /* Parameter file first name*/
4526: strcat(rfileres,"."); /* */
4527: strcat(rfileres,optionfilext); /* Other files have txt extension */
4528: if((ficres =fopen(rfileres,"w"))==NULL) {
4529: printf("Problem writing new parameter file: %s\n", fileres);goto end;
4530: fprintf(ficlog,"Problem writing new parameter file: %s\n", fileres);goto end;
4531: }
4532: fprintf(ficres,"#%s\n",version);
4533: } /* End of mle != -3 */
4534:
4535: /*-------- data file ----------*/
4536: if((fic=fopen(datafile,"r"))==NULL) {
4537: printf("Problem with datafile: %s\n", datafile);goto end;
4538: fprintf(ficlog,"Problem with datafile: %s\n", datafile);goto end;
4539: }
4540:
4541: n= lastobs;
4542: severity = vector(1,maxwav);
4543: outcome=imatrix(1,maxwav+1,1,n);
4544: num=lvector(1,n);
4545: moisnais=vector(1,n);
4546: annais=vector(1,n);
4547: moisdc=vector(1,n);
4548: andc=vector(1,n);
4549: agedc=vector(1,n);
4550: cod=ivector(1,n);
4551: weight=vector(1,n);
4552: for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */
4553: mint=matrix(1,maxwav,1,n);
4554: anint=matrix(1,maxwav,1,n);
4555: s=imatrix(1,maxwav+1,1,n);
4556: tab=ivector(1,NCOVMAX);
4557: ncodemax=ivector(1,8);
4558:
4559: i=1;
4560: linei=0;
4561: while ((fgets(line, MAXLINE, fic) != NULL) &&((i >= firstobs) && (i <=lastobs))) {
4562: linei=linei+1;
4563: for(j=strlen(line); j>=0;j--){ /* Untabifies line */
4564: if(line[j] == '\t')
4565: line[j] = ' ';
4566: }
4567: for(j=strlen(line)-1; (line[j]==' ')||(line[j]==10)||(line[j]==13);j--){
4568: ;
4569: };
4570: line[j+1]=0; /* Trims blanks at end of line */
4571: if(line[0]=='#'){
4572: fprintf(ficlog,"Comment line\n%s\n",line);
4573: printf("Comment line\n%s\n",line);
4574: continue;
4575: }
4576:
4577: for (j=maxwav;j>=1;j--){
4578: cutv(stra, strb,line,' ');
4579: errno=0;
4580: lval=strtol(strb,&endptr,10);
4581: /* if (errno == ERANGE && (lval == LONG_MAX || lval == LONG_MIN))*/
4582: if( strb[0]=='\0' || (*endptr != '\0')){
4583: printf("Error reading data around '%d' at line number %d %s for individual %d, '%s'\nShould be a status of wave %d. Setting maxwav=%d might be wrong. Exiting.\n", strb, linei,i,line,j,maxwav);
4584: exit(1);
4585: }
4586: s[j][i]=lval;
4587:
4588: strcpy(line,stra);
4589: cutv(stra, strb,line,' ');
4590: if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){
4591: }
4592: else if(iout=sscanf(strb,"%s.") != 0){
4593: month=99;
4594: year=9999;
4595: }else{
4596: printf("Error reading data around '%s' at line number %ld %s for individual %d, '%s'\nShould be a date of interview (mm/yyyy or .) at wave %d. Exiting.\n",strb, linei,i, line,j);
4597: exit(1);
4598: }
4599: anint[j][i]= (double) year;
4600: mint[j][i]= (double)month;
4601: strcpy(line,stra);
4602: } /* ENd Waves */
4603:
4604: cutv(stra, strb,line,' ');
4605: if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){
4606: }
4607: else if(iout=sscanf(strb,"%s.",dummy) != 0){
4608: month=99;
4609: year=9999;
4610: }else{
4611: printf("Error reading data around '%s' at line number %ld %s for individual %d, '%s'\nShould be a date of death (mm/yyyy or .). Exiting.\n",strb, linei,i,line);
4612: exit(1);
4613: }
4614: andc[i]=(double) year;
4615: moisdc[i]=(double) month;
4616: strcpy(line,stra);
4617:
4618: cutv(stra, strb,line,' ');
4619: if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){
4620: }
4621: else if(iout=sscanf(strb,"%s.") != 0){
4622: month=99;
4623: year=9999;
4624: }else{
4625: printf("Error reading data around '%s' at line number %ld %s for individual %d, '%s'\nShould be a date of birth (mm/yyyy or .). Exiting.\n",strb, linei,i,line,j);
4626: exit(1);
4627: }
4628: annais[i]=(double)(year);
4629: moisnais[i]=(double)(month);
4630: strcpy(line,stra);
4631:
4632: cutv(stra, strb,line,' ');
4633: errno=0;
4634: lval=strtol(strb,&endptr,10);
4635: if( strb[0]=='\0' || (*endptr != '\0')){
4636: printf("Error reading data around '%d' at line number %ld %s for individual %d\nShould be a weight. Exiting.\n",lval, i,line,linei);
4637: exit(1);
4638: }
4639: weight[i]=(double)(lval);
4640: strcpy(line,stra);
4641:
4642: for (j=ncovcol;j>=1;j--){
4643: cutv(stra, strb,line,' ');
4644: errno=0;
4645: lval=strtol(strb,&endptr,10);
4646: if( strb[0]=='\0' || (*endptr != '\0')){
4647: printf("Error reading data around '%d' at line number %ld %s for individual %d, '%s'\nShould be a covar (meaning 0 for the reference or 1). Exiting.\n",lval, linei,i, line);
4648: exit(1);
4649: }
4650: if(lval <-1 || lval >1){
4651: printf("Error reading data around '%d' at line number %ld %s for individual %d, '%s'\nShould be a value of the %d covar (meaning 0 for the reference or 1. IMaCh does not build design variables, do it your self). Exiting.\n",lval,linei, i,line,j);
4652: exit(1);
4653: }
4654: covar[j][i]=(double)(lval);
4655: strcpy(line,stra);
4656: }
4657: lstra=strlen(stra);
4658:
4659: if(lstra > 9){ /* More than 2**32 or max of what printf can write with %ld */
4660: stratrunc = &(stra[lstra-9]);
4661: num[i]=atol(stratrunc);
4662: }
4663: else
4664: num[i]=atol(stra);
4665: /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){
4666: 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;}*/
4667:
4668: i=i+1;
4669: } /* End loop reading data */
4670: fclose(fic);
4671: /* printf("ii=%d", ij);
4672: scanf("%d",i);*/
4673: imx=i-1; /* Number of individuals */
4674:
4675: /* for (i=1; i<=imx; i++){
4676: if ((s[1][i]==3) && (s[2][i]==2)) s[2][i]=3;
4677: if ((s[2][i]==3) && (s[3][i]==2)) s[3][i]=3;
4678: if ((s[3][i]==3) && (s[4][i]==2)) s[4][i]=3;
4679: }*/
4680: /* for (i=1; i<=imx; i++){
4681: if (s[4][i]==9) s[4][i]=-1;
4682: 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]));}*/
4683:
4684: /* for (i=1; i<=imx; i++) */
4685:
4686: /*if ((s[3][i]==3) || (s[4][i]==3)) weight[i]=0.08;
4687: else weight[i]=1;*/
4688:
4689: /* Calculation of the number of parameters from char model */
4690: Tvar=ivector(1,15); /* stores the number n of the covariates in Vm+Vn at 1 and m at 2 */
4691: Tprod=ivector(1,15);
4692: Tvaraff=ivector(1,15);
4693: Tvard=imatrix(1,15,1,2);
4694: Tage=ivector(1,15);
4695:
4696: if (strlen(model) >1){ /* If there is at least 1 covariate */
4697: j=0, j1=0, k1=1, k2=1;
4698: j=nbocc(model,'+'); /* j=Number of '+' */
4699: j1=nbocc(model,'*'); /* j1=Number of '*' */
4700: cptcovn=j+1;
4701: cptcovprod=j1; /*Number of products */
4702:
4703: strcpy(modelsav,model);
4704: if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){
4705: printf("Error. Non available option model=%s ",model);
4706: fprintf(ficlog,"Error. Non available option model=%s ",model);
4707: goto end;
4708: }
4709:
4710: /* This loop fills the array Tvar from the string 'model'.*/
4711:
4712: for(i=(j+1); i>=1;i--){
4713: cutv(stra,strb,modelsav,'+'); /* keeps in strb after the last + */
4714: if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyzes it */
4715: /* printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/
4716: /*scanf("%d",i);*/
4717: if (strchr(strb,'*')) { /* Model includes a product */
4718: cutv(strd,strc,strb,'*'); /* strd*strc Vm*Vn (if not *age)*/
4719: if (strcmp(strc,"age")==0) { /* Vn*age */
4720: cptcovprod--;
4721: cutv(strb,stre,strd,'V');
4722: Tvar[i]=atoi(stre); /* computes n in Vn and stores in Tvar*/
4723: cptcovage++;
4724: Tage[cptcovage]=i;
4725: /*printf("stre=%s ", stre);*/
4726: }
4727: else if (strcmp(strd,"age")==0) { /* or age*Vn */
4728: cptcovprod--;
4729: cutv(strb,stre,strc,'V');
4730: Tvar[i]=atoi(stre);
4731: cptcovage++;
4732: Tage[cptcovage]=i;
4733: }
4734: else { /* Age is not in the model */
4735: cutv(strb,stre,strc,'V'); /* strc= Vn, stre is n*/
4736: Tvar[i]=ncovcol+k1;
4737: cutv(strb,strc,strd,'V'); /* strd was Vm, strc is m */
4738: Tprod[k1]=i;
4739: Tvard[k1][1]=atoi(strc); /* m*/
4740: Tvard[k1][2]=atoi(stre); /* n */
4741: Tvar[cptcovn+k2]=Tvard[k1][1];
4742: Tvar[cptcovn+k2+1]=Tvard[k1][2];
4743: for (k=1; k<=lastobs;k++)
4744: covar[ncovcol+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];
4745: k1++;
4746: k2=k2+2;
4747: }
4748: }
4749: else { /* no more sum */
4750: /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/
4751: /* scanf("%d",i);*/
4752: cutv(strd,strc,strb,'V');
4753: Tvar[i]=atoi(strc);
4754: }
4755: strcpy(modelsav,stra);
4756: /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);
4757: scanf("%d",i);*/
4758: } /* end of loop + */
4759: } /* end model */
4760:
4761: /*The number n of Vn is stored in Tvar. cptcovage =number of age covariate. Tage gives the position of age. cptcovprod= number of products.
4762: If model=V1+V1*age then Tvar[1]=1 Tvar[2]=1 cptcovage=1 Tage[1]=2 cptcovprod=0*/
4763:
4764: /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);
4765: printf("cptcovprod=%d ", cptcovprod);
4766: fprintf(ficlog,"cptcovprod=%d ", cptcovprod);
4767:
4768: scanf("%d ",i);*/
4769:
4770: /* if(mle==1){*/
4771: if (weightopt != 1) { /* Maximisation without weights*/
4772: for(i=1;i<=n;i++) weight[i]=1.0;
4773: }
4774: /*-calculation of age at interview from date of interview and age at death -*/
4775: agev=matrix(1,maxwav,1,imx);
4776:
4777: for (i=1; i<=imx; i++) {
4778: for(m=2; (m<= maxwav); m++) {
4779: if (((int)mint[m][i]== 99) && (s[m][i] <= nlstate)){
4780: anint[m][i]=9999;
4781: s[m][i]=-1;
4782: }
4783: if((int)moisdc[i]==99 && (int)andc[i]==9999 && s[m][i]>nlstate){
4784: nberr++;
4785: 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);
4786: 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);
4787: s[m][i]=-1;
4788: }
4789: if((int)moisdc[i]==99 && (int)andc[i]!=9999 && s[m][i]>nlstate){
4790: nberr++;
4791: 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]);
4792: 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]);
4793: s[m][i]=-1; /* We prefer to skip it (and to skip it in version 0.8a1 too */
4794: }
4795: }
4796: }
4797:
4798: for (i=1; i<=imx; i++) {
4799: agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);
4800: for(m=firstpass; (m<= lastpass); m++){
4801: if(s[m][i] >0 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5){
4802: if (s[m][i] >= nlstate+1) {
4803: if(agedc[i]>0)
4804: if((int)moisdc[i]!=99 && (int)andc[i]!=9999)
4805: agev[m][i]=agedc[i];
4806: /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/
4807: else {
4808: if ((int)andc[i]!=9999){
4809: nbwarn++;
4810: printf("Warning negative age at death: %ld line:%d\n",num[i],i);
4811: fprintf(ficlog,"Warning negative age at death: %ld line:%d\n",num[i],i);
4812: agev[m][i]=-1;
4813: }
4814: }
4815: }
4816: else if(s[m][i] !=9){ /* Standard case, age in fractional
4817: years but with the precision of a month */
4818: agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);
4819: if((int)mint[m][i]==99 || (int)anint[m][i]==9999)
4820: agev[m][i]=1;
4821: else if(agev[m][i] <agemin){
4822: agemin=agev[m][i];
4823: /*printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], agemin);*/
4824: }
4825: else if(agev[m][i] >agemax){
4826: agemax=agev[m][i];
4827: /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/
4828: }
4829: /*agev[m][i]=anint[m][i]-annais[i];*/
4830: /* agev[m][i] = age[i]+2*m;*/
4831: }
4832: else { /* =9 */
4833: agev[m][i]=1;
4834: s[m][i]=-1;
4835: }
4836: }
4837: else /*= 0 Unknown */
4838: agev[m][i]=1;
4839: }
4840:
4841: }
4842: for (i=1; i<=imx; i++) {
4843: for(m=firstpass; (m<=lastpass); m++){
4844: if (s[m][i] > (nlstate+ndeath)) {
4845: nberr++;
4846: 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);
4847: 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);
4848: goto end;
4849: }
4850: }
4851: }
4852:
4853: /*for (i=1; i<=imx; i++){
4854: for (m=firstpass; (m<lastpass); m++){
4855: printf("%ld %d %.lf %d %d\n", num[i],(covar[1][i]),agev[m][i],s[m][i],s[m+1][i]);
4856: }
4857:
4858: }*/
4859:
4860:
4861: printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);
4862: fprintf(ficlog,"Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);
4863:
4864: agegomp=(int)agemin;
4865: free_vector(severity,1,maxwav);
4866: free_imatrix(outcome,1,maxwav+1,1,n);
4867: free_vector(moisnais,1,n);
4868: free_vector(annais,1,n);
4869: /* free_matrix(mint,1,maxwav,1,n);
4870: free_matrix(anint,1,maxwav,1,n);*/
4871: free_vector(moisdc,1,n);
4872: free_vector(andc,1,n);
4873:
4874:
4875: wav=ivector(1,imx);
4876: dh=imatrix(1,lastpass-firstpass+1,1,imx);
4877: bh=imatrix(1,lastpass-firstpass+1,1,imx);
4878: mw=imatrix(1,lastpass-firstpass+1,1,imx);
4879:
4880: /* Concatenates waves */
4881: concatwav(wav, dh, bh, mw, s, agedc, agev, firstpass, lastpass, imx, nlstate, stepm);
4882:
4883: /* Routine tricode is to calculate cptcoveff (real number of unique covariates) and to associate covariable number and modality */
4884:
4885: Tcode=ivector(1,100);
4886: nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);
4887: ncodemax[1]=1;
4888: if (cptcovn > 0) tricode(Tvar,nbcode,imx);
4889:
4890: codtab=imatrix(1,100,1,10); /* Cross tabulation to get the order of
4891: the estimations*/
4892: h=0;
4893: m=pow(2,cptcoveff);
4894:
4895: for(k=1;k<=cptcoveff; k++){
4896: for(i=1; i <=(m/pow(2,k));i++){
4897: for(j=1; j <= ncodemax[k]; j++){
4898: for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){
4899: h++;
4900: if (h>m) h=1;codtab[h][k]=j;codtab[h][Tvar[k]]=j;
4901: /* printf("h=%d k=%d j=%d codtab[h][k]=%d tvar[k]=%d \n",h, k,j,codtab[h][k],Tvar[k]);*/
4902: }
4903: }
4904: }
4905: }
4906: /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]);
4907: codtab[1][2]=1;codtab[2][2]=2; */
4908: /* for(i=1; i <=m ;i++){
4909: for(k=1; k <=cptcovn; k++){
4910: printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);
4911: }
4912: printf("\n");
4913: }
4914: scanf("%d",i);*/
4915:
4916: /*------------ gnuplot -------------*/
4917: strcpy(optionfilegnuplot,optionfilefiname);
4918: if(mle==-3)
4919: strcat(optionfilegnuplot,"-mort");
4920: strcat(optionfilegnuplot,".gp");
4921:
4922: if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {
4923: printf("Problem with file %s",optionfilegnuplot);
4924: }
4925: else{
4926: fprintf(ficgp,"\n# %s\n", version);
4927: fprintf(ficgp,"# %s\n", optionfilegnuplot);
4928: fprintf(ficgp,"set missing 'NaNq'\n");
4929: }
4930: /* fclose(ficgp);*/
4931: /*--------- index.htm --------*/
4932:
4933: strcpy(optionfilehtm,optionfilefiname); /* Main html file */
4934: if(mle==-3)
4935: strcat(optionfilehtm,"-mort");
4936: strcat(optionfilehtm,".htm");
4937: if((fichtm=fopen(optionfilehtm,"w"))==NULL) {
4938: printf("Problem with %s \n",optionfilehtm), exit(0);
4939: }
4940:
4941: strcpy(optionfilehtmcov,optionfilefiname); /* Only for matrix of covariance */
4942: strcat(optionfilehtmcov,"-cov.htm");
4943: if((fichtmcov=fopen(optionfilehtmcov,"w"))==NULL) {
4944: printf("Problem with %s \n",optionfilehtmcov), exit(0);
4945: }
4946: else{
4947: fprintf(fichtmcov,"<body>\n<title>IMaCh Cov %s</title>\n <font size=\"2\">%s <br> %s</font> \
4948: <hr size=\"2\" color=\"#EC5E5E\"> \n\
4949: Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n",\
4950: fileres,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);
4951: }
4952:
4953: fprintf(fichtm,"<body>\n<title>IMaCh %s</title>\n <font size=\"2\">%s <br> %s</font> \
4954: <hr size=\"2\" color=\"#EC5E5E\"> \n\
4955: Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n\
4956: \n\
4957: <hr size=\"2\" color=\"#EC5E5E\">\
4958: <ul><li><h4>Parameter files</h4>\n\
4959: - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n\
4960: - Log file of the run: <a href=\"%s\">%s</a><br>\n\
4961: - Gnuplot file name: <a href=\"%s\">%s</a><br>\n\
4962: - Date and time at start: %s</ul>\n",\
4963: fileres,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model,\
4964: fileres,fileres,\
4965: filelog,filelog,optionfilegnuplot,optionfilegnuplot,strstart);
4966: fflush(fichtm);
4967:
4968: strcpy(pathr,path);
4969: strcat(pathr,optionfilefiname);
4970: chdir(optionfilefiname); /* Move to directory named optionfile */
4971:
4972: /* Calculates basic frequencies. Computes observed prevalence at single age
4973: and prints on file fileres'p'. */
4974: freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint,strstart);
4975:
4976: fprintf(fichtm,"\n");
4977: fprintf(fichtm,"<br>Total number of observations=%d <br>\n\
4978: Youngest age at first (selected) pass %.2f, oldest age %.2f<br>\n\
4979: Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n",\
4980: imx,agemin,agemax,jmin,jmax,jmean);
4981: pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
4982: oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
4983: newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
4984: savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
4985: oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */
4986:
4987:
4988: /* For Powell, parameters are in a vector p[] starting at p[1]
4989: so we point p on param[1][1] so that p[1] maps on param[1][1][1] */
4990: p=param[1][1]; /* *(*(*(param +1)+1)+0) */
4991:
4992: globpr=0; /* To get the number ipmx of contributions and the sum of weights*/
4993:
4994: if (mle==-3){
4995: ximort=matrix(1,NDIM,1,NDIM);
4996: cens=ivector(1,n);
4997: ageexmed=vector(1,n);
4998: agecens=vector(1,n);
4999: dcwave=ivector(1,n);
5000:
5001: for (i=1; i<=imx; i++){
5002: dcwave[i]=-1;
5003: for (m=firstpass; m<=lastpass; m++)
5004: if (s[m][i]>nlstate) {
5005: dcwave[i]=m;
5006: /* printf("i=%d j=%d s=%d dcwave=%d\n",i,j, s[j][i],dcwave[i]);*/
5007: break;
5008: }
5009: }
5010:
5011: for (i=1; i<=imx; i++) {
5012: if (wav[i]>0){
5013: ageexmed[i]=agev[mw[1][i]][i];
5014: j=wav[i];
5015: agecens[i]=1.;
5016:
5017: if (ageexmed[i]> 1 && wav[i] > 0){
5018: agecens[i]=agev[mw[j][i]][i];
5019: cens[i]= 1;
5020: }else if (ageexmed[i]< 1)
5021: cens[i]= -1;
5022: if (agedc[i]< AGESUP && agedc[i]>1 && dcwave[i]>firstpass && dcwave[i]<=lastpass)
5023: cens[i]=0 ;
5024: }
5025: else cens[i]=-1;
5026: }
5027:
5028: for (i=1;i<=NDIM;i++) {
5029: for (j=1;j<=NDIM;j++)
5030: ximort[i][j]=(i == j ? 1.0 : 0.0);
5031: }
5032:
5033: p[1]=0.0268; p[NDIM]=0.083;
5034: /*printf("%lf %lf", p[1], p[2]);*/
5035:
5036:
5037: printf("Powell\n"); fprintf(ficlog,"Powell\n");
5038: strcpy(filerespow,"pow-mort");
5039: strcat(filerespow,fileres);
5040: if((ficrespow=fopen(filerespow,"w"))==NULL) {
5041: printf("Problem with resultfile: %s\n", filerespow);
5042: fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
5043: }
5044: fprintf(ficrespow,"# Powell\n# iter -2*LL");
5045: /* for (i=1;i<=nlstate;i++)
5046: for(j=1;j<=nlstate+ndeath;j++)
5047: if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
5048: */
5049: fprintf(ficrespow,"\n");
5050:
5051: powell(p,ximort,NDIM,ftol,&iter,&fret,gompertz);
5052: fclose(ficrespow);
5053:
5054: hesscov(matcov, p, NDIM, delti, 1e-4, gompertz);
5055:
5056: for(i=1; i <=NDIM; i++)
5057: for(j=i+1;j<=NDIM;j++)
5058: matcov[i][j]=matcov[j][i];
5059:
5060: printf("\nCovariance matrix\n ");
5061: for(i=1; i <=NDIM; i++) {
5062: for(j=1;j<=NDIM;j++){
5063: printf("%f ",matcov[i][j]);
5064: }
5065: printf("\n ");
5066: }
5067:
5068: printf("iter=%d MLE=%f Eq=%lf*exp(%lf*(age-%d))\n",iter,-gompertz(p),p[1],p[2],agegomp);
5069: for (i=1;i<=NDIM;i++)
5070: printf("%f [%f ; %f]\n",p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
5071:
5072: lsurv=vector(1,AGESUP);
5073: lpop=vector(1,AGESUP);
5074: tpop=vector(1,AGESUP);
5075: lsurv[agegomp]=100000;
5076:
5077: for (k=agegomp;k<=AGESUP;k++) {
5078: agemortsup=k;
5079: if (p[1]*exp(p[2]*(k-agegomp))>1) break;
5080: }
5081:
5082: for (k=agegomp;k<agemortsup;k++)
5083: lsurv[k+1]=lsurv[k]-lsurv[k]*(p[1]*exp(p[2]*(k-agegomp)));
5084:
5085: for (k=agegomp;k<agemortsup;k++){
5086: lpop[k]=(lsurv[k]+lsurv[k+1])/2.;
5087: sumlpop=sumlpop+lpop[k];
5088: }
5089:
5090: tpop[agegomp]=sumlpop;
5091: for (k=agegomp;k<(agemortsup-3);k++){
5092: /* tpop[k+1]=2;*/
5093: tpop[k+1]=tpop[k]-lpop[k];
5094: }
5095:
5096:
5097: printf("\nAge lx qx dx Lx Tx e(x)\n");
5098: for (k=agegomp;k<(agemortsup-2);k++)
5099: printf("%d %.0lf %lf %.0lf %.0lf %.0lf %lf\n",k,lsurv[k],p[1]*exp(p[2]*(k-agegomp)),(p[1]*exp(p[2]*(k-agegomp)))*lsurv[k],lpop[k],tpop[k],tpop[k]/lsurv[k]);
5100:
5101:
5102: replace_back_to_slash(pathc,path); /* Even gnuplot wants a / */
5103: printinggnuplotmort(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
5104:
5105: printinghtmlmort(fileres,title,datafile, firstpass, lastpass, \
5106: stepm, weightopt,\
5107: model,imx,p,matcov,agemortsup);
5108:
5109: free_vector(lsurv,1,AGESUP);
5110: free_vector(lpop,1,AGESUP);
5111: free_vector(tpop,1,AGESUP);
5112: } /* Endof if mle==-3 */
5113:
5114: else{ /* For mle >=1 */
5115:
5116: likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
5117: printf("First Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
5118: for (k=1; k<=npar;k++)
5119: printf(" %d %8.5f",k,p[k]);
5120: printf("\n");
5121: globpr=1; /* to print the contributions */
5122: likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
5123: printf("Second Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
5124: for (k=1; k<=npar;k++)
5125: printf(" %d %8.5f",k,p[k]);
5126: printf("\n");
5127: if(mle>=1){ /* Could be 1 or 2 */
5128: mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);
5129: }
5130:
5131: /*--------- results files --------------*/
5132: 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);
5133:
5134:
5135: fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
5136: printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
5137: fprintf(ficlog,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
5138: for(i=1,jk=1; i <=nlstate; i++){
5139: for(k=1; k <=(nlstate+ndeath); k++){
5140: if (k != i) {
5141: printf("%d%d ",i,k);
5142: fprintf(ficlog,"%d%d ",i,k);
5143: fprintf(ficres,"%1d%1d ",i,k);
5144: for(j=1; j <=ncovmodel; j++){
5145: printf("%f ",p[jk]);
5146: fprintf(ficlog,"%f ",p[jk]);
5147: fprintf(ficres,"%f ",p[jk]);
5148: jk++;
5149: }
5150: printf("\n");
5151: fprintf(ficlog,"\n");
5152: fprintf(ficres,"\n");
5153: }
5154: }
5155: }
5156: if(mle!=0){
5157: /* Computing hessian and covariance matrix */
5158: ftolhess=ftol; /* Usually correct */
5159: hesscov(matcov, p, npar, delti, ftolhess, func);
5160: }
5161: fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");
5162: printf("# Scales (for hessian or gradient estimation)\n");
5163: fprintf(ficlog,"# Scales (for hessian or gradient estimation)\n");
5164: for(i=1,jk=1; i <=nlstate; i++){
5165: for(j=1; j <=nlstate+ndeath; j++){
5166: if (j!=i) {
5167: fprintf(ficres,"%1d%1d",i,j);
5168: printf("%1d%1d",i,j);
5169: fprintf(ficlog,"%1d%1d",i,j);
5170: for(k=1; k<=ncovmodel;k++){
5171: printf(" %.5e",delti[jk]);
5172: fprintf(ficlog," %.5e",delti[jk]);
5173: fprintf(ficres," %.5e",delti[jk]);
5174: jk++;
5175: }
5176: printf("\n");
5177: fprintf(ficlog,"\n");
5178: fprintf(ficres,"\n");
5179: }
5180: }
5181: }
5182:
5183: 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");
5184: if(mle>=1)
5185: 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");
5186: 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");
5187: /* # 121 Var(a12)\n\ */
5188: /* # 122 Cov(b12,a12) Var(b12)\n\ */
5189: /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
5190: /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
5191: /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
5192: /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
5193: /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
5194: /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
5195:
5196:
5197: /* Just to have a covariance matrix which will be more understandable
5198: even is we still don't want to manage dictionary of variables
5199: */
5200: for(itimes=1;itimes<=2;itimes++){
5201: jj=0;
5202: for(i=1; i <=nlstate; i++){
5203: for(j=1; j <=nlstate+ndeath; j++){
5204: if(j==i) continue;
5205: for(k=1; k<=ncovmodel;k++){
5206: jj++;
5207: ca[0]= k+'a'-1;ca[1]='\0';
5208: if(itimes==1){
5209: if(mle>=1)
5210: printf("#%1d%1d%d",i,j,k);
5211: fprintf(ficlog,"#%1d%1d%d",i,j,k);
5212: fprintf(ficres,"#%1d%1d%d",i,j,k);
5213: }else{
5214: if(mle>=1)
5215: printf("%1d%1d%d",i,j,k);
5216: fprintf(ficlog,"%1d%1d%d",i,j,k);
5217: fprintf(ficres,"%1d%1d%d",i,j,k);
5218: }
5219: ll=0;
5220: for(li=1;li <=nlstate; li++){
5221: for(lj=1;lj <=nlstate+ndeath; lj++){
5222: if(lj==li) continue;
5223: for(lk=1;lk<=ncovmodel;lk++){
5224: ll++;
5225: if(ll<=jj){
5226: cb[0]= lk +'a'-1;cb[1]='\0';
5227: if(ll<jj){
5228: if(itimes==1){
5229: if(mle>=1)
5230: printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
5231: fprintf(ficlog," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
5232: fprintf(ficres," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
5233: }else{
5234: if(mle>=1)
5235: printf(" %.5e",matcov[jj][ll]);
5236: fprintf(ficlog," %.5e",matcov[jj][ll]);
5237: fprintf(ficres," %.5e",matcov[jj][ll]);
5238: }
5239: }else{
5240: if(itimes==1){
5241: if(mle>=1)
5242: printf(" Var(%s%1d%1d)",ca,i,j);
5243: fprintf(ficlog," Var(%s%1d%1d)",ca,i,j);
5244: fprintf(ficres," Var(%s%1d%1d)",ca,i,j);
5245: }else{
5246: if(mle>=1)
5247: printf(" %.5e",matcov[jj][ll]);
5248: fprintf(ficlog," %.5e",matcov[jj][ll]);
5249: fprintf(ficres," %.5e",matcov[jj][ll]);
5250: }
5251: }
5252: }
5253: } /* end lk */
5254: } /* end lj */
5255: } /* end li */
5256: if(mle>=1)
5257: printf("\n");
5258: fprintf(ficlog,"\n");
5259: fprintf(ficres,"\n");
5260: numlinepar++;
5261: } /* end k*/
5262: } /*end j */
5263: } /* end i */
5264: } /* end itimes */
5265:
5266: fflush(ficlog);
5267: fflush(ficres);
5268:
5269: while((c=getc(ficpar))=='#' && c!= EOF){
5270: ungetc(c,ficpar);
5271: fgets(line, MAXLINE, ficpar);
5272: puts(line);
5273: fputs(line,ficparo);
5274: }
5275: ungetc(c,ficpar);
5276:
5277: estepm=0;
5278: fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm);
5279: if (estepm==0 || estepm < stepm) estepm=stepm;
5280: if (fage <= 2) {
5281: bage = ageminpar;
5282: fage = agemaxpar;
5283: }
5284:
5285: fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");
5286: fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
5287: fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
5288:
5289: while((c=getc(ficpar))=='#' && c!= EOF){
5290: ungetc(c,ficpar);
5291: fgets(line, MAXLINE, ficpar);
5292: puts(line);
5293: fputs(line,ficparo);
5294: }
5295: ungetc(c,ficpar);
5296:
5297: 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);
5298: 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);
5299: 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);
5300: printf("begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
5301: 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);
5302:
5303: while((c=getc(ficpar))=='#' && c!= EOF){
5304: ungetc(c,ficpar);
5305: fgets(line, MAXLINE, ficpar);
5306: puts(line);
5307: fputs(line,ficparo);
5308: }
5309: ungetc(c,ficpar);
5310:
5311:
5312: dateprev1=anprev1+(mprev1-1)/12.+(jprev1-1)/365.;
5313: dateprev2=anprev2+(mprev2-1)/12.+(jprev2-1)/365.;
5314:
5315: fscanf(ficpar,"pop_based=%d\n",&popbased);
5316: fprintf(ficparo,"pop_based=%d\n",popbased);
5317: fprintf(ficres,"pop_based=%d\n",popbased);
5318:
5319: while((c=getc(ficpar))=='#' && c!= EOF){
5320: ungetc(c,ficpar);
5321: fgets(line, MAXLINE, ficpar);
5322: puts(line);
5323: fputs(line,ficparo);
5324: }
5325: ungetc(c,ficpar);
5326:
5327: 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);
5328: 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);
5329: 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);
5330: 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);
5331: 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);
5332: /* day and month of proj2 are not used but only year anproj2.*/
5333:
5334:
5335:
5336: /* freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint);*/
5337: /*,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
5338:
5339: replace_back_to_slash(pathc,path); /* Even gnuplot wants a / */
5340: printinggnuplot(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
5341:
5342: printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,\
5343: model,imx,jmin,jmax,jmean,rfileres,popforecast,estepm,\
5344: jprev1,mprev1,anprev1,jprev2,mprev2,anprev2);
5345:
5346: /*------------ free_vector -------------*/
5347: /* chdir(path); */
5348:
5349: free_ivector(wav,1,imx);
5350: free_imatrix(dh,1,lastpass-firstpass+1,1,imx);
5351: free_imatrix(bh,1,lastpass-firstpass+1,1,imx);
5352: free_imatrix(mw,1,lastpass-firstpass+1,1,imx);
5353: free_lvector(num,1,n);
5354: free_vector(agedc,1,n);
5355: /*free_matrix(covar,0,NCOVMAX,1,n);*/
5356: /*free_matrix(covar,1,NCOVMAX,1,n);*/
5357: fclose(ficparo);
5358: fclose(ficres);
5359:
5360:
5361: /*--------------- Prevalence limit (stable prevalence) --------------*/
5362:
5363: strcpy(filerespl,"pl");
5364: strcat(filerespl,fileres);
5365: if((ficrespl=fopen(filerespl,"w"))==NULL) {
5366: printf("Problem with stable prevalence resultfile: %s\n", filerespl);goto end;
5367: fprintf(ficlog,"Problem with stable prevalence resultfile: %s\n", filerespl);goto end;
5368: }
5369: printf("Computing stable prevalence: result on file '%s' \n", filerespl);
5370: fprintf(ficlog,"Computing stable prevalence: result on file '%s' \n", filerespl);
5371: fprintf(ficrespl, "#Local time at start: %s", strstart);
5372: fprintf(ficrespl,"#Stable prevalence \n");
5373: fprintf(ficrespl,"#Age ");
5374: for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);
5375: fprintf(ficrespl,"\n");
5376:
5377: prlim=matrix(1,nlstate,1,nlstate);
5378:
5379: agebase=ageminpar;
5380: agelim=agemaxpar;
5381: ftolpl=1.e-10;
5382: i1=cptcoveff;
5383: if (cptcovn < 1){i1=1;}
5384:
5385: for(cptcov=1,k=0;cptcov<=i1;cptcov++){
5386: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
5387: k=k+1;
5388: /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/
5389: fprintf(ficrespl,"\n#******");
5390: printf("\n#******");
5391: fprintf(ficlog,"\n#******");
5392: for(j=1;j<=cptcoveff;j++) {
5393: fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
5394: printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
5395: fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
5396: }
5397: fprintf(ficrespl,"******\n");
5398: printf("******\n");
5399: fprintf(ficlog,"******\n");
5400:
5401: for (age=agebase; age<=agelim; age++){
5402: prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
5403: fprintf(ficrespl,"%.0f ",age );
5404: for(j=1;j<=cptcoveff;j++)
5405: fprintf(ficrespl,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
5406: for(i=1; i<=nlstate;i++)
5407: fprintf(ficrespl," %.5f", prlim[i][i]);
5408: fprintf(ficrespl,"\n");
5409: }
5410: }
5411: }
5412: fclose(ficrespl);
5413:
5414: /*------------- h Pij x at various ages ------------*/
5415:
5416: strcpy(filerespij,"pij"); strcat(filerespij,fileres);
5417: if((ficrespij=fopen(filerespij,"w"))==NULL) {
5418: printf("Problem with Pij resultfile: %s\n", filerespij);goto end;
5419: fprintf(ficlog,"Problem with Pij resultfile: %s\n", filerespij);goto end;
5420: }
5421: printf("Computing pij: result on file '%s' \n", filerespij);
5422: fprintf(ficlog,"Computing pij: result on file '%s' \n", filerespij);
5423:
5424: stepsize=(int) (stepm+YEARM-1)/YEARM;
5425: /*if (stepm<=24) stepsize=2;*/
5426:
5427: agelim=AGESUP;
5428: hstepm=stepsize*YEARM; /* Every year of age */
5429: hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */
5430:
5431: /* hstepm=1; aff par mois*/
5432: fprintf(ficrespij, "#Local time at start: %s", strstart);
5433: fprintf(ficrespij,"#****** h Pij x Probability to be in state j at age x+h being in i at x ");
5434: for(cptcov=1,k=0;cptcov<=i1;cptcov++){
5435: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
5436: k=k+1;
5437: fprintf(ficrespij,"\n#****** ");
5438: for(j=1;j<=cptcoveff;j++)
5439: fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
5440: fprintf(ficrespij,"******\n");
5441:
5442: for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */
5443: nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
5444: nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
5445:
5446: /* nhstepm=nhstepm*YEARM; aff par mois*/
5447:
5448: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
5449: oldm=oldms;savm=savms;
5450: hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
5451: fprintf(ficrespij,"# Cov Agex agex+h hpijx with i,j=");
5452: for(i=1; i<=nlstate;i++)
5453: for(j=1; j<=nlstate+ndeath;j++)
5454: fprintf(ficrespij," %1d-%1d",i,j);
5455: fprintf(ficrespij,"\n");
5456: for (h=0; h<=nhstepm; h++){
5457: fprintf(ficrespij,"%d %3.f %3.f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );
5458: for(i=1; i<=nlstate;i++)
5459: for(j=1; j<=nlstate+ndeath;j++)
5460: fprintf(ficrespij," %.5f", p3mat[i][j][h]);
5461: fprintf(ficrespij,"\n");
5462: }
5463: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
5464: fprintf(ficrespij,"\n");
5465: }
5466: }
5467: }
5468:
5469: varprob(optionfilefiname, matcov, p, delti, nlstate, bage, fage,k,Tvar,nbcode, ncodemax,strstart);
5470:
5471: fclose(ficrespij);
5472:
5473: probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
5474: for(i=1;i<=AGESUP;i++)
5475: for(j=1;j<=NCOVMAX;j++)
5476: for(k=1;k<=NCOVMAX;k++)
5477: probs[i][j][k]=0.;
5478:
5479: /*---------- Forecasting ------------------*/
5480: /*if((stepm == 1) && (strcmp(model,".")==0)){*/
5481: if(prevfcast==1){
5482: /* if(stepm ==1){*/
5483: prevforecast(fileres, anproj1, mproj1, jproj1, agemin, agemax, dateprev1, dateprev2, mobilavproj, bage, fage, firstpass, lastpass, anproj2, p, cptcoveff);
5484: /* (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);*/
5485: /* } */
5486: /* else{ */
5487: /* erreur=108; */
5488: /* 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); */
5489: /* 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); */
5490: /* } */
5491: }
5492:
5493:
5494: /*---------- Health expectancies and variances ------------*/
5495:
5496: strcpy(filerest,"t");
5497: strcat(filerest,fileres);
5498: if((ficrest=fopen(filerest,"w"))==NULL) {
5499: printf("Problem with total LE resultfile: %s\n", filerest);goto end;
5500: fprintf(ficlog,"Problem with total LE resultfile: %s\n", filerest);goto end;
5501: }
5502: printf("Computing Total LEs with variances: file '%s' \n", filerest);
5503: fprintf(ficlog,"Computing Total LEs with variances: file '%s' \n", filerest);
5504:
5505:
5506: strcpy(filerese,"e");
5507: strcat(filerese,fileres);
5508: if((ficreseij=fopen(filerese,"w"))==NULL) {
5509: printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
5510: fprintf(ficlog,"Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
5511: }
5512: printf("Computing Health Expectancies: result on file '%s' \n", filerese);
5513: fprintf(ficlog,"Computing Health Expectancies: result on file '%s' \n", filerese);
5514:
5515: strcpy(fileresv,"v");
5516: strcat(fileresv,fileres);
5517: if((ficresvij=fopen(fileresv,"w"))==NULL) {
5518: printf("Problem with variance resultfile: %s\n", fileresv);exit(0);
5519: fprintf(ficlog,"Problem with variance resultfile: %s\n", fileresv);exit(0);
5520: }
5521: printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
5522: fprintf(ficlog,"Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
5523:
5524: /* Computes prevalence between agemin (i.e minimal age computed) and no more ageminpar */
5525: prevalence(probs, agemin, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
5526: /* 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",\
5527: ageminpar, agemax, s[lastpass][imx], agev[lastpass][imx], nlstate, imx, mint[lastpass][imx],anint[lastpass][imx], dateprev1, dateprev2, firstpass, lastpass);
5528: */
5529:
5530: if (mobilav!=0) {
5531: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
5532: if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
5533: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
5534: printf(" Error in movingaverage mobilav=%d\n",mobilav);
5535: }
5536: }
5537:
5538: for(cptcov=1,k=0;cptcov<=i1;cptcov++){
5539: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
5540: k=k+1;
5541: fprintf(ficrest,"\n#****** ");
5542: for(j=1;j<=cptcoveff;j++)
5543: fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
5544: fprintf(ficrest,"******\n");
5545:
5546: fprintf(ficreseij,"\n#****** ");
5547: for(j=1;j<=cptcoveff;j++)
5548: fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
5549: fprintf(ficreseij,"******\n");
5550:
5551: fprintf(ficresvij,"\n#****** ");
5552: for(j=1;j<=cptcoveff;j++)
5553: fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
5554: fprintf(ficresvij,"******\n");
5555:
5556: eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
5557: oldm=oldms;savm=savms;
5558: evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov, strstart);
5559:
5560: vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
5561: oldm=oldms;savm=savms;
5562: varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,0, mobilav, strstart);
5563: if(popbased==1){
5564: varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,popbased,mobilav, strstart);
5565: }
5566:
5567: fprintf(ficrest, "#Local time at start: %s", strstart);
5568: fprintf(ficrest,"#Total LEs with variances: e.. (std) ");
5569: for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);
5570: fprintf(ficrest,"\n");
5571:
5572: epj=vector(1,nlstate+1);
5573: for(age=bage; age <=fage ;age++){
5574: prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
5575: if (popbased==1) {
5576: if(mobilav ==0){
5577: for(i=1; i<=nlstate;i++)
5578: prlim[i][i]=probs[(int)age][i][k];
5579: }else{ /* mobilav */
5580: for(i=1; i<=nlstate;i++)
5581: prlim[i][i]=mobaverage[(int)age][i][k];
5582: }
5583: }
5584:
5585: fprintf(ficrest," %4.0f",age);
5586: for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){
5587: for(i=1, epj[j]=0.;i <=nlstate;i++) {
5588: epj[j] += prlim[i][i]*eij[i][j][(int)age];
5589: /* printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/
5590: }
5591: epj[nlstate+1] +=epj[j];
5592: }
5593:
5594: for(i=1, vepp=0.;i <=nlstate;i++)
5595: for(j=1;j <=nlstate;j++)
5596: vepp += vareij[i][j][(int)age];
5597: fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));
5598: for(j=1;j <=nlstate;j++){
5599: fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));
5600: }
5601: fprintf(ficrest,"\n");
5602: }
5603: free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
5604: free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);
5605: free_vector(epj,1,nlstate+1);
5606: }
5607: }
5608: free_vector(weight,1,n);
5609: free_imatrix(Tvard,1,15,1,2);
5610: free_imatrix(s,1,maxwav+1,1,n);
5611: free_matrix(anint,1,maxwav,1,n);
5612: free_matrix(mint,1,maxwav,1,n);
5613: free_ivector(cod,1,n);
5614: free_ivector(tab,1,NCOVMAX);
5615: fclose(ficreseij);
5616: fclose(ficresvij);
5617: fclose(ficrest);
5618: fclose(ficpar);
5619:
5620: /*------- Variance of stable prevalence------*/
5621:
5622: strcpy(fileresvpl,"vpl");
5623: strcat(fileresvpl,fileres);
5624: if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {
5625: printf("Problem with variance of stable prevalence resultfile: %s\n", fileresvpl);
5626: exit(0);
5627: }
5628: printf("Computing Variance-covariance of stable prevalence: file '%s' \n", fileresvpl);
5629:
5630: for(cptcov=1,k=0;cptcov<=i1;cptcov++){
5631: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
5632: k=k+1;
5633: fprintf(ficresvpl,"\n#****** ");
5634: for(j=1;j<=cptcoveff;j++)
5635: fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
5636: fprintf(ficresvpl,"******\n");
5637:
5638: varpl=matrix(1,nlstate,(int) bage, (int) fage);
5639: oldm=oldms;savm=savms;
5640: varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k,strstart);
5641: free_matrix(varpl,1,nlstate,(int) bage, (int)fage);
5642: }
5643: }
5644:
5645: fclose(ficresvpl);
5646:
5647: /*---------- End : free ----------------*/
5648: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
5649: free_ma3x(probs,1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
5650:
5651: } /* mle==-3 arrives here for freeing */
5652: free_matrix(prlim,1,nlstate,1,nlstate);
5653: free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);
5654: free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);
5655: free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);
5656: free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);
5657: free_matrix(covar,0,NCOVMAX,1,n);
5658: free_matrix(matcov,1,npar,1,npar);
5659: /*free_vector(delti,1,npar);*/
5660: free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
5661: free_matrix(agev,1,maxwav,1,imx);
5662: free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
5663:
5664: free_ivector(ncodemax,1,8);
5665: free_ivector(Tvar,1,15);
5666: free_ivector(Tprod,1,15);
5667: free_ivector(Tvaraff,1,15);
5668: free_ivector(Tage,1,15);
5669: free_ivector(Tcode,1,100);
5670:
5671: free_imatrix(nbcode,0,NCOVMAX,0,NCOVMAX);
5672: free_imatrix(codtab,1,100,1,10);
5673: fflush(fichtm);
5674: fflush(ficgp);
5675:
5676:
5677: if((nberr >0) || (nbwarn>0)){
5678: printf("End of Imach with %d errors and/or %d warnings\n",nberr,nbwarn);
5679: fprintf(ficlog,"End of Imach with %d errors and/or warnings %d\n",nberr,nbwarn);
5680: }else{
5681: printf("End of Imach\n");
5682: fprintf(ficlog,"End of Imach\n");
5683: }
5684: printf("See log file on %s\n",filelog);
5685: /* gettimeofday(&end_time, (struct timezone*)0);*/ /* after time */
5686: (void) gettimeofday(&end_time,&tzp);
5687: tm = *localtime(&end_time.tv_sec);
5688: tmg = *gmtime(&end_time.tv_sec);
5689: strcpy(strtend,asctime(&tm));
5690: printf("Local time at start %s\nLocal time at end %s",strstart, strtend);
5691: fprintf(ficlog,"Local time at start %s\nLocal time at end %s\n",strstart, strtend);
5692: printf("Total time used %s\n", asc_diff_time(end_time.tv_sec -start_time.tv_sec,tmpout));
5693:
5694: printf("Total time was %d Sec.\n", end_time.tv_sec -start_time.tv_sec);
5695: fprintf(ficlog,"Total time used %s\n", asc_diff_time(end_time.tv_sec -start_time.tv_sec,tmpout));
5696: fprintf(ficlog,"Total time was %d Sec.\n", end_time.tv_sec -start_time.tv_sec);
5697: /* printf("Total time was %d uSec.\n", total_usecs);*/
5698: /* if(fileappend(fichtm,optionfilehtm)){ */
5699: fprintf(fichtm,"<br>Local time at start %s<br>Local time at end %s<br>",strstart, strtend);
5700: fclose(fichtm);
5701: fclose(fichtmcov);
5702: fclose(ficgp);
5703: fclose(ficlog);
5704: /*------ End -----------*/
5705:
5706: chdir(path);
5707: /*strcat(plotcmd,CHARSEPARATOR);*/
5708: sprintf(plotcmd,"gnuplot");
5709: #ifndef UNIX
5710: sprintf(plotcmd,"\"%sgnuplot.exe\"",pathimach);
5711: #endif
5712: if(!stat(plotcmd,&info)){
5713: printf("Error gnuplot program not found: %s\n",plotcmd);fflush(stdout);
5714: if(!stat(getenv("GNUPLOTBIN"),&info)){
5715: printf("Error gnuplot program not found: %s Environment GNUPLOTBIN not set.\n",plotcmd);fflush(stdout);
5716: }else
5717: strcpy(pplotcmd,plotcmd);
5718: #ifdef UNIX
5719: strcpy(plotcmd,GNUPLOTPROGRAM);
5720: if(!stat(plotcmd,&info)){
5721: printf("Error gnuplot program not found: %s\n",plotcmd);fflush(stdout);
5722: }else
5723: strcpy(pplotcmd,plotcmd);
5724: #endif
5725: }else
5726: strcpy(pplotcmd,plotcmd);
5727:
5728: sprintf(plotcmd,"%s %s",pplotcmd, optionfilegnuplot);
5729: printf("Starting graphs with: %s\n",plotcmd);fflush(stdout);
5730:
5731: if((outcmd=system(plotcmd)) != 0){
5732: printf("\n Problem with gnuplot\n");
5733: }
5734: printf(" Wait...");
5735: while (z[0] != 'q') {
5736: /* chdir(path); */
5737: printf("\nType e to edit output files, g to graph again and q for exiting: ");
5738: scanf("%s",z);
5739: /* if (z[0] == 'c') system("./imach"); */
5740: if (z[0] == 'e') {
5741: printf("Starting browser with: %s",optionfilehtm);fflush(stdout);
5742: system(optionfilehtm);
5743: }
5744: else if (z[0] == 'g') system(plotcmd);
5745: else if (z[0] == 'q') exit(0);
5746: }
5747: end:
5748: while (z[0] != 'q') {
5749: printf("\nType q for exiting: ");
5750: scanf("%s",z);
5751: }
5752: }
5753:
5754:
5755:
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